U.S. patent application number 15/094908 was filed with the patent office on 2017-06-15 for compositions of adenosine deaminase-2 (ada2), variants thereof and methods of using same.
The applicant listed for this patent is Halozyme, Inc.. Invention is credited to H. Michael Shepard, Christopher D. Thanos, Lin Wang.
Application Number | 20170166878 15/094908 |
Document ID | / |
Family ID | 54601993 |
Filed Date | 2017-06-15 |
United States Patent
Application |
20170166878 |
Kind Code |
A9 |
Thanos; Christopher D. ; et
al. |
June 15, 2017 |
COMPOSITIONS OF ADENOSINE DEAMINASE-2 (ADA2), VARIANTS THEREOF AND
METHODS OF USING SAME
Abstract
Provided are variant adenosine deaminase 2 (ADA2) proteins,
conjugates thereof and compositions containing the proteins and/or
conjugates. Also provided are methods and uses of the ADA2 proteins
or conjugates for treating diseases and conditions, such as a tumor
or cancer, and in particular any disease or condition associated
with elevated adenosine or other associated marker.
Inventors: |
Thanos; Christopher D.;
(Tiburon, CA) ; Wang; Lin; (San Diego, CA)
; Shepard; H. Michael; (San Diego, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Halozyme, Inc. |
San Diego |
CA |
US |
|
|
Prior
Publication: |
|
Document Identifier |
Publication Date |
|
US 20160272960 A1 |
September 22, 2016 |
|
|
Family ID: |
54601993 |
Appl. No.: |
15/094908 |
Filed: |
April 8, 2016 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
PCT/US15/55613 |
Oct 14, 2015 |
|
|
|
15094908 |
|
|
|
|
62063936 |
Oct 14, 2014 |
|
|
|
Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A61P 37/04 20180101;
A61P 19/04 20180101; A61K 38/00 20130101; A61P 35/00 20180101; A61P
31/00 20180101; A61K 38/48 20130101; C12N 9/78 20130101; A61P 43/00
20180101; C12Y 305/04004 20130101; A61P 9/00 20180101 |
International
Class: |
C12N 9/78 20060101
C12N009/78; A61K 38/48 20060101 A61K038/48 |
Claims
1. A variant Adenosine Deaminase 2 (ADA2) protein or a
catalytically active portion thereof, comprising a modification(s)
in the sequence of amino acids of an unmodified ADA2 polypeptide or
a catalytically active portion thereof, wherein: the unmodified
ADA2 protein comprises the sequence of amino acids set forth in SEQ
ID NO:5, or a sequence of amino acids that exhibits at least 95%
sequence identity to the sequence of amino acids set forth in SEQ
ID NO:5, or is a catalytically active portion thereof; the amino
acid modification(s) are selected from among amino acid
replacement(s), deletion(s) and insertion(s); the variant ADA2
protein comprises an amino acid replacement at one or both of
positions corresponding to amino acid residue 219 and 262 with
reference to amino acid positions set forth in SEQ ID NO:5; the
variant ADA2 protein, when in dimer form, exhibits increased
adenosine deaminase activity or increased adenosine deaminase
activity and reduced heparin binding compared to the dimer form of
the unmodified ADA2 protein of SEQ ID NO:5 or dimer form of the
catalytically active portion thereof; and the variant ADA2 protein,
when in dimer form, exhibits adenosine deaminase activity to
convert adenosine to inosine.
2. The variant ADA2 protein or catalytically active portion thereof
of claim 1, wherein the unmodified ADA2 protein is a homodimer, and
the monomer form comprises the sequence of amino acid residues set
forth in SEQ ID NO:5.
3. A catalytically active portion of the variant ADA2 protein of
claim 1, wherein the unmodified ADA2 protein is a homodimer of
corresponding catalytically active portions of the polypeptide
whose sequence is set forth in SEQ ID NO:5, wherein corresponding
portions are determined by alignment.
4. The variant ADA2 protein of claim 1, wherein the unmodified ADA2
protein comprises the sequence of amino acids set forth in any of
SEQ ID NOS: 5, 326-334, 340, 375 and 380-383 or is a catalytically
active portion thereof.
5. The variant ADA2 protein of claim 1, wherein the unmodified ADA2
protein consists of the sequence of amino acids set forth in any of
SEQ ID NOS: 5, 326-334, 340, 375 and 380-383 or is a catalytically
active portion thereof.
6. The variant ADA2 protein of claim 1, wherein the unmodified ADA2
protein comprises the sequence of amino acids set forth in SEQ ID
NO: 5 or a catalytically active portion thereof.
7. The variant ADA2 protein or catalytically active portion thereof
of claim 1, wherein the variant ADA2 protein comprises one or more
amino acid replacement(s) selected from among replacements
corresponding to R219K; R219Q; R219N; R219A; S262A; S262V; S262M;
S262N; S262C; S262D; S262E; S262F; S262G; S262H; S262I; S262K;
S262L; S262P; S262Q; S262R; S262T; S262W and S262Y.
8. The variant ADA2 protein or catalytically active portion thereof
of claim 1, comprising the replacement corresponding to S262N or
S262Q.
9. The variant ADA2 protein or catalytically active portion thereof
of claim 1, comprising the replacement corresponding to R219K,
R219Q, R219N or R219A.
10. The variant ADA2 protein or catalytically active portion
thereof of claim 1, comprising the replacement corresponding to
R219Q/S262N.
11. The variant ADA2 protein or catalytically active portion
thereof of claim 10, selected from among any of
R219Q/S262N/R20N/V22S, R219Q/S262N/K371N/D373S,
R219Q/S262N/K372N/I374S, R219Q/S262N/T403N/H405S,
R219Q/S262N/G404N/P406S,
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.15,
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.10,
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.7,
R219Q/S262N/C105-T147del.fwdarw.(Gly)5,
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.3,
R219Q/S262N/R125N/P126A, R219Q/S262N/S127N/K129S,
R219Q/S262N/P126N/E128T, R219Q/S262N/R112N/I114T,
R219Q/S262N/I134N/L135C/L136T, R219Q/S262N/I134N/L135S/L136T,
R219Q/S262N/R142N/Q144S, R219Q/S262N/E137N/Y139T,
R219Q/S262N/P111N/G113S, R219Q/S262N/F119S, R219Q/S262N/F119K,
R219Q/S262N/Y224R, R219Q/S262N/Y224N, R219Q/S262N/Y191S,
R219Q/S262N/Y191D, R219Q/S262N/F183K, R219Q/S262N/Y191D/Y224R,
R219Q/S262N/F109S, R219Q/S262N/F109A, R219Q/S262N/R118D,
R219Q/S262N/R118A, R219Q/S262N/Y139T, R219Q/S262N/Y139A,
R219Q/S262N/W133S, R219Q/S262N/W133T, R219Q/S262N/P124A,
R219Q/S262N/P124S, R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.1,
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.2,
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.3,
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.1,
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.2,
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.3,
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.1,
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.2,
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.3,
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.1,
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.2,
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.3,
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.n, R219Q/S262N/K11A,
R219Q/S262N/K11D, R219Q/S262N/K11E, R219Q/S262N/K13A,
R219Q/S262N/K13D, R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.n,
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.n,
R219Q/S262N/N98-N156del, R219Q/S262N/C105-E148del,
R219Q/S262N/C105-T147del, R219Q/S262N/V99-Q144del,
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.n,
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.15,
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.10,
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.7,
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.5,
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.3,
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.n,
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.n,
R219Q/S262N/K371D/N98-N156del, R219Q/S262N/K371D/C105-E148del,
R219Q/S262N/K371D/C105-T147del, R219Q/S262N/K371D/V99-Q144del,
R219Q/S262N/K13E, R219Q/S262N/K371A, R219Q/S262N/K372A,
R219Q/S262N/K372D, R219Q/S262N/K372E, R219Q/S262N/K452A,
R219Q/S262N/K452D, R219Q/S262N/K452E, R219Q/S262N/R20A,
R219Q/S262N/R20D, R219Q/S262N/R366A, R219Q/S262N/R366D,
R219Q/S262N/R366E, R219Q/S262N/H264A, R219Q/S262N/H264Q,
R219Q/S262N/H264N, R219Q/S262N/H264G, R219K/S262N, R219N/S262N,
R219A/S262N, R219Q/S262N/L221A, R219Q/S262N/L221V,
R219Q/S262N/L221G, R219Q/S262N/E179D, R219Q/S262N/E179A,
R219Q/S262N/E179S, R219Q/S262N/E179T, R219Q/S262N/E179V,
R219Q/S262N/E179G, R219Q/S262A, R219Q/S262V, R219Q/S262M,
R219Q/S262N/K11A/R20A, R219Q/S262N/K11A/R20A/K371A,
R219Q/S262N/R20A/K371A, R219Q/S262N/K11A/K371A, R219Q/S262N/K26A,
R219Q/S262N/K26D, R219Q/S262N/K26E, R219Q/S262N/R217A,
R219Q/S262N/R217D, R219Q/S262N/R217E, R219Q/S262N/K258A,
R219Q/S262N/K258D, R219Q/S262N/K258E, R219Q/S262N/R277A,
R219Q/S262N/R277D, R219Q/S262N/R277E, R219Q/S262N/R283A,
R219Q/S262N/R283D, R219Q/S262N/R283E, R219Q/S262N/K309A,
R219Q/S262N/K309D, R219Q/S262N/K309E, R219Q/S262N/K317A,
R219Q/S262N/K317D, R219Q/S262N/K317E, R219Q/S262N/K321A,
R219Q/S262N/K321D, R219Q/S262N/K321E, R219Q/S262N/R352A,
R219Q/S262N/R352D, R219Q/S262N/R352E, R219Q/S262N/R441A,
R219Q/S262N/R441D, R219Q/S262N/R441E, R219Q/S262N/K444A,
R219Q/S262N/K444D, R219Q/S262N/K444E, R219Q/S262N/K461A,
R219Q/S262N/K461D, R219Q/S262N/K461E, R219Q/S262N/K469A,
R219Q/S262N/K469D, R219Q/S262N/K469E, R219Q/S262N/K470A,
R219Q/S262N/K470D, R219Q/S262N/K470E, R219Q/S262N/D86A,
R219Q/S262N/D86C, R219Q/S262N/D86E, R219Q/S262N/D86F,
R219Q/S262N/D86G, R219Q/S262N/D86H, R219Q/S262N/D86I,
R219Q/S262N/D86K, R219Q/S262N/D86L, R219Q/S262N/D86M,
R219Q/S262N/D86N, R219Q/S262N/D86P, R219Q/S262N/D86Q,
R219Q/S262N/D86R, R219Q/S262N/D86S, R219Q/S262N/D86T,
R219Q/S262N/D86V, R219Q/S262N/D86W, R219Q/S262N/D86Y,
R219Q/S262N/E179C, R219Q/S262N/E179F, R219Q/S262N/E179H,
R219Q/S262N/E179I, R219Q/S262N/E179K, R219Q/S262N/E179L,
R219Q/S262N/E179M, R219Q/S262N/E179N, R219Q/S262N/E179P,
R219Q/S262N/E179Q, R219Q/S262N/E179R, R219Q/S262N/E179W,
R219Q/S262N/E179Y, R219C/S262N, R219D/S262N, R219E/S262N,
R219F/S262N, R219G/S262N, R219H/S262N, R219I/S262N, R219L/S262N,
R219M/S262N, R219P/S262N, R219S/S262N, R219T/S262N, R219V/S262N,
R219W/S262N, R219Y/S262N, R219Q/S262N/L221C, R219Q/S262N/L221D,
R219Q/S262N/L221E, R219Q/S262N/L221F, R219Q/S262N/L221H,
R219Q/S262N/L221I, R219Q/S262N/L221K, R219Q/S262N/L221M,
R219Q/S262N/L221N, R219Q/S262N/L221P, R219Q/S262N/L221Q,
R219Q/S262N/L221R, R219Q/S262N/L221S, R219Q/S262N/L221T,
R219Q/S262N/L221W, R219Q/S262N/L221Y, R219Q/S262C, R219Q/S262D,
R219Q/S262E, R219Q/S262F, R219Q/S262G, R219Q/S262H, R219Q/S262I,
R219Q/S262K, R219Q/S262L, R219Q/S262P, R219Q/S262Q, R219Q/S262R,
R219Q/S262T, R219Q/S262W, R219Q/S262Y, R219Q/S262N/H264C,
R219Q/S262N/H264D, R219Q/S262N/H264E, R219Q/S262N/H264F,
R219Q/S262N/H264I, R219Q/S262N/H264K, R219Q/S262N/H264L,
R219Q/S262N/H264M, R219Q/S262N/H264P, R219Q/S262N/H264R,
R219Q/S262N/H264S, R219Q/S262N/H264T, R219Q/S262N/H264V,
R219Q/S262N/H264W, R219Q/S262N/H264Y, R219Q/S262N/S266A,
R219Q/S262N/S266C, R219Q/S262N/S266D, R219Q/S262N/S266E,
R219Q/S262N/S266F, R219Q/S262N/S266G, R219Q/S262N/S266H,
R219Q/S262N/S266I, R219Q/S262N/S266K, R219Q/S262N/S266L,
R219Q/S262N/S266M, R219Q/S262N/S266N, R219Q/S262N/S266P,
R219Q/S262N/S266Q, R219Q/S262N/S266R, R219Q/S262N/S266T,
R219Q/S262N/S266V, R219Q/S262N/S266W, R219Q/S262N/S266Y,
R219Q/S262N/K267A, R219Q/S262N/K267C, R219Q/S262N/K267D,
R219Q/S262N/K267E, R219Q/S262N/K267F, R219Q/S262N/K267G,
R219Q/S262N/K267H, R219Q/S262N/K267I, R219Q/S262N/K267L,
R219Q/S262N/K267M, R219Q/S262N/K267N, R219Q/S262N/K267P,
R219Q/S262N/K267Q, R219Q/S262N/K267R, R219Q/S262N/K267S,
R219Q/S262N/K267T, R219Q/S262N/K267V, R219Q/S262N/K267W,
R219Q/S262N/K267Y, R219Q/S262N/V296A, R219Q/S262N/V296C,
R219Q/S262N/V296D, R219Q/S262N/V296E, R219Q/S262N/V296F,
R219Q/S262N/V296G, R219Q/S262N/V296H, R219Q/S262N/V296I,
R219Q/S262N/V296K, R219Q/S262N/V296L, R219Q/S262N/V296M,
R219Q/S262N/V296N, R219Q/S262N/V296P, R219Q/S262N/V296Q,
R219Q/S262N/V296R, R219Q/S262N/V296S, R219Q/S262N/V296T,
R219Q/S262N/V296W and R219Q/S262N/V296Y.
12. The variant ADA2 protein of claim 1, wherein the variant ADA2
protein comprises amino acid replacements selected from among
R219Q/S262N/K371E, R219Q/S262N/K371D, R219Q/S262N/R20E and
R219Q/S262N/K371D/R20E.
13. The variant ADA2 protein or catalytically active portion
thereof of claim 1 that comprises the modifications corresponding
to R219Q/S262N/--.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3;
R219Q/S262N/R20N/V22S; R219Q/S262N/K371N/D373S;
R219Q/S262N/K372N/I374S; R219Q/S262N/T403N/H405S; or
R219Q/S262N/G404N/P406S
14. The variant ADA2 protein or catalytically active portion
thereof of claim 1 that comprises amino acid replacements
corresponding to R219Q/S262N/R125N/P126A; R219Q/S262N/S127N/K129S;
R219Q/S262N/P126N/E128T; R219Q/S262N/R112N/I114T;
R219Q/S262N/I134N/L135C/L136T; R219Q/S262N/I134N/L135S/L136T;
R219Q/S262N/R142N/Q144S; R219Q/S262N/E137N/Y139T; or
R219Q/S262N/P111N/G113S.
15. The variant ADA2 protein or catalytically active portion
thereof of claim 1, further comprising a modification in the
putative receptor binding (PRB) domain corresponding to one or more
of the modifications selected from among: R125N/P126A; S127N/K129S;
P126N/E128T; R112N/I114T; I134N/L135C/L136T; I134N/L135S/L136T;
R142N/Q144S; E137N/Y139T; and P111N/G113S.
16. The variant ADA2 protein or catalytically active portion
thereof of claim 1, comprising amino acid replacements selected
from among replacements corresponding to R219Q/S262N/F119S;
R219Q/S262N/F119K; R219Q/S262N/Y224R; R219Q/S262N/Y224N;
R219Q/S262N/Y191S; R219Q/S262N/Y191D; R219Q/S262N/F183K;
R219Q/S262N/Y191D/Y224R; R219Q/S262N/F109S; R219Q/S262N/F109A;
R219Q/S262N/R118D; R219Q/S262N/R118A; R219Q/S262N/Y139T;
R219Q/S262N/Y139A; R219Q/S262N/W133S; R219Q/S262N/W133T;
R219Q/S262N/P124A; and R219Q/S262N/P124S.
17. The variant ADA2 protein or catalytically active portion
thereof of claim 1 that comprises amino acid replacements selected
from among replacements corresponding to
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.15;
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.10;
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.7;
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.5;
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.3;
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.1;
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.2;
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.3;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.1;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.2;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.3;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.1;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.2;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.3;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.1;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.2;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.3;
R219Q/S262N/C105-T147del.fwdarw.(Gly)n, where n=2 to 20;
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.n, where n=1 to 5;
R219Q/S262N/N98-N156del; R219Q/S262N/C105-E148del;
R219Q/S262N/C105-T147del; R219Q/S262N/V99-Q144del;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.n, where n=2 to 20;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.15;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.10;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.7;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.5;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.3;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.n, where n=1 to 5;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.n, where n=1 to
5; R219Q/S262N/K371D/N98-N156del; R219Q/S262N/K371D/C105-E148del;
R219Q/S262N/K371D/C105-T147del; and R219Q/S262N/K371D/V99-Q144del,
with reference to amino acid positions set forth in SEQ ID
NO:5.
18. The variant ADA2 protein or catalytically active portion
thereof of claim 1, wherein the variant ADA2 protein comprises the
sequence of amino acids set forth in any of SEQ ID NOS:38-41,
51-54, 59-63, 145-159, 176-190 and 263-273 or a catalytically
active portion thereof.
19. The variant ADA2 protein or catalytically active portion
thereof of claim 1, wherein the variant ADA2 protein comprises the
sequence of amino acids set forth in any of SEQ ID NOS: 596-645 and
658-931 or a catalytically active portion thereof.
20. The variant ADA2 protein or catalytically active portion
thereof of claim 1, comprising amino acid replacements selected
from among replacements corresponding to R219Q/S262N/K371D;
R219Q/S262N/R20E; R219Q/S262N/K371E/R20E; R219Q/S262N/K371D/R20E;
R219Q/S262N; R219Q/S262N/K11A; R219Q/S262N/K11D; R219Q/S262N/K11E;
R219Q/S262N/K13A; R219Q/S262N/K13D; R219Q/S262N/K13E;
R219Q/S262N/K371A; R219Q/S262N/K372A; R219Q/S262N/K372D;
R219Q/S262N/K372E; R219Q/S262N/K452A; R219Q/S262N/K452D;
R219Q/S262N/K452E; R219Q/S262N/R20A; R219Q/S262N/R20D;
R219Q/S262N/R366A; R219Q/S262N/R366D; R219Q/S262N/R366E;
R219Q/S262N/H264A; R219Q/S262N/H264Q; R219Q/S262N/H264N;
R219Q/S262N/H264G; R219K/S262N; R219N/S262N; R219A/S262N;
R219Q/S262N/L221A; R219Q/S262N/L221V; R219Q/S262N/L221G;
R219Q/S262N/E179D; R219Q/S262N/E179A; R219Q/S262N/E179S;
R219Q/S262N/E179T; R219Q/S262N/E179V; R219Q/S262N/E179G;
R219Q/S262A; R219Q/S262V; R219Q/S262M; R219Q/S262N/K11A/R20A;
R219Q/S262N/K11A/R20A/K371A; R219Q/S262N/R20A/K371A;
R219Q/S262N/K11A/K371A; R219Q/S262N/K26A; R219Q/S262N/K26D;
R219Q/S262N/K26E; R219Q/S262N/R217A; R219Q/S262N/R217D;
R219Q/S262N/R217E; R219Q/S262N/K258A; R219Q/S262N/K258D;
R219Q/S262N/K258E; R219Q/S262N/R277A; R219Q/S262N/R277D;
R219Q/S262N/R277E; R219Q/S262N/R283A; R219Q/S262N/R283D;
R219Q/S262N/R283E; R219Q/S262N/K309A; R219Q/S262N/K309D;
R219Q/S262N/K309E; R219Q/S262N/K317A; R219Q/S262N/K317D;
R219Q/S262N/K317E; R219Q/S262N/K321A; R219Q/S262N/K321D;
R219Q/S262N/K321E; R219Q/S262N/R352A; R219Q/S262N/R352D;
R219Q/S262N/R352E; R219Q/S262N/R441A; R219Q/S262N/R441D;
R219Q/S262N/R441E; R219Q/S262N/K444A; R219Q/S262N/K444D;
R219Q/S262N/K444E; R219Q/S262N/K461A; R219Q/S262N/K461D;
R219Q/S262N/K461E; R219Q/S262N/K469A; R219Q/S262N/K469D;
R219Q/S262N/K469E; R219Q/S262N/K470A; R219Q/S262N/K470D;
R219Q/S262N/K470E; R219Q/S262N/D86A; R219Q/S262N/D86C;
R219Q/S262N/D86E; R219Q/S262N/D86F; R219Q/S262N/D86G;
R219Q/S262N/D86H; R219Q/S262N/D86I; R219Q/S262N/D86K;
R219Q/S262N/D86L; R219Q/S262N/D86M; R219Q/S262N/D86N;
R219Q/S262N/D86P; R219Q/S262N/D86Q; R219Q/S262N/D86R;
R219Q/S262N/D86S; R219Q/S262N/D86T; R219Q/S262N/D86V;
R219Q/S262N/D86W; R219Q/S262N/D86Y; R219Q/S262N/E179C;
R219Q/S262N/E179F; R219Q/S262N/E179H; R219Q/S262N/E179I;
R219Q/S262N/E179K; R219Q/S262N/E179L; R219Q/S262N/E179M;
R219Q/S262N/E179N; R219Q/S262N/E179P; R219Q/S262N/E179Q;
R219Q/S262N/E179R; R219Q/S262N/E179W; R219Q/S262N/E179Y;
R219C/S262N; R219D/S262N; R219E/S262N; R219F/S262N; R219G/S262N;
R219H/S262N; R219I/S262N; R219L/S262N; R219M/S262N; R219P/S262N;
R219S/S262N; R219T/S262N; R219V/S262N; R219W/S262N; R219Y/S262N;
R219Q/S262N/L221C; R219Q/S262N/L221D; R219Q/S262N/L221E;
R219Q/S262N/L221F; R219Q/S262N/L221H; R219Q/S262N/L221I;
R219Q/S262N/L221K; R219Q/S262N/L221M; R219Q/S262N/L221N;
R219Q/S262N/L221P; R219Q/S262N/L221Q; R219Q/S262N/L221R;
R219Q/S262N/L221S; R219Q/S262N/L221T; R219Q/S262N/L221W;
R219Q/S262N/L221Y; R219Q/S262C; R219Q/S262D; R219Q/S262E;
R219Q/S262F; R219Q/S262G; R219Q/S262H; R219Q/S262I; R219Q/S262K;
R219Q/S262L; R219Q/S262P; R219Q/S262Q; R219Q/S262R; R219Q/S262T;
R219Q/S262W; R219Q/S262Y; R219Q/S262N/H264C; R219Q/S262N/H264D;
R219Q/S262N/H264E; R219Q/S262N/H264F; R219Q/S262N/H264I;
R219Q/S262N/H264K; R219Q/S262N/H264L; R219Q/S262N/H264M;
R219Q/S262N/H264P; R219Q/S262N/H264R; R219Q/S262N/H264S;
R219Q/S262N/H264T; R219Q/S262N/H264V; R219Q/S262N/H264W;
R219Q/S262N/H264Y; R219Q/S262N/S266A; R219Q/S262N/S266C;
R219Q/S262N/S266D; R219Q/S262N/S266E; R219Q/S262N/S266F;
R219Q/S262N/S266G; R219Q/S262N/S266H; R219Q/S262N/S266I;
R219Q/S262N/S266K; R219Q/S262N/S266L; R219Q/S262N/S266M;
R219Q/S262N/S266N; R219Q/S262N/S266P; R219Q/S262N/S266Q;
R219Q/S262N/S266R; R219Q/S262N/S266T; R219Q/S262N/S266V;
R219Q/S262N/S266W; R219Q/S262N/S266Y; R219Q/S262N/K267A;
R219Q/S262N/K267C; R219Q/S262N/K267D; R219Q/S262N/K267E;
R219Q/S262N/K267F; R219Q/S262N/K267G; R219Q/S262N/K267H;
R219Q/S262N/K267I; R219Q/S262N/K267L; R219Q/S262N/K267M;
R219Q/S262N/K267N; R219Q/S262N/K267P; R219Q/S262N/K267Q;
R219Q/S262N/K267R; R219Q/S262N/K267S; R219Q/S262N/K267T;
R219Q/S262N/K267V; R219Q/S262N/K267W; R219Q/S262N/K267Y;
R219Q/S262N/V296A; R219Q/S262N/V296C; R219Q/S262N/V296D;
R219Q/S262N/V296E; R219Q/S262N/V296F; R219Q/S262N/V296G;
R219Q/S262N/V296H; R219Q/S262N/V296I; R219Q/S262N/V296K;
R219Q/S262N/V296L; R219Q/S262N/V296M; R219Q/S262N/V296N;
R219Q/S262N/V296P; R219Q/S262N/V296Q; R219Q/S262N/V296R;
R219Q/S262N/V296S; R219Q/S262N/V296T; R219Q/S262N/V296W;
R219Q/S262N/V296Y; R219Q/K11A/R20A; R219Q/K11A/R20A/K371A;
R219Q/R20A/K371A; R219Q/K11A/K371A; S262N/K11A/R20A;
S262N/K11A/R20A/K371A; S262N/R20A/K371A; and S262N/K11A/K371A, with
reference to SEQ ID NO:5.
21. The variant ADA2 protein or catalytically active portion
thereof of claim 10, wherein the sequence of the ADA2 portion is
set forth in SEQ ID NO:273.
22. The variant ADA2 protein or catalytically active portion
thereof of claim 21, wherein the ADA2 protein is PEGylated.
23. A catalytically active portion of the variant ADA2 protein or
catalytically active portion thereof of claim 1, wherein the
catalytically active portion comprises the ADA domain.
24. A variant ADA2 multimer, comprising a plurality of variant ADA2
proteins or catalytically active portions thereof of claim 1,
wherein the variant ADA2 protein or catalytically active portion
thereof are the same or different.
25. A variant ADA2 dimer, comprising a variant ADA2 protein or
catalytically active portion thereof of claim 1.
26. A variant ADA2 dimer, comprising a variant ADA2 protein or
catalytically active portion thereof of claim 10.
27. The variant ADA2 dimer or catalytically active portion thereof
of claim 25 that is a homodimer comprising two variant ADA2
proteins or catalytically active portions thereof that are the
same.
28. The variant ADA2 dimer or catalytically active portion thereof
of claim 25 that is a heterodimer comprising two variant ADA2
proteins or catalytically active portions thereof that are
different from each other.
29. A conjugate, comprising an ADA2 protein or catalytically active
portion thereof a claim 1, linked by chemical or physical
interaction directly or indirectly via a linker to a heterologous
moiety, wherein the heterologous moiety is a half-life extending
moiety.
30. The conjugate of claim 29, wherein the a half-life extending
moiety is a PEG and the ADA2 protein or catalytically active
portion thereof is PEGylated.
31. A nucleic acid encoding a variant ADA2 protein or catalytically
active portion thereof of claim 1.
32. A vector, comprising the nucleic acid molecule of claim 31.
33. An isolated cell or a cell culture, comprising the vector of
claim 32.
34. The cell or cell culture of claim 33, wherein the cell is a
selected from a tumor-infiltrating lymphocyte (TIL), a cytotoxic T
lymphocyte (CTL), a natural killer (NK) cell or a
lymphokine-activated killer (LAK) cell.
35. The cell or cell culture of claim 34, wherein the cell is a T
cell that encodes and expresses chimeric antigen receptor (CAR) and
the variant ADA2 protein or dimer, wherein the CAR is specific for
a tumor cell antigen.
36. A method of producing an ADA2 variant or catalytically active
portion thereof, comprising culturing a cell of claim 33, under
conditions whereby the ADA2 variant is expressed.
37. The method of claim 36, wherein the resulting ADA2 variant is a
dimer.
38. A method of treatment of cancer, comprising: culturing or
expanding the cell of claim 33, and administering the cells to a
human subject for treatment of a tumor.
39. A pharmaceutical composition, comprising a variant ADA2 protein
of claim 1 or a catalytically active portion thereof, or a dimer or
multimer of the ADA2 protein or catalytically active portion
thereof.
40. The pharmaceutical composition of claim 39, wherein the ADA2
variant or catalytically active portion thereof is PEGylated.
41. The pharmaceutical composition of claim 39, wherein the ADA2
variant comprises the sequence of amino acid residues set forth in
SEQ ID NO:273 or a catalytically active portion thereof.
42. The pharmaceutical composition of claim 41, wherein the ADA2
protein or catalytically active portion thereof is PEGylated.
43. A method of treating a tumor, cancer, non-cancer
hyperproliferative disease, a fibrotic disease, an infectious
disease, a vasculopathy, or an immunodeficiency disease in a
subject, comprising administering to the subject an ADA2 protein,
wherein the ADA2 protein comprises the sequence of amino acids of
SEQ ID NO:5 or a catalytically active portion thereof or variant
ADA2 protein that has at least 85%, 90% or 95% sequence identity to
the sequence of amino acids set forth in SEQ ID NO:5 or to a
corresponding catalytically active portion thereof.
Description
RELATED APPLICATIONS
[0001] This application is a continuation-in-part of International
PCT application No. PCT/US15/55613, filed Oct. 14, 2015, to
Applicant Halozyme, Inc. and inventors Christopher D. Thanos, Lin
Wang and H. Michael Shepard, entitled COMPOSITIONS OF ADENOSINE
DEAMINASE-2 (ADA2), VARIANTS THEREOF AND METHODS OF USING SAME,
which claims the benefit of priority to U.S. provisional
application Ser. No. 62/063,936, filed Oct. 14, 2014, to inventors
Christopher D Thanos, Lin Wang and H. Michael Shepard, entitled
COMPOSITIONS OF ADENOSINE DEAMINASE-2 (ADA2), VARIANTS THEREOF AND
METHODS OF USING SAME. The subject matter of these applications is
incorporated by reference in its entirety.
INCORPORATION BY REFERENCE OF SEQUENCE LISTING PROVIDED
ELECTRONICALLY
[0002] An electronic version of the Sequence Listing is filed
herewith, the contents of which are incorporated by reference in
their entirety. The electronic file was created on Apr. 8, 2016, is
3,177 kilobytes in size, and titled 3121SEQ001.txt.
FIELD OF THE INVENTION
[0003] Provided are variant adenosine deaminase 2 (ADA2) proteins.
Also provided are ADA2 conjugates and compositions containing an
ADA2 protein or ADA2 conjugate. Also provided are methods and uses
of the ADA2 proteins or conjugates for treating diseases and
conditions, such as a tumor or cancer, and in particular any
disease or condition associated with elevated adenosine or other
associated marker.
BACKGROUND
[0004] Adenosine is a well-known effector of immune function. In
T-cells, adenosine decreases T-cell receptor induced activation of
NF-.kappa.B, and inhibits IL-2, IL-4, and IFN-.gamma.. Adenosine
decreases T-cell cytotoxicity, increases T-cell anergy, and
increases T-cell differentiation to Fop3+ or Lag-3+ regulatory
(T-reg) T-cells. On NK cells, adenosine is known to decrease
IFN-.gamma. production, and suppress NK cell cytoxicity. Adenosine
is known to block neutrophil adhesion and extravasation, decrease
phagocytosis, and attenuate levels of superoxide and nitric oxide.
Adenosine also decreases the expression of TNF-.alpha., IL-12, and
MIP-1.alpha. on macrophages, attenuates MHC Class II expression,
and increases levels of IL-10 and IL-6. In addition, adenosine
decreases phagocytosis and superoxide and nitric oxide levels on
macrophages. Through these immune-related activities, and others,
aberrant or accumulated levels of adenosine is associated with a
number of diseases and conditions, including those in which the
adenosine-mediated immunosuppressive effects play a role. Hence,
there is a need for treatments of such diseases and conditions.
SUMMARY
[0005] Provided herein are variant Adenosine Deaminase 2 (ADA2)
proteins or catalytically active portions thereof that contain a
modification(s) in the sequence of amino acids of an unmodified
ADA2 protein or a catalytically active portion thereof. In some
embodiments, the unmodified ADA2 protein can include the sequence
of amino acids set forth in SEQ ID NO:5, or a sequence of amino
acids that can exhibit at least 85% sequence identity to the
sequence of amino acids set forth in SEQ ID NO:5, or is a
catalytically active portion thereof; the amino acid
modification(s) are selected from among amino acid replacement(s),
deletion(s) and insertion(s); and the variant ADA2, when in dimer
form, can exhibit one or more properties selected from among
increased adenosine deaminase activity, reduced heparin binding,
longer serum half-life, altered pH optimum, increased thermal
stability, altered receptor binding and hyperglycosylation compared
to the corresponding dimer form of the unmodified ADA2 protein. A
variety of amino acid modifications, including replacements,
deletions and insertions are provided. It is understood that the
discreet modifications that confer a particular activity or
property can be combined; as in proteins effects of mutation or
modifications generally are additive. Any of the variant ADA2 or
catalytically active portion thereof provided herein that contains
modifications, including replacements, deletions and insertions,
and nucleic acids encoding the variant ADA2 or catalytically active
portion thereof, can be used in any of the methods, compositions,
conjugates, modified forms, vectors, cells, combinations, uses and
compositions for use, and combinations for use, provided
herein.
[0006] In some embodiments, the variant ADA2 protein or
catalytically active portion thereof, when in dimer form, exhibits
increased adenosine deaminase activity or increased adenosine
deaminase activity and reduced heparin binding.
[0007] In some embodiments, the unmodified ADA2 protein is a
homodimer, and the monomer form comprises the sequence of amino
acid residues set forth in SEQ ID NO:5. In some embodiments, the
variant ADA2 is a catalytically active portion of the variant ADA2
protein as provided herein, wherein the unmodified ADA2 protein is
a homodimer of corresponding catalytically active portions of the
polypeptide whose sequence is set forth in of SEQ ID NO:5, wherein
corresponding portions are determined by alignment.
[0008] In some embodiment, the ADA2 protein or catalytically active
portion thereof does not contain a modification selected from among
an amino acid replacement corresponding to H7R, G18A, G18R, G18V,
I64T, A80D, H83Q, V90A, C108G, A120V, H121R, W133G, R125C, R140Q,
K141R, R142W, P164L, P222L, W235S, H306R, E330G, W333G, V365L,
Y424C, F464S or a deletion corresponding to R8-K14del.fwdarw.--,
with numbering with reference to amino acid residues set forth in
SEQ ID NO:5.
[0009] In some embodiments, the unmodified ADA2 protein can include
a sequence of amino acids that has at least 85%, 86%, 87%, 88%,
89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more
sequence identity to the sequence of amino acids set forth in SEQ
ID NO:5 or is a catalytically active portion thereof. For example,
the unmodified ADA2 protein has at least 95% sequence identity with
the sequence of amino acids set forth in SEQ ID NO:5 or with the
corresponding catalytically active portion thereof. For example,
the unmodified ADA2 protein includes the sequence of amino acids
set forth in any of SEQ ID NOS:5, 326-334, 340, 375 or 380-383 or
is a catalytically active portion thereof, or the unmodified ADA2
protein has a sequence of amino acids set forth in any of SEQ ID
NOS:5, 326-334, 340, 375 and 380-383 or is a catalytically active
portion thereof. In particular embodiments, the unmodified ADA2
protein includes the sequence of amino acids set forth in SEQ ID
NO:5 or is a catalytically active portion thereof.
[0010] In some embodiments, the catalytically active portion of the
ADA2 protein can be an ADA2 protein that lacks all or a portion of
the putative receptor binding (PRB) domain. For example, the
catalytically active portion of the ADA2 protein can include the
sequence of amino acids set forth in SEQ ID NOS:548-550. In some
embodiments, the catalytically active portion of the unmodified
ADA2 protein has the sequence set forth as residues 77-473 of the
protein set forth in SEQ ID NO:5.
[0011] In some embodiments, the variant ADA2 protein can include up
to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,
53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
70 or more amino acid modifications compared to the unmodified ADA2
protein. In some embodiments the variant ADA2 protein includes up
to 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid modifications. In some
embodiments, the variant ADA2 protein does not contain the sequence
of amino acids set forth in any of SEQ ID NOS: 1, 5, 68, 286-302,
326-342 or 374-383 or catalytically active fragment thereof. In
some embodiments, the primary amino acid sequence of the ADA2
protein variant is not the sequence of amino acids set forth in any
of SEQ ID NOS: 1, 5, 68, 286-302, 326-342 or 374-383.
[0012] In some embodiments, the variant ADA2 protein, when in dimer
form, exhibits adenosine deaminase activity to convert adenosine to
inosine. In some embodiments herein, the variant ADA2 protein, when
in dimer form, can exhibit a catalytic efficiency
(k.sub.cat/K.sub.M) that is at least or at least about
5.times.10.sup.3 M.sup.-1 s.sup.-1, 6.times.10.sup.3 M.sup.-1
s.sup.-1, 7.times.10.sup.3 M.sup.-1 s.sup.-1, 8.times.10.sup.3
M.sup.-1 s.sup.-1, 9.times.10.sup.3 M.sup.-1 s.sup.-1,
1.times.10.sup.4 M.sup.-1 s.sup.-1, 2.times.10.sup.4 M.sup.-1
s.sup.-1, 3.times.10.sup.4 M.sup.-1 s.sup.-1, 4.times.10.sup.4
M.sup.-1 s.sup.-1, 5.times.10.sup.4 M.sup.-1 s.sup.-1,
6.times.10.sup.4 M.sup.-1 s.sup.-1, 7.times.10.sup.4 M.sup.-1
s.sup.-1, 8.times.10.sup.4 M.sup.-1 s.sup.-1, 9.times.10.sup.4
M.sup.-1 s.sup.-1, 1.times.10.sup.5 M.sup.-1 s.sup.-1,
2.times.10.sup.5 M.sup.-1 s.sup.-1, 3.times.10.sup.5 M.sup.-1
s.sup.-1, 4.times.10.sup.5 M.sup.-1 s.sup.-1, 5.times.10.sup.5
M.sup.-1 s.sup.-1 or greater.
[0013] In some embodiments, the variant ADA2 protein, when in dimer
form, can exhibit a thermal stability with a melting temperature
(Tm) of at least 58.degree. C. For example, the Tm of the ADA2
protein is at least 59.degree. C., 60.degree. C., 61.degree. C.,
62.degree. C., 63.degree. C., 64.degree. C., 65.degree. C.,
66.degree. C., 68.degree. C., 69.degree. C., 70.degree. C.,
71.degree. C., 72.degree. C. or greater.
[0014] In some embodiments, the variant ADA2 protein can contain a
modification(s) that is an amino acid replacement(s); and the
variant ADA2 protein includes one or more amino acid replacement(s)
at an amino acid position corresponding to amino acid residue 11,
13, 20, 22, 26, 86, 179, 217, 219, 221, 258, 262, 264, 266, 267,
277, 283, 296, 309, 317, 321, 352, 366, 371, 372, 373, 374, 403,
404, 405, 406, 441, 444, 452, 461, 469 or 470, with reference to
amino acid positions set forth in SEQ ID NO:5. For example, the
amino acid replacement(s) are positions corresponding to amino acid
residue 11, 20, 219, 221, 262, 264, 366, 371, 372 or 452, with
reference to amino acid positions set forth in SEQ ID NO:5. In some
embodiments, the variant ADA2 protein can include one or more amino
acid replacement(s) selected from among K11A, K11D, K11E, K13A,
K13D, K13E, R20A, R20D, R20E, R20N, V22S, K26A, K26D, K26E, D86A,
D86C, D86E, D86F, D86G, D86H, D86I, D86K, D86L, D86M, D86N, D86P,
D86Q, D86R, D86S, D86T, D86V, D86W, D86Y, E179A, E179C, E179D,
E179F, E179G, E179H, E179I, E179K, E179L, E179M, E179N, E179P,
E179Q, E179R, E179S, E179T, E179V, E179W, E179Y, R217A, R217D,
R217E, R219A, R219C, R219D, R219E, R219F, R219G, R219H, R219I,
R219K, R219L, R219M, R219N, R219P, R219Q, R219S, R219T, R219V,
R219W, R219Y, L221A, L221C, L221D, L221E, L221F, L221G, L221H,
L221I, L221K, L221M, L221N, L221P, L221Q, L221R, L221S, L221T,
L221V, L221W, L221Y, K258A, K258D, K258E, S262A, S262C, S262D,
S262E, S262F, S262G, S262H, S262I, S262K, S262L, S262M, S262N,
S262P, S262Q, S262R, S262T, S262V, S262W, S262Y, H264A, H264C,
H264D, H264E, H264F, H264G, H264I, H264K, H264L, H264M, H264N,
H264P, H264Q, H264R, H264S, H264T, H264V, H264W, H264Y, S266A,
S266C, S266D, S266E, S266F, S266G, S266H, S266I, S266K, S266L,
S266M, S266N, S266P, S266Q, S266R, S266T, S266V, S266W, S266Y,
K267A, K267C, K267D, K267E, K267F, K267G, K267H, K267I, K267L,
K267M, K267N, K267P, K267Q, K267R, K267S, K267T, K267V, K267W,
K267Y, R277A, R277D, R277E, R283A, R283D, R283E, V296A, V296C,
V296D, V296E, V296F, V296G, V296H, V296I, V296K, V296L, V296M,
V296N, V296P, V296Q, V296R, V296S, V296T, V296W, V296Y, K309A,
K309D, K309E, K317A, K317D, K317E, K321A, K321D, K321E, R352A,
R352D, R352E, R366A, R366D, R366E, K371A, K371D, K371E, K371N,
K372A, K372D, K372E, K372N, D373S, I374S, T403N, G404N, H405S,
P406S, R441A, R441D, R441E, K444A, K444D, K444E, K452A, K452D,
K452E, K461A, K461D, K461E, K469A, K469D, K469E, K470A, K470D, and
K470E, with reference to amino acid positions set forth in SEQ ID
NO:5. For example, the variant ADA2 protein contains one or more
amino acid replacement(s) selected from among replacements
corresponding to H264A; H264Q; H264N; H264G; R219K; R219Q; R219N;
R219A; L221A; L221V; L221G; E179D; E179A; E179S; E179T; E179V;
E179G; S262A; S262V; S262M; S262N; D86A; D86C; D86E; D86F; D86G;
D86H; D86I; D86K; D86L; D86M; D86N; D86P; D86Q; D86R; D86S; D86T;
D86V; D86W; D86Y; E179C; E179F; E179H; E179I; E179K; E179L; E179M;
E179N; E179P; E179Q; E179R; E179W; E179Y; R219C; R219D; R219E;
R219F; R219G; R219H; R219I; R219L; R219M; R219P; R219S; R219T;
R219V; R219W; R219Y; L221C; L221D; L221E; L221F; L221H; L221I;
L221K; L221M; L221N; L221P; L221Q; L221R; L221S; L221T; L221W;
L221Y; S262C; S262D; S262E; S262F; S262G; S262H; S262I; S262K;
S262L; S262P; S262Q; S262R; S262T; S262W; S262Y; H264C; H264D;
H264E; H264F; H264I; H264K; H264L; H264M; H264P; H264R; H264S;
H264T; H264V; H264W; H264Y; S266A; S266C; S266D; S266E; S266F;
S266G; S266H; S266I; S266K; S266L; S266M; S266N; S266P; S266Q;
S266R; S266T; S266V; S266W; S266Y; K267A; K267C; K267D; K267E;
K267F; K267G; K267H; K267I; K267L; K267M; K267N; K267P; K267Q;
K267R; K267S; K267T; K267V; K267W; K267Y; V296A; V296C; V296D;
V296E; V296F; V296G; V296H; V296I; V296K; V296L; V296M; V296N;
V296P; V296Q; V296R; V296S; V296T; V296W; and V296Y.
[0015] In some embodiments, the variant ADA2 protein contains an
amino acid replacement at one or both of positions corresponding to
amino acid residue 219 and 262, with reference to amino acid
positions set forth in SEQ ID NO:5. For Example, the variant ADA2
protein or catalytically active portion thereof contains the
replacement corresponding to S262N or S262Q. In some embodiments,
the variant ADA2 contains the replacement corresponding to S262N.
In some embodiments, the variant ADA2 contains the replacement
corresponding to R219K, R219Q, R219N or R219A. In other
embodiments, the variant ADA2 contains the replacement
corresponding to R219Q or the replacements R219Q/R20E. In other
embodiments, the variant ADA2 contains the replacement
corresponding to R219Q/S262N. For example, the variant ADA2 protein
or catalytically active portion thereof contains modification(s)
selected from among any of
R219Q/S262N/--.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3,
R219Q/S262N/R20N/V22S, R219Q/S262N/K371N/D373S,
R219Q/S262N/K372N/I374S, R219Q/S262N/T403N/H405S,
R219Q/S262N/G404N/P406S,
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.15,
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.10,
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.7,
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.5,
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.3,
R219Q/S262N/R125N/P126A, R219Q/S262N/S127N/K129S,
R219Q/S262N/P126N/E128T, R219Q/S262N/R112N/I114T,
R219Q/S262N/I134N/L135C/L136T, R219Q/S262N/I134N/L135S/L136T,
R219Q/S262N/R142N/Q144S, R219Q/S262N/E137N/Y139T,
R219Q/S262N/P111N/G113S, R219Q/S262N/F119S, R219Q/S262N/F119K,
R219Q/S262N/Y224R, R219Q/S262N/Y224N, R219Q/S262N/Y191S,
R219Q/S262N/Y191D, R219Q/S262N/F183K, R219Q/S262N/Y191D/Y224R,
R219Q/S262N/F109S, R219Q/S262N/F109A, R219Q/S262N/R118D,
R219Q/S262N/R118A, R219Q/S262N/Y139T, R219Q/S262N/Y139A,
R219Q/S262N/W133S, R219Q/S262N/W133T, R219Q/S262N/P124A,
R219Q/S262N/P124S, R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.1,
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.2,
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.3,
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.1,
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.2,
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.3,
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.1,
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.2,
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.3,
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.1,
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.2,
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.3,
R219Q/S262N/C105-T147del.fwdarw.(Gly)n, R219Q/S262N/K11A,
R219Q/S262N/K11D, R219Q/S262N/K11E, R219Q/S262N/K13A,
R219Q/S262N/K13D, R219Q/S262N/V99-Q144del.fwdarw.(GGGGS)n,
R219Q/S262N/C105-T147del.fwdarw.(GGGGS)n, R219Q/S262N/N98-N156del,
R219Q/S262N/C105-E148del, R219Q/S262N/C105-T147del,
R219Q/S262N/V99-Q144del,
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)n,
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.15,
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.10,
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.7,
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.5,
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.3,
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS)n,
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS)n,
R219Q/S262N/K371D/N98-N156del, R219Q/S262N/K371D/C105-E148del,
R219Q/S262N/K371D/C105-T147del, R219Q/S262N/K371D/V99-Q144del,
R219Q/S262N/K13E, R219Q/S262N/K371A, R219Q/S262N/K372A,
R219Q/S262N/K372D, R219Q/S262N/K372E, R219Q/S262N/K452A,
R219Q/S262N/K452D, R219Q/S262N/K452E, R219Q/S262N/R20A,
R219Q/S262N/R20D, R219Q/S262N/R366A, R219Q/S262N/R366D,
R219Q/S262N/R366E, R219Q/S262N/H264A, R219Q/S262N/H264Q,
R219Q/S262N/H264N, R219Q/S262N/H264G, R219K/S262N, R219N/S262N,
R219A/S262N, R219Q/S262N/L221A, R219Q/S262N/L221V,
R219Q/S262N/L221G, R219Q/S262N/E179D, R219Q/S262N/E179A,
R219Q/S262N/E179S, R219Q/S262N/E179T, R219Q/S262N/E179V,
R219Q/S262N/E179G, R219Q/S262A, R219Q/S262V, R219Q/S262M,
R219Q/S262N/K11A/R20A, R219Q/S262N/K11A/R20A/K371A,
R219Q/S262N/R20A/K371A, R219Q/S262N/K11A/K371A, R219Q/S262N/K26A,
R219Q/S262N/K26D, R219Q/S262N/K26E, R219Q/S262N/R217A,
R219Q/S262N/R217D, R219Q/S262N/R217E, R219Q/S262N/K258A,
R219Q/S262N/K258D, R219Q/S262N/K258E, R219Q/S262N/R277A,
R219Q/S262N/R277D, R219Q/S262N/R277E, R219Q/S262N/R283A,
R219Q/S262N/R283D, R219Q/S262N/R283E, R219Q/S262N/K309A,
R219Q/S262N/K309D, R219Q/S262N/K309E, R219Q/S262N/K317A,
R219Q/S262N/K317D, R219Q/S262N/K317E, R219Q/S262N/K321A,
R219Q/S262N/K321D, R219Q/S262N/K321E, R219Q/S262N/R352A,
R219Q/S262N/R352D, R219Q/S262N/R352E, R219Q/S262N/R441A,
R219Q/S262N/R441D, R219Q/S262N/R441E, R219Q/S262N/K444A,
R219Q/S262N/K444D, R219Q/S262N/K444E, R219Q/S262N/K461A,
R219Q/S262N/K461D, R219Q/S262N/K461E, R219Q/S262N/K469A,
R219Q/S262N/K469D, R219Q/S262N/K469E, R219Q/S262N/K470A,
R219Q/S262N/K470D, R219Q/S262N/K470E, R219Q/S262N/D86A,
R219Q/S262N/D86C, R219Q/S262N/D86E, R219Q/S262N/D86F,
R219Q/S262N/D86G, R219Q/S262N/D86H, R219Q/S262N/D86I,
R219Q/S262N/D86K, R219Q/S262N/D86L, R219Q/S262N/D86M,
R219Q/S262N/D86N, R219Q/S262N/D86P, R219Q/S262N/D86Q,
R219Q/S262N/D86R, R219Q/S262N/D86S, R219Q/S262N/D86T,
R219Q/S262N/D86V, R219Q/S262N/D86W, R219Q/S262N/D86Y,
R219Q/S262N/E179C, R219Q/S262N/E179F, R219Q/S262N/E179H,
R219Q/S262N/E179I, R219Q/S262N/E179K, R219Q/S262N/E179L,
R219Q/S262N/E179M, R219Q/S262N/E179N, R219Q/S262N/E179P,
R219Q/S262N/E179Q, R219Q/S262N/E179R, R219Q/S262N/E179W,
R219Q/S262N/E179Y, R219C/S262N, R219D/S262N, R219E/S262N,
R219F/S262N, R219G/S262N, R219H/S262N, R219I/S262N, R219L/S262N,
R219M/S262N, R219P/S262N, R219S/S262N, R219T/S262N, R219V/S262N,
R219W/S262N, R219Y/S262N, R219Q/S262N/L221C, R219Q/S262N/L221D,
R219Q/S262N/L221E, R219Q/S262N/L221F, R219Q/S262N/L221H,
R219Q/S262N/L221I, R219Q/S262N/L221K, R219Q/S262N/L221M,
R219Q/S262N/L221N, R219Q/S262N/L221P, R219Q/S262N/L221Q,
R219Q/S262N/L221R, R219Q/S262N/L221S, R219Q/S262N/L221T,
R219Q/S262N/L221W, R219Q/S262N/L221Y, R219Q/S262C, R219Q/S262D,
R219Q/S262E, R219Q/S262F, R219Q/S262G, R219Q/S262H, R219Q/S262I,
R219Q/S262K, R219Q/S262L, R219Q/S262P, R219Q/S262Q, R219Q/S262R,
R219Q/S262T, R219Q/S262W, R219Q/S262Y, R219Q/S262N/H264C,
R219Q/S262N/H264D, R219Q/S262N/H264E, R219Q/S262N/H264F,
R219Q/S262N/H264I, R219Q/S262N/H264K, R219Q/S262N/H264L,
R219Q/S262N/H264M, R219Q/S262N/H264P, R219Q/S262N/H264R,
R219Q/S262N/H264S, R219Q/S262N/H264T, R219Q/S262N/H264V,
R219Q/S262N/H264W, R219Q/S262N/H264Y, R219Q/S262N/S266A,
R219Q/S262N/S266C, R219Q/S262N/S266D, R219Q/S262N/S266E,
R219Q/S262N/S266F, R219Q/S262N/S266G, R219Q/S262N/S266H,
R219Q/S262N/S266I, R219Q/S262N/S266K, R219Q/S262N/S266L,
R219Q/S262N/S266M, R219Q/S262N/S266N, R219Q/S262N/S266P,
R219Q/S262N/S266Q, R219Q/S262N/S266R, R219Q/S262N/S266T,
R219Q/S262N/S266V, R219Q/S262N/S266W, R219Q/S262N/S266Y,
R219Q/S262N/K267A, R219Q/S262N/K267C, R219Q/S262N/K267D,
R219Q/S262N/K267E, R219Q/S262N/K267F, R219Q/S262N/K267G,
R219Q/S262N/K267H, R219Q/S262N/K267I, R219Q/S262N/K267L,
R219Q/S262N/K267M, R219Q/S262N/K267N, R219Q/S262N/K267P,
R219Q/S262N/K267Q, R219Q/S262N/K267R, R219Q/S262N/K267S,
R219Q/S262N/K267T, R219Q/S262N/K267V, R219Q/S262N/K267W,
R219Q/S262N/K267Y, R219Q/S262N/V296A, R219Q/S262N/V296C,
R219Q/S262N/V296D, R219Q/S262N/V296E, R219Q/S262N/V296F,
R219Q/S262N/V296G, R219Q/S262N/V296H, R219Q/S262N/V296I,
R219Q/S262N/V296K, R219Q/S262N/V296L, R219Q/S262N/V296M,
R219Q/S262N/V296N, R219Q/S262N/V296P, R219Q/S262N/V296Q,
R219Q/S262N/V296R, R219Q/S262N/V296S, R219Q/S262N/V296T,
R219Q/S262N/V296W and R219Q/S262N/V296Y. In some embodiments, the
variant ADA2 protein comprises the modifications selected from
among R219Q/K11A/R20A, R219Q/K11A/R20A/K371A, R219Q/R20A/K371A,
219Q/K11A/K371A, S262N/K11A/R20A, S262N/K11A/R20A/K371A,
S262N/R20A/K371A, S262N/K11A/K371A,
R219Q/C105-T147del.fwdarw.(Gly)n,
R219Q/V99-Q144del.fwdarw.(GGGGS)n,
R219Q/C105-T147del.fwdarw.(GGGGS)n, R219Q/N98-N156del,
R219Q/C105-E148del, R219Q/C105-T147del, R219Q/V99-Q144del,
S262N/C105-T147del.fwdarw.(Gly)n,
S262N/V99-Q144del.fwdarw.(GGGGS)n,
S262N/C105-T147del.fwdarw.(GGGGS)n, S262N/N98-N156del,
S262N/C105-E148del, S262N/C105-T147del and S262N/V99-Q144del.
[0016] In some embodiments, the variant ADA2 protein, when in dimer
form, can exhibit increased adenosine deaminase activity. For
example, the variant ADA2 protein, when in dimer form, can exhibit
at least 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%,
200%, 225%, 250%, 300%, 350%, 400%, 450%, 500%, 600%, 700%, 800% or
more activity of the corresponding dimer form of the unmodified
ADA2 protein, wherein adenosine deaminase activity is assessed
under the same conditions. In some embodiments, the variant ADA2
protein, when in dimer form, can exhibit a catalytic efficiency
(k.sub.cat/K.sub.M) that is at least or at least about 1.2-fold,
1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold,
1.9-fold, 2.0-fold, 2.2-fold, 2.5-fold, 3.0-fold, 3.5-fold, 4-fold,
4.5-fold, 5.0-fold, 6.0-fold, 7.0-fold, 8.0-fold, 9.0-fold,
10.0-fold or more compared to the catalytic efficiency
(k.sub.cat/K.sub.M) of the corresponding dimer form of the
unmodified ADA2 protein, wherein catalytic efficiency of adenosine
deaminase activity is assessed under the same conditions. For
example, the variant ADA2 protein, when in dimer form, can exhibit
a catalytic efficiency (k.sub.cat/K.sub.M) that is at least or at
least about 2.times.10.sup.4M.sup.-1 s.sup.-1,
3.times.10.sup.4M.sup.-1 s.sup.-1, 4.times.10.sup.4M.sup.-1
s.sup.-1, 5.times.10.sup.4 M.sup.-1 s.sup.-1, 6.times.10.sup.4
M.sup.-1 s.sup.-1, 7.times.10.sup.4M.sup.-1 s.sup.-1,
8.times.10.sup.4M.sup.-1 s.sup.-1, 9.times.10.sup.4 M.sup.-1
s.sup.-1, 1.times.10.sup.5 M.sup.-1 s.sup.-1,
2.times.10.sup.5M.sup.-1 s.sup.-1, 3.times.10.sup.5M.sup.-1
s.sup.-1, 4.times.10.sup.5 M.sup.-1 s.sup.-1, 5.times.10.sup.5
M.sup.-1 s.sup.-1 or greater.
[0017] In some embodiments, the variant ADA2 protein or
catalytically active portion thereof contains the modifications
selected from among K371D/V99-Q144del.fwdarw.(GGGGS).sub.1,
K371D/V99-Q144del.fwdarw.(GGGGS).sub.2,
K371D/V99-Q144del.fwdarw.(GGGGS).sub.3,
K371D/C105-T147del.fwdarw.(GGGGS).sub.1,
K371D/C105-T147del.fwdarw.(GGGGS).sub.2,
K371D/C105-T147del.fwdarw.(GGGGS).sub.3,
R219Q/S262N/--.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3,
K371D/C105-T147del.fwdarw.(Gly)n,
K371D/C105-T147del.fwdarw.(Gly).sub.15,
K371D/C105-T147del.fwdarw.(Gly).sub.10,
K371D/C105-T147del.fwdarw.(Gly).sub.7,
K371D/C105-T147del.fwdarw.(Gly).sub.5,
K371D/C105-T147del.fwdarw.(Gly).sub.3,
K371D/V99-Q144del.fwdarw.(GGGGS)n,
K371D/C105-T147del.fwdarw.(GGGGS)n, K371D/N98-N156del,
K371D/C105-E148del, K371D/C105-T147del and K371D/V99-Q144del. In
some embodiments, the variant ADA2 protein or catalytically active
portion thereof contains modifications selected from among
R125N/P126A, S127N/K129S, P126N/E128T, R112N/I114T,
I134N/L135C/L136T, I134N/L135S/L136T, R142N/Q144S, E137N/Y139T,
P111N/G113S, F119S, F119K, Y224R, Y224N, Y191S, Y191D, F183K,
Y191D/Y224R, F109S, F109A, R118D, R118A, Y139T, Y139A, W133S,
W133T, P124A, P124S, V99-Q144del, V99-Q144del-*(GGGGS)n,
C105-T147del.fwdarw.(GGGGS)n, V99-Q144del.fwdarw.(GGGGS).sub.1,
V99-Q144del.fwdarw.(GGGGS).sub.2, V99-Q144del.fwdarw.(GGGGS).sub.3,
C105-T147del.fwdarw.(GGGGS).sub.1,
C105-T147del.fwdarw.(GGGGS).sub.2, and
C105-T147del.fwdarw.(GGGGS).sub.3.
[0018] In some embodiments, the variant ADA2 protein or
catalytically active portion thereof contains modifications
selected from among R125N/P126A, S127N/K129S, P126N/E128T,
R112N/I114T, I134N/L135C/L136T, I134N/L135S/L136T, R142N/Q144S,
E137N/Y139T, P111N/G113S, F119S, F119K, Y224R, Y224N, Y191S, Y191D,
F183K, Y191D/Y224R, F109S, F109A, R118D, R118A, Y139T, Y139A,
W133S, W133T, P124A, P124S, V99-Q144del,
V99-Q144del.fwdarw.(GGGGS)n, C105-T147del.fwdarw.(GGGGS)n,
V99-Q144del.fwdarw.(GGGGS).sub.1, V99-Q144del.fwdarw.(GGGGS).sub.2,
V99-Q144del.fwdarw.(GGGGS).sub.3,
C105-T147del.fwdarw.(GGGGS).sub.1,
C105-T147del.fwdarw.(GGGGS).sub.2 and
C105-T147del.fwdarw.(GGGGS).sub.3.
[0019] For example, among such variant ADA2 proteins are any that
include one or more amino acid replacement(s) at an amino acid
position corresponding to amino acid residue 11, 20, 219, 221, 262,
264, 366, 371, 372 or 452, with reference to amino acid positions
set forth in SEQ ID NO:5. For example, the variant ADA2 protein can
include one or more amino acid replacement(s) selected from among
K11A, K11E, R20A, R20E, R219K, R219Q, L221A, L221V, L221G, S262N,
H264Q, H264G, R366E, K371A, K371D, K371E, K372D, K372E, K452D and
K452E, with reference to amino acid positions set forth in SEQ ID
NO:5. In some embodiments, the variant ADA2 protein can include
amino acid replacements selected from among K11A/R20A,
K11A/R20A/K371A, R20A/K371A, K11A/K371A, S262N/K371D, S262N/K371E,
S262N/R20E, S262N/R20E/K371D, S262N/R20E/K371E, R219Q/K371E,
R219Q/K371D, R219Q/R20E, R219Q/K371E/R20E, R219Q/K371D/R20E,
R219Q/S262N/K371E, R219Q/S262N/K371D, R219Q/S262N/R20E,
R219Q/S262N/K371E/R20E, R219Q/S262N/K371D/R20E and R219Q/S262N,
with reference to amino acid positions set forth in SEQ ID
NO:5.
[0020] In some embodiments, the variant ADA2 protein, when in dimer
form, can exhibit reduced heparin binding. For example, the variant
ADA2 protein, when in dimer form, can exhibit no more than 1%, 2%,
3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%,
50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% of the heparin
binding of the corresponding dimer form of the unmodified ADA2
protein, wherein heparin binding is assessed under the same
conditions.
[0021] For example, among such the variant ADA2 proteins are any
that include one or more amino acid replacement(s) at an amino acid
position corresponding to amino acid residue 20, 262, 366, 371,
372, or 452, with reference to amino acid positions set forth in
SEQ ID NO:5. For example, the variant ADA2 protein can include one
or more amino acid replacement(s) selected from among R20A, R20D,
R20E, S262N, R366A, R366D, R366E, K371A, K371D, K371E, K372A,
K372D, K372E and K452E, with reference to amino acid positions set
forth in SEQ ID NO:5. In some embodiments, the variant ADA2 protein
can include amino acid replacements selected from among K11A/R20A,
K11A/R20A/K371A, R20A/K371A, K11A/K371A, S262N/K371D, S262N/K371E,
S262N/R20E, S262N/R20E/K371D and S262N/R20E/K371E, with reference
to amino acid positions set forth in SEQ ID NO:5.
[0022] In some embodiments, the variant ADA2 protein or
catalytically active portion thereof contains one or more amino
acid replacement(s) corresponding to K11A; K11D; K11E; K13A; K13D;
K13E; K371A; K371D; K371E; K372A; K372D; K372E; K452A; K452D;
K452E; R20A; R20D; R20E; R366A; R366D; R366E; K26A; K26D; K26E;
R217A; R217D; R217E; K258A; K258D; K258E; R277A; R277D; R277E;
R283A; R283D; R283E; K309A; K309D; K309E; K317A; K317D; K317E;
K321A; K321D; K321E; R352A; R352D; R352E; R441A; R441D; R441E;
K444A; K444D; K444E; K461A; K461D; K461E; K469A; K469D; K469E;
K470A; K470D; and K470E.
[0023] In some embodiments, the variant ADA2 protein, when in dimer
form, can exhibit a longer serum half-life (t.sub.1/2). For
example, the variant ADA2, when in dimer form, can exhibit a
half-life that is at least or at least about 110%, 120%, 130%,
140%, 150%, 160%, 170%, 180%, 190%, 200%, 225%, 250%, 300%, 350%,
400%, 450%, 500%, 600%, 700%, 800% or more longer than the
half-life of the corresponding dimer form of the unmodified ADA2
protein, wherein half-life is assessed under the same
conditions.
[0024] In some embodiments, the variant ADA2 protein, when in dimer
form, can exhibit increased thermal stability. For example, the
variant ADA2 protein, when in dimer form, can exhibit thermal
stability with a melting temperature (Tm) that is increased at
least or at least about 0.5.degree. C., 1.0.degree. C., 2.0.degree.
C., 3.0.degree. C., 4.0.degree. C., 5.0.degree. C., 6.0.degree. C.,
7.0.degree. C., 8.0.degree. C., 9.0.degree. C., 10.0.degree. C. or
more compared to the Tm of the corresponding dimer form of the
unmodified ADA2 protein, wherein Tm is assessed under the same
conditions. For example, the variant ADA2 protein can have a
melting temperature (Tm) of at least or at least about 67.6.degree.
C., 67.8.degree. C., 68.0.degree. C., 68.2.degree. C., 68.4.degree.
C., 68.6.degree. C., 68.8.degree. C., 69.0.degree. C., 69.2.degree.
C., 69.4.degree. C., 69.6.degree. C., 69.8.degree. C., 70.0.degree.
C., 70.2.degree. C., 70.4.degree. C., 70.6.degree. C., 70.8.degree.
C., 71.0.degree. C., 71.2.degree. C., 71.4.degree. C., 71.6.degree.
C., 71.8.degree. C. or higher.
[0025] In examples of any of the variant ADA2 proteins provided
herein, the adenosine deaminase activity of the variant ADA2
protein can be assessed or exhibited at or about pH 6.5.+-.0.2. In
some examples, the variant ADA2 protein, when in dimer form, can
exhibit an altered pH optimum for adenosine deaminase activity. For
example, the variant ADA2 protein, when in dimer form, can exhibit
a pH optimum for adenosine deaminase activity that is at a higher
pH compared to the pH optimum of the corresponding dimer form of
the unmodified ADA2 protein. For example, the variant ADA2 protein,
when in dimer form, can have a pH optimum with a pH that is at
least or at least about 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3,
7.4, 7.5 or higher. In other examples, the variant ADA2 protein,
when in dimer form, can exhibit a pH optimum for adenosine
deaminase activity that is at a lower pH compared to the pH optimum
of the corresponding dimer form of the unmodified ADA2 protein. For
example, the variant ADA2 protein, when in dimer form, can have a
pH optimum with a pH that is less than or less than about 6.5, 6.4,
6.3, 6.3, 6.2, 6.1, 6.0 or less.
[0026] In some embodiments, the variant ADA2 protein can include a
modification of one or more amino acids in the putative receptor
binding (PRB) domain, wherein the modification is an amino acid
deletion, insertion or replacement. In any of such examples, the
variant ADA2 protein does not contain a modification that is an
amino acid replacement corresponding to amino acid replacement
C108G, A120V, H121R, R125C, R140Q, K141R or R142W, with reference
to amino acid positions set forth in SEQ ID NO:5.
[0027] In some embodiments, the variant ADA2 protein or
catalytically active portion thereof lacks all or a portion of the
putative receptor binding (PRB) domain or has a modification of the
PRB, whereby any receptor binding or growth factor activity is
reduced or eliminated or other activity of ADA2 other than
deaminase activity is reduced or eliminated or interaction with the
ADA domain is reduced or eliminated and the PRB domain corresponds
to residues 98 to 156 set forth in SEQ ID NO:5. In some
embodiments, the variant ADA2 lacks residues 105-148 or 105 to 147
or 99 to 144, with reference to amino acid positions set forth in
SEQ ID NO:5. In some examples, the variant ADA2 protein or
catalytically active portion thereof contains the sequence of amino
acids set forth in any of SEQ ID NOS:548-550 and 579. In some
embodiments, variant ADA2 protein or catalytically active portion
thereof contains a deletion of all or a portion of the PRB domain
and optionally an insertion of peptide linker.
[0028] In some examples, the variant ADA2 protein can have a
deletion of one or more contiguous amino acid residues
corresponding to any one or more contiguous amino acid residues
between or between about amino acid residues 98 and 156 or amino
acid residues 105 and 148, inclusive, with reference to amino acid
positions set forth in SEQ ID NO:5. In any of such examples, the
variant of the ADA2 polypeptide can further include substitution of
the deleted region with a peptide linker. For example, the peptide
linker can be selected from among (Gly)n (SEQ ID NO:368), where n
is 2 to 20; (GGGGS)n (SEQ ID NO:343), where n is 1 to 6; (SSSSG)n
(SEQ ID NO:344), where n is 1 to 6; (AlaAlaProAla)n (SEQ ID
NO:350), where n is 1 to 6; GKSSGSGSESKS (SEQ ID NO:345);
GGSTSGSGKSSEGKG (SEQ ID NO:346); GSTSGSGKSSSEGSGSTKG (SEQ ID
NO:347); GSTSGSGKPGSGEGSTKG (SEQ ID NO:348); and EGKSSGSGSESKEF
(SEQ ID NO:349). For example, the peptide linker can be selected
from among GGG (SEQ ID NO:369); GGGGG (SEQ ID NO:360); GGGGGGG (SEQ
ID NO:370); GGGGGGGGGG (SEQ ID NO:371); and GGGGGGGGGGGGGGG (SEQ ID
NO:372).
[0029] In some embodiments, the variant ADA2 can contain the
variant ADA2 polypeptide that can include a modification in the PRB
domain that corresponds to C105-T147del.fwdarw.(Gly).sub.n, where n
is 2 to 20, such as C105-T147del.fwdarw.(Gly).sub.15,
C105-T147del.fwdarw.(Gly).sub.10, C105-T147del.fwdarw.(Gly).sub.7,
C105-T147del.fwdarw.(Gly).sub.5 or C105-T147del.fwdarw.(Gly).sub.3,
with reference to amino acid positions set forth in SEQ ID NO:5. In
some embodiments, the variant ADA2 can include modification in the
PRB domain that corresponds to C105-T147del.fwdarw.(Gly)n, where
n=2 to 20; C105-T147del.fwdarw.(Gly).sub.15;
C105-T147del.fwdarw.(Gly).sub.10; C105-T147del.fwdarw.(Gly).sub.7;
C105-T147del.fwdarw.(Gly).sub.5; C105-T147del.fwdarw.(Gly).sub.3;
N98-N156del; C105-E148del; C105-T147del; V99-Q144del;
V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5;
C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5;
V99-Q144del.fwdarw.(GGGGS).sub.1; V99-Q144del.fwdarw.(GGGGS).sub.2;
V99-Q144del.fwdarw.(GGGGS).sub.3;
C105-T147del.fwdarw.(GGGGS).sub.1;
C105-T147del.fwdarw.(GGGGS).sub.2; and
C105-T147del.fwdarw.(GGGGS).sub.3, with reference to amino acid
positions set forth in SEQ ID NO:5.
[0030] In some embodiments, the variant ADA2 protein or
catalytically active portion thereof contains one or more amino
acid replacement(s) selected from among replacements corresponding
to F119S; F119K; Y224R; Y224N; Y191S; Y191D; F183K; Y191D/Y224R;
F109S; F109A; R118D; R118A; Y139T; Y139A; W133S; W133T; P124A; and
P124S, with reference to amino acid positions set forth in SEQ ID
NO:5. In some embodiments, the variant ADA2 protein or
catalytically active portion thereof contains amino acid
replacements selected from among replacements corresponding to
R219Q/S262N/F119S; R219Q/S262N/F119K; R219Q/S262N/Y224R;
R219Q/S262N/Y224N; R219Q/S262N/Y191S; R219Q/S262N/Y191D;
R219Q/S262N/F183K; R219Q/S262N/Y191D/Y224R; R219Q/S262N/F109S;
R219Q/S262N/F109A; R219Q/S262N/R118D; R219Q/S262N/R118A;
R219Q/S262N/Y139T; R219Q/S262N/Y139A; R219Q/S262N/W133S;
R219Q/S262N/W133T; R219Q/S262N/P124A; and R219Q/S262N/P124S. In
some embodiments, the variant ADA2 contains modifications selected
from among K371D/V99-Q144del.fwdarw.(GGGGS).sub.1;
K371D/V99-Q144del.fwdarw.(GGGGS).sub.2;
K371D/V99-Q144del.fwdarw.(GGGGS).sub.3;
K371D/C105-T147del.fwdarw.(GGGGS).sub.1;
K371D/C105-T147del.fwdarw.(GGGGS).sub.2;
K371D/C105-T147del.fwdarw.(GGGGS).sub.3;
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.15;
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.10;
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.7;
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.5;
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.3;
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.1;
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.2;
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.3;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.1;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.2;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.3;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.1;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.2;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.3;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.1;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.2;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.3;
K371D/C105-T147del.fwdarw.(Gly)n, where n=2 to 20;
K371D/C105-T147del.fwdarw.(Gly).sub.15;
K371D/C105-T147del.fwdarw.(Gly).sub.10;
K371D/C105-T147del.fwdarw.(Gly).sub.7;
K371D/C105-T147del.fwdarw.(Gly).sub.5;
K371D/C105-T147del.fwdarw.(Gly).sub.3;
K371D/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5;
K371D/C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5;
K371D/N98-N156del; K371D/C105-E148del; K371D/C105-T147del;
K371D/V99-Q144del; R219Q/S262N/C105-T147del.fwdarw.(Gly)n, where
n=2 to 20; R219Q/S262N/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5;
R219Q/S262N/N98-N156del; R219Q/S262N/C105-E148del;
R219Q/S262N/C105-T147del; R219Q/S262N/V99-Q144del;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)n, where n=2 to 20;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.15;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.10;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.7;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.5;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.3;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5;
R219Q/S262N/K371D/N98-N156del; R219Q/S262N/K371D/C105-E148del;
R219Q/S262N/K371D/C105-T147del; R219Q/S262N/K371D/V99-Q144del;
R219Q/C105-T147del.fwdarw.(Gly)n, where n=2 to 20;
R219Q/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5;
R219Q/C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5;
R219Q/N98-N156del; R219Q/C105-E148del; R219Q/C105-T147del;
R219Q/V99-Q144del; S262N/C105-T147del.fwdarw.(Gly)n, where n=2 to
20; S262N/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5;
S262N/C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5;
S262N/N98-N156del; and S262N/C105-E148del; S262N/C105-T147del; and
S262N/V99-Q144del.
[0031] In some embodiments of a variant ADA2 protein, including
examples containing a modified PRB domain, the variant ADA2
protein, when in dimer form, can exhibit reduced binding to any one
or more adenosine receptor (ADR) selected from among A.sub.1,
A.sub.2A, A.sub.2B and A.sub.3 compared to binding of the
unmodified ADA2 protein to the same receptor when assessed under
the same conditions. For example, the variant ADA2 protein has a
binding that is reduced at least or at least about 0.5-fold,
1-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold,
8-fold, 9-fold, 10-fold or more.
[0032] In some embodiments of the variant ADA2 provided herein, the
variant ADA2 can be glycosylated, for example, at a native or a
non-native glycosylation site. In some embodiments, the variant
ADA2 protein can include a modification(s) that alters
glycosylation by introduction of a non-native glycosylation site,
whereby, when expressed in a cell capable of glycosylation, the
variant ADA2 protein is hyperglycosylated compared to the
unmodified ADA2 polypeptide. For example, the non-native
glycosylation site is introduced by amino acid replacement(s) or
insertion of one, two or three amino acids. For example, the
modifications are selected from among modifications corresponding
to --.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3, R20N/V22S, K371N/D373S,
K372N/I374S, T403N/H405S and G404N/P406S, with reference to amino
acid positions set forth in SEQ ID NO:5. In some embodiments, the
variant ADA2 or catalytically active portion thereof contains
modifications corresponding to
R219Q/S262N/--.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3;
R219Q/S262N/R20N/V22S; R219Q/S262N/K371N/D373S;
R219Q/S262N/K372N/I374S; R219Q/S262N/T403N/H405S; or
R219Q/S262N/G404N/P406S. In some embodiments, the variant ADA2
protein or catalytically active portion thereof contains a
modification in the putative receptor binding domain (PRB)
corresponding to one or more of the modifications selected from
among: R125N/P126A; S127N/K129S; P126N/E128T; R112N/I114T;
I134N/L135C/L136T; I134N/L135S/L136T; R142N/Q144S; E137N/Y139T; and
P111N/G113S. In some embodiments, the variant ADA2 protein or
catalytically active portion thereof contains amino acid
replacements corresponding to R219Q/S262N/R125N/P126A;
R219Q/S262N/S127N/K129S; R219Q/S262N/P126N/E128T;
R219Q/S262N/R112N/I114T; R219Q/S262N/I134N/L135C/L136T;
R219Q/S262N/I134N/L135S/L136T; R219Q/S262N/R142N/Q144S;
R219Q/S262N/E137N/Y139T; or R219Q/S262N/P111N/G113S.
[0033] In some embodiments, the variant ADA2 protein can be a human
ADA2. In some embodiments, the variant ADA2 protein can be isolated
or purified.
[0034] In some embodiments, the variant ADA2 protein can contain a
polypeptide that exhibits at least 65% sequence identity to SEQ ID
NO:5 or a catalytically active portion thereof. For example, the
variant ADA2 protein can contain a polypeptide that exhibits at
least 70%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%,
86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99% or more sequence identity to SEQ ID NO:5 or a catalytically
active portion thereof. For example, the variant ADA2 protein
contains a polypeptide that has the sequence of amino acids set
forth in any of SEQ ID NOS:13-63 or 71-285 or a catalytically
active portion thereof. In some embodiments, the variant ADA2
protein or catalytically active portion thereof contains the
sequence of amino acids set forth in any of SEQ ID NOS: 551-579 or
581-993 or a catalytically active portion thereof.
[0035] In some embodiments, the variant ADA2 protein or a
catalytically active portion thereof can contain amino acid
replacements selected from among replacements corresponding to
K11A/R20A; K11A/R20A/K371A; R20A/K371A; K11A/K371A; S262N/K371D;
S262N/K371E; S262N/R20E; S262N/R20E/K371D; S262N/R20E/K371E;
R219Q/K371E; R219Q/K371D; R219Q/R20E; R219Q/K371E/R20E;
R219Q/K371D/R20E; R219Q/S262N/K371E; R219Q/S262N/K371D;
R219Q/S262N/R20E; R219Q/S262N/K371E/R20E; R219Q/S262N/K371D/R20E;
R219Q/S262N; R219Q/S262N/K11A; R219Q/S262N/K11D; R219Q/S262N/K11E;
R219Q/S262N/K13A; R219Q/S262N/K13D; R219Q/S262N/K13E;
R219Q/S262N/K371A; R219Q/S262N/K372A; R219Q/S262N/K372D;
R219Q/S262N/K372E; R219Q/S262N/K452A; R219Q/S262N/K452D;
R219Q/S262N/K452E; R219Q/S262N/R20A; R219Q/S262N/R20D;
R219Q/S262N/R366A; R219Q/S262N/R366D; R219Q/S262N/R366E;
R219Q/S262N/H264A; R219Q/S262N/H264Q; R219Q/S262N/H264N;
R219Q/S262N/H264G; R219K/S262N; R219N/S262N; R219A/S262N;
R219Q/S262N/L221A; R219Q/S262N/L221V; R219Q/S262N/L221G;
R219Q/S262N/E179D; R219Q/S262N/E179A; R219Q/S262N/E179S;
R219Q/S262N/E179T; R219Q/S262N/E179V; R219Q/S262N/E179G;
R219Q/S262A; R219Q/S262V; R219Q/S262M; R219Q/S262N/K11A/R20A;
R219Q/S262N/K11A/R20A/K371A; R219Q/S262N/R20A/K371A;
R219Q/S262N/K11A/K371A; R219Q/S262N/K26A; R219Q/S262N/K26D;
R219Q/S262N/K26E; R219Q/S262N/R217A; R219Q/S262N/R217D;
R219Q/S262N/R217E; R219Q/S262N/K258A; R219Q/S262N/K258D;
R219Q/S262N/K258E; R219Q/S262N/R277A; R219Q/S262N/R277D;
R219Q/S262N/R277E; R219Q/S262N/R283A; R219Q/S262N/R283D;
R219Q/S262N/R283E; R219Q/S262N/K309A; R219Q/S262N/K309D;
R219Q/S262N/K309E; R219Q/S262N/K317A; R219Q/S262N/K317D;
R219Q/S262N/K317E; R219Q/S262N/K321A; R219Q/S262N/K321D;
R219Q/S262N/K321E; R219Q/S262N/R352A; R219Q/S262N/R352D;
R219Q/S262N/R352E; R219Q/S262N/R441A; R219Q/S262N/R441D;
R219Q/S262N/R441E; R219Q/S262N/K444A; R219Q/S262N/K444D;
R219Q/S262N/K444E; R219Q/S262N/K461A; R219Q/S262N/K461D;
R219Q/S262N/K461E; R219Q/S262N/K469A; R219Q/S262N/K469D;
R219Q/S262N/K469E; R219Q/S262N/K470A; R219Q/S262N/K470D;
R219Q/S262N/K470E; R219Q/S262N/D86A; R219Q/S262N/D86C;
R219Q/S262N/D86E; R219Q/S262N/D86F; R219Q/S262N/D86G;
R219Q/S262N/D86H; R219Q/S262N/D86I; R219Q/S262N/D86K;
R219Q/S262N/D86L; R219Q/S262N/D86M; R219Q/S262N/D86N;
R219Q/S262N/D86P; R219Q/S262N/D86Q; R219Q/S262N/D86R;
R219Q/S262N/D86S; R219Q/S262N/D86T; R219Q/S262N/D86V;
R219Q/S262N/D86W; R219Q/S262N/D86Y; R219Q/S262N/E179C;
R219Q/S262N/E179F; R219Q/S262N/E179H; R219Q/S262N/E179I;
R219Q/S262N/E179K; R219Q/S262N/E179L; R219Q/S262N/E179M;
R219Q/S262N/E179N; R219Q/S262N/E179P; R219Q/S262N/E179Q;
R219Q/S262N/E179R; R219Q/S262N/E179W; R219Q/S262N/E179Y;
R219C/S262N; R219D/S262N; R219E/S262N; R219F/S262N; R219G/S262N;
R219H/S262N; R219I/S262N; R219L/S262N; R219M/S262N; R219P/S262N;
R219S/S262N; R219T/S262N; R219V/S262N; R219W/S262N; R219Y/S262N;
R219Q/S262N/L221C; R219Q/S262N/L221D; R219Q/S262N/L221E;
R219Q/S262N/L221F; R219Q/S262N/L221H; R219Q/S262N/L221I;
R219Q/S262N/L221K; R219Q/S262N/L221M; R219Q/S262N/L221N;
R219Q/S262N/L221P; R219Q/S262N/L221Q; R219Q/S262N/L221R;
R219Q/S262N/L221S; R219Q/S262N/L221T; R219Q/S262N/L221W;
R219Q/S262N/L221Y; R219Q/S262C; R219Q/S262D; R219Q/S262E;
R219Q/S262F; R219Q/S262G; R219Q/S262H; R219Q/S262I; R219Q/S262K;
R219Q/S262L; R219Q/S262P; R219Q/S262Q; R219Q/S262R; R219Q/S262T;
R219Q/S262W; R219Q/S262Y; R219Q/S262N/H264C; R219Q/S262N/H264D;
R219Q/S262N/H264E; R219Q/S262N/H264F; R219Q/S262N/H264I;
R219Q/S262N/H264K; R219Q/S262N/H264L; R219Q/S262N/H264M;
R219Q/S262N/H264P; R219Q/S262N/H264R; R219Q/S262N/H264S;
R219Q/S262N/H264T; R219Q/S262N/H264V; R219Q/S262N/H264W;
R219Q/S262N/H264Y; R219Q/S262N/S266A; R219Q/S262N/S266C;
R219Q/S262N/S266D; R219Q/S262N/S266E; R219Q/S262N/S266F;
R219Q/S262N/S266G; R219Q/S262N/S266H; R219Q/S262N/S266I;
R219Q/S262N/S266K; R219Q/S262N/S266L; R219Q/S262N/S266M;
R219Q/S262N/S266N; R219Q/S262N/S266P; R219Q/S262N/S266Q;
R219Q/S262N/S266R; R219Q/S262N/S266T; R219Q/S262N/S266V;
R219Q/S262N/S266W; R219Q/S262N/S266Y; R219Q/S262N/K267A;
R219Q/S262N/K267C; R219Q/S262N/K267D; R219Q/S262N/K267E;
R219Q/S262N/K267F; R219Q/S262N/K267G; R219Q/S262N/K267H;
R219Q/S262N/K267I; R219Q/S262N/K267L; R219Q/S262N/K267M;
R219Q/S262N/K267N; R219Q/S262N/K267P; R219Q/S262N/K267Q;
R219Q/S262N/K267R; R219Q/S262N/K267S; R219Q/S262N/K267T;
R219Q/S262N/K267V; R219Q/S262N/K267W; R219Q/S262N/K267Y;
R219Q/S262N/V296A; R219Q/S262N/V296C; R219Q/S262N/V296D;
R219Q/S262N/V296E; R219Q/S262N/V296F; R219Q/S262N/V296G;
R219Q/S262N/V296H; R219Q/S262N/V296I; R219Q/S262N/V296K;
R219Q/S262N/V296L; R219Q/S262N/V296M; R219Q/S262N/V296N;
R219Q/S262N/V296P; R219Q/S262N/V296Q; R219Q/S262N/V296R;
R219Q/S262N/V296S; R219Q/S262N/V296T; R219Q/S262N/V296W;
R219Q/S262N/V296Y; R219Q/K11A/R20A; R219Q/K11A/R20A/K371A;
R219Q/R20A/K371A; R219Q/K11A/K371A; S262N/K11A/R20A;
S262N/K11A/R20A/K371A; S262N/R20A/K371A; and S262N/K11A/K371A, with
reference to SEQ ID NO:5.
[0036] The variant ADA2 protein can be a monomer or a dimer. In
particular, among variant ADA2 proteins provided herein are dimers
of a variant ADA2 protein, that can include any of the variant ADA2
proteins provided. In some examples, the dimer can be a homodimer.
In other examples, the dimer can be a heterodimer.
[0037] Provided are nucleic acid molecules encoding the variant
ADA2 proteins provided herein. Also provided herein is a vector
that includes the nucleic acid encoding any of the variant ADA2
proteins provided herein. The vector can be a eukaryotic or a
prokaryotic vector, such as a mammalian vector or a viral vector.
For example, the vector is an adenovirus vector, an
adeno-associated-virus vector, a retrovirus vector, a herpes virus
vector, a lentivirus vector, a poxvirus vector, or a
cytomegalovirus vector. In some embodiments, the vector is an
oncolytic vector. In some embodiments, the vector can also encode a
soluble hyaluronidase. Also provided herein are cells containing
any of the vectors provided herein. The cell can be a eukaryotic
cell, such as a mammalian cell. If human, the cells are isolated or
are provided as a cell culture. For example, the cell is a
mammalian cell, such as a Chinese Hamster Ovary (CHO) cell. In some
embodiments, the cell can expresses the variant ADA2 protein, such
as a dimer. Also provided herein are variant ADA2 proteins, such as
variant ADA2 dimers, that are produced by the cell provided herein.
In some embodiments, the cell is an isolated cell or a cell
culture, such as a eukaryotic cell, a non-human cell, a mammalian
cell, or a cell that is not a human stem cell. In some embodiments,
the cell is an immune cell, such as a T cell, a tumor-infiltrating
lymphocyte (TIL), a cytotoxic T lymphocyte (CTL), a natural killer
(NK) cell or a lymphokine-activated killer (LAK) cell. In some
embodiments, the cell is a T cell that encodes and expresses
chimeric antigen receptor (CAR) and the variant ADA2 protein or
dimer. In some examples, the CAR is specific for a tumor cell
antigen, and the tumor antigen is selected from among HER2, CD19,
HERV-K, CD20, CD22, ROR1, mesothelin, CD33/IL3Ra, c-Met, PSMA,
Glycolipid F77, EGFRvIII, GD-2, NY-ESO-1 TCR, MAGE A3 TCR and GD2
and combinations thereof.
[0038] Provided herein are conjugates include a variant ADA2
protein or a catalytically active portion of any ADA2 protein
provided herein, such as a variant ADA2 dimer provided in any
examples herein, linked directly or indirectly via a linker to a
heterologous moiety, such as a toxin or therapeutic drug.
[0039] Also provided herein are conjugates that include an ADA2
protein linked directly or indirectly via a linker to a
heterologous moiety. In any of the conjugates, the ADA2 protein can
be a monomer or a dimer. In some examples, the dimer is a
homodimer; in other it is a heterodimer. In any of the conjugates
in the examples herein, the heterologous moiety is conjugated to
one or both subunits in the dimer.
The heterologous moiety, for example, can be selected from among a
peptide, small molecule, nucleic acid, carbohydrate and
polymer.
[0040] In some embodiments of the conjugates provided herein, the
heterologous moiety is a half-life extending moiety. For example,
the half-life extending moiety is selected from among biocompatible
fatty acids and derivatives thereof, hydroxy alkyl starch (HAS),
polyethylene glycol (PEG), Poly (Gly.sub.x-Ser.sub.y).sub.n,
homo-amino-acid polymers (HAP), hyaluronic acid (HA), heparosan
polymers (HEP), phosphorylcholine-based polymers (PC polymer),
Fleximers, dextran, polysialic acids (PSA), Fc domain, Transferrin,
Albumin, elastin-like peptides, XTEN sequences, albumin binding
peptides, a CTP peptide, and any combination thereof.
[0041] In some examples, the half-life extending moiety is a PEG
and the ADA2 protein is PEGylated. For example, the PEG can be
selected from among methoxy-polyethylene glycols (mPEG),
PEG-glycidyl ethers (Epox-PEG), PEG-oxycarbonylimidazole (CDI-PEG),
branched PEGs and polyethylene oxide (PEO). In some examples, the
PEG has a molecular weight of from or from about 1 kDa to about 100
kDa. The PEG can be linear or branched. In some embodiments of
conjugates provided herein, the PEG moieties result from reaction
with a PEG reagent selected from among mPEG-Succinimidyl
Propionates (mPEG-SPA), mPEG Succinimidyl Carboxymethyl Ester
(mPEG-SCM), mPEG-Succinimidyl Butanoates (mPEG-SBA),
mPEG2-N-Hydroxylsuccinimide, mPEG-succinimidyl butanoate
(mPEG-SBA), mPEG-succinimidyl .alpha.-methylbutanoate (mPEG-SMB),
mPEG-butyrldehyde, PEG-p-nitrophenyl-carbonate and
PEG-propionaldehyde. For example, the PEG moieities result from
reaction with a PEG reagent selected from among mPEG-SCM (20 kDa),
mPEG-SCM (30 kDa), mPEG-SBA (5 kDa), mPEG-SBA (20 kDa), mPEG-SBA
(30 kDa), mPEG-SMB (20 kDa), mPEG-SMB (30 kDa), mPEG-butyrldehyde
(30 kDa), mPEG-SPA (20 kDa), mPEG-SPA (30 kDa), mPEG2-NHS (10 kDa
branched), mPEG2-NHS (20 kDa branched), mPEG2-NHS (40 kDa
branched), mPEG2-NHS (60 kDa branched), PEG-NHS-biotin (5 kDa
biotinylated), PEG-p-nitrophenyl-carbonate (30 kDa) and
PEG-propionaldehyde (30 kDa).
[0042] In embodiments of the conjugates provided herein, the ADA2
protein can contain the sequence of amino acids set forth in any of
SEQ ID NOS:5, 326-334, 340, 375 or 380-383, a sequence that
exhibits at least 85% sequence identity to the sequence of amino
acids set forth in any of SEQ ID NOS:5, 326-334, 340, 375 or
380-383 or a catalytically active form thereof. For example, the
ADA2 protein can contain a sequence of amino acids that exhibits at
least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%, 98%, 99% or more sequence identity to the sequence of amino
acids set forth in any of SEQ ID NOS:5, 326-334, 340, 375 or
380-383 or a catalytically active portion thereof. For example, the
ADA2 protein can contain a sequence of amino acids that exhibits at
least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%, 98%, 99% or more sequence identity to the sequence of amino
acids set forth in SEQ ID NOS:5 or a catalytically active portion
thereof. In another example, the ADA2 protein can include a
polypeptide having the sequence of amino acids set forth in SEQ ID
NO:5 or a catalytically active portion thereof. In embodiments of
conjugates provided herein, the ADA2 protein is a variant ADA2
protein that contains a sequence of amino acids that includes a
modification(s) in the sequence of amino acids of an unmodified
ADA2 protein or a catalytically active portion thereof, where the
unmodified ADA2 protein contains the sequence of amino acids set
forth in SEQ ID NO:5, or a sequence of amino acids that exhibits at
least 85% sequence identity to the sequence of amino acids set
forth in SEQ ID NO:5, or is a catalytically active portion thereof.
In any of such examples, the amino acid modification(s) are
selected from among amino acid replacement(s), deletion(s) and
insertion(s); and the variant ADA2 protein, when in dimer form, can
exhibit adenosine deaminase activity to convert adenosine to
inosine. In any of the conjugates provided herein, the ADA2
protein, when in dimer form, can exhibit a catalytic efficiency
(k.sub.cat/K.sub.M) that is at least or at least about
5.times.10.sup.3 M.sup.-1 s.sup.-1, 6.times.10.sup.3 M.sup.-1
s.sup.-1, 7.times.10.sup.3 M.sup.-1 s.sup.-1,
8.times.10.sup.3M.sup.-1 s.sup.-1, 9.times.10.sup.3 M.sup.-1
s.sup.-1, 1.times.10.sup.4 M.sup.-1 s.sup.-1, 2.times.10.sup.4
M.sup.-1 s.sup.-1, 3.times.10.sup.4 M.sup.-1 s.sup.-1,
4.times.10.sup.4 M.sup.-1 s.sup.-1, 5.times.10.sup.4 M.sup.-1
s.sup.-1, 6.times.10.sup.4 M.sup.-1 s.sup.-1, 7.times.10.sup.4
M.sup.-1 s.sup.-1, 8.times.10.sup.4 M.sup.-1 s.sup.-1,
9.times.10.sup.4 M.sup.-1 s.sup.-1, 1.times.10.sup.5 M.sup.-1
s.sup.-1, 2.times.10.sup.5 M.sup.-1 s.sup.-1, 3.times.10.sup.5
M.sup.-1 s.sup.-1, 4.times.10.sup.5 M.sup.-1 s.sup.-1,
5.times.10.sup.5 M.sup.-1 s.sup.-1 or greater.
[0043] In any of the embodiments of conjugates provided herein, the
modification(s) of the ADA2 protein can be an amino acid
replacement(s); and the variant ADA2 protein can include one or
more amino acid replacement(s) at an amino acid position
corresponding to amino acid residue 11, 13, 20, 22, 26, 86, 179,
217, 219, 221, 258, 262, 264, 266, 267, 277, 283, 296, 309, 317,
321, 352, 366, 371, 372, 373, 374, 403, 404, 405, 406, 441, 444,
452, 461, 469 or 470, with reference to amino acid positions set
forth in SEQ ID NO:5. For example, in some embodiments of
conjugates provided herein, the variant ADA2 protein can include
one or more amino acid replacement(s) selected from among K11A,
K11D, K11E, K13A, K13D, K13E, R20A, R20D, R20E, R20N, V22S, K26A,
K26D, K26E, D86A, D86C, D86E, D86F, D86G, D86H, D86I, D86K, D86L,
D86M, D86N, D86P, D86Q, D86R, D86S, D86T, D86V, D86W, D86Y, E179A,
E179C, E179D, E179F, E179G, E179H, E179I, E179K, E179L, E179M,
E179N, E179P, E179Q, E179R, E179S, E179T, E179V, E179W, E179Y,
R217A, R217D, R217E, R219A, R219C, R219D, R219E, R219F, R219G,
R219H, R219I, R219K, R219L, R219M, R219N, R219P, R219Q, R219S,
R219T, R219V, R219W, R219Y, L221A, L221C, L221D, L221E, L221F,
L221G, L221H, L221I, L221K, L221M, L221N, L221P, L221Q, L221R,
L221S, L221T, L221V, L221W, L221Y, K258A, K258D, K258E, S262A,
S262C, S262D, S262E, S262F, S262G, S262H, S262I, S262K, S262L,
S262M, S262N, S262P, S262Q, S262R, S262T, S262V, S262W, S262Y,
H264A, H264C, H264D, H264E, H264F, H264G, H264I, H264K, H264L,
H264M, H264N, H264P, H264Q, H264R, H264S, H264T, H264V, H264W,
H264Y, S266A, S266C, S266D, S266E, S266F, S266G, S266H, S266I,
S266K, S266L, S266M, S266N, S266P, S266Q, S266R, S266T, S266V,
S266W, S266Y, K267A, K267C, K267D, K267E, K267F, K267G, K267H,
K267I, K267L, K267M, K267N, K267P, K267Q, K267R, K267S, K267T,
K267V, K267W, K267Y, R277A, R277D, R277E, R283A, R283D, R283E,
V296A, V296C, V296D, V296E, V296F, V296G, V296H, V296I, V296K,
V296L, V296M, V296N, V296P, V296Q, V296R, V296S, V296T, V296W,
V296Y, K309A, K309D, K309E, K317A, K317D, K317E, K321A, K321D,
K321E, R352A, R352D, R352E, R366A, R366D, R366E, K371A, K371D,
K371E, K371N, K372A, K372D, K372E, K372N, D373S, I374S, T403N,
G404N, H405S, P406S, R441A, R441D, R441E, K444A, K444D, K444E,
K452A, K452D, K452E, K461A, K461D, K461E, K469A, K469D, K469E,
K470A, K470D, and K470E, with reference to amino acid positions set
forth in SEQ ID NO:5. For example, the variant ADA2 protein can
include one or more amino acid replacement(s) selected from among
K11A, K11E, R20A, R20D, R20E, R219K, R219Q, L221A, L221V, L221G,
S262N, H264Q, H264G, R366A, R366D, R366E, K371A, K371D, K371E,
K372A, K372D, K372E, K452D and K452E, with reference to amino acid
positions set forth in SEQ ID NO:5. In some examples, the variant
ADA2 protein can include amino acid replacements selected from
among K11A/R20A, K11A/R20A/K371A, R20A/K371A, K11A/K371A,
S262N/K371D, S262N/K371E, S262N/R20E, S262N/R20E/K371D,
S262N/R20E/K371E, R219Q/K371E, R219Q/K371D, R219Q/R20E,
R219Q/K371E/R20E, R219Q/K371D/R20E, R219Q/S262N/K371E,
R219Q/S262N/K371D, R219Q/S262N/R20E, R219Q/S262N/K371E/R20E,
R219Q/S262N/K371D/R20E and R219Q/S262N, with reference to amino
acid positions set forth in SEQ ID NO:5.
[0044] In some embodiments of conjugates provided herein, the
variant ADA2 protein can include a modification of one or more
amino acids in the putative receptor binding (PRB) domain that is
an amino acid deletion, insertion or replacement. For example, in
some embodiments of conjugates provided herein, the variant ADA2
protein can include deletion of one or more contiguous amino acid
residues corresponding to any one or more contiguous amino acid
residues between or between about amino acid residues 98 and 156 or
amino acid residues 105 and 148, inclusive, with reference to amino
acid positions set forth in SEQ ID NO:5. In some examples, the
variant ADA2 protein in the conjugate can further include
substitution of the deleted region with a peptide linker. For
example, the peptide linker can be selected from among (Gly)n (SEQ
ID NO:368), where n is 2 to 20; (GGGGS)n (SEQ ID NO:343), where n
is 1 to 6; (SSSSG)n (SEQ ID NO:344), where n is 1 to 6;
(AlaAlaProAla)n (SEQ ID NO:350), where n is 1 to 6; GKSSGSGSESKS
(SEQ ID NO:345); GGSTSGSGKSSEGKG (SEQ ID NO:346);
GSTSGSGKSSSEGSGSTKG (SEQ ID NO:347); GSTSGSGKPGSGEGSTKG (SEQ ID
NO:348); and EGKSSGSGSESKEF (SEQ ID NO:349). In some examples, the
peptide linker is selected from among GGG (SEQ ID NO:369); GGGGG
(SEQ ID NO:360); GGGGGGG (SEQ ID NO:370); GGGGGGGGGG (SEQ ID
NO:371); and GGGGGGGGGGGGGGG (SEQ ID NO:372). For example, the
modification in the PRB domain can correspond to
C105-T147del.fwdarw.(Gly).sub.n, where n is 2 to 20, such as,
C105-T147del.fwdarw.(Gly).sub.15, C105-T148del.fwdarw.(Gly).sub.10,
C105-T147del.fwdarw.(Gly).sub.7, C105-T147del.fwdarw.(Gly).sub.5 or
C105-T147del.fwdarw.(Gly).sub.3, with reference to amino acid
positions set forth in SEQ ID NO:5.
[0045] In some embodiments of conjugates provided herein, the ADA2
protein in the conjugate can be glycosylated at one or more native
or non-native glycosylation sites. For example, in some embodiments
of conjugates provided herein containing a variant ADA2 protein,
the variant ADA2 protein in the conjugate can include a
modification(s) that alters glycosylation by introduction of a
non-native glycosylation site. The non-native glycosylation site
can be introduced by creating the canonical glycosylation sequence
(NXT/S, where X is not Pro for N-linked carbohydrates, S/T for
O-linked) by introducing amino acid replacement(s), insertions or
deletions of one, two or three amino acids. For example, the
modifications that alter glycosylation are selected from among
modifications corresponding to
--.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3, R20N/V22S, K371N/D373S,
K372N/I374S, T403N/H405S and G404N/P406S, with reference to amino
acid positions set forth in SEQ ID NO:5.
[0046] In some embodiments of conjugates provided herein, the
variant ADA2 protein in the conjugate can have the sequence of
amino acids set forth in any of SEQ ID NOS:13-63 or 71-285 or a
catalytically active portion thereof.
[0047] In some embodiments of conjugates containing an ADA2 or
variant ADA2 protein provided herein, the conjugate retains the
adenosine deaminase activity compared to the ADA2 protein that is
not conjugated. For example, the conjugate can exhibit from or from
about 50% to 500%, 50% to 200%, 50% to 100%, 50% to 80%, 80% to
500%, 80% to 200%, 80% to 100%, 100% to 500% or 100% to 200%, each
inclusive, of the adenosine deaminase activity of the ADA2 protein
that is not conjugated, such as at least 50%, 60%, 70%, 80%, 90%,
100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%,
300%, 400%, 500% or more the adenosine deaminase activity of the
ADA2 protein that is not conjugated. In some embodiments of
conjugates provided herein, the ADA2 in the conjugate can exhibit a
catalytic efficiency (k.sub.cat/K.sub.M) that is at least or at
least about 5.times.10.sup.3 M.sup.-1 s.sup.-1, 6.times.10.sup.3
M.sup.-1 s.sup.-1, 7.times.10.sup.3 M.sup.-1 s.sup.-1,
8.times.10.sup.3M.sup.-1 s.sup.-1, 9.times.10.sup.3 M.sup.-1
s.sup.-1, 1.times.10.sup.4M.sup.-1 s.sup.-1,
2.times.10.sup.4M.sup.-1 s.sup.-1, 3.times.10.sup.4M.sup.-1
s.sup.-1, 4.times.10.sup.4M.sup.-1 s.sup.-1,
5.times.10.sup.4M.sup.-1 s.sup.-1, 6.times.10.sup.4M.sup.-1
s.sup.-1, 7.times.10.sup.4M.sup.-1 s.sup.-1,
8.times.10.sup.4M.sup.-1 s.sup.-1, 9.times.10.sup.4M.sup.-1
s.sup.-1, 1.times.10.sup.5 M.sup.-1 s.sup.-1, 2.times.10.sup.5
M.sup.-1 s.sup.-1, 3.times.10.sup.5 M.sup.-1 s.sup.-1,
4.times.10.sup.5 M.sup.-1 s.sup.-1, 5.times.10.sup.5M.sup.-1
s.sup.-1 or greater.
[0048] Provided herein are combinations containing any of the
variant ADA2 proteins or a catalytically active portion thereof
provided herein, any variant ADA2 dimer provided herein or any
conjugate of any of the examples provided herein, and a therapeutic
agent. Also provided herein are combinations containing any ADA2
protein; and a therapeutic agent. In any examples of the
combination provided herein, the ADA2 protein can be a monomer or a
dimer. For example, the ADA2 protein can be a dimer, such as a
homodimer.
[0049] In some embodiments of combinations provided herein, the
therapeutic agent can be selected from among an antibody, cytotoxic
agent, chemotherapeutic agents, cytokine, growth inhibitory agent,
anti-hormonal agent, kinase inhibitor, anti-angiogenic agent,
cardioprotectant, immunostimulatory agent, immunosuppressive agent,
immune checkpoint inhibitor, antibiotic and angiogenesis inhibitor.
For example, the therapeutic agent can be an anti-cancer agent. In
some embodiments of combinations provided herein, the anti-cancer
agent can be an anti-cancer antibody, a chemotherapeutic agent, a
radioimmunotherapeutic, an anti-angiogenic agent or an immune
checkpoint inhibitor.
[0050] For example, the anti-cancer agent can be an immune
checkpoint inhibitor; and the target of the immune checkpoint
inhibitor can be selected from among CTLA4, PD-1, and PD-L1. In
some embodiments of combinations provided herein, the immune
checkpoint inhibitor can be an antibody, a fusion protein, an
aptamer, or an immune checkpoint protein-binding fragment thereof.
For example, the immune checkpoint inhibitor is an anti-immune
checkpoint protein antibody or antigen-binding fragment thereof. In
particular examples, the immune checkpoint inhibitor is selected
from among: an anti-CTLA4 antibody, derivative thereof, or
antigen-binding fragment thereof; an anti-PD-L1 antibody,
derivative thereof, or antigen-binding fragment thereof; and an
anti-PD-1 antibody, derivative thereof, or antigen-binding fragment
thereof. For example, the immune checkpoint inhibitor can be
selected from among: Ipilimumab, a derivative thereof, or an
antigen-binding fragment thereof; Tremelimumab, a derivative
thereof, or an antigen-binding fragment thereof, Nivolumab, a
derivative thereof, or an antigen-binding fragment thereof, and
Pidilizumab, a derivative thereof, or an antigen-binding fragment
thereof.
[0051] In some embodiments of combinations provided herein, the
therapeutic agent can be an anti-hyaluronan agent. For example, the
anti-hyaluronan agent can be a soluble hyaluronidase. In some
embodiments of combinations provided herein, the soluble
hyaluronidase can exhibit hyaluronidase activity at neutral pH. In
particular, the soluble hyaluronidase can be selected from among
bovine, ovine or a C-terminal truncated human PH20 that lacks all
or a portion of the glycosylphosphatidylinositol (GPI) anchor
attachment sequence. For example, the soluble hyaluronidase is a
C-terminally truncated human PH20 that lacks all or a portion of
the GPI anchor attachment sequence, such as those set forth in any
of SEQ ID NOS:481-488, 493-514, or 526-532, or that has a sequence
of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%,
92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity to a
sequence of amino acids set forth in any of SEQ ID NOS:481-488,
493-514, or 526-532 and is soluble and retains hyaluronidase
activity. In some embodiments of combinations provided herein, the
anti-hyaluronan agent or soluble hyaluronidase can be conjugated to
a polymer, such as a PEG moiety.
[0052] In some embodiments of combinations provided herein, the
ADA2 protein can include a polypeptide having the sequence of amino
acids set forth in any of SEQ ID NOS:5, 326-334, 340, 375 or
380-383, a sequence that can exhibit at least 85% sequence identity
to the sequence of amino acids set forth in SEQ ID NOS:5, 326-334,
340, 375 or 380-383 or a catalytically active form thereof. For
example, the ADA2 protein can include a protein having a sequence
of amino acids that can exhibit at least 86%, 87%, 88%, 89%, 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence
identity to the sequence of amino acids set forth in SEQ ID NOS:5,
326-334, 340, 375 or 380-383 or a catalytically active portion
thereof. In particular examples, the ADA2 protein can contain a
sequence of amino acids that can exhibit at least 86%, 87%, 88%,
89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more
sequence identity to the sequence of amino acids set forth in SEQ
ID NO:5. For example, the ADA2 protein can contain the sequence of
amino acids set forth in SEQ ID NO:5.
[0053] In some embodiments of combinations provided herein, the
ADA2 protein is a variant ADA2 protein having a sequence of amino
acids that includes a modification(s) in the sequence of amino
acids of an unmodified ADA2 polypeptide or a catalytically active
portion thereof. In any of such examples, the unmodified ADA2
protein can include the sequence of amino acids set forth in SEQ ID
NO:5, or a sequence of amino acids that can exhibit at least 85%
sequence identity to the sequence of amino acids set forth in SEQ
ID NO:5, or is a catalytically active portion thereof; the amino
acid modification(s) are selected from among amino acid
replacement(s), deletion(s) and insertion(s); and the variant ADA2
protein, when in dimer form, can exhibit adenosine deaminase
activity to convert adenosine to inosine.
[0054] In some embodiments of combinations provided herein, the
ADA2 protein, when in dimer form, can exhibit a catalytic
efficiency (k.sub.cat/K.sub.M) that is at least or at least about
5.times.10.sup.3 M.sup.-1 s.sup.-1, 6.times.10.sup.3 M.sup.-1
s.sup.-1, 7.times.10.sup.3 M.sup.-1 s.sup.-1,
8.times.10.sup.3M.sup.-1 s.sup.-1, 9.times.10.sup.3 M.sup.-1
s.sup.-1, 1.times.10.sup.4 M.sup.-1 s.sup.-1, 2.times.10.sup.4
M.sup.-1 s.sup.-1, 3.times.10.sup.4 M.sup.-1 s.sup.-1,
4.times.10.sup.4 M.sup.-1 s.sup.-1, 5.times.10.sup.4 M.sup.-1
s.sup.-1, 6.times.10.sup.4 M.sup.-1 s.sup.-1, 7.times.10.sup.4
M.sup.-1 8.times.10.sup.4 M.sup.-1 s.sup.-1, 9.times.10.sup.4
M.sup.-1 s.sup.-1, 1.times.10.sup.5 M.sup.-1 s.sup.-1,
2.times.10.sup.5 M.sup.-1 s.sup.-1, 3.times.10.sup.5 M.sup.-1
s.sup.-1, 4.times.10.sup.5 M.sup.-1 s.sup.-1, 5.times.10.sup.5
M.sup.-1 s.sup.-1 or greater.
[0055] In some embodiments of combinations provided herein, the
modification(s) in the sequence of amino acids of an unmodified
ADA2 protein can include an amino acid replacement(s); and the
variant ADA2 protein can include one or more amino acid
replacement(s) at an amino acid position corresponding to amino
acid residue 11, 13, 20, 22, 26, 86, 179, 217, 219, 221, 258, 262,
264, 266, 267, 277, 283, 296, 309, 317, 321, 352, 366, 371, 372,
373, 374, 403, 404, 405, 406, 441, 444, 452, 461, 469 or 470, with
reference to amino acid positions set forth in SEQ ID NO:5. For
example, the variant ADA2 protein can include one or more amino
acid replacement(s) selected from among K11A, K11D, K11E, K13A,
K13D, K13E, R20A, R20D, R20E, R20N, V22S, K26A, K26D, K26E, D86A,
D86C, D86E, D86F, D86G, D86H, D86I, D86K, D86L, D86M, D86N, D86P,
D86Q, D86R, D86S, D86T, D86V, D86W, D86Y, E179A, E179C, E179D,
E179F, E179G, E179H, E179I, E179K, E179L, E179M, E179N, E179P,
E179Q, E179R, E179S, E179T, E179V, E179W, E179Y, R217A, R217D,
R217E, R219A, R219C, R219D, R219E, R219F, R219G, R219H, R219I,
R219K, R219L, R219M, R219N, R219P, R219Q, R219S, R219T, R219V,
R219W, R219Y, L221A, L221C, L221D, L221E, L221F, L221G; L221H,
L221I, L221K, L221M, L221N, L221P, L221Q, L221R, L221S, L221T,
L221V, L221W, L221Y, K258A, K258D, K258E, S262A, S262C, S262D,
S262E, S262F, S262G, S262H, S262I, S262K, S262L, S262M, S262N,
S262P, S262Q, S262R, S262T, S262V, S262W, S262Y, H264A, H264C,
H264D, H264E, H264F, H264G, H264I, H264K, H264L, H264M, H264N,
H264P, H264Q, H264R, H264S, H264T, H264V, H264W, H264Y, S266A,
S266C, S266D, S266E, S266F, S266G, S266H, S266I, S266K, S266L,
S266M, S266N, S266P, S266Q, S266R, S266T, S266V, S266W, S266Y,
K267A, K267C, K267D, K267E, K267F, K267G, K267H, K267I, K267L,
K267M, K267N, K267P, K267Q, K267R, K267S, K267T, K267V, K267W,
K267Y, R277A, R277D, R277E, R283A, R283D, R283E, V296A, V296C,
V296D, V296E, V296F, V296G, V296H, V296I, V296K, V296L, V296M,
V296N, V296P, V296Q, V296R, V296S, V296T, V296W, V296Y, K309A,
K309D, K309E, K317A, K317D, K317E, K321A, K321D, K321E, R352A,
R352D, R352E, R366A, R366D, R366E, K371A, K371D, K371E, K371N,
K372A, K372D, K372E, K372N, D373S, I374S, T403N, G404N, H405S,
P406S, R441A, R441D, R441E, K444A, K444D, K444E, K452A, K452D,
K452E, K461A, K461D, K461E, K469A, K469D, K469E, K470A, K470D, and
K470E, with reference to amino acid positions set forth in SEQ ID
NO:5. In particular examples, the variant ADA2 protein can include
one or more amino acid replacement(s) selected from among K11A,
K11E, R20A, R20D, R20E, R219K, R219Q, L221A, L221V, L221G, S262N,
H264Q, H264G, R366A, R366D, R366E, K371A, K371D, K371E, K372A,
K372D, K372E, K452D and K452E, with reference to amino acid
positions set forth in SEQ ID NO:5. In some examples of the
combinations provided herein, the variant ADA2 protein can include
amino acid replacements selected from among K11A/R20A,
K11A/R20A/K371A, R20A/K371A, K11A/K371A, S262N/K371D, S262N/K371E,
S262N/R20E, S262N/R20E/K371D, S262N/R20E/K371E, R219Q/K371E,
R219Q/K371D, R219Q/R20E, R219Q/K371E/R20E, R219Q/K371D/R20E,
R219Q/S262N/K371E, R219Q/S262N/K371D, R219Q/S262N/R20E,
R219Q/S262N/K371E/R20E, R219Q/S262N/K371D/R20E and R219Q/S262N,
with reference to amino acid positions set forth in SEQ ID
NO:5.
[0056] In some embodiments of combinations provided herein, the
variant ADA2 protein can include a modification of one or more
amino acids in the putative receptor binding (PRB) domain, wherein
the modification is an amino acid deletion, insertion or
replacement. For example, the variant ADA2 can include deletion of
one or more contiguous amino acid residues corresponding to any one
or more contiguous amino acid residues between or between about
amino acid residues 98 and 156 or amino acid residues 105 and 148,
inclusive, with reference to amino acid positions set forth in SEQ
ID NO:5. In some embodiments, the variant of ADA2 polypeptide can
further include substitution of the deleted region with a peptide
linker. For example, the peptide linker can be selected from among
(Gly)n (SEQ ID NO:368), where n is 2 to 20; (GGGGS)n (SEQ ID
NO:343), where n is 1 to 6; (SSSSG)n (SEQ ID NO:344), where n is 1
to 6; (AlaAlaProAla)n (SEQ ID NO:350), where n is 1 to 6;
GKSSGSGSESKS (SEQ ID NO:345); GGSTSGSGKSSEGKG (SEQ ID NO:346);
GSTSGSGKSSSEGSGSTKG (SEQ ID NO:347); GSTSGSGKPGSGEGSTKG (SEQ ID
NO:348); and EGKSSGSGSESKEF (SEQ ID NO:349). In particular
examples, the peptide linker is selected from among GGG (SEQ ID
NO:369); GGGGG (SEQ ID NO:360); GGGGGGG (SEQ ID NO:370); GGGGGGGGGG
(SEQ ID NO:371); and GGGGGGGGGGGGGGG (SEQ ID NO:372). In some
embodiments of combinations provided herein, the modification in
the PRB domain of the variant ADA2 polypeptide corresponds to
C105-T147del.fwdarw.(Gly).sub.n, where n is 2 to 20, such as
C105-T147del.fwdarw.(Gly).sub.15, C105-T147del.fwdarw.(Gly).sub.10,
C105-T147del.fwdarw.(Gly).sub.7, C105-T147del.fwdarw.(Gly).sub.5 or
C105-T147del.fwdarw.(Gly).sub.3, with reference to amino acid
positions set forth in SEQ ID NO:5.
[0057] In some embodiments of combinations provided herein, the
ADA2 protein in the combination can be glycosylated at one or more
native or non-native glycosylation sites. For example, in some
embodiments of combinations provided herein containing a variant
ADA2 protein, the variant ADA2 protein in the combination include a
modification(s) that alters glycosylation by introduction of a
non-native glycosylation site. The non-native glycosylation site is
introduced by amino acid replacement(s) or insertion of one, two or
three amino acids. For example, the modifications that alter
hyperglycosylation can be selected from among modifications
corresponding to --.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3, R20N/V22S,
K371N/D373S, K372N/I374S, T403N/H405S and G404N/P406S, with
reference to amino acid positions set forth in SEQ ID NO:5.
[0058] In some embodiments of combinations provided herein, the
variant ADA2 polypeptide has the sequence of amino acids set forth
in any of SEQ ID NOS:13-63 or 71-285 or a catalytically active
portion thereof.
[0059] Provided herein are pharmaceutical compositions that can
include any of the variant ADA2 proteins or a catalytically active
portion thereof provided herein, any variant ADA2 dimer provided
herein or any conjugate provided herein, in a pharmaceutically
acceptable vehicle. In some embodiments, the pharmaceutical
composition can be formulated for local or systemic administration.
For example, the pharmaceutical composition is formulated for
intravenous administration.
[0060] Provided herein are methods of treating a tumor or cancer in
a subject, that can include administering to the subject any of the
variant ADA2 proteins or a catalytically active portion thereof
provided herein, any variant ADA2 dimer provided herein, any
conjugate provided herein, or any combination provided herein. Also
provided are medical uses or pharmaceutical compositions for use of
any of the variant ADA2 proteins or a catalytically active portion
thereof provided herein, any variant ADA2 dimer provided herein or
any conjugate provided herein for treating a tumor or a cancer in a
subject. Also provided are combinations for use of any of the
combinations provided herein for use in treating a tumor or
cancer.
[0061] Also provided herein are methods of treating a tumor or
cancer in a subject that can include administering to the subject
any ADA2 protein. Also provided are medical uses of an ADA2 protein
or pharmaceutical composition for use containing an ADA2 protein
for treating a tumor or a cancer. Also provided are combinations
for use containing an ADA2 protein and a therapeutic agent for
treating a tumor or cancer.
[0062] In some embodiments of methods, uses, pharmaceutical
compositions for use or uses provided herein, the tumor can be a
solid tumor or a metastatic tumor. In particular examples, the
tumor can be a carcinoma, gliomas, sarcoma, adenocarcinoma,
adenosarcoma, or adenoma. In some embodiments, the tumor can be a
tumor of the breast, heart, lung, small intestine, colon, spleen,
kidney, bladder, head and neck, ovary, prostate, brain, pancreas,
skin, bone, bone marrow, blood, thymus, uterus, testicles, cervix
or liver.
[0063] In some embodiments of methods provided herein, the subject
can be selected for treatment based on elevated levels of plasma
adenosine, tumor-associated expression of adenosine receptor (ADR)
or tumor-associated expression of a nucleotidase. In particular
examples, the ADR is A2A or A2B. In particular examples, the
nucleotidase is CD39 or CD73. In some embodiments of methods
provided herein, the elevated level is at least 0.5-fold, 1-fold,
2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold,
10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold,
70-fold, 80-fold, 90-fold, 100-fold, 150-fold, 200-fold, 500-fold,
1000-fold or more, compared to the predetermined level or
predetermined amount or control sample.
[0064] In some embodiments of methods provided herein, the method
of treating a tumor or cancer in a subject can further include
administration of one or more anticancer agents or treatments. For
example, the anti-cancer agent can be selected from among an
anti-cancer antibody, a chemotherapeutic agent, a
radioimmunotherapeutic, an anti-angiogenic agent and an immune
checkpoint inhibitor.
[0065] Provided herein are methods of treating a disease or
condition in a subject, that can include administering to the
subject any of the variant ADA2 proteins or a catalytically active
portion thereof provided herein, any variant ADA2 dimer provided
herein, any conjugate provided herein, or any combination provided
herein for treating a disease or condition that is a non-cancer
hyperproliferative disease, a fibrotic disease, an infectious
disease, a vasculopathy or Severe Combined Immunodeficiency (SCID).
Also provided are medical uses or pharmaceutical compositions for
use of any of the variant ADA2 proteins or a catalytically active
portion thereof provided herein, any variant ADA2 dimer provided
herein or any conjugate provided herein for treating a non-cancer
hyperproliferative disease, a fibrotic disease, an infectious
disease, a vasculopathy or Severe Combined Immunodeficiency (SCID)
in a subject. Also provided are combinations for use of any of the
combinations provided herein for use in treating a non-cancer
hyperproliferative disease, a fibrotic disease, an infectious
disease, a vasculopathy or Severe Combined Immunodeficiency (SCID).
Also provided herein are methods of treating a disease or condition
in a subject, that can include administering to the subject any
ADA2 protein, for treating a disease or condition that is a
non-cancer hyperproliferative disease, a fibrotic disease, an
infectious disease, a vasculopathy or Severe Combined
Immunodeficiency (SCID). Also provided are medical uses of an ADA2
protein or pharmaceutical compositions for use containing an ADA2
protein for treating a disease or condition that is a non-cancer
hyperproliferative disease, a fibrotic disease, an infectious
disease, a vasculopathy or Severe Combined Immunodeficiency (SCID).
Also provided are combinations for use containing an ADA2 protein
and a therapeutic agent for treating a disease or condition that is
a non-cancer hyperproliferative disease, a fibrotic disease, an
infectious disease, a vasculopathy or Severe Combined
Immunodeficiency (SCID)
[0066] In some embodiments of methods, uses, pharmaceutical
compositions for use or uses provided herein, the ADA2 protein can
be a monomer or a dimer. For example, the ADA2 protein can be a
dimer, in particular, a homodimer. In some embodiments of methods,
uses, pharmaceutical compositions for use or combinations for use
provided herein, the ADA2 protein can contain the sequence of amino
acids set forth in any of SEQ ID NOS:5, 326-334, 340, 375 or
380-383, a sequence that can exhibit at least 85% sequence identity
to the sequence of amino acids set forth in SEQ ID NOS:5, 326-334,
340, 375 or 380-383 or a catalytically active form thereof. For
example, the ADA2 protein can contain a sequence of amino acids
that can exhibit at least 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the
sequence of amino acids set forth in SEQ ID NOS:5, 326-334, 340,
375 or 380-383 or a catalytically active portion thereof. In
particular examples, the ADA2 protein can contain a sequence of
amino acids that can exhibit at least 86%, 87%, 88%, 89%, 90%, 91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to
the sequence of amino acids set forth in SEQ ID NOS:5 or a
catalytically active portion thereof. For example, the ADA2 protein
can contain the sequence of amino acids set forth in SEQ ID
NO:5.
[0067] In some embodiments of methods, uses, pharmaceutical
compositions for use, or combinations for use provided herein, the
ADA2 protein is a variant ADA2 protein that includes
modification(s) in the sequence of amino acids of an unmodified
ADA2 polypeptide or a catalytically active portion thereof. In any
of such examples, the unmodified ADA2 protein can include the
sequence of amino acids set forth in SEQ ID NO:5, or a sequence of
amino acids that can exhibit at least 85% sequence identity to the
sequence of amino acids set forth in SEQ ID NO:5, or is a
catalytically active portion thereof; the amino acid
modification(s) are selected from among amino acid replacement(s),
deletion(s) and insertion(s); and the variant ADA2 protein, when in
dimer form, can exhibit adenosine deaminase activity to convert
adenosine to inosine.
[0068] In some embodiments of methods, uses, pharmaceutical
compositions for use or combinations for use provided herein, the
ADA2 protein, when in dimer form, can exhibit a catalytic
efficiency (k.sub.cat/K.sub.M) that is at least or at least about
5.times.10.sup.3 M.sup.-1 s.sup.-1, 6.times.10.sup.3 M.sup.-1
s.sup.-1, 7.times.10.sup.3 M.sup.-1 s.sup.-1,
8.times.10.sup.3M.sup.-1 s.sup.-1, 9.times.10.sup.3 M.sup.-1
s.sup.-1, 1.times.10.sup.4 M.sup.-1 s.sup.-1, 2.times.10.sup.4
M.sup.-1 s.sup.-1, 3.times.10.sup.4 M.sup.-1 s.sup.-1,
4.times.10.sup.4 M.sup.-1 s.sup.-1, 5.times.10.sup.4 M.sup.-1
s.sup.-1, 6.times.10.sup.4 M.sup.-1 s.sup.-1, 7.times.10.sup.4
M.sup.-1 s.sup.-1, 8.times.10.sup.4 M.sup.-1 s.sup.-1,
9.times.10.sup.4 M.sup.-1 s.sup.-1, 1.times.10.sup.5 M.sup.-1
s.sup.-1, 2.times.10.sup.5 M.sup.-1 s.sup.-1, 3.times.10.sup.5
M.sup.-1 s.sup.-1, 4.times.10.sup.5 M.sup.-1 s.sup.-1,
5.times.10.sup.5 M.sup.-1 s.sup.-1 or greater.
[0069] In some embodiments of methods, uses, pharmaceutical
compositions for use, or combinations for use provided herein, the
modification(s) in the sequence of amino acids of an unmodified
ADA2 polypeptide can include an amino acid replacement(s); and the
variant ADA2 protein can include one or more amino acid
replacement(s) at an amino acid position corresponding to amino
acid residue 11, 13, 20, 22, 26, 86, 179, 217, 219, 221, 258, 262,
264, 266, 267, 277, 283, 296, 309, 317, 321, 352, 366, 371, 372,
373, 374, 403, 404, 405, 406, 441, 444, 452, 461, 469 or 470, with
reference to amino acid positions set forth in SEQ ID NO:5. For
example, the variant ADA2 protein can include one or more amino
acid replacement selected from among K11A, K11D, K11E, K13A, K13D,
K13E, R20A, R20D, R20E, R20N, V22S, K26A, K26D, K26E, D86A, D86C,
D86E, D86F, D86G, D86H, D86I, D86K, D86L, D86M, D86N, D86P, D86Q,
D86R, D86S, D86T, D86V, D86W, D86Y, E179A, E179C, E179D, E179F,
E179G, E179H, E179I, E179K, E179L, E179M, E179N, E179P, E179Q,
E179R, E179S, E179T, E179V, E179W, E179Y, R217A, R217D, R217E,
R219A, R219C, R219D, R219E, R219F, R219G, R219H, R219I, R219K,
R219L, R219M, R219N, R219P, R219Q, R219S, R219T, R219V, R219W,
R219Y, L221A, L221C, L221D, L221E, L221F, L221 G, L221H, L221I,
L221K, L221M, L221N, L221P, L221Q, L221R, L221S, L221T, L221V,
L221W, L221Y, K258A, K258D, K258E, S262A, S262C, S262D, S262E,
S262F, S262G, S262H, S262I, S262K, S262L, S262M, S262N, S262P,
S262Q, S262R, S262T, S262V, S262W, S262Y, H264A, H264C, H264D,
H264E, H264F, H264G, H264I, H264K, H264L, H264M, H264N, H264P,
H264Q, H264R, H654S, H264T, H264V, H264W, H264Y, S266A, S266C,
S266D, S266E, S266F, S266G, S266H, S266I, S266K, S266L, S266M,
S266N, S266P, S266Q, S266R, S266T, S266V, S266W, S266Y, K267A,
K267C, K267D, K267E, K267F, K267G, K267H, K267I, K267L, K267M,
K267N, K267P, K267Q, K267R, K267S, K267T, K267V, K267W, K267Y,
R277A, R277D, R277E, R283A, R283D, R283E, V296A, V296C, V296D,
V296E, V296F, V296G, V296H, V296I, V296K, V296L, V296M, V296N,
V296P, V296Q, V296R, V296S, V296T, V296W, V296Y, K309A, K309D,
K309E, K317A, K317D, K317E, K321A, K321D, K321E, R352A, R352D,
R352E, R366A, R366D, R366E, K371A, K371D, K371E, K371N, K372A,
K372D, K372E, K372N, D373S, I374S, T403N, G404N, H405S, P406S,
R441A, R441D, R441E, K444A, K444D, K444E, K452A, K452D, K452E,
K461A, K461D, K461E, K469A, K469D, K469E, K470A, K470D, and K470E,
with reference to amino acid positions set forth in SEQ ID
NO:5.
[0070] In particular examples, the variant ADA2 protein can include
one or more amino acid replacement(s) selected from among K11A,
K11E, R20A, R20D, R20E, R219K, R219Q, L221A, L221V, L221G, S262N,
H264Q, H264G, R366A, R366D, R366E, K371A, K371D, K371E, K372A,
K372D, K372E, K452D and K452E, with reference to amino acid
positions set forth in SEQ ID NO:5. In some embodiments of methods,
uses, pharmaceutical compositions for use or combinations for use
provided herein, the variant ADA2 protein can include amino acid
replacements selected from among K11A/R20A, K11A/R20A/K371A,
R20A/K371A, K11A/K371A, S262N/K371D, S262N/K371E, S262N/R20E,
S262N/R20E/K371D, S262N/R20E/K371E, R219Q/K371E, R219Q/K371D,
R219Q/R20E, R219Q/K371E/R20E, R219Q/K371D/R20E, R219Q/S262N/K371E,
R219Q/S262N/K371D, R219Q/S262N/R20E, R219Q/S262N/K371E/R20E,
R219Q/S262N/K371D/R20E and R219Q/S262N, with reference to amino
acid positions set forth in SEQ ID NO:5.
[0071] In some embodiments of methods, uses, pharmaceutical
compositions for use or combinations for use provided herein, the
variant ADA2 protein can include a modification of one or more
amino acids in the putative receptor binding (PRB) domain, such as
an amino acid deletion, insertion or replacement. For example, the
variant ADA2 can include deletion of one or more contiguous amino
acid residues corresponding to any one or more contiguous amino
acid residues between or between about amino acid residues 98 and
156 or amino acid residues 105 and 148, inclusive, with reference
to amino acid positions set forth in SEQ ID NO:5. In any of such
examples of methods, uses, pharmaceutical compositions for use or
combinations for use provided herein, the variant of ADA2 protein
can further include substitution of the deleted region with a
peptide linker. For example, the peptide linker is selected from
among (Gly)n (SEQ ID NO:368), where n is 2 to 20; (GGGGS)n (SEQ ID
NO:343), where n is 1 to 6; (SSSSG)n (SEQ ID NO:344), where n is 1
to 6; (AlaAlaProAla)n (SEQ ID NO:350), where n is 1 to 6;
GKSSGSGSESKS (SEQ ID NO:345); GGSTSGSGKSSEGKG (SEQ ID NO:346);
GSTSGSGKSSSEGSGSTKG (SEQ ID NO:347); GSTSGSGKPGSGEGSTKG (SEQ ID
NO:348); and EGKSSGSGSESKEF (SEQ ID NO:349). In particular examples
the peptide linker is selected from among GGG (SEQ ID NO:369);
GGGGG (SEQ ID NO:360); GGGGGGG (SEQ ID NO:370); GGGGGGGGGG (SEQ ID
NO:371); and GGGGGGGGGGGGGGG (SEQ ID NO:372).
For example, the modification in the PRB domain of the ADA2 protein
corresponds to C105-T147del.fwdarw.(Gly) where n is 2 to 20, such
as C105-T147del.fwdarw.(Gly).sub.15,
C105-T147del.fwdarw.(Gly).sub.10, C105-T147del.fwdarw.(Gly).sub.7,
C105-T147del.fwdarw.(Gly).sub.5 or C105-T147del.fwdarw.(Gly).sub.3,
with reference to amino acid positions set forth in SEQ ID
NO:5.
[0072] In some embodiments of methods, uses, pharmaceutical
compositions for use or combinations for use provided herein, the
ADA2 protein can be glycosylated at one or more native or
non-native glycosylation sites. For example, in some embodiments
provided herein containing a variant ADA2 protein, the variant ADA2
protein includes a modification(s) that alters glycosylation by
introduction of a non-native glycosylation site. For example, the
non-native glycosylation site is introduced by amino acid
replacement(s) or insertion of one, two or three amino acids. In
particular examples, the modifications that alter glycosylation are
selected from among modifications corresponding to
--.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3, R20N/V22S, K371N/D373S,
K372N/I374S, T403N/H405S and G404N/P406S, with reference to amino
acid positions set forth in SEQ ID NO:5.
[0073] In some embodiments of methods, uses, pharmaceutical
compositions for use or combinations for use provided herein, the
variant ADA2 can include a polypeptide that has the sequence of
amino acids set forth in any of SEQ ID NOS:13-63 or 71-285 or a
catalytically active portion thereof.
[0074] In some embodiments of methods, uses, pharmaceutical
compositions for use or uses provided herein, the subject can be a
mammal, in particular a human. In some embodiments of methods
provided herein, the pharmaceutical composition can be administered
parenterally, locally, or systemically. For example, the
pharmaceutical composition can be administered intranasally,
intramuscularly, intradermally, intraperitoneally, intravenously,
subcutaneously, orally, or by pulmonary administration.
[0075] In some embodiments, in the variant ADA2 protein or
catalytically active portion thereof provided herein, the variant
ADA2 protein in the methods, compositions, conjugates, modified
forms, vectors, cells, combinations, uses and compositions for use,
and the nucleic acids encoding the variant ADA2 provided herein and
vectors that include the nucleic acids, the modifications can be
from any one or more of the following amino acid replacement(s),
insertion(s), deletion(s), and any combination thereof. The
modification(s) listed below are with reference to mature
numbering, as set forth in the amino acid positions set forth in
SEQ ID NO:5.
Exemplary of ADA2 variants provided herein are the following; it is
understood that the different types of mutants (amino acid
modifications) can be combined to exploit the properties of each
type of mutation. It is understood by those of skill in the art
that, in general, the effects of mutations in proteins are at least
additive, and can be synergistic.
[0076] 1. Heparin Binding Mutants
[0077] The following modifications can confer reduced heparin
binding. Binding to heparin can deplete circulating levels of
administered ADA2. Thus, the following ADA2 variants can increase
the bioavailability and pharmacokinetics of the administered
ADA2:
[0078] K11A; K11D; K11E; K13A; K13D; K13E; K371A; K371D; K371E;
K372A; K372D; K372E; K452A; K452D; K452E; R20A; R20D; R20E; R366A;
R366D; R366E; K26A; K26D; K26E; R217A; R217D; R217E; K258A; K258D;
K258E; R277A; R277D; R277E; R283A; R283D; R283E; K309A; K309D;
K309E; K317A; K317D; K317E; K321A; K321D; K321E; R352A; R352D;
R352E; R441A; R441D; R441E; K444A; K444D; K444E; K461A; K461D;
K461E; K469A; K469D; K469E; K470A; K470D; and K470E.
[0079] Examples of Heparin Binding Mutants Containing these
Replacements:
[0080] K11A (SEQ ID NO:13); K11D (SEQ ID NO:14); K11E (SEQ ID
NO:15); K13A (SEQ ID NO:16); K13D (SEQ ID NO:17); K13E (SEQ ID
NO:18); K371A (SEQ ID NO:19); K371D (SEQ ID NO:20); K371E (SEQ ID
NO:21); K372A (SEQ ID NO:22); K372D (SEQ ID NO:23); K372E (SEQ ID
NO:24); K452A (SEQ ID NO:25); K452D (SEQ ID NO:26); K452E (SEQ ID
NO:27); R20A (SEQ ID NO:28); R20D (SEQ ID NO:29); R20E (SEQ ID
NO:30); R366A (SEQ ID NO:31); R366D (SEQ ID NO:32); R366E (SEQ ID
NO:33); K26A (SEQ ID NO:71); K26D (SEQ ID NO:72); K26E (SEQ ID
NO:73); R217A (SEQ ID NO:74); R217D (SEQ ID NO:75); R217E (SEQ ID
NO:76); K258A (SEQ ID NO:77); K258D (SEQ ID NO:78); K258E (SEQ ID
NO:79); R277A (SEQ ID NO:80); R277D (SEQ ID NO:81); R277E (SEQ ID
NO:82); R283A (SEQ ID NO:83); R283D (SEQ ID NO:84); R283E (SEQ ID
NO:85); K309A (SEQ ID NO:86); K309D (SEQ ID NO:87); K309E (SEQ ID
NO:88); K317A (SEQ ID NO:89); K317D (SEQ ID NO:90); K317E (SEQ ID
NO:91); K321A (SEQ ID NO:92); K321D (SEQ ID NO:93); K321E (SEQ ID
NO:94); R352A (SEQ ID NO:95); R352D (SEQ ID NO:96); R352E (SEQ ID
NO:97); R441A (SEQ ID NO:98); R441D (SEQ ID NO:99); R441E (SEQ ID
NO:100); K444A (SEQ ID NO:101); K444D (SEQ ID NO:102); K444E (SEQ
ID NO:103); K461A (SEQ ID NO:104); K461D (SEQ ID NO:105); K461E
(SEQ ID NO:106); K469A (SEQ ID NO:107); K469D (SEQ ID NO:108);
K469E (SEQ ID NO:109); K470A (SEQ ID NO:110); K470D (SEQ ID
NO:111); and K470E (SEQ ID NO:112).
[0081] 2. Active Site Mutants
[0082] The following modifications can confer increased catalytic
efficiency. The modifications are in select residues of the active
site, and can effect improved catalytic efficiency
(k.sub.cat/K.sub.m) for adenosine. Binding to heparin can deplete
circulating levels of administered ADA2. Thus, the following ADA2
variants can confer increased adenosine deaminase activity:
[0083] H264A; H264Q; H264N; H264G; R219K; R219Q; R219N; R219A;
L221A; L221V; L221G; E179D; E179A; E179S; E179T; E179V; E179G;
S262A; S262V; S262M; S262N; D86A; D86G; D86E; D86F; D86G; D86H;
D86I; D86K; D86L; D86M; D86N; D86P; D86Q; D86R; D86S; D86T; D86V;
D86W; D86Y; E179G; E179F; E179H; E179I; E179K; E179L; E179M; E179N;
E179P; E179Q; E179R; E179W; E179Y; R219C; R219D; R219E; R219F;
R219G; R219H; R219I; R219L; R219M; R219P; R219S; R219T; R219V;
R219W; R219Y; L221C; L221D; L221E; L221F; L221H; L221I; L221K;
L221M; L221N; L221P; L221Q; L221R; L221S; L221T; L221W; L221Y;
S262C; S262D; S262E; S262F; S262G; S262H; S262I; S262K; S262L;
S262P; S262Q; S262R; S262T; S262W; S262Y; H264C; H264D; H264E;
H264F; H264I; H264K; H264L; H264M; H264P; H264R; H264S; H264T;
H264V; H264W; H264Y; S266A; S266C; S266D; S266E; S266F; S266G;
S266H; S266I; S266K; S266L; S266M; S266N; S266P; S266Q; S266R;
S266T; S266V; S266W; S266Y; K267A; K267C; K267D; K267E; K267F;
K267G; K267H; K267I; K267L; K267M; K267N; K267P; K267Q; K267R;
K267S; K267T; K267V; K267W; K267Y; V296A; V296C; V296D; V296E;
V296F; V296G; V296H; V296I; V296K; V296L; V296M; V296N; V296P;
V296Q; V296R; V296S; V296T; V296W; and V296Y.
[0084] Examples of Active Site Mutants Containing these
Replacements:
H264A (SEQ ID NO:34); H264Q (SEQ ID NO:35); H264N (SEQ ID NO:36);
H264G (SEQ ID NO:37); R219K (SEQ ID NO:38); R219Q (SEQ ID NO:39);
R219N (SEQ ID NO:40); R219A (SEQ ID NO:41); L221A (SEQ ID NO:42);
L221V (SEQ ID NO:43); L221G (SEQ ID NO:44); E179D (SEQ ID NO:45);
E179A (SEQ ID NO:46); E179S (SEQ ID NO:47); E179T (SEQ ID NO:48);
E179V (SEQ ID NO:49); E179G (SEQ ID NO:50); S262A (SEQ ID NO:51);
S262V (SEQ ID NO:52); S262M (SEQ ID NO:53); S262N (SEQ ID NO:54);
D86A (SEQ ID NO:113); D86C (SEQ ID NO:114); D86E (SEQ ID NO:115);
D86F (SEQ ID NO:116); D86G (SEQ ID NO:117); D86H (SEQ ID NO:118);
D86I (SEQ ID NO:119); D86K (SEQ ID NO:120); D86L (SEQ ID NO:121);
D86M (SEQ ID NO:122); D86N (SEQ ID NO:123); D86P (SEQ ID NO:124);
D86Q (SEQ ID NO:125); D86R (SEQ ID NO:126); D86S (SEQ ID NO:127);
D86T (SEQ ID NO:128); D86V (SEQ ID NO:129); D86W (SEQ ID NO:130);
D86Y (SEQ ID NO:131); E179C (SEQ ID NO:132); E179F (SEQ ID NO:133);
E179H (SEQ ID NO:134); E179I (SEQ ID NO:135); E179K (SEQ ID
NO:136); E179L (SEQ ID NO:137); E179M (SEQ ID NO:138); E179N (SEQ
ID NO:139); E179P (SEQ ID NO:140); E179Q (SEQ ID NO:141); E179R
(SEQ ID NO:142); E179W (SEQ ID NO:143); E179Y (SEQ ID NO:144);
R219C (SEQ ID NO:145); R219D (SEQ ID NO:146); R219E (SEQ ID
NO:147); R219F (SEQ ID NO:148); R219G (SEQ ID NO:149); R219H (SEQ
ID NO:150); R219I (SEQ ID NO:151); R219L (SEQ ID NO:152); R219M
(SEQ ID NO:153); R219P (SEQ ID NO:154); R219S (SEQ ID NO:155);
R219T (SEQ ID NO:156); R219V (SEQ ID NO:157); R219W (SEQ ID
NO:158); R219Y (SEQ ID NO:159); L221C (SEQ ID NO:160); L221D (SEQ
ID NO:161); L221E (SEQ ID NO:162); L221F (SEQ ID NO:163); L221H
(SEQ ID NO:164); L221I (SEQ ID NO:165); L221K (SEQ ID NO:166);
L221M (SEQ ID NO:167); L221N (SEQ ID NO:168); L221P (SEQ ID
NO:169); L221Q (SEQ ID NO:170); L221R (SEQ ID NO:171); L221S (SEQ
ID NO:172); L221T (SEQ ID NO:173); L221W (SEQ ID NO:174); L221Y
(SEQ ID NO:175); S262C (SEQ ID NO:176); S262D (SEQ ID NO:177);
S262E (SEQ ID NO:178); S262F (SEQ ID NO:179); S262G (SEQ ID
NO:180); S262H (SEQ ID NO:181); S262I (SEQ ID NO:182); S262K (SEQ
ID NO:183); S262L (SEQ ID NO:184); S262P (SEQ ID NO:185); S262Q
(SEQ ID NO:186); S262R (SEQ ID NO:187); S262T (SEQ ID NO:188);
S262W (SEQ ID NO:189); S262Y (SEQ ID NO:190); H264C (SEQ ID
NO:191); H264D (SEQ ID NO:192); H264E (SEQ ID NO:193); H264F (SEQ
ID NO:194); H264I (SEQ ID NO:195); H264K (SEQ ID NO:196); H264L
(SEQ ID NO:197); H264M (SEQ ID NO:198); H264P (SEQ ID NO:199);
H264R (SEQ ID NO:200); H264S (SEQ ID NO:201); H264T (SEQ ID
NO:202); H264V (SEQ ID NO:203); H264W (SEQ ID NO:204); H264Y (SEQ
ID NO:205); S266A (SEQ ID NO:206); S266C (SEQ ID NO:207); S266D
(SEQ ID NO:208); S266E (SEQ ID NO:209); S266F (SEQ ID NO:210);
S266G (SEQ ID NO:211); S266H (SEQ ID NO:212); S266I (SEQ ID
NO:213); S266K (SEQ ID NO:214); S266L (SEQ ID NO:215); S266M (SEQ
ID NO:216); S266N (SEQ ID NO:217); S266P (SEQ ID NO:218); S266Q
(SEQ ID NO:219); S266R (SEQ ID NO:220); S266T (SEQ ID NO:221);
S266V (SEQ ID NO:222); S266W (SEQ ID NO:223); S266Y (SEQ ID
NO:224); K267A (SEQ ID NO:225); K267C (SEQ ID NO:226); K267D (SEQ
ID NO:227); K267E (SEQ ID NO:228); K267F (SEQ ID NO:229); K267G
(SEQ ID NO:230); K267H (SEQ ID NO:231); K267I (SEQ ID NO:232);
K267L (SEQ ID NO:233); K267M (SEQ ID NO:234); K267N (SEQ ID
NO:235); K267P (SEQ ID NO:236); K267Q (SEQ ID NO:237); K267R (SEQ
ID NO:238); K267S (SEQ ID NO:239); K267T (SEQ ID NO:240); K267V
(SEQ ID NO:241); K267W (SEQ ID NO:242); K267Y (SEQ ID NO:243);
V296A (SEQ ID NO:244); V296C (SEQ ID NO:245); V296D (SEQ ID
NO:246); V296E (SEQ ID NO:247); V296F (SEQ ID NO:248); V296G (SEQ
ID NO:249); V296H (SEQ ID NO:250); V296I (SEQ ID NO:251); V296K
(SEQ ID NO:252); V296L (SEQ ID NO:253); V296M (SEQ ID NO:254);
V296N (SEQ ID NO:255); V296P (SEQ ID NO:256); V296Q (SEQ ID
NO:257); V296R (SEQ ID NO:258); V296S (SEQ ID NO:259); V296T (SEQ
ID NO:260); V296W (SEQ ID NO:261); and V296Y (SEQ ID NO:262).
[0085] 3. Hyperglycosylation Mutants
[0086] The following modifications introduce a non-native
glycosylation site in ADA2. Introduction of non-native
glycosylation sites, such as N-linked glycosylation sites, can
confer an increase in stability and pharmacokinetic profiles. Thus,
the following ADA2 variants can effect hyperglycosylation of ADA2,
and increase the stability and pharmacokinetic profiles of the
administered ADA2:
[0087] --.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3; R20N/V22S;
K371N/D373S; K372N/I374S; T403N/H405S; and G404N/P406S.
[0088] Examples of Hyperglycosylation Mutants Containing these
Replacements:
--.fwdarw.N1/--.fwdarw.A2/--.fwdarw.53 (SEQ ID NO:274); R20N/V22S
(SEQ ID NO:275); K371N/D373S (SEQ ID NO:276); K372N/I374S (SEQ ID
NO:277); T403N/H405S (SEQ ID NO:278); and G404N/P406S (SEQ ID
NO:279).
[0089] 4. PRB Deletion and Replacement Mutants
[0090] The following variants contain a modified PRB domain. The
modifications of the PRB domain can include deletion of all or a
portion of the PRB domain (i.e. deletion of one or more residues of
the PRB domain), insertion of one or more amino acid residues into
the PRB domain, amino acid replacement of one or more residues of
the PRB domain or a combination thereof. Deletion and/or
substitution of the PRB domain can confer altered activity, e.g.,
reduction in binding to a receptor and/or the activity mediated by
the receptor.
[0091] C105-T147del.fwdarw.(Gly)n, where n=2 to 20;
C105-T147del.fwdarw.(Gly)15; C105-T147del.fwdarw.(Gly)10;
C105-T147del.fwdarw.(Gly)7; C105-T147del.fwdarw.(Gly)5;
C105-T147del.fwdarw.(Gly)3; N98-N156del; C105-E148del;
C105-T147del; V99-Q144del; V99-Q144del.fwdarw.(GGGGS)n, where n=1
to 5; C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5;
V99-Q144del.fwdarw.(GGGGS)1; V99-Q144del.fwdarw.(GGGGS)2;
V99-Q144del.fwdarw.(GGGGS)3; C105-T147del.fwdarw.(GGGGS)1;
C105-T147del.fwdarw.(GGGGS)2; and C105-T147del.fwdarw.(GGGGS)3.
[0092] Examples of PRB Deletion and Replacement Mutants Containing
these Replacements:
[0093] C105-T147del.fwdarw.(Gly)n (SEQ ID NO:280);
C105-T147del.fwdarw.(Gly)15 (SEQ ID NO:281);
C105-T147del.fwdarw.(Gly)10 (SEQ ID NO:282);
C105-T147del.fwdarw.(Gly)7 (SEQ ID NO:283);
C105-T147del.fwdarw.(Gly)5 (SEQ ID NO:284);
C105-T147del.fwdarw.(Gly)3 (SEQ ID NO:285); N98-N156del (SEQ ID
NO:548); C105-E148del (SEQ ID NO:549); C105-T147del (SEQ ID
NO:550); V99-Q144del (SEQ ID NO:579); V99-Q144del.fwdarw.(GGGGS)n,
where n=1 to 5 (SEQ ID NO:581); C105-T147del.fwdarw.(GGGGS)n, where
n=1 to 5 (SEQ ID NO:582); V99-Q144del.fwdarw.(GGGGS)1 (SEQ ID
NO:583); V99-Q144del.fwdarw.(GGGGS)2 (SEQ ID NO:584);
V99-Q144del.fwdarw.(GGGGS)3 (SEQ ID NO:585);
C105-T147del.fwdarw.(GGGGS)1 (SEQ ID NO:586);
C105-T147del.fwdarw.(GGGGS)2 (SEQ ID NO:587); and
C105-T147del.fwdarw.(GGGGS)3 (SEQ ID NO:588)
[0094] 5. PRB Hyperglycosylation Mutants
[0095] The following modifications can introduce a non-native
glycosylation site in the PRB domain. Introduction of non-native
glycosylation sites, such as N-linked glycosylation sites, in the
PRB domain can confer an increase in stability and pharmacokinetic
profiles and/or other activities, e.g., reduction in binding to a
receptor. Thus, the following ADA2 variants can effect
hyperglycosylation of the ADA2 in the PRB domain, reduce receptor
binding, and increase the stability and pharmacokinetic profiles of
the administered ADA2:
[0096] R125N/P126A; S127N/K129S; P126N/E128T; R112N/I114T;
I134N/L135C/L136T; I134N/L135S/L136T; R142N/Q144S; E137N/Y139T; and
P111N/G113S.
[0097] Examples of PRB Hyperglycosylation Mutants Containing these
Replacements:
[0098] R125N/P126A (SEQ ID NO:552); S127N/K129S (SEQ ID NO:553);
P126N/E128T (SEQ ID NO:554); R112N/I114T (SEQ ID NO:555);
I134N/L135C/L136T (SEQ ID NO:556); I134N/L135S/L136T (SEQ ID
NO:557); R142N/Q144S (SEQ ID NO:558); E137N/Y139T (SEQ ID NO:559);
and P111N/G113S (SEQ ID NO:560).
[0099] 6. PRB-ADA Domain Interaction Mutants
[0100] The following modifications can confer altered interaction
between the PRB domain and the rest of ADA2 (e.g., the adenosine
deaminase (ADA) domain). Altering the interaction between PRB
domain and the rest of ADA2, such as the ADA domain, can confer an
activity, e.g., an increase in the adenosine deaminse activity and
a reduction in receptor binding:
[0101] F119S; F119K; Y224R; Y224N; Y191S; Y191D; F183K;
Y191D/Y224R; F109S; F109A; R118D; R118A; Y139T; Y139A; W133S;
W133T; P124A; and P124S.
[0102] Examples of PRB-ADA Domain Interaction Mutants Containing
these Replacements:
[0103] F119S (SEQ ID NO:561); F119K (SEQ ID NO:562); Y224R (SEQ ID
NO:563); Y224N (SEQ ID NO:564); Y191S (SEQ ID NO:565); Y191D (SEQ
ID NO:566); F183K (SEQ ID NO:567); Y191D/Y224R (SEQ ID NO:568);
F109S (SEQ ID NO:569); F109A (SEQ ID NO:570); R118D (SEQ ID
NO:571); R118A (SEQ ID NO:572); Y139T (SEQ ID NO:573); Y139A (SEQ
ID NO:574); W133S (SEQ ID NO:575); W133T (SEQ ID NO:576); P124A
(SEQ ID NO:577); and P124S (SEQ ID NO:578).
[0104] 7. Combinations of Mutations with Hyperglycosylation
Mutants
[0105] The following variants combine modifications that effect
improved catalytic efficiency (kcat/Km) for adenosine, such as
R219Q and/or S262N, with modifications that introduce non-native
glycosylation sites:
[0106] R219Q/S262N/--.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3;
R219Q/S262N/R20N/V22S; R219Q/S262N/K371N/D373S;
R219Q/S262N/K372N/I374S; R219Q/S262N/T403N/H405S; and
R219Q/S262N/G404N/P406S.
[0107] Combination with Hyperglycosylation Mutants Containing these
Replacements:
[0108] R219Q/S262N/--.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3 (SEQ ID
NO:596); R219Q/S262N/R20N/V22S (SEQ ID NO:597);
R219Q/S262N/K371N/D373S (SEQ ID NO:598); R219Q/S262N/K372N/I374S
(SEQ ID NO:599); R219Q/S262N/T403N/H405S (SEQ ID NO:600); and
R219Q/S262N/G404N/P406S (SEQ ID NO:601).
[0109] 8. Combinations of Mutations with PRB Hyperglycosylation
Mutants
[0110] The following variants combine modifications that effect
improved catalytic efficiency (kcat/Km) for adenosine, such as
R219Q and/or S262N, with modifications that introduce non-native
glycosylation sites in the PRB domain:
[0111] R219Q/S262N/R125N/P126A; R219Q/S262N/S127N/K129S;
R219Q/S262N/P126N/E128T; R219Q/S262N/R112N/I114T;
R219Q/S262N/I134N/L135C/L136T; R219Q/S262N/I134N/L135S/L136T;
R219Q/S262N/R142N/Q144S; R219Q/S262N/E137N/Y139T; and
R219Q/S262N/P111N/G113S.
[0112] Examples of Combinations with PRB Hyperglycosylation Mutants
Containing these Replacements:
[0113] R219Q/S262N/R125N/P126A (SEQ ID NO:607);
R219Q/S262N/S127N/K129S (SEQ ID NO:608); R219Q/S262N/P126N/E128T
(SEQ ID NO:609); R219Q/S262N/R112N/I114T (SEQ ID NO:610);
R219Q/S262N/I134N/L135C/L136T (SEQ ID NO:611);
R219Q/S262N/I134N/L135S/L136T (SEQ ID NO:612);
R219Q/S262N/R142N/Q144S (SEQ ID NO:613); R219Q/S262N/E137N/Y139T
(SEQ ID NO:614); and R219Q/S262N/P111N/G113S (SEQ ID NO:615).
[0114] 9. Combinations with PRB-ADA Domain Interaction Mutants
[0115] The following variants combine modifications that effect
improved catalytic efficiency (kcat/Km) for adenosine, such as
R219Q and/or S262N, with modifications that alter the interaction
between the PRB domain and the rest of ADA2 (e.g., the adenosine
deaminase (ADA) domain):
[0116] R219Q/S262N/F119S; R219Q/S262N/F119K; R219Q/S262N/Y224R;
R219Q/S262N/Y224N; R219Q/S262N/Y191S; R219Q/S262N/Y191D;
R219Q/S262N/F183K; R219Q/S262N/Y191D/Y224R; R219Q/S262N/F109S;
R219Q/S262N/F109A; R219Q/S262N/R118D; R219Q/S262N/R118A;
R219Q/S262N/Y139T; R219Q/S262N/Y139A; R219Q/S262N/W133S;
R219Q/S262N/W133T; R219Q/S262N/P124A; and R219Q/S262N/P124S.
[0117] Combinations with PRB-ADA Domain Interaction Mutants
Containing these Replacements:
[0118] R219Q/S262N/F119S (SEQ ID NO:616); R219Q/S262N/F119K (SEQ ID
NO:617); R219Q/S262N/Y224R (SEQ ID NO:618); R219Q/S262N/Y224N (SEQ
ID NO:619); R219Q/S262N/Y191S (SEQ ID NO:620); R219Q/S262N/Y191D
(SEQ ID NO:621); R219Q/S262N/F183K (SEQ ID NO:622);
R219Q/S262N/Y191D/Y224R (SEQ ID NO:623); R219Q/S262N/F109S (SEQ ID
NO:624); R219Q/S262N/F109A (SEQ ID NO:625); R219Q/S262N/R118D (SEQ
ID NO:626); R219Q/S262N/R118A (SEQ ID NO:627); R219Q/S262N/Y139T
(SEQ ID NO:628); R219Q/S262N/Y139A (SEQ ID NO:629);
R219Q/S262N/W133S (SEQ ID NO:630); R219Q/S262N/W133T (SEQ ID
NO:631); R219Q/S262N/P124A (SEQ ID NO:632); and R219Q/S262N/P124S
(SEQ ID NO:633).
[0119] 10. Combinations with PRB Deletion Mutants
[0120] The following variants combine modifications that effect
improved catalytic efficiency (kcat/Km) for adenosine, such as
R219Q and/or S262N, and/or modifications that confer reduced
heparin binding, such as K371D, with modifications, e.g.,
deletions, insertions, substitutions, and/or replacements, in the
PRB domain:
[0121] K371D/V99-Q144del.fwdarw.(GGGGS)1;
K371D/V99-Q144del.fwdarw.(GGGGS)2;
K371D/V99-Q144del.fwdarw.(GGGGS)3;
K371D/C105-T147del.fwdarw.(GGGGS)1;
K371D/C105-T147del.fwdarw.(GGGGS)2;
K371D/C105-T147del.fwdarw.(GGGGS)3;
R219Q/S262N/C105-T147del.fwdarw.(Gly)15;
R219Q/S262N/C105-T147del.fwdarw.(Gly)10;
R219Q/S262N/C105-T147del.fwdarw.(Gly)7;
R219Q/S262N/C105-T147del.fwdarw.(Gly)5;
R219Q/S262N/C105-T147del.fwdarw.(Gly)3;
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS)1;
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS)2;
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS)3;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS)1;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS)2;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS)3;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS)1;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS)2;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS)3;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS)1;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS)2;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS)3;
K371D/C105-T147del.fwdarw.(Gly)n, where n=2 to 20;
K371D/C105-T147del.fwdarw.(Gly)15;
K371D/C105-T147del.fwdarw.(Gly)10;
K371D/C105-T147del.fwdarw.(Gly)7; K371D/C105-T147del.fwdarw.(Gly)5;
K371D/C105-T147del.fwdarw.(Gly)3;
K371D/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5;
K371D/C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5;
K371D/N98-N156del; K371D/C105-E148del; K371D/C105-T147del;
K371D/V99-Q144del; R219Q/S262N/C105-T147del.fwdarw.(Gly)n, where
n=2 to 20; R219Q/S262N/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5;
R219Q/S262N/N98-N156del; R219Q/S262N/C105-E148del;
R219Q/S262N/C105-T147del; R219Q/S262N/V99-Q144del;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)n, where n=2 to 20;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)15;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)10;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)7;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)5;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)3;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5;
R219Q/S262N/K371D/N98-N156del; R219Q/S262N/K371D/C105-E148del;
R219Q/S262N/K371D/C105-T147del; R219Q/S262N/K371D/V99-Q144del;
R219Q/C105-T147del.fwdarw.(Gly)n, where n=2 to 20;
R219Q/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5;
R219Q/C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5;
R219Q/N98-N156del; R219Q/C105-E148del; R219Q/C105-T147del;
R219Q/V99-Q144del; S262N/C105-T147del.fwdarw.(Gly)n, where n=2 to
20; S262N/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5;
S262N/C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5;
S262N/N98-N156del; and S262N/C105-E148del; S262N/C105-T147del; and
S262N/V99-Q144del.
[0122] Examples of Combination with PRB Deletion Mutants Containing
these Replacements:
[0123] K371D/V99-Q144del.fwdarw.(GGGGS)1 (SEQ ID NO:589);
K371D/V99-Q144del.fwdarw.(GGGGS)2 (SEQ ID NO:590);
K371D/V99-Q144del.fwdarw.(GGGGS)3 (SEQ ID NO:591);
K371D/C105-T147del.fwdarw.(GGGGS)1 (SEQ ID NO:592);
K371D/C105-T147del.fwdarw.(GGGGS)2 (SEQ ID NO:593);
K371D/C105-T147del.fwdarw.(GGGGS)3 (SEQ ID NO:594);
R219Q/S262N/C105-T147del.fwdarw.(Gly)15 (SEQ ID NO:602);
R219Q/S262N/C105-T147del.fwdarw.(Gly)10 (SEQ ID NO:603);
R219Q/S262N/C105-T147del.fwdarw.(Gly)7 (SEQ ID NO:604);
R219Q/S262N/C105-T147del.fwdarw.(Gly)5 (SEQ ID NO:605);
R219Q/S262N/C105-T147del.fwdarw.(Gly)3 (SEQ ID NO:606);
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS)1 (SEQ ID NO:634);
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS)2 (SEQ ID NO:635);
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS)3 (SEQ ID NO:636);
R219Q/S262N/C105-T147del.fwdarw.(GGGGS)1 (SEQ ID NO:637);
R219Q/S262N/C105-T147del.fwdarw.(GGGGS)2 (SEQ ID NO:638);
R219Q/S262N/C105-T147del.fwdarw.(GGGGS)3 (SEQ ID NO:639);
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS)1 (SEQ ID NO:640);
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS)2 (SEQ ID NO:641);
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS)3 (SEQ ID NO:642);
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS)1 (SEQ ID NO:643);
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS)2 (SEQ ID NO:644);
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS)3 (SEQ ID NO:645);
K371D/C105-T147del.fwdarw.(Gly)n, where n=2 to 20 (SEQ ID NO:646);
K371D/C105-T147del.fwdarw.(Gly)15 (SEQ ID NO:647);
K371D/C105-T147del.fwdarw.(Gly)10 (SEQ ID NO:648);
K371D/C105-T147del.fwdarw.(Gly)7 (SEQ ID NO:649);
K371D/C105-T147del.fwdarw.(Gly)5 (SEQ ID NO:650);
K371D/C105-T147del.fwdarw.(Gly)3 (SEQ ID NO:651);
K371D/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5 (SEQ ID NO:652);
K371D/C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5 (SEQ ID NO:653);
K371D/N98-N156del (SEQ ID NO:654); K371D/C105-E148del (SEQ ID
NO:655); K371D/C105-T147del (SEQ ID NO:656); K371D/V99-Q144del (SEQ
ID NO:657); R219Q/S262N/C105-T147del.fwdarw.(Gly)n, where n=2 to 20
(SEQ ID NO:658); R219Q/S262N/V99-Q144del.fwdarw.(GGGGS)n, where n=1
to 5 (SEQ ID NO:664); R219Q/S262N/C105-T147del.fwdarw.(GGGGS)n,
where n=1 to 5 (SEQ ID NO:665); R219Q/S262N/N98-N156del (SEQ ID
NO:666); R219Q/S262N/C105-E148del (SEQ ID NO:667);
R219Q/S262N/C105-T147del (SEQ ID NO:668); R219Q/S262N/V99-Q144del
(SEQ ID NO:669); R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)n,
where n=2 to 20 (SEQ ID NO:670);
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)15 (SEQ ID NO:671);
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)10 (SEQ ID NO:672);
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)7 (SEQ ID NO:673);
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)5 (SEQ ID NO:674);
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)3 (SEQ ID NO:675);
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5 (SEQ
ID NO:676); R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS)n, where
n=1 to 5 (SEQ ID NO:677); R219Q/S262N/K371D/N98-N156del (SEQ ID
NO:678); R219Q/S262N/K371D/C105-E148del (SEQ ID NO:679);
R219Q/S262N/K371D/C105-T147del (SEQ ID NO:680);
R219Q/S262N/K371D/V99-Q144del (SEQ ID NO:681);
R219Q/C105-T147del.fwdarw.(Gly)n, where n=2 to 20 (SEQ ID NO:918);
R219Q/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5 (SEQ ID NO:919);
R219Q/C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5 (SEQ ID NO:920);
R219Q/N98-N156del (SEQ ID NO:921); R219Q/C105-E148del (SEQ ID
NO:922); R219Q/C105-T147del (SEQ ID NO:923); R219Q/V99-Q144del (SEQ
ID NO:924); S262N/C105-T147del.fwdarw.(Gly)n, where n=2 to 20 (SEQ
ID NO:925); S262N/V99-Q144del.fwdarw.(GGGGS)n, where n=1 to 5 (SEQ
ID NO:926); S262N/C105-T147del.fwdarw.(GGGGS)n, where n=1 to 5 (SEQ
ID NO:927); S262N/N98-N156del (SEQ ID NO:928); S262N/C105-E148del
(SEQ ID NO:929); S262N/C105-T147del (SEQ ID NO:930); and
S262N/V99-Q144del (SEQ ID NO:931).
[0124] 11. Other Combination Mutants
[0125] The following variants combine various modifications, such
as modifications that effect improved catalytic efficiency
(kcat/Km) for adenosine, such as R219Q and/or S262N, modifications
that confer reduced heparin binding, such as K371D, and other
modifications:
[0126] K11A/R20A; K11A/R20A/K371A; R20A/K371A; K11A/K371A;
S262N/K371D; S262N/K371E; S262N/R20E; S262N/R20E/K371D;
S262N/R20E/K371E; R219Q/K371E; R219Q/K371D; R219Q/R20E;
R219Q/K371E/R20E; R219Q/K371D/R20E; R219Q/S262N/K371E;
R219Q/S262N/K371D; R219Q/S262N/R20E; R219Q/S262N/K371E/R20E;
R219Q/S262N/K371D/R20E; R219Q/S262N; R219Q/S262N/K11A;
R219Q/S262N/K11D; R219Q/S262N/K11E; R219Q/S262N/K13A;
R219Q/S262N/K13D; R219Q/S262N/K13E; R219Q/S262N/K371A;
R219Q/S262N/K372A; R219Q/S262N/K372D; R219Q/S262N/K372E;
R219Q/S262N/K452A; R219Q/S262N/K452D; R219Q/S262N/K452E;
R219Q/S262N/R20A; R219Q/S262N/R20D; R219Q/S262N/R366A;
R219Q/S262N/R366D; R219Q/S262N/R366E; R219Q/S262N/H264A;
R219Q/S262N/H264Q; R219Q/S262N/H264N; R219Q/S262N/H264G;
R219K/S262N; R219N/S262N; R219A/S262N; R219Q/S262N/L221A;
R219Q/S262N/L221V; R219Q/S262N/L221G; R219Q/S262N/E179D;
R219Q/S262N/E179A; R219Q/S262N/E179S; R219Q/S262N/E179T;
R219Q/S262N/E179V; R219Q/S262N/E179G; R219Q/S262A; R219Q/S262V;
R219Q/S262M; R219Q/S262N/K11A/R20A; R219Q/S262N/K11A/R20A/K371A;
R219Q/S262N/R20A/K371A; R219Q/S262N/K11A/K371A; R219Q/S262N/K26A;
R219Q/S262N/K26D; R219Q/S262N/K26E; R219Q/S262N/R217A;
R219Q/S262N/R217D; R219Q/S262N/R217E; R219Q/S262N/K258A;
R219Q/S262N/K258D; R219Q/S262N/K258E; R219Q/S262N/R277A;
R219Q/S262N/R277D; R219Q/S262N/R277E; R219Q/S262N/R283A;
R219Q/S262N/R283D; R219Q/S262N/R283E; R219Q/S262N/K309A;
R219Q/S262N/K309D; R219Q/S262N/K309E; R219Q/S262N/K317A;
R219Q/S262N/K317D; R219Q/S262N/K317E; R219Q/S262N/K321A;
R219Q/S262N/K321D; R219Q/S262N/K321E; R219Q/S262N/R352A;
R219Q/S262N/R352D; R219Q/S262N/R352E; R219Q/S262N/R441A;
R219Q/S262N/R441D; R219Q/S262N/R441E; R219Q/S262N/K444A;
R219Q/S262N/K444D; R219Q/S262N/K444E; R219Q/S262N/K461A;
R219Q/S262N/K461D; R219Q/S262N/K461E; R219Q/S262N/K469A;
R219Q/S262N/K469D; R219Q/S262N/K469E; R219Q/S262N/K470A;
R219Q/S262N/K470D; R219Q/S262N/K470E; R219Q/S262N/D86A;
R219Q/S262N/D86C; R219Q/S262N/D86E; R219Q/S262N/D86F;
R219Q/S262N/D86G; R219Q/S262N/D86H; R219Q/S262N/D86I;
R219Q/S262N/D86K; R219Q/S262N/D86L; R219Q/S262N/D86M;
R219Q/S262N/D86N; R219Q/S262N/D86P; R219Q/S262N/D86Q;
R219Q/S262N/D86R; R219Q/S262N/D86S; R219Q/S262N/D86T;
R219Q/S262N/D86V; R219Q/S262N/D86W; R219Q/S262N/D86Y;
R219Q/S262N/E179C; R219Q/S262N/E179F; R219Q/S262N/E179H;
R219Q/S262N/E179I; R219Q/S262N/E179K; R219Q/S262N/E179L;
R219Q/S262N/E179M; R219Q/S262N/E179N; R219Q/S262N/E179P;
R219Q/S262N/E179Q; R219Q/S262N/E179R; R219Q/S262N/E179W;
R219Q/S262N/E179Y; R219C/S262N; R219D/S262N; R219E/S262N;
R219F/S262N; R219G/S262N; R219H/S262N; R219I/S262N; R219L/S262N;
R219M/S262N; R219P/S262N; R219S/S262N; R219T/S262N; R219V/S262N;
R219W/S262N; R219Y/S262N; R219Q/S262N/L221C; R219Q/S262N/L221D;
R219Q/S262N/L221E; R219Q/S262N/L221F; R219Q/S262N/L221H;
R219Q/S262N/L221I; R219Q/S262N/L221K; R219Q/S262N/L221M;
R219Q/S262N/L221N; R219Q/S262N/L221P; R219Q/S262N/L221Q;
R219Q/S262N/L221R; R219Q/S262N/L221S; R219Q/S262N/L221T;
R219Q/S262N/L221W; R219Q/S262N/L221Y; R219Q/S262C; R219Q/S262D;
R219Q/S262E; R219Q/S262F; R219Q/S262G; R219Q/S262H; R219Q/S262I;
R219Q/S262K; R219Q/S262L; R219Q/S262P; R219Q/S262Q; R219Q/S262R;
R219Q/S262T; R219Q/S262W; R219Q/S262Y; R219Q/S262N/H264C;
R219Q/S262N/H264D; R219Q/S262N/H264E; R219Q/S262N/H264F;
R219Q/S262N/H264I; R219Q/S262N/H264K; R219Q/S262N/H264L;
R219Q/S262N/H264M; R219Q/S262N/H264P; R219Q/S262N/H264R;
R219Q/S262N/H264S; R219Q/S262N/H264T; R219Q/S262N/H264V;
R219Q/S262N/H264W; R219Q/S262N/H264Y; R219Q/S262N/S266A;
R219Q/S262N/S266C; R219Q/S262N/S266D; R219Q/S262N/S266E;
R219Q/S262N/S266F; R219Q/S262N/S266G; R219Q/S262N/S266H;
R219Q/S262N/S266I; R219Q/S262N/S266K; R219Q/S262N/S266L;
R219Q/S262N/S266M; R219Q/S262N/S266N; R219Q/S262N/S266P;
R219Q/S262N/S266Q; R219Q/S262N/S266R; R219Q/S262N/S266T;
R219Q/S262N/S266V; R219Q/S262N/S266W; R219Q/S262N/S266Y;
R219Q/S262N/K267A; R219Q/S262N/K267C; R219Q/S262N/K267D;
R219Q/S262N/K267E; R219Q/S262N/K267F; R219Q/S262N/K267G;
R219Q/S262N/K267H; R219Q/S262N/K267I; R219Q/S262N/K267L;
R219Q/S262N/K267M; R219Q/S262N/K267N; R219Q/S262N/K267P;
R219Q/S262N/K267Q; R219Q/S262N/K267R; R219Q/S262N/K267S;
R219Q/S262N/K267T; R219Q/S262N/K267V; R219Q/S262N/K267W;
R219Q/S262N/K267Y; R219Q/S262N/V296A; R219Q/S262N/V296C;
R219Q/S262N/V296D; R219Q/S262N/V296E; R219Q/S262N/V296F;
R219Q/S262N/V296G; R219Q/S262N/V296H; R219Q/S262N/V296I;
R219Q/S262N/V296K; R219Q/S262N/V296L; R219Q/S262N/V296M;
R219Q/S262N/V296N; R219Q/S262N/V296P; R219Q/S262N/V296Q;
R219Q/S262N/V296R; R219Q/S262N/V296S; R219Q/S262N/V296T;
R219Q/S262N/V296W; R219Q/S262N/V296Y; R219Q/K11A/R20A;
R219Q/K11A/R20A/K371A; R219Q/R20A/K371A; R219Q/K11A/K371A;
S262N/K11A/R20A; S262N/K11A/R20A/K371A; S262N/R20A/K371A; and
S262N/K11A/K371A.
[0127] Examples of these Combination Mutants Containing these
Replacements:
[0128] K11A/R20A (SEQ ID NO:55); K11A/R20A/K371A (SEQ ID NO:56);
R20A/K371A (SEQ ID NO:57); K11A/K371A (SEQ ID NO:58); S262N/K371D
(SEQ ID NO:59); S262N/K371E (SEQ ID NO:60); S262N/R20E (SEQ ID
NO:61); S262N/R20E/K371D (SEQ ID NO:62); S262N/R20E/K371E (SEQ ID
NO:63); R219Q/K371E (SEQ ID NO:263); R219Q/K371D (SEQ ID NO:264);
R219Q/R20E (SEQ ID NO:265); R219Q/K371E/R20E (SEQ ID NO:266);
R219Q/K371D/R20E (SEQ ID NO:267); R219Q/S262N/K371E (SEQ ID
NO:268); R219Q/S262N/K371D (SEQ ID NO:269); R219Q/S262N/R20E (SEQ
ID NO:270); R219Q/S262N/K371E/R20E (SEQ ID NO:271);
R219Q/S262N/K371D/R20E (SEQ ID NO:272); R219Q/S262N (SEQ ID
NO:273); R219Q/S262N/K11A (SEQ ID NO:659); R219Q/S262N/K11D (SEQ ID
NO:660); R219Q/S262N/K11E (SEQ ID NO:661); R219Q/S262N/K13A (SEQ ID
NO:662); R219Q/S262N/K13D (SEQ ID NO:663); R219Q/S262N/K13E (SEQ ID
NO:682); R219Q/S262N/K371A (SEQ ID NO:683); R219Q/S262N/K372A (SEQ
ID NO:684); R219Q/S262N/K372D (SEQ ID NO:685); R219Q/S262N/K372E
(SEQ ID NO:686); R219Q/S262N/K452A (SEQ ID NO:687);
R219Q/S262N/K452D (SEQ ID NO:688); R219Q/S262N/K452E (SEQ ID
NO:689); R219Q/S262N/R20A (SEQ ID NO:690); R219Q/S262N/R20D (SEQ ID
NO:691); R219Q/S262N/R366A (SEQ ID NO:692); R219Q/S262N/R366D (SEQ
ID NO:693); R219Q/S262N/R366E (SEQ ID NO:694); R219Q/S262N/H264A
(SEQ ID NO:695); R219Q/S262N/H264Q (SEQ ID NO:696);
R219Q/S262N/H264N (SEQ ID NO:697); R219Q/S262N/H264G (SEQ ID
NO:698); R219K/S262N (SEQ ID NO:699); R219N/S262N (SEQ ID NO:700);
R219A/S262N (SEQ ID NO:701); R219Q/S262N/L221A (SEQ ID NO:702);
R219Q/S262N/L221V (SEQ ID NO:703); R219Q/S262N/L221G (SEQ ID
NO:704); R219Q/S262N/E179D (SEQ ID NO:705); R219Q/S262N/E179A (SEQ
ID NO:706); R219Q/S262N/E179S (SEQ ID NO:707); R219Q/S262N/E179T
(SEQ ID NO:708); R219Q/S262N/E179V (SEQ ID NO:709);
R219Q/S262N/E179G (SEQ ID NO:710); R219Q/S262A (SEQ ID NO:711);
R219Q/S262V (SEQ ID NO:712); R219Q/S262M (SEQ ID NO:713);
R219Q/S262N/K11A/R20A (SEQ ID NO:714); R219Q/S262N/K11A/R20A/K371A
(SEQ ID NO:715); R219Q/S262N/R20A/K371A (SEQ ID NO:716);
R219Q/S262N/K11A/K371A (SEQ ID NO:717); R219Q/S262N/K26A (SEQ ID
NO:718); R219Q/S262N/K26D (SEQ ID NO:719); R219Q/S262N/K26E (SEQ ID
NO:720); R219Q/S262N/R217A (SEQ ID NO:721); R219Q/S262N/R217D (SEQ
ID NO:722); R219Q/S262N/R217E (SEQ ID NO:723); R219Q/S262N/K258A
(SEQ ID NO:724); R219Q/S262N/K258D (SEQ ID NO:725);
R219Q/S262N/K258E (SEQ ID NO:726); R219Q/S262N/R277A (SEQ ID
NO:727); R219Q/S262N/R277D (SEQ ID NO:728); R219Q/S262N/R277E (SEQ
ID NO:729); R219Q/S262N/R283A (SEQ ID NO:730); R219Q/S262N/R283D
(SEQ ID NO:731); R219Q/S262N/R283E (SEQ ID NO:732);
R219Q/S262N/K309A (SEQ ID NO:733); R219Q/S262N/K309D (SEQ ID
NO:734); R219Q/S262N/K309E (SEQ ID NO:735); R219Q/S262N/K317A (SEQ
ID NO:736); R219Q/S262N/K317D (SEQ ID NO:737); R219Q/S262N/K317E
(SEQ ID NO:738); R219Q/S262N/K321A (SEQ ID NO:739);
R219Q/S262N/K321D (SEQ ID NO:740); R219Q/S262N/K321E (SEQ ID
NO:741); R219Q/S262N/R352A (SEQ ID NO:742); R219Q/S262N/R352D (SEQ
ID NO:743); R219Q/S262N/R352E (SEQ ID NO:744); R219Q/S262N/R441A
(SEQ ID NO:745); R219Q/S262N/R441D (SEQ ID NO:746);
R219Q/S262N/R441E (SEQ ID NO:747); R219Q/S262N/K444A (SEQ ID
NO:748); R219Q/S262N/K444D (SEQ ID NO:749); R219Q/S262N/K444E (SEQ
ID NO:750); R219Q/S262N/K461A (SEQ ID NO:751); R219Q/S262N/K461D
(SEQ ID NO:752); R219Q/S262N/K461E (SEQ ID NO:753);
R219Q/S262N/K469A (SEQ ID NO:754); R219Q/S262N/K469D (SEQ ID
NO:755); R219Q/S262N/K469E (SEQ ID NO:756); R219Q/S262N/K470A (SEQ
ID NO:757); R219Q/S262N/K470D (SEQ ID NO:758); R219Q/S262N/K470E
(SEQ ID NO:759); R219Q/S262N/D86A (SEQ ID NO:760); R219Q/S262N/D86C
(SEQ ID NO:761); R219Q/S262N/D86E (SEQ ID NO:762); R219Q/S262N/D86F
(SEQ ID NO:763); R219Q/S262N/D86G (SEQ ID NO:764); R219Q/S262N/D86H
(SEQ ID NO:765); R219Q/S262N/D86I (SEQ ID NO:766); R219Q/S262N/D86K
(SEQ ID NO:767); R219Q/S262N/D86L (SEQ ID NO:768); R219Q/S262N/D86M
(SEQ ID NO:769); R219Q/S262N/D86N (SEQ ID NO:770); R219Q/S262N/D86P
(SEQ ID NO:771); R219Q/S262N/D86Q (SEQ ID NO:772); R219Q/S262N/D86R
(SEQ ID NO:773); R219Q/S262N/D86S (SEQ ID NO:774); R219Q/S262N/D86T
(SEQ ID NO:775); R219Q/S262N/D86V (SEQ ID NO:776); R219Q/S262N/D86W
(SEQ ID NO:777); R219Q/S262N/D86Y (SEQ ID NO:778);
R219Q/S262N/E179C (SEQ ID NO:779); R219Q/S262N/E179F (SEQ ID
NO:780); R219Q/S262N/E179H (SEQ ID NO:781); R219Q/S262N/E179I (SEQ
ID NO:782); R219Q/S262N/E179K (SEQ ID NO:783); R219Q/S262N/E179L
(SEQ ID NO:784); R219Q/S262N/E179M (SEQ ID NO:785);
R219Q/S262N/E179N (SEQ ID NO:786); R219Q/S262N/E179P (SEQ ID
NO:787); R219Q/S262N/E179Q (SEQ ID NO:788); R219Q/S262N/E179R (SEQ
ID NO:789); R219Q/S262N/E179W (SEQ ID NO:790); R219Q/S262N/E179Y
(SEQ ID NO:791); R219C/S262N (SEQ ID NO:792); R219D/S262N (SEQ ID
NO:793); R219E/S262N (SEQ ID NO:794); R219F/S262N (SEQ ID NO:795);
R219G/S262N (SEQ ID NO:796); R219H/S262N (SEQ ID NO:797);
R219I/S262N (SEQ ID NO:798); R219L/S262N (SEQ ID NO:799);
R219M/S262N (SEQ ID NO:800); R219P/S262N (SEQ ID NO:801);
R219S/S262N (SEQ ID NO:802); R219T/S262N (SEQ ID NO:803);
R219V/S262N (SEQ ID NO:804); R219W/S262N (SEQ ID NO:805);
R219Y/S262N (SEQ ID NO:806); R219Q/S262N/L221C (SEQ ID NO:807);
R219Q/S262N/L221D (SEQ ID NO:808); R219Q/S262N/L221E (SEQ ID
NO:809); R219Q/S262N/L221F (SEQ ID NO:810); R219Q/S262N/L221H (SEQ
ID NO:811); R219Q/S262N/L221I (SEQ ID NO:812); R219Q/S262N/L221K
(SEQ ID NO:813); R219Q/S262N/L221M (SEQ ID NO:814);
R219Q/S262N/L221N (SEQ ID NO:815); R219Q/S262N/L221P (SEQ ID
NO:816); R219Q/S262N/L221Q (SEQ ID NO:817); R219Q/S262N/L221R (SEQ
ID NO:818); R219Q/S262N/L221S (SEQ ID NO:819); R219Q/S262N/L221T
(SEQ ID NO:820); R219Q/S262N/L221W (SEQ ID NO:821);
R219Q/S262N/L221Y (SEQ ID NO:822); R219Q/S262C (SEQ ID NO:823);
R219Q/S262D (SEQ ID NO:824); R219Q/S262E (SEQ ID NO:825);
R219Q/S262F (SEQ ID NO:826); R219Q/S262G (SEQ ID NO:827);
R219Q/S262H (SEQ ID NO:828); R219Q/S262I (SEQ ID NO:829);
R219Q/S262K (SEQ ID NO:830); R219Q/S262L (SEQ ID NO:831);
R219Q/S262P (SEQ ID NO:832); R219Q/S262Q (SEQ ID NO:833);
R219Q/S262R (SEQ ID NO:834); R219Q/S262T (SEQ ID NO:835);
R219Q/S262W (SEQ ID NO:836); R219Q/S262Y (SEQ ID NO:837);
R219Q/S262N/H264C (SEQ ID NO:838); R219Q/S262N/H264D (SEQ ID
NO:839); R219Q/S262N/H264E (SEQ ID NO:840); R219Q/S262N/H264F (SEQ
ID NO:841); R219Q/S262N/H264I (SEQ ID NO:842); R219Q/S262N/H264K
(SEQ ID NO:843); R219Q/S262N/H264L (SEQ ID NO:844);
R219Q/S262N/H264M (SEQ ID NO:845); R219Q/S262N/H264P (SEQ ID
NO:846); R219Q/S262N/H264R (SEQ ID NO:847); R219Q/S262N/H264S (SEQ
ID NO:848); R219Q/S262N/H264T (SEQ ID NO:849); R219Q/S262N/H264V
(SEQ ID NO:850); R219Q/S262N/H264W (SEQ ID NO:851);
R219Q/S262N/H264Y (SEQ ID NO:852); R219Q/S262N/S266A (SEQ ID
NO:853); R219Q/S262N/S266C (SEQ ID NO:854); R219Q/S262N/S266D (SEQ
ID NO:855); R219Q/S262N/S266E (SEQ ID NO:856); R219Q/S262N/S266F
(SEQ ID NO:857); R219Q/S262N/S266G (SEQ ID NO:858);
R219Q/S262N/S266H (SEQ ID NO:859); R219Q/S262N/S266I (SEQ ID
NO:860); R219Q/S262N/S266K (SEQ ID NO:861); R219Q/S262N/S266L (SEQ
ID NO:862); R219Q/S262N/S266M (SEQ ID NO:863); R219Q/S262N/S266N
(SEQ ID NO:864); R219Q/S262N/S266P (SEQ ID NO:865);
R219Q/S262N/S266Q (SEQ ID NO:866); R219Q/S262N/S266R (SEQ ID
NO:867); R219Q/S262N/S266T (SEQ ID NO:868); R219Q/S262N/S266V (SEQ
ID NO:869); R219Q/S262N/S266W (SEQ ID NO:870); R219Q/S262N/S266Y
(SEQ ID NO:871); R219Q/S262N/K267A (SEQ ID NO:872);
R219Q/S262N/K267C (SEQ ID NO:873); R219Q/S262N/K267D (SEQ ID
NO:874); R219Q/S262N/K267E (SEQ ID NO:875); R219Q/S262N/K267F (SEQ
ID NO:876); R219Q/S262N/K267G (SEQ ID NO:877); R219Q/S262N/K267H
(SEQ ID NO:878); R219Q/S262N/K267I (SEQ ID NO:879);
R219Q/S262N/K267L (SEQ ID NO:880); R219Q/S262N/K267M (SEQ ID
NO:881); R219Q/S262N/K267N (SEQ ID NO:882); R219Q/S262N/K267P (SEQ
ID NO:883); R219Q/S262N/K267Q (SEQ ID NO:884); R219Q/S262N/K267R
(SEQ ID NO:885); R219Q/S262N/K267S (SEQ ID NO:886);
R219Q/S262N/K267T (SEQ ID NO:887); R219Q/S262N/K267V (SEQ ID
NO:888); R219Q/S262N/K267W (SEQ ID NO:889); R219Q/S262N/K267Y (SEQ
ID NO:890); R219Q/S262N/V296A (SEQ ID NO:891); R219Q/S262N/V296C
(SEQ ID NO:892); R219Q/S262N/V296D (SEQ ID NO:893);
R219Q/S262N/V296E (SEQ ID NO:894); R219Q/S262N/V296F (SEQ ID
NO:895); R219Q/S262N/V296G (SEQ ID NO:896); R219Q/S262N/V296H (SEQ
ID NO:897); R219Q/S262N/V296I (SEQ ID NO:898); R219Q/S262N/V296K
(SEQ ID NO:899); R219Q/S262N/V296L (SEQ ID NO:900);
R219Q/S262N/V296M (SEQ ID NO:901); R219Q/S262N/V296N (SEQ ID
NO:902); R219Q/S262N/V296P (SEQ ID NO:903); R219Q/S262N/V296Q (SEQ
ID NO:904); R219Q/S262N/V296R (SEQ ID NO:905); R219Q/S262N/V296S
(SEQ ID NO:906); R219Q/S262N/V296T (SEQ ID NO:907);
R219Q/S262N/V296W (SEQ ID NO:908); R219Q/S262N/V296Y (SEQ ID
NO:909); R219Q/K11A/R20A (SEQ ID NO:910); R219Q/K11A/R20A/K371A
(SEQ ID NO:911); R219Q/R20A/K371A (SEQ ID NO:912); R219Q/K11A/K371A
(SEQ ID NO:913); S262N/K11A/R20A (SEQ ID NO:914);
S262N/K11A/R20A/K371A (SEQ ID NO:915); S262N/R20A/K371A (SEQ ID
NO:916); and S262N/K11A/K371A (SEQ ID NO:917).
BRIEF DESCRIPTION OF THE FIGURES
[0129] FIGS. 1A-1F depict exemplary alignments of precursor human
adenosine deaminase 2 (ADA2) set forth in SEQ ID NO:2 (residues
30-511 corresponding to mature ADA2 set forth in SEQ ID NO:5) with
other ADA2 proteins. A "*" means that the aligned residues are
identical, a ":" means that aligned residues are not identical, but
are similar and contain conservative amino acids residues at the
aligned position, and a "." means that the aligned residues are
similar and contain semi-conservative amino acid residues at the
aligned position. Residues corresponding to the putative receptor
binding domain (PRB) are underlined. Exemplary, non-limiting,
corresponding positions for amino acid replacements are indicated
by highlighting. For example, FIG. 1A depicts the alignment of ADA2
set forth in SEQ ID NO:2 with chimpanzee ADA2 set forth in SEQ ID
NO:286. FIG. 1B depicts the alignment of a ADA2 set forth in SEQ ID
NO:2 with gorilla ADA2 set forth in SEQ ID NO:287. FIG. 1C depicts
the alignment of a ADA2 set forth in SEQ ID NO:2 with pygmy
chimpanzee set forth in SEQ ID NO:288. FIG. 1D depicts the
alignment of ADA2 set forth in SEQ ID NO:2 with Sumatran orangutan
ADA2 set forth in SEQ ID NO:289. FIG. 1E depicts the alignment of
ADA2 set forth in SEQ ID NO:2 with northern white-cheeked gibbon
ADA2 set forth in SEQ ID NO:290. FIG. 1F depicts the alignment of
ADA2 set forth in SEQ ID NO:2 with crab-eating macaque ADA2 set
forth in SEQ ID NO:291.
[0130] FIG. 2 depicts the biosynthesis and catabolism of
extracellular adenosine, and adenosine receptor signaling (adapted
from Antonioli et al. (2013) Nat Rev Can 13:842-857). Physiological
conditions such as hypoxia, ischemia, inflammation, tumor
environment or trauma can promote the extracellular accumulation of
ATP, which is metabolized to AMP by the cell surface enzyme CD39.
AMP is in turn metabolized to adenosine by CD73. Extracellular
adenosine can bind to four different G-protein-coupled adenosine
receptors (ADRs; i.e. A1, A2A, A2B and A3), expressed on the cell
surface of nearby immune, tumor or other cells, to mediate various
downstream adenosine-mediated signaling and activities, such as
immunosuppression, cancer cell proliferation, cancer cell migration
and/or metastasis, angiogenesis, and other effects. Nucleoside
transporters (NTs) facilitate uptake of extracellular adenosine
into cells. Adenosine deaminase 2 (ADA2), including exogenous ADA2
or variants as provided herein, can breakdown extracellular
adenosine by catalyzing the conversion of adenosine to inosine.
DETAILED DESCRIPTION
Outline
[0131] A. Definitions
[0132] B. Adenosine Deaminase 2 (ADA2) and Modulation of
Adenosine-Mediated
[0133] Tumor Immunosuppression [0134] 1. Tumor Immunity and Immune
Evasion [0135] 2. Adenosine Immunomodulation in Cancer and Tumor
Microenvironment (TME) [0136] 3. Adenosine Deaminase and Targeting
Adenosine in Treatment of Cancer
[0137] C. Adenosine Deaminase 2 (ADA2) and Variants Thereof [0138]
1. Structure and Activity of ADA2 [0139] a. Structure of ADA2
[0140] b. Activities of ADA2 [0141] 2. ADA2 Variants [0142] a.
Exemplary Modifications [0143] i. Amino Acid Replacements [0144]
ii. Modification(s) of PRB Domain [0145] iv. Hyperglycosylation
[0146] b. Nucleic Acid Molecules [0147] c. Production of Variant
ADA2 Proteins
[0148] D. ADA2 Conjugates and Fusion Proteins [0149] 1. Half-Life
Extending Moieties [0150] a. Low Complexity Polypeptides [0151] b.
C-terminal peptide (CTP) of the .beta. Subunit of Human Chorionic
Gonadotropin [0152] c. Immunoglobulin Constant Region (Fc) or
Portions Thereof [0153] d. Albumin or Fragment, or Variant Thereof
[0154] e. Albumin Binding Moiety [0155] f. PAS Sequences [0156] g.
HAP Sequences [0157] h. XTEN Sequences [0158] i. Transferrin or
Fragment thereof [0159] j. Polymer conjugation [0160] i.
Polyethylene Glycol (PEG) [0161] ii. Hydroxyethyl Starch (HES)
[0162] iii. Polysialic Acids (PSA) [0163] iv. Other polymers [0164]
2. Methods of Producing Conjugates or Fusion Proteins [0165]
Linkers [0166] i. Peptide Linkers [0167] ii. Heterobifunctional
linking agents
E. Methods of Producing Nucleic Acids Encoding ADA2 and
Polypeptides Thereof
[0167] [0168] 1. Isolation or Preparation of Nucleic Acids Encoding
ADA2 Polypeptides [0169] 2. Generation of Mutant or Modified
Nucleic Acid and Encoding Polypeptides [0170] 3. Vectors and Cells
Immune cells that encode and express the ADA2 variants provided
herein [0171] 4. Expression [0172] a. Prokaryotic Cells [0173] b.
Yeast Cells [0174] c. Insect Cells [0175] d. Mammalian Cells [0176]
e. Plants [0177] 5. Purification Techniques
[0178] F. Methods of Assessing Activity and Physical Properties of
ADA2 [0179] 1. Adenosine Deaminase Assay [0180] 2. Methods of
Assessing Heparin Binding [0181] a. Affinity Assay [0182] b. ELISA
Assay [0183] c. Dot Blot and other Radiolabeled Heparin Binding
Assays [0184] 3. Methods for Assessing Stability [0185] a.
Conditions [0186] i. Stability in Plasma [0187] ii. Thermal
Stability [0188] iii. Stability in pH or pH Optima [0189] iv. Other
Conditions [0190] b. Determination of Physical Properties [0191] i.
Enzymatic Activity [0192] ii. Chromatographic Analysis of Protein
Purity [0193] iii. Differential Scanning calorimetry [0194] iv.
Differential Scanning Fluorimetry [0195] v. Intrinsic Fluorescence
Spectroscopy [0196] vi. Circular Dichroism [0197] vii. Dynamic
Light Scattering [0198] viii. Static Light Scattering [0199] ix.
Turbidity Measurements [0200] x. Other Methods to Determine
Stability [0201] 4. Assay for Therapeutic Activity [0202] a. In
vitro Tests [0203] b. In vivo Animal Models [0204] i. Tumor
Metabolic Activity [0205] ii. Tumor Size and Volume [0206] c.
Clinical Monitoring [0207] 5. Pharmacodynamics/Pharmacokinetics and
Tolerability
[0208] G. Pharmaceutical Compositions and Formulations [0209] 1.
Formulations--liquids, injectables, emulsions [0210] Lyophilized
Powders [0211] 2. Compositions for Other Routes of Administration
[0212] 3. Dosages and Administration [0213] 4. Packaging and
Articles of Manufacture
[0214] H. Methods of Treatment with an Adenosine Deaminase 2 (ADA2)
[0215] 1. Exemplary Diseases and Conditions [0216] a. Cancers and
Tumors [0217] b. Non-Cancer Hyperproliferative Diseases [0218] c.
Fibrotic Diseases [0219] d. Infectious Diseases [0220] e. Other
Diseases and Conditions [0221] 2. Methods of Patient Selection
[0222] a. Adenosine-associated Biomarkers [0223] i. Plasma
Adenosine Levels [0224] ii. Adenosine Receptors (ADRs) [0225] iii.
Ectonucleotidases CD39 and CD73 [0226] b. Patient Selection [0227]
3. Dosages and Administration [0228] 4. Combination Therapies
[0229] a. Anticancer Agents [0230] i. Anticancer Antibodies [0231]
ii. Chemotherapeutic Agents [0232] iii. Radiation Therapy [0233]
iv. Anti-angiogenic Agents [0234] v. Immune Checkpoint Inhibitors
[0235] (a) Anti-CTLA4 Therapies [0236] (b) Anti-PD-1 and Anti-PD-L1
Therapies [0237] b. Other Immunomodulatory Agents [0238] c.
Hyaluronan-Degrading Enzyme [0239] Soluble hyaluronan degrading
enzymes (e.g. soluble PH20) [0240] d. Antibodies to Treat
Infectious Diseases [0241] e. Antibiotics and Antifungals
[0242] I. Examples
A. DEFINITIONS
[0243] Unless defined otherwise, all technical and scientific terms
used herein have the same meaning as is commonly understood by one
of skill in the art to which the invention(s) belong. All patents,
patent applications, published applications and publications,
Genbank sequences, databases, websites and other published
materials referred to throughout the entire disclosure herein,
unless noted otherwise, are incorporated by reference in their
entirety. In the event that there are a plurality of definitions
for terms herein, those in this section prevail. Where reference is
made to a URL or other such identifier or address, it understood
that such identifiers can change and particular information on the
internet can come and go, but equivalent information can be found
by searching the internet. Reference thereto evidences the
availability and public dissemination of such information.
[0244] As used herein, "adenosine" refers to a purine nucleoside
that is composed of a molecule of adenine attached to a ribose
sugar molecule (ribofuranose) moiety via a
.beta.-N.sub.9-glycosidic bond. Adenosine can modulate a variety of
physiological processes through its interaction with adenosine
receptors.
[0245] As used herein, "Michaelis constant" or K.sub.m is a measure
of the substrate concentration required for effective catalysis to
occur. For example, an enzyme with a high K.sub.m can require a
higher substrate concentration to achieve a given reaction velocity
than an enzyme with a lower K.sub.m for the substrate. K.sub.m can
represent the affinity of the enzyme for a substrate.
[0246] As used herein, "catalytic efficiency" is the efficiency
with which an enzyme reacts with a substrate to form a product. It
is represented by the k.sub.cat/K.sub.m (M.sup.-1 s.sup.-1 or
1/Ms). Methods to assess kinetic parameters of catalytic activity,
including k.sub.cat/K.sub.m, are well known to a skilled artisan.
Generally, k.sub.cat/K.sub.m is measured under steady state
conditions.
[0247] As used herein, "adenosine deaminase" or "ADA" refers to an
enzyme that catalyzes the hydrolytic deamination of adenosine to
form inosine. An ADA also can deaminate 2'deoxyadenosine to
2'deoxyinosine, and hence includes enzymes that have
2'deoxyadenosine deaminase activity. In humans there are two ADA
isozymes, designated ADA1 and ADA2, that differ in their molecular
weight, catalytic parameters and other properties.
[0248] As used herein, "adenosine deaminase 1" or ADA1 refers to an
ADA that lacks a signal peptide and is ubiquitously expressed
inside cells. It is produced as a monomer. Exemplary of ADA1 is
human ADA1 having the sequence of nucleotides set forth in SEQ ID
NO:11 and encoding the sequence of amino acids set forth in SEQ ID
NO:12. In humans, wild-type ADA1 is characterized by a Km of or of
about 5.2.times.10.sup.-5 M, has a pH optimum of from or from about
7 to 7.5, and exhibits a similar affinity for both adenosine and
2'deoxyadenosine. For example, ADA1 has a
2'deoxyadenosine/adenosine deaminase ratio of at least or at least
about 0.70, such at least or at least about 0.75. Reference to ADA1
includes wild-type or native ADA1 present in mammalian, including
human and non-human, subjects. For example, reference to ADA1
includes human ADA1 that contains a polypeptide having the sequence
of amino acids set forth in SEQ ID NO:12. Reference to ADA1 also
includes variants thereof, such as allelic variants, species
variants, splice variants and other variants that include a
polypeptide having a sequence of amino acids that has at least 65%,
70%, 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO:12,
and that exhibit adenosine deaminase activity.
[0249] As used herein, "adenosine deaminase 2," or "ADA2" refers to
an ADA that is present in extracellular environments, including in
the plasma. ADA2 is produced from a precursor polypeptide that
contains a signal peptide (e.g. ADA2 set forth in SEQ ID NO:2),
which is removed to yield a mature protein lacking the signal
peptide (e.g. ADA2 set forth in SEQ ID NO:5). The secreted ADA2 is
a homodimer containing two identical polypeptide chains that
interact via non-polar interactions between residues of each
subunit. In humans, wild-type ADA2 is characterized with a Km that
is or is about 200.times.10.sup.-5 M, has a pH optimum of or of
about 6.5.+-.0.2, and exhibits a weak affinity for
2'deoxyadenosine. For example, ADA2 has a
2'deoxyadenosine/adenosine deaminase ratio of less than 0.40, such
less than or about 0.30 or less than or about 0.25. Reference to
ADA2 includes wild-type or native ADA2 present in mammalian,
including human and non-human, subjects. For example, reference to
ADA2 includes human ADA2 that contains a polypeptide having the
sequence of amino acids set forth in SEQ ID NO:2, the mature form
set forth in SEQ ID NO:5, catalytically active portions of SEQ ID
NO:5, and dimer forms thereof. Reference to ADA2 also includes
precursor, mature, catalytically active forms, and dimer forms that
are variants thereof, such as allelic variants, species variants,
splice variants and other variants that include a polypeptide
having a sequence of amino acids that has at least 40%, 50%, 60%,
65%, 70%, 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the
precursor polypeptide set forth in SEQ ID NO:2 or the mature form
thereof set forth in SEQ ID NO:5, and that, when in active form,
exhibit adenosine deaminase activity. Such variants, when in active
form, exhibit at least 40%, 50%, 70%, 90%, 90%, 100%, 110%, 120%,
130%, 140%, 150%, 160%, 170%, 180%, 190%, 200% 300%, 400%, 500%,
600%, 700%, 800%, 900%, 1000% or more activity than the activity of
a native or wildtype ADA2 polypeptide. As used herein, wild-type"
or "native" with reference to ADA2 refers to a ADA2 protein
containing a polypeptide encoded by a native or naturally occurring
ADA2 gene, including allelic variants, that is present in an
organism, including a human and other animals, in nature. Reference
to wild-type ADA2 without reference to a species is intended to
encompass any species of a wild-type ADA2. Included among wild-type
ADA2 polypeptides are the encoded precursor polypeptide, fragments
thereof, and processed forms thereof, such as a mature form lacking
the signal peptide, as well as any pre- or post-translationally
processed or modified forms thereof. Also included among native
ADA2 proteins are those that are post-translationally modified,
including, but not limited to, modification by glycosylation,
carboxylation and hydroxylation. Native ADA2 proteins also include
the polypeptide monomer as well as dimer forms. For example, humans
express native ADA2. Wild-type human ADA2 is set forth in SEQ ID
NO:2 (precursor) and SEQ ID NO:5 (mature), and includes
catalytically active forms thereof as described herein, and allelic
variants (precursor or mature) set forth in any of SEQ ID
NOS:376-383, or isoforms of an ADA2 such as ADA2 set forth in SEQ
ID NO:68. Wildtype or native ADA2 from non-human species include,
but are not limited to, ADA2 from Pan troglodytes (chimpanzee;
precursor form SEQ ID NO:286, mature form SEQ ID NO:326; NCBI Acc.
No. XP_003317127.1); Gorilla gorilla (gorilla; precursor form SEQ
ID NO:287, mature form SEQ ID NO:327; NCBI Acc. No.
XP_004063024.1); Pan paniscus (pygmy chimpanzee; precursor form SEQ
ID NO:288, mature form SEQ ID NO:328; NCBI Acc. No.
XP_003828345.1); Pongo abelii (Sumatran orangutan; precursor form
SEQ ID NO:289, mature form SEQ ID NO:329; NCBI Acc. No.
NP_001125360.1); Nomascus leucogenys (Northern white-cheeked
gibbon; precursor form SEQ ID NO:290, mature form SEQ ID NO:330;
NCBI Acc. No. XP_004088517.1); Macaca fascicularis (crab-eating
macaque; precursor form SEQ ID NO:291, mature form SEQ ID NO:331;
NCBI Acc. No. XP_005568111.1); Chlorocebus sabaeus (green monkey;
precursor form SEQ ID NO:292, mature form SEQ ID NO:332; NCBI Acc.
No. XP_007972990.1); Macaca mulatta (Rhesus macaque; precursor form
SEQ ID NOS:293, 337, mature form SEQ ID NOS:333, 340; GenBank Acc.
Nos. AFH32795.1, EHH20002.1); Callithrix jacchus (marmoset;
precursor form SEQ ID NOS:294, 374, mature form SEQ ID NO:334, 375;
NCBI Acc. No. XP_009004591.1, XP_009004586.1); Xenopus laevis
(African clawed frog; precursor form SEQ ID NO:295, mature form SEQ
ID NO:335; NCBI Acc. No. NP_001090531.1); Drosophila melanogaster
(fruit fly; precursor form SEQ ID NOS:296-300, mature form SEQ ID
NOS:336, 338, 339; AAL40913.1, AAL40920.1, AAL40911.1, AAL40912.1,
and AAL40910.1); Bombyx mori (silk moth; precursor form SEQ ID
NO:301, mature form SEQ ID NO:341; NCBI Acc. No. NP 001098698.1);
and Sarcophaga perigrina (flesh fly; precursor form SEQ ID NO:302,
mature form SEQ ID NO:342; GenBank Acc. No. BAA11812.1).
[0250] As used herein, a precursor ADA2 refers to a non-secreted
form of an ADA2 that contains an N-terminal signal peptide that
targets the protein for secretion. The signal peptide is cleaved
off in the endoplasmic reticulum. Exemplary of an ADA2 precursor
polypeptide is the polypeptide set forth in SEQ ID NO:2, or an
allelic or species variant or other variant thereof such as those
set forth in any of SEQ ID NOS:286-302, 337 or 376-379.
[0251] As used herein, a "mature ADA2" refers to an ADA2 that lacks
a signal sequence. An exemplary mature ADA2 is set forth in SEQ ID
NO:5, and also includes variants thereof such as species and
allelic variants and other variants, such as those set forth in any
of SEQ ID NOS:326-336, 338-342, 375, and 380-383. Reference to
mature ADA2 includes dimer forms thereof.
[0252] As used herein, species variants refer to variants in
polypeptides among different species, including different mammalian
species, such as mouse and human.
[0253] As used herein, allelic variants refer to variations in
proteins among members of the same species.
[0254] As used herein, domain (typically a sequence of three or
more, generally 5 or 7 or more amino acids) refers to a portion of
a molecule, such as proteins or the encoding nucleic acids, that is
structurally and/or functionally distinct from other portions of
the molecule and is identifiable. For example, domains include
those portions of a polypeptide chain that can form an
independently folded structure within a protein made up of one or
more structural motifs and/or that is recognized by virtue of a
functional activity, such as proteolytic activity. A protein can
have one, or more than one, distinct domains. For example, a domain
can be identified, defined or distinguished by homology of the
sequence therein to related family members, such as homology to
motifs that define a protease domain. In another example, a domain
can be distinguished by its function, such as by proteolytic
activity, or an ability to interact with a biomolecule, such as DNA
binding, ligand binding, and dimerization. A domain independently
can exhibit a biological function or activity such that the domain
independently or fused to another molecule can perform an activity,
such as, for example proteolytic activity or ligand binding. A
domain can be a linear sequence of amino acids or a non-linear
sequence of amino acids. Many polypeptides contain a plurality of
domains. Such domains are known, and can be identified by those of
skill in the art. For exemplification herein, definitions are
provided, but it is understood that it is well within the skill in
the art to recognize particular domains by name. If needed
appropriate software can be employed to identify domains.
[0255] As used herein "catalytic domain" or "ADA domain" refers to
the domain that confers adenosine deaminase activity. The catalytic
domain of an enzyme contains all of the requisite properties of
that protein required for its enzymatic, such as adenosine
deaminase activity. The ADA domain is structurally composed of an
eight-stranded, parallel .beta.-sheet that closes into a barrel and
is surrounded by classical .alpha./.beta.-TIM barrel motif helices
and five additional, located between .beta.1 and .alpha.1 (H1, H2,
and H3) and at the C terminus (H4 and H5) (Zavialov et al. (2010)
J. Biol. Chem. 285:12367-12377). Loops between .beta.-strands and
.alpha.-helices contain many of the active site residues required
for activity. Active site residues include residues that coordinate
zinc binding, active site proton donor and acceptor residues, and
substrate binding residues. Exemplary of such residues in human
ADA2 are set forth in Table 4. In reference to human ADA2, the ADA
domain is contained in the region corresponding to residues 106-502
of the precursor sequence of amino acids set forth in SEQ ID NO:2
(corresponding to residues 77-473 of the mature protein set forth
in SEQ ID NO:5), except that residues corresponding to the putative
receptor binding (PRB) domain contained therein are not required
for catalytic activity.
[0256] As used herein, "a catalytically active portion thereof" or
"a catalytically active fragment thereof" refers to an ADA2
polypeptide that contains less than the full-length sequence of a
mature ADA2 polypeptide, but contains a contiguous portion of amino
acids of an ADA2, including all or part of the catalytic domain,
sufficient for adenosine deaminase activity. For example, a
catalytically active portion of ADA2 is one that includes a
polypeptide containing a contiguous sequence of amino acids of the
mature sequence of an ADA2 polypeptide that includes amino acid
residues corresponding to residues 83, 85, 327, 330, 355, and 412
with reference to amino acid residues set forth in SEQ ID NO:5, but
does not include the full amino acid sequence of the mature ADA2
polypeptide. For example, a catalytically active portion is one
that includes a polypeptide containing a contiguous sequence of
amino acids of the mature sequence of ADA2 set forth in SEQ ID NO:5
that includes amino acid residues 83, 85, 327, 330, 355, and 412,
but that does not include the full length sequence of amino acids
set forth in SEQ ID NO:5. An ADA2 that contains a catalytically
active portion of an ADA2 polypeptide, when in active form,
exhibits at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%,
30%, 40%, 50%, 60%, 70%, 80%, 90%, or more of the activity, such as
at least 120%, 130%, 140%, 150%, 200%, 300%, 400%, 500% or more of
the activity, compared to the ADA2 containing a full-length mature
ADA2 polypeptide. In one example, a catalytically active portion of
an ADA2 polypeptide includes a polypeptide that lacks all or a
portion of the putative receptor binding (PRB) domain. In another
example, a catalytically active portion of an ADA2 polypeptide
includes a polypeptide that lacks one or more C-terminal amino
acids of the mature polypeptide, i.e. is truncated at the
C-terminus, by up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,
49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65,
66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82,
83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99,
100 or more contiguous C-terminal amino acid residues compared to
the mature ADA2 polypeptide. It is understood that reference herein
to a variant ADA2 or catalytically active portion thereof means
that the catalytically active portion contains the modification(s)
(e.g. amino acid replacement(s)).
[0257] As used herein, "putative receptor binding domain" or "PRB
domain" refers to a portion of ADA2 that forms an independently
folded structure composed of an .alpha.- and .beta.-fold containing
a three-stranded antiparallel .beta.-sheets designated SR1-SR2-SR3,
surrounded by the HR and partially H2 .alpha.-helices on one side
and the proline-rich SR2-SR3 loop on the other side (Zavialov et
al. (2010) J. Biol. Chem. 285:12367-12377). The PRB domain contains
conserved cysteine residues that form a disulfide bond between C137
and C159 of precursor ADA2 set forth in SEQ ID NO:2 (positions C108
and C130 of mature ADA2 set forth in SEQ ID NO:5). The PRB domain
is reported to be involved in binding of ADA2 to its receptors. It
is understood that the particular residues that make up the domain
can vary (e.g. longer or shorter), for example, depending on
methods used to identify the domain. In reference to human ADA2,
the PRB domain is reported to correspond to residues 127-185 or
134-177 of precursor ADA2 set forth in SEQ ID NO:2 (residues 98-156
or 105-148, respectively, of mature ADA2 set forth in SEQ ID
NO:5).
[0258] As used herein, a protein lacking all or a portion of a
domain, such as all or a portion of the PRB domain, refers a
polypeptide that has a deletion of one or more amino acids or all
of the amino acids of the domain, such as the PRB domain, compared
to a reference or unmodified protein. Amino acids deleted in a
polypeptide lacking all or part of a domain can be contiguous, but
need not be contiguous amino acids within the domain of the cognate
polypeptide. Polypeptides that lack all or a part of a domain can
include the loss or reduction of an activity of the polypeptide
compared to the activity of a reference or unmodified protein.
[0259] As used herein, "active form" refers to any ADA2 enzyme that
exhibits adenosine deaminase activity. An active form of an enzyme
can contain a full-length sequence of amino acids or can be a
catalytically active portion thereof. An active form of an enzyme
can be a monomer or a dimer. Typically, an active enzyme is a
dimer. An active enzyme is any form that exhibits a catalytic
efficiency (k.sub.cat/K.sub.M) that is at least or at least about
5.times.10.sup.3 M.sup.-1 s.sup.-1, 6.times.10.sup.3 M.sup.-1
s.sup.-1, 7.times.10.sup.3 M.sup.-1 s.sup.-1,
8.times.10.sup.3M.sup.-1 s.sup.-1, 9.times.10.sup.3 M.sup.-1
s.sup.-1, 1.times.10.sup.4 M.sup.-1 s.sup.-1, 2.times.10.sup.4
M.sup.-1 s.sup.-1, 3.times.10.sup.4 M.sup.-1 s.sup.-1,
4.times.10.sup.4 M.sup.-1 s.sup.-1, 5.times.10.sup.4 M.sup.-1
s.sup.-1, 6.times.10.sup.4 M.sup.-1 s.sup.-1, 7.times.10.sup.4
M.sup.-1 s.sup.-1, 8.times.10.sup.4 M.sup.-1 s.sup.-1,
9.times.10.sup.4 M.sup.-1 s.sup.-1, 1.times.10.sup.5 M.sup.-1
s.sup.-1, 2.times.10.sup.5 M.sup.-1 s.sup.-1, 3.times.10.sup.5
M.sup.-1 s.sup.-1, 4.times.10.sup.5 M.sup.-1 s.sup.-1,
5.times.10.sup.5 M.sup.-1 s.sup.-1, 6.times.10.sup.5M.sup.-1
s.sup.-1, 7.times.10.sup.5M.sup.-1 s.sup.-1,
8.times.10.sup.5M.sup.-1 s.sup.-1, 9.times.10.sup.5M.sup.-1
s.sup.-1, 1.times.10.sup.6M.sup.-1 s.sup.-1,
2.times.10.sup.6M.sup.-1 s.sup.-1, 3.times.10.sup.6M.sup.-1
s.sup.-1, 4.times.10.sup.6M.sup.-1 s.sup.-1,
5.times.10.sup.6M.sup.-1 s.sup.-1 or greater.
[0260] As used herein, a "multimer" refers to a molecule composed
of several identical or different subunits held together or
associated, for example, by non-covalent interactions.
[0261] As used herein, a "dimer" refers to a molecule that contains
two polypeptides linked together. Typically, the polypeptides are
non-covalently linked. For example, an ADA2 dimer is formed by
nonpolar intersubunit interactions, including hydrophobic
interaction, between residues of two polypeptides.
[0262] As used herein, a "homodimer" refers to a dimer that is
formed by two identical polypeptides.
[0263] As used herein, a "heterodimer" refers to a dimer that is
formed by two different polypeptides.
[0264] As used herein, a "monomer" refers to a single protein or
polypeptide unit. A monomer has a relatively low molecular weight
compared to dimers or other multimers. A monomer can exist
independently, or it can associate with other molecules to form a
dimer or other multimer.
[0265] As used herein a "corresponding form" with reference to an
ADA2 protein means that when comparing a property or activity of
two ADA2 proteins, the property is compared using the same
structural form of the protein. For example, if its stated that an
ADA2 protein has less activity compared to the activity of the
corresponding form of a first ADA2 protein, that means that a
particular form, such as a dimer, has less activity compared to the
dimer of the first ADA2 protein.
[0266] As used herein, a "polypeptide" refers to a linear organic
polymer containing a large number of amino acid residues bonded
together in a chain, forming part of, or the whole of, a protein
molecule.
[0267] As used herein, a "protein" or "protein molecule" or
variations thereof refers to a large molecule composed of one or
more polypeptide chains made up of a linear sequence of amino
acids. Hence, a protein can be a monomer, or can be a dimer or
other multimer. A protein can exhibit structural, mechanical,
biochemical or signaling activities. As used herein, a "polypeptide
subunit" or "protein subunit" refers to a single polypeptide or
monomer that is capable of assembling with other polypeptides or
monomers to form a protein molecule that is a multimeric complex.
One subunit is made up of one polypeptide chain.
[0268] As used herein, "variant ADA2 protein" refers to an ADA2
protein, including any form thereof such as a full-length,
catalytically active portion, monomer, or dimer, that has one or
more amino acid differences compared to an unmodified ADA2 protein.
The one or more amino acid differences can be amino acid mutations,
such as one or more amino acid replacements (substitutions),
insertions or deletions, or can be insertions or deletions of
entire domains, and any combination thereof. Typically, a variant
ADA2 protein has one or more modifications in primary sequence
compared to an unmodified ADA2 protein. For example, a variant ADA2
provided herein can have at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85 or more
amino acid differences compared to an unmodified ADA2 protein. Any
modification is contemplated as long as the resulting protein
exhibits adenosine deaminase activity.
[0269] As used herein, modification refers to modification of a
sequence of amino acid residues of a polypeptide or a sequence of
nucleotides in a nucleic acid molecule and includes deletions,
insertions, and replacements of amino acids and nucleotides,
respectively. Modifications also can include post-translational
modifications or other changes to the molecule that can occur due
to conjugation or linkage, directly or indirectly, to another
moiety. Methods of modifying a polypeptide are routine to those of
skill in the art, such as by using recombinant DNA
methodologies.
[0270] As used herein, "deletion," when referring to modification
of a nucleic acid or polypeptide sequence, refers to the removal of
one or more nucleotides or amino acids compared to a sequence, such
as a target polynucleotide or polypeptide or a native or wild-type
sequence. Thus, an amino acid sequence or nucleic acid molecule
that contains one or more deletions compared to a wild-type
sequence, contains one or more fewer amino acids or nucleotides
within the linear length of the sequence.
[0271] As used herein, "insertion" when referring to modification
of a nucleic acid or amino acid sequence, describes the inclusion
of one or more additional nucleotides or amino acids, within a
target, native, wild-type or other related sequence. Thus, an amino
acid or nucleic acid molecule that contains one or more insertions
compared to a wild-type sequence, contains one or more additional
amino acids or nucleotides within the linear length of the
sequence.
[0272] As used herein, "additions" to nucleic acid and amino acid
sequences describe addition of nucleotides or amino acids onto
either termini compared to another sequence.
[0273] As used herein, "substitution" or "replacement" with respect
to a modification refers to the replacing of one or more
nucleotides or amino acids in a native, target, wild-type or other
nucleic acid or polypeptide sequence with an alternative nucleotide
or amino acid, without changing the length (as described in numbers
of residues) of the molecule. Thus, one or more substitutions in a
molecule does not change the number of amino acid residues or
nucleotides of the molecule. Amino acid replacements compared to a
particular polypeptide can be expressed in terms of the number of
the amino acid residue along the length of the polypeptide sequence
or a reference polypeptide sequence. For example, a modified
polypeptide having a modification in the amino acid at the
19.sup.th position of the amino acid sequence that is a
substitution of Isoleucine (Ile; I) for cysteine (Cys; C) can be
expressed as "replacement with Cys or C at a position corresponding
to position 19," I19C, Ile19Cys, or simply C19, to indicate that
the amino acid at the modified 19.sup.th position is a cysteine. In
this example, the molecule having the substitution has a
modification at Ile 19 of the unmodified polypeptide.
[0274] As used herein, "unmodified polypeptide" or "unmodified
ADA2" and grammatical variations thereof refer to a starting
polypeptide that is selected for modification as provided herein.
The starting polypeptide can be a naturally-occurring, wild-type
form of a polypeptide. Exemplary of an unmodified ADA2 polypeptide
is human ADA2 set forth in SEQ ID NO:5, or a catalytically active
portion thereof. In addition, the starting polypeptide can be
altered or mutated, such that it differs from a native wild type
isoform but is nonetheless referred to herein as a starting
unmodified polypeptide relative to the subsequently modified
polypeptides produced herein. Thus, existing proteins known in the
art that have been modified to have a desired increase or decrease
in a particular activity or property compared to an unmodified
reference protein can be selected and used as the starting
unmodified polypeptide. For example, a protein that has been
modified from its native form by one or more single amino acid
changes and possesses either an increase or decrease in a desired
property, such as a change in an amino acid residue or residues to
alter glycosylation, can be a target protein, referred to herein as
unmodified, for further modification of either the same or a
different property.
[0275] As used herein, "corresponding residues" refers to residues
that occur at aligned loci. For purposes herein, the amino acid
sequence of a protein is aligned to precursor ADA2 set forth in SEQ
ID NO:2 or its mature form set forth in SEQ ID NO:5 (see FIG. 1) or
to the ADA2 sequence used for Zavialov numbering, the numbering of
residues used in Zavialov et al. (2010) J. Biol. Chem.
285:12367-12377 and in PDB accession Nos. 3LGG and 3LGD, set forth
in SEQ ID NO:4. Related or variant polypeptides are aligned by any
method known to those of skill in the art. Such methods typically
maximize matches, and include methods such as using manual
alignments and by using the numerous alignment programs available
(for example, BLASTP) and others known to those of skill in the
art. By aligning the sequences of ADA2 polypeptides, one of skill
in the art can identify corresponding residues, using conserved and
identical amino acid residues as guides. Generally, recitation that
amino acids of a polypeptide correspond to amino acids in a
disclosed sequence refers to amino acids identified upon alignment
of the polypeptide with the disclosed sequence to maximize identity
or homology (where conserved amino acids are aligned) using a
standard alignment algorithm, such as the GAP algorithm.
[0276] As used herein, a "property" of an ADA2 refers to a physical
or structural property, such as three-dimensional structure, pI,
half-life, conformation and other such physical
characteristics.
[0277] As used herein, an "activity" of an ADA2 or "ADA2 activity"
refers to any activity exhibited by the active form of an ADA2
protein, typically the dimer form. Such activities can be tested in
vitro and/or in vivo and include, but are not limited to, adenosine
deaminase activity, growth factor activity, ability to bind heparin
and/or ability to bind to an adenosine receptor (ADR). Activity can
be assessed in vitro or in vivo using recognized assays, for
example, by measuring adenosine deaminase activity in vitro or in
vivo. The results of such assays indicate that a polypeptide
exhibits an activity that can be correlated to activity of the
polypeptide in vivo, in which in vivo activity can be referred to
as biological activity. Assays to determine functionality or
activity of modified forms of ADA2 are known to those of skill in
the art, and exemplary assays are described herein.
[0278] As used herein, "adenosine deaminase activity" refers to the
ability of an enzyme to catalyze the hydrolytic deamination of
adenosine to form inosine. ADA2 activity can be assessed, directly
or indirectly, by measuring the rate of production of a product of
the enzymatic reaction. For example, the production of inosine or
ammonia can be directly or indirectly measured. In other examples,
the decrease of the substrate of the enzyme, e.g., adenosine or
2-deoxyadenosine, is measured. Assays to assess adenosine deaminase
activity are known to those of skill in the art, and include but
are not limited to, assays in which the decrease of the substrate,
or the increase of the product, is measured directly by
spectrophotometry, or indirectly, by subsequent enzymatic or
oxidation-reduction reactions that use chromogenic substrates or
change the absorbance spectra of the reaction.
[0279] As used herein, "increased adenosine deaminase activity"
refers to an enhanced ability of an ADA2 protein, for example a
variant ADA2 protein, to exhibit adenosine deaminase activity as
compared with a reference protein. For example, the ability of a
variant ADA2 protein to exhibit adenosine deaminase activity can be
greater than the adenosine deaminase activity of the unmodified
ADA2 protein. The adenosine deaminase activity can be increased by
at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%,
40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, 600%,
700%, 800%, 900%, 1000%, or more compared to the adenosine
deaminase activity of reference or an unmodified protein.
[0280] As used herein, a glycosylation site refers to an amino
position in a polypeptide to which a carbohydrate moiety can be
attached. Typically, a glycosylated protein contains one or more
amino acid residues, such as asparagine or serine, for the
attachment of the carbohydrate moieties.
[0281] As used herein, a native glycosylation site refers to an
amino position to which a carbohydrate moiety is attached in a
wild-type polypeptide. There are four N-linked native glycosylation
sites in ADA2 corresponding to residues N98, N145, N156 and N349
with reference to SEQ ID NO:5.
[0282] As used herein, a non-native glycosylation site refers to an
amino position to which a carbohydrate moiety is attached in a
modified polypeptide that is not present in a wild-type
polypeptide. Non-native glycosylation sites can be introduced into
a ADA2 polypeptide by amino acid replacement. O-glycosylation sites
can be created, for example, by amino acid replacement of a native
residue with a serine or threonine. N-glycosylation sites can be
created, for example, by establishing the motif
Asn-Xaa-Ser/Thr/Cys, where Xaa is not proline. Creation of this
consensus sequence by amino acid modification can involve, for
example, a single amino acid replacement of a native amino acid
residue with an asparagine, a single amino acid replacement of a
native amino acid residue with a serine, threonine or cysteine, or
a double amino acid replacement involving a first amino acid
replacement of a native residue with an asparagine and a second
amino acid replacement of native residue with a serine, threonine
or cysteine, or an insertion of a non-native N-glycosylation motif,
such as the motif Asn-Xaa-Ser/Thr/Cys, where Xaa is not
proline.
[0283] As used herein, "level of glycosylation" refers to the
number of glycosylation sites capable of being occupied by a
glycan, for example, upon expression in a host cell capable of
glycosylation.
[0284] As used herein, increases with reference to the level of
glycosylation means that there is a greater number of glycosylation
sites capable of being occupied by a glycan with reference to an
unmodified or wildtype ADA2. A variant ADA2 that exhibits an
increased level of glycosylation can be hyperglycosylated if there
is a greater number of glycosylation sites occupied by a glycan
compared to the unmodified or wildtype ADA2.
[0285] As used herein, "protein stability" refers to a measure of
the maintenance of one or more physical properties of a protein in
response to an environmental condition (e.g. an elevated
temperature). In one embodiment, the physical property is the
maintenance of the covalent structure of the protein (e.g. the
absence of proteolytic cleavage, unwanted oxidation or
deamidation). In another embodiment, the physical property is the
presence of the protein in a properly folded state (e.g. the
absence of soluble or insoluble aggregates or precipitates). In one
embodiment, stability of a protein is measured by assaying a
biophysical property of the protein, for example thermal stability,
pH unfolding profile, stable removal of glycosylation, solubility,
biochemical function (e.g., ability to bind to a protein such as a
receptor or enzymatic activity) and/or combinations thereof. In
another embodiment, biochemical function is demonstrated by the
binding affinity of an interaction. Stability can be measured using
methods known in the art and/or described herein.
[0286] As used herein, "half-life" refers to the time that a living
body requires to eliminate one half of the quantity of an
administered substance through its normal channels of elimination.
The normal channels of elimination generally include the kidneys
and liver, but can include other excretion pathways. A half-life
can be described as the time it takes the concentration of a
substance to halve its concentration from steady state or from a
certain point on the elimination curve. A half-life typically is
measured in the plasma and can be determined by giving a single
dose of drug, and then measuring the concentration of the drug in
the plasma at times to determine the relationship between time and
decline in concentration as the substance is eliminated.
[0287] As used herein, "increased half-life" refers to a longer
half-life of a protein molecule compared to a reference protein.
Hence, it means that the time that it takes the concentration of a
substance to halve its concentration is longer than for the time it
takes the concentration of a reference protein to halve. The
half-life can be increased by at least 1%, 2%, 3%, 4%, 5%, 6%, 7%,
8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%,
300%, 400%, 500%, 600%, 700%, 800%, 900%, 1000%, 1100%, 1200%,
1300%, 1400%, 1500%, 1600%, 1700%, 1800%, 1900%, 2000%, 3000%,
4000%, 5000%, 6000%, 7000%, 8000%, 9000%, 10000% or more compared
to the half-life of an unmodified polypeptide. Assays to assess
half-life are known and standard in the art.
[0288] As used herein, "thermal stability" refers to the measure of
the resistance to denaturation of a protein that occurs upon
exposure to high or elevated temperatures, and hence is the ability
of a protein to function at a particular temperature. A polypeptide
is thermally stable at a temperature if it retains at least 50%,
55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more of an activity
or a property of the polypeptide at the temperature. Thermal
stability can be measured either by known procedures or by the
methods described herein. In certain embodiments, thermal stability
is evaluated by measuring the melting temperature (Tm) of a protein
or by a thermal challenge assay (Tc).
[0289] As used herein, "increased thermal stability" refers to a
higher degree of resistance to denaturation of a protein. For
example, it can mean that a protein is thermally stable at a higher
temperature than a reference proteins. It also can mean that a
protein exhibits greater retained activity at a particular
temperature compared to the activity of a reference protein at the
same temperature. In some cases, an increased thermal stability
means that a protein has a greater melting temperature Tm compared
to a reference protein. For example, the thermal stability is
increased if the Tm of a protein is at least 0.1.degree. C.,
0.2.degree. C., 0.3.degree. C., 0.4.degree. C., 0.5.degree. C.,
0.6.degree. C., 0.7.degree. C., 0.8.degree. C., 0.9.degree. C.,
1.0.degree. C., 1.5.degree. C., 2.0.degree. C. 2.5.degree. C.
3.0.degree. C., 4.0.degree. C., 5.0.degree. C. or more greater than
a reference or unmodified protein.
[0290] As used herein, the melting temperature (Tm; also called
transition temperature) is the temperature at the midpoint of a
thermal transition curve where 50% of molecules of a composition
are in a folded state. Hence, it is the temperature at which 50% of
a macromolecule becomes denatured, and is a standard parameter for
describing the thermal stability of a protein. Methods to determine
Tm are well-known to a skilled artisan and include, for example,
analytical spectroscopy methods such as, but are not limited to,
differential scanning calorimetry (DSC), circular dichroism (CD)
spectroscopy), fluorescence emission spectroscopy or nuclear
magnetic resonance (NMR) spectroscopy.
[0291] As used herein, "pH optima" or "pH optimum" refers to the pH
at which any enzymatic reaction, such as adenosine deaminase
activity, is most effective under a given set of conditions. With
respect to its adenosine deaminase activity, ADA2 exhibits a pH
optima that is or is about 6.5.
[0292] As used herein, "altered pH optima" or "altered pH optimum"
refers to a change (increased or decreased) in the pH that is the
optimal pH for adenosine deaminase activity. An increased pH
optimum occurs if the pH optimum is greater than 0.1, 0.2, 0.3,
0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.0,
2.5 or more compared to the pH optimum of a reference or unmodified
protein. A decreased pH optimum occurs if the pH optimum is lower
than or less than 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0,
1.1, 1.2, 1.3, 1.4, 1.5, 1.0, 2.5 or more less to the pH optimum of
a reference or unmodified protein.
[0293] As used herein, "bind," "bound" or grammatical variations
thereof refers to the participation of a molecule in any attractive
interaction with another molecule, resulting in a stable
association in which the two molecules are in close proximity to
one another. Binding includes, but is not limited to, non-covalent
bonds, covalent bonds (such as reversible and irreversible covalent
bonds), and includes interactions between molecules such as, but
not limited to, proteins, nucleic acids, carbohydrates, lipids, and
small molecules, such as chemical compounds including drugs.
Typically, bind involves the association of two or more molecules
by one or more noncovalent bonds. Binding can be assessed by
standard methods known in the art, including but not limited to,
equilibrium dialysis, radioimmunoassay radiolabeled target antigen,
immunoassays (e.g. enzyme linked immunosorbent assay (ELISA)),
surface plasmon resonance (SPR), isothermal titration calorimetry
(ITC) and other methods well known to a skilled artisan.
[0294] As used herein, binding activity refer to characteristics of
a molecule, e.g. a polypeptide, relating to whether or not, and
how, it binds one or more binding partners. Binding activities
include the ability to bind the binding partner(s), the affinity
with which it binds to the binding partner (e.g. high affinity),
the avidity with which it binds to the binding partner, the
strength of the bond with the binding partner and/or specificity
for binding with the binding partner.
[0295] As used herein, "heparin binding" refers to the ability of
ADA2 to bind heparin, which is a highly sulfated glycosaminoglycan
made up of variably sulfated repeating disaccharide units.
Commonly, a heparin disaccharide unit is made up of a 2-O-sulfated
iduronic acid and 6-O-sulfated, N-sulfated glucosamine,
IdoA(2S)-GlcNS(6S).
[0296] As used herein, "reduced heparin binding" or "attenuated
heparin binding" refers to a lessening or reduced binding activity
for heparin. For example, it can mean that the level or degree of
binding of an ADA2 protein, such as a variant ADA2, is less than a
reference protein. For example, the heparin binding is reduced if
the level or degree of binding of an ADA2 protein to heparin is no
more than 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%,
30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or
95% of the binding of a reference or unmodified ADA2 protein to
heparin. In some cases, heparin binding is reduced at least or at
least about 0.5-fold, 1-fold, 1.5-fold, 2-fold, 3-fold, 4-fold,
5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold or more compared to
the heparin binding of a reference or unmodified ADA2 protein.
[0297] As used herein, "adenosine receptor" or ADR refers to a
class of G-protein coupled receptors that bind adenosine. Adenosine
receptors also can bind to ADA2. There are four types of adenosine
receptors. For example, in humans, the ADRs are designated A.sub.1
(SEQ ID NO:533), A.sub.2A(SEQ ID NO:534), A.sub.2B (SEQ ID NO:535)
and A.sub.3 (SEQ ID NOS:536-538).
[0298] As used herein, "receptor binding" refers to the ability of
ADA2 to bind an adenosine receptor.
[0299] As used herein, "reduced receptor binding" refers to a
lessening or reduced binding activity for an adenosine receptor.
For example, it can mean that the level or degree of binding of an
ADA2 protein, such as a variant ADA2, is less than the binding of a
reference protein for the same adenosine receptor. For example,
receptor binding is reduced if the level or degree of an ADA2
protein for an adenosine receptor is no more than 1%, 2%, 3%, 4%,
5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%,
55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% of the binding of a
reference or unmodified ADA2 protein for the same adenosine
receptor. In some cases, receptor binding is reduced at least or at
least about 0.5-fold, 1-fold, 1.5-fold, 2-fold, 3-fold, 4-fold,
5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold or more compared to
the receptor binding of a reference or unmodified ADA2 protein for
the same adenosine receptor.
[0300] As used herein, recitation that proteins are "compared under
the same conditions" means that different proteins are treated
identically or substantially identically such that any one or more
conditions that can influence the activity or properties of a
protein or agent are not varied or not substantially varied between
the test agents. For example, when the adenosine deaminase activity
of an ADA2 is compared to an unmodified ADA2 protein any one or
more conditions such as the amount or concentration of the protein;
presence, including amount, of excipients, carriers or other
components in a formulation other than the active agent;
temperature; pH and/or other conditions are identical or
substantially identical between and among the compared
polypeptides.
[0301] As used herein, "immune checkpoints" refer to inhibitory
pathways of the immune system that are responsible for maintaining
self-tolerance and modulating the duration and amplitude of
physiological immune responses in peripheral tissues in order to
minimize collateral tissue damage. Immune checkpoints are regulated
by immune checkpoint proteins.
[0302] An "immune checkpoint protein" is a protein, typically a
receptor (e.g., CTLA4 or PD-1) or a ligand (e.g., PD-L1) that
regulates or modulates the extent of an immune response. The immune
checkpoint proteins can be inhibitory or stimulatory. In
particular, the immune checkpoint proteins are inhibitory to the
activation of the immune response. Thus, inhibition of an
inhibitory immune checkpoint protein acts to stimulate or activate
an immune response, such as T cell activation and
proliferation.
[0303] As used herein, an "immune checkpoint inhibitor" or "immune
checkpoint inhibiting agent," or "immune checkpoint blocking agent"
refers to an agent that binds an inhibitory immune checkpoint
protein and blocks its activity. The inhibition can be competitive
or non-competitive inhibition that can be steric or allosteric. In
cases where an immune checkpoint protein is an immune stimulating
protein, an immune checkpoint inhibitor acts to promote the
activity of the immune stimulating protein, such as by binding and
activating the stimulatory immune checkpoint protein or by
inhibiting by interfering with, such as by binding or deactivating,
inhibitors of the stimulatory immune checkpoint protein. An example
of an immune checkpoint inhibitor is an anti-immune checkpoint
protein antibody.
[0304] A "target" of an immune checkpoint inhibitor is the immune
checkpoint protein to which the immune checkpoint inhibitor or
immune checkpoint inhibiting agent binds to block activity.
Typically, the immune checkpoint inhibitor specifically binds to
the target. For example, the target of the exemplary anti-CTLA4
antibody designated ipilimumab is CTLA4.
[0305] As used herein, an anti-immune checkpoint protein antibody,
refers to any antibody that specifically binds to an immune
checkpoint protein or a soluble fragment thereof and blocks. An
anti-immune checkpoint protein antibody typically binds an immune
checkpoint ligand protein or an immune checkpoint receptor protein
and blocks the binding of a receptor to the target immune
checkpoint ligand protein or a ligand to the target immune
checkpoint receptor protein, thereby preventing the inhibitory
signal transduction that suppresses an immune response. Hence,
anti-immune checkpoint protein antibodies are immune checkpoint
inhibitors. Reference to anti-immune checkpoint protein antibodies
herein include full-length antibodies and antigen-binding fragments
thereof that specifically bind to an immune checkpoint ligand or
receptor protein. Exemplary anti-immune checkpoint protein
antibodies include, but are not limited to, anti-cytotoxic
T-lymphocyte-associated protein 4 (CTLA4) antibodies and
anti-programmed cell death protein 1 (PD-1) antibodies.
[0306] As used herein, an antigen-binding fragment of an
anti-immune checkpoint protein antibody refers to an antibody
derived from an anti-immune checkpoint protein antibody but that is
less than the full length sequence of the anti-immune checkpoint
protein antibody but contains at least a portion of the variable
regions (heavy and light) of the antibody sufficient to form an
antigen binding site (e.g., one or more CDRs, and generally all
CDRs) and thus retains the binding specificity and/or activity of
the anti-immune checkpoint protein antibody.
[0307] As used herein, anti-CTLA4 antibody refers to any antibody
that specifically binds to cytotoxic T-lymphocyte-associated
protein 4 (CTLA4) or a soluble fragment thereof and blocks the
binding of ligands to CTLA4, thereby resulting in competitive
inhibition of CTLA4 and inhibition of CTLA4-mediated inhibition of
T cell activation. Hence, anti-CTLA4 antibodies are CTLA4
inhibitors. Reference to anti-CTLA4 antibodies herein include a
full-length antibody and derivatives thereof, such as
antigen-binding fragments thereof that specifically bind to CTLA4.
Exemplary anti-CTLA4 antibodies include, but are not limited to,
Ipilimumab or Tremelimumab, or a derivative or antigen-binding
fragment thereof.
[0308] As used herein, anti-PD-1 antibody refers to any antibody
that specifically binds to programmed cell death protein 1 (PD-1)
or a soluble fragment thereof and blocks the binding of ligands to
PD-1, thereby resulting in competitive inhibition of PD-1 and
inhibition of PD-1-mediated inhibition of T cell activation. Hence,
anti-PD-1 antibodies are PD-1 inhibitors. Reference to anti-PD-1
antibodies herein include a full-length antibody and derivatives
thereof, such as antigen-binding fragments thereof that
specifically bind to PD-1. Exemplary anti-PD-1 antibodies include,
but are not limited to, Nivolumab, MK-3475, Pidilizumab, or a
derivative or antigen-binding fragment thereof.
[0309] As used herein, anti-PD-L1 antibody refers to an antibody
that specifically binds to programmed death-ligand 1 (PD-L1) or a
soluble fragment thereof and blocking the binding of the ligand to
PD-1, thereby resulting in competitive inhibition of PD-1 and
inhibition of PD-1-mediated inhibition of T cell activity. Hence,
anti-PD-L1 antibodies are PD-1 inhibitors. Reference to anti-PD-L1
antibodies herein include a full-length antibody and derivatives
thereof, such as antigen-binding fragments thereof that
specifically bind to PD-L1. Exemplary anti-PD-L1 antibodies
include, but are not limited to, BMS-936559, MPDL3280A, MEDI4736 or
a derivative or antigen-binding fragment thereof.
[0310] As used herein, "antibody" refers to immunoglobulins and
immunoglobulin fragments, whether natural or partially or wholly
synthetically, such as recombinantly, produced, including any
fragment thereof containing at least a portion of the variable
heavy chain and light region of the immunoglobulin molecule that is
sufficient to form an antigen binding site and, when assembled, to
specifically bind antigen. Hence, an antibody includes any protein
having a binding domain that is homologous or substantially
homologous to an immunoglobulin antigen-binding domain (antibody
combining site). For example, an antibody refers to an antibody
that contains two heavy chains (which can be denoted H and H') and
two light chains (which can be denoted L and L'), where each heavy
chain can be a full-length immunoglobulin heavy chain or a portion
thereof sufficient to form an antigen binding site (e.g., heavy
chains include, but are not limited to, VH chains, VH-CH1 chains
and VH-CH1-CH2-CH3 chains), and each light chain can be a
full-length light chain or a portion thereof sufficient to form an
antigen binding site (e.g., light chains include, but are not
limited to, VL chains and VL-CL chains). Each heavy chain (H and
H') pairs with one light chain (L and L', respectively). Typically,
antibodies minimally include all or at least a portion of the
variable heavy (VH) chain and/or the variable light (VL) chain. The
antibody also can include all or a portion of the constant
region.
[0311] For purposes herein, the term antibody includes full-length
antibodies and portions thereof including antibody fragments.
Antibody fragments, include, but are not limited to, Fab fragments,
Fab' fragments, F(ab').sub.2 fragments, Fv fragments,
disulfide-linked Fvs (dsFv), Fd fragments, Fd' fragments,
single-chain Fvs (scFv), single-chain Fabs (scFab), diabodies,
anti-idiotypic (anti-Id) antibodies, or antigen-binding fragments
of any of the above. Antibody also includes synthetic antibodies,
recombinantly produced antibodies, multispecific antibodies (e.g.,
bispecific antibodies), human antibodies, non-human antibodies,
humanized antibodies, chimeric antibodies, and intrabodies.
Antibodies provided herein include members of any immunoglobulin
type (e.g., IgG IgM, IgD, IgE, IgA and IgY), any class (e.g., IgG1,
IgG2, IgG3, IgG4, IgA1 and IgA2) or subclass (e.g., IgG2a and
IgG2b).
[0312] As used herein, the phrase "derived from" or "derivative"
when referring to antibody fragments derived from another antibody,
such as a monoclonal antibody, refers to the engineering of
antibody fragments (e.g., Fab, F(ab'), F(ab').sub.2, single-chain
Fv (scFv), Fv, dsFv, diabody, Fd and Fd' fragments) that retain the
binding specificity of the original or parent antibody. Such
fragments can be derived by a variety of methods known in the art,
including, but not limited to, enzymatic cleavage, chemical
crosslinking, recombinant means or combinations thereof. Generally,
the derived antibody fragment shares the identical or substantially
identical heavy chain variable region (V.sub.H) and light chain
variable region (V.sub.L) of the parent antibody, such that the
antibody fragment and the parent antibody bind the same
epitope.
[0313] As used herein, an anti-hyaluronan agent refers to any agent
that modulates hyaluronan (HA) synthesis or degradation, thereby
altering hyaluronan levels in a tissue or cell. For purposes
herein, anti-hyaluronan agents reduce hyaluronan levels in a tissue
or cell compared to the absence of the agent. Such agents include
compounds that modulate the expression of genetic material encoding
HA synthase (HAS) and other enzymes or receptors involved in
hyaluronan metabolism, or that modulate the proteins that
synthesize or degrade hyaluronan including HAS function or
activity. The agents include small-molecules, nucleic acids,
peptides, proteins or other compounds. For example, anti-hyaluronan
agents include, but are not limited to, antisense or sense
molecules, antibodies, enzymes, small molecule inhibitors and HAS
substrate analogs.
[0314] As used herein, a hyaluronan degrading enzyme refers to an
enzyme that catalyzes the cleavage of a hyaluronan polymer (also
referred to as hyaluronic acid or HA) into smaller molecular weight
fragments. Exemplary hyaluronan degrading enzymes are
hyaluronidases, and particular chondroitinases and lyases that have
the ability to depolymerize hyaluronan Exemplary chondroitinases
that are hyaluronan degrading enzymes include, but are not limited
to, chondroitin ABC lyase (also known as chondroitinase ABC),
chondroitin AC lyase (also known as chondroitin sulfate lyase or
chondroitin sulfate eliminase) and chondroitin C lyase.
[0315] As used herein, hyaluronidase refers to a class of
hyaluronan degrading enzymes. Hyaluronidases include bacterial
hyaluronidases (EC 4.2.2.1 or EC 4.2.99.1), hyaluronidases from
leeches, other parasites, and crustaceans (EC 3.2.1.36), and
mammalian type hyaluronidases (EC 3.2.1.35). Hyaluronidases include
any of non-human origin including, but not limited to, murine,
canine, feline, leporine, avian, bovine, ovine, porcine, equine,
piscine, ranine, bacterial, and any from leeches, other parasites,
and crustaceans. For example, hyaluronidases include those of human
origin. Exemplary human hyaluronidases include HYAL1, HYAL2, HYAL3,
HYAL4, and PH20 (SEQ ID NO:480 and 551). Also included amongst
hyaluronidases are soluble hyaluronidases, including, ovine and
bovine PH20, soluble human PH20 and soluble rHuPH20. Examples of
commercially available bovine or ovine soluble hyaluronidases
include Vitrase.RTM. (ovine hyaluronidase), Amphadase.RTM. (bovine
hyaluronidase) and Hydase.TM. (bovine hyaluronidase).
[0316] Reference to hyaluronan degrading enzymes or hyaluronidase
includes precursor hyaluronan degrading enzyme polypeptides and
mature hyaluronan degrading enzyme polypeptides (such as those in
which a signal sequence has been removed), truncated forms thereof
that have activity, and includes allelic variants and species
variants, variants encoded by splice variants, and other variants,
including polypeptides that have at least 40%, 45%, 50%, 55%, 65%,
70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence
identity to the precursor polypeptides, or the mature forms
thereof. Hyaluronan degrading enzymes and hyaluronidase also
include those that contain chemical or posttranslational
modifications and those that do not contain chemical or
posttranslational modifications. Such modifications include, but
are not limited to, PEGylation, albumination, glycosylation,
farnesylation, carboxylation, hydroxylation, phosphorylation, and
other polypeptide modifications known in the art. A truncated PH20
hyaluronidase is any C-terminal shortened form thereof,
particularly forms that are truncated and neutral active when
N-glycosylated.
[0317] As used herein, "bovine PH20" refers to a bovine
hyaluronidase purified from bovine testicular extracts (see U.S.
Pat. Nos. 2,488,564, 2,488,565, 2,806,815, 2,808,362, 2,676,139,
2,795,529, 5,747,027 and 5,827,721). Examples of commercially
available purified bovine testicular hyaluronidases include
Amphadase.RTM. and Hydase.TM., and bovine hyaluronidases,
including, but not limited to, those available from Sigma Aldrich,
Abnova, EMD Chemicals, GenWay Biotech, Inc., Raybiotech, Inc., and
Calzyme. Also included are recombinantly produced bovine
hyaluronidases.
[0318] As used herein, "ovine PH20" refers to an ovine
hyaluronidase purified from ovine testicular extracts (see U.S.
Pat. Nos. 2,488,564, 2,488,565 and 2,806,815 and International PCT
Publication No. WO2005/118799). Examples of commercially available
purified ovine testicular extract include Vitrase.RTM., and ovine
hyaluronidases, including, but not limited to, those available from
Sigma Aldrich, Cell Sciences, EMD Chemicals, GenWay Biotech, Inc.,
Mybiosource.com and Raybiotech, Inc. Also included are
recombinantly produced ovine hyaluronidases.
[0319] As used herein, "PH20" refers to a type of hyaluronidase
that occurs in sperm and is neutral-active. PH-20 occurs on the
sperm surface, and in the lysosome-derived acrosome, where it is
bound to the inner acrosomal membrane. PH20 includes those of any
origin including, but not limited to, human, chimpanzee, Cynomolgus
monkey, Rhesus monkey, murine, bovine, ovine, guinea pig, rabbit
and rat origin. Exemplary PH20 polypeptides include those from
human (precursor set forth in SEQ ID NO:551 and mature set forth in
SEQ ID NO:480).
[0320] As used herein, a "soluble PH20" refers to any form of PH20
that is soluble under physiologic conditions. A soluble PH20 can be
identified, for example, by its partitioning into the aqueous phase
of a Triton.RTM. X-114 solution at 37.degree. C. (Bordier et al.,
(1981) J. Biol. Chem., 256:1604-7). Membrane-anchored PH20, such as
lipid-anchored PH20, including GPI-anchored PH20, will partition
into the detergent-rich phase, but will partition into the
detergent-poor or aqueous phase following treatment with
Phospholipase-C. Included among soluble PH20 are membrane-anchored
PH20 in which one or more regions associated with anchoring of the
PH20 to the membrane has been removed or modified, where the
soluble form retains hyaluronidase activity. Soluble PH20 also
includes recombinant soluble PH20 and those contained in or
purified from natural sources, such as, for example, testes
extracts from sheep or cows. An example of such soluble PH20 is
soluble human PH20. Exemplary soluble human PH20 polypeptides are
set forth in any of SEQ ID NOS:481-488, 493-514, or 526-532, or has
a sequence of amino acids that is at least 85%, 86%, 87%, 88%, 89%,
90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence
identity to a sequence of amino acids set forth in any of SEQ ID
NOS:481-488, 493-514, or 526-532 and is soluble and retains
hyaluronidase activity.
[0321] As used herein, "soluble recombinant human PH20 (rHuPH20)"
refers to a composition containing soluble form of human PH20 as
recombinantly expressed and secreted in Chinese Hamster Ovary (CHO)
cells. Soluble rHuPH20 is encoded by nucleic acid molecule that
includes the signal sequence and encodes the polypeptide set forth
in SEQ ID NO:481. The nucleic acid encoding soluble rHuPH20 is
expressed in CHO cells which secrete the mature polypeptide. As
produced in the culture medium, there is heterogeneity at the
C-terminus so that the product includes a mixture of species that
can include any one or more of SEQ ID NO:481-486 in various
abundance.
[0322] As used herein, "hyaluronidase activity" refers to the
ability to enzymatically catalyze the cleavage of hyaluronic acid.
The United States Pharmacopeia (USP) XXII assay for hyaluronidase
determines hyaluronidase activity indirectly by measuring the
amount of higher molecular weight hyaluronic acid, or hyaluronan,
(HA) substrate remaining after the enzyme is allowed to react with
the HA for 30 min at 37.degree. C. (USP XXII-NF XVII (1990) 644-645
United States Pharmacopeia Convention, Inc., Rockville, Md.). A
Reference Standard solution can be used in an assay to ascertain
the relative activity, in units, of any hyaluronidase. In vitro
assays to determine the hyaluronidase activity of hyaluronidases,
such as PH20, including soluble PH20 and esPH20, are known in the
art and described herein. Exemplary assays include the
microturbidity assay that measures cleavage of hyaluronic acid by
hyaluronidase indirectly by detecting the insoluble precipitate
formed when the uncleaved hyaluronic acid binds with serum albumin
and the biotinylated-hyaluronic acid assay that measures the
cleavage of hyaluronic acid indirectly by detecting the remaining
biotinylated-hyaluronic acid non-covalently bound to microtiter
plate wells with a streptavidin-horseradish peroxidase conjugate
and a chromogenic substrate. Reference Standards can be used, for
example, to generate a standard curve to determine the activity in
Units of the hyaluronidase being tested.
[0323] As used herein, "neutral active" refers to the ability of a
PH20 polypeptide to enzymatically catalyze the cleavage of
hyaluronic acid at neutral pH (e.g., at or about pH 7.0).
[0324] As used herein, an anti-cancer agent or chemotherapeutic
agent refers to an agent that is capable of killing cells that
divide rapidly, such as cancer cells. One of skill in the art is
familiar with anti-cancer agents, including chemotherapeutic
agents. Exemplary agents are described herein.
[0325] As used herein, "biological activity" refers to the in vivo
activities of a compound or physiological responses that result
upon in vivo administration of a compound, composition or other
mixture. Biological activity, thus, encompasses therapeutic effects
and pharmaceutical activity of such compounds, compositions and
mixtures. Biological activities can be observed in in vitro systems
designed to test or use such activities. Thus, for purposes herein
a biological activity of a ADA2 encompasses adenosine deaminase
activity.
[0326] As used herein the term "assess", and grammatical variations
thereof, is intended to include quantitative and qualitative
determination in the sense of obtaining an absolute value for the
activity of a polypeptide, and also of obtaining an index, ratio,
percentage, visual or other value indicative of the level of the
activity. Assessment can be direct or indirect. For example,
detection of cleavage of a substrate by a polypeptide can be by
direct measurement of the product, or can be indirectly measured by
determining the resulting activity of the cleaved substrate.
[0327] As used herein, "mature numbering" or "standard numbering"
refers to the numbering of residues in order based on a mature ADA2
polypeptide. For purposes herein, mature numbering is based on the
numbering of residues of mature ADA2 set forth in SEQ ID NO:5.
[0328] As used herein, "Zavialov numbering" refers to the numbering
of residues used in Zavialov et al. (2010) J. Biol. Chem.
285:12367-12377 and in PDB accession Nos. 3LGG and 3LGD. Zavialov
numbering is based on the numbering of residues of ADA2 as set
forth in SEQ ID NO:4. Hence Zavialov numbering can be determined by
alignment with SEQ ID NO:4. Table 1 below sets forth the
corresponding position numbers between mature numbering and
Zavialov numbering. Table 1 provides the sequence of amino acids
set forth in SEQ ID NO:4 (reference sequence for Zavialov
numbering), its position numbers and the corresponding position
numbers for SEQ ID NO:5 (reference sequence for mature numbering as
used herein).
TABLE-US-00001 TABLE 1 Corresponding Position Numbers for Mature
Numbering (SEQ ID NO: 5) and Zavialov Numbering (SEQ ID NO: 4) SEQ
ID NO: 5 (mature) 1 2 3 4 5 6 7 SEQ ID NO: 4 (Zavialov) 1 2 3 4 5 6
7 8 9 10 Sequence (SEQ ID NO: 4) G G S I D E T R A H SEQ ID NO: 5
(mature) 8 9 10 11 12 13 14 15 16 17 SEQ ID NO: 4 (Zavialov) 11 12
13 14 15 16 17 18 19 20 Sequence (SEQ ID NO: 4) L L L K E K M M R L
SEQ ID NO: 5 (mature) 18 19 20 21 22 23 24 25 26 27 SEQ ID NO: 4
(Zavialov) 21 22 23 24 25 26 27 28 29 30 Sequence (SEQ ID NO: 4) G
G R L V L N T K E SEQ ID NO: 5 (mature) 28 29 30 31 32 33 34 35 36
37 SEQ ID NO: 4 (Zavialov) 31 32 33 34 35 36 37 38 39 40 Sequence
(SEQ ID NO: 4) E L A N E R L M T L SEQ ID NO: 5 (mature) 38 39 40
41 42 43 44 45 46 47 SEQ ID NO: 4 (Zavialov) 41 42 43 44 45 46 47
48 49 50 Sequence (SEQ ID NO: 4) K I A E M K E A M R SEQ ID NO: 5
(mature) 48 49 50 51 52 53 54 55 56 57 SEQ ID NO: 4 (Zavialov) 51
52 53 54 55 56 57 58 59 60 Sequence (SEQ ID NO: 4) T L I F P P S M
H F SEQ ID NO: 5 (mature) 58 59 60 61 62 63 64 65 66 67 SEQ ID NO:
4 (Zavialov) 61 62 63 64 65 66 67 68 69 70 Sequence (SEQ ID NO: 4)
F Q A K H L I E R S SEQ ID NO: 5 (mature) 68 69 70 71 72 73 74 75
76 77 SEQ ID NO: 4 (Zavialov) 71 72 73 74 75 76 77 78 79 80
Sequence (SEQ ID NO: 4) Q V F N I L R M M P SEQ ID NO: 5 (mature)
78 79 80 81 82 83 84 85 86 87 SEQ ID NO: 4 (Zavialov) 81 82 83 84
85 86 87 88 89 90 Sequence (SEQ ID NO: 4) K G A A L H L H D I SEQ
ID NO: 5 (mature) 88 89 90 91 92 93 94 95 96 97 SEQ ID NO: 4
(Zavialov) 91 92 93 94 95 96 97 98 99 100 Sequence (SEQ ID NO: 4) G
I V T M D W L V R SEQ ID NO: 5 (mature) 98 99 100 101 102 103 104
105 106 107 SEQ ID NO: 4 (Zavialov) 101 102 103 104 105 106 107 108
109 110 Sequence (SEQ ID NO: 4) N V T Y R P H C H I SEQ ID NO: 5
(mature) 108 109 110 111 112 113 114 115 116 117 SEQ ID NO: 4
(Zavialov) 111 112 113 114 115 116 117 118 119 120 Sequence (SEQ ID
NO: 4) C F T P R G I M Q F SEQ ID NO: 5 (mature) 118 119 120 121
122 123 124 125 126 127 SEQ ID NO: 4 (Zavialov) 121 122 123 124 125
126 127 128 129 130 Sequence (SEQ ID NO: 4) R F A H P T P R P S SEQ
ID NO: 5 (mature) 128 129 130 131 132 133 134 135 136 137 SEQ ID
NO: 4 (Zavialov) 131 132 133 134 135 136 137 138 139 140 Sequence
(SEQ ID NO: 4) E K C S K W I L L E SEQ ID NO: 5 (mature) 138 139
140 141 142 143 144 145 146 147 SEQ ID NO: 4 (Zavialov) 141 142 143
144 145 146 147 148 149 150 Sequence (SEQ ID NO: 4) D Y R K R V Q N
V T SEQ ID NO: 5 (mature) 148 149 150 151 152 153 154 155 156 157
SEQ ID NO: 4 (Zavialov) 151 152 153 154 155 156 157 158 159 160
Sequence (SEQ ID NO: 4) E F D D S L L R N F SEQ ID NO: 5 (mature)
158 159 160 161 162 163 164 165 166 167 SEQ ID NO: 4 (Zavialov) 161
162 163 164 165 166 167 168 169 170 Sequence (SEQ ID NO: 4) T L V T
Q H P E V I SEQ ID NO: 5 (mature) 168 169 170 171 172 173 174 175
176 177 SEQ ID NO: 4 (Zavialov) 171 172 173 174 175 176 177 178 179
180 Sequence (SEQ ID NO: 4) Y T N Q N V V W S K SEQ ID NO: 5
(mature) 178 179 180 181 182 183 184 185 186 187 SEQ ID NO: 4
(Zavialov) 181 182 183 184 185 186 187 188 189 190 Sequence (SEQ ID
NO: 4) F E T I F F T I S G SEQ ID NO: 5 (mature) 188 189 190 191
192 193 194 195 196 197 SEQ ID NO: 4 (Zavialov) 191 192 193 194 195
196 197 198 199 200 Sequence (SEQ ID NO: 4) L I H Y A P V F R D SEQ
ID NO: 5 (mature) 198 199 200 201 202 203 204 205 206 207 SEQ ID
NO: 4 (Zavialov) 201 202 203 204 205 206 207 208 209 210 Sequence
(SEQ ID NO: 4) Y V F R S M Q E F Y SEQ ID NO: 5 (mature) 208 209
210 211 212 213 214 215 216 217 SEQ ID NO: 4 (Zavialov) 211 212 213
214 215 216 217 218 219 220 Sequence (SEQ ID NO: 4) E D N V L Y M E
I R SEQ ID NO: 5 (mature) 218 219 220 221 222 223 224 225 226 227
SEQ ID NO: 4 (Zavialov) 221 222 223 224 225 226 227 228 229 230
Sequence (SEQ ID NO: 4) A R L L P V Y E L S SEQ ID NO: 5 (mature)
228 229 230 231 232 233 234 235 236 237 SEQ ID NO: 4 (Zavialov) 231
232 233 234 235 236 237 238 239 240 Sequence (SEQ ID NO: 4) G E H H
D E E W S V SEQ ID NO: 5 (mature) 238 239 240 241 242 243 244 245
246 247 SEQ ID NO: 4 (Zavialov) 241 242 243 244 245 246 247 248 249
250 Sequence (SEQ ID NO: 4) K T Y Q E V A Q K F SEQ ID NO: 5
(mature) 248 249 250 251 252 253 254 255 256 257 SEQ ID NO: 4
(Zavialov) 251 252 253 254 255 256 257 258 259 260 Sequence (SEQ ID
NO: 4) V E T H P E F I G I SEQ ID NO: 5 (mature) 258 259 260 261
262 263 264 265 266 267 SEQ ID NO: 4 (Zavialov) 261 262 263 264 265
266 267 268 269 270 Sequence (SEQ ID NO: 4) K I I Y S D H R S K SEQ
ID NO: 5 (mature) 268 269 270 271 272 273 274 275 276 277 SEQ ID
NO: 4 (Zavialov) 271 272 273 274 275 276 277 278 279 280 Sequence
(SEQ ID NO: 4) D V A V I A E S I R SEQ ID NO: 5 (mature) 278 279
280 281 282 283 284 285 286 287 SEQ ID NO: 4 (Zavialov) 281 282 283
284 285 286 287 288 289 290 Sequence (SEQ ID NO: 4) M A M G L R I K
F P SEQ ID NO: 5 (mature) 288 289 290 291 292 293 294 295 296 297
SEQ ID NO: 4 (Zavialov) 291 292 293 294 295 296 297 298 299 300
Sequence (SEQ ID NO: 4) T V V A G F D L V G SEQ ID NO: 5 (mature)
298 299 300 301 302 303 304 305 306 307 SEQ ID NO: 4 (Zavialov) 301
302 303 304 305 306 307 308 309 310 Sequence (SEQ ID NO: 4) H E D T
G H S L H D SEQ ID NO: 5 (mature) 308 309 310 311 312 313 314 315
316 317 SEQ ID NO: 4 (Zavialov) 311 312 313 314 315 316 317 318 319
320 Sequence (SEQ ID NO: 4) Y K E A L M I P A K SEQ ID NO: 5
(mature) 318 319 320 321 322 323 324 325 326 327 SEQ ID NO: 4
(Zavialov) 321 322 323 324 325 326 327 328 329 330 Sequence (SEQ ID
NO: 4) D G V K L P Y F F H SEQ ID NO: 5 (mature) 328 329 330 331
332 333 334 335 336 337 SEQ ID NO: 4 (Zavialov) 331 332 333 334 335
336 337 338 339 340 Sequence (SEQ ID NO: 4) A G E T D W Q G T S SEQ
ID NO: 5 (mature) 338 339 340 341 342 343 344 345 346 347 SEQ ID
NO: 4 (Zavialov) 341 342 343 344 345 346 347 348 349 350 Sequence
(SEQ ID NO: 4) I D R N I L D A L M SEQ ID NO: 5 (mature) 348 349
350 351 352 353 354 355 356 357 SEQ ID NO: 4 (Zavialov) 351 352 353
354 355 356 357 358 359 360 Sequence (SEQ ID NO: 4) L N T T R I G H
G F SEQ ID NO: 5 (mature) 358 359 360 361 362 363 364 365 366 367
SEQ ID NO: 4 (Zavialov) 361 362 363 364 365 366 367 368 369 370
Sequence (SEQ ID NO: 4) A L S K H P A V R T SEQ ID NO: 5 (mature)
368 369 370 371 372 373 374 375 376 377 SEQ ID NO: 4 (Zavialov) 371
372 373 374 375 376 377 378 379 380 Sequence (SEQ ID NO: 4) Y S W K
K D I P I E SEQ ID NO: 5 (mature) 378 379 380 381 382 383 384 385
386 387 SEQ ID NO: 4 (Zavialov) 381 382 383 384 385 386 387 388 389
390 Sequence (SEQ ID NO: 4) V C P I S N Q V L K SEQ ID NO: 5
(mature) 388 389 390 391 392 393 394 395 396 397 SEQ ID NO: 4
(Zavialov) 391 392 393 394 395 396 397 398 399 400 Sequence (SEQ ID
NO: 4) L V S D L R N H P V SEQ ID NO: 5 (mature) 398 399 400 401
402 403 404 405 406 407 SEQ ID NO: 4 (Zavialov) 401 402 403 404 405
406 407 408 409 410 Sequence (SEQ ID NO: 4) A T L M A T G H P M SEQ
ID NO: 5 (mature) 408 409 410 411 412 413 414 415 416 417 SEQ ID
NO: 4 (Zavialov) 411 412 413 414 415 416 417 418 419 420 Sequence
(SEQ ID NO: 4) V I S S D D P A M F SEQ ID NO: 5 (mature) 418 419
420 421 422 423 424 425 426 427 SEQ ID NO: 4 (Zavialov) 421 422 423
424 425 426 427 428 429 430 Sequence (SEQ ID NO: 4) G A K G L S Y D
F Y SEQ ID NO: 5 (mature) 428 429 430 431 432 433 434 435 436 437
SEQ ID NO: 4 (Zavialov) 431 432 433 434 435 436 437 438 439 440
Sequence (SEQ ID NO: 4) E V F M G I G G M K SEQ ID NO: 5 (mature)
438 439 440 441 442 443 444 445 446 447 SEQ ID NO: 4 (Zavialov) 441
442 443 444 445 446 447 448 449 450 Sequence (SEQ ID NO: 4) A D L R
T L K Q L A SEQ ID NO: 5 (mature) 448 449 450 451 452 453 454 455
456 457 SEQ ID NO: 4 (Zavialov) 451 452 453 454 455 456 457 458 459
460 Sequence (SEQ ID NO: 4) M N S I K Y S T L L SEQ ID NO: 5
(mature) 458 459 460 461 462 463 464 465 466 467 SEQ ID NO: 4
(Zavialov) 461 462 463 464 465 466 467 468 469 470 Sequence (SEQ ID
NO: 4) E S E K N T F M E I SEQ ID NO: 5 (mature) 468 469 470 471
472 473 474 475 476 477 SEQ ID NO: 4 (Zavialov) 471 472 473 474 475
476 477 478 479 480 Sequence (SEQ ID NO: 4) W K K R W D K F I A SEQ
ID NO: 5 (mature) 478 479 480 481 482 SEQ ID NO: 4 (Zavialov) 481
482 483 484 485 Sequence (SEQ ID NO: 4) D V A T K
[0329] As used herein, a "conjugate" refers to a polypeptide linked
directly or indirectly to one or more other polypeptides or
chemical moieties. Such conjugates include fusion proteins, those
produced by chemical conjugates and those produced by any other
methods. For example, a conjugate refers to an ADA2 protein linked
directly or indirectly to one or more other polypeptides or
chemical moieties, whereby at least one ADA2 polypeptide subunit is
linked, directly or indirectly to another polypeptide or chemical
moiety so long as the conjugate retains adenosine deaminase
activity.
[0330] As used herein, "coupled" or "conjugated" means attached via
a covalent or noncovalent interaction.
[0331] As used herein, a chimeric polypeptide refers to a
polypeptide that contains portions from at least two different
polypeptides or from two non-contiguous portions of a single
polypeptide. Thus, a chimeric polypeptide generally includes a
sequence of amino acid residues from all or part of one polypeptide
and a sequence of amino acids from all or part of another different
polypeptide. The two portions can be linked directly or indirectly
and can be linked via peptide bonds, other covalent bonds covalent
interactions of sufficient strength to maintain the integrity of a
substantial portion of the chimeric polypeptide under equilibrium
conditions and physiologic conditions, such as in isotonic pH 7
buffered saline.
[0332] As used herein, a fusion protein is a polypeptide engineered
to contain sequences of amino acids corresponding to two distinct
polypeptides, which are joined together, such as by expressing the
fusion protein from a vector containing two nucleic acids, encoding
the two polypeptides, in close proximity, e.g., adjacent, to one
another along the length of the vector. Accordingly, a fusion
protein refers to a chimeric protein containing two, or portions
from two, or more proteins or peptides that are linked directly or
indirectly via peptide bonds. The two molecules can be adjacent in
the construct or separated by a linker, or spacer polypeptide.
[0333] As used herein, "linker" or "spacer" peptide refers to short
sequences of amino acids that join two polypeptide sequences (or
nucleic acid encoding such an amino acid sequence). "Peptide
linker" refers to the short sequence of amino acids joining the two
polypeptide sequences. Exemplary of polypeptide linkers are linkers
joining a peptide transduction domain to an antibody or linkers
joining two antibody chains in a synthetic antibody fragment such
as an scFv fragment. Linkers are well-known and any known linkers
can be used in the provided methods. Exemplary of polypeptide
linkers are (Gly-Ser).sub.n amino acid sequences, with some Glu or
Lys residues dispersed throughout to increase solubility. Other
exemplary linkers are described herein; any of these and other
known linkers can be used with the provided compositions and
methods.
[0334] As used herein, a multimerization domain refers to a
sequence of amino acids that promotes stable interaction of a
polypeptide molecule with one or more additional polypeptide
molecules, each containing a complementary multimerization domain,
which can be the same or a different multimerization domain to form
a stable multimer with the first domain. Generally, a polypeptide
is joined directly or indirectly to the multimerization domain.
Exemplary multimerization domains include the immunoglobulin
sequences or portions thereof, leucine zippers, hydrophobic
regions, hydrophilic regions, and compatible protein-protein
interaction domains. The multimerization domain, for example, can
be an immunoglobulin constant region or domain, such as, for
example, the Fc domain or portions thereof from IgG, including
IgG1, IgG2, IgG3 or IgG4 subtypes, IgA, IgE, IgD and IgM and
modified forms thereof.
[0335] As used herein, a "moiety" or "heterologous moiety" refers
to a molecule that is capable of associating with another molecule,
either directly or indirectly by a covalent or non-covalent
interaction. Typically, the molecule is derived from a distinct
entity from that of the entity to which it is being associated. In
one embodiment, a heterologous moiety can be a polypeptide fused to
another polypeptide to produce a fusion polypeptide or protein. In
another embodiment, a heterologous moiety can be a non-polypeptide
such as a polymer, such as a PEG conjugated to a polypeptide or
protein.
[0336] As used herein, a "half-life extending moiety" is
heterologous moiety that facilitates the increased half-life of the
molecule to which it is conjugated.
[0337] As used herein, "Fc" or "Fc region" or "Fc domain" refers to
a polypeptide containing the constant region of an antibody heavy
chain, excluding the first constant region immunoglobulin domain.
Thus, Fc refers to the last two constant region immunoglobulin
domains of IgA, IgD, and IgE, or the last three constant region
immunoglobulin domains of IgE and IgM. Optionally, an Fc domain can
include all or part of the flexible hinge N-terminal to these
domains. For IgA and IgM, Fc can include the J chain. For an
exemplary Fc domain of IgG Fc contains immunoglobulin domains
C.gamma.2 and C.gamma.3, and optionally, all or part of the hinge
between C.gamma.1 and C.gamma.2. The boundaries of the Fc region
can vary, but typically, include at least part of the hinge region.
In addition, Fc also includes any allelic or species variant or any
variant or modified form, such as any variant or modified form that
alters the binding to an FcR or alters an Fc-mediated effector
function.
[0338] As used herein, "Fc chimera" refers to a chimeric
polypeptide in which one or more polypeptides is linked, directly
or indirectly, to an Fc region or a derivative thereof. Typically,
an Fc chimera combines the Fc region of an immunoglobulin with
another polypeptide. Derivatives of or modified Fc polypeptides are
known to those of skill in the art.
[0339] As used herein, a "polymer" refers to any high molecular
weight natural or synthetic moiety that is conjugated to, i.e.
stably linked directly or indirectly via a linker, to a
polypeptide. Such polymers, typically increase serum half-life, and
include, but are not limited to sialic moieties, PEGylation
moieties, dextran, and sugar and other moieties, such as for
glycosylation. For example, ADA2 proteins, such as a variant ADA2,
can be conjugated to a polymer.
[0340] As used herein, "PEGylated" refers to covalent or other
stable attachment of polymeric molecules, such as polyethylene
glycol (PEGylation moiety PEG) to proteins, including an ADA2, such
as a variant ADA2. PEGylation can increase half-life of the
ADA2.
[0341] As used herein, nucleic acids include DNA, RNA and analogs
thereof, including peptide nucleic acids (PNA) and mixtures
thereof. Nucleic acids can be single or double-stranded. When
referring to probes or primers, which are optionally labeled, such
as with a detectable label, such as a fluorescent or radiolabel,
single-stranded molecules are contemplated. Such molecules are
typically of a length such that their target is statistically
unique or of low copy number (typically less than 5, generally less
than 3) for probing or priming a library. Generally a probe or
primer contains at least 14, 16 or 30 contiguous nucleotides of
sequence complementary to or identical to a gene of interest.
Probes and primers can be 10, 20, 30, 50, 100 or more nucleotides
long.
[0342] As used herein, a peptide refers to a polypeptide that is
from 2 to 40 amino acids in length.
[0343] As used herein, the amino acids that occur in the various
sequences of amino acids provided herein are identified according
to their known, three-letter or one-letter abbreviations (Table 2).
The nucleotides which occur in the various nucleic acid fragments
are designated with the standard single-letter designations used
routinely in the art.
[0344] As used herein, an "amino acid" is an organic compound
containing an amino group and a carboxylic acid group. A
polypeptide contains two or more amino acids. For purposes herein,
amino acids include the twenty naturally-occurring amino acids,
non-natural amino acids and amino acid analogs (i.e., amino acids
wherein the .alpha.-carbon has a side chain).
[0345] In keeping with standard polypeptide nomenclature described
in J. Biol. Chem., 243: 3557-3559 (1968), and adopted in 37 C.F.R.
.sctn..sctn.1.821-1.822, abbreviations for the amino acid residues
are shown in Table 2:
TABLE-US-00002 TABLE 2 Table of Correspondence SYMBOL 1-Letter
3-Letter AMINO ACID Y Tyr Tyrosine G Gly Glycine F Phe
Phenylalanine M Met Methionine A Ala Alanine S Ser Serine I Ile
Isoleucine L Leu Leucine T Thr Threonine V Val Valine P Pro proline
K Lys Lysine H His Histidine Q Gln Glutamine E Glu glutamic acid Z
Glx Glu and/or Gln W Trp Tryptophan R Arg Arginine D Asp aspartic
acid N Asn asparagine B Asx Asn and/or Asp C Cys Cysteine X Xaa
Unknown or other
[0346] All amino acid residue sequences represented herein by
formulae have a left to right orientation in the conventional
direction of amino-terminus to carboxyl-terminus. In addition, the
phrase "amino acid residue" is broadly defined to include the amino
acids listed in the Table of Correspondence (Table 2) and modified
and unusual amino acids, such as those referred to in 37 C.F.R.
.sctn..sctn.1.821-1.822, and incorporated herein by reference. A
dash at the beginning or end of an amino acid residue sequence
indicates a peptide bond to a further sequence of one or more amino
acid residues, to an amino-terminal group such as NH.sub.2 or to a
carboxyl-terminal group such as COOH.
[0347] As used herein, a "hydrophobic amino acid" includes any one
of the amino acids determined to be hydrophobic using the Eisenberg
hydrophobicity consensus scale. Exemplary are the naturally
occurring hydrophobic amino acids, such as isoleucine,
phenylalanine, valine, leucine, tryptophan, methionine, alanine,
glycine, cysteine and tyrosine (Eisenberg et al., (1982) Faraday
Symp. Chem. Soc. 17:109-120). Non-naturally-occurring hydrophobic
amino acids also are included.
[0348] As used herein, an "acidic amino acid" includes among the
naturally-occurring amino acids aspartic acid and glutamic acid
residues. Non-naturally-occurring acidic amino acids also are
included.
[0349] As used herein, a "polar amino acid" refers to an amino acid
that is a hydrophile, such that the side chains prefer to reside in
an aqueous (i.e. water) environment. Such amino acids generally are
located on the surface of a protein. Such amino acids generally are
classified if they include those with polar side chains that have a
functional group such as an acid, amide, alcohol or amine that
contains oxygens or nitrogens that can participate in hydrogen
bonding with water. Exemplary of such amino acids are Arg (R), Asn
(N), Asp (D), Glu (E), Gln (Q), His (H), Lys (K), Ser (S), Thr (T),
and Tyr (Y). Cys (C) and Trp (W), which are also considered to be
weakly polar.
[0350] As used herein, a polar and neutral amino acid is a polar
amino acid that contains a neutral side chain. Exemplary of such
amino acid residues for replacement are Asn (N), Gln (Q), Ser (S),
Thr (T), Cys (C) or Tyr (Y).
[0351] As used herein, "naturally occurring amino acids" refer to
the 20 L-amino acids that occur in polypeptides.
[0352] As used herein, "non-natural amino acid" refers to an
organic compound containing an amino group and a carboxylic acid
group that is not one of the naturally-occurring amino acids listed
in Table 2. Non-naturally occurring amino acids thus include, for
example, amino acids or analogs of amino acids other than the 20
naturally-occurring amino acids and include, but are not limited
to, the D-stereoisomer of amino acids. Exemplary non-natural amino
acids are known to those of skill in the art and can be included in
a modified ADA2 polypeptide.
[0353] As used herein, suitable conservative substitutions of amino
acids are known to those of skill in the art and can be made
generally without altering the biological activity of the resulting
molecule. Those of skill in the art recognize that, in general,
single amino acid substitutions in non-essential regions of a
polypeptide do not substantially alter biological activity (see,
e.g., Watson et al. Molecular Biology of the Gene, 4th Edition,
1987, The Benjamin/Cummings Pub. co., p. 224). Such substitutions
can be made in accordance with those set forth in Table 3 as
follows:
TABLE-US-00003 TABLE 3 Original residue Exemplary conservative
substitution Ala (A) Gly; Ser Arg (R) Lys Asn (N) Gln; His Cys (C)
Ser Gln (Q) Asn Glu (E) Asp Gly (G) Ala; Pro His (H) Asn; Gln Ile
(I) Leu; Val Leu (L) Ile; Val Lys (K) Arg; Gln; Glu Met (M) Leu;
Tyr; Ile Phe (F) Met; Leu; Tyr Ser (S) Thr Thr (T) Ser Trp (W) Tyr
Tyr (Y) Trp; Phe Val (V) Ile; Leu
[0354] Other substitutions also are permissible and can be
determined empirically or in accord with known conservative
substitutions.
[0355] As used herein, a DNA construct is a single or double
stranded, linear or circular DNA molecule that contains segments of
DNA combined and juxtaposed in a manner not found in nature. DNA
constructs exist as a result of human manipulation, and include
clones and other copies of manipulated molecules.
[0356] As used herein, a DNA segment is a portion of a larger DNA
molecule having specified attributes. For example, a DNA segment
encoding a specified polypeptide is a portion of a longer DNA
molecule, such as a plasmid or plasmid fragment, which, when read
from the 5' to 3' direction, encodes the sequence of amino acids of
the specified polypeptide.
[0357] As used herein, the term polynucleotide means a single- or
double-stranded polymer of deoxyribonucleotides or ribonucleotide
bases read from the 5' to the 3' end. Polynucleotides include RNA
and DNA, and can be isolated from natural sources, synthesized in
vitro, or prepared from a combination of natural and synthetic
molecules. The length of a polynucleotide molecule is given herein
in terms of nucleotides (abbreviated "nt") or base pairs
(abbreviated "bp"). The term nucleotides is used for single- and
double-stranded molecules where the context permits. When the term
is applied to double-stranded molecules it is used to denote
overall length and will be understood to be equivalent to the term
base pairs. It will be recognized by those skilled in the art that
the two strands of a double-stranded polynucleotide can differ
slightly in length and that the ends thereof can be staggered; thus
all nucleotides within a double-stranded polynucleotide molecule
cannot be paired. Such unpaired ends will, in general, not exceed
20 nucleotides in length.
[0358] As used herein, "primary sequence" refers to the sequence of
amino acid residues in a polypeptide.
[0359] As used herein, "similarity" between two proteins or nucleic
acids refers to the relatedness between the sequence of amino acids
of the proteins or the nucleotide sequences of the nucleic acids.
Similarity can be based on the degree of identity and/or homology
of sequences of residues and the residues contained therein.
Methods for assessing the degree of similarity between proteins or
nucleic acids are known to those of skill in the art. For example,
in one method of assessing sequence similarity, two amino acid or
nucleotide sequences are aligned in a manner that yields a maximal
level of identity between the sequences. "Identity" refers to the
extent to which the amino acid or nucleotide sequences are
invariant. Alignment of amino acid sequences, and to some extent
nucleotide sequences, also can take into account conservative
differences and/or frequent substitutions in amino acids (or
nucleotides). Conservative differences are those that preserve the
physico-chemical properties of the residues involved. Alignments
can be global (alignment of the compared sequences over the entire
length of the sequences and including all residues) or local (the
alignment of a portion of the sequences that includes only the most
similar region or regions).
[0360] As used herein, the terms "homology" and "identity" are used
interchangeably, but homology for proteins can include conservative
amino acid changes. In general to identify corresponding positions
the sequences of amino acids are aligned so that the highest order
match is obtained (see, e.g.: Computational Molecular Biology,
Lesk, A. M., ed., Oxford University Press, New York, 1988;
Biocomputing: Informatics and Genome Projects, Smith, D. W., ed.,
Academic Press, New York, 1993; Computer Analysis of Sequence Data,
Part I, Griffin, A. M., and Griffin, H. G, eds., Humana Press, New
Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje,
G, Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M.
and Devereux, J., eds., M Stockton Press, New York, 1991; Carrillo
et al. (1988) SIAM J Applied Math 48:1073).
[0361] As use herein, "sequence identity" refers to the number of
identical amino acids (or nucleotide bases) in a comparison between
a test and a reference polypeptide or polynucleotide. Homologous
polypeptides refer to a pre-determined number of identical or
homologous amino acid residues. Homology includes conservative
amino acid substitutions as well as identical residues. Sequence
identity can be determined by standard alignment algorithm programs
used with default gap penalties established by each supplier.
Homologous nucleic acid molecules refer to a pre-determined number
of identical or homologous nucleotides. Homology includes
substitutions that do not change the encoded amino acid (i.e.,
"silent substitutions") as well identical residues. Substantially
homologous nucleic acid molecules hybridize typically at moderate
stringency or at high stringency all along the length of the
nucleic acid or along at least about 70%, 80% or 90% of the
full-length nucleic acid molecule of interest. Also contemplated
are nucleic acid molecules that contain degenerate codons in place
of codons in the hybridizing nucleic acid molecule. (For
determination of homology of proteins, conservative amino acids can
be aligned as well as identical amino acids; in this case,
percentage of identity and percentage homology varies). Whether any
two nucleic acid molecules have nucleotide sequences (or any two
polypeptides have amino acid sequences) that are at least 80%, 85%,
90%, 95%, 96%, 97%, 98% or 99% "identical" can be determined using
known computer algorithms such as the "FAST A" program, using for
example, the default parameters as in Pearson et al. Proc. Natl.
Acad. Sci. USA 85: 2444 (1988) (other programs include the GCG
program package (Devereux, J., et al., Nucleic Acids Research
12(I): 387 (1984)), BLASTP, BLASTN, FASTA (Altschul, S. F., et al.,
J. Molec. Biol. 215:403 (1990); Guide to Huge Computers, Martin J.
Bishop, ed., Academic Press, San Diego (1994), and Carrillo et al.
SIAM J Applied Math 48: 1073 (1988)). For example, the BLAST
function of the National Center for Biotechnology Information
database can be used to determine identity. Other commercially or
publicly available programs include DNAStar "MegAlign" program
(Madison, Wis.) and the University of Wisconsin Genetics Computer
Group (UWG) "Gap" program (Madison Wis.)). Percent homology or
identity of proteins and/or nucleic acid molecules can be
determined, for example, by comparing sequence information using a
GAP computer program (e.g., Needleman et al. J. Mol. Biol. 48: 443
(1970), as revised by Smith and Waterman (Adv. Appl. Math. 2: 482
(1981)). Briefly, a GAP program defines similarity as the number of
aligned symbols (i.e., nucleotides or amino acids) that are
similar, divided by the total number of symbols in the shorter of
the two sequences. Default parameters for the GAP program can
include: (1) a unary comparison matrix (containing a value of 1 for
identities and 0 for non identities) and the weighted comparison
matrix of Gribskov et al. Nucl. Acids Res. 14: 6745 (1986), as
described by Schwartz and Dayhoff, eds., Atlas of Protein Sequence
and Structure, National Biomedical Research Foundation, pp. 353-358
(1979); (2) a penalty of 3.0 for each gap and an additional 0.10
penalty for each symbol in each gap; and (3) no penalty for end
gaps.
[0362] Therefore, as used herein, the term "identity" represents a
comparison between a test and a reference polypeptide or
polynucleotide. In one non-limiting example, "at least 90%
identical to" refers to percent identities from 90 to 100% relative
to the reference polypeptides. Identity at a level of 90% or more
is indicative of the fact that, assuming for exemplification
purposes a test and reference polynucleotide length of 100 amino
acids are compared, no more than 10% (i.e., 10 out of 100) of amino
acids in the test polypeptide differs from that of the reference
polypeptides. Similar comparisons can be made between a test and
reference polynucleotides. Such differences can be represented as
point mutations randomly distributed over the entire length of an
amino acid sequence or they can be clustered in one or more
locations of varying length up to the maximum allowable, e.g.,
10/100 amino acid difference (approximately 90% identity).
Differences are defined as nucleic acid or amino acid
substitutions, insertions or deletions. At the level of homologies
or identities above about 85-90%, the result should be independent
of the program and gap parameters set; such high levels of identity
can be assessed readily, often without relying on software.
[0363] As used herein, it also is understood that the terms
"substantially identical" or "similar" varies with the context as
understood by those skilled in the relevant art, but that those of
skill can assess such.
[0364] As used herein, an aligned sequence refers to the use of
homology (similarity and/or identity) to align corresponding
positions in a sequence of nucleotides or amino acids. Typically,
two or more sequences that are related by 50% or more identity are
aligned. An aligned set of sequences refers to 2 or more sequences
that are aligned at corresponding positions and can include
aligning sequences derived from RNAs, such as ESTs and other cDNAs,
aligned with genomic DNA sequence.
[0365] As used herein, "specifically hybridizes" refers to
annealing, by complementary base-pairing, of a nucleic acid
molecule (e.g. an oligonucleotide) to a target nucleic acid
molecule.
[0366] Those of skill in the art are familiar with in vitro and in
vivo parameters that affect specific hybridization, such as length
and composition of the particular molecule. Parameters particularly
relevant to in vitro hybridization further include annealing and
washing temperature, buffer composition and salt concentration.
Exemplary washing conditions for removing non-specifically bound
nucleic acid molecules at high stringency are 0.1.times.SSPE, 0.1%
SDS, 65.degree. C., and at medium stringency are 0.2.times.SSPE,
0.1% SDS, 50.degree. C. Equivalent stringency conditions are known
in the art. The skilled person can readily adjust these parameters
to achieve specific hybridization of a nucleic acid molecule to a
target nucleic acid molecule appropriate for a particular
application.
[0367] As used herein, isolated or purified polypeptide or protein
or biologically-active portion thereof is substantially free of
cellular material or other contaminating proteins from the cell or
tissue from which the protein is derived, or substantially free
from chemical precursors or other chemicals when chemically
synthesized. Preparations can be determined to be substantially
free if they appear free of readily detectable impurities as
determined by standard methods of analysis, such as thin layer
chromatography (TLC), gel electrophoresis and high performance
liquid chromatography (HPLC), used by those of skill in the art to
assess such purity, or sufficiently pure such that further
purification would not detectably alter the physical and chemical
properties, such as enzymatic and biological activities, of the
substance. Methods for purification of the compounds to produce
substantially chemically pure compounds are known to those of skill
in the art. A substantially chemically pure compound, however, can
be a mixture of stereoisomers. In such instances, further
purification might increase the specific activity of the
compound.
[0368] Hence, reference to an isolated or purified protein or
catalytically active protein thereof means that it is substantially
free of cellular material or other contaminating proteins from the
cell of tissue from which the protein is derived, or substantially
free from chemical precursors or other chemicals when chemically
synthesized. Preparations can be determined to be substantially
free if they appear free of readily detectable impurities as
determined by standard methods of analysis, such as thin layer
chromatography (TLC), gel electrophoresis and high performance
liquid chromatography (HPLC), used by those of skill in the art to
assess such purity, or sufficiently pure such that further
purification would not detectably alter the physical and chemical
properties, such as proteolytic and biological activities, of the
substance. Methods for purification of the proteins to produce
substantially pure polypeptides are known to those of skill in the
art.
[0369] The term substantially free of cellular material includes
preparations of proteins in which the protein is separated from
cellular components of the cells from which it is isolated or
recombinantly-produced. In one embodiment, the term substantially
free of cellular material includes preparations of protease
proteins having less than about 30% (by dry weight) of non-protease
proteins (also referred to herein as a contaminating protein),
generally less than about 20% of non-protease proteins or 10% of
non-protease proteins or less that about 5% of non-protease
proteins. When the protease protein or active portion thereof is
recombinantly produced, it also is substantially free of culture
medium, i.e., culture medium represents less than, about, or equal
to 20%, 10% or 5% of the volume of the protease protein
preparation.
[0370] As used herein, the term substantially free of chemical
precursors or other chemicals includes preparations of protease
proteins in which the protein is separated from chemical precursors
or other chemicals that are involved in the synthesis of the
protein. The term includes preparations of protease proteins having
less than about 30% (by dry weight), 20%, 10%, 5% or less of
chemical precursors or non-protease chemicals or components.
[0371] As used herein, production by recombinant methods by using
recombinant DNA methods refers to the use of the well-known methods
of molecular biology for expressing proteins encoded by cloned
DNA.
[0372] As used herein, vector (or plasmid) refers to discrete
elements that are used to introduce heterologous nucleic acid into
cells for either expression or replication thereof. The vectors
typically remain episomal, but can be designed to effect
integration of a gene or portion thereof into a chromosome of the
genome. Also contemplated are vectors that are artificial
chromosomes, such as bacterial artificial chromosomes, yeast
artificial chromosomes and mammalian artificial chromosomes.
Selection and use of such vehicles are well known to those of skill
in the art.
[0373] As used herein, expression refers to the process by which
nucleic acid is transcribed into mRNA and translated into peptides,
polypeptides, or proteins. If the nucleic acid is derived from
genomic DNA, expression can, if an appropriate eukaryotic host cell
or organism is selected, include processing, such as splicing of
the mRNA.
[0374] As used herein, an expression vector includes vectors
capable of expressing DNA that is operatively linked with
regulatory sequences, such as promoter regions, that are capable of
effecting expression of such DNA fragments. Such additional
segments can include promoter and terminator sequences, and
optionally can include one or more origins of replication, one or
more selectable markers, an enhancer, a polyadenylation signal, and
the like. Expression vectors are generally derived from plasmid or
viral DNA, or can contain elements of both. Thus, an expression
vector refers to a recombinant DNA or RNA construct, such as a
plasmid, a phage, recombinant virus or other vector that, upon
introduction into an appropriate host cell, results in expression
of the cloned DNA. Appropriate expression vectors are well known to
those of skill in the art and include those that are replicable in
eukaryotic cells and/or prokaryotic cells and those that remain
episomal or those which integrate into the host cell genome.
[0375] As used herein, vector also includes "virus vectors" or
"viral vectors." Viral vectors are engineered viruses that are
operatively linked to exogenous genes to transfer (as vehicles or
shuttles) the exogenous genes into cells.
[0376] As used herein, "operably" or "operatively linked" when
referring to DNA segments means that the segments are arranged so
that they function in concert for their intended purposes, e.g.,
transcription initiates downstream of the promoter and upstream of
any transcribed sequences. The promoter is usually the domain to
which the transcriptional machinery binds to initiate transcription
and proceeds through the coding segment to the terminator.
[0377] As used herein, a human protein is one encoded by a nucleic
acid molecule, such as DNA, present in the genome of a human,
including all allelic variants and conservative variations thereof.
A variant or modification of a protein is a human protein if the
modification is based on the wildtype or prominent sequence of a
human protein.
[0378] As used herein, a "composition" refers to any mixture of two
or more products or compounds. It can be a solution, a suspension,
liquid, powder, a paste, aqueous, non-aqueous, or any combination
thereof.
[0379] As used herein, "a combination" refers to any association
between two or among more items or elements, for example, two or
more items that can be used together. For example, a combination
can include an ADA2 protein and another therapeutic agent. Such
combinations can be packaged as kits.
[0380] As used herein, a kit is a packaged combination, optionally,
including instructions for use of the combination and/or other
reactions and components for such use.
[0381] As used herein, an "article of manufacture" is a product
that is made and sold. As used throughout this application, the
term is intended to encompass ADA2 proteins, for example variant
ADA2 proteins contained in articles of packaging.
[0382] As used herein, direct administration refers to a
composition that is administered without dilution.
[0383] As used herein, a single dosage formulation refers to a
formulation for use only once. Typically, a single dosage
formulation is for direct administration.
[0384] As used herein, a multiple dosage formulation refers to a
formulation for use in repeat administrations.
[0385] As used herein, when referencing dosage based on mg/kg of
the subject, an average human subject is considered to have a mass
of about 70 kg-75 kg, such as 70 kg and a body surface area (BSA)
of 1.73 m.sup.2.
[0386] As used herein, "disease or disorder" refers to a
pathological condition in an organism resulting from cause or
condition including, but not limited to, infections, acquired
conditions, genetic conditions, and characterized by identifiable
symptoms. Diseases and disorders of interest herein include any
associated with aberrant or high adenosine levels.
[0387] As used herein, a tumor, also known as a neoplasm, is an
abnormal mass of tissue that results when cells proliferate at an
abnormally high rate. Tumors can show partial or total lack of
structural organization and functional coordination with normal
tissue. Tumors can be benign (not cancerous), or malignant
(cancerous). As used herein, a tumor is intended to encompass
hematopoietic tumors as well as solid tumors.
[0388] Malignant tumors can be broadly classified into three major
types. Carcinomas are malignant tumors arising from epithelial
structures (e.g. breast, prostate, lung, colon, pancreas). Sarcomas
are malignant tumors that originate from connective tissues, or
mesenchymal cells, such as muscle, cartilage, fat or bone.
Leukemias and lymphomas are malignant tumors affecting
hematopoietic structures (structures pertaining to the formation of
blood cells) including components of the immune system. Other
malignant tumors include, but are not limited to, tumors of the
nervous system (e.g. neurofibromatomas), germ cell tumors, and
blastic tumors.
[0389] As used herein, neoplastic disease refers to any disorder
involving cancer, including tumor development, growth, metastasis
and progression.
[0390] As used herein, cancer is a term for diseases caused by or
characterized by any type of malignant tumor, including metastatic
cancers, lymphatic tumors, and blood cancers. Exemplary cancers
include, but are not limited to, cancers of the bladder, brain,
breast, bone marrow, cervix, colon/rectum, kidney, liver,
lung/bronchus, ovary, pancreas, prostate, skin, stomach, thyroid,
or uterus.
[0391] As used herein, "intravenous administration" refers to
delivery of a therapeutic directly into a vein.
[0392] As used herein, a control refers to a sample that is
substantially identical to the test sample, except that it is not
treated with a test parameter, or, if it is a plasma sample, it can
be from a normal volunteer not affected with the condition of
interest. A control also can be an internal control.
[0393] As used herein, normal levels or values can be defined in a
variety of ways known to one of skill in the art. Typically, normal
levels refer to the expression levels of a marker (e.g. adenosine,
ADR or nucleosidase) across a healthy population. The normal levels
(or reference levels) are based on measurements of healthy
subjects, such as from a specified source (i.e., blood, serum,
tissue, or other source). Often, a normal level will be specified
as a "normal range", which typically refers to the range of values
of the median 95% of the healthy population. Reference value is
used interchangeably herein with normal level but can be different
from normal levels depending on the subjects or the source.
Reference levels are typically dependent on the normal levels of a
particular segment of the population. Thus, for purposes herein, a
normal or reference level is a predetermined standard or control by
which a test patient can be compared.
[0394] As used herein, elevated level refers to the any level of
amount or expression of a marker above a recited or normal
threshold.
[0395] As used herein, biological sample refers to any sample
obtained from a living or viral source or other source of
macromolecules and biomolecules, and includes any cell type or
tissue of a subject from which nucleic acid or protein or other
macromolecule can be obtained. The biological sample can be a
sample obtained directly from a biological source or to sample that
is processed. For example, isolated nucleic acids that are
amplified constitute a biological sample. Biological samples
include, but are not limited to, body fluids, such as blood,
plasma, serum, cerebrospinal fluid, synovial fluid, urine and
sweat, and tissue and organ samples from animals, including
biopsied tumor samples.
[0396] As used herein, detection includes methods that permit
visualization (by eye or equipment) of a protein or marker. A
protein can be visualized using an antibody specific to the
protein. Detection of a protein can also be facilitated by fusion
of a protein with a tag including an epitope tag or label.
[0397] As used herein, "treating" a subject with a disease or
condition means that the subject's symptoms are partially or
totally alleviated, or remain static following treatment. Hence
treatment encompasses prophylaxis, therapy and/or cure. Prophylaxis
refers to prevention of a potential disease and/or a prevention of
worsening of symptoms or progression of a disease.
[0398] As used herein, a pharmaceutically effective agent includes
any therapeutic agent or bioactive agents, including, but not
limited to, for example, chemotherapeutics, anesthetics,
vasoconstrictors, dispersing agents, conventional therapeutic
drugs, including small molecule drugs and therapeutic proteins.
[0399] As used herein, treatment means any manner in which the
symptoms of a condition, disorder or disease or other indication,
are ameliorated or otherwise beneficially altered.
[0400] As used herein, therapeutic effect means an effect resulting
from treatment of a subject that alters, typically improves or
ameliorates the symptoms of a disease or condition or that cures a
disease or condition. A therapeutically effective amount refers to
the amount of a composition, molecule or compound which results in
a therapeutic effect following administration to a subject.
[0401] As used herein, amelioration of the symptoms of a particular
disease or disorder by a treatment, such as by administration of a
pharmaceutical composition or other therapeutic, refers to any
lessening, whether permanent or temporary, lasting or transient, of
the symptoms or, adverse effects of a condition, such as, for
example, reduction of adverse effects associated with or that occur
upon administration of an ADA2, such as a variant ADA2.
[0402] As used herein, prevention or prophylaxis refers to
reduction in the risk of developing a disease or condition.
[0403] As used herein, a "therapeutically effective amount" or a
"therapeutically effective dose" refers to the quantity of an
agent, compound, material, or composition containing a compound
that is at least sufficient to produce a therapeutic effect. Hence,
it is the quantity necessary for preventing, curing, ameliorating,
arresting or partially arresting a symptom of a disease or
disorder.
[0404] As used herein, unit dose form refers to physically discrete
units suitable for human and animal subjects and packaged
individually as is known in the art.
[0405] As used herein, the term "subject" refers to an animal,
including a mammal, such as a human being. The subject can include
any animal, such as, but are not limited to primates including
humans, gorillas and monkeys; rodents, such as mice and rats; fowl,
such as chickens; ruminants, such as goats, cows, deer, sheep; pigs
and other animals. Non-human animals exclude humans as the
contemplated animal.
[0406] As used herein, a patient refers to a human subject
exhibiting symptoms of a disease or disorder.
[0407] As used herein, about the same means within an amount that
one of skill in the art would consider to be the same or to be
within an acceptable range of error. For example, typically, for
pharmaceutical compositions, within at least 1%, 2%, 3%, 4%, 5% or
10% is considered about the same. Such amount can vary depending
upon the tolerance for variation in the particular composition by
subjects.
[0408] As used herein, the singular forms "a," "an" and "the"
include plural referents unless the context clearly dictates
otherwise. Thus, for example, reference to a compound comprising or
containing "an extracellular domain" includes compounds with one or
a plurality of extracellular domains.
[0409] As used herein, ranges and amounts can be expressed as
"about" a particular value or range. About also includes the exact
amount. Hence "about 5 bases" means "about 5 bases" and also "5
bases."
[0410] As used herein, "optional" or "optionally" means that the
subsequently described event or circumstance does or does not
occur, and that the description includes instances where said event
or circumstance occurs and instances where it does not. For
example, an optionally substituted group means that the group is
unsubstituted or is substituted.
[0411] As used herein, the abbreviations for any protective groups,
amino acids and other compounds, are, unless indicated otherwise,
in accord with their common usage, recognized abbreviations, or the
IUPAC-IUB Commission on Biochemical Nomenclature (see, (1972)
Biochem. 11:1726).
B. ADENOSINE DEAMINASE 2 (ADA2) AND MODULATION OF
ADENOSINE-MEDIATED TUMOR IMMUNOSUPPRESSION
[0412] Provided herein are methods of treating diseases or
conditions such as a cancer or a tumor by administering any
Adenosine Deaminase 2 (ADA2) protein, including variants or
conjugates thereof, to a subject. Extracellular adenosine is
responsible for the regulation of critical biological processes,
such as immunomodulation (Blay, J. (2012) Encyclopedia of Cancer
pp. 49-52). In pathophysiological conditions such as the tumor
microenvironment (TME), extracellular adenosine concentration
rapidly increases in certain parts of the TME, generating an
immunosuppressive niche that promotes tumor growth. ADA2 modulates
adenosine levels in the extracellular environment, thereby
affecting adenosine signaling and adenosine-dependent
immunosuppression. ADA2 can decrease the extracellular adenosine
levels by converting adenosine to inosine, to overcome the
immunosuppressive effects in the TME. For example, as shown herein,
administration of ADA2 can reverse the adenosine-dependent
immunosuppression and can reduce tumor growth in vivo.
[0413] 1. Tumor Immunity and Immune Evasion
[0414] Cancerous cells contain tumor-specific antigens that are
recognized by the immune system. In tumor immunity, the goal of the
immune system is to attack and eradicate these cancerous cells
through the actions of immune cells, including cytotoxic T cells,
Natural Killer (NK) cells and macrophages. For example, CD4+ and
CD8+ T cells can become activated upon recognition of antigenic
peptides presented on antigen-presenting cells on major
histocompatibility complex (MHC) class I or class II molecules,
respectively. Activated CD8+ cells, or cytotoxic T cells, can kill
tumor cells expressing the antigen, which can be helped by the
presence of CD4+ T cells. In addition to the direct killing effects
of cytotoxic T cells, T cells also produce various cytokines and
chemokines that can recruit other effector immune cells, such as
neutrophils, macrophages or NK cells to the tumor microenvironment.
NK cells also can directly kill cancer cells.
[0415] Studies have demonstrated that the immune system can prevent
tumor growth. For example, immunodeficient mice develop more
cancers than wild-type mice (Dunn et al. (2004) Immunity,
21:137-48). Lymphocytes and IFN-gamma have been shown to
collaborate to prevent the formation of carcinogen-induced sarcoma
and spontaneous epithelial carcinomas (Shankaran et al. (2001)
Nature, 410:1107-1111). Further, gene-targeted and lymphocyte
subset-depleted mice have demonstrated a role for NK cells in tumor
rejection. For example, mice depleted for both NK and NK1.1+ T
cells were found to have increased susceptibility to tumor
formation compared to control mice, and a similar result was
observed upon treatment of mice with antisialo-GM1, which
selectively eliminates NK cells (Smyth et al. (2001) Int Immunol.,
13; 459-63). In addition, the number, type and location of tumor
immune infiltrates in primary tumors are prognostic factors for
survival of cancer in human patients (Pages et al. (2005) N Engl J
Med, 353:2654-2666).
[0416] Most tumors, however, can evade the immune system. The tumor
microenvironment is complex, and includes a variety of
immunosuppressive mechanisms that can be intrinsic to tumor cells
or mediated by other cells or molecules. Through these mechanisms,
alone or in combination, the immune system can promote tumor
progression. These mechanisms include, but are not limited to,
eliminating tumor cell antigens that elicit immune response;
preventing or downregulating the expression of ligands required for
immune activation, such as major histocompatibility complex class I
(MHC I); production of immunosuppressive mediators, such as
interleukin-10 (IL-10), transforming growth factor-0 or adenosine;
recruitment of immune cell subsets that suppress effector immune
cell function, such as T regulatory cells (Tregs) or
myeloid-derived suppressor cell (MDSC); or the upregulation of
checkpoint inhibitors, such as cytotoxic T-lymphocyte antigen 4
(CTLA4), that can attenuate effector T-cell function. For example,
adenosine is a prominent immunosuppressive agent in the tumor
microenvironment.
[0417] 2. Adenosine Immunomodulation in Cancer and Tumor
Microenvironment (TME)
[0418] Adenosine (adenine-9-.beta.-D-ribofuranoside; Ado) is a
nucleoside that exists as a part of adenine nucleotides (AMP, ADP,
and ATP) which participate widely in cellular energy metabolism and
act as precursor molecules in many processes. Adenosine can exist
in the free form both inside and outside of cells.
[0419] Adenosine is an important in vivo signaling molecule,
especially for the immune system. In particular, adenosine is a
well-known effector of immune function. In T-cells, adenosine
decreases T-cell receptor induced activation of NF-.kappa.B, and
inhibits IL-2, IL-4, and IFN-.gamma.. Adenosine decreases T-cell
cytotoxicity, increases T-cell anergy, and increases T-cell
differentiation to Foxp3.sup.+ or Lag-3.sup.+ regulatory T cells.
Adenosine decreases IFN-.gamma. production by NK cells and
suppresses NK cell cytotoxicity. Adenosine blocks neutrophil
adhesion and extravasation, decreases phagocytosis, and attenuates
levels of superoxide and nitric oxide. Adenosine also decreases the
expression of TNF-.alpha., IL-12, and MIP-1.alpha. on macrophages,
attenuates MHC Class II expression, and increases levels of IL-10
and IL-6. In addition, adenosine decreases phagocytosis and
superoxide and nitric oxide levels on macrophages (Stagg and Smyth
(2010) Oncogene 29:5346-5358).
[0420] FIG. 2 sets forth the biosynthesis and catabolism of
adenosine. Extracellular adenosine is produced by the sequential
activities of membrane associated ectoenzymes, CD39 and CD73, which
together produce adenosine by phosphohydrolysis of ATP or ADP
produced from dead or dying cells. CD39 (also called ectonucleoside
triphosphate diphosphohydrolase; SEQ ID NO:542) converts
extracellular ATP (or ADP) to 5'AMP. Then, CD73 (also called
5'nucleotidase; SEQ ID NO:543) converts 5'AMP to adenosine. The
activity of CD39 is reversible by the actions of NDP kinase and
adenylate kinase, whereas the activity of CD73 is irreversible.
CD39 and CD73 are expressed on tumor stromal cells, including
endothelial cells and Tregs, and also on many cancer cells. For
example, the expression of CD39 and CD73 on endothelial cells is
increased under the hypoxic conditions of the tumor
microenvironment. Tumor hypoxia can result from inadequate blood
supply and disorganized tumor vasculature, impairing delivery of
oxygen (Carroll and Ashcroft (2005), Expert. Rev. Mol. Med.
7(6):1-16). Hypoxia also inhibits adenylate kinase (AK), which
converts adenosine to AMP, leading to very high extracellular
adenosine concentration. Thus, adenosine is released at high
concentrations in response to hypoxia, which is a condition that
frequently occurs the tumor microenvironment (TME), in or around
solid tumors.
[0421] Thus, while the concentration of adenosine is typically low
in the tissues and blood, the local adenosine concentration can
increase significantly as a result of damage or stress, e.g.,
inflammation, ischemia, and hypoxia. For example, the extracellular
concentration of adenosine in the hypoxic tumor microenvironment
can be up to 10 .mu.M adenosine, which is up to about 100-fold
higher than the typical extracellular adenosine concentration of
approximately 0.1 .mu.M (Antonioli et al. (2013) Nat Rev Can
13:842-857). Since the hypoxic regions in tumors are centered
around the microvessels, the local concentration of adenosine in
regions of the tumor can actually be higher.
[0422] Adenosine immunomodulation activity occurs after its release
into the extracellular space of the tumor and activation of
adenosine receptors (ADRs) on the surface of target immune cells,
cancer cells or endothelial cells. There are four types of ADRs,
A.sub.1 (SEQ ID NO:533), A.sub.2A (SEQ ID NO:534), A.sub.2B (SEQ ID
NO:535) and A.sub.3 (SEQ ID NOS:536-538), which are each G-protein
coupled receptors with different affinity for adenosine and
different downstream signaling pathways. Activation of the A.sub.1
and A.sub.3 receptors decrease intracellular cyclic AMP (cAMP)
levels, and the activation of A.sub.2A and A.sub.2B receptors
increase cAMP levels through the activation of adenylyl cyclase.
Each of the A.sub.1, A.sub.2A, and A.sub.3 can be activated at
physiological concentrations of adenosine (e.g. 30-300 nM), but
A.sub.2B has a lower affinity for adenosine and requires higher
levels of adenosine for activation (Stagg et al. (2010) Oncogene,
29:5346-5358). The result of activation of the ADRs differs
depending on the cell type and the receptor type: it can lead to
activation or suppression of cell function and cell death
(Antonioli et al. (2013) Nat Rev Can 13:842-857). All four types of
receptors can exist on cells in the tumor microenvironment,
including on cancer cells, stromal cells, endothelial cells, and
inflammatory and immune cells, and all can be activated at
adenosine concentrations present in the tumor microenvironment.
[0423] The high adenosine levels in the tumor microenvironment
results in local immunosuppression, which limits the capacity of
the immune system to eliminate cancer cells. For example, adenosine
can suppress various functions of T lymphocytes, natural killer
(NK) cells, polymorphonuclear granulocytes, and phagocytic cells
such as tissue macrophages. In particular, the A.sub.2A receptor is
known to be expressed on monocytes, macrophages, mast cells,
granulocytes, lymphocytes, dendritic cells (DCs), NK cells and
endothelial cells, and its expression on many cell types is induced
by hypoxia (Stagg and Smyth (2010) Oncogene, 29:5346-5358).
Activation of A.sub.2A has been shown to suppress NK cell
functions, inhibit T-cell proliferation, inhibit T cell
cytotoxicity and cytokine production, and inhibit macrophage
activation (Stagg and Smyth (2010); Antonioli et al. (2013)).
Activation of A.sub.2B has been shown to suppress DC
differentiation to limit T cell activation and to promote expansion
and accumulation of MSDC (Stagg and Smyth (2010); Antonioli et al.
(2013)).
[0424] In addition to direct effects to inhibit the immune system,
adenosine also can control cancer cell growth and dissemination by
effects on cancer cell proliferation, apoptosis and angiogenesis.
For example, adenosine can promote angiogenesis, primarily through
the stimulation of A.sub.2A and A.sub.2B receptors. Stimulation of
the receptors on endothelial cells can regulate the expression of
intercellular adhesion molecule 1 (ICAM-1) and E-selectin on
endothelial cells, maintain vascular integrity, and promote vessel
growth (Antonioli et al. (2013)). In addition, activation of one or
more of A.sub.2A, A.sub.2B or A.sub.3 on various cells by adenosine
can stimulate the production of the pro-angiogenic factors, such as
vascular endothelial growth factor (VEGF), interleukin-8 (IL-8) or
angiopoietin 2 (Antonioli et al. (2013)).
[0425] Adenosine also can directly regulate tumor cell
proliferation, apoptosis and metastasis through interaction with
receptors on cancer cells. For example, studies have shown that the
activation of A.sub.1 and A.sub.2A receptors promote tumor cell
proliferation in some breast cancer cell lines, and activation of
A.sub.2B receptors have cancer growth-promoting properties in
colonic carcinoma cells (Antonioli et al. (2013)). Adenosine also
can trigger apoptosis of cancer cells, and various studies have
correlated this activity to activation of the extrinsic apoptotic
pathway through A.sub.3 or the intrinsic apoptotic pathway through
A.sub.2A and A.sub.2B (Antonioli et al. (2013)). In addition,
adenosine can promote tumor cell migration and metastasis, by
increasing cell motility, adhesion to the extracellular matrix, and
expression of cell attachment proteins and receptors to promote
cell movement motility.
[0426] 3. Adenosine Deaminase and Targeting Adenosine in Treatment
of Cancer
[0427] The levels of adenosine can be regulated by the actions of
adenosine deaminase (ADA), which is an enzyme that converts
adenosine to inosine or 2'-deoxyadenosine to 2'-deoxyinosine. In
particular, ADA converts either adenosine or deoxyadenosine, in the
presence or water, into inosine or dexoyinosine and ammonia as
follows: adenosine+H.sub.2O=inosine+NH.sub.3 or
2'-deoxyadenosine+H.sub.2O=2'-deoxyinosine+NH.sub.3. The increase
in ammonia in the local tumor microenvironment can increase the
pH.
[0428] There are two types of ADA in humans, ADA1 and ADA2. ADA1 is
ubiquitously present inside cells, and exhibits a similar binding
affinity for adenosine and 2'deoxyadenosine with a Km of about
5.2.times.10.sup.-5 M. ADA1 principally functions intracellularly,
to reduce the levels of adenosine that can be toxic to cells, such
as lymphocytes. For example, deficiency of adenosine deaminase 1
(ADA1) is associated with mild immunodeficiency to severe combined
immunodeficiency (SCID), due to the toxic accumulation of adenosine
in immature lymphoid cells, thereby resulting in apoptotic death of
lymphocytes and a profound depletion of T, B, and NK cells
(Hershfield, M. S. (2005) Eur. J. Immunol. 35:25-30). In contrast,
ADA2 contains a secretion signal sequence, and is the predominant
extracellular ADA. The majority of ADA activity in normal human
serum or plasma are from ADA2 (Neidzwicki and Aberneth (1991)
Biochemical Pharmacology 41:1615-1624). ADA2 has a much lower
binding affinity for adenosine with a Km of about
200.times.10.sup.-5 M, and exhibits even weaker affinity for
2'deoxyadenosine. Also, unlike ADA1, ADA2 has an acidic pH
optimum.
[0429] Decreasing the tumor-specific accumulation of adenosine in
the TME is an attractive therapeutic option for treating tumors and
cancers. It is found herein that recombinant forms of ADA2 can be
administered to a subject to selectively target the TME, where it
can decrease the extracellular adenosine levels by deaminating
adenosine to inosine, thereby reversing the immunosuppressive
effect of adenosine. In particular, ADA2 is an extracellular
adenosine deaminase adapted for high adenosine concentrations. As
discussed above, adenosine is actively produced in the TME, and
regions of the TME can have up to about a 100-fold higher adenosine
concentration than other tissue environments. Because of the
hydrophobic subpocket for substrate binding, discussed further
below, the K.sub.m of ADA2 for adenosine is approximately 100 times
higher than that of ADA1. The turnover rate (k.sub.cat), however,
is similar to that of ADA1. Because ADA2 has a similar turnover
rate but a lower affinity to adenosine, it can be specifically
active in environments with high adenosine concentrations, such as
the TME or site of inflammation, without affecting adenosine
metabolism in normal microenvironments that have lower adenosine
concentrations.
[0430] The results herein demonstrate that recombinant ADA2 is
selectively targeted to the tumor environment. In addition, results
provided herein confirm that adenosine-mediates immunosuppression
in T cells and NK cells, and that this suppression can be reversed
by administered adenosine deaminase 2 (ADA2). The selective
activity of ADA2 for decreasing adenosine levels in the TME can
limit undesired or unwanted side effects, which can occur if the
activity of ADA2 were more ubiquitous. For example, many existing
tumor therapeutics are limited because they can result in adverse
side effects in the subject due to lack of specificity or
selectivity. The use of ADA2, or variants or conjugates thereof, in
methods provided herein can result in fewer or lesser undesirable
side-effects and/or exhibit improved efficacy by virtue of the
ability to dose higher.
[0431] Thus, ADA2 offers advantages compared to ADA1. In addition
to differences in binding affinity for adenosine that permits the
use of ADA2 as a selective tumor-targeting molecule, ADA1 also is
not adapted for use in an extracellular environment. For example,
ADA1 is primarily intracellular in vivo and is substantially less
stable in the extracellular environment, such as in the plasma, as
shown in the results provided herein. In contrast, ADA2 shows
increased stability in the extracellular environment due to the
extensive glycosylation that protect the molecule from proteolysis
in the extracellular environment and conserved disulfide bonds.
ADA2 also is substantially more stable at higher temperature
compared to ADA1 (Daddona and Kelley (1981) Biochim. Biophys. Acta
658:280-290). It is found herein that ADA2 has a higher thermal
stability, and that ADA2 is also more stable than ADA1 in
extracellular environments, such as the plasma.
[0432] ADA2 also shows optimal activity in environments commonly
found in the TME, such as environments having an acidic pH. For
example, the optimal pH of wildtype ADA2 is approximately pH 6.5,
whereas it is pH 7.5 for ADA'. The TME is a complex
microenvironment in and surrounding the tumor that is made of
diverse cell types and extracellular conditions. The TME commonly
has regions where the extracellular environment is acidic, caused
by lactic acid and other acidic metabolites produced by anaerobic
glycolysis in hypoxic conditions of the tumor (Kato et al. (2013)
Cancer Cell International 13:89).
[0433] In addition, ADA2 also overcomes other problems encountered
with existing therapeutics, including those that target adenosine.
For example, since adenosine has multiple receptors, it is
difficult to target adenosine using an anti-ADR antibody, since all
four ADR receptors are present in the TME and can be activated by
adenosine. Hence, targeting of a single receptor would not achieve
complete attenuation of adenosine immunomodulation activity.
[0434] Thus, the methods provided include methods of treatment
using any ADA2, for example recombinant human ADA2 (rHuADA2) or
variants and/or conjugates thereof, for treatment of diseases or
conditions, such as a cancer or a tumor and other diseases or
conditions involving aberrant or accumulated production of
adenosine. Also provided herein are ADA2 variants and modified
forms that possess altered properties, such as decreased heparin
binding, increased catalytic efficiency, increased stability,
altered glycosylation state and/or altered pH optimum. Any of the
ADA2 proteins can be used in the methods of treatment provided
herein. Also provided herein are methods of combination therapy
using any ADA2 and other immunomodulatory agents, chemotherapeutic
agents, immune checkpoint inhibitors or hyaluronan-degrading
enzyme, such as a soluble hyaluronidase or polymer-conjugated
soluble hyaluronidase (e.g. PEGPH20).
C. ADENOSINE DEAMINASE 2 (ADA2) AND VARIANTS THEREOF
[0435] Provided herein are methods of treatment using an adenosine
deaminase 2 (ADA2), including wildtype human ADA2, ADA2 variants
and/or conjugates or other modified forms thereof. Also provided
herein are variants of ADA2 with altered properties. ADA2 can be
used to regulate adenosine levels in environments where regulation
of adenosine-dependent immunomodulation or other
adenosine-dependent activity is needed, such as in a tumor
microenvironment or for inflammation.
[0436] 1. Structure and Activity of ADA2
[0437] Adenosine deaminases are enzymes that convert adenosine to
inosine. There are three known ADAs: ADA1, ADA2 and ADA3, although
the activity of ADA3 is not known. With respect to proteins with
known adenosine deaminase activity, humans have both ADA2 and ADA1,
whereas in flies, homologues of ADA2 (known as ADGF homologues) are
the only active adenosine deaminase enzymes, and rodents only have
ADA1, indicating that the two proteins have overlapping yet also
distinct functions. Distinct functions relate to the difference in
expression, cellular location and kinetic properties of the
enzymatic activity, difference in other structural features, as
well as the additional growth factor and heparin binding properties
(Zavialov et al. (2010) J. Biol. Chem. 285:12367-12377).
[0438] ADA1 and ADA2 are structurally similar, and exhibit a shared
catalytic mechanism to convert adenosine to inosine, but exhibit
little sequence similarity. ADA2 has a nucleotide sequence set
forth in SEQ ID NO:1, which encodes a 511 amino acid protein, set
forth in SEQ ID NO:2, that contains a signal sequence
(corresponding to amino acid residues 1-29 of SEQ ID NO:2). Mature
ADA2 is a secreted protein that lacks the signal sequence and has
the sequence of amino acids set forth in SEQ ID NO:5. ADA1 has a
nucleotide sequence set forth in SEQ ID NO:11, which encodes a 363
amino acid protein that does not contain a signal sequence, and has
the sequence of amino acids set forth in SEQ ID NO:12. The
N-terminal methionine residue is cleaved, resulting in the mature
362 amino acid protein, set forth in SEQ ID NO:66.
[0439] As discussed in more detail below, compared to ADA1, ADA2 is
considerably longer and includes an 80-100-amino acid extension at
the N terminus that is involved in dimerization and
glycosaminoglycan (e.g. heparin) binding (Maier et al. (2005) Mol
Evol 61:776-794). ADA2 also has an additional putative receptor
binding (PRB) domain that is reported to mediate binding to cell
surface receptors and/or contribute to its growth factor or other
signaling functions. Also, unlike ADA1, ADA2 is dimeric and
secreted, whereas ADA1 is monomeric and largely intracellular. ADA2
also is extensively glycosylated and has a conserved disulfide
bond. The structural and functional features of ADA2 offer
advantages as a therapeutic molecule, including, but not limited
to, greater stability and increased tumor selectivity. [0440] a.
Structure of ADA2
[0441] ADA2, also known as dendritic cell derived growth factor
(DCDGF) or adenosine deaminase growth factor (ADGF), is a member of
the adenosine ADGF family of proteins. ADA2 is found only in
eukaryotes, and primarily in multicellular organisms. In contrast,
ADA1 is found in both prokaryotes and eukaryotes. In particular
ADA2/ADGF homologs, have been characterized in insects and other
vertebrates such as Xenopus laevis, as well as in humans. ADGF
family proteins in insects were initially identified as proteins
having growth factor activity, and later found to also possess
adenosine deaminase activity.
[0442] In humans, ADA2 is encoded by the cat eye syndrome critical
region gene 1 (CECR1) gene (Riazi et al. (2000) Genomics
64:277-285). The human CECR1 gene (nucleotide sequence of the
coding region set forth in SEQ ID NO:1) encodes a 511 amino acid
precursor protein (sequence set forth in SEQ ID NO:2; Uniprot
Accession No. Q9NZK5). ADA2 has an N-terminal 29 residue signal
sequence (amino acid residues positions 1-29 of SEQ ID NO:2) that
is cleaved following transport to the ER to form the 482 amino acid
mature protein (sequence set forth in SEQ ID NO:5). The mature ADA2
protein exists as a homodimer due to nonpolar interactions between
two polypeptide chains. Other sequences of human ADA2 also have
been reported, see e.g. U.S. Pat. No. 5,968,780 (precursor form SEQ
ID NO:376 and mature form SEQ ID NO:380), NCBI Acc. No. BAG369969.1
(precursor form SEQ ID NO:377 and mature form SEQ ID NO:381); NCBI
Acc. No. AAF65941 (precursor form SEQ ID NO:378 and mature form SEQ
ID NO:382); and NCBI Acc. No. AAH51755 (precursor form SEQ ID
NO:379 and mature form SEQ ID NO:383). A non-canonical second
isoform, formed by alternative splicing of the mRNA, encodes a
shorter protein of 270 amino acids (sequence set forth in SEQ ID
NO:68; Uniprot Accession No. Q9NZK5-2), missing the N-terminal 241
amino acids and containing a 10-amino acid sequence in the
N-terminus that is different from the canonical isoform.
[0443] Exemplary ADA2 homologs in other species include, but are
not limited to, ADA2 from Pan troglodytes (chimpanzee; precursor
form SEQ ID NO:286, mature form SEQ ID NO:326; NCBI Acc. No.
XP_003317127.1); Gorilla gorilla (gorilla; precursor form SEQ ID
NO:287, mature form SEQ ID NO:327; NCBI Acc. No. XP.sub.--
004063024.1); Pan paniscus (pygmy chimpanzee; precursor form SEQ ID
NO:288, mature form SEQ ID NO:328; NCBI Acc. No. XP_003828345.1);
Pongo abelii (Sumatran orangutan; precursor form SEQ ID NO:289,
mature form SEQ ID NO:329; NCBI Acc. No. NP_001125360.1); Nomascus
leucogenys (Northern white-cheeked gibbon; precursor form SEQ ID
NO:290, mature form SEQ ID NO:330; NCBI Acc. No. XP_004088517.1);
Macaca fascicularis (crab-eating macaque; precursor form SEQ ID
NO:291, mature form SEQ ID NO:331; NCBI Acc. No. XP_005568111.1);
Chlorocebus sabaeus (green monkey; precursor form SEQ ID NO:292,
mature form SEQ ID NO:332; NCBI Acc. No. XP_007972990.1); Macaca
mulatta (Rhesus macaque; precursor form SEQ ID NOS:293, 337, mature
form SEQ ID NOS:333, 340; GenBank Acc. Nos. AFH32795.1,
EHH20002.1); Callithrix jacchus (marmoset; precursor form SEQ ID
NOS:294, 374, mature form SEQ ID NO:334, 375; NCBI Acc. No.
XP_009004591.1, XP_009004586.1); Xenopus laevis (African clawed
frog; precursor form SEQ ID NO:295, mature form SEQ ID NO:335; NCBI
Acc. No. NP_001090531.1); Drosophila melanogaster (fruit fly;
precursor form SEQ ID NOS:296-300, mature form SEQ ID NOS:336, 338,
339; AAL40913.1, AAL40920.1, AAL40911.1, AAL40912.1, and
AAL40910.1); Bombyx mori (silk moth; precursor form SEQ ID NO:301,
mature form SEQ ID NO:341; NCBI Acc. No. NP 001098698.1); and
Sarcophaga perigrina (flesh fly; precursor form SEQ ID NO:302,
mature form SEQ ID NO:342; GenBank Acc. No. BAA11812.1).
[0444] The domain organization of ADA2 is described in Zavialov et
al. (2010) J. Biol. Chem. 285:12367-12377. ADA2 contains a core ADA
domain or catalytic domain that makes up more than 70% of the amino
acid sequence, and is structurally similar to the ADA domain in
ADA1. In the monomer, the ADA domain is folded into eight strands
of parallel .alpha./.beta. barrels, which surround a central deep
pocket that is the active site. In addition, the ADA domain also
contains three additional helices located between the .beta.1
strand and the .alpha.1 helix (designated H1, H2 and H3) and two
additional helices at the C terminus (designated H4 and H5). The
ADA domain is contained in the region corresponding to residues
106-502 of the precursor ADA2 set forth in SEQ ID NO:2
(corresponding to residues 77-473 of the mature ADA2 set forth in
SEQ ID NO:5). In the ADA region, ADA2 contains insertions of amino
acid residues compared to ADA1, including residues that make up the
putative receptor-binding (PRB) domain (discussed below), and which
are not involved in the catalytic function of ADA2. The ADA domain
does not have high sequence homology with that of ADA1 (18-21%
identical residues), but the two ADA domains have high structural
similarity. Table 4 summarizes the residues in the active site
involved in substrate binding and catalysis.
TABLE-US-00004 TABLE 4 Residue (numbering of precursor set forth in
SEQ ID NO: 2) Active Site 112 Zn.sup.2+ coordination, catalytic 114
Zn.sup.2+ coordination, catalytic 115 substrate binding 116
substrate binding 204 substrate binding 207 substrate binding 208
substrate binding 211 substrate binding 293 substrate binding 325
substrate binding 326 substrate binding 356 Zn.sup.2+ coordination,
catalytic 359 active site proton donor, substrate binding 384
active site proton acceptor, substrate binding 415 substrate
binding 441 Zn.sup.2+ coordination, catalytic, substrate binding
442 substrate binding
[0445] Based on the crystal structure as reported in Zavialov et
al. (2010) J. Biol. Chem. 285:12367-12377 of ADA2 with coformycin
(CF), a transition state inhibitor that mimics the tetrahedral
intermediate at the C6 position of adenine, residues involved in
substrate binding have been identified. These include residues
D115, 1116, W204, F207, E208, F211, H293, V325, G326, E359, H384,
L415, D441, and D442 of precursor ADA2 set forth in SEQ ID NO:2
(corresponding to residues D86, 187, W175, F178, E179, F182, H254,
V296, G297, E330, H355, L386, D412 and D413 of mature ADA2 set
forth in SEQ ID NO:5). Although the structural features of the
catalytic site are similar between ADA2 and ADA1, the hydrophobic
substrate-binding subpocket in the ADA domain of ADA2 is more open
and contains fewer hydrophobic residues. These differences could
account for the lower affinity of ADA2 for adenosine.
[0446] ADA2 is a zinc-dependent hydrolase that requires
coordination with a bound zinc for activity, which acts as a
powerful electrophile activating the attacking water to a hydroxide
ion. Amino acid residues H112, H114, H356 and D441 of precursor
ADA2 set forth in SEQ ID NO:2 (corresponding to H83, H85, H327,
D412 of mature ADA2 set forth in SEQ ID NO:5) are involved in
coordinating the zinc active center. During catalysis, the
Zn.sup.++ promotes nucleophilic attack on the carbonyl carbon by
the oxygen atom of a water molecule at the active site. The
combination of E359, H384 and D441 of precursor ADA2 set forth in
SEQ ID NO:2 (corresponding to E330, H355 and D412 of mature ADA2
set forth in SEQ ID NO:5) participate as zinc ligands. H384 and
D441 position the attacking water, E359 is the active site
catalytic proton donor residue that facilitates the reaction by
extracting a proton from the attacking water molecule, and H384
serves as the proton acceptor. The catalytic active site residues
structurally mirror the corresponding active site residues of ADA1,
indicating that the catalytic mechanism is similar between the two
adenosine deaminases (Zavialov et al. (2010) J. Biol. Chem.
285:12367-12377).
[0447] Active ADA2 exists as a homodimer. Dimerization of ADA2 is
mediated by residues in the N-terminal .alpha.-helices of ADA2
designated HN1, HN2, HN3 and HN4 (corresponding to residues 29-105
of precursor ADA2 set forth in SEQ ID NO:2, or residues 1-76 of
mature ADA2 set forth in SEQ ID NO:5), as well as residues in the
C-terminal .alpha.-helix designated H5 (corresponding to residues
503-511 of precursor ADA2 set forth in SEQ ID NO:2 or residues
474-482 of mature ADA2 set forth in SEQ ID NO:5). Because these
regions are responsible for more than 70% of the nonpolar
intersubunit interaction, they are designated the dimerization
domain. The first N-terminal helix, HN1, forms a helix anchor due
to ionic interactions between residues R34 and E41 (residues R5 and
E12 of mature ADA2 set forth in SEQ ID NO:5) with D373 and H391
(residues D344 and H362 of mature ADA2 set forth in SEQ ID NO:5) of
the neighboring subunit, and hydrophobic interactions between
residues I30, T33, L37, L38, K40 and M44 (residues I1, T4, L8, L9,
K11 and M15 of mature ADA2 set forth in SEQ ID NO:5) with residues
in the neighboring subunit. A hydrophobic binding pocket is formed
with residues M71, A74, M75, L78 and F80, which accommodates the
W336 (residues M42, A45, M46, L49 and F51 of mature ADA2 set forth
in SEQ ID NO:5) residue from the neighboring subunit.
[0448] ADA1, which does not form a dimer, does not contain the
residues that make up the "dimerization domain." Also, compared to
ADA1, residue W336 in ADA2 is inserted into a region of the active
site between .beta.5 and .alpha.5, where it indirectly contributes
to catalytic activity due to its involvement in dimerization.
Substitution W336G results in an ADA2 molecule that partly
dissociates into monomers, and which exhibits altered catalytic
activity (Zavialov et al. (2010) J. Biol. Chem. 285:12367-12377).
In addition to affecting full enzymatic activity, dimerization also
is involved in the secretion of ADA2. Deletion of amino acids T33
and E41 (corresponding to T4 and E12 of mature ADA2 set forth in
SEQ ID NO:5) abolishes secretion of ADA2 into the culture medium
(Zavialov et al. (2010) J. Biol. Chem. 285:12367-12377).
[0449] ADA2 binds glycosaminoglycans (GAGs), including heparin and
its analogs, such as heparan sulfate, and chondroitin sulfate.
Protein dimerization results in a large, highly positively charged
surface at the interface of dimer, which forms the GAG-binding site
(Zavialov et al. (2010) J. Biol. Chem. 285:12367-12377). In
particular, the GAG-binding site involves amino acid residues near
positions I30-R45, S389-T396 and R422-T428 of precursor ADA2
(corresponding to I1-R16, S360-T367, and R393-T399 of mature ADA2
set forth in SEQ ID NO:5). The interaction with GAGs appears to
play a role in stabilizing the ADA2 dimer.
[0450] ADA2 has an insertion sequence within the catalytic domain,
designated the putative receptor-binding (PRB) domain, which is
reported to correspond to residues 127-185 or 134-177 of precursor
ADA2 set forth in SEQ ID NO:2 (positions 98-156 or 105-148,
respectively, of mature ADA2 set forth in SEQ ID NO:5). The PRB
domain folds into a chemokine-like domain made up of an .alpha.-
and .beta.-fold composed of a three-stranded antiparallel
.beta.-sheet surrounded by .alpha.-helices on one side and a
proline-rich loop on the other side. A disulfide bond between
positions 137 and 159 of precursor ADA2 (positions 108 and 130 of
mature ADA2 set forth in SEQ ID NO:5) is present in the PRB domain,
which is required for ADA2 secretion and structural stability. The
crystal structure of ADA2 shows that the PRB domain, while not
involved in the catalytic function of ADA2, sits on the top of the
adenosine deaminase (ADA) domain at the edge of the active site.
When ADA2 dimerizes, the two PRB domains in the dimer are present
on the same side of the dimer, and could bind dimeric receptors or
induce receptor dimerization (Zavialov et al. (2010) J. Biol. Chem.
285:12367-12377; Zavialov et al. (2010) J. Leukoc. Biol.
88:279-290). ADA2 binds adenosine receptors (ADRs) which are
dimeric receptors. The PRB domain is implicated in its growth
factor activity through the receptor binding activity (Zavialov et
al. (2010) J. Biol. Chem. 285:12367-12377; Zavialov et al. (2010)
J. Leukoc. Biol. 88:279-290). Thus, elimination or modification of
this domain can reduce, attenuate or eliminate this activity.
[0451] ADA2 has four (4) native N-linked glycosylation sites, at
N127, N174, N185 and N378 of precursor ADA2 (corresponding to N98,
N145, N156 and N349 of mature ADA2 set forth in SEQ ID NO:5). Three
N-glycosylation sites are present in the PRB domain, at N127, N174,
and N185, and one is present on the opposite side of the molecule,
at N378. The oligosaccharide chains located on three different
faces of the ADA2 molecule protects the enzyme against proteolysis
in the extracellular environment, providing increased stability
(Zavialov et al. (2010) J. Biol. Chem. 285:12367-12377).
[0452] b. Activities of ADA2
[0453] ADA2 has several activities. ADA2 has adenosine deaminase
(ADA) activity, which catalyzes adenosine to inosine
(adenosine+H.sub.2O=inosine+NH.sub.3) and 2'-deoxyadenosine to
2'-deoxyinosine
(2'-deoxyadenosine+H.sub.2O=2'-deoxyinosine+NH.sub.3) reactions.
Coformycin and 2'-deoxycoformycin are potent inhibitors of ADA1 and
ADA2. Due to differences in the substrate binding pocket, however,
the inhibitor (+)-erythro-9-(2-hydroxy-3-nonyl)adenine (EHNA)
selectively inhibits ADA1, but does not inhibit ADA2. Also, the
differences in the substrate binding pocket account for differences
in substrate binding affinity between ADA1 and ADA2. For example,
while the k.sub.cat values for adenosine are similar due to the
high structural similarity of the catalytic residues in ADA2 and
ADA1, the K.sub.m for adenosine are different. The K.sub.m of ADA2
for adenosine is approximately 2.25 mM. Because ADA2 has a
hydrophobic subpocket for substrate binding, the affinity for ADA2
for substrates is different from that of ADA1. The K.sub.m of ADA2
for adenosine is approximately 100 times higher than that of ADA1,
which is approximately 0.1 mM.
[0454] The optimal pH for activity of ADA2 is around pH 6.5, and
its activity decreases at a pH higher than 7 0 In contrast, the
optimal pH for ADA1 is around pH 7.5. Different substrate affinity
and pH optimum indicate that ADA2 is adapted for specific
microenvironments, and serve overlapping yet different functions in
regulation of adenosine concentration and signaling (Zavialov et
al. (2005) Biochem. J. 391:51-57). The acidic optimum pH for ADA2
and requirement for high adenosine concentration indicates that
ADA2 can be active specific environments, such as sites of
inflammation or tumors, where adenosine concentration is elevated
and pH is lower. In the tumor microenvironment, tumor cells can
undergo extensive glycolysis due to the hypoxic environment, and
the extracellular microenvironment becomes acidic (pH 6.5-6.9) in
certain regions.
[0455] In humans, ADA2 is widely expressed, with most abundant
expression in adult heart, lung, lymphoblasts, and placenta as well
as fetal lung, liver, and kidney. ADA2 is also detected in blood
plasma at the protein level. The majority of ADA activity in normal
human serum or plasma are from ADA2 (Neidzwicki and Aberneth (1991)
Biochemical Pharmacology 41:1615-1624). ADA2 is secreted by
activated cells, including activated monocytes and other immune
cells, and to a more limited extent, by unstimulated lymphocytes
(Iwaki-Egawa et al. (2006) Biol. Chem. 387:319-321). Immune cells,
such as monocytes, are activated in inflammatory sites and tumors,
where extracellular adenosine deaminase is accumulated (Sitkovsky
et al. (2004) Annu. Rev. Immunol. 22:657-682). ADA2 could be
involved in the regulation of adenosine levels in these specific
environments (Zavialov et al. (2010) J. Leukoc. Biol. 88:279-290).
For example, ADA2 could function to reduce the level of adenosine
in environments with high adenosine concentrations, such as at
inflammation sites or in the tumor microenvironment with hypoxic
conditions.
[0456] ADA2 activity is elevated in plasma from patients suffering
from liver diseases, such as chronic hepatitis and cirrhosis, AIDS,
adult T-cell leukemia, acute lymphoblastic leukemia, tuberculosis
and diabetes mellitus. (Zavialov et al. (2005) Biochem. J.
391:51-57). In addition, ADA2 levels are elevated in tuberculosis
pleural effusion in recent Mycobacterium tuberculosis (MTB)
infections (Valdez) or in visceral leishmaniasis (Tripathi et al.,
Clinica Chimica Acta 388 (2008) 135-138). The pleural effusion of
MTB infection contain a high number of macrophages and CD4+ cells,
indicating that ADA2 secretion by macrophages could modulate the
immune response during MTB infection (Zavialov et al. (2010) J.
Leukoc. Biol. 88:279-290).
[0457] ADA2 binds to the cell surface via GAG proteoglycans (e.g.
heparin) and ADRs. Heparin analogs such as heparan sulfate
proteoglycan (HSPG), or chondroitin sulfate (CS)-containing
proteoglycans are present on the cell surface and are involved in
protein localization and cell signaling. ADA2 can bind various
types of cells via these heparin analogs, and the binding is
tighter to a more highly sulfated heparin sulfate than to less
sulfated heparin, indicating that the binding involves extensive
ionic interaction. In contrast to ADA2, ADA1 does not bind to
heparin (Zavialov et al. (2005) Biochem. J. 391:51-57, Zavialov et
al. (2010) J. Biol. Chem. 285:12367-12377).
[0458] In addition to heparin analogs containing proteoglycans,
ADA2 dimer binds to adenosine receptors (ADRs), which function as
dimers (Zavialov et al. (2005) Biochem. J. 391:51-57, Zavialov et
al. (2010) J. Biol. Chem. 285:12367-12377). ADA2 is reported to
interact with cells to mediate growth factor activity. ADA2 can
also directly bind to some dimeric adenosine receptors, stimulate
proliferation of monocyte-activated CD4 T cells independently of
its catalytic activity, induce T cell-dependent differentiation of
monocytes into macrophages and stimulate macrophage proliferation.
For example, ADA2 increases the rate of proliferation of
monocyte-activated CD4 T cells independently of its catalytic
activity, and induces T cell-dependent differentiation of monocytes
into macrophages and stimulates macrophage proliferation (Zavialov
et al. (2010) J. Leukoc. Biol. 88:279-290).
[0459] Defects or deficiencies in ADA2 have been associated with
increased vascular inflammation and vasculopathy, in particular
associated with Polyarteritis nodosa or Sneddon syndrome (Zhou et
al. (2014) N. Engl. J. Med 370:911-920; Navon Elkan et al. (2014)
N. Engl. J. Med 370:921-931; Garg et al. (2014) Eur. J. Pediatr
173:827-830; Bras et al. (2014) New Eng. J. Med., 371:479-48; Belot
et al. (2014) Pediatric Rheumatology 12:44). For example,
vasculitis is associated with recessive mutations in the gene
encoding for ADA2 characterized by mutations G47A, G47R, G47V,
A109D, H112Q, V119A, G142S, R169Q, P193L, P251L, W264S, Y453C with
reference to precursor ADA2 set forth in SEQ ID NO:2 (Navon Elkan
et al. (2014) N. Engl. J. Med 370:921-931; Zhou et al. (2014) N.
Engl. J. Med 370:911-920; Bras et al. (2014) New Eng. J. Med.,
371:479-480).
[0460] 2. ADA2 Variants
[0461] Provided herein are variants or mutants of ADA2 containing a
polypeptide that contains one or more amino acid modifications
(i.e. changes in amino acid sequence) compared to a reference or
unmodified ADA2. The modifications can be in any reference or
unmodified ADA2 polypeptide, so long as the reference ADA2 does not
already contain the amino acid change at the modified position(s).
For example, the modification(s) can be in an ADA2 polypeptide that
contains the sequence of amino acids set forth in any of SEQ ID
NOS:5 or 326-336, 338-342, 375 or 380-383, a catalytically active
fragment thereof or a sequence of amino acids that exhibits at
least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%, 98%, 99% or more sequence identity to any of SEQ ID NOS:5 or
326-336, 338-342, 375 or 380-383 or a catalytically active fragment
thereof but does not contain the modification(s).
[0462] In particular examples, the modifications are in an ADA2
polypeptide set forth in SEQ ID NO:5, a catalytically active
fragment thereof or in a sequence of amino acids that exhibits at
least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%, 98%, 99% or more sequence identity to SEQ ID NO:5 or a
catalytically active fragment thereof but does not contain the
modification(s). For example, modifications can be in an ADA2
having a sequence of amino acids set forth in any of SEQ ID NOS:5,
326-334, 340, 375 or 380-383. Modifications also can be in a
catalytically active portion of SEQ ID NO:5. For example, a
catalytically active ADA2 can be one that lacks all or a portion of
the PRB domain, such as those set forth in any of SEQ ID
NOS:548-550 or 579. In particular examples, modifications are in a
human ADA2 containing the sequence of amino acids set forth in SEQ
ID NO:5.
[0463] In examples of a variant ADA2 polypeptide provided herein,
the variant ADA2 does not have the sequence of amino acids set
forth in any of SEQ ID NOS:1, 5, 68, 286-302, 326-342 or 374-383.
Also, in examples herein, the variant ADA2 polypeptide does not
contain modifications that are deletion R8-K14del.fwdarw.-- or that
are an amino acid replacement H7R, G18A, G18R, G18V, I64T, A80D,
H83Q, V90A, C108G, H121R, W133G, R140Q, K141R, P164L, P222L, W235S,
H306R, E330G, W333G, V365L, Y424C, F464S, with numbering with
reference to amino acid residues set forth in SEQ ID NO:5.
[0464] The variant ADA2 can be a monomer or can be a dimer, such as
a heterodimer or a homodimer. The variant ADA2 polypeptides
provided herein exhibit adenosine deaminase activity to catalyze
the conversion of adenosine to inosine. It is understood that such
activity is exhibited when the variant ADA2 polypeptide is in
active form, such as when it is present as a dimer. Typically, such
activity is present when the ADA2 is in dimer form. Hence, any of
the variants provided herein can be used to regulate adenosine
levels in environments where regulation of adenosine-dependent
immunomodulation or other adenosine-dependent activity is needed,
such as in a tumor microenvironment or for inflammation. Hence, any
of the variants provided herein can be used in methods of treating
tumor or cancer as described herein.
[0465] When in active form, such as when in dimer form, the variant
ADA2 containing the variant ADA2 polypeptide can exhibit about 50%
to 500%, such as about 50% to 400%, 50% to 300%, 50% to 200%, 50%
to 150%, 50% to 100%, 50% to 80%, 80% to 400%, 80% to 300%, 80% to
200%, 80% to 150%, 80% to 100%, 100% to 400%, 100% to 300%, 100% to
200% or 100% to 150% of the adenosine deaminase activity compared
to the corresponding form of the ADA2 polypeptide not containing
the modification(s) (i.e. the unmodified ADA2), such as an ADA2
homodimer containing the sequence of amino acids set forth in SEQ
ID NO:5, 326-334, 340, 375 or 380-383 or a catalytically active
fragment thereof. For example, when in active form, such as when in
dimer form, the variant ADA2 containing the variant ADA2
polypeptide can exhibit at least 50%, 60%, 70%, 75%, 80%, 85%, 90%,
95%, 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%,
200%, 210%, 220%, 230%, 240%, 250%, 260%, 270%, 280%, 290%, 300%,
350%, 400%, 450%, 500% or more of the adenosine deaminase activity
compared to the corresponding form of the ADA2 polypeptide not
containing the modification(s) (i.e. the unmodified ADA2), such as
an ADA2 homodimer containing the sequence of amino acids set forth
in SEQ ID NO:5, 326-334, 340, 375 or 380-383 or a catalytically
active fragment thereof. Typically, a variant ADA2 containing a
variant ADA2 polypeptide provided herein, when in dimer form,
retains adenosine deaminase activity of the corresponding form of
the ADA2 homodimer containing the sequence of amino acids set forth
in SEQ ID NO:5 or a catalytically active fragment thereof, such
that the variant ADA2, when in dimer form, exhibits at least 50%,
60%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 110%, 120%, 130%, 140%,
150%, 160%, 170%, 180%, 190%, 200%, 210%, 220%, 230%, 240%, 250%,
260%, 270%, 280%, 290%, 300%, 350%, 400%, 450%, 500% or more of the
adenosine deaminase activity of the ADA2 homodimer containing the
sequence of amino acids set forth in SEQ ID NO:5 or a catalytically
active fragment thereof.
[0466] Typically, the catalytic efficiency or k.sub.cat/K.sub.M
(M.sup.-1 s.sup.-1) of variant ADA2 containing a variant ADA2
polypeptide provided herein is at least 5,000, such is generally
from or from about 5.times.10.sup.3 to 5.times.10.sup.6,
5.times.10.sup.3 to 2.5.times.10.sup.6, 5.times.10.sup.3 to
1.times.10.sup.6, 5.times.10.sup.3 to 5.times.10.sup.5,
5.times.10.sup.3 to 2.5.times.10.sup.5, 5.times.10.sup.3 to
1.times.10.sup.5, 5.times.10.sup.3 to 8.times.10.sup.4,
5.times.10.sup.3 to 5.times.10.sup.4, 5.times.10.sup.3 to
2.5.times.10.sup.4, 5.times.10.sup.3 to 1.times.10.sup.4,
1.times.10.sup.4 to 5.times.10.sup.5, 1.times.10.sup.4 to
2.5.times.10.sup.5, 1.times.10.sup.4 to 1.times.10.sup.5,
1.times.10.sup.4 to 8.times.10.sup.4, 1.times.10.sup.4 to
5.times.10.sup.4, 1.times.10.sup.4 to 2.5.times.10.sup.4,
2.5.times.10.sup.4 to 5.times.10.sup.6, 2.5.times.10.sup.4 to
2.5.times.10.sup.6, 2.5.times.10.sup.4 to 1.times.10.sup.6,
2.5.times.10.sup.4 to 5.times.10.sup.5, 2.5.times.10.sup.4 to
2.5.times.10.sup.5, 2.5.times.10.sup.4 to 1.times.10.sup.5,
2.5.times.10.sup.4 to 8.times.10.sup.4, 2.5.times.10.sup.4 to
5.times.10.sup.4, 5.times.10.sup.4 to 5.times.10.sup.6,
5.times.10.sup.4 to 2.5.times.10.sup.6, 5.times.10.sup.4 to
1.times.10.sup.6, 5.times.10.sup.4 to 5.times.10.sup.5,
5.times.10.sup.4 to 2.5.times.10.sup.5, 5.times.10.sup.4 to
1.times.10.sup.5, 5.times.10.sup.4 to 8.times.10.sup.4,
8.times.10.sup.4 to 5.times.10.sup.6, 8.times.10.sup.4 to
2.5.times.10.sup.6, 8.times.10.sup.4 to 1.times.10.sup.6,
8.times.10.sup.4 to 5.times.10.sup.5, 8.times.10.sup.4 to
2.5.times.10.sup.5, 8.times.10.sup.4 to 1.times.10.sup.5,
1.times.10.sup.5 to 5.times.10.sup.6, 1.times.10.sup.5 to
2.5.times.10.sup.6, 1.times.10.sup.5 to 1.times.10.sup.6,
1.times.10.sup.5 to 5.times.10.sup.5, 1.times.10.sup.5 to
2.5.times.10.sup.5, 2.5.times.10.sup.5 to 5.times.10.sup.6,
2.5.times.10.sup.5 to 2.5.times.10.sup.6, 2.5.times.10.sup.5 to
1.times.10.sup.6, 2.5.times.10.sup.5 to 5.times.10.sup.5,
5.times.10.sup.5 to 5.times.10.sup.6, 5.times.10.sup.5 to
2.5.times.10.sup.6, or 5.times.10.sup.5 to 1.times.10.sup.6
M.sup.-1 s.sup.-1. For example, variant ADA2 containing a variant
ADA2 polypeptide provided herein has a catalytic efficiency of
k.sub.cat/K.sub.M (M.sup.-1 s.sup.-1) of at least 5.times.10.sup.3,
6.times.10.sup.3, 7.times.10.sup.3, 8.times.10.sup.3,
9.times.10.sup.3, 1.times.10.sup.4, 2.times.10.sup.4,
3.times.10.sup.4, 4.times.10.sup.4, 5.times.10.sup.4,
6.times.10.sup.4, 7.times.10.sup.4, 8.times.10.sup.4,
9.times.10.sup.4, 1.times.10.sup.5, 2.times.10.sup.5,
3.times.10.sup.5, 4.times.10.sup.5, 5.times.10.sup.5, or greater,
or 6.times.10.sup.5, 7.times.10.sup.5, 8.times.10.sup.5,
9.times.10.sup.5, 1.times.10.sup.6, 2.times.10.sup.6,
3.times.10.sup.6, 4.times.10.sup.6, 5.times.10.sup.6M.sup.-1
s.sup.-1 or greater.
[0467] The variant ADA2 polypeptide provided herein can contain
amino acid replacements (i.e. substitutions), additions (i.e.
insertions), deletions, truncations or combinations thereof. The
variant ADA2 can contain modification(s) in any region or domain of
an ADA2 polypeptide provided the resulting variant ADA2, when in
active form, for example as a dimer, at least retains adenosine
deaminase activity. For purposes herein, reference to
modification(s) in an ADA2 polypeptide is with respect to residues
of the mature ADA2 polypeptide set forth in SEQ ID NO:5. Amino acid
replacements can be made at corresponding residues of any ADA2
polypeptide or catalytically active fragment thereof, including in
any ADA2 polypeptide or variant ADA2 polypeptide known in the art.
Corresponding residues can be identified by alignment with the
mature polypeptide set forth in SEQ ID NO:5 (see e.g. FIG. 1, Table
1). Reference also is made throughout the application and Examples
to numbering based on Zavialov (Zavialov et al. (2010) J. Biol.
Chem. 285:12367-12377), which is based on the numbering of amino
acids residues set forth in SEQ ID NO:4. See Table 1, which sets
forth the corresponding position numbers of Zavialov numbering (SEQ
ID NO:4) and mature ADA2 numbering (SEQ ID NO:5).
[0468] To retain adenosine deaminase activity, modifications
typically are not at those positions that are less tolerant to
change Such positions can be within domains or regions that are
required for catalytic activity, substrate binding and/or
dimerization. For example, such positions include regions that are
highly conserved, such as residues required for zinc coordination
or active site residues. A skilled artisan knows or can readily
identify amino acid residues that are required for activity and
should not be changed. Also, in some instances if a modification is
at these positions, it generally is a conservative amino acid
substitution. One of skill in the art understands conservative
amino acid substitutions, such as those provided in Table 3, can be
used to reduce the likelihood of a modification resulting in a
reduction in activity.
[0469] Variant ADA2 proteins provided herein can contain a
polypeptide subunit that exhibits at least 85%, 86%, 87%, 88%, 89%,
90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence
identity to the polypeptide sequence of the unmodified or reference
ADA2 polypeptide, such as those set forth in any of SEQ ID NOS:5,
326-334, 340, 375 or 380-383, or a catalytically active fragment
thereof. In particular, variant ADA2 proteins provided herein
contain a polypeptide subunit that exhibits at least 85%, 86%, 87%,
88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more
sequence identity to the polypeptide sequence set forth in SEQ ID
NO:5 or a catalytically active fragment thereof. The variant ADA2
proteins provided herein can contain a polypeptide subunit that can
contain at least or about or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,
30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46,
47, 48, 49, 50 or more amino acid modification(s) compared to the
polypeptide sequence of the unmodified or reference ADA2
polypeptide. It is understood that when present as a dimer or
multimer, the variant ADA2 can contain at least or about or 1, 2,
3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 12, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54,
55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88,
89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 or more amino acid
modification(s).
[0470] For purposes herein, amino acid replacements are denoted by
the replaced amino acid, the amino acid position and the replacing
amino acid (e.g. K11A by mature numbering, which represents that
the amino acid at a position corresponding to amino acid residue 11
in SEQ ID NO:5, e.g. lysine, is replaced by alanine). For purposes
herein, amino acid replacements can also be denoted by the replaced
amino acid, the amino acid position and the replacing amino acid
(e.g. K14A by Zavialov numbering, which represents that the amino
acid at a position corresponding to amino acid residue 14 in SEQ ID
NO:4, e.g. lysine, is replaced by alanine). See Table 1, which sets
forth the corresponding position numbers of Zavialov numbering (SEQ
ID NO:4) and mature ADA2 numbering (SEQ ID NO:5). Nomenclature also
is employed herein to represent the insertion (--.fwdarw.followed
by position of insertion) or deletion (e.g. position of deletion
(del) followed by .fwdarw.--) of an amino acid residue at a
corresponding position in SEQ ID NO:5, by mature numbering, and/or
by SEQ ID NO:4, by Zavialov numbering. For example, --.fwdarw.N1 by
mature numbering means that the residue at position 1 is inserted
compared to the corresponding sequence of mature ADA2 set forth in
SEQ ID NO:5. For example, --.fwdarw.N4 by Zavialov numbering means
that the residue at position 4 is inserted compared to the
corresponding sequence of ADA2 set forth in SEQ ID NO:4. It is
understood that in some cases, due to deletions or insertions of
amino acid residues, the numbering of residues in a variant ADA2
polypeptide is altered compared to the numbering of residues set
forth in SEQ ID NO:5. In such instances, it is within the level of
a skilled artisan to identify residues in the corresponding variant
ADA2 polypeptide that correspond to residues in SEQ ID NO:5, for
example by alignment as demonstrated in FIG. 1. For example, the
numbering of residues in a variant ADA2 polypeptide can be numbered
based on Zavialov (Zavialov et al. (2010) J. Biol. Chem.
285:12367-12377), which is based on the numbering of amino acids
residues set forth in SEQ ID NO:4. See Table 1, which sets forth
the corresponding position numbers of Zavialov numbering (SEQ ID
NO:4) and mature ADA2 numbering (SEQ ID NO:5).
[0471] Exemplary modifications in a variant ADA2 polypeptide
provided herein are described in further detail below. The variant
ADA2 provided herein include those that, when in active form,
exhibit altered or improved activities or properties compared to
the corresponding form of the reference or wildtype ADA2 not
containing the modification(s) (i.e. the unmodified ADA2). For
example, the variant ADA2 provided herein include those that, when
in active form, exhibit altered or improved activities or
properties compared to the corresponding form of an unmodified ADA2
containing an ADA2 polypeptide having a sequence of amino acids
that exhibits at least 85% sequence identity to SEQ ID NO:5 or a
catalytically active fragment thereof, such as those set forth in
any of SEQ ID NOS:5, 326-334, 340, 375 or 380-383, or a
catalytically active fragment thereof. In particular, the
modifications provided herein can affect any one or more activities
from among increased adenosine deaminase activity, attenuated
heparin binding, increased half-life, altered pH optimum, increased
thermal stability, reduced receptor binding, or hyperglycosylation
compared to the corresponding form of the ADA2 not containing the
modifications (i.e. the unmodified ADA2).
[0472] In particular, the active form is the dimer form, such as
the homodimer form, that contains the variant ADA2 polypeptide.
Thus, in examples herein, variant ADA2 proteins containing a
variant ADA2 polypeptide provided herein, when in dimer form,
exhibit altered or improved activities or properties compared to
the corresponding dimer form of the reference or wildtype ADA2 not
containing the modifications. For example, the variant ADA2
provided herein include those that, when in dimer form, exhibit
altered or improved activities or properties compared to the
corresponding dimer form of an unmodified ADA2 containing an ADA1
polypeptide having a sequence of amino acids that exhibits at least
85% sequence identity to SEQ ID NO:5 or a catalytically active
fragment thereof, such as those set forth in any of SEQ ID NOS:5,
326-334, 340, 375 or 380-383, or a catalytically active portion
thereof. For example, provided are variant ADA2 containing a
variant ADA2 polypeptide provided herein that, when in dimer form,
exhibit altered or improved activities or properties compared to
the ADA2 homodimer containing the sequence of amino acids set forth
in SEQ ID NO:5 or a catalytically active fragment thereof. In
particular, the modifications provided herein can affect any one or
more activities from among increased adenosine deaminase activity,
attenuated heparin binding, increased half-life, altered pH
optimum, increased thermal stability, reduced receptor binding, or
hyperglycosylation compared to the corresponding form of the ADA2
not containing the modifications (i.e. the unmodified ADA2).
[0473] For example, provided herein are variant ADA2 proteins that,
when in active form such as dimer form, exhibit increased adenosine
deaminase activity. For example, the variant ADA2 protein, when in
active form such as dimer form, can exhibit at least 110%, 120%,
130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 225%, 250%, 300%,
350%, 400%, 450%, 500%, 600%, 700%, 800%, 900%, 1000% or more
activity of the corresponding form of the unmodified ADA2, wherein
adenosine deaminase activity is assessed under the same conditions.
The catalytic efficiency (k.sub.cat/K.sub.M) of a variant ADA2 that
exhibits increased adenosine deaminase activity is at least or at
least about 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold,
1.7-fold, 1.8-fold, 1.9-fold, 2.0-fold, 2.2-fold, 2.5-fold,
3.0-fold, 3.5-fold, 4-fold, 4.5-fold, 5.0-fold, 6.0-fold, 7.0-fold,
8.0-fold, 9.0-fold, 10.0-fold greater or more, or 11.0-fold,
12.0-fold, 13.0-fold, 14.0-fold, 15.0-fold greater or more compared
to the catalytic efficiency (k.sub.cat/K.sub.M) of the
corresponding form of the unmodified ADA2, wherein catalytic
efficiency of adenosine deaminase activity is assessed under the
same conditions. For example, when in dimer form, the variant ADA2
provided herein exhibits a catalytic efficiency (k.sub.cat/K.sub.M)
that is at least 2.times.10.sup.4 M.sup.-1 s.sup.-1,
3.times.10.sup.4M.sup.-1 s.sup.-1, 4.times.10.sup.4M.sup.-1
s.sup.-1, 5.times.10.sup.4M.sup.-1 s.sup.-1, 6.times.10.sup.4
M.sup.-1 s.sup.-1, 7.times.10.sup.4 M.sup.-1 s.sup.-1,
8.times.10.sup.4 M.sup.-1 s.sup.-1, 9.times.10.sup.4M.sup.-1
s.sup.-1, 1.times.10.sup.5 M.sup.-1 s.sup.-1, 2.times.10.sup.5
M.sup.-1 s.sup.-1, 3.times.10.sup.5 M.sup.-1 s.sup.-1,
4.times.10.sup.5M.sup.-1 s.sup.-1, 5.times.10.sup.5 or greater, or
6.times.10.sup.5M.sup.-1 s.sup.-1, 7.times.10.sup.5M.sup.-1
s.sup.-1, 8.times.10.sup.5 M.sup.-1 s.sup.-1,
9.times.10.sup.5M.sup.-1 s.sup.-1, 1.times.10.sup.6M.sup.-1
s.sup.-1, 2.times.10.sup.6M.sup.-1 s.sup.-1,
3.times.10.sup.6M.sup.-1 s.sup.-1, 4.times.10.sup.6M.sup.-1
s.sup.-1, 5.times.10.sup.6M.sup.-1s.sup.-1 or greater.
[0474] In examples herein, provided herein are variant ADA2
proteins that, when in active form such as dimer form, exhibit
reduced binding to any one or more adenosine receptor (ADR)
selected from among A.sub.1, A.sub.2A, A.sub.2B and A.sub.3, and
typically one or both of A.sub.2A or A.sub.2B. Without being bound
by theory, it is contemplated herein that the activity of the
adenosine deaminase activity provided herein for converting
adenosine to inosine is greater or more efficient if binding of the
ADA2 to an ADR is reduced. For example, provided herein are variant
ADA2, when in active form such as dimer form, in which binding to
one or more ADR is reduced at least or at least about 0.5-fold,
1-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold,
8-fold, 9-fold, 10-fold or more compared to the corresponding form
of the unmodified ADA2.
[0475] In examples herein, provided herein are variant ADA2
proteins that, when in active form such as dimer form, exhibit
reduced or attenuated heparin binding. ADA2 binds
glycosaminoglycans (GAGs), including heparin and its analogs, such
as heparan sulfate, and chondroitin sulfate. High-affinity binding
to heparin/GAGs is mediated by a large, highly positively charged
surface at the interface of dimer, and dimerization of ADA2 forms
the heparin binding site. Because glycosaminoglycan is widely
present throughout the body, it could interact with the
administered ADA2 and act as a peripheral sink. Therefore, an ADA2
with reduced heparin binding can increase the bioavailability and
pharmacokinetics of the administered ADA2. For example, ADA2
variants with attenuated heparin binding provided herein, result in
improved bioavailability and pharmacokinetics, such as increased
half-life, when administered, because the administered ADA2
molecules will not be sequestered in the peripheral sink by binding
to the GAGs. In particular, provided herein are variant ADA2
proteins that, when in active form such as dimer form, exhibit no
more than 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%,
30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or
95% of the heparin binding of the corresponding form of the
unmodified ADA2, wherein heparin binding is assessed under the same
conditions.
[0476] In examples herein, provided are variant ADA2 proteins that,
when in active form such as dimer form, exhibit an increased or
longer plasma or serum half-life (t.sub.1/2). For example, variant
ADA2 provided herein, when in active form such as dimer form,
exhibit a half-life that is at least or at least about 110%, 120%,
130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 225%, 250%, 300%,
350%, 400%, 450%, 500%, 600%, 700%, 800% or more longer, or 900%,
1000%, 1100%, 1200%, 1300%, 1400%, 1500%, 1600%, 1700%, 1800%,
1900%, 2000%, 3000%, 4000%, 5000%, 6000%, 7000%, 8000%, 9000%,
10000%, or more longer than the half-life of the corresponding form
of the unmodified ADA2, wherein half-life is assessed under the
same conditions.
[0477] In examples herein, provided are variant ADA2 proteins that,
when in active form such as dimer form, exhibit an increased
thermal stability. For example, when in active form such as dimer
form, variant ADA2 provided herein exhibit thermal stability with a
melting temperature (Tm) that is increased at least or at least
about 0.5.degree. C., 1.0.degree. C., 2.0.degree. C., 3.0.degree.
C., 4.0.degree. C., 5.0.degree. C., 6.0.degree. C., 7.0.degree. C.,
8.0.degree. C., 9.0.degree. C., 10.0.degree. C. or more compared to
the Tm of the corresponding form of the unmodified ADA2, wherein Tm
is assessed under the same conditions. The melting temperature (Tm)
of variant ADA2, when in active form such as dimer form, provided
herein can be at least or at least about 67.6.degree. C.,
67.8.degree. C., 68.0.degree. C., 68.2.degree. C., 68.4.degree. C.,
68.6.degree. C., 68.8.degree. C., 69.0.degree. C., 69.2.degree. C.,
69.4.degree. C., 69.6.degree. C., 69.8.degree. C., 70.0.degree. C.,
70.2.degree. C., 70.4.degree. C., 70.6.degree. C., 70.8.degree. C.,
71.0.degree. C., 71.2.degree. C., 71.4.degree. C., 71.6.degree. C.,
71.8.degree. C. or higher.
[0478] In examples herein, the adenosine deaminase activity of ADA2
or variants can be exhibited at a pH optima of from or from about
pH 6.0 to pH 7.6, such as a pH of at least pH 6, 6.25, 6.5, 6.75,
7, 7.25 or 7.5. For example, ADA2 has a pH optima of at or about pH
6.5.+-.0.2. Variant ADA2 proteins provided herein can exhibit a pH
optima for adenosine deaminase activity of from or from about pH
6.0 to 6.8, such as at or about pH 6.5.+-.0.2. In some cases, the
variant ADA2 exhibits an altered pH optimum and the catalytic
activity can be exhibited at a higher pH that is from or from about
pH 6.8 to pH 7.6, such as from or from about pH 7.0 to pH 7.5 or pH
7.2 to pH 7.4, each inclusive. Since proliferating tissue near
blood vessels in the TME can have a more neutral pH, such variants
could be more active in particular tumor environments. For example,
ADA2 variant can exhibit a pH optima for adenosine deaminase
activity of at least pH 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6
or higher. Based on this description, it is within the level of one
of skill in the art to generate a variant ADA2 containing any one
or more of the described modification(s), and test each for
adenosine deaminase activity and/or one or more of properties from
among heparin binding, half-life, pH optimum, thermal stability,
receptor binding and/or glycosylation as described herein.
a. EXEMPLARY MODIFICATIONS
i. Amino Acid Replacements
[0479] In one example, the modification(s) can be an amino acid
replacement(s). Provided herein are variant ADA2 polypeptides that
contain one or more amino acid replacements in an ADA2 polypeptide
at an amino acid position corresponding to amino acid residue 11,
13, 20, 22, 26, 86, 109, 118, 119, 124, 133, 139, 179, 183, 191,
217, 219, 221, 224, 258, 262, 264, 266, 267, 277, 283, 296, 309,
317, 321, 352, 366, 371, 372, 373, 374, 403, 404, 405, 406, 441,
444, 452, 461, 469 or 470, by mature numbering, with reference to
amino acid residues set forth in SEQ ID NO:5. For example, the
amino replacement can be at an amino acid position corresponding to
amino acid residue K11, K13, R20, V22, K26, D86, F109, R118, F119,
P124, W133, Y139, E179, F183, Y191, R217, R219, L221, Y224, K258,
S262, H264, S266, K267, R277, R283, V296, K309, K317, K321, R352,
R366, K371, K372, D373, I374, T403, G404, H405, P406, R441, K444,
K452, K461, K469 or K470, by mature numbering, with reference to
amino acid residues set forth in SEQ ID NO:5.
[0480] For example, provided herein are variant ADA2 polypeptides
that contain one or more amino acid replacements in an ADA2
polypeptide that is any one or more of: K11A, K11D, K11E, K13A,
K13D, K13E, R20A, R20D, R20E, R20N, V22S, K26A, K26D, K26E, D86A,
D86C, D86E, D86F, D86G, D86H, D86I, D86K, D86L, D86M, D86N, D86P,
D86Q, D86R, D86S, D86T, D86V, D86W, D86Y, F109S, F109A, R118D,
R118A, F119S, F119K, P124A, P124S, W133S, W133T, Y139T, Y139A,
E179A, E179C, E179D, E179F, E179G, E179H, E179I, E179K, E179L,
E179M, E179N, E179P, E179Q, E179R, E179S, E179T, E179V, E179W,
E179Y, F183K, Y191S, Y191D, R217A, R217D, R217E, R219A, R219C,
R219D, R219E, R219F, R219G, R219H, R219I, R219K, R219L, R219M,
R219N, R219P, R219Q, R219S, R219T, R219V, R219W, R219Y, L221A,
L221C, L221D, L221E, L221F, L221 G, L221H, L221I, L221K, L221M,
L221N, L221P, L221Q, L221R, L221S, L221T, L221V, L221W, L221Y,
Y224R, Y224N, K258A, K258D, K258E, S262A, S262C, S262D, S262E,
S262F, S262G, S262H, S262I, S262K, S262L, S262M, S262N, S262P,
S262Q, S262R, S262T, S262V, S262W, S262Y, H264A, H264C, H264D,
H264E, H264F, H264G, H264I, H264K, H264L, H264M, H264N, H264P,
H264Q, H264R, H264S, H264T, H264V, H264W, H264Y, S266A, S266C,
S266D, S266E, S266F, S266G, S266H, S266I, S266K, S266L, S266M,
S266N, S266P, S266Q, S266R, S266T, S266V, S266W, S266Y, K267A,
K267C, K267D, K267E, K267F, K267G; K267H, K267I, K267L, K267M,
K267N, K267P, K267Q, K267R, K267S, K267T, K267V, K267W, K267Y,
R277A, R277D, R277E, R283A, R283D, R283E, V296A, V296C, V296D,
V296E, V296F, V296G, V296H, V296I, V296K, V296L, V296M, V296N,
V296P, V296Q, V296R, V296S, V296T, V296W, V296Y, K309A, K309D,
K309E, K317A, K317D, K317E, K321A, K321D, K321E, R352A, R352D,
R352E, R366A, R366D, R366E, K371A, K371D, K371E, K371N, K372A,
K372D, K372E, K372N, D373S, I374S, T403N, G404N, H405S, P406S,
R441A, R441D, R441E, K444A, K444D, K444E, K452A, K452D, K452E,
K461A, K461D, K461E, K469A, K469D, K469E, K470A, K470D, and K470E,
by mature numbering, with reference to amino acid residues set
forth in SEQ ID NO:5.
[0481] In particular, provided herein are variant ADA2 polypeptides
that contain one or more amino acid replacements in an ADA2
polypeptide that is any one or more of: K11A, K11E, R20A, R20D,
R20E, R219K, R219Q, L221A, L221V, L221G, S262N, H264Q, H264G R366A,
R366D, R366E, K371A, K371D, K371E, K372A, K372D, K372E and K452E,
by mature numbering, with reference to amino acid residues set
forth in SEQ ID NO:5. For example, provided herein are variant ADA2
polypeptides that contain one or more amino acid replacements in an
ADA2 polypeptide that is any one or more of: K11A, K11E, R20A,
R20E, R219K, R219Q, L221A, L221V, L221G, S262N, H264Q, H264G,
R366E, K371A, K371D, K371E, K372D, K372E, K452D and K452E, by
mature numbering, with reference to amino acid residues set forth
in SEQ ID NO:5. In another example, provided herein are variant
ADA2 polypeptides that contain one or more amino acid replacements
in an ADA2 polypeptide that is any one or more of R20A, R20D, R20E,
S262N, R366A, R366D, R366E, K371A, K371D, K371E, K372A, K372D,
K372E and K452E, by mature numbering, with reference to amino acid
residues set forth in SEQ ID NO:5. In examples, provided herein are
variant ADA2 polypeptides that contain one or more amino acid
replacements in an ADA2 polypeptide that is any one or more of
K11A, R20A, R20E, R219Q, S262N, K371A, K371D or K371E, by mature
numbering, with reference to amino acid residues set forth in SEQ
ID NO:5.
[0482] Also provided herein are variant ADA2 polypeptides that
contain 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19 or 20 amino acid replacements compared to the reference ADA2
polypeptide not containing the modifications (i.e. the unmodified
ADA2). Variant ADA2 polypeptides can contain any two or more amino
acid replacements provided above, so long as the resulting ADA2
variant exhibits or retains adenosine deaminase activity. The two
or more amino acid replacements can confer the same altered
activity or a different altered activity. For example, one amino
acid replacement can confer altered heparin binding and the other
can confer increased adenosine deaminase activity. Hence, the
resulting ADA2 polypeptide variants exhibit two or more altered
activities or properties.
[0483] For example, provided herein are variant ADA2 polypeptides
that contain amino acid replacements K11A/R20A; K11A/R20A/K371A;
R20A/K371A; K11A/K371A; S262N/K371D; S262N/K371E; S262N/R20E;
S262N/R20E/K371D; S262N/R20E/K371E; R219Q/K371E; R219Q/K371D;
R219Q/R20E; R219Q/K371E/R20E; R219Q/K371D/R20E; R219Q/S262N/K371E;
R219Q/S262N/K371D; R219Q/S262N/R20E; R219Q/S262N/K371E/R20E;
R219Q/S262N/K371D/R20E; or R219Q/S262N, by mature numbering, with
reference to amino acid residues set forth in SEQ ID NO:5.
[0484] For example, provided herein are variant ADA2 polypeptides
that contain amino acid replacements K11A/R20A; K11A/R20A/K371A;
R20A/K371A; K11A/K371A; S262N/K371D; S262N/K371E; S262N/R20E;
S262N/R20E/K371D; S262N/R20E/K371E; R219Q/K371E; R219Q/K371D;
R219Q/R20E; R219Q/K371E/R20E; R219Q/K371D/R20E; R219Q/S262N/K371E;
R219Q/S262N/K371D; R219Q/S262N/R20E; R219Q/S262N/K371E/R20E;
R219Q/S262N/K371D/R20E; or R219Q/S262N, by mature numbering, with
reference to amino acid residues set forth in SEQ ID NO:5.
[0485] Exemplary of such variant ADA2 polypeptides are any set
forth in any of SEQ ID NOS:13-63 or 71-273, or a catalytically
active portion thereof.
[0486] In other examples, also provided herein are variant ADA2
polypeptides that contain amino acid replacements R219Q/S262N/K11A;
R219Q/S262N/K11D; R219Q/S262N/K11E; R219Q/S262N/K13A;
R219Q/S262N/K13D; R219Q/S262N/K13E; R219Q/S262N/K371A;
R219Q/S262N/K372A; R219Q/S262N/K372D; R219Q/S262N/K372E;
R219Q/S262N/K452A; R219Q/S262N/K452D; R219Q/S262N/K452E;
R219Q/S262N/R20A; R219Q/S262N/R20D; R219Q/S262N/R366A;
R219Q/S262N/R366D; R219Q/S262N/R366E; R219Q/S262N/H264A;
R219Q/S262N/H264Q; R219Q/S262N/H264N; R219Q/S262N/H264G;
R219K/S262N; R219N/S262N; R219A/S262N; R219Q/S262N/L221A;
R219Q/S262N/L221V; R219Q/S262N/L221G; R219Q/S262N/E179D;
R219Q/S262N/E179A; R219Q/S262N/E179S; R219Q/S262N/E179T;
R219Q/S262N/E179V; R219Q/S262N/E179G; R219Q/S262A; R219Q/S262V;
R219Q/S262M; R219Q/S262N/K11A/R20A; R219Q/S262N/K11A/R20A/K371A;
R219Q/S262N/R20A/K371A; R219Q/S262N/K11A/K371A; R219Q/S262N/K26A;
R219Q/S262N/K26D; R219Q/S262N/K26E; R219Q/S262N/R217A;
R219Q/S262N/R217D; R219Q/S262N/R217E; R219Q/S262N/K258A;
R219Q/S262N/K258D; R219Q/S262N/K258E; R219Q/S262N/R277A;
R219Q/S262N/R277D; R219Q/S262N/R277E; R219Q/S262N/R283A;
R219Q/S262N/R283D; R219Q/S262N/R283E; R219Q/S262N/K309A;
R219Q/S262N/K309D; R219Q/S262N/K309E; R219Q/S262N/K317A;
R219Q/S262N/K317D; R219Q/S262N/K317E; R219Q/S262N/K321A;
R219Q/S262N/K321D; R219Q/S262N/K321E; R219Q/S262N/R352A;
R219Q/S262N/R352D; R219Q/S262N/R352E; R219Q/S262N/R441A;
R219Q/S262N/R441D; R219Q/S262N/R441E; R219Q/S262N/K444A;
R219Q/S262N/K444D; R219Q/S262N/K444E; R219Q/S262N/K461A;
R219Q/S262N/K461D; R219Q/S262N/K461E; R219Q/S262N/K469A;
R219Q/S262N/K469D; R219Q/S262N/K469E; R219Q/S262N/K470A;
R219Q/S262N/K470D; R219Q/S262N/K470E; R219Q/S262N/D86A;
R219Q/S262N/D86C; R219Q/S262N/D86E; R219Q/S262N/D86F;
R219Q/S262N/D86G; R219Q/S262N/D86H; R219Q/S262N/D86I;
R219Q/S262N/D86K; R219Q/S262N/D86L; R219Q/S262N/D86M;
R219Q/S262N/D86N; R219Q/S262N/D86P; R219Q/S262N/D86Q;
R219Q/S262N/D86R; R219Q/S262N/D86S; R219Q/S262N/D86T;
R219Q/S262N/D86V; R219Q/S262N/D86W; R219Q/S262N/D86Y;
R219Q/S262N/E179C; R219Q/S262N/E179F; R219Q/S262N/E179H;
R219Q/S262N/E179I; R219Q/S262N/E179K; R219Q/S262N/E179L;
R219Q/S262N/E179M; R219Q/S262N/E179N; R219Q/S262N/E179P;
R219Q/S262N/E179Q; R219Q/S262N/E179R; R219Q/S262N/E179W;
R219Q/S262N/E179Y; R219C/S262N; R219D/S262N; R219E/S262N;
R219F/S262N; R219G/S262N; R219H/S262N; R219I/S262N; R219L/S262N;
R219M/S262N; R219P/S262N; R219S/S262N; R219T/S262N; R219V/S262N;
R219W/S262N; R219Y/S262N; R219Q/S262N/L221C; R219Q/S262N/L221D;
R219Q/S262N/L221E; R219Q/S262N/L221F; R219Q/S262N/L221H;
R219Q/S262N/L221I; R219Q/S262N/L221K; R219Q/S262N/L221M;
R219Q/S262N/L221N; R219Q/S262N/L221P; R219Q/S262N/L221Q;
R219Q/S262N/L221R; R219Q/S262N/L221S; R219Q/S262N/L221T;
R219Q/S262N/L221W; R219Q/S262N/L221Y; R219Q/S262C; R219Q/S262D;
R219Q/S262E; R219Q/S262F; R219Q/S262G; R219Q/S262H; R219Q/S262I;
R219Q/S262K; R219Q/S262L; R219Q/S262P; R219Q/S262Q; R219Q/S262R;
R219Q/S262T; R219Q/S262W; R219Q/S262Y; R219Q/S262N/H264C;
R219Q/S262N/H264D; R219Q/S262N/H264E; R219Q/S262N/H264F;
R219Q/S262N/H264I; R219Q/S262N/H264K; R219Q/S262N/H264L;
R219Q/S262N/H264M; R219Q/S262N/H264P; R219Q/S262N/H264R;
R219Q/S262N/H264S; R219Q/S262N/H264T; R219Q/S262N/H264V;
R219Q/S262N/H264W; R219Q/S262N/H264Y; R219Q/S262N/S266A;
R219Q/S262N/S266C; R219Q/S262N/S266D; R219Q/S262N/S266E;
R219Q/S262N/S266F; R219Q/S262N/S266G; R219Q/S262N/S266H;
R219Q/S262N/S266I; R219Q/S262N/S266K; R219Q/S262N/S266L;
R219Q/S262N/S266M; R219Q/S262N/S266N; R219Q/S262N/S266P;
R219Q/S262N/S266Q; R219Q/S262N/S266R; R219Q/S262N/S266T;
R219Q/S262N/S266V; R219Q/S262N/S266W; R219Q/S262N/S266Y;
R219Q/S262N/K267A; R219Q/S262N/K267C; R219Q/S262N/K267D;
R219Q/S262N/K267E; R219Q/S262N/K267F; R219Q/S262N/K267G;
R219Q/S262N/K267H; R219Q/S262N/K267I; R219Q/S262N/K267L;
R219Q/S262N/K267M; R219Q/S262N/K267N; R219Q/S262N/K267P;
R219Q/S262N/K267Q; R219Q/S262N/K267R; R219Q/S262N/K267S;
R219Q/S262N/K267T; R219Q/S262N/K267V; R219Q/S262N/K267W;
R219Q/S262N/K267Y; R219Q/S262N/V296A; R219Q/S262N/V296C;
R219Q/S262N/V296D; R219Q/S262N/V296E; R219Q/S262N/V296F;
R219Q/S262N/V296G; R219Q/S262N/V296H; R219Q/S262N/V296I;
R219Q/S262N/V296K; R219Q/S262N/V296L; R219Q/S262N/V296M;
R219Q/S262N/V296N; R219Q/S262N/V296P; R219Q/S262N/V296Q;
R219Q/S262N/V296R; R219Q/S262N/V296S; R219Q/S262N/V296T;
R219Q/S262N/V296W; R219Q/S262N/V296Y; R219Q/K11A/R20A;
R219Q/K11A/R20A/K371A; R219Q/R20A/K371A; R219Q/K11A/K371A;
S262N/K11A/R20A; S262N/K11A/R20A/K371A; S262N/R20A/K371A; or
S262N/K11A/K371A, by mature numbering, with reference to amino acid
residues set forth in SEQ ID NO:5.
[0487] Exemplary of such variant ADA2 polypeptides are any set
forth in any of SEQ ID NOS:659-663 or 682-917, or a catalytically
active portion thereof.
ii. Modification(s) of PRB Domain
[0488] In other examples, also provided herein are modified ADA2
polypeptides that contain a modified PRB domain. The PRB domain is
not required for catalytic activity, and, hence, as shown herein,
can be removed so that the ADA2 variant proteins activities other
than deaminase activity, mediated by ADA2, are reduced or
eliminated. According to the reported domain organization of ADA2,
the PRB domain corresponds to residues 98-156 or 105-148 of mature
ADA2 set forth in SEQ ID NO:5. The modifications of the PRB domain
can include deletion of all or a portion of the PRB domain (i.e.
deletion of one or more residues of the PRB domain), insertion of
one or more amino acid residues into the PRB domain, amino acid
replacement of one or more residues of the PRB domain or a
combination thereof to thereby reduce or inhibit binding of the
domain to a receptor or other activity thereof. For example, the
PRB domain can contain up to or about or 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,
27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,
44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, or 59
modified positions, such as generally up to or about 1, 2, 3, 4, 5,
6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,
41, 42, 43 or 44 modified positions.
[0489] In one example, as described in more detail below, all or a
portion of the PRB domain can be deleted, such as by deletion of
one or more contiguous amino acid residues of the PRB domain. For
example, provided herein are variant ADA2 in which one or more
contiguous amino acid residues between or about between amino acid
residues 98 and 156 or amino acid residues 105 and 148 or amino
acid residues 105 and 147 or amino acid residues 99 and 144,
inclusive, with reference to residues set forth in SEQ ID NO:5, are
deleted. Exemplary of such ADA2 polypeptides are deletion of
contiguous amino acid residues corresponding to contiguous residues
98-156, 105-148, 105-147, 102-147 or 108-150, by mature numbering,
with reference to the sequence of amino acids set forth in SEQ ID
NO:5. For example, exemplary of such ADA2 polypeptides include
polypeptides ADA2_del98-156 (98-156del; SEQ ID NO:548);
ADA2_del105-148 (105-148del; SEQ ID NO:549); ADA2_del105-147
(105-147del; SEQ ID NO:550); and ADA2_del99-144 (99-144del; SEQ ID
NO:579), by mature numbering, with reference to the sequence of
amino acids set forth in SEQ ID NO:5.
[0490] In some examples, the variant ADA2 that contains a
modification in the PRB domain, such as a deletion of contiguous
residues, also contains a substitution of the modified or deleted
region with a peptide linker. As a result, all or a portion of the
PRB domain can be replaced with a sterically acceptable peptide
linker sequence. In such examples, at least 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,
27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,
44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59 or
all more contiguous amino acids from the PRB domain can be
substituted or replaced with amino acids of a peptide linker that
generally does not exceed 60 amino acids, and generally does not
exceed 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, or 50
amino acids. Any suitable linker can be selected so long as the
resulting variant ADA2 exhibits adenosine deaminase activity.
[0491] Examples of peptide linkers include, but are not limited to:
(Gly)n, where n is 2 to 20 (SEQ ID NO:368); -Gly-Gly-; GGG (SEQ ID
NO:369); GGGG (SEQ ID NO:362); GGGGG (SEQ ID NO:360); GGGGGGG (SEQ
ID NO:370); GGGGGGGGGG (SEQ ID NO:371); GGGGGGGGGGGGGGG (SEQ ID
NO:372); GGGGS or (GGGGS)n (SEQ ID NO:343); GGGGSGGGGS (SEQ ID
NO:580); GGGGSGGGGSGGGGS (SEQ ID NO:367); SSSSG or (SSSSG)n (SEQ ID
NO:344); GKSSGSGSESKS (SEQ ID NO:345); GGSTSGSGKSSEGKG (SEQ ID
NO:346); GSTSGSGKSSSEGSGSTKG (SEQ ID NO:347); GSTSGSGKPGSGEGSTKG
(SEQ ID NO:348); EGKSSGSGSESKEF (SEQ ID NO:349); or AlaAlaProAla or
(AlaAlaProAla)n (SEQ ID NO:350), where n is 1 to 6, such as 1, 2,
3, or 4. In particular examples, the peptide linker is GGG (SEQ ID
NO:369); GGGGG (SEQ ID NO:360); GGGGGGG (SEQ ID NO:370); GGGGGGGGGG
(SEQ ID NO:371); GGGGGGGGGGGGGGG (SEQ ID NO:372); GGGGS (SEQ ID
NO:343); GGGGSGGGGS (SEQ ID NO:580); or GGGGSGGGGSGGGGS (SEQ ID
NO:367).
[0492] Exemplary of such a modification is a variant ADA2
designated C105-T147del.fwdarw.(Gly).sub.n (SEQ ID NO:280), where n
is 2 to 20, whereby the PRB domain in the region corresponding to
residues 105-147 with reference to numbering in SEQ ID NO:5 is
replaced with a glycine linker of 2 to 20 amino acid residues in
length. For example, the variant ADA2 can be
C105-T147del.fwdarw.(Gly).sub.15(SEQ ID NO:281),
C105-T147del.fwdarw.(Gly).sub.10 (SEQ ID NO:282),
C105-T147del.fwdarw.(Gly).sub.7 (SEQ ID NO:283);
C105-T147del.fwdarw.(Gly).sub.5 (SEQ ID NO:284) or
C105-T147del.fwdarw.(Gly).sub.3 (SEQ ID NO:285). Further examples
of such a modification is a variant ADA designated
V99-Q144del.fwdarw.(GGGGS).sub.n (SEQ ID NO:581), where n is 1 to
5, whereby the PRB domain in the region corresponding to residues
99-144 with reference to numbering in SEQ ID NO:5 is replaced with
a (GGGGS).sub.n linker where the sequence of amino acids in the
linker is repeated 1 to 5 times such that the linker is 5, 10, 15,
20 or 25 amino acid residues in length. For example, the variant
ADA2 can be V99-Q144del.fwdarw.(GGGGS).sub.1 (SEQ ID NO:583);
V99-Q144del.fwdarw.(GGGGS).sub.2 (SEQ ID NO:584); or
V99-Q144del.fwdarw.(GGGGS).sub.3 (SEQ ID NO:585). Further examples
of such a modification is a variant ADA designated
C105-T147del.fwdarw.(GGGGS).sub.n (SEQ ID NO:582), where n is 1 to
5, whereby the PRB domain in the region corresponding to residues
105-147 with reference to numbering in SEQ ID NO:5 is replaced with
a (GGGGS).sub.n linker where the sequence of amino acids in the
linker is repeated 1 to 5 times such that the linker is 5, 10, 15,
20 or 25 amino acid residues in length. For example, the variant
ADA2 can be C105-T147del.fwdarw.(GGGGS).sub.1 (SEQ ID NO:586);
C105-T147del.fwdarw.(GGGGS).sub.2 (SEQ ID NO:587); or
C105-T147del.fwdarw.(GGGGS).sub.3 (SEQ ID NO:588), by mature
numbering, with reference to the sequence of amino acids set forth
in SEQ ID NO:5. Exemplary of such variant ADA2 polypeptides are any
set forth in any of SEQ ID NOS:281-285 and 583-588, or a
catalytically active portion thereof.
[0493] Also provided herein are variant ADA2 polypeptides that
contain deletions, insertions, substitutions and/or amino acid
replacements in the PRB domain, combined with other deletions,
insertions, substitutions and/or amino acid replacements provided
herein. For example, provided are variant ADA2 polypeptides that
contain a deletion of all or a portion of the PRB domain, such as
by deletion of one or more contiguous amino acid residues of the
PRB domain, combined with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19 or 20 additional amino acid replacements
compared to the unmodified reference ADA2. Also provided herein are
variant ADA2 polypeptides that contain a modification in the PRB
domain, such as a deletion of contiguous residues and also contains
a substitution of the modified or deleted region with a peptide
linker, combined with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19 or 20 additional amino acid replacements
compared to the unmodified reference ADA2. For example, the variant
ADA2 polypeptides that contain both a deletion of all or portion of
the PRB domain and any one or more amino acid replacements provided
above, so long as the resulting ADA2 variant exhibits or retains
adenosine deaminase activity. The deletion and/or amino acid
replacements can confer the same altered activity or a different
altered activity. For example, deletion and/or substitution of the
PRB domain can confer one altered activity, e.g., reduction in
binding to a receptor, and amino acid replacement(s) can confer
increased adenosine deaminase activity. Hence, the resulting ADA2
polypeptide variants exhibit two or more altered activities or
properties.
[0494] For example, provided herein are variant ADA2 polypeptides
that contain the following combination of deletions and/or
substitutions and/or amino acid replacements:
K371D/V99-Q144del.fwdarw.(GGGGS).sub.1;
K371D/V99-Q144del.fwdarw.(GGGGS).sub.2;
K371D/V99-Q144del.fwdarw.(GGGGS).sub.3;
K371D/C105-T147del.fwdarw.(GGGGS).sub.1;
K371D/C105-T147del.fwdarw.(GGGGS).sub.2;
K371D/C105-T147del.fwdarw.(GGGGS).sub.3;
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.15;
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.10;
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.7;
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.5;
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.3;
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.1;
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.2;
R219Q/S262N/V99-Q144del.fwdarw.(GGGGS).sub.3;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.1;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.2;
R219Q/S262N/C105-T147del.fwdarw.(GGGGS).sub.3;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.1;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.2;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS).sub.3;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.1;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.2;
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS).sub.3;
K371D/C105-T147del.fwdarw.(Gly)n (where n is 2 to 20);
K371D/C105-T147del.fwdarw.(Gly).sub.15;
K371D/C105-T147del.fwdarw.(Gly).sub.10;
K371D/C105-T147del.fwdarw.(Gly).sub.7;
K371D/C105-T147del.fwdarw.(Gly).sub.5;
K371D/C105-T147del.fwdarw.(Gly).sub.3;
K371D/V99-Q144del.fwdarw.(GGGGS)n (where n is 1 to 5);
K371D/C105-T147del.fwdarw.(GGGGS)n (where n is 1 to 5);
K371D/N98-N156del; K371D/C105-E148del; K371D/C105-T147del;
K371D/V99-Q144del; R219Q/S262N/C105-T147del.fwdarw.(Gly)n (where n
is 2 to 20); R219Q/S262N/V99-Q144del.fwdarw.(GGGGS)n (where n is 1
to 5); R219Q/S262N/C105-T147del.fwdarw.(GGGGS)n (where n is 1 to
5); R219Q/S262N/N98-N156del; R219Q/S262N/C105-E148del;
R219Q/S262N/C105-T147del; R219Q/S262N/V99-Q144del;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly)n (where n is 2 to 20);
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.15;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.10;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.7;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.5;
R219Q/S262N/K371D/C105-T147del.fwdarw.(Gly).sub.3;
R219Q/S262N/K371D/V99-Q144del.fwdarw.(GGGGS)n (where n is 1 to 5);
R219Q/S262N/K371D/C105-T147del.fwdarw.(GGGGS)n (where n is 1 to 5);
R219Q/S262N/K371D/N98-N156del; R219Q/S262N/K371D/C105-E148del;
R219Q/S262N/K371D/C105-T147del; R219Q/S262N/K371D/V99-Q144del;
R219Q/C105-T147del.fwdarw.(Gly)n (where n is 2 to 20);
R219Q/V99-Q144del.fwdarw.(GGGGS)n (where n is 1 to 5);
R219Q/C105-T147del.fwdarw.(GGGGS)n (where n is 1 to 5);
R219Q/N98-N156del; R219Q/C105-E148del; R219Q/C105-T147del;
R219Q/V99-Q144del; S262N/C105-T147del.fwdarw.(Gly)n (where n is 2
to 20); S262N/V99-Q144del.fwdarw.(GGGGS)n (where n is 1 to 5);
S262N/C105-T147del.fwdarw.(GGGGS)n (where n is 1 to 5);
S262N/N98-N156del; S262N/C105-E148del; S262N/C105-T147del; and
S262N/V99-Q144del, by mature numbering, with reference to amino
acid residues set forth in SEQ ID NO:5.
[0495] Exemplary of such variant ADA2 polypeptides are any set
forth in any of SEQ ID NOS:589-594, 602-606, 634-658, 664-681,
918-931, or a catalytically active portion thereof.
iii. Amino Acid Replacement(s) with Altered Interaction Between the
PRB Domain and Other Regions of ADA2
[0496] In yet other examples, also provided herein are modified
ADA2 polypeptides that contain amino acid replacements that confer
altered interaction between the PRB domain and the rest of ADA2
(e.g., the adenosine deaminase (ADA) domain). For example,
according to the reported domain organization of ADA2, the PRB
domain corresponds to residues 98-156 or 105-148 of mature ADA2 set
forth in SEQ ID NO:5. Provided herein are variant ADA2 polypeptides
that contain one or more amino acid replacements in an ADA2
polypeptide at an amino acid position corresponding to amino acid
residue 109, 118, 119, 124, 133, 139, 183, 191 or 224, by mature
numbering, with reference to amino acid residues set forth in SEQ
ID NO:5. For example, the amino replacement can be at an amino acid
position corresponding to amino acid residue F109, R118, F119,
P124, W133, Y139, F183, Y191 or Y224 with reference to amino acid
residues set forth in SEQ ID NO:5. Modifications at each position,
or combination thereof, can alter the interaction between the PRB
domain and other domains in ADA2, such as the ADA domain.
[0497] For example, provided herein are variant ADA2 polypeptides
that contain one or more amino acid replacements in an ADA2
polypeptide that is any one or more of: F109S, F109A, R118D, R118A,
F119S, F119K, P124A, P124S, W133S, W133T, Y139T, Y139A, F183K,
Y191S, Y191D, Y224R or Y224N, by mature numbering, with reference
to amino acid residues set forth in SEQ ID NO:5.
[0498] Also provided herein are variant ADA2 polypeptides that
contain amino acid replacements that confer altered interaction
between the PRB domain and the rest of ADA2, combined with other
deletions, insertions, substitutions and/or amino acid replacements
provided herein. For example, provided are variant ADA2
polypeptides that contain 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19 or 20 amino acid replacements compared to
the reference ADA2 polypeptide not containing the modifications
(i.e. the unmodified ADA2). Variant ADA2 polypeptides can contain
any two or more amino acid replacements provided above, so long as
the resulting ADA2 variant exhibits or retains adenosine deaminase
activity. The two or more amino acid replacements can confer the
same altered activity or a different altered activity. For example,
one amino acid replacement can confer altered interaction between
the PRB domain the ADA domain, and the other can confer increased
adenosine deaminase activity. Hence, the resulting ADA2 polypeptide
variants exhibit two or more altered activities or properties.
[0499] For example, provided herein are variant ADA2 polypeptides
that contain amino acid replacements Y191D/Y224R;
R219Q/S262N/F119S; R219Q/S262N/F119K; R219Q/S262N/Y224R;
R219Q/S262N/Y224N; R219Q/S262N/Y191S; R219Q/S262N/Y191D;
R219Q/S262N/F183K; R219Q/S262N/Y191D/Y224R; R219Q/S262N/F109S;
R219Q/S262N/F109A; R219Q/S262N/R118D; R219Q/S262N/R118A;
R219Q/S262N/Y139T; R219Q/S262N/Y139A; R219Q/S262N/W133S;
R219Q/S262N/W133T; R219Q/S262N/P124A; or R219Q/S262N/P124S, by
mature numbering, with reference to amino acid residues set forth
in SEQ ID NO:5.
[0500] Exemplary of such variant ADA2 polypeptides are any set
forth in any of SEQ ID NOS:561-578 or 616-633, or a catalytically
active portion thereof.
iv. Hyperglycosylation
[0501] Included among the variant ADA2 provided herein are those
that have been modified by altering the level and/or type of
glycosylation compared to an unmodified ADA2. Glycosylation can be
increased or decreased compared to the unmodified ADA2 polypeptide.
In some instances, the level or extent of glycosylation is
increased, resulting in a hyperglycosylated ADA2 polypeptide or
protein. This can be achieved, for example, by incorporation of at
least one non-native glycosylation site not found in the unmodified
ADA2 polypeptide or protein to which a carbohydrate is linked.
Hyperglycosylated ADA2 polypeptides also can be generated by
linkage of a carbohydrate moiety to at least one native
glycosylation site found but not glycosylated in the unmodified
ADA2 polypeptide.
[0502] The variant ADA2 proteins provided herein can contain
altered, such as new, 0-linked glycosylation, N-linked
glycosylation or O-linked and N-linked glycosylation. In some
examples, a variant ADA2 includes 1, 2, 3, 4, 5 or more
carbohydrate moieties, each linked to different glycosylation
sites. The glycosylation site(s) can be a native glycosylation
site(s) and/or a non-native glycosylation site(s). In some
examples, the variant ADA2 is glycosylated at more than one
non-native glycosylation site. For example, a variant ADA2 can be
modified to introduce 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more
non-native glycosylation sites.
[0503] Non-native glycosylation sites can be introduced by amino
acid replacement. O-glycosylation sites can be created, for
example, by amino acid replacement of a native residue with a
serine or threonine. N-linked glycosylation sites can be created by
creating the motif Asn-Xaa-Ser/Thr/Cys, where Xaa is not proline.
Creation of this consensus sequence by amino acid modification can
involve replacement of a native amino acid residue with an
asparagine, replacement of a native amino acid residue with a
serine, threonine or cysteine, or replacement of a native amino
acid residue with an asparagine and amino acid replacement of
native residue with a serine, threonine or cysteine. Non-native
glycosylation sites can be created in any region in an ADA2
polypeptide. The level of glycosylation (e.g. the number of
introduced non-native glycosylation sites) can be increased by at
least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%,
50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more
compared to the level of glycosylation of the corresponding form of
the unmodified or wild-type ADA2.
[0504] Exemplary modifications provided herein include introducing
a non-native glycosylation site by modification with one or more
amino acid replacement(s) that include, but are not limited to,
replacement with: N at a position corresponding to position 20 and
S at a position corresponding to position 22; N at a position
corresponding to position 371 and S at a position corresponding to
position 373; N at a position corresponding to position 372 and S
at a position corresponding to position 374; N at a position
corresponding to position 403 and S at a position corresponding to
position 405; and N at a position corresponding to position 404 and
S at a position corresponding to position 406, each by mature
numbering, with reference to positions set forth in SEQ ID NO:5.
For example, amino acid replacement(s) to introduce a non-native
glycosylation site can include: R20N/V22S; K371N/D373S;
K372N/I374S; T403N/H405S; or G404N/P406S, by mature numbering, with
reference to amino acid residues set forth in SEQ ID NO:5.
[0505] In other examples, modifications provided herein include
introducing a non-native glycosylation site by modification with
one or more amino acid replacement(s) in or near the PRB domain.
Exemplary modifications provided herein include introducing a
non-native glycosylation site by modification with one or more
amino acid replacement(s) that include, but are not limited to,
replacement with:
N at a position corresponding to position 125 and A at a position
corresponding to position 126; N at a position corresponding to
position 127 and S at a position corresponding to position 129; N
at a position corresponding to position 126 and T at a position
corresponding to position 128; N at a position corresponding to
position 112 and T at a position corresponding to position 114; N
at a position corresponding to position 134, C at a position
corresponding to position 135 and T at a position corresponding to
position 136; N at a position corresponding to position 134, S at a
position corresponding to position 135 and Tat a position
corresponding to position 136; N at a position corresponding to
position 142 and S at a position corresponding to position 144; N
at a position corresponding to position 137 and T at a position
corresponding to position 139; N at a position corresponding to
position 111 and S at a position corresponding to position 113,
each by mature numbering, with reference to positions set forth in
SEQ ID NO:5. For example, amino acid replacement(s) to introduce a
non-native glycosylation site in or near the PRB domain can
include: R125N/P126A; S127N/K129S; P126N/E128T; R112N/I114T;
I134N/L135C/L136T; I134N/L135S/L136T; R142N/Q144S; E137N/Y139T; or
P111N/G113S, by mature numbering, with reference to amino acid
residues set forth in SEQ ID NO:5.
[0506] In other examples, also provided herein are modified ADA2
polypeptides that contain addition (i.e. insertion) of one or more
contiguous residues at the N-terminus or the C-terminus. Such
replacements can introduce a non-native glycosylation site. The
modified ADA2 polypeptides can contain insertion of up to or about
or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20 or more amino acid residues at one or both of the N-terminus
or C-terminus. For example, addition or insertion of amino acids
can provide for altered glycosylation sites in the encoded protein.
Exemplary of a modification is insertion
--.fwdarw.N--.fwdarw.A2/--.fwdarw.S3 at the N-terminus, by mature
numbering, with reference to the amino acid positions set forth in
SEQ ID NO:5.
[0507] Exemplary of such variant ADA2 polypeptides are any set
forth in any of SEQ ID NOS:274-279 and 552-560.
[0508] Also provided herein are variant ADA2 polypeptides that
contain one or more amino acid replacement(s) that introduce a
non-native glycosylation site, combined with other deletions,
insertions, substitutions and/or amino acid replacements provided
herein. For example, provided are variant ADA2 polypeptides that
contain 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19 or 20 amino acid replacements compared to the reference ADA2
polypeptide not containing the modifications (i.e. the unmodified
ADA2). Variant ADA2 polypeptides can contain any two or more amino
acid replacements provided above, so long as the resulting ADA2
variant exhibits or retains adenosine deaminase activity. The two
or more amino acid replacements can confer the same altered
activity or a different altered activity. For example, one or more
amino acid replacement(s) can introduce a non-native glycosylation
site, and another amino acid replacement(s) can confer increased
adenosine deaminase activity. Hence, the resulting ADA2 polypeptide
variants exhibit two or more altered activities or properties.
[0509] For example, provided herein are variant ADA2 polypeptides
that contain amino acid replacements
R219Q/S262N/--.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3;
R219Q/S262N/R20N/V22S; R219Q/S262N/K371N/D373S;
R219Q/S262N/K372N/I374S; R219Q/S262N/T403N/H405S;
R219Q/S262N/G404N/P406S; R219Q/S262N/R125N/P126A;
R219Q/S262N/S127N/K129S; R219Q/S262N/P126N/E128T;
R219Q/S262N/R112N/I114T; R219Q/S262N/I134N/L135C/L136T;
R219Q/S262N/I134N/L135S/L136T; R219Q/S262N/R142N/Q144S;
R219Q/S262N/E137N/Y139T; or R219Q/S262N/P111N/G113S, by mature
numbering, with reference to amino acid residues set forth in SEQ
ID NO:5.
[0510] Exemplary of such variant ADA2 polypeptides are any set
forth in any of SEQ ID NOS:596-601 or 607-615, or a catalytically
active portion thereof.
b. NUCLEIC ACID MOLECULES
[0511] Also provided herein are nucleic acid molecules that encode
any of the variant ADA2 polypeptides provided herein. A modified
nucleic acid molecule that encodes any of the variant ADA2
polypeptides provided herein includes codon changes corresponding
to modifications provided herein (e.g. replacement or substitution,
insertion or addition, or deletion of one or more nucleotides). It
is within the level of a skilled artisan, who is familiar with
codons that correspond to various amino acids, to identify such
codon changes based on exemplification of the modified amino acids
herein. In particular examples, the nucleic acid sequence can be
codon optimized, for example, to increase expression levels of the
encoded sequence. The particular codon usage is dependent on the
host organism in which the modified polypeptide is expressed. One
of skill in the art is familiar with optimal codons for expression
in mammalian or human cells, bacteria or yeast, including for
example Escherichia coli or Saccharomyces cerevisiae. For example,
codon usage information is available from the Codon Usage Database
available at kazusa. or jp.codon (see e.g. Richmond (2000) Genome
Biology, 1:241 for a description of the database). See also,
Forsburg (2004) Yeast, 10:1045-1047; Brown et al. (1991) Nucleic
Acids Research, 19:4298; Sharp et al. (1988) Nucleic Acids Res.,
12:8207-8211; Sharp et al. (1991) Yeast, 657-78). Vectors contain
the nucleic acid molecules for expression and production of the
ADA2 polypeptides are provided.
c. PRODUCTION OF VARIANT ADA2 PROTEINS
[0512] The variant ADA2 polypeptides and encoding nucleic acid
molecules provided herein can be produced by standard recombinant
DNA techniques known to one of skill in the art.
[0513] Any method known in the art to effect mutation of any one or
more amino acids in a target protein can be employed. Methods
include standard site-directed or random mutagenesis of encoding
nucleic acid molecules, or solid phase polypeptide synthesis
methods. In particular, total chemical synthesis methods, including
peptide synthesis followed by peptide ligation can be employed.
Nucleic acid molecules encoding an ADA2 polypeptide can be
subjected to mutagenesis, such as random mutagenesis of the
encoding nucleic acid, error-prone PCR, site-directed mutagenesis
(using e.g., a kit, such as kit such as QuikChange available from
Stratagene), overlap PCR, gene shuffling, or other recombinant
methods. The nucleic acid encoding the polypeptides can then be
introduced into a host cell to be expressed heterologously. In some
examples, the variant ADA2 polypeptides are produced synthetically,
such as using total chemical synthesis, solid phase or solutions
phase peptide synthesis.
[0514] Exemplary methods for producing and expressing a nucleic
acid molecule encoding an ADA2 polypeptide, including any variant
ADA2 polypeptide, are described in Section E. Depending on how the
variant ADA2 molecule is produced, or the particular nature of the
modification(s), the variant ADA2 polypeptides provided herein can
be produced as a monomer, dimer, or other multimer. For example,
the variant ADA2 is a heterodimer or homodimer.
[0515] In particular, ADA2 normally exists as a homodimer that is
composed of two identical polypeptide chains. As described above,
nonpolar interactions between residues of two identical polypeptide
subunits mediate formation of the homodimer upon secretion of ADA2
from cells. Since wildtype ADA2 is a homodimer, it is understood
that mention of an amino acid sequence of the reference or
unmodified ADA2 polypeptide refers to the sequence of amino acids
of a single ADA2 polypeptide subunit. The variant ADA2 can contain
one or more ADA2 polypeptide subunits, that are the same (i.e.
homodimer) or different (i.e. heterodimer). For example, a variant
ADA2 homodimer is readily produced and secreted by cells
transformed with a nucleic acid molecule encoding a variant ADA2
polypeptide, such as nucleic acid encoding a polypeptide that has
the sequence of amino acids set forth in any of SEQ ID NOS:13-63,
71-285 or 552-931, or a catalytically active fragment thereof. If
cells are encoded with two or more different nucleic acid
molecules, each encoding a different ADA2 polypeptide, a
heterodimer can be produced.
[0516] In one example, the variant ADA2 polypeptide provided herein
is a dimer. For example, the resulting variant ADA2 polypeptide is
a homodimer that contains a first and second polypeptide subunit
that are the same, i.e. each has the same amino acid sequence
containing the identical modification(s) with respect to the amino
acid sequence of the reference or unmodified ADA2 polypeptide. The
homodimer can be formed by transforming a nucleic acid molecule
encoding the variant polypeptide into a cell, which, upon
secretion, results in nonpolar interaction between residues of two
variant polypeptide subunits to mediate formation of the dimer.
[0517] In another example, the resulting ADA2 polypeptide is a
heterodimer that contains a first and second polypeptide subunit
that are different. In such an example, one or both of the first or
second polypeptide subunit contains a sequence of amino acids
containing a modification(s) with respect to the amino acid
sequence of the reference or unmodified ADA2 polypeptide. In some
cases, both the first and second polypeptide subunit can contain a
sequence of amino acids containing a modification(s) compared to
the reference of unmodified ADA2 polypeptide, but the nature of the
modification(s) are different. The heterodimer can be formed by
transforming into a cell both a first nucleic acid molecule
encoding a first variant polypeptide subunit and a second nucleic
acid molecule encoding a second different polypeptide subunit. The
second nucleic acid molecule can encode a polypeptide subunit
containing the sequence of amino acids of the reference or wildtype
ADA2, or can encode a variant polypeptide subunit containing a
sequence of amino acids containing modification(s) with respect to
the amino acid sequence of the reference or unmodified ADA2. The
heterodimer is produced upon expression and secretion from a cell
as a result of nonpolar interaction between residues of the two
polypeptide subunits to mediate formation of the dimer. In such
processes, generally a mixture of dimeric molecules is formed,
including homodimers and heterodimers. For the generation of
heterodimers, additional steps for purification can be necessary.
For example, the first and second polypeptide can be engineered to
include a tag with metal chelates or other epitope, where the tags
are different. The tagged domains can be used for rapid
purification by metal-chelate chromatography, and/or by antibodies,
to allow for detection by western blots, immunoprecipitation, or
activity depletion/blocking in bioassays.
[0518] In other examples, the variant ADA2 polypeptide is a
monomer. A monomer can be produced by mutation of one or more
residues that are involved in protein dimerization, so long as the
adenosine deaminase activity is retained. Exemplary of residues
that can be targeted for mutagenesis include, but are not limited
to, amino acid residues 1, 4, 5, 8, 9, 11, 12, 15, 344, 362 or 366,
with reference to amino acid residues set forth in SEQ ID NO:5. The
residues can be replaced with one of the other nineteen amino acid
residues at the position. It is within the level of a skilled
artisan to generate and assess monomer formation of a polypeptide.
For example, monomer formation can be assessed, and monomers
purified, by size-exclusion chromatography (SEC). Adenosine
deaminase activity also can be assessed, such as using any of the
assays described herein or known in the art.
[0519] In some examples, dimeric or other multimeric molecules of a
variant ADA2 can be formed by conjugation or fusion of the encoded
variant ADA2 polypeptide to any moiety or other polypeptide that
are themselves able to interact to form a stable structure. For
example, separate encoded ADA2 polypeptides, where at least one is
a variant ADA2 polypeptide, can be joined by multimerization,
whereby multimerization of the polypeptides is mediated by a
multimerization domain. The variant ADA2 dimers or multimers can be
formed by generation of a chimeric molecule where a variant ADA2 is
linked, directly or indirectly, to a multimerization domain. A
nucleic acid molecule encoding a variant ADA2 can be joined
(directly or indirectly) with a nucleic acid encoding a
multimerization domain. For example, a variant ADA2 dimer provided
herein can contain a first ADA2 polypeptide subunit linked directly
or indirectly via a linker to a multimerization domain and a second
ADA2 polypeptide subunit linked directly or indirectly via a linker
to a multimerization domain, wherein one or both of the first and
second polypeptide are a variant ADA2 polypeptide. The first and
second ADA2 polypeptide can be the same or different. Exemplary of
a multimerization domain is an Fc domain, which is described
further below.
[0520] Homo- or heteromultimeric polypeptides can be generated from
co-expression of separate nucleic acid molecules encoding ADA2
polypeptides. Chimeric ADA2 polypeptides can be readily produced
and secreted by cells, such as mammalian cells, transformed with
the appropriate nucleic acid molecule. For example, a cell can be
transformed with a first nucleic acid molecule encoding a variant
ADA2 and a second nucleic acid molecule encoding the same or
different ADA2. The second nucleic acid molecule can encode a
polypeptide subunit containing the sequence of amino acids of the
reference or wildtype ADA2, or can encode a variant polypeptide
subunit containing a sequence of amino acids containing
modification(s) with respect to the amino acid sequence of the
reference or unmodified ADA2. The secreted forms of the ADA2
polypeptide include those where the variant ADA2 is a homodimer of
the first encoded variant ADA2 polypeptide, a homodimer of the
second encoded ADA2 polypeptide, such as wildtype or second variant
ADA2 polypeptide, and ADA2 heterodimers containing two polypeptide
subunits that are different. In some cases, higher ordered
multimers can form.
[0521] Multimerization domains are well known to a skilled artisan.
Generally, a multimerization domain includes any capable of forming
a stable protein-protein interaction. The multimerization domains
can interact via an immunoglobulin sequence (e.g. Fc domain; see
e.g., International Patent Pub. Nos. WO 93/10151 and WO
2005/063816; U.S. Pub. No. 2006/0024298; U.S. Pat. No. 5,457,035),
leucine zipper (e.g. from nuclear transforming proteins fos and jun
or the proto-oncogene c-myc or from General Control of Nitrogen
(GCN4)), a hydrophobic region, a hydrophilic region, or a free
thiol which forms an intermolecular disulfide bond between the
chimeric molecules of a homo- or heteromultimer. In addition, a
multimerization domain can include an amino acid sequence
containing a protuberance complementary to an amino acid sequence
comprising a hole, such as is described, for example, in U.S. Pat.
No. 5,731,168; International Patent Pub. Nos. WO 98/50431 and WO
2005/063816; Ridgway et al. (1996) Protein Engineering, 9:617-621.
Such a multimerization region can be engineered such that steric
interactions not only promote stable interaction, but further
promote the formation of heterodimers over homodimers from a
mixture of chimeric monomers. Generally, protuberances are
constructed by replacing small amino acid side chains from the
interface of the first polypeptide with larger side chains (e.g.,
tyrosine or tryptophan) Compensatory cavities of identical or
similar size to the protuberances are optionally created on the
interface of the second polypeptide by replacing large amino acid
side chains with smaller ones (e.g., alanine or threonine).
[0522] An ADA2 polypeptide, such as any variant ADA2 polypeptide
provided herein, can be joined anywhere, but typically via its N-
or C-terminus, to the N- or C-terminus of a multimerization domain
to form a chimeric polypeptide. The linkage can be direct or
indirect via a linker. Also, the chimeric polypeptide can be a
fusion protein or can be formed by chemical linkage, such as
through covalent or non-covalent interactions. For example, when
preparing a chimeric polypeptide containing a multimerization
domain, nucleic acid encoding an ADA2 polypeptide can be operably
linked to nucleic acid encoding the multimerization domain
sequence, directly or indirectly or optionally via a linker domain.
The construct can encode a chimeric protein where the C-terminus of
the ADA2 polypeptide is joined to the N-terminus of the
multimerization domain. In some instances, a construct can encode a
chimeric protein where the N-terminus of the ADA2 polypeptide is
joined to the N- or C-terminus of the multimerization domain.
[0523] In examples where the multimerization domain is a
polypeptide, a gene fusion encoding the ADA2-multimerization domain
chimeric polypeptide is inserted into an appropriate expression
vector. The resulting ADA2-multimerization domain chimeric proteins
can be expressed in host cells transformed with the recombinant
expression vector, and allowed to assemble into multimers, where
the multimerization domains interact to form multivalent
polypeptides. Chemical linkage of multimerization domains to ADA2
polypeptides can also be effected using heterobifunctional
linkers.
[0524] The resulting chimeric polypeptides, and multimers formed
therefrom, can be purified by any suitable method such as, for
example, by affinity chromatography over Protein A or Protein G
columns. Where two nucleic acid molecules encoding different ADA2
chimeric polypeptides are transformed into cells, formation of
homo- and heterodimers will occur. Conditions for expression can be
adjusted so that heterodimer formation is favored over homodimer
formation. For example, for multimers formed by interaction of
disulfide-linkage of an Fc multimerization domain, homodimers can
be reduced under conditions that favor the disruption of
inter-chain disulfides, but do not affect intra-chain disulfides.
Alternatively, the formation of this type of heterodimer can be
biased by genetically engineering and expressing ADA2 fusion
molecules using a multimerization domain that promotes formation of
heterodimers, such as using a c-jun and c-fos leucine zipper
combination. Since the leucine zippers form predominantly
heterodimers, they can be used to drive the formation of the
heterodimers when desired. The ADA2 polypeptides contain an Fc
region or other multimerization domain also can be engineered to
include a tag to permit purification of desired heterodimers. The
products of the nuclear oncogenesfos and jun contain leucine zipper
domains that preferentially form a heterodimer (O'Shea et al.
(1989) Science, 245:646; Turner and Tijian (1989) Science,
243:1689). For example, the leucine zipper domains of the human
transcription factors c-jun and c-fos have been shown to form
stable heterodimers with a 1:1 stoichiometry (see e.g., Busch and
Sassone-Corsi (1990) Trends Genetics, 6:36-40; Gentz et al. (1989)
Science, 243:1695-1699). Although jun-jun homodimers also have been
shown to form, they are about 1000-fold less stable than jun-fos
heterodimers.
D. ADA2 CONJUGATES AND FUSION PROTEINS
[0525] Any ADA2 molecule, including any provided herein, can be
conjugated, directly or indirectly, to one or more heterologous
moiety. The ADA2 can be a wildtype ADA2, including allelic and
species variants, or can be any variant described herein in Section
C.2. above. The ADA2 molecule in the conjugate can be a monomer or
a dimer, for example, a heterodimer or a homodimer. Typically, the
ADA2 in the conjugate is a homodimer. The heterologous moiety can
be conjugated to one or both polypeptide subunits of the dimer.
[0526] For example, the ADA2 can be any that contains a polypeptide
having the sequence of amino acids set forth in any of SEQ ID NOS:5
or 326-336, 338-342, 375 or 380-383, or a sequence of amino acids
that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any of
SEQ ID NOS:5 or 326-336, 338-342, 375 or 380-383, or a
catalytically active fragment thereof. In one example, the ADA2 in
the conjugate provided herein can contain a polypeptide having the
sequence of amino acids set forth in any of SEQ ID NOS:5 or
326-336, 338-342, 375 or 380-383 or a catalytically active fragment
thereof, such as any of SEQ ID NOS:5, 326-334, 340, 375 or 380-383,
or a catalytically active fragment thereof. For example, the ADA2
in the conjugate provided herein can contain a polypeptide having
the sequence of amino acids set forth in SEQ ID NO:5, or a
catalytically active portion thereof. The catalytically active
portion can be one that lacks all or a portion of the PRB domain,
such as those set forth in any of SEQ ID NOS:548-550 or 579.
[0527] In other examples of conjugates provided herein, the
conjugate contains a variant ADA2 polypeptide, such as any
described herein. For example, conjugates provided herein can be an
ADA2 that contains the variant polypeptide set forth in any of SEQ
ID NOS:13-63, 71-285 or 552-931.
[0528] The heterologous moiety can include protein or polypeptide
moieties or non-polypeptide moieties. For example, the heterologous
moiety can be, but is not limited to, a peptide, small molecule,
nucleic acid, carbohydrate and polymer. The heterologous moiety can
be linked, directly or indirectly, to the ADA2 protein molecule.
For example, the heterologous moiety can be a protein or
polypeptide moiety, which can be directly or indirectly conjugated
to the ADA2 polypeptide, or produced as fusion proteins that are
directly or indirectly fused. In other cases, the heterologous
moiety is a non-peptide moiety that is conjugated to the ADA2
molecules.
[0529] The ADA2 protein can be conjugated to one or more
heterologous moieties, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or
more heterologous moieties. A heterologous moiety can be a
heterologous polypeptide moiety, or a heterologous non-polypeptide
moiety, or both. In other examples, the heterologous moieties can
include a combination of a heterologous polypeptide and a
non-polypeptide moiety. In some examples, all the heterologous
moieties are identical. In some examples, at least one heterologous
moiety is different from the other heterologous moieties. In some
examples, any ADA2 provided herein can be conjugated to two, three
or more than three heterologous moieties in tandem. In other
examples, any ADA2 provided herein can be conjugated to two, three,
or more heterologous moieties wherein at least an additional moiety
is interposed between two heterologous moieties (e.g., an ADA2
polypeptide, a linker, a protease-cleavable substrate, a
self-immolative spacer, or combinations thereof).
[0530] Conjugation with heterologous moieties can confer beneficial
properties compared to an ADA2 molecule that is not conjugated with
the heterologous moiety. Exemplary heterologous moieties are
moieties that increase the in vivo half-life of the molecule. Other
exemplary beneficial properties provided by a heterologous moiety
include, but are not limited to, increased protein expression in
mammalian expression systems, improved biophysical properties such
as stability and solubility, improved protein purification and
detection, visualization and localization and/or increased
enzymatic activity. For example, a heterologous moiety can be one
that facilitates detection, visualization or localization of an
ADA2 protein molecule or a fragment thereof containing the
heterologous moiety. Detection, visualization and/or location of
any ADA2 fragment thereof can be in vivo, in vitro, ex vivo, or
combinations thereof.
[0531] In some cases, when conjugated to an ADA2 or fragment
thereof, the heterologous moiety increases stability of the ADA2 or
a fragment thereof. For example, the presence of the heterologous
moiety can maintain one or more physical properties of an ADA2 in
response to an environmental condition (e.g., an elevated
temperature or low or high pH conditions) compared to the physical
property in the absence of the heterologous moiety. In some
examples, the physical property can include maintenance of the
covalent structure of an ADA2 (e.g., the absence of proteolytic
cleavage, unwanted oxidation or deamidation). In other examples,
the physical property can be the maintenance of a properly folded
state (e.g., the absence of soluble or insoluble aggregates or
precipitates). The stability of any ADA2 or ADA2 conjugate can be
measured by assaying a biophysical property of the protein, for
example thermal stability, pH unfolding profile, stable removal of
glycosylation, solubility, biochemical function (e.g. adenosine
deaminase activity or heparin binding activity) and/or combinations
thereof. Stability can be measured using methods known in the art,
such as, HPLC (high performance liquid chromatography), SEC (size
exclusion chromatography), DLS (dynamic light scattering). Methods
to measure thermal stability include, but are not limited to
differential scanning calorimetry (DSC), differential scanning
fluorimetry (DSF), circular dichroism (CD), and thermal challenge
assay. Exemplary methods to assess the stability of any ADA2 or
conjugate are described below in Section F.
[0532] In some examples, when conjugated to an ADA2 or fragment
thereof, the presence of the heterologous moiety reduces or
attenuates binding of ADA2 to heparin and other glycosaminoglycans
(GAGs) compared to the ADA2 protein not containing the heterologous
moiety (i.e. the free or non-conjugated ADA2). For example, ADA2
conjugates provided herein include those that exhibit no more than
1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%,
40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% of
the heparin binding of the ADA2 protein not containing the
heterologous moiety (i.e. the free or non-conjugated ADA2). For
example, it is shown herein that PEGylated ADA2 exhibits reduced
heparin binding compared to the corresponding non-PEGylated ADA2
(see e.g. Example 8). Typically, the heparin binding is exhibited
when the ADA2 is in dimer form, and the ADA2 conjugate is a dimer.
It also is understood the comparison of binding between the
conjugated and non-conjugated form is assessed under the same or
substantially the same conditions. In particular, the reduction in
binding in the presence of the heterologous moiety in the conjugate
can be due to steric blockage and/or alteration of electrostatic
charges on the surface.
[0533] In examples of conjugates provided herein, the heterologous
moiety improves one or more properties of the ADA2 (e g. half-life)
without substantially affecting the biological activity or function
of the ADA2 protein (e.g., adenosine deaminase activity). For
example, ADA2 conjugates provided herein exhibit about 50% to 500%,
such as about 50% to 400%, 50% to 300%, 50% to 200%, 50% to 150%,
50% to 100%, 50% to 80%, 80% to 400%, 80% to 300%, 80% to 200%, 80%
to 150%, 80% to 100%, 100% to 400%, 100% to 300%, 100% to 200% or
100% to 150% of the adenosine deaminase activity compared to the
ADA2 protein not containing the heterologous moiety (i.e. the free
or non-conjugated ADA2). For example, the ADA2 conjugate can
exhibit at least 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 100%,
110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 210%,
220%, 230%, 240%, 250%, 260%, 270%, 280%, 290%, 300%, 350%, 400%,
450%, 500% or more of the adenosine deaminase activity compared to
the ADA2 polypeptide not containing the heterologous moiety (i.e.
the free or non-conjugated ADA2). In some cases, ADA2 conjugates
provided herein exhibit increased or improved adenosine deaminase
activity compared to the ADA2 polypeptide not containing the
heterologous moiety (i.e. the free or non-conjugated ADA2), such as
greater than 100% or more adenosine deaminase activity. Typically,
the adenosine deaminase activity is exhibited when the ADA2 is in
dimer form, and the ADA2 conjugate is a dimer. It also is
understood the comparison of adenosine binding between the
conjugated and non-conjugated form is assessed under the same or
substantially the same conditions.
[0534] 1. Half-Life Extending Moieties
[0535] Non-limiting examples of heterologous moieties include any
that, when conjugated or linked (directly or indirectly) to the
ADA2 molecule, confers an increase in the in vivo and/or in vitro
half-life compared to the free- or non-conjugated ADA2. Half-life
of any ADA2 provided herein can be determined by any method known
to those of skill in the art and/or described herein, e.g.,
adenosine deaminase activity assays. Exemplary of such half-life
extending moieties are described in the following subsections.
[0536] For example, the heterologous moieties are peptides and
polypeptides with either unstructured or structured characteristics
that are associated with the prolongation of in vivo half-life when
conjugated to an ADA2. Non-limiting examples include albumin,
albumin fragments, Fc fragments of immunoglobulins, the .beta.
subunit of the C-terminal peptide (CTP) of the .beta. subunit of
human chorionic gonadotropin, HAP sequences, XTEN sequences, a
transferrin or a fragment thereof, a PAS polypeptide, polyglycine
linkers, polyserine linkers, albumin-binding moieties, non-natural
amino acid based conjugation or half-life extension, or any
fragments, derivatives, variants, or combinations of these
polypeptides.
[0537] The heterologous moiety can be a half-life extending moiety,
i.e., a heterologous moiety that increases the in vivo half-life of
any ADA2 provided herein compared to the in vivo half-life of the
ADA2 lacking such heterologous moiety. In vivo half-life of any
ADA2 provided herein can be determined by any method known to those
of skill in the art and/or described herein, e.g., adenosine
deaminase activity assays.
[0538] Exemplary half-life extending moieties that can be
conjugated, directly or indirectly, to any ADA2 provided herein
include: biocompatible fatty acids and derivatives thereof, hydroxy
alkyl starch (HAS) (e.g. hydroxy ethyl starch (HES)), polyethylene
glycol (PEG), Poly (Gly.sub.x-Ser.sub.y).sub.n, homo-amino-acid
polymers (HAP), hyaluronic acid (HA), heparosan polymers (HEP),
phosphorylcholine-based polymers (PC polymer), Fleximers, dextran,
polysialic acids (PSA), Fc domain, Transferrin, Albumin,
elastin-like peptides, XTEN sequences, albumin binding peptides, a
CTP peptide, a non-natural amino acid or non-natural amino acid
conjugate, and any combination thereof.
[0539] In some example, when conjugated to an ADA2 or fragment
thereof, the presence of one or more half-life extending moieties
results in the half-life of any ADA2 provided herein to be
increased compared to the half-life of the ADA2 lacking such one or
more half-life extending moieties (i.e. the free or non-conjugated
ADA2). For example, ADA2 conjugates provided herein exhibit a
half-life that is at least about 110%, 120%, 130%, 140%, 150%,
160%, 170%, 180%, 190%, 200%, 225%, 250%, 300%, 350%, 400%, 450%,
500%, 600%, 700%, 800% or more longer than the half-life of ADA2
polypeptide not containing the heterologous moiety (i.e. the free
or non-conjugated ADA2), or 900%, 1000%, 1100%, 1200%, 1300%,
1400%, 1500%, 1600%, 1700%, 1800%, 1900%, 2000%, 3000%, 4000%,
5000%, 6000%, 7000%, 8000%, 9000%, 10000%, or more longer than the
half-life of ADA2 polypeptide not containing the heterologous
moiety (i.e. the free or non-conjugated ADA2). In some examples,
the half-life of any ADA2 conjugate provided herein that is linked,
directly or indirectly, to a half-life extending moiety exhibits a
half-life that is about 1.5-fold to about 20-fold, about 1.5-fold
to about 15-fold, about 1.5-fold to about 10-fold longer, about
2-fold to about 10-fold, about 2-fold to about 9-fold, about 2-fold
to about 8-fold, about 2-fold to about 7-fold, about 2-fold to
about 6-fold, about 2-fold to about 5-fold, about 2-fold to about
4-fold, about 2-fold to about 3-fold, about 2.5-fold to about
10-fold, about 2.5-fold to about 9-fold, about 2.5-fold to about
8-fold, about 2.5-fold to about 7-fold, about 2.5-fold to about
6-fold, about 2.5-fold to about 5-fold, about 2.5-fold to about
4-fold, about 2.5-fold to about 3-fold, about 3-fold to about
10-fold, about 3-fold to about 9-fold, about 3-fold to about
8-fold, about 3-fold to about 7-fold, about 3-fold to about 6-fold,
about 3-fold to about 5-fold, about 3-fold to about 4-fold, about
4-fold to about 6 fold, about 5-fold to about 7-fold, or about
6-fold to about 8-fold longer than the half-life of the
corresponding ADA2 lacking such half-life extending moiety.
Typically, the half-life for activity in vivo is exhibited when the
ADA2 is in dimer form, and the ADA2 conjugate is a dimer. It also
is understood the comparison of half-life between the conjugated
and non-conjugated form is assessed under the same or substantially
the same conditions.
[0540] In some examples, the half-life of any ADA2 conjugate
provided herein that is linked, directly or indirectly, to a
half-life extending moiety can be or is at least or at least about
10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16
hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours, 22 hours,
23 hours, 24 hours, 25 hours, 26 hours, 27 hours, 28 hours, 29
hours, 30 hours, 32 hours, 34 hours, 36 hours, 38 hours, 40 hours,
42 hours, 46 hours, 48 hours, 50 hours, 55 hours, 60 hours, 65
hours, 70 hours, 75 hours, 80 hours or more. For example, the
half-life of any ADA2 conjugate provided herein can be 10 hours to
60 hours, such as 12 hours to 48 hours or 13 hours to 36 hours. For
example, Example 9 shows that an ADA2 conjugate that is a PEGylated
ADA2 exhibits a half-life of about or approximately 12 to 14 hours,
and PEGylated variant ADA2 molecules (e.g. R20E or K371D) exhibit
an even greater half-life of about or approximately 16 hours to 24
hours. Example 14 shows that other PEGylated variant ADA2 molecules
(e.g. R219Q/S262N) exhibit an even greater half-life of about or
approximately 39 hours to 47 hours.
[0541] The following sub-sections describe exemplary half-life
extending moieties in the ADA2 conjugates provided herein.
[0542] a. Low Complexity Polypeptides
[0543] An ADA2 conjugate provided herein can include an ADA2 that
is linked, directly or indirectly, to at least one heterologous
moiety that is a polypeptide with low compositional and/or
structural complexity (e.g., a disordered polypeptide with no
secondary or tertiary structure in solution under physiologic
conditions). In one example, the low complexity polypeptide
sequences are made of unstructured, hydrophilic amino acid
polymers. The low complexity polypeptides can provide beneficial
properties, for example, if the protein is subjected to higher
temperature or harsh conditions, such as HPLC purification.
[0544] b. C-Terminal Peptide (CTP) of the .beta. Subunit of Human
Chorionic Gonadotropin
[0545] An ADA2 conjugate provided herein can include an ADA2 that
is linked, directly or indirectly, to a heterologous moiety that
includes one C-terminal peptide (CTP) of the .beta. subunit of
human chorionic gonadotropin, or fragment, variant, or derivative
thereof. One or more CTP peptides inserted into a recombinant
protein is known to increase the in vivo half-life of that protein
(see, e.g., U.S. Pat. No. 5,712,122). Exemplary CTP peptides
include DPRFQDSSSSKAPPPSLPSPSRLPGPSDTPIL (SEQ ID NO:303) or
SSSSKAPPPSLPSPSRLPGPSDTPILPQ. (SEQ ID NO:304) (See, e.g., U.S.
Patent Publication No. US 2009/0087411).
[0546] c. Immunoglobulin Constant Region (Fc) or Portions
Thereof
[0547] An ADA2 conjugate provided herein can include an ADA2 that
is linked, directly or indirectly, to an Fc domain or variant
thereof. Fc domains, fragments, variants, and derivatives are known
to one of skill in the art and are described, e.g., in U.S. Pat.
No. 5,457,035; U.S. Patent Publication No. US 2006/0024298,
International PCT Publication Nos. WO 2011/069164, WO 2012/006623,
WO 2012/006635, or WO 2012/006633, each of which is incorporated by
reference herein in its entirety. Preparations of fusion proteins
containing polypeptides fused to various portions of
antibody-derived polypeptides (including the Fc domain) has been
described, see e.g., Ashkenazi et al. (1991) PNAS 88: 10535; Byrn
et al. (1990) Nature, 344:667; and Hollenbaugh and Aruffo, (2002)
"Construction of Immunoglobulin Fusion Proteins," in Current
Protocols in Immunology, Ch. 10, pp. 10.19.1-10.19.11.
[0548] An Fc region has domains denoted C.sub.H (constant heavy)
domains (C.sub.HI, C.sub.H2, C.sub.H3 (optionally C.sub.H4)).
Depending on the isotype, (i.e. IgG, IgM, IgA IgD or IgE), the Fc
region can have three or four CH domains. Some isotypes (e.g. IgG)
Fc regions also contain a hinge region (see Janeway et al. 2001,
Immunobiology, Garland Publishing, N.Y., N.Y). In humans, there are
five antibody isotypes classified based on their heavy chains
denoted as delta (.delta.), gamma (.gamma.), mu (.mu.), and alpha
(.alpha.) and epsilon (.epsilon.), giving rise to the IgD, IgG,
IgM, IgA, and IgE classes of antibodies, respectively. The IgA and
IgG classes contain the subclasses IgA1, IgA2, IgG1, IgG2, IgG3,
and IgG4. Sequence differences between immunoglobulin heavy chains
cause the various isotypes to differ in, for example, the number of
C domains, the presence of a hinge region, and the number and
location of interchain disulfide bonds. For example, IgM and IgE
heavy chains contain an extra C domain (C.sub.H4), that replaces
the hinge region. The Fc regions of IgG IgD, and IgA pair with each
other through their C.gamma.3, C.delta.3, and C.alpha.3 domains,
whereas the Fc regions of IgM and IgE dimerize through their C.mu.4
and C.epsilon.4 domains. IgM and IgA form multimeric structures
with ten and four antigen-binding sites, respectively.
[0549] Fc regions are known to a skilled artisan, and any can be
used in the conjugates provided herein so long as the resulting
conjugate retains adenosine deaminase activity. An Fc region or a
portion thereof for producing any ADA2 provided herein can be
obtained from a number of different sources. In some examples, an
Fc region or a portion thereof is derived from a human
immunoglobulin. The Fc region or a portion thereof can also be
derived from an immunoglobulin of another mammalian species,
including for example, a rodent (e.g. a mouse, rat, rabbit, guinea
pig) or non-human primate (e.g. chimpanzee, macaque) species.
Moreover, the Fc region or a portion thereof can be derived from
any immunoglobulin class, including IgG (including human subclasses
IgG1, IgG2, IgG3, or IgG4), IgA (including human subclasses IgA1
and IgA2), IgD, IgE, and IgM. In one example, the human isotype
IgG1 is used. An ADA2 provided herein that is conjugated to an Fc
region of an immunoglobulin can confer several desirable properties
including increased stability, increased serum half-life (see Capon
et al. (1989) Nature 337:525) as well as binding to Fc receptors
such as the neonatal Fc receptor (FcRn) (U.S. Pat. Nos. 6,086,875,
6,485,726, 6,030,613; WO 03/077834; US 2003/0235536, each of which
is incorporated by reference herein in its entirety). In other
examples, where effector functions mediated by the Fc-Fc receptor
(FcR) interactions are to be minimized, fusion with IgG isotypes
that poorly recruit complement or effector cells, such as for
example, the Fc of IgG2 or IgG4, is contemplated. Further, linkers
can be used to covalently link Fc to another polypeptide to
generate a Fc chimera.
[0550] Exemplary sequences of heavy chain constant regions for
human IgG sub-types are set forth in SEQ ID NO:355 (IgG1), SEQ ID
NO:356 (IgG2), SEQ ID NO:357 (IgG3), and SEQ ID NO:358 (IgG4). For
example, for the exemplary heavy chain constant region set forth in
SEQ ID NO:355, the C.sub.H1 domain corresponds to amino acids 1-98,
the hinge region corresponds to amino acids 99-110, the C.sub.H2
domain corresponds to amino acids 111-223, and the C.sub.H3 domain
corresponds to amino acids 224-330.
[0551] Modified Fc domains also are contemplated herein for
conjugation to any ADA2 provided herein. In some examples, the Fc
region is modified such that it exhibits altered binding to an FcR
to result in altered (i.e. more or less) effector function compared
to the effector function of an Fc region of a wild-type
immunoglobulin heavy chain Thus, a modified Fc domain can have
altered affinity, including but not limited to, increased or low or
no affinity for the Fc receptor. For example, the different IgG
subclasses have different affinities for the Fc.gamma. receptors
(Fc.gamma.Rs), with IgG1 and IgG3 typically binding substantially
better to the receptors than IgG2 and IgG4. In addition, different
Fc.gamma.Rs mediate different effector functions. Fc.gamma.R1,
Fc.gamma.RIIa/c, and Fc.gamma.RIIIa are positive regulators of
immune complex triggered activation, characterized by having an
intracellular domain that has an immunoreceptor tyrosine-based
activation motif (ITAM). Fc.gamma.RIIb, however, has an
immunoreceptor tyrosine-based inhibition motif (ITIM) and is
therefore inhibitory. In some instances, an ADA2 conjugate
including an Fc domain provided herein can be modified to enhance
binding to the complement protein C1q.
[0552] In certain examples, Fc region for conjugation to any ADA2
provided herein can include one or more truncated Fc regions that
are nonetheless sufficient to confer Fc receptor (FcR) binding
properties to the Fc region. For example, the portion of an Fc
region that binds to FcRn (i.e., the FcRn binding portion) can
include from about amino acids 282-438 of IgG1, with the primary
contact sites being amino acids 248, 250-257, 272, 285, 288,
290-291, 308-311, and 314 of the C.sub.H2 domain and amino acid
residues 385-387, 428, and 433-436 of the C.sub.H3 domain (amino
acid numbering based on the EU numbering system; see Edelman et al.
(1969) PNAS 63:78-85 and Kabat et al. (1991) Sequences of Proteins
of Immunological Interest, Fifth Edition, U.S. Department of Health
and Human Services, NIH Publication No. 91-3242). Thus, an Fc
region in any ADA2 provided herein can include an FcRn binding
portion. FcRn binding portions can be derived from heavy chains of
any isotype, including IgG1, IgG2, IgG3 and IgG4. Altering the
affinity of an Fc region for a receptor can modulate the effector
functions and/or pharmacokinetic properties associated by the Fc
domain. Modified Fc domains are known to one of skill in the art
and described in the literature, see e.g. U.S. Pat. No. 5,457,035;
U.S. Patent Publication No. US 2006/0024298; and International
Patent Publication No. WO 2005/063816 for exemplary
modifications.
[0553] In certain examples, an Fc region for conjugation to any
ADA2 provided herein can include at least one of: a hinge (e.g.,
upper, middle, and/or lower hinge region) domain (about amino acids
216-230 of an antibody Fc region based on EU numbering), a C.sub.H2
domain (about amino acids 231-340 of an antibody Fc region based on
EU numbering), a C.sub.H3 domain (about amino acids 341-438 of an
antibody Fc region based on EU numbering), a C.sub.H4 domain, or a
variant, portion, or fragment thereof. In other examples, an Fc
region can include a complete Fc domain (i.e., a hinge domain, a
C.sub.H2 domain, and a C.sub.H3 domain). In some examples, an Fc
region can include, a hinge domain (or a portion thereof) fused to
a C.sub.H3 domain (or a portion thereof), a hinge domain (or a
portion thereof) fused to a C.sub.H2 domain (or a portion thereof),
a C.sub.H2 domain (or a portion thereof) fused to a C.sub.H3 domain
(or a portion thereof), a C.sub.H2 domain (or a portion thereof)
fused to both a hinge domain (or a portion thereof) and a C.sub.H
domain (or a portion thereof). In still other examples, an Fc
region lacks at least a portion of a C.sub.H2 domain (e.g., all or
part of a C.sub.H2 domain). In a particular example, an Fc region
can include amino acids corresponding 221 to 447 (based on the EU
numbering system; see Edelman et al. (1969) PNAS 63:78-85 and Kabat
et al. (1991) Sequences of Proteins of Immunological Interest,
Fifth Edition, U.S. Department of Health and Human Services, NIH
Publication No. 91-3242)
[0554] An Fc region for conjugation to any ADA2 provided herein can
include, for example, a modification (e.g., an amino acid
substitution) at one or more of the amino acid positions disclosed
in International. PCT Pub. Nos. WO88/07089, WO96/14339, WO98/05787,
WO98/23289, WO99/51642, WO99/58572, WO00/09560, WO00/32767,
WO00/42072, WO02/44215, WO02/060919, WO03/074569, WO04/016750,
WO04/029207, WO04/035752, WO04/063351, WO04/074455, WO04/099249,
WO05/040217, WO04/044859, WO05/070963, WO05/077981, WO05/092925,
WO05/123780, WO06/019447, WO06/047350, and WO06/085967; U.S. Pat.
Publ. Nos. US 2007/0231329, US2007/0231329, US2007/0237765,
US2007/0237766, US2007/0237767, US2007/0243188, US2007/0248603,
US2007/0286859, US2008/0057056; or U.S. Pat. Nos. 5,648,260;
5,739,277; 5,834,250; 5,869,046; 6,096,871; 6,121,022; 6,194,551;
6,242,195; 6,277,375; 6,528,624; 6,538,124; 6,737,056; 6,821,505;
6,998,253; 7,083,784; 7,404,956; and 7,317,091, each of which is
incorporated by reference herein in its entirety. In one example,
the specific modification (e.g., the specific substitution of one
or more amino acids disclosed in the art) can be made at one or
more of the disclosed amino acid positions. In another example, a
different change at one or more of the disclosed amino acid
positions (e.g., the different substitution of one or more amino
acid position disclosed in the art) can be made.
[0555] In some examples, any ADA2 provided herein can be conjugated
to at least one Fc region as a fusion protein. Typically, such a
fusion retains at least a functionally active hinge, C.sub.H2 and
C.sub.H3 domains of the constant region of an immunoglobulin heavy
chain. For example, a full-length Fc sequence of IgG1 includes
amino acids 99-330 of the sequence set forth in SEQ ID NO:355. An
exemplary Fc sequence for hIgG1 is set forth in SEQ ID NO:359, and
contains almost all of the hinge sequence, and the complete
sequence for the C.sub.H2 and C.sub.H3 domain as set forth in SEQ
ID NO:355. Another exemplary Fc polypeptide is the Fc polypeptide
set forth in SEQ ID NO:361. Another exemplary Fc polypeptide is set
forth in PCT Pub. No. WO 93/10151, and is a single chain
polypeptide extending from the N-terminal hinge region to the
native C-terminus of the Fc region of a human IgG1 antibody (SEQ ID
NO:359). The precise site at which the linkage is made is not
critical: particular sites are well known and can be selected in
order to optimize the biological activity, secretion, or binding
characteristics of the ADA2 protein molecule. For example, other
exemplary Fc polypeptide sequences begin at amino acid C109 or P113
of the sequence set forth in SEQ ID NO:355 (see e.g., U.S. Pub. No.
2006/0024298).
[0556] An Fc region for conjugation to any ADA2 provided herein can
also contain amino acid substitution which alters the glycosylation
of the chimeric protein known in the art. For example, the Fc
region of any ADA2 provided herein can be conjugated to an Fc
region having a mutation leading to reduced glycosylation (e.g., N-
or O-linked glycosylation) or to an altered glycoform of the
wild-type Fc moiety (e.g., a low fucose or fucose-free glycan).
[0557] An Fc region for conjugation to any ADA2 provided herein
also can be engineered to include a tag with metal chelates or
other epitope. The tagged domain can be used for rapid purification
by metal-chelate chromatography, and/or by antibodies, to allow by
detection of western blots, immunoprecipitation, or activity
depletion/blocking in bioassays.
[0558] d. Albumin or Fragment, or Variant Thereof
[0559] An ADA2 conjugate provided herein can include an ADA2 that
is linked, directly or indirectly, to a heterologous moiety that
includes albumin or a functional fragment thereof. Human serum
albumin (HSA, or HA), a protein of 609 amino acids in its
full-length form (exemplary sequence set forth in SEQ ID NO:305),
is responsible for a significant proportion of the osmotic pressure
of serum and also functions as a carrier of endogenous and
exogenous ligands. Albumin can be a full-length albumin or a
functional fragment, variant, derivative, or analog thereof.
Examples of albumin or the fragments or variants thereof are
disclosed in US Pat. Publ. Nos. 2008/0194481, 2008/0004206,
2008/0161243, 2008/0261877, or 2008/0153751 or PCT Publ. Nos.
2008/033413, 2009/058322, or 2007/021494, each of which is
incorporated by reference herein in its entirety.
[0560] In some examples, any ADA2 provided herein can include
albumin, a fragment, or a variant thereof which is further linked
to a heterologous moiety selected from an immunoglobulin constant
region or portion thereof (e.g., an Fc region), a PAS sequence,
HES, XTEN sequences, PEG, or any combinations thereof.
[0561] e. Albumin Binding Moiety
[0562] An ADA2 conjugate provided herein can include an ADA2 that
is linked, directly or indirectly, to a heterologous moiety that is
an albumin binding moiety, for example, an albumin binding peptide,
a bacterial albumin binding domain, an albumin-binding antibody
fragment, a fatty acid, or any combinations thereof.
[0563] For example, the albumin binding protein can be a bacterial
albumin binding protein, an antibody or an antibody fragment
including domain antibodies (see U.S. Pat. No. 6,696,245). An
albumin binding protein, for example, can be a bacterial albumin
binding domain, such as the one of Streptococcal protein G (Konig,
T. and A. Skerra, A. (1998) J Immunol. Methods 218:73-83). Other
examples of albumin binding peptides that can be used to conjugate
to any ADA2 provided herein are, for instance, those having a
Cys-Xaa.sub.1-Xaa.sub.2-Xaa.sub.3-Xaa.sub.4-Cys consensus sequence
(SEQ ID NO:306), wherein Xaa.sub.1 is Asp, Asn, Ser, Thr, or Trp;
Xaa.sub.2 is Asn, Gln, His, Ile, Leu, or Lys; Xaa.sub.3 is Ala,
Asp, Phe, Trp, or Tyr; and Xaa.sub.4 is Asp, Gly, Leu, Phe, Ser, or
Thr (US Patent Pub. No. 2003/0069395; Dennis et al. (2002) J. Biol.
Chem. 277: 35035-35043).
[0564] Domain 3 from Streptococcal protein G (Kraulis et al, (1996)
FEBS Lett. 378:190-194; Linhult et al. (2002) Protein Sci.
11:206-213) is an example of a bacterial albumin-binding domain.
Examples of albumin-binding peptides include a series of peptides
having the core sequence DICLPRWGCLW (SEQ ID NO:307). (See, e.g.,
Dennis et al. (2002) J. Biol. Chem. 277: 35035-35043). Other
examples of albumin-binding peptides include: RLIEDICLPRWGCLWEDD
(SEQ ID NO:308); QRLMEDICLPRWGCLWEDDF (SEQ ID NO:309);
QGLIGDICLPRWGCLWGDSVK (SEQ ID NO:310), and GEWWEDICLPRWGCLWEEED
(SEQ ID NO:311).
[0565] Examples of albumin-binding antibody fragments that can be
conjugated to any ADA2 provided herein include those disclosed in
Muller and Kontermann, Curr. Opin. Mol. Ther. (2007) 9:319-326;
Roovers et al. (2007), Cancer Immunol. Immunother. 56:303-317; Holt
et al. (2008) Prot. Eng. Design Sci., 21:283-288, each of which is
incorporated by reference herein in its entirety. An example of
such albumin binding moiety is the
2-(3-maleimidopropanamido)-6-(4-(4-iodophenyl)butanamido) hexanoate
("Albu" tag) (Trussel et al. (2009) Bioconjugate Chem.
20:2286-2292).
[0566] Fatty acids, in particular long chain fatty acids (LCFA) and
long chain fatty acid-like albumin-binding compounds can be used to
extend the in vivo half-life of any ADA2 provided herein. An
example of an LCFA-like albumin-binding compound is
16-(1-(3-(9-(((2,5-dioxopyrrolidin-1-yloxy)
carbonyloxy)-methyi)-7-sulfo-9H-fluoren-2-ylamino)-3-oxopropyl)-2,5-dioxo-
pyrrolidin-3-ylthio) hexadecanoic acid (see, e.g., WO
2010/140148).
[0567] f. PAS Sequences
[0568] An ADA2 conjugate provided herein can include an ADA2 that
is linked, directly or indirectly, to at least one heterologous
moiety that is a PAS sequence, which is an amino acid sequence that
includes mainly alanine and serine residues or that includes mainly
alanine, serine, and proline residues. The amino acid sequences
form random coil conformation under physiological conditions.
Accordingly, the PAS sequence is a building block, an amino acid
polymer, or a sequence cassette made of alanine, serine, and
proline, which can be used as a part of the heterologous moiety
conjugated to any ADA2 provided herein.
[0569] One of skilled in the art is aware that an amino acid
polymer also can form a random coil conformation when residues
other than alanine, serine, and proline are added as a minor
constituent in the PAS sequence. Minor constituents include amino
acids other than alanine, serine, and proline that can be added in
the PAS sequence to a certain degree, e.g., up to about 12%, i.e.,
about 12 of 100 amino acids of the PAS sequence, up to about 10%,
i.e. about 10 of 100 amino acids of the PAS sequence, up to about
9%, i.e., about 9 of 100 amino acids, up to about 8%, i.e., about 8
of 100 amino acids, about 6%, i.e., about 6 of 100 amino acids,
about 5%, i.e., about 5 of 100 amino acids, about 4%, i.e., about 4
of 100 amino acids, about 3%, i.e., about 3 of 100 amino acids,
about 2%, i.e., about 2 of 100 amino acids, or about 1%, i.e.,
about 1 of 100 of the amino acids. The amino acids different from
alanine, serine and proline can be selected from Arg, Asn, Asp,
Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Tyr, or
Val.
[0570] Under physiological conditions, the PAS sequence stretch
forms a random coil conformation and thereby can mediate an
increased in vivo and/or in vitro stability to any ADA2 provided
herein. Since the random coil domain does not adopt a stable
structure or function by itself, the biological activity mediated
by any ADA2 provided herein is essentially preserved. In other
examples, the PAS sequences that form random coil domains are
biologically inert, especially with respect to proteolysis in blood
plasma, immunogenicity, isoelectric point/electrostatic behavior,
binding to cell surface receptors or internalization, but are still
biodegradable, which provides clear advantages over synthetic
polymers such as PEG
[0571] Non-limiting examples of the PAS sequences forming random
coil conformation include an amino acid sequence such as
ASPAAPAPASPAAPAPSAPA (SEQ ID NO:312), AAPASPAPAAPSAPAPAAPS (SEQ ID
NO:313), APSSPSPSAPSSPSPASPSS (SEQ ID NO:314), APSSPSPSAPSSPSPASPS
(SEQ ID NO:315), SSPSAPSPSSPASPSPSSPA (SEQ ID NO:316),
AASPAAPSAPPAAASPAAPSAPPA (SEQ ID NO:317), ASAAAPAAASAAASAPSAAA (SEQ
ID NO:318) or any combinations thereof. Additional examples of PAS
sequences are known in the art (see, e.g., US Pat. Publ. No.
2010/0292130 and International PCT Publ. No. WO 2008/155134)
[0572] g. HAP Sequences
[0573] An ADA2 conjugate provided herein can include an ADA2 that
is linked, directly or indirectly, to at least one heterologous
moiety that is a glycine-rich homo-amino-acid polymer (HAP). The
HAP sequence can include a repetitive sequence of glycine, which
has at least 50 amino acids, at least 100 amino acids, 120 amino
acids, 140 amino acids, 160 amino acids, 180 amino acids, 200 amino
acids, 250 amino acids, 300 amino acids, 350 amino acids, 400 amino
acids, 450 amino acids, or 500 amino acids in length. In one
example, the HAP sequence is capable of extending half-life of a
moiety fused to or linked to the HAP sequence. Non-limiting
examples of the HAP sequence includes, but are not limited to
(Gly).sub.n(SEQ ID NO:368), (Gly.sub.4Ser).sub.n(SEQ ID NO:343) or
Ser(Gly.sub.4Ser).sub.n(SEQ ID NO:595), wherein n is 1, 2, 3, 4, 5,
6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20. In one
example, n is 20, 21, 22, 23, 24, 25, 26, 26, 28, 29, 30, 31, 32,
33, 34, 35, 36, 37, 38, 39, or 40. In another example, n is 50, 60,
70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or
200.
[0574] h. XTEN Sequences
[0575] An ADA2 conjugate provided herein can include an ADA2 that
is linked, directly or indirectly, to at least one heterologous
moiety that includes an XTEN sequence, polypeptide or fragment,
variant, or derivative thereof. XTEN sequence is an extended length
polypeptide sequence with non-naturally occurring, substantially
non-repetitive sequences that are composed mainly of small
hydrophilic amino acids, with the sequence having a low degree or
no secondary or tertiary structure under physiologic conditions
(Schellenberger et al. (2009) Nat Biotechnol. 27(12):1186-1190). An
exemplary XTEN sequence is an unstructured recombinant polypeptide
of 864 amino acids (SEQ ID NO:373), which extends the plasma
half-life of the protein fused to the moiety. As a heterologous
moiety, XTEN sequences can function as a half-life extension
moiety. In addition, XTEN sequences can provide desirable
properties including, but are not limited to, enhanced
pharmacokinetic parameters and solubility characteristics. For
example, conjugation of XTEN sequences to any ADA2 provided herein
can confer one or more of the following advantageous properties:
conformational flexibility, enhanced aqueous solubility, high
degree of protease resistance, low immunogenicity, low binding to
mammalian receptors, or increased hydrodynamic (or Stokes) radii.
In some examples, an XTEN sequence can increase pharmacokinetic
properties such as longer in vivo half-life or increased area under
the curve (AUC), such that any ADA2 provided herein stays in vivo
and retains adenosine deaminase activity for an increased period of
time compared to the same ADA2 without the XTEN heterologous
moiety.
[0576] Examples of XTEN sequences that can be used as heterologous
moieties conjugated to any ADA2 provided herein include any of
those described in U.S. Pat. Nos. 7,855,279 and 7,846,445, U.S.
Patent Publication Nos. 2009/0092582, 2010/0239554, 2010/0323956,
2011/0046060, 2011/0046061, 2011/0077199, 2011/0172146,
2012/0178691, 2013/0017997, or 2012/0263701, or International
Patent Publication Nos. WO 2010091122, WO 2010144502, WO
2010144508, WO 2011028228, WO 2011028229, or WO 2011028344, each of
which is incorporated by reference herein in its entirety.
[0577] i. Transferrin or Fragment Thereof
[0578] An ADA2 conjugate provided herein can include an ADA2 that
is linked, directly or indirectly, to at least one heterologous
moiety that is a transferrin or a fragment thereof. Any transferrin
can be conjugated to any ADA2 provided herein. For example,
wildtype human Tf (Tf) is a 679 amino acid protein (amino acid
sequence set forth in SEQ ID NOS:320 and 324; GenBank Acc. Nos. NP
001054.1 and AAB22049.1; nucleic acid sequence set forth in SEQ ID
NOS:319 and 322-323, GenBank Acc. Nos. NM001063, M12530, XM039845,
and S95936), of approximately 75 kDa (excluding glycosylation),
with two main domains, the N terminal domain (about 330 amino
acids) and the C terminal domain (about 340 amino acids), which
appear to originate from a gene duplication. The N domain includes
two subdomains, N1 domain and N2 domain, and the C domain includes
two subdomains, C1 domain and C2 domain.
[0579] In one example, the transferrin heterologous moiety includes
a transferrin splice variant. In one example, a transferrin splice
variant can be a splice variant of human transferrin (SEQ ID
NO:325; Genbank Acc. No. AAA61140). In another example, the
transferrin portion of the chimeric protein includes one or more
domains of the transferrin sequence, e.g., N domain, C domain, N1
domain, N2 domain, C1 domain, C2 domain or any combinations
thereof.
[0580] j. Polymer Conjugation
[0581] An ADA2 conjugate provided herein can include an ADA2 that
is linked, directly or indirectly, to at least one heterologous
moiety that is a polymeric molecule (polymer).
[0582] Exemplary of polymers are such as polyols (i.e., poly-OH),
polyamines (i.e., poly-NH.sub.2) and polycarboxyl acids (i.e.,
poly-COOH), and further heteropolymers i.e., polymers containing
one or more different coupling groups e.g., a hydroxyl group and
amine groups. Examples of suitable polymeric molecules include
polymeric molecules selected from among polyalkylene oxides (PAO),
such as polyalkylene glycols (PAG), including polyethylene glycols
(PEG), ethylene glycol/propylene glycol copolymers,
methoxypolyethylene glycols (mPEG) and polypropylene glycols,
PEG-glycidyl ethers (Epox-PEG), PEG-oxycarbonylimidazole (CDI-PEG)
branched polyethylene glycols (PEGs), polyvinyl alcohol (PVA),
polycarboxylates, polyvinylpyrrolidone, polyoxazoline,
polyacryloylmorpholine, poly-D,L-amino acids,
polyethylene-co-maleic acid anhydride, polystyrene-co-maleic acid
anhydride, dextrans including carboxymethyl-dextrans, heparin,
homologous albumin, celluloses, including methylcellulose,
carboxymethylcellulose, ethylcellulose, hydroxyethylcellulose
carboxyethylcellulose and hydroxypropylcellulose, hydrolysates of
chitosan, starches such as hydroxyethyl-starches and
hydroxypropyl-starches, glycogen, agaroses and derivatives thereof,
guar gum, pullulan, inulin, xanthan gum, carrageenan, pectin,
alginic acid hydrolysates, bio-polymer, and those disclosed in the
art, for example, in U.S. Pat. No. 8,741,283 and International PCT
Publication No. WO 2007/149686.
[0583] For example, polymer conjugated to any ADA2 provided herein
can generally correspond to the following formula:
[R--NH].sub.z-(ADA2)
[0584] wherein (ADA2) represents any ADA2 described herein, such as
wildtype, variants or modified forms thereof;
[0585] NH-- is an amino group of an amino acid found on the ADA2
provided herein for the attachment to the polymer;
[0586] z is a positive integer, such as from about 1 to about 32,
or 1-3, 2-4, 3-5, 4-6, 5-7, 6-8, 7-9, 8-10, 9-1 1, 10-12, 11-13,
12-14, 13-15, 14-16, 15-17, 16-18, 17-19, 18-20, 19-21, 20-22,
21-23, 22-24, 23-25, 24-26, 25-27, 26-28, 27-29, 28-30, 29-31 or
30-32;
[0587] R is a substantially non-antigenic polymer molecule that is
attached to the ADA2 provided herein in a releasable or
non-releasable form. Exemplary non-antigenic polymeric molecule can
be any described herein and those disclosed in the art, for
example, in U.S. Pat. No. 8,741,283 and International PCT
Publication No. WO 2007/149686.
[0588] For example, any ADA2 described herein can be conjugated to
least one polyethylene glycol (PEG) molecule. In some examples, the
polymer can be water-soluble. In some examples, any ADA2 provided
herein is conjugated to a PEG heterologous moiety and further
includes a heterologous moiety selected from an immunoglobulin
constant region or portion thereof (e.g., an Fc region), a PAS
sequence, hydroxyethyl starch (HES) and albumin or fragment or
variant thereof, an XTEN sequence, or any combinations thereof.
[0589] Covalent or other stable attachment (conjugation) of
polymeric molecules, such as polyethylene glycol (PEGylation moiety
(PEG)), to any ADA2 polypeptide, including variant ADA2
polypeptides, impart beneficial properties to the resulting
ADA2-polymer composition. Such properties include improved
biocompatibility, extension of protein (and enzymatic activity)
half-life in the plasma, cells and/or in other tissues within a
subject, effective shielding of the protein from proteases and
hydrolysis, improved biodistribution, enhanced pharmacokinetics
and/or pharmacodynamics, increased stability, decreased
immunogenicity, prolonged/sustained treatment effects in a subject,
and increased water solubility (see U.S. Pat. No. 4,179,337).
[0590] i. Polyethylene Glycol (PEG)
[0591] Polyethylene glycol (PEG) has been widely used in
biomaterials, biotechnology and medicine primarily because PEG is a
biocompatible, nontoxic, water-soluble polymer that is typically
nonimmunogenic (Zhao and Harris, ACS Symposium Series 680: 458-72,
1997). In the area of drug delivery, PEG derivatives have been
widely used in covalent attachment (i.e., "PEGylation") to proteins
to reduce immunogenicity, proteolysis and kidney clearance and to
enhance solubility (Zalipsky, Adv. Drug Del. Rev. 16:157-82, 1995).
Similarly, PEG has been attached to low molecular weight,
relatively hydrophobic drugs to enhance solubility, reduce toxicity
and alter biodistribution. Typically, PEGylated drugs are injected
as solutions.
[0592] A closely related application is synthesis of crosslinked
degradable PEG networks or formulations for use in drug delivery
since much of the same chemistry used in design of degradable,
soluble drug carriers can also be used in design of degradable gels
(Sawhney et al., Macromolecules 26: 581-87, 1993). It also is known
that intermacromolecular complexes can be formed by mixing
solutions of two complementary polymers. Such complexes are
generally stabilized by electrostatic interactions
(polyanion-polycation) and/or hydrogen bonds (polyacid-polybase)
between the polymers involved, and/or by hydrophobic interactions
between the polymers in an aqueous surrounding (Krupers et al.,
Eur. Polym J. 32:785-790, 1996). For example, mixing solutions of
polyacrylic acid (PAAc) and polyethylene oxide (PEO) under the
proper conditions results in the formation of complexes based
mostly on hydrogen bonding. Dissociation of these complexes at
physiologic conditions has been used for delivery of free drugs
(i.e., non-PEGylated). In addition, complexes of complementary
polymers have been formed from both homopolymers and
copolymers.
[0593] Numerous reagents for PEGylation have been described in the
art. Such reagents include, but are not limited to,
N-hydroxysuccinimidyl (NHS) activated PEG; succinimidyl mPEG,
mPEG.sub.2-N-hydroxysuccinimide, mPEG succinimidyl
alpha-methylbutanoate, mPEG succinimidyl propionate, mPEG
succinimidyl butanoate, mPEG carboxymethyl 3-hydroxybutanoic acid
succinimidyl ester, homobifunctional PEG-succinimidyl propionate,
homobifunctional PEG propionaldehyde, homobifunctional PEG
butyraldehyde, PEG maleimide, PEG hydrazide,
p-nitrophenyl-carbonate PEG; mPEG-benzotriazole carbonate,
propionaldehyde PEG, mPEG butryaldehyde, branched mPEG.sub.2
butyraldehyde, mPEG acetyl, mPEG piperidone, mPEG methylketone,
mPEG "linkerless" maleimide, mPEG vinyl sulfone, mPEG thiol, mPEG
orthopyridylthioester, mPEG orthopyridyl disulfide, Fmoc-PEG-NHS,
Boc-PEG-NHS, vinylsulfone PEG-NHS, acrylate PEG-NHS, fluorescein
PEG-NHS, and biotin PEG-NHS (see e.g., Monfardini et al.,
Bioconjugate Chem. 6:62-69, 1995; Veronese et al., J. Bioactive
Compatible Polymers 12:197-207, 1997; U.S. Pat. No. 5,672,662; U.S.
Pat. No. 5,932,462; U.S. Pat. No. 6,495,659; U.S. Pat. No.
6,737,505; U.S. Pat. No. 4,002,531; U.S. Pat. No. 4,179,337; U.S.
Pat. No. 5,122,614; U.S. Pat. No. 5,324,844; U.S. Pat. No.
5,446,090; U.S. Pat. No. 5,612,460; U.S. Pat. No. 5,643,575; U.S.
Pat. No. 5,766,581; U.S. Pat. No. 5,795,569; U.S. Pat. No.
5,808,096; U.S. Pat. No. 5,900,461; U.S. Pat. No. 5,919,455; U.S.
Pat. No. 5,985,263; U.S. Pat. No. 5,990,237; U.S. Pat. No.
6,113,906; U.S. Pat. No. 6,214,966; U.S. Pat. No. 6,258,351; U.S.
Pat. No. 6,340,742; U.S. Pat. No. 6,413,507; U.S. Pat. No.
6,420,339; U.S. Pat. No. 6,437,025; U.S. Pat. No. 6,448,369; U.S.
Pat. No. 6,461,802; U.S. Pat. No. 6,828,401; U.S. Pat. No.
6,858,736; U.S. Pat. No. 8,741,283; US 2001/0021763; US
2001/0044526; US 2001/0046481; US 2002/0052430; US 2002/0072573; US
2002/0156047; US 2003/0114647; US 2003/0143596; US 2003/0158333; US
2003/0220447; US 2004/0013637; US 2004/0235734; WO 05000360; US
2005/0114037; US 2005/0171328; US 2005/0209416; EP 1064951; EP
0822199; WO 01076640; WO 0002017; WO 0249673; WO 94/28024; and WO
01/87925).
[0594] In particular, the polymer is a polyethylene glycol (PEG).
Suitable polymeric molecules for attachment to any ADA2
polypeptide, including variant ADA2 polypeptides, include, but are
not limited to, polyethylene glycol (PEG) and PEG derivatives such
as methoxy-polyethylene glycols (mPEG), PEG-glycidyl ethers
(Epox-PEG), PEG-oxycarbonylimidazole (CDI-PEG), branched PEGs, and
polyethylene oxide (PEO) (see e.g., Roberts et al., Advanced Drug
Delivery Review (2002) 54: 459-476; Harris and Zalipsky, S (eds.)
"Poly(ethylene glycol), Chemistry and Biological Applications" ACS
Symposium Series 680, 1997; Mehvar et al., J. Pharm. Pharmaceut.
Sci., 3(1):125-136, 2000; Harris, (2003) Nature Reviews Drug
Discovery 2:214-221; and Tsubery, (2004) J Biol. Chem
279(37):38118-24).
[0595] The polymeric moiety, such as the PEG moiety, can be of a
molecular weight typically ranging from about 1 kDa to about 100
kDa. In some embodiments the polymeric molecule that is conjugated
to a protein, such as any ADA2 provided herein, has a molecular
weight of at least or at least about or 5, 10, 15, 20, 25, 30, 35,
40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 kDa or more
than 1000 kDa. Other sizes can be used, depending on the desired
profile (e.g., the duration of sustained release desired, the
effects, if any on biological activity, the ease in handling, the
degree or lack of antigenicity and other known effects of the
polyethylene glycol to a protein or analog).
[0596] The PEG moiety can be of any molecular weight, and can be
branched or unbranched. In some examples, the heterologous polymer
is a PEG with a branched structure. Branched polyethylene glycols
are described, for example, in U.S. Pat. No. 5,643,575; Morpurgo et
al. (1996) Appl. Biochem. Biotechnol. 56:59-72; Vorobjev et al.
(1999) Nucleosides Nucleotides 18:2745-2750; and Caliceti et al.
(1999) Bioconjug. Chem. 10:638-646, each of which is incorporated
herein by reference in its entirety.
[0597] While numerous reactions have been described for PEGylation,
those that are most generally applicable confer directionality,
utilize mild reaction conditions, and do not necessitate extensive
downstream processing to remove toxic catalysts or byproducts. For
instance, monomethoxy PEG (mPEG) has only one reactive terminal
hydroxyl, and thus its use limits some of the heterogeneity of the
resulting PEG-protein product mixture. Activation of the hydroxyl
group at the end of the polymer opposite to the terminal methoxy
group is generally necessary to accomplish efficient protein
PEGylation, with the aim being to make the derivatised PEG more
susceptible to nucleophilic attack. The attacking nucleophile is
usually the epsilon-amino group of a lysine residue, but other
amines also can react (e.g. the N-terminal alpha-amine or the ring
amines of histidine) if local conditions are favorable.
[0598] A more directed attachment is possible in proteins
containing a single lysine or cysteine. The latter residue can be
targeted by PEG-maleimide for thiol-specific modification.
Alternatively, PEG hydrazide can be reacted with a periodate
oxidized protein and reduced in the presence of NaCNBH.sub.3. More
specifically, PEGylated CMP sugars can be reacted with a protein in
the presence of appropriate glycosyl-transferases. Alternatively,
pegyaltion of ADA2 can occur in variants containing substitutions
with non-natural amino acids that allow for site-specific chemical
conjugation at optimized positions within the protein. PEGylation
techniques can allow where a number of polymeric molecules are
coupled to the polypeptide in question. When using this technique
the immune system has difficulties in recognizing the epitopes on
the polypeptide's surface responsible for the formation of
antibodies, thereby reducing the immune response. For polypeptides
introduced directly into the circulatory system of the human body
to give a particular physiological effect (i.e. pharmaceuticals)
the typical potential immune response is an IgG and/or IgM
response, while polypeptides which are inhaled through the
respiratory system (i.e. industrial polypeptide) potentially can
cause an IgE response (i.e. allergic response). One of the theories
explaining the reduced immune response is that the polymeric
molecule(s) shield(s) epitope(s) on the surface of the polypeptide
responsible for the immune response leading to antibody formation.
Another theory or at least a partial factor is that the heavier the
conjugate is, the more reduced immune response is obtained.
[0599] Typically, to make the PEGylated ADA2 polypeptides provided
herein, including variant ADA2 polypeptides, PEG moieties are
conjugated, via covalent attachment, to the polypeptides.
Techniques for PEGylation include, but are not limited to,
specialized linkers and coupling chemistries (see e.g., Roberts et
al., Adv. Drug Deliv. Rev. 54:459-476, 2002), attachment of
multiple PEG moieties to a single conjugation site (such as via use
of branched PEGs; see e.g., Guiotto et al., Bioorg. Med. Chem.
Lett. 12:177-180, 2002), site-specific PEGylation and/or
mono-PEGylation (see e.g., Chapman et al., Nature Biotech.
17:780-783, 1999), and site-directed enzymatic PEGylation (see
e.g., Sato, Adv. Drug Deliv. Rev., 54:487-504, 2002). Methods and
techniques described in the art can produce proteins having at
least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more than 10 PEG or PEG
derivatives attached to a single protein molecule (see e.g., U.S.
2006/0104968).
[0600] The number of polyethylene glycol moieties attached to each
ADA2 molecule can also vary. For example, any ADA2 provided herein
can be conjugated to, on average, at least 1, 2, 3, 4, 5, 6, 7, 8,
9, 10, 12, 15, 17, 20, 25, 30 or more polyethylene glycol
molecules. For example, the PEGylated ADA2 polypeptides, including
variant ADA2 polypeptides generally contains at least 5 PEG
moieties per molecule. In other examples, the range of number of
PEG molecules per protein molecule can be 1-3, 2-4, 3-5, 4-6, 5-7,
6-8, 7-9, 8-10, 9-1 1, 10-12, 11-13, 12-14, 13-15, 14-16, 15-17,
16-18, 17-19, 18-20, 19-21, 20-22, 21-23, 22-24, 23-25, 24-26,
25-27, 26-28, 27-29, 28-30, 29-31 or 30-32. For example, the ADA2
polypeptides, including variant ADA2 polypeptides can have a PEG to
protein molar ratio between 32:1 and 1:1, such as about or up to
30:1, 20:1, 15:1, 10:1 and 5:1. The number of PEG molecules per
protein can be varied in order to modify the physical and kinetic
properties of the combined conjugate to fit any particular clinical
situation, as determined by one of skill in the art. Methods for
determining the PEG to protein molar ratio is disclosed in the art,
for example, in Delgado et al. (1992) Crit. Rev. Thera. Drug
Carrier Sys. 9:249-304).
[0601] Covalent attachment of the PEG to the drug (known as
"PEGylation") can be accomplished by known chemical synthesis
techniques. For example, the PEGylation of protein can be
accomplished by reacting NHS-activated PEG with the protein under
suitable reaction conditions. Various methods of modifying
polypeptides by covalently attaching (conjugating) a PEG or PEG
derivative (i.e., "PEGylation") are known in the art (see e.g.,
U.S. Pat. No. 5,672,662; U.S. Pat. No. 6,737,505; U.S.
2004/0235734; U.S. 2006/0104968). Covalent attachment of a variety
of polymers, such as PEG or PEG derivatives, is described in U.S.
Pat. No. 8,741,283.
[0602] Activated polymers and derivatives can be employed to
facilitate the conjugation of the polymer to any ADA2 provided
herein. Activated polymers and derivatives have a leaving or
activating group, which facilitates the attachment of the polymer
system to an amine group found on the polypeptide, such as an ADA2
provided herein. For example, activated groups are those groups
which are capable of reacting with an amine group (nucleophile)
found on any ADA2 provided herein, such as the epsilone amine group
of lysine. Exemplary activating groups include:
##STR00001##
and other suitable leaving or activating groups such as
N-hydroxybenzotriazolyl, halogen, N-hydroxyphthalimidyl,
imidazolyl, O-acyl ureas, pentafluorophenol, 2,4,6-tri-chlorophenol
or other suitable leaving groups apparent to one of skill in the
art.
[0603] Exemplary activated PEGs include, for example, those
disclosed in the art, such as in U.S. Pat. Nos. 5,122,614,
5,324,844, 5,612,460 and 5,808,096 (succinimidyl
carbonate-activated polyethylene glycol (SC-PEG) and related
activated PEGs), and U.S. Pat. No. 5,349,001 (cyclic imide thione
activated PEGs). Conjugation reactions typically are carried out in
a suitable buffer using a several-fold molar excess of activated
PEG. In some examples, conjugates are made with linear PEGs, such
as SC-PEG; and can contain, on average, from about 1 to about 32
PEG molecules per protein molecule. Consequently, for these, molar
excesses of several hundred fold, e.g., about 200 to about
1000-fold can be employed. The molar excess used for branched
polymers and polymers attached to the enzyme will be lower and can
be determined using the techniques known in the art.
[0604] In some examples, the activated polymer linkers of the
polymeric systems based on benzyl elimination or trimethyl lock
lactonization, as described in U.S. Pat. Nos. 6,180,095, 6,720,306,
5,965,119, 6,624,142 and 6,303,569. In other examples, polymer
conjugation of any ADA2 provided herein can be achieved using
bicine polymer residues, as described in the art, for example, in
U.S. Pat. Nos. 7,122,189, 7,087,229 and 8,741,283. In other
examples, polymer conjugation of any ADA2 provided herein can be
achieved using branched polymer residues, such as those described
in U.S. Pat. Nos. 5,681,567, 5,756,593, 5,643,575; 5,919,455,
6,113,906, 6,153,655, 6,395,266 and 6,638,499, 6,251,382,
6,824,766, and 8,741,283. In other examples, polymer conjugation of
any ADA2 provided herein can be achieved using a hindered
ester-based linker, such as those described in International PCT
Pub. No. WO 2008/034119. In some examples, the activated
polyethylene glycol is one which provides a urethane linkage or
amide-linkage with the protein such as any ADA2 provided
herein.
[0605] Methods of preparing polymers having terminal carboxylic
acids in high purity are described in the art, for example in U.S.
Pat. Pub. No. 2007/0173615. The methods include first preparing a
tertiary alkyl ester of a polyalkylene oxide followed by conversion
to the carboxylic acid derivative thereof. The first step of the
preparation of the PAO carboxylic acids of the process includes
forming an intermediate such as t-butyl ester of polyalkylene oxide
carboxylic acid. This intermediate is formed by reacting a PAO with
a t-butyl haloacetate in the presence of a base such as potassium
t-butoxide. Once the t-butyl ester intermediate has been formed,
the carboxylic acid derivative of the polyalkylene oxide can be
readily provided in purities exceeding 92%, such as exceeding 97%,
99%, or 99.5%.
[0606] In other examples, polymers having terminal amine groups can
be employed to make conjugates to ADA2 provided herein. The methods
of preparing polymers containing terminal amines in high purity are
described in the art, for example in U.S. Pat. Nos. 7,868,131 and
7,569,657. For example, polymers having azides react with
phosphine-based reducing agent such as triphenylphosphine or an
alkali metal borohydride reducing agent such as NaBH.sub.4.
Alternatively, polymers including leaving groups react with
protected amine salts such as potassium salt of methyl-tert-butyl
imidodicarbonate (KNMeBoc) or the potassium salt of di-tert-butyl
imidodicarbonate (KNBoc.sub.2) followed by deprotecting the
protected amine group. The purity of the polymers containing the
terminal amines formed by these processes is greater than about
95%, such as greater than 99%.
[0607] In some examples, the PEG portion of the polymer conjugate
of ADA2 provided herein can be selected from among:
J-O--(CH.sub.2CH.sub.2O).sub.u--
J-O--(CH.sub.2CH.sub.2O).sub.u--CH.sub.2C(O)--O--,
J-O--(CH.sub.2CH.sub.2O).sub.u--CH.sub.2CH.sub.2NR--, and
J-O--(CH.sub.2CH.sub.2O).sub.u--CH.sub.2CH.sub.2SH--, [0608] where
u is the degree of polymerization, i.e. from about 10 to about
2,300; [0609] R is selected from among hydrogen, C.sub.1-6 alkyls,
C.sub.2-6 alkenyls, C.sub.2-6 alkynyls, C.sub.3-12 branched alkyls,
C.sub.3-8 cycloalkyls, C.sub.1-6 substituted alkyls, C.sub.2-6
substituted alkenyls, C.sub.2-6 substituted alkynyls, C.sub.3-8
substituted cycloalkyls, aryls substituted aryls, aralkyls,
C.sub.1-6 heteroalkyls, substituted C.sub.1-6 heteroalkyls,
C.sub.1-6 alkoxy, phenoxy and C.sub.1-6 heteroalkoxy, and
[0610] J is a capping group, i.e., a group which is found on the
terminal of the polymer and, in some aspects, can be selected from
among NH.sub.2 (or CH.sub.2CH.sub.2NH.sub.2), H, SH (or
CH.sub.2CH.sub.2SH), CO.sub.2H (or CH.sub.2CO.sub.2H), C.sub.1-6
alkyls, such as a methyl, or other PEG terminal activating groups
known in the art.
[0611] For example, the PEG portion of the polymer conjugate can be
selected from among CH.sub.3--O--(CH.sub.2CH.sub.2O).sub.u--,
CH.sub.3--O--(CH.sub.2CH.sub.2O).sub.u--CH.sub.2C(O)--O--,
CH.sub.3--O--(CH.sub.2CH.sub.2O).sub.u--CH.sub.2CH.sub.2NH-- and
CH.sub.3--O--(CH.sub.2CH.sub.2O).sub.u--CH.sub.2CH.sub.2SH--, where
u is a positive integer, such that the average total molecular
weight of the polymer portion ranges from about 2 kDa to about 100
kDa.
[0612] In other examples, the PEG portion of the polymer conjugate
of ADA2 provided herein can be selected from among:
--Y.sub.1--(CH.sub.2CH.sub.2O).sub.u--CH.sub.2CH.sub.2Y.sub.1--,
Y.sub.1--(CH.sub.2CH.sub.2O).sub.u--CH.sub.2C(.dbd.Y.sub.2)--Y.sub.1--,
--Y.sub.1--C(.dbd.Y.sub.2)--(CH.sub.2)a.sub.1-Y.sub.3--(CH.sub.2CH.sub.2-
O).sub.u--CH.sub.2CH.sub.2--Y.sub.3--(CH.sub.2)a.sub.1-C(.dbd.Y.sub.2)--Y.-
sub.1--,
--Y.sub.1--(CR.sub.2R.sub.3)a.sub.2-Y.sub.3--(CH.sub.2)b.sub.1-O--(CH.su-
b.2CH.sub.2O)b.sub.1-(CH.sub.2)b.sub.1-Y.sub.3--(CR.sub.2R.sub.3)a.sub.2-Y-
.sub.1--,
Y.sub.1--(CH.sub.2CH.sub.2O).sub.u--CH.sub.2CH.sub.2--,
Y.sub.1--(CH.sub.2CH.sub.2O).sub.u--CH.sub.2C(.dbd.Y.sub.2)--,
--C(.dbd.Y.sub.2)--(CH.sub.2)a.sub.1-Y.sub.3--(CH.sub.2CH.sub.2O).sub.u--
-CH.sub.2CH.sub.2--Y.sub.3--(CH.sub.2)a.sub.1-C(.dbd.Y.sub.2)--,
and
--(CR.sub.2R.sub.3)a.sub.2-Y.sub.3--(CH.sub.2)b.sub.1-O--(CH.sub.2CH.sub-
.2O).sub.u--(CH.sub.2)b.sub.1-Y.sub.3--(CR.sub.2R.sub.3)a.sub.2-,
[0613] wherein: Y.sub.1 and Y.sub.3 are independently O, S, SO,
SO.sub.2, NR.sub.4 or a bond;
[0614] Y.sub.2 is O, S, or NR.sub.5;
[0615] R.sub.2-R.sub.5 are independently selected from among
hydrogen, C.sub.1-6 alkyl, C.sub.2-6 alkenyl, C.sub.2-6 alkynyl,
C.sub.3-19 branched alkyl, C.sub.3-8 cycloalkyl, C.sub.1-6
substituted alkyl, C.sub.2-6 substituted alkenyl, C.sub.2-6
substituted alkynyl, C.sub.3-8 substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, C.sub.1-6
heteroalkyl, substituted C.sub.1-6 heteroalkyl, C.sub.1-6 alkoxy,
aryloxy, C.sub.1-6 heteroalkoxy, heteroaryloxy, C.sub.2-6 alkanoyl,
arylcarbonyl, C.sub.2-6 alkoxycarbonyl, aryloxycarbonyl, C.sub.2-6
alkanoyloxy, arylcarbonyloxy, C.sub.2-6 substituted alkanoyl,
substituted arylcarbonyl, C.sub.2-6 substituted alkanoyloxy,
substituted aryloxycarbonyl, C.sub.2-6 substituted alkanoyloxy and
substituted arylcarbonyloxy;
[0616] a.sub.1, a.sub.2, and b.sub.1 are independently zero or a
positive integer from 1 to 6, for example, 0, 1 or 2; and
[0617] u is an integer from about 10 to about 2300.
[0618] In other examples, the PEG portion of the polymer conjugate
of ADA.sub.2 provided herein
can be functionalized, for example, in the following manner:
--C(.dbd.Y.sub.4)--(CH.sub.2).sub.m--(CH.sub.2CH.sub.2O).sub.6--,
--C(.dbd.Y.sub.4)--Y--(CH.sub.2).sub.m--(CH.sub.2CH.sub.2O).sub.6--,
--C(.dbd.Y.sub.4)--NR.sub.2--(CH.sub.2).sub.m--(CH.sub.2CH.sub.2O).sub.6-
--,
--CR.sub.6R.sub.7--(CH.sub.2).sub.m--(CH.sub.2CH.sub.2O).sub.6--
[0619] wherein: R.sub.2, R.sub.6 and R.sub.7 are independently
selected from among H, C.sub.1-6 alkyls, aryls, substituted aryls,
aralkyls, heteroalkyls, substituted heteroalkyls and substituted
C.sub.1-6 alkyls;
[0620] m is zero or is a positive integer, such as 1 or 2,
[0621] Y.sub.4 is O or S; and
[0622] u represents the degree of polymerization.
[0623] In some examples, the polymer conjugates of ADA2 provided
herein can be made by methods which include converting the
multi-arm PEG-OH or "star-PEG" products, such made by NOF Corp,
Tokyo, Japan, into a suitably activated polymer, using the
activation techniques described in U.S. Pat. No. 5,122,614 or
5,808,096. In one example, the multi-arm polymers can contain four
or more polymer arms and preferably four or eight polymer arms. In
some examples, four of the PEG arms are converted to suitable
functional groups, such as succinimidyl carbonate (SC), for
facilitating attachment to the polypeptide, such as any ADA2
provided herein.
[0624] The polymeric conjugates provided herein can be
water-soluble at room temperature. A non-limiting list of such
polymers include polyalkylene oxide homopolymers such as
polyethylene glycol (PEG) or polypropylene glycols,
polyoxyethylenated polyols, copolymers thereof and block copolymers
thereof.
[0625] As an exemplary illustrative method for making PEGylated
ADA2 polypeptides, including variant ADA2 polypeptides, PEG
aldehydes, succinimides and carbonates have each been applied to
conjugate PEG moieties, typically succinimidyl PEGs. Exemplary
succinimidyl monoPEG (mPEG) reagents including mPEG-Succinimidyl
Propionates (mPEG-SPA), mPEG Succinimidyl Carboxymethyl Ester
(mPEG-SCM), mPEG-Succinimidyl Butanoates (mPEG-SBA), and (for
attaching "branched" PEGs) mPEG2-N-Hydroxylsuccinimide. These
PEGylated succinimidyl esters contain different length carbon
backbones between the PEG group and the activated cross-linker, and
either a single or branched PEG group. These differences can be
used, for example, to provide for different reaction kinetics and
to potentially restrict sites available for PEG attachment to ADA2
during the conjugation process. Such PEGylated ADA2 compositions
can be readily purified to yield compositions having at least about
90% to about 100% PEGylated ADA2 molecules, and being substantially
free of non-PEGylated ADA2 (less than 5% non-PEGylated).
[0626] In one example, the PEGylation includes conjugation of
mPEG-SCM, for example, mPEG-SCM-20K (having a molecular weight of
about 20 kDa) or another succinimidyl carboxymethyl esters of PEG
derivative, to any ADA2 polypeptide, including variant ADA2
polypeptides. Succinimidyl carboxymethyl esters of PEG derivatives,
such as mPEG-SCM-20K readily couple to amino groups of lysines in
proteins or the N-terminal amine in biological active molecules.
For example, covalent conjugation of m-PEG-SCM-20K and ADA2 (which
is approximately 59 kDa in size as a monomer) provides stable amide
bonds between ADA2 and mPEG. Typically, the mPEG-SCM-20K or other
PEG is added to any ADA2 polypeptide, including variant ADA2
polypeptides, at a PEG:polypeptide molar ratio of 15:1 in a
suitable buffer, followed by sterilization, e.g., sterile
filtration, and continued conjugation, for example, with stirring,
overnight at 4.degree. C. in a cold room.
[0627] Other methods of coupling succinimidyl esters of PEG,
including butanoic acid derivatives such as mPEG-SBA-30K, to a
polypeptide are known in the art (see e.g., U.S. Pat. No.
5,672,662; U.S. Pat. No. 6,737,505; U.S. Pat. No. 8,784,791; U.S.
2004/0235734 and U.S. 2005/0158273). For example, a polypeptide,
such as any ADA2 provided herein, can be coupled to an NHS
activated PEG derivative by reaction in a borate buffer (0.1 M, pH
8.0) for one hour at 4.degree. C. The resulting PEGylated protein
can be purified by ultrafiltration. Alternatively, PEGylation of a
bovine alkaline phosphatase can be accomplished by mixing the
phosphatase with mPEG-SBA in a buffer containing 0.2 M sodium
phosphate and 0.5 M NaCl (pH 7.5) at 4.degree. C. for 30 minutes.
Unreacted PEG can be removed by ultrafiltration or using resin
columns such as Capto Phenyl resin columns (GE Healthcare). Another
method reacts polypeptide with mPEG-SBA in deionized water to which
triethylamine is added to raise the pH to 7.2-9. The resulting
mixture is stirred at room temperature for several hours to
complete the PEGylation.
[0628] As shown herein, PEGylation of variant ADA2 confers
reduction in heparin binding property to the ADA2. The reduction in
heparin binding can be in addition to any attenuated heparin
binding resulting from amino acid replacement(s) that reduce
heparin binding. Thus, PEGylation of ADA2 also improves
pharmacokinetic properties of the ADA2, and PEGylation can be used
in place of or in addition to amino acid replacement(s) to
attenuate heparin binding.
[0629] ii. Hydroxyethyl Starch (HES)
[0630] In some examples, at least one heterologous moiety is a
polymer, e.g., hydroxyethyl starch (HES) or a derivative thereof.
Hydroxyethyl starch (HES) is a derivative of naturally occurring
amylopectin and is degraded by alpha-amylase in the body. HES is a
substituted derivative of the carbohydrate polymer amylopectin,
which is present in corn starch at a concentration of up to 95% by
weight. HES exhibits advantageous biological properties and is used
as a blood volume replacement agent and in hemodilution therapy in
the clinics.
[0631] Amylopectin contains glucose moieties, wherein in the main
chain .alpha.-1,4-glycosidic bonds are present and at the branching
sites .alpha.-1,6-glycosidic bonds are found. The physical-chemical
properties of this molecule are mainly determined by the type of
glycosidic bonds. Due to the nicked .alpha.-1,4-glycosidic bond,
helical structures with about six glucose-monomers per turn are
produced. The physicochemical as well as the biochemical properties
of the polymer can be modified via substitution. The introduction
of a hydroxyethyl group can be achieved via alkaline
hydroxyethylation. By adapting the reaction conditions it is
possible to exploit the different reactivity of the respective
hydroxy group in the unsubstituted glucose monomer with respect to
hydroxyethylation. One of skill in the art can determine the
substitution pattern. HES is mainly characterized by the molecular
weight distribution and the degree of substitution (DS), which
refers to the molar ratio of the substitution.
[0632] In one example, hydroxyethyl starch has a mean molecular
weight (weight mean) of from 1 to 300 kD, from 2 to 200 kD, from 3
to 100 kD, or from 4 to 70 kD. Hydroxyethyl starch can further
exhibit a molar degree of substitution (DS) of from 0.1 to 3,
preferably 0.1 to 2, more preferred, 0.1 to 0.9, preferably 0.1 to
0.8, and a ratio between C2:C6 substitution in the range of from 2
to 20 with respect to the hydroxyethyl groups. A non-limiting
example of HES having a mean molecular weight of about 130 kD is a
HES with a DS of 0.2 to 0.8, such as 0.2, 0.3, 0.4, 0.5, 0.6, 0.7,
or 0.8, and in particular, a DS of 0.4 to 0.7 such as 0.4, 0.5,
0.6, or 0.7.
[0633] In one example, the HES can have a mean molecular weight of
about 130 kD, and is VOLUVEN.RTM. (Fresenius Kabi, Germany).
VOLUVEN.RTM. is an artificial colloid, employed, e.g., for volume
replacement used in the therapeutic indication for therapy and
prophylaxis of hypovolemia. The characteristics of VOLUVEN.RTM. are
a mean molecular weight of 130.+-.20 kDa, with a molar substitution
of 0.4 and a C2:C6 ratio of about 9:1. In other examples, ranges of
the mean molecular weight of hydroxyethyl starch are, e.g., 4 to 70
kDa or 10 to 70 kDa or 12 to 70 kDa or 18 to 70 kDa or 50 to 70 kDa
or 4 to 50 kDa or 10 to 50 kDa or 12 to 50 kDa or 18 to 50 kDa or 4
to 18 kDa or 10 to 18 kDa or 12 to 18 kDa or 4 to 12 kDa or 10 to
12 kDa or 4 to 10 kDa. In other examples, the mean molecular weight
of hydroxyethyl starch employed is in the range of from more than 4
kDa and below 70 kDa, such as about 10 kDa, or in the range of from
9 to 10 kDa or from 10 to 11 kDa or from 9 to 11 kDa, or about 12
kDa, or in the range of from 11 to 12 kDa) or from 12 to 13 kDa or
from 11 to 13 kDa, or about 18 kDa, or in the range of from 17 to
18 kDa or from 18 to 19 kDa or from 17 to 19 kDa, or about 30 kDa,
or in the range of from 29 to 30, or from 30 to 31 kDa, or about 50
kDa, or in the range of from 49 to 50 kDa or from 50 to 51 kDa or
from 49 to 51 kDa.
[0634] In some examples, the heterologous moiety can be a mixture
of hydroxyethyl starches having different mean molecular weights
and/or different degrees of substitution and/or different ratios of
C2: C6 substitution. Therefore, mixtures of hydroxyethyl starches
can be employed having different mean molecular weights and
different degrees of substitution and different ratios of C2: C6
substitution, or having different mean molecular weights and
different degrees of substitution and the same or about the same
ratio of C2:C6 substitution, or having different mean molecular
weights and the same or about the same degree of substitution and
different ratios of C2:C6 substitution, or having the same or about
the same mean molecular weight and different degrees of
substitution and different ratios of C2:C6 substitution, or having
different mean molecular weights and the same or about the same
degree of substitution and the same or about the same ratio of
C2:C6 substitution, or having the same or about the same mean
molecular weights and different degrees of substitution and the
same or about the same ratio of C2:C6 substitution, or having the
same or about the same mean molecular weight and the same or about
the same degree of substitution and different ratios of C2:C6
substitution, or having about the same mean, molecular weight and
about the same degree of substitution and about the same ratio of
C2:C6 substitution.
[0635] iii. Polysialic Acids (PSA)
[0636] In certain examples, at least one heterologous moiety is a
polymer, e.g., polysialic acids (PSAs) or a derivative thereof.
Polysialic acids (PSAs) are naturally occurring unbranched polymers
of sialic acid produced by certain bacterial strains and in mammals
in certain cells (Roth J., et al. (1993) in Polysialic Acid: From
Microbes to Man, eds Roth J., Rutishauser U., Troy F. A.
(Birkhauser Verlag, Basel, Switzerland), pp 335-348). They can be
produced in various degrees of polymerization from about 80 or more
sialic acid residues to about 2, by limited acid hydrolysis or by
digestion with neuraminidases, or by fractionation of the natural,
bacterially derived forms of the polymer.
[0637] The composition of different polysialic acids also varies
such that there are homopolymeric forms i.e. the .alpha.-2,8-linked
polysialic acid of the capsular polysaccharide of E. coli strain K1
and the group-B meningococci, which is also found on the embryonic
form of the neuronal cell adhesion molecule (N-CAM).
Heteropolymeric forms also exist, such as the alternating
.alpha.-2,8 .alpha.-2,9 polysialic acid of E. coli strain K92 and
group C polysaccharides of N. meningitidis. Sialic acid can also be
found in alternating copolymers with monomers other than sialic
acid such as group W135 or group Y of N. meningitidis. Polysialic
acids have important biological functions including the evasion of
the immune and complement systems by pathogenic bacteria and the
regulation of glial adhesiveness of immature neurons during fetal
development (wherein the polymer has an anti-adhesive function)
(Cho and Troy, (1994) P.N.A.S. 91:11427-11431), although there are
no known receptors for polysialic acids in mammals.
[0638] In other examples, the .alpha.-2,8-linked polysialic acid of
E. coli strain K1, also known as colominic acid, are used (in
various lengths). Various methods of attaching or conjugating
polysialic acids to a polypeptide have been described (see e.g.,
U.S. Pat. No. 5,846,951; WO 01/87922, and US 2007/0191597, each of
which is incorporated herein by reference in its entirety).
[0639] iv. Other Polymers
[0640] In other examples, the polymer moiety for conjugation to any
ADA2 provided herein can be selected from among one or more
effectively non-antigenic materials such as dextran, polyvinyl
alcohols, carbohydrate-based polymers, hydroxypropylmeth-acrylamide
(HPMA), polyalkylene oxides, and/or copolymers thereof, including
other polymers known in the art and/or described in U.S. Pat. No.
6,153,655. It is within the level of one of skill in the art to
select the polymer based on the purpose of use, and to select the
suitable conjugation methods.
[0641] 2. Methods of Producing Conjugates or Fusion Proteins
Heterologous moieties can be conjugated directly or indirectly to
any ADA2 provided herein. For example, the heterologous moieties
can be conjugated in a post-translational manner, after the
recombinant production of the ADA2 polypeptide, by direct chemical
linkage or indirectly via a linker. In other examples, heterologous
moieties that are protein or polypeptide moieties, can be directly
or indirectly conjugated to any ADA2 provided herein. In one
example, the protein or polypeptide moieties can be directly
linked, for example, as a fusion protein. In other examples, the
heterologous moiety is conjugated indirectly, via a linker. In
other examples, the heterologous moiety can be linked by disulfide
bonds formed between a thiol group in the heterologous moiety and
the cysteine residues in the ADA2 provided herein.
[0642] Linkers
[0643] Linkers, or spacers, can be used to connect heterologous
moieties and polypeptides, such as any ADA2 provided herein. A
linker refers to a peptide or polypeptide sequence (e.g. a
synthetic peptide or polypeptide sequence), or a non-peptide linker
for which its main function is to connect two moieties, such as an
ADA2 provided herein and the heterologous moiety. Linkers can be
used to maintain the structural flexibility and other
conformational characteristics of the individual residues or at the
secondary, tertiary, or quaternary structural levels of domains or
moieties of the polypeptide conjugate or fusion protein, in order
to maintain functional properties of the moieties. Linkers can also
provide additional beneficial properties to the polypeptide
conjugate or fusion protein, such as increased protein expression
in mammalian expression systems, improved biophysical properties
such as stability and solubility, improved protein purification and
detection and/or increased enzymatic activity. In some examples,
two or more linkers can be linked in tandem. Linkers can be peptide
linkers that link a protein or polypeptide moiety to the ADA2
polypeptide. Other exemplary linkers include chemical linking
agents and heterobifunctional linking agents.
[0644] When multiple linkers are present between the ADA2 and the
heterologous moiety, each of the linkers can be the same or
different. Generally, linkers provide flexibility to the
polypeptide molecule. Linkers are not typically cleaved; however in
certain examples, such cleavage can be desirable. Accordingly, in
some embodiments a linker can contain one or more
protease-cleavable sites, which can be located within the sequence
of the linker or flanking the linker at either end of the linker
sequence.
[0645] Linkers can be introduced into polypeptide sequences, such
as any ADA2 provided herein, using techniques known in the art
(e.g., chemical conjugation, recombinant techniques, or peptide
synthesis). Modifications can be confirmed by DNA sequence
analysis. In some examples, the linkers can be introduced using
recombinant techniques. In other examples, the linkers can be
introduced using solid phase peptide synthesis. In other examples,
the polypeptide, such as any ADA2 provided herein, can contain
simultaneously one or more linkers that have been introduced using
recombinant techniques and one or more linkers that have been
introduced using solid phase peptide synthesis or methods of
chemical conjugation known in the art.
[0646] i. Peptide Linkers
[0647] Peptide linkers can be used to link the heterologous moiety
to the ADA2 polypeptide provided herein. In one example, peptide
linkers can be fused to the C-terminal end of a first polypeptide
(e.g., the ADA2 polypeptide) and the N-terminal end of a second
polypeptide (e.g., a protein or polypeptide heterologous moiety).
This structure can be repeated multiple times such that at least
one, preferably 2, 3, 4, or more polypeptides are linked to one
another via peptide linkers at their respective termini.
[0648] For example, two molecules (e.g., the ADA2 polypeptide and
the heterologous moiety) can be adjacent in the construct or
separated by a linker polypeptide that contains, 1, 2, 3, or more,
amino acids. In some examples, the peptide linker can contain at
least two amino acids, at least three, at least four, at least
five, at least 10, at least 20, at least 30, at least 40, at least
50, at least 60, at least 70, at least 80, at least 90, or at least
100 amino acids. In other examples, the peptide linker can contain
at least 200, at least 300, at least 400, at least 500, at least
600, at least 700, at least 800, at least 900, or at least 1,000
amino acids. In some examples, the peptide linker can contain at
least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300,
400, 500, 600, 700, 800, 900, 1000, 1 100, 1200, 1300, 1400, 1500,
1600, 1700, 1800, 1900, or 2000 amino acids. The peptide linker can
contain 1-5 amino acids, 1-10 amino acids, 1-20 amino acids, 10-50
amino acids, 50-100 amino acids, 100-200 amino acids, 200-300 amino
acids, 300-400 amino acids, 400-500 amino acids, 500-600 amino
acids, 600-700 amino acids, 700-800 amino acids, 800-900 amino
acids, or 900-1000 amino acids. The linker is of a length such that
the two variable domains are bridged without substantial
interference. For example, a linker polypeptide can have a sequence
Z.sub.1--X--Z.sub.2, where Z.sub.1 and Z.sub.2 are the ADA2
polypeptide and the heterologous moiety, respectively, and where X
is a sequence of a peptide linker. In another example, the
polypeptide has a sequence of Z.sub.1--X--Z.sub.2(--X--Z).sub.n,
where "n" is any integer, i.e. generally 1 or 2.
[0649] Typically, the peptide linker is of a sufficient length to
allow both the ADA2 polypeptide and the heterologous moiety to
retain their conformational structure and functions. Examples of
peptide linkers include, but are not limited to: -Gly-Gly-, GGGG
(SEQ ID NO:362), GGGGG (SEQ ID NO:360), GGGGS or (GGGGS)n (SEQ ID
NO:343), SSSSG or (SSSSG)n (SEQ ID NO:344), GKSSGSGSESKS (SEQ ID
NO:345), GGSTSGSGKSSEGKG (SEQ ID NO:346), GSTSGSGKSSSEGSGSTKG (SEQ
ID NO:347), GSTSGSGKPGSGEGSTKG (SEQ ID NO:348), EGKSSGSGSESKEF (SEQ
ID NO:349), AlaAlaProAla or (AlaAlaProAla)n (SEQ ID NO:350),
SGGSGGS (SEQ ID NO:363), GGSGGSGGSGGSGGG (SEQ ID NO:364),
GGSGGSGGGGSGGGGS (SEQ ID NO:365), GGSGGSGGSGGSGGSGGS (SEQ ID
NO:366), GGGGSGGGGSGGGGS (SEQ ID NO:367), Ser(Gly.sub.4Ser).sub.n
(SEQ ID NO:595) or (Gly-Ser).sub.n residues with some Glu or Lys
residues dispersed throughout to increase solubility, where n can
be an integer from 1 to 20, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, or 20. Other exemplary linkers
include peptide linkers with the formula
[(Gly).sub.x-Ser.sub.y].sub.z where x is from 1 to 4, y is 0 or 1,
and z is from 1 to 50. In other examples, the peptide linker
includes the sequence G.sub.n, where n can be an integer from 1 to
100. In another example, the sequence of the peptide linker can be
(GA).sub.n or (GGS).sub.n. Other exemplary linkers include:
[0650] (1) Gly.sub.4Ser with NcoI ends (SEQ ID NO:351)
[0651] CCATGGGCGG CGGCGGCTCT GCCATGG
[0652] (2) (Gly.sub.4Ser).sub.2 with NcoI ends (SEQ ID NO:352)
[0653] CCATGGGCGG CGGCGGCTCT GGCGGCGGCG GCTCTGCCAT GG
[0654] (3) (Ser.sub.4Gly).sub.4 with NcoI ends (SEQ ID NO:353)
[0655] CCATGGCCTC GTCGTCGTCG GGCTCGTCGT CGTCGGGCTC GTCGTCGTCG
GGCTCGTCGT CGTCGGGCGC CATGG
[0656] (4) (Ser.sub.4Gly).sub.2 with NcoI ends (SEQ ID NO:354)
[0657] CCATGGCCTC GTCGTCGTCG GGCTCGTCGT CGTCGGGCGC CATGG
[0658] Linking moieties are described, for example, in Huston et
al. (1988) PNAS 85:5879-5883, Whitlow et al. (1993) Protein
Engineering 6:989-995, and Newton et al., (1996) Biochemistry
35:545-553. Other suitable peptide linkers include any of those
described in U.S. Pat. No. 4,751,180 or 4,935,233, which are hereby
incorporated by reference. A polynucleotide encoding a desired
peptide linker can be inserted between, and in the same reading
frame as a polynucleotide encoding any ADA2 provided herein and the
protein or polypeptide heterologous moiety, using any suitable
conventional technique. Linking moieties can also include
derivatives and analogs of the naturally occurring amino acids, as
well as various non-naturally occurring amino acids (D- or L-),
hydrophobic or non-hydrophobic, known in the art.
[0659] In some examples, a peptide linker includes peptides (or
polypeptides) (e.g., natural, or non-naturally occurring peptides)
which includes an amino acid sequence that links or genetically
fuses a first linear sequence of amino acids to a second linear
sequence of amino acids to which it is not naturally linked or
genetically fused in nature. For example, the peptide linker can
include non-naturally occurring polypeptides which are modified
forms of naturally occurring polypeptides (e.g., that includes a
mutation such as an addition, substitution or deletion). In another
example, the peptide linker can include non-naturally occurring
amino acids. In another example, the peptide linker can include
naturally occurring amino acids occurring in a linear sequence that
does not occur in nature. In still another example, the peptide
linker can include a naturally occurring polypeptide sequence.
[0660] ii. Heterobifunctional Linking Agents
[0661] Linkage of any ADA2 provided herein and a heterologous
moiety can be direct or indirect. For example, the linkage can be
achieved by chemical linkage or facilitated by bifunctional or
heterobifunctional linkers, such as any known in the art or
provided herein.
[0662] Numerous heterobifunctional cross-linking reagents that are
used to form covalent bonds between amino groups and thiol groups
and to introduce thiol groups into proteins, are known to those of
skill in the art (see, e.g., the PIERCE CATALOG, ImmunoTechnology
Catalog & Handbook, 1992-1993, which describes the preparation
of and use of such reagents and provides a commercial source for
such reagents; see, also, e.g., Cumber et al. (1992) Bioconjugate
Chem. 3:397-401; Thorpe et al. (1987) Cancer Res. 47:5924-5931;
Gordon et al. (1987) Proc. Natl. Acad Sci. 84:308-312; Walden et
al. (1986) J. Mol. Cell Immunol. 2:191-197; Carlsson et al. (1978)
Biochem. J. 173: 723-737; Mahan et al. (1987) Anal. Biochem.
162:163-170; Wawrzynczak et al. (1992) Br J. Cancer 66:361-366;
Fattom et al. (1992) Infection & Immun. 60:584-589). These
reagents can be used to form covalent bonds between the N-terminal
portion of the heterologous moiety and the C-terminal portion of
the ADA2 provided herein, or between each of those portions and a
linker. These reagents include, but are not limited to:
N-succinimidyl-3-(2-pyridyldithio)propionate (SPDP; disulfide
linker); sulfosuccinimidyl
6-[3-(2-pyridyldithio)proponamido]hexanoate (sulfo-LC-SPDP);
succinimidyloxycarbonyl-.alpha.-methyl benzyl thiosulfate (SMBT,
hindered disulfate linker); succinimidyl 6-[3-(2-pyridyldithio)
propionamido]hexanoate (LC-SPDP); sulfosuccinimidyl
4-(N-maleimidomethyl)cyclohexane-1-carboxylate (sulfo-SMCC);
succinimidyl 3-(2-pyridyldithio)butyrate (SPDB; hindered disulfide
bond linker); sulfosuccinimidyl
2-(7-azido-4-methylcoumarin-3-acetamide)
ethyl-1,3'-dithiopropionate (SAED); sulfo-succinimidyl
7-azido-4-methylcoumarin-3-acetate (SAMCA);
sulfosuccinimidyl-6-[alpha-methyl-alpha-(2-pyridyldithio)toluamido]-hexan-
oate (sulfo-LC-SMPT);
1,4-di-[3'-(2'-pyridyldithio)propionamido]butane (DPDPB);
4-succinimidyloxycarbonyl-.alpha.-methyl-.alpha.-(2-pyridylthio)-
toluene (SMPT, hindered disulfate linker);
sulfosuccinimidyl-6-[.alpha.-methyl-.alpha.-(2-pyrimiyldi-thio)toluamido]-
hexanoate (sulfo-LC-SMPT); m-maleimidobenzoyl-N-hydroxysuccinimide
ester (MBS); m-maleimidobenzoyl-N-hydroxysulfo-succinimide ester
(sulfo-MBS); N-succinimidyl(4-iodoacetyl)aminobenzoate (SIAB;
thioether linker); sulfosuccinimidyl-(4-iodoacetyl)amino benzoate
(sulfo-SIAB); succinimidyl-4-(p-maleimidophenyl)butyrate (SMPB);
sulfosuccinimidyl-4-(p-maleimido-phenyl)butyrate (sulfo-SMPB);
azidobenzoyl hydrazide (ABH); maleimido caproyl (MC); maleimido
propanoyl (MP); succinimidyl
4-(K-maleimidomethyl)-cyclohexane-1-carboxylate (SMCC);
m-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS);
N-succinimidyl(4-iodoacetyl)aminobenzonate (SIAB); and succinimidyl
6-[3-(2-pyridyldithio)-propionamide hexanoate (LC-SPDP) (see, e.g.,
U.S. Pat. No. 7,375,078). Other exemplary linkers include, but are
not limited to linkers with the formula:
--C(O)CH.sub.2OCH.sub.2C(O)--;
--C(O)CH.sub.2NHCH.sub.2C(O)--;
--C(O)CH.sub.2SCH.sub.2C(O)--;
--C(O)CH.sub.2CH.sub.2CH.sub.2C(O)--, and
--C(O)CH.sub.2CH.sub.2C(O)--.
[0663] These linkers, for example, can be used in combination with
peptide linkers, such as those that increase flexibility or
solubility or that provide for or eliminate steric hindrance. Any
other linkers known to those of skill in the art for linking a
polypeptide molecule to another molecule can be employed. General
properties are such that the resulting molecule retains the
adenosine deaminase function and stability of the protein. For in
vivo use of the ADA2 conjugate or fusion protein, generally the
linker must be biocompatible for administration to animals,
including humans.
E. METHODS OF PRODUCING NUCLEIC ACIDS ENCODING ADA2 AND
POLYPEPTIDES THEREOF
[0664] Polypeptides of any ADA2 as described herein, including
variants or modified forms thereof, can be obtained by methods well
known in the art for protein purification and recombinant protein
expression. Polypeptides also can be synthesized chemically.
Modified or variant forms can be engineered from a wildtype
polypeptide using standard recombinant DNA methods. For example,
any ADA2, including variants or modified forms can be engineered
from a wildtype polypeptide, such as by site-directed
mutagenesis.
[0665] 1. Isolation or Preparation of Nucleic Acids Encoding ADA2
Polypeptides
[0666] Polypeptides can be cloned or isolated using any available
methods known in the art for cloning and isolating nucleic acid
molecules. Such methods include PCR amplification of nucleic acids
and screening of libraries, including nucleic acid hybridization
screening, antibody-based screening and activity-based screening.
For example, when the polypeptides are produced by recombinant
means, any method known to those of skill in the art for
identification of nucleic acids that encode desired genes can be
used. Any method available in the art can be used to obtain a full
length or partial (i.e., encompassing the entire coding region)
cDNA or genomic DNA clone encoding the ADA2 polypeptide, such as
from a cell or tissue source.
[0667] Methods for amplification of nucleic acids can be used to
isolate nucleic acid molecules encoding a desired polypeptide,
including for example, polymerase chain reaction (PCR) methods.
Examples of such methods include use of a Perkin-Elmer Cetus
thermal cycler and Taq polymerase (Gene Amp, Applied Biosystems,
Carlsbad, Calif.). A nucleic acid containing material can be used
as a starting material from which a desired polypeptide-encoding
nucleic acid molecule can be isolated. For example, DNA and mRNA
preparations, cell extracts, tissue extracts, fluid samples (e.g.,
blood, serum, saliva), samples from healthy and/or diseased
subjects can be used in amplification methods. The source can be
from any eukaryotic species including, but not limited to,
vertebrate, mammalian, human, porcine, bovine, feline, avian,
equine, canine, and other primate sources. Nucleic acid libraries
also can be used as a source of starting material. Primers can be
designed to amplify a desired polypeptide. For example, primers can
be designed based on expressed sequences from which a desired
polypeptide is generated. Primers can be designed based on
back-translation of a polypeptide amino acid sequence. If desired,
degenerate primers can be used for amplification. Oligonucleotide
primers that hybridize to sequences at the 3' and 5' termini of the
desired sequence can be uses as primers to amplify by PCR sequences
from a nucleic acid sample. Primers can be used to amplify the
full-length ADA2. Nucleic acid molecules generated by amplification
can be sequenced and confirmed to encode a desired polypeptide.
[0668] In addition, nucleic acid molecules encoding the ADA2
polypeptide can be chemically synthesized or produced in a
semi-synthetic manner. The synthetically or semi-synthetically
produced nucleic acid molecule can encode the amino acid sequence
of any ADA2, such as any described herein in Section C above. For
example, the synthesized or semi-synthetically produced nucleic
acid molecule can be encoded by a nucleic acid molecule having a
sequence of nucleotides of any as described herein. Chemically
synthesized nucleic acid molecules can span the entire length of
the wildtype ADA2 gene, or a truncated sequence thereof. Chemical
gene synthesis can be achieved by any methods known in the art,
such as annealing chemically synthesized oligonucleotides.
Semi-synthetic gene assembly, such as the Gibson assembly method,
can also be used to produce the nucleic acid molecule encoding any
of the ADA2 polypeptides, including variants, as described
herein.
[0669] The nucleic acid encoding any of the ADA2 polypeptides can
be a codon-optimized nucleic acid molecule, where the codon is
optimized for the expression system used to produce the polypeptide
(i.e., codons that are preferred in the organism of the expression
system are used more frequently in the synthesized nucleic acid).
For example, for production of the polypeptide in an Escherichia
coli expression system, the codons for each amino acid can be
optimized such that the most preferred codon in E. coli are used
for each amino acid.
[0670] Additional nucleotide sequences can be joined to a
polypeptide-encoding nucleic acid molecule, including linker
sequences containing restriction endonuclease sites for the purpose
of cloning the synthetic gene into a vector, for example, a protein
expression vector or a vector designed for the amplification of the
core protein coding DNA sequences. Furthermore, additional
nucleotide sequences specifying functional DNA elements can be
operatively linked to a polypeptide-encoding nucleic acid molecule.
Examples of such sequences include, but are not limited to,
promoter sequences designed to facilitate intracellular protein
expression, and secretion sequences, for example heterologous
signal sequences, designed to facilitate protein secretion. Such
sequences are known to those of skill in the art. Additional
nucleotide residue sequences such as sequences of bases specifying
protein binding regions also can be linked to enzyme-encoding
nucleic acid molecules. Such regions include, but are not limited
to, sequences of residues that facilitate or encode proteins that
facilitate uptake of an enzyme into specific target cells, or
otherwise alter pharmacokinetics of a product of a synthetic
gene.
[0671] In addition, tags or other moieties can be added, for
example, to aid in detection or affinity purification of the
polypeptide. For example, additional nucleotide residue sequences
such as sequences of bases specifying an epitope tag or other
detectable marker also can be linked to enzyme-encoding nucleic
acid molecules. Examples of such sequences include nucleic acid
sequences encoding the FLAG.RTM. tag or the Strep tag.
[0672] The identified and isolated nucleic acids can then be
inserted into an appropriate cloning vector. A large number of
vector-host systems known in the art can be used. Possible vectors
include, but are not limited to, plasmids or modified viruses, but
the vector system must be compatible with the host cell used. Such
vectors include, but are not limited to, bacteriophages such as
lambda derivatives, or plasmids such as pCMV4, pCMV-Script (Agilent
Technologies, Santa Clara, Calif.), pBR322, pUC plasmid derivatives
or pBluescript vectors (Stratagene, La Jolla, Calif.). The
insertion into a cloning vector can, for example, be accomplished
by ligating the DNA fragment into a cloning vector which has
complementary cohesive termini. Insertion can be effected using
TOPO cloning vectors (Invitrogen, Carlsbad, Calif.).
[0673] If the complementary restriction sites used to fragment the
DNA are not present in the cloning vector, the ends of the DNA
molecules can be enzymatically modified. Alternatively, any site
desired can be produced by ligating nucleotide sequences (linkers)
onto the DNA termini; these ligated linkers can contain specific
chemically synthesized oligonucleotides encoding restriction
endonuclease recognition sequences. In an alternative method, the
cleaved vector and protein gene can be modified by homopolymeric
tailing.
[0674] Recombinant molecules can be introduced into host cells via,
for example, transformation, transfection, infection,
electroporation and sonoporation, so that many copies of the gene
sequence are generated. In specific embodiments, transformation of
host cells with recombinant DNA molecules that incorporate the
isolated protein gene, cDNA, or synthesized DNA sequence enables
generation of multiple copies of the gene. Thus, the gene can be
obtained in large quantities by growing transformants, isolating
the recombinant DNA molecules from the transformants and, when
necessary, retrieving the inserted gene from the isolated
recombinant DNA.
[0675] In addition to recombinant production, any ADA2, including
variants or modified forms thereof provided herein can be produced
by direct peptide synthesis using solid-phase techniques (see e.g.,
Stewart et al. (1969) Solid-Phase Peptide Synthesis, WH Freeman
Co., San Francisco; Merrifield J (1963) J Am Chem Soc.,
85:2149-2154). In vitro protein synthesis can be performed using
manual techniques or by automation. Automated synthesis can be
achieved, for example, using Applied Biosystems 431A Peptide
Synthesizer (Perkin Elmer, Foster City Calif.) in accordance with
the instructions provided by the manufacturer. Various fragments of
a polypeptide can be chemically synthesized separately and combined
using chemical methods.
[0676] 2. Generation of Mutant or Modified Nucleic Acid and
Encoding Polypeptides
[0677] The modifications provided herein can be made by standard
recombinant DNA techniques such as are routine to one of skill in
the art. Any method known in the art to effect mutation of any one
or more amino acids in a target protein can be employed. Methods
include standard site-directed mutagenesis (using e.g., a kit, such
as QuikChange available from Stratagene) of encoding nucleic acid
molecules, or by solid phase polypeptide synthesis methods.
Site-specific variations to the wildtype ADA2 or any of the ADA2
variants provided herein can also be introduced during the chemical
gene synthesis or the semi-synthetic gene assembly if such methods
are used to generate the nucleic acid sequence encoding the
ADA2.
[0678] 3. Vectors and Cells
[0679] For recombinant expression of one or more of the desired
proteins, such as any ADA2 polypeptide described herein, the
nucleic acid containing all or a portion of the nucleotide sequence
encoding the protein can be inserted into an appropriate expression
vector, i.e., a vector that contains the necessary elements for the
transcription and translation of the inserted protein coding
sequence. The necessary transcriptional and translational signals
also can be supplied by the native promoter for enzyme genes,
and/or their flanking regions.
[0680] Also provided are vectors that contain a nucleic acid
encoding the enzyme. Cells containing the vectors also are
provided. The cells include eukaryotic and prokaryotic cells, and
the vectors are any suitable for use therein.
[0681] Prokaryotic and eukaryotic cells, including endothelial
cells, containing the vectors are provided. Such cells include
bacterial cells, yeast cells, fungal cells, Archea, plant cells,
insect cells and animal cells. The cells are used to produce a
protein thereof by growing the above-described cells under
conditions whereby the encoded protein is expressed by the cell,
and recovering the expressed protein. For purposes herein, for
example, the enzyme can be secreted into the medium.
[0682] Provided are vectors that contain a sequence of nucleotides
that encodes any ADA2 polypeptide or variants, coupled to the
native or heterologous signal sequence, as well as multiple copies
thereof. The vectors can be selected for expression of the enzyme
protein in the cell or such that the enzyme protein is expressed as
a secreted protein.
[0683] Any of the variety of host-vector systems well known to
those of skill in the art can be used to express the protein coding
sequence. These include but are not limited to mammalian cell
systems infected with virus (e.g., vaccinia virus, adenovirus and
other viruses); insect cell systems infected with virus (e.g.,
baculovirus); microorganisms such as yeast containing yeast
vectors; or bacteria transformed with bacteriophage, DNA, plasmid
DNA, or cosmid DNA. The expression elements of vectors vary in
their strengths and specificities. Depending on the host-vector
system used, any one of a number of suitable transcription and
translation elements can be used.
[0684] Any methods known to those of skill in the art for the
insertion of DNA fragments into a vector can be used to construct
expression vectors containing a chimeric gene containing
appropriate transcriptional/translational control signals and
protein coding sequences. These methods can include in vitro
recombinant DNA and synthetic techniques and in vivo recombinants
(genetic recombination). Expression of nucleic acid sequences
encoding protein, or domains, derivatives, fragments or homologs
thereof, can be regulated by a second nucleic acid sequence so that
the genes or fragments thereof are expressed in a host transformed
with the recombinant DNA molecule(s). For example, expression of
the proteins can be controlled by any promoter/enhancer known in
the art. In a specific embodiment, the promoter is not native to
the genes for a desired protein. Promoters which can be used
include but are not limited to the SV40 early promoter (Bernoist
and Chambon, Nature 290:304-310 (1981)), the promoter contained in
the 3' long terminal repeat of Rous sarcoma virus (Yamamoto et al.,
Cell 22:787-797 (1980)), the herpes thymidine kinase promoter
(Wagner et al., Proc. Natl. Acad. Sci. USA 78:1441-1445 (1981)),
the regulatory sequences of the metallothionein gene (Brinster et
al., Nature 296:39-42 (1982)); prokaryotic expression vectors such
as the .beta.-lactamase promoter (Jay et al., Proc. Natl. Acad.
Sci. USA 78:5543 (1981)) or the tac promoter (DeBoer et al., Proc.
Natl. Acad. Sci. USA 80:21-25 (1983); see also "Useful Proteins
from Recombinant Bacteria": in Scientific American 242:74-94
(1980)); plant expression vectors containing the nopaline
synthetase promoter (Herrera-Estrella et al., Nature 303:209-213
(1984)) or the cauliflower mosaic virus 35S RNA promoter (Gardner
et al., Nucleic Acids Res. 9:2871 (1981)), and the promoter of the
photosynthetic enzyme ribulose bisphosphate carboxylase
(Herrera-Estrella et al., Nature 310:115-120 (1984)); promoter
elements from yeast and other fungi such as the Gal4 promoter, the
alcohol dehydrogenase promoter, the phosphoglycerol kinase
promoter, the alkaline phosphatase promoter, and the following
animal transcriptional control regions that exhibit tissue
specificity and have been used in transgenic animals: elastase I
gene control region which is active in pancreatic acinar cells
(Swift et al., Cell 38:639-646 (1984); Ornitz et al., Cold Spring
Harbor Symp. Quant. Biol. 50:399-409 (1986); MacDonald, Hepatology
7: 425-515 (1987)); insulin gene control region which is active in
pancreatic beta cells (Hanahan et al., Nature 315:115-122 (1985)),
immunoglobulin gene control region which is active in lymphoid
cells (Grosschedl et al., Cell 38:647-658 (1984); Adams et al.,
Nature 318:533-538 (1985); Alexander et al., Mol. Cell Biol.
7:1436-1444 (1987)), mouse mammary tumor virus control region which
is active in testicular, breast, lymphoid and mast cells (Leder et
al., Cell 45:485-495 (1986)), albumin gene control region which is
active in liver (Pinkert et al., Genes and Devel. 1:268-276
(1987)), alpha-fetoprotein gene control region which is active in
liver (Krumlauf et al., Mol. Cell. Biol. 5:1639-1648 (1985); Hammer
et al., Science 235:53-58 (1987)), alpha-1 antitrypsin gene control
region which is active in liver (Kelsey et al., Genes and Devel.
1:161-171 (1987)), beta globin gene control region which is active
in myeloid cells (Magram et al., Nature 315:338-340 (1985); Kollias
et al., Cell 46:89-94 (1986)), myelin basic protein gene control
region which is active in oligodendrocyte cells of the brain
(Readhead et al., Cell 48:703-712 (1987)), myosin light chain-2
gene control region which is active in skeletal muscle (Shani,
Nature 314:283-286 (1985)), and gonadotrophic releasing hormone
gene control region which is active in gonadotrophs of the
hypothalamus (Mason et al., Science 234:1372-1378 (1986)).
[0685] In a specific example, a vector is used that contains a
promoter operably linked to nucleic acids encoding a desired
protein, or a domain, fragment, derivative or homolog, thereof, one
or more origins of replication, and optionally, one or more
selectable markers (e.g., an antibiotic resistance gene). Exemplary
plasmid vectors for transformation of E. coli cells, include, for
example, the pQE expression vectors (available from Qiagen,
Valencia, Calif.). pQE vectors enable placement of a 6.times.His
tag at either the N- or C-terminus of the recombinant protein. Such
plasmids include pQE32, pQE30, and pQE31 which provide multiple
cloning sites for all three reading frames and provide for the
expression of N-terminally 6.times.His tagged proteins. (need to
fill I w/pCMV stuff). Other exemplary plasmid vectors for
transformation of E. coli cells include, for example, pD444-SR
(DNA2.0, Menlo Park, Calif.), which contains an Isopropyl
.beta.-D-1-thiogalactopyranoside (IPTG) inducible T5 promoter, a
strong ribosome bind site (RBS) and a pUC derived origin of
replication. Other exemplary plasmid vectors for transformation of
E. coli cells, include, for example, the pET expression vectors
(see, U.S. Pat. No. 4,952,496; available from Novagen, Madison,
Wis.; see, also literature published by Novagen describing the
system). Such plasmids include pET11a, which contains the T7lac
promoter, T7 terminator, the inducible E. coli lac operator, and
the lac repressor gene; pET12a-c, which contains the T7 promoter,
T7 terminator, and the E. coli ompT secretion signal; and pET15b
and pET19b (Novagen, Madison, Wis.), which contain a His-Tag.TM.
leader sequence for use in purification with a His column and a
thrombin cleavage site that permits cleavage following purification
over the column, the T7-lac promoter region and the T7
terminator.
[0686] Exemplary of a vector for mammalian cell expression is the
pCMV-Script expression vector (Agilent Technologies, Santa Clara,
Calif.; Cat. No. 212220). The pCMV-Script vector is derived from a
high-copy-number pUC-based plasmid, and contains the human
cytomegalovirus (CMV) immediate early promoter for constitutive
expression of cloned inserts in a wide variety of cell lines. The
vector contains DNA encoding the .beta.-lactamase promoter and the
SV40 early promoter linked to the neomycin/kanamycin resistance
gene (neo/kan), an f1 origin of replication, a (CMV) immediate
early promoter, an SV40 late polyadenylation signal (SV40), and the
herpes simplex virus (HSV)-thymidine kinase (TK) polyA signal.
Another example of a mammalian expression vector is the HZ24
expression vector, derived from the pCI vector backbone (Promega).
It contains DNA encoding the Beta-lactamase resistance gene (AmpR),
an F1 origin of replication, a Cytomegalovirus immediate-early
enhancer/promoter region (CMV), and an SV40 late polyadenylation
signal (SV40). The expression vector also has an internal ribosome
entry site (IRES) from the ECMV virus (Clontech) and the mouse
dihydrofolate reductase (DHFR) gene.
[0687] Any of the ADA2 variants provided herein also can be encoded
in expression vectors for in vivo expression, particularly tumor
targeted or oncolytic vectors for expression in tumor cells.
Vectors for in vivo expression include oncolytic vectors for
delivery to tumors and expression therein or targeted for delivery
to other cells and tissues, or gene therapy vectors. Oncolytic
vectors for delivery include viral vectors for Newcastle Disease
virus, parvovirus, vaccinia virus, reovirus, measles virus,
vesticular stomatitis virus (VSV), oncolytic adenoviruses and
herpes viruses. Oncolytic viral vectors for targeted delivery are
well known to one of skill in the art and include, for example,
vesicular stomatitis virus, see, e.g., U.S. Pat. Nos. 7,731,974,
7,153,510, 6,653,103 and U.S. Pat. Pub. Nos. 2010/0178684,
2010/0172877, 2010/0113567, 2007/0098743, 20050260601, 20050220818
and EP Pat. Nos. 1385466, 1606411 and 1520175; herpes simplex
virus, see, e.g., U.S. Pat. Nos. 7,897,146, 7,731,952, 7,550,296,
7,537,924, 6,723,316, 6,428,968 and U.S. Pat. Pub. Nos.
2011/0177032, 2011/0158948, 2010/0092515, 2009/0274728,
2009/0285860, 2009/0215147, 2009/0010889, 2007/0110720,
2006/0039894 and 20040009604; retroviruses, see, e.g., U.S. Pat.
Nos. 6,689,871, 6,635,472, 6,639,139, 5,851,529, 5,716,826,
5,716,613 and U.S. Pat. Pub. No. 20110212530; and adeno-associated
viruses, see, e.g., U.S. Pat. Nos. 8,007,780, 7,968,340, 7,943,374,
7,906,111, 7,927,585, 7,811,814, 7,662,627, 7,241,447, 7,238,526,
7,172,893, 7,033,826, 7,001,765, 6,897,045, and 6,632,670. The
vectors can be introduced into cells for cell therapy, such as
immune cells for immunotherapy as described herein.
[0688] The vectors for targeted delivery of any of the ADA2
variants provided herein can also encode additional agents, such as
agents for combination therapies that are proteins or polypeptides,
for example, other immunomodulatory agents, chemotherapeutic
agents, immune checkpoint inhibitors or hyaluronan-degrading
enzyme, such as a soluble hyaluronidase or polymer-conjugated
soluble hyaluronidase (e.g. PEGPH20). For example, in addition to
any of the ADA2 variants provided herein, hyaluronan degrading
enzymes can be encoded in expression vectors for in vivo
expression, particularly tumor targeted or oncolytic vectors for
expression in tumor cells (see, e.g., U.S. Pat. No. 8,450,470, and
U.S. Patent Pub. No. 2011/0152359; see also U.S. Patent Pub. No.
2012/0148535).
[0689] Immune Cells that Encode and Express the ADA2 Variants
Provided Herein
[0690] Any of the modified adenosine deaminase 2 (ADA2) variants
provided herein can be employed in methods of adoptive
immunotherapy. Methods for adoptive immunotherapy using immune
cells modified to express a therapeutic protein or other protein,
and optionally other proteins and receptors that increase immune
response to overcome the immunosuppressive effect of cancers and/or
to target the immune cells to specific cells are well known to
those of skill in the art. Accordingly, provided are immune cells
that encode one or more of the ADA2 variants provided herein, and
optionally additional molecules to enhance tumor targeting and
immune responses, particularly to overcome the immunosuppressive
effect of certain tumors. The immune cells include, but are not
limited to, tumor-infiltrating lymphocytes (TIL), cytotoxic T
lymphocytes (CTL), natural killer (NK) cells, lymphokine-activated
killer (LAK) cells, and immune cells, such as T-cells, that express
chimeric antigen receptor (CAR).
[0691] Methods for immunotherapy by administration of immune cells
are well known.
[0692] Immune cells, which can be autologous or heterologous, but
typically are autologous cells harvested from the subject to be
treated, modified to express nucleic acid encoding any one or more
of the ADA2 variants provided herein, and treated to remove tumor
cells as needed, and expanded, if necessary. Nucleic acid can be
introduced, for example, in an expression vector or in a vector or
artificial chromosome that results in incorporation of the DNA
encoding the ADA2 variant(s) into a chromosome or chromosomes of
the immune cells. The immune cells are cultured, expanded and
introduced into a subject having a tumor for treatment. In some
embodiments, the immune cells are targeted to tumor cells. For
example, in some embodiments, the cells encode an ADA2 variant and
also express a chimeric antigen receptor (CAR). Cells containing
CARS targeted to particular tumor antigens and methods for
preparing such cells are known to those of skill in the art (see,
e.g., International PCT Pub. No. WO 2014/186469).
[0693] CARs are well known, see e.g., any of International PCT Pub.
Nos. WO 2012/031744, WO 2012/079000, WO 2013/059593, WO
2015/112626, WO 2014/011988 and U.S. Pat. No. 8,465,743, which
describe CARs and cells expressing them and the uses thereof and
improvements thereof; see also U.S. Patent Pub. No. US 20150064154,
which describes cells and expression systems for producing immune
cells that target tumors for use in cell therapy. The cell can be
transfected, transduced or otherwise modified to express these
heterologous proteins using standard methods known to those of
skill in the art. The CAR can be engineered to target any tumor
cell antigen of interest, including, but not limited to, HER2,
CD19, HERV-K, CD20, CD22, ROR1, mesothelin, CD33/IL3Ra, c-Met,
PSMA, Glycolipid F77, EGFRvIII, GD-2, NY-ESO-1 TCR, MAGE A3 TCR and
GD2 and combinations thereof. Exemplary tumor antigens recognized
by CARs are known to those of skill in the art (see, e.g., Renkvist
et al. Cancer Immunol Immunother. 50(1):3-15 (2001) and Novelino et
al. Cancer Immunol Immunother. 54(3):187-207 (2005)). The antigen
binding region can include, for example, a fragment of the VH and
VL chains of a single-chain variable fragment (scFv) derived from a
particular human monoclonal antibody specific for a tumor cell
antigen or can include a plurality of antigen binding domains of a
human antigen-specific antibody. The scFv, for example can be
linked to a flexible transmembrane domain followed by a
tyrosine-based activation motif (see, e.g., Sadelain et al. Curr.
Opin. Immunol. 21, 215-223 (2009)). CARS can include additional
activation domains from co-stimulatory molecules such as CD28 and
CD137 to enhance T cell survival and proliferation. The CARs and/or
cells expressing them can further encode and express a
costimulatory signaling regions that include, for example,
intracellular domain of a costimulatory molecule, such as the
intracellular domain of CD27, CD28, 4-1BB, OX40, CD30, CD40, PD-1,
lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT,
NKG2C, B7-H3, a ligand that specifically binds with CD83, and any
combination thereof.
[0694] A variety of CAR constructs and expression vectors for the
same are known in the art. The expression vector can be one that
remains episomal, or one that results in incorporation of nucleic
acid encoding the CAR and/or the ADA2 variant into a chromosome,
such as by homologous integration or by inclusion of transposon
sequences, such that the presence of a transposase allows the
coding sequence to integrate into a chromosome of a transfected
cell. The nucleic acid encoding the ADA2 variant and CAR can be
incorporated into the same vector or can be introduced in separate
vectors. If transposon(s) are used, the cells can express a
transposase that facilitates integration of the nucleic acid
encoding the CAR and/or ADA2 variant into a chromosome of the
transfected cells. Transposon systems are known (see, e.g.,
International PCT Pub. No. WO 2014/186469). The transposase can be
provided in a DNA expression vector or as an expressible RNA or a
protein for transient expression. Transposon systems are known to
those of skill in the art such that long-term expression of the
transposase does not occur in the transgenic cells. Any transposase
system can be used in accordance with the embodiments. In other
aspects, cells can be infected with a lentivirus to facilitate
integration of the CAR coding sequence and the nucleic acid
sequence that encodes the ADA2 variant into the genome of the
cell.
[0695] 4. Expression
[0696] Any adenosine deaminase 2 (ADA2) polypeptides including
variant ADA2 polypeptides, can be produced by any method known to
those of skill in the art including in vivo and in vitro methods.
Desired proteins can be expressed in any organism suitable to
produce the required amounts and forms of the proteins, such as for
example, the amounts and forms needed for administration and
treatment. Expression hosts include prokaryotic and eukaryotic
organisms such as E. coli, yeast, plants, insect cells, mammalian
cells, including human cell lines and transgenic animals.
Expression hosts can differ in their protein production levels as
well as the types of post-translational modifications that are
present on the expressed proteins. The choice of expression host
can be made based on these and other factors, such as regulatory
and safety considerations, production costs and the need and
methods for purification. Any of the ADA2 variants provided herein
also can be encoded in expression vectors for in vivo expression,
particularly tumor targeted or oncolytic vectors for expression in
tumor cells.
[0697] Many expression vectors are available and known to those of
skill in the art and can be used for expression of proteins. The
choice of expression vector will be influenced by the choice of
host expression system. In general, expression vectors can include
transcriptional promoters and optionally enhancers, translational
signals, and transcriptional and translational termination signals.
Expression vectors that are used for stable transformation
typically have a selectable marker which allows selection and
maintenance of the transformed cells. In some cases, an origin of
replication can be used to amplify the copy number of the
vector.
[0698] The ADA2 polypeptides, including variant ADA2 polypeptides,
also can be utilized or expressed as protein fusions. For example,
an enzyme fusion can be generated to add additional functionality
to an enzyme. Examples of enzyme fusion proteins include, but are
not limited to, fusions of a signal sequence, a tag such as for
localization, e.g., a His.sub.6 tag or a FLAG.TM. tag, or a tag for
purification, for example, a GST fusion, and a sequence for
directing protein secretion and/or membrane association.
[0699] a. Prokaryotic Cells
[0700] Prokaryotes, especially Escherichia coli, provide a system
for producing large amounts of proteins. Transformation of E. coli
is a simple and rapid technique well known to those of skill in the
art. Expression vectors for E. coli can contain inducible
promoters, such promoters are useful for inducing high levels of
protein expression and for expressing proteins that exhibit some
toxicity to the host cells. Examples of inducible promoters include
the lac promoter, the trp promoter, the hybrid tac promoter, the T7
and SP6 RNA promoters and the temperature regulated .lamda.PL
promoter.
[0701] Proteins, such as any provided herein, can be expressed in
the cytoplasmic environment of E. coli. The cytoplasm is a reducing
environment and for some molecules, this can result in the
formation of insoluble inclusion bodies. Reducing agents such as
dithiothreitol and .beta.-mercaptoethanol and denaturants, such as
guanidine-HCl and urea can be used to resolubilize the proteins. An
alternative approach is the expression of proteins in the
periplasmic space of bacteria which provides an oxidizing
environment and chaperonin-like and disulfide isomerases and can
lead to the production of soluble protein. Typically, a leader
sequence is fused to the protein to be expressed which directs the
protein to the periplasm. The leader is then removed by signal
peptidases inside the periplasm. Examples of periplasmic-targeting
leader sequences include the pelB leader from the pectate lyase
gene and the leader derived from the alkaline phosphatase gene. In
some cases, periplasmic expression allows leakage of the expressed
protein into the culture medium. The secretion of proteins allows
quick and simple purification from the culture supernatant.
Proteins that are not secreted can be obtained from the periplasm
by osmotic lysis. Similar to cytoplasmic expression, in some cases
proteins can become insoluble and denaturants and reducing agents
can be used to facilitate solubilization and refolding. Temperature
of induction and growth also can influence expression levels and
solubility, typically temperatures between 25.degree. C. and
37.degree. C. are used. Typically, bacteria produce aglycosylated
proteins. Thus, if proteins require glycosylation for function,
glycosylation can be added in vitro after purification from host
cells.
[0702] b. Yeast Cells
[0703] Yeasts such as Saccharomyces cerevisae, Schizosaccharomyces
pombe, Yarrowia lipolytica, Kluyveromyces lactis and Pichia
pastoris are well known yeast expression hosts that can be used for
production of proteins, such as any described herein. Yeast can be
transformed with episomal replicating vectors or by stable
chromosomal integration by homologous recombination. Typically,
inducible promoters are used to regulate gene expression. Examples
of such promoters include GAL1, GAL7 and GAL5 and metallothionein
promoters, such as CUP1, AOX1 or other Pichia or other yeast
promoter. Expression vectors often include a selectable marker such
as LEU2, TRP1, HIS3 and URA3 for selection and maintenance of the
transformed DNA. Proteins expressed in yeast are often soluble.
Co-expression with chaperonins such as Bip and protein disulfide
isomerase can improve expression levels and solubility.
Additionally, proteins expressed in yeast can be directed for
secretion using secretion signal peptide fusions such as the yeast
mating type alpha-factor secretion signal from Saccharomyces
cerevisae and fusions with yeast cell surface proteins such as the
Aga2p mating adhesion receptor or the Arxula adeninivorans
glucoamylase. A protease cleavage site such as for the Kex-2
protease, can be engineered to remove the fused sequences from the
expressed polypeptides as they exit the secretion pathway. Yeast
also is capable of glycosylation at Asn-X-Ser/Thr motifs.
[0704] c. Insect Cells
[0705] Insect cells, particularly using baculovirus expression, are
useful for expressing polypeptides such as any ADA2 polypeptides or
variants. Insect cells express high levels of protein and are
capable of most of the post-translational modifications used by
higher eukaryotes. Baculovirus have a restrictive host range which
improves the safety and reduces regulatory concerns of eukaryotic
expression. Typical expression vectors use a promoter for high
level expression such as the polyhedrin promoter of baculovirus.
Commonly used baculovirus systems include the baculoviruses such as
Autographa californica nuclear polyhedrosis virus (AcNPV), and the
Bombyx mori nuclear polyhedrosis virus (BmNPV) and an insect cell
line such as Sf9 derived from Spodoptera frugiperda, Pseudaletia
unipuncta (A7S) and Danaus plexippus (DpN1). For high-level
expression, the nucleotide sequence of the molecule to be expressed
is fused immediately downstream of the polyhedrin initiation codon
of the virus. Mammalian secretion signals are accurately processed
in insect cells and can be used to secrete the expressed protein
into the culture medium. In addition, the cell lines Pseudaletia
unipuncta (A7S) and Danaus plexippus (DpN1) produce proteins with
glycosylation patterns similar to mammalian cell systems.
[0706] An alternative expression system in insect cells is the use
of stably transformed cells. Cell lines such as the Schneider 2
(S2) and Kc cells (Drosophila melanogaster) and C7 cells (Aedes
albopictus) can be used for expression. The Drosophila
metallothionein promoter can be used to induce high levels of
expression in the presence of heavy metal induction with cadmium or
copper. Expression vectors are typically maintained by the use of
selectable markers such as neomycin and hygromycin.
[0707] d. Mammalian Cells
[0708] Mammalian expression systems can be used to express proteins
including any ADA2 polypeptides, including variant ADA2
polypeptides. Expression constructs can be transferred to mammalian
cells by viral infection such as adenovirus or by direct DNA
transfer such as liposomes, calcium phosphate, DEAE-dextran and by
physical means such as electroporation and microinjection.
Expression vectors for mammalian cells typically include an mRNA
cap site, a TATA box, a translational initiation sequence (Kozak
consensus sequence) and polyadenylation elements. IRES elements
also can be added to permit bicistronic expression with another
gene, such as a selectable marker. Such vectors often include
transcriptional promoter-enhancers for high-level expression, for
example the SV40 promoter-enhancer, the human cytomegalovirus (CMV)
promoter and the long terminal repeat of Rous sarcoma virus (RSV).
These promoter-enhancers are active in many cell types. Tissue and
cell-type promoters and enhancer regions also can be used for
expression. Exemplary promoter/enhancer regions include, but are
not limited to, those from genes such as elastase I, insulin,
immunoglobulin, mouse mammary tumor virus, albumin, alpha
fetoprotein, alpha 1 antitrypsin, beta globin, myelin basic
protein, myosin light chain 2, and gonadotropic releasing hormone
gene control. Selectable markers can be used to select for and
maintain cells with the expression construct. Examples of
selectable marker genes include, but are not limited to, hygromycin
B phosphotransferase, adenosine deaminase, xanthine-guanine
phosphoribosyl transferase, aminoglycoside phosphotransferase,
dihydrofolate reductase (DHFR) and thymidine kinase. For example,
expression can be performed in the presence of methotrexate to
select for only those cells expressing the DHFR gene. Fusion with
cell surface signaling molecules such as TCR-.zeta. and
Fc.sub..epsilon.RT-.gamma. can direct expression of the proteins in
an active state on the cell surface.
[0709] Many cell lines are available for mammalian expression
including mouse, rat human, monkey, chicken and hamster cells.
Exemplary cell lines include but are not limited to CHO, Balb/3T3,
HeLa, MT2, mouse NS0 (nonsecreting) and other myeloma cell lines,
hybridoma and heterohybridoma cell lines, lymphocytes, fibroblasts,
Sp2/0, COS, NIH3T3, HEK293, 293S, 2B8, and HKB cells. Cell lines
also are available adapted to serum-free media which facilitate
purification of secreted proteins from the cell culture media.
Examples include CHO-S cells (Invitrogen, Carlsbad, Calif., cat
#11619-012) and the serum free EBNA-1 cell line (Pham et al.,
(2003) Biotechnol. Bioeng. 84:332-342). Cell lines also are
available that are adapted to grow in special media optimized for
maximal expression. For example, DG44 CHO cells are adapted to grow
in suspension culture in a chemically defined, animal product-free
medium.
[0710] e. Plants
[0711] Transgenic plant cells and plants can be used to express
proteins such as any described herein. Expression constructs are
typically transferred to plants using direct DNA transfer such as
microprojectile bombardment and PEG-mediated transfer into
protoplasts, and with agrobacterium-mediated transformation.
Expression vectors can include promoter and enhancer sequences,
transcriptional termination elements and translational control
elements. Expression vectors and transformation techniques are
usually divided between dicot hosts, such as Arabidopsis and
tobacco, and monocot hosts, such as corn and rice. Examples of
plant promoters used for expression include the cauliflower mosaic
virus promoter, the nopaline synthetase promoter, the ribose
bisphosphate carboxylase promoter and the ubiquitin and UBQ3
promoters. Selectable markers such as hygromycin, phosphomannose
isomerase and neomycin phosphotransferase are often used to
facilitate selection and maintenance of transformed cells.
Transformed plant cells can be maintained in culture as cells,
aggregates (callus tissue) or regenerated into whole plants.
Transgenic plant cells also can include algae engineered to produce
any ADA2 polypeptides. Because plants have different glycosylation
patterns than mammalian cells, this can influence the choice of
protein produced in these hosts.
[0712] 5. Purification Techniques
[0713] Method for purification of polypeptides, including any ADA2
polypeptides, including variant ADA2 polypeptides, from host cells
will depend on the chosen host cells and expression systems. For
secreted molecules, proteins are generally purified from the
culture media after removing the cells. For intracellular
expression, cells can be lysed and the proteins purified from the
extract. When transgenic organisms such as transgenic plants and
animals are used for expression, tissues or organs can be used as
starting material to make a lysed cell extract. Additionally,
transgenic animal production can include the production of
polypeptides in milk or eggs, which can be collected, and if
necessary, the proteins can be extracted and further purified using
standard methods in the art.
[0714] Proteins, such as ADA2 polypeptides, can be purified using
standard protein purification techniques known in the art including
but not limited to, SDS-PAGE, size fraction and size exclusion
chromatography, ammonium sulfate precipitation and ionic exchange
chromatography, such as anion exchange chromatography. Affinity
purification techniques also can be utilized to improve the
efficiency and purity of the preparations. For example, antibodies,
receptors and other molecules that bind ADA2 enzymes can be used in
affinity purification. Expression constructs also can be engineered
to add an affinity tag to a protein such as a FLAG.TM. epitope, GST
fusion or His.sub.6 and affinity purified with an anti-FLAG.TM.
antibody, glutathione resin and Ni-resin, respectively.
[0715] When proteins are expressed by transformed bacteria in large
amounts, typically after promoter induction, although expression
can be constitutive, the polypeptides can form insoluble
aggregates. There are several protocols that are suitable for
purification of polypeptide inclusion bodies known to one of skill
in the art. Numerous variations will be apparent to those of skill
in the art. For example, in one method, the cell suspension is
generally centrifuged and the pellet containing the inclusion
bodies resuspended in buffer which does not dissolve but washes the
inclusion bodies, e.g., 20 mM Tris-HCl (pH 7.2), 1 mM EDTA, 150 mM
NaCl and 2% Triton-X 100, a non-ionic detergent. It can be
necessary to repeat the wash step to remove as much cellular debris
as possible. The remaining pellet of inclusion bodies can be
resuspended in an appropriate buffer (e.g., 20 mM sodium phosphate,
pH 6.8, 150 mM NaCl). Other appropriate buffers are apparent to
those of skill in the art.
[0716] Alternatively, proteins can be purified from bacteria
periplasm. Where the protein is exported into the periplasm of the
bacteria, the periplasmic fraction of the bacteria can be isolated
by cold osmotic shock in addition to other methods known to those
of skill in the art. For example, in one method, to isolate
recombinant polypeptides from the periplasm, the bacterial cells
are centrifuged to form a pellet. The pellet can be resuspended in
a suitable buffer containing 20% sucrose. To lyse the cells, the
bacteria can be centrifuged and the pellet resuspended in ice-cold
5 mM MgSO.sub.4 and kept in an ice bath for approximately 10
minutes. The cell suspension is centrifuged and the supernatant
decanted and saved. Recombinant proteins present in the supernatant
can be separated from the host proteins by standard separation
techniques well known to those of skill in the art, such as the
separation techniques described herein. These methods include, but
are not limited to, the following steps: solubility fractionation,
size differential filtration, and column chromatography.
[0717] ADA2 protein molecules having a molecular weight of from or
from about 95 kDa to 120 kDa, and generally from or from about 100
kDa to 110 kDa, inclusive, can be collected and purified. When in
monomer form, or when assessed under reducing conditions on an SDS
PAGE gel, the molecular weight of ADA2 is generally from or from
about 50 kDa to 60 kDa, such as generally from or from about 57 kDa
to 59 kDa. It is understood that variants or other modified forms
can exhibit higher or lower molecular weights. For example,
typically hyperglycosylated variants or conjugates as provided
herein can exhibit higher molecular weights.
[0718] Purity can be assessed by any method known in the art
including gel electrophoresis and staining and spectrophotometric
techniques. Any ADA2 polypeptides, including variant ADA2
polypeptides, can be purified to 60%, 70%, 80% purity and typically
at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% purity.
Purity can be assessed by standard methods such as by SDS-PAGE and
coomassie staining.
F. METHODS OF ASSESSING ACTIVITY AND PHYSICAL PROPERTIES OF
ADA2
[0719] Assays can be used to assess the physical properties,
stability and/or activity of any of the ADA2 protein molecules
provided herein, including wildtype and variants and modified forms
thereof. The properties and activities can be related to biological
activities and/or tumor treatment activities. The assays can be
performed in vitro or in vivo. For example, the assays can be used
to assess the adenosine deaminase activity of the ADA2, heparin
binding, thermal stability, pH optima, pharmacokinetics, tumor
growth inhibitor activity and other activities and properties. In
another example, the assays can be used to assess the effects of
administering any ADA2 provided herein, including effects of dose
and route of administration. The assays also can be used make minor
adjustments to the formulations provided herein while retaining the
activity of ADA2 for therapeutic use. Such assays are well known to
a skilled artisan. Non-limiting exemplary assays are described in
the following subsections.
[0720] 1. Adenosine Deaminase Assay
[0721] The adenosine deaminase (ADA; EC 3.5.4.4) activity of any of
the ADA2 described herein, including a wildtype, variant or
conjugate, can be assessed using methods well known in the art. ADA
activity assays commonly measure, directly or indirectly, the rate
of production a product of the enzymatic reaction. For example, the
production of inosine or ammonia can be directly or indirectly
measured. In other examples, the decrease of the substrate of the
enzyme, e.g., adenosine or 2-deoxyadenosine, is measured. The
decrease of the substrate, or the increase of the product, can be
measured directly by spectrophotometry, or indirectly, by
subsequent enzymatic or oxidation-reduction reactions that use
chromogenic substrates or change the absorbance spectra of the
reaction.
[0722] For example, some commercially available adenosine deaminase
(ADA) assays, such as ADA assay kits available from BQ Kits (San
Diego, Calif.; Cat. No. BQ014EALD) and Diazyme (Poway, C A; Cat.
No. DZ117A-K), utilize colorimetric substrate and
spectrophotometric reading to determine the conversion of adenosine
to inosine by ADA enzymes. In these assays, the production of
inosine is detected by multi-step enzymatic reactions that produce
a chromogenic dye. Enzymatic deamination of adenosine produces
inosine, which is converted to hypoxanthine by the inosine-specific
purine nucleoside phosphorylase (PNP; EC 2.4.2.1) present in the
reaction. Hypoxanthine is then converted to uric acid and hydrogen
peroxide (H.sub.2O.sub.2) by xanthine oxidase (XOD; EC 1.1.3.22).
H.sub.2O.sub.2 is further reacted with
N-Ethyl-N-(2-hydroxy-3-sulfopropyl)-3-methylaniline (EHSPT) and
4-aminoantipyrine (4-AA) in the presence of peroxidase (POD) to
generate a quinone dye which is detectable in a kinetic manner
using a UV spectrophotometer at 556 nm. Bovine liver adenosine
deaminase can be used as standards. The change in absorbance at 556
nm (.DELTA.A.sub.556) over time, at 37.degree. C., is measured. One
unit of ADA is defined as the amount of ADA that generates one
.mu.mole of inosine from adenosine per minute at 37.degree. C.
Adenosine deaminase activity in mU/mL is calculated using the
following formula:
1
mU/mL=(.DELTA.A.sub.556/min.times.T.sub.v)/(S.sub.v.times..epsilon..ti-
mes.1)
[0723] where T.sub.v=total volume of reaction; S.sub.v=sample
volume, .epsilon.=32.2.times.10.sup.-3 .mu.M.sup.-1 cm.sup.-1,
1=0.5 cm.
[0724] ADA activity can be visualized using other colorimetric
methods (see, e.g., Manchenko, G. P., Handbook of Detection of
Enzymes on Electrophoretic Gels, CRC Press, pp. 453-454). For
example, the H.sub.2O.sub.2 produced in the ADA assay described
above, can be visualized by the addition of phenazine methosulfate
(PMS), which is converted to dihydroPMS by H.sub.2O.sub.2, then the
dihydroPMS converts nitroblue tetrazolium chloride (NBT) to
formazan. Absorbance of formazan can be determined at 570 nm.
[0725] Another method to measure ADA activity is by measuring the
release of ammonia from adenosine, when it is deaminated to form
inosine. Ammonia release can be measured using commercially
available kits, such as the Ammonia Assay kit (Cat. No. A0853,
Sigma-Aldrich, St. Louis, Mo.). The kit contains dry reagents
containing .alpha.-ketoglutaric acid and NADPH. Ammonia reacts with
.alpha.-ketogluaric acid (KGA) and reduced nicotinamide adenine
dinucleotide phosphate (NADPH) in the presence of L-glutamate
dehydrogenase (GDH; Cat. No. G2294, Sigma-Aldrich). The decrease in
absorbance at 340 nm, due to the oxidation of NADPH to NADP+, is
proportional to the ammonia concentration, and hence the adenosine
deaminase activity. The decrease in absorbance can be measured
using a spectrophotometer. Adenosine deaminase activity in mU/mL
(.mu.M/min equivalent) is calculated using the following
formula:
1
mU/mL=(.DELTA.A/min.times.T.sub.v)/(S.sub.v.times..epsilon..times.1)
[0726] where T.sub.v=total volume, S.sub.v=sample volume,
.epsilon.=6.22.times.10.sup.-3 .mu.M.sup.-1 cm.sup.-1, 1=1 cm.
[0727] Other spectrophotometry-based adenosine deaminase assays
include the continuous optical assay, which directly measures the
changes in adenosine absorbance. Absorbance of adenosine can be
measured at 265 nm, and the decrease of absorbance at 265 nm, as
adenosine is deaminated to inosine, is measured over time. The
samples are prepared in a 100 mM potassium phosphate buffer, pH 7.5
at 25.degree. C. containing 0.1% (w/v) bovine serum albumin (BSA),
and is incubated with 1.35 mM adenosine solution, pH 7.0 at
25.degree. C. The decrease in absorbance at 265 nm
(.DELTA.A.sub.265) is measured for approximately 5 minutes. In this
assay, ADA activity in U/mL is calculated using the following
formula:
Units/mL enzyme=(.DELTA.A.sub.265/min)(T.sub.v)(df))/(8.1)(V.sub.E)
[0728] where T.sub.v=Total volume (in mL) of assay; df=Dilution
Factor; 8.1=Millimolar extinction coefficient of adenosine at 265
nm; V.sub.E=Volume (in milliliters) of enzyme used.
[0729] One unit will deaminate 1.0 .mu.mole of adenosine to inosine
per minute at pH 7.5 at 25.degree. C. Such method can be performed
in a larger scale format such as in a 96-well microtiter plate
format (see, for example, Lu et al. (2012) Clinica Chimica Acta
413:1637-1640).
[0730] A variation of this method can be used, with necessary
corrections made to the absorbance measurements. UV absorption peak
of adenosine and inosine are at 261 nm and 249 nm, respectively,
and the spectra overlap significantly. During the deamination
reaction, the absorbance of Adenosine decreases while that of
inosine increases with time. To determine the relative adenosine,
whose spectra overlap with that of inosine, two spectrophotometric
measurements are made. The isobestic point, where adenosine and
inosine have the same extinction coefficient and remains unchanged,
is at 253 nm, and is concentration independent. The isobestic point
is also measured as the reference point to correct for volume or
intensity discrepancies. The ratio of absorbance at 261
nm/absorbance at 253 nm (A.sub.261/A.sub.253) is used to measure
changes in adenosine concentration, based on a standard curve.
[0731] 2. Methods of Assessing Heparin Binding
[0732] Heparin binding, or binding to another GAG; by any ADA2
described herein, including a wildtype, variant or conjugate, can
be assessed using methods well known in the art. These methods and
other methods known in the art to assess binding to GAGs, can be
used to assess binding and/or select ADA2 variants with altered
heparin binding, e.g.
[0733] attenuated heparin binding or increased heparin binding.
Generally, heparin-binding is sensitive to the presence of metal
ions, urea, and detergents (anionic, nonionic, and zwitterionic).
Ca.sup.2+ and Mg.sup.2+ and the zwitterionic detergent
3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate increases
heparin binding. The presence of NaCl, urea, sodium dodecylsulfate,
and La.sup.3+ reduces heparin binding.
[0734] a. Affinity Assay
[0735] The ability of ADA2 to bind heparin can be assessed using
affinity binding assays with immobilized heparin. Heparin is a
highly sulfated glycosaminoglycan, and is widely used as a general
affinity ligand. Its high degree of sulfation imparts a strong
acidic nature to the molecule, therefore it binds many substances,
including ADA2, by ionic interaction. In addition, heparin contains
unique carbohydrate sequences, which act as specific binding sites
for some proteins. Columns containing immobilized heparin are used
to assess binding of and purify proteins with high affinity for
heparin, such as DNA-binding proteins, coagulation factors,
lipoproteins, and protein synthesis factors. For example,
commercially available heparin resin columns, such as HiTrap
Heparin HP loaded with heparin-Sepharose.TM. resin (GE Healthcare,
Pittsburgh, Pa.; Cat. No. 17-0998-01), can be used to assess
binding of a specific protein, such as ADA2. In the
heparin-Sepharose.TM. resin, heparin is coupled to the Sepharose
High Performance base matrix via the N-hydroxysuccinamide coupling
method, to provide high capacity, performance, and low leakage
levels.
[0736] Heparin binding can be assessed by an affinity assay using
the heparin-Sepharose.TM. resin. In such an exemplary assay, 35
.mu.L of ADA2, wildtype or variants, is mixed with 20 .mu.L
heparin-Sepharose.TM. resin (GE Healthcare, Pittsburgh, Pa.; Cat.
No. 17-0998-01), followed by incubating at room temperature for 30
min. The mixture is then centrifuged through a 0.22 .mu.m
centrifuge filter and the flow-through, containing the unbound
protein, is collected for analysis on an SDS-PAGE gel. 35 .mu.L of
1.5 M NaCl is added to heparin-Sepharose resin and incubated at
room temperature (RT) for 10 min to elute the remaining
heparin-bound protein from the heparin-Sepharose. Degree of heparin
binding is assessed by SDS-PAGE, by comparing the amount of ADA2,
wildtype and variants, bound to the resins and the flowthrough to
the amount in the input.
[0737] b. ELISA Assay
[0738] Heparin binding of a protein, such as any ADA2 provided
herein, can also be assessed using enzyme-linked immunosorbent
assay (ELISA) based methods. ELISA-based methods use heparin
immobilized on a surface, such as a microtiter plate. The protein
of interest which binds to heparin, such as any ADA2 provided
herein, is incubated in the heparin coated plate, and binding is
detected using antibodies that detect the protein of interest, such
as any ADA2 provided herein.
[0739] For example, a 96-well plate coated with 100 .mu.L of 200
.mu.g/mL heparin sodium salt (Calibochem, EMD Milipore, Billerica,
Mass.; Cat. No. 375095) in Na.sub.2CO.sub.3 buffer (pH 9.6) can be
used to test ADA2 binding to heparin. After binding of ADA2, such
as wildtype or variants or modified forms thereof, the wells are
washed and incubated with a horseradish peroxidase (HRP)-conjugated
detection antibody, e.g., HRP-anti-FLAG antibody (Abcam, Cambridge,
UK; Cat. No. Ab1238) to detect the FLAG tag on the protein of
interest, such as any ADA2 provided herein. After incubation and
washing, the degree of binding of the protein of interest to the
immobilized heparin on the plate is visualized by a chromogenic
substrate, such as 3,3',5,5'-Tetramethylbenzidine (TMB) substrate
solution (Pierce, Thermo Fisher Scientific, Rockford, Ill.) for
HRP, is added for color development. The optical density (OD) of
each reaction is measured on a plate reader.
[0740] In another example, heparin is immobilized by incubating
Streptavidin-coated microtiter plates, such as the
Streptavidin-coated 96-well plate (Thermo Fisher Scientific,
Rockford, Ill.; Cat. No. 15520), with biotinylated heparin, such as
biotin-heparin (Sigma-Aldrich, St. Louis, Mo.; Cat No. B9806-10MG).
After binding of ADA2, wildtype or variants or modified forms
thereof, the wells are washed and incubated with a horseradish
peroxidase (HRP)-conjugated detection antibody, e.g., HRP-anti-FLAG
antibody (Abcam, Cambridge, UK; Cat. No. Ab1238) to detect the FLAG
tag on the protein of interest, such as any ADA2 provided herein.
After incubation and washing, the degree of binding of the protein
of interest to the immobilized heparin on the plate is visualized
by a chromogenic substrate, such as 3,3',5,5'-Tetramethylbenzidine
(TMB) substrate solution (Pierce, Thermo Fisher Scientific,
Rockford, Ill.) for HRP, is added for color development. The
optical density (OD) of each reaction is measured on a plate
reader.
[0741] Any variations of these methods known in the art can also be
used. For example, it is within the level of one of skill in the
art to select a suitable solid support depending on the particular
assay conditions, such as a particular pH condition. Nickel coated
microplates can be less suitable for binding of His-tagged
proteins, since buffer pH can affect antigen coating to Ni-coated
but not high-bind plates. In addition, various methods can be used
to immobilize heparin to the plate, such as conjugation with bovine
serum albumin (BSA) or other carriers coating with protamine
sulfate with an excess of heparin.
[0742] Buffers, blocking solutions and reaction conditions can also
be selected based on the desired binding assay. For example,
blocking solutions include those containing human, bovine, horse or
other serum albumin or gelatin. Blocking of a solid support, such
as a plate, can be performed using a binding assay buffer to which
one or more blocking agents are added. Exemplary blocking agents
include 1-5% Bovine Serum Albumin (BSA), 1-5% non-fat dry milk,
0.1-1% gelatin and 25% human serum. Detergents, such as Tween-20,
and preservatives, such as thimerosal, can be added to the blocking
solution. Binding assay buffers include i.e. the tumor
microenvironment buffer or the normal physiologic buffer. The
aqueous protein solution-solid support mixture is typically
maintained for a time period of 30 minutes, 1 hour, or longer, and
can vary as a function of the temperature. The blocking reaction
can be performed at any temperature, and generally can be performed
4.degree. C.-37.degree. C., such as 4.degree. C., room temperature
(i.e., 22.degree. C.) or 37.degree. C. In some examples, the
reaction is allowed to proceed for at least one hour at a
temperature of about 4.degree. C.-37.degree. C. For example,
blocking can be achieved at room temperature for one hour. After
incubation and blocking, the resulting solid phase can be
thereafter rinsed free of unbound protein prior to contact with the
test molecule (e.g. ADA2 wildtype, variants and modified forms
provided herein).
[0743] Examples of enzyme labels include horseradish peroxidase,
alkaline phosphatase, and .beta.-D-galactosidase. Examples of
enzyme substrates that can be added to develop the signal include
PNPP (p-Nitrophenyl Phosphate, Disodium Salt), ABTS (2,2'-Azinobis
[3-ethylbenzothiazoline-6-sulfonic acid]-diammonium salt), OPD
(o-phenylenediamine dihydrochloride), and TMB
(3,3',5,5'-tetramethylbenzidine) (SOMA Labs, Romeo, Mich.),
including Sureblue TMB Microwell Peroxidase Substrate 1-component
(KPL, #52-00-03). The reaction can be stopped by adding a stopping
reagent (e.g. TMB stop solution). The absorbance at a suitable
wavelength (i.e. 450 nm) can be determined.
[0744] For fluorescence, a large number of fluorometers are
available. For chemiluminescence detection, such as detection of
horseradish peroxidase (HRP) substrates, luminometers or films are
available. With enzymes, a fluorescent, chemiluminescent, or
colored product can be determined or measured fluorometrically,
luminometrically, spectrophotometrically or visually. For example,
an anti-tag reagent can be conjugated to horseradish peroxidase
(HRP) or other detectable agent.
[0745] Detection can be facilitated by the presence of a
fluorescent, radioactive or other detectable moiety. For example,
any ADA2 polypeptides provided herein, including wildtype and
variant polypeptides and modified forms thereof, can harbor an N-
or C-terminal tag, such as a FLAG tag, and can be detected using an
anti-tag reagent, such as an anti-FLAG antibody. The choice of
anti-tag reagent is a function of the tag that is employed with the
binding molecule or protein. In addition, an anti-tag reagent is
chosen that is compatible with the environment conditions (e.g. pH)
used in the assay. It is within the level of one of skill in the
art to identify or select such reagents, and test their
compatibility with the assay conditions. Anti-tag reagents are
readily available such as from commercial sources or other sources.
Exemplary anti-tag reagents that can be used for detection in the
methods herein include, but are not limited to an anti-FLAG
antibody or anti-Myc antibody (available from vendors such as
Abcam, Cambridge, Mass.; GeneTex, Irvine, Calif.). In addition,
depending on the protein of interest and strength of signal, other
antibodies and/or chromogenic substrates can be used in a variant
version of the ELISA. For example, for native proteins that do not
harbor a tag, detection can be achieved using two antibodies, e.g.,
primary antibody recognizing the native target and a secondary
antibody conjugated with enzymes used for detection.
[0746] Typically, in the methods herein, the method of detection of
the bound complex is one that is capable of being quantitated. For
example, a label can produce a signal, such as a colorimetric
signal, a chemiluminescent signal, a chemifluorescent signal or a
radioactive signal. Depending upon the nature of the label, various
techniques can be employed for detecting or detecting and
quantitating the label. For example, methods of quantitation
include, but are not limited to, spectrophotometric, fluorescent
and radioactive methods.
[0747] c. Dot Blot and Other Radiolabeled Heparin Binding
Assays
[0748] The degree of heparin binding can also be detected using
blot-based methods with radiolabeled heparin. For example, a dot
blot method can be used to detect and quantitate picomole amounts
of heparin-binding protein of interest. Proteins are spotted on
nitrocellulose and then incubated with .sup.125I-heparin. Binding
of heparin to the proteins is detected by radioautography and
quantitated by scanning densitometry; proteins are quantitated by
densitometric analysis of the amido black stained nitrocellulose
(Hirose et al. (1986) Analytical Biochemistry 156(2):320-325). In
another example, radiolabeled heparin, such as .sup.3H-heparin is
incubated in a 96-well microtiter format with the heparin binding
protein of interest, such as any ADA2 provided herein, including
wildtype, variants or modified forms thereof. The mixture is then
transferred to a 96-well microtiter filter plates which filters out
the unbound heparin and protein of interest. Binding is detected by
scintillation counting (see Proudfoot et al. (2003). PNAS
100(4):1885-1890).
[0749] 3. Methods for Assessing Stability
[0750] Stability of any of the ADA2 provided herein in specific
conditions can be determined by any method known to one of skill in
the art used to assess protein stability. Stability in a specific
condition (e.g., high temperature condition for thermal stability,
high or low pH conditions for pH tolerance, plasma conditions for
plasma stability, and long-term storage for long-term stability)
can be assessed by determining changes in physical properties of
the polypeptide, including but not limited to, structural
configuration or conformation, enzymatic activity, protein
unfolding, aggregation, and solubility, before and after without
exposure to the specific condition. Stability also can be assessed
by comparing any one or more of activity, aggregation or other
physical properties in the presence of one or more denaturation
conditions compared to a native, wildtype or reference ADA2
polypeptide.
[0751] Protein stability includes a measure of the maintenance of
one or more physical properties of a protein in response to an
environmental condition (e.g. an elevated temperature). In one
example, the physical property is the maintenance of the covalent
structure of the protein (e.g. the absence of proteolytic cleavage,
unwanted oxidation or deamidation). In another example, the
physical property is the presence of the protein in a properly
folded state (e.g. the absence of soluble or insoluble aggregates
or precipitates). In one example, stability of a protein is
measured by assaying a biophysical property of the protein, for
example thermal stability, pH unfolding profile, stable removal of
glycosylation, solubility, biochemical function (e.g., enzymatic
activity, ability to bind to a protein (e.g., a ligand, a receptor,
an antigen, etc.) or chemical moiety, etc.), and/or combinations
thereof. In another example, biochemical function is demonstrated
by the binding affinity of an interaction. In addition, stability
can be assessed by visual inspection, percent recovery, protein
purity and apparent melting temperature. Stability measurements
also provide important biological information; a decrease in
stability can be a sign of protein unfolding, misfolding and
aggregation, which can lead to polypeptides ineffective for
treatment. Such assays can be performed under any conditions that
can result in protein instability, and can be assessed on any
physical or functional properties associated with an ADA2 protein.
Stability can be measured using any methods known in the art and/or
described herein.
[0752] a. Conditions
[0753] i. Stability in Plasma
[0754] For therapeutic uses, such as for treatment of tumors or
cancers, it is desirable to administer to the subject a dosage of
ADA2 that will maintain plasma adenosine deaminase (ADA) activity
for a sufficient time for therapeutic effect. Hence, sufficient
retention of stability in the plasma and tumor microenvironment
(TME) is necessary for effectiveness of the treatment. The plasma
stability of any ADA2 described herein, such as a wildtype, variant
or conjugate, can be determined by measuring the changes in
enzymatic activity and/or other physical properties, before and
after incubation in plasma, e.g., ex vivo mammalian plasma.
[0755] Stability can be assessed in vitro or in vivo. For example,
stability can be tested after exposure to plasma for a desired
length of time, which can be empirically determined or selected by
a skilled artisan depending on the desired length of time. For
example, the incubation time can be at least 1 hour, such as at
least 2, 3, 4, 5, 10, 15, 20, 24, 30, 36, 48, 60, 72 hours or more.
The protein can be directly administered systemically, such as
intravenously, and activity can be assessed. In other examples, the
protein can be subject to appropriate incubation conditions in
vitro. In one example, the stability of ADA activity of any ADA2
provided herein can be measured after incubation at 37.degree. C.,
in 25% ex vivo plasma or serum, such as human or non-human plasma
or serum, for example, mouse plasma. For example, as shown herein,
ADA2 is more stable than ADA1 after a long incubation (e.g., 24
hours) in plasma. Other conditions, such as temperature, type of
plasma and buffer conditions, can also be selected based on the
desired conditions to be tested.
[0756] ii. Thermal Stability
[0757] Proteins differ in their degrees of thermal stability (or
thermostability). In particular, proteins with biological
activities, such as enzymes, can have different optimal
temperatures. Thermostability, the quality of a protein to resist
irreversible change in its chemical or physical structure at a
relatively high temperature, can be indicative of overall stability
of a protein. Increased temperature usually induces protein
unfolding, and disruption of secondary, tertiary and quaternary
structure of proteins, leading to destabilization of protein.
Thermostability of a protein, such as any ADA2 polypeptide provided
herein, can be determined by measuring the changes in enzymatic
activity and/or other physical properties, before and after
incubation in relatively high or low temperatures.
[0758] The stability of a protein can be determined by measuring
the activity of the protein as a function of time. The melting
temperature (T.sub.m) of the protein can be used as a marker of
solution stability and in vivo stability for proteins. The
unfolding temperature of a particular protein refers to that
temperature at which the protein loses its secondary structure and
typically, its activity and can be determined using methods known
to those of skill in the art and described herein, such as
differential scanning calorimetry (DSM). In another example, other
methods to determine the physical property of the protein, such as
dynamic light scattering (DLS), can be used to characterize the
stability of proteins as a function of temperature. In other
examples, the thermal stability can be measured biochemically. An
exemplary biochemical method for assessing thermal stability is a
thermal challenge assay. In a "thermal challenge assay," a
polypeptide is subjected to a range of elevated temperatures for a
set period of time. For example, in one embodiment, test
polypeptides are subject to a range of increasing temperatures,
e.g., for 10 minutes. The activity of the protein is then assayed
by a relevant biochemical assay (e.g., adenosine deaminase assay).
The thermal challenge assay can be used to determine the
temperature at which 50% adenosine deaminase (ADA) activity is
retained (i.e., the T.sub.C value or T.sub.50). The T.sub.C or
T.sub.50 values are not necessarily equivalent to the biophysically
derived T.sub.m values. Such an assay can be performed to assess
the thermal stability of any of the ADA2 provided herein, including
wildtype, variants, conjugates and other modified forms
thereof.
[0759] iii. Stability in pH or pH Optima
[0760] Proteins also differ in their ability to tolerate changes in
pH, or can have different optimal pH for biological activity.
Variations in pH in the environment can result in changes in the
charge on the basic and acidic groups of amino acid side chains in
a protein causing changes in electrostatic interactions that can
destabilize the native structure. Relatively small changes in pH
can result in fairly dramatic decreases in protein conformational
stability, and the changes in conformational stability can also
lead to aggregation of the proteins. The ionic strength in solution
and the isoelectric point (pI) of the solution also contribute to
the stability of the protein in solution in different pH
conditions.
[0761] For example, the pH environment of the tumor, and the pH
optima of a particular protein, can affect the therapeutic efficacy
of an ADA2 protein. For example, the tumor microenvironment (TME)
has regions, which generally are in hypoxic areas, with relatively
acidic pH, such as pH 6.5-6.9 or lower. On the other hand, in
regions with proliferating tissue, such as near blood vessels, the
TME pH is more neutral. Thus, the pH optima of an ADA2 protein can
be an important factor in determination of dosage and formulation
of proteins used in methods of treating tumors as described
herein.
[0762] The stability of a protein, such as any ADA2 polypeptide
provided herein, in a specific pH environment, can be determined by
measuring the changes in enzymatic activity and/or other physical
properties, before and after incubation in relatively high or low
pH. For example, the enzymatic activity of any of the ADA2 provided
herein can be measured using an ADA activity assay described
herein, at various pH conditions (e.g. at pH ranging from or from
about 6.0 to 8.0, such as from or from about 6.5 to 7.5, inclusive,
for example 6.5.+-.0.2 or 7.4.+-.0.2). In another example, other
methods to determine the physical property of the protein, such as,
dynamic light scattering (DLS), can be used to characterize the
stability of proteins as a function of solution pH.
[0763] iv. Other Conditions
[0764] Other conditions in the environment or the formulation, such
as ionic strength, buffer compositions, presence of other
substances such as other proteins in the tumor microenvironment,
presence of pharmaceutical excipients, or presence of other agents
used for combination therapy, can contribute to the stability of
the polypeptide used in the method of treatment, such as any of the
ADA2 polypeptides provided herein. Stability of the polypeptide in
conditions that are can affect protein stability and function can
be tested using methods described below, but after incubation in
the specific condition to be tested. The assays can be used make
minor adjustments to the formulations provided herein while
retaining the stability of ADA2 and/or other agents used in
combination therapy.
[0765] b. Determination of Physical Properties
[0766] Stability of a polypeptide, such as any ADA2 polypeptide
provided herein, can be determined by measuring changes in physical
or functional properties or activities of the polypeptide, such as
enzymatic activity, structural configuration or conformation,
enzymatic activity, protein unfolding, aggregation, and solubility,
using any methods known in the art. The functional or physical
property that is assessed can be compared in the presence and
absence of the condition (e.g. plasma, temperature, pH or other
condition). It is understood that the assay to compare or assess
the stability of the protein in the presence of a condition
compared to its absence is substantially the same, except for the
presence of or the extent of the condition present.
[0767] Proteins are stabilized by physical forces such as hydrogen
bonds, hydrophobic interactions, electrostatic interactions,
disulfide bonds, and van der Waals force. Disruption of any of
these forces can destabilize the protein, and the disruption of
these forces can be measured using a variety of methods known in
the art. Also, in certain conditions, such as specific pH or
temperature, or high protein concentration during overexpression,
the polypeptide can form protein aggregates. Protein aggregates are
the irreversibly assembled protein molecules to form higher-order
oligomers with native or non-native protein structures that can be
soluble or insoluble in nature. Aggregation often results in
conformational destabilization of the protein.
[0768] Methods to determine changes in physical properties include
spectroscopy, thermodynamic methods, hydrodynamic methods,
chromatography, electrophoresis, analysis of biological activity,
and analysis of protein-protein interaction (see, e.g., Uversky, V.
and E. Permiakov, eds., Methods in Protein Structure and Stability
Analysis, Nova Science Publishers, New York (2007); Chaudhury et
al. (2014) The AAPS Journal 16(1):48-64). An increase in particle
size and/or a decrease in the melting temperature also can indicate
denaturation and subsequent aggregation of the ADA2 polypeptide. In
addition, protein stability can be assessed by visual inspection of
protein integrity by electrophoretic methods, calculating percent
recovery, protein purity and apparent melting temperature.
Exemplary assays to assess protein stability are described
below.
[0769] i. Enzymatic Activity
[0770] Disruption of stability can cause changes in tertiary
structure of the active site of an enzyme, leading to a disruption
of enzymatic activity. Biological activity is often closely
correlated with changes in other physical properties of the
protein, such as circular dichroism spectra. Functional assays,
such as enzymatic activity assays, including any of the adenosine
deaminase (ADA) activity assays described above, can be used as a
measure of protein stability in the presence and absence of an
assessed condition. For example, the stability of adenosine
deaminase (ADA) can be measured before and after exposure to
specific conditions, e.g., conditions described above in Section
F.2.a, to assess the stability of any ADA2 provided herein.
Exposure to a specific condition, such as incubation in plasma, can
be performed at a fixed time point, or assessed over several time
points.
[0771] ii. Chromatographic Analysis of Protein Purity
[0772] Methods to assess the purity of the native protein can be
used as a measure to determine the state of degradation or other
destabilizing events for a protein. Protein purity can be measured
using chromatographic methods, for example, by reversed phase high
performance liquid chromatography (RP-HPLC). Protein purity, as
determined by RP-HPLC, is the percent of the main ADA2 protein peak
present, as compared to all of the protein species present. Thus,
RP-HPLC, and similar methods known to one of skill in the art, can
assess degradation of the enzyme. Protein purity can be assessed
over time. Protein purity can be assessed in the presence of one or
more conditions, such as conditions described above in Section
F.2.a, and in varying amounts thereof. Percent recovery also can be
determined as the relative percentage of the polypeptide in the
presence of various conditions for different lengths of time as
compared to a reference sample. The stability of any ADA2
polypeptides provided herein, including wildtype, variants,
conjugates or other modified forms thereof, also can be determined
by measuring the oxidation of the polypeptide by RP-HPLC. Percent
oxidation is a measure of sum of the peak areas of the major (ox-1)
and minor (ox-2) peaks.
[0773] In another example, other chromatographic methods such as
size exclusion chromatography (SEC) can be used to determine the
folding of a protein or the state of multimerization. SEC can be
performed under native solution conditions, preserving
macromolecular interactions. Size exclusion chromatography measures
the hydrodynamic volume (not molecular weight), allowing folded and
unfolded versions of the same protein to be distinguished.
Quantitative assessment of aggregate levels in protein formulations
by SEC is typically accomplished by UV detection, sometimes at
multiple wavelengths, and often in combination with molecular
weight characterization by multi-angle light scattering detection.
SEC can also be employed to study reversible protein
self-association (Chaudhury et al. (2014) The AAPS Journal
16(1):48-64).
[0774] iii. Differential Scanning Calorimetry
[0775] The thermostability of a polypeptide in solution, such as
any ADA2 provided herein, including wildtype, variants and modified
forms thereof can be determined using differential scanning
calorimetry (DSC). In DSC, a sample cell (containing protein and
buffer) and a reference cell (buffer only) are heated together to
raise the temperature at a constant rate, and the excess heat
required in the sample cell for maintaining equal temperature in
both cells (due to transition from a folded, native state of
protein to unfolded forms as temperature is increased) is recorded.
The midpoint temperature of the thermal transition (or thermal
melting temperature, T.sub.m) is commonly used as an indicator of
thermostability. DSC can also provide detailed information on the
thermodynamic parameters of protein unfolding, including the change
in enthalpy (.DELTA.H), entropy (.DELTA.S), Gibb's free energy
(.DELTA.G), and heat capacity (.DELTA.Cp), if the experimental
conditions allow reversible thermal transitions. DSC can be used to
determine the effect of solution conditions (pH, ionic strength)
and excipients on protein stability during protein formulation
(Chaudhury et al. (2014) The AAPS Journal 16(1):48-64).
[0776] iv. Differential Scanning Fluorimetry
[0777] Differential scanning fluorimetry (DSF), also referred to as
fluorescence thermal shift assay, is a method used to monitor
thermal transitions of proteins, such as unfolding, in the presence
of a fluorescent dye. The polarity-sensitive fluorescent dyes used
for DSF are highly fluorescent in non-polar environment (e.g., in
hydrophobic pockets of (partially) unfolded proteins), whereas the
fluorescence is quenched in aqueous solution and/or in presence of
native protein. DSF can be used to determine conformational
stability of proteins. When the fluorescence intensity of the dye
in presence of protein is plotted as a function of the temperature,
the midpoints of transition temperatures (T.sub.h) of the protein
can be derived from the inflection point of the resulting sigmoidal
graph. The T.sub.h values for various proteins in different
solutions, as obtained from DSF experiments, are well correlated
with thermal melting temperature (T.sub.m) values determined by
differential scanning calorimetry. In addition, information about
the cooperative (two-state) or complex unfolding transitions in
multi-domain proteins can be obtained by DSF (Chaudhury et al.
(2014) The AAPS Journal 16(1):48-64).
[0778] The dye can be a small molecule, a peptide or a nucleic
acid, and can be performed using a conventional real-time PCR
instrument. Commonly used fluorescent dyes include SYRPO Orange,
ANS, ROX.TM. and Nile red. For example, the melting temperature of
any ADA2 provided herein, including wildtype, variants, conjugates
or other modified forms, can be assessed using the ROX.TM. protein
thermal shift dye (Applied Biosystems, Carlsbad, Calif.; Cat. No.
4461146) as the fluorescent dye, and the ViiA7 RT-PCR System
(Applied Biosystems, Carlsbad, Calif.) to measure the shift in
fluorescence as the temperature of the samples were increased.
[0779] v. Intrinsic Fluorescence Spectroscopy
[0780] The stability of a polypeptide, such as any ADA2 provided
herein, including wildtype, variants, conjugates and other modified
forms thereof can be determined by measuring changes in its
intrinsic fluorescence. Intrinsic fluorescence spectroscopy detects
the fluorescence from the internal fluorophores of proteins, such
as the aromatic amino acid residues tryptophan and tyrosine.
Properties of the fluorescence of tryptophan including its
intensity and wavelength of maximum emission are especially
sensitive to their local environment. As a result, the emission can
often be used as probe to study changes in the higher-order
structure of proteins. Protein unfolding is often accompanied by a
decrease in fluorescence intensity and shift of maximum emission of
Trp residues to longer wavelengths (red shift). Fluorometers
equipped with plate reader and temperature control capability can
be employed to assess the conformational stability of protein
therapeutics. (Chaudhury et al. (2014) The AAPS Journal
16(1):48-64).
[0781] vi. Circular Dichroism
[0782] Circular dichroism (CD) spectroscopy measures the
differential absorption of left and right circularly polarized
light, and is a popular tool for characterizing a protein's
secondary structure content (i.e., .alpha.-helix and .beta.-sheet)
as a function of temperature and solution conditions. Far-UV CD
spectra (160-250 nm) are used this purpose, while near-UV CD
spectra (230-320 nm) can provide information about the local
environment of aromatic amino acid side chains and disulfides,
which can be then be used to monitor changes in tertiary structure.
CD is incompatible with certain buffers and additives possessing
high UV absorption (Chaudhury et al. (2014) The AAPS Journal
16(1):48-64).
[0783] vii. Dynamic Light Scattering
[0784] Dynamic light scattering (DLS), also known as photon
correlation spectroscopy or quasi-elastic light scattering, is used
to monitor changes in protein hydrodynamic properties in solution
(e.g., aggregation) as well as making absolute size measurements.
DLS measures the time-dependent fluctuation in the intensity of
scattered light from a solution, and through autocorrelation
analysis can provide information including diffusion coefficients,
hydrodynamic radii, and size distribution of particles with sizes
of a few nanometers up to about 1 .mu.m. A DLS signal is very
sensitive to the presence of the largest sized particle in
solution. DLS is useful for detection of higher-order protein
oligomers and aggregates. DLS has been employed to characterize the
colloidal stability of protein therapeutics, such as monoclonal
antibodies as a function of solution pH and temperature. DLS has
also been applied to assess the aggregation propensity of proteins
in response to the physical stresses present during the production,
delivery and administration of many proteins (Chaudhury et al.
(2014) The AAPS Journal 16(1):48-64). Formation of ADA2 aggregates
after exposure to specific conditions can be determined by
measuring the hydrodynamic radius of particles by dynamic light
scattering under various conditions (e.g., denaturation conditions
or other storage conditions).
[0785] viii. Static Light Scattering
[0786] Static light scattering (SLS) is a technique that measures
the time-averaged intensity of scattered light, providing
information about the size of particles suspended in solution.
Multi-angle light scattering (MALS), a technique that collects and
analyzes static light scattering intensity from multiple angles,
can be used to determine the absolute molecular weight and radius
of gyration of proteins and larger molecular weight oligomers. MALS
detection can be coupled to size exclusion chromatography (SEC) or
flow field fractionation (FFF) to separate and then characterize
protein aggregates. Light scattering can also be measured with the
fluorescence detection by simply scanning through the entire
spectral region containing both the fluorescence and light
scattering. This permits both conformational stability and
aggregation data to be obtained (Chaudhury et al. (2014) The AAPS
Journal 16(1):48-64).
[0787] ix. Turbidity Measurements
[0788] The magnitude of the turbidity (or optical density) of a
solution is proportional to both the size and quantity of protein
aggregates in solution (Optical density=Absorbance+Light
scattering). Turbidity is usually measured in the wavelength range
of 320-400 nm because proteins typically do not have significant
absorbance in this wavelength range, and the magnitude of the light
scattering signal is greater as the wavelength is lowered. During
stability testing, the aggregation propensity of proteins in
various formulations can be evaluated by either a temperature ramp
method (measuring turbidity changes as a function of increasing
temperature) or a kinetic method (measuring turbidity changes as a
function of time at a constant temperature (Chaudhury et al. (2014)
The AAPS Journal 16(1):48-64).
[0789] x. Other Methods to Determine Stability
[0790] Other methods known to one of skill in the art that can be
used to determine the stability of any ADA2 provided herein,
including wildtype, variants and modified forms thereof in the
method of treatment provided herein, include polyacrylamide gel
electrophoresis (PAGE) and visual analysis of protein integrity,
immunoblotting, nuclear magnetic resonance (NMR) spectroscopy,
isothermal titration calorimetry, transverse urea gradient
electrophoresis (TUG-PAGE), neutron scattering, analytical
ultracentrifugation, tritium planigraphy and viscometric analysis.
Visual analysis of protein integrity can include, for example,
observation of lower molecular weight degradation products or
higher molecular weight aggregation products in PAGE gels.
[0791] 4. Assay for Therapeutic Activity
[0792] The therapeutic activity, such as an anticancer activity, of
any of the ADA2 used in the method of treatment provided herein,
can be measured using in vitro and in vivo functional assays.
Provided herein are exemplary assays and systems used to monitor
the therapeutic effect of treatment with any ADA2 provided
herein.
[0793] a. In Vitro Tests
[0794] Anticancer activity of any ADA2 provided herein, including
wildtype and variants, conjugates and other modified forms thereof,
and combination therapy using any ADA2 provided herein and other
agents, can be examined in vitro, for example, by incubating a
cancer cell culture with the derivative, and then evaluating cell
growth inhibition in the culture. Suitable cells for such testing
include, but are not limited to, murine P388 leukemia, B16 melanoma
and Lewis lung cancer cells, as well as MCF7 human breast cancer
cells, OVCAR-3 cancer cells, A549 lung cancer cells, MX-1 human
breast tumor cells, HT29 colon cancer cell line, HepG2 liver cancer
cells, HCT116 colon cancer cells, Caco-2 human colonic cancer
cells, U138MG human glioma cell line, DU 145 human prostate cancer
cells, L1210 lymphatic leukemia cells, L4946 lymphatic leukemia
cells, 6C3HED lymphosarcoma cells, TA3 mammary adenocarcinoma
cells, E2 Ehrlich carcinoma cells, 755 adenocarcinoma cells, 180
sarcoma cells, and B16 melanoma cells.
[0795] Reversal of adenosine-mediated immunosuppression by any ADA2
provided herein, including wildtype and variants, conjugates and
other modified forms thereof, and combination therapy using any
ADA2 provided herein and other agents, can be examined in vitro,
for example, by performing proliferation assays. Such assays
include, but are not limited to T-cell proliferation assays or a
mixture of NK and T (NK/T) cell proliferation assays, in the
presence of adenosine and/or any ADA2 provided herein and/or any
other combination therapy agents. For example, the
immunosuppressive effect of adenosine on various immune cells, such
as lymphocytes, natural killer (NK) cells, polymorphonuclear
granulocytes, and phagocytic cells such as tissue macrophages, can
be assessed by proliferation assays using the immune cells or
mixtures thereof, such as the mixture of NK and T (NK/T) cells
prepared from peripheral blood mononuclear cells (PBMC). The effect
of any ADA2 provided herein and any other combination therapy
agents provided herein, can be assessed by comparing the results of
such proliferation assays in the presence of adenosine, with or
without the addition of any ADA2 provided herein and/or any other
combination therapy agents provided herein, including immune
checkpoint inhibitors. Combination therapy agents are described in
Section H.4 below.
[0796] Proliferation assays can be used to measure the activity of
any ADA2 provided herein, including wildtype and variants,
conjugates and other modified forms thereof, and combination
therapy using any ADA2 provided herein and other agents, in the
presence of adenosine. The assays can measure proliferation of
immune cells whose activity is suppressed by the addition of
adenosine. Cells can be incubated for a sufficient time for cells
to exhibit proliferation (such as, for example, 12 hours, or 1, 2,
3, 4, 5, 6, 7 days, 2, 3, 4, 5 weeks or longer). Cell proliferation
can be measured by any method known in the art, including
.sup.3H-thymidine incorporation assay, 5-bromo-2-deoxyuridine
(BrdU), ELISA, tetrazolium microplate assay and acid phosphatase
assay (e.g., Maghni et al. (1999) J. Immunol. Method.
223(2):185-194). Cell proliferation also can be measured using kits
available from Invitrogen (Cyquant NF cell proliferation assay
kit), Cambrex (ViaLight HS (high sensitivity) BioAssay), Promega
(CellTiter-Glo Luminescent Cell Viability Assay), Guava
Technologies (CellGrowth assay), Stratagene (Quantos cell
proliferation assay) (e.g., Assays for Cell Proliferation Studies,
Genetic Eng. Biotechnol. News. 26(6)). In some examples, the cell
proliferation can be normalized to proliferation of cells in the
presence of adenosine. In some examples, the cell proliferation can
be normalized to proliferation of cells in the absence of
adenosine. In exemplary proliferation assays, cells can be added to
a well of a 96-well plate in normal growth medium that includes
adenosine and any ADA2 provided herein or any other combination
therapy agents to be assayed.
[0797] b. In Vivo Animal Models
[0798] Animal models can be used to assess the effects of
therapeutic activity, such as tumor growth inhibition activity,
provided herein, using any ADA2 provided herein. For example,
animal models can be used to assess tumor size, volume or growth.
In addition, animal models can be used to assess the
pharmacokinetics or tolerability of the compositions or
combinations.
[0799] Animal models can include, but are not limited to, mice,
rats, rabbits, dogs, guinea pigs and non-human primate models, such
as cynomolgus monkeys or rhesus macaques. Animal models including
genetic models as well as xenograft models. For example, xenograft
models include those in which, prior to testing the agents, tumors
can be established in suitable test animals, such as
immunodeficient or immunocompetent animals. In some examples,
immunodeficient mice, such as nude mice or SCID mice, are
transplanted with a tumor cell line, such as from an
adenosine-associated cancer, to establish an animal model of that
cancer. In other cases, syngeneic models employing immunocompetent
animals are used.
[0800] Exemplary cell lines, including cancers associated with
adenosine signaling, include, but are not limited to, CT26 murine
colon cancer cells, MCF7 human breast cancer cells, HepG2 liver
cancer cells, Caco-2 human colonic cancer cells, U138MG human
glioma cell line, DU 145 human prostate cancer cells, L1210
lymphatic leukemia cells, L4946 lymphatic leukemia cells, 6C3HED
lymphosarcoma cells, TA3 mammary adenocarcinoma cells, E2 Ehrlich
carcinoma cells, 755 adenocarcinoma cells, 180 sarcoma cells, and
B16 melanoma cells. Other cancer cells that can be used in animal
xenograft models include PC3 prostate carcinoma cells, BxPC-3
pancreatic adenocarcinoma cells, MDA-MB-231 breast carcinoma cells,
BT474 breast tumor cells, Tramp C2 prostate tumor cells, Mat-LyLu
prostate cancer cells, MH194 mouse pancreatic carcinoma cells and
KLN205 murine lung cancer cells.
[0801] Exemplary of an animal tumor model that can be used to
assess the effect of cancer treatment using ADA2 provided herein is
the CT26 syngeneic tumor model. This model is created by
subcutaneous injection of CT26 murine primary colon carcinoma (ATCC
CRL-2638) cells into syngeneic BALB/c mice. The mice are staged
until the tumor is established, then the agent used for treatment,
such as any ADA2 provided herein or combination therapy including
ADA2 treatment, are administered. Another example of an animal
tumor model of pancreatic cancer involves the generation of tumors
in animals using BxPC-3 pancreatic adenocarcinoma cells (see e.g.
Von Hoff et al. (2011) J. Clin. Oncol., 29:4548-54). Other examples
of animal tumor models include the murine MH194+PSC4 syngeneic
tumor model and the murine lung cancer KLN205 syngeneic tumor
model.
[0802] Other animal models, such as mouse models developed to study
cancer immunotherapies or combination therapies, can be used to
assess the therapeutic effect of treatment using ADA2. For example,
mouse models developed to study both the efficacy of cancer
immunotherapy and the immune-related adverse events (irAEs), can be
used. Some cancer immunotherapies that target immunomodulatory
receptors, such as anti-CTLA4 and anti-PD-1 combination therapy,
can also elicit irAEs, such as rash, diarrhea, colitis and liver
damage. Therefore, using mouse models that can mimic the kinetics
of response that are observed in the clinic and models that can
reflect possible irAEs can be used to assess both the efficacy and
possible adverse events associated with treatment. Such models
include those that are carcinogen-induced, such as
methylcholanthrene (MCA)-induced fibrosarcomas and
7,12-dimethylbenz[.alpha.]anthracene
(DMBA)/12-O-tetradecanoylphorbol-13-acetate (TPA)-induced skin
papillomas or genetically engineered mouse tumour models, which
have enforced expression of oncogenes and/or the loss of function
of tumour suppressors, often in a tissue-specific and/or temporally
controlled manner. Examples include the Her2/neu or PyMT transgenic
mice to mimic breast cancer, the MT/ret model of spontaneous
metastatic melanoma and BrafCATyr-creERT2Ptenfl/fl mice in which
4-hydroxytamoxifen (4-HT) induces de novo melanoma as well as the
use of adenoviral vectors encoding Cre recombinase to selectively
introduce mutations in the oncogene Kras and the tumour-suppressor
gene Tp53 in the pulmonary epithelia to induce autochthonous lung
tumours. Carcinogen-induced mouse models of cancer better mimic
cancers that are immunogenic. Alternatively, in tumor explant
models, tumors can be transplanted orthotopically, i.e. at the
normal place of occurrance, rather than subcutaneously, to more
accurately reflect the tumor microenvironment. Another exemplary
mouse model to assess the efficacy and irAE of combination cancer
immunotherapy is the Foxp3-DTR mice, which can be conditionally
depleted of their Tregs to mimic the maximum suppression on all
immune cells. This model allows the assessment of the efficacy of
modulating co-inhibitory/co-stimulatory receptors or with other
therapies to attenuate anti-tumour immunity/irAEs (Liu et al.
(2014) Clinical & Translational Immunology 3:e22)
[0803] Genetic models also can be used in which animals are
rendered to be deficient in one or more genes that results in tumor
generation or formation. Such genetically engineered mouse models
(GEMM) can recapitulate the molecular and clinical features of
disease. For example, an exemplary pancreatic cancer genetic model
involves the pancreatic specific expression of endogenous mutants
Kras and Trp53 alleles, which results in mutant mice that exhibit a
deficient phenotype (termed KPC mice; LSL-Kras.sup.G12D,
LSL-Trp53.sup.R172H, Pdx-1-Cre). The KPC mice develop primary
pancreatic tumors that exhibit features similar to human disease,
including resistance to the nucleoside analog gemcitabine (see e.g.
Frese et al. (2012) Cancer Discovery, 2:260-269).
[0804] i. Tumor Metabolic Activity
[0805] A reduction in tumor metabolic activity can be tested for
ADA2 treatment provided herein. Tumor metabolic activity can be
assessed using standard procedures known in the art. For example,
[.sup.18F]-fluorodeoxyglucose positron emission tomography
(FDG-PET) can be used. PET is a non-invasive diagnostic that
provides images and quantitative parameters of perfusion, cell
viability, proliferation and/or metabolic activity of tissues. The
images result from the use of different biological substances
(e.g., sugars, amino acids, metabolic precursors, hormones)
labelled with positron emitting radioisotopes. For example, FDG is
an analogue of glucose and is taken up by living cells via the
first stages of normal glucose pathway. In cancers, increased
glycolytic activity exists resulting in trapping of FDG in the
cancer cell. A decrease in FDG trapping correlates with a decreased
tumor metabolic activity and anticancer activity. Guidelines for
PET imaging are known to one of skill in the art and should be
followed by any treating physician or technician.
[0806] ii. Tumor Size and Volume
[0807] For example, the tumor and/or metastasis size and location
can be monitored. Tumor and or metastasis size can be monitored by
any of a variety of methods known in the art, including external
assessment methods or tomographic or magnetic imaging methods, such
as the detection methods described herein. Monitoring size over
several time points can provide information regarding the efficacy
of the therapeutic methods provided herein. In addition, monitoring
the increase or decrease in size of a tumor or metastasis, and can
also provide information regarding the presence (i.e., detection
and/or diagnosis) of additional tumors and/or metastases in the
subject. Monitoring tumor size over several time points can provide
information regarding the development of a neoplastic disease in a
subject, including the efficacy of treatments of a neoplastic
disease in a subject, such as the treatment provided herein.
[0808] In particular examples, reductions in tumor size and/or
volume indicate that therapy is working. Tumor size and volume can
be monitored based on techniques known to one of skill in the art.
For example, tumor size and volume can be monitored by radiography,
ultrasound imaging, necropsy, by use of calipers, by microCT or by
.sup.18F-FDG-PET. Tumor size also can be assessed visually. In
particular examples, tumor size (diameter) is measured directly
using calipers.
[0809] In other examples, tumor volume can be measured using an
average of measurements of tumor diameter (D) obtained by caliper
or ultrasound assessments. For example, tumor volume can be
determined using VisualSonics Vevo 770 high-resolution ultrasound
or other similar ultrasound. The volume can be determined from the
formula V=D.sup.3.times..pi./6 (for diameter measured using
calipers) or V=D.sup.2.times.d.times..pi./6 (for diameter measured
using ultrasound where d is the depth or thickness). For example,
caliper measurements can be made of the tumor length (l) and width
(w) and tumor volume calculated as
length.times.width.sup.2.times.0.52. In another example, microCT
scans can be used to measure tumor volume (see e.g., Huang et al.
(2009) PNAS, 106:3426-3430). As an example, mice can be injected
with Optiray Pharmacy ioversol injection 74% contrast medium (e.g.,
741 mg of ioversol/mL), mice anesthetized, and CT scanning done
using a MicroCat 1A scanner or other similar scanner (e.g., IMTek)
(40 kV, 600 .mu.A, 196 rotation steps, total angle or
rotation=196). The images can be reconstructed using software
(e.g., RVA3 software program; ImTek). Tumor volumes can be
determined by using available software (e.g., Amira 3.1 software;
Mercury Computer Systems). Tumor volume or size also can be
determined based on size or weight of a tumor.
[0810] The percent of tumor growth inhibition can be calculated
based on the volume using the equation: %
TGI=[1-(T.sub.n-T.sub.0)/(C.sub.n-C.sub.0)].times.100%, where
"T.sub.n" is the average tumor volume for the treatment group at
day "n" after the final dose of ADA2; "T.sub.0" is the average
tumor volume in that treatment group at day 0, before treatment;
"C.sub.n" is the average tumor volume for the corresponding control
group at day "n"; and "C.sub.0" is the average tumor volume in the
control group at day 0, before treatment. Statistical analysis of
tumor volumes can be determined.
[0811] c. Clinical Monitoring
[0812] The methods provided herein can further include one or more
steps of monitoring treatment effect, such as tumor treatment using
any of the ADA2 provided herein. Subjects can be monitored by
monitoring the tumor, the general health of the subject and/or
course of disease in the subject. Any of a variety of monitoring
steps can be included in the methods provided herein, including,
but not limited to, monitoring tumor size, monitoring anti-(tumor
antigen) antibody titer, monitoring the presence and/or size of
metastases, monitoring the subject's lymph nodes, and monitoring
the subject's weight or other health indicators including blood or
urine markers. The purpose of the monitoring can be for assessing
the health state of the subject or the progress of therapeutic
treatment of the subject, or can be for determining whether or not
further administration of ADA2 is warranted, or for determining
when or whether or not to administer a further agent or treatment,
or can be for determining whether or not to administer or continue
combination therapy.
[0813] Parameters indicative of the health of a subject also can be
monitored. Monitoring the health of a subject can be used to
determine the efficacy of the therapeutic method, as is known in
the art. Any of a variety of health diagnostic methods for
monitoring disease such as neoplastic disease or other disease can
be monitored, as is known in the art. For example, the weight,
blood pressure, pulse, breathing, color, temperature or other
observable state of a subject can indicate the health of a subject.
In addition, the presence or absence or level of one or more
components in a sample from a subject can indicate the health of a
subject. Typical samples can include blood and urine samples, where
the presence or absence or level of one or more components can be
determined by performing, for example, a blood panel or a urine
panel diagnostic test. Exemplary components indicative of a
subject's health include, but are not limited to, white blood cell
count, hematocrit, or reactive protein concentration.
[0814] 5. Pharmacodynamics/Pharmacokinetics and Tolerability
[0815] The effect of administration of any ADA2 provided herein,
including wildtype, variants and modified forms thereof, alone or
in combination with another therapeutic agent, on the
pharmacokinetic and pharmacodynamic properties of any administered
agent also can be assessed in vivo using animal models and/or human
subjects, such as in the setting of a clinical trial.
Pharmacokinetic or pharmacodynamic studies can be performed using
animal models or can be performed during studies with patients
administered with any ADA2 provided herein, including wildtype,
variants and modified forms thereof.
[0816] Animal models include, but are not limited to, mice, rats,
rabbits, dogs, guinea pigs and non-human primate models, such as
cynomolgus monkeys or rhesus macaques. In some instances,
pharmacokinetic or pharmacodynamic studies are performed using
healthy animals. In other examples, the studies are performed using
animal models of a disease for which therapy with ADA2 is
considered, such as animal models of any adenosine-associated
disease or disorder, for example a tumor model.
[0817] The pharmacokinetic properties of any ADA2 provided herein,
including wildtype, variants and modified forms thereof, can be
assessed by measuring such parameters as the maximum (peak)
concentration (C.sub.max), the peak time (i.e., when maximum
concentration occurs; T.sub.max), the minimum concentration (i.e.,
the minimum concentration between doses; C.sub.max), the
elimination half-life (T.sub.1/2) and area under the curve (i.e.,
the area under the curve generated by plotting time versus
concentration; AUC), following administration. The absolute
bioavailability of the ADA2 can be determined by comparing the area
under the curve of ADA2 following subcutaneous delivery (AUCsc)
with the AUC of ADA2 following intravenous delivery (AUC.sub.iv).
Absolute bioavailability (F), can be calculated using the formula:
F=([AUC].sub.sc.times.dose.sub.sc)/([AUC].sub.iv.times.dose.sub.iv).
A range of doses and different dosing frequency of dosing can be
administered in the pharmacokinetic studies to assess the effect of
increasing or decreasing concentrations of the enzyme, such as any
ADA2 provided herein, including wildtype, variants and modified
forms thereof, in the dose.
[0818] Studies to assess the safety and tolerability of a treatment
also are known in the art and can be used herein. Following
administration of any of the ADA2 provided herein, or any
combination therapy provided herein, the development of any adverse
reactions can be monitored. Adverse reactions can include, but are
not limited to, injection site reactions, such as edema or
swelling, headache, fever, fatigue, chills, flushing, dizziness,
urticaria, wheezing or chest tightness, nausea, vomiting, rigors,
back pain, chest pain, muscle cramps, seizures or convulsions,
changes in blood pressure and anaphylactic or severe
hypersensitivity responses. Typically, a range of doses and
different dosing frequencies can be administered in the safety and
tolerability studies to assess the effect of increasing or
decreasing concentrations of any ADA2 or agents used in combination
therapy in the dose.
G PHARMACEUTICAL COMPOSITIONS AND FORMULATIONS
[0819] Provided herein are pharmaceutical compositions containing
an adenosine deaminase 2 (ADA2), such as a wildtype ADA2, variants,
conjugates or other modified forms thereof, and a pharmaceutically
acceptable excipient or additive. The pharmaceutical compositions
can be use in treatment of diseases or conditions associated with
elevated adenosine levels (e.g., hyperproliferative disease or
condition, such as a tumor or cancer). Any of the ADA2 can be
administered in a single agent therapy, or can be administered in a
combination therapy with a further agent or treatment as described
herein. The compositions can be formulated for single dosage
administration or for multiple dosage administration. The agents
can be formulated for direct administration. The compositions can
be provided as a liquid or lyophilized formulation.
[0820] Pharmaceutically acceptable compositions are prepared in
view of approvals for a regulatory agency or other agency prepared
in accordance with generally recognized pharmacopeia for use in
animals and in humans. The compositions can be prepared as
solutions, suspensions, powders, or sustained release formulations.
Typically, the compounds are formulated into pharmaceutical
compositions using techniques and procedures well known in the art
(see e.g., Ansel Introduction to Pharmaceutical Dosage Forms,
Fourth Edition, 1985, 126). The formulation should suit the mode of
administration.
[0821] Compositions can be formulated for administration by any
route known to those of skill in the art including intramuscular,
intravenous, intradermal, intralesional, intraperitoneal injection,
subcutaneous, intratumoral, epidural, nasal, oral, vaginal, rectal,
topical, local, otic, inhalational, buccal (e.g., sublingual), and
transdermal administration or any route. Other modes of
administration also are contemplated. Administration can be local,
topical or systemic depending upon the locus of treatment. Local
administration to an area in need of treatment can be achieved by,
for example, but not limited to, local infusion during surgery,
topical application, e.g., in conjunction with a wound dressing
after surgery, by injection, by means of a catheter, by means of a
suppository, or by means of an implant. Compositions also can be
administered with other biologically active agents, either
sequentially, intermittently or in the same composition.
Administration also can include controlled release systems
including controlled release formulations and device controlled
release, such as by means of a pump.
[0822] The most suitable route in any given case depends on a
variety of factors, such as the nature of the disease, the progress
of the disease, the severity of the disease and the particular
composition which is used. Pharmaceutical compositions can be
formulated in dosage forms appropriate for each route of
administration. In particular, the compositions can be formulated
into any suitable pharmaceutical preparations for systemic,
intraperitoneal, oral or direct administration. For example, the
compositions can be formulated for administration subcutaneously,
intramuscularly, intratumorally, intravenously or intradermally. In
some embodiments, the compositions contain nucleic acids that
encode the variant ADA2 polypeptide provided herein, such as
oncolytic viral vectors or gene therapy vectors, or cells, such as
modified immune cells for adoptive immunotherapy, and particular
compositions can be formulated in dosage forms appropriate for the
particular composition.
[0823] Administration methods can be employed to decrease the
exposure of the active agent to degradative processes, such as
proteolytic degradation and immunological intervention via
antigenic and immunogenic responses. Examples of such methods
include local administration at the site of treatment or continuous
infusion (e.g., of ADA2 polypeptide or variant thereof).
[0824] The compounds can be formulated into suitable pharmaceutical
preparations such as solutions, suspensions, tablets, dispersible
tablets, pills, capsules, powders, sustained release formulations
or elixirs, for oral administrations well as transdermal patch
preparation and dry powder inhalers. Typically, the compounds are
formulated into pharmaceutical compositions using techniques and
procedures well known in the art (see e.g., Ansel Introduction to
Pharmaceutical Dosage Forms, Fourth Edition, 1985, 126). Generally,
the mode of formulation is a function of the route of
administration. Generally, the compositions are formulated in
lyophilized or liquid form. Where the compositions are provided in
lyophilized form they can be reconstituted just prior to use by an
appropriate buffer, for example, a sterile saline solution.
[0825] 1. Formulations--Liquids, Injectables, Emulsions
[0826] The formulation generally is made to suit the route of
administration. Parenteral administration, generally characterized
by injection or infusion, either subcutaneously, intramuscularly,
intravenously or intradermally is contemplated herein. Preparations
for parenteral administration include sterile solutions ready for
injection, sterile dry soluble products, such as lyophilized
powders, ready to be combined with a solvent just prior to use,
including hypodermic tablets, sterile suspensions ready for
injection, sterile dry insoluble products ready to be combined with
a vehicle just prior to use and sterile emulsions. Injectables can
be prepared in conventional forms, either as liquid solutions or
suspensions, solid forms suitable for solution or suspension in
liquid prior to injection, or as emulsions. Lyophilized
formulations are ideal for storage of large unit doses for later
use or storage.
[0827] In one example, pharmaceutical preparation can be in liquid
form, for example, solutions, syrups or suspensions. If provided in
liquid form, the pharmaceutical preparations can be provided as a
concentrated preparation to be diluted to a therapeutically
effective concentration before use. The pharmaceutical preparations
also can be provided in a dosage form that does not require
dilution for use. Such liquid preparations can be prepared by
conventional means with pharmaceutically acceptable additives such
as suspending agents (e.g., sorbitol syrup, cellulose derivatives
or hydrogenated edible fats); emulsifying agents (e.g., lecithin or
acacia); non-aqueous vehicles (e.g., almond oil, oily esters, or
fractionated vegetable oils); and preservatives (e.g., methyl or
propyl-p-hydroxybenzoates or sorbic acid). In another example,
pharmaceutical preparations can be presented in lyophilized form
for reconstitution with water or other suitable vehicle before
use.
[0828] Injectables are designed for local and systemic
administration. Injectables can be prepared in conventional forms,
either as liquid solutions or suspensions, solid forms suitable for
solution or suspension in liquid prior to injection, or as
emulsions. Suitable excipients are, for example, water, saline,
dextrose, glycerol or ethanol Preparations for parenteral
administration include sterile solutions ready for injection,
sterile dry soluble products, such as lyophilized powders, ready to
be combined with a solvent just prior to use, including hypodermic
tablets, sterile suspensions ready for injection, sterile dry
insoluble products ready to be combined with a vehicle just prior
to use and sterile emulsions. The solutions can be either aqueous
or nonaqueous. If administered intravenously, suitable carriers
include physiological saline or phosphate buffered saline (PBS),
and solutions containing thickening and solubilizing agents, such
as glucose, polyethylene glycol, and polypropylene glycol and
mixtures thereof.
[0829] Pharmaceutical compositions can include carriers or other
excipients. For example, pharmaceutical compositions provided
herein can contain any one or more of a diluents(s), adjuvant(s),
antiadherent(s), binder(s), coating(s), filler(s), flavor(s),
color(s), lubricant(s), glidant(s), preservative(s), detergent(s),
sorbent(s) or sweetener(s) and a combination thereof or vehicle
with which a modified PH20 polypeptide is administered. For
example, pharmaceutically acceptable carriers or excipients used in
parenteral preparations include aqueous vehicles, nonaqueous
vehicles, antimicrobial agents, isotonic agents, buffers,
antioxidants, local anesthetics, suspending and dispersing agents,
emulsifying agents, sequestering or chelating agents and other
pharmaceutically acceptable substances. Formulations, including
liquid preparations, can be prepared by conventional means with
pharmaceutically acceptable additives or excipients.
[0830] Pharmaceutical compositions can include carriers such as a
diluent, adjuvant, excipient, or vehicle with which the composition
are administered. Examples of suitable pharmaceutical carriers are
described in "Remington's Pharmaceutical Sciences" by E. W. Martin.
Such compositions will contain a therapeutically effective amount
of the compound or agent, generally in purified form or partially
purified form, together with a suitable amount of carrier so as to
provide the form for proper administration to the patient. Such
pharmaceutical carriers can be sterile liquids, such as water and
oils, including those of petroleum, animal, vegetable or synthetic
origin, such as peanut oil, soybean oil, mineral oil, and sesame
oil. Water is a typical carrier. Saline solutions and aqueous
dextrose and glycerol solutions also can be employed as liquid
carriers, particularly for injectable solutions. Compositions can
contain along with an active ingredient: a diluent such as lactose,
sucrose, dicalcium phosphate, or carboxymethylcellulose; a
lubricant, such as magnesium stearate, calcium stearate and talc;
and a binder such as starch, natural gums, such as gum acacia,
gelatin, glucose, molasses, polyvinylpyrrolidine, celluloses and
derivatives thereof, povidone, crospovidones and other such binders
known to those of skill in the art. Suitable pharmaceutical
excipients include starch, glucose, lactose, sucrose, gelatin,
malt, rice, flour, chalk, silica gel, sodium stearate, glycerol
monostearate, talc, sodium chloride, dried skim milk, glycerol,
propylene, glycol, water, and ethanol. For example, suitable
excipients are, for example, water, saline, dextrose, glycerol or
ethanol. A composition, if desired, also can contain other minor
amounts of non-toxic auxiliary substances such as wetting or
emulsifying agents, pH buffering agents, stabilizers, solubility
enhancers, and other such agents, such as for example, sodium
acetate, sorbitan monolaurate, triethanolamine oleate and
cyclodextrins.
[0831] Pharmaceutically acceptable carriers used in parenteral
preparations include aqueous vehicles, nonaqueous vehicles,
antimicrobial agents, isotonic agents, buffers, antioxidants, local
anesthetics, suspending and dispersing agents, emulsifying agents,
sequestering or chelating agents and other pharmaceutically
acceptable substances. Examples of aqueous vehicles include Sodium
Chloride Injection, Ringers Injection, Isotonic Dextrose Injection,
Sterile Water Injection, Dextrose and Lactated Ringers Injection.
Nonaqueous parenteral vehicles include fixed oils of vegetable
origin, cottonseed oil, corn oil, sesame oil and peanut oil.
Antimicrobial agents in bacteriostatic or fungistatic
concentrations can be added to parenteral preparations packaged in
multiple-dose containers, which include phenols or cresols,
mercurials, benzyl alcohol, chlorobutanol, methyl and propyl
p-hydroxybenzoic acid esters, thimerosal, benzalkonium chloride and
benzethonium chloride. Isotonic agents include sodium chloride and
dextrose. Buffers include phosphate and citrate. Antioxidants
include sodium bisulfate. Local anesthetics include procaine
hydrochloride. Suspending and dispersing agents include sodium
carboxymethylcellulose, hydroxypropyl methylcellulose and
polyvinylpyrrolidone. Emulsifying agents include Polysorbate 80
(TWEEN 80). A sequestering or chelating agent of metal ions include
EDTA. Pharmaceutical carriers also include ethyl alcohol,
polyethylene glycol and propylene glycol for water miscible
vehicles and sodium hydroxide, hydrochloric acid, citric acid or
lactic acid for pH adjustment.
[0832] In particular, antimicrobial agents (e.g., preservatives) in
bacteriostatic or fungistatic concentrations (e.g., an
anti-microbial effective amount) can be added to parenteral
preparations packaged in multiple-dose containers, which include
phenols or cresols, mercurials, benzyl alcohol, chlorobutanol,
methyl and propyl p-hydroxybenzoic acid esters, thimerosal,
benzalkonium chloride and benzethonium chloride.
[0833] The pharmaceutical compositions also can contain other minor
amounts of non-toxic auxiliary substances such as wetting or
emulsifying agents, pH buffering agents, stabilizers, solubility
enhancers, and other such agents, such as for example, sodium
acetate, sorbitan monolaurate, triethanolamine oleate and
cyclodextrins. Implantation of a slow-release or sustained-release
system, such that a constant level of dosage is maintained (see,
e.g., U.S. Pat. No. 3,710,795) also is contemplated herein. The
percentage of active compound contained in such parenteral
compositions is highly dependent on the specific nature thereof, as
well as the activity of the compound and the needs of the
subject.
[0834] Lyophilized Powders
[0835] Of interest herein are lyophilized powders, which can be
reconstituted for administration as solutions, emulsions and other
mixtures. They can also be reconstituted and formulated as solids
or gels. The lyophilized powders can be prepared from any of the
solutions described above. The pharmaceutical preparations can be
presented in lyophilized form for reconstitution with water or
other suitable vehicle before use.
[0836] The sterile, lyophilized powder is prepared by dissolving a
compound in a buffer solution. The buffer solution can contain an
excipient which improves the stability or other pharmacological
component of the powder or reconstituted solution, prepared from
the powder. Subsequent sterile filtration of the solution followed
by lyophilization under standard conditions known to those of skill
in the art provides the desired formulation. Briefly, the
lyophilized powder is prepared by dissolving an excipient, such as
dextrose, sorbitol, fructose, corn syrup, xylitol, glycerin,
glucose, sucrose or other suitable agent, in a suitable buffer,
such as citrate, sodium or potassium phosphate or other such buffer
known to those of skill in the art. Then, a selected enzyme, agent
or compound is added to the resulting mixture, and stirred until it
dissolves. The resulting mixture is sterile filtered or treated to
remove particulates and to insure sterility, and apportioned into
vials for lyophilization. Each vial will contain a single dosage (1
mg-1 g, generally 1-100 mg, such as 1-5 mg) or other dosages as
described herein, or multiple dosages of the compound. The
lyophilized powder can be stored under appropriate conditions, such
as at about 4.degree. C. to room temperature.
[0837] Reconstitution of this lyophilized powder with a buffer
solution provides a formulation for use in parenteral
administration. The precise amount depends upon the indication
treated and selected compound. Such amount can be empirically
determined.
[0838] 2. Compositions for Other Routes of Administration
[0839] Depending upon the condition treated other routes of
administration, such as topical application, transdermal patches,
oral and rectal administration are also contemplated herein.
[0840] For example, pharmaceutical dosage forms for rectal
administration are rectal suppositories, capsules and tablets for
systemic effect. Rectal suppositories include solid bodies for
insertion into the rectum which melt or soften at body temperature
releasing one or more pharmacologically or therapeutically active
ingredients. Pharmaceutically acceptable substances utilized in
rectal suppositories are bases or vehicles and agents to raise the
melting point. Examples of bases include cocoa butter (theobroma
oil), glycerin-gelatin, carbowax (polyoxyethylene glycol) and
appropriate mixtures of mono-, di- and triglycerides of fatty
acids. Combinations of the various bases can be used. Agents to
raise the melting point of suppositories include spermaceti and
wax. Rectal suppositories can be prepared either by the compressed
method or by molding. The typical weight of a rectal suppository is
about 2 to 3 gm. Tablets and capsules for rectal administration are
manufactured using the same pharmaceutically acceptable substance
and by the same methods as for formulations for oral
administration. Formulations suitable for rectal administration can
be provided as unit dose suppositories. These can be prepared by
admixing the active compound with one or more conventional solid
carriers, for example, cocoa butter, and then shaping the resulting
mixture.
[0841] For oral administration, pharmaceutical compositions can
take the form of, for example, tablets or capsules prepared by
conventional means with pharmaceutically acceptable excipients such
as binding agents (e.g., pregelatinized maize starch, polyvinyl
pyrrolidone or hydroxypropyl methylcellulose); fillers (e.g.,
lactose, microcrystalline cellulose or calcium hydrogen phosphate);
lubricants (e.g., magnesium stearate, talc or silica);
disintegrants (e.g., potato starch or sodium starch glycolate); or
wetting agents (e.g., sodium lauryl sulphate). The tablets can be
coated by methods well-known in the art.
[0842] Formulations suitable for buccal (sublingual) administration
include, for example, lozenges containing the active compound in a
flavored base, usually sucrose and acacia or tragacanth; and
pastilles containing the compound in an inert base such as gelatin
and glycerin or sucrose and acacia.
[0843] Topical mixtures are prepared as described for the local and
systemic administration. The resulting mixtures can be solutions,
suspensions, emulsion or the like and are formulated as creams,
gels, ointments, emulsions, solutions, elixirs, lotions,
suspensions, tinctures, pastes, foams, aerosols, irrigations,
sprays, suppositories, bandages, dermal patches or any other
formulations suitable for topical administration.
[0844] The compounds or pharmaceutically acceptable derivatives
thereof can be formulated as aerosols for topical application, such
as by inhalation (see, e.g., U.S. Pat. Nos. 4,044,126, 4,414,209,
and 4,364,923, which describe aerosols for delivery of a steroid
useful for treatment of inflammatory diseases, particularly
asthma). These formulations, for administration to the respiratory
tract, can be in the form of an aerosol or solution for a
nebulizer, or as a microfine powder for insufflation, alone or in
combination with an inert carrier such as lactose. In such a case,
the particles of the formulation will typically have diameters of
less than 50 microns, or less than 10 microns.
[0845] The compounds can be formulated for local or topical
application, such as for topical application to the skin and mucous
membranes, such as in the eye, in the form of gels, creams, and
lotions and for application to the eye or for intracisternal or
intraspinal application. Topical administration is contemplated for
transdermal delivery and also for administration to the eyes or
mucosa, or for inhalation therapies. Nasal solutions of the active
compound alone or in combination with other pharmaceutically
acceptable excipients also can be administered.
[0846] Formulations suitable for transdermal administration are
provided. They can be provided in any suitable format, such as
discrete patches adapted to remain in intimate contact with the
epidermis of the recipient for a prolonged period of time. Such
patches contain the active compound in an optionally buffered
aqueous solution of, for example, 0.1 to 0.2 M concentration with
respect to the active compound. Formulations suitable for
transdermal administration also can be delivered by iontophoresis
(see, e.g., Tyle, P, Pharmaceutical Research 3(6):318-326 (1986))
and typically take the form of an optionally buffered aqueous
solution of the active compound.
[0847] Pharmaceutical compositions also can be administered by
controlled release formulations and/or delivery devices (see e.g.,
in U.S. Pat. Nos. 3,536,809; 3,598,123; 3,630,200; 3,845,770;
3,916,899; 4,008,719; 4,769,027; 5,059,595; 5,073,543; 5,120,548;
5,591,767; 5,639,476; 5,674,533 and 5,733,566).
[0848] 3. Dosages and Administration
[0849] The ADA2 in the composition, such as any described herein
including wildtype, variant, conjugate or other modified form, can
be formulated as pharmaceutical compositions for single dosage or
multiple dosage administration. The protein can be included in an
amount sufficient to exert a therapeutically useful effect in the
absence of undesirable side effects on the patient treated. For
example, the concentration of the pharmaceutically active compound
is adjusted so that an injection provides an effective amount to
produce the desired pharmacological effect. The therapeutically
effective concentration can be determined empirically by testing
the protein in known in vitro and in vivo systems such as by using
the assays described herein or known in the art. For example,
standard clinical techniques can be employed. In addition, in vitro
assays and animal models can be employed to help identify optimal
dosage ranges. The precise dose, which can be determined
empirically, can depend on the age, weight and condition of the
patient or animal, the particular ADA2 molecule being administered,
the route of administration, the type of disease to be treated and
the seriousness of the disease.
[0850] Hence, it is understood that the precise dosage and duration
of treatment is a function of the disease being treated and can be
determined empirically using known testing protocols or by
extrapolation from in vivo or in vitro test data. It is to be noted
that concentrations and dosage values also can vary with the
severity of the condition to be alleviated. It is to be further
understood that for any particular subject, specific dosage
regimens should be adjusted over time according to the individual
need and the professional judgment of the person administering or
supervising the administration of the compositions, and that the
concentration ranges set forth herein are exemplary only and are
not intended to limit the scope or use of compositions and
combinations containing them. The compositions can be administered
hourly, daily, weekly, monthly, yearly or once. Generally, dosage
regimens are chosen to limit toxicity. It should be noted that the
attending physician would know how to and when to terminate,
interrupt or adjust therapy to lower dosage due to toxicity, or
bone marrow, liver or kidney or other tissue dysfunctions.
Conversely, the attending physician would also know how to and when
to adjust treatment to higher levels if the clinical response is
not adequate (precluding toxic side effects).
[0851] Compositions of an ADA2 protein, such as a wildtype,
variant, conjugate or other modified forms thereof, are included in
the composition in an amount sufficient to exert a therapeutically
useful effect. For example, the amount is one that achieves a
therapeutic effect in the treatment of a hyperproliferative disease
or condition, such as cancer. Generally, compositions contain 0.5
.mu.g to 100 grams of an ADA2 protein, for example, 20 .mu.g to 10
gram, 20 .mu.g to 50 grams, 20 .mu.g to 1 grams, 20 .mu.g to 500
mg, 20 .mu.g to 200 mg, 20 .mu.g to 5 mg, 20 .mu.g to 0.5 mg, 0.5
mg to 100 grams, 0.5 mg to 10 grams, 0.5 mg to 5 grams, 0.5 mg to 1
gram, 0.5 mg to 500 mg, 0.5 mg to 200 mg, 0.5 mg to 5 mg, 5 mg to
100 gram, 5 mg to 10 grams, 5 mg to 5 grams, 5 mg to 1 gram, 5 mg
to 500 mg, 5 mg to 200 mg, 100 mg to 100 gram, 100 mg to 10 grams,
100 mg to 5 grams, 100 mg to 1 gram, 100 mg to 500 mg, 100 mg to
200 mg, 200 mg to 100 gram, 200 mg to 10 grams, 200 mg to 5 grams,
200 mg to 1 gram, 200 mg to 500 mg, 500 mg to 100 gram, 500 mg to
10 grams, 500 mg to 5 grams, 500 mg to 1 gram, 1 gram to 100 gram,
1 gram to 10 grams, 1 gram to 5 grams, 5 grams to 100 grams, 5
grams to 10 grams, or 10 grams to 100 grams. For example, the
composition can contain an amount of ADA2 that is at least or at
least about or is 1 mg, 5 mg, 10 mg, 20 mg, 30 mg, 40 mg, 50 mg, 60
mg, 70 mg, 80 mg, 90 mg, 100 mg, 200 mg, 300 mg, 400 mg, 500 mg,
600 mg, 700 mg, 800 mg, 900 mg, 1 gram, 5 grams, 10 grams, 20
grams, 30 grams, 40 grams, 50 grams, 60 grams, 70 grams, 80 grams,
90 grams, 100 grams, 200 grams, 300 grams or more.
[0852] In further examples, the composition contains between or
between about 1 milliunits (mU) and 10,000 units (U), 1 mU and
1,000 U, 1 mU and 100 U, 1 mU and 10 U, 1 mU and 1 U, 1 mU and 100
mU, 1 mU and 10 mU, 10 mU and 10,000 U, 10 mU and 1,000 U, 10 mU
and 100 U, 10 mU and 10 U, 10 mU and 1 U, 10 mU and 100 mU, 100 mU
and 10,000 U, 100 mU and 1,000 U, 100 mU and 100 U, 100 mU and 10
U, 100 mU and 1 U, 1 U and 10,000 U, 1 U and 1,000 U, 1 U and 100
U, 1 U and 10 U, 10 U and 10,000 U, 10 U and 1,000 U, 10 U and 100
U, 100 U and 10,000 U, 100 U and 1,000 U, 1,000 U and 10,000 U, of
ADA2. For example, the composition can contain an amount of ADA2
that is at least or at least about or is 1 mU, 2 mU, 3 mU, 4 mU, 5
mU, 6 mU, 7 mU, 8 mU, 9 mU, 10 mU, 20 mU, 30 mU, 40 mU, 50 mU, 60
mU, 70 mU, 80 mU, 90 mU, 100 mU, 200 mU, 300 mU, 400 mU, 500 mU,
600 mU, 700 mU, 800 mU, 900 mU, 1 U, 10U, 20 U, 30 U, 40 U, 50 U,
60 U, 70 U, 80 U, 90 U, 100 U, 200 U, 300 U, 400 U, 500 U, 600 U,
700 U, 800 U, 900 U, 1000 U, 2000 U, 3000 U, 4000 U, 5000 U, 6000
U, 7000 U, 8000 U, 9000 U, 10000 U or more.
[0853] The volume of the composition containing the ADA2 provided
herein can be between or can be between about 0.1 mL and 100 mL,
such as 0.5 mL and 100 mL, 0.5 mL and 50 mL, 0.5 mL and 10 mL, 1 mL
and 100 mL, 1 mL and 50 mL, 1 mL and 40 mL, 1 mL and 20 mL, 1 mL
and 10 mL, or 3 mL and 10 mL. Typically, volumes of injections or
infusions of a composition are at least or at least about 0.01 mL,
0.05 mL, 0.1 mL, 0.2 mL, 0.3 mL, 0.4 mL, 0.5 mL, 1 mL, 2 mL, 3 mL,
4 mL, 5 mL, 6 mL, 7 mL, 8 mL, 9 mL, 10 mL, 20 mL, 30 mL, 40 mL, 50
mL or more.
[0854] Any ADA2 provided herein, wildtype, variants or conjugate
(e.g. PEGylated ADA2), can be provided at a concentration of at or
about or at least or at least about 1 mU/mL, 10 mU/mL, 20 mU/mL, 10
mU/mL, 20 mU/mL, 30 mU/mL, 40 mU/mL, 50 mU/mL, 60 mU/mL, 70 mU/mL,
80 mU/mL, 90 mU/mL, 100 mU/mL, 200 mU/mL, 300 mU/mL, 400 mU/mL, 500
mU/mL, 600 mU/mL, 700 mU/mL, 800 mU/mL, 900 mU/mL, 1 U/mL, 2 U/mL,
3 U/mL, 4 U/mL, 5 U/mL, 6 U/mL, 7 U/mL, 8 U/mL, 9 U/mL, 10 U/mL, 20
U/mL, 30 U/mL, 40 U/mL, 50 U/mL, 100 U/mL, 150 U/mL, 200 U/mL, 250
U/mL, 400 U/mL, 500 U/mL, 1000 U/mL, 2000 Units/mL, 3000 U/mL, 4000
U/mL, 5000 U/mL, 6000 U/mL, 7000 U/mL, 8000 U/mL, 9000 U/mL, or
10,000 U/mL. The composition can be prepared for use directly or
for dilution to the effective concentration prior to use.
[0855] Pharmaceutically and therapeutically active compounds and
derivatives thereof are typically formulated and administered in
unit dosage forms or multiple dosage forms. Each unit dose contains
a predetermined quantity of therapeutically active compound
sufficient to produce the desired therapeutic effect, in
association with the required pharmaceutical carrier, vehicle or
diluent. Unit dosage forms, include, but are not limited to,
tablets, capsules, pills, powders, granules, sterile parenteral
solutions or suspensions, and oral solutions or suspensions, and
oil water emulsions containing suitable quantities of the compounds
or pharmaceutically acceptable derivatives thereof. Unit dose forms
can be contained in ampoules and syringes or individually packaged
tablets or capsules. Unit dose forms can be administered in
fractions or multiples thereof. A multiple dose form is a plurality
of identical unit dosage forms packaged in a single container to be
administered in segregated unit dose form. Examples of multiple
dose forms include vials, bottles of tablets or capsules or bottles
of pints or gallons. Hence, multiple dose form is a multiple of
unit doses that are not segregated in packaging. Generally, dosage
forms or compositions containing active ingredient in the range of
0.005% to 100% with the balance made up from non-toxic carrier can
be prepared. Pharmaceutical composition can be formulated in dosage
forms appropriate for each route of administration.
[0856] The unit-dose parenteral preparations are packaged in an
ampoule, a vial or a syringe with a needle. The volume of liquid
solution or reconstituted powder preparation, containing the
pharmaceutically active compound, is a function of the disease to
be treated and the particular article of manufacture chosen for
package. All preparations for parenteral administration must be
sterile, as is known and practiced in the art.
[0857] As indicated, compositions provided herein can be formulated
for any route known to those of skill in the art including, but not
limited to, subcutaneous, intramuscular, intravenous, intradermal,
intralesional, intraperitoneal injection, epidural, vaginal,
rectal, local, otic, transdermal administration or any route of
administration. Formulations suited for such routes are known to
one of skill in the art. Compositions also can be administered with
other biologically active agents, either sequentially,
intermittently or in the same composition.
[0858] Pharmaceutical compositions can be administered by
controlled release formulations and/or delivery devices (see, e.g.,
in U.S. Pat. Nos. 3,536,809; 3,598,123; 3,630,200; 3,845,770;
3,847,770; 3,916,899; 4,008,719; 4,687,660; 4,769,027; 5,059,595;
5,073,543; 5,120,548; 5,354,556; 5,591,767; 5,639,476; 5,674,533
and 5,733,566).
[0859] Various delivery systems are known and can be used to
administer selected compositions, such as but not limited to,
encapsulation in liposomes, microparticles, microcapsules,
recombinant cells capable of expressing the compound, receptor
mediated endocytosis, and delivery of nucleic acid molecules
encoding an ADA2, such as wildtype, variant or modified forms
thereof, or other agent such as retrovirus delivery systems. In
some embodiments, the compositions contain nucleic acids that
encode the variant ADA2 polypeptide provided herein, such as
oncolytic viral vectors or gene therapy vectors, or cells, such as
modified immune cells for adoptive immunotherapy, and particular
compositions can be administered in delivery systems appropriate
for the particular composition.
[0860] Hence, in certain embodiments, liposomes and/or
nanoparticles also can be employed with administration of
compositions and combinations herein. Liposomes are formed from
phospholipids that are dispersed in an aqueous medium and
spontaneously form multilamellar concentric bilayer vesicles (also
termed multilamellar vesicles (MLVs)). MLVs generally have
diameters of from 25 nm to 4 .mu.m. Sonication of MLVs results in
the formation of small unilamellar vesicles (SUVs) with diameters
in the range of 200 to 500 angstroms containing an aqueous solution
in the core. In some embodiments, the liposomes can be
multivesicular liposomes (MVL).
[0861] Phospholipids can form a variety of structures other than
liposomes when dispersed in water, depending on the molar ratio of
lipid to water. At low ratios, the liposomes form. Physical
characteristics of liposomes depend on pH, ionic strength and the
presence of divalent cations. Liposomes can show low permeability
to ionic and polar substances, but at elevated temperatures undergo
a phase transition which markedly alters their permeability. The
phase transition involves a change from a closely packed, ordered
structure, known as the gel state, to a loosely packed,
less-ordered structure, known as the fluid state. This occurs at a
characteristic phase-transition temperature and results in an
increase in permeability to ions, sugars and drugs.
[0862] Liposomes interact with cells via different mechanisms:
endocytosis by phagocytic cells of the reticuloendothelial system
such as macrophages and neutrophils; adsorption to the cell
surface, either by nonspecific weak hydrophobic or electrostatic
forces, or by specific interactions with cell-surface components;
fusion with the plasma cell membrane by insertion of the lipid
bilayer of the liposome into the plasma membrane, with simultaneous
release of liposomal contents into the cytoplasm; and by transfer
of liposomal lipids to cellular or subcellular membranes, or vice
versa, without any association of the liposome contents. Varying
the liposome formulation can alter which mechanism is operative,
although more than one can operate at the same time. Nanocapsules
can generally entrap compounds in a stable and reproducible way. To
avoid side effects due to intracellular polymeric overloading, such
ultrafine particles (sized around 0.1 .mu.m) should be designed
using polymers able to be degraded in vivo. Biodegradable
polyalkyl-cyanoacrylate nanoparticles that meet these requirements
are contemplated for use herein, and such particles can be easily
made.
[0863] 4. Packaging and Articles of Manufacture
[0864] Also provided are articles of manufacture containing
packaging materials, any pharmaceutical composition provided
herein, and a label that indicates that the compositions are to be
used for treatment of diseases or conditions as described herein.
For example, the label can indicate that the treatment is for a
tumor or cancer. The label also can indicate that the treatment is
for a disease or condition associated with an elevated marker as
described herein, such as elevated or accumulated adenosine levels
on tissues or cells, elevated adenosine receptor (ADR) and/or
elevated CD73 or CD39 levels.
[0865] Combinations of an ADA2 protein described herein, including
a variant, conjugate (e.g. PEGylated ADA2) or other modified form,
and another therapeutic agent also can be packaged in an article of
manufacture. In one example, the article of manufacture contains a
pharmaceutical composition containing an ADA2, such as any ADA2
provided herein, and no further agent or treatment. In other
examples, the article of manufacture contains a pharmaceutical
composition containing an ADA2 and another further therapeutic
agent. For example, the article of manufacture contains a
pharmaceutical composition containing an ADA2 and another treatment
such as an immune checkpoint inhibitor agent or an antitumor agent.
In this example, the agents can be provided together or separately,
for packaging as articles of manufacture.
[0866] The articles of manufacture provided herein contain
packaging materials. Packaging materials for use in packaging
pharmaceutical products are well known to those of skill in the
art. See, for example, U.S. Pat. Nos. 5,323,907, 5,052,558 and
5,033,252, each of which is incorporated herein in its entirety.
Examples of pharmaceutical packaging materials include, but are not
limited to, blister packs, bottles, tubes, inhalers, pumps, bags,
vials, containers, syringes, bottles, and any packaging material
suitable for a selected formulation and intended mode of
administration and treatment. Exemplary of articles of manufacture
are containers including single chamber and dual chamber
containers. The containers include, but are not limited to, tubes,
bottles and syringes. The containers can further include a needle
for intravenous administration.
[0867] The choice of package depends on the agents, and whether
such compositions will be packaged together or separately. In
general, the packaging is non-reactive with the compositions
contained therein. In other examples, some of the components can be
packaged as a mixture. In other examples, all components are
packaged separately. Thus, for example, the components can be
packaged as separate compositions that, upon mixing just prior to
administration, can be directly administered together.
Alternatively, the components can be packaged as separate
compositions for administration separately.
[0868] Selected compositions including articles of manufacture
thereof also can be provided as kits. Kits can include a
pharmaceutical composition described herein and an item for
administration provided as an article of manufacture. For example
an ADA2 can be supplied with a device for administration, such as a
syringe, an inhaler, a dosage cup, a dropper, or an applicator. The
compositions can be contained in the item for administration or can
be provided separately to be added later. The kit can, optionally,
include instructions for application including dosages, dosing
regimens and instructions for modes of administration. Kits also
can include a pharmaceutical composition described herein and an
item for diagnosis.
H. METHOD OF TREATMENT WITH AN ADENOSINE DEAMINASE 2 (ADA2)
[0869] The methods provided herein include methods of administering
or using any adenosine deaminase 2 (ADA2) described herein, such as
wildtype, variant, conjugate (e.g. PEGylated ADA2) or other
modified forms thereof, for treating subjects having a disease or
condition whose symptoms can be ameliorated or lessened by a
reduction in adenosine or deoxyadenosine levels in the subject. For
example, the disease or condition is one that is associated with
elevated adenosine levels. For example, since ADA2 exhibits a low
binding affinity for adenosine with a Km of about
200.times.10.sup.-5M, it preferentially exhibits activity under
conditions of elevated or higher levels of adenosine. Thus, the use
of ADA2 as a therapeutic offers the benefit of exhibiting
specificity for disease or aberrant environments, while not
exhibiting activity under normal environments in which adenosine
levels are lower. In particular examples, as described below, the
disease or condition is a tumor or a cancer. The subject can be
selected based on levels of extracellular adenosine, level of
adenosine receptor (ADR) expression, and/or level of
ectonucleotidase expression. Additionally, methods of combination
therapies with one or more additional agents for treatment, such as
an anticancer agent or an anti-hyaluronan agent, also are
provided.
[0870] 1. Exemplary Diseases and Conditions
[0871] The concentrations of adenosine, which is physiologically
present in the interstitial fluids of unstressed tissues at low
levels, can rapidly increase in response to pathological
conditions, such as hypoxia, ischemia, tumor environment or trauma.
When released into the extracellular space, adenosine functions as
a danger signal and through the activation of adenosine receptors
(ADRs), various cellular responses are generated to restore tissue
homeostasis. Adenosine is associated with a variety of activities
that can contribute to the etiology of diseases and conditions,
including, but not limited to, stimulation of tumor growth and
angiogenesis, inhibition of cytokine synthesis and adhesion of
immune cells to the endothelial wall, inhibition of the function of
T-cells, macrophages, and natural killer cells, and promotion of
tumor metastasis.
[0872] Adenosine deaminases, such as any ADA2 or variants,
conjugates or other modified forms thereof described herein, can
modulate the extracellular adenosine levels in such conditions by
deaminating the adenosine molecules to inosine. Hence, any of such
diseases can be treated with an ADA2 described herein, such as a
wildtype, variant, conjugate (e.g. PEGylated ADA2) or other
modified form. In particular, ADA2 possesses properties that
contribute to extracellular stability, such as extensive
glycosylation and presence of conserved disulfide bonds, that make
it a desirable therapeutic. Provided herein are exemplary diseases
and conditions in which ADA2 treatment can be used.
[0873] Compositions containing an ADA2 can be administered by any
route that is desired for treatment of the disease or condition.
The particular route of administration can depend on the particular
disease or condition, the severity of the disease or condition, the
particular formulation and other factors within the level of a
skilled artisan. Typically, the compositions are administered by
intravenous route, although other routes of administration are
contemplated, such as any route known to those of skill in the art
including intramuscular, intraperitoneal, intravenous, intradermal,
intralesional, intraperitoneal injection, epidural, vaginal,
rectal, local, otic, transdermal administration or any route of
administration.
[0874] a. Cancers and Tumors
[0875] ADA2, such as any described herein, including a wildtype,
variant, conjugate (e.g. PEGylated ADA2) or other modified form,
can be used to treat a tumor or cancer. High extracellular
adenosine in the tumor microenvironments (TME) creates a local
immunosuppressive environment, and suppresses the activity of T and
NK cells. Through the generation of immunosuppressive TME and ADR
signaling to specific tumor and immune cells, adenosine generally
creates a TME that is favorable to tumor growth, vascularization
and metastasis.
[0876] Agents that modulate adenosine signaling have been shown to
have effects in inhibiting tumor growth and modulating downstream
cell signaling in a variety of cancer types, such as breast cancer,
lung cancer, colon carcinoma, prostate cancer and melanoma cells
(Antonioli et al. (2013) Nat Rev Can 13:842-857). Adenosine
deaminases, such as any ADA2 or variants, conjugates, or modified
forms thereof described herein, can modulate the extracellular
adenosine levels in the tumor environment, by deaminating the
adenosine molecules to inosine. Thus, any ADA2, variant, conjugate
(e.g. PEGylated ADA2), or modified forms thereof can be used as an
agent to modulate adenosine levels and signaling, reverse
immunosuppression of anti-tumor immune response, and ultimately
reduce tumor growth.
[0877] In particular, the diseases and conditions that can be
treated or ameliorated by the methods provided herein include, for
example, those in which tumor growth is stimulated through high
adenosine concentration and/or adenosine receptor (ADR) signaling.
For example, TME that actively produces a high concentration of
adenosine, thereby creating a local immunosuppressive environment,
can be more susceptible to ADA2 treatment. Compared to normal
adenosine levels of about or approximately 0.1 micromolar, the
adenosine levels in the TME rise to about 10 micromolar. Since ADA2
has a high Km and is preferentially active in conditions containing
elevated adenosine, as commonly present in the tumor
microenvironment (TME), ADA2 can reduce the adenosine levels in the
TME by its adenosine deaminase activity. Any ADA2 provided herein,
including ADA2 wildtype, variants and modified forms thereof, can
be used to treat tumors, including solid tumors, with a high
adenosine concentration in the TME.
[0878] In addition, as shown herein, ADA2, or variants, also
exhibit various pH optima that can preferentially target regions
within the TME. For example, hypoxic regions of the TME generally
have a low pH of about or approximately pH 6.5, which is the same
as the pH optimum of ADA2. For example, an altered pH is a common
microenvironment found in disease states such as in the TME (see
e.g. Fogh Andersen et al. (1995) Clin. Chem., 41:1522-1525;
Bhujwalla et al. (2002) NMR Biomed., 15:114-119; Helmlinger et al.
(1997) Nature Med., 3:177; Gerweck and Seetharaman (1996), Cancer
Res. 56(6):1194-1198). For example, in many tumors, Warburg effect
creates a microenvironment with a pH ranging from about 5.6 to
about 6.8, such as less than or about or pH 5.6, 5.7, 5.8, 5.9,
6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, or 6.8. Thus, ADA2 that are
more active at acidic pH than at neutral pH, such as ADA2 wildtype
or variants described herein, can be used to treat tumors within
the low pH TME, while minimizing activity in non-target disease
cells or tissues.
[0879] Thus, administering any ADA2 provided herein to reduce the
adenosine concentration in the TME by the enzymatic conversion of
adenosine to inosine can be used to prevent tumor growth and
metastasis, while minimizing activity at non-target disease cells
or tissues.
[0880] The methods provided herein are applicable to treating all
types of tumors, including cancers, that are associated with
elevated adenosine levels and/or susceptible to a reduction in
adenosine or deoxyadenosine levels in the subject to be treated.
Broadly, these include tumors of the blood as well as solid tumors.
Included among the tumors are those whose growth is suppressed when
adenosine levels are reduced. Included among the tumors are those
in which reduced adenosine levels allow the subject's immune system
to more effectively suppress the growth of the tumor, and/or tumors
whose growth is suppressed when reduced levels of adenosine
inhibits the blood supply, e.g., hypoxic tumors. In particular,
solid tumors are susceptible to treatment by the methods provided
herein, because they are more sensitive to the reduction in tumor
angiogenesis, resulting from the reduced adenosine levels. High
adenosine levels in sections of the TME promotes angiogenesis, and
the reduction of adenosine levels using the methods provided herein
can result in reduction of the angiogenic effect of adenosine. In
addition, high adenosine levels and CD73 activity are associated
with cancer cell dissemination and metastasis. Thus, reduction of
adenosine levels, effected by the administration of any ADA2
provided herein, can result in the suppression of cancer cell
dissemination and metastasis.
[0881] Tumors subject to treatment by the methods provided herein
include, but are not limited to, those that originate in the immune
system, skeletal system, muscles and heart, breast,
gastrointestinal tract, central and peripheral nervous system,
renal system, reproductive system, respiratory system, skin,
connective tissue systems, including joints, fatty tissues, and
circulatory system, including blood vessel walls. Examples of
tumors that can be treated by administering any ADA2 or variant or
modified form thereof provided herein include carcinomas, gliomas,
sarcomas (including liposarcoma), adenocarcinomas, adenosarcomas,
and adenomas. Such tumors can occur in virtually all parts of the
body, including, for example, breast, heart, lung, small intestine,
colon, spleen, kidney, bladder, head and neck, ovary, prostate,
brain, pancreas, skin, bone, bone marrow, blood, thymus, uterus,
testicles, cervix or liver.
[0882] Tumors of the skeletal system include, for example, sarcomas
and blastomas such as osteosarcoma, chondrosarcoma, and
chondroblastoma. Muscle and heat tumors include tumors of both
skeletal and smooth muscles, e.g., leiomyomas (benign tumors of
smooth muscle), leiomyosarcomas, rhabdomyomas (benign tumors of
skeletal muscle), rhabdomyosarcomas, cardiac sarcoma. Tumors of the
gastrointestinal tract include e.g., tumors of the mouth,
esophagus, stomach, small intestine, colon and colorectal tumors,
as well as tumors of gastrointestinal secretory organs such as
salivary glands, liver, pancreas, and the biliary tract. Tumors of
the central nervous system include tumors of the brain, retina, and
spinal cord, and can also originate in associated connective
tissue, bone, blood vessels or nervous tissue. Treatment of tumors
of the peripheral nervous system are also contemplated. Tumors of
the peripheral nervous system include malignant peripheral nerve
sheath tumors. Tumors of the renal system include those of the
kidneys, e.g., renal cell carcinoma, as well as tumors of the
ureters and bladder. Tumors of the reproductive system include
tumors of the cervix, uterus, ovary, prostate, testes and related
secretory glands. Tumors of the immune system include both blood
based and solid tumors, including lymphomas, e.g., both Hodgkin's
and non-Hodgkin's. Tumors of the respiratory system include tumors
of the nasal passages, bronchi and lungs. Tumors of the breast
include, e.g., both lobular and ductal carcinoma.
[0883] Other examples of tumors that can be treated with any ADA2
or variant or modified form thereof provided herein include
Kaposi's sarcoma, CNS neoplasms, neuroblastomas, capillary
hemangioblastomas, meningiomas and cerebral metastases, melanoma,
gastrointestinal and renal carcinomas and sarcomas,
rhabdomyosarcoma, glioblastoma (such as glioblastoma multiforme)
and leiomyosarcoma. Examples of cancer that can be treated with any
ADA2 or variant or modified form thereof provided herein include
but are not limited to lymphoma, blastoma, neuroendocrine tumors,
mesothelioma, schwannoma, meningioma, melanoma, and leukemia or
lymphoid malignancies. Examples of such cancers include hematologic
malignancies, such as Hodgkin's lymphoma; non-Hodgkin's lymphomas
(Burkitt's lymphoma, small lymphocytic lymphoma/chronic lymphocytic
leukemia, mycosis fungoides, mantle cell lymphoma, follicular
lymphoma, diffuse large B-cell lymphoma, marginal zone lymphoma,
hairy cell leukemia and lymphoplasmacytic leukemia), tumors of
lymphocyte precursor cells, including B-cell acute lymphoblastic
leukemia/lymphoma, and T-cell acute lymphoblastic
leukemia/lymphoma, thymoma, tumors of the mature T and NK cells,
including peripheral T-cell leukemias, adult T-cell leukemia/T-cell
lymphomas and large granular lymphocytic leukemia, Langerhans cell
histocytosis, myeloid neoplasias such as acute myelogenous
leukemias, including AML with maturation, AML without
differentiation, acute promyelocytic leukemia, acute myelomonocytic
leukemia, and acute monocytic leukemias, myelodysplastic syndromes,
and chronic myeloproliferative disorders, including chronic
myelogenous leukemia; tumors of the central nervous system such as
glioma, glioblastoma, neuroblastoma, astrocytoma, medulloblastoma,
ependymoma, and retinoblastoma; solid tumors of the head and neck
(e.g., nasopharyngeal cancer, salivary gland carcinoma, and
esophageal cancer), lung (e.g., small-cell lung cancer, non-small
cell lung cancer, adenocarcinoma of the lung and squamous carcinoma
of the lung), digestive system (e.g., gastric or stomach cancer
including gastrointestinal cancer, cancer of the bile duct or
biliary tract, colon cancer, rectal cancer, colorectal cancer, and
anal carcinoma), reproductive system (e.g., testicular, penile, or
prostate cancer, uterine, vaginal, vulval, cervical, ovarian, and
endometrial cancer), skin (e.g., melanoma, basal cell carcinoma,
squamous cell cancer, actinic keratosis, cutaneous melanoma), liver
(e.g., liver cancer, hepatic carcinoma, hepatocellular cancer, and
hepatoma), bone (e.g., osteoclastoma, and osteolytic bone cancers)
additional tissues and organs (e.g., pancreatic cancer, bladder
cancer, kidney or renal cancer, thyroid cancer, breast cancer,
cancer of the peritoneum, and Kaposi's sarcoma), tumors of the
vascular system (e.g., angiosarcoma and hemangiopericytoma), Wilms'
tumor, retinoblastoma, osteosarcoma and Ewing's sarcoma.
[0884] b. Non-Cancer Hyperproliferative Diseases
[0885] Any ADA2 described herein, such as a wildtype, variant,
conjugate (e.g. PEGylated ADA2) or other modified form thereof, can
be used to treat a non-cancer hyperproliferative disease in a
subject. Adenosine and ADR signaling play a role in various
signaling pathways that include G-protein-coupled receptors
(GPCRs), cyclic AMP (cAMP) signaling, and/or cytokine signaling, to
a variety of cellular responses such as mitogen activated protein
kinase activation, gene transcription and proliferation. Activation
of certain adenosine receptors (ADRs), such as the A1 receptor, can
initiate cellular pathways leading to cellular proliferation.
Overexpression and/or overstimulation can result in
hyperproliferation. Any ADA2 provided herein can be used to treat
non-cancer hyperproliferative disorders by reducing the activation
of ADRs in cells involved in the hyperproliferative disorders.
[0886] Examples of hyperproliferative diseases that can be treated
by any ADA2 provided herein, including wildtype, variants and
modified forms thereof provided herein include any
hyperproliferative diseases, including, for example, psoriasis,
actinic keratoses, and seborrheic keratoses, warts, keloid scars,
and eczema. Also included are hyperproliferative diseases caused by
virus infections, such as papilloma virus infection. Different
types of psoriasis can display characteristics such as pus-like
blisters (pustular psoriasis), severe sloughing of the skin I
(erythrodermic psoriasis), drop-like dots (guttae psoriasis) and
smooth inflamed lesions (inverse psoriasis). It is understood that
treatment of psoriasis includes treatment of all types of psoriasis
(e.g., psoriasis vulgaris, psoriasis pustulosa, psoriasis
erythrodermica, psoriasis arthropathica, parapsoriasis,
palmoplantar pustulosis).
[0887] c. Fibrotic Diseases
[0888] Any ADA2 described herein, such as a wildtype, variant,
conjugate (e.g. PEGylated ADA2) or other modified form thereof, can
be used to treat fibrotic diseases, and particularly those
associated with elevated adenosine. Adenosine levels are elevated
in stressed conditions, such as hypoxia, ischemia, inflammation,
tumor environment or trauma. In these conditions, extracellular
adenosine works as a danger signal, and promotes various responses
for tissue homeostasis. However, the persistence of increased
adenosine concentrations beyond the acute-injury phase can become
detrimental to tissues by activating pathways that trigger immune
suppression or promote an unremitting wound-healing process, which
leads to fibrotic remodeling (Antonioli et al. (2013) Nat Rev Can
13:842-857). Administration of ADA2 provided herein, which can
reduce the stress-related increase in extracellular adenosine, can
be used to treat diseases or conditions associated with excessive
fibrotic tissue deposition, such as fibrosis, the formation of
excess fibrous connective tissue in an organ or tissue in a
reparative or reactive process. Diseases or conditions associated
with fibrosis include, for example, fibrosis of the lungs,
including Idiopathic pulmonary fibrosis and cystic fibrosis;
fibrosis of the liver, including cirrhosis; fibrosis of the heart,
including endomyocardial fibrosis, myocardial infarction, atrial
fibrosis; and other fibrosis conditions, including mediastinal
fibrosis (fibrosis of the soft tissue of the mediastinum),
myelofibrosis (fibrosis of the bone marrow), retroperitoneal
fibrosis (fibrosis of the soft tissue of the retroperitoneum),
progressive massive fibrosis (fibrosis of the lungs), nephrogenic
systemic fibrosis (fibrosis of the skin), Crohn's Disease (fibrosis
of the intestine), keloid (fibrosis of the skin),
scleroderma/systemic sclerosis (fibrosis of the skin, lungs),
arthrofibrosis (fibrosis of the knee, shoulder, other joints),
Peyronie's disease (fibrosis of the penis), Dupuytren's contracture
(fibrosis of the hands, fingers), and adhesive capsulitis (fibrosis
of the shoulder).
[0889] d. Infectious Diseases
[0890] Any ADA2 described herein, such as a wildtype, variant,
conjugate (e.g. PEGylated ADA2) or other modified form thereof, can
be used to treat infectious diseases associated with elevated
adenosine. Invasive pathogens can take advantage of the host's
endogenous immunosuppressive mechanisms, such as adenosine-mediated
immunosuppression, to promote spread or survival within the host.
For example, Candida albicans hyphae release adenosine to suppress
the neutrophil-mediated killing of the organism, and Staphylococcus
aureus also produce adenosine to suppress the host's immune
response. In addition, increased susceptibility to infection in
neonates and the elderly is also associated with elevated adenosine
levels signaling (Hasko et al. (2013) Front Immunol. 4:85).
[0891] Therefore, in certain infectious diseases, ADA2 can be used
as treatment to decrease the adenosine-mediated immunosuppression.
Any ADA2 provided herein, including wildtype, variants and modified
forms thereof, can be used to treat infectious diseases. Infectious
diseases that can be treated by any ADA2 provided herein include,
but are not limited to, diseases caused by pathogens such as
viruses, bacteria, fungi, protozoa, and parasites. Infectious
diseases can be caused by viruses including adenovirus,
cytomegalovirus, dengue, Epstein-Barr, hanta, hepatitis A,
hepatitis B, hepatitis C, herpes simplex type I, herpes simplex
type II, human immunodeficiency virus, (HIV), human papilloma virus
(HPV), influenza, measles, mumps, papova virus, polio, respiratory
syncytial virus, rinderpest, rhinovirus, rotavirus, rubella, SARS
virus, smallpox and viral meningitis. Infectious diseases can also
be caused by bacteria including Bacillus anthracia, Borrelia
burgdorferi, Campylobacter jejuni, Chlamydia trachomatis,
Clostridium botulinum, Clostridium tetani, Diphtheria, Escherichia
coli, Legionella, Helicobacter pylori, Mycobacterium rickettsia,
Mycobacterium tuberculosis, Mycoplasma Neisseria, Pertussis,
Pseudomonas aeruginosa, Streptococcus pneumoniae, Streptococcus,
Staphylococcus, Vibrio cholerae and Yersinia pestis. Infectious
diseases can also be caused by fungi such as Aspergillus fumigatus,
Blastomyces dermatitidis, Candida albicans, Coccidioides immitis,
Cryptococcus neoformans, Histoplasma capsulatum and Penicillium
marneffei. Infectious diseases can also be caused by protozoa and
parasites such as chlamydia, kokzidiose, leishmania, malaria,
rickettsia, and trypanosoma.
[0892] e. Other Diseases and Conditions
[0893] Individuals who harbor deleterious mutations in the ADA1
gene can develop varying degrees of immunodeficiency disorder, from
mild to severe. Such immunodeficiency disorder is due to the toxic
accumulation of the enzyme substrates, adenosine and
deoxyadenosine, in the immature lymphoid cells. The onset of the
disorder can also range from early childhood to adults, depending
on the mutations inherited. Deficiencies of ADA1 are one of the
leading causes of severe combined immunodeficiency disease (SCID)
in children and is one of the leading targets for gene therapy
approaches (R. Parkman et al., 2000, "Gene therapy for adenosine
deaminase deficiency," Ann. Rev. Med. 51:33-47).
[0894] An ADA2 provided herein, such as wildtype, variant,
conjugate (e.g. PEGylated ADA2), or other modified forms, can be
used in the treatment of SCID or other ADA1-mediated
immunodeficiencies. Immunodeficiencies are generally categorized as
either acquired immunodeficiencies or inherited immunodeficiencies.
Acquired immunodeficiencies include human immunodeficiency virus-1
(HIV-1) infection, herpes virus infections, Epstein-Barr virus
infections, lepromatous leprosy and diminished immune capacity
resulting from skin burns in burn patients, i.e. burn-related
immunodeficiency. Inherited immunodeficiencies include several
genetically different forms of SCID, including adenosine deaminase
deficiency dependent SCID (ADA SCID), SCID autosomal recessive with
and without B cells (no ADA deficiency), SCID X-linked recessive
without B cells, SCID autosomal recessive (with ADA deficiency),
purine nucleotide phosphorylase deficiency (PNP SCID), severe
combined immune deficiency (IL-2 receptor deficiency; i.e. X-linked
SCID), and bare lymphocyte syndrome. Other immunodeficiencies
include various forms of congenital or genetically determined
hematopoietic abnormalities, several high risk leukemias and
several forms of severe life-threatening aplastic anemia. Still
other immunodeficiencies that can be treated include
Wiskott-Aldrich syndrome; Blackfan-Diamond syndrome; Fanconi
anemia; severe neutrophil dysfunction; chronic granulomatous
disease of childhood; severe (Kostman-type) agranulocytosis;
immunodeficiency and neutropenia of cartilage-hair hypoplasia;
infantile and late onset osteoporosis; aplastic anemia-toxic
chemical, idiopathic, immunological, and genetic (non-Fanconi);
acute myeloid leukemia; chronic myeloid leukemia; Burkitt lymphoma,
and recurrent acute lymphatic leukemia. In particular examples, the
immune system disorder that is treated is adenosine deaminase
deficiency-dependent severe combined immunodeficiency (ADA
SCID).
[0895] 2. Methods of Patient Selection
[0896] Provided herein are methods of patient selection for
treatment with any ADA2 provided herein, based on the level of
adenosine-associated biomarkers described herein. Exemplary
adenosine-associated biomarkers include plasma adenosine levels,
adenosine receptor (ADR) levels and ectonucleotidase levels.
[0897] For example, subjects with elevated adenosine levels in the
plasma or other samples, can be more responsive to treatment using
ADA2, as the effects of ADA2 administration directly reduce the
elevated extracellular adenosine levels. In another example,
subjects that express elevated or high levels of ADRs, such as the
A2A and A2B adenosine receptors in samples, such as tumor samples,
can be more responsive to treatments using ADA2, as the effects on
adenosine and tumor growth can be mediated directly by binding to
ADRs expressed on tumor cells. In a further example, subjects with
elevated levels or expression of the CD39 and CD73
ectonucleotidases in the tumor sample or other samples can be more
responsive to treatment using ADA2, as the increased expression of
CD39 and CD73 lead to elevated adenosine levels, and elevated
adenosine levels, via signaling through the ADRs, have downstream
cancer promoting effects. Thus, these biomarkers can be used to
select or identify patients predicted to be responsive to treatment
and/or to monitor treatment and efficacy of treatment, thereby
providing an improved treatment regimen of adenosine-associated
diseases or conditions, such as a tumor or a cancer, using any ADA2
provided herein.
[0898] a. Adenosine-Associated Biomarkers
[0899] Provided herein are methods of selecting patients that have
tumors in which treatment with ADA2 is applicable. The methods
provided herein are applicable to treating conditions and diseases
that are associated with elevated adenosine levels and/or
susceptible to a reduction in adenosine or deoxyadenosine levels in
the subject to be treated. For example, such conditions or diseases
include a tumor or a cancer. Levels of adenosine-associated
biomarkers, such as plasma adenosine levels, adenosine receptor
(ADR) levels and ectonucleotidase levels, can be used for diagnosis
or prognosis of an adenosine-associated disease or condition, to
predict responsiveness of a subject having an adenosine-associated
disease or condition to any ADA2 or combination therapy provided
herein, and/or to monitor or predict efficacy of treatment of a
subject having an adenosine-associated disease or condition that
has been treated with an ADA2 provided herein, including wildtype,
variants and modified forms thereof.
[0900] In any examples provided herein, the adenosine-associated
diseases or conditions are diseases and conditions in which
adenosine levels are elevated as cause, consequence or otherwise
observed in the disease or condition. Exemplary
adenosine-associated diseases or conditions, include, but are not
limited to, a cancer, a tumor, an inflammatory disease, an
infection, and other conditions and diseases associated with
elevated adenosine levels and/or is susceptible to a reduction in
adenosine or deoxyadenosine levels in the subject to be treated. In
particular, adenosine-associated diseases and conditions, include,
but are not limited to, cancers with elevated adenosine levels in
the extracellular environment, for example, tumors, including solid
tumors that are hypoxic. Provided herein are methods of treatment
that includes measurement of adenosine-associated biomarkers and
selection of subjects for treatment with any ADA2 provided
herein.
[0901] i. Plasma Adenosine Levels
[0902] In one example, a patient or subject can be selected for
treatment with any ADA2 provided herein, based on the levels or
expression of extracellular adenosine in the sample, such as the
plasma. In other examples, the level of extracellular adenosine in
the tumor microenvironment of a specific tumor can be used. Plasma
adenosine level can be measured using any methods known in the art,
including chromatography-based methods. It is within the level of
one of skill in the art to assess, quantify, determine and/or
detect adenosine levels in a plasma sample using assays known in
the art. Assays include in vitro or in vivo assays. Exemplary
assays that can be used to assess, evaluate, determine, quantify
and/or otherwise specifically detect adenosine levels in a sample
include, but are not limited to, high performance liquid
chromatography (HPLC)-based assays (see, e.g., Jackson and Ohnishi
(1987) Hypertension 10:189-197), spectrophotometric methods,
radioenzymatic assays (see, e.g., German and Kredich (1984) Anal
Biochem. 142(2):536-541), microelectrode-based detection, and in
vivo imaging methods, such as bioluminescence-based methods. In
some examples, plasma adenosine levels can be detected using a
modified HPLC method that utilizes a reaction that converts
adenosine into a fluorescent derivative, such as
1,N6-ethanoadenosine for detection of adenosine levels. (Howard et
al. (1998) Investigative Opthalmology & Visual Science,
39(10):1942-1946).
[0903] ii. Adenosine Receptors (ADRs)
[0904] The level of expression of adenosine receptors (ADRs) can be
used as biomarkers for the selection of patients or subjects for
treatment with any ADA2 provided herein. In particular, ADRs that
are expressed in tumor cells and/or immune cells involved in tumor
immunity, such as the A2A (amino acid sequence set forth in SEQ ID
NO:534) and A2B (amino acid sequence set forth in SEQ ID NO:535)
adenosine receptors, can be used. Tumors that express elevated or
high levels of ADRs, such as the A2A and A2B adenosine receptors,
can be more responsive to treatments using ADA2, as the effects on
adenosine and tumor growth can be mediated by adenosine binding to
ADRs expressed on tumor cells. Some tumors have elevated expression
of ADRs, in particular, A2A and A2B, and the expression of these
receptors have downstream cancer-promoting effects. In other
examples, adenosine signaling, through the stimulation of A2A and
A2B receptors, regulate endothelial inflammatory processes and
tumor angiogenesis. In other examples, expression of ADRs, such as
the A2A and A2B adenosine receptors, have inhibitory effects on
activation and differentiation of immune cells, such as macrophages
and dendritic cells. Therefore, measurements of ADRs, such as the
A2A and A2B adenosine receptors can be used to select tumors,
including cancers, that are associated with elevated adenosine
levels and/or susceptible to a reduction in adenosine or
deoxyadenosine levels. Levels of ADRs, such as the A2A and A2B
adenosine receptors, can be used to select or identify patients
predicted to be responsive to treatment and/or to monitor treatment
and efficacy of treatment, thereby providing an improved treatment
regimen of adenosine-associated diseases or conditions, such as a
tumor or a cancer.
[0905] For example, a patient or subject can be selected for
treatment with any ADA2 provided herein, based on the levels or
expression of the A2A and A2B adenosine receptors in a sample, such
as a tumor or fluid sample from a subject having a tumor or
suspected of having a tumor. Level of expression of ADRs, for
example, the A2A and A2B adenosine receptors, can be measured using
any methods known in the art for determining levels of
extracellular receptors on a cell. It is within the level of one of
skill in the art to assess, quantify, determine and/or detect
levels of ADRs, such as those of A2A and A2B adenosine receptors,
in a sample using assays known in the art. Assays include in vitro
or in vivo assays. Exemplary assays that can be used to assess,
evaluate, determine, quantify and/or otherwise specifically detect
levels of ADRs, such as those of A2A and A2B adenosine receptors,
in a sample include, but are not limited to, solid phase binding
assays (e.g. enzyme linked immunosorbent assay (ELISA)),
radioimmunoassay (RIA), immunoradiometric assay, fluorescence
assay, chemiluminescent assay, bioluminescent assay, western blot
and histochemistry methods, such as immunohistochemistry (IHC) or
pseudo immunohistochemistry using a non-antibody binding agent. In
solid phase binding assay methods, such as ELISA methods, for
example, the assay can be a sandwich format or a competitive
inhibition format. In other examples, in vivo imaging methods can
be used.
[0906] The methods provided herein are directed to measurement of
ADR protein levels, such as that of the A2A and A2B adenosine
receptors, in a sample, such as a tumor or fluid sample from a
subject having a tumor or suspected of having a tumor, using
antibodies against ADRs, such as the A2A and A2B adenosine
receptors. Exemplary antibodies against adenosine receptor A2A
include those from Santa Cruz Biotechnology (Dallas, Tex.; Cat no.
sc-70321), Abcam (Cambridge, UK; Cat no. ab3461), and EMD Milipore
(Billerica, Mass.; Cat no. AB1559P). Exemplary antibodies against
adenosine receptor A2B include those from Santa Cruz Biotechnology
(Dallas, Tex.; Cat no. sc-7505), Abcam (Cambridge, UK; Cat no.
ab40002), and EMD Milipore (Billerica, Mass.; Cat no. AB1589P). The
antibodies can be used to detect the ADR protein levels in samples,
using methods such as immunohistochemistry, ELISA, RIA,
immunoradiometric assay, fluorescence assay, chemiluminescent
assay, bioluminescent assay, and western blot. The antibodies can
be modified by conjugation, directly or indirectly, to biotin, a
fluorescent moiety, a radiolabel or other detectable label. In
other examples, secondary antibodies, which are conjugated to a
detectable label, can be used.
[0907] ADR levels, such as that of the A2A and A2B adenosine
receptors, can also be determined using in vivo imaging methods.
For example, positron emission tomography (PET) with the
administration of xanthine derivatives, which have A2A receptor
antagonist activity, radiolabeled with the positron emitter
carbon-11 (.sup.11C), such as .sup.11C-SCH442416, .sup.11C-KF1783,
.sup.11C-KF18446, .sup.11C-KF19631, .sup.11C-KW-6002 and
.sup.11C-TMSX (Grachev et al. (2014) Journal of Diagnostic Imaging
in Therapy 1(1):1-19).
[0908] Other methods of determining ADR levels, such as that of the
A2A and A2B adenosine receptors, include nucleic acid based
methods, such as reverse transcriptase-polymerase chain reaction
(RT-PCR), microarrays, quantitative PCR, high-throughput
transcriptome sequencing, and other such methods.
[0909] iii. Ectonucleotidases CD39 and CD73
[0910] The level of expression of ectonucleotidases CD39 and CD73
that are expressed in tumor cells can be used as biomarkers for the
selection of patients or subjects for treatment with any ADA2
provided herein. CD39 and CD73 are the ectonucleotidases that
generate extracellular adenosine from adenosine triphosphate (ATP).
CD39 (Ectonucleoside triphosphate diphosphohydrolase 1; EC 3.6.1.5;
amino acid sequence set forth in SEQ ID NO:542) metabolizes
extracellular ATP to generate adenosine diphosphate (ADP) and
adenosine monophosphate (AMP), and CD73 (ecto-5'-nucleotidase; EC
3.1.3.5; amino acid sequence set forth in SEQ ID NO:543)
metabolizes AMP to generate adenosine. CD39 and CD73 are the major
source of extracellular adenosine during conditions associated with
a rapid elevation of adenosine levels, such as hypoxia, ischemia,
inflammation, tumor environment or trauma. In these conditions,
extracellular ATP increases, which leads to a subsequent increase
in adenosine levels, by the action of CD39 and CD73
ectonucleotidases. In certain cancer types, the level of CD39 and
CD73 are overexpressed, and elevated CD73 levels are associated
with poor prognosis and high early tumor recurrence. Thus, the
level of expression of ectonucleotidases CD39 and CD73 can be used
as a biomarker for tumors associated with elevated adenosine levels
and for selection of patients for treatment with any ADA2 provided
herein.
[0911] For example, a patient or subject can be selected for
treatment with any ADA2 provided herein, based on the levels or
expression of the CD39 and CD73 ectonucleotidases in a sample, such
as a tumor or fluid sample from a subject having a tumor or
suspected of having a tumor, or immune cells. Level of expression
of CD39 and CD73 ectonucleotidases can be measured using any
methods known in the art for determining levels of plasma membrane
or extracellular proteins. It is within the level of one of skill
in the art to assess, quantify, determine and/or detect the level
of expression CD39 and CD73 ectonucleotidases in a sample using
assays known in the art. Assays include in vitro or in vivo assays.
Exemplary assays that can be used to assess, evaluate, determine,
quantify and/or otherwise specifically detect the level of
expression CD39 and CD73 ectonucleotidases in a sample include, but
are not limited to, solid phase binding assays (e.g. enzyme linked
immunosorbent assay (ELISA)), radioimmunoassay (RIA),
immunoradiometric assay, fluorescence assay, chemiluminescent
assay, bioluminescent assay, western blot and histochemistry
methods, such as immunohistochemistry (IHC) or pseudo
immunohistochemistry using a non-antibody binding agent. In solid
phase binding assay methods, such as ELISA methods, for example,
the assay can be a sandwich format or a competitive inhibition
format. In other examples, in vivo imaging methods can be used.
[0912] The methods provided herein are directed to measurement of
CD39 and CD73 ectonucleotidases in a sample, such as a tumor or
fluid sample from a subject having a tumor or suspected of having a
tumor, using antibodies against CD39 and CD73 ectonucleotidases.
Exemplary antibodies against CD39 include those from Santa Cruz
Biotechnology (Dallas, Tex.; Cat no. sc-65262), Abcam (Cambridge,
UK; Cat no. ab49580), and EMD Milipore (Billerica, Mass.; Cat no.
04-973). Exemplary antibodies against CD73 include those from Santa
Cruz Biotechnology (Dallas, Tex.; Cat no. sc-8502), Abcam
(Cambridge, UK; Cat no. ab4056), and EMD Milipore (Billerica,
Mass.; Cat no. IHCR2023-6). The antibodies can be used to detect
the ADR protein levels in samples, using methods such as
immunohistochemistry, ELISA, RIA, immunoradiometric assay,
fluorescence assay, chemiluminescent assay, bioluminescent assay,
and western blot. The antibodies can be modified by conjugation,
directly or indirectly, to biotin, a fluorescent moiety, a
radiolabel or other detectable label. In other examples, secondary
antibodies, which are conjugated to a detectable label, can be
used.
[0913] Other methods of determining CD39 and CD73 ectonucleotidase
levels include nucleic acid based methods, such as reverse
transcriptase-polymerase chain reaction (RT-PCR), microarrays,
quantitative PCR, high-throughput transcriptome sequencing, and
other such methods.
[0914] b. Patient Selection
[0915] Once the amount of the level of biomarkers, such as plasma
adenosine levels, levels of ADRs such as A2A or A2B, or levels of
CD39 and CD73 ectonucleotidases, is determined the amount can be
compared to a control or threshold level. The control or threshold
level is generally a predetermined threshold level or amount that
is indicative of disease or condition associated with elevated
adenosine levels (e.g. a tumor or cancer). Such level or amount can
be empirically determined by one of skill in the art. It is
understood that the particular predetermined selection or
classification criteria for the methods herein are dependent on the
particular assay that is used to detect the level of
adenosine-associated biomarkers and the particular sample that is
being tested. It is within the level of one of skill in the art to
determine if an assay is compatible with testing a particular
sample. In vitro solid phase assays or high performance liquid
chromatography (HPLC) based assays can be used for testing body
fluid samples. Assays such as histochemistry or
immunohistochemistry can be used for testing tissue samples. It
also is understood that in methods involving comparisons to a
predetermined level or amount or to a control or reference sample
that the references are made with the same type of sample and using
the same assay and reagents (including the same detectable moiety
and detection method).
[0916] For example, the predetermined threshold level can be
determined based on the level or amount of the marker in a
reference or control sample, such as the median or mean level or
amount of the marker in a population of subjects, in order to
assess differences in levels or expression. In one example, the
predetermined threshold level can represent the mean or median
level or amount of the adenosine-associated biomarker in a sample
from a healthy subject or a subject known to have a condition or
disease associated with elevated adenosine levels (e.g. a tumor or
cancer). In one embodiment, the predetermined level or amount of
the adenosine-associated biomarker from a normal tissue or bodily
fluid sample is the mean level or amount observed in normal samples
(e.g., all normal samples analyzed). In another embodiment, the
level or amount of the adenosine-associated biomarker from a normal
tissue or bodily fluid sample is the median value for the level or
amount observed in normal samples. The predetermined threshold
level also can be based on the level or amount of the
adenosine-associated biomarker in a cell line or other control
sample (e.g. tumor cell line). As described herein, these
predetermined values can be determined by comparison or knowledge
of the adenosine-associated biomarker levels in a corresponding
normal sample as determined by the same assay of detection and
using the same reagents, for example, the same antibody and
detection method.
[0917] The reference or control sample can be another tissue, cell
or body fluid, such as a normal tissue, cell or body fluid, for
example, a tissue, cell or body fluid that is analogous to the
sample being tested, but isolated from a different subject. The
control or reference subject can be a subject or a population of
subjects that is normal (i.e. does not have a disease or
condition), a subject that has a disease but does not have the type
of disease or condition that the subject being tested has or is
suspected of having, for example, a subject that does not have a
condition or disease associated with elevated adenosine levels
(e.g. a tumor or cancer), or an analogous tissue from another
subject that has a similar disease or condition, but whose disease
is not as severe and/or expresses relatively less of the
adenosine-associated biomarker. For example, when the cell, tissue
or fluid being tested is a subject or a population of subjects
having a cancer, the level or amount of the marker can be compared
to the level or amount of the marker in a tissue, cell or fluid
from a subject having a less severe cancer, such as an early stage,
differentiated or other type of cancer. In another example, a
control or reference sample is a fluid, tissue, extract (e.g.
cellular or nuclear extract), nucleic acid or peptide preparation,
cell line, biopsy, standard or other sample, with a known amount or
relative amount of the adenosine-associated biomarker, such as a
sample, for example a tumor cell line or tumors from tumor models
generated using such cell lines.
[0918] In any method herein, the level(s) of the
adenosine-associated biomarker in samples from subjects suspected
or known to have a condition or disease associated with elevated
adenosine levels (e.g., cancer) can be determined concurrently with
the determination of level(s) of the adenosine-associated biomarker
in reference or normal tissues. Alternatively, the levels of the
adenosine-associated biomarker in samples from subjects suspected
or known to have a condition or disease associated with elevated
adenosine levels (e.g. cancer) can be compared to the level(s) of
the adenosine-associated biomarker previously determined in normal
tissue or bodily fluid. Thus, the level of the adenosine-associated
biomarker in normal or healthy samples or other reference samples
employed in any detection, comparison, determination, or evaluation
can be a level or amount determined prior to any detection,
determination, or evaluation of the level or amount of the
adenosine-associated biomarker in a sample from a human
patient.
[0919] The level or amount of the adenosine-associated biomarker of
is determined and/or scored and compared to predetermined
phenotypes of the adenosine-associated biomarker associated with
disease. It is within the level of one of skill in the art to
determine the threshold level for disease diagnosis depending on
the particular disease, the assay being used for detection of the
adenosine-associated biomarker and/or the detection reagent being
used. It is within the level of one of skill in the art to
determine the threshold level of the adenosine-associated biomarker
for classifying responsiveness to treatment with any ADA2 provided
herein. Exemplary methods for stratification of tumor samples or
bodily fluid samples for diagnosis, prognosis or selection of
subjects for treatment are provided herein.
[0920] It is understood that the particular change, e.g. increase
in or decrease of the adenosine-associated biomarker is dependent
on the assay used. In an ELISA, the fold increase or decrease in
absorbance at a particular wavelength or in quantity of protein
(e.g. as determined by using a standard curve) can be expressed
relative to a control. In a PCR assay, such as RT-PCR, expression
levels can be compared to control expression levels (e.g. expressed
as fold change) using methods known to those in the art, such as
using standards.
[0921] In particular examples of the methods herein, a subject is
selected as a candidate for therapy with any ADA2 provided herein,
if the amount of the adenosine-associated biomarker is determined
to be elevated in the sample. For example, elevated or accumulated
adenosine-associated biomarker levels in a diseased subject
compared to a healthy or normal subject is indicative of a
condition or disease associated with elevated adenosine levels
(e.g. tumor or cancer). The adenosine-associated biomarker can be
elevated 0.5-fold, 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold,
7-fold, 8-fold, 9-fold, 10-fold, 15-fold, 20-fold, 30-fold,
40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold,
150-fold, 200-fold, 500-fold, 1000-fold or more. Thus, in examples
of the methods herein, when the amount of the adenosine-associated
biomarker in a sample from a subject is being tested, detection of
the marker can be determining that the amount of the
adenosine-associated biomarker in the sample (e.g. cancerous cell,
tissue or fluid) from the subject is elevated compared to a
predetermined level or amount or control sample. In one example,
the subject is determined to have a condition or disease associated
with elevated adenosine levels if the amount of the
adenosine-associated biomarker in the tissue, cell or fluid is
elevated at or about 0.5-fold, 1-fold, 2-fold, 3-fold, 4-fold,
5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 15-fold, 20-fold,
30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold,
100-fold, 150-fold, 200-fold, 500-fold, 1000-fold or more, compared
to the predetermined level or amount or control sample.
[0922] A subject can be selected as a candidate for therapy with
any ADA2 provided herein, including wildtype, variants and modified
forms thereof, based on the level or amount of adenosine levels in
a sample (e.g. plasma) from the subject. For example, plasma
adenosine levels greater than 0.1 mM, such as 0.1 mM, 0.2 mM, 0.3
mM, 0.4 mM, 0.5 mM, 0.6 mM, 0.7 mM, 0.8 mM, 0.9 mM, 1 mM, 2 mM, 3
mM, 4 mM, 5 mM, 6 mM, 7 mM, 8 mM, 9 mM, 10 mM or higher, correlates
to the presence of a tumor or cancer. Using such methods, in
exemplary methods provided herein, a subject can be selected for
treatment with any ADA2 provided herein if the adenosine level in
the fluid sample, such as a plasma sample, is greater than 0.1 mM,
such as 0.1 mM, 0.2 mM, 0.3 mM, 0.4 mM, 0.5 mM, 0.6 mM, 0.7 mM, 0.8
mM, 0.9 mM, 1 mM, 2 mM, 3 mM, 4 mM, 5 mM, 6 mM, 7 mM, 8 mM, 9 mM,
10 mM or higher.
[0923] A subject can be selected as a candidate for therapy with
any ADA2 provided herein, based on the level or amount of the
adenosine-associated biomarker, such as ADRs, such as the A2A (SEQ
ID NO:534) and A2B (SEQ ID NO:535) adenosine receptors or CD39 (SEQ
ID NO:542) and CD73 (SEQ ID NO:543) ectonucleotidases, in a cell or
tissue sample. In such an example, if the level is indicative of
disease, then the patient is diagnosed with a condition or disease
associated with elevated adenosine levels. For example, a high
percentage of staining indicates the subject has a tumor with
elevated the adenosine-associated biomarker, such as ADRs, such as
the A2A and A2B adenosine receptors or CD39 and CD73
ectonucleotidase, indicative of the presence of a tumor that would
benefit from treatment with any ADA2 provided herein and thus is a
candidate for treatment with any ADA2 provided herein. In other
examples, a subject can be selected for treatment with any ADA2
provided herein, based on the percentage of staining, for example,
if the degree of the adenosine-associated biomarker staining is
10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%,
75%, 80%, 85%, 90%, 95% or more of the total staining area, and
generally at least 25% or more. Using histochemical methods, the
amount of the adenosine-associated biomarker detected is quantified
and given as a percentage of the adenosine-associated biomarker
positive pixels and/or a score. For example, the amount of the
adenosine-associated biomarker detected in the sample can be
quantified as a percentage of the adenosine-associated biomarker
positive pixels. In some examples, the amount of the
adenosine-associated biomarker present in a sample is quantified as
the percentage of area stained, e.g., the percentage of the
adenosine-associated biomarker positive pixels. For example, a
sample can have at least or at least about or about 0, 1%, 2%, 3%,
4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%,
18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%,
31%, 32%, 33%, 34%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%,
80%, 85%, 90%, 95% or more of the adenosine-associated biomarker
positive pixels as compared to the total staining area.
[0924] Efficacy of treatment with any ADA2 provided herein or
responsiveness to treatment also can be monitored by comparing the
level or amount of adenosine-associated biomarkers in a subject
over time. Changes in the level or amount of adenosine-associated
biomarkers can be used to optimize dosing or scheduling of
treatment with any ADA2 provided herein. In the method, the level
of adenosine-associated biomarkers in samples, from treated
subjects, are compared to a predetermined level of
adenosine-associated biomarkers.
[0925] For purposes of monitoring treatment, the predetermined
level of the adenosine-associated biomarker can be from a normal or
healthy subject, a baseline adenosine-associated biomarker value
prior to treatment, the prior measured adenosine-associated
biomarker level in the same subject at an earlier time after
treatment, or a classification or stratification of the
adenosine-associated biomarker levels known to be associated with
disease progression or regression. For example, if the
adenosine-associated biomarker level is about the same as or below
(or decreased) as compared reference or control sample, the
treatment is indicated to be efficacious and the treatment can be
continued or discontinued or altered. For example, the
predetermined level of the adenosine-associated biomarker can be an
adenosine-associated biomarker level from a normal or healthy
tissue sample, and if the level of the adenosine-associated
biomarker measured in the subject after treatment is higher than
the normal the adenosine-associated biomarker levels, then
treatment is resumed or continued. For example, the predetermined
level of the adenosine-associated biomarker can be the
adenosine-associated biomarker levels as determined from a baseline
adenosine-associated biomarker value prior to treatment, and the
course of treatment determined accordingly. For example, if the
level of the adenosine-associated biomarker is the same as baseline
levels, then treatment is continued or resumed; if the level of the
adenosine-associated biomarker is higher than baseline levels, then
treatment is continued or resumed or treatment is accelerated or
increased (e.g. by increasing the dosage of ADA2 or increasing the
dose schedule in a dosage regimen cycle); if the level of the
adenosine-associated biomarker is less than baseline levels, then
treatment is continued or resumed, terminated or is reduced or
decreased (e.g. by decreasing the dosage of ADA2 or decreasing the
dose schedule in a dosage regimen cycle). In a further example, the
predetermined level of the adenosine-associated biomarker can be an
adenosine-associated biomarker level as determined in a prior
measurement in an earlier course of treatment of the same subject.
For example, if the level of the adenosine-associated biomarker is
the same as the earlier measured levels, then treatment is
continued or resumed; if the level of the adenosine-associated
biomarker is higher than the earlier measured levels, then
treatment is continued or resumed or treatment is accelerated or
increased (e.g. by increasing the dosage of ADA2 or increasing the
dose schedule in a dosage regimen cycle); if the level of the
adenosine-associated biomarker is less than the earlier measured
levels, then treatment is continued or resumed, terminated or is
reduced or decreased (e.g. by decreasing the dosage of ADA2 or
decreasing the dose schedule in a dosage regimen cycle).
[0926] In the monitoring methods or methods of determining efficacy
of treatment, the particular therapy can be altered during the
course of treatment to maximize individual response. Dosing and
scheduling of treatment can be modified in response to changing
levels. Combination therapy using other therapeutic agents, such as
other anti-cancer agents, also can be employed in such treatment
methods. It is within the level of the skill of the treating
physician to determine the exact course of treatment. For example,
the treatment can be altered, such that the dosing amount, schedule
(e.g frequency of administration), or regime is adjusted
accordingly, such as discontinued, decreased or made less frequent,
or combined with another treatment for the disease or condition. On
the other hand, if the adenosine-associated biomarker level is
above a compared reference or control sample, the patient is
indicated to be not responding to the treatment. In such instances,
the particular nature and type of the therapeutic agent, such as
ADA2 or combination therapy can be modified or changed. In other
instances, the dosing, amount, schedule and/or regime can be
adjusted accordingly, such as increased or made more frequent. It
is within the level of the treating physician to determine the
exact course of treatment.
[0927] For purposes of monitoring efficacy of treatment,
predetermined levels or amounts of the adenosine-associated
biomarker can be empirically determined, whereby the level or
amount indicates that the treatment is working. These predetermined
values can be determined by comparison or knowledge of the
adenosine-associated biomarker levels in a corresponding normal
sample or samples of disease subjects as determined by the same
assay of detection and using the same reagent. For example, high
levels of the adenosine-associated biomarker as assessed by
immunohistochemistry methods using a quantitative score scheme or
percentage of tumor staining for the adenosine-associated biomarker
of greater than 25% correlate to the existence of malignant disease
across a range of cancer types, and indicate that a patient is not
responding to treatment.
[0928] In the methods herein, the comparison to a predetermined
level or to levels of a control or reference sample can be
determined by any method known of skill in the art. For example,
the comparison of the level of the adenosine-associated biomarker
with a reference, control or predetermined level can be done by an
automated system, such as software program or intelligence system
that is part of, or compatible with, the equipment (e.g. computer
platform) on which the assay is carried out. Alternatively, this
comparison can be done by a physician or other trained or
experienced professional or technician.
[0929] 3. Dosages and Administration
[0930] Any ADA2 provided herein, including wildtype, variants and
modified forms thereof, can be formulated as pharmaceutical
compositions for single dosage or multiple dosage administration.
The ADA2 polypeptide is included in the composition in an amount
sufficient to exert a therapeutically useful effect in the absence
of undesirable side effects on the patient treated. The
therapeutically effective concentration can be determined
empirically by testing the polypeptides in known in vitro and in
vivo systems such as by using the assays provided herein or known
in the art (see e.g., Taliani et al. (1996) Anal. Biochem., 240:
60-67; Filocamo et al. (1997) J Virology, 71: 1417-1427; Sudo et
al. (1996) Antiviral Res. 32: 9-18; Bouffard et al. (1995)
Virology, 209:52-59; Bianchi et al. (1996) Anal. Biochem., 237:
239-244; Hamatake et al. (1996) Intervirology 39:249-258;
Steinkuhler et al. (1998) Biochem., 37:8899-8905; D'Souza et al.
(1995) J Gen. Virol., 76:1729-1736; Takeshita et al. (1997) Anal.
Biochem., 247:242-246; see also e.g., Shimizu et al. (1994) J
Virol. 68:8406-8408; Mizutani et al. (1996) J Virol. 70:7219-7223;
Mizutani et al. (1996) Biochem. Biophys. Res. Commun., 227:822-826;
Lu et al. (1996) Proc. Natl. Acad. Sci., 93:1412-1417; Hahm et al.,
(1996) Virology, 226:318-326; Ito et al. (1996) J Gen. Virol.,
77:1043-1054; Mizutani et al. (1995) Biochem. Biophys. Res.
Commun., 212:906-911; Cho et al. (1997) J Virol. Meth. 65:201-207)
and then extrapolated therefrom for dosages for humans.
[0931] The amount of any ADA2 provided herein to be administered
for the treatment of a disease or condition can be determined by
standard clinical techniques. In addition, in vitro assays and
animal models can be employed to help identify optimal dosage
ranges. The precise dosage, which can be determined empirically,
can depend on the particular agent, the route of administration,
the type of disease to be treated and the seriousness of the
disease. In some embodiments, the compositions administered can
contain nucleic acids that encode the variant ADA2 polypeptide
provided herein, such as oncolytic viral vectors or gene therapy
vectors, or cells, such as modified immune cells for adoptive
immunotherapy. Particular dosage can depend on the particular route
of administration, the particular disease or condition, the
severity of the disease or condition, the particular formulation
and other factors within the level of a skilled artisan.
[0932] Hence, it is understood that the precise dosage and duration
of treatment is a function of the disease being treated and can be
determined empirically using known testing protocols or by
extrapolation from in vivo or in vitro test data. It is to be noted
that concentrations and dosage values also can vary with the
severity of the condition to be alleviated. It is to be further
understood that for any particular subject, specific dosage
regimens should be adjusted over time according to the individual
need and the professional judgment of the person administering or
supervising the administration of the compositions, and that the
concentration ranges set forth herein are exemplary only and are
not intended to limit the scope or use of compositions and
combinations containing them. The compositions can be administered
hourly, daily, weekly, monthly, yearly or once. Generally, dosage
regimens are chosen to limit toxicity. It should be noted that the
attending physician would know how to and when to terminate,
interrupt or adjust therapy to lower dosage due to toxicity, or
bone marrow, liver or kidney or other tissue dysfunctions.
Conversely, the attending physician would also know how to and when
to adjust treatment to higher levels if the clinical response is
not adequate (precluding toxic side effects).
[0933] One of skill in the art can, in a clinical setting,
determine the individual dosage of ADA2 provided herein for
administration, depending on the clinical response of the tumor and
the side effect profile of an individual subject, such as a human
or an animal. For example, compositions of PEGylated ADA2 provided
herein, can be formulated at 25 U/mL. If a 25 g mouse is injected
with 0.2 mL of this formulation, this would translate into 200 U/kg
body weight. One of skill in the art can determine the human
equivalent dose (HED), based on body surface area, of approximately
16 U/kg body weight for humans. Appropriate HED can be calculated
using body surface area or body weight-based conversion
(Reagan-Shaw et al. (2008) The FASEB Journal 22(3):659-661).
[0934] The range of doses of any ADA2 provided herein can be from
or from about 10 mU/kg body weight to about 50 U/kg body weight or
higher. For example, a single dose can be 10 mU/kg body weight, 10
mU/kg, 20 mU/kg, 30 mU/kg, 40 mU/kg, 50 mU/kg, 60 mU/kg, 70 mU/kg,
80 mU/kg, 90 mU/kg, 100 mU/kg, 200 mU/kg, 300 mU/kg, 400 mU/kg, 500
mU/kg, 600 mU/kg, 700 mU/kg, 800 mU/kg, 900 mU/kg, 1 U/kg, 2 U/kg,
3 U/kg, 4 U/kg, 5 U/kg, 6 U/kg, 7 U/kg, 8 U/kg, 9 U/kg, 10 U/kg, 20
U/kg, 30 U/kg, 40 U/kg, or 50 U/kg body weight. In other examples,
a single dose can be between or between about 10 mU/kg body weight
and 50 U/kg body weight, 10 mU/kg and 40 U/kg, 10 mU/kg and 30
U/kg, 10 mU/kg and 20 U/kg, 10 mU/kg and 10 U/kg, 10 mU/kg and 9
U/kg, 10 mU/kg and 8 U/kg, 10 mU/kg and 7 U/kg, 10 mU/kg and 6
U/kg, 10 mU/kg and 5 U/kg, 10 mU/kg and 4 U/kg, 10 mU/kg and 3
U/kg, 10 mU/kg and 2 U/kg, 10 mU/kg and 1 U/kg, 10 mU/kg and 900
mU/kg, 10 mU/kg and 800 mU/kg, 10 mU/kg and 700 mU/kg, 10 mU/kg and
600 mU/kg, 10 mU/kg and 500 mU/kg, 10 mU/kg and 400 mU/kg, 10 mU/kg
and 300 mU/kg, 10 mU/kg and 200 mU/kg, 10 mU/kg and 100 mU/kg, 100
mU/kg and 50 U/kg, 100 mU/kg and 40 U/kg, 100 mU/kg and 30 U/kg,
100 mU/kg and 20 U/kg, 100 mU/kg and 10 U/kg, 100 mU/kg and 9 U/kg,
100 mU/kg and 8 U/kg, 100 mU/kg and 7 U/kg, 100 mU/kg and 6 U/kg,
100 mU/kg and 5 U/kg, 100 mU/kg and 4 U/kg, 100 mU/kg and 3 U/kg,
100 mU/kg and 2 U/kg, 100 mU/kg and 1 U/kg, 100 mU/kg and 900
mU/kg, 100 mU/kg and 800 mU/kg, 100 mU/kg and 700 mU/kg, 100 mU/kg
and 600 mU/kg, 100 mU/kg and 500 mU/kg, 100 mU/kg and 400 mU/kg,
100 mU/kg and 300 mU/kg, 100 mU/kg and 200 mU/kg, 500 mU/kg and 50
U/kg, 500 mU/kg and 40 U/kg, 500 mU/kg and 30 U/kg, 500 mU/kg and
20 U/kg, 500 mU/kg and 10 U/kg, 500 mU/kg and 9 U/kg, 500 mU/kg and
8 U/kg, 500 mU/kg and 7 U/kg, 500 mU/kg and 6 U/kg, 500 mU/kg and 5
U/kg, 500 mU/kg and 4 U/kg, 500 mU/kg and 3 U/kg, 500 mU/kg and 2
U/kg, 500 mU/kg and 1 U/kg, 500 mU/kg and 900 mU/kg, 500 mU/kg and
800 mU/kg, 500 mU/kg and 700 mU/kg, 500 mU/kg and 600 mU/kg, 1 U/kg
and 50 U/kg, 1 U/kg and 40 U/kg, 1 U/kg and 30 U/kg, 1 U/kg and 20
U/kg, 1 U/kg and 10 U/kg, 1 U/kg and 9 U/kg, 1 U/kg and 8 U/kg, 1
U/kg and 7 U/kg, 1 U/kg and 6 U/kg, 1 U/kg and 5 U/kg, 1 U/kg and 4
U/kg, 1 U/kg and 3 U/kg, 1 U/kg and 2 U/kg, 5 U/kg and 50 U/kg, 5
U/kg and 40 U/kg, 5 U/kg and 30 U/kg, 5 U/kg and 20 U/kg, 5 U/kg
and 10 U/kg, 5 U/kg and 9 U/kg, 5 U/kg and 8 U/kg, 5 U/kg and 7
U/kg, 5 U/kg and 6 U/kg, 10 U/kg and 50 U/kg, 10 U/kg and 40 U/kg,
10 U/kg and 30 U/kg, and 10 U/kg body weight and 20 U/kg body
weight.
[0935] In another example, the range of doses of any ADA2 provided
herein can be between or between about 0.1 mg/kg body weight and 50
mg/kg body weight, 0.1 mg/kg and 40 mg/kg, 0.1 mg/kg and 30 mg/kg,
0.1 mg/kg and 20 mg/kg, 0.1 mg/kg and 10 mg/kg, 0.1 mg/kg and 9
mg/kg, 0.1 mg/kg and 8 mg/kg, 0.1 mg/kg and 7 mg/kg, 0.1 mg/kg and
6 mg/kg, 0.1 mg/kg and 5 mg/kg, 0.1 mg/kg and 4 mg/kg, 0.1 mg/kg
and 3 mg/kg, 0.1 mg/kg and 2 mg/kg, 0.1 mg/kg and 1 mg/kg, 0.1
mg/kg and 0.9 mg/kg, 0.1 mg/kg and 0.8 mg/kg, 0.1 mg/kg and 0.7
mg/kg, 0.1 mg/kg and 0.6 mg/kg, 0.1 mg/kg and 0.5 mg/kg, 0.1 mg/kg
and 0.4 mg/kg, 0.1 mg/kg and 0.3 mg/kg, 0.1 mg/kg and 0.2 mg/kg,
0.5 mg/kg and 50 mg/kg, 0.5 mg/kg and 40 mg/kg, 0.5 mg/kg and 30
mg/kg, 0.5 mg/kg and 20 mg/kg, 0.5 mg/kg and 10 mg/kg, 0.5 mg/kg
and 9 mg/kg, 0.5 mg/kg and 8 mg/kg, 0.5 mg/kg and 7 mg/kg, 0.5
mg/kg and 6 mg/kg, 0.5 mg/kg and 5 mg/kg, 0.5 mg/kg and 4 mg/kg,
0.5 mg/kg and 3 mg/kg, 0.5 mg/kg and 2 mg/kg, 0.5 mg/kg and 1
mg/kg, 0.5 mg/kg and 0.9 mg/kg, 0.5 mg/kg and 0.8 mg/kg, 0.5 mg/kg
and 0.7 mg/kg, 0.5 mg/kg and 0.6 mg/kg, 1 mg/kg and 50 mg/kg, 1
mg/kg and 40 mg/kg, 1 mg/kg and 30 mg/kg, 1 mg/kg and 20 mg/kg, 1
mg/kg and 10 mg/kg, 1 mg/kg and 9 mg/kg, 1 mg/kg and 8 mg/kg, 1
mg/kg and 7 mg/kg, 1 mg/kg and 6 mg/kg, 1 mg/kg and 5 mg/kg, 1
mg/kg and 4 mg/kg, 1 mg/kg and 3 mg/kg, 1 mg/kg and 2 mg/kg, 2
mg/kg and 50 mg/kg, 2 mg/kg and 40 mg/kg, 2 mg/kg and 30 mg/kg, 2
mg/kg and 20 mg/kg, 2 mg/kg and 10 mg/kg, 2 mg/kg and 9 mg/kg, 2
mg/kg and 8 mg/kg, 2 mg/kg and 7 mg/kg, 2 mg/kg and 6 mg/kg, 2
mg/kg and 5 mg/kg, 2 mg/kg and 4 mg/kg, 2 mg/kg and 3 mg/kg, 5
mg/kg and 50 mg/kg, 5 mg/kg and 40 mg/kg, 5 mg/kg and 30 mg/kg, 5
mg/kg and 20 mg/kg, 5 mg/kg and 10 mg/kg, 5 mg/kg and 9 mg/kg, 5
mg/kg and 8 mg/kg, 5 mg/kg and 7 mg/kg, 5 mg/kg and 6 mg/kg, 10
mg/kg and 50 mg/kg, 10 mg/kg and 40 mg/kg, 10 mg/kg and 30 mg/kg,
10 mg/kg and 20 mg/kg, 20 mg/kg and 50 mg/kg, 20 mg/kg and 40
mg/kg, 20 mg/kg and 30 mg/kg, 30 mg/kg and 50 mg/kg, 30 mg/kg and
40 mg/kg, and 40 mg/kg body weight and 50 mg/kg body weight. The
dose can be administered a single time, or a multiple times.
Appropriate dose amount can be determined by one of skill in the
art, based on the regimen of administration. Total dose over a
specific period of time can also be selected by one of skill in the
art.
[0936] The optimal dose range for administration of compositions
containing any ADA2 provided herein, including wildtype, variants
and modified forms thereof, can be adjusted by plasma monitoring.
The dose of administration can be such that the subject will
maintain plasma ADA activity in the range of from about 10 to 1,000
mM/hr, and demonstrate a decline in erythrocyte adenosine, i.e.,
dATP less than or equal to about 0.001 to about 0.057 mM, for
example, about 0.005 to about 0.015 mM in packed erythrocytes, or
less than or equal to about 1% of the total erythrocyte adenosine
(i.e., ATP+dATP content), of the normal adenosine level, as
measured in a pre-administration sample. The normal value of dATP
is less than about 0.001 mM.
[0937] Accordingly, the method provided herein includes a method of
treating a tumor comprising administering an effective amount of
ADA2 to the subject. An effective amount is readily determined by
one of skill in the art to reduce tissue levels of adenosine or
deoxyadenosine in the subject, and wherein growth or spread of the
tumor is inhibited by substantially reduced tissue levels of
adenosine in the subject. Also provided herein are methods to
assess the level of adenosine-associated biomarkers in a subject to
select a subject for treatment with any ADA2 provided herein. Doses
or treatment regimen can be varied or adjusted based on the
susceptibility of the patient to the treatment, as determined by
one of skill in the art using the methods provided herein.
[0938] When ADA2 provided herein is co-formulated or
co-administered with another therapeutic agent, such as an immune
checkpoint inhibitor agent, a hyaluronan-degrading enzyme or an
antitumor agent, dosages can be provided as a ratio of the amount
of the ADA2 polypeptide to the amount of the other therapeutic
agent administered. For example, an ADA2 polypeptide can be
administered at 1 U ADA:1 U other therapeutic agent (1:1) to 50:1
or more, for example, at or about 1:1, 2:1, 3:1, 4:1, 5:1, 6:1,
7:1, 8:1, 9:1, 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 20:1, 25:1,
30:1, 35:1, 40:1, 45:1, 50:1 or more. In other examples, an ADA2
polypeptide can be administered at 1 U ADA:1 U other therapeutic
agent (1:1) to 1:50 or less, for example, at or about 1:2, 1:3,
1:4, 1:5, 1:6, 1:7, 1:8, 1:9, 1:10, 1:11, 1:12, 1:13, 1:14, 1:15,
1:20, 1:25, 1:30, 1:35, 1:40, 1:45, 1:50 or less.
[0939] 4. Combination Therapies
[0940] In the methods provided herein, ADA2 provided herein,
including wildtype, variants and modified forms thereof, can be
administered before, after, or concomitantly with one or more other
therapeutic regimens or agents. The skilled medical practitioner
can determine empirically, or by considering the pharmacokinetics
and modes of action of the agents, the appropriate dose or doses of
each therapeutic regimen or agent, as well as the appropriate
timings and methods of administration. The additional therapeutic
regimes or agents can improve the efficacy or safety of the ADA2
provided herein. In some examples, the additional therapeutic
regimes or agents can treat the same disease or a comorbidity
rather than to alter the action of the ADA2 provided herein. In
some examples, the additional therapeutic regimes or agents can
ameliorate, reduce or eliminate one or more side effects that are
associated with administration of any ADA2 provided herein.
[0941] For example, an ADA2 described herein can be administered
with chemotherapy, radiation therapy, or both chemotherapy and
radiation therapy. Any ADA2 provided herein, including wildtype,
variants and modified forms thereof can be administered in
combination with one or more other prophylactic or therapeutic
agents, including but not limited to antibodies, cytotoxic agents,
chemotherapeutic agents, cytokines, growth inhibitory agents,
anti-hormonal agents, kinase inhibitors, anti-angiogenic agents,
cardioprotectants, immunostimulatory agents, immunosuppressive
agents, immune checkpoint inhibitors, antibiotics, angiogenesis
inhibitors, or other therapeutic agents. The other therapeutic
agent used in combination with the treatment using ADA2 provided
herein, can be, for example, a protein, a peptide, a nucleic acid,
a small molecule agent, a toxin, a lipid, a carbohydrate or
combinations thereof, or any other type of therapeutic agent. In
other examples, the additional therapeutic regime can be radiation
therapy.
[0942] The one or more additional agents can be administered
simultaneously, sequentially or intermittently with any of the ADA2
provided herein thereof. The agents can be co-administered with the
ADA2 thereof, for example, as part of the same pharmaceutical
composition or same method of delivery. In some examples, the
agents can be co-administered with the ADA2 provided herein at the
same time as the ADA2 thereof, but by a different means of
delivery. The agents also can be administered at a different time
than administration of the ADA2 thereof, but close enough in time
to the administration of the ADA2 to have a combined prophylactic
or therapeutic effect. In some examples, the one or more additional
agents are administered subsequent to or prior to the
administration of the ADA2 provided herein, separated by a selected
time period. In some examples, the time period is 1 day, 2 days, 3
days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 1 month, 2
months, or 3 months. In some examples, the one or more additional
agents are administered multiple times and/or the ADA2 provided
herein is administered multiple times. In other examples, the ADA2
variants provided herein and the one or more additional agents that
are proteins, can be encoded in one or more expression vectors for
in vivo expression, particularly, tumor targeted or oncolytic
vectors for expression in tumor cells. In yet another example, the
ADA2 variant provided herein and the one or more additional agents
that are proteins, can be expressed in modified immune cells, and
the modified immune cells can be administered for adoptive
immunotherapy which can target and deliver ADA2 and additional
agent(s) to tumor cells in particular.
[0943] a. Anticancer Agents
[0944] The method of treatment using ADA2 provided herein can be
administered in combination with one or more anticancer agents
known in the art. The combination treatment of the present
invention includes administering ADA2 with an effective amount of
the anticancer agents described herein or known in the art,
simultaneously or sequentially. The anticancer agent can be, for
example, a chemotherapeutic, an antibody, a peptide, or a gene
therapy vector, virus or DNA or combinations thereof.
[0945] Exemplary of anticancer agents for the combination treatment
include, for example, Taxol.TM., bevacizumab (Avastin.RTM.),
vincristine, vinblastine, neomycin, combretastatin(s),
podophyllotoxin(s), TNF-.alpha., angiostatin, endostatin,
vasculostatin, .alpha.v-.beta.3 antagonists, calcium ionophores,
calcium-flux inducing agents, and any derivative or prodrug
thereof. The anticancer agents for combination therapy also include
chemotherapeutic agents, radiotherapeutic agents, cytokines,
anti-angiogenic agents, apoptosis-inducing agents or anticancer
immunotoxins or coaguligands, for example, Erbitux.RTM.
(cetuximab). Exemplary chemotherapeutic agents include but are not
limited to, 5-azacytidine, 5-fluorouracil, optionally in
combination with leucovorin, 5-fluorodeoxyuridine,
6-mercaptopurine, 6-thioguanine, mitoxantrone,
aziridinylbenzoquinone (AZQ), Carmustine (BCNU or BCNU;
Bristol-Myers Squibb), bleomycin, carboplatin (CBDCA), Lomustine
(CCNU), methyl-CCNU or MeCCNU, chlorambucil, chlorodeoxyadenosine,
cisplatin, cyclophosphamide, cytarabine, dactinomycin,
daunorubicin, deoxycoformycin, doxorubicin, doxycoformycin, DTIC
(dacarbazine), epirubicin, etoposide (VP-16), fludarabine,
hexamethylmelamine, hydroxyurea, idarubicin, ifosfamide, ifosfamide
and mesna, levamisol, N-acetylcysteine (NAC), 1-phenylalanine
mustard, 4'-(9-acridinylamino)methanesulfon-m-anisidide (mAMSA),
inhibitors of multiple drug resistance (i.e., MDR inhibitors),
melphalan, methotrexate, optionally in combination with leucovorin,
mithramycin, mitomycin-c, inhibitors of multidrug resistance
related protein ("MRP" inhibitors), paclitaxel, procarbazine,
streptozotocin, N,N'N'-triethylenethiophosphoramide ("thioTEPA"),
inhibitors of topoisomerase I and/or topoisomerase II, taxol,
vinblastine, vincristein, vincristine, vindesine, and teniposide
(VM-26.RTM.).
[0946] Other exemplary anti-cancer agents that can be administered
after, coincident with or before administration of any ADA2
provided herein, including wildtype, variants and modified forms
thereof, include, but are not limited to Acivicins; Aclarubicins;
Acodazoles; Acronines; Adozelesins; Aldesleukins; Alemtuzumabs;
Alitretinoins (9-Cis-Retinoic Acids); Allopurinols; Altretamines;
Alvocidibs; Ambazones; Ambomycins; Ametantrones; Amifostines;
Aminoglutethimides; Amsacrines; Anastrozoles; Anaxirones;
Ancitabines; Anthramycins; Apaziquones; Argimesnas; Arsenic
Trioxides; Asparaginases; Asperlins; Atrimustines; Azacitidines;
Azetepas; Azotomycins; Banoxantrones; Batabulins; Batimastats; BCG
Live; Benaxibines; Bendamustines; Benzodepas; Bexarotenes;
Bevacizumab; Bicalutamides; Bietaserpines; Biricodars; Bisantrenes;
Bisantrenes; Bisnafide Dimesylates; Bizelesins; Bleomycins;
Bortezomibs; Brequinars; Bropirimines; Budotitanes; Busulfans;
Cactinomycins; Calusterones; Canertinibs; Capecitabines;
Caracemides; Carbetimers; Carboplatins; Carboquones; Carmofurs;
Carmustines with Polifeprosans; Carmustines; Carubicins;
Carzelesins; Cedefingols; Celecoxibs; Cemadotins; Chlorambucils;
Cioteronels; Ciplactin; Cirolemycins; Cisplatins; Cladribines;
Clanfenurs; Clofarabines; Crisnatols; Cyclophosphamides; Cytarabine
liposomals; Cytarabines; Dacarbazines; Dactinomycins; Darbepoetin
Alfas; Daunorubicin liposomals; Daunorubicins/Daunomycins;
Daunorubicins; Decitabines; Denileukin Diftitoxes; Dexniguldipines;
Dexonas; Dexrazoxanes; Dezaguanines; Diaziquones; Dibrospidiums;
Dienogests; Dinalins; Disermolides; Docetaxels; Dofequidars;
Doxifluridines; Doxorubicin liposomals; Doxorubicin HCL;
Doxorubicin HCL liposome injection; Doxorubicins; Droloxifenes;
Dromostanolone Propionates; Duazomycins; Ecomustines; Edatrexates;
Edotecarins; Eflornithines; Elacridars; Elinafides; Elliott's B
Solutions; Elsamitrucins; Emitefurs; Enloplatins; Enpromates;
Enzastaurins; Epipropidines; Epirubicins; Epoetin alfas;
Eptaloprosts; Erbulozoles; Esorubicins; Estramustines;
Etanidazoles; Etoglucids; Etoposide phosphates; Etoposide VP-16s;
Etoposides; Etoprines; Exemestanes; Exisulinds; Fadrozoles;
Fazarabines; Fenretinides; Filgrastims; Floxuridines; Fludarabines;
Fluorouracils; 5-fluorouracils; Fluoxymesterones; Flurocitabines;
Fosquidones; Fostriecins; Fostriecins; Fotretamines; Fulvestrants;
Galarubicins; Galocitabines; Gemcitabines; Gemtuzumabs/Ozogamicins;
Geroquinols; Gimatecans; Gimeracils; Gloxazones; Glufosfamides;
Goserelin acetates; Hydroxyureas; Ibritumomabs/Tiuxetans;
Idarubicins; Ifosfamides; Ilmofosines; Ilomastats; Imatinib
mesylates; Imexons; Improsulfans; Indisulams; Inproquones;
Interferon alfa-2as; Interferon alfa-2bs; Interferon Alfas;
Interferon Betas; Interferon Gammas; Interferons; Interleukin-2s
and other Interleukins (including recombinant Interleukins);
Intoplicines; Iobenguanes [131-I]; Iproplatins; Irinotecans;
Irsogladines; Ixabepilones; Ketotrexates; L-Alanosines;
Lanreotides; Lapatinibs; Ledoxantrones; Letrozoles; Leucovorins;
Leuprolides; Leuprorelins (Leuprolides); Levamisoles;
Lexacalcitols; Liarozoles; Lobaplatins; Lometrexols;
Lomustines/CCNUs; Lomustines; Lonafarnibs; Losoxantrones;
Lurtotecans; Mafosfamides; Mannosulfans; Marimastats; Masoprocols;
Maytansines; Mechlorethamines; Mechlorethamines/Nitrogen mustards;
Megestrol acetates; Megestrols; Melengestrols; Melphalans;
Melphalan L-PAMs; Menogarils; Mepitiostanes; Mercaptopurines;
6-Mecaptopurine; Mesnas; Metesinds; Methotrexates; Methoxsalens;
Metomidates; Metoprines; Meturedepas; Miboplatins; Miproxifenes;
Misonidazoles; Mitindomides; Mitocarcins; Mitocromins;
Mitoflaxones; Mitogillins; Mitoguazones; Mitomalcins; Mitomycin Cs;
Mitomycins; Mitonafides; Mitoquidones; Mitospers; Mitotanes;
Mitoxantrones; Mitozolomides; Mivobulins; Mizoribines; Mofarotenes;
Mopidamols; Mubritinibs; Mycophenolic Acids; Nandrolone
Phenpropionates; Nedaplatins; Nelarabines; Nemorubicins;
Nitracrines; Nocodazoles; Nofetumomabs; Nogalamycins; Nolatrexeds;
Nortopixantrones; Octreotides; Oprelvekins; Ormaplatins;
Ortataxels; Oteracils; Oxaliplatins; Oxisurans; Oxophenarsines;
Paclitaxels; Pamidronates; Patupilones; Pegademases; Pegaspargases;
Pegfilgrastims; Peldesines; Peliomycins; Pelitrexols; Pemetrexeds;
Pentamustines; Pentostatins; Peplomycins; Perfosfamides;
Perifosines; Picoplatins; Pinafides; Pipobromans; Piposulfans;
Pirfenidones; Piroxantrones; Pixantrones; Plevitrexeds; Plicamycin
Mithramycins; Plicamycins; Plomestanes; Plomestanes; Porfimer
sodiums; Porfimers; Porfiromycins; Prednimustines; Procarbazines;
Propamidines; Prospidiums; Pumitepas; Puromycins; Pyrazofurins;
Quinacrines; Ranimustines; Rasburicases; Riboprines; Ritrosulfans;
Rituximabs; Rogletimides; Roquinimexs; Rufocromomycins;
Sabarubicins; Safingols; Sargramostims; Satraplatins; Sebriplatins;
Semustines; Simtrazenes; Sizofirans; Sobuzoxanes; Sorafenibs;
Sparfosates; Sparfosic Acids; Sparsomycins; Spirogermaniums;
Spiromustines; Spiroplatins; Spiroplatins; Squalamines;
Streptonigrins; Streptovarycins; Streptozocins; Sufosfamides;
Sulofenurs; Sunitinib Malate; 6-TG; Tacedinalines; Talcs;
Talisomycins; Tallimustines; Tamoxifens; Tariquidars;
Tauromustines; Tecogalans; Tegafurs; Teloxantrones; Temoporfins;
Temozolomides; Teniposides/VM-26s; Teniposides; Teroxirones;
Testolactones; Thiamiprines; Thioguanines; Thiotepas; Tiamiprines;
Tiazofurins; Tilomisoles; Tilorones; Timcodars; Timonacics;
Tirapazamines; Topixantrones; Topotecans; Toremifenes;
Tositumomabs; Trabectedins (Ecteinascidin 743); Trastuzumabs;
Trestolones; Tretinoins/ATRA; Triciribines; Trilostanes;
Trimetrexates; Triplatin Tetranitrates; Triptorelins;
Trofosfamides; Tubulozoles; Ubenimexs; Uracil Mustards; Uredepas;
Valrubicins; Valspodars; Vapreotides; Verteporfins; Vinblastines;
Vincristines; Vindesines; Vinepidines; Vinflunines; Vinformides;
Vinglycinates; Vinleucinols; Vinleurosines; Vinorelbines;
Vinrosidines; Vintriptols; Vinzolidines; Vorozoles; Xanthomycin A's
(Guamecyclines); Zeniplatins; Zilascorbs [2-H]; Zinostatins;
Zoledronate; Zorubicins; and Zosuquidars; Aldesleukins (e.g.,
PROLEUKIN.RTM.); Alemtuzumabs (e.g., CAMPATH.RTM.); Alitretinoins
(e.g., PANRETIN.RTM.); Allopurinols (e.g., ZYLOPRIM.RTM.);
Altretamines (e.g., HEXALEN.RTM.); Amifostines (e.g., ETHYOL.RTM.);
Anastrozoles (e.g., ARIMIDEX.RTM.); Arsenic Trioxides (e.g.,
TRISENOX.RTM.); Asparaginases (e.g., ELSPAR.RTM.); BCG Live (e.g.,
TICE.RTM. BCG); Bexarotenes (e.g., TARGRETIN.RTM.); Bevacizumab
(AVASTIN.RTM.); Bleomycins (e.g., BLENOXANE.RTM.); Busulfan
intravenous (e.g., BUSULFEX.RTM.); Busulfan orals (e.g.,
MYLERAN.TM.); Calusterones (e.g., METHOSARB.RTM.); Capecitabines
(e.g., XELODA.RTM.); Carboplatins (e.g., PARAPLATIN.RTM.);
Carmustines (e.g., BCNU.RTM., BiCNU.RTM.); Carmustines with
Polifeprosans (e.g., GLIADEL.RTM. Wafer); Celecoxibs (e.g.,
CELEBREX.RTM.); Chlorambucils (e.g., LEUKERAN.RTM.); Cisplatins
(e.g., PLATINOL.RTM.); Cladribines (e.g., LEUSTATIN.RTM.,
2-CdA.RTM.); Cyclophosphamides (e.g., CYTOXAN.RTM., NEOSAR.RTM.);
Cytarabines (e.g., CYTOSAR-U.RTM.); Cytarabine liposomals (e.g.,
DepoCyt.RTM.); Dacarbazines (e.g., DTIC-Domeu): Dactinomycins
(e.g., COSMEGEN.RTM.); Darbepoetin Alfas (e.g., ARANESP.RTM.);
Daunorubicin liposomals (e.g. DAUNOXOME.RTM.);
Daunorubicins/Daunomycins (e.g., CERUBIDINE.RTM.); Denileukin
Diftitoxes (e.g., ONTAK.RTM.); Dexrazoxanes (e.g., ZINECARD.RTM.);
Docetaxels (e.g., TAXOTERE.RTM.); Doxorubicins (e.g.,
ADRIAMYCIN.RTM., RUBEX.RTM.); Doxorubicin liposomals, including
Doxorubicin HCL liposome injections (e.g., DOXIL.RTM.);
Dromostanolone propionates (e.g., DROMOSTANOLONE.RTM. and
MASTERONE.RTM. Injection); Elliott's B Solutions (e.g., Elliott's B
Solution.RTM.); Epirubicins (e.g., ELLENCE.RTM.); Epoetin alfas
(e.g., EPOGEN.RTM.); Estramustines (e.g., EMCYT.RTM.); Etoposide
phosphates (e.g., ETOPOPHOS.RTM.); Etoposide VP-16s (e.g.,
VEPESID.RTM.); Exemestanes (e.g., AROMASIN.RTM.); Filgrastims
(e.g., NEUPOGEN.RTM.); Floxuridines (e.g., FUDR.RTM.); Fludarabines
(e.g., FLUDARA.RTM.); Fluorouracils incl. 5-FUs (e.g.,
ADRUCIL.RTM.); Fulvestrants (e.g., FASLODEX.RTM.); Gemcitabines
(e.g., GEMZAR.RTM.); Gemtuzumabs/Ozogamicins (e.g., MYLOTARG.RTM.);
Goserelin acetates (e.g., ZOLADEX.RTM.); Hydroxyureas (e.g.,
HYDREA.RTM.); Ibritumomabs/Tiuxetans (e.g., ZEVALIN.RTM.);
Idarubicins (e.g., IDAMYCIN.RTM.); Ifosfamides (e.g., IFEX.RTM.);
Imatinib mesylates (e.g., GLEEVEC.RTM.); Interferon alfa-2as (e.g.,
ROFERON-A.RTM.); Interferon alfa-2bs (e.g., INTRON A.RTM.);
Irinotecans (e.g., CAMPTOSAR.RTM.); Letrozoles (e.g., FEMARA.RTM.);
Leucovorins (e.g., WELLCOVORIN.RTM., LEUCOVORIN.RTM.); Levamisoles
(e.g., ERGAMISOL.RTM.); Lomustines/CCNUs (e.g., CeeNU.RTM.);
Mechlorethamines/Nitrogen mustards (e.g., MUSTARGEN.RTM.);
Megestrol acetates (e.g., MEGACE.RTM.); Melphalans/L-PAMs (e.g.,
ALKERAN.RTM.); Mercaptopurine incl. 6-MPs (e.g., PURINETHOL.RTM.);
Mesnas (e.g., MESNEX.RTM.); Methotrexates; Methoxsalens (e.g.,
UVADEX.RTM.); Mitomycin Cs (e.g., MUTAMYCIN.RTM., MITOZYTREX.RTM.);
Mitotanes (e.g., LYSODREN.RTM.); Mitoxantrones (e.g.,
NOVANTRONE.RTM.); Nandrolone Phenpropionates (e.g.,
DURABOLIN-50.RTM.); Nofetumomabs (e.g., VERLUMA.RTM.); Oprelvekins
(e.g., NEUMEGA.RTM.); Oxaliplatins (e.g., ELOXATIN.RTM.);
Paclitaxels (e.g., PAXENE.RTM., TAXOL.RTM.); Pamidronates (e.g.,
AREDIA.RTM.); Pegademases (e.g., ADAGEN.RTM.); Pegaspargases (e.g.,
ONCASPAR.RTM.); Pegfilgrastims (e.g., NEULASTA.RTM.); Pentostatins
(e.g., NIPENT.RTM.); Pipobromans (e.g., VERCYTE.RTM.);
Plicamycin/Mithramycins (e.g., MITHRACIN.RTM.); Porfimer sodiums
(e.g., PHOTOFRIN.RTM.); Procarbazines (e.g., MATULANE.RTM.);
Quinacrines (e.g., ATABRINE.RTM.); Rasburicases (e.g.,
ELITEK.RTM.); Rituximabs (e.g., RITUXAN.RTM.); Sargramostims (e.g.,
PROKINE.RTM.); Streptozocins (e.g., ZANOSAR.RTM.); Sunitinib
Malates (e.g., SUTENT.RTM.); Talcs (e.g., SCLEROSOL.RTM.);
Tamoxifens (e.g., NOLVADEX.RTM.); Temozolomides (e.g.,
TEMODAR.RTM.); Teniposides/VM-26s (e.g., VUMON.RTM.); Testolactones
(e.g., TESLAC.RTM.); Thioguanines incl. 6-TG; Thiotepas (e.g.,
THIOPLEX.RTM.); Topotecans (e.g., HYCAMTIN.RTM.); Toremifenes
(e.g., FARESTON.RTM.); Tositumomabs (e.g., BEXXAR.RTM.);
Trastuzumabs (e.g., HERCEPTIN.RTM.); Tretinoins/ATRA (e.g.,
VESANOID.RTM.); Uracil Mustards; Valrubicins (e.g., VALSTAR.RTM.);
Vinblastines (e.g., VELBAN.RTM.); Vincristines (e.g.,
ONCOVIN.RTM.); Vinorelbines (e.g., NAVELBINE.RTM.); and
Zoledronates (e.g., ZOMETA.RTM.). Any ADA2 provided herein can be
used in combination therapy with other anticancer agents, such as
those provided herein and/or those described in Goodman and
Gilman's The Pharmacological Basis of Therapeutics, Eds. Hardman
and Limbird, Tenth edition (2002).
[0947] i. Anticancer Antibodies
[0948] Examples of anti-cancer antibodies that can be
co-administered with any ADA2 provided herein include, but are not
limited to, anti 17-IA cell surface antigen antibodies such as
Panorex.RTM. (edrecolomab); anti-4-1BB antibodies; anti-4Dc
antibodies; anti-A33 antibodies such as A33 and CDP-833;
anti-.alpha.1 integrin antibodies such as natalizumab;
anti-.alpha.4.beta.7 integrin antibodies such as LDP-02;
anti-.alpha.V.beta.1 integrin antibodies such as F-200, M-200, and
SJ-749; anti-.alpha.B.beta.3 integrin antibodies such as abciximab,
CNTO-95, Mab-17E6, and Vitaxin.RTM.; anti-complement factor 5 (C5)
antibodies such as 5G1.1; anti-CA125 antibodies such as OvaRex.RTM.
(oregovomab); anti-CD3 antibodies such as Nuvion.RTM. (visilizumab)
and Rexomab; anti-CD4 antibodies such as IDEC-151, MDX-CD4, OKT4A;
anti-CD6 antibodies such as Oncolysin B and Oncolysin CD6; anti-CD7
antibodies such as HB2; anti-CD19 antibodies such as B43, MT-103,
and Oncolysin B; anti-CD20 antibodies such as 2H7, 2H7.v16,
2H7.v114, 2H7.v115, Bexxar.RTM. (tositumomab), Rituxan.RTM.
(rituximab), and Zevalin.RTM. (Ibritumomab tiuxetan); anti-CD22
antibodies such as Lymphocide.RTM. (epratuzumab); anti-CD23
antibodies such as IDEC-152; anti-CD25 antibodies such as
basiliximab and Zenapax.RTM. (daclizumab); anti-CD30 antibodies
such as AC10, MDX-060, and SGN-30; anti-CD33 antibodies such as
Mylotarg.RTM. (gemtuzumab ozogamicin), Oncolysin M, and Smart MI
95; anti-CD38 antibodies; anti-CD40 antibodies such as SGN-40 and
toralizumab; anti-CD40L antibodies such as 5c8, Antova.RTM., and
IDEC-131; anti-CD44 antibodies such as bivatuzumab; anti-CD46
antibodies; anti-CD52 antibodies such as Campath.RTM.
(alemtuzumab); anti-CD55 antibodies such as SC-1; anti-CD56
antibodies such as huN901-DM1; anti-CD64 antibodies such as MDX-33;
anti-CD66e antibodies such as XR-303; anti-CD74 antibodies such as
IMMU-1 10; anti-CD80 antibodies such as galiximab and IDEC-1 14;
anti-CD89 antibodies such as MDX-214; anti-CD123 antibodies;
anti-CD138 antibodies such as B-B4-DM1; anti-CD146 antibodies such
as AA-98; anti-CD148 antibodies; anti-CEA antibodies such as
cT84.66, labetuzumab, and Pentacea.RTM.; anti-CTLA4 antibodies such
as MDX-101; anti-CXCR4 antibodies; anti-EGFR antibodies such as
ABX-EGF, Erbitux.RTM. (cetuximab), IMC-C225, and Merck Mab 425;
anti-EpCAM antibodies such as Crucell's anti-EpCAM, ING-1, and
IS-IL-2; anti-ephrin B2/EphB4 antibodies; anti-Her2 antibodies such
as Herceptin.RTM.), MDX-210; anti-FAP (fibroblast activation
protein) antibodies such as sibrotuzumab; anti-ferritin antibodies
such as NXT-211; anti-FGF-1 antibodies; anti-FGF-3 antibodies;
anti-FGF-8 antibodies; anti-FGFR antibodies, anti-fibrin
antibodies; anti-G250 antibodies such as WX-G250 and Rencarex.RTM.;
anti-GD2 ganglioside antibodies such as EMD-273063 and TriGem;
anti-GD3 ganglioside antibodies such as BEC2, KW-2871, and
mitumomab; anti-gpIIb/IIIa antibodies such as ReoPro;
anti-heparinase antibodies; anti-Her2/ErbB2 antibodies such as
Herceptin.RTM. (trastuzumab), MDX-210, and pertuzumab; anti-HLA
antibodies such as Oncolym.RTM., Smart 1D10; anti-HM1.24
antibodies; anti-ICAM antibodies such as ICM3; anti-IgA receptor
antibodies; anti-IGF-1 antibodies such as CP-751871 and EM-164;
anti-IGF-1R antibodies such as IMC-A12; anti-IL-6 antibodies such
as CNTO-328 and elsilimomab; anti-IL-15 antibodies such as
HuMax.RTM.-IL15; anti-KDR antibodies; anti-laminin 5 antibodies;
anti-Lewis Y antigen antibodies such as Hu3S193 and IGN-311;
anti-MCAM antibodies; anti-Muc1 antibodies such as BravaRex and
TriAb; anti-NCAM antibodies such as ERIC-1 and ICRT; anti-PEM
antigen antibodies such as Theragyn and Therex; anti-PSA
antibodies; anti-PSCA antibodies such as IG8; anti-Ptk antibodies;
anti-PTN antibodies; anti-RANKL antibodies such as AMG-162;
anti-RLIP76 antibodies; anti-SK-1 antigen antibodies such as
Monopharm C; anti-STEAP antibodies; anti-TAG72 antibodies such as
CC49-SCA and MDX-220; anti-TGF-.beta. antibodies such as CAT-152;
anti-TNF-.alpha. antibodies such as CDP571, CDP870, D2E7,
Humira.RTM. (adalimumab), and Remicade.RTM. (infliximab);
anti-TRAIL-R1 and TRAIL-R2 antibodies; anti-VE-cadherin-2
antibodies; and anti-VLA-4 antibodies such as Antegren.RTM..
Furthermore, anti-idiotype antibodies including but not limited to
the GD3 epitope antibody BEC2 and the gp72 epitope antibody 105AD7,
can be used. In addition, bispecific antibodies including but not
limited to the anti-CD3/CD20 antibody Bi20 can be used.
[0949] ii. Chemotherapeutic Agents
[0950] In some examples, any ADA2 provided herein, including
wildtype, variants and modified forms thereof, is administered with
one or more chemotherapeutic agents. Examples of chemotherapeutic
agents include but are not limited to alkylating agents such as
thiotepa and cyclophosphamide (CYTOXAN.RTM.); alkyl sulfonates such
as busulfan, improsulfan and piposulfan; androgens such as
calusterone, dromostanolone propionate, epitiostanol, mepitiostane,
testolactone; anti-adrenals such as aminoglutethimide, mitotane,
trilostane; anti-androgens such as flutamide, nilutamide,
bicalutamide, leuprolide, and goserelin; antibiotics such as
aclacinomycins, actinomycin, anthramycin, azaserine, bleomycins,
cactinomycin, calicheamicin, carubicin, carminomycin,
carzinophilin, chromomycins, dactinomycin, daunorubicin,
detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin, epirubicin,
esorubicin, idarubicin, marcellomycin, mitomycins, mycophenolic
acid, nogalamycin, olivomycins, peplomycin, porfiromycin,
puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin,
tubercidin, ubenimex, zinostatin, zorubicin; anti estrogens
including for example tamoxifen, raloxifene, aromatase inhibiting
4(5)-imidazoles, 4-hydroxytamoxifen, trioxifene, keoxifene, LY
117018, onapristone, and toremifene (Fareston); anti-metabolites
such as methotrexate and 5-fluorouracil (5-FU); folic acid
analogues such as denopterin, methotrexate, pteropterin,
trimetrexate; aziridines such as benzodepa, carboquone, meturedepa,
and uredepa; ethylenimines and methylmelamines including
altretamine, triethylenemelamine, triethylenephosphoramide,
triethylenethiophosphoramide and trimethylol melamine; folic acid
replenisher such as folinic acid; nitrogen mustards such as
chlorambucil, chlornaphazine, chlorophosphamide, estramustine,
ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride,
melphalan, novembichin, phenesterine, prednimustine, trofosfamide,
uracil mustard; nitrosoureas such as carmustine, chlorozotocin,
fotemustine, lomustine, nimustine, ranimustine; platinum analogs
such as cisplatin and carboplatin; vinblastine; platinum; proteins
such as arginine deiminase and asparaginase; purine analogs such as
fludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidine
analogs such as ancitabine, azacitidine, 6-azauridine, carmofur,
cytarabine, dideoxyuridine, doxifluridine, enocitabine,
floxuridine, 5-FU; taxanes, e.g. paclitaxel (TAXOL.RTM.,
Bristol-Myers Squibb Oncology, Princeton, N.J.) and docetaxel
(TAXOTERE.RTM.), Rhone-Poulenc Rorer, Antony, France);
topoisomerase inhibitor RFS 2000; thymidylate synthase inhibitor
(such as Tomudex); additional chemotherapeutics including
aceglatone; aldophosphamide glycoside; aminolevulinic acid;
amsacrine; bestrabucil; bisantrene; edatrexate; defosfamide;
demecolcine; diaziquone; difluoromethylornithine (DMFO);
eflornithine; elliptinium acetate; etoglucid; gallium nitrate;
hydroxyurea; lentinan; lonidamine; mitoguazone; mitoxantrone;
mopidamol; nitracrine; pentostatin; phenamet; pirarubicin;
podophyllinic acid; 2-ethylhydrazide; procarbazine; PSK.RTM.;
razoxane; sizofiran; spirogermanium; tenuazonic acid; triaziquone;
2,2',2''-trichlorotriethylamine; urethan; vindesine; dacarbazine;
mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine;
arabinoside ("Ara-C"); cyclophosphamide; thiotepa; chlorambucil;
gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; etoposide
(VP-16); ifosfamide; mitomycin C; mitoxantrone; vincristine;
vinorelbine; Navelbine; Novantrone; teniposide; daunomycin;
aminopterin; Xeloda; ibandronate; CPT-11; retinoic acid;
esperamycins; capecitabine; and topoisomerase inhibitors such as
irinotecan. Pharmaceutically acceptable salts, acids or derivatives
of any of the above can also be used.
[0951] A chemotherapeutic agent can be administered as a prodrug.
Examples of prodrugs that can be administered with any ADA2
provided herein include, but are not limited to,
phosphate-containing prodrugs, thiophosphate-containing prodrugs,
sulfate-containing prodrugs, peptide-containing prodrugs, D-amino
acid-modified prodrugs, glycosylated prodrugs,
beta-lactam-containing prodrugs, optionally substituted phenoxy
acetamide-containing prodrugs or optionally substituted
phenylacetamide-containing prodrugs, 5-fluorocytosine and other
5-fluorouridine prodrugs which can be converted into the more
active cytotoxic free drug.
[0952] iii. Radiation Therapy
[0953] Any ADA2 provided herein, including wildtype, variants and
modified forms thereof, can be combined with other therapeutic
regimens. For example, in one embodiment, the patient to be treated
with any ADA2 provided herein can receive radiation therapy.
Radiation therapy can be administered according to protocols
commonly employed in the art and known to the skilled artisan. Such
therapy includes but is not limited to cesium, iridium, iodine,
cobalt radiation, irradiation with X-rays, gamma rays, including
both direct irradiation and with tomographic targeting, treatment
of cancerous tissues with implanted radioactive pellets or "seeds,"
neutron beam irradiation of tissues primed with boron compounds,
and/or other types of particle beam therapy known in the art. The
radiation therapy can be whole body irradiation, or can be directed
locally to a specific site or tissue in or on the body, such as the
lung, bladder, or prostate. Typically, radiation therapy is
administered in pulses over a period of time from about 1 to 2
weeks. The radiation therapy can, however, be administered over
longer periods of time. For instance, radiation therapy can be
administered to patients having head and neck cancer for about 6 to
about 7 weeks. Optionally, the radiation therapy can be
administered as a single dose or as multiple, sequential doses. The
skilled medical practitioner can determine empirically the
appropriate dose or doses of radiation therapy useful herein. In
some examples, any ADA2 provided herein, including wildtype,
variants and modified forms thereof and optionally one or more
other anti-cancer therapies are employed to treat cancer cells ex
vivo. It is contemplated that such ex vivo treatment can be useful
in bone marrow transplantation and particularly, autologous bone
marrow transplantation. For instance, treatment of cells or
tissue(s) containing cancer cells with any ADA2 provided herein and
one or more anti-cancer therapies can be employed to deplete or
substantially deplete the cancer cells prior to transplantation in
a recipient patient. Radiation therapy can also comprise treatment
with an isotopically labeled molecule, such as an antibody.
Examples of radioimmunotherapeutics include but Zevalin.RTM. (Y-90
labeled anti-CD20), LymphoCide.RTM. (Y-90 labeled anti-CD22) and
Bexxar.RTM. (1-131 labeled anti-CD20). In addition, it is
contemplated that any ADA2 provided herein, including wildtype,
variants and modified forms thereof, can be administered to a
patient or subject in combination with still other therapeutic
techniques such as surgery or phototherapy.
[0954] iv. Anti-Angiogenic Agents
[0955] In some examples, any ADA2 provided herein, including
wildtype, variants and modified forms thereof, is administered with
one or more anti-angiogenic agents. For example, the
anti-angiogenic factor can be a small molecule or a protein (e.g.,
an antibody, Fc fusion, or cytokine) that binds to a growth factor
or growth factor receptor involved in promoting angiogenesis.
Examples of anti-angiogenic agents include but are not limited to
antibodies that bind to Vascular Endothelial Growth Factor (VEGF)
or that bind to VEGF-R, RNA-based therapeutics that reduce levels
of VEGF or VEGF-R expression, VEGF-toxin fusions, Regeneron's
VEGF-trap, angiostatin (plasminogen fragment), antithrombin III,
angiozyme, ABT-627, Bay 12-9566, BeneFin, bevacizumab,
bisphosphonates, BMS-275291, cartilage-derived inhibitor (CDI),
CAI, CD59 complement fragment, CEP-7055, Col 3, Combretastatin A-4,
endostatin (collagen XVIII fragment), farnesyl transferase
inhibitors, fibronectin fragment, gro-beta, halofuginone,
heparinases, heparin hexasaccharide fragment, HMV833, human
chorionic gonadotropin (hCG), IM-862, interferon alpha, interferon
beta, interferon gamma, interferon inducible protein 10 (IP-10),
interleukin-12, kringle 5 (plasminogen fragment), marimastat,
metalloproteinase inhibitors (e.g. TIMPs), 2-methoxyestradiol, MMI
270 (CGS 27023A), plasminogen activator inhibitor (PAI), platelet
factor-4 (PF4), prinomastat, prolactin 16 kDa fragment,
proliferin-related protein (PRP), PTK 787/ZK 222594, retinoids,
solimastat, squalamine, SS3304, SU5416, SU6668, SU11248,
tetrahydrocortisol-S, tetrathiomolybdate, thalidomide,
thrombospondin-1 (TSP-1), TNP470, transforming growth factor beta
(TGF-.beta.), vasculostatin, vasostatin (calreticulin fragment),
ZS6126, and ZD6474.
[0956] v. Immune Checkpoint Inhibitors
[0957] In some examples, any ADA2 provided herein, including
wildtype, variants and modified forms thereof, is administered with
one or more agents that increases the immune response by blocking
an immune checkpoint protein (i.e., immune checkpoint inhibitor).
In the combination therapies provided herein, the immune checkpoint
inhibitor can be an antibody directed against an immune checkpoint
protein, such as an antibody directed against cytotoxic
T-lymphocyte antigen 4 (CTLA4 or CD152), programmed cell death
protein 1 (PD-1), or programmed cell death protein 1 ligand 1
(PD-L1).
[0958] In particular, the combination therapy provided herein is
applicable to treating all types of tumors, including cancers, that
are associated with elevated adenosine levels and/or susceptible to
a reduction in adenosine or deoxyadenosine levels in the subject to
be treated. Broadly, these include tumors of the blood as well as
solid tumors. Exemplary cancers include, but are not limited to,
those that originate in the immune system, skeletal system, muscles
and heart, breast, gastrointestinal tract, central and peripheral
nervous system, renal system, reproductive system, respiratory
system, skin, connective tissue systems, including joints, fatty
tissues, and circulatory system, including blood vessel walls.
[0959] Therapies for treating cancers include immunotherapies
(e.g., inhibitory checkpoint protein antagonists or agonists) that
inhibit immunosuppressive signaling or enhance immunostimulant
signaling Instead of directly targeting the tumor itself, such
therapies use the host's endogenous defenses to combat the tumor.
For example, inhibitory checkpoint protein antagonists and/or
agonists of co-stimulatory receptors can stimulate a host's
endogenous anti-tumor immune response by amplifying
antigen-specific T cell responses. Enhancing the host's immune
response offers the advantage over cytotoxic therapies in that the
effects can be long lasting, such that the subject can develop a
durable anti-tumor response that can persist for months to years
after cessation of treatment.
[0960] In particular examples, the combination therapies provided
herein employ an agent (e.g., antibody) that targets an inhibitory
checkpoint protein. Exemplary inhibitory immune checkpoint target
proteins and therapeutic antibodies for the targets are provided in
Table 5.
TABLE-US-00005 TABLE 5 Exemplary inhibitory immune checkpoint
target proteins and inhibitors Antibody/fusion Target Target
Function protein Synonyms and Code Names CTLA4 Inhibitory receptor
Ipilimumab (MDX-CTLA4; BMS-734016; MDX- Tremelimumab 010)
(ticilimumab; CP-675,206) PD-1 Inhibitory receptor MK-3475
(Pembrolizumab; Lambrolizumab; SCH AMP-224 900475) Nivolumab
(anti-PD-1 fusion protein AMP-224) Pidilizumab (BMS-936558;
MDX-1106; ONO- 4538) (CT-011) PD-L1 Ligand for PD-1 MDX-1105
(RG7446) BMS-936559 MED14736 MPDL33280A LAG3 Inhibitory receptor
IMP321 ImmuFact B7-H3 Inhibitory ligand MGA271 B7-H4 Inhibitory
ligand TIM3 Inhibitory receptor CD25 inhibitory receptor subunit
CD137 stimulatory receptor OX40 stimulatory receptor 4-1BB
co-stimulatory Aptamer ligand receptor IDO immunosuppressive
enzyme
[0961] In particular, inhibitors of the immunologic inhibitory
molecules CTLA4, PD-1 and PD-L1 are contemplated for the
combinations and methods provided herein. While both CTLA4 and PD-1
function as negative regulators, each places a non-redundant role
in modulating immune responses: CTLA4 is involved in attenuating
the early activation of naive and memory (resting) T cells, whereas
PD-1 plays a role in modulating T cell activity in peripheral
tissues (see, e.g., Keir et al. (2008) Annu Rev Immunol.
26:677-704; Pardoll, (2012) Nat Rev Cancer. 12(4):252-264; Quezada
et al., (2013) Br J Cancer. 108(8): 1560-1565; Callahan et al.,
(2010) Semin Oncol. 37(5):473-84).
[0962] Cytotoxic T-lymphocyte-associated antigen 4 (CTLA4; also
called CD152; SEQ ID NO:544) is a co-inhibitory receptor that is
packaged in vesicles that are maintained in the cytoplasm of naive
or resting T cells. When T cell activation is initiated,
transportation of the vesicles containing CTLA4 to the surface of
the T cell is also triggered. The inhibitory activity of CTLA4 acts
to dampen the amplitude of the stimulatory signals. In this role,
CTLA4 functions to reduce T-cell activity and thereby limit
autoimmunity. CTLA4 also plays a role in down-modulation of helper
T cell activity and in enhancing regulatory T (T.sub.reg) cell
activity Inhibition of CTLA4, for example by administering
anti-CTLA4 antibodies, can enhance the immune response by
increasing the activity of CTLs, increasing the presence of
effector and helper T cells and/or by inhibiting the suppressive
functions of T.sub.reg cells. Inhibition of CTLA4 allows full
activation of the T cells during the priming phase of the immune
response.
[0963] Upon T cell activation and entry into the bloodstream,
expression of programmed cell death protein 1 (PD-1; SEQ ID
NO:545), a receptor that inhibits T cell activation, is induced.
PD-1 also is present on regulatory T (T.sub.reg) cells, exhausted T
cells, activated B cells, natural killer (NK) cells, dendritic
cells (DCs) and activated monocytes. PD-1 has two principal
ligands, PD-1 ligand 1 (PD-L1; also called B7-H1 or CD274; SEQ ID
NO:546) and PD-L2 (also called B7-DC or CD273). Inflammatory
signals in tissues induce the expression of PD-L1 and PD-L2. Upon
binding one of its ligands, PD-1 acts to attenuate T cell activity,
by inhibiting signaling of the T cell receptor (TCR),
downregulation the secretion of immunostimulatory cytokines and
expression of survival proteins, and increasing T cell production
of the immunosuppressive cytokine IL-10. These activities serve to
limit collateral tissue damage and limit autoimmunity during an
immune response under normal conditions. Blocking the PD-1
signaling pathway, for example by administering anti-PD-1 or
anti-PD-L1 antibodies, results in restoration of T cell effector
functions, such as tumor-specific T cell effector functions, such
as killing tumor cells and secretion of immunostimulatory
cytokines, such as interferon gamma (IFN-.gamma.), interleukin-2
(IL-2) and tumor necrosis factor alpha (TNF-.alpha.).
[0964] Other immune checkpoint ligands and receptors are involved
in modulating the immune response and can be targets for therapies
aimed at enhancing antitumor immunity. Further, blockade of two or
more of coordinately expressed receptors or ligands can produce
additive or synergistic antitumor activities. Targets include B7
inhibitory ligands, other than PD-L1 an PD-L2, such B7-H3 and
B7-H4, which are upregulated on tumor cells or tumor infiltrating
cells. Other targets, which are associated with inhibition of
lymphocyte activity, include lymphocyte activation gene 3 (LAG3;
also called CD223), 2B4 (also called CD244), B and T lymphocyte
attenuator (BTLA; or CD272), T cell membrane protein 3 (TIM3; or
HAVcr2), Adenosine A2a receptor (A2aR), and the family of killer
inhibitory receptors. Many of these immune checkpoint receptors
regulate the activity of effector T cells and T.sub.reg cells. For
example, LAG3 is highly expressed on T.sub.reg cells (which help
prevent autoimmunity), where it is thought to be important for
amplifying immunosuppressive activity. LAG3 also is associated with
inhibition of effector T-cell activity and can induce T-cell anergy
(Pardoll, (2012) Nat Rev Cancer. 12(4):252-264. Antibody targeting
of these proteins alone or in combination can enhance antitumor
immunity in animal cancer models. Because many tumor cells express
multiple inhibitory ligands, and tumor infiltrating lymphocytes
express multiple inhibitory receptors, a combinatorial approach to
inhibiting these proteins can be effective in enhancing antitumor
immunity (see Pardoll, (2012) Nat Rev Cancer. 12(4):252-264 for a
review). In addition to secreted or membrane-bound inhibitory
ligands, metabolic enzymes such as indoleamine 2,3 dioxygenase
(IDO) and arginase, which are expressed by inhibitory
myeloid-derived suppressor cells that commonly infiltrate tumors,
can locally inhibit immune responses by depleting amino acids
essential for anabolic metabolism of T cells. These enzymes can be
inhibited by small molecule drugs.
[0965] Since immune checkpoint inhibitors act on immune cells to
enhance immune responses, the increased response when provided in
combination with any ADA2 provided herein, including wildtype,
variants and modified forms thereof, can be due to effects on
increasing access of immune cells (e.g., CTLs) to the tumor. For
example, as described above, tumor and stromal cells produce a high
level of adenosine, which can exert immunosuppressive effects. By
reducing the adenosine-mediated immunosuppression, there can be an
increased activity of circulating immune cells against the tumors,
thereby increasing the number of cytotoxic and other immune cells
available to kill tumor cells. The efficacy of anti-tumor agents or
drugs, such as immune checkpoint inhibitors (e.g., anti-CTLA4
antibody), can also be increased.
[0966] Hence, the use of any ADA2 provided herein, including
wildtype, variants and modified forms thereof, for example,
PEGylated ADA2), can sensitize a tumor to immune-mediated
responses, which can be further increased in the presence of an
immune checkpoint inhibitor (e.g., anti-CTLA4 antibody, and
anti-PD1 antibody or an anti-PD-L1 antibody). Enhancing the
activity of immune cells against the tumor, i.e. reducing the
effect of adenosine-mediated immunosuppression, by any ADA2
provided herein, can allow for reduced dosage of the immune
checkpoint inhibitor, while maintaining or enhancing therapeutic
efficacy. The ability to more effectively fine tune the antibody
dosage can result in a reduction in adverse events that can be
associated with the antibody therapy. Thus, the combination therapy
provided herein can facilitate an enhanced anti-tumor immune
response for the eradication of tumors and tumor treatment.
[0967] The combination therapy, including compositions,
combinations and methods and use thereof, provided herein contains
inhibitors of immune checkpoint proteins that block an immune
checkpoint protein to stimulate an anti-tumor immune response. Such
immune checkpoint inhibitors are known in the art. Examples of such
inhibitors are provided herein, and include any inhibitory agent
that targets an inhibitory checkpoint protein described in Table 5.
For example, the immune checkpoint inhibitor or inhibitory agent is
an inhibitor of CTLA4, PD-1 and PD-L1. In particular examples, the
immune checkpoint inhibitor is an antibody or an aptamer. Exemplary
inhibitors of CTLA4, PD-1 and PD-L1 include anti-CTLA4, anti-PD-1
and anti-PD-L1 antibodies and aptamers.
[0968] An inhibitor that is an aptamer can be employed in the
combination therapy provided herein. An aptamer includes
oligonucleotide (DNA, RNA, or XNA) or peptide aptamers. An aptamer
can be monovalent or multivalent, such as bivalent or tetravalent.
In some cases, the aptamer can be modified by polymers, such as
cholesterol or polyethylene glycol (PEG) to extend the half-life of
circulating aptamers.
[0969] In particular examples, the immune checkpoint inhibitor is
an antibody that blocks an immune checkpoint molecule (e.g.
anti-CTLA4, anti-PD-1 and anti-PD-L1). The antibody can be a
full-length antibody or an antigen-binding fragment thereof that
immunospecifically binds to the immune checkpoint molecule (e.g.,
CTLA4, PD-1 and PD-L1). Other immunomodulatory agents which are
contemplated for use in the combinations, methods, and uses
provided herein include inhibitory agents targeted against the
inhibitory receptors lymphocyte-activation gene 3 (LAG3) and T cell
membrane protein 3 (TIM3), inhibitory ligands such as PD-L2 (or
B7-H2), B7-H3, B7-H4, and CD25, and the immunosuppressive enzyme
Indoleamine 2,3-dioxygenase (IDO). Agents directed against LAG3
(e.g., fusion protein IMP321 and multiple mAbs) and anti B7-H3
antibodies (e.g., MGA271) have been characterized and are in use in
clinical trials. Antibodies or inhibitory agents of B7-H4 and TIM3
are in preclinical development (Pardoll, Nat Rev Cancer. 2012 Mar.
22; 12(4):252-264). Any one of more of these agents can be included
in any of the combinations provided herein. In addition, variants
and modified forms of the antibodies can also be used in the method
of combination therapy provided herein.
[0970] (a) Anti-CTLA4 Therapies
[0971] Two antibodies that block CTLA4, Ipilimumab and
Tremelimumab, have been used for the effective treatment of some
cancers, such as melanoma, pancreatic cancer, ovarian cancer,
prostate cancer, renal cell cancer (RCC), colorectal cancer (CRC),
gastric cancer, and NSCLC (see Kyi et al., (2014) FEBS Letters
588:368-376 for a review). Therapeutic CTLA4 blockade can effect
tumor regression months to years after completion of therapy
(Prieto et al., (2012) Clin Cancer Res. 18(7):2039-2047; Kirckwood
et al., (2010) Clin Cancer Res. 16(3):1042-1048), but also can
reduce tolerance to other host tissues, leading to adverse events,
such as immune-related adverse events (irAEs).
[0972] The combination therapies provided herein, including
compositions and methods and uses thereof, can include therapeutic
agents that inhibit CTLA4 Inhibitors include antibodies and
aptamers. Antibody and aptamer inhibitors that bind to CTLA4 and
inhibit CTLA4 signaling are known. Exemplary aptamers which bind
CTLA4, inhibit CTLA4 function, and enhance tumor immunity have been
described and are set forth in SEQ ID NOS:384-388, 539-541
(Santulli-Marotto (2003) Cancer Res. 63(21):7483-7489; Gilboa et
al., (2013) Clin Cancer Res 19(5): 1054-1062).
[0973] Several antibodies, which bind and inhibit CTLA4 activity,
have been described which have been used in anti-tumor
immunotherapy. Anti-CTLA4 antibodies include, but are not limited
to, any of those described in U.S. Pat. Nos. 6,682,736, 6,984,720;
U.S. Publ. Nos. 2002/0086014; 2009/0074787; EP 1262193; and WO
2000/037504. In particular, anti-CTLA4 antibodies include
Ipilimumab (also called MDX-010, MDX-101, 10D1; Drug Bank Accession
No. DB06186) and Tremelimumab (also called Ticilimumab, CP-675,206
or 11.2.1).
[0974] For example, an anti-CTLA4 antibody for use in the
combination therapy provided herein can include Ipilimumab (also
called MDX-010, MDX-101, 10D1; Drug Bank Accession No. DB06186) or
derivatives thereof, such as variants or antigen-binding fragments
of Ipilimumab. Ipilimumab is a fully human IgG1.kappa. monoclonal
antibody that specifically binds human CTLA4 (see, e.g., antibody
designated 10D1 in US Patent Publication No. 2002/0086014 and U.S.
Pat. No. 6,984,720). The heavy chain of Ipilimumab has a variable
domain (V.sub.H) with the sequence of amino acids set forth in SEQ
ID NO:390, encoded by the sequence of nucleotides set forth in SEQ
ID NO:389. The complementarity determining regions (CDRs) of the
heavy chain include V.sub.H CDR 1 (set forth in SEQ ID NO:393);
V.sub.H CDR 2 (set forth in SEQ ID NO:394); and V.sub.H CDR 3 (set
forth in SEQ ID NO:395). The light chain of Ipilimumab has a
variable domain (V.sub.L) with the sequence of amino acids set
forth in SEQ ID NO:392, encoded by the sequence of nucleotides set
forth in SEQ ID NO:391. The CDRs of the light chain include,
V.sub.L CDR 1 (set forth in SEQ ID NO:396); V.sub.L CDR 2 (set
forth in SEQ ID NO:397); and V.sub.L CDR 3 (set forth in SEQ ID
NO:398). When recombinantly produced, Ipilimumab is made up of four
polypeptide chains; two identical heavy chains of 447 amino acids
each and two identical kappa light chains of 215 amino acids each.
Each heavy and light chain pair is linked through an interchain
disulfide bond.
[0975] In another example, an anti-CTLA4 antibody for use in the
combination therapy provided herein can include Tremelimumab (also
called Ticilimumab, CP-675,206 or 11.2.1) or derivatives thereof,
such as variants or antigen-binding fragments of Tremelimumab.
Tremelimumab is a fully human IgG2 monoclonal antibody that
specifically binds human CTLA4 (see e.g., antibody designated
11.2.1 of WO 00/37504). The heavy chain of Tremelimumab has a
variable domain (V.sub.H) with the sequence of amino acids set
forth in SEQ ID NO:400, encoded by the sequence of nucleotides set
forth in SEQ ID NO:399. The complementarity determining regions
(CDRs) of the heavy chain include V.sub.H CDR 1 (set forth in SEQ
ID NO:471); V.sub.H CDR 2 (set forth in SEQ ID NO:472); and V.sub.H
CDR 3 (set forth in SEQ ID NO:473). The light chain of Tremelimumab
has a variable domain (V.sub.L) with the sequence of amino acids
set forth in SEQ ID NO:402, encoded by the sequence of nucleotides
set forth in SEQ ID NO:401. The CDRs of the light chain include,
V.sub.L CDR 1 (set forth in SEQ ID NO:474); V.sub.L CDR 2 (set
forth in SEQ ID NO:475); and V.sub.L CDR 3 (set forth in SEQ ID
NO:476). When recombinantly produced, Tremelimumab is made up of
four polypeptide chains; two identical heavy chains and two
identical kappa light chains. Each heavy and light chain pair is
linked through an interchain disulfide bond.
[0976] These anti-CTLA4 antibodies have been involved in numerous
clinical trials for the treatment of cancers. Ipilimumab is FDA
approved for the treatment of melanoma and has been in clinical
trials for other cancers, such as prostate cancer, lung cancer, and
RCC. Tremelimumab has been investigated in clinical trials for the
treatment of CRC, gastric cancer, melanoma and NSCLC.
[0977] The anti-CTLA4 antibodies in the combination therapy
provided herein also can include variants of Ipilimumab or
Tremelimumab, or antigen-binding fragments thereof that include the
variations, where the variant antibody immunospecifically binds
CTLA4. The variations can be, for example, amino acid replacements,
insertion or deletion of amino acids.
[0978] (b) Anti-PD-1 and Anti-PD-L1 Therapies
[0979] The combination therapies provided herein, including
compositions and methods and uses thereof, include therapeutic
agents that inhibit PD-1 or PD-L1 Inhibitors that include
antibodies and fusion proteins, aptamers, Antibody, aptamer and
fusion protein inhibitors that bind to PD-1 or PD-L1 and inhibit
PD-1 inhibitory signaling are known. Exemplary fusion proteins
include AMP-224 (also known as B7-DCIg), which is a PD-L2-Fc fusion
soluble receptor described in WO2010/027827 and WO2011/066342.
[0980] Several antibodies, which bind PD-1 or PD-L1 and inhibit
PD-1-inhibitory activity, have been described which have been used
in anti-tumor immunotherapy. Anti-PD-1 antibodies include, but are
not limited to, any of those described in U.S. Pat. Nos. 7,943,743,
8,008,449, 8,779,105, 8,735,553; U.S. Publication Nos. 2005/0180969
2007/0166281; and International Patent Pub. No. WO 2008/156712.
Anti-PD-L1 antibodies include, but are not limited to, any of those
described in U.S. Publ. Nos. 2013/0034559 and 2013/0045202; U.S.
Pat. Nos. 7,943,743, 8,217,149, 8,679,767, and 8,779,108; and Intl.
Publ. Nos. WO 2010/077634 and WO 2013/019906.
[0981] In particular, anti-PD-1 antibodies include Nivolumab (also
known as BMS-936558, MDX-1106, ONO-4538 or 5C4), MK-3475 (also
known as Pembrolizumab, Lambrolizumab or h409A11), Pidilizumab
(also known as hBAT-1 or CT-011), and AMP-224 (also known as
B7-DCIg). These anti-PD-1 antibodies have been involved in numerous
clinical trials for the treatment of cancers, such as melanoma,
NSCLC, RCC, hematologic malignancies, lymphomas, leukemias,
pancreatic cancer, prostate cancer, lung cancer, and multiple
myeloma.
[0982] For example, an anti-PD-1 antibody for use in the
combination therapy provided herein can include Nivolumab (also
known as BMS-936558, MDX-1106, ONO-4538 or 5C4) or derivatives
thereof, such as variants or antigen-binding fragments of
Nivolumab. Nivolumab is a fully human IgG4 monoclonal antibody that
specifically binds human PD-1 (see, e.g., antibody designated 5C4
in U.S. Pat. No. 8,008,449). The heavy chain of Nivolumab has a
variable domain (VH) with the sequence of amino acids set forth in
SEQ ID NO:404, encoded by the sequence of nucleotides set forth in
SEQ ID NO:403. The complementarity determining regions (CDRs) of
the heavy chain include VH CDR 1 (set forth in SEQ ID NO:407); VH
CDR 2 (set forth in SEQ ID NO:408); and VH CDR 3 (set forth in SEQ
ID NO:409). The light chain of Nivolumab has a variable domain (VL)
with the sequence of amino acids set forth in SEQ ID NO:406,
encoded by the sequence of nucleotides set forth in SEQ ID NO:405.
The CDRs of the light chain include, VL CDR 1 (set forth in SEQ ID
NO:410); VL CDR 2 (set forth in SEQ ID NO:411); and VL CDR 3 (set
forth in SEQ ID NO:412). When recombinantly produced, Nivolumab is
made up of four polypeptide chains; two identical heavy chains and
two identical kappa light chains. Each heavy and light chain pair
is linked through an interchain disulfide bond.
[0983] In another example, an anti-PD-1 antibody for use in the
combination therapy provided herein can include MK-3475 (also
called Pembrolizumab, Lambrolizumab or h409A11) or derivatives
thereof, such as variants or antigen-binding fragments of MK-3475.
MK-3475 is a humanized IgG4K monoclonal antibody that specifically
binds human PD-1 (see, e.g., antibody designated h409A11 in WO
2008/156712). The complete heavy chain of MK-3475 has the sequence
of amino acids set forth in SEQ ID NO:414, encoded by a sequence of
nucleotides set forth in SEQ ID NO:413, and the complete light
chain has the sequence of amino acids set forth in SEQ ID NO:416,
encoded by a sequence of nucleotides set forth in SEQ ID NO:415.
The heavy chain is composed of a variable domain (VH), with an
amino acid sequence set forth in SEQ ID NO:418, encoded by a
sequence of nucleotides set forth in SEQ ID NO:417). The light
chain is composed of a variable domain (VL) with an amino acid
sequence set forth in SEQ ID NO:420, encoded by a sequence of
nucleic acids set forth in SEQ ID NO:419) and a humanized kappa
light constant region. When recombinantly produced, MK-3475 is made
up of four polypeptide chains; two identical heavy chains of 447
amino acids each and two identical kappa light chains of 218 amino
acids each. Each heavy and light chain pair is linked through an
interchain disulfide bond.
[0984] The CDRs of MK-3475 include, VH CDR 1 (SEQ ID NO:421); VH
CDR 2 (SEQ ID NO:422); VH CDR 3 (SEQ ID NO:423); VL CDR 1 (SEQ ID
NO:424); VL CDR 2 (SEQ ID NO:425); and VL CDR 3 (SEQ ID
NO:426).
[0985] In another example, an anti-PD-1 antibody for use in the
combination therapy provided herein can include Pidilizumab (also
called hBAT-1 or CT-011) or derivatives thereof, such as variants
or antigen-binding fragments of Pidilizumab. Pidilizumab is a
humanized IgG1 monoclonal antibody that was generated from a murine
antibody (BAT), which was raised against B lymphoid cell membranes,
and has been shown to elicit T-cell- and NK-cell-based activities.
Pidilizumab binds human PD-1 (see, e.g., antibody designated BAT-1
R.kappa.D/RHC in US 2005/0180969). The complete heavy chain of
Pidilizumab has the sequence of amino acids set forth in SEQ ID
NO:428, encoded by a sequence of nucleotides set forth in SEQ ID
NO:427, and the complete light chain has the sequence of amino
acids set forth in SEQ ID NO:430, encoded by a sequence of
nucleotides set forth in SEQ ID NO:429. The heavy chain is composed
of a variable domain (VH), with an amino acid sequence set forth in
SEQ ID NO:432, encoded by a sequence of nucleotides set forth in
SEQ ID NO:431. The light chain is composed of a variable domain
(VL,) with an amino acid sequence set forth in SEQ ID NO:434,
encoded by a sequence of nucleic acids set forth in SEQ ID NO:433,
and a humanized kappa light constant region. When recombinantly
produced, Pidilizumab is made up of four polypeptide chains; two
identical heavy chains and two identical kappa light chains Each
heavy and light chain pair is linked through an interchain
disulfide bond.
[0986] The CDRs of Pidilizumab include, VH CDR 1 (amino acid
sequence set forth in SEQ ID NO:435); VH CDR 2 (amino acid sequence
set forth in SEQ ID NO:436); VH CDR 3 (amino acid sequence set
forth in SEQ ID NO:437); VL CDR 1 (amino acid sequence set forth in
SEQ ID NO:438); VL CDR 2 (amino acid sequence set forth in SEQ ID
NO:439); and VL CDR 3 (amino acid sequence set forth in SEQ ID
NO:440).
[0987] The anti-PD-1 antibodies in the combination therapy provided
herein also can include variants of Nivolumab, MK-3475,
Pidilizumab, and AMP-224, or antigen-binding fragments thereof that
include the variations, where the variant antibody
immunospecifically binds PD-1. The variations can be, for example,
amino acid replacements, insertion or deletion of amino acids.
[0988] In particular, anti-PD-L1 (or anti-B7H1) antibodies include,
but are not limited to, the antibodies called BMS-936559 (also
known as MDX-1105 or 12A4), MPDL3280A (also known as RG7446), and
MEDI4736. These anti-PD-L1 antibodies have been involved in
numerous clinical trials for the treatment of cancers, such as
melanoma, NSCLC, ovarian cancer, RCC, and lung cancer.
[0989] For example, an anti-PD-L1 antibody for use in the
combination therapy provided herein can include BMS-936559 (also
known as MDX-1105 or 12A4) or derivatives thereof, such as variants
or antigen-binding fragments of BMS-936559. BMS-936559 is a fully
human IgG4 monoclonal antibody that specifically binds human PD-L1
(see, e.g., antibody designated 12A4 in U.S. Pat. No. 7,943,743).
The heavy chain of BMS-936559 has a variable domain (VH) with the
sequence of amino acids set forth in SEQ ID NO:442, encoded by the
sequence of nucleotides set forth in SEQ ID NO:441. The
complementarity determining regions (CDRs) of the heavy chain
include VH CDR 1 (set forth in SEQ ID NO:445); VH CDR 2 (set forth
in SEQ ID NO:446); and VH CDR 3 (set forth in SEQ ID NO:447). The
light chain of BMS-936559 has a variable domain (VL) with the
sequence of amino acids set forth in SEQ ID NO:444, encoded by the
sequence of nucleotides set forth in SEQ ID NO:443. The CDRs of the
light chain include, VL CDR 1 (set forth in SEQ ID NO:448); VL CDR
2 (set forth in SEQ ID NO:449); and VL CDR 3 (set forth in SEQ ID
NO:450). When recombinantly produced, BMS-936559 is made up of four
polypeptide chains; two identical heavy chains and two identical
kappa light chains. Each heavy and light chain pair is linked
through an interchain disulfide bond.
[0990] In another example, an anti-PD-L1 antibody for use in the
combination therapy provided herein can include MPDL3280A (also
known as RG7446) or derivatives thereof, such as variants or
antigen-binding fragments of MPDL3280A. MPDL3280A is a fully human
IgG4 monoclonal antibody that specifically binds human PD-L1 (see,
e.g., U.S. Pat. No. 8,217,149 and WO 2013/019906). MPDL3280A
contains a heavy chain variable domain (VH) with the sequence of
amino acids set forth in SEQ ID NO:463 and a light chain variable
domain (VL) with the sequence of amino acids set forth in SEQ ID
NO:464. The full-length antibody contains a heavy chain sequence of
amino acids set forth in SEQ ID NO:477 or 479 and a light chain
sequence of amino acids set forth in SEQ ID NO:478. The full-length
antibody also is reported to contain a heavy chain sequence of
amino acids set forth in SEQ ID NO:461 and light chain sequence set
forth in SEQ ID NO:462 (see WO 2013019906). The complementarity
determining regions (CDRs) of the heavy chain include VH CDR 1 (set
forth in SEQ ID NO:465); VH CDR 2 (set forth in SEQ ID NO:466); and
VH CDR 3 (set forth in SEQ ID NO:467). The CDRs of the light chain
include, VL CDR 1 (set forth in SEQ ID NO:468); VL CDR 2 (set forth
in SEQ ID NO:469); and VL CDR 3 (set forth in SEQ ID NO:470). When
recombinantly produced, MPDL3280A is made up of four polypeptide
chains; two identical heavy chains and two identical kappa light
chains. Each heavy and light chain pair is linked through an
interchain disulfide bond.
[0991] In another example, an anti-PD-L1 antibody for use in the
combination therapy provided herein can include MEDI4736 or
derivatives thereof, such as variants or antigen-binding fragments
of MEDI4736. MEDI4736 is a fully human IgG1.kappa. monoclonal
antibody that specifically binds human PD-L1 (see, e.g., antibody
designated 2.7A4OPT in U.S. Publ. No. 2013/0034559). The heavy
chain of MEDI4736 has a variable domain (VH) with the sequence of
amino acids set forth in SEQ ID NO:452, encoded by the sequence of
nucleotides set forth in SEQ ID NO:451. The complementarity
determining regions (CDRs) of the heavy chain include VH CDR 1 (set
forth in SEQ ID NO:455); VH CDR 2 (set forth in SEQ ID NO:456); and
VH CDR 3 (set forth in SEQ ID NO:457). The light chain of MEDI4736
has a variable domain (VL) with the sequence of amino acids set
forth in SEQ ID NO:454, encoded by the sequence of nucleotides set
forth in SEQ ID NO:453. The CDRs of the light chain include, VL CDR
1 (set forth in SEQ ID NO:458); VL CDR 2 (set forth in SEQ ID
NO:459); and VL CDR 3 (set forth in SEQ ID NO:460). When
recombinantly produced, MEDI4736 is made up of four polypeptide
chains; two identical heavy chains and two identical kappa light
chains Each heavy and light chain pair is linked through an
interchain disulfide bond.
[0992] The anti-PD-L1 antibodies in the combination therapy
provided herein also can include variants of BMS-936559, MPDL3280A,
and MEDI4736, or antigen-binding fragments thereof that include the
variations, where the variant antibody immunospecifically binds
PD-L1. The variations can be, for example, amino acid replacements,
insertion or deletion of amino acids.
[0993] b. Other Immunomodulatory Agents
[0994] In some examples, any ADA2 provided herein, including
wildtype, variants and modified forms thereof, is administered with
one or more immunomodulatory agents. Such agents can increase or
decrease production of one or more cytokines, up- or down-regulate
self-antigen presentation, mask MHC antigens, or promote the
proliferation, differentiation, migration, or activation state of
one or more types of immune cells. Examples of immunomodulatory
agents include but are not limited to non-steroidal
anti-inflammatory drugs (NSAIDs) such as aspirin, ibuprofen,
celecoxib, diclofenac, etodolac, fenoprofen, indomethacin,
ketorolac, oxaprozin, nabumetone, sulindac, tolmetin, rofecoxib,
naproxen, ketoprofen, and nabumetone; steroids (e.g.
glucocorticoids, dexamethasone, cortisone, hydroxycortisone,
methylprednisolone, prednisone, prednisolone, triamcinolone,
azulfidine eicosanoids such as prostaglandins, thromboxanes, and
leukotrienes; as well as topical steroids such as anthralin,
calcipotriene, clobetasol, and tazarotene); cytokines such as TGFb,
IFNa, IFNb, IFNg, IL-2, IL4, IL-10; cytokine, chemokine, or
receptor antagonists including antibodies, soluble receptors, and
receptor-Fc fusions against BAFF, B7, CCR2, CCR5, CD2, CD3, CD4,
CD6, CD7, CD8, CD11, CD14, CD15, CD17, CD18, CD20, CD23, CD28,
CD40, CD40L, CD44, CD45, CD52, CD64, CD80, CD86, CD147, CD152,
complement factors (C5, D) CTLA4, eotaxin, Fas, ICAM, ICOS,
IFN.alpha., IFN.beta., IFN.gamma., IFNAR, IgE, IL-1, IL-2, IL-2R,
IL-4, IL-5R, IL-6, IL-8, IL-9 IL-12, IL-13, IL-13R1, IL-15, IL-18R,
IL-23, integrins, LFA-1, LFA-3, MHC, selectins, TGF.beta.,
TNF.alpha., TNF.beta., TNF-R1, T-cell receptor, including
Enbrel.RTM. (etanercept), Humira.RTM. (adalimumab), and
Remicade.RTM. (infliximab); heterologous anti-lymphocyte globulin;
other immunomodulatory molecules such as 2-amino-6-aryl-5
substituted pyrimidines, anti-idiotypic antibodies for MHC binding
peptides and MHC fragments, azathioprine, brequinar, Bromocryptine,
cyclophosphamide, cyclosporine A, D-penicillamine, deoxyspergualin,
FK506, glutaraldehyde, gold, hydroxychloroquine, leflunomide,
malononitriloamides (e.g. leflunomide), methotrexate, minocycline,
mizoribine, mycophenolate mofetil, rapamycin, and
sulfasalazine.
[0995] In some examples, any ADA2 provided herein, including
wildtype, variants and modified forms thereof, is administered with
one or more cytokines. Examples of cytokines include but are not
limited to lymphokines, monokines, and traditional polypeptide
hormones. Included among the cytokines are growth hormone such as
human growth hormone, N-methionyl human growth hormone, and bovine
growth hormone; parathyroid hormone; thyroxine; insulin;
proinsulin; relaxin; prorelaxin; glycoprotein hormones such as
follicle stimulating hormone (FSH), thyroid stimulating hormone
(TSH), and luteinizing hormone (LH); hepatic growth factor;
fibroblast growth factor; prolactin; placental lactogen; tumor
necrosis factor-alpha and -beta; mullerian-inhibiting substance;
mouse gonadotropin-associated peptide; inhibin; activin; vascular
endothelial growth factor; integrin; thrombopoietin (TPO); nerve
growth factors such as NGF-beta; platelet-growth factor;
transforming growth factors (TGFs) such as TGF-alpha and TGF-beta;
insulin-like growth factor-I and -II; erythropoietin (EPO);
osteoinductive factors; interferons such as interferon-alpha, beta,
and -gamma; colony stimulating factors (CSFs) such as
macrophage-CSF (M-CSF); granulocyte-macrophage-CSF (GM-CSF); and
granulocyte-CSF (G-CSF); interleukins (ILs) such as IL-1,
IL-1alpha, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10,
IL-11, IL-12; IL-15, a tumor necrosis factor such as TNF-alpha or
TNF-beta; and other polypeptide factors including LIF and kit
ligand (KL).
[0996] In addition to inhibitory antibodies that target and inhibit
immune checkpoint proteins, agonistic antibodies, which are capable
of stimulating an immune response by binding its target
protein/receptor, are contemplated for use in the combinations,
methods, and uses provided herein. For example, Urelumab (also
known as BMS-663513 and anti-4-1BB) is an agonistic humanized
monoclonal antibody targeting the CD137 co-receptor, that is a
member of the tumor necrosis factor (TNF)/nerve growth factor (NGF)
family of receptors and is expressed on dendritic cells, follicular
dendritic cells, natural killer cells, granulocytes and cells of
blood vessel walls at sites of inflammation, with immunostimulatory
properties. Urelumab specifically binds to and activates
CD137-expressing immune cells, stimulating an immune response, in
particular a cytotoxic T cell response, which can be mounted
against tumor cells when administered as a part of a combination
therapy provided herein (see, e.g., Vinay et al., (2012) Mol Cancer
Ther. 11(5):1062-1070). Other 4-1BB agonists also can be included
in the combinations provided herein, such as any described by Snell
et al. in Immunol Rev. 244:197-217 (2011). OX40 (also known as
CD134) is another immunostimulatory receptor, of the TNF family,
which can be targeted by incorporating OX40 agonists, such as those
described by Weinberg et al. in Immunol Rev. 244(1):218-231 (2011),
into the combinations provided herein. Aptamer ligands which bind
and stimulate 4-1BB or OX40 signaling also have been described
(Gilboa et al., Clin Cancer Res. 19(5):1054-1062) and are
contemplated for inclusion in the combination therapies provided
herein.
[0997] In some examples, any ADA2 provided herein, including
wildtype, variants and modified forms thereof, is administered with
one or more cytokines or other agents that stimulate cells of the
immune system and enhance desired effector function. For example,
agents that stimulate NK cells, including but not limited to IL-2
can be administered with an any ADA2 provided herein. In another
embodiment, agents that stimulate macrophages, including but not
limited to C5a, formyl peptides such as
N-formyl-methionyl-leucyl-phenylalanine (Beigier-Bompadre et. al.
(2003) Scand. J. Immunol. 57: 221-8), can be administered with any
ADA2 provided herein. Also, agents that stimulate neutrophils,
including but not limited to G-CSF and GM-CSF, can be administered
with any ADA2 provided herein. Furthermore, agents that promote
migration of such immunostimulatory cytokines can be administered
with any ADA2 provided herein. Also additional agents including but
not limited to interferon gamma, IL-3 and IL-7 can promote one or
more effector functions. In some examples, any ADA2 provided herein
is administered with one or more cytokines or other agents that
inhibit effector cell function.
[0998] c. Hyaluronan-Degrading Enzyme
[0999] The combination therapy, including combinations and methods
and use thereof, provided herein can contain, in addition to the
ADA2 provided herein, an anti-hyaluronan agent, such as a soluble
hyaluronan-degrading enzyme. Hyaluronan-degrding enzymes are
enzymes that catalyze the hydrolysis of hyaluronan, and can
temporarily degrade hyaluronan Hyaluronan is a component of the
extracellular matrix and a major constituent of the interstitial
barrier. Hyaluronan degrading enzymes act to degrade hyaluronan by
cleaving hyaluronan polymers, which are composed of repeating
disaccharides units, D-glucuronic acid (GlcA) and
N-acetyl-D-glucosamine (GlcNAc), linked together via alternating
.beta.-1.fwdarw.4 and .beta.-1.fwdarw.3 glycosidic bonds.
Hyaluronan chains can reach about 25,000 disaccharide repeats or
more in length and polymers of hyaluronan can range in size from
about 5,000 to 20,000,000 Da in vivo. By catalyzing the hydrolysis
of hyaluronan, a major constituent of the interstitial barrier,
hyaluronan degrading enzymes lower the viscosity of hyaluronan,
thereby increasing tissue permeability. As such, hyaluronan
degrading enzymes, such as hyaluronidases, have been used, for
example, as spreading or dispersing agents in conjunction with
other agents, drugs and proteins to enhance their dispersion and
delivery.
[1000] Certain diseases also are associated with expression and/or
production of hyaluronan, including inflammatory diseases and
cancers. HA is linked to a variety of biological processes involved
with progression of such diseases (see e.g. Itano et al. (2008)
Semin Cancer Biol 18(4):268-274; Tammi et al. (2008) Semin Cancer
Biol 18(4):288-295). For example, HA is linked to biological
processes associated with tumor progression, including
epithelial-mesenchymal transition, and the p53 tumor suppressor
pathway. Also, HA is involved in increased water uptake and
interstitial fluid pressure (IFP) in disease tissues, such as
tumors, thereby resulting in compressed tumor vasculature. For
example, at sites of inflammation or in a tumor focus, there is
rapid accumulation of hyaluronan, other matrix components and
water. Because of this rapid accumulation, the diseased site cannot
come to equilibrium with its environment and therefore has a higher
interstitial fluid pressure than normal tissues.
[1001] Treatment with hyaluronan degrading enzymes, such as
polymer-conjugated soluble hyaluronidase (e.g. PEGPH20) can degrade
HA on accumulated tissues and cells, including on tumor cells. This
treatment can reduce the hyaluronan such that the tissue deflates,
the blood vessels expand, and more blood can flow through the site.
Accordingly, treatment with a hyaluronan-degrading enzyme, such as
a soluble hyaluronidase or polymer-conjugated soluble hyaluronidase
(e.g. PEGPH20), can diminish interstitial fluid pressure (IFP) and
water content at the tissue site and associated increased vascular
perfusion, thereby treating hyaluronan-associated diseases and
conditions, such as tumors and cancers. Accordingly, hyaluronan
degrading enzymes for the combinations, uses and methods provided
include any enzyme having the ability to catalyze the cleavage of a
hyaluronan disaccharide chain or polymer.
[1002] Hyaluronan-degrading enzymes include hyaluronidases, as well
as other enzymes such as chondrotinases and lyases that have the
ability to cleave hyaluronan. Hyaluronidases are members of a large
family of hyaluronan degrading enzymes. There are three general
classes of hyaluronidases: mammalian-type hyaluronidases, bacterial
hyaluronidases and hyaluronidases from leeches, other parasites and
crustaceans. Mammalian-type hyaluronidases (EC 3.2.1.35) are
endo-.beta.-N-acetyl-hexosaminidases that hydrolyze the
.beta.-1.fwdarw.4 glycosidic bond of hyaluronan into various
oligosaccharide lengths such as tetrasaccharides and
hexasaccharides. These enzymes have both hydrolytic and
transglycosidase activities, and can degrade hyaluronan and
chondroitin sulfates (CS), generally C4-S and C6-S. Five
hyaluronidase-like genes have been identified in the human genome,
PH20 (or SPAM1), HYAL1, HYAL2, HYAL3, HYAL4 and HYALP1.
[1003] Mammalian hyaluronidases can be further subdivided into
those that are neutral active, predominantly found in testes
extracts, and acid active, predominantly found in organs such as
the liver. HYALP1 is a pseudogene, and HYAL3 has not been shown to
possess enzyme activity toward any known substrates. HYAL4 is a
chondroitinase and exhibits little activity towards hyaluronan
HYAL1 is the prototypical acid-active enzyme and PH20 (precursor
polypeptide set forth in SEQ ID NO:551 and mature protein set forth
in SEQ ID NO:480) is the prototypical neutral-active enzyme.
Acid-active hyaluronidases, such as HYAL1 and HYAL2 generally lack
catalytic activity at neutral pH (i.e., pH 7). For example, HYAL1
has little catalytic activity in vitro over pH 4.5 (Frost et al.
(1997) Anal. Biochem. 251:263-269). HYAL2 is an acid-active enzyme
with a very low specific activity in vitro. The hyaluronidase-like
enzymes also can be characterized by those which are generally
attached to the plasma membrane via a glycosylphosphatidyl inositol
(GPI) anchor such as human HYAL2 and human PH20
(Danilkovitch-Miagkova et al. (2003) Proc Natl Acad Sci USA
100(8):4580-4585), and those which are generally soluble such as
human HYAL1 (Frost et al. (1997) Biochem Biophys Res Commun.
236(1):10-15). Many hyaluronidases also are glycosylated, and
require glycosylation for activity. For example, human PH20
contains six N-linked glycosylation sites at N82, N166, N235, N254,
N368, N393 and S490 of the polypeptide exemplified in SEQ ID
NO:551.
[1004] PH20 is naturally involved in sperm-egg adhesion and aids
penetration by sperm of the layer of cumulus cells by digesting
hyaluronic acid. PH20 is located on the sperm surface, and in the
lysosome-derived acrosome, where it is bound to the inner acrosomal
membrane. The human PH20 mRNA transcript is normally translated to
generate a 509 amino acid precursor polypeptide (SEQ ID NO:551)
containing a 35 amino acid signal sequence at the N-terminus (amino
acid residue positions 1-35) and a 19 amino acid
glycosylphosphatidylinositol (GPI) anchor attachment signal
sequence at the C-terminus (amino acid residue positions 491-509).
The mature PH20 therefore, is a 474 amino acid polypeptide set
forth in SEQ ID NO:480. Following transport of the precursor
polypeptide to the ER and removal of the signal peptide, the
C-terminal GPI-attachment signal peptide is cleaved to facilitate
covalent attachment of a GPI anchor to the newly-formed C-terminal
amino acid at the amino acid position corresponding to position 490
of the precursor polypeptide set forth in SEQ ID NO:551. In
contrast, clear GPI anchors are not predicted in many other PH20
species besides humans. Thus, PH20 polypeptides produced from ovine
and bovine naturally exist as soluble forms. Though bovine PH20
exists very loosely attached to the plasma membrane, it is not
anchored via a phospholipase sensitive anchor (Lalancette et al.
(2001) Biol Reprod. 65(2):628-636). This unique feature of bovine
hyaluronidase has permitted the use of the soluble bovine testes
hyaluronidase enzyme as an extract for clinical use (Wydase.RTM.,
Hyalase.RTM.).
[1005] Hence, hyaluronan-degrading enzymes exist in membrane-bound
or soluble forms that are secreted from cells. Hyaluronan-degrading
enzymes can be made soluble to be expressed and secreted from
cells. For example, where hyaluronan-degrading enzymes include a
glycosylphosphatidylinositol (GPI) anchor and/or are otherwise
membrane-anchored or insoluble, hyaluronan-degrading enzymes can be
provided in soluble form by truncation or deletion of all or a
portion of the GPI anchor to render the enzyme secreted and
soluble. Soluble hyaluronan-degrading enzymes can be used in the
method of combination therapy provided herein. Thus,
hyaluronan-degrading enzymes include truncated variants, e.g.
truncated to remove all or a portion of a GPI anchor. Examples of
such soluble hyaluronidases include soluble PH20 hyaluronides, such
as any set forth in U.S. Pat. No. 7,767,429; U.S. Publication Nos.
US20040268425, US20100143457 or US20130302275, see also exemplary
soluble human PH20 hyaluronidases set forth in any of SEQ ID
NOS:481-488, 493-514, or 526-532).
[1006] Various forms of hyaluronan degrading enzymes, including
hyaluronidases have been prepared and approved for therapeutic use
in subjects, including humans. For example, animal-derived
hyaluronidase preparations include Vitrase.RTM. (ISTA
Pharmaceuticals), a purified ovine testicular hyaluronidase,
Amphadase.RTM. (Amphastar Pharmaceuticals), a bovine testicular
hyaluronidase and Hydase.TM. (Prima Pharm Inc.), a bovine
testicular hyaluronidase. Hylenex.RTM. (Halozyme Therapeutics) is a
human recombinant hyaluronidase produced by genetically engineered
Chinese Hamster Ovary (CHO) cells containing nucleic acid encoding
soluble forms of PH20, designated rHuPH20 (see e.g., U.S.
Publication Nos. US20040268425; U.S. Pat. No. 7,767,429). It is
understood that any hyaluronidase preparation can be used in the
method of combination therapy provided herein (see, e.g., U.S. Pat.
Nos. 2,488,564, 2,488,565, 2,676,139, 2,795,529, 2,806,815,
2,808,362, 5,747,027 and 5,827,721 and International PCT
Publication No. WO2005/118799; U.S. Publication Nos. US20040268425;
U.S. Pat. No. 7,767,429; or any provided herein).
[1007] Described herein is a non-limiting examples of
hyaluronan-degrading enzymes, such as hyaluronidase enzymes or
soluble hyaluronidase enzyme, for example PH20, for use in the
combinations and methods provided herein. Generally, such
hyaluronan-degrading enzymes include those that are conjugated to a
polymer. The hyaluronan-degrading enzyme, such as a hyaluronidase,
can be, for example, of human origin, mammalian origin, bacterial
origin, or other biological origin. In other examples, the
hyaluronan-degrading enzyme can be modified, for example, by
conjugation to a polymer.
[1008] Soluble Hyaluronan Degrading Enzymes (e.g. Soluble PH20)
[1009] In particular, provided herein is a method of combination
therapy and compositions that include any ADA2 protein provided
herein, such as any variant ADA2 protein, and a soluble hyaluronan
degrading enzymes, such as a soluble hyaluronidase (e.g. soluble
PH20). Soluble hyaluronan degrading enzymes include any hyaluronan
degrading enzymes that are secreted from cells (e.g. CHO cell) upon
expression and exist in soluble form. Such enzymes include, but are
not limited to, soluble hyaluronidases, including non-human soluble
hyaluronidases, including non-human animal soluble hyaluronidases,
bacterial soluble hyaluronidases and human hyaluronidases, Hyal1,
bovine PH20 and ovine PH20, allelic variants thereof and other
variants thereof. For example, included among soluble hyaluronan
degrading enzymes are any hyaluronan degrading enzymes that have
been modified to be soluble. For example, hyaluronan degrading
enzymes that contain a GPI anchor can be made soluble by truncation
of and removal of all or a portion of the GPI anchor. In one
example, the human hyaluronidase PH20, which is normally membrane
anchored via a GPI anchor, can be made soluble by truncation of and
removal of all or a portion of the GPI anchor at the
C-terminus.
[1010] Soluble hyaluronan degrading enzymes also include neutral
active and acid active hyaluronidases. Depending on factors, such
as, but not limited to, the desired level of activity of the enzyme
following administration and/or site of administration, neutral
active and acid active hyaluronidases can be selected. In a
particular example, the hyaluronan degrading enzyme is a soluble
neutral active hyaluronidase, such as a soluble PH20
polypeptide
[1011] The soluble PH20 polypeptide can be an ovine PH20, bovine
PH20 or a soluble PH20 that is C-terminally truncated and lacks all
or a portion of the GPI anchor attachment sequence. For example,
exemplary of a soluble hyaluronidase is PH20 from any species or
truncated forms thereof lacking all or a portion of the C-terminal
GPI anchor, so long as the hyaluronidase is soluble (secreted upon
expression) and retains hyaluronidase activity. In some instances,
the soluble hyaluronan degrading enzyme, such as soluble PH20 is
normally GPI-anchored (such as, for example, human PH20) and is
rendered soluble by truncation at the C-terminus. Such truncation
can remove all of the GPI anchor attachment signal sequence, or can
remove only some of the GPI anchor attachment signal sequence. For
example, up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45 or more C-terminal
amino acid residues can be removed. The resulting polypeptide,
however, is soluble. In instances where the soluble hyaluronan
degrading enzyme, such as a soluble PH20, retains a portion of the
GPI anchor attachment signal sequence, up to 1, 2, 3, 4, 5, 6, 7,
8, 9 or more amino acid residues in the GPI-anchor attachment
signal sequence can be retained, provided the polypeptide is
soluble. One of skill in the art can determine whether a
polypeptide is GPI-anchored using methods well known in the art.
Such methods include, but are not limited to, using known
algorithms to predict the presence and location of the GPI-anchor
attachment signal sequence and .omega.-site, and performing
solubility analyses before and after digestion with
phosphatidylinositol-specific phospholipase C (PI-PLC) or D
(PI-PLD).
[1012] Typically, the soluble hylauronan degrading enzyme, such as
a soluble PH20, is human. Although hylauronan degrading enzymes,
such as PH20, from other animals can be utilized, such preparations
are potentially immunogenic, since they are animal proteins. For
example, a significant proportion of patients demonstrate prior
sensitization secondary to ingested foods, and since these are
animal proteins, all patients have a risk of subsequent
sensitization. Thus, non-human preparations may not be suitable for
chronic use. If non-human preparations are desired, it is
contemplated herein that such polypeptides can be prepared to have
reduced immunogenicity. Such modifications are within the level of
one of skill in the art and can include, for example, removal
and/or replacement of one or more antigenic epitopes on the
molecule.
[1013] Exemplary of a soluble hyaluronidase is soluble human PH20.
Soluble forms of recombinant human PH20 have been produced and are
known. The production of such soluble forms of PH20 is described in
U.S. Published Patent Application Nos. US20040268425;
US20050260186, US20060104968, US20100143457 and International PCT
application No. WO2009111066. Included among these polypeptides are
soluble PH20 polypeptides that completely lack all or a portion of
the GPI-anchor attachment signal sequence. For example, a soluble
PH20 (esPH20) polypeptides can contain at least one amino acid of
the GPI anchor or can lack all amino acid residues of the GPI
anchor. Thus, instead of having a GPI-anchor covalently attached to
the C-terminus of the protein in the ER and being anchored to the
extracellular leaflet of the plasma membrane, these polypeptides
are secreted and are soluble. C-terminally truncated PH20
polypeptides can be C-terminally truncated by 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40,
45, 50, 55, 60 or more amino acids compared to the full length wild
type polypeptide, such as a full length wild type polypeptide with
a sequence set forth in SEQ ID NO:480, or allelic or species
variants or other variants thereof.
[1014] Soluble forms of human PH20 generally include those that
contain amino acids 36-464 set forth in SEQ ID NO:551. For example,
soluble forms include, but are not limited to, C-terminal truncated
polypeptides of human PH20 set forth in SEQ ID NO:551 having a
C-terminal amino acid residue 465, 466, 467, 468, 469, 470, 471,
472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484,
485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497,
498, 499 or 500 of the sequence of amino acids set forth in SEQ ID
NO:551, mature forms thereof, or polypeptides that exhibit at least
85% identity thereto. For example, when expressed in mammalian
cells, the 35 amino acid N-terminal signal sequence is cleaved
during processing, and the mature form of the protein is produced
and can be secreted. Thus, the mature soluble polypeptides contain
amino acids 36 to 464, 465, 466, 467, 468, 469, 470, 471, 472, 473,
474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486,
487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499 or
500 of SEQ ID NO:441. Table 6 provides non-limiting examples of
exemplary C-terminally truncated soluble PH20 polypeptides,
including precursor and mature forms thereof. In Table 6 below, the
length (in amino acids) of the precursor and mature polypeptides,
and the sequence identifier (SEQ ID NO) in which exemplary amino
acid sequences of the precursor and mature polypeptides of the
C-terminally truncated PH20 proteins are set forth, are provided.
The wild-type PH20 polypeptide also is included in Table 6 for
comparison.
TABLE-US-00006 TABLE 6 Exemplary C-terminally truncated PH20
polypeptides Mature Precursor amino amino acids acids of of SEQ ID
length SEQ ID SEQ ID SEQ ID NO: 551 (aa) NO NO: 551 length (aa) NO
1-509 509 551 36-509 474 480 1-500 500 36-500 465 526 1-499 499
36-499 464 493 1-498 498 36-498 463 527 1-497 497 36-497 462 494
1-496 496 36-496 461 528 1-495 495 36-495 460 495 1-494 494 36-494
459 529 1-493 493 36-493 458 496 1-492 492 36-492 457 530 1-491 491
36-491 456 497 1-490 490 36-490 455 499 1-489 489 36-489 454 498
1-488 488 36-488 453 531 1-487 487 36-487 452 500 1-486 486 36-486
451 532 1-485 485 36-485 450 501 1-484 484 36-484 449 502 1-483 483
36-483 448 488 1-482 482 36-482 447 481 1-481 481 36-481 446 482
1-480 480 36-480 445 483 1-479 479 36-479 444 484 1-478 478 36-478
443 485 1-477 477 36-477 442 486 1-476 476 36-476 441 503 1-475 475
36-475 440 504 1-474 474 36-474 439 505 1-473 473 36-473 438 506
1-472 472 36-472 437 507 1-471 471 36-471 436 508 1-470 470 36-470
435 509 1-469 469 36-469 434 510 1-468 468 36-468 433 511 1-467 467
36-467 432 487 1-466 466 36-466 431 512 1-465 465 36-465 430 513
1-464 464 36-464 429 514
[1015] For example, soluble forms of PH20 for use in combinations
provided herein include, for example, polypeptide that has the
sequence of amino acids set forth in any of SEQ ID NOS:481-488,
493-514, or 526-532, or a sequence of amino acids that exhibits at
least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%, 98% or 99% sequence identity to a sequence of amino acids set
forth in any of SEQ ID NOS:481-488, 493-514, or 526-532 and are
soluble and retain hyaluronidase activity. Amino acid variants
include conservative and non-conservative mutations. It is
understood that residues that are important or otherwise required
for the activity of a hyaluronidase, such as any described above or
known to skill in the art, are generally invariant and cannot be
changed. These include, for example, active site residues. Thus,
for example, amino acid residues 111, 113 and 176 (corresponding to
residues in the mature PH20 polypeptide set forth in SEQ ID NO:551)
of a human PH20 polypeptide, or soluble form thereof, are generally
invariant and are not altered. Other residues that confer
glycosylation and formation of disulfide bonds required for proper
folding also can be invariant.
[1016] In particular, a soluble human PH20 polypeptide is a
polypeptide that is truncated after amino acid 482 of the sequence
set forth in SEQ ID NO:551. Such a polypeptide can be generated
from a nucleic acid molecule containing a signal sequence and
encoding amino acids 36-482. The signal sequence can be the native
signal sequence, an IgG kappa signal sequence or other signal
sequence capable of processing the protein for secretion. Post
translational processing removes the signal sequence, leaving a 474
amino acid soluble recombinant human PH20 (SEQ ID NO:480). A
product produced upon expression results in a secreted product,
designated rHuPH20, in the culture medium that exhibits
heterogeneity at the C-terminus such that the product includes a
mixture of species that can include any one or more of SEQ ID
NOS:481-486 in various abundance. Typically, rHuPH20 is produced in
cells that facilitate correct N-glycosylation to retain activity,
such as mammalian cells, for example CHO cells (e.g., DG44 CHO
cells). Hylenex.RTM. (Halozyme) is a human recombinant
hyaluronidase produced by genetically engineered Chinese Hamster
Ovary (CHO) cells containing nucleic acid encoding a truncated
human PH20 polypeptide (designated rHuPH20).
[1017] Variants of PH20, such as a human PH20 (e.g., a soluble
human PH20) are known and are described in U.S. published appl. No.
US201310302275. Any PH20 variant described in U.S. published appl.
No. US2013/0302275 can be incorporated into a soluble PH20
polypeptide for use in the combination provided herein. Such
variants include those that exhibit increased resistance to a
denaturation condition (e.g., a phenolic preservative) or increased
activity. An example of such a polypeptide is a soluble human PH20
containing the amino acid replacement F204P, V58K or V58R with
reference to the sequence of amino acids set forth in full length
human PH20 set forth in SEQ ID NO:480 or in a soluble human PH20
set forth in any of SEQ ID NOS:481-488, 493-514, or 526-532.
[1018] Generally soluble forms of PH20 are produced using protein
expression systems that facilitate correct N-glycosylation to
ensure the polypeptide retains activity, since glycosylation is
important for the catalytic activity and stability of
hyaluronidases. Such cells include, for example Chinese Hamster
Ovary (CHO) cells (e.g., DG44 CHO cells).
[1019] Hyaluronan degrading enzymes, including hyaluronidases
(e.g., PH20), in the combinations provided herein can be
recombinantly produced or can be purified or partially-purified
from natural sources, such as, for example, from testes extracts.
Methods for production of recombinant proteins, including
recombinant hyaluronan degrading enzymes, are provided elsewhere
herein and are well known in the art.
[1020] The hyaluronan degrading enzymes can be administered in
forms that increase half-life. For example, the hyaluronan
degrading enzyme can be provided as part of a liposome or
multicellular laminar vesicle or other such delivery vehicle (see,
e.g., Example 24 herein). The hyaluronan degrading enzyme can be
encoded in a vector, such as an oncolytic vector or targeted vector
for delivery.
[1021] The hyaluronan-degrading enzyme, such as a soluble
hyaluronidase (e.g. a soluble PH20 polypeptide) provided in the
combinations herein can be modified by a polymer. In some examples,
the polymer is a polyalkylene glycol, dextran, pullulan or
cellulose. Polyalkylene glycol polymers, which can modify the
hyaluronan-degrading enzyme include polyethylene glycol (PEG) and
methoxypolyethylene glycol (mPEG). In examples where the
hyaluroanan-degrading enzyme is modified by PEG, the PEG can by
branched or linear. In some embodiments, the polymer can be
produced by reaction with methoxy-poly(ethylene
glycol)-succinimidyl butanoate (mPEG-SBA) (5 kDa);
methoxy-poly(ethylene glycol)-succinimidyl butanoate (mPEG-SBA) (20
kDa); methoxy-poly(ethylene glycol)-succinimidyl butanoate
(mPEG-SBA) (30 kDa); methoxy-poly(ethylene glycol)-succinimidyl
.alpha.-methylbutanoate (mPEG-SMB) (20 kDa); methoxy-poly(ethylene
glycol)-succinimidyl .alpha.-methylbutanoate (mPEG-SMB) (30 kDa);
methoxy-poly(ethylene glycol)-butyraldehyde (mPEG-butyraldehyde)
(30 kDa), methoxy-poly(ethylene glycol)-succinimidyl propionate
(mPEG-SPA) (20 kDa); methoxy-poly(ethylene glycol)-succinimidyl
propionate (mPEG-SPA) (30 kDa); (methoxy-poly(ethylene
glycol)).sub.2-N-hydroxysuccinimide ester (mPEG.sub.2-NHS) (10 kDa
branched); (methoxy-poly(ethylene
glycol)).sub.2-N-hydroxysuccinimide ester (mPEG.sub.2-NHS) (20 kDa
branched); (methoxy-poly(ethylene
glycol)).sub.2-N-hydroxysuccinimide ester (mPEG.sub.2-NHS) (40 kDa
branched); (methoxy-poly(ethylene
glycol)).sub.2-N-hydroxysuccinimide ester (mPEG.sub.2-NHS) (60 kDa
branched); biotin-poly(ethylene glycol)-N-hydroxysuccinimide ester
(biotin-PEG-NHS) (5 kDa biotinylated); poly(ethylene
glycol)-p-nitrophenyl carbonate (PEG-p-nitrophenyl-carbonate) (30
kDa); or poly(ethylene glycol)-propionaldehyde
(PEG-propionaldehyde) (30 kDa). In some embodiments, the polymer
can be a PEG that has a molecular weight of 30 or about 30
kilodaltons.
[1022] d. Antibodies to Treat Infectious Diseases
[1023] In some examples, any ADA2 provided herein, such as a
wildtype, variants and modified forms thereof, is administered with
one or more antibodies or antibody fragments to treat infectious
diseases. Examples of antibodies that can be co-administered to
treat infectious diseases include, but are not limited to,
anti-anthrax antibodies such as ABthrax, anti-CMV antibodies such
as CytoGam and sevirumab, anti-cryptosporidium antibodies such as
CryptoGAM, Sporidin-G, anti-helicobacter antibodies such as
Pyloran, anti-hepatitis B antibodies such as HepeX-B, Nabi-HB,
anti-HIV antibodies such as HRG-214, anti-RSV antibodies such as
felvizumab, HNK-20, palivizumab, RespiGam, and anti-staphylococcus
antibodies such as Aurexis, Aurograb, BSYX-A110, and SE-Mab.
[1024] e. Antibiotics and Antifungals
[1025] In some examples, any ADA2 provided herein, including
wildtype, variants and modified forms thereof, is administered with
one or more antibiotics, including but not limited to:
aminoglycoside antibiotics (e.g. apramycin, arbekacin,
bambermycins, butirosin, dibekacin, gentamicin, kanamycin,
neomycin, netilmicin, paromomycin, ribostamycin, sisomicin,
spectinomycin), aminocyclitols (e.g. spectinomycin), amphenicol
antibiotics (e.g. azidamfenicol, chloramphenicol, florfenicol, and
thiamphenicol), ansamycin antibiotics (e.g. rifamide and rifampin),
carbapenems (e.g. imipenem, meropenem, panipenem); cephalosporins
(e.g. cefaclor, cefadroxil, cefamandole, cefatrizine, cefazedone,
cefozopran, cefpimizole, cefpiramide, cefpirome, cefprozil,
cefuroxime, cefixime, cephalexin, cephradine), cephamycins
(cefbuperazone, cefoxitin, cefininox, cefmetazole, and cefotetan);
lincosamides (e.g. clindamycin, lincomycin); macrolide (e.g.
azithromycin, brefeldin A, clarithromycin, erythromycin,
roxithromycin, tobramycin), monobactams (e.g. aztreonam, carumonam,
and tigemonam); mupirocin; Oxacephems (e.g. flomoxef, latamoxef,
and moxalactam); penicillins (e.g. amdinocillin, amdinocillin
pivoxil, amoxicillin, bacampicillin, benzylpenicillinic acid,
benzylpenicillin sodium, epicillin, fenbenicillin, floxacillin,
penamecillin, penethamate hydriodide, penicillin o-benethamine,
penicillin O, penicillin V, penicillin V benzoate, penicillin V
hydrabamine, penimepicycline, and phenethicillin potassium);
polypeptides (e.g. bacitracin, colistin, polymixin B, teicoplanin,
vancomycin); quinolones (amifloxacin, cinoxacin, ciprofloxacin,
enoxacin, enrofloxacin, fleroxacin, flumequine, gatifloxacin,
gemifloxacin, grepafloxacin, lomefloxacin, moxifloxacin, nalidixic
acid, norfloxacin, ofloxacin, oxolinic acid, pefloxacin, pipemidic
acid, rosoxacin, rufloxacin, sparfloxacin, temafloxacin,
tosufloxacin, and trovafloxacin); rifampin; streptogramins (e.g.
quinupristin, dalfopristin); sulfonamides (sulfanilamide,
sulfamethoxazole); tetracyclines (chlortetracycline, demeclocycline
hydrochloride, demethylchlortetracycline, doxycycline, Duramycin,
minocycline, neomycin, oxytetracycline, streptomycin, tetracycline,
and vancomycin).
[1026] In some examples, any ADA2 provided herein, including
wildtype, variants and modified forms thereof, is administered with
one or more anti-fungal agents, including but not limited to
amphotericin B, ciclopirox, clotrimazole, econazole, fluconazole,
flucytosine, itraconazole, ketoconazole, miconazole, nystatin,
terbinafine, terconazole, and tioconazole. In some examples, an
ADA2 provided herein is administered with one or more antiviral
agents, including but not limited to protease inhibitors, reverse
transcriptase inhibitors, and others, including type I interferons,
viral fusion inhibitors, neuraminidase inhibitors, acyclovir,
adefovir, amantadine, amprenavir, clevudine, enfuvirtide,
entecavir, foscarnet, ganciclovir, idoxuridine, indinavir,
lopinavir, pleconaril, ribavirin, rimantadine, ritonavir,
saquinavir, trifluridine, vidarabine, and zidovudine.
I. EXAMPLES
[1027] The following examples are included for illustrative
purposes only and are not intended to limit the scope of the
invention.
Example 1
Cloning of Human Adenosine Deaminase 2 (ADA2) and Generation of
ADA2 Variants
[1028] A. Cloning of Wildtype (WT) ADA2
[1029] The wild type human adenosine deaminase (ADA2) gene
including its signal sequence (nucleic acid sequence set forth in
SEQ ID NO:1; encoding the amino acid sequence set forth in SEQ ID
NO:2 (precursor)) was amplified and cloned between the ScaI and
XhoI restriction sites of the pCMV-Script vector (Agilent
Technologies, Santa Clara, Calif.; Cat. No. 212220; sequence set
forth in SEQ ID NO:6). At the C-terminal end of the coding
sequence, the stop codon was replaced by nucleic acid sequence
encoding the FLAG.TM. tag (nucleic acid sequence set forth in SEQ
ID NO:8; encoding the amino acid sequence set forth in SEQ ID NO:9)
and a stop codon, for purposes of protein purification and/or
detection. The resulting construct pCMV-Script-hADA2-FLAG encodes
the WT recombinant human ADA2-FLAG polypeptide (amino acid sequence
set forth in SEQ ID NO:7).
[1030] B. Generation of ADA2 Variants
[1031] This resulting construct encoding the WT rHuADA2 described
above was used to introduce site-specific amino acid substitutions
to create ADA2 variants. As described in the subsections below,
site-specific amino acid substitutions were generated based on
modeling studies of ADA2 to identify residues indicated to be
involved in heparin binding, catalytic activity, and/or to
attenuate protein-protein interactions between ADA2 and any other
receptors to which ADA2 binds. Each of the generated ADA2 variant
was made from the pCMV-Script-hADA2-FLAG vector described above,
with site-specific substitutions using the QuikChange Lightning
Multi Site-Directed Mutagenesis Kit (Agilent Technologies, Santa
Clara, Calif.; Cat. No. 210514) according to the manufacturer's
instructions.
[1032] The generated variants are set forth in Table 7-12 below.
The variants are designated with Zavialov numbering, adopted from
the numbering used in the PDB accession Nos. 3LGG and 3LGD (amino
acid sequence of the polypeptide used for crystal structure set
forth in SEQ ID NO:4; based on Zavialov et al., J. Biol. Chem.
285:12367-12377 (2010)), and with mature ADA2 numbering, based on
the mature human ADA2 amino acid sequence set forth in SEQ ID NO:5
(based on Uniprot accession No. Q9NZK5; the precursor amino acid
sequence, containing amino acids residues 1-29 of the signal
sequence, is set forth in SEQ ID NO:2). Table 1 sets forth the
corresponding position numbers of Zavialov numbering (SEQ ID NO:4)
and mature ADA2 numbering (SEQ ID NO:5).
[1033] a. Candidate Variants with Altered Heparin Binding
[1034] Heparin is a naturally occurring glycosaminoglycan, widely
present on the surface of tissue throughout the body. ADA2 is known
to physically interact with heparin (Zavialov et al., J. Biol.
Chem. 285:12367-12377 (2010)), binding to heparin could deplete
circulating levels of administered ADA2. To generate ADA2 variants
with improved pharmacokinetics, replacement of residues identified
herein, based on modeling studies, as involved in heparin binding
were made. Two available crystal structures of human ADA2, as
described in Zavialov et al., J. Biol. Chem. 285:12367-12377
(2010), were used to identify candidate positions for mutagenesis:
crystal structure of ADA2 lacking bound heparin and expressed from
drosophila cells (RCSB Protein Data Bank (PDB) No. 3LGG; human ADA2
bound to the transition state analog coformycin); and human ADA2 in
the apo form (Protein Data Bank accession No. 3LGD; empty enzyme
without any cofactors or substrates bound). From the crystal
structures, electrostatic surface potential was calculated to
identify surfaces on ADA2 that possess positive electrostatic
potential, using the open source 3D molecular visualization package
PyMOL. Surfaces with positive electrostatic potential can form
complementary electrostatic interactions with the highly negatively
charged heparin sulfate. From the electrostatic surface potential
calculations, a set of lysine and arginine residues were identified
as candidate sites for substitution with the amino acids alanine
(for replacement of the positively charged lysine or arginine side
chain with a methylene group without impacting the protein phi-psi
angles), aspartate or glutamate (the two known negatively charged
amino acids), to generate a charge repulsion between heparin and
the ADA2 variant.
[1035] Based on the modeling, amino acid residues 14, 16, 23, 29,
220, 261, 280, 286, 312, 320, 324, 369, 374, 375, 444, 447, 455,
464, 472 or 473 by Zavialov numbering (corresponding to residues
11, 13, 20, 26, 217, 258, 277, 283, 309, 317, 321, 352, 366, 371,
372, 441, 444, 452, 461, 469 or 470, respectively, by mature
numbering) were targeted for mutagenesis. ADA2 variants were
generated by amino acid replacement of the amino acid at the
position to alanine, aspartate or glutamate. Single amino acid
replacements, as well as double and triple amino acid replacements
also were made. Table 7 sets forth the amino acid replacements in
exemplary candidate variants. Example 7 describes studies assessing
the heparin binding and adenosine deaminase activity of select
candidate variants set forth in Table 7.
TABLE-US-00007 TABLE 7 Candidate ADA2 Variants for Attenuated
Heparin Binding Properties (HBP) Replacement (Zavialov Replacement
(mature ADA2 numbering) numbering) SEQ ID NO: K14A K11A 13 K14D
K11D 14 K14E K11E 15 K16A K13A 16 K16D K13D 17 K16E K13E 18 R23A
R20A 28 R23D R20D 29 R23E R20E 30 K29A K26A 71 K29D K26D 72 K29E
K26E 73 R220A R217A 74 R220D R217D 75 R220E R217E 76 K261A K258A 77
K261D K258D 78 K261E K258E 79 R280A R277A 80 R280D R277D 81 R280E
R277E 82 R286A R283A 83 R286D R283D 84 R286E R283E 85 K312A K309A
86 K312D K309D 87 K312E K309E 88 K320A K317A 89 K320D K317D 90
K320E K317E 91 K324A K321A 92 K324D K321D 93 K324E K321E 94 R355A
R352A 95 R355D R352D 96 R355E R352E 97 R369A R366A 31 R369D R366D
32 R369E R366E 33 K374A K371A 19 K374D K371D 20 K374E K371E 21
K375A K372A 22 K375D K372D 23 K375E K372E 24 R444A R441A 98 R444D
R441D 99 R444E R441E 100 K447A K444A 101 K447D K444D 102 K447E
K444E 103 K455A K452A 25 K455D K452D 26 K455E K452E 27 K464A K461A
104 K464D K461D 105 K464E K461E 106 K472A K469A 107 K472D K469D 108
K472E K469E 109 K473A K470A 110 K473D K470D 111 K473E K470E 112
K14A/R23A K11A/R20A 55 K14A/R23A/K374A K11A/R20A/K371A 56
R23A/K374A R20A/K371A 57 K14A/K374A K11A/K371A 58
b. Candidate Active Site (AS) Variants
[1036] To generate ADA2 variants with improved catalytic
efficiency, candidate variants were generated by replacement of
amino acid residues in the active site as identified based on
molecular modeling studies. The crystal structures of human ADA2,
bound to the transition state analog coformycin (Protein Data Bank
accession No. 3LGG) and in the apo form (Protein Data Bank
accession No. 3LGD), as described above, were visualized using the
open source 3D molecular modeling program PyMol. In silico site
directed mutagenesis was performed using PyMol to evaluate the
packing of introduced amino acid side chains to adenosine or
adjacent residues within the active site, assess packing to
adjacent residues near the active site or on the active pocket
cleft, measure distances and potential for steric clashes of
introduced residues, asses changes to the relative concavity of the
active site pocket, and assess the potential for adenosine to
access the active site. The selected residues targeted for
mutagenesis were those identified herein as candidates for
effecting improved catalytic efficiency (k.sub.cat/K.sub.m) for
adenosine, and thereby have increased adenosine deaminase
activity.
[1037] Based on the modeling, amino acid residues 89, 182, 222,
224, 265, 267, 269, 270 and 299 by Zavialov numbering
(corresponding to residues 86, 179, 219, 221, 262, 264, 266, 267,
or 296, by mature numbering) were targeted for mutagenesis. ADA2
variants were generated by amino acid replacement of the amino acid
at the position to all nineteen other amino acids. Table 8 sets
forth the amino acid replacements of exemplary candidate variants.
Example 10 describes studies assessing the adenosine deaminase
activity of select candidate variants.
TABLE-US-00008 TABLE 8 Candidate rHuADA2 Active Site (AS) variants
Replacement (Zavialov Replacement (mature numbering) numbering) SEQ
ID NO: D89A D86A 113 D89C D86C 114 D89E D86E 115 D89F D86F 116 D89G
D86G 117 D89H D86H 118 D89I D86I 119 D89K D86K 120 D89L D86L 121
D89M D86M 122 D89N D86N 123 D89P D86P 124 D89Q D86Q 125 D89R D86R
126 D89S D86S 127 D89T D86T 128 D89V D86V 129 D89W D86W 130 D89Y
D86Y 131 E182A E179A 46 E182C E179C 132 E182D E179D 45 E182F E179F
133 E182G E179G 50 E182H E179H 134 E182I E179I 135 E182K E179K 136
E182L E179L 137 E182M E179M 138 E182N E179N 139 E182P E179P 140
E182Q E179Q 141 E182R E179R 142 E182S E179S 47 E182T E179T 48 E182V
E179V 49 E182W E179W 143 E182Y E179Y 144 R222A R219A 41 R222C R219C
145 R222D R219D 146 R222E R219E 147 R222F R219F 148 R222G R219G 149
R222H R219H 150 R222I R219I 151 R222K R219K 38 R222L R219L 152
R222M R219M 153 R222N R219N 40 R222P R219P 154 R222Q R219Q 39 R222S
R219S 155 R222T R219T 156 R222V R219V 157 R222W R219W 158 R222Y
R219Y 159 L224A L221A 42 L224C L221C 160 L224D L221D 161 L224E
L221E 162 L224F L221F 163 L224G L221G 44 L224H L221H 164 L224I
L221I 165 L224K L221K 166 L224M L221M 167 L224N L221N 168 L224P
L221P 169 L224Q L221Q 170 L224R L221R 171 L224S L221S 172 L224T
L221T 173 L224V L221V 43 L224W L221W 174 L224Y L221Y 175 S265A
S262A 51 S265C S262C 176 S265D S262D 177 S265E S262E 178 S265F
S262F 179 S265G S262G 180 S265H S262H 181 S265I S262I 182 S265K
S262K 183 S265L S262L 184 S265M S262M 53 S265N S262N 54 S265P S262P
185 S265Q S262Q 186 S265R S262R 187 S265T S262T 188 S265V S262V 52
S265W S262W 189 S265Y S262Y 190 H267A H264A 34 H267C H264C 191
H267D H264D 192 H267E H264E 193 H267F H264F 194 H267G H264G 37
H267I H264I 195 H267K H264K 196 H267L H264L 197 H267M H264M 198
H267N H264N 36 H267P H264P 199 H267Q H264Q 35 H267R H264R 200 H267S
H264S 201 H267T H264T 202 H267V H264V 203 H267W H264W 204 H267Y
H264Y 205 S269A S266A 206 S269C S266C 207 S269D S266D 208 S269E
S266E 209 S269F S266F 210 S269G S266G 211 S269H S266H 212 S269I
S266I 213 S269K S266K 214 S269L S266L 215 S269M S266M 216 S269N
S266N 217 S269P S266P 218 S269Q S266Q 219 S269R S266R 220 S269T
S266T 221 S269V S266V 222 S269W S266W 223 S269Y S266Y 224 K270A
K267A 225 K270C K267C 226 K270D K267D 227 K270E K267E 228 K270F
K267F 229 K270G K267G 230 K270H K267H 231 K270I K267I 232 K270L
K267L 233 K270M K267M 234 K270N K267N 235 K270P K267P 236 K270Q
K267Q 237 K270R K267R 238 K270S K267S 239 K270T K267T 240 K270V
K267V 241 K270W K267W 242 K270Y K267Y 243 V299A V296A 244 V299C
V296C 245 V299D V296D 246 V299E V296E 247 V299F V296F 248 V299G
V296G 249 V299H V296H 250 V299I V296I 251 V299K V296K 252 V299L
V296L 253 V299M V296M 254 V299N V296N 255 V299P V296P 256 V299Q
V296Q 257 V299R V296R 258 V299S V296S 259 V299T V296T 260 V299W
V296W 261 V299Y V296Y 262
c. Candidate Variants with Altered Glycosylation
[1038] To generate ADA2 variants that are hyperglycosylated,
candidate variants were generated by mutation (e.g. insertion
and/or amino acid replacement) of residues to create an
N-glycosylation site by incorporation of a new N-glycosylation site
motif (Asn-Xaa-Ser/Thr). Table 9 sets forth the mutations of
exemplary candidate variants.
TABLE-US-00009 TABLE 9 Candidate rHuADA2 hyperglycosylation
variants Mutation (Zavialov numbering) Mutation (mature numbering)
SEQ ID NO: --.fwdarw.N4/--.fwdarw.A5/--.fwdarw.S6
--.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3 274 R23N/V25S R20N/V22S 275
K374N/D376S K371N/D373S 276 K375N/I377S K372N/I374S 277 T406N/H408S
T403N/H405S 278 G407N/P409S G404N/P406S 279
[1039] d. Candidate Variants Lacking the Receptor Binding (PRB)
Domain
[1040] To generate ADA2 variants that lack the receptor binding
(PRB) domain, residues V102-Q147 (V99-Q144 by mature numbering) or
C108-T150 (C105-T147 by mature numbering) were deleted and replaced
with a glycine linker of various lengths (e.g., 3, 5, 7, 10 or 15;
see SEQ ID NO:280) or (GGGGS)n linker of various length (e.g., n=1,
2 or 3; see SEQ ID NOS:581 and 582). Table 10 sets forth the
mutations of exemplary candidate variants.
TABLE-US-00010 TABLE 10 Candidate rHuADA2 PRB domain deletion
variants SEQ ID Mutation (Zavialov numbering) Mutation (mature
numbering) NO: C108-T150del.fwdarw.(Gly).sub.15
C105-T147del.fwdarw.(Gly).sub.15 281
C108-T150del.fwdarw.(Gly).sub.10 C105-T147del.fwdarw.(Gly).sub.10
282 C108-T150del.fwdarw.(Gly).sub.7 C105-T147del.fwdarw.(Gly).sub.7
283 C108-T150del.fwdarw.(Gly).sub.5 C105-T147del.fwdarw.(Gly).sub.5
284 C108-T150del.fwdarw.(Gly).sub.3 C105-T147del.fwdarw.(Gly).sub.3
285 V102-Q147del.fwdarw.(GGGGS).sub.1
V99-Q144del.fwdarw.(GGGGS).sub.1 583
V102-Q147del.fwdarw.(GGGGS).sub.2 V99-Q144del.fwdarw.(GGGGS).sub.2
584 V102-Q147del.fwdarw.(GGGGS).sub.3
V99-Q144del.fwdarw.(GGGGS).sub.3 585
C108-T150del.fwdarw.(GGGGS).sub.1 C105-T147del.fwdarw.(GGGGS).sub.1
586 C108-T150del.fwdarw.(GGGGS).sub.2
C105-T147del.fwdarw.(GGGGS).sub.2 587
C108-T150del.fwdarw.(GGGGS).sub.3 C105-T147del.fwdarw.(GGGGS).sub.3
588
[1041] e. Candidate Variants with Altered Glycosylation in the
Receptor Binding (PRB) Domain
[1042] To disrupt the potential interaction of ADA2 with potential
receptors through the receptor binding (PRB), ADA2 candidate
variants were generated by introducing mutation (e.g. insertion
and/or amino acid replacement) of residues to create an
N-glycosylation site by incorporation of a new N-glycosylation site
motif (Asn-Xaa-Ser/Thr) in the PRB domain. Table 11 sets forth the
mutations of exemplary candidate variants.
TABLE-US-00011 TABLE 11 Candidate rHuADA2 PRB domain
hyperglycosylation variants Mutation (Zavialov Mutation (mature
numbering) numbering) SEQ ID NO: R128N/P129A R125N/P126A 552
S130N/K132S S127N/K129S 553 P129N/E131T P126N/E128T 554 R115N/I117T
R112N/I114T 555 I137N/L138C/L139T I134N/L135C/L136T 556
I137N/L138S/L139T I134N/L135S/L136T 557 R145N/Q147S R142N/Q144S 558
E140N/Y142T E137N/Y139T 559 P114N/G116S P111N/G113S 560
[1043] f. Candidate Variants with Altered Interaction Between
Receptor Binding (PRB) Domain and the ADA Domain
[1044] To generate ADA2 variants that have altered interaction
between the receptor binding (PRB) domain and the rest of ADA2
(e.g., the adenosine deaminase (ADA) domain), mutation(s) were
introduced in individual or multiple amino acids in the PRB domain.
Structure based design was used to identify residues on the surface
of ADA2 in the context of its three dimensional structure that
could disrupt the ability of the PRB domain to interact with other
contact residues outside of the PRB domain in ADA2. Table 12 sets
forth the mutations of exemplary candidate variants.
TABLE-US-00012 TABLE 12 Candidate rHuADA2 PRB domain interaction
variants Mutation (Zavialov numbering) Mutation (mature numbering)
SEQ ID NO: F122S F119S 561 F122K F119K 562 Y227R Y224R 563 Y227N
Y224N 564 Y194S Y191S 565 Y194D Y191D 566 F186K F183K 567
Y194D/Y227R Y191D/Y224R 568 F112S F109S 569 F112A F109A 570 R121D
R118D 571 R121A R118A 572 Y142T Y139T 573 Y142A Y139A 574 W136S
W133S 575 W136T W133T 576 P127A P124A 577 P127S P124S 578
Example 2
Production of Recombinant Human Adenosine Deaminase 2 (rHuADA2) and
Variants
[1045] A. Transient Expression
[1046] For transient expression of wildtype ADA2 and variants
generated in Example 1, 300 ml of 1.0.times.10.sup.6 cells/ml CHO-S
cells (Invitrogen, Cat. No. 11619-012) were transfected with 375
.mu.g of pCMV-Script-hADA2-FLAG plasmid or variant plasmid using
FreeStyle.TM. MAX Reagent (Life Technologies, Carlsbad, Calif.;
Cat. No. 16447-500). Transfected cells were grown for 4 days, and
culture supernatant was collected by centrifugation at 100 rpm for
10 min.
[1047] The collected supernatant was used to purify the protein,
either mature ADA2 set forth in SEQ ID NO:5 or a mature variant
(e.g. variants set forth in Tables 7-12), each with a FLAG tag.
Batch purification was performed using an anti-FLAG M2 affinity
resin (Sigma-Aldrich, St. Louis, Mo., Cat. No. A2220), following
the manufacturer's instructions. ADA2 were eluted from the resin
using FLAG.TM. peptide. Purity of the eluted protein was assessed
using SDS-PAGE and size-exclusion chromatography (SEC). SEC results
confirmed that the purified protein was a dimer. N-terminal
sequencing also was performed and confirmed the signal sequence
corresponds to amino acid residues 1-29 of SEQ ID NO:2, such that
the mature protein as purified begins with amino acid residues IDET
as set forth in SEQ ID NO:5.
[1048] C. Cloning and Stable Expression
[1049] The wild type human ADA2 gene (nucleic acid sequence set
forth in SEQ ID NO:1) or variant with a C-terminal FLAG.TM. tag
(nucleic acid sequence set forth in SEQ ID NO:8; encoding the amino
acid sequence set forth in SEQ ID NO:9) was subcloned into the
multiple cloning site (MCS) of lentiviral expression vector
pLV-EF1a-MCS-IRES-GFP-Bsd. The resulting expression vector,
pLV-EF1a-hADA2-Flag-IRES-GFP-Bsd (nucleic acid sequence set forth
in SEQ ID NO:10) was used to generate a lentivirus capable of
stably transfecting CHO-S cells. In the expression vector,
expression of the recombinant human ADA2 gene was driven by the
EF1a promoter. An IRES sequence was inserted after the transgene
followed by the cDNA for green fluorescent protein (GFP) used for
identification of transduced cells by microscopy, in combination
with the blasticidin resistance gene (Bsd) used for selection of
transduced cells. The Woodchuck Hepatitis Virus Posttranscriptional
Regulatory Element (WPRE) was inserted after the GFP-Bsd sequence
to enhance gene expression.
[1050] The constructed lentivirus expression vector
pLV-EF1a-hADA2-Flag-IRES-GFP-Bsd was used to produce lentivirus as
described in the ViraPower.TM. (Invitrogen, Carlsbad, Calif.)
manufacturer's instruction manual. Briefly, 293FT cells were plated
at 6.times.10.sup.6 cells onto 10 cm tissue culture plates. After
24 hours, 9 .mu.g of the ViraPower.TM. Packaging Mix (containing a
mixture of the pLP1, pLP2, and pLP/VSVG plasmids at 1 .mu.g/.mu.l
in TE Buffer, pH 8.0 as supplied by manufacturer) and 3 .mu.g of
the pLV-EF1a-hADA2-Flag-IRES-GFP-Bsd lentiviral expression plasmid
were mixed in 1.5 mL Opti-MEM (Life Technologies) medium. 36 .mu.L
of Lipofectamine.TM. 2000 (LF2000; Life Technologies, Carlsbad,
Calif.) were diluted into 1.5 mL Opti-MEM (Life Technologies). The
DNA and LF2000 were mixed gently, and incubated at room temperature
for 20 minutes to allow the DNA and lipid to form complexes. In the
meantime, the overnight culture medium was replaced with 5.0 mL
Opti-MEM+10% FBS without antibiotics. The DNA-LF2000 complexes were
added to the 293FT cells for transfection. The cells were incubated
overnight at 37.degree. C. in a humidified 5% CO.sub.2 incubator.
The medium containing the DNA-LF2000 complexes was replaced with 10
mL complete medium and the cells were incubated overnight at
37.degree. C. in a humidified 5% CO.sub.2 incubator. The
supernatant was collected at 48 hours post-transfection and the
medium was transferred to a sterile storage tube. The
virus-containing medium was centrifuged at 3000 rpm for 5 minutes
to pellet any 293FT cells that were carried over during collection.
The supernatant was carefully transferred to a sterile storage
tube.
[1051] For transduction, CHO-S cells (Life Technologies, Carlsbad,
Calif.; Cat. No. 16447-500) were cultured in CD CHO medium (Life
Technologies, Carlsbad, Calif.; Cat. No. 10743-029). Transduction
of the CHO-S cell line was performed in six-well plates containing
2.times.10.sup.7 lentiviral infectious units (IU) and
2.times.10.sup.6 CHO-S cells in 2 mL of CD-CHO medium supplemented
with 4 mM Glutamax (Invitrogen, Carlsbad Calif.) and 4 .mu.g/mL
hexadimethrine bromide (Polybrene; Biosettia, San Diego, Calif.).
Infected cells were incubated with shaking at about 30 rpm at
37.degree. C. in a humidified-air incubator with 5% CO.sub.2 for 6
hours. The cells were then harvested and centrifuged at low speed
(1000.times.g, 5 min) and the transduction medium was removed and
replaced with fresh CD-CHO medium. The cells were transferred to a
T-25 mL vented flask and returned to the incubator. Four days after
initial infection, the medium was supplemented with 1 .mu.g/mL of
blasticidin (Invitrogen, Carlsbad, Calif.). The medium was changed
every 3-4 days until the confluency of the CHO-S cells reached
approximately 90% and cells began to detach from the flasks. The
cells were transferred to shaker flasks for expansion, cell banking
and protein production.
[1052] Conditioned medium was collected to purify the protein,
either mature ADA2 set forth in SEQ ID NO:5 or a mature variant
(e.g. set forth in Tables 7-12), each with a FLAG tag. Two to five
liters of conditioned medium was harvested and passed over an
anti-FLAG M2 affinity resin (Sigma-Aldrich, St. Louis, Mo., Cat.
No. A2220). The resin was equilibrated with approximately 10 bed
volumes of wash buffer (Tris Buffered Saline (TBS), pH 7.5) at a
flow rate of 4 mL/min before loading the conditioned medium. The
loaded column was then washed with .about.10 bed volumes of TBS and
then connected to an AKTA Purifier (GE Healthcare, Pittsburgh,
Pa.), and the bound protein was eluted using a low pH buffer (0.1 M
of Glycine-HCl at pH 2.7). The fractions were immediately
neutralized with 1/10 volume of 1 M Tris-HCl, pH 8.8.
[1053] The fractions of purified protein were pooled and dialyzed
in 4 liters of PBS with two buffer changes using a Slide-A-Lyzer
Dialysis Cassette (20 kD MWCO; Thermo Fisher Scientific, Rockford,
Ill.). The dialyzed protein product was then concentrated using an
Amicon Ultra centrifugal concentrator (30 kD MWCO; EMD Milipore,
Billerica, Mass.) and the final protein concentration determined
using the Pierce.TM. BCA Protein Assay Kit (Thermo Fisher
Scientific, Rockford, Ill.). Purity of the preparation was assessed
using SDS-PAGE, and adenosine deaminase activity was tested as
described below in Example 4.
[1054] Purity of the rHuADA2-FLAG protein preparation, as assessed
by SDS-PAGE was 95% or greater. The preparation was also
characterized by size-exclusion chromatography (SEC), which showed
that the rHuADA2-FLAG protein was present as a single molecular
weight species with greater than 95% purity as assessed by area
under the curve (AUC) calculations.
[1055] Alternatively, the wild type rHuADA2 and variants were
expressed using the CHO Freedom CHO-S Kit (Invitrogen) according to
the manufacturer's specification and purified as described
above.
Example 3
Production of Recombinant Human Adenosine Deaminase 1 (rHuADA1)
[1056] A. Cloning of Wildtype (WT) ADA1
[1057] The human adenosine deaminase 1 (ADA1) gene (nucleic acid
sequence set forth in SEQ ID NO:11; encoding the amino acid
sequence set forth in SEQ ID NO:12) was amplified and cloned into
the pD444-SR: T5-sRBS-ORF (DNA 2.0, Menlo Park, Calif.; Cat. No.
FPB-27-444) E. coli expression vector, under the control of an
Isopropyl-.beta.-D-thiogalactopyranoside (IPTG) inducible promoter
(DNA 2.0, Menlo Park, Calif.). The construct also contained a
linker (amino acid sequence set forth in SEQ ID NO:64) and a
C-terminal Strep-tag (amino acid sequence set forth in SEQ ID
NO:65) to facilitate affinity purification of the protein. The
amino acid sequence of the encoded ADA1-Strep is set forth in SEQ
ID NO:3. In the mature form of the protein, the N-terminal
methionine residue is removed, so that the mature ADA1-Strep
polypeptide has the amino acid sequence set forth in SEQ ID NO:67
(corresponding to a mature polypeptide sequence set forth in SEQ ID
NO:66, without the Strep tag).
[1058] B. Generation of ADA1 Variants
[1059] This resulting construct encoding the WT rHuADA1-Strep was
used to introduce site-specific amino acid substitutions to create
ADA1 variant C74S, with numbering based on the mature ADA1 set
forth in SEQ ID NO:67 (corresponding to C75S with number based on
polypeptide set forth in SEQ ID NO:12). The variant was generated
as a candidate to stabilize activity because a solvent exposed
cysteine residue in ADA1 could be oxidized in plasma and negatively
impact enzymatic activity in the plasma. Site-specific substitution
was made using the QuikChange Lightning Multi Site-Directed
Mutagenesis Kit (Agilent Technologies, Santa Clara, Calif.; Cat.
No. 210514) according to the manufacturer's instructions. In the
mature form of the protein, the mature C74S-ADA1-Strep variant has
the sequence of amino acids set forth in SEQ ID NO:69
(corresponding to a mature polypeptide sequence set forth in SEQ ID
NO:70, without the Strep tag).
[1060] C. Expression in E. coli
[1061] For expression of wildtype ADA1 and variant, the resulting
cloned construct was transformed into Escherichia coli BL21-DE3
(Calbiochem, San Diego, Calif.). The transformed bacteria were
plated onto Luria Broth (LB) agar-ampicilin plates (TekNova,
Hollister, Calif.) and single colony selected for large scale
culture. The bacteria from the selected colony was grown overnight
(37.degree. C., 200 rpm) in LB medium supplemented with the
antibiotic carbenicillin (50 .mu.g/mL; EMD Millipore, Billerica,
Mass.). The culture was used to seed large shaker cultures. The
culture was allowed to grow until it reached an OD.sub.600 of
approximately 0.8 and then expression of protein was induced by the
addition of 1 mM IPTG The culture was then transferred to a
25.degree. C. incubator and allowed to grow overnight (.about.15
hours) with shaking at 200 rpm. The following day, the bacterial
cells were centrifuged at 9000.times.g for 30 min and the cells in
the pellet were lysed by sonication using a Branson Sonifier 250
(Emerson, Danbury, Conn.) using repeated pulsing on ice at 20% duty
cycle for approximately 5 min. The bacterial lysate was then
incubated with lysozyme (100 .mu.g/mL; Sigma-Aldrich, St. Louis,
Mo.) and Benzonase (50 U/mL; Sigma-Aldrich, St. Louis, Mo.) for
four hours at 4.degree. C. with gentle stirring. The bacterial
lysate was centrifuged (5000.times.g; 45 min) to remove cell
debris.
[1062] The culture lysate was used to purify the protein, either
mature ADA1 set forth in SEQ ID NO:66 or a mature C74S-ADA1 variant
set forth in SEQ ID NO:69, each with a Strep tag. The clarified
lysate was removed and sterile filtered prior to being loaded onto
a StrepTrap.TM. columns containing StrepTactin.TM. affinity resins
(5 mL capacity; GE Healthcare, Pittsburgh, Pa.). The column was
then connected to an AKTA purifier and protein was eluted using a
solution of 2.5 mM d-desthiobiotin in buffer (100 mM Tris-HCl, pH
8.0, 150 mM NaCl, 1 mM EDTA). The fractions containing the purified
protein were pooled and dialyzed at 4.degree. C. in 4 liters of
1.times. Phosphate Buffered Saline (PBS) buffer for 4 hours with
two buffer changes using a Slide-A-Lyzer Dialysis Cassette (20 kD
MWCO; Thermo Fisher Scientific, Rockford, Ill.). The protein
preparation was then concentrated using an Amicon Ultra centrifugal
concentrator (30 kD MWCO; EMD Milipore, Billerica, Mass.) and the
final protein concentration determined using the Pierce.TM. BCA
Protein Assay Kit (Thermo Fisher Scientific, Rockford, Ill.). The
purity of the protein preparation, as assessed by SDS-PAGE was 95%
or greater.
Example 4
Adenosine Deaminase Enzymatic Activity Test
[1063] Adenosine deaminase activity was determined using an
adenosine deaminase (ADA) assay kit (Genway, San Diego, Calif.;
Cat. No. BQ014EALD) with minor modifications. The ADA assay is
based on the enzymatic deamination of adenosine to inosine, which
is converted to hypoxanthine by purine nucleoside phosphorylase
(PNP). Hypoxanthine is then converted to uric acid and hydrogen
peroxide by xanthine oxidase (XOD). Hydrogen peroxide is further
reacted with N-Ethyl-N-(2-hydroxy-3-sulfopropyl)-3-methylaniline
(EHSPT) and 4-aminoantipyrine (4-AA) in the presence of peroxidase
(POD) to generate quinone dye, which is monitored in a kinetic
manner.
[1064] Briefly, 5 .mu.L samples in duplicates (at appropriate
dilutions to measure steady-state, non-saturating enzyme activity)
were added to 120 .mu.L R1 reagent (provided by the manufacturer;
50 mM Tris HCL, pH 8.0, 2 mM 4-AA, 0.1 U/mL PNP, 0.2 U/mL XOD, 0.6
U/mL peroxidase) in a 96 well plate, according to manufacturer's
instructions. The mixtures were incubated at 37.degree. C. for
approximately 5 min and 60 .mu.L of R2 reagent (provided by the
manufacturer; 50 mM Tris HCl, pH 4.0, 10 mM Adenosine, 2 mM EHSPT)
was added to the mixtures. Then, change in absorbance (AA) at 556
nm over time at 37.degree. C. was measured. One unit of ADA is the
amount of ADA that generates one .mu.mole of inosine from adenosine
per minute at 37.degree. C. Adenosine deaminase activity in mU/mL
was calculated using the following formula:
1
mU/mL=(.DELTA.A/min.times.T.sub.v)/(S.sub.v.times..epsilon..times.1)
[1065] where T.sub.v=total volume (185 .mu.L), S.sub.v=sample
volume (5 .mu.L), .epsilon.=32.2.times.10.sup.-3 .mu.M.sup.-1
cm.sup.-1, 1=0.5 cm.
Example 5
In Vitro Plasma Stability of ADA1 Versus ADA2
[1066] The enzymatic activity of the purified preparation of WT
rHuADA1, rHuADA1-C74S and rHuADA2, before and after incubation in
mammalian plasma over a 24 hour time period, was assayed to test
the stability of the recombinant protein preparations. The variant
rHuADA1-C74S also was tested to determine whether stability in
plasma can be improved by substitution of the solvent-exposed
cysteine residue.
[1067] A. Incubation of Purified rHuADA1 and rHuADA2 Preparations
in Plasma
[1068] Purified rHuADA1, rHuADA2 and rHuADA1-C74S preparations were
individually added to ex vivo 25% BALB/c mouse plasma at a final
concentration of 0.17 mg/ml (corresponding to an approximate
equivalent dose of 10 mg/kg equivalent in a mouse). The samples
were incubated at 37.degree. C. for 24 hours. As a control,
proteins were individually incubated at a concentration of 0.17
mg/ml in PBS containing 0.2% BSA (as a stabilizer). At 0, 4 and 24
hours after incubation, 3 small aliquots of each plasma incubated
sample and each PBS incubated controls were removed and stored at
-20.degree. C. until subsequent analysis.
[1069] The stability of the proteins in ex vivo plasma after
incubation was determined by comparing the changes in adenosine
deaminase enzymatic activity using the method described in Example
4. The molecular weight and stability of the protein also was
examined by Western blot to detect any possible protein
degradation. Approximately 200 ng of protein were individually
assayed using Western blot and the protein bands were detected
using ECL (Bio-Rad Laboratories, Hercules, Calif.).
Rabbit-anti-human ADA1 (Abcam, Cambridge, Mass.) and
goat-anti-rabbit-horseradish peroxidase (HRP) (EMD Millipore,
Billerica, Mass.) were used as primary and secondary antibodies,
respectively, for rHuADA1. Anti-FLAG-HRP (Abcam) was used to detect
rHuADA2.
[1070] B. Results
[1071] 1. rHuADA1 Stability
[1072] Table 13 shows the mean and standard deviation (stdev) of
the adenosine deaminase activity test of WT rHuADA1 and
rHuADA1-C74S. The results show that there was a significant
reduction of rHuADA1 activity after a 24-hour incubation in plasma
at 37.degree. C. For example, less than 1% of activity was retained
after treatment with plasma for 24 hours, whereas greater than 80%
of activity was retained when in the PBS/BSA control for the same
time period. The observed decrease in activity was not caused by
protein degradation, since the protein level was relatively
constant at all time-points, as measured by western blot.
[1073] The results also show that the solvent-exposed cysteine
residue (C74) does not account for the negative impact on enzyme
activity in plasma, since similar results were obtained for the
C74S variant. For example, despite not possessing the exposed thiol
at position 74, the variant still showed a strong decrease in
activity after a 24 hour incubation in plasma. The results showed
that after 24 hours, about 1% of activity of the variant enzyme was
retained after treatment with plasma, whereas greater than 80% of
activity was retained when in the PBS/BSA control.
[1074] Normally, ADA1 is expressed in an intracellular manner and
is known to translocate and associate with extracellular dipeptidyl
peptidase-4 (DPPIV). These results demonstrate that outside of this
environment, ADA1 is rapidly inactivated by exposure to plasma, and
that the mutation of the surface exposed cysteine 74 did not
prevent inactivation.
TABLE-US-00013 TABLE 13 rHuADA1 and rHuADA1-C74S activity after
serum incubation PBS Plasma incubated incubated PBS Plasma mean
mean incubated incubated Time (hr) (mU/mL) (mU/mL) Stdev Stdev
rHuADA1 0 61,077.0 71,663.6 2,352.2 2,461.4 4 59,544.8 46,772.1
3,352.5 4,645.3 24 50,287.9 673.6 700.5 135.7 rHuADA1- 0 43,031.9
59,632.4 2,695.6 4,890.5 C74S 4 44,682.4 39,636.7 3,739.6 1,671.4
24 37,492.2 616.6 751.4 44.7
[1075] 2. rHuADA2 Stability
[1076] Table 14 below shows the mean and standard deviation (stdev)
of the adenosine deaminase activity test of rHuADA2 after a 24 hour
incubation with plasma. In contrast to the results for ADA1, the
results show that ADA2 was substantially more stable in plasma
after a 24-hour incubation at 37.degree. C. For example, about 65%
of activity was retained after treatment with plasma for 24 hours,
whereas no change in activity was observed when treated with
PBS/BSA control for the same time period.
TABLE-US-00014 TABLE 14 rHuADA2 activity after serum incubation
Plasma Time PBS incubated Plasma incubated PBS incubated incubated
(hr) mean (mU/mL) mean (mU/mL) Stdev Stdev 0 9,140.5 10,988.4
1,058.8 1,827.9 4 9,584.6 10,936.1 1,697.8 1,784.5 24 9,832.1
7,147.8 1,310.6 1,014.8
Example 6
Effect of ADA2 on Adenosine-Mediated Modulation of Immune
Response
[1077] Extracellular adenosine is an inflammatory modulator of
immune responses, and elevated levels of adenosine in the tumor
microenvironment could reduce and/or inhibit the effector function
of T and NK cells, thus favoring tumor growth. To assess if effects
of adenosine can be monitored by assessing immune cell
proliferation, proliferation experiments were performed with a
mixture of NK and T cells (NK/T). In addition, experiments were
performed to assess if rHuADA2, through its enzymatic conversion of
adenosine to inosine, can rescue the immune cells from
adenosine-mediated proliferation inhibition.
[1078] A. Assessing Effects of Adenosine on NK/T Cell
Proliferation
[1079] A mixture of NK and T cells (NK/T) were prepared from
healthy donor's peripheral blood mononuclear cells (PBMC). Briefly,
10.times.10.sup.7 HumanPBMCs were cultured for 6-7 days in Stem
cell growth medium (SCGM; Order No. 20802-0500, CellGenix,
Freiburg, Germany) with 5% human serum from donors with blood type
AB (human AB serum; Cat. No. 35-060-C1, Mediatech, Mannassas, Va.)
in the presence of 20 ng/mL anti-CD3 eBioscience, San Diego,
Calif.; Cat. No. 16-0039) and 500 IU/mL recombinant human
interleukin 2 (rhIL-2; Cat. No. 200-02, PeproTech, Rocky Hill,
N.J.). The cells were then cultured for an additional 2-3 weeks in
SCGM in the presence of 500 IU/mL rhIL-2. NK/T cells cultured for
2-4 weeks were used in experiments.
[1080] To test the adenosine-mediated inhibition of NK/T cells
proliferation, NK/T cells (10,000 cells/well) were plated in a 96
well white plate with clear bottoms in 200 .mu.L volume. The cells
were treated with 20 .mu.L adenosine (SKU No. A925, Sigma Aldrich)
at concentrations resulting from a 3-fold dilution series starting
at 1 mM, i.e. 1 mM, 300 .mu.M, 100 .mu.M, 30 .mu.M, 10 .mu.M, 3
.mu.M, 1 .mu.M, 0.3 .mu.M and 0.1 .mu.M. The NK/T cells were
allowed to grow for 5 days in a humidified tissue culture incubator
at 37.degree. C. with 5% CO.sub.2. After 5 days of treatment, the
cells were centrifuged in a 96 well plate at 12,000 rpm for 5 min.
100 .mu.L of medium was removed from each well of cells, followed
by addition of 100 .mu.L of Cell Titer Glow (CTG) reagent (Cat. No.
G7570, Promega, Madison, Wis.) and incubated at room temperature
for 15 min before measuring luminescence on the SpectraMax M3 plate
reader according to the manufacturer's instructions. The mean cell
survival (%) was determined by comparison of the measured
luminescence to control cells not treated with adenosine
[1081] The results are set forth in Table 15. The results showed
that treatment of the NK/T cells with adenosine for 5 days resulted
in a dose-dependent adenosine inhibition of NK/T cells
proliferation. The IC.sub.50, the concentration of adenosine where
the response is reduced by half, was 16.2
TABLE-US-00015 TABLE 15 Adenosine-mediated inhibition of NK/T
proliferation Adenosine Concentration (.mu.M) Mean Cell survival
(%) Standard Deviation 1000 15.82 0.44 300 13.65 1.04 100 26.01
1.51 30 36.84 0.96 10 70.33 1.33 3 110.07 2.07 1 121.11 1.8 0.3
101.19 1.14 0.1 106.67 1.21
[1082] B. Assessing Effects of ADA2 on Adenosine-Mediated
Inhibition of Proliferation of NK/T Cells
[1083] rHuADA2 was tested to assess whether it can reverse the
adenosine-mediated inhibition of NK/T cell proliferation at 1 mM
adenosine. NK/T cells (10,000 cells/well) were plated in 96 well
white plates with clear bottoms in a total volume of 180 .mu.L. The
cells were treated with 20 .mu.L rHuADA2 at concentrations
resulting from 3-fold dilution series, to give a final rHuADA2
concentration of 100 nM, 30 nM, 10 nM, 3 nM, 1 nM, 0.3 nM, 0.1 nM,
and 0.03 nm, and then each well also was treated with 20 .mu.L of
adenosine at 1 mM. After treatment, the NK/T cells were cultured,
processed and luminescence measured as described above. The mean
cell survival (%) was determined by comparison of the measured
luminescence to control cells not treated with adenosine or
rHuADA2.
[1084] The results are set forth in Table 16. The results showed
that rHuADA2 rescued the adenosine-mediated inhibition of NK/T cell
proliferation, in a dose-dependent manner. The EC.sub.50, the
concentration of rHuADA2 that induces a response halfway between
the baseline and maximum, was 8.5 nM.
TABLE-US-00016 TABLE 16 ADA2 rescue of adenosine-mediated
proliferation inhibition (1 mM adenosine) rHuADA2 Conc (nM) Mean
cell survival (%) Standard Deviation 100 nM 120.6 2.76 30 nM 105.5
2.86 10 nM 83.82 2.17 3 nM 41.98 0.9 1 nM 25.73 0.3 0.3 nM 18.33
0.12 0.1 nM 18.4 0.72 0.03 nM 16.03 0.47
[1085] Experiments also were performed to assess the effect of
rHuADA2 to reverse adenosine-mediated inhibition of NK/T cell
proliferation at various concentrations of adenosine. The
experiments were conducted in a similar manner as described above,
with final adenosine concentration of 1 mM, 100, 50, or 25 .mu.M
and final rHuADA2 concentration of 100 nM, 30 nM, 10 nM, 3 nM, 1
nM, 0.3 nM, 0.1 nM, and 0.03 nM.
[1086] The results are set forth in Table 17. Similar to the
results above, a dose-dependent rescue of NK/T cells proliferation
by rHuADA2 was observed at varying adenosine concentrations. The
EC.sub.50 values for rHuADA2 at different fixed concentrations of
adenosine is set forth in Table 18. The results show that adenosine
inhibits NK/T cells proliferation and that the addition of rHuADA2
can rescue human NK/T cells from the adenosine-mediated inhibition
of proliferation.
TABLE-US-00017 TABLE 17 ADA2 rescue of adenosine-mediated
proliferation inhibition at varying adenosine and ADA2
concentrations 1 mM 100 .mu.M 50 .mu.M 25 .mu.M ADA2 Adenosine
Adenosine Adenosine Adenosine (nM) MS % SD MS % SD MS % SD MS % SD
100 nM 96.3 1.2 109 2.3 116.9 1.5 120.6 2.5 30 nM 79.1 1.5 114.4
2.6 114.7 2.3 117.2 1.3 10 nM 67.1 1.4 108.3 2.1 105.9 1.2 121.2
1.1 3 nM 41.4 1 91.6 2.3 94 0.9 107.4 1.1 1 nM 22.6 0.5 71.7 1.7
80.2 0.6 99.3 1.5 0.3 nM 18.3 0.1 57.8 0.7 64.8 0.8 90.5 1 0.1 nM
16.3 0.2 43.8 0.8 76.6 0.9 89.6 0.9 0.03 nM 15.6 0.2 45.9 1.6 71.2
0.5 81.7 1 MS % = mean survival (%) SD--standard deviation
TABLE-US-00018 TABLE 18 EC.sub.50 values for ADA2 and various
concentrations of Adenosine Adenosine Concentration EC.sub.50 for
rHuADA2 1 mM 7.2 nM 100 .mu.M 1.5 nM 50 .mu.M 3.8 nM 25 .mu.M 1.5
nM
Example 7
Identification of ADA2 Heparin Binding Site Variants that Exhibit
Reduced Heparin Binding
[1087] Selected candidate variants described in Table 7 above, that
have an amino acid substitution in a residue that involved in
heparin binding, were screened to assess if any exhibit attenuated
heparin binding. Table 19 lists the variants that were tested.
Heparin binding was assessed using heparin-affinity chromatography
and/or using an enzyme-linked immunosorbent assay (ELISA). In
addition, the adenosine deaminase activity of variants also was
assessed. To perform the experiments, purified WT rHuADA2 and
tested variants were prepared at 0.3 mg/mL concentration to
normalize the amount of protein in each experiment.
[1088] A. Heparin Binding
[1089] 1. Heparin-Affinity Chromatography
[1090] To assess binding of variants to heparin, heparin-affinity
chromatography was employed to identify heparin-bound variants.
Heparin binding was tested by mixing 35 .mu.L of rHuADA2 WT and
variants with 20 .mu.L heparin-Sepharose.TM. resin (GE Healthcare,
Pittsburgh, Pa.; Cat. No. 17-0998-01), followed by incubating at
room temperature for 30 min. The mixture was then centrifuged
through a 0.22 .mu.m centrifuge filter and the flow-through,
containing the unbound protein, was collected for analysis on an
SDS-PAGE gel. 35 .mu.L of 1.5 M NaCl was added to heparin-Sepharose
resin and incubated at room temperature (RT) for 10 min to elute
the remaining heparin-bound protein from the heparin-Sepharose.
Samples of purified WT rHuADA2 and tested variants, before and
after mixing with the heparin-Sepharose resin, were analyzed by
SDS-PAGE to compare the degree of heparin binding.
[1091] The results are set forth in Table 19. The results show that
a reduced elution of protein was achieved for 16 out of the 25
tested variants, indicating that these variants exhibit attenuated
heparin binding compared to WT rHuADA2. The other variants
exhibited elution similar to WT rHuADA2.
TABLE-US-00019 TABLE 19 Heparin Column Binding of ADA2 HBP variants
Substitution (Zavialov Substitution (mature numbering) numbering)
Heparin Column Binding K14A K11A Similar to WT K14D K11D Similar to
WT K14E K11E Similar to WT K16A K13A Similar to WT K16D K13D
Similar to WT K16E K13E Similar to WT K374A K371A Reduced K374D
K371D Reduced K374E K371E Reduced K375A K372A Reduced K375D K372D
Reduced K375E K372E Reduced K455A K452A Similar to WT K455D K452D
Similar to WT K455E K452E Reduced R23A R20A Reduced R23D R20D
Reduced R23E R20E Reduced R369A R366A Reduced R369D R366D Reduced
R369E R366E Reduced K14A/R23A K11A/R20A Reduced K14A/R23A/K374A
K11A/R20A/K371A Reduced R23A/K374A R20A/K371A Reduced K14A/K374A
K11A/K371A Reduced
[1092] 2. ELISA Assay for Heparin Binding Property
[1093] An enzyme-linked immunosorbent assay (ELISA) using a heparin
coated microtiter plate was performed to confirm the attenuated
heparin binding properties of the rHuADA2 HBP variants screened
above. A 96-well plate was coated with 100 .mu.L of 200 .mu.g/mL
heparin sodium salt (Calibochem, EMD Milipore, Billerica, Mass.;
Cat. No. 375095) in Na.sub.2CO.sub.3 buffer (pH 9.6), overnight at
4.degree. C. The wells were blocked with 5% milk in PBS, and washed
6 times with PBS. 3 .mu.M of select rHuADA2 variants (see Table
20), WT rHuADA2 (positive control) and WT rHuADA1 (negative
control) were added to the wells individually and incubated for 2
hours at room temperature, followed by washing 6 times with PBS.
100 .mu.L of 1:1000 diluted horseradish peroxidase (HRP)-anti-FLAG
antibody (Abcam, Cambridge, UK; Cat. No. Ab1238) was added to the
wells to detect binding and incubated at room temperature for 1
hour. The ELISA reactions were developed by adding the
3,3',5,5'-Tetramethylbenzidine (TMB) substrate solution (Pierce,
Thermo Fisher Scientific, Rockford, Ill.) according the
manufacturer's instructions and reading the optical density at 450
nm (OD.sub.450) on a plate reader.
[1094] The results are set forth in Table 20, which sets forth the
average OD.sub.450 reading and the standard deviation (Stdev) for
tested variants. The results showed that WT ADA2 had the highest
measured OD of any tested protein indicating binding to heparin,
while the negative control ADA1 did not result in a detectable
signal. The results showed that all tested variants, which are
variants identified above that exhibit reduced binding to heparin,
exhibit a lower measured OD reading than WT ADA2 and hence reduced
binding to heparin-coated plates. Hence, consistent with the
results above, the results showed attenuated binding to heparin,
compared to wild-type human rHuADA2.
TABLE-US-00020 TABLE 20 Heparin Binding ELISA assay of selected
ADA2 HBP variants Substitution Substitution (Zavialov (mature
numbering) numbering) Average OD.sub.450 Stdev Set 1 K374D K371D
0.15 0.02 K374E K371E 0.11 0.01 K375D K372D 0.2 0.07 K375E K372E
0.21 0.05 WT ADA2 WT ADA2 0.49 0.02 WT ADA1 WT ADA1 0.07 0.01 Set 2
K455E K452E 0.26 1 R23E R20E 0.2 0 R369E R366E 0.18 0.04 R23A/R374A
R20A/R371A 0.17 0.08 WT ADA2 WT ADA2 0.55 0.15 WT ADA1 WT ADA1 0.06
0.01
[1095] B. Adenosine Deaminase Activity Assay
[1096] Adenosine deaminase activity of WT rHuADA2 and variants
tested above were determined using the adenosine deaminase activity
(ADA) assay described in Example 4. Activity was assessed on
purified rHuADA2 WT and variants that were diluted to 5 .mu.g/mL,
and then serially diluted 2 fold to generate 4 measurements.
[1097] Table 21 sets forth the results. The last column sets forth
the relative enzymatic activity (% activity vs. WT) compared to the
rHuADA2 WT.
[1098] The results show that most variants that exhibit reduced
heparin binding exhibit either similar or increased adenosine
deaminase activity compared to WT ADA2. In particular, variants
R23E, K374D, K374E, K375D, K375E, K455D, K455E, and R369E by
Zavialov numbering (R20E, K371D, K371E, K372D, K372E, K452D, K452E
and R366E, respectively, by mature numbering) not only show
attenuated heparin binding, but also exhibit improved enzymatic
activity.
[1099] In contrast, variants R23A, R23D and R369A (R20A, R20D and
R366A, respectively, by mature numbering) exhibit reduced heparin
binding, but also exhibit reduced adenosine deaminase activity.
[1100] The results show that K14E variant (K11E by mature
numbering) and K455D variant (K452D by mature numbering) exhibit
improved enzymatic activity relative to the WT rHuADA2, while the
heparin binding property was not attenuated.
TABLE-US-00021 TABLE 21 Adenosine Deaminase Activity of ADA2
variants Substitution % (Zavialov Substitution (mature .DELTA.A/
mU/ activity numbering) numbering) min mL stdev vs. WT K14A K11A
4.9 11.4 1.2 14.6 K14D K11D 8.1 18.7 0.2 24 K14E K11E 38.8 89.1 2.8
114.2 K16A K13A 12.2 28 1.8 35.9 K16D K13D 29.3 67.3 18.1 86.3 K16E
K13E 7.1 16.3 2.4 20.9 K374A K371A 25.8 59.2 16.3 75.9 K374D K371D
117.3 269.8 6.4 345.9 K374E K371E 136.5 313.8 17 402.3 K375A K372A
35.5 81.8 15.4 104.8 K375D K372D 53.7 123.5 10.9 158.3 K375E K372E
47 108.1 10 138.6 K455A K452A 6.1 14 2.8 18 K455D K452D 42.6 97.9
12.6 125.5 K455E K452E 55.4 127.3 6.1 163.2 R23A R20A 23.2 53.3 4.8
68.4 R23D R20D 6.9 15.9 4.2 20.3 R23E R20E 70.2 161.6 26.3 207.1
R369A R366A 14.9 34.3 5.5 44 R369D R366D 34.9 80.2 3.6 102.8 R369E
R366E 50.4 115.9 28.9 148.5 K14A/R23A K11A/R20A 42.1 96.9 0.7 124.2
K14A/R23A/K374A K11A/R20A/K371A 31.7 72.8 10.1 93.3 R23A/K374A
R20A/K371A 51.1 117.6 7.1 150.7 K14A/K374A K11A/K371A 34.1 78.4 2.2
100.5 WT ADA2 WT ADA2 33.9 78 1.2 100
Example 8
PEGylation of rHuADA2 and Assessment of Adenosine Deaminase
Activity and Heparin Binding
[1101] rHuADA2, K374D-ADA2 variant (K371D by mature numbering) or
R23E-ADA2 variant (R20E by mature numbering) were PEGylated on
surface exposed lysines by reaction with linear PEG-20K. The
PEGylated-rHuADA2 or variants were assessed for heparin binding and
adenosine deaminase activity.
[1102] A. PEGylation
[1103] To PEGylate the enzyme, 3 mg/mL WT rHuADA2, rHuADA2-K374D
(K371D by mature numbering) or rHuADA2-R23E (R20E by mature
numbering) variants were each individually mixed with linear
PEG-20K (JenKem Technology, Plano, Tex.; Cat. No. M-SCM-20K) at
1:15 molar ratio and incubated at 4.degree. C. for 16 hours. The
reaction mixture was centrifuged through a 0.22 .mu.m centrifuge
filter and the flow-through containing the PEGylated enzyme was
collected.
[1104] The extent of PEGylation was assessed by SDS-PAGE analysis.
The results show that at least 80% of the WT rHuADA2, rHuADA2-K374D
(K371D by mature numbering), and rHuADA2-R23E (R20E by mature
numbering) were PEGylated under the reaction conditions, as
indicated by a decrease in intensity of the unmodified rHuADA2 band
accompanied by the appearance of multiple larger bands representing
the PEGylated rHuADA2 molecules.
[1105] B. Heparin Binding ELISA
[1106] Heparin binding of PEGylated rHuADA2 or variants was
assessed by capture ELISA. Binding of rHuADA1 was assessed as a
negative control. 100 .mu.L of 0.2 mg/mL biotin-heparin
(Sigma-Aldrich, St. Louis, Mo.; Cat No. B9806-10MG) was added to a
streptavidin coated 96-well plate (Thermo Fisher Scientific,
Rockford, Ill.; Cat. No. 15520), and incubated at room temperature
for 1 hour. The plate was washed 6 times with PBS. Then, 150 .mu.L
of 1 PEGylated rHuADA2 was added to the heparin coated plate,
titrated in 3.times. serial dilutions, and incubated at room
temperature for 2 hours. The plate was then washed 6 times with
PBS. A 1000.times. dilution of goat HRP-anti-FLAG pAb (Abcam,
Cambridge, UK; Cat. No. Ab1238) was added to the ELISA plate and
incubated at room temperature for 1 hour. The ELISA plate was then
washed 6 times with phosphate buffered saline with Tween (PBST) and
developed with the 3,3',5,5'-Tetramethylbenzidine (TMB) substrate
solution (Pierce, Thermo Fisher Scientific, Rockford, Ill.)
according the manufacturer's instructions and reading the optical
density at 450 nm (OD.sub.450) on a plate reader.
[1107] Table 22 sets forth the average OD.sub.450 reading and the
standard deviation (Stdev) from the heparin binding capture ELISA
assay of PEGylated rHuADA2 wild-type and variants. The results show
that PEGylated rHuADA2 and variants have a significant reduction in
heparin binding. For PEGylated rHuADA2-K374D (K371D by mature
numbering) and rHuADA2-R23E (R20E by mature numbering) variants,
PEGylation conferred additional reduction in heparin binding
property compared to the non-PEGylated forms with reduced heparin
binding. Thus, these results indicate that modification of the
rHuADA2 protein with the PEG moiety reduces heparin binding by
steric blockade and/or alteration of electrostatic charges on the
surface of rHuADA2.
TABLE-US-00022 TABLE 22 Heparin Binding ELISA assay of PEGylated
ADA2 WT and variants Variant (Zavialov Variant (mature numbering)
numbering) Average OD.sub.450 Stdev K374D K371D 0.87 0.03 PEG-K374D
PEG-K371D 0.15 0.05 R23E R20E 0.71 0.04 PEG-R23E PEG-R20E 0.55 0.02
WT ADA2 WT ADA2 2.31 0.01 PEG-WT ADA2 PEG-WT ADA2 0.75 0.04 WT ADA1
WT ADA1 <0.02 0
[1108] C. Adenosine Deaminase Activity Assay
[1109] Adenosine deaminase activity of PEGylated rHuADA2 and
variants was assessed using the method described in Example 4, and
compared to the activity of the corresponding non-PEGylated
form.
[1110] The results are set forth in Table 23. The results show that
PEGylated WT rHuADA2 had comparable adenosine deaminase activity
compared to the non-PEGylated form. Similarly, the PEGylated
rHuADA2-K374D (K371D by mature numbering) and rHuADA2-R23E (R20E by
mature numbering) variants also showed comparable adenosine
deaminase activity compared to the non-PEGylated forms. Although WT
rHuADA2 contains 32 lysine residues as a monomer, and 64 lysine
residues as a dimer, PEGylation at the lysine residues had no
impact on the adenosine deaminase activity of rHuADA2.
TABLE-US-00023 TABLE 23 Adenosine Deaminase Activity of PEGylated
ADA2 WT and variants Variant (Zavialov Variant (mature numbering)
numbering) mU/mL stdev % of WT K374D K371D 162.9 2.2 134 R23E R20E
129.9 0.4 106.8 WT WT 121.6 2.3 100 PEG-K374D PEG-K371D 142 7.1
116.8 PEG-R23E PEG-R20E 115.6 3.9 95.1 PEG-WT PEG-WT 124.2 5.5
102.2
[1111] D. Conclusion
[1112] The results of the experiments demonstrate that PEGylation
of rHuADA2 variants reduces heparin binding in addition to the
attenuated heparin binding resulting from the amino acid
substitution, but without loss of adenosine deaminase activity.
Thus, the results show that PEGylation of heparin-binding variants
can improve the pharmacokinetic properties of the rHuADA2 variants
without affecting the adenosine deaminase activity. PEGylation can
be used in place of mutation to attenuate heparin binding.
Example 9
In Vivo Pharmacokinetic Analysis of rHuADA2, ADA2 Variants, and
PEGylated Forms
[1113] The pharmacokinetics (PK) of non-PEGylated and PEGylated
forms of WT rHuADA2, ADA2-K374D and ADA2-R23E variants by Zavialov
numbering (K371D and R20E, respectively, by mature numbering) were
analyzed in an immunocompetent mouse model.
[1114] A. Study Design
[1115] Fifty four (54) male BALB/c mice were divided into six (6)
dosing groups, and were further divided into three (3) groups each
for sampling of blood at different time points. Thus, the mice were
randomized into eighteen (18) groups total. Mice were weighed prior
to the start of the study, and randomized into the 18 groups based
upon their body weights. In each sampling group, three groups of
(3) mice were used for dosing each test article to prevent
oversampling of the blood from the animals. For measurement of
baseline ADA2 levels, a blood sample was obtained from 12 randomly
chosen mice and plasma was prepared using the anti-coagulant
potassium (K.sub.3) ethylene diamine tetraacetic acid
(K.sub.3-EDTA). All blood was collected by submandibular
venipuncture.
[1116] Each mouse was injected by intravenous tail-vein injection
with a 7.5 mg/kg dose of one of six ADA2 test article as set forth
in Table 24, i.e. rHuADA2-K374D (K371D by mature numbering),
PEG-rHuADA2-K374D (PEG-K371D by mature numbering), rHuADA2-R23E
(R20E by mature numbering), PEG-rHuADA2-R23E (PEG-R20E by mature
numbering), or WT ADA2 and PEG-WT ADA2. PEGylated ADA2 variants
were prepared using the PEGylation method as described in Example
8.A. The concentration of each test article was 1.5 mg/mL, which
resulted in a dose volume range from 93-119 .mu.L depending on the
body weight (BW) of the mouse. Dose volumes and body weights for
individual animals are provided in Table 25.
[1117] Blood was collected at designated sampling time points from
appropriate groups of mice as indicated below in Table 24 and kept
on ice until plasma preparation. Plasma was prepared by
centrifuging the blood (500.times.g for 5 min at 4.degree. C.),
transferring the plasma to a fresh tube and immediately freezing at
-80.degree. C. until the adenosine deaminase activity assay.
Adenosine deaminase activity was determined as described in Example
4. The half-life, or time taken for the activity of ADA2 proteins
to be reduced by half, was calculated. Also, total exposure was
measured by calculating the Area Under the Concentration-time Curve
(AUC).
TABLE-US-00024 TABLE 24 Pharmacokinetics Study Design for PEGylated
ADA2 WT and variants Blood Collection Time points post Test Article
No. of dosing Group # (ZavialoNo.) (Mature No.) Animals Dose
(hours) 1 K374D K371D 3 7.5 mg/kg 0.25, 2 2 3 1, 8 3 3 4, 24 4
PEG-K374D PEG-K371D 3 7.5 mg/kg 0.25, 2 5 3 1, 8 6 3 4, 24 7 R23E
R20E 3 7.5 mg/kg 0.25, 2 8 3 1, 8 9 3 4, 24 10 PEG-R23E PEG-R20E 3
7.5 mg/kg 0.25, 2 11 3 1, 8 12 3 4, 24 13 WT ADA2 WT ADA2 3 7.5
mg/kg 0.25, 2 14 3 1, 8 15 3 4, 24 16 PEG-WT PEG-WT 3 7.5 mg/kg
0.25, 2 17 ADA2 ADA2 3 1, 8 18 3 4, 24
TABLE-US-00025 TABLE 25 Body weight and dosing for pharmacokinetics
analysis of PEGylated ADA2 WT and variants Test Article (Zavialov
(Mature Animal mg of test vol numbering) numbering) Group # ID# BW
article (.mu.L) K374D K371D 1 817 17.7 0.1328 89 850 21 0.1575 105
832 23.7 0.1778 119 2 822 18.6 0.1395 93 830 21 0.1575 105 819 23.7
0.1778 119 3 821 18.9 0.1418 95 812 21.1 0.1583 106 844 23.3 0.1748
117 PEG-K374D PEG-K371D 4 823 19.2 0.144 96 801 20.9 0.1568 105 848
22.8 0.171 114 5 841 19.3 0.1448 97 836 21.1 0.1583 106 837 22.8
0.171 114 6 826 19.7 0.1478 99 835 20.8 0.156 104 853 22.6 0.1695
113 R23E R20E 7 828 19.8 0.1485 99 807 21.2 0.159 106 834 22.4
0.168 112 8 820 19.9 0.1493 100 840 20.7 0.1553 104 839 22.3 0.1673
112 9 810 20 0.15 100 809 21.2 0.159 106 842 22.2 0.1665 111
PEG-R23E PEG-R20E 10 815 20 0.15 100 813 20.6 0.1545 103 827 22.2
0.1665 111 11 824 20 0.15 100 852 21.2 0.159 106 833 22.1 0.1658
111 12 825 20 0.15 100 808 20.6 0.1545 103 845 22 0.165 110 WT ADA2
WT ADA2 13 838 20 0.15 100 818 21.3 0.1598 107 843 21.9 0.1643 110
14 846 20 0.15 100 814 20.5 0.1538 103 805 21.8 0.1635 109 15 849
20 0.15 100 851 21.3 0.1598 107 803 21.8 0.1635 109 PEG-WT PEG-WT
16 811 20.2 0.1515 101 ADA2 ADA2 829 20.4 0.153 102 831 21.7 0.1628
109 17 802 20.3 0.1523 102 854 21.4 0.1605 107 804 21.7 0.1628 109
18 806 20.3 0.1523 102 847 20.3 0.1523 102 816 21.5 0.1613 108
[1118] B. Results
[1119] 1. Pharmacokinetics of Non-PEGylated rHuADA2 WT and
Variants
[1120] The pharmacokinetics (PK) properties of WT rHuADA2 compared
to variants ADA2-K374D and ADA2-R23E by Zavialov numbering (K371D
and R20E, respectively, by mature numbering) are set forth in
Tables 26 and 27. Table 26 sets forth the total exposure measured
using an Area Under the Curve (AUC) calculation and Table 27 sets
forth the half-life (t.sub.1/2). The results show that each of the
variants exhibited improved pharmacokinetic parameters compared to
the wildtype ADA2. For example, variant rHuADA2-R23E (R20E by
mature numbering) exhibited an AUC that was 19% higher than for WT
rHuADA2 and a half-life that was 119% longer than WT rHuADA2.
Variant rHuADA2-K374D, exhibited an AUC that was 128% higher than
for WT rHuADA2 and a half-life that was 230% longer than for WT
rHuADA2.
TABLE-US-00026 TABLE 26 Comparison of Total Exposure - Area under
the Curve (AUC): ADA2 WT and HBP variants Test Article Test article
Percent increase in (Zavialov (Mature AUC compared to WT numbering)
numbering) AUC (mU * h)/mL ADA2 WT WT 32,883 -- R23E R20E 39,033 19
K374D K371D 74,983 128
TABLE-US-00027 TABLE 27 Comparison of half-life (t.sub.1/2): ADA2
WT and HBP variants Test Article Test article Percent increase in
t.sub.1/2 (Zavialov (Mature Half life slow (t.sub.1/2) compared
numbering) numbering) (min) to WT ADA2 WT WT 69 -- R23E R20E 151
119 K374D K371D 228 230
[1121] 2. Pharmacokinetics of PEGylated rHuADA2 WT and Variants
[1122] The pharmacokinetics (PK) properties of native and PEGylated
WT rHuADA2 compared to PEGylated forms of variants, PEG-R23E (R20E
by mature numbering) and PEG-K374D (K371D by mature numbering), are
set forth in Tables 28 and 29. Table 28 sets forth the total
exposure measured using an Area Under the Curve (AUC) calculation
and Table 29 sets forth the half-life (t.sub.1/2).
[1123] For wildtype ADA2, the results show that PEGylation
substantially improves the pharmacokinetic profile. The results
show that PEG-WT ADA2 exhibits an AUC that was 4291% higher than
the non-PEGylated WT ADA2 and a half-life that was 1078% longer
than the non-PEGylated WT ADA2. Likewise, PEGylation of the variant
forms also resulted in improved pharmacokinetics compared to
non-PEGylated forms. Thus, for both of the PK components measured,
AUC and t.sub.1/2, PEGylation led to improved PK values compared to
the non-PEGylated forms.
[1124] The results also show that that the PEGylated forms of ADA2
variants also exhibit improvements in one or both PK components
compared to PEG-WT ADA2, although these improvements were greater
for the variant PEG-K374D (K371D by mature numbering) than for
PEG-R23E (R20E by mature numbering). For example, PEG-R23E (R20E by
mature numbering), exhibited an AUC that was 4271% higher (compared
to 4291% for PEG-WT ADA2) than the non-PEGylated WT ADA2 and a
half-life that was 1420% longer (compared to 1078% for PEG-WT ADA2)
than the non-PEGylated WT ADA2. In contrast, PEG-K374D (K371D by
mature numbering), exhibited an AUC that was 8187% higher (compared
to 4291% for PEG-WT ADA2) than the non-PEGylated WT ADA2 and a
half-life that was 1791% longer (compared to 1078% for PEG-WT ADA2)
than the non-PEGylated WT ADA2.
TABLE-US-00028 TABLE 28 Comparison of Total Exposure - Area under
the Curve (AUC): PEGylated ADA2 WT and HBP variants Percent
increase Test Article Test article in AUC (Zavialov (Mature AUC
compared to WT numbering) numbering) (mU * h)/mL ADA2 WT ADA2 WT
ADA2 32,883 -- PEG-WT ADA2 PEG-WT ADA2 1,444,000 4291 PEG-R23E
PEG-R20E 1,437,333 4271 PEG-K374D PEG-K371D 2,725,000 8187
TABLE-US-00029 TABLE 29 Comparison of half-life (t.sub.1/2):
PEGylated ADA2 WT and HBP variants Test Article Test article Half
life Percent increase in t.sub.1/2 (Zavialov (Mature slow
(t.sub.1/2) compared to WT numbering) numbering) (min) ADA2 WT ADA2
WT ADA2 69 -- PEG-WT ADA2 PEG-WT ADA2 813 1078 PEG-R23E PEG-R20E
1049 1420 PEG-K374D PEG-K371D 1305 1791
Example 10
Identification of ADA2 Active Site Variants with Increased
Enzymatic Activity
[1125] Selected candidate variants described in Table 8 above,
containing an amino acid substitution in a residue that play a role
in enzymatic activity, were assessed for their adenosine deaminase
activity using the method described in Example 4. Table 30 lists
the variants that were tested. To perform the experiments, purified
WT rHuADA2 and tested variants were prepared at 5 .mu.g/mL
concentration to normalize the amount of protein in each
experiment.
[1126] The results of the adenosine deaminase activity assay are
set forth in Table 30 below. The percent (%) activity of each
variant compared to WT-ADA2 is indicated. The results show that the
activity of all tested variants containing a substitution at
position 182 (position 179 by mature numbering) was substantially
reduced, indicating that the glutamic acid (E) residue is important
for enzymatic activity.
[1127] In contrast, other substitutions retain or exhibit increased
enzymatic activity. In particular, identified variants with
increased activity included: R222Q variant (R219Q by mature
numbering) with 170% activity of WT, H267Q variant (H264Q by mature
numbering) with 114% activity of WT, H267G (H264G by mature
numbering) with 153% activity of WT, R222K (R219K by mature
numbering) with 152% activity of WT, L224A (L221A by mature
numbering) with 128% activity of WT, L224V (L221V by mature
numbering) with 123% activity of WT, L224G (L221G by mature
numbering) with 113% activity of WT, and S265N (S262N by mature
numbering) with 211% activity relative of WT.
TABLE-US-00030 TABLE 30 Adenosine deaminase activity of variants
designed for improved rHuADA2 activity Substitution Substitution
(Zavialov (mature % of WT numbering) numbering) .DELTA.A/min mU/ml
std activity H267A H264A 30.8 70.9 8.6 91 H267Q H264Q 38.8 89.3
16.2 114 H267N H264N 21.9 50.4 8 65 H267G H264G 51.8 119.1 10.9 153
R222K R219K 51.5 118.5 6.9 152 R222Q R219Q 57.8 132.9 11.6 170
R222N R219N 35.4 81.5 10.7 104 R222A R219A 13.6 31.2 5.7 40 L224A
L221A 43.5 100.1 10.9 128 L224V L221V 41.8 96.1 13.3 123 L224G
L221G 38.3 88.2 1.6 113 E182D E179D 7.8 18.1 2.1 23 E182A E179A 3.7
8.6 0.8 11 E182S E179S 4.1 9.5 0.1 12 E182T E179T 2.7 6.2 0.2 8
E182V E179V 3.5 8 0.7 10 E182G E179G 3 6.9 0.7 9 S265A S262A 20.5
47.1 2.5 60 S265V S262V 28.8 66.1 6.8 85 S265M S262M 35.5 81.6 3.4
105 S265N S262N 71.7 164.8 21.4 211 WT ADA2 WT ADA2 33.9 78 1.2
100
Example 11
Generation of Combination Variants
[1128] Combinations variants were generated containing amino acid
substitution(s) that increased enzymatic activity and that
attenuated heparin binding. In particular, the amino acid
substitution S265N and/or R222Q (S262N and/or R219Q, by mature
numbering) which conferred the greatest increases in enzymatic
activity as described in Example 10, were combined with one or more
of amino acid substitutions K374D, K374E and/or R23E (K371D, K371E
and/or R20E, respectively, by mature numbering) identified in
Example 7. Variants were generated as described above in Example 1
using the QuikChange Lightning Multi Site-Directed Mutagenesis Kit.
The generated combination variants are set forth in Table 31. The
combination variants and corresponding single amino acid
substitutions were assessed for kinetic parameters of adenosine
deaminase activity and for heparin binding.
TABLE-US-00031 TABLE 31 Active Site and Attenuated Heparin Binding
Combination Variants Substitution (Zavialov Substitution (mature
SEQ numbering) numbering) ID NO: S265N/K374D S262N/K371D 59
S265N/K374E S262N/K371E 60 S265N/R23E S262N/R20E 61
S265N/R23E/K374D S262N/R20E/K371D 62 S265N/R23E/K374E
S262N/R20E/K371E 63 R222Q/K374E R219Q/K371E 263 R222Q/K374D
R219Q/K371D 264 R222Q/R23E R219Q/R20E 265 R222Q/K374E/R23E
R219Q/K371E/R20E 266 R222Q/K374D/R23E R219Q/K371D/R20E 267
R222Q/S265N/K374E R219Q/S262N/K371E 268 R222Q/S265N/K374D
R219Q/S262N/K371D 269 R222Q/S265N/R23E R219Q/S262N/R20E 270
R222Q/S265N/K374E/R23E R219Q/S262N/K371E/R20E 271
R222Q/S265N/K374D/R23E R219Q/S262N/K371D/R20E 272 R222Q/S265N
R219Q/S262N 273
[1129] The combination variants containing the mutations S265N
(S262N by mature numbering), set forth in SEQ ID NOS:59-63, and/or
R222Q (R219Q by mature numbering), set forth in SEQ ID NOS:263-273,
and corresponding single amino acid substitutions, were assessed
for kinetic parameters of adenosine deaminase activity. The
combination variants containing the mutation S265N (S262N by mature
numbering), set forth in SEQ ID NOS: 59-63 and corresponding single
amino acid substitutions, were assessed for heparin binding
activities.
[1130] A. Kinetic Assessment of Adenosine Deaminase Activity
[1131] 1. Assay Method
[1132] Adenosine deaminase activity was determined by the
measurement of ammonia released from adenosine when broken down to
inosine. Ammonia was measured using a commercially available
Ammonia Assay kit (Cat. No. AA0100, Sigma-Aldrich, St. Louis, Mo.).
The kit contains dry reagents containing .alpha.-ketoglutaric acid
and NADPH, which were reconstituted with 5 mL water prior to use in
the assay. Ammonia reacts with .alpha.-ketogluaric acid (KGA) and
reduced nicotinamide adenine dinucleotide phosphate (NADPH) in the
presence of L-glutamate dehydrogenase (GDH). The decrease in
absorbance at 340 nm, due to the oxidation of NADPH, is
proportional to the ammonia concentration, and hence the adenosine
deaminase activity.
[1133] Kinetics parameters of rHuADA2 WT and variants were compared
using this assay at different adenosine concentrations at pH 7.6
and 6.5. Adenosine concentrations ranging from 20 .mu.M to 20 mM
were used. Sub-molar concentration of adenosine stock was prepared
in 1N NaOH.
[1134] For the enzymatic assays at pH 7.6, adenosine was serially
diluted with 100 mM sodium acetate (NaOAc), pH 4.9. A 2.times.
reaction mixture was prepared, containing reconstituted ammonia
assay reagent (containing about 4 mM .alpha.-ketoglutarate and
about 300 .mu.M NADPH), WT rHuADA2 or variants at 1 .mu.g/mL (17
nM) and glutamate dehydrogenase (GDH, 1:50 dilution). 85 .mu.L of
adenosine was added to 85 .mu.L 2.times. mixture in duplicate in a
UV-transparent half-area plate. The change in absorbance (.DELTA.A)
at 340 nm over time at room temperature was monitored.
[1135] For the enzymatic assay at pH 6.5, adenosine was serially
diluted with 200 mM piperazine-N,N'-bis(2-ethanesulfonic acid)
(PIPES), pH 6.5. A 2.times. reaction mixture in 200 mM PIPES, pH
6.5 was prepared, containing 4 mM .alpha.-ketoglutarate, 300 .mu.M
NADPH, 1 .mu.g/mL (17 nM) rHuADA2 or variants and 50 U/mL GDH (Cat
No. G2626, Sigma-Aldrich). The enzymatic reaction was initiated by
adding equal volume of adenosine to the 2.times. mixture in a
UV-transparent half-area plate as described above, and the change
in absorbance (AA) at 340 nm over time at room temperature was
monitored.
[1136] Adenosine deaminase activity in mU/mL (.mu.M/min equivalent)
was calculated using the following formula:
1
mU/mL=-(-.DELTA.A/min.times.T.sub.v)/(S.sub.v.times..epsilon..times.1)
[1137] where T.sub.v=total volume (170 .mu.L), S.sub.v=sample
volume (85 .mu.L), .epsilon.=6.22.times.10.sup.-3 .mu.M.sup.-1
cm.sup.-1, 1=1 cm.
[1138] The activity data were fitted with non-linear regression of
Michaelis-Menten equation using Graphpad Prism software to obtain
K.sub.m and V.sub.max. Other kinetics parameters such as k.sub.cat
and k.sub.cat/K.sub.m were also determined.
[1139] k.sub.cat(1/s)=V.sub.max/[E].sub.0
[1140] V.sub.max unit=.mu.M/min
[1141] [E].sub.0=8.5 nM or 0.0085 .mu.M
[1142] k.sub.cat=V.sub.max/0.0085/60
[1143] k.sub.cat/K.sub.m unit=1/Ms
[1144] 2. Results
[1145] Tables 32 and 33 set forth the kinetic parameters of the
rHuADA2 wild-type and variants, at pH 7.6 and pH 6.5, respectively.
The K.sub.m of WT rHuADA2 was 5.25 mM at pH 7.6 and 3.66 mM at pH
6.5, and the catalytic efficiency (k.sub.cat/K.sub.m) of WT rHuADA2
was 9,753 at pH 7.6 and 17,060 at pH 6.5. Thus, these results show
that WT rHuADA2 exhibits greater activity at pH 6.5. All tested
variants exhibited improved enzyme kinetics compared to WT-ADA2.
Generally, improved enzyme kinetics for the designed variants was
observed more prominently at pH 6.5 than at pH 7.6.
[1146] For example, S265N (S262N by mature numbering) had
significantly improved kinetics properties compared to the WT.
Substitution of serine residue 265 (262 by mature numbering) to an
asparagine at the active site of rHuADA2 lowered the K.sub.m value
to 3.02 mM at pH 7.6 and 1.49 mM at pH 6.5, and increased the
catalytic efficiency (k.sub.cat/K.sub.m) from 9,753 to 52,208
(1/Ms) at pH 7.6, and from 17,060 to 60,339 (1/Ms) at pH 6.5. R222Q
(R219Q by mature numbering) also had significantly improved
kinetics properties compared to the WT. Substitution of lysine
residue 222 (219 by mature numbering) to an glutamine lowered the
K.sub.m value to 1.92 mM at pH 7.6 and 0.994 mM at pH 6.5, and
increased the catalytic efficiency (k.sub.cat/K.sub.m) from 9,753
to 60,697 (1/Ms) at pH 7.6, and from 17,060 to 83,146 (1/Ms) at pH
6.5.
[1147] The ADA2 variants K374D, K374E and R23E in Zavialov
numbering (K371D, K371E and R20E, respectively, by mature
numbering), identified as conferring attenuated heparin binding,
also exhibited improved kinetics properties compared to WT, which
was greater at pH 6.5. The combination variants containing S265N
(S262N by mature numbering) further exhibited improved catalytic
activity compared to WT. In particular, the combination variants
S265N/K374E, S265N/R23E and S265N/R23E/K374E exhibited the greatest
improvements in catalytic activity at pH 6.5 among the tested
variants.
[1148] The results also show that combination variants containing
R222Q (R219Q by mature numbering) have significantly improved
kinetic properties compared to WT ADA2 and R222Q (R219Q by mature
numbering). Among the tested ADA2 combination variants, double
mutant R222Q/S265N (R219Q/S262N by mature numbering) exhibited the
greatest improvement on kinetic properties, showing a 4.7-fold
lower K.sub.m and 15-fold higher catalytic efficiency
(k.sub.cat/K.sub.m) at pH 7.6, and a 5.0-fold lower K.sub.m and
8.2-fold higher catalytic efficiency (k.sub.cat/K.sub.m) at pH 6.5,
compared to the WT ADA2. The results also show that ADA2 WT and all
tested R222Q (R219Q by mature numbering) containing variants have
lower K.sub.m at pH 6.5 than that at pH 7.6.
TABLE-US-00032 TABLE 32 Kinetic parameters of ADA2 WT and variants
at pH 7.6; [E] = 8.5 nM Replacement Replacement Vmax K.sub.m
k.sub.cat/K.sub.m (Zavialov numbering) (mature numbering)
(.mu.M/min) (mM) k.sub.cat (1/s) (1/Ms) WT WT 26.09 5.25 51.16
9,753 K374D K371D 28.25 4.88 55.39 11,349 K374E K371E 35.13 4.77
68.88 14,438 R23E R20E 29.08 5.06 57.02 11,275 S265N S262N 80.49
3.02 157.82 52,208 R222Q R219Q 59.28 1.92 116.24 60,697 S265N/K374D
S262N/K371D 78.29 2.86 153.51 53,637 S265N/K374E S262N/K371E 87.44
2.54 171.45 67,554 S265N/R23E S262N/R20E 63.13 2.9 123.78 42,743
S265N/R23E/K374D S262N/R20E/K371D 72.78 3.13 142.71 45,564
S265N/R23E/K374E S262N/R20E/K371E 82.38 2.87 161.53 56,262
R222Q/K374E R219Q/K371E 87.27 1.58 171.12 108,508 R222Q/K374D
R219Q/K371D 77.01 1.71 151.00 88,252 R222Q/R23E R219Q/R20E 84.71
1.46 166.10 114,078 R222Q/K374E/R23E R219Q/K371E/R20E 78.42 1.92
153.76 80,086 R222Q/K374D/R23E R219Q/K371D/R20E 88.43 1.34 173.39
129,687 R222Q/S265N/K374E R219Q/S262N/K371E 65.43 1.35 128.29
95,103 R222Q/S265N/K374D R219Q/S262N/K371D 70.96 1.19 139.14
117,218 R222Q/S265N/R23E R219Q/S262N/R20E 67.24 1.29 131.84 102,602
R222Q/S265N/K374E/ R219Q/S262N/K371E/ 90.91 1.24 178.25 143,407
R23E R20E R222Q/S265N/K374D/ R219Q/S262N/K371D/ 72.58 1.23 142.31
115,514 R23E R20E R222Q/S265N R219Q/S262N 87.79 1.10 172.14
157,203
TABLE-US-00033 TABLE 33 Kinetic parameters of ADA2 WT and variants
at pH 6.5; [E] = 8.5 nM Replacement Replacement Vmax K.sub.m
k.sub.cat/K.sub.m (Zavialov numbering) (mature numbering)
(.mu.M/min) (mM) k.sub.cat (1/s) (1/Ms) WT WT 31.81 3.66 62.37
17,060 K374D K371D 42.98 3.16 84.27 26,635 K374E K371E 41.93 3.18
82.22 25,895 R23E R20E 37.16 3.29 72.86 22,167 S265N S262N 45.79
1.49 89.78 60,339 R222Q R219Q 42.15 0.994 82.65 83,146 S265N/K374D
S262N/K371D 43.85 1.51 85.98 56,978 S265N/K374E S262N/K371E 57.13
1.41 112.02 79,390 S265N/R23E S262N/R20E 53.25 1.43 104.41 72,812
S265N/R23E/K374D S262N/R20E/K371D 43.42 1.50 85.14 56,948
S265N/R23E/K374E S262N/R20E/K371E 63.74 1.29 124.98 96,585
R222Q/K374E R219Q/K371E 58.56 0.99 114.82 115,937 R222Q/K374D
R219Q/K371D 60.87 0.79 119.35 150,584 R222Q/R23E R219Q/R20E 60.47
0.84 118.57 141,778 R222Q/K374E/R23E R219Q/K371E/R20E 54.48 0.86
106.82 124,474 R222Q/K374D/R23E R219Q/K371D/R20E 60.68 0.67 118.98
177,795 R222Q/S265N/K374E R219Q/S262N/K371E 45.53 0.80 89.27
111,985 R222Q/S265N/K374D R219Q/S262N/K371D 50.89 0.76 99.78
131,054 R222Q/S265N/R23E R219Q/S262N/R20E 40.59 1.01 79.59 79,192
R222Q/S265N/K374E/ R219Q/S262N/K371E/ 54.82 0.77 107.49 140,199
R23E R20E R222Q/S265N/K374D/ R219Q/S262N/K371D/ 45.78 0.81 89.76
111,150 R23E R20E R222Q/S265N R219Q/S262N 56.75 0.80 111.27
139,775
[1149] B. Heparin Binding of Combination Variants
[1150] Heparin binding activity of single mutants and combination
variants containing S265N (S262N by mature numbering) was assessed
using the ELISA-based heparin binding assay described in Example
7.A above. The results are set forth in Table 34. The results
confirmed that the variants K374D, K374E and R23E exhibit
attenuated binding to heparin compared to WT-ADA2. In addition, the
S265N (S262N by mature numbering) variant, designed for improved
enzymatic activity by modification of an active site residue, also
possessed attenuated binding to heparin coated plates, indicating
that modifications of the enzyme active site can impact heparin
binding in an allosteric manner. Further, all of the tested
combination variants showed significantly attenuated binding to
heparin, illustrating that combinations of variants can be created
that exhibit improved enzyme activity towards adenosine and
attenuated binding to heparin.
TABLE-US-00034 TABLE 34 Heparin Binding ELISA assay of ADA2 WT and
combination variants Heparin Binding Substitution (Zavialov
Substitution (mature ELISA Average numbering) numbering) OD.sub.450
stdev. K374D K371D 0.87 0.03 K374E K371E 0.03 0.01 R23E R20E 0.71
0.04 S265N S262N 0.88 0.19 S265N/K374D S262N/K371D 0.92 0.13
S265N/K374E S262N/K371E 0.6 0.12 S265N/R23E S262N/R20E 1.03 0.02
S265N/R23E/K374D S262N/R20E/K371D 0.69 0.07 S265N/R23E/K374E
S262N/R20E/K371E 0.93 0.11 WT ADA2 WT ADA2 2.31 0.01 WT ADA1 WT
ADA1 -0.02 0
Example 12
Thermal Stability of rHuADA2 WT and Variants
[1151] The stability of the rHuADA2 WT and variants was measured by
differential scanning fluorimetry (DSF) at increasing temperatures.
DSF measures conformational stability, which correlates with
thermal stability. The melting temperature (Tm) in DSF is defined
as the midpoint of the protein unfolding transition.
[1152] Non-PEGylated WT rHuADA2, non-PEGylated rHuADA2 variants,
and PEGylated forms of WT rHuADA2 and rHuADA2 variants were
prepared at concentrations of 0.1-1 mg/mL and mixed with the
ROX.TM. protein thermal shift dye (Applied Biosystems, Carlsbad,
Calif.; Cat. No. 4461146) to a final dye concentration that
corresponds to a 125-fold dilution of the stock ROX.TM. solution.
Protein samples were then loaded into 96-well plate at a volume of
20 .mu.L/well in triplicate. A ViiA7 RT-PCR System (Applied
Biosystems, Carlsbad, Calif.) was used to measure the shift in
fluorescence as the temperature of the samples were increased. The
reactions were subjected to the following steps: incubation at
25.degree. C. for 2 min; ramping of temperature from 25 to
99.degree. C. at a rate of 0.05.degree. C. per second; followed by
a 99.degree. C. incubation for 2 min. The wavelengths used for
emission and excitation were 623 nanometers (nm) and 580 nm,
respectively.
[1153] Table 35 sets forth the melting temperature (Tm) determined
from the DSF analysis. The results show that the Tm of variant
K374E (K371E by mature numbering) is 1.4.degree. C. higher than WT
ADA2, which indicates an improvement in thermal stability of the
variant. The other tested variants show comparable or slightly
lower Tm than WT ADA2. The results show that all PEGylated forms
exhibited a higher Tm than the corresponding non-PEGylated from,
which also indicates that PEGylation improves the thermal stability
of the enzymes.
TABLE-US-00035 TABLE 35 Melting temperature (Tm) of ADA2 WT,
variants and PEGylated forms Replacement (Zavialov Replacement
(mature numbering) numbering) Tm (.degree. C.) WT ADA2 WT ADA2 67.1
K374D K371D 66.8 K374E K371E 69.7 R23E R20E 65.2 S265N S262N 60.8
S265N/K374D S262N/K371D 60.8 S265N/K374E S262N/K371E 61.3
S265N/R23E S262N/R20E 59.6 S265N/R23E/K374D S262N/R20E/K371D 59.8
S265N/R23E/K374E S262N/R20E/K371E 60.4 PEG-WT ADA2 PEG-WT ADA2
68.81 PEG-K374D PEG-K371D 67.81 PEG-R23E PEG-R20E 66.4
Example 13
pH Optimum of rHuADA2 WT and Variants
[1154] Adenosine deaminase activity of rHuADA2 and variants at
varying pH were assessed to determine the pH optimum of each. The
adenosine deaminase activity was determined spectrophotometrically
by direct measurement of changes in adenosine absorbance. The UV
absorption spectra of adenosine (ADO) and inosine (INO) are very
similar and they overlap significantly, with respective absorbance
peaks at 261 nm and 249 nm. During the deamination reaction, the
absorbance of ADO decreases while that of INO increases with time.
Since the dynamic changes in absorbance make it difficult to
monitor activity at a single wavelength, the relative ADO activity
was determined as a ratio of the ADO peak to isobestic point (i.e.
the wavelength where ADO and INO have the same extinction
coefficient). The isobestic point, which is 253 nm, remains
unchanged and is concentration independent, so that it is the
reference point to correct for volume or intensity discrepancies.
Therefore, changes in adenosine concentration, and hence adenosine
deaminase activity, was assessed as the ratio of absorbance at 261
nm/absorbance at 253 nm (A.sub.261/A.sub.253), based on a standard
curve.
[1155] A. Standard Curve
[1156] To construct the standard curve for ADO and INO, a series of
solution mixtures in 0.001% Tween-20 containing different
concentrations of ADO and INO were prepared. The total
concentration of ADO and INO mix was 50 .mu.M, in 1.times.PBS (10
mM phosphate, 137 mM NaCl, 2.7 mM KCl), pH 7.4. The samples were
scanned with the wavelengths between 220 nm and 300 nm to determine
the isosbestic point, where all spectra cross. Table 36 sets forth
the measurements for the standard curve. The A.sub.261/A.sub.253
ratio was plotted against ADO concentration and linear fitting
resulted in a standard curve of
A.sub.261/A.sub.253=0.0249[ADO]-0.0152 (R.sup.2=0.999).
TABLE-US-00036 TABLE 36 Standard curve for Spectrophotometric
determination of adenosine concentration [ADO] (.mu.M) A.sub.261
A.sub.253 A.sub.261/A.sub.253 50 0.669 0.5455 1.2264 49.5 0.6543
0.5366 1.2193 49 0.6493 0.5388 1.2051 48.5 0.6418 0.5378 1.1934 48
0.6352 0.5386 1.1794 47.5 0.6306 0.5406 1.1665 47 0.6244 0.5406
1.1550 46.5 0.6134 0.5363 1.1438 46 0.6108 0.5402 1.1307 45.5
0.6026 0.5395 1.1170 45 0.5965 0.5404 1.1038
[1157] B. Adenosine Deaminase Activity Spectrophotometric Assay
[1158] For performing the spectrophotometric adenosine deaminase
assay of ADA2 and variants, a 2.times. solution containing 10 mM
ADO in 100 mM potassium phosphate buffer (KPB), 0.1% Tween-20 at
different pHs (i.e. 5.5, 6, 6.5, 6.75, 7, 7.25, 7.4, 7.75 and 8)
were prepared. A separate 2.times. solution containing 2 .mu.g/mL
WT rHuADA2 or variants were prepared in the same 100 mM potassium
phosphate buffer (KPB), 0.1% Tween-20 at the respective pH (i.e.
5.5, 6, 6.5, 6.75, 7, 7.25, 7.4, 7.75 and 8). An equal volume of
the ADO solution and the ADA2 solution (wildtype or variants) were
mixed to initiate reaction. At each time point (i.e. 1, 3, 5, 7, 9,
11, 13 and 15 min), a small aliquot (4 .mu.l) was removed and
diluted 50 times by adding to 196 .mu.l 1.times.PBS, pH 7.4. The
diluted samples were further diluted 2 fold (in duplicates) by
adding 85 .mu.l samples to 85 .mu.l 1.times.PBS in a UV-transparent
half area plate. The absorbance at 253 nm and 261 nm were measured
of each diluted sample.
[1159] Adenosine concentration was determined using the
A.sub.261/A.sub.253 ratio and the standard curve. Adenosine
deaminase activity was measured by negative change in ADO
concentration per min.times.100.
[1160] Table 37 sets forth the results of the adenosine deaminase
activity, as measured by the spectrophotometric assay, at various
pH. The results showed that the optimal pH (highest deaminase
activity) for WT rHuADA2 activity is approximately 6.5. ADA2
variants K374D (K371D by mature numbering) and K374E (K371E by
mature numbering) have a similar activity pH profile as WT
rHuADA2.
[1161] In contrast, the ADA2 S265N variant (S262N by mature
numbering) has a pH optimum at a higher pH of 7.25. Double- and
triple-variants containing the S265N mutation (S262N by mature
numbering) also results in a similar pH optimum at 7.25.
TABLE-US-00037 TABLE 37 Adenosine deaminase activity of ADA2 and
variants at varying pH Replacement Replacement Adenosine deaminase
activity .DELTA. [ADO]/min .times. (-100) at pH (Zavialov No.)
(mature No.) 5.5 6 6.5 6.75 7 7.25 7.4 7.75 8 WT ADA2 WT ADA2 21.11
22.06 33.77 29.76 28.70 24.47 21.77 6.65 3.58 K374D K371D 12.19
10.68 14.22 12.90 13.22 12.86 10.55 1.55 3.46 K374E K371E 15.76
19.15 27.09 25.72 24.63 21.88 18.32 5.98 4.25 R23E R20E 22.84 25.64
29.18 29.47 28.53 21.71 19.37 7.41 5.33 S265N S262N 24.61 31.59
41.30 44.46 45.16 50.99 45.81 25.16 3.70 S265N/K374D S262N/K371D
22.89 33.51 39.06 41.58 45.98 42.69 43.37 22.29 4.36 S265N/K374E
S262N/K371E 31.84 44.31 50.23 54.55 59.68 60.07 57.15 28.28 1.77
S265N/R23E S262N/R20E 27.34 38.26 45.58 48.49 51.90 56.12 50.44
24.42 4.63 S265N/R23E/K374D S262N/R20E/K371D 20.27 28.16 35.51
33.24 40.08 42.28 34.66 18.46 4.94 S265N/R23E/K374E
S262N/R20E/K371E 37.94 52.70 66.08 67.95 74.68 77.81 67.77 35.97
2.04
Example 14
In Vivo Pharmacokinetic Analysis of PEGylated rHuADA2 Combination
Variants
[1162] The pharmacokinetics (PK) of the PEGylated ADA2-K374D,
PEGylated ADA2-R222Q/S265N and PEGylated ADA2-R222Q/S265N/K374D
variants by Zavialov numbering (K371D, R219Q/S262N and
R219Q/S262N/K371D, respectively, by mature numbering) were analyzed
in an immunocompetent mouse model.
[1163] A. Study Design
[1164] Twenty-seven (27) male BALB/c mice were divided into three
(3) dosing groups, and were further divided into three (3) groups
each for sampling of blood at different time points.
[1165] Thus, the mice were randomized into nine (9) groups total.
Mice were weighed prior to the start of the study, and randomized
into the 9 groups based upon their body weights. In each sampling
group, three groups of (3) mice were used for dosing each test
article to prevent oversampling of the blood from the animals. For
measurement of baseline ADA2 levels, a blood sample was obtained
from 12 randomly chosen mice and plasma was prepared using the
anti-coagulant potassium (K.sub.3) ethylene diamine tetraacetic
acid (K.sub.3-EDTA). All blood was collected by submandibular
venipuncture.
[1166] Each mouse was injected by intravenous tail-vein injection
with a 3 mg/kg dose of one of three PEGylated ADA2 variant test
article as set forth in Table 38, i.e., PEG-rHuADA2-K374D (K371D by
mature numbering), PEG-rHuADA2-R222Q/S265N (R219Q/S262N by mature
numbering) or PEG-rHuADA2-R222Q/S265N/K374D (R219Q/S262N/K371D by
mature numbering). PEGylated ADA2 variants were prepared using the
PEGylation method as described in Example 8.A, with minor
modifications. Briefly, all ADA2 variants at 10 mg/mL were
PEGylated with linear PEG-20K (JenKem Technology, Plano, Tex.; Cat.
No. M-SCM-20K) at 1:15 molar ratio and incubated first at
37.degree. for 30 min, then at 4.degree. C. for 16 hours. SDS-PAGE
and analytical SEC results show that 100% of the ADA2 variants were
PEGylated under the optimized PEGylation condition and all
PEGylated ADA2 variants retained 100% enzymatic activity.
[1167] Approximately 200 .mu.L of whole blood was collected at
designated sampling time points from appropriate groups of mice as
indicated below in Table 38 and kept on ice until plasma
preparation. The initial two (2) blood samples were collected by
submandibular venipuncture. The final sample was collected from a
terminal bleed. Plasma was prepared by centrifuging the blood
(500.times.g for 5 min at 4.degree. C.), transferring the plasma to
a fresh tube and immediately freezing at -80.degree. C. until the
adenosine deaminase activity assay. Adenosine deaminase activity
was determined as described in Example 4.
[1168] Non-compartmental analysis (NCA) was conducted using the
Phoenix WinNonlin version 6.3 (Pharsight Corp, St. Louis, Mo.
63101). The half-life, or time taken for the activity of ADA2
proteins to be reduced by half, was calculated. Also, total
exposure was measured by calculating the Area Under the
Concentration-time Curve (AUC). The AUC and half-life values were
obtained from the unweighted average from each test article group.
The following options in the Phoenix WinNonlin program were used
for data analysis: (i) linear trapezoidal/linear interpolation
option for AUC; (ii) best-fit slope selection option for terminal
slope; and (iii) uniform weighting of the data.
TABLE-US-00038 TABLE 38 Pharmacokinetics Study Design for PEGylated
ADA2 WT and variants Blood Collection Time points post Test Article
No. of dosing Group # (ZavialoNo.) (Mature No.) Animals Dose
(hours) 1 PEG-K374D PEG-K371D 3 3 mg/kg 0.25, 8, 48 2 3 1, 4, 72 3
3 2, 24, 168 4 PEG-R222Q/ PEG-R219Q/ 3 3 mg/kg 0.25, 8, 48 5 S265N
S262N 3 1, 4, 72 6 3 2, 24, 168 7 PEG- PEG- 3 3 mg/kg 0.25, 8, 48 8
R222Q/ R219Q/ 3 1, 4, 72 S265N/ S262N/ K374D K371D 9 3 2, 24,
168
[1169] B. Results
[1170] 1. Pharmacokinetics of Non-PEGylated rHuADA2 WT and
Variants
[1171] The pharmacokinetics (PK) properties of PEGylated ADA2
variants PEG-K374D (K371D by mature numbering),
PEG-R222Q/S265N(R219Q/S262N by mature numbering) and
PEG-R222Q/S265N/K374D (R219Q/S262N/K371D by mature numbering) are
set forth in Tables 39 and 40. Table 39 sets forth the total
exposure measured using an Area Under the Curve (AUC) calculation
and Table 40 sets for the half-life (t.sub.1/2) of the tested
PEGylated rHuADA2 variants.
[1172] The results show that PEGylation substantially improves the
pharmacokinetic profile of ADA2 and all tested PEGylated ADA2
variants exhibited significant higher AUC and longer half-life than
the non-PEGylated WT rHuADA2 (see Example 9 and Tables 26 and 27).
PEG-R222Q/S265N (R219Q/S262N by mature numbering) exhibited the
largest improvement, with an AUC that is 49661% higher than the
non-PEGylated WT rHuADA2, and a half-life that was 4043% longer
than the non-PEGylated WT rHuADA2. The PEG-K374D (K371D by mature
numbering) exhibited a greater improvement of PK properties
compared to the same test article group in Example 9 and Tables 26
and 27, which can be attributed to the optimized PEGylation
conditions used in preparing the test articles.
TABLE-US-00039 TABLE 39 Comparison of Total Exposure - Area under
the Curve (AUC): PEGylated ADA2 combination variants Test Percent
increase Article (Zavialov Test article (Mature AUC in AUC compared
numbering) numbering) (U * h)/mL to WT ADA2 PEG-K374D PEG-K371D
4,662 14,177 PEG-R222Q/ PEG-R219Q/S262N 16,330 49,661 S265N
PEG-K374D/ PEG-K371D/ 9,340 28,404 R222Q/S265N R219Q/S262N
TABLE-US-00040 TABLE 40 Comparison of half-life (t.sub.1/2):
PEGylated ADA2 variants Test Half-life Percent increase Article
(Zavialov Test article (Mature slow (t.sub.1/2) in t.sub.1/2
compared numbering) numbering) (min) to WT ADA2 PEG-K374D PEG-K371D
2,256 3,269 PEG-R222Q/S265N PEG-R219Q/S262N 2,790 4,043 PEG-K374D/
PEG-K371D/ 2,364 3,426 R222Q/S265N R219Q/S262N
Example 15
Generation of Additional Combination Variants
[1173] Additional combinations variants were generated, combining
amino acid substitution(s) that increased enzymatic activity and/or
amino acid substitution(s) that confer attenuated heparin binding,
with other modifications, such as
deletions/insertions/substitutions and amino acid replacement(s)
that confer other altered activity. In particular, the amino acid
substitution S265N and/or R222Q (S262N and/or R219Q, by mature
numbering) which conferred the greatest increases in enzymatic
activity as described in Example 10, were combined with other ADA2
modifications described in previous Examples. The amino acid
replacement K374D (K371D by mature numbering) was also combined
with other ADA2 modifications described in previous Examples. The
combination variants are set forth in Table 41.
TABLE-US-00041 TABLE 41 Other Combination Variants SEQ ID
Substitution (Zavialov numbering) Substitution (mature numbering)
NO: K374D/V102-Q147del.fwdarw.(GGGGS).sub.1
K371D/V99-Q144del.fwdarw.(GGGGS).sub.1 589
K374D/V102-Q147del.fwdarw.(GGGGS).sub.2
K371D/V99-Q144del.fwdarw.(GGGGS).sub.2 590
K374D/V102-Q147del.fwdarw.(GGGGS).sub.3
K371D/V99-Q144del.fwdarw.(GGGGS).sub.3 591
K374D/C108-T150del.fwdarw.(GGGGS).sub.1
K371D/C105-T147del.fwdarw.(GGGGS).sub.1 592
K374D/C108-T150del.fwdarw.(GGGGS).sub.2
K371D/C105-T147del.fwdarw.(GGGGS).sub.2 593
K374D/C108-T150del.fwdarw.(GGGGS).sub.3
K371D/C105-T147del.fwdarw.(GGGGS).sub.3 594
R222Q/S265N/--.fwdarw.N4/--.fwdarw.A5/--.fwdarw.S6
R219Q/S262N/--.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3 596
R222Q/S265N/R23N/V25S R219Q/S262N/R20N/V22S 597
R222Q/S265N/K374N/D376S R219Q/S262N/K371N/D373S 598
R222Q/S265N/K375N/I377S R219Q/S262N/K372N/I374S 599
R222Q/S265N/T406N/H408S R219Q/S262N/T403N/H405S 600
R222Q/S265N/G407N/P409S R219Q/S262N/G404N/P406S 601
R222Q/S265N/C108-T150del.fwdarw.(Gly).sub.15
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.15 602
R222Q/S265N/C108-T150del.fwdarw.(Gly).sub.10
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.10 603
R222Q/S265N/C108-T150del.fwdarw.(Gly).sub.7
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.7 604
R222Q/S265N/C108-T150del.fwdarw.(Gly).sub.5
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.5 605
R222Q/S265N/C108-T150del.fwdarw.(Gly).sub.3
R219Q/S262N/C105-T147del.fwdarw.(Gly).sub.3 606
R222Q/S265N/R128N/P129A R219Q/S262N/R125N/P126A 607
R222Q/S265N/S130N/K132S R219Q/S262N/S127N/K129S 608
R222Q/S265N/P129N/E131T R219Q/S262N/P126N/E128T 609
R222Q/S265N/R115N/I117T R219Q/S262N/R112N/I114T 610
R222Q/S265N/I137N/L138C/L139T R219Q/S262N/I134N/L135C/L136T 611
R222Q/S265N/I137N/L138S/L139T R219Q/S262N/I134N/L135S/L136T 612
R222Q/S265N/R145N/Q147S R219Q/S262N/R142N/Q144S 613
R222Q/S265N/E140N/Y142T R219Q/S262N/E137N/Y139T 614
R222Q/S265N/P114N/G116S R219Q/S262N/P111N/G113S 615
R222Q/S265N/F122S R219Q/S262N/F119S 616 R222Q/S265N/F122K
R219Q/S262N/F119K 617 R222Q/S265N/Y227R R219Q/S262N/Y224R 618
R222Q/S265N/Y227N R219Q/S262N/Y224N 619 R222Q/S265N/Y194S
R219Q/S262N/Y191S 620 R222Q/S265N/Y194D R219Q/S262N/Y191D 621
R222Q/S265N/F186K R219Q/S262N/F183K 622 R222Q/S265N/Y194D/Y227R
R219Q/S262N/Y191D/Y224R 623 R222Q/S265N/F112S R219Q/S262N/F109S 624
R222Q/S265N/F112A R219Q/S262N/F109A 625 R222Q/S265N/R121D
R219Q/S262N/R118D 626 R222Q/S265N/R121A R219Q/S262N/R118A 627
R222Q/S265N/Y142T R219Q/S262N/Y139T 628 R222Q/S265N/Y142A
R219Q/S262N/Y139A 629 R222Q/S265N/W136S R219Q/S262N/W133S 630
R222Q/S265N/W136T R219Q/S262N/W133T 631 R222Q/S265N/P127A
R219Q/S262N/P124A 632 R222Q/S265N/P127S R219Q/S262N/P124S 633
R222Q/S265N/V102- R219Q/S262N/V99- 634 Q147del.fwdarw.(GGGGS).sub.1
Q144del.fwdarw.(GGGGS).sub.1 R222Q/S265N/V102- R219Q/S262N/V99- 635
Q147del.fwdarw.(GGGGS).sub.2 Q144del.fwdarw.(GGGGS).sub.2
R222Q/S265N/V102- R219Q/S262N/V99- 636 Q147del.fwdarw.(GGGGS).sub.3
Q144del.fwdarw.(GGGGS).sub.3 R222Q/S265N/C108- R219Q/S262N/C105-
637 T150del.fwdarw.(GGGGS).sub.1 T147del.fwdarw.(GGGGS).sub.1
R222Q/S265N/C108- R219Q/S262N/C105- 638
T150del.fwdarw.(GGGGS).sub.2 T147del.fwdarw.(GGGGS).sub.2
R222Q/S265N/C108- R219Q/S262N/C105- 639
T150del.fwdarw.(GGGGS).sub.3 T147del.fwdarw.(GGGGS).sub.3
R222Q/S265N/K374D/V102- R219Q/S262N/K371/V99- 640
Q147del.fwdarw.(GGGGS).sub.1 Q144del.fwdarw.(GGGGS).sub.1
R222Q/S265N/K374D/V102- R219Q/S262N/K371D/V99- 641
Q147del.fwdarw.(GGGGS).sub.2 Q144del.fwdarw.(GGGGS).sub.2
R222Q/S265N/K374D/V102- R219Q/S262N/K371D/V99- 642
Q147del.fwdarw.(GGGGS).sub.3 Q144del.fwdarw.(GGGGS).sub.3
R222Q/S265N/K374D/C108- R219Q/S262N/K371D/C105- 643
T150del.fwdarw.(GGGGS).sub.1 T147del.fwdarw.(GGGGS).sub.1
R222Q/S265N/K374D/C108- R219Q/S262N/K371D/C105- 644
T150del.fwdarw.(GGGGS).sub.2 T147del.fwdarw.(GGGGS).sub.2
R222Q/S265N/K374D/C108- R219Q/S262N/K371D/C105- 645
T150del.fwdarw.(GGGGS).sub.3 T147del.fwdarw.(GGGGS).sub.3
K374D/C108-T150del.fwdarw.(Gly).sub.15
K371D/C105-T147del.fwdarw.(Gly).sub.15 647
K374D/C108-T150del.fwdarw.(Gly).sub.10
K371D/C105-T147del.fwdarw.(Gly).sub.10 648
K374D/C108-T150del.fwdarw.(Gly).sub.7
K371D/C105-T147del.fwdarw.(Gly).sub.7 649
K374D/C108-T150del.fwdarw.(Gly).sub.5
K371D/C105-T147del.fwdarw.(Gly).sub.5 650
K374D/C108-T150del.fwdarw.(Gly).sub.3
K371D/C105-T147del.fwdarw.(Gly).sub.3 651 R222Q/S265N/K374D/C108-
R219Q/S262N/K371D/C105- 671 T150del.fwdarw.(Gly).sub.15
T147del.fwdarw.(Gly).sub.15 R222Q/S265N/K374D/C108-
R219Q/S262N/K371D/C105- 672 T150del.fwdarw.(Gly).sub.10
T147del.fwdarw.(Gly).sub.10 R222Q/S265N/K374D/C108-
R219Q/S262N/K371D/C105- 673 T150del.fwdarw.(Gly).sub.7
T147del.fwdarw.(Gly).sub.7 R222Q/S265N/K374D/C108-
R219Q/S262N/K371D/C105- 674 T150del.fwdarw.(Gly).sub.5
T147del.fwdarw.(Gly).sub.5 R222Q/S265N/K374D/C108-
R219Q/S262N/K371D/C105- 675 T150del.fwdarw.(Gly).sub.3
T147del.fwdarw.(Gly).sub.3 R222Q/S265N/K14A R219Q/S262N/K11A 659
R222Q/S265N/K14D R219Q/S262N/K11D 660 R222Q/S265N/K14E
R219Q/S262N/K11E 661 R222Q/S265N/K16A R219Q/S262N/K13A 662
R222Q/S265N/K16D R219Q/S262N/K13D 663 R222Q/S265N/K16E
R219Q/S262N/K13E 682 R222Q/S265N/K374A R219Q/S262N/K371A 683
R222Q/S265N/K375A R219Q/S262N/K372A 684 R222Q/S265N/K375D
R219Q/S262N/K372D 685 R222Q/S265N/K375E R219Q/S262N/K372E 686
R222Q/S265N/K455A R219Q/S262N/K452A 687 R222Q/S265N/K455D
R219Q/S262N/K452D 688 R222Q/S265N/K455E R219Q/S262N/K452E 689
R222Q/S265N/R23A R219Q/S262N/R20A 690 R222Q/S265N/R23D
R219Q/S262N/R20D 691 R222Q/S265N/R369A R219Q/S262N/R366A 692
R222Q/S265N/R369D R219Q/S262N/R366D 693 R222Q/S265N/R369E
R219Q/S262N/R366E 694 R222Q/S265N/H267A R219Q/S262N/H264A 695
R222Q/S265N/H267Q R219Q/S262N/H264Q 696 R222Q/S265N/H267N
R219Q/S262N/H264N 697 R222Q/S265N/H267G R219Q/S262N/H264G 698
R222K/S265N R219K/S262N 699 R222N/S265N R219N/S262N 700 R222A/S265N
R219A/S262N 701 R222Q/S265N/L224A R219Q/S262N/L221A 702
R222Q/S265N/L224V R219Q/S262N/L221V 703 R222Q/S265N/L224G
R219Q/S262N/L221G 704 R222Q/S265N/E182D R219Q/S262N/E179D 705
R222Q/S265N/E182A R219Q/S262N/E179A 706 R222Q/S265N/E182S
R219Q/S262N/E179S 707 R222Q/S265N/E182T R219Q/S262N/E179T 708
R222Q/S265N/E182V R219Q/S262N/E179V 709 R222Q/S265N/E182G
R219Q/S262N/E179G 710 R222Q/S265A R219Q/S262A 711 R222Q/S265V
R219Q/S262V 712 R222Q/S265M R219Q/S262M 713 R222Q/S265N/K14A/R23A
R219Q/S262N/K11A/R20A 714 R222Q/S265N/K14A/R23A/K374A
R219Q/S262N/K11A/R20A/K371A 715 R222Q/S265N/R23A/K374A
R219Q/S262N/R20A/K371A 716 R222Q/S265N/K14A/K374A
R219Q/S262N/K11A/K371A 717 R222Q/S265N/K29A R219Q/S262N/K26A 718
R222Q/S265N/K29D R219Q/S262N/K26D 719 R222Q/S265N/K29E
R219Q/S262N/K26E 720 R222Q/S265N/R220A R219Q/S262N/R217A 721
R222Q/S265N/R220D R219Q/S262N/R217D 722 R222Q/S265N/R220E
R219Q/S262N/R217E 723 R222Q/S265N/K261A R219Q/S262N/K258A 724
R222Q/S265N/K261D R219Q/S262N/K258D 725 R222Q/S265N/K261E
R219Q/S262N/K258E 726 R222Q/S265N/R280A R219Q/S262N/R277A 727
R222Q/S265N/R280D R219Q/S262N/R277D 728 R222Q/S265N/R280E
R219Q/S262N/R277E 729 R222Q/S265N/R286A R219Q/S262N/R283A 730
R222Q/S265N/R286D R219Q/S262N/R283D 731 R222Q/S265N/R286E
R219Q/S262N/R283E 732 R222Q/S265N/K312A R219Q/S262N/K309A 733
R222Q/S265N/K312D R219Q/S262N/K309D 734 R222Q/S265N/K312E
R219Q/S262N/K309E 735 R222Q/S265N/K320A R219Q/S262N/K317A 736
R222Q/S265N/K320D R219Q/S262N/K317D 737 R222Q/S265N/K320E
R219Q/S262N/K317E 738 R222Q/S265N/K324A R219Q/S262N/K321A 739
R222Q/S265N/K324D R219Q/S262N/K321D 740 R222Q/S265N/K324E
R219Q/S262N/K321E 741 R222Q/S265N/R355A R219Q/S262N/R352A 742
R222Q/S265N/R355D R219Q/S262N/R352D 743 R222Q/S265N/R355E
R219Q/S262N/R352E 744 R222Q/S265N/R444A R219Q/S262N/R441A 745
R222Q/S265N/R444D R219Q/S262N/R441D 746 R222Q/S265N/R444E
R219Q/S262N/R441E 747 R222Q/S265N/K447A R219Q/S262N/K444A 748
R222Q/S265N/K447D R219Q/S262N/K444D 749 R222Q/S265N/K447E
R219Q/S262N/K444E 750 R222Q/S265N/K464A R219Q/S262N/K461A 751
R222Q/S265N/K464D R219Q/S262N/K461D 752 R222Q/S265N/K464E
R219Q/S262N/K461E 753 R222Q/S265N/K472A R219Q/S262N/K469A 754
R222Q/S265N/K472D R219Q/S262N/K469D 755 R222Q/S265N/K472E
R219Q/S262N/K469E 756 R222Q/S265N/K473A R219Q/S262N/K470A 757
R222Q/S265N/K473D R219Q/S262N/K470D 758 R222Q/S265N/K473E
R219Q/S262N/K470E 759 R222Q/S265N/D89A R219Q/S262N/D86A 760
R222Q/S265N/D89C R219Q/S262N/D86C 761 R222Q/S265N/D89E
R219Q/S262N/D86E 762 R222Q/S265N/D89F R219Q/S262N/D86F 763
R222Q/S265N/D89G R219Q/S262N/D86G 764 R222Q/S265N/D89H
R219Q/S262N/D86H 765 R222Q/S265N/D89I R219Q/S262N/D86I 766
R222Q/S265N/D89K R219Q/S262N/D86K 767 R222Q/S265N/D89L
R219Q/S262N/D86L 768 R222Q/S265N/D89M R219Q/S262N/D86M 769
R222Q/S265N/D89N R219Q/S262N/D86N 770 R222Q/S265N/D89P
R219Q/S262N/D86P 771 R222Q/S265N/D89Q R219Q/S262N/D86Q 772
R222Q/S265N/D89R R219Q/S262N/D86R 773 R222Q/S265N/D89S
R219Q/S262N/D86S 774 R222Q/S265N/D89T R219Q/S262N/D86T 775
R222Q/S265N/D89V R219Q/S262N/D86V 776 R222Q/S265N/D89W
R219Q/S262N/D86W 777 R222Q/S265N/D89Y R219Q/S262N/D86Y 778
R222Q/S265N/E182C R219Q/S262N/E179C 779 R222Q/S265N/E182F
R219Q/S262N/E179F 780 R222Q/S265N/E182H R219Q/S262N/E179H 781
R222Q/S265N/E182I R219Q/S262N/E179I 782 R222Q/S265N/E182K
R219Q/S262N/E179K 783 R222Q/S265N/E182L R219Q/S262N/E179L 784
R222Q/S265N/E182M R219Q/S262N/E179M 785 R222Q/S265N/E182N
R219Q/S262N/E179N 786 R222Q/S265N/E182P R219Q/S262N/E179P 787
R222Q/S265N/E182Q R219Q/S262N/E179Q 788 R222Q/S265N/E182R
R219Q/S262N/E179R 789 R222Q/S265N/E182W R219Q/S262N/E179W 790
R222Q/S265N/E182Y R219Q/S262N/E179Y 791 R222C/S265N R219C/S262N 792
R222D/S265N R219D/S262N 793 R222E/S265N R219E/S262N 794 R222F/S265N
R219F/S262N 795 R222G/S265N R219G/S262N 796 R222H/S265N R219H/S262N
797 R222I/S265N R219I/S262N 798 R222L/S265N R219L/S262N 799
R222M/S265N R219M/S262N 800 R222P/S265N R219P/S262N 801 R222S/S265N
R219S/S262N 802 R222T/S265N R219T/S262N 803 R222V/S265N R219V/S262N
804 R222W/S265N R219W/S262N 805 R222Y/S265N R219Y/S262N 806
R222Q/S265N/L224C R219Q/S262N/L221C 807 R222Q/S265N/L224D
R219Q/S262N/L221D 808 R222Q/S265N/L224E R219Q/S262N/L221E 809
R222Q/S265N/L224F R219Q/S262N/L221F 810 R222Q/S265N/L224H
R219Q/S262N/L221H 811 R222Q/S265N/L224I R219Q/S262N/L221I 812
R222Q/S265N/L224K R219Q/S262N/L221K 813 R222Q/S265N/L224M
R219Q/S262N/L221M 814 R222Q/S265N/L224N R219Q/S262N/L221N 815
R222Q/S265N/L224P R219Q/S262N/L221P 816 R222Q/S265N/L224Q
R219Q/S262N/L221Q 817 R222Q/S265N/L224R R219Q/S262N/L221R 818
R222Q/S265N/L224S R219Q/S262N/L221S 819
R222Q/S265N/L224T R219Q/S262N/L221T 820 R222Q/S265N/L224W
R219Q/S262N/L221W 821 R222Q/S265N/L224Y R219Q/S262N/L221Y 822
R222Q/S265C R219Q/S262C 823 R222Q/S265D R219Q/S262D 824 R222Q/S265E
R219Q/S262E 825 R222Q/S265F R219Q/S262F 826 R222Q/S265G R219Q/S262G
827 R222Q/S265H R219Q/S262H 828 R222Q/S265I R219Q/S262I 829
R222Q/S265K R219Q/S262K 830 R222Q/S265L R219Q/S262L 831 R222Q/S265P
R219Q/S262P 832 R222Q/S265Q R219Q/S262Q 833 R222Q/S265R R219Q/S262R
834 R222Q/S265T R219Q/S262T 835 R222Q/S265W R219Q/S262W 836
R222Q/S265Y R219Q/S262Y 837 R222Q/S265N/H267C R219Q/S262N/H264C 838
R222Q/S265N/H267D R219Q/S262N/H264D 839 R222Q/S265N/H267E
R219Q/S262N/H264E 840 R222Q/S265N/H267F R219Q/S262N/H264F 841
R222Q/S265N/H267I R219Q/S262N/H264I 842 R222Q/S265N/H267K
R219Q/S262N/H264K 843 R222Q/S265N/H267L R219Q/S262N/H264L 844
R222Q/S265N/H267M R219Q/S262N/H264M 845 R222Q/S265N/H267P
R219Q/S262N/H264P 846 R222Q/S265N/H267R R219Q/S262N/H264R 847
R222Q/S265N/H267S R219Q/S262N/H264S 848 R222Q/S265N/H267T
R219Q/S262N/H264T 849 R222Q/S265N/H267V R219Q/S262N/H264V 850
R222Q/S265N/H267W R219Q/S262N/H264W 851 R222Q/S265N/H267Y
R219Q/S262N/H264Y 852 R222Q/S265N/S269A R219Q/S262N/S266A 853
R222Q/S265N/S269C R219Q/S262N/S266C 854 R222Q/S265N/S269D
R219Q/S262N/S266D 855 R222Q/S265N/S269E R219Q/S262N/S266E 856
R222Q/S265N/S269F R219Q/S262N/S266F 857 R222Q/S265N/S269G
R219Q/S262N/S266G 858 R222Q/S265N/S269H R219Q/S262N/S266H 859
R222Q/S265N/S269I R219Q/S262N/S266I 860 R222Q/S265N/S269K
R219Q/S262N/S266K 861 R222Q/S265N/S269L R219Q/S262N/S266L 862
R222Q/S265N/S269M R219Q/S262N/S266M 863 R222Q/S265N/S269N
R219Q/S262N/S266N 864 R222Q/S265N/S269P R219Q/S262N/S266P 865
R222Q/S265N/S269Q R219Q/S262N/S266Q 866 R222Q/S265N/S269R
R219Q/S262N/S266R 867 R222Q/S265N/S269T R219Q/S262N/S266T 868
R222Q/S265N/S269V R219Q/S262N/S266V 869 R222Q/S265N/S269W
R219Q/S262N/S266W 870 R222Q/S265N/S269Y R219Q/S262N/S266Y 871
R222Q/S265N/K270A R219Q/S262N/K267A 872 R222Q/S265N/K270C
R219Q/S262N/K267C 873 R222Q/S265N/K270D R219Q/S262N/K267D 874
R222Q/S265N/K270E R219Q/S262N/K267E 875 R222Q/S265N/K270F
R219Q/S262N/K267F 876 R222Q/S265N/K270G R219Q/S262N/K267G 877
R222Q/S265N/K270H R219Q/S262N/K267H 878 R222Q/S265N/K270I
R219Q/S262N/K267I 879 R222Q/S265N/K270L R219Q/S262N/K267L 880
R222Q/S265N/K270M R219Q/S262N/K267M 881 R222Q/S265N/K270N
R219Q/S262N/K267N 882 R222Q/S265N/K270P R219Q/S262N/K267P 883
R222Q/S265N/K270Q R219Q/S262N/K267Q 884 R222Q/S265N/K270R
R219Q/S262N/K267R 885 R222Q/S265N/K270S R219Q/S262N/K267S 886
R222Q/S265N/K270T R219Q/S262N/K267T 887 R222Q/S265N/K270V
R219Q/S262N/K267V 888 R222Q/S265N/K270W R219Q/S262N/K267W 889
R222Q/S265N/K270Y R219Q/S262N/K267Y 890 R222Q/S265N/V299A
R219Q/S262N/V296A 891 R222Q/S265N/V299C R219Q/S262N/V296C 892
R222Q/S265N/V299D R219Q/S262N/V296D 893 R222Q/S265N/V299E
R219Q/S262N/V296E 894 R222Q/S265N/V299F R219Q/S262N/V296F 895
R222Q/S265N/V299G R219Q/S262N/V296G 896 R222Q/S265N/V299H
R219Q/S262N/V296H 897 R222Q/S265N/V299I R219Q/S262N/V296I 898
R222Q/S265N/V299K R219Q/S262N/V296K 899 R222Q/S265N/V299L
R219Q/S262N/V296L 900 R222Q/S265N/V299M R219Q/S262N/V296M 901
R222Q/S265N/V299N R219Q/S262N/V296N 902 R222Q/S265N/V299P
R219Q/S262N/V296P 903 R222Q/S265N/V299Q R219Q/S262N/V296Q 904
R222Q/S265N/V299R R219Q/S262N/V296R 905 R222Q/S265N/V299S
R219Q/S262N/V296S 906 R222Q/S265N/V299T R219Q/S262N/V296T 907
R222Q/S265N/V299W R219Q/S262N/V296W 908 R222Q/S265N/V299Y
R219Q/S262N/V296Y 909 R222Q/K14A/R23A R219Q/K11A/R20A 910
R222Q/K14A/R23A/K374A R219Q/K11A/R20A/K371A 911 R222Q/R23A/K374A
R219Q/R20A/K371A 912 R222Q/K14A/K374A R219Q/K11A/K371A 913
S265N/K14A/R23A S262N/K11A/R20A 914 S265N/K14A/R23A/K374A
S262N/K11A/R20A/K371A 915 S265N/R23A/K374A S262N/R20A/K371A 916
S265N/K14A/K374A S262N/K11A/K371A 917
Example 16
Kinetic Assessment of Adenosine Deaminase Activity of rHuADA2 PRB
Domain Deletion Combination Variants
[1174] Combination variants containing the K374D mutation (K371D by
mature numbering) and PRB deletions replaced with (GGGGS).sub.n
linker, set forth in SEQ ID NOS:588-593, were assessed for kinetic
parameters of adenosine deaminase activity, using the assay method
described in Example 11.A above. The first set of variants contain
a deletion of residues V102-Q147 (V99-Q144, by mature numbering),
replaced with (GGGGS).sub.n linker of various length (e.g., n=1, 2
or 3; set forth in SEQ ID NOS: 588-590), and the second set of
variants contain a deletion of residues C108-T150 (C105-T147, by
mature numbering), replaced with (GGGGS).sub.n linker of various
length (e.g., n=1, 2 or 3; set forth in SEQ ID NOS: 591-593.
Kinetic parameters were tested at pH 7.6, and the results are set
forth in Table 42.
[1175] The results indicate that all tested ADA2 PRB domain
deletion mutants remain enzymatic activity, and generally exhibit
approximately 5 to 7-fold lower K.sub.m and 8 to 11-fold higher
catalytic efficiency (k.sub.cat/K.sub.m) at pH 7.6, compared to the
WT ADA2.
TABLE-US-00042 TABLE 42 Kinetic parameters of ADA2 WT and variants
at pH 7.6; [E] = 8.5 nM Replacement (Zavialov Replacement Vmax
K.sub.m k.sub.cat k.sub.cat/K.sub.m numbering) (mature numbering)
(.mu.M/min) (mM) (1/s) (1/Ms) K374D/V102- K371D/V99- 43.46 0.89
85.22 95,748 Q147del.fwdarw.(GGGGS).sub.1
Q144del.fwdarw.(GGGGS).sub.1 K374D/V102- K371D/V99- 44.52 0.87
87.29 100,338 Q147del.fwdarw.(GGGGS).sub.2
Q144del.fwdarw.(GGGGS).sub.2 K374D/V102- K371D/V99- 43.01 0.82
84.33 102,846 Q147del.fwdarw.(GGGGS).sub.3
Q144del.fwdarw.(GGGGS).sub.3 K374D/C108- K371D/C105- 43.1 0.91
84.51 92,532 T150del.fwdarw.(GGGGS).sub.1
T147del.fwdarw.(GGGGS).sub.1 K374D/C108- K371D/C105- 36.92 0.85
72.39 85,167 T150del.fwdarw.(GGGGS).sub.2
T147del.fwdarw.(GGGGS).sub.2 K374D/C108- K371D/C105- 38.12 0.77
74.75 97,223 T150del.fwdarw.(GGGGS).sub.3
T147del.fwdarw.(GGGGS).sub.3
Example 17
Tumor Growth Inhibition (TGI) Assessment of PEGylated rHuADA2-K374D
Using the CT26 Syngeneic Tumor Model
[1176] The murine CT26 syngeneic tumor model was used to assess the
antitumor activity of ADA2.
[1177] A. Syngeneic Tumor Model and Treatment
[1178] Forty-four (44) male BALB/c mice were inoculated
subcutaneously with 5.times.10.sup.6 murine colon cancer tumor
cells (CT26, ATCC CRL-2638) in 0.1 mL injection volume per animal.
Tumor volume was determined using digital calipers by caliper
measurement of the length (L) and width (W) of the solid tumor
masses. Tumor volume (TV) was calculated as: (L.times.W.sup.2)/2.
Tumors were allowed to grow and tumor bearing mice were staged
until when the tumors were palpable and measured to be about 50-100
mm.sup.3.
[1179] PEGylated rHuADA2-K374D (K371D by mature numbering) was
prepared as described in Example 8.A, with minor modifications to
generate a preparation in which approximately 100% of the molecules
were PEGylated as assessed by SDS-PAGE. Briefly, a preparation of
rHuADA2-K374D (K371D by mature numbering) at 10 mg/mL was mixed
with linear PEG-20K (JenKem Technology, Plano, Tex.; Cat. No.
M-SCM-20K) at 1:15 molar ratio and incubated first at 4.degree. C.
for 16 hours, and then at 30.degree. C. for 60 min.
[1180] For treatment, animals were randomized into four groups
(n=8/group). CT26 tumor bearing mice were then injected
intravenously (IV) every other day, at 3 mg/kg body weight, 10
mg/kg body weight or 30 mg/kg body weight doses of PEG-K374D
(PEG-K371D by mature numbering) or vehicle control (buffer only)
every other day. Tumor volume was measured at day 0 and 8 using
caliper measurement as described above. Percent Tumor Growth
Inhibition (TGI) for each respective tumor model was calculated
using the following equation:
% TGI=[1-(T.sub.n-T.sub.0)/(C.sub.n-C.sub.0)].times.100%
where "T.sub.n" is the average tumor volume for the treatment group
at day "n" after the final dose of PEG-K374D or control; "T.sub.0"
is the average tumor volume in that treatment group at day 0,
before treatment; "C.sub.n" is the average tumor volume for the
corresponding control group at day "n"; and "C.sub.0" is the
average tumor volume in the control group at day 0, before
treatment. One mouse from the vehicle group was excluded due to
significant tumor growth inhibition.
[1181] B. Results
[1182] Table 43 sets forth the results of the average tumor volume
and tumor growth inhibition at day 8 in the mice administered with
PEG-K374D compared to the vehicle injected control. At day 8, the
average tumor volume for the vehicle control group was 446.67
mm.sup.3 (n=7). For the group injected with 3 mg/kg of PEG-K374D,
the average tumor volume was 257.72 mm.sup.3, indicating a tumor
growth inhibition (TGI) of 50% (n=8; p-value=0.037). For the group
injected with 10 mg/kg of PEG-K374D, the average tumor volume was
207.84 mm.sup.3, indicating a TGI of 63% (n=8; p-value=0.0056). For
the group injected with 30 mg/kg of PEG-K374D, the average tumor
volume was 187.32 mm.sup.3, indicating a TGI of 68% (n=8;
p-value=0.0085). The results show that administration of PEG-K374D
results in significant tumor growth inhibition.
TABLE-US-00043 TABLE 43 Tumor volume and tumor growth inhibition
(TGI) in mice administered with PEG-K374D No. of Tumor Mice per
Average Tumor Growth p value (t-Test) Dose group Volume (mm.sup.3)
Inhibition compared to vehicle Vehicle 7 446.67 0% 3 mg/kg 8 257.72
50% 0.037 10 mg/kg 8 207.84 63% 0.0056 30 mg/kg 8 187.32 68%
0.0085
Example 18
Tumor Growth Inhibition (TGI) Assessment of Combination Therapy
with PEGYLATED rHuADA2, Anti-PD-1 and Anti-CTLA4
[1183] The murine CT26 syngeneic tumor model was used to compare
the antitumor activity of combination therapy using PEGylated ADA2
with checkpoint inhibitors anti-PD-1 and anti-CTLA4 antibodies.
CT26 syngeneic tumors were produced by injecting 2.times.10.sup.5
CT26 cells in 0.05 mL injection volume per animal into the right
peritibial muscle of male Balb/C mice. Tumor bearing mice were
staged into treatment groups when the average tumor size reached
150 mm.sup.3.
[1184] For treatment, animals were randomized into 8 groups
(n=8/group) as follows: 1) saline vehicle control, 2)
PEG-ADA2-K374D, 3) .alpha.-CTLA4 antibody (Clone 9D9, Cat. No.
BE0164; BioXCell, West Lebanon, N.H., 4) .alpha.-PD-1 antibody
(Clone RMP1-14, Cat. No. BE0146; BioXCell, West Lebanon, N.H.), 5)
PEG-ADA2-K374D+.alpha.-CTLA4; 6) PEG-K374D+.alpha.-PD-1; 7)
.alpha.-CTLA4+.alpha.-PD-1, or 8) Triple combo
(PEG-ADA2-K374D+.alpha.-CTLA4+.alpha.-PD-1). PEG-ADA2-K374D was
dosed intravenously 3.times. weekly at 10 mg/kg, .alpha.-CTLA4 was
dosed intraperiotoneally biweekly at 4 mg/kg, and .alpha.-PD-1 was
dosed intraperitoneally biweekly at 4 mg/kg. The sequence of dosing
in the combination groups was as follows: PEG-ADA2-K374D followed
by .alpha.-CTLA4 followed by .alpha.-PD-1.
[1185] Tumor volume was assessed twice weekly via ultrasound
imaging using the Vevo2100 (Visual Sonics, Toronto, Canada) to
determine tumor growth inhibition (TGI). Animals were anesthetized
using light isoflurane anesthesia while the tumor volumes were
measured. For tumor measurement, the region of interest was covered
in ultrasound gel (Parker Laboratories, Fairfield, N.J.), and the
RMV-716 (focal depth=17.5 mm) scan head was positioned directly
over the region of interest. While in 2D-Mode, the approximate
center of the tumor was located, and subsequently an image
(.about.150-200 frames) was captured using 3D-mode. Approximately
15-30 frames out of 150-200 frames were analyzed and a tumor volume
calculated and expressed in mm.sup.3. Tumor growth Inhibition (TGI)
was calculated as described above.
[1186] The results are presented in Table 44. Table 44 depicts the
average tumor volume per group, on study day 10 (SD10), 48 hours
after PEG-ADA2-K374D and 72 hours after .alpha.-CTLA4 and
.alpha.-PD-1, and the range of tumor volume of all animals in the
group. The TGI compared to vehicle control also is depicted. The
results show that PEG-ADA2-K374D, .alpha.-CTLA4 and .alpha.-PD-1
each individually exhibited tumor growth inhibition activity, with
.alpha.-CTLA4 exhibiting greater tumor growth reduction than the
other single treatments. The results show a slight synergistic
effect of the combination therapy of PEG-ADA2-K374D with either
.alpha.-CTLA4 or .alpha.-PD-1. A further increase in tumor growth
inhibition was observed in the triple combination therapy. In
contrast, the combination therapy of .alpha.-CTLA4 and .alpha.-PD-1
only slightly increased tumor growth inhibition as compared to
treatment with .alpha.-CTLA4.
TABLE-US-00044 TABLE 44 Tumor Growth Inhibition of Combination
Therapy Average Group Tumor Volume, Treatment SD10 Volume Range TGI
Vehicle 1567.53 1389-1890 -- PEG-ADA2-K374D 1499.11 1213-1594 5%
.alpha.-CTLA4 1050.78 860-1232 37% .alpha.-PD-1 1359.2 1131-1616
15% PEG-ADA2-K374D + 965.21 731-1207 43% .alpha.-CTLA4
PEG-ADA2-K374D + 1244.43 687-1539 23% .alpha.-PD-1 .alpha.-CTLA4 +
.alpha.-PD-1 993.97 763-1252 41% Triple Combo 835.77 687-989
52%
Example 19
PEG-ADA2 Distribution in CT26 Peritibial Tumors or Normal
Organs
[1187] To assess the distribution and elimination of administered
PEG-ADA2-K374D in the tumor microenvironment or in normal organs,
immunofluorescence was used to assess the presence of
PEG-ADA2-K374D administered to mice. PEG-ADA2-K374D was labeled at
room temperature for 60 minutes with DyLight755 Sulfydryl-Reactive
Dye (DL755), a near-IR fluor, using the DyLight 755 Antibody
Labeling Kit (Thermo Scientific, Rockford, Ill.). Alexa Fluor 750
(AF 750) labeled bovine serum albumin (BSA, 1 mg/mL) was purchased
from (Life Technology, Carlsbad, Calif.).
[1188] A. Distribution in CT26 Peritibial Tumors
[1189] CT26 syngeneic tumors were produced by injecting
2.times.10.sup.5 cells in 0.05 mL injection volume per animal into
the right peritibial muscle of male Balb/C mice. When average tumor
size reached 600 mm.sup.3, tumor-bearing mice were staged into 2
groups (n=4/group) to receive either PEG-ADA2-K374D.sup.DL755 at
0.5 mg/kg or BSA.sup.AF750 at 0.5 mg/kg intravenously. The
distribution of DL755 labeled PEG-ADA2-K374D
(PEG-ADA2-K374D.sup.DL755) and AF 750 labeled BSA (BSA.sup.AF750)
in mouse tumors was assessed using the IVIS Caliper fluorescent
imaging system with an excitation wavelength of 745 nm and an
emission wavelength of 800 nm (Caliper Life Sciences, Alameda,
Calif.) and signal intensity was measured with LivingImage
software. Images were captured before administration of labeled
proteins and at 10 minute, 2, 6 hours and daily after
administration of labeled proteins.
[1190] The results are set forth in Table 45. The images showed a
strong fluorescent intensity at the tumor site in all treatment
groups. Fluorescent intensity of images demonstrated
PEG-ADA2-K374D.sup.DL755 rapidly accessed to CT26 tumor and reached
the plateau at 48 hours. Only 30% of PEG-ADA2-K374D.sup.DL755 was
eliminated from tumors on day 6 post PEG-ADA2-K374D.sup.DL755
injection. In contrast, less control agent BSA.sup.AF750 accessed
to the tumors, and the fluorescent intensity was reduced quickly.
Nearly 100% of BSA.sup.AF750 was eliminated from the tumors on day
6. Thus, the results demonstrate that PEG-ADA2-K374D.sup.DL755 has
a high affinity to CT26 tumors.
TABLE-US-00045 TABLE 45 Tumor Distribution BSA.sup.AF750
PEG-ADA2-K374D.sup.DL755 Hour (Fluorescent intensity) (Fluorescent
intensity) -1 7.86E+08 .+-.6.92E7 7.80E+08 .+-.5.67E7 0.2 2.95E+09
.+-.9.69E7 4.52E+09 .+-.5.72E8 2 3.92E+09 .+-.2.93E8 4.64E+09
.+-.6.06E8 6 4.64E+09 .+-.7.81E8 6.54E+09 .+-.6.44E8 24 3.18E+09
.+-.4.88E8 9.48E+09 .+-.1.30E9 48 1.94E+09 .+-.7.70E7 1.12E+10
.+-.8.26E8 72 1.30E+09 .+-.1.40E8 8.95E+09 .+-.7.40E8 96 9.86E+08
.+-.2.98E7 1.07E+10 .+-.8.26E8 144 7.78E+08 .+-.3.45E7 4.83E+09
.+-.5.80E8 168 6.39E+08 .+-.7.03E7 3.64E+09 .+-.3.10E8 196 6.59E+08
.+-.3.42E7 2.68E+09 .+-.4.09E8
[1191] B. Comparison of Distribution in CT26-Tumor Bearing Mice or
Balb/C Naive Mice
[1192] To compare the distribution in naive mice, CT26-tumor
bearing mice were generated as described above, and were
intravenously administered PEG-ADA2-K374D.sup.DL755 at 0.5 mg/kg
(n=3). Separately, naive Balb/c mice also were intravenously
administered PEG-ADA2-K374D.sup.DL755 at 0.5 mg/kg (n=4). The mice
were sacrificed and transcardically perfused with heparin normal
saline 24 hours post PEG-ADA2-K374D.sup.DL755 injection. Tumors
from tumor-bearing mice and organs from naive mice were collected
and imaged with IVIS image system, and DL755 signal intensity was
measured with LivingImage software as described above. Signal
intensity was normalized by tissue organ weight.
[1193] The results are set forth in Table 46. Signal intensity or
each organ was compared to the signal intensity of the tumor, and
set forth as a ratio (tumor/organ). The results showed that
compared to the other organs, the highest signal intensity was
observed in the tumor. The liver and spleen did show high
fluorescent intensity, which was 1.5-fold and 2.1-fold less,
respectively, than in the tumor. Other organs, such as the brain
and heart, showed low signal intensity with 29-fold and 11-fold,
respectively, less signal intensity than the tumor. Thus, the
results show that PEG-ADA2-K374D.sup.DL755 has a lower affinity to
normal organs.
TABLE-US-00046 TABLE 46 Distribution in Normal Organs vs. Tumors
PEG-ADA2-K374D, 24 hr (Fluorescent intensity/ Signal Intensity
Organ Tissue Weight) - Baseline (Tumor vs Organ) Lung 1.22E+06
.+-.1.11E6 5.1 Heart 5.55E+05 .+-.1.88E5 11.2 Liver 4.02E+06
.+-.5.17E5 1.5 Spleen 2.98E+06 .+-.7.44E5 2.1 Kidney 8.61E+05
.+-.8.23E5 7.2 Colon 9.13E+05 .+-.3.01E5 6.8 Brain 2.11E+05
.+-.1.86E5 29.5 Bone 1.82E+06 .+-.7.04E5 3.4 Tumor 6.22E+06
.+-.2.29E6 --
Example 20
Tumor Growth Inhibition (TGI) and Survival Assessment of PEGylated
rHuADA2-R222Q/S265N Using the MH194+PSC4 Syngeneic Tumor Model
[1194] The murine MH194+PSC4 syngeneic tumor model was used to
assess the antitumor efficacy of PEGylated a recombinant adenosine
deaminase 2 (ADA2), PEGylated rHuADA2-R222Q/S265N (PEG-R222Q/S265N;
PEG-R219Q/S262N by mature numbering). The MH194 mouse pancreatic
carcinoma cells are derived from the
KrasLSL.G12D/+p53R172H/+PdxCretg/+ genetically engineered mouse
model The PSC4 cells are isolated and immortalized pancreatic
stellate cells.
[1195] A. Syngeneic Tumor Model
[1196] The murine MH194+PSC4 syngeneic tumor model was used to
assess the antitumor efficacy of PEGylated a recombinant adenosine
deaminase 2 (ADA2), PEGylated rHuADA2-R222Q/S265N (PEG-R222Q/S265N;
PEG-R219Q/S262N by mature numbering).
[1197] The PSC4 cells are isolated and immortalized pancreatic
stellate cells. To generate the PSC4 cells, pancreas from C57BL/6
mice were minced with razor blades and placed in 2 mL of a
digestion buffer containing 0.05% collagenase P, 0.1% DNAse, and
0.02% Pronase in Gey's balanced salt solution (GBSS). Following two
15 min digestion incubations at 37.degree. C. with thorough mixing
after each incubation, the resulting cell suspension was filtered
through a 100 .mu.m nylon mesh, washed twice in GBSS with 0.3%
bovine serum albumin (BSA), and resuspended in 10 mL GBSS/BSA.
Eight mL of Histodenz (Sigma, Cat. No. D2158) was added to the cell
suspension, and the entire volume was pipetted under 6 mL GBSS/BSA
in order to generate a discontinuous density gradient. Following
centrifugation for 20 min at 1,400 g with the brake set at zero,
the desired cells were harvested from the interface between the two
density volumes and washed once with PBS and once with DMEM medium
supplemented with 2 mM L-glutamine, 10% fetal bovine serum, and 1%
amphotericin-B (complete DMEM). Cells were immortalized using
Lenti-SV40 (Capital Biosciences, Cat. No. CIP-0011) using
manufacturer's protocol. The resulting cell line, designated PSC4,
were maintained in tissue culture as an adherent monolayer in
complete DMEM at 37.degree. C. and 5% CO.sub.2. The MH194 mouse
pancreatic carcinoma cells are derived from the
KrasLSL.G12D/+p53R172H/+PdxCretg/+ genetically engineered mouse
model.
[1198] To generate the MH194+PSC4 syngeneic tumor model, mice (male
C57BL/6 mice obtained at 4-6 weeks from Taconic Farms and housed
4/cage) were injected with 50 .mu.L of cell suspension containing
parental MH194 cells along with 5.times.10.sup.5 PSC4
(5.times.10.sup.6 cells total) intramuscularly, adjacent to the
right tibial periosteum.
[1199] Thirty-nine (39) male C57BL/6 mice were co-inoculated
subcutaneously with 5.times.10.sup.6 of a mixture of murine MH194
pancreatic cancer tumor cells and murine PSC4 pancreatic stellate
cells in 0.1 mL injection volume per animal. Tumor volume was
determined using digital calipers via measurement of length (L) and
width (W) of the solid tumor masses. Tumor volume (TV) was
calculated as: (L.times.W.sup.2)/2. Tumors were allowed to grow and
tumor bearing mice were staged for test article administration when
the tumors were palpable and measured to be approximately 50-100
mm.sup.3.
[1200] PEG-R222Q/S265N was prepared using similar methods as
described in Example 8.A, with minor modifications to generate a
preparation in which approximately 100% of the molecules were
PEGylated as assessed by SDS-PAGE. Briefly, a preparation of
rHuADA2-R222Q/S265N (R219Q/S262N by mature numbering) at 10 mg/mL
was mixed with linear PEG-20K (JenKem Technology, Plano, Tex.; Cat.
No. M-SCM-20K) at 1:15 molar ratio and incubated first at 4.degree.
C. for 16 hours, and then at 30.degree. C. for 60 min.
[1201] For treatment, MH194+PSC4 tumor bearing mice were randomized
into five treatment groups (n=.ltoreq.8); vehicle control (buffer
only) or PEG-R222Q/S265N at four treatment doses. MH194+PSC4 tumor
bearing mice were then injected intravenously (IV) every other day,
at 0.003 mg/kg body weight, 0.03 mg/kg body weight, 0.3 mg/kg body
weight and 3 mg/kg body weight of PEG-R222Q/S265N, or vehicle.
Tumor volume was measured at day 0 and 8 using caliper measurement
as described above. Percent Tumor Growth Inhibition (TGI) for each
respective tumor model was calculated using the following
equation:
% TGI=[1-(T.sub.n-T.sub.0)/(C.sub.n-C.sub.0)].times.100%
where "T.sub.n" is the average tumor volume for the treatment group
at day "n" after the final dose of PEG-R222Q/S265N or control;
"T.sub.0" is the average tumor volume in that treatment group at
day 0, before treatment; "C.sub.n" is the average tumor volume for
the corresponding control group at day "n"; and "C.sub.0" is the
average tumor volume in the control group at day 0, before
treatment. Median survival time (MST) (in days) was calculated as
the time at which 50% of the mice of the individual groups reached
one of the following endpoints: (1) tumor volume reaches 2000
mm.sup.3, (2) the animal loses >25% of its body weight, or (3)
the animal appears moribund.
[1202] B. Results
[1203] Table 47 sets forth the results of the average tumor volume
and tumor growth inhibition at day 11 in the mice administered with
PEG-R222Q/S265N compared to vehicle control. At day 11, the average
tumor volume for the vehicle control group was approximately 840
mm.sup.3. For the group treated with PEG-R222Q/S265N (0.003 mg/kg),
the average tumor volume was approximately 324 mm.sup.3, a tumor
growth inhibition (TGI) of approximately 72% (n=8; p=0.036),
relative to the control group, demonstrating that PEG-R222Q/S265N
administration results in significant tumor growth inhibition.
[1204] Table 48 sets forth the results of the median survival time
of the mice administered PEG-R222Q/S265N, relative to the vehicle
control group. All mice in the control group died between day 13
and day 36, resulting in a median survival time (MST) of 27 days.
Five out of eight PEG-R222Q/S265N injected mice (at the 0.003 mg/kg
dose) survived beyond 41 days, with an MST of 46 days for
PEG-R222Q/S265N treated mice, at the 0.003 mg/kg dose. The results
indicate that PEG-R222Q/S265N administration significantly prolongs
survival in mice bearing MH194+PSC4 tumors.
TABLE-US-00047 TABLE 47 Tumor volume and tumor growth inhibition
(TGI) in mice administered with PEG-R222Q/S265N No. of Average p
value (t-Test) Dose Mice per Tumor Volume Tumor Growth compared to
(mg/kg) group (mm.sup.3) Inhibition vehicle Vehicle 7 840.1 0%
0.003 8 323.9 72% 0.0357 0.03 8 680.45 21% 0.56 0.3 8 700.59 20%
0.6 3 8 678.58 22% 0.53
TABLE-US-00048 TABLE 48 Median Survival Time (MST) in mice
administered with PEG- R222Q/S265N No. of Survival **p value (Log-
Dose Mice per time MST Increase in rank) compared (mg/kg) group
(days) (days) MST to vehicle Vehicle 7 13-36 27 -- 0.003 8 22-48+
46 70% 0.041 0.03 8 13-48+ 26 0% 0.72 0.3 8 13-41 32.5 20% 0.49 3 8
13-48+ 23.5 0% 0.83 **Log-rank (Mantel-Cox) test
Example 21
Tumor Growth Inhibition (TGI) Assessment of Combination Therapy
with PEGylated rHuADA2 and Anti-PD-1
[1205] The murine lung cancer KLN205 syngeneic tumor model was used
to compare the antitumor activity of PEGylated ADA2-K374D
(PEG-K374D; PEG-K371D by mature numbering) combined with checkpoint
inhibitor anti-PD-1 antibody.
[1206] KLN205 syngeneic tumor models were produced by injecting
thirty-two (32) DBA/2 mice with 5.times.10.sup.5 KLN205 murine lung
cancer tumor cells (ATCC CRL-1453), in 0.1 mL injection volume per
animal, subcutaneously. Tumor bearing mice were staged into
treatment groups when the average tumor size reached approximately
100 mm.sup.3.
[1207] For treatment, animals were randomized into 4 groups
(n=8/group): 1) saline vehicle control, 2) PEG-K374D, 3)
.alpha.-PD-1 antibody (Clone RMP1-14, Cat. No. BE0146; BioXCell,
West Lebanon, N.H.), or 4) PEG-K374D+.alpha.-PD-1. PEG-K374D was
dosed intravenously biweekly at 0.3 mg/kg, and .alpha.-PD-1 was
dosed intraperitoneally biweekly at 2 mg/kg). The sequence of
dosing in the combination group was PEG-K374D immediately followed
by .alpha.-PD-1.
Tumor volume was measured twice weekly using caliper measurement as
described above in Example 17.A. Percent Tumor Growth Inhibition
(TGI) for each respective tumor model was calculated using the
following equation:
% TGI=[1-(T.sub.n-T.sub.0)/(C.sub.n-C.sub.0)].times.100%
[1208] where "T.sub.n" is the average tumor volume for the
treatment group at day "n" after the final dose of PEG-K374D and
.alpha.-PD-1 or control; "T.sub.0" is the average tumor volume in
that treatment group at day 0, before treatment; "C.sub.n" is the
average tumor volume for the corresponding control group at day
"n"; and "C.sub.0" is the average tumor volume in the control group
at day 0, before treatment.
[1209] The results are presented in Table 49. Table 49 depicts the
average tumor volume per group, on study day 14 (SD14). The results
show that PEG-K374D alone, .alpha.-PD-1 alone and the combination
of PEG-K374D+.alpha.-PD-1 all inhibited tumor growth, compared to
the control group. PEG-K374D alone exhibited greater tumor growth
inhibition than either .alpha.-PD-1 treatment alone or the
PEG-K374D+.alpha.-PD-1 combination therapy.
TABLE-US-00049 TABLE 49 Tumor Growth Inhibition of Combination
Therapy in KLN205 Tumor Model Average p value No. of Tumor Tumor
(t-Test) Mice per Volume Growth compared to Dose group (mm.sup.3)
Inhibition vehicle Vehicle 8 899.41 0% PEG-K374D, 0.3 mg/kg 8
264.56 78% 0.013 .alpha.-PD-1, 2 mg/kg 8 545.73 43% 0.16 PEG-K374D
+ .alpha.-PD-1 8 417.79 59% 0.053
Example 22
Removal of Free PEGylation Moieties
[1210] Unconjugated, free PEGylation moieties were removed from
reactions to PEGylate ADA2 variants using the Capto Phenyl resin
columns. Free PEG was removed from the preparations of PEGylated
ADA2-K374D (PEG-K374D; PEG-K371D by mature numbering) and PEGylated
rHuADA2-R222Q/S265N (PEG-R222Q/S265N; PEG-R219Q/S262N by mature
numbering), prepared using the PEGylation method as described in
Examples 8.A and 20.A.
[1211] To remove free PEG from the PEG-K374D (polypeptide of SEQ ID
NO:20) preparation, 3.5M ammonium sulfate was added to the
PEG-K374D in PBS to achieve a final concentration of 0.70 M
ammonium sulfate in PBS. The PEG-K374D with ammonium sulfate was
then applied to a Capto Phenyl resin column (GE Healthcare)
pre-equilibrated with 0.70M ammonium sulfate in PBS, at a ratio of
5 mg PEGylated protein per ml of resin. The loaded Capto Phenyl
resin was washed with 10 column volumes of 0.70M ammonium sulfate
in PBS. The PEG-K374D was eluted with a decreasing gradient from
0.70M ammonium sulfate in PBS to 0 M ammonium sulfate in PBS. The
fractions eluted after 40% gradient elution (0.42M ammonium sulfate
in PBS) were pooled. The pooled elution fraction was concentrated
to a concentration of 1 to 2 mg/mL, and analyzed by SDS-PAGE. Free
PEG was detected using a Corona.TM. Charged Aerosol Detector
(Thermo Scientific, Sunnyvale, Calif.).
[1212] To remove free PEG from PEG-R222Q/S265N (polypeptide of SEQ
ID NO:273), 3.5M ammonium sulfate was added to the PEG-R222Q/S265N
in PBS to achieve a final concentration of 0.64 M ammonium sulfate
in PBS. The PEG-R222Q/S265N with ammonium sulfate was then applied
to a Capto Phenyl resin column (GE Healthcare) pre-equilibrated
with 0.64M ammonium sulfate in PBS, at a ratio of 5 mg PEGylated
protein per ml of resin. The loaded Capto Phenyl resin was washed
with 10 column volumes of 0.64M ammonium sulfate in PBS. The
PEG-R222Q/S265N was eluted with a decreasing gradient from 0.64M
ammonium sulfate in PBS to 0 M ammonium sulfate in PBS. The
fractions eluted after 60% gradient elution (0.256M ammonium
sulfate in PBS) were pooled. An additional elution with 20 column
volumes of 15 mM sodium phosphate, pH 7.0 was also pooled with the
first pooled elution fraction. The pooled elution fractions were
concentrated to a concentration of 1 to 2 mg/mL, and analyzed by
SDS-PAGE. Free PEG was detected using a Corona.TM. Charged Aerosol
Detector (Thermo Scientific, Sunnyvale, Calif.).
[1213] The results of free PEG removal are presented in Table 50.
The results show that the amount of free PEG decreased from
approximately 3.7 mg free PEG/mg protein, to 0.13 mg free PEG/mg
protein for the PEG-K374D preparation, and from 3.8 mg free PEG/mg
protein to 0.2 mg/free PEG/mg protein for the PEG-R222Q/S265N
preparation.
TABLE-US-00050 TABLE 50 Removal of free PEG from PEGylated ADA2
variant preparations PEG-K374D PEG-R222Q/S265N Starting protein
amount 6 mg 50 mg Free PEG before Capto 3.7 mg free PEG/ 3.8 mg
free PEG/ Phenyl resin column mg protein mg protein Free PEG after
Capto 0.13 mg free PEG/mg 0.2 mg free PEG/ Phenyl resin column
protein mg protein Amount of protein 4.5 mg 28.5 mg recovered after
free PEG removal Protein recovery yield after 75% 57% free PEG
removal
Example 23
Multivesicular Liposome (MVL) PH20 Formulations
[1214] For systemic administration, hyaluronidases, including
soluble hyaluronidases, can be prepared in lipids vesicles, such as
liposomes. Exemplary of these are multivesicular liposomes (MVL).
Various extended release multivesicular liposome PH20 (MVL-PH20)
formulations were prepared using the following general procedure,
see also, International PCT Pub. No. WO 2012/109387 and US Patent
Pub. No. 2013/0251786. The lipid solutions contained mixtures of
various neutral lipids, including triglycerides (TG) triolein
(C.sub.18:1), tricaprylin (C.sub.8:0) and cholesterol, and lipids
with both positive and negative charges, including
phosphatidylcholines (PC), dioleoylphosphatidylcholine (DOPC,
C.sub.18:1), dierucoyl phosphatidylcholine (DEPC, C.sub.22:1) and
dipalmitoyl phosphorylglycerol (DPPG; C.sub.16:1). Total PC
concentration was up to 19.8 mM, cholesterol concentration was 30
mM, TG concentration was up to 3.9 mM and DPPG concentration was
4.2 mM.
[1215] A. Generation of MVL-PH20 Formulations
[1216] MVL formulations containing varying mole percent of DEPC and
DOPC (0-100%) and varying mole percent of triolein and tricaprylin
(0-100%), DPPG, cholesterol, and 0.1, 0.25, 0.5, 1 or 2 mg/mL PH20
were prepared. In the first step, the lipids in chloroform (oil
phase) and PH20 in a first aqueous solution (water phase) were
combined and emulsified to form a water-in-oil emulsion, whereby
the PH20 was encapsulated by the phospholipid monolayer. In the
second step, a second aqueous solution was added and emulsified,
whereby a water-in-oil-in-water emulsion was formed. After addition
of a second aliquot of the second aqueous solution, the chloroform
solvent was evaporated and the resulting product containing
multivesicular liposomes was washed multiple times in a third
aqueous solution and resuspended to approximately 50% lipocrit
(packed particle volume) and stored at 2-8.degree. C.
[1217] Exemplary formulations were prepared using either a mini
vortex or were prepared on a larger scale using an Omni mixer (Omni
Macro ES, Omni International, Kennesaw, Ga.). In the latter Omni
mixer method, the lipid solution in chloroform (6 mL) was
emulsified at 7,000 rpm for 8 min with an Omni Mixer with 6 mL of
the first aqueous solution (10 mM His-HCl, pH 6.5 with 5% sucrose
containing varying concentrations of PH20) producing a water-in-oil
emulsion. A subsequent emulsification at 4500 rpm for 1-3 min with
20 mL of a second aqueous solution of 3.2% glucose containing 40 mM
lysine, pH 10.0, resulted in a water-in-oil-in-water second
emulsion. The second emulsion was transferred equally into two
Erlenmeyer flasks and another 50 mL aliquot of the second aqueous
solution was added to both flasks. Chloroform was removed by
flushing nitrogen over the surface of the emulsion at 35.degree. C.
The MVL particles containing PH20 were washed three times with 50
mL third aqueous solution (25 mM His-HCl buffer, pH 6.0 containing
120 mM NaCl) by adding the solution, mixing the centrifuge tube by
inversion, and centrifugation at 3500 rpm for 10 min at 4.degree.
C. in a refrigerated table top centrifuge. Finally, the MVL
particles were resuspended in the third aqueous solution to form an
approximately 50% lipocrit formulation and stored refrigerated at
2-8.degree. C. The mini vortex procedure was similar, using the
parameters set forth in Table 30.
[1218] Table 51 below summarizes the first, second and third
aqueous solutions. Table 51 also summarizes the volumes, reagent
concentrations and other parameters of each step of the MVL
process.
TABLE-US-00051 TABLE 51 MVL-PH20 formulation and process parameters
1st Aqueous Solution 10 mM His-HCl, pH 6.5 with 5% sucrose 2nd
Aqueous Solution 3.2% glucose containing 40 mM lysine, pH 10.0 3rd
Aqueous Solution 25 mM His-HCl buffer, pH 6.0 containing 120 mM
NaCl 1.sup.st Emulsion Mixing Vortex Mixer Omni Mixer PH20 in 1st
aqueous 600 .mu.L 6 mL solution Lipid Solution in 600 .mu.L 6 mL
chloroform Total Volume 1.2 mL 12 mL 1.sup.st Emulsification Speed
Maximum RPM 7000 RPM Time 8 min 8 min Starting PH20 protein 0.25
mg/mL 0.5 mg/mL 0.5 mg/mL 1.0 mg/mL 2.0 mg/mL concentration
(activity) (30,000 U/mL) (60,000 U/mL) (60,000 U/mL) (120,000 U/mL)
(240,000 U/mL) PC 15.8-19.8 mM 15.8-19.8 mM Cholesterol 30 mM 30 mM
TG 3.75-3.9 mM 3.75-3.9 mM DPPG 4.2 mM 4.2 mM Blade Type 1 Not
applicable Sharp on the sides Blade Type 2 Not applicable Sharp on
the sides and on the inside Blade Type 3 Not applicable Flat all
over, not sharp 2.sup.nd Emulsion Mixing Vortex Mixer Omni Mixer
2nd Aqueous Solution 2.5 mL 20 mL Total Volume 3.7 mL 32 mL Speed
Maximum RPM 4500 RPM Time 15 sec 1-3 min Solvent Evaporation Vortex
Mixer Omni Mixer 2nd Aqueous Solution 10 mL 100 mL Total Volume
13.7 mL 132 mL Shaking Water Bath Speed 100-130 RPM 100-130 RPM
Time 11 min 15 min Temperature 35.degree. C. 35.degree. C. Washing,
buffer exchange Vortex Mixer Omni Mixer and resuspension Sample
Entire Sample 17 mL 3rd Aqueous Solution 50 mL 50 mL Total Volume
50 mL 200 mL Centrifugation Speed 3500 RPM 3500 RPM Time 10 min 10
min Number of Washes 3 3 Resuspension Volume 0.3-0.5 mL 3-5 mL
LIPOCRIT Vortex Mixer Omni Mixer Pellet volume Varies Varies 3rd
Aqueous Solution Varies Varies Speed 3500 rpm 3500 rpm Time (min)
10 min 10 min Solution + Pellet Volume Varies Varies % Lipocrit
Adjusted to ~50% ~50%
[1219] B. Summary of Exemplary MVL-PH20 Formulations
[1220] Several MVL-PH20 formulations containing varying molar
ratios of lipids, PH20 and other additives were prepared using the
same general procedures as described above. The various additional
additives were included in the first aqueous solution to enhance
and preserve the stability of encapsulated PH20. For example,
formulations F68 and F69 contained calcium chloride. Formulation
F82 contained 150 .mu.L glycerol as an interphase separating the
600 .mu.L chloroform phase and 600 .mu.L first aqueous solution
phase. Formulation F83 contained 0.1% dextran 40,000 and 0.1%
PEG-6000. Formulations F85-F87 contained hyaluronic acid (HA)
oligomers. Several formulations varied in their
mixing/emulsification procedures. For example, for formulation F66,
the first emulsification step was carried out for 4 minutes,
instead of 8 minutes, resulting in smaller liposomal pellets.
Formulation F67 was mixed with a rotor wheel, instead of a mini
vortex to generate lesser shear during mixing.
[1221] Table 52 below sets forth various MVL-PH20 formulations,
including the formulation number, the formulation PC
(phosphatidylcholine) and TG (triglyceride) molar % ratios, the
starting concentration of PH20 in mg/mL, the mixer used for making
the emulsions, and any additives that were included in the first
aqueous solution.
TABLE-US-00052 TABLE 52 MVL Formulations with PH20 Starting PH20
Formulation PC & TG concentration Additives in First
Formulation mol % ratio mg/mL Mixer Aqueous Solution F40 DEPC with
Triolein 0.25 Mini N/A Vortex F41 DEPC with Triolein 0 Mini N/A
Vortex F42 DEPC with Triolein 0.25 Mini AlexaFluor 488 fluorescent
Vortex labeled PH20 labeled F53 25/75 DEPC/DOPC; 0.25 Mini N/A
25/75 Triolein/Tricap Vortex F54 50/50 DEPC/DOPC; 0.25 Mini N/A
50/50 Triolein/Tricap Vortex F55 75/25 DEPC/DOPC; 0.25 Mini N/A
75/25 Triolein/Tricap Vortex F56 90/10 DEPC/DOPC; 0.25 Mini N/A
90/10 Triolein/Tricap Vortex F61 50/50 DEPC/DOPC; 0.25 Omni N/A
50/50 Triolein/Tricap F66 50/50 DEPC/DOPC; 0.25 Mini N/A 50/50
Triolein/Tricap Vortex.sup.1 F67 50/50 DEPC/DOPC; 0.25 Rotor N/A
50/50 Triolein/Tricap Wheel F68 50/50 DEPC/DOPC; 0.25 Mini 20 mM
CaCl.sub.2 50/50 Triolein/Tricap Vortex F69 50/50 DEPC/DOPC; 0.25
Mini 10 mM CaCl.sub.2 50/50 Triolein/Tricap Vortex F70 50/50
DEPC/DOPC; 0.0 Omni N/A 50/50 Triolein/Tricap F71 50/50 DEPC/DOPC;
0.25 Omni N/A 50/50 Triolein/Tricap F72 50/50 DEPC/DOPC; 0.5 Omni
N/A 50/50 Triolein/Tricap F73 50/50 DEPC/DOPC; 0.5 Omni N/A 50/50
Triolein/Tricap F74 50/50 DEPC/DOPC; 1.0 Omni N/A 50/50
Triolein/Tricap F75 50/50 DEPC/DOPC; 2.0 Omni N/A 50/50
Triolein/Tricap F77.sup.2 50/50 DEPC/DOPC; 1.0 Omni 50/50
Triolein/Tricap F78 DEPC with Triolein 1.0 Omni N/A F79 DEPC with
Triolein 1.0 Omni N/A F80 50/50 DEPC/DOPC; 1.0 Omni N/A 50/50
Triolein/Tricap F81 DEPC with Triolein 0.5 Omni N/A F82 50/50
DEPC/DOPC; 0.5 Mini 150 .mu.L Glycerol as 50/50 Triolein/Tricap
Vortex interphase F83 50/50 DEPC/DOPC; 1.0 Omni 0.1% Dextran 50/50
Triolein/Tricap 40,000 0.1% PEG-6000 F84 50/50 DEPC/DOPC; 1.0
Omni.sup.3 N/A 50/50 Triolein/Tricap F85 50/50 DEPC/DOPC; 1.0 Omni
15 mg/mL HA 74,000 50/50 Triolein/Tricap F85R1 50/50 DEPC/DOPC; 1.0
Omni 15 mg/mL HA 74,000 50/50 Triolein/Tricap F86 50/50 DEPC/DOPC;
1.0 Omni 50 mg/mL HA 74,000 50/50 Triolein/Tricap F87 50/50
DEPC/DOPC; 1.0 Omni 100 mM Proline 50/50 Triolein/Tricap F88 50/50
DEPC/DOPC; 1.0 Omni 100 mM Arg-HCl, pH 50/50 Triolein/Tricap 6.44
F89 50/50 DEPC/DOPC; 1.0 Omni 6% Sorbitol 50/50 Triolein/Tricap F90
50/50 DEPC/DOPC; 1.0 Omni 6% Trehalose 50/50 Triolein/Tricap
.sup.1Shorter first emulsion mixing time (4 min) .sup.2Animal
derived cholesterol used instead of plant derived cholesterol in
the lipid solution .sup.3Shorter first emulsion mixing time (4 min)
and shorter second emulsion mixing time (30 sec)
Example 24
PEGADA2 Variant R222Q/S265N Significantly Reduces Adenosine in
MH194+PSC4 Tumor Extracellular Matrix
[1222] To assess the effects of PEGADA2 on adenosine in tumor
extracellular matrix, mice bearing peritibial MH194+PSC4 tumors
received vehicle, the polypeptide whose sequence is set forth in
SEQ ID NO:20, which contains the amino acid replacement K374D
(Zavialov numbering; K371D mature numbering), at 0.03 mg/kg, or the
polypeptide whose sequence is set forth in SEQ ID NO: 273, which
contains the amino acid replacements R222Q/S265N (Zavialov
numbering; R219Q/5262 mature numbering), at 0.03 mg/kg, 24 or 48
hours prior to microdialysis. Each of the polypeptides were
PEGylated as described above in Examples 8 and 22). The mice were
anesthetized using isofluorane, and a heating pad was used to
maintain body temperature. A small incision was made on the tumor.
A microdialysis probe with 55,000 Da molecular weight cut-off (CMA,
Stockholm, Sweden) was inserted into the tumor, via a guided
cannula. The length of the microdialysis probe used in this study
was 10 mm. Once the probe was in position, the cannula was
withdrawn leaving the probe completely embedded in the tumor
tissue. Dulbecco's phosphate buffered saline (DPBS; Thermo Fisher
Scientific) with ADA inhibitors (Pentostatin and 5-iodotubercindin)
was perfused through the probe at a flow rate of 1 .mu.l/min for 30
minutes. Then the samples were collected at a flow rate of 0.5
.mu.l/min for 60 minutes. Microdialysis perfusates were analyzed by
Liquid chromatography-mass spectrometry (LC/MS) at MicroConstants
(9050 Camino Santa Fe, San Diego, Calif. 92121).
[1223] LC/MS analysis reveals average concentration of adenosine in
MH194+PSC4 peritibial tumors was 17.8 .mu.M (n=8). 24 hours post
K374D treatment, adenosine concentration was 19.5 .mu.M (n=8),
which is above control due to outlier value from one tumor (49
.mu.M). The trend toward reduced adenosine (11 .mu.M) was observed
in K374D-treated mice at 48 hours. In contrast, the adenosine is
significantly reduced to 6.9 .mu.M (n=8) at 24 hours and 9.8 .mu.M
(n=8) at 48 hours post R222Q/S265N treatment (P.ltoreq.0.05).
TABLE-US-00053 TABLE 53 R222Q/S265N reduces adenosine in tumor ECM
Adenosine (.mu.M) Group (n = 8) Mean .+-. SD P Vehicle control 17.8
.+-. 6.1 -- NME8 @ 24 hours 19.5 .+-. 15.3 >0.05 NME8 @ 48 hours
11.1 .+-. 10.9 >0.05 NME62 @ 24 hours 6.9 .+-. 9.0 .ltoreq.0.05
NME62 @ 48 hours 9.8 .+-. 8.3 .ltoreq.0.05
TABLE-US-00054 TABLE 54 Adenosine concentration (.mu.M) in ECM
R222Q/ R222Q/ Vehicle K374D @ K374D @ S265N S265N control 24 hours
48 hours @ 24 hours @ 48 hours 14.33 7.48 1.64 21.48 4.15 11.08
2.04 27.54 0.48 14.26 10.48 29.30 5.95 5.80 3.43 24.43 49.02 23.13
0.08 13.06 16.17 12.72 0.07 20.54 1.96 17.25 29.64 6.47 1.08 20.36
21.85 13.58 2.77 0.62 20.62 27.02 12.54 20.92 4.94 0.35 Mean 17.83
19.54 11.06 6.88 9.77 SD 6.09 15.35 10.95 8.98 8.30 P (t-test) 0.77
0.15 0.01 0.04
Example 25
Tabular Summary of Exemplary ADA2 Variants and Region of the
Protein Modified
[1224] Table 55 provides a summary of the variant ADA2 polypeptides
exemplified herein. The table provides the position of modification
based on Zavialov and mature sequence numbering, and an exemplary
SEQ ID NOS: of an ADA2 variant protein that contains such
modification. It is understood that modifications can be combined
and that additional variants are contemplated. The noted amino acid
residues generally can be replaced with conservative amino acid
substitutions (see, e.g., Table 3), except in instances, such as
hyperglycosylation where a conservative substitution will not
create a glycosylation site. Hence, for example, N can be replaced
with Q or H. ADA2 variant polypeptides comprising each of the noted
modifications are provided. Included among these are the
polypeptides whose sequence is referenced with a sequence
identifier. Combinations of any of the modifications also are
provided. Also provided are modified ADA2 variant dimers, including
homodimers and heterodimers. Also provided are multimers of the
variants. Also provide are conjugates containing the variants and
multimers and dimers, as are methods of treatment, uses for
treatment, combinations and pharmaceutical compositions as
described herein. The last column identifies the region or domain
of the modification, or the activity the modification confers. In
general, the mutations, for example, increase activity, decrease
heparin binding, introduce glycosylation to interfere with
undesirable interactions and/or to increase serum half-life,
interfere with or decrease interactions of the PRB domain with the
ADA catalytically active portions and/or decrease activities other
than the deaminase activity, such as growth factor activity of ADA2
by interfering with binding to receptors that mediate such
activities.
TABLE-US-00055 TABLE 55 Variant ADA2 polypeptides comprising the
listed mutations SEQ ID NO. of an Zavialov numbering (SEQ ID Mature
numbering (SEQ ID exemplary NO: 4) NO: 5) polypeptides Type K14A
K11A 13 Heparin Binding K14D K11D 14 Heparin Binding K14E K11E 15
Heparin Binding K16A K13A 16 Heparin Binding K16D K13D 17 Heparin
Binding K16E K13E 18 Heparin Binding K374A K371A 19 Heparin Binding
K374D K371D 20 Heparin Binding K374E K371E 21 Heparin Binding K375A
K372A 22 Heparin Binding K375D K372D 23 Heparin Binding K375E K372E
24 Heparin Binding K455A K452A 25 Heparin Binding K455D K452D 26
Heparin Binding K455E K452E 27 Heparin Binding R23A R20A 28 Heparin
Binding R23D R20D 29 Heparin Binding R23E R20E 30 Heparin Binding
R369A R366A 31 Heparin Binding R369D R366D 32 Heparin Binding R369E
R366E 33 Heparin Binding H267A H264A 34 Active Site H267Q H264Q 35
Active Site H267N H264N 36 Active Site H267G H264G 37 Active Site
R222K R219K 38 Active Site R222Q R219Q 39 Active Site R222N R219N
40 Active Site R222A R219A 41 Active Site L224A L221A 42 Active
Site L224V L221V 43 Active Site L224G L221G 44 Active Site E182D
E179D 45 Active Site E182A E179A 46 Active Site E182S E179S 47
Active Site E182T E179T 48 Active Site E182V E179V 49 Active Site
E182G E179G 50 Active Site S265A S262A 51 Active Site S265V S262V
52 Active Site S265M S262M 53 Active Site S265N S262N 54 Active
Site K14A/R23A K11A/R20A 55 Combination K14A/R23A/K374A
K11A/R20A/K371A 56 Combination R23A/K374A R20A/K371A 57 Combination
K14A/K374A K11A/K371A 58 Combination S265N/K374D S262N/K371D 59
Combination S265N/K374E S262N/K371E 60 Combination S265N/R23E
S262N/R20E 61 Combination S265N/R23E/K374D S262N/R20E/K371D 62
Combination S265N/R23E/K374E S262N/R20E/K371E 63 Combination K29A
K26A 71 Heparin Binding K29D K26D 72 Heparin Binding K29E K26E 73
Heparin Binding R220A R217A 74 Heparin Binding R220D R217D 75
Heparin Binding R220E R217E 76 Heparin Binding K261A K258A 77
Heparin Binding K261D K258D 78 Heparin Binding K261E K258E 79
Heparin Binding R280A R277A 80 Heparin Binding R280D R277D 81
Heparin Binding R280E R277E 82 Heparin Binding R286A R283A 83
Heparin Binding R286D R283D 84 Heparin Binding R286E R283E 85
Heparin Binding K312A K309A 86 Heparin Binding K312D K309D 87
Heparin Binding K312E K309E 88 Heparin Binding K320A K317A 89
Heparin Binding K320D K317D 90 Heparin Binding K320E K317E 91
Heparin Binding K324A K321A 92 Heparin Binding K324D K321D 93
Heparin Binding K324E K321E 94 Heparin Binding R355A R352A 95
Heparin Binding R355D R352D 96 Heparin Binding R355E R352E 97
Heparin Binding R444A R441A 98 Heparin Binding R444D R441D 99
Heparin Binding R444E R441E 100 Heparin Binding K447A K444A 101
Heparin Binding K447D K444D 102 Heparin Binding K447E K444E 103
Heparin Binding K464A K461A 104 Heparin Binding K464D K461D 105
Heparin Binding K464E K461E 106 Heparin Binding K472A K469A 107
Heparin Binding K472D K469D 108 Heparin Binding K472E K469E 109
Heparin Binding K473A K470A 110 Heparin Binding K473D K470D 111
Heparin Binding K473E K470E 112 Heparin Binding D89A D86A 113
Active Site D89C D86C 114 Active Site D89E D86E 115 Active Site
D89F D86F 116 Active Site D89G D86G 117 Active Site D89H D86H 118
Active Site D89I D86I 119 Active Site D89K D86K 120 Active Site
D89L D86L 121 Active Site D89M D86M 122 Active Site D89N D86N 123
Active Site D89P D86P 124 Active Site D89Q D86Q 125 Active Site
D89R D86R 126 Active Site D89S D86S 127 Active Site D89T D86T 128
Active Site D89V D86V 129 Active Site D89W D86W 130 Active Site
D89Y D86Y 131 Active Site E182C E179C 132 Active Site E182F E179F
133 Active Site E182H E179H 134 Active Site E182I E179I 135 Active
Site E182K E179K 136 Active Site E182L E179L 137 Active Site E182M
E179M 138 Active Site E182N E179N 139 Active Site E182P E179P 140
Active Site E182Q E179Q 141 Active Site E182R E179R 142 Active Site
E182W E179W 143 Active Site E182Y E179Y 144 Active Site R222C R219C
145 Active Site R222D R219D 146 Active Site R222E R219E 147 Active
Site R222F R219F 148 Active Site R222G R219G 149 Active Site R222H
R219H 150 Active Site R222I R219I 151 Active Site R222L R219L 152
Active Site R222M R219M 153 Active Site R222P R219P 154 Active Site
R222S R219S 155 Active Site R222T R219T 156 Active Site R222V R219V
157 Active Site R222W R219W 158 Active Site R222Y R219Y 159 Active
Site L224C L221C 160 Active Site L224D L221D 161 Active Site L224E
L221E 162 Active Site L224F L221F 163 Active Site L224H L221H 164
Active Site L224I L221I 165 Active Site L224K L221K 166 Active Site
L224M L221M 167 Active Site L224N L221N 168 Active Site L224P L221P
169 Active Site L224Q L221Q 170 Active Site L224R L221R 171 Active
Site L224S L221S 172 Active Site L224T L221T 173 Active Site L224W
L221W 174 Active Site L224Y L221Y 175 Active Site S265C S262C 176
Active Site S265D S262D 177 Active Site S265E S262E 178 Active Site
S265F S262F 179 Active Site S265G S262G 180 Active Site S265H S262H
181 Active Site S265I S262I 182 Active Site S265K S262K 183 Active
Site S265L S262L 184 Active Site S265P S262P 185 Active Site S265Q
S262Q 186 Active Site S265R S262R 187 Active Site S265T S262T 188
Active Site S265W S262W 189 Active Site S265Y S262Y 190 Active Site
H267C H264C 191 Active Site H267D H264D 192 Active Site H267E H264E
193 Active Site H267F H264F 194 Active Site H267I H264I 195 Active
Site H267K H264K 196 Active Site H267L H264L 197 Active Site H267M
H264M 198 Active Site H267P H264P 199 Active Site H267R H264R 200
Active Site H267S H264S 201 Active Site H267T H264T 202 Active Site
H267V H264V 203 Active Site H267W H264W 204 Active Site H267Y H264Y
205 Active Site S269A S266A 206 Active Site S269C S266C 207 Active
Site S269D S266D 208 Active Site S269E S266E 209 Active Site S269F
S266F 210 Active Site S269G S266G 211 Active Site S269H S266H 212
Active Site S269I S266I 213 Active Site S269K S266K 214 Active Site
S269L S266L 215 Active Site S269M S266M 216 Active Site S269N S266N
217 Active Site S269P S266P 218 Active Site S269Q S266Q 219 Active
Site S269R S266R 220 Active Site S269T S266T 221 Active Site S269V
S266V 222 Active Site S269W S266W 223 Active Site S269Y S266Y 224
Active Site K270A K267A 225 Active Site K270C K267C 226 Active Site
K270D K267D 227 Active Site K270E K267E 228 Active Site K270F K267F
229 Active Site K270G K267G 230 Active Site K270H K267H 231 Active
Site K270I K267I 232 Active Site K270L K267L 233 Active Site K270M
K267M 234 Active Site K270N K267N 235 Active Site K270P K267P 236
Active Site K270Q K267Q 237 Active Site K270R K267R 238 Active Site
K270S K267S 239 Active Site K270T K267T 240 Active Site K270V K267V
241 Active Site K270W K267W 242 Active Site K270Y K267Y 243 Active
Site V299A V296A 244 Active Site V299C V296C 245 Active Site V299D
V296D 246 Active Site V299E V296E 247 Active Site V299F V296F 248
Active Site V299G V296G 249 Active Site V299H V296H 250 Active Site
V299I V296I 251 Active Site V299K V296K 252 Active Site V299L V296L
253 Active Site V299M V296M 254 Active Site V299N V296N 255 Active
Site V299P V296P 256 Active Site V299Q V296Q 257 Active Site V299R
V296R 258 Active Site V299S V296S 259 Active Site V299T V296T 260
Active Site V299W V296W 261 Active Site
V299Y V296Y 262 Active Site R222Q/K374E R219Q/K371E 263 Combination
R222Q/K374D R219Q/K371D 264 Combination R222Q/R23E R219Q/R20E 265
Combination R222Q/K374E/R23E R219Q/K371E/R20E 266 Combination
R222Q/K374D/R23E R219Q/K371D/R20E 267 Combination R222Q/S265N/K374E
R219Q/S262N/K371E 268 Combination R222Q/S265N/K374D
R219Q/S262N/K371D 269 Combination R222Q/S265N/R23E R219Q/S262N/R20E
270 Combination R222Q/S265N/K374E/R23E R219Q/S262N/K371E/R20E 271
Combination R222Q/S265N/K374D/R23E R219Q/S262N/K371D/R20E 272
Combination R222Q/S265N R219Q/S262N 273 Combination
--.fwdarw.N4/--.fwdarw.A5/--.fwdarw.S6
--.fwdarw.N1/--.fwdarw.A2/--.fwdarw.S3 274 Hyperglycosylation
R23N/V25S R20N/V22S 275 Hyperglycosylation K374N/D376S K371N/D373S
276 Hyperglycosylation K375N/I377S K372N/I374S 277
Hyperglycosylation T406N/H408S T403N/H405S 278 Hyperglycosylation
G407N/P409S G404N/P406S 279 Hyperglycosylation
C108-T150del.fwdarw.(Gly).sub.n C105-T147del.fwdarw.(Gly).sub.n 280
PRB deletion C108-T150del.fwdarw.(Gly).sub.15
C105-T147del.fwdarw.(Gly).sub.15 281 PRB deletion
C108-T150del.fwdarw.(Gly).sub.10 C105-T147del.fwdarw.(Gly).sub.10
282 PRB deletion C108-T150del.fwdarw.(Gly).sub.7
C105-T147del.fwdarw.(Gly).sub.7 283 PRB deletion
C108-T150del.fwdarw.(Gly).sub.5 C105-T147del.fwdarw.(Gly).sub.5 284
PRB deletion C108-T150del.fwdarw.(Gly).sub.3
C105-T147del.fwdarw.(Gly).sub.3 285 PRB deletion N101-N159del
N98-N156del 548 PRB deletion C108-E151del C105-E148del 549 PRB
deletion C108-T150del C105-T147del 550 PRB deletion R128N/P129A
R125N/P126A 552 PRB hyperglycosylation S130N/K132S S127N/K129S 553
PRB hyperglycosylation P129N/E131T P126N/E128T 554 PRB
hyperglycosylation R115N/I117T R112N/I114T 555 PRB
hyperglycosylation I137N/L138C/L139T I134N/L135C/L136T 556 PRB
hyperglycosylation I137N/L138S/L139T I134N/L135S/L136T 557 PRB
hyperglycosylation R145N/Q147S R142N/Q144S 558 PRB
hyperglycosylation E140N/Y142T E137N/Y139T 559 PRB
hyperglycosylation P114N/G116S P111N/G113S 560 PRB
hyperglycosylation F122S F119S 561 PRB-ADA interaction F122K F119K
562 PRB-ADA interaction Y227R Y224R 563 PRB-ADA interaction Y227N
Y224N 564 PRB-ADA interaction Y194S Y191S 565 PRB-ADA interaction
Y194D Y191D 566 PRB-ADA interaction F186K F183K 567 PRB-ADA
interaction Y194D/Y227R Y191D/Y224R 568 PRB-ADA interaction F112S
F109S 569 PRB-ADA interaction F112A F109A 570 PRB-ADA interaction
R121D R118D 571 PRB-ADA interaction R121A R118A 572 PRB-ADA
interaction Y142T Y139T 573 PRB-ADA interaction Y142A Y139A 574
PRB-ADA interaction W136S W133S 575 PRB-ADA interaction W136T W133T
576 PRB-ADA interaction P127A P124A 577 PRB-ADA interaction P127S
P124S 578 PRB-ADA interaction V102-Q147del V99-Q144del 579 PRB
deletion V102-Q147del.fwdarw.(GGGGS)n V99-Q144del.fwdarw.(GGGGS)n
581 PRB deletion C108-T150del.fwdarw.(GGGGS)n
C105-T147del.fwdarw.(GGGGS)n 582 PRB deletion
V102-Q147del.fwdarw.(GGGGS).sub.1 V99-Q144del.fwdarw.(GGGGS).sub.1
583 PRB deletion V102-Q147del.fwdarw.(GGGGS).sub.2
V99-Q144del.fwdarw.(GGGGS).sub.2 584 PRB deletion
V102-Q147del.fwdarw.(GGGGS).sub.3 V99-Q144del.fwdarw.(GGGGS).sub.3
585 PRB deletion C108-T150del.fwdarw.(GGGGS).sub.1
C105-T147del.fwdarw.(GGGGS).sub.1 586 PRB deletion
C108-T150del.fwdarw.(GGGGS).sub.2 C105-T147del.fwdarw.(GGGGS).sub.2
587 PRB deletion C108-T150del.fwdarw.(GGGGS).sub.3
C105-T147del.fwdarw.(GGGGS).sub.3 588 PRB deletion K374D/V102-
K371D/V99- 589 Combination w/ Q147del.fwdarw.(GGGGS).sub.1
Q144del.fwdarw.(GGGGS).sub.1 PRB deletion K374D/V102- K371D/V99-
590 Combination w/ Q147del.fwdarw.(GGGGS).sub.2
Q144del.fwdarw.(GGGGS).sub.2 PRB deletion K374D/V102- K371D/V99-
591 Combination w/ Q147del.fwdarw.(GGGGS).sub.3
Q144del.fwdarw.(GGGGS).sub.3 PRB deletion K374D/C108- K371D/C105-
592 Combination w/ T150del.fwdarw.(GGGGS).sub.1
T147del.fwdarw.(GGGGS).sub.1 PRB deletion K374D/C108- K371D/C105-
593 Combination w/ T150del.fwdarw.(GGGGS).sub.2
T147del.fwdarw.(GGGGS).sub.2 PRB deletion K374D/C108- K371D/C105-
594 Combination w/ T150del.fwdarw.(GGGGS).sub.3
T147del.fwdarw.(GGGGS).sub.3 PRB deletion
R222Q/S265N/--.fwdarw.N4/-- R219Q/S262N/--.fwdarw.N1/-- 596
Combination w/ .fwdarw.A5/--.fwdarw.S6 .fwdarw.A2/--.fwdarw.S3
hyperglycosylation R222Q/S265N/R23N/V25S R219Q/S262N/R20N/V22S 597
Combination w/ hyperglycosylation R222Q/S265N/K374N/D376S
R219Q/S262N/K371N/D373S 598 Combination w/ hyperglycosylation
R222Q/S265N/K375N/I377S R219Q/S262N/K372N/I374S 599 Combination w/
hyperglycosylation R222Q/S265N/T406N/H408S R219Q/S262N/T403N/H405S
600 Combination w/ hyperglycosylation R222Q/S265N/G407N/P409S
R219Q/S262N/G404N/P406S 601 Combination w/ hyperglycosylation
R222Q/S265N/C108- R219Q/S262N/C105- 602 Combination w/
T150del.fwdarw.(Gly).sub.15 T147del.fwdarw.(Gly).sub.15 PRB
deletion R222Q/S265N/C108- R219Q/S262N/C105- 603 Combination w/
T150del.fwdarw.(Gly).sub.10 T147del.fwdarw.(Gly).sub.10 PRB
deletion R222Q/S265N/C108- R219Q/S262N/C105- 604 Combination w/
T150del.fwdarw.(Gly).sub.7 T147del.fwdarw.(Gly).sub.7 PRB deletion
R222Q/S265N/C108- R219Q/S262N/C105- 605 Combination w/
T150del.fwdarw.(Gly).sub.5 T147del.fwdarw.(Gly).sub.5 PRB deletion
R222Q/S265N/C108- R219Q/S262N/C105- 606 Combination w/
T150del.fwdarw.(Gly).sub.3 T147del.fwdarw.(Gly).sub.3 PRB deletion
R222Q/S265N/R128N/P129A R219Q/S262N/R125N/P126A 607 Combination w/
PRB hyperglycosylation R222Q/S265N/S130N/K132S
R219Q/S262N/S127N/K129S 608 Combination w/ PRB hyperglycosylation
R222Q/S265N/P129N/E131T R219Q/S262N/P126N/E128T 609 Combination w/
PRB hyperglycosylation R222Q/S265N/R115N/I117T
R219Q/S262N/R112N/I114T 610 Combination w/ PRB hyperglycosylation
R222Q/S265N/I137N/L138C/ R219Q/S262N/I134N/L135C/ 611 Combination
w/ L139T L136T PRB hyperglycosylation R222Q/S265N/I137N/L138S/
R219Q/S262N/I134N/L135S/ 612 Combination w/ L139T L136T PRB
hyperglycosylation R222Q/S265N/R145N/Q147S R219Q/S262N/R142N/Q144S
613 Combination w/ PRB hyperglycosylation R222Q/S265N/E140N/Y142T
R219Q/S262N/E137N/Y139T 614 Combination w/ PRB hyperglycosylation
R222Q/S265N/P114N/G116S R219Q/S262N/P111N/G113S 615 Combination w/
PRB hyperglycosylation R222Q/S265N/F122S R219Q/S262N/F119S 616
Combination w/ PRB-ADA interaction R222Q/S265N/F122K
R219Q/S262N/F119K 617 Combination w/ PRB-ADA interaction
R222Q/S265N/Y227R R219Q/S262N/Y224R 618 Combination w/ PRB-ADA
interaction R222Q/S265N/Y227N R219Q/S262N/Y224N 619 Combination w/
PRB-ADA interaction R222Q/S265N/Y194S R219Q/S262N/Y191S 620
Combination w/ PRB-ADA interaction R222Q/S265N/Y194D
R219Q/S262N/Y191D 621 Combination w/ PRB-ADA interaction
R222Q/S265N/F186K R219Q/S262N/F183K 622 Combination w/ PRB-ADA
interaction R222Q/S265N/Y194D/Y227R R219Q/S262N/Y191D/Y224R 623
Combination w/ PRB-ADA interaction R222Q/S265N/F112S
R219Q/S262N/F109S 624 Combination w/ PRB-ADA interaction
R222Q/S265N/F112A R219Q/S262N/F109A 625 Combination w/ PRB-ADA
interaction R222Q/S265N/R121D R219Q/S262N/R118D 626 Combination w/
PRB-ADA interaction R222Q/S265N/R121A R219Q/S262N/R118A 627
Combination w/ PRB-ADA interaction R222Q/S265N/Y142T
R219Q/S262N/Y139T 628 Combination w/ PRB-ADA interaction
R222Q/S265N/Y142A R219Q/S262N/Y139A 629 Combination w/ PRB-ADA
interaction R222Q/S265N/W136S R219Q/S262N/W133S 630 Combination w/
PRB-ADA interaction R222Q/S265N/W136T R219Q/S262N/W133T 631
Combination w/ PRB-ADA interaction R222Q/S265N/P127A
R219Q/S262N/P124A 632 Combination w/ PRB-ADA interaction
R222Q/S265N/P127S R219Q/S262N/P124S 633 Combination w/ PRB-ADA
interaction R222Q/S265N/V102- R219Q/S262N/V99- 634 Combination w/
Q147del.fwdarw.(GGGGS).sub.1 Q144del.fwdarw.(GGGGS).sub.1 PRB
deletion R222Q/S265N/V102- R219Q/S262N/V99- 635 Combination w/
Q147del.fwdarw.(GGGGS).sub.2 Q144del.fwdarw.(GGGGS).sub.2 PRB
deletion R222Q/S265N/V102- R219Q/S262N/V99- 636 Combination w/
Q147del.fwdarw.(GGGGS).sub.3 Q144del.fwdarw.(GGGGS).sub.3 PRB
deletion R222Q/S265N/C108- R219Q/S262N/C105- 637 Combination w/
T150del.fwdarw.(GGGGS).sub.1 T147del.fwdarw.(GGGGS).sub.1 PRB
deletion R222Q/S265N/C108- R219Q/S262N/C105- 638 Combination w/
T150del.fwdarw.(GGGGS).sub.2 T147del.fwdarw.(GGGGS).sub.2 PRB
deletion R222Q/S265N/C108- R219Q/S262N/C105- 639 Combination w/
T150del.fwdarw.(GGGGS).sub.3 T147del.fwdarw.(GGGGS).sub.3 PRB
deletion R222Q/S265N/K374D/V102- R219Q/S262N/K371D/V99- 640
Combination w/ Q147del.fwdarw.(GGGGS).sub.1
Q144del.fwdarw.(GGGGS).sub.1 PRB deletion R222Q/S265N/K374D/V102-
R219Q/S262N/K371D/V99- 641 Combination w/
Q147del.fwdarw.(GGGGS).sub.2 Q144del.fwdarw.(GGGGS).sub.2 PRB
deletion R222Q/S265N/K374D/V102- R219Q/S262N/K371D/V99- 642
Combination w/ Q147del.fwdarw.(GGGGS).sub.3
Q144del.fwdarw.(GGGGS).sub.3 PRB deletion R222Q/S265N/K374D/C108-
R219Q/S262N/K371D/C105- 643 Combination w/
T150del.fwdarw.(GGGGS).sub.1 T147del.fwdarw.(GGGGS).sub.1 PRB
deletion R222Q/S265N/K374D/C108- R219Q/S262N/K371D/C105- 644
Combination w/ T150del.fwdarw.(GGGGS).sub.2
T147del.fwdarw.(GGGGS).sub.2 PRB deletion R222Q/S265N/K374D/C108-
R219Q/S262N/K371D/C105- 645 Combination w/
T150del.fwdarw.(GGGGS).sub.3 T147del.fwdarw.(GGGGS).sub.3 PRB
deletion K374D/C108- K371D/C105- 646 Combination w/
T150del.fwdarw.(Gly)n T147del.fwdarw.(Gly)n PRB deletion
K374D/C108- K371D/C105- 647 Combination w/
T150del.fwdarw.(Gly).sub.15 T147del.fwdarw.(Gly).sub.15 PRB
deletion K374D/C108- K371D/C105- 648 Combination w/
T150del.fwdarw.(Gly).sub.10 T147del.fwdarw.(Gly).sub.10 PRB
deletion K374D/C108- K371D/C105- 649 Combination w/
T150del.fwdarw.(Gly).sub.7 T147del.fwdarw.(Gly).sub.7 PRB deletion
K374D/C108- K371D/C105- 650 Combination w/
T150del.fwdarw.(Gly).sub.5 T147del.fwdarw.(Gly).sub.5 PRB deletion
K374D/C108- K371D/C105- 651 Combination w/
T150del.fwdarw.(Gly).sub.3 T147del.fwdarw.(Gly).sub.3 PRB deletion
K374D/V102- K371D/V99- 652 Combination w/ Q147del.fwdarw.(GGGGS)n
Q144del.fwdarw.(GGGGS)n PRB deletion K374D/C108- K371D/C105- 653
Combination w/ T150del.fwdarw.(GGGGS)n T147del.fwdarw.(GGGGS)n PRB
deletion K374D/N101-N159del K371D/N98-N156del 654 Combination w/
PRB deletion K374D/C108-E151del K371D/C105-E148del 655 Combination
w/ PRB deletion K374D/C108-T150del K371D/C105-T147del 656
Combination w/ PRB deletion K374D/V102-Q147del K371D/V99-Q144del
657 Combination w/ PRB deletion R222Q/S265N/C108- R219Q/S262N/C105-
658 Combination w/ T150del.fwdarw.(Gly)n T147del.fwdarw.(Gly)n PRB
deletion R222Q/S265N/K14A R219Q/S262N/K11A 659 Combination
R222Q/S265N/K14D R219Q/S262N/K11D 660 Combination R222Q/S265N/K14E
R219Q/S262N/K11E 661 Combination R222Q/S265N/K16A R219Q/S262N/K13A
662 Combination R222Q/S265N/K16D R219Q/S262N/K13D 663 Combination
R222Q/S265N/V102- R219Q/S262N/V99- 664 Combination w/
Q147del.fwdarw.(GGGGS)n Q144del.fwdarw.(GGGGS)n PRB deletion
R222Q/S265N/C108- R219Q/S262N/C105- 665 Combination w/
T150del.fwdarw.(GGGGS)n T147del.fwdarw.(GGGGS)n PRB deletion
R222Q/S265N/N101-N159del R219Q/S262N/N98-N156del 666 Combination w/
PRB deletion R222Q/S265N/C108-E151del R219Q/S262N/C105-E148del 667
Combination w/ PRB deletion R222Q/S265N/C108-T150del
R219Q/S262N/C105-T147del 668 Combination w/ PRB deletion
R222Q/S265N/V102-Q147del R219Q/S262N/V99-Q144del 669 Combination w/
PRB deletion R222Q/S265N/K374D/C108- R219Q/S262N/K371D/C105- 670
Combination w/ T150del.fwdarw.(Gly)n T147del.fwdarw.(Gly)n PRB
deletion R222Q/S265N/K374D/C108- R219Q/S262N/K371D/C105- 671
Combination w/ T150del.fwdarw.(Gly).sub.15
T147del.fwdarw.(Gly).sub.15 PRB deletion R222Q/S265N/K374D/C108-
R219Q/S262N/K371D/C105- 672 Combination w/
T150del.fwdarw.(Gly).sub.10 T147del.fwdarw.(Gly).sub.10 PRB
deletion R222Q/S265N/K374D/C108- R219Q/S262N/K371D/C105- 673
Combination w/ T150del.fwdarw.(Gly).sub.7
T147del.fwdarw.(Gly).sub.7 PRB deletion R222Q/S265N/K374D/C108-
R219Q/S262N/K371D/C105- 674 Combination w/
T150del.fwdarw.(Gly).sub.5 T147del.fwdarw.(Gly).sub.5 PRB deletion
R222Q/S265N/K374D/C108- R219Q/S262N/K371D/C105- 675 Combination w/
T150del.fwdarw.(Gly).sub.3 T147del.fwdarw.(Gly).sub.3 PRB deletion
R222Q/S265N/K374D/V102- R219Q/S262N/K371D/V99- 676 Combination w/
Q147del.fwdarw.(GGGGS)n Q144del.fwdarw.(GGGGS)n PRB deletion
R222Q/S265N/K374D/C108- R219Q/S262N/K371D/C105- 677 Combination w/
T150del.fwdarw.(GGGGS)n T147del.fwdarw.(GGGGS)n PRB deletion
R222Q/S265N/K374D/N101- R219Q/S262N/K371D/N98- 678 Combination w/
N159del N156del PRB deletion R222Q/S265N/K374D/C108-
R219Q/S262N/K371D/C105- 679 Combination w/ E151del E148del PRB
deletion R222Q/S265N/K374D/C108- R219Q/S262N/K371D/C105- 680
Combination w/ T150del T147del PRB deletion R222Q/S265N/K374D/V102-
R219Q/S262N/K371D/V99- 681 Combination w/ Q147del Q144del PRB
deletion R222Q/S265N/K16E R219Q/S262N/K13E 682 Combination
R222Q/S265N/K374A R219Q/S262N/K371A 683 Combination
R222Q/S265N/K375A R219Q/S262N/K372A 684 Combination
R222Q/S265N/K375D R219Q/S262N/K372D 685 Combination
R222Q/S265N/K375E R219Q/S262N/K372E 686 Combination
R222Q/S265N/K455A R219Q/S262N/K452A 687 Combination
R222Q/S265N/K455D R219Q/S262N/K452D 688 Combination
R222Q/S265N/K455E R219Q/S262N/K452E 689 Combination
R222Q/S265N/R23A R219Q/S262N/R20A 690 Combination R222Q/S265N/R23D
R219Q/S262N/R20D 691 Combination R222Q/S265N/R369A
R219Q/S262N/R366A 692 Combination R222Q/S265N/R369D
R219Q/S262N/R366D 693 Combination R222Q/S265N/R369E
R219Q/S262N/R366E 694 Combination R222Q/S265N/H267A
R219Q/S262N/H264A 695 Combination R222Q/S265N/H267Q
R219Q/S262N/H264Q 696 Combination R222Q/S265N/H267N
R219Q/S262N/H264N 697 Combination R222Q/S265N/H267G
R219Q/S262N/H264G 698 Combination R222K/S265N R219K/S262N 699
Combination R222N/S265N R219N/S262N 700 Combination R222A/S265N
R219A/S262N 701 Combination R222Q/S265N/L224A R219Q/S262N/L221A 702
Combination R222Q/S265N/L224V R219Q/S262N/L221V 703 Combination
R222Q/S265N/L224G R219Q/S262N/L221G 704 Combination
R222Q/S265N/E182D R219Q/S262N/E179D 705 Combination
R222Q/S265N/E182A R219Q/S262N/E179A 706 Combination
R222Q/S265N/E182S R219Q/S262N/E179S 707 Combination
R222Q/S265N/E182T R219Q/S262N/E179T 708 Combination
R222Q/S265N/E182V R219Q/S262N/E179V 709 Combination
R222Q/S265N/E182G R219Q/S262N/E179G 710 Combination R222Q/S265A
R219Q/S262A 711 Combination R222Q/S265V R219Q/S262V 712 Combination
R222Q/S265M R219Q/S262M 713 Combination R222Q/S265N/K14A/R23A
R219Q/S262N/K11A/R20A 714 Combination R222Q/S265N/K14A/R23A/K374A
R219Q/S262N/K11A/R20A/K371A 715 Combination R222Q/S265N/R23A/K374A
R219Q/S262N/R20A/K371A 716 Combination R222Q/S265N/K14A/K374A
R219Q/S262N/K11A/K371A 717 Combination R222Q/S265N/K29A
R219Q/S262N/K26A 718 Combination R222Q/S265N/K29D R219Q/S262N/K26D
719 Combination R222Q/S265N/K29E R219Q/S262N/K26E 720 Combination
R222Q/S265N/R220A R219Q/S262N/R217A 721 Combination
R222Q/S265N/R220D R219Q/S262N/R217D 722 Combination
R222Q/S265N/R220E R219Q/S262N/R217E 723 Combination
R222Q/S265N/K261A R219Q/S262N/K258A 724 Combination
R222Q/S265N/K261D R219Q/S262N/K258D 725 Combination
R222Q/S265N/K261E R219Q/S262N/K258E 726 Combination
R222Q/S265N/R280A R219Q/S262N/R277A 727 Combination
R222Q/S265N/R280D R219Q/S262N/R277D 728 Combination
R222Q/S265N/R280E R219Q/S262N/R277E 729 Combination
R222Q/S265N/R286A R219Q/S262N/R283A 730 Combination
R222Q/S265N/R286D R219Q/S262N/R283D 731 Combination
R222Q/S265N/R286E R219Q/S262N/R283E 732 Combination
R222Q/S265N/K312A R219Q/S262N/K309A 733 Combination
R222Q/S265N/K312D R219Q/S262N/K309D 734 Combination
R222Q/S265N/K312E R219Q/S262N/K309E 735 Combination
R222Q/S265N/K320A R219Q/S262N/K317A 736 Combination
R222Q/S265N/K320D R219Q/S262N/K317D 737 Combination
R222Q/S265N/K320E R219Q/S262N/K317E 738 Combination
R222Q/S265N/K324A R219Q/S262N/K321A 739 Combination
R222Q/S265N/K324D R219Q/S262N/K321D 740 Combination
R222Q/S265N/K324E R219Q/S262N/K321E 741 Combination
R222Q/S265N/R355A R219Q/S262N/R352A 742 Combination
R222Q/S265N/R355D R219Q/S262N/R352D 743 Combination
R222Q/S265N/R355E R219Q/S262N/R352E 744 Combination
R222Q/S265N/R444A R219Q/S262N/R441A 745 Combination
R222Q/S265N/R444D R219Q/S262N/R441D 746 Combination
R222Q/S265N/R444E R219Q/S262N/R441E 747 Combination
R222Q/S265N/K447A R219Q/S262N/K444A 748 Combination
R222Q/S265N/K447D R219Q/S262N/K444D 749 Combination
R222Q/S265N/K447E R219Q/S262N/K444E 750 Combination
R222Q/S265N/K464A R219Q/S262N/K461A 751 Combination
R222Q/S265N/K464D R219Q/S262N/K461D 752 Combination
R222Q/S265N/K464E R219Q/S262N/K461E 753 Combination
R222Q/S265N/K472A R219Q/S262N/K469A 754 Combination
R222Q/S265N/K472D R219Q/S262N/K469D 755 Combination
R222Q/S265N/K472E R219Q/S262N/K469E 756 Combination
R222Q/S265N/K473A R219Q/S262N/K470A 757 Combination
R222Q/S265N/K473D R219Q/S262N/K470D 758 Combination
R222Q/S265N/K473E R219Q/S262N/K470E 759 Combination
R222Q/S265N/D89A R219Q/S262N/D86A 760 Combination R222Q/S265N/D89C
R219Q/S262N/D86C 761 Combination R222Q/S265N/D89E R219Q/S262N/D86E
762 Combination R222Q/S265N/D89F R219Q/S262N/D86F 763 Combination
R222Q/S265N/D89G R219Q/S262N/D86G 764 Combination R222Q/S265N/D89H
R219Q/S262N/D86H 765 Combination R222Q/S265N/D89I R219Q/S262N/D86I
766 Combination R222Q/S265N/D89K R219Q/S262N/D86K 767 Combination
R222Q/S265N/D89L R219Q/S262N/D86L 768 Combination R222Q/S265N/D89M
R219Q/S262N/D86M 769 Combination R222Q/S265N/D89N R219Q/S262N/D86N
770 Combination R222Q/S265N/D89P R219Q/S262N/D86P 771 Combination
R222Q/S265N/D89Q R219Q/S262N/D86Q 772 Combination R222Q/S265N/D89R
R219Q/S262N/D86R 773 Combination R222Q/S265N/D89S R219Q/S262N/D86S
774 Combination R222Q/S265N/D89T R219Q/S262N/D86T 775 Combination
R222Q/S265N/D89V R219Q/S262N/D86V 776 Combination R222Q/S265N/D89W
R219Q/S262N/D86W 777 Combination R222Q/S265N/D89Y R219Q/S262N/D86Y
778 Combination R222Q/S265N/E182C R219Q/S262N/E179C 779 Combination
R222Q/S265N/E182F R219Q/S262N/E179F 780 Combination
R222Q/S265N/E182H R219Q/S262N/E179H 781 Combination
R222Q/S265N/E182I R219Q/S262N/E179I 782 Combination
R222Q/S265N/E182K R219Q/S262N/E179K 783 Combination
R222Q/S265N/E182L R219Q/S262N/E179L 784 Combination
R222Q/S265N/E182M R219Q/S262N/E179M 785 Combination
R222Q/S265N/E182N R219Q/S262N/E179N 786 Combination
R222Q/S265N/E182P R219Q/S262N/E179P 787 Combination
R222Q/S265N/E182Q R219Q/S262N/E179Q 788 Combination
R222Q/S265N/E182R R219Q/S262N/E179R 789 Combination
R222Q/S265N/E182W R219Q/S262N/E179W 790 Combination
R222Q/S265N/E182Y R219Q/S262N/E179Y 791 Combination R222C/S265N
R219C/S262N 792 Combination R222D/S265N R219D/S262N 793 Combination
R222E/S265N R219E/S262N 794 Combination R222F/S265N R219F/S262N 795
Combination R222G/S265N R219G/S262N 796 Combination R222H/S265N
R219H/S262N 797 Combination R222I/S265N R219I/S262N 798 Combination
R222L/S265N R219L/S262N 799 Combination R222M/S265N R219M/S262N 800
Combination R222P/S265N R219P/S262N 801 Combination R222S/S265N
R219S/S262N 802 Combination R222T/S265N R219T/S262N 803 Combination
R222V/S265N R219V/S262N 804 Combination R222W/S265N R219W/S262N 805
Combination R222Y/S265N R219Y/S262N 806 Combination
R222Q/S265N/L224C R219Q/S262N/L221C 807 Combination
R222Q/S265N/L224D R219Q/S262N/L221D 808 Combination
R222Q/S265N/L224E R219Q/S262N/L221E 809 Combination
R222Q/S265N/L224F R219Q/S262N/L221F 810 Combination
R222Q/S265N/L224H R219Q/S262N/L221H 811 Combination
R222Q/S265N/L224I R219Q/S262N/L221I 812 Combination
R222Q/S265N/L224K R219Q/S262N/L221K 813 Combination
R222Q/S265N/L224M R219Q/S262N/L221M 814 Combination
R222Q/S265N/L224N R219Q/S262N/L221N 815 Combination
R222Q/S265N/L224P R219Q/S262N/L221P 816 Combination
R222Q/S265N/L224Q R219Q/S262N/L221Q 817 Combination
R222Q/S265N/L224R R219Q/S262N/L221R 818 Combination
R222Q/S265N/L224S R219Q/S262N/L221S 819 Combination
R222Q/S265N/L224T R219Q/S262N/L221T 820 Combination
R222Q/S265N/L224W R219Q/S262N/L221W 821 Combination
R222Q/S265N/L224Y R219Q/S262N/L221Y 822 Combination R222Q/S265C
R219Q/S262C 823 Combination R222Q/S265D R219Q/S262D 824 Combination
R222Q/S265E R219Q/S262E 825 Combination R222Q/S265F R219Q/S262F 826
Combination R222Q/S265G R219Q/S262G 827 Combination R222Q/S265H
R219Q/S262H 828 Combination R222Q/S265I R219Q/S262I 829 Combination
R222Q/S265K R219Q/S262K 830 Combination R222Q/S265L R219Q/S262L 831
Combination R222Q/S265P R219Q/S262P 832 Combination R222Q/S265Q
R219Q/S262Q 833 Combination R222Q/S265R R219Q/S262R 834 Combination
R222Q/S265T R219Q/S262T 835 Combination R222Q/S265W R219Q/S262W 836
Combination R222Q/S265Y R219Q/S262Y 837 Combination
R222Q/S265N/H267C R219Q/S262N/H264C 838 Combination
R222Q/S265N/H267D R219Q/S262N/H264D 839 Combination
R222Q/S265N/H267E R219Q/S262N/H264E 840 Combination
R222Q/S265N/H267F R219Q/S262N/H264F 841 Combination
R222Q/S265N/H267I R219Q/S262N/H264I 842 Combination
R222Q/S265N/H267K R219Q/S262N/H264K 843 Combination
R222Q/S265N/H267L R219Q/S262N/H264L 844 Combination
R222Q/S265N/H267M R219Q/S262N/H264M 845 Combination
R222Q/S265N/H267P R219Q/S262N/H264P 846 Combination
R222Q/S265N/H267R R219Q/S262N/H264R 847 Combination
R222Q/S265N/H267S R219Q/S262N/H264S 848 Combination
R222Q/S265N/H267T R219Q/S262N/H264T 849 Combination
R222Q/S265N/H267V R219Q/S262N/H264V 850 Combination
R222Q/S265N/H267W R219Q/S262N/H264W 851 Combination
R222Q/S265N/H267Y R219Q/S262N/H264Y 852 Combination
R222Q/S265N/S269A R219Q/S262N/S266A 853 Combination
R222Q/S265N/S269C R219Q/S262N/S266C 854 Combination
R222Q/S265N/S269D R219Q/S262N/S266D 855 Combination
R222Q/S265N/S269E R219Q/S262N/S266E 856 Combination
R222Q/S265N/S269F R219Q/S262N/S266F 857 Combination
R222Q/S265N/S269G R219Q/S262N/S266G 858 Combination
R222Q/S265N/S269H R219Q/S262N/S266H 859 Combination
R222Q/S265N/S269I R219Q/S262N/S266I 860 Combination
R222Q/S265N/S269K R219Q/S262N/S266K 861 Combination
R222Q/S265N/S269L R219Q/S262N/S266L 862 Combination
R222Q/S265N/S269M R219Q/S262N/S266M 863 Combination
R222Q/S265N/S269N R219Q/S262N/S266N 864 Combination
R222Q/S265N/S269P R219Q/S262N/S266P 865 Combination
R222Q/S265N/S269Q R219Q/S262N/S266Q 866 Combination
R222Q/S265N/S269R R219Q/S262N/S266R 867 Combination
R222Q/S265N/S269T R219Q/S262N/S266T 868 Combination
R222Q/S265N/S269V R219Q/S262N/S266V 869 Combination
R222Q/S265N/S269W R219Q/S262N/S266W 870 Combination
R222Q/S265N/S269Y R219Q/S262N/S266Y 871 Combination
R222Q/S265N/K270A R219Q/S262N/K267A 872 Combination
R222Q/S265N/K270C R219Q/S262N/K267C 873 Combination
R222Q/S265N/K270D R219Q/S262N/K267D 874 Combination
R222Q/S265N/K270E R219Q/S262N/K267E 875 Combination
R222Q/S265N/K270F R219Q/S262N/K267F 876 Combination
R222Q/S265N/K270G R219Q/S262N/K267G 877 Combination
R222Q/S265N/K270H R219Q/S262N/K267H 878 Combination
R222Q/S265N/K270I R219Q/S262N/K267I 879 Combination
R222Q/S265N/K270L R219Q/S262N/K267L 880 Combination
R222Q/S265N/K270M R219Q/S262N/K267M 881 Combination
R222Q/S265N/K270N R219Q/S262N/K267N 882 Combination
R222Q/S265N/K270P R219Q/S262N/K267P 883 Combination
R222Q/S265N/K270Q R219Q/S262N/K267Q 884 Combination
R222Q/S265N/K270R R219Q/S262N/K267R 885 Combination
R222Q/S265N/K270S R219Q/S262N/K267S 886 Combination
R222Q/S265N/K270T R219Q/S262N/K267T 887 Combination
R222Q/S265N/K270V R219Q/S262N/K267V 888 Combination
R222Q/S265N/K270W R219Q/S262N/K267W 889 Combination
R222Q/S265N/K270Y R219Q/S262N/K267Y 890 Combination
R222Q/S265N/V299A R219Q/S262N/V296A 891 Combination
R222Q/S265N/V299C R219Q/S262N/V296C 892 Combination
R222Q/S265N/V299D R219Q/S262N/V296D 893 Combination
R222Q/S265N/V299E R219Q/S262N/V296E 894 Combination
R222Q/S265N/V299F R219Q/S262N/V296F 895 Combination
R222Q/S265N/V299G R219Q/S262N/V296G 896 Combination
R222Q/S265N/V299H R219Q/S262N/V296H 897 Combination
R222Q/S265N/V299I R219Q/S262N/V296I 898 Combination
R222Q/S265N/V299K R219Q/S262N/V296K 899 Combination
R222Q/S265N/V299L R219Q/S262N/V296L 900 Combination
R222Q/S265N/V299M R219Q/S262N/V296M 901 Combination
R222Q/S265N/V299N R219Q/S262N/V296N 902 Combination
R222Q/S265N/V299P R219Q/S262N/V296P 903 Combination
R222Q/S265N/V299Q R219Q/S262N/V296Q 904 Combination
R222Q/S265N/V299R R219Q/S262N/V296R 905 Combination
R222Q/S265N/V299S R219Q/S262N/V296S 906 Combination
R222Q/S265N/V299T R219Q/S262N/V296T 907 Combination
R222Q/S265N/V299W R219Q/S262N/V296W 908 Combination
R222Q/S265N/V299Y R219Q/S262N/V296Y 909 Combination R222Q/K14A/R23A
R219Q/K11A/R20A 910 Combination R222Q/K14A/R23A/K374A
R219Q/K11A/R20A/K371A 911 Combination R222Q/R23A/K374A
R219Q/R20A/K371A 912 Combination R222Q/K14A/K374A R219Q/K11A/K371A
913 Combination S265N/K14A/R23A S262N/K11A/R20A 914 Combination
S265N/K14A/R23A/K374A S262N/K11A/R20A/K371A 915 Combination
S265N/R23A/K374A S262N/R20A/K371A 916 Combination S265N/K14A/K374A
S262N/K11A/K371A 917 Combination R222Q/C108- R219Q/C105- 918
Combination w/ T150del.fwdarw.(Gly)n T147del.fwdarw.(Gly)n PRB
deletion R222Q/V102- R219Q/V99- 919 Combination w/
Q147del.fwdarw.(GGGGS)n Q144del.fwdarw.(GGGGS)n PRB deletion
R222Q/C108- R219Q/C105- 920 Combination w/ T150del.fwdarw.(GGGGS)n
T147del.fwdarw.(GGGGS)n PRB deletion R222Q/N101-N159del
R219Q/N98-N156del 921 Combination w/ PRB deletion
R222Q/C108-E151del R219Q/C105-E148del 922 Combination w/ PRB
deletion R222Q/C108-T150del R219Q/C105-T147del 923 Combination w/
PRB deletion R222Q/V102-Q147del R219Q/V99-Q144del 924 Combination
w/ PRB deletion S265N/C108- S262N/C105- 925 Combination w/
T150del.fwdarw.(Gly)n T147del.fwdarw.(Gly)n PRB deletion
S265N/V102- S262N/V99- 926 Combination w/ Q147del.fwdarw.(GGGGS)n
Q144del.fwdarw.(GGGGS)n PRB deletion S265N/C108- S262N/C105- 927
Combination w/ T150del.fwdarw.(GGGGS)n T147del.fwdarw.(GGGGS)n PRB
deletion S265N/N101-N159del S262N/N98-N156del 928 Combination w/
PRB deletion S265N/C108-E151del S262N/C105-E148del 929 Combination
w/ PRB deletion S265N/C108-T150del S262N/C105-T147del 930
Combination w/ PRB deletion S265N/V102-Q147del S262N/V99-Q144del
931 Combination w/ PRB deletion
[1225] Since modifications will be apparent to those of skill in
the art, it is intended that this invention be limited only by the
scope of the appended claims.
Sequence CWU 0 SQTB SEQUENCE LISTING The patent application
contains a lengthy "Sequence Listing" section. A copy of the
"Sequence Listing" is available in electronic form from the USPTO
web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20170166878A9).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
0 SQTB SEQUENCE LISTING The patent application contains a lengthy
"Sequence Listing" section. A copy of the "Sequence Listing" is
available in electronic form from the USPTO web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20170166878A9).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
* * * * *
References