U.S. patent application number 12/096009 was filed with the patent office on 2008-12-25 for compositions containing, methods involving, and uses of non-natural amino acids and polypeptides.
This patent application is currently assigned to Ambrx, Inc.. Invention is credited to Junjie Liu, Zhenwei Miao, Thea Norman.
Application Number | 20080317670 12/096009 |
Document ID | / |
Family ID | 38163532 |
Filed Date | 2008-12-25 |
United States Patent
Application |
20080317670 |
Kind Code |
A1 |
Miao; Zhenwei ; et
al. |
December 25, 2008 |
Compositions Containing, Methods Involving, and Uses of Non-Natural
Amino Acids and Polypeptides
Abstract
Disclosed herein are non-natural amino acids and polypeptides
that include at least one non-natural amino acid, and methods for
making such non-natural amino acids and polypeptides. The
non-natural amino acids, by themselves or as a part of a
polypeptide, can include a wide range of possible functionalities,
but typical have at least one aromatic amine group. Also disclosed
herein are non-natural amino acid polypeptides that are further
modified post-translationally, methods for effecting such
modifications, and methods for purifying such polypeptides.
Typically, the modified non-natural amino acid polypeptides include
at least one alkylated amine group. Further disclosed are methods
for using such non-natural amino acid polypeptides and modified
non-natural amino acid polypeptides, including therapeutic,
diagnostic, and other biotechnology uses.
Inventors: |
Miao; Zhenwei; (San Diego,
CA) ; Liu; Junjie; (San Diego, CA) ; Norman;
Thea; (San Diego, CA) |
Correspondence
Address: |
ATTN: JOHN W. WALLEN, III;AMBRX, INC.
10975 NORTH TORREY PINES ROAD, SUITE 100
LA JOLLA
CA
92037
US
|
Assignee: |
Ambrx, Inc.
La Jolla
CA
|
Family ID: |
38163532 |
Appl. No.: |
12/096009 |
Filed: |
December 13, 2006 |
PCT Filed: |
December 13, 2006 |
PCT NO: |
PCT/US06/47822 |
371 Date: |
August 21, 2008 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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60743041 |
Dec 14, 2005 |
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60743040 |
Dec 14, 2005 |
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Current U.S.
Class: |
424/9.1 ;
424/130.1; 424/85.2; 424/85.4; 424/85.5; 424/85.6; 424/85.7;
424/94.4; 514/1.1; 530/324; 530/350; 562/443 |
Current CPC
Class: |
A61P 35/00 20180101;
C07C 229/42 20130101; C07K 2/00 20130101; A61P 43/00 20180101; C07K
1/006 20130101; A61P 3/10 20180101 |
Class at
Publication: |
424/9.1 ;
562/443; 530/324; 530/350; 514/12; 424/130.1; 514/8; 424/85.4;
424/85.7; 424/85.6; 424/85.5; 424/85.2; 424/94.4 |
International
Class: |
A61K 49/00 20060101
A61K049/00; C07C 229/34 20060101 C07C229/34; C07K 14/00 20060101
C07K014/00; A61K 38/16 20060101 A61K038/16; A61K 39/395 20060101
A61K039/395; A61P 43/00 20060101 A61P043/00; A61K 38/14 20060101
A61K038/14; A61K 38/21 20060101 A61K038/21; A61K 38/20 20060101
A61K038/20; A61K 38/44 20060101 A61K038/44 |
Claims
1. A compound or salt thereof selected from the group consisting
of: ##STR00095## wherein each R.sub.a is independently selected
from the group consisting of H, halogen, alkyl, --NO.sub.2, --CN,
substituted alkyl, --N(R').sub.2, --C(O).sub.kR',
--C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where k is 1, 2, or
3; M is H or --CH.sub.2R.sub.5; or the M-N--C(R.sub.5) moiety may
form a 4 to 7 membered ring structure; R.sub.1 is H, an amino
protecting group, resin, amino acid, polypeptide, or
polynucleotide; R.sub.2 is OH, an ester protecting group, resin,
amino acid, polypeptide, or polynucleotide; R.sub.5 is alkyl,
substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR'; or
R.sub.5 is L-X, where, X is a selected from the group consisting of
a label; a dye; a polymer; a water-soluble polymer; a derivative of
polyethylene glycol; a photocrosslinker; a cytotoxic compound; a
drug; an affinity label; a photoaffinity label; a reactive
compound; a resin; a second protein or polypeptide or polypeptide
analog; an antibody or antibody fragment; a metal chelator; a
cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a
RNA; an antisense polynucleotide; a saccharide, a water-soluble
dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin
label; a fluorophore, a metal-containing moiety; a radioactive
moiety; a novel functional group; a group that covalently or
noncovalently interacts with other molecules; a photocaged moiety;
an actinic radiation excitable moiety; a ligand; a
photoisomerizable moiety; biotin; a biotin analogue; a moiety
incorporating a heavy atom; a chemically cleavable group; a
photocleavable group; an elongated side chain; a carbon-linked
sugar; a redox-active agent; an amino thioacid; a toxic moiety; an
isotopically labeled moiety; a biophysical probe; a phosphorescent
group; a chemiluminescent group; an electron dense group; a
magnetic group; an intercalating group; a chromophore; an energy
transfer agent; a biologically active agent; a detectable label; a
small molecule; an inhibitory ribonucleic acid; a radionucleotide;
a neutron-capture agent; a derivative of biotin; quantum dot(s); a
nanotransmitter; a radiotransmitter; an abzyme, an activated
complex activator, a virus, an adjuvant, an aglycan, an allergan,
an angiostatin, an antihormone, an antioxidant, an aptamer, a guide
RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a
receptor, a reverse micelle, and any combination thereof; and L is
optional, and when present is a linker selected from the group
consisting of alkylene, substituted alkylene, alkenylene,
substituted alkenylene, --O--, --O-(alkylene or substituted
alkylene)-, -(alkylene or substituted alkylene)-O--, --C(O)--,
--C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; or
R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; and each R' is independently H, alkyl, or
substituted alkyl.
2. The compound of claim 1, wherein R.sub.1 is H and R.sub.2 is
OH.
3. The compound of claim 1, wherein R.sub.a is a halogen.
4. The compound of claim 1, wherein both R.sub.1 and R.sub.2 are
polypeptides.
5. The compound of claim 1, wherein X is a biologically active
agent selected from the group consisting of a peptide, protein,
enzyme, antibody, drug, dye, lipid, nucleosides, oligonucleotide,
cell, virus, liposome, microparticle, and micelle.
6. The compound of claim 5, wherein X is a drug selected from the
group consisting of an antibiotic, fungicide, anti-viral agent,
anti-inflammatory agent, anti-tumor agent, cardiovascular agent,
anti-anxiety agent, hormone, growth factor, and steroidal
agent.
7. The compound of claim 5, wherein X is an enzyme selected from
the group consisting of horseradish peroxidase, alkaline
phosphatase, .beta.-galactosidase, and glucose oxidase.
8. The compound of claim 1, wherein X is a detectable label
selected from the group consisting of a fluorescent,
phosphorescent, chemiluminescent, chelating, electron dense,
magnetic, intercalating, radioactive, chromophoric, and energy
transfer moiety.
9. The compound of claim 1, wherein X is a polymer comprising
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, alkaryl, substituted alkaryl, aralkyl, or substituted
aralkyl.
10. The compound of claim 9, wherein the polymer comprises
polyalkylene oxide or substituted polyalkylene oxide.
11. The compound of claim 9, wherein the polymer comprises
-[(alkylene or substituted alkylene)-O-(hydrogen, alkyl, or
substituted alkyl)].sub.x, wherein x is from 20-10,000.
12. The compound of claim 9, wherein the polymer is m-PEG having a
molecular weight ranging from about 2 to about 40 KDa.
13. A polypeptide, or salt thereof, containing at least one
compound of claim 1 selected from the group: ##STR00096##
##STR00097## ##STR00098## ##STR00099## wherein X is a halogen.
14. A polypeptide, or salt thereof, containing at least one
compound of claim 1 selected from the group: ##STR00100##
##STR00101## ##STR00102## ##STR00103##
15. A polypeptide, or salt thereof, containing at least one
compound of claim 1 selected from the group: ##STR00104##
##STR00105## ##STR00106## ##STR00107## wherein X is a halogen.
16. A compound or salt thereof having the structure: ##STR00108##
wherein each R.sub.a is independently selected from the group
consisting of H, halogen, alkyl, --NO.sub.2, --CN, substituted
alkyl, --N(R').sub.2, --C(O).sub.kR', --C(O)N(R').sub.2, --OR', and
--S(O).sub.kR', where k is 1, 2, or 3; R.sub.1 is H, an amino
protecting group, resin, amino acid, polypeptide, or
polynucleotide; and R.sub.2 is OH, an ester protecting group,
resin, amino acid, polypeptide, or polynucleotide; each of R.sub.3
and R.sub.4 is independently H, halogen, lower alkyl, or
substituted lower alkyl, or R.sub.3 and R.sub.4 or two R.sub.3
groups optionally form a cycloalkyl or a heterocycloalkyl; M is H
or --CH.sub.2R.sub.5; R.sub.5 is alkyl, substituted alkyl, alkenyl,
substituted alkenyl, alkynyl, substituted alkynyl, alkoxy,
substituted alkoxy, alkylalkoxy, substituted alkylalkoxy,
polyalkylene oxide, substituted polyalkylene oxide, cycloalkyl,
substituted cycloalkyl, aryl, substituted aryl, heteroaryl,
substituted heteroaryl, heterocycle, substituted heterocycle,
alkaryl, substituted alkaryl, aralkyl, substituted aralkyl,
--C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2, --C(O)NHCH(R'').sub.2,
-(alkylene or substituted alkylene)-N(R'').sub.2, -(alkenylene or
substituted alkenylene)-N(R'').sub.2, -(alkylene or substituted
alkylene)-(aryl or substituted aryl), -(alkenylene or substituted
alkenylene)-(aryl or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR'; or
R.sub.5 is L-X, where, X is a selected from the group consisting of
a label; a dye; a polymer; a water-soluble polymer; a derivative of
polyethylene glycol; a photocrosslinker; a cytotoxic compound; a
drug; an affinity label; a photoaffinity label; a reactive
compound; a resin; a second protein or polypeptide or polypeptide
analog; an antibody or antibody fragment; a metal chelator; a
cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a
RNA; an antisense polynucleotide; a saccharide, a water-soluble
dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin
label; a fluorophore, a metal-containing moiety; a radioactive
moiety; a novel functional group; a group that covalently or
noncovalently interacts with other molecules; a photocaged moiety;
an actinic radiation excitable moiety; a ligand; a
photoisomerizable moiety; biotin; a biotin analogue; a moiety
incorporating a heavy atom; a chemically cleavable group; a
photocleavable group; an elongated side chain; a carbon-linked
sugar; a redox-active agent; an amino thioacid; a toxic moiety; an
isotopically labeled moiety; a biophysical probe; a phosphorescent
group; a chemiluminescent group; an electron dense group; a
magnetic group; an intercalating group; a chromophore; an energy
transfer agent; a biologically active agent; a detectable label; a
small molecule; an inhibitory ribonucleic acid; a radionucleotide;
a neutron-capture agent; a derivative of biotin; quantum dot(s); a
nanotransmitter; a radiotransmitter; an abzyme, an activated
complex activator, a virus, an adjuvant, an aglycan, an allergan,
an angiostatin, an antihormone, an antioxidant, an aptamer, a guide
RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a
receptor, a reverse micelle, and any combination thereof; and L is
optional, and when present is a linker selected from the group
consisting of alkylene, substituted alkylene, alkenylene,
substituted alkenylene, --O--, --O-(alkylene or substituted
alkylene)-, -(alkylene or substituted alkylene)-O--, --C(O)--,
--C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; or two
R.sub.5 groups optionally form a cycloalkyl or a heterocycloalkyl;
or R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; with a proviso that when R.sub.1 is H then
R.sub.2 is not OH, or when R.sub.2 is OH then R.sub.1 is not H; and
G is an amine protecting group.
17. The compound of claim 16, wherein the amine protecting group is
selected from the group consisting of: ##STR00109##
18. The compound of claim 16, wherein both R.sub.1 and R.sub.2 are
polypeptides.
19. A compound or salt thereof having the structure of:
##STR00110## wherein L is optional, and when present is lower
alkylene, substituted lower alkylene, lower cycloalkylene,
substituted lower cycloalkylene, lower alkenylene, substituted
lower alkenylene, alkynylene, lower heteroalkylene, substituted
heteroalkylene, lower heterocycloalkylene, substituted lower
heterocycloalkylene, arylene, substituted arylene, heteroarylene,
substituted heteroarylene, alkarylene, substituted alkarylene,
aralkylene, or substituted aralkylene; Q is optional, and when
present is a linker selected from the group consisting of lower
alkylene, substituted lower alkylene, lower alkenylene, substituted
lower alkenylene, lower heteroalkylene, substituted lower
heteroalkylene, --O-(alkylene or substituted alkylene)-,
--S-(alkylene or substituted alkylene)-, where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(O)-(alkylene
or substituted alkylene)-, --C(S)-(alkylene or substituted
alkylene)-, --NR'-(alkylene or substituted alkylene)-,
--CON(R'')-(alkylene or substituted alkylene)-, --CSN(R')-(alkylene
or substituted alkylene)-, --N(R')CO-(alkylene or substituted
alkylene)-, and where each R' is independently H, alkyl, or
substituted alkyl; R.sub.1 is H, an amino protecting group, resin,
amino acid, polypeptide, or polynucleotide; and R.sub.2 is OH, an
ester protecting group, resin, amino acid, polypeptide, or
polynucleotide; each of R.sub.3 and R.sub.4 is independently H,
halogen, lower alkyl, or substituted lower alkyl, or R.sub.3 and
R.sub.4 or two R.sub.3 groups optionally form a cycloalkyl or a
heterocycloalkyl; each R.sub.a is independently selected from the
group consisting of H, halogen, alkyl, --NO.sub.2, --CN,
substituted alkyl, --N(R').sub.2, --C(O).sub.kR',
--C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where k is 1, 2, or
3; R.sub.6 is a protected aldehyde or a masked aldehyde, wherein
the protecting group includes, but is not limited to, ##STR00111##
where each X.sub.1 is independently selected from the group
consisting of --O--, --S--, --N(H)--, --N(R)--, --N(Ac)--, and
--N(OMe)-; X.sub.2 is --OR, --OAc, --SR, --N(R).sub.2, --N(R)(Ac),
--N(R)(OMe), or N.sub.3, and where each R' and R is independently
H, alkyl, or substituted alkyl.
20. The compound of claim 19 wherein X.sub.1 is O.
21. The compound of claim 19 wherein both R.sub.1 and R.sub.2 are
polypeptides.
22. A polypeptide containing at least one compound of claim 19
selected from the group: ##STR00112## ##STR00113## ##STR00114##
23. A method of making a compound containing at least one
non-natural amino acid selected from the group consisting of:
##STR00115## wherein the compound is formed by a reductive
alkylation of an aromatic amino moiety on at least one non-natural
amino acid with at least one reactant comprising at least one
aldehyde moiety; each R.sub.a is independently selected from the
group consisting of H, halogen, alkyl, --NO.sub.2, --CN,
substituted alkyl, --N(R').sub.2, --C(O).sub.kR',
--C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where k is 1, 2, or
3; M is H or --CH.sub.2R.sub.5; or the M-N--C(R.sub.5) moiety may
form a 4 to 7 membered ring structure; R.sub.1 is H, an amino
protecting group, resin, amino acid, polypeptide, or
polynucleotide; R.sub.2 is OH, an ester protecting group, resin,
amino acid, polypeptide, or polynucleotide; R.sub.5 is alkyl,
substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR'; or
R.sub.5 is L-X, where, X is a selected from the group consisting of
a label; a dye; a polymer; a water-soluble polymer; a derivative of
polyethylene glycol; a photocrosslinker; a cytotoxic compound; a
drug; an affinity label; a photoaffinity label; a reactive
compound; a resin; a second protein or polypeptide or polypeptide
analog; an antibody or antibody fragment; a metal chelator; a
cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a
RNA; an antisense polynucleotide; a saccharide, a water-soluble
dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin
label; a fluorophore, a metal-containing moiety; a radioactive
moiety; a novel functional group; a group that covalently or
noncovalently interacts with other molecules; a photocaged moiety;
an actinic radiation excitable moiety; a ligand; a
photoisomerizable moiety; biotin; a biotin analogue; a moiety
incorporating a heavy atom; a chemically cleavable group; a
photocleavable group; an elongated side chain; a carbon-linked
sugar; a redox-active agent; an amino thioacid; a toxic moiety; an
isotopically labeled moiety; a biophysical probe; a phosphorescent
group; a chemiluminescent group; an electron dense group; a
magnetic group; an intercalating group; a chromophore; an energy
transfer agent; a biologically active agent; a detectable label; a
small molecule; an inhibitory ribonucleic acid; a radionucleotide;
a neutron-capture agent; a derivative of biotin; quantum dot(s); a
nanotransmitter; a radiotransmitter; an abzyme, an activated
complex activator, a virus, an adjuvant, an aglycan, an allergan,
an angiostatin, an antihormone, an antioxidant, an aptamer, a guide
RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a
receptor, a reverse micelle, and any combination thereof; and L is
optional, and when present is a linker selected from the group
consisting of alkylene, substituted alkylene, alkenylene,
substituted alkenylene, --O--, --O-(alkylene or substituted
alkylene)-, -(alkylene or substituted alkylene)-O--, --C(O)--,
--C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; or
R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; and each R' is independently H, alkyl, or
substituted alkyl.
24. The method of claim 23, wherein R.sub.1 and R.sub.2 of the at
least one non-natural amino acid is H and OH respectively.
25. The method of claim 23, wherein R.sub.a of the at least one
non-natural amino acid is a halogen.
26. The method of claim 23, wherein both R.sub.1 and R.sub.2 of the
at least one non-natural amino acid are polypeptides.
27. The method of claim 23, wherein X of the at least one
non-natural amino acid is a biologically active agent selected from
the group consisting of a peptide, protein, enzyme, antibody, drug,
dye, lipid, nucleosides, oligonucleotide, cell, virus, liposome,
microparticle, and micelle.
28. The method of claim 27, wherein X of the at least one
non-natural amino acid is a drug selected from the group consisting
of an antibiotic, fungicide, anti-viral agent, anti-inflammatory
agent, anti-tumor agent, cardiovascular agent, anti-anxiety agent,
hormone, growth factor, and steroidal agent.
29. The method of claim 27, wherein X of the at least one
non-natural amino acid is an enzyme selected from the group
consisting of horseradish peroxidase, alkaline phosphatase,
.beta.-galactosidase, and glucose oxidase.
30. The method of claim 23, wherein X of the at least one
non-natural amino acid is a detectable label selected from the
group consisting of a fluorescent, phosphorescent,
chemiluminescent, chelating, electron dense, magnetic,
intercalating, radioactive, chromophoric, and energy transfer
moiety.
31. The method of claim 23, wherein X of the non-natural amino acid
is a polymer comprising alkyl, substituted alkyl, alkenyl,
substituted alkenyl, alkynyl, substituted alkynyl, alkoxy,
substituted alkoxy, alkylalkoxy, substituted alkylalkoxy,
polyalkylene oxide, substituted polyalkylene oxide, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, alkaryl,
substituted alkaryl, aralkyl, or substituted aralkyl.
32. The method of claim 31, wherein the polymer comprises
polyalkylene oxide or substituted polyalkylene oxide.
33. The method of claim 31, wherein the polymer comprises
-[(alkylene or substituted alkylene)-O-(hydrogen, alkyl, or
substituted alkyl)].sub.x, wherein x is from 20-10,000.
34. The method of claim 31, wherein the polymer is m-PEG having a
molecular weight ranging from about 2 to about 40 KDa.
35. The method of claim 23 wherein the at least one non-natural
amino acid is selected from a group: ##STR00116## ##STR00117##
##STR00118##
36. The method of claim 23 wherein the at least one non-natural
amino acid is selected from a group: ##STR00119## ##STR00120##
##STR00121## ##STR00122##
37. The method of claim 23 wherein the at least one non-natural
amino acid is selected from a group: ##STR00123## ##STR00124##
##STR00125##
38. A method of making a polypeptide containing at least one
non-natural amino acid selected from the group consisting of:
##STR00126## wherein the polypeptide is formed by a reductive
alkylation of an aromatic amino moiety on at least one non-natural
amino acid with at least one reactant comprising at least one
aldehyde moiety; each R.sub.a is independently selected from the
group consisting of H, halogen, alkyl, --NO.sub.2, --CN,
substituted alkyl, --N(R').sub.2, --C(O).sub.kR',
--C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where k is 1, 2, or
3; R.sub.1 is H, an amino protecting group, resin, amino acid,
polypeptide, or polynucleotide; and R.sub.2 is OH, an ester
protecting group, resin, amino acid, polypeptide, or
polynucleotide; each of R.sub.3 and R.sub.4 is independently H,
halogen, lower alkyl, or substituted lower alkyl, or R.sub.3 and
R.sub.4 or two R.sub.3 groups optionally form a cycloalkyl or a
heterocycloalkyl; M is --CH.sub.2R.sub.5; R.sub.5 is alkyl,
substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR'; or
R.sub.5 is L-X, where, X is a selected from the group consisting of
a label; a dye; a polymer; a water-soluble polymer; a derivative of
polyethylene glycol; a photocrosslinker; a cytotoxic compound; a
drug; an affinity label; a photoaffinity label; a reactive
compound; a resin; a second protein or polypeptide or polypeptide
analog; an antibody or antibody fragment; a metal chelator; a
cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a
RNA; an antisense polynucleotide; a saccharide, a water-soluble
dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin
label; a fluorophore, a metal-containing moiety; a radioactive
moiety; a novel functional group; a group that covalently or
noncovalently interacts with other molecules; a photocaged moiety;
an actinic radiation excitable moiety; a ligand; a
photoisomerizable moiety; biotin; a biotin analogue; a moiety
incorporating a heavy atom; a chemically cleavable group; a
photocleavable group; an elongated side chain; a carbon-linked
sugar; a redox-active agent; an amino thioacid; a toxic moiety; an
isotopically labeled moiety; a biophysical probe; a phosphorescent
group; a chemiluminescent group; an electron dense group; a
magnetic group; an intercalating group; a chromophore; an energy
transfer agent; a biologically active agent; a detectable label; a
small molecule; an inhibitory ribonucleic acid; a radionucleotide;
a neutron-capture agent; a derivative of biotin; quantum dot(s); a
nanotransmitter; a radiotransmitter; an abzyme, an activated
complex activator, a virus, an adjuvant, an aglycan, an allergan,
an angiostatin, an antihormone, an antioxidant, an aptamer, a guide
RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a
receptor, a reverse micelle, and any combination thereof; and L is
optional, and when present is a linker selected from the group
consisting of alkylene, substituted alkylene, alkenylene,
substituted alkenylene, --O--, --O-(alkylene or substituted
alkylene)-, -(alkylene or substituted alkylene)-O--, --C(O)--,
--C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; or two
R.sub.5 groups optionally form a cycloalkyl or a heterocycloalkyl;
or R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; with a proviso that when R.sub.1 is H then
R.sub.2 is not OH, or when R.sub.2 is OH then R.sub.1 is not H; and
G is an amine protecting group.
39. The method of claim 38 wherein the amine protecting group is
selected from the group consisting of: ##STR00127##
40. The method of claim 38 wherein both R.sub.1 and R.sub.2 are
polypeptides.
41. The method of claim 38 wherein the at least one aldehyde moiety
has the structure corresponding to: ##STR00128## wherein: R.sub.5
is alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR'; or
R.sub.5 is L-X, where, X is a selected from the group consisting of
a label; a dye; a polymer; a water-soluble polymer; a derivative of
polyethylene glycol; a photocrosslinker; a cytotoxic compound; a
drug; an affinity label; a photoaffinity label; a reactive
compound; a resin; a second protein or polypeptide or polypeptide
analog; an antibody or antibody fragment; a metal chelator; a
cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a
RNA; an antisense polynucleotide; a saccharide, a water-soluble
dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin
label; a fluorophore, a metal-containing moiety; a radioactive
moiety; a novel functional group; a group that covalently or
noncovalently interacts with other molecules; a photocaged moiety;
an actinic radiation excitable moiety; a ligand; a
photoisomerizable moiety; biotin; a biotin analogue; a moiety
incorporating a heavy atom; a chemically cleavable group; a
photocleavable group; an elongated side chain; a carbon-linked
sugar; a redox-active agent; an amino thioacid; a toxic moiety; an
isotopically labeled moiety; a biophysical probe; a phosphorescent
group; a chemiluminescent group; an electron dense group; a
magnetic group; an intercalating group; a chromophore; an energy
transfer agent; a biologically active agent; a detectable label; a
small molecule; an inhibitory ribonucleic acid; a radionucleotide;
a neutron-capture agent; a derivative of biotin; quantum dot(s); a
nanotransmitter; a radiotransmitter; an abzyme, an activated
complex activator, a virus, an adjuvant, an aglycan, an allergan,
an angiostatin, an antihormone, an antioxidant, an aptamer, a guide
RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a
receptor, a reverse micelle, and any combination thereof; and L is
optional, and when present is a linker selected from the group
consisting of alkylene, substituted alkylene, alkenylene,
substituted alkenylene, --O--, --O-(alkylene or substituted
alkylene)-, -(alkylene or substituted alkylene)-O--, --C(O)--,
--C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--.
42. A method for treating a disorder, condition or disease
comprising administering a therapeutically effective amount of a
polypeptide comprising at least one non-natural amino acid selected
from the group consisting of: ##STR00129## wherein each R.sub.a is
independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; M is H or --CH.sub.2R.sub.5; or the
M-N--C(R.sub.5) moiety may form a 4 to 7 membered ring structure;
R.sub.1 is H, an amino protecting group, resin, amino acid,
polypeptide, or polynucleotide; R.sub.2 is OH, an ester protecting
group, resin, amino acid, polypeptide, or polynucleotide; R.sub.5
is alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR'; or
R.sub.5 is L-X, where, X is a selected from the group consisting of
a label; a dye; a polymer; a water-soluble polymer; a derivative of
polyethylene glycol; a photocrosslinker; a cytotoxic compound; a
drug; an affinity label; a photoaffinity label; a reactive
compound; a resin; a second protein or polypeptide or polypeptide
analog; an antibody or antibody fragment; a metal chelator; a
cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a
RNA; an antisense polynucleotide; a saccharide, a water-soluble
dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin
label; a fluorophore, a metal-containing moiety; a radioactive
moiety; a novel functional group; a group that covalently or
noncovalently interacts with other molecules; a photocaged moiety;
an actinic radiation excitable moiety; a ligand; a
photoisomerizable moiety; biotin; a biotin analogue; a moiety
incorporating a heavy atom; a chemically cleavable group; a
photocleavable group; an elongated side chain; a carbon-linked
sugar; a redox-active agent; an amino thioacid; a toxic moiety; an
isotopically labeled moiety; a biophysical probe; a phosphorescent
group; a chemiluminescent group; an electron dense group; a
magnetic group; an intercalating group; a chromophore; an energy
transfer agent; a biologically active agent; a detectable label; a
small molecule; an inhibitory ribonucleic acid; a radionucleotide;
a neutron-capture agent; a derivative of biotin; quantum dot(s); a
nanotransmitter; a radiotransmitter; an abzyme, an activated
complex activator, a virus, an adjuvant, an aglycan, an allergan,
an angiostatin, an antihormone, an antioxidant, an aptamer, a guide
RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a
receptor, a reverse micelle, and any combination thereof; and L is
optional, and when present is a linker selected from the group
consisting of alkylene, substituted alkylene, alkenylene,
substituted alkenylene, --O--, --O-(alkylene or substituted
alkylene)-, -(alkylene or substituted alkylene)-O--, --C(O)--,
--C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; or
R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; and each R' is independently H, alkyl, or
substituted alkyl. with a proviso that when R.sub.1 is H then
R.sub.2 is not OH, or when R.sub.2 is OH then R.sub.1 is not H.
43. The method of claim 42, further comprising administering a
pharmaceutically acceptable carrier with the therapeutically
effective amount of the polypeptide.
44. The method of claim 42, wherein R.sub.1 and R.sub.2 are both
polypeptides.
45. The method of claim 42, wherein X is a water-soluble
polymer.
46. The method of claim 42, wherein X is a derivative of
polyethylene glycol.
47. The method of claim 42, wherein X is a cytotoxic compound.
48. The method of claim 42, wherein X is a drug.
49. The method of claim 42, wherein X is a second polypeptide.
50. The method of claim 49, wherein the second polypeptide is a
peptide containing a non-natural amino acid polypeptide.
51. The method of claim 42, wherein the polypeptide is a protein
homologous to a therapeutic protein selected from the group
consisting of: alpha-1 antitrypsin, angiostatin, antihemolytic
factor, antibody, antibody fragment, apolipoprotein, apoprotein,
atrial natriuretic factor, atrial natriuretic polypeptide, atrial
peptide, C-X-C chemokine, T39765, NAP-2, ENA-78, gro-a, gro-b,
gro-c, IP-10, GCP-2, NAP-4, SDF-1, PF4, MIG, calcitonin, c-kit
ligand, cytokine, CC chemokine, monocyte chemoattractant protein-1,
monocyte chemoattractant protein-2, monocyte chemoattractant
protein-3, monocyte inflammatory protein-1 alpha, monocyte
inflammatory protein-i beta, RANTES, 1309, R83915, R91733, HCC1,
T58847, D31065, T64262, CD40, CD40 ligand, c-kit ligand, collagen,
colony stimulating factor (CSF), complement factor 5a, complement
inhibitor, complement receptor 1, cytokine, epithelial neutrophil
activating peptide-78, MIP-16, MCP-1, epidermal growth factor
(EGF), epithelial neutrophil activating peptide, erythropoietin
(EPO), exfoliating toxin, Factor IX, Factor VII, Factor VIII,
Factor X, fibroblast growth factor (FGF), fibrinogen, fibronectin,
four-helical bundle protein, G-CSF, glp-1, GM-CSF,
glucocerebrosidase, gonadotropin, growth factor, growth factor
receptor, grf, hedgehog protein, hemoglobin, hepatocyte growth
factor (hGF), hirudin, human growth hormone (hGH), human serum
albumin, ICAM-1, ICAM-1 receptor, LFA-1, LFA-1 receptor, insulin,
insulin-like growth factor (IGF), IGF-I, IGF-II, interferon (IFN),
IFN-alpha, IFN-beta, IFN-gamma, interleukin (IL), IL-1, IL-2, IL-3,
IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12,
keratinocyte growth factor (KGF), lactoferrin, leukemia inhibitory
factor, luciferase, neurturin, neutrophil inhibitory factor (NIF),
oncostatin M, osteogenic protein, oncogene product, paracitonin,
parathyroid hormone, PD-ECSF, PDGF, peptide hormone, pleiotropin,
protein A, protein G, pth, pyrogenic exotoxin A, pyrogenic exotoxin
B, pyrogenic exotoxin C, pyy, relaxin, renin, SCF, small
biosynthetic protein, soluble complement receptor I, soluble I-CAM
1, soluble interleukin receptor, soluble TNF receptor, somatomedin,
somatostatin, somatotropin, streptokinase, superantigens,
staphylococcal enterotoxin, SEA, SEB, SEC1, SEC2, SEC3, SED, SEE,
steroid hormone receptor, superoxide dismutase, toxic shock
syndrome toxin, thymosin alpha 1, tissue plasminogen activator,
tumor growth factor (TGF), tumor necrosis factor, tumor necrosis
factor alpha, tumor necrosis factor beta, tumor necrosis factor
receptor (TNFR), VLA-4 protein, VCAM-1 protein, vascular
endothelial growth factor (VEGF), urokinase, mos, ras, raf, met,
p53, tat, fos, myc, jun, myb, rel, estrogen receptor, progesterone
receptor, testosterone receptor, aldosterone receptor, LDL
receptor, and corticosterone.
52. The method of claim 42, wherein the at least one non-natural
acid is incorporated at a specific site within the polypeptide.
53. The method of claim 42, wherein the non-natural amino acid is
incorporated using a translation system.
54. The method of claim 42, wherein the non-natural amino acid is
incorporated into the polypeptide using a translation system and a
post translation modification system.
55. The method of claim 42, wherein the polypeptide comprising at
least one non-natural amino acid is stable for at least 1
month.
56. The method of claim 42, wherein the polypeptide comprising at
least one non-natural amino acid is stable for at least 2
weeks.
57. A method for detecting the presence of a polypeptide in a
patient, the method comprising administering an effective amount of
a homologous non-natural amino acid polypeptide comprising at least
one non-natural amino acid selected from the group consisting of:
##STR00130## and detecting an indicator on the polypeptide selected
from the group consisting of a label; a dye; an affinity label; a
photoaffinity label; a spin label; a second protein or polypeptide
or polypeptide analog; a fluorophore; a radioactive moiety; a
moiety incorporating a heavy atom; an isotopically labeled moiety;
a biophysical probe; a phosphorescent group; a chemiluminescent
group; biotin, a biotin analogue; an electron dense group; a
magnetic group; a chromophore; an energy transfer agent; a
detectable label; a radiotransmitter, and any combination of the
above; wherein each R.sub.a is independently selected from the
group consisting of H, halogen, alkyl, --NO.sub.2, --CN,
substituted alkyl, --N(R').sub.2, --C(O).sub.kR',
--C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where k is 1, 2, or
3; M is H or --CH.sub.2R.sub.5; or the M-N--C(R.sub.5) moiety may
form a 4 to 7 membered ring structure; R.sub.1 is H, an amino
protecting group, resin, amino acid, polypeptide, or
polynucleotide; R.sub.2 is OH, an ester protecting group, resin,
amino acid, polypeptide, or polynucleotide; R.sub.5 is L-X, where,
X is a selected from the group consisting of a label; a dye; an
affinity label; a photoaffinity label; a spin label; a second
protein or polypeptide or polypeptide analog; a fluorophore; a
radioactive moiety; a moiety incorporating a heavy atom; an
isotopically labeled moiety; a biophysical probe; a phosphorescent
group; a chemiluminescent group; biotin, a biotin analogue; an
electron dense group; a magnetic group; a chromophore; an energy
transfer agent; a detectable label; a radiotransmitter, and any
combination of the above; and L is optional, and when present is a
linker selected from the group consisting of alkylene, substituted
alkylene, alkenylene, substituted alkenylene, --O--, --O-(alkylene
or substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; or
R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; each R' is independently H, alkyl, or substituted
alkyl; and with a proviso that when R.sub.1 is H then R.sub.2 is
not OH, or when R.sub.2 is OH then R.sub.1 is not H.
58. The method of claim 57, wherein the at least one non-natural
acid is incorporated at a specific site within the polypeptide.
59. The method of claim 57, wherein the non-natural amino acid is
incorporated using a translation system.
60. The method of claim 57, wherein the non-natural amino acid is
incorporated into the polypeptide using a translation system and a
post translation modification system.
61. The method of claim 57, wherein the at least one non-natural
amino acid is stable in aqueous solution for at least 1 month.
62. The method of claim 57, wherein the at least one non-natural
amino acid is stable for at least 2 weeks.
63. The method of claim 57, wherein the at least one non-natural
amino acid is stable for at least 5 days.
64. The method of claim 57, wherein the polypeptide is a protein
homologous to a therapeutic protein selected from the group
consisting of: alpha-1 antitrypsin, angiostatin, antihemolytic
factor, antibody, apolipoprotein, apoprotein, atrial natriuretic
factor, atrial natriuretic polypeptide, atrial peptide, C-X-C
chemokine, T39765, NAP-2, ENA-78, gro-a, gro-b, gro-c, IP-10,
GCP-2, NAP-4, SDF-1, PF4, MIG, calcitonin, c-kit ligand, cytokine,
CC chemokine, monocyte chemoattractant protein-1, monocyte
chemoattractant protein-2, monocyte chemoattractant protein-3,
monocyte inflammatory protein-1 alpha, monocyte inflammatory
protein-i beta, RANTES, 1309, R83915, R91733, HCC1, T58847, D31065,
T64262, CD40, CD40 ligand, c-kit ligand, collagen, colony
stimulating factor (CSF), complement factor 5a, complement
inhibitor, complement receptor 1, cytokine, epithelial neutrophil
activating peptide-78, MIP-16, MCP-1, epidermal growth factor
(EGF), epithelial neutrophil activating peptide, erythropoietin
(EPO), exfoliating toxin, Factor IX, Factor VII, Factor VIII,
Factor X, fibroblast growth factor (FGF), fibrinogen, fibronectin,
four-helical bundle protein, G-CSF, glp-1, GM-CSF,
glucocerebrosidase, gonadotropin, growth factor, growth factor
receptor, grf, hedgehog protein, hemoglobin, hepatocyte growth
factor (hGF), hirudin, human growth hormone (hGH), human serum
albumin, ICAM-1, ICAM-1 receptor, LFA-1, LFA-1 receptor, insulin,
insulin-like growth factor (IGF), IGF-I, IGF-II, interferon (IFN),
IFN-alpha, IFN-beta, IFN-gamma, interleukin (IL), IL-1, IL-2, IL-3,
IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12,
keratinocyte growth factor (KGF), lactoferrin, leukemia inhibitory
factor, luciferase, neurturin, neutrophil inhibitory factor (NIF),
oncostatin M, osteogenic protein, oncogene product, paracitonin,
parathyroid hormone, PD-ECSF, PDGF, peptide hormone, pleiotropin,
protein A, protein G, pth, pyrogenic exotoxin A, pyrogenic exotoxin
B, pyrogenic exotoxin C, pyy, relaxin, renin, SCF, small
biosynthetic protein, soluble complement receptor I, soluble I-CAM
1, soluble interleukin receptor, soluble TNF receptor, somatomedin,
somatostatin, somatotropin, streptokinase, superantigens,
staphylococcal enterotoxin, SEA, SEB, SEC1, SEC2, SEC3, SED, SEE,
steroid hormone receptor, superoxide dismutase, toxic shock
syndrome toxin, thymosin alpha 1, tissue plasminogen activator,
tumor growth factor (TGF), tumor necrosis factor, tumor necrosis
factor alpha, tumor necrosis factor beta, tumor necrosis factor
receptor (TNFR), VLA-4 protein, VCAM-1 protein, vascular
endothelial growth factor (VEGF), urokinase, mos, ras, raf, met,
p53, tat, fos, myc, jun, myb, rel, estrogen receptor, progesterone
receptor, testosterone receptor, aldosterone receptor, LDL
receptor, and corticosterone.
Description
RELATED APPLICATIONS
[0001] This application claims benefit of U.S. Provisional
Application No. 60/743,041 entitled "Compositions Containing,
Methods Involving, and Uses of Non-natural Amino Acids and
Polypeptides" filed Dec. 14, 2005 and U.S. Provisional Application
No. 60/743,040 entitled "Compositions Containing, Methods
Involving, and Uses of Non-natural Amino Acids and Polypeptides"
filed Dec. 14, 2005, both of which are incorporated by
reference.
FIELD OF THE INVENTION
[0002] Described herein are methods and compositions for making and
using non-natural amino acid agents.
BACKGROUND OF THE INVENTION
[0003] The ability to incorporate non-genetically encoded amino
acids (i.e., "non-natural amino acids") into proteins permits the
introduction of chemical functional groups that could provide
valuable alternatives to the naturally-occurring functional groups,
such as the epsilon --NH.sub.2 of lysine, the sulfhydryl --SH of
cysteine, the imino group of histidine, etc. Certain chemical
functional groups are known to be inert to the functional groups
found in the 20 common, genetically-encoded amino acids but react
cleanly and efficiently to form stable linkages with functional
groups that can be incorporated onto non-natural amino acids.
[0004] Methods are now available to selectively introduce chemical
functional groups that are not found in proteins, that are
chemically inert to all of the functional groups found in the 20
common, genetically-encoded amino acids and that may be used to
react efficiently and selectively with reagents comprising certain
functional groups to form stable covalent linkages.
SUMMARY OF THE INVENTION
[0005] Described herein are methods, compositions, techniques and
strategies for making, purifying, characterizing, and using
non-natural amino acids, non-natural amino acid polypeptides and
modified non-natural amino acid polypeptides. In one aspect are
methods, compositions, techniques and strategies for derivatizing a
non-natural amino acid and/or a non-natural amino acid polypeptide.
In one embodiment, such methods, compositions, techniques and
strategies involved chemical derivatization, in other embodiments,
biological derivatization, in other embodiments, physical
derivatization, in other embodiments a combination of
derivatizations. In further or additional embodiments, such
derivatizations are regioselective. In further or additional
embodiments, such derivatizations are regiospecific. In further or
additional embodiments, such derivations are stoichiometric, near
stoichiometric or stoichiometric-like in both the non-natural amino
acid containing reagent and the derivatizing reagent. In further or
additional embodiments are provided methods which allow the
stoichiometric, near stoichiometric or stoichiometric-like
incorporation of a desired group onto a non-natural amino acid
polypeptide. In further or additional embodiments are provided
strategies, reaction mixtures, synthetic conditions which allow the
stoichiometric, near stoichiometric or stoichiometric-like
incorporation of a desired group onto a non-natural amino acid
polypeptide. In further or additional embodiments, such
derivatizations are rapid at ambient temperature. In further or
additional embodiments, such derivatizations occur in aqueous
solutions. In further or additional embodiments, such
derivatizations occur at a pH between about 4 and about 10. In
further or additional embodiments, such derivatizations occur at a
pH between about 4 and about 7. In further or additional
embodiments, such derivatizations occur at a pH between about 4 and
about 5. In further or additional embodiments, such derivatizations
occur at a pH of about 5. In further or additional embodiments,
such derivatizations occur at a pH of about 4.
[0006] In one aspect are non-natural amino acids for the chemical
derivatization of peptides and proteins based upon the reactivity
of an aromatic amine group. In further or additional embodiments,
at least one of the aforementioned non-natural amino acids is
incorporated into a polypeptide, that is, such embodiments are
non-natural amino acid polypeptides. In further or additional
embodiments, the non-natural amino acids are functionalized on
their sidechains such that their reaction with a derivatizing
molecule generates an amine linkage. In further or additional
embodiments, the non-natural amino acids are selected from amino
acids having aromatic amine sidechains. In further or additional
embodiments, the non-natural amino acids comprise a masked
sidechain, including a masked aromatic amine group.
[0007] In further or additional embodiments, the non-natural amino
acids comprise aromatic amine sidechains where the aromatic amine
is selected from an aryl amine or a heteroaryl amine. In a further
or additional embodiment, the non-natural amino acids resemble a
natural amino acid in structure but contain aromatic amine groups.
In another or further embodiment the non-natural amino acids
resemble phenylalanine or tyrosine (aromatic amino acids). In one
embodiment, the non-natural amino acids have properties that are
distinct from those of the natural amino acids. In one embodiment,
such distinct properties are the chemical reactivity of the
sidechain; in a further embodiment this distinct chemical
reactivity permits the sidechain of the non-natural amino acid to
undergo a reaction while being a unit of a polypeptide even though
the sidechains of the naturally-occurring amino acid units in the
same polypeptide do not undergo the aforementioned reaction. In a
further embodiment, the sidechain of the non-natural amino acid has
a chemistry orthogonal to those of the naturally-occurring amino
acids. In a further embodiment, the sidechain of the non-natural
amino acid comprises a nucleophile-containing moiety; in a further
embodiment, the nucleophile-containing moiety on the sidechain of
the non-natural amino acid can undergo a reaction to generate an
amine derivatized protein. In a further embodiment, the sidechain
of the non-natural amino acid comprises an electrophile-containing
moiety; in a further embodiment, the electrophile-containing moiety
on the sidechain of the non-natural amino acid can undergo
nucleophilic attack to generate an amine derivatized protein. In
any of the aforementioned embodiments in this paragraph, the
non-natural amino acid may exist as a separate molecule or may be
incorporated into a polypeptide of any length; if the latter, then
the polypeptide may further incorporate naturally-occurring or
non-natural amino acids.
[0008] In another aspect are carbonyl-substituted molecules such
as, by way of example, aldehydes, and ketones, for the production
of derivatized non-natural amino acid polypeptides based upon an
amine linkage. In a further embodiment are aldehyde-substituted
molecules used to derivatize aromatic amine-containing non-natural
amino acid polypeptides via the formation of an amine linkage
between the derivatizing molecule and the aromatic amine-containing
non-natural amino acid polypeptide. In further or additional
embodiments, the aldehyde-substituted molecules comprise a group
selected from: a label; a dye; a polymer; a water-soluble polymer;
a derivative of polyethylene glycol; a photocrosslinker; a
cytotoxic compound; a drug; an affinity label; a photoaffinity
label; a reactive compound; a resin; a second protein or
polypeptide or polypeptide analog; an antibody or antibody
fragment; a metal chelator; a cofactor; a fatty acid; a
carbohydrate; a polynucleotide; a DNA; a RNA; an antisense
polynucleotide; a saccharide, a water-soluble dendrimer, a
cyclodextrin, a biomaterial; a nanoparticle; a spin label; a
fluorophore, a metal-containing moiety; a radioactive moiety; a
novel functional group; a group that covalently or noncovalently
interacts with other molecules; a photocaged moiety; an actinic
radiation excitable moiety; a ligand; a photoisomerizable moiety;
biotin; a biotin analogue; a moiety incorporating a heavy atom; a
chemically cleavable group; a photocleavable group; an elongated
side chain; a carbon-linked sugar; a redox-active agent; an amino
thioacid; a toxic moiety; an isotopically labeled moiety; a
biophysical probe; a phosphorescent group; a chemiluminescent
group; an electron dense group; a magnetic group; an intercalating
group; a chromophore; an energy transfer agent; a biologically
active agent; a detectable label; a small molecule; an inhibitory
ribonucleic acid; a radionucleotide; a neutron-capture agent; a
derivative of biotin; quantum dot(s); a nanotransmitter; a
radiotransmitter, an abzyme, an activated complex activator, a
virus, an adjuvant, an aglycan, an allergan, an angiostatin, an
antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a
shuttle vector, a macromolecule, a mimotope, a receptor, a reverse
micelle, and any combination thereof. In further or additional
embodiments, the aldehyde-substituted molecules are
aldehyde-substituted polyethylene glycol (PEG) molecules. In a
further embodiment, the sidechain of the non-natural amino acid has
a chemistry orthogonal to those of the naturally-occurring amino
acids that allows the non-natural amino acid to react selectively
with the aldehyde-substituted molecules. In a further embodiment,
the sidechain of the non-natural amino acid comprises an aromatic
amine-containing moiety that reacts selectively with the
aldehyde-containing molecule; in a further embodiment, the aromatic
amine-containing moiety on the sidechain of the non-natural amino
acid can undergo reaction to generate an alkylated
amine-derivatized protein. In a further aspect related to the
embodiments described in this paragraph are the modified
non-natural amino acid polypeptides that result from the reaction
of the derivatizing molecule with the non-natural amino acid
polypeptides. Further embodiments include any further modifications
of the already modified non-natural amino acid polypeptides.
[0009] In another aspect are aromatic amine-substituted molecules
such as, by way of example, aryl amines and heteroaryl amines, for
the production of derivatized non-natural amino acid polypeptides
based upon an amine linkage. In a further embodiment are aromatic
amine-substituted molecules used to derivatize aldehyde-containing
non-natural amino acid polypeptides via the formation of an amine
linkage between the derivatizing molecule and the
aldehyde-containing non-natural amino acid polypeptide. In further
or additional embodiments, the aromatic amine-substituted molecules
comprise a group selected from: a label; a dye; a polymer; a
water-soluble polymer; a derivative of polyethylene glycol; a
photocrosslinker; a cytotoxic compound; a drug; an affinity label;
a photoaffinity label; a reactive compound; a resin; a second
protein or polypeptide or polypeptide analog; an antibody or
antibody fragment; a metal chelator; a cofactor; a fatty acid; a
carbohydrate; a polynucleotide; a DNA; a RNA; an antisense
polynucleotide; a saccharide, a water-soluble dendrimer, a
cyclodextrin, a biomaterial; a nanoparticle; a spin label; a
fluorophore, a metal-containing moiety; a radioactive moiety; a
novel functional group; a group that covalently or noncovalently
interacts with other molecules; a photocaged moiety; an actinic
radiation excitable moiety; a ligand; a photoisomerizable moiety;
biotin; a biotin analogue; a moiety incorporating a heavy atom; a
chemically cleavable group; a photocleavable group; an elongated
side chain; a carbon-linked sugar; a redox-active agent; an amino
thioacid; a toxic moiety; an isotopically labeled moiety; a
biophysical probe; a phosphorescent group; a chemiluminescent
group; an electron dense group; a magnetic group; an intercalating
group; a chromophore; an energy transfer agent; a biologically
active agent; a detectable label; a small molecule; an inhibitory
ribonucleic acid; a radionucleotide; a neutron-capture agent; a
derivative of biotin; quantum dot(s); a nanotransmitter; a
radiotransmitter; an abzyme, an activated complex activator, a
virus, an adjuvant, an aglycan, an allergan, an angiostatin, an
antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a
shuttle vector, a macromolecule, a mimotope, a receptor, a reverse
micelle, and any combination thereof. In further or additional
embodiments, the aromatic amine-substituted molecules are aromatic
amine-substituted polyethylene glycol (PEG) molecules. In a further
embodiment, the sidechain of the non-natural amino acid has a
chemistry orthogonal to those of the naturally-occurring amino
acids that allows the non-natural amino acid to react selectively
with the aromatic amine-substituted molecules. In a further
embodiment, the sidechain of the non-natural amino acid comprises
an aldehyde-containing moiety that reacts selectively with the
aromatic amine-containing molecule; in a further embodiment, the
aldehyde-containing moiety on the sidechain of the non-natural
amino acid can undergo reaction to generate an alkylated
amine-derivatized protein. In a further aspect related to the
embodiments described in this paragraph are the modified
non-natural amino acid polypeptides that result from the reaction
of the derivatizing molecule with the non-natural amino acid
polypeptides. Further embodiments include any further modifications
of the already modified non-natural amino acid polypeptides.
[0010] In another aspect are mono-, bi- and multi-functional
linkers for the generation of derivatized non-natural amino acid
polypeptides based upon an amine linkage. In one embodiment are
molecular linkers (bi- and multi-functional) that can be used to
connect aromatic amine-containing non-natural amino acid
polypeptides to other molecules. In another embodiment the aromatic
amine-containing non-natural amino acid polypeptides comprise an
aryl amine or a heteroaryl amine sidechain. In an embodiment
utilizing an aromatic amine-containing non-natural amino acid
polypeptide, the molecular linker contains an aldehyde group at one
of its termini. In further or additional embodiments, the
aldehyde-substituted linker molecules are aldehyde-substituted
polyethylene glycol (PEG) linker molecules. In further embodiments,
the phrase "other molecules" includes, by way of example only,
proteins, other polymers and small molecules. In further or
additional embodiments, the aldehyde-containing molecular linkers
comprise the same or equivalent groups on all termini so that upon
reaction with an aromatic amine-containing non-natural amino acid
polypeptide, the resulting product is the homo-multimerization of
the aromatic amine-containing non-natural amino acid polypeptide.
In further embodiments, the homo-multimerization is a
homo-dimerization. In further or additional embodiments, the
molecular linkers comprise at least one aldehyde group and a
different group on all termini so that upon reaction with an
aromatic amine-containing non-natural amino acid polypeptide, the
resulting product is the hetero-multimerization of the aromatic
amine-containing non-natural amino acid polypeptide. In further
embodiments, the hetero-multimerization is a hetero-dimerization.
In a further embodiment, the sidechain of the non-natural amino
acid has a chemistry orthogonal to those of the naturally-occurring
amino acids that allows the non-natural amino acid to react
selectively with the aldehyde-substituted linker molecules. In a
further aspect related to the embodiments described in this
paragraph are the linked modified or unmodified non-natural amino
acid polypeptides that result from the reaction of the linker
molecule with the non-natural amino acid polypeptides. Further
embodiments include any further modifications of the already linked
modified or unmodified non-natural amino acid polypeptides.
[0011] In one aspect are methods to derivatize proteins via the
reaction of aromatic amines and aldehyde reactants to alkylated
amine-derivatized protein. Included within this aspect are methods
for the derivatization of proteins based upon the reductive
alkylation of aromatic amine- and aldehyde-containing reactants to
generate alkylated amine-derivatized protein adduct. In additional
or further embodiments are methods to derivatize aromatic
amine-containing proteins with aldehyde-functionalized polyethylene
glycol (PEG) molecules. In yet additional or further aspects, the
aldehyde-substituted molecule can include proteins, other polymers
(non-branched and branched), and small molecules.
[0012] In another aspect are methods for the chemical synthesis of
aldehyde-substituted molecules for the derivatization of aromatic
amine-substituted proteins. In one embodiment, the
aldehyde-substituted molecule can comprise peptides, other polymers
(non-branched and branched) and small molecules. In one embodiment
are methods for the preparation of aldehyde-substituted molecules
suitable for the derivatization of aromatic amine-containing
non-natural amino acid polypeptides. In a further or additional
embodiment, the non-natural amino acids, including, but not limited
to, aromatic amine-containing non natural amino acids, are
incorporated site-specifically during the in vivo translation of
proteins. In further or alternative embodiments, the non-natural
amino acids, including, but not limited to, aromatic
amine-containing non natural amino acids, are incorporated
site-specifically by ribosomal translation. In further or
alternative embodiments, the non-natural amino acids, including,
but not limited to, aromatic amine-containing non natural amino
acids, are incorporated site-specifically during the in vitro
translation. In a further or additional embodiment, the
aldehyde-substituted molecules allow for the site-specific
derivatization of aromatic amine-containing non-natural amino acids
via reductive alkylation of the aromatic amine moiety to form an
alkylated amine-derivatized polypeptide in a site-specific fashion.
In a further or additional embodiment, the method for the
preparation of aldehyde-substituted molecules provides access to a
wide variety of site-specifically derivatized polypeptides. In a
further or additional embodiment are methods for synthesizing
aldehyde-functionalized polyethylene glycol (PEG) molecules.
[0013] In another aspect are methods for the chemical
derivatization of aromatic amine-substituted non-natural amino acid
polypeptides using an aldehyde-containing bi-functional linker. In
one embodiment are methods for attaching an aldehyde-substituted
linker to an aromatic amine-substituted protein via a reductive
alkylation reaction to generate an amine linkage. In further or
additional embodiments, the aromatic amine-substituted non-natural
amino acid is an aryl amine or a heteroaryl amine-substituted
non-natural amino acid. In further or additional embodiments, the
non-natural amino acid polypeptides are derivatized
site-specifically and/or with precise control of three-dimensional
structure, using an aldehyde-containing bi-functional linker. In
one embodiment, such methods are used to attach molecular linkers
(mono- bi- and multi-functional) to aromatic amine-containing
non-natural amino acid polypeptides, wherein at least one of the
linker termini contains an aldehyde group which can link to the
aromatic amine-containing non-natural amino acid polypeptides via
an amine linkage. In a further or additional embodiment, these
linkers are used to connect the aromatic amine-containing
non-natural amino acid polypeptides to other molecules, including
by way of example, proteins, other polymers (branched and
non-branched) and small molecules.
[0014] In some embodiments, the non-natural amino acid polypeptide
is linked to a water soluble polymer. In some embodiments, the
water soluble polymer comprises a polyethylene glycol moiety. In
some embodiments, the poly(ethylene glycol) molecule is a
bifunctional polymer. In some embodiments, the bifunctional polymer
is linked to a second polypeptide. In some embodiments, the second
polypeptide is identical to the first polypeptide, in other
embodiments; the second polypeptide is a different polypeptide. In
some embodiments, the non-natural amino acid polypeptide comprises
at least two amino acids linked to a water soluble polymer
comprising a polyethylene glycol moiety.
[0015] In some embodiments, the non-natural amino acid polypeptide
comprises a substitution, addition or deletion that increases
affinity of the non-natural amino acid polypeptide for a receptor.
In some embodiments, the non-natural amino acid polypeptide
comprises a substitution, addition, or deletion that increases the
stability of the non-natural amino acid polypeptide. In some
embodiments, the non-natural amino acid polypeptide comprises a
substitution, addition, or deletion that increases the aqueous
solubility of the non-natural amino acid polypeptide. In some
embodiments, the non-natural amino acid polypeptide comprises a
substitution, addition, or deletion that increases the solubility
of the non-natural amino acid polypeptide produced in a host cell.
In some embodiments, the non-natural amino acid polypeptide
comprises a substitution, addition, or deletion that modulates
protease resistance, serum half-life, immunogenicity, and/or
expression relative to the amino-acid polypeptide without the
substitution, addition or deletion.
[0016] In some embodiments, the non-natural amino acid polypeptide
is an agonist, partial agonist, antagonist, partial antagonist, or
inverse agonist. In some embodiments, the agonist, partial agonist,
antagonist, partial antagonist, or inverse agonist comprises a
non-natural amino acid linked to a water soluble polymer. In some
embodiments, the water polymer comprises a polyethylene glycol
moiety. In some embodiments, the polypeptide comprising a
non-natural amino acid linked to a water soluble polymer, for
example, may prevent dimerization of the corresponding receptor. In
some embodiments, the polypeptide comprising a non-natural amino
acid linked to a water soluble polymer modulates binding of the
polypeptide to a binding partner, ligand or receptor. In some
embodiments, the polypeptide comprising a non-natural amino acid
linked to a water soluble polymer modulates one or more properties
or activities of the polypeptide.
[0017] In some embodiments, the selector codon is selected from the
group consisting of an amber codon, ochre codon, opal codon, a
unique codon, a rare codon, an unnatural codon, a five-base codon,
and a four-base codon.
[0018] In further or additional embodiments, the non-natural
aromatic amine amino acid polypeptides and/or modified non-natural
aromatic amine amino acid polypeptides described herein have at
least one of the following characteristics: (1) the amine moiety of
the aromatic amine is a primary amine; (2) the amine moiety of the
aromatic amine is a secondary amine; (3) the aromatic moiety of the
aromatic amine is a heteroaromatic moiety; (4) the aromatic moiety
of the aromatic amine is an aryl moiety; (5) the aromatic amine
reacts with aldehyde functionalized groups; (6) is coupled to a
water soluble polymer; (7) is PEGylated; (8) has increased
therapeutic half-life relative to the corresponding polypeptide
without the non-natural aromatic amine amino acid; (9) has
increased serum half-life relative to the corresponding polypeptide
without the non-natural aromatic amine amino acid; (10) has
increased circulation time relative to the corresponding
polypeptide without the non-natural aromatic amine amino acid; (11)
has increased water solubility relative to the corresponding
polypeptide without the non-natural aromatic amine amino acid; (12)
has enhanced bioavailability relative to the corresponding
polypeptide without the non-natural aromatic amine amino acid; (13)
has modulated immunogenicity relative to the corresponding
polypeptide without the non-natural aromatic amine amino acid; (14)
has modulated biological activity relative to the corresponding
polypeptide without the non-natural aromatic amine amino acid; (15)
is part of a pharmaceutical composition; (16) is obtained from cell
culture; (17) is chemically synthesized; (18) is used in library
screening methods; (19) is used with arrays; (20) is used with
protein arrays; (21) is used for gene expression analysis; (22) is
coupled to at least one agent; (23) is coupled to a label; (24) is
coupled to a dye; (25) is coupled to a polymer; (26) is coupled to
a cytotoxic compound; (27) is coupled to a drug; (28) is coupled to
a second protein or polypeptide or polypeptide analog; (29) is
coupled to an antibody or antibody fragment; (30) is coupled to a
carbohydrate; (31) is coupled to a polynucleotide; (32) is coupled
to an antisense polynucleotide; (33) is coupled to a saccharide,
(34) is coupled to a fluorophore, (35) is coupled to a chemically
cleavable group; (36) is coupled to a photocleavable group; (37) is
coupled to an energy transfer agent; (38) is coupled to a
radionucleotide; (39) may be post-translationally modified; (40)
may be post-translationally modified by reductive alkylation; (41)
may be post-translationally modified by reductive alkylation in a
pH range between about 4 to about 10; (42) may be site-specifically
derivatized by post-translational reductive alkylation; (43) may be
rapidly post-translationally modified by reductive alkylation at
room temperature, (44) may be post-translationally modified by
reductive alkylation in aqueous conditions; (45) may be
post-translationally modified by reductive alkylation with
stoichiometric reaction conditions; (46) may be
post-translationally modified by reductive alkylation with
near-stoichiometric reaction conditions; (47) may be
post-translationally modified by reductive alkylation with
stoichiometric-like reaction conditions; (48) is used to treat a
mammal suffering from a disease, disorder or condition; (49) is
used to treat a human suffering from a disease, disorder or
condition; (50) is used to diagnose a mammal suffering from a
disease, disorder or condition; (51) is used to diagnose a human
suffering from a disease, disorder or condition; (52) is part of a
sustained-release compositions; (53) the amine moiety is formed by
post-translational reduction of a masked amine moiety; (54) the
amine moiety is formed by post-translational reduction of an imine
moiety; (55) the amine moiety is formed by post-translational
reduction of an azide moiety; (56) the amine moiety is formed by
post-translational reduction of a hydrazine moiety; (57) the amine
moiety is formed by post-translational reduction of a nitro moiety,
(58) is coupled to a pro-drug; (59) is obtained from cell lysate;
(60) is ribosomally translated; (61) may be post-translationally
modified by reductive alkylation in a pH range between about 4 to
about 7; (62) may be post-translationally modified by reductive
alkylation in a pH range between about 4 to about 5; (63) may be
post-translationally modified by reductive alkylation at a pH of
about 5; (64) may be post-translationally modified by reductive
alkylation at a pH of about 4; (65) reacts rapidly in reductive
alkylation reactions; (66) reacts in less than about 10 hours in
reductive alkylation reactions; (67) reacts in less than about 8
hours in reductive alkylation reactions; (68) reacts in less than
about 6 hours in reductive alkylation reactions; (68) reacts in
less than about 4 hours in reductive alkylation reactions; (69)
reacts in less than about 2 hours in reductive alkylation
reactions; (70) reacts in less than about 1 hour in reductive
alkylation reactions, or (71) reacts in less than about 30 minutes
in reductive alkylation reactions.
[0019] In further or alternative embodiments the non-natural
aromatic amine amino acid polypeptides and/or modified non-natural
aromatic amine amino acid polypeptides described herein have at
least two of the aforementioned characteristics. In further or
alternative embodiments the non-natural aromatic amine amino acid
polypeptides and/or modified non-natural aromatic amine amino acid
polypeptides described herein have at least three of the
aforementioned characteristics. In further or alternative
embodiments the non-natural aromatic amine amino acid polypeptides
and/or modified non-natural aromatic amine amino acid polypeptides
described herein have at least four of the aforementioned
characteristics. In further or alternative embodiments the
non-natural aromatic amine amino acid polypeptides and/or modified
non-natural aromatic amine amino acid polypeptides described herein
have at least five of the aforementioned characteristics.
[0020] In further or additional embodiments, the non-natural
aldehyde-based amino acid polypeptides and/or modified non-natural
aldehyde-based amino acid polypeptides described herein have at
least one of the following characteristics: (1) contains a
protected or masked aldehyde moiety; (2) contains a deprotected or
unmasked aldehyde moiety (3) contains a deprotected or unmasked
aldehyde moiety which can react with an aromatic amine; (4)
contains a deprotected or unmasked aldehyde moiety which can react
with a heteroaromatic amine; (5) contains a deprotected or unmasked
aldehyde moiety which can react with an aromatic amine or a
heteroaromatic amine by reductive amination; (6) is coupled to a
water soluble polymer; (7) is PEGylated; (8) has increased
therapeutic half-life relative to the corresponding polypeptide
without the non-natural aldehyde-based amino acid; (9) has
increased serum half-life relative to the corresponding polypeptide
without the non-natural aldehyde-based amino acid; (10) has
increased circulation time relative to the corresponding
polypeptide without the non-natural aldehyde-based amino acid; (11)
has increased water solubility relative to the corresponding
polypeptide without the non-natural aldehyde-based amino acid; (12)
has enhanced bioavailability relative to the corresponding
polypeptide without the non-natural aldehyde-based amino acid; (13)
has modulated immunogenicity relative to the corresponding
polypeptide without the non-natural aldehyde-based amino acid; (14)
has modulated biological activity relative to the corresponding
polypeptide without the non-natural aldehyde-based amino acid; (15)
is part of a pharmaceutical composition; (16) is obtained from cell
culture; (17) is chemically synthesized; (18) is used in library
screening methods; (19) is used with arrays; (20) is used with
protein arrays; (21) is used for gene expression analysis; (22) can
be coupled to an agent via reductive amination; (23) is coupled to
a label; (24) is coupled to a dye; (25) is coupled to a polymer;
(26) is coupled to a cytotoxic compound; (27) is coupled to a drug;
(28) is coupled to a second protein or polypeptide or polypeptide
analog; (29) is coupled to an antibody or antibody fragment; (30)
is coupled to a carbohydrate; (31) is coupled to a polynucleotide;
(32) is coupled to an antisense polynucleotide; (33) is coupled to
a saccharide, (34) is coupled to a fluorophore, (35) is coupled to
a chemically cleavable group; (36) is coupled to a photocleavable
group; (37) is coupled to an energy transfer agent; (38) is coupled
to a radionucleotide; (39) may be post translationally modified;
(40) may be post-translationally modified by reductive amination;
(41) may be post-translationally modified by reductive amination in
a pH range between about 4 to about 10; (42) may be
site-specifically derivatized by post-translation reductive
amination; (43) may be rapidly post-translationally modified by
reductive amination at room temperature, (44) may be
post-translationally modified by reductive amination in aqueous
conditions; (45) may be post-translationally modified by reductive
amination with stoichiometric reaction conditions; (46) may be
post-translationally modified by reductive amination with
near-stoichiometric reaction conditions; (47) may be
post-translationally modified by reductive amination with
stoichiometric-like reaction conditions; (48) is used treat a
mammal suffering from a disease, disorder or condition; (49) is
used treat a human suffering from a disease, disorder or condition;
(50) is used diagnose a mammal suffering from a disease, disorder
or condition; (51) is used diagnose a human suffering from a
disease, disorder or condition; (52) is part of a sustained-release
compositions; (53) is coupled to a pro-drug; (54) is obtained from
cell lysate; (55) is ribosomally translated; (56) may be
post-translationally modified by reductive amination in a pH range
between about 4 to about 7; (57) may be post-translationally
modified by reductive amination in a pH range between about 4 to
about 5; (58) may be post-translationally modified by reductive
amination at a pH of about 5; (59) may be post-translationally
modified by reductive amination at a pH of about 4; (60) reacts
rapidly in reductive amination reactions; (61) reacts in less than
about 10 hours in reductive amination reactions; (62) reacts in
less than about 8 hours in reductive amination reactions; (63)
reacts in less than about 6 hours in reductive amination reactions;
(68) reacts in less than about 4 hours in reductive amination
reactions; (64) reacts in less than about 2 hours in reductive
amination reactions; (65) reacts in less than about 1 hour in
reductive amination reactions, or (66) reacts in less than about 30
minutes in reductive amination reactions.
[0021] In further or alternative embodiments the non-natural
aldehyde-based amino acid polypeptides and/or modified non-natural
aldehyde-based amino acid polypeptides described herein have at
least two of the aforementioned characteristics: In further or
alternative embodiments the non-natural aldehyde-based amino acid
polypeptides and modified non-natural aldehyde-based amino acid
polypeptides described herein have at least three of the
aforementioned characteristics. In further or alternative
embodiments the non-natural aldehyde-based amino acid polypeptides
and/or modified non-natural aldehyde-based amino acid polypeptides
described herein have at least four of the aforementioned
characteristics. In further or alternative embodiments the
non-natural aldehyde-based amino acid polypeptides and/or modified
non-natural aldehyde-based amino acid polypeptides described herein
have at least five of the aforementioned characteristics.
[0022] Also described herein are methods of making a non-natural
amino acid polypeptide linked to a water soluble polymer. In some
embodiments, the method comprises contacting an isolated
polypeptide comprising a non-natural amino acid with a water
soluble polymer comprising a moiety that reacts with the
non-natural amino acid. In some embodiments, the non-natural amino
acid incorporated into is reactive toward a water soluble polymer
that is otherwise unreactive toward any of the 20 common amino
acids. In some embodiments, the water polymer comprises a
polyethylene glycol moiety. The molecular weight of the polymer may
be of a wide range, including but not limited to, between about 100
Da and about 100,000 Da or more. The molecular weight of the
polymer may be between about 100 Da and about 100,000 Da, including
but not limited to, 100,000 Da, 95,000 Da, 90,000 Da, 85,000 Da,
80,000 Da, 75,000 Da, 70,000 Da, 65,000 Da, 60,000 Da, 55,000 Da,
50,000 Da, 45,000 Da, 40,000 Da, 35,000 Da, 30,000 Da, 25,000. Da,
20,000 Da, 15,000 Da, 10,000 Da, 9,000 Da, 8,000 Da, 7,000 Da,
6,000 Da, 5,000 Da, 4,000 Da, 3,000 Da, 2,000 Da, 1,000 Da, 900 Da,
800 Da, 700 Da, 600 Da, 500 Da, 400 Da, 300 Da, 200 Da, and 100 Da.
In some embodiments, the molecular weight of the polymer is between
about 100 Da and about 50,000 Da. In some embodiments, the
molecular weight of the polymer is between about 100 Da and about
40,000 Da. In some embodiments, the molecular weight of the polymer
is between about 1,000 Da and about 40,000 Da. In some embodiments,
the molecular weight of the polymer is between about 5,000 Da and
about 40,000 Da. In some embodiments, the molecular weight of the
polymer is between about 10,000 Da and about 40,000 Da. In some
embodiments, the polyethylene glycol molecule is a branched
polymer. The molecular weight of the branched chain PEG may be
between about 1,000 Da and about 100,000 Da, including but not
limited to, 100,000 Da, 95,000 Da, 90,000 Da, 85,000 Da, 80,000 Da,
75,000 Da, 70,000 Da, 65,000 Da, 60,000 Da, 55,000 Da, 50,000 Da,
45,000 Da, 40,000 Da, 35,000 Da, 30,000 Da, 25,000 Da, 20,000 Da,
15,000 Da, 10,000 Da, 9,000 Da, 8,000 Da, 7,000 Da, 6,000 Da, 5,000
Da, 4,000 Da, 3,000 Da, 2,000 Da, and 1,000 Da. In some
embodiments, the molecular weight of the branched chain PEG is
between about 1,000 Da and about 50,000 Da. In some embodiments,
the molecular weight of the branched chain PEG is between about
1,000 Da and about 40,000 Da. In some embodiments, the molecular
weight of the branched chain PEG is between about 5,000 Da and
about 40,000 Da. In some embodiments, the molecular weight of the
branched chain PEG is between about 5,000 Da and about 20,000
Da.
[0023] Also described herein are compositions comprising a
polypeptide comprising at least one of the non-natural amino acids
described herein and a pharmaceutically acceptable carrier. In some
embodiments, the non-natural amino acid is linked to a water
soluble polymer. Also described herein are pharmaceutical
compositions comprising a pharmaceutically acceptable carrier and a
polypeptide, wherein at least one amino acid is substituted by a
non-natural amino acid. In some embodiments, the non-natural amino
acid comprises a saccharide moiety. In some embodiments, the water
soluble polymer is linked to the polypeptide via a saccharide
moiety.
[0024] Also described herein are cells comprising a polynucleotide
encoding the polypeptide comprising a selector codon. In some
embodiments, the cells comprise an orthogonal RNA synthetase and/or
an orthogonal tRNA for substituting a non-natural amino acid into
the polypeptide. In some embodiments the cells are in a cell
culture, whereas in other embodiments the cells of part of a
multicellular organism, including amphibians, reptiles, birds, and
mammals. In any of the cell embodiments, further embodiments
include expression of the polynucleotide to produce the non-natural
amino acid polypeptide. In some embodiments, the non-natural amino
acid polypeptide is produced in vitro. In some embodiments, the
non-natural amino acid polypeptide is produced in cell lysate. In
some embodiments, the non-natural amino acid polypeptide is
produced by ribosomal translation.
[0025] Also described herein are methods of making a polypeptide
comprising a non-natural amino acid. In some embodiments, the
methods comprise culturing cells comprising a polynucleotide or
polynucleotides encoding a polypeptide, an orthogonal RNA
synthetase and/or an orthogonal tRNA under conditions to permit
expression of the polypeptide; and purifying the polypeptide from
the cells and/or culture medium.
[0026] Also described herein are libraries of the non-natural amino
acids described herein or libraries of the non-natural amino acid
polypeptides described herein, or libraries of the modified
non-natural amino acid polypeptides described herein, or
combination libraries thereof. Also described herein are arrays
containing at least one non-natural amino acid, at least one
non-natural amino acid polypeptide, and/or at least one modified
non-natural amino acid. Also described herein are arrays containing
at least one polynucleotide encoding a polypeptide comprising a
selector codon. The arrays described herein may be used to screen
for the production of the non-natural amino acid polypeptides in an
organism (either by detecting transcription of the polynucleotide
encoding the polypeptide or by detecting the translation of the
polypeptide).
[0027] Also described herein are methods for screening libraries
described herein for a desired activity, or for using the arrays
described herein to screen the libraries described herein, or for
other libraries of compounds and/or polypeptides and/or
polynucleotides for a desired activity. Also described herein is
the use of such activity data from library screening to develop and
discover new therapeutic agents, as well as the therapeutic agents
themselves.
[0028] Also described herein are methods of increasing therapeutic
half-life, serum half-life or circulation time of a polypeptide. In
some embodiments, the methods comprise substituting at least one
non-natural amino acid for any one or more amino acids in a
naturally occurring polypeptide and/or linking the polypeptide to a
water soluble polymer.
[0029] Also described herein are methods of treating a patient, in
need of such treatment, with an effective amount of a
pharmaceutical composition which comprises a polypeptide comprising
a non-natural amino acid and a pharmaceutically acceptable carrier.
In some embodiments, the non-natural amino acid is linked to a
water soluble polymer.
[0030] It is to be understood that the methods and compositions
described herein are not limited to the particular methodology,
protocols, cell lines, constructs, and reagents described herein
and as such may vary. It is also to be understood that the
terminology used herein is for the purpose of describing particular
embodiments only, and is not intended to limit the scope of the
methods and compositions described herein, which will be limited
only by the appended claims.
[0031] As used herein and in the appended claims, the singular
forms "a," "an," and "the" include plural reference unless the
context clearly indicates otherwise.
[0032] Unless defined otherwise, all technical and scientific terms
used herein have the same meaning as commonly understood to one of
ordinary skill in the art to which the inventions described herein
belong. Although any methods, devices, and materials similar or
equivalent to those described herein can be used in the practice or
testing of the inventions described herein, the preferred methods,
devices and materials are now described.
[0033] All publications and patents mentioned herein are
incorporated herein by reference in their entirety for the purpose
of describing and disclosing, for example, the constructs and
methodologies that are described in the publications, which might
be used in connection with the presently described inventions. The
publications discussed herein are provided solely for their
disclosure prior to the filing date of the present application.
Nothing herein is to be construed as an admission that the
inventors described herein are not entitled to antedate such
disclosure by virtue of prior invention or for any other
reason.
[0034] The term "affinity label," as used herein, refers to a label
which reversibly or irreversibly binds another molecule, either to
modify it, destroy it, or form a compound with it. By way of
example, affinity labels include enzymes and their substrates, or
antibodies and their antigens.
[0035] The terms "alkoxy," "alkylamino" and "alkylthio" are used in
their conventional sense, and refer to alkyl groups linked to
molecules via an oxygen atom, an amino group, a sulfur atom,
respectively.
[0036] The term "alkyl," by itself or as part of another molecule,
means, unless otherwise stated, a straight or branched chain, or
cyclic hydrocarbon radical, or combination thereof, which may be
fully saturated, mono- or polyunsaturated and can include di- and
multivalent radicals, having the number of carbon atoms designated
(i.e. C.sub.1-C.sub.10 means one to ten carbons). Examples of
saturated hydrocarbon radicals include, but are not limited to,
groups such as methyl, ethyl, n-propyl, isopropyl, n-butyl,
t-butyl, isobutyl, sec-butyl, cyclohexyl, (cyclohexyl)methyl,
cyclopropylmethyl, homologs and isomers of, for example, n-pentyl,
n-hexyl, n-heptyl, n-octyl, and the like. An unsaturated alkyl
group is one having one or more double bonds or triple bonds.
Examples of unsaturated alkyl groups include, but are not limited
to, vinyl, 2-propenyl, crotyl, 2-isopentenyl, 2-(butadienyl),
2,4-pentadienyl, 3-(1,4-pentadienyl), ethynyl, 1- and 3-propynyl,
3-butynyl, and the higher homologs and isomers. The term "alkyl,"
unless otherwise noted, is also meant to include those derivatives
of alkyl defined in more detail below, such as "heteroalkyl",
"haloalkyl" and "homoalkyl".
[0037] The term "alkylene" by itself or as part of another molecule
means a divalent radical derived from an alkane, as exemplified by
(--CH.sub.2--).sub.n, wherein n may be 1 to about 24. By way of
example only, such groups include, but are not limited to, groups
having 10 or fewer carbon atoms such as the structures
--CH.sub.2CH.sub.2-- and CH.sub.2CH.sub.2CH.sub.2CH.sub.2--. A
"lower alkyl" or "lower alkylene" is a shorter chain alkyl or
alkylene group, generally having eight or fewer carbon atoms. The
term "alkylene," unless otherwise noted, is also meant to include
those groups described below as "heteroalkylene."
[0038] The term "amino acid" refers to naturally occurring and
non-natural amino acids, as well as amino acid analogs and amino
acid mimetics that function in a manner similar to the naturally
occurring amino acids. Naturally encoded amino acids are the 20
common amino acids (alanine, arginine, asparagine, aspartic acid,
cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine,
leucine, lysine, methionine, phenylalanine, proline, serine,
threonine, tryptophan, tyrosine, and valine) and pyrrolysine and
selenocysteine. Amino acid analogs refers to compounds that have
the same basic chemical structure as a naturally occurring amino
acid, by way of example, an at carbon that is bound to a hydrogen,
a carboxyl group, an amino group, and an R group. Such analogs may
have modified R groups (by way of example, norleucine) or may have
modified peptide backbones, while still retaining the same basic
chemical structure as a naturally occurring amino acid.
Non-limiting examples of amino acid analogs include homoserine,
norleucine, methionine sulfoxide, methionine methyl sulfonium.
[0039] Amino acids may be referred to herein by either their name,
their commonly known three letter symbols or by the one-letter
symbols recommended by the IUPAC-IUB Biochemical Nomenclature
Commission. Additionally, nucleotides, may be referred to by their
commonly accepted single-letter codes.
[0040] An "amino terminus modification group" refers to any
molecule that can be attached to a terminal amine group. By way of
example, such terminal amine groups may be at the end of polymeric
molecules, wherein such polymeric molecules include, but are not
limited to, polypeptides, polynucleotides, and polysaccharides.
Terminus modification groups include but are not limited to,
various water soluble polymers, peptides or proteins. By way of
example only, terminus modification groups include polyethylene
glycol or serum albumin. Terminus modification groups may be used
to modify therapeutic characteristics of the polymeric molecule,
including but not limited to increasing the serum half-life of
peptides.
[0041] By "antibody fragment" is meant any form of an antibody
other than the full-length form. Antibody fragments herein include
antibodies that are smaller components that exist within
full-length antibodies, and antibodies that have been engineered.
Antibody fragments include but are not limited to Fv, Fc, Fab, and
(Fab').sub.2, single chain Fv (scFv), diabodies, triabodies,
tetrabodies, bifunctional hybrid antibodies, CDR1, CDR2, CDR3,
combinations of CDR's, variable regions, framework regions,
constant regions, heavy chains, light chains, and variable regions,
and alternative scaffold non-antibody molecules, bispecific
antibodies, and the like (Maynard & Georgiou, 2000, Annu. Rev.
Biomed Eng. 2:339-76; Hudson, 1998, Curr. Opin. Biotechnol.
9:395-402). Another functional substructure is a single chain Fv
(scFv), comprised of the variable regions of the immunoglobulin
heavy and light chain, covalently connected by a peptide linker
(S-z Hu et al., 1996, Cancer Research, 56, 3055-3061). These small
(Mr 25,000) proteins generally retain specificity and affinity for
antigen in a single polypeptide and can provide a convenient
building block for larger, antigen-specific molecules. Unless
specifically noted otherwise, statements and claims that use the
term "antibody" or "antibodies" specifically includes "antibody
fragment" and "antibody fragments."
[0042] The term "aromatic amine," as used herein, refers to an aryl
moiety which contains an amino moiety. Such amino moieties may
include, but are not limited to primary amines, secondary amines,
tertiary amines, masked amines, or protected amines. Such tertiary
amines, masked amines, or protected amines may be converted to
primary amine or secondary amine moieties. Additionally, the amine
moiety may include an amine-like moiety which has similar chemical
characteristics as amine moieties, including but not limited to
chemical reactivity.
[0043] The term "aromatic" or "aryl", as used herein, refers to a
closed ring structure which has at least one ring having a
conjugated pi electron system and includes both carbocyclic aryl
and heterocyclic aryl (or "heteroaryl" or "heteroaromatic") groups.
The carbocyclic or heterocyclic aromatic group may contain from 5
to 20 ring atoms. The term includes monocyclic rings linked
covalently or fused-ring polycyclic (i.e., rings which share
adjacent pairs of carbon atoms) groups. An aromatic group can be
unsubstituted or substituted. Non-limiting examples of "aromatic"
or "aryl", groups include phenyl, 1-naphthyl, 2-naphthyl,
4-biphenyl, anthracenyl, and phenanthracenyl. Substituents for each
of the above noted aryl and heteroaryl ring systems are selected
from the group of acceptable substituents described below.
[0044] For brevity, the term "aromatic" or "aryl" when used in
combination with other terms (including but not limited to,
aryloxy, arylthioxy, aralkyl) includes both aryl and heteroaryl
rings as defined above. Thus, the term "aralkyl" or "alkaryl" is
meant to include those radicals in which an aryl group is attached
to an alkyl group (including but not limited to, benzyl, phenethyl,
pyridylmethyl and the like) including those alkyl groups in which a
carbon atom (including but not limited to, a methylene group) has
been replaced by a heteroatom, by way of example only, by an oxygen
atom. Examples of such aryl groups include, but are not limited to,
phenoxymethyl, 2-pyridyloxymethyl, 3-(1-naphthyloxy)propyl, and the
like.
[0045] A "bifunctional polymer", also referred to as a
"bifunctional linker", refers to a polymer comprising two
functional groups that are capable of reacting specifically with
other moieties to form covalent or non-covalent linkages. Such
moieties may include, but are not limited to, the side groups on
natural or non-natural amino acids or peptides which contain such
natural or non-natural amino acids. By way of example only, a
bifunctional linker may have a functional group reactive with a
group on a first peptide, and another functional group which is
reactive with a group on a second peptide, whereby forming a
conjugate that includes the first peptide, the bifunctional linker
and the second peptide. Many procedures and linker molecules for
attachment of various compounds to peptides are known. See, e.g.,
European Patent Application No. 188,256; U.S. Pat. Nos. 4,671,958,
4,659,839, 4,414,148, 4,699,784; 4,680,338; and 4,569,789 which are
incorporated by reference herein in their entirety. A
"multi-functional polymer" also referred to as a "multi-functional
linker", refers to a polymer comprising two or more functional
groups that are capable of reacting with other moieties. Such
moieties may include, but are not limited to, the side groups on
natural or non-natural amino acids or peptides which contain such
natural or non-natural amino acids (including but not limited to,
amino acid side groups) to form covalent or non-covalent linkages.
A bi-functional polymer or multi-functional polymer may be any
desired length or molecular weight, and may be selected to provide
a particular desired spacing or conformation between one or more
molecules linked to a compound and molecules it binds to or the
compound.
[0046] The term "bioavailability," as used herein, refers to the
rate and extent to which a substance or its active moiety is
delivered from a pharmaceutical form and becomes available at the
site of action or in the general circulation.
[0047] The term "biologically active molecule", "biologically
active moiety" or "biologically active agent" when used herein
means any substance which can affect any physical or biochemical
properties of a biological system, pathway, molecule, or
interaction relating to an organism, including but not limited to,
viruses, bacteria, bacteriophage, transposon, prion, insects,
fungi, plants, animals, and humans. In particular, as used herein,
biologically active molecules include but are not limited to any
substance intended for diagnosis, cure, mitigation, treatment, or
prevention of disease in humans or other animals, or to otherwise
enhance physical or mental well-being of humans or animals.
Examples of biologically active molecules include, but are not
limited to, peptides, proteins, enzymes, small molecule drugs, hard
drugs, soft drugs, carbohydrates, inorganic atoms or molecules,
dyes, lipids, nucleosides, radionuclides, oligonucleotides, toxins,
cells, viruses, liposomes, microparticles and micelles. Classes of
biologically active agents that are suitable for use with the
methods and compositions described herein include, but are not
limited to, drugs, prodrugs, radionuclides, imaging agents,
polymers, antibiotics, fungicides, anti-viral agents,
anti-inflammatory agents, anti-tumor agents, cardiovascular agents,
anti-anxiety agents, hormones, growth factors, steroidal agents,
microbially derived toxins, and the like.
[0048] The term "biomaterial," as used herein, refers to a
biologically-derived material, including but not limited to
material obtained from bioreactors and/or from recombinant methods
and techniques.
[0049] The term "biophysical probe," as used herein, refers to
probes which can detect or monitor structural changes in molecules.
Such molecules include, but are not limited to, proteins and the
"biophysical probe" may be used to detect or monitor interaction of
proteins with other macromolecules. Examples of biophysical probes
include, but are not limited to, spin-labels, a fluorophores, and
photoactivatable groups.
[0050] The term "biotin analogue," or also referred to as "biotin
mimic", as used herein, is any molecule, other than biotin, which
bind with high affinity to avidin and/or streptavidin.
[0051] The term "carboxy terminus modification group" refers to any
molecule that can be attached to a terminal carboxy group. By way
of example, such terminal carboxy groups may be at the end of
polymeric molecules, wherein such polymeric molecules include, but
are not limited to, polypeptides, polynucleotides, and
polysaccharides. Terminus modification groups include but are not
limited to, various water soluble polymers, peptides or proteins.
By way of example only, terminus modification groups include
polyethylene glycol or serum albumin. Terminus modification groups
may be used to modify therapeutic characteristics of the polymeric
molecule, including but not limited to increasing the serum
half-life of peptides.
[0052] The term "chemically cleavable group," also referred to as
"chemically labile", as used herein, refers to a group which breaks
or cleaves upon exposure to acid, base, oxidizing agents, reducing
agents, chemical initiators, or radical initiators.
[0053] The term "chemiluminescent group," as used herein, refers to
a group which emits light as a result of a chemical reaction
without the addition of heat. By way of example only, luminol
(5-amino-2,3-dihydro-1,4-phthalazinedione) reacts with oxidants
like hydrogen peroxide (H.sub.2O.sub.2) in the presence of a base
and a metal catalyst to produce an excited state product
(3-aminophthalate, 3-APA).
[0054] The term "chromophore," as used herein, refers to a molecule
which absorbs light of visible wavelengths, UV wavelengths or IR
wavelengths.
[0055] The term "cofactor," as used herein, refers to an atom or
molecule essential for the action of a large molecule. Cofactors
include, but are not limited to, inorganic ions, coenzymes,
proteins, or some other factor necessary for the activity of
enzymes. Examples include, heme in hemoglobin, magnesium in
chlorophyll, and metal ions for proteins.
[0056] "Cofolding," as used herein, refers to refolding processes,
reactions, or methods which employ at least two molecules which
interact with each other and result in the transformation of
unfolded or improperly folded molecules to properly folded
molecules. By way of example only, "cofolding," employ at least two
polypeptides which interact with each other and result in the
transformation of unfolded or improperly folded polypeptides to
native, properly folded polypeptides. Such polypeptides may contain
natural amino acids and/or at least one non-natural amino acid.
[0057] A "comparison window," as used herein, refers a segment of
any one of contiguous positions used to compare a sequence to a
reference sequence of the same number of contiguous positions after
the two sequences are optimally aligned. Such contiguous positions
include, but are not limited to a group consisting of from about 20
to about 600 sequential units, including about 50 to about 200
sequential units, and about 100 to about 150 sequential units. By
way of example only, such sequences include polypeptides and
polypeptides containing non-natural amino acids, with the
sequential units including, but are not limited to natural and
non-natural amino acids. In addition, by way of example only, such
sequences include polynucleotides with nucleotides being the
corresponding sequential units. Methods of alignment of sequences
for comparison are well-known in the art. Optimal alignment of
sequences for comparison can be conducted, including but not
limited to, by the local homology algorithm of Smith and Waterman
(1970) Adv. Appl. Math. 2:482c, by the homology alignment algorithm
of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search
for similarity method of Pearson and Lipman (1988) Proc. Nat'l.
Acad. Sci. USA 85:2444, by computerized implementations of these
algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin
Genetics Software Package, Genetics Computer Group, 575 Science
Dr., Madison, Wis.), or by manual alignment and visual inspection
(see, e.g., Ausubel et al., Current Protocols in Molecular Biology
(1995 supplement)).
[0058] By way of example, an algorithm which may be used to
determine percent sequence identity and sequence similarity are the
BLAST and BLAST 2.0 algorithms, which are described in Altschul et
al. (1997) Nuc. Acids Res. 25:3389-3402, and Altschul et al. (1990)
J. Mol. Biol. 215:403-410, respectively. Software for performing
BLAST analyses is publicly available through the National Center
for Biotechnology Information. The BLAST algorithm parameters W, T,
and X determine the sensitivity and speed of the alignment. The
BLASTN program (for nucleotide sequences) uses as defaults a
wordlength (W) of 11, an expectation (E) or 10, M=5, N=-4 and a
comparison of both strands. For amino acid sequences, the BLASTP
program uses as defaults a wordlength of 3, and expectation (E) of
10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff
(1992) Proc. Natl. Acad. Sci. USA 89:10915) alignments (B) of 50,
expectation (E) of 10, M=5, N=-4, and a comparison of both strands.
The BLAST algorithm is typically performed with the "low
complexity" filter turned off.
[0059] The BLAST algorithm also performs a statistical analysis of
the similarity between two sequences (see, e.g., Karlin and
Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5787). One
measure of similarity provided by the BLAST algorithm is the
smallest sum probability (P(N)), which provides an, indication of
the probability by which a match between two nucleotide or amino
acid sequences would occur by chance. For example, a nucleic acid
is considered similar to a reference sequence if the smallest sum
probability in a comparison of the test nucleic acid to the
reference nucleic acid is less than about 0.2, more or less than
about 0.01, or less than about 0.001.
[0060] The term "conservatively modified variants" applies to both
natural and non-natural amino acid and natural and non-natural
nucleic acid sequences, and combinations thereof. With respect to
particular nucleic acid sequences, "conservatively modified
variants" refers to those natural and non-natural nucleic acids
which encode identical or essentially identical natural and
non-natural amino acid sequences, or where the natural and
non-natural nucleic acid does not encode a natural and non-natural
amino acid sequence, to essentially identical sequences. By way of
example, because of the degeneracy of the genetic code, a large
number of functionally identical nucleic acids encode any given
protein. For instance, the codons GCA, GCC, GCG and GCU all encode
the amino acid alanine. Thus, at every position where an alanine is
specified by a codon, the codon can be altered to any of the
corresponding codons described without altering the encoded
polypeptide. Such nucleic acid variations are "silent variations,"
which are one species of conservatively modified variations. Thus
by way of example every natural or non-natural nucleic acid
sequence herein which encodes a natural or non-natural polypeptide
also describes every possible silent variation of the natural or
non-natural nucleic acid. One of ordinary skill in the art will
recognize that each codon in a natural or non-natural nucleic acid
(except AUG, which is ordinarily the only codon for methionine, and
TGG, which is ordinarily the only codon for tryptophan) can be
modified to yield a functionally identical molecule. Accordingly,
each silent variation of a natural and non-natural nucleic acid
which encodes a natural and non-natural polypeptide is implicit in
each described sequence.
[0061] As to amino acid sequences, individual substitutions,
deletions or additions to a nucleic acid, peptide, polypeptide, or
protein sequence which alters, adds or deletes a single natural and
non-natural amino acid or a small percentage of natural and
non-natural amino acids in the encoded sequence is a
"conservatively modified variant" where the alteration results in
the deletion of an amino acid, addition of an amino acid, or
substitution of a natural and non-natural amino acid with a
chemically similar amino acid. Conservative substitution tables
providing functionally similar natural amino acids are well known
in the art. Such conservatively modified variants are in addition
to and do not exclude polymorphic variants, interspecies homologs,
and alleles of the methods and compositions described herein.
[0062] Conservative substitution tables providing functionally
similar amino acids are known to those of ordinary skill in the
art. The following eight groups each contain amino acids that are
conservative substitutions for one another:
1) Alanine (A), Glycine (G);
[0063] 2) Aspartic acid (D), Glutamic acid (E);
3) Asparagine (N), Glutamine (Q);
4) Arginine (R), Lysine (K);
5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V);
6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W);
7) Serine (S), Threonine (T); and
8) Cysteine (C), Methionine (M)
[0064] (see, e.g., Creighton, Proteins: Structures and Molecular
Properties (W H Freeman & Co.; 2nd edition (December 1993)
[0065] The terms "cycloalkyl" and "heterocycloalkyl", by themselves
or in combination with other terms, represent, unless otherwise
stated, cyclic versions of "alkyl" and "heteroalkyl", respectively.
Thus, a cycloalkyl or heterocycloalkyl include saturated, partially
unsaturated and fully unsaturated ring linkages. Additionally, for
heterocycloalkyl, a heteroatom can occupy the position at which the
heterocycle is attached to the remainder of the molecule. The
heteroatom may include, but is not limited to, oxygen, nitrogen or
sulfur. Examples of cycloalkyl include, but are not limited to,
cyclopentyl, cyclohexyl, 1-cyclohexenyl, 3-cyclohexenyl,
cycloheptyl, and the like. Examples of heterocycloalkyl include,
but are not limited to, 1-(1,2,5,6-tetrahydropyridyl),
1-piperidinyl, 2-piperidinyl, 3-piperidinyl, 4-morpholinyl,
3-morpholinyl, tetrahydrofuran-2-yl, tetrahydrofuran-3-yl,
tetrahydrothien-2-yl, tetrahydrothien-3-yl, 1-piperazinyl,
2-piperazinyl, and the like. Additionally, the term encompasses
multicyclic structures, including but not limited to, bicyclic and
tricyclic ring structures. Similarly, the term
"heterocycloalkylene" by itself or as part of another molecule
means a divalent radical derived from heterocycloalkyl, and the
term "cycloalkylene" by itself or as part of another molecule means
a divalent radical derived from cycloalkyl.
[0066] The term "cyclodextrin," as used herein, refers to cyclic
carbohydrates consisting of at least six to eight glucose molecules
in a ring formation. The outer part of the ring contains water
soluble groups; at the center of the ring is a relatively nonpolar
cavity able to accommodate small molecules.
[0067] The term "cytotoxic," as used herein, refers to a compound
which harms cells.
[0068] "Denaturing agent" or "denaturant," as used herein, refers
to any compound or material which will cause a reversible unfolding
of a polymer. By way of example only, "denaturing agent" or
"denaturants," may cause a reversible unfolding of a protein. The
strength of a denaturing agent or denaturant will be determined
both by the properties and the concentration of the particular
denaturing agent or denaturant. By way of example, denaturing
agents or denaturants include, but are not limited to, chaotropes,
detergents, organic, water miscible solvents, phospholipids, or a
combination thereof. Non-limiting examples of chaotropes include,
but are not limited to, urea, guanidine, and sodium thiocyanate.
Non-limiting examples of detergents may include, but are not
limited to, strong detergents such as sodium dodecyl sulfate, or
polyoxyethylene ethers (e.g. Tween or Triton detergents), Sarkosyl,
mild non-ionic detergents (e.g., digitonin), mild cationic
detergents such as
N.fwdarw.2,3-(Dioleyoxy)-propyl-N,N,N-trimethylammonium, mild ionic
detergents (e.g. sodium cholate or sodium deoxycholate) or
zwitterionic detergents including, but not limited to,
sulfobetaines (Zwittergent),
3-(3-chlolamidopropyl)dimethylammonio-1-propane sulfate (CHAPS),
and 3-(3-chlolamidopropyl)dimethylammonio-2-hydroxy-1-propane
sulfonate (CHAPSO). Non-limiting examples of organic, water
miscible solvents include, but are not limited to, acetonitrile,
lower alkanols (especially C.sub.2-C.sub.4 alkanols such as ethanol
or isopropanol), or lower alkandiols (C.sub.2-C.sub.4 alkandiols
such as ethylene-glycol) may be used as denaturants. Non-limiting
examples of phospholipids include, but are not limited to,
naturally occurring phospholipids such as phosphatidylethanolamine,
phosphatidylcholine, phosphatidylserine, and phosphatidylinositol
or synthetic phospholipid derivatives or variants such as
dihexanoylphosphatidylcholine or
diheptanoylphosphatidylcholine.
[0069] The term "detectable label," as used herein, refers to a
label which may be observable using analytical techniques
including, but not limited to, fluorescence, chemiluminescence,
electron-spin resonance, ultraviolet/visible absorbance
spectroscopy, mass spectrometry, nuclear magnetic resonance,
magnetic resonance, and electrochemical methods.
[0070] The term "dicarbonyl," as used herein refers to a group
containing at least two moieties selected from the group consisting
of --C(O)--, --S(O)--, --S(O).sub.2--, and --C(S)--, including, but
not limited to, 1,2-dicarbonyl groups, a 1,3-dicarbonyl groups, and
1,4-dicarbonyl groups, and groups containing a least one ketone
group, and/or at least one aldehyde groups, and/or at least one
ester group, and/or at least one carboxylic acid group, and/or at
least one thioester group. Such dicarbonyl groups include
diketones, ketoaldehydes, ketoacids, ketoesters, and
ketothioesters. In addition, such groups may be part of linear,
branched, or cyclic molecules.)
[0071] The term "drug," as used herein, refers to any substance
used in the prevention, diagnosis, alleviation, treatment, or cure
of a disease or condition.
[0072] The term "dye," as used herein, refers to a soluble,
coloring substance which contains a chromophore.
[0073] The term "effective amount," as used herein, refers to a
sufficient amount of an agent or a compound being administered
which will relieve to some extent one or more of the symptoms of
the disease or condition being treated. The result can be reduction
and/or alleviation of the signs, symptoms, or causes of a disease,
or any other desired alteration of a biological system. By way of
example, an agent or a compound being administered includes, but,
is not limited to, a natural amino acid polypeptide, non-natural
amino acid polypeptide, modified natural amino acid polypeptide, or
modified non-amino acid polypeptide. Compositions containing such
natural amino acid polypeptides, non-natural amino acid
polypeptides, modified natural amino acid polypeptides, or modified
non-natural amino acid polypeptides can be administered for
prophylactic, enhancing, and/or therapeutic treatments. An
appropriate "effective" amount in any individual case may be
determined using techniques, such as a dose escalation study.
[0074] The term "electron dense group," as used herein, refers to a
group which scatters electrons when irradiated with an electron
beam. Such groups include, but are not limited to, ammonium
molybdate, bismuth subnitrate cadmium iodide, 99%, carbohydrazide,
ferric chloride hexahydrate, hexamethylene tetramine, 98.5%, indium
trichloride anhydrous, lanthanum nitrate, lead acetate trihydrate,
lead citrate trihydrate, lead nitrate, periodic acid,
phosphomolybdic acid, phosphotungstic acid, potassium ferricyanide,
potassium ferrocyanide, ruthenium red, silver nitrate, silver
proteinate (Ag Assay: 8.0-8.5%) "Strong", silver tetraphenylporphin
(S-TPPS), sodium chloroaurate, sodium tungstate, thallium nitrate,
thiosemicarbazide (TSC), uranyl acetate, uranyl nitrate, and
vanadyl sulfate.
[0075] The term "energy transfer agent," as used herein, refers to
a molecule which can either donate or accept energy from another
molecule. By way of example only, fluorescence resonance energy
transfer (FRET) is a dipole-1-dipole coupling process by which the
excited-state energy of a fluorescence donor molecule is
non-radiatively transferred to an unexcited acceptor molecule which
then fluorescently emits the donated energy at a longer
wavelength.
[0076] The terms "enhance" or "enhancing" means to increase or
prolong either in potency or duration a desired effect. By way of
example, "enhancing" the effect of therapeutic agents refers to the
ability to increase or prolong, either in potency or duration, the
effect of therapeutic agents on during treatment of a disease,
disorder or condition. An "enhancing-effective amount," as used
herein, refers to an amount adequate to enhance the effect of a
therapeutic agent in the treatment of a disease, disorder or
condition. When used in a patient, amounts effective for this use
will depend on the severity and course of the disease, disorder or
condition, previous therapy, the patient's health status and
response to the drugs, and the judgment of the treating
physician.
[0077] As used herein, the term "eukaryote" refers to organisms
belonging to the phylogenetic domain Eucarya, including but not
limited to animals (including but not limited to, mammals, insects,
reptiles, birds, etc.), ciliates, plants (including but not limited
to, monocots, dicots, and algae), fungi, yeasts, flagellates,
microsporidia, and protists.
[0078] The term "fatty acid," as used herein, refers to carboxylic
acids with about C.sub.6 or longer hydrocarbon side chain.
[0079] The term "fluorophore," as used herein, refers to a molecule
which upon excitation emits photons and is thereby fluorescent.
[0080] The terms "functional group", "active moiety", "activating
group", "leaving group", "reactive site", "chemically reactive
group" and "chemically reactive moiety," as used herein, refer to
portions or units of a molecule at which chemical reactions occur.
The terms are somewhat synonymous in the chemical arts and are used
herein to indicate the portions of molecules that perform some
function or activity and are reactive with other molecules.
[0081] The term "halogen" includes fluorine, chlorine, iodine, and
bromine.
[0082] The term "haloacyl," as used herein, refers to acyl groups
which contain halogen moieties, including, but not limited to,
--C(O)CH.sub.3, --C(O)CF.sub.3, --C(O)CH.sub.2OCH.sub.3, and the
like.
[0083] The term "haloalkyl," as used herein, refers to alkyl groups
which contain halogen moieties, including, but not limited to,
--CF.sub.3 and --CH.sub.2CF.sub.3 and the like.
[0084] The term "heteroalkyl," as used herein, refers to straight
or branched chain, or cyclic hydrocarbon radicals, or combinations
thereof, consisting of an alkyl group and at least one heteroatom
selected from the group consisting of O, N, Si and S, and wherein
the nitrogen and sulfur atoms may optionally be oxidized and the
nitrogen heteroatom may optionally be quaternized. The
heteroatom(s) O, N and S and Si may be placed at any interior
position of the heteroalkyl group or at the position at which the
alkyl group is attached to the remainder of the molecule. Examples
include, but are not limited to, --CH.sub.2--CH.sub.2--O--CH.sub.3,
--CH.sub.2--CH.sub.2--NH--CH.sub.3,
--CH.sub.2--CH.sub.2--N(CH.sub.3)--CH.sub.3,
--CH.sub.2--S--CH.sub.2--CH.sub.3, --CH.sub.2--CH.sub.2,
--S(O)--CH.sub.3, --CH.sub.2--CH.sub.2--S(O).sub.2--CH.sub.3,
--CH.dbd.CH--O--CH.sub.3, --Si(CH.sub.3).sub.3,
--CH.sub.2--CH.dbd.N--OCH.sub.3, and
--CH.dbd.CH--N(CH.sub.3)--CH.sub.3. In addition, up to two
heteroatoms may be consecutive, such as, by way of example,
--CH.sub.2--NH--OCH.sub.3 and
--CH.sub.2--O--Si(CH.sub.3).sub.3.
[0085] The term "heteroalkylene," as used herein, refers to a
divalent radical derived from heteroalkyl, as exemplified, but not
limited by, --CH.sub.2--CH.sub.2--S--CH.sub.2--CH.sub.2-- and
--CH.sub.2--S--CH.sub.2--CH.sub.2--NH--CH.sub.2--. For
heteroalkylene groups, the same or different heteroatoms can also
occupy either or both of the chain termini (including but not
limited to, alkyleneoxy, alkylenedioxy, alkyleneamino,
alkylenediamino, aminooxyalkylene, and the like). Still further,
for alkylene and heteroalkylene linking groups, no orientation of
the linking group is implied by the direction in which the formula
of the linking group is written. By way of example, the formula
--C(O).sub.2R'-- represents both --C(O).sub.2R'-- and
--R'C(O).sub.2--.
[0086] The term "heteroaryl" or "heteroaromatic," as used herein,
refers to aryl groups which contain at least one heteroatom
selected from N, O, and S; wherein the nitrogen and sulfur atoms
may be optionally oxidized, and the nitrogen atom(s) may be
optionally quaternized. Heteroaryl groups may be substituted or
unsubstituted. A heteroaryl group may be attached to the remainder
of the molecule through a heteroatom. Non-limiting examples of
heteroaryl groups include 1-pyrrolyl, 2-pyrrolyl, 3-pyrrolyl,
3-pyrazolyl, 2-imidazolyl, 4-imidazolyl, pyrazinyl, 2-oxazolyl,
4-oxazolyl, 2-phenyl-4-oxazolyl, 5-oxazolyl, 3-isoxazolyl,
4-isoxazolyl, 5-isoxazolyl, 2-thiazolyl, 4-thiazolyl, 5-thiazolyl,
2-furyl, 3-furyl, 2-thienyl, 3-thienyl, 2-pyridyl, 3-pyridyl,
4-pyridyl, 2-pyrimidyl, 4-pyrimidyl, 5-benzothiazolyl, purinyl,
2-benzimidazolyl, 5-indolyl, 1-isoquinolyl, 5-isoquinolyl,
2-quinoxalinyl, 5-quinoxalinyl, 3-quinolyl, and 6-quinolyl.
[0087] The term "homoalkyl," as used herein refers to alkyl groups
which are hydrocarbon groups.
[0088] The term "identical," as used herein, refers to two or more
sequences or subsequences which are the same. In addition, the term
"substantially identical," as used herein, refers to two or more
sequences which have a percentage of sequential units which are the
same when compared and aligned for maximum correspondence over a
comparison window, or designated region as measured using a
comparison algorithm or by manual alignment and visual inspection.
By way of example only, two or more sequences may be "substantially
identical" if the sequential units are about 60% identical, about
65% identical, about 70% identical, about 75% identical, about 80%
identical, about 85% identical, about 90% identical, or about 95%
identical over a specified region. Such percentages to describe the
"percent identity" of two or more sequences. The identity of a
sequence can exist over a region that is at least about 75-100
sequential units in length, over a region that is about 50
sequential units in length, or, where not specified, across the
entire sequence. This definition also refers to the complement of a
test sequence. By way of example only, two or more polypeptide
sequences are identical when the amino acid residues are the same,
while two or more polypeptide sequences are "substantially
identical" if the amino acid residues are about 60% identical,
about 65% identical, about 70% identical, about 75% identical,
about 80% identical, about 85% identical, about 90% identical, or
about 95% identical over a specified region. The identity can exist
over a region that is at least about 75-100 amino acids in length,
over a region that is about 50 amino acids in length, or, where not
specified, across the entire sequence of a polypeptide sequence. In
addition, by way of example only, two or more polynucleotide
sequences are identical when the nucleic acid residues are the
same, while two or more polynucleotide sequences are "substantially
identical" if the nucleic acid residues are about 60% identical,
about 65% identical, about 70% identical, about 75% identical,
about 80% identical, about 85% identical, about 90% identical, or
about 95% identical over a specified region. The identity can exist
over a region that is at least about 75-100 nucleic acids in
length, over a region that is about 50 nucleic acids in length, or,
where not specified, across the entire sequence of a polynucleotide
sequence.
[0089] For sequence comparison, typically one sequence acts as a
reference sequence, to which test sequences are compared. When
using a sequence comparison algorithm, test and reference sequences
are entered into a computer, subsequence coordinates are
designated, if necessary, and sequence algorithm program parameters
are designated. Default program parameters can be used, or
alternative parameters can be designated. The sequence comparison
algorithm then calculates the percent sequence identities for the
test sequences relative to the reference sequence, based on the
program parameters.
[0090] The term "intercalating agent," also referred to as
"intercalating group," as used herein, refers to a chemical that
can insert into the intramolecular space of a molecule or the
intermolecular space between molecules. By way of example only an
intercalating agent or group may be a molecule which inserts into
the stacked bases of the DNA double helix.
[0091] The term "isolated," as used herein, refers to separating
and removing a component of interest from components not of
interest. Isolated substances can be in either a dry or semi-dry
state, or in solution, including but not limited to an aqueous
solution. The isolated component can be in a homogeneous state or
the isolated component can be a part of a pharmaceutical
composition that comprises additional pharmaceutically acceptable
carriers and/or excipients. Purity and homogeneity may be
determined using analytical chemistry techniques including, but not
limited to, polyacrylamide gel electrophoresis or high performance
liquid chromatography. In addition, when a component of interest is
isolated and is the predominant species present in a preparation,
the component is described herein as substantially purified. The
term "purified," as used herein, may refer to a component of
interest which is at least 85% pure, at least 90% pure, at least
95% pure, at least 99% or greater pure. By way of example only,
nucleic acids or proteins are "isolated" when such nucleic acids or
proteins are free of at least some of the cellular components with
which it is associated in the natural state, or that the nucleic
acid or protein has been concentrated to a level greater than the
concentration of its in vivo or in vitro production. Also, by way
of example, a gene is isolated when separated from open reading
frames which flank the gene and encode a protein other than the
gene of interest.
[0092] The term "label," as used herein, refers to a substance
which is incorporated into a compound and is readily detected,
whereby its physical distribution may be detected and/or
monitored.
[0093] The term "linkage," as used herein to refer to bonds or
chemical moiety formed from a chemical reaction between the
functional group of a linker and another molecule. Such bonds may
include, but are not limited to, covalent linkages and non-covalent
bonds, while such chemical moieties may include, but are not
limited to, esters, carbonates, imines phosphate esters,
hydrazones, acetals, orthoesters, peptide linkages, and
oligonucleotide linkages. Hydrolytically stable linkages means that
the linkages are substantially stable in water and do not react
with water at useful pH values, including but not limited to, under
physiological conditions for an extended period of time, perhaps
even indefinitely. Hydrolytically unstable or degradable linkages
means that the linkages are degradable in water or in aqueous
solutions, including for example, blood. Enzymatically unstable or
degradable linkages means that the linkage can be degraded by one
or more enzymes. By way of example only, PEG and related polymers
may include degradable linkages in the polymer backbone or in the
linker group between the polymer backbone and one or more of the
terminal functional groups of the polymer molecule. Such degradable
linkages include, but are not limited to, ester linkages formed by
the reaction of PEG carboxylic acids or activated PEG carboxylic
acids with alcohol groups on a biologically active agent, wherein
such ester groups generally hydrolyze under physiological
conditions to release the biologically active agent. Other
hydrolytically degradable linkages include but are not limited to
carbonate linkages; imine linkages resulted from reaction of an
amine and an aldehyde; phosphate ester linkages formed by reacting
an alcohol with a phosphate group; hydrazone linkages which are
reaction product of a hydrazide and an aldehyde; acetal linkages
that are the reaction product of an aldehyde and an alcohol;
orthoester linkages that are the reaction product of a formate and
an alcohol; peptide linkages formed by an amine group, including
but not limited to, at an end of a polymer such as PEG, and a
carboxyl group of a peptide; and oligonucleotide linkages formed by
a phosphoramidite group, including but not limited to, at the end
of a polymer, and a 5' hydroxyl group of an oligonucleotide.
[0094] The terms "medium" or "media," as used herein, refer to any
culture medium used to grow and harvest cells and/or products
expressed and/or secreted by such cells. Such "medium" or "media"
include, but are not limited to, solution, solid, semi-solid, or
rigid supports that may support or contain any host cell,
including, by way of example, bacterial host cells, yeast host
cells, insect host cells, plant host cells, eukaryotic host cells,
mammalian host cells, CHO cells, prokaryotic host cells, E. coli,
or Pseudomonas host cells, and cell contents. Such "medium" or
"media" includes, but is not limited to, medium or media in which
the host cell has been grown into which a polypeptide has been
secreted, including medium either before or after a proliferation
step. Such "medium" or "media" also includes, but is not limited
to, buffers or reagents that contain host cell lysates, by way of
example a polypeptide produced intracellularly and the host cells
are lysed or disrupted to release the polypeptide.
[0095] The term "metabolite," as used herein, refers to a
derivative of a natural amino acid polypeptide, a non-natural amino
acid polypeptide, a modified natural amino acid polypeptide, or a
modified non-natural amino acid polypeptide that is formed when the
natural amino acid polypeptide, non-natural amino-acid polypeptide,
modified natural amino acid polypeptide, or modified non-natural
amino acid polypeptide is metabolized. The term "active metabolite"
refers to a biologically active derivative of a natural amino acid
polypeptide, a non-natural amino acid polypeptide, a modified
natural amino acid polypeptide, or a modified non-natural amino
acid polypeptide that is formed when the natural amino acid
polypeptide, non-natural amino acid polypeptide, modified natural
amino acid polypeptide, or modified non-natural amino acid
polypeptide is metabolized.
[0096] The term "metabolized," as used herein, refers to the sum of
the processes by which a particular substance is changed by an
organism. Such processes include, but are not limited to,
hydrolysis reactions and reactions catalyzed by enzymes. Further
information on metabolism may be obtained from The Pharmacological
Basis of Therapeutics, 9th Edition, McGraw-Hill (1996). By way of
example only, metabolites of natural amino acid polypeptides,
non-natural amino acid polypeptides, modified natural amino acid
polypeptides, or modified non-natural amino acid polypeptides may
be identified either by administration of the natural amino acid
polypeptides, non-natural amino acid polypeptides, modified natural
amino acid polypeptides, or modified non-natural amino acid
polypeptides to a host and analysis of tissue samples from the
host, or by incubation of natural amino acid polypeptides,
non-natural amino acid polypeptides, modified natural amino acid
polypeptides, or modified non-natural amino acid polypeptides with
hepatic cells in vitro and analysis of the resulting compounds.
[0097] The term "metal chelator," as used herein, refers to a
molecule which forms a metal complex with metal ions. By way of
example, such molecules may form two or more coordination bonds
with a central metal ion and may form ring structures.
[0098] The term "metal-containing moiety," as used herein, refers
to a group which contains a metal ion, atom or particle. Such
moieties include, but are not limited to, cisplatin, chelated
metals ions (such as nickel, iron, and platinum), and metal
nanoparticles (such as nickel, iron, and platinum).
[0099] The term "moiety incorporating a heavy atom," as used
herein, refers to a group which incorporates an ion of atom which
is usually heavier than carbon. Such ions or atoms include, but are
not limited to, silicon, tungsten, gold, lead, and uranium.
[0100] The term "modified," as used herein refers to the presence
of a change to a natural amino acid, a non-natural amino acid, a
natural amino acid polypeptide or a non-natural amino acid
polypeptide. Such changes, or modifications, may be obtained by
post synthesis modifications of natural amino acids, non-natural
amino acids, natural amino acid polypeptides or non-natural amino
acid polypeptides, or by post-translational modification of natural
amino acids, non-natural amino acids, natural amino acid
polypeptides or non-natural amino acid polypeptides. The form
"(modified)" means that the natural amino acid, non-natural amino
acid, natural amino acid polypeptide or non-natural amino acid
polypeptide being discussed are optionally modified, that is, he
natural amino acid, non-natural amino acid, natural amino acid
polypeptide or non-natural amino acid polypeptide under discussion
can be modified or unmodified.
[0101] As used herein, the term "modulated serum half-life" refers
to positive or negative changes in the circulating half-life of a
modified biologically active molecule relative to its non-modified
form. By way of example, the modified biologically active molecules
include, but are not limited to, natural amino acid, non-natural
amino acid, natural amino acid polypeptide or non-natural amino
acid polypeptide. By way of example, serum half-life is measured by
taking blood samples at various time points after administration of
the biologically active molecule or modified biologically active
molecule, and determining the concentration of that molecule in
each sample. Correlation of the serum concentration with time
allows calculation of the serum half-life. By way of example,
modulated serum half-life may be an increased in serum half-life,
which may enable an improved dosing regimens or avoid toxic
effects. Such increases in serum may be at least about two fold, at
least about three-fold, at least about five-fold, or at least about
ten-fold.
[0102] The term "modulated therapeutic half-life," as used herein,
refers to positive or negative change in the half-life of the
therapeutically effective amount of a modified biologically active
molecule, relative to its non-modified form. By way of example, the
modified biologically active molecules include, but are not limited
to, natural amino acid, non-natural amino acid, natural amino acid
polypeptide or non-natural amino acid polypeptide. By way of
example, therapeutic half-life is measured by measuring
pharmacokinetic and/or pharmacodynamic properties of the molecule
at various time points after administration. Increased therapeutic
half-life may enable a particular beneficial dosing regimen, a
particular beneficial total dose, or avoids an undesired effect. By
way of example, the increased therapeutic half-life may result from
increased potency, increased or decreased binding of the modified
molecule to its target, an increase or decrease in another
parameter or mechanism of action of the non-modified molecule, or
an increased or decreased breakdown of the molecules by enzymes
such as, by way of example only, proteases.
[0103] The term "nanoparticle," as used herein, refers to a
particle which has a particle size between about 500 nm to about 1
nm.
[0104] The term "near-stoichiometric," as used herein, refers to
the ratio of the moles of compounds participating in a chemical
reaction being about 0.75 to about 1.5 relative to the number of
hydrogens on the aromatic amine side chain of the non-natural amino
acid polypeptide. By way of example, a primary aromatic amine has 2
hydrogens, whereas a secondary amine has one hydrogen.)
[0105] As used herein, the term "non-eukaryote" refers to
non-eukaryotic organisms. By way of example, a non-eukaryotic
organism may belong to the Eubacteria, (which includes but is not
limited to, Escherichia coli, Thermus thermophilus, or Bacillus
stearothermophilus, Pseudomonas fluorescens, Pseudomonas
aeruginosa, Pseudomonas putida), phylogenetic domain, or the
Archaea, which includes, but is not limited to, Methanococcus
jannaschii, Methanobacterium thermoautotrophicum, Archaeoglobus
fulgidus, Pyrococcus furiosus, Pyrococcus horikoshii, Aeuropyrum
pernix, or Halobacterium such as Haloferax volcanii and
Halobacterium species NRC-1, or phylogenetic domain.
[0106] A "non-natural amino acid" refers to an amino acid that is
not one of the 20 common amino acids or pyrolysine or
selenocysteine. Other terms that may be used synonymously with the
term "non-natural amino acid" is "non-naturally encoded amino
acid," "unnatural amino acid," "non-naturally-occurring amino
acid," and variously hyphenated and non-hyphenated versions
thereof. The term "non-natural amino acid" includes, but is not
limited to, amino acids which occur naturally by modification of a
naturally encoded amino acid (including but not limited to, the 20
common amino acids or pyrrolysine and selenocysteine) but are not
themselves incorporated into a growing polypeptide chain by the
translation complex. Examples of naturally-occurring amino acids
that are not naturally-encoded include, but are not limited to,
N-acetylglucosaminyl-L-serine, N-acetylglucosaminyl-L-threonine,
and O-phosphotyrosine. Additionally, the term "non-natural amino
acid" includes, but is not limited to, amino acids which do not
occur naturally and may be obtained synthetically or may be
obtained by modification of non-natural amino acids.
[0107] The term "nucleic acid," as used herein, refers to
deoxyribonucleotides, deoxyribonucleosides, ribonucleosides or
ribonucleotides and polymers thereof in either single- or
double-stranded form. By way of example only, such nucleic acids
and nucleic acid polymers include, but are not limited to, (i)
analogues of natural nucleotides which have similar binding
properties as a reference nucleic acid and are metabolized in a
manner similar to naturally occurring nucleotides; (ii)
oligonucleotide analogs including, but are not limited to, PNA
(peptidonucleic acid), analogs of DNA used in antisense technology
(phosphorothioates, phosphoroamidates, and the like); (iii)
conservatively modified variants thereof (including but not limited
to, degenerate codon substitutions) and complementary sequences and
sequence explicitly indicated. By way of example, degenerate codon
substitutions may be achieved by generating sequences in which the
third position of one or more selected (or all) codons is
substituted with mixed-base and/or deoxyinosine residues (Batzer et
al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol.
Chem. 260:2605-2608 (1985); and Rossolini et al., Mol. Cell. Probes
8:91-98 (1994)).
[0108] The term "oxidizing agent," as used herein, refers to a
compound or material which is capable of removing an electron from
a compound being oxidized. By way of example oxidizing agents
include, but are not limited to, oxidized glutathione, cystine,
cystamine, oxidized dithiothreitol, oxidized erythreitol, and
oxygen. A wide variety of oxidizing agents are suitable for use in
the methods and compositions described herein.
[0109] The term "photoaffinity label," as used herein, refers to a
label with a group, which, upon exposure to light, forms a linkage
with a molecule for which the label has an affinity. By way of
example only, such a linkage may be covalent or non-covalent.
[0110] The term "photocaged moiety," as used herein, refers to a
group which, upon illumination at certain wavelengths, covalently
or non-covalently binds other ions or molecules.
[0111] The term "photocleavable group," as used herein, refers to a
group which breaks upon exposure to light.
[0112] The term "photocrosslinker," as used herein, refers to a
compound comprising two or more functional groups which, upon
exposure to light, are reactive and form a covalent or non-covalent
linkage with two or more monomeric or polymeric molecules.
[0113] The term "photoisomerizable moiety," as used herein, refers
to a group wherein upon illumination with light changes from one
isomeric form to another.
[0114] The term "polyalkylene glycol," as used herein, refers to
linear or branched polymeric polyether polyols. Such polyalkylene
glycols, including, but are not limited to, polyethylene glycol,
polypropylene glycol, polybutylene glycol, and derivatives thereof.
Other exemplary embodiments are listed, for example, in commercial
supplier catalogs, such as Shearwater Corporation's catalog
"Polyethylene Glycol and Derivatives for Biomedical Applications"
(2001). By way of example only, such polymeric polyether polyols
have average molecular weights between about 0.1 kDa to about 100
kDa. By way of example, such polymeric polyether polyols include,
but are not limited to, between about 100 Da and about 100,000 Da
or more. The molecular weight of the polymer may be between about
100 Da and about 100,000 Da, including but not limited to, 100,000
Da, 95,000 Da, 90,000 Da, 85,000 Da, 80,000 Da, 75,000 Da, 70,000
Da, 65,000 Da, 60,000 Da, 55,000 Da, 50,000 Da, 45,000 Da, 40,000
Da, 35,000 Da, 30,000 Da, 25,000 Da, 20,000 Da, 15,000 Da, 10,000
Da, 9,000 Da, 8,000 Da, 7,000 Da, 6,000 Da, 5,000 Da, 4,000 Da,
3,000 Da, 2,000 Da, 1,000 Da, 900 Da, 800 Da, 700 Da, 600 Da, 500
Da, 400 Da, 300 Da, 200 Da, and 100 Da. In some embodiments, the
molecular weight of the polymer is between about 100 Da and about
50,000 Da. In some embodiments, the molecular weight of the polymer
is between about 100 Da and about 40,000 Da. In some embodiments,
the molecular weight of the polymer is between about 1,000 Da and
about 40,000 Da. In some embodiments, the molecular weight of the
polymer is between about 5,000 Da and about 40,000 Da. In some
embodiments, the molecular weight of the polymer is between about
10,000 Da and about 40,000 Da. In some embodiments, the
poly(ethylene glycol) molecule is a branched polymer. The molecular
weight of the branched chain PEG may be between about 1,000 Da and
about 100,000 Da, including but not limited to, 100,000 Da, 95,000
Da, 90,000 Da, 85,000 Da, 80,000 Da, 75,000 Da, 70,000 Da, 65,000
Da, 60,000 Da, 55,000 Da, 50,000 Da, 45,000 Da, 40,000 Da, 35,000
Da, 30,000 Da, 25,000 Da, 20,000 Da, 15,000 Da, 10,000 Da, 9,000
Da, 8,000 Da, 7,000 Da, 6,000 Da, 5,000 Da, 4,000 Da, 3,000 Da,
2,000 Da, and 1,000 Da. In some embodiments, the molecular weight
of the branched chain PEG is between about 1,000 Da and about
50,000 Da. In some embodiments, the molecular weight of the
branched chain PEG is between about 1,000 Da and about 40,000 Da.
In some embodiments, the molecular weight of the branched chain PEG
is between about 5,000 Da and about 40,000 Da. In some embodiments,
the molecular weight of the branched chain PEG is between about
5,000 Da and about 20,000 Da.
[0115] The term "polymer," as used herein, refers to a molecule
composed of repeated subunits. Such molecules include, but are not
limited to, polypeptides, polynucleotides, or polysaccharides or
polyalkylene glycols.
[0116] The terms "polypeptide," "peptide" and "protein" are used
interchangeably herein to refer to a polymer of amino acid
residues. That is, a description directed to a polypeptide applies
equally to a description of a peptide and a description of a
protein, and vice versa. The terms apply to naturally occurring
amino acid polymers as well as amino acid polymers in which one or
more amino acid residues is a non-natural amino acid. Additionally,
such "polypeptides," "peptides" and "proteins" include amino acid
chains of any length, including full length proteins, wherein the
amino acid residues are linked by covalent peptide bonds.
[0117] The term "post-translationally modified" refers to any
modification of a natural or non-natural amino acid which occurs
after such an amino acid has been translationally incorporated into
a polypeptide chain. Such modifications include, but are not
limited to, co-translational in vivo modifications,
co-translational in vitro modifications (such as in a cell-free
translation system), post-translational in vivo modifications, and
post-translational in vitro modifications.
[0118] The term "prodrug," as used herein, refers to an agent that
is converted into the parent drug in vivo or in vitro. The benefits
of such prodrugs include, but are not limited to, (i) ease of
administration compared with the parent drug; (ii) the prodrug may
be bioavailable by oral administration whereas the parent is not;
and (iii) the prodrug may also have improved solubility in
pharmaceutical compositions compared with the parent drug. A
prodrug includes a pharmacologically inactive, or reduced-activity,
derivative of an active drug. Prodrugs may be designed to modulate
the amount of a drug or biologically active molecule that reaches a
desired site of action through the manipulation of the properties
of a drug, such as physiochemical, biopharmaceutical, or
pharmacokinetic properties. Prodrugs are converted into active drug
within the body through enzymatic or non-enzymatic reactions.
Prodrugs may provide improved physiochemical properties such as
better solubility, enhanced delivery characteristics, such as
specifically targeting a particular cell, tissue, organ or ligand,
and improved therapeutic value of the drug.
[0119] The term "prophylactically effective amount," as used
herein, refers that amount of a composition containing at least one
non-natural amino acid polypeptide or at least one modified
non-natural amino acid polypeptide prophylactically applied to a
patient which will relieve to some extent one or more of the
symptoms of a disease, condition or disorder being treated. In such
prophylactic applications, such amounts may depend on the patient's
state of health, weight, and the like. It is considered well within
the skill of the art for one to determine such prophylactically
effective amounts by routine experimentation, including, but not
limited to, a dose escalation clinical trial.
[0120] The term "protected," as used herein, refers to the presence
of a "protecting group" or moiety that prevents reaction of the
chemically reactive functional group under certain reaction
conditions. The protecting group will vary depending on the type of
chemically reactive group being protected. By way of example only,
(i) if the chemically reactive group is an amine or a hydrazide,
the protecting group may be selected from tert-butyloxycarbonyl
(t-Boc) and 9-fluorenylmethoxycarbonyl (Fmoc); (ii) if the
chemically reactive group is a thiol, the protecting group may be
orthopyridyldisulfide; and (iii) if the chemically reactive group
is a carboxylic acid, such as butanoic or propionic acid, or a
hydroxyl group, the protecting group may be benzyl or an alkyl
group such as methyl, ethyl, or tert-butyl.
[0121] By way of example only, blocking/protecting groups may also
be selected from:
##STR00001##
[0122] Additionally, protecting groups include, but are not limited
to, including photolabile groups such as Nvoc and MeNvoc and other
protecting groups known in the art. Other protecting groups are
described in Greene and Wuts, Protective Groups in Organic
Synthesis, 3rd Ed., John Wiley & Sons, New York, N.Y., 1999,
which is incorporated herein by reference in its entirety.
[0123] The term "radioactive moiety," as used herein, refers to a
group whose nuclei spontaneously give off nuclear radiation, such
as alpha, beta, or gamma particles; wherein, alpha particles are
helium nuclei, beta particles are electrons, and gamma particles
are high energy photons.
[0124] The term "reactive compound," as used herein, refers to a
compound which under appropriate conditions is reactive toward
another atom, molecule or compound.
[0125] The term "recombinant host cell," also referred to as "host
cell," refers to a cell which includes an exogenous polynucleotide,
wherein the methods used to insert the exogenous polynucleotide
into a cell include, but are not limited to, direct uptake,
transduction, f-mating, or other methods known in the art to create
recombinant host cells. By way of example only, such exogenous
polynucleotide may be a nonintegrated vector, including but not
limited to a plasmid, or may be integrated into the host
genome.
[0126] The term "redox-active agent," as used herein, refers to a
molecule which oxidizes or reduces another molecule, whereby the
redox active agent becomes reduced or oxidized. Examples of redox
active agent include, but are not limited to, ferrocene, quinones,
Ru.sup.2+/3+ complexes, Co.sup.2+/3+ complexes, and Os.sup.2+/3+
complexes.
[0127] The term "reducing agent," as used herein, refers to a
compound or material which is capable of adding an electron to a
compound being reduced. By way of example reducing agents include,
but are not limited to, dithiothreitol (DTT), 2-mercaptoethanol,
dithioerythritol, cysteine, cysteamine (2-aminoethanethiol), and
reduced glutathione. Such reducing agents may be used, by way of
example only, to maintain sulfhydryl groups in the reduced state
and to reduce intra- or intermolecular-disulfide bonds.
[0128] "Refolding," as used herein describes any process, reaction
or method which transforms an improperly folded or unfolded state
to a native or properly folded conformation. By way of example
only, refolding transforms disulfide bond containing polypeptides
from an improperly folded or unfolded state to a native or properly
folded conformation with respect to disulfide bonds. Such disulfide
bond containing polypeptides may be natural amino acid polypeptides
or non-natural amino acid polypeptides.
[0129] The term "resin," as used herein, refers to high molecular
weight, insoluble polymer beads. By way of example only, such beads
may be used as supports for solid phase peptide synthesis, or sites
for attachment of molecules prior to purification.
[0130] The term "saccharide," as used herein, refers to a series of
carbohydrates including but not limited to sugars, monosaccharides,
oligosaccharides, and polysaccharides.
[0131] The phrase "selectively hybridizes to" or "specifically
hybridizes to," as used herein, refers to the binding, duplexing,
or hybridizing of a molecule to a particular nucleotide sequence
under stringent hybridization conditions when that sequence is
present in a complex mixture including but not limited to, total
cellular or library DNA or RNA.
[0132] The term "spin label," as used herein, refers to molecules
which contain an atom or a group of atoms exhibiting an unpaired
electron spin (i.e. a stable paramagnetic group) that can be
detected by electron spin resonance spectroscopy and can be
attached to another molecule. Such spin-label molecules include,
but are not limited to, nitryl radicals and nitroxides, and may be
single spin-labels or double spin-labels.
[0133] The term "stoichiometric," as used herein, refers to the
ratio of the moles of compounds participating in a chemical
reaction being about 0.9 to about 1.1 relative to the number of
hydrogen's on the aromatic amine side chain of the non-natural
amino acid polypeptide. By way of example, a primary aromatic amine
has 2 hydrogen's, whereas a secondary amine has one hydrogen.
[0134] The term "stoichiometric-like," as used herein, refers to a
chemical reaction which becomes stoichiometric or
near-stoichiometric upon changes in reaction conditions or in the
presence of additives. Such changes in reaction conditions include,
but are not limited to, an increase in temperature or change in pH.
Such additives include, but are not limited to, accelerants.
[0135] The phrase "stringent hybridization conditions" refers to
hybridization of sequences of DNA, RNA, PNA or other nucleic acid
mimics, or combinations thereof, under conditions of low ionic
strength and high temperature. By way of example, under stringent
conditions a probe will hybridize to its target subsequence in a
complex mixture of nucleic acid (including but not limited to,
total cellular or library DNA or RNA) but does not hybridize to
other sequences in the complex mixture. Stringent conditions are
sequence-dependent and will be different in different
circumstances. By way of example, longer sequences hybridize
specifically at higher temperatures. Stringent hybridization
conditions include, but are not limited to, (i) about 5-10.degree.
C. lower than the thermal melting point (T.sub.m) for the specific
sequence at a defined ionic strength and pH; (ii) the salt
concentration is about 0.01 M to about 1.0 M at about pH 7.0 to
about pH 8.3 and the temperature is at least about 30.degree. C.
for short probes (including but not limited to, 10 to 50
nucleotides) and at least about 60.degree. C. for long probes
(including but not limited to, greater than 50 nucleotides); (iii)
the addition of destabilizing agents including, but not limited to,
formamide, (iv) 50% formamide, 5.times.SSC, and 1% SDS, incubating
at 42.degree. C., or 5.times.SSC, 1% SDS, incubating at 65.degree.
C., with wash in 0.2.times.SSC, and 0.1% SDS at 65.degree. C. for
between about 5 minutes to about 120 minutes. By way of example
only; detection of selective or specific hybridization, includes,
but is not limited to, a positive signal at least two times
background. An extensive guide to the hybridization of nucleic
acids is found in Tijssen, Laboratory Techniques in Biochemistry
and Molecular Biology--Hybridization with Nucleic Probes, "Overview
of principles of hybridization and the strategy of nucleic acid
assays" (1993).
[0136] The term "subject" as used herein, refers to an animal which
is the object of treatment, observation or experiment. By way of
example only, a subject may be, but is not limited to, a mammal
including, but not limited to, a human.
[0137] The term "substantially purified," as used herein, refers to
a component of interest that may be substantially or essentially
free of other components which normally accompany or interact with
the component of interest prior to purification. By way of example
only, a component of interest may be "substantially purified" when
the preparation of the component of interest contains less than
about 30%, less than about 25%, less than about 20%, less than
about 15%, less than about 10%, less than about 5%, less than about
4%, less than about 3%, less than about 2%, or less than about 1%
(by dry weight) of contaminating components. Thus, a "substantially
purified" component of interest may have a purity level of about
70%, about 75%, about 80%, about 85%, about 90%, about 95%, about
96%, about 97%, about 98%, about 99% or greater. By way of example
only, a natural amino acid polypeptide or a non-natural amino acid
polypeptide may be purified from a native cell, or host cell in the
case of recombinantly produced natural amino acid polypeptides or
non-natural amino acid polypeptides. By way of example a
preparation of a natural amino acid polypeptide or a non-natural
amino acid polypeptide may be "substantially purified" when the
preparation contains less than about 30%, less than about 25%, less
than about 20%, less than about 15%, less than about 10%, less than
about 5%, less than about 4%, less than about 3%, less than about
2%, or less than about 1% (by dry weight) of contaminating
material. By way of example when a natural amino acid polypeptide
or a non-natural amino acid polypeptide is recombinantly produced
by host cells, the natural amino acid polypeptide or non-natural
amino acid polypeptide may be present at about 30%, about 25%,
about 20%, about 15%, about 10%, about 5%, about 4%, about 3%,
about 2%, or about 1% or less of the dry weight of the cells. By
way of example when a natural amino acid polypeptide or a
non-natural amino acid polypeptide is recombinantly produced by
host cells, the natural amino acid polypeptide or non-natural amino
acid polypeptide may be present in the culture medium at about 5
g/L, about 4 g/L, about 3 g/L, about 2 g/L, about 1 g/L, about 750
mg/L, about 500 mg/L, about 250 mg/L, about 100 mg/L, about 50
mg/L, about 10 mg/L, or about 1 mg/L or less of the dry weight of
the cells. By way of example, "substantially purified" natural
amino acid polypeptides or non-natural amino acid polypeptides may
have a purity level of about 30%, about 35%, about 40%, about 45%,
about 50%, about 55%, about 60%, about 65%, about 70%, about 75%,
about 80%, about 85%, about 90%, about 95%, about 99% or greater as
determined by appropriate methods, including, but not limited to,
SDS/PAGE analysis, RP-HPLC, SEC, and capillary electrophoresis.
[0138] The term "substituents" also referred to as "non-interfering
substituents" "refers to groups which may be used to replace
another group on a molecule. Such groups include, but are not
limited to, halo, C.sub.1-C.sub.10 alkyl, C.sub.2-C.sub.10 alkenyl,
C.sub.2-C.sub.10 alkynyl, C.sub.1-C.sub.10 alkoxy, C.sub.5-C.sub.12
aralkyl, C.sub.3-C.sub.12 cycloalkyl, C.sub.4-C.sub.12
cycloalkenyl, phenyl, substituted phenyl, toluoyl, xylenyl,
biphenyl, C.sub.2-C.sub.12 alkoxyalkyl, C.sub.5-C.sub.12
alkoxyaryl, C.sub.5-C.sub.12 aryloxyalkyl, C.sub.7-C.sub.12
oxyaryl, C.sub.1-C.sub.6 alkylsulfinyl, C.sub.1-C.sub.10
alkylsulfonyl, --(CH.sub.2).sub.m--O--(C.sub.1-C.sub.10 alkyl)
wherein m is from 1 to 8, aryl, substituted aryl, substituted
alkoxy, fluoroalkyl, heterocyclic radical, substituted heterocyclic
radical, nitroalkyl, --NO.sub.2, --CN, --NRC(O)--(C.sub.1-C.sub.10
alkyl), --C(O)--(C.sub.1-C.sub.10 alkyl), C.sub.2-C.sub.10
alkthioalkyl, --C(O)O--(C.sub.1-C.sub.10 alkyl), --OH, --SO.sub.2,
.dbd.S, --COOH, --NR.sub.2, carbonyl, --C(O)--(C.sub.1-C.sub.10
alkyl)-CF.sub.3, --C(O)--CF.sub.3, --C(O)NR.sub.2,
--(C.sub.1-C.sub.10 aryl)-S--(C.sub.6-C.sub.10 aryl),
--C(O)--(C.sub.6-C.sub.10 aryl),
--(CH.sub.2).sub.m--O--(CH.sub.2).sub.m--O--(C.sub.1-C.sub.10
alkyl) wherein each m is from 1 to 8, --C(O)NR.sub.2,
--C(S)NR.sub.2, --SO.sub.2NR.sub.2, --NRC(O)NR.sub.2,
--NRC(S)NR.sub.2, salts thereof, and the like. Each R group in the
preceding list includes, but is not limited to, H, alkyl or
substituted alkyl, aryl or substituted aryl, or alkaryl. Where
substituent groups are specified by their conventional chemical
formulas, written from left to right, they equally encompass the
chemically identical substituents that would result from writing
the structure from right to left, for example, --CH.sub.2O-- is
equivalent to --OCH.sub.2--.
[0139] By way of example only, substituents for alkyl and
heteroalkyl radicals (including those groups referred to as
alkylene, alkenyl, heteroalkylene, heteroalkenyl, alkynyl,
cycloalkyl, heterocycloalkyl, cycloalkenyl, and heterocycloalkenyl)
includes, but is not limited to: --OR, .dbd.O, .dbd.NR, .dbd.N--OR,
--NR.sub.2, --SR, -halogen, --SiR.sub.3, --OC(O)R, --C(O)R,
--CO.sub.2R, --CONR.sub.2, --OC(O)NR.sub.2, --NRC(O)R,
--NR--C(O)NR.sub.2, --NR(O).sub.2R, --NR--C(NR.sub.2).dbd.NR,
--S(O)R, --S(O).sub.2R, --S(O).sub.2NR.sub.2, --NRSO.sub.2R, --CN
and --NO.sub.2. Each R group in the preceding list includes, but is
not limited to, hydrogen, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted aryl, including but not limited to,
aryl substituted with 1-3 halogens, substituted or unsubstituted
alkyl, alkoxy or thioalkoxy groups, or aralkyl groups. When two R
groups are attached to the same nitrogen atom, they can be combined
with the nitrogen atom to form a 5-, 6-, or 7-membered ring. For
example, --NR.sub.2 is meant to include, but not be limited to,
1-pyrrolidinyl and 4-morpholinyl.
[0140] By way of example, substituents for aryl and heteroaryl
groups include, but are not limited to, --OR, .dbd.O, .dbd.NR,
.dbd.N--OR, --NR.sub.2, --SR, -halogen, --SiR.sub.3, --OC(O)R,
--C(O)R, --CO.sub.2R, --CONR.sub.2, --OC(O)NR.sub.2, --NRC(O)R,
--NR--C(O)NR.sub.2, --NR(O).sub.2R, --NR--C(NR.sub.2).dbd.NR,
--S(O)R, --S(O).sub.2R, --S(O).sub.2NR.sub.2, --NRSO.sub.2R, --CN,
--NO.sub.2, --R, --N.sub.3, --CH(Ph).sub.2,
fluoro(C.sub.1-C.sub.4)alkoxy, and fluoro(C.sub.1-C.sub.4)alkyl, in
a number ranging from zero to the total number of open valences on
the aromatic ring system; and where each R group in the preceding
list includes, but is not limited to, hydrogen, alkyl, heteroalkyl,
aryl and heteroaryl.
[0141] The term "therapeutically effective amount," as used herein,
refers to the amount of a composition containing at least one
non-natural amino acid polypeptide and/or at least one modified
non-natural amino acid polypeptide administered to a patient
already suffering from a disease, condition or disorder, sufficient
to cure or at least partially arrest, or relieve to some extent one
or more of the symptoms of the disease, disorder or condition being
treated. The effectiveness of such compositions depend conditions
including, but not limited to, the severity and course of the
disease, disorder or condition, previous therapy, the patient's
health status and response to the drugs, and the judgment of the
treating physician. By way of example only, therapeutically
effective amounts may be determined by routine experimentation,
including but not limited to a dose escalation clinical trial.
[0142] The term "thioalkoxy," as used herein, refers to sulfur
containing alkyl groups linked to molecules via an oxygen atom.
[0143] The term "thermal melting point" or T.sub.m is the
temperature (under defined ionic strength, pH, and nucleic
concentration) at which 50% of probes complementary to a target
hybridize to the target sequence at equilibrium.
[0144] The term "toxic moiety," as used herein, refers to a
compound which can cause harm or death.
[0145] The terms "treat," "treating" or "treatment", as used
herein, include alleviating, abating or ameliorating a disease or
condition symptoms, preventing additional symptoms, ameliorating or
preventing the underlying metabolic causes of symptoms, inhibiting
the disease or condition, e.g., arresting the development of the
disease or condition, relieving the disease or condition, causing
regression of the disease or condition, relieving a condition
caused by the disease or condition, or stopping the symptoms of the
disease or condition. The terms "treat," "treating" or "treatment",
include, but are not limited to, prophylactic and/or therapeutic
treatments.
[0146] As used herein, the term "water soluble polymer" refers to
any polymer that is soluble in aqueous solvents. Such water soluble
polymers include, but are not limited to, polyethylene glycol,
polyethylene glycol propionaldehyde, mono C.sub.1-C.sub.10 alkoxy
or aryloxy derivatives thereof (described in U.S. Pat. No.
5,252,714 which is incorporated by reference herein),
monomethoxy-polyethylene glycol, polyvinyl pyrrolidone, polyvinyl
alcohol, polyamino acids, divinylether maleic anhydride,
N-(2-Hydroxypropyl)-methacrylamide, dextran, dextran derivatives
including dextran sulfate, polypropylene glycol, polypropylene
oxide/ethylene oxide copolymer, polyoxyethylated polyol, heparin,
heparin fragments, polysaccharides, oligosaccharides, glycans,
cellulose and cellulose derivatives, including but not limited to
methylcellulose and carboxymethyl cellulose, serum albumin, starch
and starch derivatives, polypeptides, polyalkylene glycol and
derivatives thereof, copolymers of polyalkylene glycols and
derivatives thereof, polyvinyl ethyl ethers, and
alpha-beta-poly[(2-hydroxyethyl)-DL-aspartamide, and the like, or
mixtures thereof. By way of example, linkage of such water soluble
polymers to a natural amino acid polypeptide or a non-natural
polypeptide can result in changes including, but not limited to,
increased or modulated serum half-life, increased or modulated
therapeutic half-life relative to the unmodified form, modulated
immunogenicity, modulated physical association characteristics
including, but not limited to, aggregation and multimer formation,
altered receptor binding, altered binding to one or more binding
partners, and altered receptor dimerization or multimerization. In
addition, such water soluble polymers may or may not have their own
biological activity.
[0147] Unless otherwise indicated, conventional methods of mass
spectroscopy, NMR, HPLC, protein chemistry, biochemistry,
recombinant DNA techniques and pharmacology, within the skill of
the art are employed.
[0148] Compounds, (including, but not limited to non-natural amino
acids, non-natural amino acid polypeptides and modified non-natural
amino acid polypeptides, and reagents for producing the
aforementioned compounds) presented herein include
isotopically-labeled compounds, which are identical to those
recited in the various formulas and structures presented herein,
but for the fact that one or more atoms are replaced by an atom
having an atomic mass or mass number different from the atomic mass
or mass number usually found in nature. Examples of isotopes that
can be incorporated into the present compounds include isotopes of
hydrogen, carbon, nitrogen, oxygen, fluorine and chlorine, such as
.sup.2H, .sup.3H, .sup.13C, .sup.14C, .sup.15N, .sup.18O, .sup.17O,
.sup.35S, .sup.18F, .sup.36Cl, respectively. Certain
isotopically-labeled compounds described herein, for example those
into which radioactive isotopes such as 3H and .sup.14C are
incorporated, are useful in drug and/or substrate tissue
distribution assays. Further, substitution with isotopes such as
deuterium, i.e., .sup.2H, can afford certain therapeutic advantages
resulting from greater metabolic stability, for example increased
in vivo half-life or reduced dosage requirements.
[0149] Some of the compounds herein (including, but not limited to
non-natural amino acids, non-natural amino acid polypeptides and
modified non-natural amino acid polypeptides, and reagents for
producing the aforementioned compounds) have asymmetric carbon
atoms and can therefore exist as enantiomers or diastereomers.
Diasteromeric mixtures can be separated into their individual
diastereomers on the basis of their physical chemical differences
by methods known, for example, by chromatography and/or fractional
crystallization. Enantiomers can be separated by converting the
enantiomeric mixture into a diastereomeric mixture by reaction with
an appropriate optically active compound (e.g., alcohol),
separating the diastereomers and converting (e.g., hydrolyzing) the
individual diastereomers to the corresponding pure enantiomers. All
such isomers, including diastereomers, enantiomers, and mixtures
thereof are considered as part of the compositions described
herein.
[0150] In additional or further embodiments, the compounds
described herein (including, but not limited to non-natural amino
acids, non-natural amino acid polypeptides and modified non-natural
amino acid polypeptides, and reagents for producing the
aforementioned compounds) are used in the form of pro-drugs. In
additional or further embodiments, the compounds described herein
((including, but not limited to non-natural amino acids,
non-natural amino acid polypeptides and modified non-natural amino
acid polypeptides, and reagents for producing the aforementioned
compounds) are metabolized upon administration to an organism in
need to produce a metabolite that is then used to produce a desired
effect, including a desired therapeutic effect. In further or
additional embodiments are active metabolites of non-natural amino
acids and modified or unmodified non-natural amino acid
polypeptides.
[0151] The methods and formulations described herein include the
use of N-oxides, crystalline forms (also known as polymorphs), or
pharmaceutically acceptable salts of non-natural amino acids,
non-natural amino acid polypeptides and modified non-natural amino
acid polypeptides. In certain embodiments, non-natural amino acids,
non-natural amino acid polypeptides and modified non-natural amino
acid polypeptides may exist as tautomers. All tautomers are
included within the scope of the non-natural amino acids,
non-natural amino acid polypeptides and modified non-natural amino
acid polypeptides presented herein. In addition, the non-natural
amino acids, non-natural amino acid polypeptides and modified
non-natural amino acid polypeptides described herein can exist in
unsolvated as well as solvated forms with pharmaceutically
acceptable solvents such as water, ethanol, and the like. The
solvated forms of the non-natural amino acids, non-natural amino
acid polypeptides and modified non-natural amino acid polypeptides
presented herein are also considered to be disclosed herein.
[0152] Some of the compounds herein (including, but not limited to
non-natural amino acids, non-natural amino acid polypeptides and
modified non-natural amino acid polypeptides and reagents for
producing the aforementioned compounds) may exist in several
tautomeric forms. All such tautomeric forms are considered as part
of the compositions described herein. Also, for example all
enol-keto forms of any compounds (including, but not limited to
non-natural amino acids, non-natural amino acid polypeptides and
modified non-natural amino acid polypeptides and reagents for
producing the aforementioned compounds) herein are considered as
part of the compositions described herein.
[0153] Some of the compounds herein (including, but not limited to
non-natural amino acids, non-natural amino acid polypeptides and
modified non-natural amino acid polypeptides and reagents for
producing either of the aforementioned compounds) are acidic and
may form a salt with a pharmaceutically acceptable cation. Some of
the compounds herein (including, but not limited to non-natural
amino acids, non-natural amino acid polypeptides and modified
non-natural amino acid polypeptides and reagents for producing the
aforementioned compounds) can be basic and accordingly, may form a
salt with a pharmaceutically acceptable anion. All such salts,
including di-salts are within the scope of the compositions
described herein and they can be prepared by conventional methods.
For example, salts can be prepared by contacting the acidic and
basic entities, in either an aqueous, non-aqueous or partially
aqueous medium. The salts are recovered by using at least one of
the following techniques: filtration, precipitation with a
non-solvent followed by filtration, evaporation of the solvent, or,
in the case of aqueous solutions, lyophilization.
[0154] Salts, for example, include: (1) acid addition salts, formed
with inorganic acids such as hydrochloric acid, hydrobromic acid,
sulfuric acid, nitric acid, phosphoric acid, and the like; or
formed with organic acids such as acetic acid, propionic acid,
hexanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic
acid, lactic acid, malonic acid, succinic acid, malic acid, maleic
acid, fumaric acid, tartaric acid, citric acid, benzoic acid,
3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, mandelic acid,
methanesulfonic acid, ethanesulfonic acid, 1,2-ethanedisulfonic
acid, 2-hydroxyethanesulfonic acid, benzenesulfonic acid,
2-naphthalenesulfonic acid,
4-methylbicyclo-[2.2.2]oct-2-ene-1-carboxylic acid, glucoheptonic
acid, 4,4'-methylenebis-(3-hydroxy-2-ene-1-carboxylic acid),
3-phenylpropionic acid, trimethylacetic acid, tertiary butylacetic
acid, lauryl sulfuric acid, gluconic acid, glutamic acid,
hydroxynaphthoic acid, salicylic acid, stearic acid, muconic acid,
and the like; (2) salts formed when an acidic proton present in the
parent compound either is replaced by a metal ion, e.g., an alkali
metal ion, an alkaline earth ion, or an aluminum ion; or
coordinates with an organic base. Acceptable organic bases include
ethanolamine, diethanolamine, triethanolamine, tromethamine,
N-methylglucamine, and the like. Acceptable inorganic bases include
aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium
carbonate, sodium hydroxide, and the like.
[0155] It should be understood that a reference to a salt includes
the solvent addition forms or crystal forms thereof, particularly
solvates or polymorphs. Solvates contain either stoichiometric or
non-stoichiometric amounts of a solvent, and are often formed
during the process of crystallization. Hydrates are formed when the
solvent is water, or alcoholates are formed when the solvent is
alcohol. Polymorphs include the different crystal packing
arrangements of the same elemental composition of a compound.
Polymorphs usually have different X-ray diffraction patterns,
infrared spectra, melting points, density, hardness, crystal shape,
optical and electrical properties, stability, and solubility.
Various factors such as the recrystallization solvent, rate of
crystallization, and storage temperature may cause a single crystal
form to dominate.
BRIEF DESCRIPTION OF THE FIGURES
[0156] A better understanding of the features and advantages of the
present methods and compositions may be obtained by reference to
the following detailed description that sets forth illustrative
embodiments, in which the principles of our methods, compositions,
devices and apparatuses are utilized, and the accompanying drawings
of which:
[0157] FIG. 1 illustrates a non-limiting aspect of methods for
selecting and designing a polypeptide to be modified using the
methods, compositions and techniques described herein.
[0158] FIG. 2 presents illustrative, non-limiting examples of the
types of non-natural amino acids described herein. Such non-natural
amino acids may be used in or incorporated into any of the methods,
compositions, techniques and strategies for making, purifying,
characterizing, and using non-natural amino acids, non-natural
amino acid polypeptides and modified non-natural amino acid
polypeptides described herein.
[0159] FIG. 3 presents illustrative, non-limiting examples of the
types of non-natural amino acids described herein. Such non-natural
amino acids may be used in or incorporated into any of the methods,
compositions, techniques and strategies for making, purifying,
characterizing, and using non-natural amino acids, non-natural
amino acid polypeptides and modified non-natural amino acid
polypeptides described herein. For FIG. 3 only, X represents a
halogen.
[0160] FIG. 4 presents illustrative, non-limiting examples of the
types of non-natural amino acids described herein. Such non-natural
amino acids may be used in of incorporated into any of the methods,
compositions, techniques and strategies for making, purifying,
characterizing, and using non-natural amino acids, non-natural
amino acid polypeptides and modified non-natural amino acid
polypeptides described herein.
[0161] FIG. 5 presents illustrative, non-limiting examples of the
types of non-natural amino acids described herein. Such non-natural
amino acids may be used in or incorporated into any of the methods,
compositions, techniques and strategies for making, purifying,
characterizing, and using non-natural amino acids, non-natural
amino acid polypeptides and modified non-natural amino acid
polypeptides described herein.
[0162] FIG. 6 presents illustrative, non-limiting examples of the
types of non-natural amino acids described herein. Such non-natural
amino acids may be used in or incorporated into any of the methods,
compositions, techniques and strategies for making, purifying,
characterizing, and using non-natural amino acids, non-natural
amino acid polypeptides and modified non-natural amino acid
polypeptides described herein. For FIG. 6 only, X represents a
halogen.
[0163] FIG. 7 presents illustrative, non-limiting examples of the
types of non-natural amino acids described herein. Such non-natural
amino acids may be used in or incorporated into any of the methods,
compositions, techniques and strategies for making, purifying,
characterizing, and using non-natural amino acids, non-natural
amino acid polypeptides and modified non-natural amino acid
polypeptides described herein.
[0164] FIG. 8 presents illustrative, non-limiting examples of the
types of non-natural amino acids described herein. Such non-natural
amino acids may be used in or incorporated into any of the methods,
compositions, techniques and strategies for making, purifying,
characterizing, and using non-natural amino acids, non-natural
amino acid polypeptides and modified non-natural amino acid
polypeptides described herein.
[0165] FIG. 9 presents illustrative, non-limiting examples of the
types of non-natural amino acids described herein. Such non-natural
amino acids may be used in or incorporated into any of the methods,
compositions, techniques and strategies for making, purifying,
characterizing, and using non-natural amino acids, non-natural
amino acid polypeptides and modified non-natural amino acid
polypeptides described herein. For FIG. 9 only, X represents a
halogen.
[0166] FIG. 10 presents illustrative, non-limiting examples of the
types of non-natural amino acids described herein. Such non-natural
amino acids may be used in or incorporated into any of the methods,
compositions, techniques and strategies for making, purifying,
characterizing, and using non-natural amino acids, non-natural
amino acid polypeptides and modified non-natural amino acid
polypeptides described herein.
[0167] FIG. 11 presents an illustrative, non-limiting example of
the synthetic methodology used to make the non-natural amino acids
described herein. Such non-natural amino acids may be used in or
incorporated into any of the methods, compositions, techniques and
strategies for making, purifying, characterizing, and using
non-natural amino acids, non-natural amino acid polypeptides and
modified non-natural amino acid polypeptides described herein.
[0168] FIG. 12 presents an illustrative, non-limiting example of
the synthetic methodology used to make the non-natural amino acids
described herein. Such non-natural amino acids may be used in or
incorporated into any of the methods, compositions, techniques and
strategies for making, purifying, characterizing, and using
non-natural amino acids, non-natural amino acid polypeptides and
modified non-natural amino acid polypeptides described herein.
[0169] FIG. 13 presents an illustrative, non-limiting example of
the synthetic methodology used to make the non-natural amino acids
described herein. Such non-natural amino acids may be used in or
incorporated into any of the methods, compositions, techniques and
strategies for making, purifying, characterizing, and using
non-natural amino acids, non-natural amino acid polypeptides and
modified non-natural amino acid polypeptides described herein.
[0170] FIG. 14 presents illustrative, non-limiting examples of
non-natural amino acids described herein which contain masked
and/or protected amine moieties which can be converted to unmasked
and/or deprotected amine moieties. Such non-natural amino acids may
be used in or incorporated into any of the methods, compositions,
techniques and strategies for making, purifying, characterizing,
and using non-natural amino acids, non-natural amino acid
polypeptides and modified non-natural amino acid polypeptides
described herein.
[0171] FIG. 15 presents illustrative, non-limiting examples of
non-natural amino acids described herein which contain masked
and/or protected amine side chains for reductive amination with an
aldehyde-containing reagent. Such non-natural amino acids may be
used in or incorporated into any of the methods, compositions,
techniques and strategies for making, purifying, characterizing,
and using non-natural amino acids, non-natural amino acid
polypeptides and modified non-natural amino acid polypeptides
described herein.
[0172] FIG. 16 presents illustrative, non-limiting examples of the
formation of polypeptides with aromatic amine-containing
non-natural amino acids by reductive alkylations with
aldehyde-containing reagents.
[0173] FIG. 17 presents illustrative, non-limiting examples of
aromatic protected aldehyde containing non natural amino acids
described herein. Such non-natural amino acids may be used in or
incorporated into any of the methods, compositions, techniques and
strategies for making, purifying, characterizing, and using
non-natural amino acids, non-natural amino acid polypeptides and
modified non-natural amino acid polypeptides described herein.
[0174] FIG. 18 presents illustrative, non-limiting examples of the
formation of polypeptides with aldehyde-containing non-natural
amino acids by post-translational deprotecting/unmasking of a
protected/masked precursor followed by reductive aminations with
aromatic amine-containing reagents.
[0175] FIG. 19 presents illustrative, non-limiting examples of the
site selective reductive alkylation and reductive amination of
non-natural amino acid polypeptides.
[0176] FIG. 20 presents illustrative, non-limiting examples of the
reductive alkylations of reduced urotension-II (UT-II-SH) with
propionaldehyde (I) and benzaldehyde (II) and the corresponding
HPLC chromatograms.
[0177] FIG. 21 presents illustrative, non-limiting examples of
reductive alkylations of urotension-II (UT-II) with propionaldehyde
(I) and benzaldehyde (II) and the corresponding HPLC
chromatograms.
[0178] FIG. 22 presents illustrative, non-limiting examples of
reductive alkylations of peptide XT-8 with propionaldehyde (I) and
benzaldehyde (II), isobutaldehyde (III) and pivalaldehyde (IV) and
the corresponding HPLC chromatograms.
[0179] FIG. 23 presents illustrative, non-limiting examples of
reductive alkylations of peptide SXT-9 with propionaldehyde (I),
benzaldehyde (II), isobutaldehyde (III) and pivalaldehyde (IV) and
the corresponding HPLC chromatograms.
[0180] FIG. 24 presents illustrative, non-limiting examples of
reductive alkylations of peptide HXT-9 with propionaldehyde (I),
benzaldehyde (II), isobutaldehyde (III) and pivalaldehyde (IV) and
the corresponding HPLC chromatograms.
[0181] FIG. 25 presents illustrative, non-limiting examples of
reductive alkylations of peptide WXT-9 with propionaldehyde (I),
benzaldehyde (II) and isobutaldehyde (III) and the corresponding
HPLC chromatograms.
[0182] FIG. 26 presents illustrative, non-limiting examples of
reductive alkylations of peptide NXT-9 with propionaldehyde (I) and
benzaldehyde (II) and the corresponding HPLC chromatograms.
[0183] FIG. 27 presents illustrative, non-limiting examples of
reductive alkylations of peptide RXT-10 with propionaldehyde (I)
and benzaldehyde (II) and the corresponding HPLC chromatograms.
[0184] FIG. 28 presents illustrative, non-limiting examples of
reductive alkylations of peptide AXT-11 with propionaldehyde (I)
and benzaldehyde (II) and the corresponding HPLC chromatograms.
[0185] FIG. 29 presents illustrative, non-limiting examples of
reductive alkylations of peptide AXT-11 with different aldehydes
(I-III) and the corresponding HPLC chromatograms.
[0186] FIG. 30 presents illustrative, non-limiting examples of
reductive alkylations of peptide AXT-11 with different aldehydes
(IV-VII) and the corresponding HPLC chromatograms.
[0187] FIG. 31 presents illustrative, non-limiting examples of
competitive reactions of peptide AXT-11 with an aldehyde and a
1,3-diketone (I-III) and the corresponding HPLC chromatograms.
[0188] FIG. 32 presents illustrative, non-limiting examples of
competitive reactions of peptide NXT-9 with an aldehyde and a
1,2-diketone (I-III) and the corresponding HPLC chromatograms.
[0189] FIG. 33 presents illustrative, non-limiting examples of
competitive reactions of peptide MXT-9 with different aldehydes and
ketones (I-V) and the corresponding HPLC chromatograms.
[0190] FIG. 34 presents illustrative, non-limiting examples of
reduction of peptide MXT-9-N3 to MXT-9NH2 (I), followed by
reductive alkylations with propionaldehyde (II) and benzaldehyde
(III) and the corresponding HPLC chromatograms.
[0191] FIG. 35 presents illustrative, non-limiting examples and
comparison PEGylation of peptides by N-terminal PEGylation and
PEGylation of aromatic amine-containing non-natural amino acids
described herein.
[0192] FIG. 36 presents illustrative, non-limiting examples of PEG
aldehyde reagents used to PEGylate aromatic amine-containing
non-natural amino acids incorporated into peptides.
[0193] FIG. 37 presents illustrative, non-limiting examples of
PEGylation of MT-9 by N-terminal reductive alkylation.
[0194] FIG. 38 presents illustrative, non-limiting examples of
PEGylation of MXT-9 by reductive alkylation of aromatic
amine-containing non-natural amino acid incorporated into
MXT-9.
[0195] FIG. 39 presents illustrative, non-limiting examples of
PEGylation of hGH and IFN.alpha. by reductive alkylation of
aromatic amine-containing non-natural amino acid incorporated into
hGH and IFN.alpha..
[0196] FIG. 40 presents illustrative, non-limiting image of an
electrophoresis gel of various hGH PEGylations.
DETAILED DESCRIPTION OF THE INVENTION
I. Introduction
[0197] Recently, an entirely new technology in the protein sciences
has been reported, which promises to overcome many of the
limitations associated with site-specific modifications of
proteins. Specifically, new components have been added to the
protein biosynthetic machinery of the prokaryote Escherichia coli
(E. coli) (e.g., L. Wang, et al., (2001), Science 292:498-500) and
the eukaryote Saccharomyces cerevisiae (S. cerevisiae) (e.g., J.
Chin et al., Science 301:964-7 (2003)), which has enabled the
incorporation of non-natural amino acids to proteins in vivo. A
number of new amino acids with novel chemical, physical or
biological properties, including photoaffinity labels and
photoisomerizable amino acids, photocrosslinking amino acids (See,
e.g., Chin, J. W., et al. (2002) Proc. Natl. Acad. Sci. U.S.A.
99:11020-11024; and, Chin, J. W., et al., (2002) J. Am. Chem. Soc.
124:9026-9027), heavy atom containing amino acids, keto amino
acids, and glycosylated amino acids have been incorporated
efficiently and with high fidelity into proteins in E. coli and in
yeast in response to the amber codon, TAG, using this methodology.
See, e.g., J. W. Chin et al., (2002), Journal of the American
Chemical Society 124:9026-9027 (incorporated by reference in its
entirety); J. W. Chin, & P. G. Schultz, (2002), Chem Bio Chem
3(11):1135-1137 (incorporated by reference in its entirety); J. W.
Chin, et al., (2002), PNAS United States of America 99:11020-11024
(incorporated by reference in its entirety); and, L. Wang, & P.
G. Schultz, (2002), Chem. Comm., 1:1-11 (incorporated by reference
in its entirety). These studies have demonstrated that it is
possible to selectively and routinely introduce chemical functional
groups that are not found in proteins, that are chemically inert to
all of the functional groups found in the 20 common,
genetically-encoded amino acids and that may be used to react
efficiently and selectively to form stable covalent linkages.
II. Overview
[0198] FIG. 1 presents an overview of the compositions, methods and
techniques that are described herein. At one level, described
herein are the tools (methods, compositions, techniques) for
creating and using a polypeptide comprising at least one
non-natural amino acid or modified non-natural amino acid with an
aromatic amine or a heteroaromatic amine. The heteroaromatic group
includes, but is not limited to, furans, pyrroles, thiophenes,
pyridines, quinolines, isoquinolines, imidazole, thiazoles,
pyrimidines, pyridazines, pyrazines, benzothiazoles,
thiazolopyridines, oxazoles, benzoxazoles, oxazolopyridines,
thiazolopyrimidines, oxazolopyrimidines, benzoxazines, and
benzothiazines. Such non-natural amino acids may contain further
functionality, including but not limited to, a label; a dye; a
polymer; a water-soluble polymer; a derivative of polyethylene
glycol; a photocrosslinker; a cytotoxic compound; a drug; an
affinity label; a photoaffinity label; a reactive compound; a
resin; a second protein or polypeptide or polypeptide analog; an
antibody or antibody fragment; a metal chelator; a cofactor; a
fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an
antisense polynucleotide; a saccharide, a water-soluble dendrimer,
a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a
fluorophore, a metal-containing moiety; a radioactive moiety; a
novel functional group; a group that covalently or noncovalently
interacts with other molecules; a photocaged moiety; an actinic
radiation excitable moiety; a ligand; a photoisomerizable moiety;
biotin; a biotin analogue; a moiety incorporating a heavy atom; a
chemically cleavable group; a photocleavable group; an elongated
side chain; a carbon-linked sugar; a redox-active agent; an amino
thioacid; a toxic moiety; an isotopically labeled moiety; a
biophysical probe; a phosphorescent group; a chemiluminescent
group; an electron dense group; a magnetic group; an intercalating
group; a chromophore; an energy transfer agent; a biologically
active agent; a detectable label; a small molecule; an inhibitory
ribonucleic acid; a radionucleotide; a neutron-capture agent; a
derivative of biotin; quantum dot(s); a nanotransmitter; a
radiotransmitter; an abzyme, an activated complex activator, a
virus, an adjuvant, an aglycan, an allergan, an angiostatin, an
antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a
shuttle vector, a macromolecule, a mimotope, a receptor, a reverse
micelle, and any combination thereof.
[0199] As shown in FIG. 1, in one aspect are methods for selecting
and designing a polypeptide to be modified using the methods,
compositions and techniques described herein. The new polypeptide
may be designed de novo, including by way of example only, as part
of high-throughput screening process (in which case numerous
polypeptides may be designed, synthesized, characterized and/or
tested) or based on the interests of the researcher. The new
polypeptide may also be designed based on the structure of a known
or partially characterized polypeptide. By way of example only, the
Growth Hormone Gene Superfamily (see infra) has been the subject of
intense study by the scientific community; a new polypeptide may be
designed based on the structure of a member or members of this gene
superfamily. The principles for selecting which amino acid(s) to
substitute and/or modify are described separately herein. The
choice of which modification to employ is also described herein,
and can be used to meet the need of the experimenter or end user.
Such needs may include, but are not limited to, manipulating the
therapeutic effectiveness of the polypeptide, improving the safety
profile of the polypeptide, adjusting the pharmacokinetics,
pharmacologics and/or pharmacodynamics of the polypeptide, such as,
by way of example only, increasing water solubility,
bioavailability, increasing serum half-life, increasing therapeutic
half-life, modulating immunogenicity, modulating biological
activity, or extending the circulation time. In addition, such
modifications include, by way of example only, providing additional
functionality to the polypeptide, incorporating a tag, label or
detectable signal into the polypeptide, easing the isolation
properties of the polypeptide, and any combination of the
aforementioned modifications.
[0200] Also described herein are non-natural amino acids that have
or can be modified to contain an aromatic amine or a heteroaromatic
amine. The heteroaromatic group includes, but is not limited to,
furans, pyrroles, thiophenes, pyridines, quinolines; isoquinolines,
imidazole, thiazoles, pyrimidines, pyridazines, pyrazines,
benzothiazoles, thiazolopyridines, oxazoles, benzoxazoles,
oxazolopyridines, thiazolopyrimidines, oxazolopyrimidines,
benzoxazines, and benzothiazines. Included with this aspect are
methods for producing, purifying, characterizing and using such
non-natural amino acids. In another aspect described herein are
methods, strategies and techniques for incorporating at least one
such non-natural amino acids into a polypeptide. Also included with
this aspect are methods for producing, purifying, characterizing
and using such polypeptides containing at least one such
non-natural amino acids. Also included with this aspect are
compositions of and methods for producing, purifying,
characterizing and using oligonucleotides (including DNA and RNA)
that can be used to produce, at least in part, a polypeptide
containing at least one non-natural amino acid. Also included with
this aspect are compositions of and methods for producing,
purifying, characterizing and using cells that can express such
oligonucleotides that can be used to produce, at least in part, a
polypeptide containing at least one non-natural amino acid.
[0201] Thus, polypeptides comprising at least one non-natural amino
acid or modified non-natural amino acid with an aromatic amine or a
heteroaromatic amine are provided and described herein. The
heteroaromatic group includes, but is not limited to, furans,
pyrroles, thiophenes, pyridines, quinolines, isoquinolines,
imidazole, thiazoles, pyrimidines, pyridazines, pyrazines,
benzothiazoles, thiazolopyridines, oxazoles, benzoxazoles,
oxazolopyridines, thiazolopyrimidines, oxazolopyrimidines,
benzoxazines, and benzothiazines. In certain embodiments,
polypeptides with at least one non-natural amino acid or modified
non-natural amino acid with an aromatic amine or a heteroaromatic
amine include at least one post-translational modification at some
position on the polypeptide. In such embodiments, the heterocycle
modified non-natural amino acids may include, but are not limited
to, furans, pyrroles, thiophenes, pyridines, quinolines,
isoquinolines, imidazole, thiazoles, pyrimidines, pyridazines,
pyrazines, benzothiazoles, thiazolopyridines, oxazoles,
benzoxazoles, oxazolopyridines, thiazolopyrimidines,
oxazolopyrimidines, benzoxazines, and benzothiazines. In some
embodiments the post-translational modification occurs via the
cellular machinery (e.g., glycosylation, acetylation, acylation,
lipid-modification, palmitoylation, palmitate addition,
phosphorylation, glycolipid-linkage modification, and the like), in
many instances, such cellular-machinery-based post-translational
modifications occur at the naturally occurring amino acid sites on
the polypeptide, however, in certain embodiments, the
cellular-machinery-based post-translational modifications occur on
the non-natural amino acid site(s) on the polypeptide.
[0202] In other embodiments the post-translational modification
does not utilize cellular machinery, but the functionality is
instead provided by attachment of a molecule (including but not
limited to, a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof) comprising a second reactive group to the at least one
non-natural amino acid comprising a first reactive group (including
but not limited to, non-natural amino acid containing an aromatic
amine or a heteroaromatic amine functional group) utilizing
reductive alkylation methodology. In certain embodiments, such
second reactive groups may be carbonyl containing groups,
including, but not limited to, aldehydes and ketones. In certain
embodiments, the post-translational modification is made in vivo in
a eukaryotic cell or in a non-eukaryotic cell. In certain
embodiments, the post-translational modification is made in vitro.
Also included with this aspect are methods for producing,
purifying, characterizing and using such polypeptides containing at
least one such post-translationally modified non-natural amino
acids.
[0203] Also included within the scope of the methods, compositions,
strategies and techniques described herein are reagents capable of
reacting with a non-natural amino acid (containing either an
aromatic amine group, a heteroaromatic amine group, or protected
forms thereof) that is part of a polypeptide so as to produce any
of the aforementioned post-translational modifications. In general,
the resulting post-translationally modified non-natural amino acid
will contain at least one reductively aminated aldehyde or ketone,
which may undergo further modification reactions. Also included
with this aspect are methods for producing, purifying,
characterizing and using such reagents that are capable of any such
post-translational modifications of such non-natural amino
acid(s).
[0204] In certain embodiments, the protein includes at least one
post-translational modification that is made in vivo by one host
cell, where the post-translational modification is not normally
made by another host cell type. In certain embodiments, the protein
includes at least one post-translational modification that is made
in viva by a eukaryotic cell, where the post-translational
modification is not normally made by a non-eukaryotic cell.
Examples of such post-translational modifications include, but are
not limited to, glycosylation, acetylation, acylation,
lipid-modification, palmitoylation, palmitate addition,
phosphorylation, glycolipid-linkage modification, and the like. In
one embodiment, the post-translational modification comprises
attachment of an oligosaccharide to an asparagine by a
GlcNAc-asparagine linkage (including but not limited to, where the
oligosaccharide comprises (GlcNAc-Man).sub.2-Man-GlcNAc-GlcNAc, and
the like). In another embodiment, the post-translational
modification comprises attachment of an oligosaccharide (including
but not limited to, Gal-GalNAc, Gal-GlcNAc, etc.) to a serine or
threonine by a GalNAc-serine, a GalNAc-threonine, a GlcNAc-serine,
or a GlcNAc-threonine linkage. Examples of secretion signal
sequences include, but are not limited to, a prokaryotic secretion
signal sequence, a eukaryotic secretion signal sequence, a
eukaryotic secretion signal sequence 5'-optimized for bacterial
expression, a novel secretion signal sequence, pectate lyase
secretion signal sequence, Omp A secretion signal sequence, and a
phage secretion signal sequence. Examples of secretion signal
sequences, include, but are not limited to, STII (prokaryotic), Fd
GIII and M13 (phage), Bgl2 (yeast), and the signal sequence bla
derived from a transposon. In certain embodiments, a protein or
polypeptide can comprise a secretion or localization sequence, an
epitope tag, a FLAG tag, a polyhistidine tag, a GST fusion, and/or
the like. Also included with this aspect are methods for producing,
purifying, characterizing and using such polypeptides containing at
least one such post-translational modification. In other
embodiments, the glycosylated non-natural amino acid polypeptide is
produced in a non-glycosylated form. Such a non-glycosylated form
of a glycosylated non-natural amino acid may be produced by methods
that include chemical or enzymatic removal of oligosaccharide
groups from an isolated or substantially purified or unpurified
glycosylated non-natural amino acid polypeptide; production of the
non-natural amino acid in a host that does not glycosylate such a
non-natural amino acid polypeptide (such a host including,
prokaryotes or eukaryotes engineered or mutated to not glycosylate
such a polypeptide), the introduction of a glycosylation inhibitor
into the cell culture medium in which such a non-natural amino acid
polypeptide is being produced by a eukaryote that normally would
glycosylate such a polypeptide, or a combination of any such
methods. Also described herein are such non-glycosylated forms of
normally-glycosylated non-natural amino acid polypeptides (by
normally-glycosylated is meant a polypeptide that would be
glycosylated when produced under conditions in which
naturally-occurring polypeptides are glycosylated). Of course, such
non-glycosylated forms of normally-glycosylated non-natural amino
acid polypeptides may be in an unpurified form, a substantially
purified form, or in an isolated form.
[0205] In certain embodiments, the protein includes at least one
post-translational modification that is made in vitro, wherein the
post-translational modification is stoichiometric,
stoichiometric-like, or -near-stoichiometric. Examples of such
post-translational modifications include, but are not limited to,
reductive alkylations of aromatic amine groups or heteroaromatic
amine groups with carbonyl containing reagents using a reducing
agent. In certain embodiments, such post-translational
modifications include, but are not limited to, reductive
alkylations of aromatic amine groups or heteroaromatic amine groups
with aldehyde containing reagents using a reducing agent. In
certain embodiments, such post-translational modifications include,
but are not limited to, reductive alkylations of aromatic amine
groups or heteroaromatic amine groups with aldehyde containing
reagents using sodium cyanoborohydride reducing agent.
[0206] The non-natural amino acid containing polypeptide can
contain at least one, at least two, at least three, at least four,
at least five, at least six, at least seven, at least eight, at
least nine, or ten or more non-natural amino acids containing an
aromatic amine, heteroaromatic amine, or protected forms thereof.
The non-natural amino acids can be the same or different, for
example, there can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, or more different sites in the protein
that comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, or more different non-natural amino acids. In
certain embodiments, at least one, but fewer than all, of a
particular amino acid present in a naturally occurring version of
the protein is substituted with a non-natural amino acid. The
non-natural amino acid polypeptide may also contain one or more
non-natural amino acids that are not non-material amino acids
containing an aromatic amine, heteroaromatic amine, or protected
forms thereof.
[0207] The methods and compositions provided and described herein
include polypeptides comprising at least one non-natural amino acid
containing an aromatic amine, heteroaromatic amine, or protected
forms thereof. Introduction of at least one such non-natural amino
acid into a polypeptide can allow for the application of
conjugation chemistries that involve specific chemical reactions,
including, but not limited to, with one or more non-natural amino
acids while not reacting with the commonly occurring 20 amino
acids. Such specific chemical reactions involving such incorporated
the amino acid side chains includes, but is not limited to,
reductive alkylation chemistry methodologies suitable for the
particular functional groups or substituents present. Once
incorporated, the amino acid side chains can then be modified by
utilizing chemistry methodologies known to those of ordinary skill
in the art to be suitable for the particular functional groups or
substituents present in the naturally encoded amino acid.
[0208] The non-natural amino acid methods and compositions
described herein provides conjugates of substances having a wide
variety of functional groups, substituents or moieties, with other
substances including but not limited to a label; a dye; a polymer;
a water-soluble polymer; a derivative of polyethylene glycol; a
photocrosslinker; a cytotoxic compound; a drug; an affinity label;
a photoaffinity label; a reactive compound; a resin; a second
protein or polypeptide or polypeptide analog; an antibody or
antibody fragment; a metal chelator; a cofactor; a fatty acid; a
carbohydrate; a polynucleotide; a DNA; a RNA; an antisense
polynucleotide; a saccharide, a water-soluble dendrimer, a
cyclodextrin, a biomaterial; a nanoparticle; a spin label; a
fluorophore, a metal-containing moiety; a radioactive moiety; a
novel functional group; a group that covalently or noncovalently
interacts with other molecules; a photocaged moiety; an actinic
radiation excitable moiety; a ligand; a photoisomerizable moiety;
biotin; a biotin analogue; a moiety incorporating a heavy atom; a
chemically cleavable group; a photocleavable group; an elongated
side chain; a carbon-linked sugar; a redox-active agent; an amino
thioacid; a toxic moiety; an isotopically labeled moiety; a
biophysical probe; a phosphorescent group; a chemiluminescent
group; an electron dense group; a magnetic group; an intercalating
group; a chromophore; an energy transfer agent; a biologically
active agent; a detectable label; a small molecule; an inhibitory
ribonucleic acid; a radionucleotide; a neutron-capture agent; a
derivative of biotin; quantum dot(s); a nanotransmitter; a
radiotransmitter; an abzyme, an activated complex activator, a
virus, an adjuvant, an aglycan, an allergan, an angiostatin, an
antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a
shuttle vector, a macromolecule, a mimotope, a receptor, a reverse
micelle, and any combination thereof.
[0209] In another aspect of the compositions, methods, techniques
and strategies described herein are methods for studying or using
any of the aforementioned modified or unmodified non-natural amino
acid polypeptides. Included within this aspect, by way of example
only, are therapeutic, diagnostic, assay-based, industrial,
cosmetic, plant biology, environmental, energy-production, and/or
military uses which would benefit from a polypeptide comprising a
modified or unmodified non-natural amino acid polypeptide or
protein.
III. Location of Non-Natural Amino Acids in Polypeptides
[0210] The methods and compositions described herein include
incorporation of one or more non-natural amino acids into a
polypeptide. One or more non-natural amino acids may be
incorporated at one or more particular position which does not
disrupt activity of the polypeptide. This can be achieved by making
"conservative" substitutions, including but not limited to,
substituting hydrophobic amino acids with non-natural or natural
hydrophobic amino acids, bulky amino acids for non-natural or
natural bulky amino acids, hydrophilic amino acids for non-natural
or natural hydrophilic amino acids and/or inserting the non-natural
amino acid in a location that is not required for activity.
[0211] A variety of biochemical and structural approaches can be
employed to select the desired sites for substitution with a
non-natural amino acid within the polypeptide. Any position of the
polypeptide chain is suitable for selection to incorporate a
non-natural amino acid, and selection may be based on rational
design or by random selection for any or no particular desired
purpose. Selection of desired sites may be for producing a
non-natural amino acid polypeptide (which may be further modified
or remain unmodified) having any desired property or activity,
including but not limited to agonists, super-agonists, inverse
agonists, antagonists, receptor binding modulators, receptor
activity modulators, modulators of binding to binder partners,
binding partner activity modulators, binding partner conformation
modulators, dimer or multimer formation, no change to activity or
property compared to the native molecule, or manipulating any
physical or chemical property of the polypeptide such as
solubility, aggregation, or stability. For example, locations in
the polypeptide required for biological activity of a polypeptide
can be identified using point mutation analysis, alanine scanning
or homolog scanning methods known in the art. Residues other than
those identified as critical to biological activity by alanine or
homolog scanning mutagenesis may be good candidates for
substitution with a non-natural amino acid depending on the desired
activity sought for the polypeptide. Alternatively, the sites
identified as critical to biological activity may also be good
candidates for substitution with a non-natural amino acid, again
depending on the desired activity sought for the polypeptide.
Another alternative would be to simply make serial substitutions in
each position on the polypeptide chain with a non-natural amino
acid and observe the effect on the activities of the polypeptide.
Any means, technique, or method for selecting a position for
substitution with a non-natural amino acid into any polypeptide is
suitable for use in the methods, techniques and compositions
described herein.
[0212] The structure and activity of naturally-occurring mutants of
a polypeptide that contain deletions can also be examined to
determine regions of the protein that are likely to be tolerant of
substitution with a non-natural amino acid. Once residues that are
likely to be intolerant to substitution with non-natural amino
acids have been eliminated, the impact of proposed substitutions at
each of the remaining positions can be examined from the
three-dimensional structure of the relevant polypeptide, and any
associated ligands or binding proteins. X-ray crystallographic
and
[0213] NMR structures of many polypeptides are available in the
Protein Data Bank (PDB, www.rcsb.org), a centralized database
containing three-dimensional structural data of large molecules of
proteins and nucleic acids. In addition, models may be made
investigating the secondary and tertiary structure of polypeptides,
if three-dimensional structural data is not available. Thus, the
identity of amino acid positions that can be substituted with
non-natural amino acids can be readily obtained.
[0214] Exemplary sites of incorporation of a non-natural amino acid
include, but are not limited to, those that are excluded from
potential receptor binding regions or regions for binding to
binding proteins or ligands, may be fully or partially solvent
exposed, have minimal or no hydrogen-bonding interactions with
nearby residues, may be minimally exposed to nearby reactive
residues, and may be in regions that are highly flexible as
predicted by the three-dimensional crystal structure of a
particular polypeptide with its associated receptor, ligand or
binding proteins.
[0215] A wide variety of non-natural amino acids can be substituted
for, or incorporated into, a given position in a polypeptide. In
general, a particular non-natural amino acid is selected for
incorporation based on an examination of the three dimensional
crystal structure of a polypeptide with its associated ligand,
receptor and/or binding proteins, a preference for conservative
substitutions (i.e., aryl-based non-natural amino acids, such as
p-acetylphenylalanine or O-propargyltyrosine substituting for Phe,
Tyr or Trp), and the specific conjugation chemistry that one
desires to introduce into the polypeptide protein.
[0216] In one embodiment, the method further includes incorporating
into the protein the non-natural amino acid, where the non-natural
amino acid comprises a first reactive group; and contacting the
protein with a molecule (including but not limited to a label; a
dye; a polymer; a water-soluble polymer; a derivative of
polyethylene glycol; a photocrosslinker; a cytotoxic compound; a
drug; an affinity label; a photoaffinity label; a reactive
compound; a resin, a second protein or polypeptide or polypeptide
analog; an antibody or antibody fragment; a metal chelator; a
cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a
RNA; an antisense polynucleotide; a saccharide, a water-soluble
dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin
label; a fluorophore, a metal-containing moiety; a radioactive
moiety; a novel functional group; a group that covalently or
noncovalently interacts with other molecules; a photocaged moiety;
an actinic radiation excitable moiety; a ligand; a
photoisomerizable moiety; biotin; a biotin analogue; a moiety
incorporating a heavy atom; a chemically cleavable group; a
photocleavable group; an elongated side chain; a carbon-linked
sugar; a redox-active agent; an amino thioacid; a toxic moiety; an
isotopically labeled moiety; a biophysical probe; a phosphorescent
group; a chemiluminescent group; an electron dense group; a
magnetic group; an intercalating group; a chromophore; an energy
transfer agent; a biologically active agent; a detectable label; a
small molecule; an inhibitory ribonucleic acid; a radionucleotide;
a neutron-capture agent; a derivative of biotin; quantum dot(s); a
nanotransmitter; a radiotransmitter; an abzyme, an activated
complex activator, a virus, an adjuvant, an aglycan, an allergan,
an angiostatin, an antihormone, an antioxidant, an aptamer, a guide
RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a
receptor, a reverse micelle, and any combination thereof) that
comprises a second reactive group. In certain embodiments, the
first reactive group is an amine moiety on an aromatic amine and
the second reactive group is an aldehyde, wherein the amine group
is reductively alkylated upon contact with the aldehyde in the
presence of a reducing agent, such as sodium cyanborohydride. In
other embodiments, the first reactive group is an amine moiety on a
heteroaromatic amine and the second reactive group is an aldehyde,
wherein the amine group is reductively alkylated upon contact with
the aldehyde in the presence of a reducing agent, such as sodium
cyanborohydride.
[0217] In some cases, the non-natural amino acid substitution(s) or
incorporation(s) will be combined with other additions,
substitutions, or deletions within the polypeptide to affect other
biological traits. In some cases, the other additions,
substitutions or deletions may increase the stability (including
but not limited to, resistance to proteolytic degradation) of the
polypeptide or increase affinity of the polypeptide for its
appropriate receptor, ligand and/or binding proteins. In some
cases, the other additions, substitutions or deletions may increase
the solubility (including but not limited to, when expressed in E.
coli or other host cells) of the polypeptide. In some embodiments
sites are selected for substitution with a naturally encoded or
non-natural amino acid in addition to another site for
incorporation of a non-natural amino acid for the purpose of
increasing the polypeptide solubility following expression in E.
coli or other recombinant host cells. In some embodiments, the
polypeptides comprise another addition, substitution, or deletion
that modulates affinity for the associated ligand, binding
proteins, and/or receptor, modulates (including but not limited to,
increases or decreases) receptor dimerization, stabilizes receptor
dimers, modulates circulating half-life, modulates release or
bio-availability, facilitates purification, or improves or alters a
particular route of administration. Similarly, polypeptide can
comprise chemical or enzyme cleavage sequences, protease cleavage
sequences, reactive groups, antibody-binding domains (including but
not limited to, FLAG or poly-His) or other affinity based sequences
(including but not limited to, FLAG, poly-His, GST, etc.) or linked
molecules (including but not limited to, biotin) that improve
detection (including but not limited to, GFP), purification
transport thru tissues or cell membranes, prodrug release or
activation, size reduction, or other traits of the polypeptide.
IV. Growth Hormone Supergene Family as Exemplar
[0218] The methods, compositions, strategies and techniques
described herein are not limited to a particular type, class or
family of polypeptides or proteins. Indeed, virtually any
polypeptides may be designed or modified to include at least one
modified or unmodified non-natural amino acids described herein. By
way of example only, the polypeptide can be homologous to a
therapeutic protein selected from the group consisting of: alpha-1
antitrypsin, angiostatin, antihemolytic factor, antibody, antibody
fragment, apolipoprotein, apoprotein, atrial natriuretic factor,
atrial natriuretic polypeptide, atrial peptide, C-X-C chemokine,
T39765, NAP-2, ENA-78, gro-a, gro-b, gro-c, IP-10, GCP-2, NAP-4,
SDF-1, PF4, MIG, calcitonin, c-kit ligand, cytokine, CC chemokine,
monocyte chemoattractant protein-1, monocyte chemoattractant
protein-2, monocyte chemoattractant protein-3, monocyte
inflammatory protein-1 alpha, monocyte inflammatory protein-i beta,
RANTES, 1309, R83915, R91733, HCC1, T58847, D31065, T64262, CD40,
CD40 ligand, c-kit ligand, collagen, colony stimulating factor
(CSF), complement factor 5a, complement inhibitor, complement
receptor 1, cytokine, epithelial neutrophil activating peptide-78,
MIP-16, MCP-1, epidermal growth factor (EGF), epithelial neutrophil
activating peptide, erythropoietin (EPO), exfoliating toxin, Factor
IX, Factor VII, Factor VIII, Factor X, fibroblast growth factor
(FGF), fibrinogen, fibronectin, four-helical bundle protein, G-CSF,
glp-1, GM-CSF, glucocerebrosidase, gonadotropin, growth factor,
growth factor receptor, grf, hedgehog protein, hemoglobin,
hepatocyte growth factor (hGF), hirudin, human growth hormone
(hGH), human serum albumin, ICAM-1, ICAM-1 receptor, LFA-1, LFA-1
receptor, insulin, insulin-like growth factor (IGF), IGF-I, IGF-II,
interferon (IFN), IFN-alpha, IFN-beta, IFN-gamma, any
interferon-like molecule or member of the IFN family, interleukin
(IL), IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10,
IL-11, IL-12, keratinocyte growth factor (KGF), lactoferrin,
leukemia inhibitory factor, luciferase, neurturin, neutrophil
inhibitory factor (NIF), oncostatin M, osteogenic protein, oncogene
product, paracitonin, parathyroid hormone, PD-ECSF, PDGF, peptide
hormone, pleiotropin, protein A, protein G, pth, pyrogenic exotoxin
A, pyrogenic exotoxin B, pyrogenic exotoxin C, pyy, relaxin, renin,
SCF, small biosynthetic protein, soluble complement receptor I,
soluble I-CAM 1, soluble interleukin receptor, soluble TNF
receptor; somatomedin, somatostatin, somatotropin, streptokinase,
superantigens, staphylococcal enterotoxin, SEA, SEB, SEC1, SEC2,
SEC3, SED, SEE, steroid hormone receptor, superoxide dismutase,
toxic shock syndrome toxin, thymosin alpha 1, tissue plasminogen
activator, tumor growth factor (TGF), tumor necrosis factor, tumor
necrosis factor alpha, tumor necrosis factor beta, tumor necrosis
factor receptor (TNFR), VLA4 protein, VCAM-1 protein, vascular
endothelial growth factor (VEGF), urokinase, mos, ras, raf, met,
p53, tat, fos, myc, jun, myb, rel, estrogen receptor, progesterone
receptor, testosterone receptor, aldosterone receptor, LDL
receptor, and corticosterone.
[0219] Thus, the following description of the growth hormone (GH)
supergene family is provided for illustrative purposes and by way
of example only, and not as a limit on the scope of the methods,
compositions, strategies and techniques described herein. Further,
reference to GH polypeptides in this application is intended to use
the generic term as an example of any member of the GH supergene
family. Thus, it is understood that the modifications and
chemistries described herein with reference to GH polypeptides or
protein can be equally applied to any member of the GH supergene
family, including those specifically listed herein.
[0220] The following proteins include those encoded by genes of the
growth hormone (GH) supergene family (Bazan, F., Immunology Today
11: 350-354 (1990); Bazan, J. F. Science 257: 410-413 (1992); Mott,
H. R. and Campbell, I. D., Current Opinion in Structural Biology 5:
114-121 (1995); Silvennoinen, O. and Ihle, J. N., SIGNALLING BY THE
HEMATOPOIETIC CYTOKNE RECEPTORS (1996)): growth hormone, prolactin,
placental lactogen, erythropoietin (EPO), thrombopoietin (TPO);
interleukin-2 (IL-2), IL-3, IL-4, IL-5, IL-6, IL-7, IL-9, IL-10,
IL-11, IL-12 (p35 subunit), IL-13, IL-15, oncostatin M, ciliary
neurotrophic factor, leukemia inhibitory factor, alpha interferon,
beta interferon, epsilon interferon, gamma interferon, omega
interferon, tau interferon, granulocyte-colony stimulating factor
(G-CSF), granulocyte-macrophage colony stimulating factor (GM-CSF),
macrophage colony stimulating factor (M-CSF) and cardiotrophin-1
(CT-1) ("the GH supergene family"). It is anticipated that
additional members of this gene family will be identified in the
future through gene cloning and sequencing. Members of the GH
supergene family have similar secondary and tertiary structures,
despite the fact that they generally have limited amino acid or DNA
sequence identity. The shared structural features allow new members
of the gene family to be readily identified and the non-natural
amino acid methods and compositions described herein similarly
applied.
[0221] Structures of a number of cytokines, including G-CSF (Zink
et al., FEBS Lett. 314:435 (1992); Zink et al., Biochemistry
33:8453 (1994); Hill et al., Proc. Natl. Acad. Sci. USA 90:5167
(1993)), GM-CSF (Diederichs, K., et al. Science 154: 1779-1782
(1991); Walter et al., J. Mol. Biol. 224:1075-1085 (1992)), IL-2
(Bazan, J. F. and McKay, D. B. Science 257: 410-413 (1992)), IL-4
(Redfield et al., Biochemistry 30: 11029-11035 (1991); Powers et
al., Science 256:1673-1677 (1992)), and IL-5 (Milburn et al.,
Nature 363: 172-176 (1993)) have been determined by X-ray
diffraction and NMR studies and show striking conservation with the
GH structure, despite a lack of significant primary sequence
homology. IFN is considered to be a member of this family based
upon modeling and other studies (Lee et al., J. Interferon.
Cytokine Res. 15:341 (1995); Murgolo et al., Proteins 17:62 (1993);
Radhakrishnan et al., Structure 4:1453 (1996); Klaus et al., J.
Mol. Biol. 274:661 (1997)). A large number of additional cytokines
and growth factors including ciliary neurotrophic factor (CNTF),
leukemia inhibitory factor (LIF), thrombopoietin (TPO), oncostatin
M, macrophage colony stimulating factor (M-CSF), IL-3, IL-6, IL-7,
IL-9, IL-12, IL-13, IL-15, and granulocyte-colony stimulating
factor (G-CSF), as well as the IFN's such as alpha, beta, omega,
tau, epsilon, and gamma interferon belong to this family (reviewed
in Mott and Campbell, Current Opinion in Structural Biology 5:
114-121 (1995); Silvennoinen and Ihle (1996) SIGNALLING BY THE
HEMATOPOIETIC CYTOKINE RECEPTORS). All of the above cytokines and
growth factors are now considered to comprise one large gene
family.
[0222] In addition to sharing similar secondary and tertiary
structures, members of this family share the property that they
must oligomerize cell surface receptors to activate intracellular
signaling pathways. Some GH family members, including but not
limited to; GH and EPO, bind a single type of receptor and cause it
to form homodimers. Other family members, including but not limited
to, IL-2, IL4. and IL-6, bind more than one type of receptor and
cause the receptors to form heterodimers or higher order aggregates
(Davis et al., (1993) Science 260: 1805-1808; Paonessa et al.,
1995) EMBO J. 14: 1942-1951; Mott and Campbell, Current Opinion in
Structural Biology 5: 114-121 (1995)). Mutagenesis studies have
shown that, like GH, these other cytokines and growth factors
contain multiple receptor binding sites, typically two, and bind
their cognate receptors sequentially. (Mott and Campbell, Current
Opinion in Structural Biology 5: 114-121 (1995); Matthews et al.,
(1996) Proc. Natl. Acad. Sci. USA 93: 9471-9476). Like GH, the
primary receptor binding sites for these other family members occur
primarily in the four alpha helices and the A-B loop. The specific
amino acids in the helical bundles that participate in receptor
binding differ amongst the family members. Most of the cell surface
receptors that interact with members of the GH supergene family are
structurally related and comprise a second large multi-gene family.
See, e.g. U.S. Pat. No. 6,608,183, which is herein incorporated by
reference in its entirety.
[0223] A general conclusion reached from mutational studies of
various members of the GH supergene family is that the loops
joining the alpha helices generally tend to not be involved in
receptor binding. In particular the short B-C loop appears to be
non-essential for receptor binding in most, if not all, family
members. For this reason, the B-C loop may be substituted with
non-natural amino acids as described herein in members of the GH
supergene family. The A-B loop, the C-D loop (and D-E loop of
interferon/IL-10-like members of the GH superfamily) may also be
substituted with a non-natural amino acid. Amino acids proximal to
helix A and distal to the final helix also tend not to be involved
in receptor binding and also may be sites for introducing
non-natural amino acids. In some embodiments, a non-natural amino
acid is substituted at any position within a loop structure
including but not limited to the first 1, 2, 3, 4, 5, 6, 7, or more
amino acids of the A-B, B-C, C-D or D-E loop. In some embodiments,
a non-natural amino acid is substituted within the last 1, 2, 3, 4,
5, 6, 7, or more amino acids of the A-B, B-C, C-D or D-E loop.
[0224] Certain members of the GH family, including but not limited
to, EPO, IL-2, IL-3, IL4, IL-6, GM-CSF, TPO, IL-10, IL-12 p35,
IL-13, IL-15 and beta interferon contain N-linked and/or O-linked
sugars. The glycosylation sites in the proteins occur almost
exclusively in the loop regions and not in the alpha helical
bundles. Because the loop regions generally are not involved in
receptor binding and because they are sites for the covalent
attachment of sugar groups, they may be useful sites for
introducing non-natural amino acid substitutions into the proteins.
Amino acids that comprise the N- and O-linked glycosylation sites
in the proteins may be sites for non-natural amino acid
substitutions because these amino acids are surface-exposed.
Therefore, the natural protein can tolerate bulky sugar groups
attached to the proteins at these sites and the glycosylation sites
tend to be located away from the receptor binding sites.
[0225] Additional members of the GH gene family are likely to be
discovered in the future. New members of the GH supergene family
can be identified through computer-aided secondary and tertiary
structure analyses of the predicted protein sequences, and by
selection techniques designed to identify molecules that bind to a
particular target. Members of the GH supergene family typically
possess four or five amphipathic helices joined by non-helical
amino acids (the loop regions). The proteins may contain a
hydrophobic signal sequence at their N-terminus to promote
secretion from the cell. Such later discovered members of the GH
supergene family also are included within the methods and
compositions described herein.
V. Non-Natural Amino Acids
[0226] A very wide variety of non-natural amino acids are suitable
for use in the methods and compositions described herein as long as
they have at least one of the following four properties: (1) at
least one functional group on the sidechain of the non-natural
amino acid has at least one characteristics and/or activity and/or
reactivity orthogonal to the chemical reactivity of the 20 common,
genetically-encoded amino acids (i.e., alanine, arginine,
asparagine, aspartic acid, cysteine, glutamine, glutamic acid,
glycine, histidine, isoleucine, leucine, lysine, methionine,
phenylalanine, proline, serine, threonine, tryptophan, tyrosine,
and valine), or at least orthogonal to the chemical reactivity of
the naturally occurring amino acids present in the polypeptide that
includes the non-natural amino acid; (2) the introduced non-natural
amino acids are substantially chemically inert toward the 20
common, genetically-encoded amino acids; (3) the non-natural amino
acid can be stably incorporated into a polypeptide, preferably with
the stability commensurate with the naturally-occurring amino acids
or under typical physiological conditions, and further preferably
such incorporation can occur via an in vivo system; and (4) the
non-natural amino acid includes an aromatic amine or heteroaromatic
amine, or a functional group that can be transformed into an
aromatic amine or heteroaromatic amine, by reacting with a reagent,
preferably under conditions that do not destroy the biological
properties of the polypeptide that includes the non-natural amino
acid (unless of course such a destruction of biological properties
is the purpose of the modification/transformation), or where the
transformation can occur under aqueous conditions at a pH between
about 4 and about 10, or where the reactive site on the non-natural
amino acid is an nucleophilic site. Illustrative, non-limiting
examples of amino acids that satisfy these four properties for
non-natural amino acids that can be used with the compositions and
methods described herein are presented throughout the Figures and
the text herein. Any number of non-natural amino acids can be
introduced into the polypeptide. Non-natural amino acids may also
include a protected or masked aromatic amine or heteroaromatic
amine, whereby upon deprotection or unmasking, the protected or
masked aromatic amine or heteroaromatic amine are transformed into
an aromatic amine or heteroaromatic amine.
[0227] Non-natural amino acids of interest that may be suitable for
use in the methods and compositions described herein include, but
are not limited to, amino acids comprising a photoactivatable
cross-linker, spin-labeled amino acids, fluorescent amino acids,
metal binding amino acids, metal-containing amino acids,
radioactive amino acids, amino acids with novel functional groups,
amino acids that covalently or noncovalently interact with other
molecules, photocaged and/or photoisomerizable amino acids, amino
acids comprising biotin or a biotin analogue, glycosylated amino
acids such as a sugar substituted serine, other carbohydrate
modified amino acids, keto-containing amino acids, amino acids
comprising polyethylene glycol or polyether, heavy atom substituted
amino acids, chemically cleavable and/or photocleavable amino
acids, amino acids with an elongated side chains as compared to
natural amino acids, including but not limited to, polyethers or
long chain hydrocarbons, including but not limited to, greater than
about 5 or greater than about 10 carbons, carbon-linked
sugar-containing amino acids, redox-active amino acids, amino
thioacid containing amino acids, and amino acids comprising one or
more toxic moiety.
[0228] In some embodiments, non-natural amino acids comprise a
saccharide moiety. Examples of such amino acids include
N-acetyl-L-glucosaminyl-L-serine,
N-acetyl-L-galactosaminyl-L-serine,
N-acetyl-L-glucosaminyl-L-threonine,
N-acetyl-L-glucosaminyl-L-asparagine and O-mannosaminyl-L-serine.
Examples of such amino acids also include examples where the
naturally-occurring N- or O-linkage between the amino acid and the
saccharide is replaced by a covalent linkage not commonly found in
nature--including but not limited to, an amine linkage, and the
like. Examples of such amino acids also include saccharides that
are not commonly found in naturally-occurring proteins such as
2-deoxy-glucose, 2-deoxygalactose and the like.
[0229] The chemical moieties via non-natural amino acids that can
be incorporated into proteins offer a variety of advantages and
manipulations of the protein. For example, a heavy atom non-natural
amino acid, for example, can be useful for phasing x-ray structure
data. The site-specific introduction of heavy atoms using
non-natural amino acids also provides selectivity and flexibility
in choosing positions for heavy atoms. Photoreactive non-natural
amino acids (including but not limited to, amino acids with
benzophenone and arylazides (including but not limited to,
phenylazide) side chains), for example, allow for efficient in vivo
and in vitro photocrosslinking of protein. Examples of
photoreactive non-natural amino acids include, but are not limited
to, p-azido-phenylalanine and p-benzoyl-phenylalanine. The protein
with the photoreactive non-natural amino acids can then be
crosslinked at will by excitation of the photoreactive
group-providing temporal control. In one example, the methyl group
of a non-natural amino can be substituted with an isotopically
labeled, including but not limited to, methyl group, as a probe of
local structure and dynamics, including but not limited to, with
the use of nuclear magnetic resonance and vibrational
spectroscopy.
A. Structure and Synthesis of Non-Natural Amino Acids: Alkylated
Aromatic Amine Groups
[0230] Non-natural amino acids with nucleophilic reactive groups,
such as, by way of example only, an aromatic amine group (including
secondary and tertiary amine groups), a masked aromatic amine group
(which can be readily converted into a aromatic amine group), or a
protected aromatic amine group (which has reactivity similar to an
aromatic amine group upon deprotection) allow for a variety of
reactions to link molecules via various reactions, including but
not limited to, reductive alkylation reactions with aldehyde
containing reagents. Such aromatic amine containing non-natural
amino acids include amino acids having the structure of Formula
(A):
##STR00002##
wherein:
##STR00003##
is selected from the group consisting of a monocyclic aryl ring, a
bicyclic aryl ring, a multicyclic aryl ring, a monocyclic
heteroaryl ring, a bicyclic heteroaryl ring, and a multicyclic
heteroaryl ring; [0231] A is independently CR.sub.a, or N; [0232] B
is independently CR.sub.a, N, O, or S; [0233] each R.sub.a is
independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; and n is 0, 1, 2, 3, 4, 5, or 6; [0234] R.sub.1 is
H, an amino protecting group, resin, amino acid, polypeptide, or
polynucleotide; and [0235] R.sub.2 is OH, an ester protecting
group, resin, amino acid, polypeptide, or polynucleotide; [0236]
each of R.sub.3 and R.sub.4 is independently H, halogen, lower
alkyl, or substituted lower alkyl, or R.sub.3 and R.sub.4 or two
R.sub.3 groups optionally form a cycloalkyl or a heterocycloalkyl;
[0237] M is H or --CH.sub.2R.sub.5; or the M-N--C(R.sub.5) moiety
may form a 4 to 7 membered ring structure; [0238] R.sub.5 is alkyl,
substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0239] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--;
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd., --C(R').sub.2--N--,
and --C(R').sub.2--N(R')--N(R')--; [0240] or two R.sub.5 groups
optionally form a cycloalkyl or a heterocycloalkyl; [0241] or
R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; and [0242] each R' is independently H, alkyl, or
substituted alkyl. Such non-natural amino acids may also be in the
form of a salt, or may be incorporated into a non-natural amino
acid polypeptide, polymer, polysaccharide, or a polynucleotide and
optionally reductively alkylated. The structure
##STR00004##
[0242] (as presented in all examples herein) does not present the
relative orientations of "A," "B," "NH-M" and "R.sub.a"; rather
these four features of this structure may be oriented in any
chemically-sound manner (along with other features of this
structure), as illustrated by example herein.
[0243] Non-natural amino acids containing an aromatic amine moiety
having the structure of Formula (A) include non-natural amino acids
having the structure of Formula (I), Formula (II), Formula (III),
Formula (IV), and Formula (V):
##STR00005##
wherein, each A' is independently selected from CR.sub.a, N, or
##STR00006##
and up to two A' may be
##STR00007##
[0244] with the remaining A' selected from CR.sub.n, or N. Such
non-natural amino acids may also be in the form of a salt, or may
be incorporated into a non-natural amino acid polypeptide, polymer,
polysaccharide, or a polynucleotide and optionally reductively
alkylated.
[0245] Non-limiting examples of non-natural amino acids containing
an aromatic amine moiety having the structure of Formula (A)
include non-natural amino acids having the structure of Formula
(VI), and Formula (VII),
##STR00008##
wherein; G is an amine protecting group, including, but not limited
to,
##STR00009##
Such non-natural amino acids may be in the form of a salt, or may
be incorporated into a non-natural amino acid polypeptide, polymer,
polysaccharide, or a polynucleotide and optionally reductively
alkylated.
[0246] Non-natural amino acids containing an aromatic amine moiety
have the following structures:
##STR00010## [0247] wherein each R.sub.a is independently selected
from the group consisting of H, halogen, alkyl, --NO.sub.2, --CN,
substituted alkyl, --N(R').sub.2, --C(O).sub.kR',
--C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where k is 1, 2, or
3; [0248] M is H or --CH.sub.2R.sub.5; or the M-N--C(R.sub.5)
moiety may form a 4 to 7 membered ring structure; [0249] R.sub.1 is
H, an amino protecting group, resin, amino acid, polypeptide, or
polynucleotide; [0250] R.sub.2 is OH, an ester protecting group,
resin, amino acid, polypeptide, or polynucleotide; [0251] R.sub.5
is alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0252] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; [0253]
or R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; and [0254] each R' is independently H, alkyl, or
substituted alkyl. Such non-natural amino acids may also be in the
form of a salt, or may be incorporated into a non-natural amino
acid polypeptide, polymer, polysaccharide, or a polynucleotide.
[0255] Other non-limiting examples of non-natural amino acids
containing an aromatic amine moiety having the structure of Formula
(A) are shown in FIGS. 2-10. Such non-natural amino acids may also
be in the form of a salt, or may be incorporated into a non-natural
amino acid polypeptide, polymer, polysaccharide, or a
polynucleotide.
[0256] Non-limiting examples of syntheses of compounds of Formula
(A) are shown in FIGS. 11-13. Such examples show the syntheses of
non-natural amino acids containing aromatic amine moieties, wherein
the amine moiety created is a primary or secondary amine. Such
non-natural amino acids may be in the form of a salt, or may be
incorporated into a non-natural amino acid polypeptide, polymer,
polysaccharide, or a polynucleotide and optionally reductively
alkylated.
[0257] A non-limiting formation of an aromatic amine-containing
non-natural amino acid having the structure of Formula (A) is shown
in FIG. 14, wherein by way of example only, non-natural amino acids
of Formula (A) may be formed by reduction of protected or masked
amine moieties on the aromatic moiety of a non-natural amino acid.
Such protected or masked amine moieties include, but are not
limited to, imines, hydrazines, nitro, or azide substituents. The
reducing agents used to reduce such protected or masked amine
moieties include, but are not limited to, TCEP, Na.sub.2S,
Na.sub.2S.sub.2O.sub.4, LiAlH.sub.4, NaBH.sub.4 or NaBCNH.sub.3.
Such non-natural amino acids containing the protected or masked
amine moieties on an aromatic moiety have the structure of Formula
(B),
##STR00011##
wherein:
##STR00012##
is selected from the group consisting of a monocyclic aryl ring, a
bicyclic aryl ring, a multicyclic aryl ring, a monocyclic
heteroaryl ring, a bicyclic heteroaryl ring, and a multicyclic
heteroaryl ring; [0258] A is independently CR.sub.a, or N; [0259] B
is independently CR.sub.a, N, O, or S; [0260] each R.sub.a is
independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; and n is 0, 1, 2, 3, 4, 5, or 6; [0261] R.sub.1 is
H, an amino protecting group, resin, amino acid, polypeptide, or
polynucleotide; and [0262] R.sub.2 is OH, an ester protecting
group, resin, amino acid, polypeptide, or polynucleotide; [0263]
each of R.sub.3 and R.sub.4 is independently H, halogen, lower
alkyl, or substituted lower alkyl, or R.sub.3 and R.sub.4 or two
R.sub.3 groups optionally form a cycloalkyl or a heterocycloalkyl;
[0264] Y is --NH--NH.sub.2, --NH--NHR', --CR'.dbd.NR', --NO.sub.2,
or --N.sub.3, and [0265] each R' is independently H, alkyl, or
substituted alkyl. Such protected non-natural amino acids may be in
the form of a salt, or may be incorporated into a non-natural amino
acid polypeptide, polymer, polysaccharide, or polynucleotide. The
structure
##STR00013##
[0265] (as presented in all examples herein) does not present the
relative orientations of "A," "B," "Y" and "R.sub.a"; rather these
four features of this structure may be oriented in any
chemically-sound manner (along with other features of this
structure), as illustrated by example herein.
[0266] Non-natural amino acids containing an aromatic amine moiety
having the structure of Formula (B) include non-natural amino acids
having the structures of Formula (VIII), Formula (IX), Formula (X),
and Formula (XI),
##STR00014##
Such protected non-natural amino acids may be in the form of a
salt, or may be incorporated into a non-natural amino acid
polypeptide, polymer, polysaccharide, or polynucleotide. Such
non-natural amino acids may also be translationally incorporated
into a non-natural amino acid polypeptide and then
post-translationally modified by reduction to form non-natural
amino acids having the structure of Formula (A) as part of the
non-natural amino acid polypeptide. In addition, non-natural amino
acids having the structure of Formula (B) may also be incorporated
into a polymer, polysaccharide, polynucleotide or chemically
synthesized polypeptide, and are then reduced to form non-natural
amino acids having the structure of Formula (A) as part of the
polymer, polysaccharide, polynucleotide or chemically synthesized
polypeptide. Such incorporated non-natural amino acids having the
structure of Formula (A) may then be optionally reductively
alkylated.
[0267] Other non-limiting examples of such non-natural amino acids
containing protected or masked amine moieties are shown in FIG.
15
B. Structure and Synthesis of Non-Natural Amino Acids: Alkylated
Aromatic Amine Groups
[0268] Non-natural amino acids with nucleophilic reactive groups,
such as, by way of example only, an aromatic amine group (including
secondary and tertiary amine groups), a masked aromatic amine group
(which can be readily converted into a aromatic amine group), or a
protected aromatic amine group (which has reactivity similar to a
aromatic amine group upon deprotection) allow for a variety of
reactions to link molecules via various reactions, including but
not limited to, reductive alkylation reactions with aldehyde
containing reagents. Such alkylated non-natural amino acids include
amino acids having the structure of Formula (C):
##STR00015##
wherein:
##STR00016##
is selected from the group consisting of a monocyclic aryl ring, a
bicyclic aryl ring, a multicyclic aryl ring, a monocyclic
heteroaryl ring, a bicyclic heteroaryl ring, and a multicyclic
heteroaryl ring; [0269] A is independently CR.sub.a, or N; [0270] B
is independently CR.sub.a, N, O, or S; [0271] each R.sub.a is
independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; and n is 0, 1, 2, 3, 4, 5, or 6; [0272] R.sub.1 is
H, an amino protecting group, resin, amino acid, polypeptide, or
polynucleotide; and [0273] R.sub.2 is OH, an ester protecting
group, resin, amino acid, polypeptide, or polynucleotide; [0274]
each of R.sub.3 and R.sub.4 is independently H, halogen, lower
alkyl, or substituted lower alkyl, or R.sub.3 and R.sub.4 or two
R.sub.3 groups optionally form a cycloalkyl or a heterocycloalkyl;
[0275] M is H or --CH.sub.2R.sub.5; or the M-N--C(R.sub.5) moiety
may form a 4 to 7 membered ring structure; [0276] R.sub.5 is alkyl,
substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0277] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R')--N(R')--N(R')--; [0278] or
two R.sub.5 groups optionally form a cycloalkyl or a
heterocycloalkyl; [0279] or R.sub.5 and any R.sub.a optionally form
a cycloalkyl or a heterocycloalkyl; and [0280] each R' is
independently H, alkyl, or substituted alkyl. Such non-natural
amino acids may also be in the form of a salt, or may be
incorporated into a non-natural amino acid polypeptide, polymer,
polysaccharide, or a polynucleotide and optionally reductively
alkylated. The structure
##STR00017##
[0280] (as presented in all examples herein) does not present the
relative orientations of "A," "B," "N(M)CH.sub.2R.sub.5" and
"R.sub.a"; rather these four features of this structure may be
oriented in any chemically-sound manner (along with other features
of this structure), as illustrated by example herein.
[0281] Non-natural amino acids containing an aromatic amine moiety
having the structure of Formula (C) include non-natural amino acids
having the structure of Formula (XII), Formula (XIII), Formula
(XIV), Formula (XV), and Formula (XVI):
##STR00018##
wherein, each A' is independently selected from CR.sub.a, N, or
##STR00019##
and up to two A' may be
##STR00020##
[0282] with the remaining A'-selected from CR.sub.a, or N. Such
non-natural amino acids may also be in the form of a salt, or may
be incorporated into a non-natural amino acid polypeptide, polymer,
polysaccharide, or a polynucleotide and optionally reductively
alkylated.
[0283] Other non-limiting examples of non-natural amino acids
containing an aromatic amine moiety having the structure of Formula
(C) are shown in FIGS. 8-10. Such non-natural amino acids may also
be in the form of a salt, or may be incorporated into a non-natural
amino acid polypeptide, polymer, polysaccharide, or a
polynucleotide and optionally reductively alkylated.
[0284] Compounds of Formula (C) may be formed by the reductive
alkylation of compounds of Formula (A) with carbonyl containing
reagents such as, by way of example, ketones, esters, thioesters,
and aldehydes. By way of example, such aldehyde containing reagents
may have the structure corresponding to
##STR00021##
wherein; [0285] R.sub.5 is alkyl, substituted alkyl, alkenyl,
substituted alkenyl, alkynyl, substituted alkynyl, alkoxy,
substituted alkoxy, alkylalkoxy, substituted alkylalkoxy,
polyalkylene oxide, substituted polyalkylene oxide, cycloalkyl,
substituted cycloalkyl, aryl, substituted aryl, heteroaryl,
substituted heteroaryl, heterocycle, substituted heterocycle,
alkaryl, substituted alkaryl, aralkyl, substituted aralkyl,
--C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2, --C(O)NHCH(R'').sub.2,
-(alkylene or substituted alkylene)-N(R'').sub.2, -(alkenylene or
substituted alkenylene)-N(R'').sub.2, -(alkylene or substituted
alkylene)-(aryl or substituted aryl), -(alkenylene or substituted
alkenylene)-(aryl or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0286] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'--(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N--, --C(R').dbd.N--.,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; each
R' is independently H, alkyl, or substituted alkyl.
[0287] Other non-natural amino acids having the structure of
Formula (B) are non-limiting examples described herein:
##STR00022## [0288] wherein each R.sub.a is independently selected
from the group consisting of H, halogen, alkyl, --NO.sub.2, --CN,
substituted alkyl, --N(R').sub.2, --C(O).sub.kR',
--C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where k is 1, 2, or
3; [0289] M is H or --CH.sub.2R.sub.5; or the M-N--C(R.sub.5)
moiety may form a 4 to 7 membered ring structure; [0290] R.sub.5 is
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0291] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; [0292]
or R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; and [0293] each R' is independently H, alkyl, or
substituted alkyl.
[0294] The following non-natural amino acids having the structure
of Formula (C) are non-limiting examples of alkylated non-natural
amino acids described herein:
##STR00023## ##STR00024## ##STR00025##
Such non-natural amino acids may also be in the form of a salt, or
may be incorporated into a non-natural amino acid polypeptide,
polymer, polysaccharide, or a polynucleotide and optionally
reductively alkylated.
[0295] Non-limiting exemplary syntheses of non-natural amino acid
polypeptides containing amino acids of Formula (C) is presented in
FIG. 15, wherein the masked amine moieties of non-natural amino
acids Formula (B) contained in polypeptides are initially reduced
to give non-natural amino acids of Formula (A) containing aromatic
amine moieties incorporated into non-natural amino acid
polypeptides. Such aromatic amine moieties are then reductive
alkylated with carbonyl-containing reagents described above to give
polypeptides containing non-natural amino acids of Formula (C).
Such reactions may also be applied to non-natural amino acids
incorporated into synthetic polymers, polysaccharides, or
polynucleotides. Additionally, such reactions may be applied to
non-incorporated non-natural amino acids. By way of example the
reducing agent used to reduce masked amine moieties includes, but
is not limited to, TCEP, Na.sub.2S, Na.sub.2S.sub.2O.sub.4,
LiAlH.sub.4, B.sub.2H6, and NaBH.sub.4. By way of example only,
reductive alkylation may occur in aqueous buffers with a pH of
about 4 to about 7 and using a mild reducing agent, such as, by way
of example only, sodium cyanoborohydride (NaBCNH.sub.3). In
addition, other reducing agents may be used for reductive
alkylation including, but not limited to, TCEP, Na.sub.2S,
Na.sub.2S.sub.2O.sub.4, LiAlH.sub.4, B.sub.2H.sub.6, and
NaBH.sub.4.
[0296] Presented in FIG. 16 are non-limiting exemplary syntheses of
non-natural amino acid polypeptides containing amino acids of
Formula (C) by reductive alkylation of secondary aromatic amine
moieties, contained in non-natural amino acids of Formula (A), with
carbonyl-containing reagents described above. Such reductive
alkylations give polypeptides containing non-natural amino acids
with tertiary aromatic amine moieties. Such reactions may also be
applied to non-natural amino acids incorporated into synthetic
polymers, polysaccharides, or polynucleotides. Additionally, such
reactions may be applied to non-incorporated non-natural amino
acids. By way of example only, reductive alkylation may occur in
aqueous buffers with a pH of about 4 to about 7 and using a mild
reducing agent, such as, by way of example only, sodium
cyanoborohydride (NaBCNH.sub.3). In addition, other reducing agents
may be used for reductive alkylation including, but not limited to,
TCEP, Na.sub.2S, Na.sub.2S.sub.2O.sub.4, LiAlH.sub.4,
B.sub.2H.sub.6, and NaBH.sub.4.
[0297] Compounds of Formula (C) may also be formed by the reductive
alkylation of compounds of Formula (A) with reagents containing at
least two carbonyl moieties, including, but not limited to,
diketones, ketoaldehydes and dialdehydes. By way of example, such
reagents may have the structure corresponding to
##STR00026##
wherein; [0298] each R.sub.1 is independently selected from H,
optionally substituted alkyl, optionally substituted alkene,
optionally substituted alkyne, optionally substituted cycloalkyl,
optionally substituted heterocycle, optionally substituted aryl, or
optionally substituted heteroaryl; [0299] R.sub.5 is alkylene,
substituted alkylene, alkenylene, substituted alkenylene,
alkynylene, substituted alkynylene, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkylene, substituted cycloalkylene,
arylene, substituted arylene, heteroarylene, substituted
heteroarylene, heterocycloalkylene, substituted
heterocycloalkylene, --C(O)R''--, --C(O)OR''--, --C(O)N(R'')--,
-(alkylene or substituted alkylene)-N(R'')--, -(alkenylene or
substituted alkenylene)-N(R'')--, -(alkylene or substituted
alkylene)-ON(R'')--, -(alkylene or substituted
alkylene)-C(O)SR''--, wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl; alkoxy,
substituted alkoxy, substituted alkylene, alkenylene, substituted
alkenylene, alkynylene, substituted alkynylene, aryl, substituted
aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted
heterocycle, alkaryl, substituted alkaryl, aralkyl, or substituted
aralkyl; [0300] or R.sub.5 is L-X, where, X is a selected from the
group consisting of a label; a dye; a polymer; a water-soluble
polymer; a derivative of polyethylene glycol; a photocrosslinker; a
cytotoxic compound; a drug; an affinity label; a photoaffinity
label; a reactive compound; a resin; a second protein or
polypeptide or polypeptide analog; an antibody or antibody
fragment; a metal chelator; a cofactor; a fatty acid; a
carbohydrate; a polynucleotide; a DNA; a RNA; an antisense
polynucleotide; a saccharide, a water-soluble dendrimer, a
cyclodextrin, a biomaterial; a nanoparticle; a spin label; a
fluorophore, a metal-containing moiety; a radioactive moiety; a
novel functional group; a group that covalently or noncovalently
interacts with other molecules; a photocaged moiety; an actinic
radiation excitable moiety; a ligand; a photoisomerizable moiety;
biotin; a biotin analogue; a moiety incorporating a heavy atom; a
chemically cleavable group; a photocleavable group; an elongated
side chain; a carbon-linked sugar; a redox-active agent; an amino
thioacid; a toxic moiety; an isotopically labeled moiety; a
biophysical probe; a phosphorescent group; a chemiluminescent
group; an electron dense group; a magnetic group; an intercalating
group; a chromophore; an energy transfer agent; a biologically
active agent; a detectable label; a small molecule; an inhibitory
ribonucleic acid; a radionucleotide; a neutron-capture agent; a
derivative of biotin; quantum dot(s); a nanotransmitter; a
radiotransmitter; an abzyme, an activated complex activator, a
virus, an adjuvant, an aglycan, an allergan, an angiostatin, an
antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a
shuttle vector, a macromolecule, a mimotope, a receptor, a reverse
micelle, and any combination thereof; and L is optional, and when
present is a linker selected from the group consisting of alkylene,
substituted alkylene, alkenylene, substituted alkenylene, --O--,
--O-(alkylene or substituted alkylene)-, -(alkylene or substituted
alkylene)-O--, --C(O)--, --C(O)-(alkylene or substituted
alkylene)-, -(alkylene or substituted alkylene)-C(O)--,
--C(O)N(R')--, --C(O)N(R')-(alkylene or substituted alkylene)-,
-(alkylene or substituted alkylene)-C(O)N(R'), --OC(O)N(R')--,
--OC(O)N(R')-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-OC(O)N(R')--, --N(R')C(O)--,
--NR'C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-NR'C(O)--, --S--, --S-(alkylene or
substituted alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R')--N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; each
R' is independently H, alkyl, or substituted alkyl; n is 1, 2, or
3.
C. Structure and Synthesis of Non-Natural Amino Acids: Aminated
Amino Acids
[0301] Non-natural amino acids with electrophilic reactive groups,
such as, by way of example only, an aldehyde group, a masked
aldehyde group (which is a functional group which can be readily
converted into an aldehyde group), or a protected aldehyde group
(which has reactivity similar to an aldehyde group upon
deprotection) allow for a variety of reactions to link molecules
via various reactions, including but not limited to, reductive
amination reactions with aromatic amine containing reagents. Such
aminated non-natural amino acids include amino acids having the
structure of Formula (D):
##STR00027##
wherein: [0302] L is optional, and when present is lower alkylene,
substituted lower alkylene, lower cycloalkylene, substituted lower
cycloalkylene, lower alkenylene, substituted lower alkenylene,
alkynylene, lower heteroalkylene, substituted heteroalkylene, lower
heterocycloalkylene, substituted lower heterocycloalkylene,
arylene, substituted arylene, heteroarylene, substituted
heteroarylene, alkarylene, substituted alkarylene, aralkylene, or
substituted aralkylene; [0303] Q is optional, and when present is a
linker selected from the group consisting of lower alkylene,
substituted lower alkylene, lower alkenylene, substituted lower
alkenylene, lower heteroalkylene, substituted lower heteroalkylene,
--O--, --O-(alkylene or substituted alkylene)-, --S--,
--S-(alkylene or substituted alkylene)-, --S(O).sub.k-- where k is
1, 2, or 3, --S(O).sub.k(alkylene or substituted alkylene)-,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --N(R')--,
--NR'-(alkylene or substituted alkylene)-, --C(O)N(R')--,
--CON(R'')-(alkylene or substituted alkylene)-, --CSN(R'')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO--,
--N(R')CO-(alkylene or substituted alkylene)-, --N(R')C(O)O--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R'')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R'').dbd.N--,
--C(R')--N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R--).sub.2--N(R')--N(R')--, where
each R' is independently H, alkyl, or substituted alkyl; [0304]
R.sub.1 is H, an amino protecting group, resin, amino acid,
polypeptide, or polynucleotide; and [0305] R.sub.2 is OH, an ester
protecting group, resin, amino acid, polypeptide, or
polynucleotide; [0306] each of R.sub.3 and R.sub.4 is independently
H, halogen, lower alkyl, or substituted lower alkyl, or R.sub.3 and
R.sub.4 or two R.sub.3 groups optionally form a cycloalkyl or a
heterocycloalkyl; [0307] each R.sub.a is independently selected
from the group consisting of H, halogen, alkyl, --NO.sub.2, --CN,
substituted alkyl, --N(R').sub.2, --C(O).sub.kR',
--C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where k is 1, 2, or
3; [0308] M is H or --CH.sub.2R.sub.5; [0309] R.sub.5 is alkyl,
substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0310] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; [0311]
or R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; [0312] each R' is independently H, alkyl, or
substituted alkyl;
##STR00028##
[0312] is selected from the group consisting of a monocyclic aryl
ring, a bicyclic aryl ring, a multicyclic aryl ring, a monocyclic
heteroaryl ring, a bicyclic heteroaryl ring, and a multicyclic
heteroaryl ring; [0313] A is independently CR.sub.a, or N; and
[0314] B is independently CR.sub.a, N, O, or S. The structure
##STR00029##
[0314] (as presented in all examples herein) does not present the
relative orientations of "A," "B," "R.sub.a," and the other
substituent represented by the line and squiggle; rather these four
features of this structure may be oriented in any chemically-sound
manner (along with other features of this structure), as
illustrated by example herein.
[0315] One embodiment of the non-natural amino acid containing a
protected aldehyde moiety has the structure of Formula (E),
##STR00030##
wherein: [0316] L is optional, and when present is lower alkylene,
substituted lower alkylene, lower cycloalkylene, substituted lower
cycloalkylene, lower alkenylene, substituted lower alkenylene,
alkynylene, lower heteroalkylene, substituted heteroalkylene, lower
heterocycloalkylene, substituted lower heterocycloalkylene,
arylene, substituted arylene, heteroarylene, substituted
heteroarylene, alkarylene, substituted alkarylene, aralkylene, or
substituted aralkylene; [0317] Q is optional, and when present is a
linker selected from the group consisting of lower alkylene,
substituted lower alkylene, lower alkenylene, substituted lower
alkenylene, lower heteroalkylene, substituted lower heteroalkylene,
--O-(alkylene or substituted alkylene)-, --S-(alkylene or
substituted alkylene)-, where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(O)-(alkylene
or substituted alkylene)-, --C(S)-(alkylene or substituted
alkylene)-, --NR'-(alkylene or substituted alkylene)-,
--CON(R'')-(alkylene or substituted alkylene)-, --CSN(R'')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, and where each R' is independently H,
alkyl, or substituted alkyl; [0318] R.sub.1 is H, an amino
protecting group, resin, amino acid, polypeptide, or
polynucleotide; and [0319] R.sub.2 is OH, an ester protecting
group, resin, amino acid, polypeptide, or polynucleotide; [0320]
each of R.sub.3 and R.sub.4 is independently H, halogen, lower
alkyl, or substituted lower alkyl, or R.sub.3 and R.sub.4 or two
R.sub.3 groups optionally form a cycloalkyl or a heterocycloalkyl;
[0321] each R.sub.a is independently selected from the group
consisting of H, halogen, alkyl, --NO.sub.2, --CN, substituted
alkyl, --N(R').sub.2, --C(O).sub.kR', --C(O)N(R').sub.2, --OR', and
--S(O).sub.kR', where k is 1, 2, or 3; [0322] R.sub.6 is an
aldehyde, a protected aldehyde or a masked aldehyde, wherein the
protecting group includes, but is not limited to,
##STR00031##
[0322] where each X.sub.1 is independently selected from the group
consisting of --O--, --S--, --N(H)--, --N(R)--, --N(Ac)--, and
--N(OMe)-; X.sub.2 is --OR, --OAc, --SR, --N(R).sub.2, --N(R)(Ac),
--N(R)(OMe), or N.sub.3, and where each R' and R is independently
H, alkyl, or substituted alkyl. Such non-natural amino acids may
also be in the form of a salt, or may be incorporated into a
non-natural amino acid polypeptide, polymer, or a polynucleotide.
Such non-natural amino acids may also be incorporated into a
non-natural amino acid polypeptide and then post-translationally
modified by deprotecting to form an aldehyde group "in-situ"
followed by reductive amination of the aldehyde with an aromatic
amine containing reagent, thereby forming non-natural amino acids
having the structure of Formula (D) as part of the non-natural
amino acid polypeptide. In addition, non-natural amino acids having
the structure of Formula (E) may also be incorporated into a
polymer or a polynucleotide and are deprotecting to form an
aldehyde group "in-situ" followed by reductive amination of the
aldehyde with an aromatic amine containing reagent thereby forming
non-natural amino acids having the structure of Formula (D) as part
of the polymer, or polynucleotide.
[0323] Non-limiting examples of such non-natural amino acids
containing protected aldehyde moieties are shown in FIG. 17.
[0324] Compounds of Formula (D) may be formed, after deprotection
of the aldehyde group of compounds of Formula (E), followed by the
reductive amination of compounds of Formula (D) with aromatic amine
containing reagents. Such aromatic amine containing reagents have
the structure corresponding to
##STR00032##
wherein,
##STR00033##
is selected from the group consisting of a monocyclic aryl ring, a
bicyclic aryl ring, a multicyclic aryl ring, a monocyclic
heteroaryl ring, a bicyclic heteroaryl ring, and a multicyclic
heteroaryl ring; [0325] A is independently CR.sub.a, or N; and
[0326] B is independently CR.sub.a, N, O, or S. [0327] each R.sub.5
is independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; n is 0, 1, 2, 3, 4, 5, or 6; [0328] M is H or
--CH.sub.2R.sub.5; [0329] R.sub.5 is alkyl, substituted alkyl,
alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy,
substituted alkoxy, alkylalkoxy, substituted alkylalkoxy,
polyalkylene oxide, substituted polyalkylene oxide, cycloalkyl,
substituted cycloalkyl, aryl, substituted aryl, heteroaryl,
substituted heteroaryl, heterocycle, substituted heterocycle,
alkaryl, substituted alkaryl, aralkyl, substituted aralkyl,
--C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2, --C(O)NHCH(R'').sub.2,
-(alkylene or substituted alkylene)-N(R'').sub.2, -(alkenylene or
substituted alkenylene)-N(R'').sub.2, -(alkylene or substituted
alkylene)-(aryl or substituted aryl), -(alkenylene or substituted
alkenylene)-(aryl or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0330] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof, and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N--N.dbd., and --C(R').sub.2--N(R')--N(R')--;
wherein each R' is independently hydrogen, alkyl, substituted
alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy,
substituted alkylene, alkenylene, substituted alkenylene,
alkynylene, substituted alkynylene, aryl, substituted aryl,
heteroaryl, substituted heteroaryl, heterocycle, substituted
heterocycle, alkaryl, substituted alkaryl, aralkyl, or substituted
aralkyl.
[0331] A non-limiting exemplary synthesis of non-natural amino acid
polypeptides containing amino acids of Formula (D) as presented in
FIG. 18, wherein protected aldehyde moieties of non-natural amino
acids of Formula (E) contained in polypeptides are initially
deprotected to give non-natural amino acids containing aldehyde
moieties incorporated into non-natural amino acid polypeptides.
Such aldehyde moieties are then reductively aminated with aromatic
amine-containing reagents described above to give polypeptides
containing non-natural amino acids of Formula (D). Such reactions
may also be applied to non-natural amino acids incorporated into
synthetic polymers, polysaccharides, or polynucleotides.
Additionally, such reactions may be applied to non-incorporated
non-natural amino acids. By way of example the protected aldehyde
is deprotected by acid catalyzed deprotection. By way of example
only, reductive amination may occur in aqueous buffers with a pH of
about 4 to about 7 and using a mild reducing agent, such as, by way
of example only, sodium cyanoborohydride (NaBCNH.sub.3). In
addition, other reducing agents may be used for reductive
alkylation including, but not limited to, TCEP, Na.sub.2S,
Na.sub.2S.sub.2O.sub.4, LiAlH.sub.4, B.sub.2H.sub.6, and
NaBH.sub.4.
[0332] Shown in FIG. 19 are a non-limiting representation of the
formation of non-natural amino acids of Formula (C) by reductive
alkylation of the aromatic amine moiety of non-natural amino acids
of Formula (A), and a non-limiting representation of the formation
of non-natural amino acids of Formula (D) by reductive amination of
a deprotected aldehyde moiety on non-natural amino acids of Formula
(E). Depicted in FIG. 19 is the specificity and selectivity of the
reductive alkylation reaction, wherein only the aromatic amine
moiety of non-natural amino acids of Formula (A) is reductively
alkylated while other amine moieties, thiols and disulfide bonds
are not reduced or do not react under the reaction conditions used.
Also depicted in FIG. 19 is the specificity and selectivity of the
reductive amination reaction, wherein only the deprotected aldehyde
moiety of non-natural amino acids of Formula (E) is reductively
aminated while other carboxylate moieties, thiols and disulfide
bonds are not reduced or do not react under the reaction conditions
used. Such selective, site-specific derivatizations, reductive
alkylation or reductive amination reactions may allow for
modification of polypeptides/proteins to design agonists and/or
antagonists, site-specific pegylation of polypeptides/proteins,
site-specific conjugation of polypeptides/proteins, prodrug design,
polypeptide/protein glycosylation, polypeptide/protein
dimerization, small molecule drug conjugates of
polypeptides/proteins, and small molecule drug conjugates of
antibodies.
[0333] Modification of non-natural amino acids described herein
using reductive alkylation or reductive amination reactions have
any or all of the following advantages. First, aromatic amines can
be reductively alkylated with carbonyl-containing compounds,
including aldehydes, and ketones, in a pH range of about 4 to about
10 (and in certain embodiments in a pH range of about 4 to about 7)
to generate substituted amine, including secondary and tertiary
amine, linkages. Second, under these reaction conditions the
chemistry is selective for non-natural amino acids as the
sidechains of naturally occurring amino acids are unreactive. This
allows for site-specific derivatization of polypeptides which have
incorporated non-natural amino acids containing aromatic amine
moieties or protected aldehyde moieties, including, by way of
example, recombinant proteins. Such derivatized polypeptides and
proteins can thereby be prepared as defined homogeneous products.
Third, the mild conditions needed to effect the reaction of an
aromatic amine moiety on an amino acid, which has been incorporated
into a polypeptide, with an aldehyde-containing reagent generally
do not irreversibly destroy the tertiary structure of the
polypeptide (excepting, of course, where the purpose of the
reaction is to destroy such tertiary structure). Similarly, the
mild conditions needed to effect the reaction of an aldehyde moiety
on an amino acid, which has been incorporated into a polypeptide
and deprotected, with an aromatic amine-containing reagent
generally do not irreversibly destroy the tertiary structure of the
polypeptide (excepting, of course, where the purpose of the
reaction is to destroy such tertiary structure). Fourth, the
reaction occurs rapidly at room temperature, which allows the use
of many types of polypeptides or reagents that would otherwise be
unstable at higher temperatures. Fifth, the reaction occurs readily
is aqueous conditions, again allowing use of polypeptides and
reagents incompatible (to any extent) with non-aqueous solutions.
Six, the reaction occurs readily even when the ratio of polypeptide
or amino acid to reagent is stoichiometric, stoichiometric-like, or
near-stoichiometric, so that it is unnecessary to add excess
reagent or polypeptide to obtain a useful amount of reaction
product. Seventh, the resulting amine can be produced
regioselectively and/or regiospecifically, depending upon the
design of the amine and carbonyl portions of the reactants.
Finally, the reductive alkylation of aromatic amines with
aldehyde-containing reagents, and the reductive amination of
aldehydes with aromatic amine containing reagents, generates amine,
including secondary and tertiary amine, linkages which are stable
under biological conditions.
[0334] Shown in FIG. 20 are non-limiting examples of the
specificity and selectivity of the reductive alkylation of aromatic
amine moieties on amino acid residues next to a cysteine residue.
The reductive alkylation of reduced urotensin-II (UT-II-SH) with
propionaldehyde (I) or benzaldehyde (II) demonstrates that one
product is predominantly formed from the respective reactions, and
that the free thiol group did not react. Also shown in FIG. 20 are
the speed of the reactions, which was about 2 hours, and the
stoichiometric or near-stoichiometric relationship between the
reduced urotensin-II (UT-II-SH) and the respective aldehyde
containing reagents. Additionally, the MS data for UT-II-SH, I, and
II are presented.
[0335] Shown in FIG. 21 are non-limiting examples of the
specificity and selectivity of the reductive alkylation of aromatic
amine moieties on amino acid residues next to a cysteine residue.
The reductive alkylation of urotensin-II (UT-II) with
propionaldehyde (I) or benzaldehyde (II) demonstrates that one
product was predominantly formed from the respective reactions, and
that the disulfide bond did not react. Also shown in FIG. 21 are
the speed of the reactions, which was about 2 hours, and the
stoichiometric or near-stoichiometric relationship between the
urotensin-II (UT-II) and the respective aldehyde containing
reagents. Additionally, the MS data for UT-II-SH, I, and II are
presented.
[0336] Further non-limiting examples of the specificity and
selectivity of the reductive alkylation reactions of aromatic amine
moieties on terminal amino acid residues are shown in FIG. 22,
wherein the reductive alkylation of peptide XT-8 with
propionaldehyde (I), benzaldehyde (II), isobutaldehyde (III) and
pivalaldehyde (IV), demonstrates that one product was predominantly
formed from the respective reactions, and that the disulfide bond
did not react. Also shown in FIG. 22 are the speed of the
reactions, which was about 2 hours, and the stoichiometric or
near-stoichiometric relationship between the XT-8 and the
respective aldehyde containing reagents. Additionally, the MS data
for XT-8, I, II, III, and IV are presented.
[0337] Further non-limiting examples of the specificity and
selectivity of the reductive alkylation reactions of aromatic amine
moieties on amino acid residues which are next to various
N-terminal amino acids are shown in FIGS. 23-27. In FIG. 23 the
reductive alkylation of peptide SXT-9 (N-terminal serine) with
propionaldehyde (I), benzaldehyde (II), isobutaldehyde (III) and
pivalaldehyde (IV), shows the speed of the reactions, which was
about 2 hours, and the stoichiometric or near-stoichiometric
relationship between the SXT-9 and the respective aldehyde
containing reagents. In addition, FIG. 23 demonstrates that one
product was predominantly formed from the respective reactions,
that the disulfide bond did not react, and that the N-Ser residue
has minimal effect on the selectivity. Additionally, the MS data
for SXT-9, I, II, III, and IV are presented.
[0338] In FIG. 24 the reductive alkylation of peptide HXT-9
(N-terminal histidine) with propionaldehyde (I), benzaldehyde (II),
isobutaldehyde (III) and pivalaldehyde (IV), shows the speed of the
reactions, which was about 2 hours, and the stoichiometric or
near-stoichiometric relationship between the HXT-9 and the
respective aldehyde containing reagents. In addition, FIG. 24
demonstrates that one product was predominantly formed from the
respective reactions, that the disulfide bond did not react, and
that the N-His residue has minimal effect on the selectivity. Also,
the MS data for HXT-9, I, II, III, and IV are shown.
[0339] In FIG. 25 the reductive alkylation of peptide WXT-9
(N-terminal tryptophan) with propionaldehyde (I), benzaldehyde
(II), isobutaldehyde (III) and pivalaldehyde (IV), shows the speed
of the reactions, which was about 2 hours, and the stoichiometric
or near-stoichiometric relationship between the WXT-9 and the
respective aldehyde containing reagents. In addition, FIG. 25
demonstrates that one product was predominantly formed from the
respective reactions, that the disulfide bond did not react, and
that the N-Trp residue has minimal effect on the selectivity. Also,
the MS data for WXT-9, I, II, and III are shown.
[0340] In FIG. 26 the reductive alkylation of peptide NXT-9
(N-terminal asparagine) with propionaldehyde (I), benzaldehyde
(II), isobutaldehyde (III) and pivalaldehyde (IV), shows the speed
of the reactions, which was about 2 hours, and the stoichiometric
or near-stoichiometric relationship between the NXT-9 and the
respective aldehyde containing reagents. In addition, FIG. 26
demonstrates that one product was predominantly formed from the
respective reactions, that the disulfide bond did not react, and
that the N-Asn residue has minimal effect on the selectivity. Also,
the MS data for NXT-9, I, and II are shown.
[0341] In FIG. 27 the reductive alkylation of peptide RXT-10
(N-terminal arginine) with propionaldehyde (I) and benzaldehyde
(II) shows the speed of the reactions, which was about 2 hours, and
the stoichiometric or near-stoichiometric relationship between the
RXT-10 and the respective aldehyde containing reagents. In
addition, FIG. 27 demonstrates that one product was predominantly
formed from the respective reactions, that the disulfide bond did
not react, and that the N-Arg residue has minimal effect on the
selectivity. Also, the MS data for RXT-10, I, and II are
shown.)
[0342] A further non-limiting example of the specificity and
selectivity of the reductive alkylation reactions of aromatic amine
moieties on amino acid residues in a peptide is shown in FIG. 28,
wherein the reductive alkylation of peptide AXT-11 with
propionaldehyde (I) and benzaldehyde (II) shows the speed of the
reactions, which was about 2 hours, and the stoichiometric or
near-stoichiometric relationship between the AXT-11 and the
respective aldehyde containing reagents. In addition, FIG. 28
demonstrates that one product was predominantly formed from the
respective reactions, that the disulfide bond did not react, and
that the N-Ala residue has minimal effect on the selectivity. Also
MS data for AXT-11, I, and II are presented.
[0343] Further non-limiting examples of the specificity and
selectivity of the reductive alkylation reactions of aromatic amine
moieties on amino acid residues in a peptide with various aldehyde
containing reagents are shown in FIGS. 29-30. In FIG. 29 the
reductive alkylation of peptide AXT-11 with various aldehyde
containing reagents shows the speed of the reactions, which was
about 5 hours, and the stoichiometric or near-stoichiometric
relationship between the AXT-11 and the respective aldehyde
containing reagents. In addition, FIG. 29 demonstrates that one
product was predominantly formed from the respective reactions, and
that the disulfide bond did not react. Also, MS data for AXT-11, I,
II, and III are presented. In FIG. 30 the reductive alkylation of
peptide AXT-11 with various heteroaromatic aldehyde containing
reagents shows the speed of the reactions, which was about 5 hours,
and the stoichiometric or near-stoichiometric relationship between
the AXT-11 and the respective aldehyde containing reagents. In
addition, FIG. 30 demonstrates that one product was predominantly
formed from the respective reactions, and that the disulfide bond
did not react. Also, MS data for AXT-11, IV, V, VI are
presented.
[0344] FIGS. 31-33 show non-limiting examples of the specificity
and selectivity of the reductive alkylation reactions of aromatic
amine moieties on amino acid residues in a peptide, wherein the
aromatic amine moieties are reacted with either an aldehyde
containing reagent, a ketone containing reagent or a mixture
thereof. In FIG. 31 the reductive alkylation of peptide AXT-11 with
an aldehyde containing reagent, a ketone containing reagent or a
mixture thereof shows the speed of the reactions, which was about 2
hours, and the stoichiometric or near-stoichiometric relationship
between the AXT-11 and the respective aldehyde containing reagents.
In addition, FIG. 31 demonstrates that under the reaction
conditions used, only the aldehyde containing reagent reacted with
the aromatic amine moiety and only one product was predominantly
formed. Again, the disulfide bond did not react. In FIG. 32 the
reductive alkylation of peptide NXT-9 with an aldehyde containing
reagent, a ketone containing reagent or a mixture thereof shows the
speed of the reactions, which was about 2 hours, and the
stoichiometric or near-stoichiometric relationship between the
NXT-10 and the respective aldehyde containing reagents. In
addition, FIG. 32 demonstrates that under the reaction conditions
used, only the aldehyde containing reagent reacted with the
aromatic amine moiety and only one product was predominantly
formed. Again, the disulfide bond did not react. In FIG. 33 the
reductive alkylation of peptide MXT-9 with an aldehyde containing
reagent, a ketone containing reagent or a mixture thereof
demonstrates that under the reaction conditions used, only the
aldehyde containing reagent reacted with the aromatic amine moiety
and only one product was predominantly formed. Again, the disulfide
bond did not react.
[0345] A non-limiting example of the deprotecting (or unmasking) of
a protected (or masked) aromatic amine moiety on an amino acid in a
peptide, followed by reductive alkylation of the resulting aromatic
amine moiety with various aldehyde containing reagents is shown in
FIG. 34. Reduction of the azide on peptide MXT-9-N3 with TCEP gave
the primary aromatic amine moiety on peptide MXT-9NH2 (I).
Subsequent reductive alkylations of MXT-9NH2 (I) with
propionaldehyde (II) or benzaldehyde (III) then yields the
corresponding alkylated peptides. FIG. 34 demonstrates the ability
to form aromatic amine moieties after incorporation of a
non-natural amino acid containing a protected or masked amine
group. Also shown are the speed of the reactions, which was about 1
hour, the stoichiometric or near-stoichiometric relationship
between the MXT-9NH2 (I) and the respective aldehyde containing
reagents, only one product was predominantly formed, and the thiol
groups did not react.
D. Cellular Uptake of Non-Natural Amino Acids
[0346] Non-natural amino acid uptake by a cell is one issue that is
considered when designing and selecting non-natural amino acids,
including but not limited to, for incorporation into a protein. For
example, the high charge density of .alpha.-amino acids suggests
that these compounds are unlikely to be cell permeable. Natural
amino acids are taken up into the eukaryotic cell via a collection
of protein-based transport systems. A rapid screen can be done
which assesses which non-natural amino acids, if any, are taken up
by cells. See, e.g., the toxicity assays in, e.g., the U.S. Patent
Publication No. 2004/198637 entitled "Protein Arrays," which is
herein incorporated by reference in its entirety; and Liu, D. R.
& Schultz, P. G. (1999) Progress toward the evolution of an
organism with an expanded genetic code. PNAS United States
96:4780-4785. Although uptake is easily analyzed with various
assays, an alternative to designing non-natural amino acids that
are amenable to cellular uptake pathways is to provide biosynthetic
pathways to create amino acids in vivo.
E. Biosynthesis of Non-Natural Amino Acids
[0347] Many biosynthetic pathways already exist in cells for the
production of amino acids and other compounds. While a biosynthetic
method for a particular non-natural amino acid may not exist in
nature, including but not limited to, in a cell, the methods and
compositions described herein provide such methods. For example,
biosynthetic pathways for non-natural amino; acids are optionally
generated in host cell by adding new enzymes or modifying existing
host cell pathways. Additional new enzymes are optionally naturally
occurring enzymes or artificially evolved enzymes. For example, the
biosynthesis of p-aminophenylalanine (as presented in an example in
WO 2002/085923 entitled "In vivo incorporation of unnatural amino
acids") relies ori the addition of a combination of known enzymes
from other organisms. The genes for these enzymes can be introduced
into a eukaryotic cell by transforming the cell with a plasmid
comprising the genes. The genes, when expressed in the cell,
provide an enzymatic pathway to synthesize the desired compound.
Examples of the types of enzymes that are optionally added are
provided in the examples below. Additional enzymes sequences are
found, for example, in Genbank. Artificially evolved enzymes are
also optionally added into a cell in the same manner. In this
manner, the cellular machinery and resources of a cell are
manipulated to produce non-natural amino acids.
[0348] A variety of methods are available for producing novel
enzymes for use in biosynthetic pathways or for evolution of
existing pathways. For example, recursive recombination, including
but not limited to, as developed by Maxygen, Inc. (available on the
world wide web at www.maxygen.com), is optionally used to develop
novel enzymes and pathways. See, e.g., Stemmer (1994), Rapid
evolution of a protein in vitro by DNA shuffling, Nature
370(4):389-391; and, Stemmer, (1994), DNA shuffling by random
fragmentation and reassembly: In vitro recombination for molecular
evolution, Proc. Natl. Acad. Sci. USA., 91:10747-10751. Similarly
DesignPath.TM., developed by Genencor (available on the world wide
web at genencor.com) is optionally used for metabolic pathway
engineering, including but not limited to, to engineer a pathway to
create O-methyl-L-tyrosine in a cell. This technology reconstructs
existing pathways in host organisms using a combination of new
genes, including but not limited to, those identified through
functional genomics, and molecular evolution and design. Diversa
Corporation (available on the world wide web at diversa.com) also
provides technology for rapidly screening libraries of genes and
gene pathways, including but not limited to, to create new
pathways.
[0349] Typically, the non-natural amino acid produced with an
engineered biosynthetic pathway as described herein is produced in
a concentration sufficient for efficient protein biosynthesis,
including but not limited to, a natural cellular amount, but not to
such a degree as to affect the concentration of the other amino
acids or exhaust cellular resources. Typical concentrations
produced in vivo in this manner are about 10 mM to about 0.05 mM.
Once a cell is transformed with a plasmid comprising the genes used
to produce enzymes desired for a specific pathway and a non-natural
amino acid is generated, in vivo selections are optionally used to
further optimize the production of the non-natural amino acid for
both ribosomal protein synthesis and cell growth.
F. Additional Synthetic Methodology
[0350] The non-natural amino acids described herein may be
synthesized using methodologies described in the art or using the
techniques described herein or by a combination thereof. As an aid,
the following table provides various starting electrophiles and
nucleophiles that may be combined to create a desired functional
group. The information provided is meant to be illustrative and not
limiting to the synthetic techniques described herein.
TABLE-US-00001 TABLE Examples of Covalent Linkages and Precursors
Thereof Covalent Linkage Product Electrophile Nucleophile
Carboxamides Activated esters amines/anilines Carboxamides acyl
azides amines/anilines Carboxamides acyl halides amines/anilines
Esters acyl halides alcohols/phenols Esters acyl nitriles
alcohols/phenols Carboxamides acyl nitriles amines/anilines Imines
Aldehydes amines/anilines Hydrazones aldehydes or ketones
Hydrazines Oximes aldehydes or ketones Hydroxylamines Alkyl amines
alkyl halides amines/anilines Esters alkyl halides carboxylic acids
Thioethers alkyl halides Thiols Ethers alkyl halides
alcohols/phenols Thioethers alkyl sulfonates Thiols Esters alkyl
sulfonates carboxylic acids Ethers alkyl sulfonates
alcohols/phenols Esters Anhydrides alcohols/phenols Carboxamides
Anhydrides amines/anilines Thiophenols aryl halides Thiols Aryl
amines aryl halides Amines Thioethers Azindines Thiols Boronate
esters Boronates Glycols Carboxamides carboxylic acids
amines/anilines Esters carboxylic acids Alcohols N-acylureas or
Anhydrides carbodiimides carboxylic acids Esters diazoalkanes
carboxylic acids Thioethers Epoxides Thiols Thioethers
haloacetamides Thiols Ammotriazines halotriazines amines/anilines
Triazinyl ethers halotriazines alcohols/phenols Amidines imido
esters amines/anilines Ureas Isocyanates amines/anilines Urethanes
Isocyanates alcohols/phenols Thioureas isothiocyanates
amines/anilines Thioethers Maleimides Thiols Phosphite esters
phosphoramidites Alcohols Silyl ethers silyl halides Alcohols Alkyl
amines sulfonate esters amines/anilines Thioethers sulfonate esters
Thiols Esters sulfonate esters carboxylic acids Ethers sulfonate
esters Alcohols Sulfonamides sulfonyl halides amines/anilines
Sulfonate esters sulfonyl halides phenols/alcohols
[0351] In general, carbon electrophiles are susceptible to attack
by complementary nucleophiles, including carbon nucleophiles,
wherein an attacking nucleophile brings an electron pair to the
carbon electrophile in order to form a new bond between the
nucleophile and the carbon electrophile.
[0352] Suitable carbon nucleophiles include, but are not limited to
alkyl, alkenyl, aryl and alkynyl Grignard, organolithium,
organozinc, alkyl-, alkenyl, aryl- and alkynyl-tin reagents
(organostannanes), alkyl-, alkenyl-, aryl- and alkynyl-borane
reagents (organoboranes and organoboronates); these carbon
nucleophiles have the advantage of being kinetically stable in
water or polar organic solvents. Other carbon nucleophiles include
phosphorus ylids, enol and enolate reagents; these carbon
nucleophiles have the advantage of being relatively easy to
generate from precursors well known to those skilled in the art of
synthetic organic chemistry. Carbon nucleophiles, when used in
conjunction with carbon electrophiles, engender new carbon-carbon
bonds between the carbon nucleophile and carbon electrophile.
[0353] Non-carbon nucleophiles suitable for coupling to carbon
electrophiles include but are not limited to primary and secondary
amines, thiols, thiolates, and thioethers, alcohols, alkoxides,
azides, semicarbazides, and the like. These non-carbon
nucleophiles, when used in conjunction with carbon electrophiles,
typically generate heteroatom linkages (C-X-C), wherein X is a
heteroatom, e.g, oxygen or nitrogen.
VI. Polypeptides with Non-Natural Amino Acids
[0354] The compositions and methods described herein provide for
the incorporation of at least one non-natural amino acid into a
polypeptide. The non-natural amino acid may be present at any
location on the polypeptide, including any terminal position or any
internal position of the polypeptide. Preferably, the non-natural
amino acid does not destroy the activity and/or the tertiary
structure of the polypeptide relative to the homologous
naturally-occurring amino acid polypeptide, unless such destruction
of the activity and/or tertiary structure was one of the purposes
of incorporating the non-natural amino acid into the polypeptide.
Further, the incorporation of the non-natural amino acid into the
polypeptide may modify to some extent the activity (e.g.,
manipulating the therapeutic effectiveness of the polypeptide,
improving the safety profile of the polypeptide, adjusting the
pharmacokinetics, pharmacologics and/or pharmacodynamics of the
polypeptide (e.g., increasing water solubility, bioavailability,
increasing serum half-life, increasing therapeutic half-life,
modulating immunogenicity, modulating biological activity, or
extending the circulation time), providing additional functionality
to the polypeptide, incorporating a tag, label or detectable signal
into the polypeptide, easing the isolation properties of the
polypeptide, and any combination of the aforementioned
modifications) and/or tertiary structure of the polypeptide
relative to the homologous naturally-occurring amino acid
polypeptide without fully causing destruction of the activity
and/or tertiary structure. Such modifications of the activity
and/or tertiary structure are often one of the goals of effecting
such incorporations, although of course, the incorporation of the
non-natural amino acid into the polypeptide may also have little
effect on the activity and/or tertiary structure of the polypeptide
relative to the homologous naturally-occurring amino acid
polypeptide. Correspondingly, non-natural amino acid polypeptides,
compositions comprising non-natural amino acid polypeptides,
methods for making such polypeptides and polypeptide compositions,
methods for purifying, isolating, and characterizing such
polypeptides and polypeptide compositions, and methods for using
such polypeptides and polypeptide compositions are considered
within the scope of the present disclosure. Further, the
non-natural amino acid polypeptides described herein may also be
ligated to another polypeptide (including, by way of example, a
non-natural amino acid polypeptide or a naturally-occurring amino
acid polypeptide).
[0355] The non-natural amino acid polypeptides described herein may
be produced biosynthetically or non-biosynthetically. By
biosynthetically is meant any method utilizing a translation system
(cellular or non-cellular), including use of at least one of the
following components: a polynucleotide, a codon, a tRNA, and a
ribosome. By non-biosynthetically is meant any method not utilizing
a translation system: this approach can be further divided into
methods utilizing solid state peptide synthetic methods, solid
phase peptide synthetic methods, methods that utilize at least one
enzyme, and methods that do not utilize at least one enzyme; in
addition any of this sub-divisions may overlap and many methods may
utilize a combination of these sub-divisions.
[0356] The methods, compositions, strategies and techniques
described herein are not limited to a particular type, class or
family of polypeptides or proteins. Indeed, virtually any
polypeptides may include at least one non-natural amino acids
described herein. By way of example only, the polypeptide can be
homologous to a therapeutic protein selected from the group
consisting of: alpha-1 antitrypsin, angiostatin, antihemolytic
factor, antibody, apolipoprotein, apoprotein, atrial natriuretic
factor, atrial natriuretic polypeptide, atrial peptide, C-X-C
chemokine, T39765, NAP-2, ENA-78, gro-a, gro-b, gro-c, IP-10,
GCP-2, NAP-4, SDF-1, PF4, MIG, calcitonin, c-kit ligand, cytokine,
CC chemokine, monocyte chemoattractant protein-1, monocyte
chemoattractant protein-2, monocyte chemoattractant protein-3,
monocyte inflammatory protein-1 alpha, monocyte inflammatory
protein-i beta, RANTES, 1309, R83915, R91733, HCC1, T58847, D31065,
T64262, CD40, CD40 ligand, c-kit ligand, collagen, colony
stimulating factor (CSF), complement factor 5a, complement
inhibitor, complement receptor 1, cytokine, epithelial neutrophil
activating peptide-78, MIP-16, MCP-1, epidermal growth factor
(EGF), epithelial neutrophil activating peptide, erythropoietin
(EPO), exfoliating toxin, Factor IX, Factor VII, Factor VIII,
Factor X, fibroblast growth factor (FGF), fibrinogen, fibronectin,
four-helical bundle protein, G-CSF, glp-1, GM-CSF,
glucocerebrosidase, gonadotropin, growth factor, growth factor
receptor, grf, hedgehog protein, hemoglobin, hepatocyte growth
factor (hGF), hirudin, human growth hormone (hGH), human serum
albumin, ICAM-1, ICAM-1 receptor, LFA-1, LFA-1 receptor, insulin,
insulin-like growth factor (IGF), IGF-I, IGF-II, interferon (IFN),
IFN-alpha, IFN-beta, IFN-gamma, any interferon-like molecule or
member of the IFN family, interleukin (IL), IL-1, IL-2, IL-3, IL-4,
IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, keratinocyte
growth factor (KGF), lactoferrin, leukemia inhibitory factor,
luciferase, neurturin, neutrophil inhibitory factor (NIF),
oncostatin M, osteogenic protein, oncogene product, paracitonin,
parathyroid hormone, PD-ECSF, PDGF, peptide hormone, pleiotropin,
protein A, protein G, pth, pyrogenic exotoxin A, pyrogenic exotoxin
B, pyrogenic exotoxin C, pyy, relaxin, renin, SCF, small
biosynthetic protein, soluble complement receptor I, soluble I-CAM
1, soluble interleukin receptor, soluble TNF receptor, somatomedin,
somatostatin, somatotropin, streptokinase, superantigens,
staphylococcal enterotoxin, SEA, SEB, SEC1, SEC2, SEC3, SED, SEE,
steroid hormone receptor, superoxide dismutase, toxic shock
syndrome toxin, thymosin alpha 1, tissue plasminogen activator,
tumor growth factor (TGF), tumor necrosis factor, tumor necrosis
factor alpha, tumor necrosis factor beta, tumor necrosis factor
receptor (TNFR), VLA-4 protein, VCAM-1 protein, vascular
endothelial growth factor (VEGF), urokinase, mos, ras, raf, met,
p53, tat, fos, myc, jun, myb, rel, estrogen receptor, progesterone
receptor, testosterone receptor, aldosterone receptor, LDL
receptor, and corticosterone. The non-natural amino acid
polypeptide may also be homologous to any polypeptide member of the
growth hormone supergene family. Non-limiting examples of
peptides/proteins which may incorporate non-natural amino acids
containing an aromatic amine moiety are shown in FIGS. 20-34.
[0357] The non-natural amino acid polypeptides may be further
modified as described elsewhere in this disclosure or the
non-natural amino acid polypeptide may be used without further
modification. Incorporation of a non-natural amino acid into a
polypeptide can be done for a variety of purposes, including but
not limited to, tailoring changes in protein structure and/or
function, changing size, acidity, nucleophilicity, hydrogen
bonding, hydrophobicity, accessibility of protease target sites,
targeting to a moiety (including but not limited to, for a protein
array), etc. Proteins that include a non-natural amino acid can
have enhanced or even entirely new catalytic or biophysical
properties. By way of example only, the following properties are
optionally modified by inclusion of a non-natural amino acid into a
protein: toxicity, biodistribution, structural properties,
spectroscopic properties, chemical and/or photochemical properties,
catalytic ability, half-life (including but not limited to, serum
half-life), ability to react with other molecules, including but
not limited to, covalently or noncovalently, and the like. The
compositions including proteins that include at least one
non-natural amino acid are useful for, including but not limited
to, novel therapeutics, diagnostics, catalytic enzymes, industrial
enzymes, binding proteins (including but not limited to,
antibodies), and including but not limited to, the study of protein
structure and function. See, e.g., Dougherty, (2000) Unnatural
Amino Acids as Probes of Protein Structure and Function, Current
Opinion in Chemical Biology 4:645-652.
[0358] Further, the sidechain of the non-natural amino acid
component(s) of a polypeptide can provide a wide range of
additional functionality to the polypeptide; by way of example
only, and not as a limitation, the sidechain of the non-natural
amino acid portion of a polypeptide may include any of the
following: a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof.
[0359] In one aspect, a composition includes at least one protein
with at least one, including but not limited to, at least two, at
least three, at least four, at least five, at least six, at least
seven, at least eight, at least nine, or at least ten or more
non-natural amino acids. The non-natural amino acids can be the
same or different, including but not limited to, there can be 1, 2,
3, 4, 5, 6, 7, 8, 9, 10 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or
more different sites in the protein that comprise 1, 2, 3, 4, 5, 6,
7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more
different non-natural amino acids. In another aspect, a composition
includes a protein with at least one, but fewer than all, of a
particular amino acid present in the protein is substituted with
the non-natural amino acid. For a given protein with more than one
non-natural amino acids, the non-natural amino acids can be
identical or different (including but not limited to, the protein
can include two or more different types of non-natural amino acids,
or can include two of the same non-natural amino acid). For a given
protein with more than two non-natural amino acids, the non-natural
amino acids can be the same or different.
[0360] Although embodiments of the non-natural amino acid
polypeptides described herein may be chemically synthesized via
solid phase peptide synthesis methods (e.g., on a solid resin), by
solution phase peptide synthesis methods, and/or without the aid of
enzymes, other embodiments of the non-natural amino acid
polypeptides described herein allow synthesis via a cell membrane,
cellular extract, or lysate system or via an in vivo system, i.e.,
using the cellular machinery of a prokaryotic or eukaryotic cell.
In further or additional embodiments, one of the key features of
the non-natural amino acid polypeptides described herein is that
they may be synthesized utilizing ribosomes. In further or
additional embodiments of the non-natural amino acid polypeptides
described herein, the non-natural amino acid polypeptides may be
synthesized by a combination of solid resins, without the aid of
enzymes, via the aid of ribosomes, via an in vitro system, via an
in vivo system or any combination thereof.
[0361] Synthesis of non-natural amino acid polypeptides via
ribosomes and/or an in viva system has distinct advantages and
characteristic from a non-natural amino acid polypeptide
synthesized on a solid resin or without the aid of enzymes. These
advantages or characteristics include different impurity profiles,
a system utilizing ribosomes and/or an in vivo system will have
impurities stemming from the biological system utilized including
host cell proteins, membrane portions, and lipids, whereas the
impurity profile from a system utilizing a solid resin and/or
without the aid of enzymes will include organic solvents,
protecting groups, resin materials, coupling reagents and other
chemicals used in the synthetic procedures. In addition, the
isotopic pattern of the non-natural amino acid polypeptide
synthesized via the use of ribosomes and/or an in vivo system will
mirror the isotopic pattern of the feedstock utilized for the
cells; on the other hand, the isotopic pattern of the non-natural
amino acid polypeptide synthesized on a solid resin and/or without
the aid of enzymes will mirror the isotopic pattern of the amino
acids utilized in the synthesis. Further, the non-natural amino
acid synthesized via the use of ribosomes and/or an in vivo system
will be substantially free of the D-isomers of the amino acids
and/or will be able to readily incorporate internal cysteine amino
acids into the structure of the polypeptide, and/or will rarely
provide internal amino acid deletion polypeptides. On the other
hand, a non-natural amino acid polypeptide synthesized via a solid
resin and/or without the use of enzymes will have a higher content
of D-isomers of the amino acids and/or a lower content of internal
cysteine amino acids and/or a higher percentage of internal amino
acid deletion polypeptides. Furthermore, one of skill in the art
will be able to differentiate a non-natural amino acid polypeptide
synthesized by use of a ribosome and/or an in viva system from a
non-natural amino acid polypeptide synthesized via a solid resin
and/or without the use of enzymes.
[0362] In a certain embodiment is a method of making a compound or
salt thereof containing at least one non-natural amino acid
selected from the group consisting of:
##STR00034##
wherein the compound is formed by a reductive alkylation of an
aromatic amino moiety on at least one non-natural amino acid
comprising the aromatic amino moiety with at least one reactant
comprising at least one aldehyde moiety; each R.sub.a is
independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; M is H or --CH.sub.2R.sub.5; or the
M-N--C(R.sub.5) moiety may form a 4 to 7 membered ring structure;
R.sub.1 is H, an amino protecting group, resin, amino acid,
polypeptide, or polynucleotide; R.sub.2 is OH, an ester protecting
group, resin, amino acid, polypeptide, or polynucleotide; R.sub.5
is alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroalkyl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR'; or
R.sub.5 is L-X, where, X is a selected from the group consisting of
a label; a dye; a polymer; a water-soluble polymer; a derivative of
polyethylene glycol; a photocrosslinker; a cytotoxic compound; a
drug; an affinity label; a photoaffinity label; a reactive
compound; a resin; a second protein or polypeptide or polypeptide
analog; an antibody or antibody fragment; a metal chelator; a
cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a
RNA; an antisense polynucleotide; a saccharide, a water-soluble
dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin
label; a fluorophore, a metal-containing moiety; a radioactive
moiety; a novel functional group; a group that covalently or
noncovalently interacts with other molecules; a photocaged moiety;
an actinic radiation excitable moiety; a ligand; a
photoisomerizable moiety; biotin; a biotin analogue; a moiety
incorporating a heavy atom; a chemically cleavable group; a
photocleavable group; an elongated side chain; a carbon-linked
sugar; a redox-active agent; an amino thioacid; a toxic moiety; an
isotopically labeled moiety; a biophysical probe; a phosphorescent
group; a chemiluminescent group; an electron dense group; a
magnetic group; an intercalating group; a chromophore; an energy
transfer agent; a biologically active agent; a detectable label; a
small molecule an inhibitory ribonucleic acid; a radionucleotide; a
neutron-capture agent; a derivative of biotin; quantum dot(s); a
nanotransmitter; a radiotransmitter; an abzyme, an activated
complex activator, a virus, an adjuvant, an aglycan, an allergan,
an angiostatin, an antihormone, an antioxidant, an aptamer, a guide
RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a
receptor, a reverse micelle, and any combination thereof; and L is
optional, and when present is a linker selected from the group
consisting of alkylene, substituted alkylene, alkenylene,
substituted alkenylene, --O--, --O-(alkylene or substituted
alkylene)-, -(alkylene or substituted alkylene)-O--, --C(O)--,
--C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; or
R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; and each R' is independently H, alkyl, or
substituted alkyl.
[0363] In other embodiments is a method of making a compound or
salt thereof, wherein R.sub.1 and R.sub.2 of at least one
non-natural amino acid is H and OH respectively. In some
embodiments is a method of making a compound, wherein R.sub.a of at
least one non-natural amino acid is a halogen. In other embodiments
is a method of making a compound or salt thereof, wherein both
R.sub.1 and R.sub.2 of at least one non-natural amino acid are
polypeptides. In some embodiments is a method of making a compound
or salt thereof, wherein X of at least one non-natural amino acid
is a biologically active agent selected from the group consisting
of a peptide, protein, enzyme, antibody, drug, dye, lipid,
nucleosides, oligonucleotide, cell, virus, liposome, microparticle,
and micelle. In some embodiments is a method of making a compound
or salt thereof, wherein X of at least one non-natural amino acid
is a drug selected from the group consisting of an antibiotic,
fungicide, anti-viral agent, anti-inflammatory agent, anti-tumor
agent, cardiovascular agent, anti-anxiety agent, hormone, growth
factor, and steroidal agent. In other embodiments is a method of
making a compound or salt thereof, wherein X of at least one
non-natural amino acid is an enzyme selected from the group
consisting of horseradish peroxidase, alkaline phosphatase,
.beta.-galactosidase, and glucose oxidase. In some embodiments is a
method of making a compound or salt thereof, wherein X of at least
one non-natural amino acid is a detectable label selected from the
group consisting of a fluorescent, phosphorescent,
chemiluminescent, chelating, electron dense, magnetic,
intercalating, radioactive, chromophoric, and energy transfer
moiety. In further embodiments is a method of making a compound or
salt thereof, wherein X of the non-natural amino acid is a polymer
comprising alkyl, substituted alkyl, alkenyl, substituted alkenyl,
alkynyl, substituted alkynyl, alkoxy, substituted alkoxy,
alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide,
substituted polyalkylene oxide, aryl, substituted aryl, heteroaryl,
substituted heteroaryl, alkaryl, substituted alkaryl, aralkyl, or
substituted aralkyl.
[0364] In other embodiments is a method of making a compound or
salt thereof, wherein the polymer comprises polyalkylene oxide or
substituted polyalkylene oxide. In some embodiments is a method of
making a compound or salt thereof, wherein the polymer comprises
-[(alkylene or substituted alkylene)-O-(hydrogen, alkyl, or
substituted alkyl)].sub.x, wherein x is from 20-10,000. In other
embodiments is a method of making a compound or salt thereof,
wherein the polymer is m-PEG having a molecular weight ranging from
about 2 to about 40 KDa.
[0365] In further embodiments is a method of making a compound or
salt thereof wherein at least one non-natural amino acid is
selected from a group:
##STR00035## ##STR00036## ##STR00037##
wherein X is a halogen.
[0366] In some embodiments is a method of making a compound or salt
thereof wherein at least one non-natural amino acid is selected
from a group:
##STR00038## ##STR00039## ##STR00040##
[0367] In further embodiments is a method of making a compound or
salt thereof wherein at least one non-natural amino acid is
selected from a group:
##STR00041## ##STR00042## ##STR00043##
wherein X is a halogen.
[0368] In other embodiments is a method of making a compound or
salt thereof containing at least one non-natural amino acid
selected from the group consisting of:
##STR00044## [0369] wherein the compound is formed by a reductive
alkylation of an aromatic amino moiety on the at least one
non-natural amino acid comprising the aromatic amino moiety with at
least one reactant comprising at least one aldehyde moiety; [0370]
each R.sub.a is independently selected from the group consisting of
H, halogen, alkyl, --NO.sub.2, --CN, substituted alkyl,
--N(R').sub.2, --C(O).sub.kR', --C(O)N(R').sub.2, --OR', and
--S(O).sub.kR', where k is 1, 2, or 3; [0371] R.sub.1 is H, an
amino protecting group, resin, amino acid, polypeptide, or
polynucleotide; and [0372] R.sub.2 is OH, an ester protecting
group, resin, amino acid, polypeptide, or polynucleotide; [0373]
each of R.sub.3 and R.sub.4 is independently H, halogen, lower
alkyl, or substituted lower alkyl, or R.sub.3 and R.sub.4 or two
R.sub.3 groups optionally form a cycloalkyl or a heterocycloalkyl;
[0374] M is H or --CH.sub.2R.sub.5; [0375] R.sub.5 is alkyl,
substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0376] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; [0377]
or two R.sub.5 groups optionally form a cycloalkyl or a
heterocycloalkyl; or R.sub.5 and any R.sub.a optionally form a
cycloalkyl or a heterocycloalkyl; with a proviso that when R.sub.1
is H then R.sub.2 is not OH, or when R.sub.2 is OH then R.sub.1 is
not H; and G is an amine protecting group. In some embodiments is a
method of making a compound or salt thereof wherein the amine
protecting group is selected from the group consisting of:
##STR00045##
[0377] In other embodiments is a method of making a compound or
salt thereof wherein both R.sub.1 and R.sub.2 are polypeptides.
[0378] In some embodiments is a method of making a compound or salt
thereof wherein at least one aldehyde moiety has the structure
corresponding to:
##STR00046##
wherein; R.sub.5 is alkyl, substituted alkyl, alkenyl, substituted
alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy,
alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide,
substituted polyalkylene oxide, cycloalkyl, substituted cycloalkyl,
aryl, substituted aryl, heteroaryl, substituted heteroaryl,
heterocycle, substituted heterocycle, alkaryl, substituted alkaryl,
aralkyl, substituted aralkyl, --C(O)R'', --C(O)OR'',
--C(O)N(R'').sub.2, --C(O)NHCH(R'').sub.2, -(alkylene or
substituted alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR'; or
R.sub.5 is L-X, where, X is a selected from the group consisting of
a label; a dye; a polymer; a water-soluble polymer; a derivative of
polyethylene glycol; a photocrosslinker; a cytotoxic compound; a
drug; an affinity label; a photoaffinity label; a reactive
compound; a resin; a second protein or polypeptide or polypeptide
analog; an antibody or antibody fragment; a metal chelator; a
cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a
RNA; an antisense polynucleotide; a saccharide, a water-soluble
dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin
label; a fluorophore, a metal-containing moiety; a radioactive
moiety; a novel functional group; a group that covalently or
noncovalently interacts with other molecules; a photocaged moiety;
an actinic radiation excitable moiety; a ligand; a
photoisomerizable moiety; biotin; a biotin analogue; a moiety
incorporating a heavy atom; a chemically cleavable group; a
photocleavable group; an elongated side chain; a carbon-linked
sugar; a redox-active agent; an amino thioacid; a toxic moiety; an
isotopically labeled moiety; a biophysical probe; a phosphorescent
group; a chemiluminescent group; an electron dense group; a
magnetic group; an intercalating group; a chromophore; an energy
transfer agent; a biologically active agent; a detectable label; a
small molecule; an inhibitory ribonucleic acid; a radionucleotide;
a neutron-capture agent; a derivative of biotin; quantum dot(s); a
nanotransmitter; a radiotransmitter; an abzyme, an activated
complex activator, a virus, an adjuvant, an aglycan, an allergan,
an angiostatin, an antihormone, an antioxidant, an aptamer, a guide
RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a
receptor, a reverse micelle, and any combination thereof; and L is
optional, and when present is a linker selected from the group
consisting of alkylene, substituted alkylene, alkenylene,
substituted alkenylene, --O--, --O-(alkylene or substituted
alkylene)-, -(alkylene or substituted alkylene)-O--, --C(O)--,
--C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--.
[0379] In other embodiments is a method of making a compound or
salt thereof having the structure of:
##STR00047##
wherein L is optional, and when present is lower alkylene,
substituted lower alkylene, lower cycloalkylene, substituted lower
cycloalkylene, lower alkenylene, substituted lower alkenylene,
alkynylene, lower heteroalkylene, substituted heteroalkylene, lower
heterocycloalkylene, substituted lower heterocycloalkylene,
arylene, substituted arylene, heteroarylene, substituted
heteroarylene; alkarylene, substituted alkarylene, aralkylene, or
substituted aralkylene; Q is optional, and when present is a linker
selected from the group consisting of lower alkylene, substituted
lower alkylene, lower alkenylene, substituted lower alkenylene,
lower heteroalkylene, substituted lower heteroalkylene,
--O-(alkylene or substituted alkylene)-, --S-(alkylene or
substituted alkylene)-, --S(O).sub.k(alkylene or substituted
alkylene)-, where k is 1, 2, or 3, --C(O)-(alkylene or substituted
alkylene)-, --C(S)-(alkylene or substituted alkylene)-,
--NR'-(alkylene or substituted alkylene)-, --CON(R'')-(alkylene or
substituted alkylene)-, --CSN(R')-(alkylene or substituted
alkylene)-, --N(R')CO-(alkylene or substituted alkylene)-, where
each R' is independently H, alkyl, or substituted alkyl; R.sub.1 is
H, an amino protecting group, resin, amino acid, polypeptide, or
polynucleotide; and R.sub.2 is OH, an ester protecting group,
resin, amino acid, polypeptide, or polynucleotide; each of R.sub.3
and R.sub.4 is independently H, halogen, lower alkyl, or
substituted lower alkyl, or R.sub.3 and R.sub.4 or two R.sub.3
groups optionally form a cycloalkyl or a heterocycloalkyl; each
R.sub.a is independently selected from the group consisting of H,
halogen, alkyl, --NO.sub.2, --CN, substituted alkyl; --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; R.sub.6 is a protected aldehyde or a masked
aldehyde, wherein the protecting group includes, but is not limited
to,
##STR00048##
where each X.sub.1 is independently selected from the group
consisting of --O--, --S--, --N(H)--, --N(R)--, --N(Ac)--, and
--N(OMe)-; X.sub.2 is --OR, --OAc, --SR, --N(R).sub.2, --N(R)(Ac),
--N(R)(OMe), or N.sub.3, and where each R' and R is independently
H, alkyl, or substituted alkyl.
[0380] In other embodiments is a method of making a compound or
salt thereof wherein X.sub.1 is O. In some embodiments is a method
of making a compound or salt thereof wherein both R.sub.1 and
R.sub.2 are polypeptides.
VII. Compositions and Methods Comprising Nucleic Acids and
Oligonucleotides
A. General Recombinant Nucleic Acid Methods for Use Herein
[0381] In numerous embodiments of the methods and compositions
described herein, nucleic acids encoding a polypeptide of interest
(including by way of example a GH polypeptide) will be isolated,
cloned and often altered using recombinant methods. Such
embodiments are used, including but not limited to, for protein
expression or during the generation of variants, derivatives,
expression cassettes, or other sequences derived from a
polypeptide. In some embodiments, the sequences encoding the
polypeptides are operably linked to a heterologous promoter.
[0382] Also described herein are cells that can produce non-natural
amino acid polypeptides wherein at least one non-natural amino acid
on the polypeptide comprises a side-chain having an aromatic amine
moiety or a masked or protected aldehyde moiety. Cells that
biosynthesize at least one non-natural amino acid polypeptide may
be produced using the techniques, methods, compositions and
strategies described herein or variants thereof.
[0383] A nucleotide sequence encoding a polypeptide comprising a
non-natural amino acid may be synthesized on the basis of the amino
acid sequence of the parent polypeptide, and then changing the
nucleotide sequence so as to effect introduction (i.e.,
incorporation or substitution) or removal (i.e., deletion or
substitution) of the relevant amino acid residue(s). The nucleotide
sequence may be conveniently modified by site-directed mutagenesis
in accordance with conventional methods. Alternatively, the
nucleotide sequence may be prepared by chemical synthesis,
including but not limited to, by using an oligonucleotide
synthesizer, wherein oligonucleotides are designed based on the
amino acid sequence of the desired polypeptide, and preferably
selecting those codons that are favored in the host cell in which
the recombinant polypeptide will be produced. For example, several
small oligonucleotides coding for portions of the desired
polypeptide may be synthesized and assembled by PCR, ligation or
ligation chain reaction. See, e.g., Barany, et al., Proc. Natl.
Acad. Sci. 88: 189-193 (1991); U.S. Pat. No. 6,521,427 which are
incorporated by reference herein.
[0384] The non-natural amino acid methods and compositions
described herein utilize routine techniques in the field of
recombinant genetics. Basic texts disclosing the general methods of
use for the non-natural amino acid methods and compositions
described herein include Sambrook et al., Molecular Cloning, A
Laboratory Manual (3rd ed. 2001); Kriegler, Gene Transfer and
Expression: A Laboratory Manual (1990); and Current Protocols in
Molecular Biology (Ausubel et al., eds., 1994)).
[0385] General texts which describe molecular biological techniques
include Berger and Kimmel, Guide to Molecular Cloning Techniques.
Methods in Enzymology volume 152 Academic Press, Inc., San Diego,
Calif. (Berger); Sambrook et al., Molecular Cloning--A Laboratory
Manual (2nd Ed.). Vol. 1-3, Cold Spring Harbor Laboratory, Cold
Spring Harbor, N.Y., 1989 ("Sambrook") and Current Protocols in
Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a
joint venture between Greene Publishing Associates, Inc. and John
Wiley & Sons, Inc., (supplemented through 1999) ("Ausubel")).
These texts describe mutagenesis, the use of vectors, promoters and
many other relevant topics related to, including but not limited
to, the generation of genes or polynucleotides which include
selector codons for production of proteins that include non-natural
amino acids, orthogonal tRNAs, orthogonal synthetases, and pairs
thereof.
[0386] Various types of mutagenesis are used in the non-natural
amino acid methods and compositions described herein for a variety
of purposes, including but not limited to, to produce novel
synthetases or tRNAs, to mutate tRNA molecules, to mutate
polynucleotides encoding synthetases, to produce libraries of
tRNAs, to produce libraries of synthetases, to produce selector
codons, to insert selector codons that encode non-natural amino
acids in a protein or polypeptide of interest. They include but are
not limited to site-directed, random point mutagenesis, homologous
recombination, DNA shuffling or other recursive mutagenesis
methods, chimeric construction, mutagenesis using uracil containing
templates, oligonucleotide-directed mutagenesis,
phosphorothioate-modified DNA mutagenesis, mutagenesis using gapped
duplex DNA or the like, or any combination thereof. Additional
suitable methods include point mismatch repair, mutagenesis using
repair-deficient host strains, restriction-selection and
restriction-purification, deletion mutagenesis, mutagenesis by
total gene synthesis, double-strand break repair, and the like.
Mutagenesis, including but not limited to, involving chimeric
constructs, are also included in the non-natural amino acid methods
and compositions described herein. In one embodiment, mutagenesis
can be guided by known information of the naturally occurring
molecule or altered or mutated naturally occurring molecule,
including but not limited to, sequence, sequence comparisons,
physical properties, crystal structure or the like.
[0387] The texts and examples found herein describe these
procedures. Additional information is found in the following
publications and references cited within: Ling et al., Approaches
to DNA mutagenesis: an overview, Anal Biochem. 254(2): 157-178
(1997); Dale et al., Oligonucleotide-directed random mutagenesis
using the phosphorothioate method, Methods Mol. Biol. 57:369-374
(1996); Smith, In vitro mutagenesis, Ann. Rev. Genet. 19:423-462
(1985); Botstein & Shortle, Strategies and applications of in
vitro mutagenesis, Science 229:1193-1201 (1985); Carter,
Site-directed mutagenesis, Biochem. J. 237:1-7 (1986); Kunkel, The
efficiency of oligonucleotide directed mutagenesis, in Nucleic
Acids & Molecular Biology (Eckstein, F. and Lilley, D. M. J.
eds., Springer Verlag, Berlin)) (1987); Kunkel, Rapid and efficient
site-specific mutagenesis without phenotypic selection, Proc. Natl.
Acad. Sci. USA 82:488-492 (1985); Kunkel et al., Rapid and
efficient site-specific mutagenesis without phenotypic selection,
Methods in Enzymol. 154, 367-382 (1987); Bass et al., Mutant Trp
repressors with new DNA-binding specificities, Science 242:240-245
(1988); Zoller & Smith, Oligonucleotide-directed mutagenesis
using M13-derived vectors: an efficient and general procedure for
the production of point mutations in any DNA fragment, Nucleic
Acids Res. 10:6487-6500 (1982); Zoller & Smith,
Oligonucleotide-directed mutagenesis of DNA fragments cloned into
M13 vectors, Methods in Enzymol. 100:468-500 (1983); Zoller &
Smith, Oligonucleotide-directed mutagenesis: a simple method using
two oligonucleotide primers and a single-stranded DNA template,
Methods in Enzymol. 154:329-350 (1987); Taylor et al., The use of
phosphorothioate-modified DNA in restriction enzyme reactions to
prepare nicked DNA, Nucl. Acids Res. 13: 8749-8764 (1985); Taylor
et al., The rapid generation of oligonucleotide-directed mutations
at high frequency using phosphorothioate-modified DNA, Nucl. Acids
Res. 13: 8765-8785 (1985); Nakamaye & Eckstein, Inhibition of
restriction endonuclease Nci I cleavage by phosphorothioate groups
and its application to oligonucleotide-directed mutagenesis, Nucl.
Acids Res. 14: 9679-9698 (1986); Sayers et al., 5'-3' Exonucleases
in phosphorothioate-based oligonucleotide-directed mutagenesis,
Nucl. Acids Res. 16:791-802 (1988); Sayers et al., Strand specific
cleavage of phosphorothioate-containing DNA by reaction with
restriction endonucleases in the presence of ethidium bromide,
(1988) Nucl. Acids Res. 16: 803-814; Kramer et al., The gapped
duplex DNA approach to oligonucleotide-directed mutation
construction, Nucl. Acids Res. 12: 9441-9456 (1984); Kramer &
Fritz Oligonucleotide-directed construction of mutations via gapped
duplex DNA, Methods in Enzymol. 154:350-367 (1987); Kramer et al.,
Improved enzymatic in vitro reactions in the gapped duplex DNA
approach to oligonucleotide-directed construction of mutations,
Nucl Acids Res. 16: 7207 (1988); Fritz et al.,
Oligonucleotide-directed construction of mutations: a gapped duplex
DNA procedure without enzymatic reactions in vitro, Nucl. Acids
Res. 16: 6987-6999 (1988); Kramer et al., Point Mismatch Repair,
Cell 38:879-887 (1984); Carter et al., Improved oligonucleotide
site-directed mutagenesis using M13 vectors, Nucl. Acids Res. 13:
4431-4443 (1985); Carter, Improved oligonucleotide-directed
mutagenesis using M13 vectors, Methods in Enzymol. 154: 382-403
(1987); Eghtedarzadeh & Henikoff, Use of oligonucleotides to
generate large deletions, Nucl. Acids Res. 14: 5115 (1986); Wells
et al., Importance of hydrogen-bondformation in stabilizing the
transition state of subtilisin, Phil. Trans. R. Soc. Lond. A 317:
415-423 (1986); Nambiar et al., Total synthesis and cloning of a
gene coding for the ribonuclease S protein, Science 223: 1299-1301
(1984); Sakmar and Khorana, Total synthesis and expression of a
gene for the alpha subunit of bovine rod outer segment guanine
nucleotide-binding protein (transducin), Nucl. Acids Res. 14:
6361-6372 (1988); Wells et al., Cassette mutagenesis: an efficient
method for generation of multiple mutations at defined sites, Gene
34:315-323 (1985); Grundstrom et al., Oligonucleotide-directed
mutagenesis by microscale `shot-gun` gene synthesis, Nucl. Acids
Res. 13: 3305-3316 (1985); Mandecki, Oligonucleotide-directed
double-strand break repair in plasmids of Escherichia coli: a
method for site-specific mutagenesis, Proc. Natl. Acad. Sci. USA,
83:7177-7181 (1986); Arnold, Protein engineering for unusual
environments, Current Opinion in Biotechnology 4:450-455 (1993);
Sieber, et al., Nature Biotechnology, 19:456-460 (2001). W. P. C.
Stemmer, Nature 370, 389-91 (1994); and, I. A. Lorimer, I. Pastan,
Nucleic Acids Res. 23, 3067-8 (1995). Additional details on many of
the above methods can be found in Methods in Enzymology Volume 154,
which also describes useful controls for trouble-shooting problems
with various mutagenesis methods.
[0388] The methods and compositions described herein also include
use of eukaryotic host cells, non-eukaryotic host cells, and
organisms for the in vivo incorporation of a non-natural amino acid
via orthogonal tRNA/RS pairs. Host cells are genetically engineered
(including but not limited to, transformed, transduced or
transfected) with the polynucleotides corresponding to the
polypeptides described herein or constructs which include a
polynucleotide corresponding to the polypeptides described herein,
including but not limited to, a vector corresponding to the
polypeptides described herein, which can be, for example, a cloning
vector or an expression vector. For example, the coding regions for
the orthogonal tRNA, the orthogonal tRNA synthetase, and the
protein to be derivatized are operably linked to gene expression
control elements that are functional in the desired host cell. The
vector can be, for example, in the form of a plasmid, a cosmid, a
phage, a bacterium, a virus, a naked polynucleotide, or a
conjugated polynucleotide. The vectors are introduced into cells
and/or microorganisms by standard methods including electroporation
(Fromm et al., Proc. Natl. Acad. Sci. USA 82, 5824 (1985),
infection by viral vectors, high velocity ballistic penetration by
small particles with the nucleic acid either within the matrix of
small beads or particles, or on the surface (Klein et al., Nature
327, 70-73 (1987)), and/or the like.
[0389] The engineered host cells can be cultured in conventional
nutrient media modified as appropriate for such activities as, for
example, screening steps, activating promoters or selecting
transformants. These cells can optionally be cultured into
transgenic organisms. Other useful references, including but not
limited to for cell isolation and culture (e.g., for subsequent
nucleic acid isolation) include Freshney (1994) Culture of Animal
Cells, a Manual of Basic Technique, third edition, Wiley-Liss, New
York and the references cited therein; Payne et al. (1992) Plant
Cell and Tissue Culture in Liquid Systems John Wiley & Sons,
Inc. New York, N.Y.; Gamborg and Phillips (eds) (1995) Plant Cell,
Tissue and Organ Culture; Fundamental Methods Springer Lab Manual,
Springer-Verlag (Berlin Heidelberg N.Y.) and Atlas and Parks (eds)
The Handbook of Microbiological Media (1993) CRC Press, Boca Raton,
Fla.
[0390] Several well-known methods of introducing target nucleic
acids into cells are available, any of which can be used in methods
and compositions described herein. These include: fusion of the
recipient cells with bacterial protoplasts containing the DNA,
electroporation, projectile bombardment, and infection with viral
vectors (discussed further, below), etc. Bacterial cells can be
used to amplify the number of plasmids containing DNA constructs
corresponding to the polypeptides described herein. The bacteria
are grown to log phase and the plasmids within the bacteria can be
isolated by a variety of methods known in the art (see, for
instance, Sambrook). In addition, kits are commercially available
for the purification of plasmids from bacteria, (see, e.g.,
EasyPrep.TM., FlexiPrep.TM., both from Pharmacia Biotech;
StrataClean.TM., from Stratagene; and, QIAprep.TM. from Qiagen).
The isolated and purified plasmids are then further manipulated to
produce other plasmids, used to transfect cells or incorporated
into related vectors to infect organisms. Typical vectors contain
transcription and translation terminators, transcription and
translation initiation sequences, and promoters useful for
regulation of the expression of the particular target nucleic acid.
The vectors optionally comprise generic expression cassettes
containing at least one independent terminator sequence, sequences
permitting replication of the cassette in eukaryotes, or
prokaryotes, or both, (including but not limited to, shuttle
vectors) and selection markers for both prokaryotic and eukaryotic
systems. Vectors are suitable for replication and integration in
prokaryotes, eukaryotes, or both. See, Gillam & Smith, Gene
8:81 (1979); Roberts, et al., Nature, 328:731 (1987); Schneider,
E., et al., Protein Expr. Purif. 6(1):10-14 (1995); Ausubel,
Sambrook, Berger (all supra). A catalogue of bacteria and
bacteriophages useful for cloning is provided, e.g., by the ATCC,
e.g., The ATCC Catalogue of bacteria and bacteriophage (1992)
Gherna et al. (eds) published by the ATCC. Additional basic
procedures for sequencing, cloning and other aspects of molecular
biology and underlying theoretical considerations are also found in
Watson et al. (1992) Recombinant DNA Second Edition Scientific
American Books, NY. In addition, essentially any nucleic acid (and
virtually any labeled nucleic acid, whether standard or
non-standard) can be custom or standard ordered from any of a
variety of commercial sources, such as the Midland Certified
Reagent Company (Midland, Tex. mcrc.com), The Great American Gene
Company (Ramona, Calif. available on the World Wide Web at
genco.com), ExpressGen Inc. (Chicago, Ill. available on the World
Wide Web at expressgen.com), Operon Technologies Inc. (Alameda,
Calif.) and many others.)
B. Selector Codons
[0391] Selector codons encompassed within the methods and
compositions described herein expand the genetic codon framework of
protein biosynthetic machinery. For example, a selector codon
includes, but is not limited to, a unique three base codon, a
nonsense codon, such as a stop codon, including but not limited to,
an amber codon (UAG), an ochre codon, or an opal codon (UGA), a
unnatural codon, a four or more base codon, a rare codon, or the
like. There is a wide range in the number of selector codons that
can be introduced into a desired gene or polynucleotide including
but not limited to, one or more, two or more, three or more, 4, 5,
6, 7, 8, 9, 10 or more in a single polynucleotide encoding at least
a portion of a polypeptide of interest.
[0392] In one embodiment, the methods involve the use of a selector
codon that is a stop codon for the incorporation of one or more
non-natural amino acids in vivo. For example, an O-tRNA is produced
that recognizes the stop codon, including but not limited to, UAG,
and is aminoacylated by an O--RS with a desired non-natural amino
acid. This O-tRNA is not recognized by the naturally occurring
host's aminoacyl-tRNA synthetases. Conventional site-directed
mutagenesis can be used to introduce the stop codon, including but
not limited to, TAG, at the site of interest in a polypeptide of
interest. See, e.g., Sayers, J. R., et al. (1988), 5'-3'
Exonuclease in phosphorothioate-based oligonucleotide-directed
mutagenesis. Nucleic Acids Res. 16:791-802. When the O--RS, O-tRNA
and the nucleic acid that encodes the polypeptide of interest are
combined in vivo, the non-natural amino acid is incorporated in
response to the UAG codon to give a polypeptide containing the
non-natural amino acid at the specified position.
[0393] Non-natural amino acids can also be encoded with rare
codons. For example, when the arginine concentration in an in vitro
protein synthesis reaction is reduced, the rare arginine codon,
AGG, has proven to be efficient for insertion of Ala by a synthetic
tRNA acylated with alanine. See, e.g., Ma et al., Biochemistry.
32:7939 (1993). In this case, the synthetic tRNA competes with the
naturally occurring tRNAArg, which exists as a minor species in
Escherichia coli. Some organisms do not use all triplet codons. An
unassigned codon AGA in Micrococcus luteus has been utilized for
insertion of amino acids in an in vitro transcription/translation
extract. See, e.g., Kowal and Oliver, Nucl. Acid. Res., 25:4685
(1997). Components of the present invention can be generated to use
these rare codons in vivo.
[0394] The incorporation of non-natural amino acids in vivo can be
done without significant perturbation of the eukaryotic host cell.
For example, because the suppression efficiency for the UAG codon
depends upon the competition between the O-tRNA, including but not
limited to, the amber suppressor tRNA, and a eukaryotic release
factor (including but not limited to, eRF) (which binds to a stop
codon and initiates release of the growing peptide from the
ribosome), the suppression efficiency can be modulated by,
including but not limited to, increasing the expression level of
O-tRNA, and/or the suppressor tRNA.
[0395] Selector codons also comprise extended codons, including but
not limited to, four or more base codons, such as, four, five, six
or more base codons. Examples of four base codons include, but are
not limited to, AGGA, CUAG, UAGA, CCCU and the like. Examples of
five base codons include, but are not limited to, AGGAC, CCCCU,
CCCUC, CUAGA, CUACU, UAGGC and the like. A feature of the methods
and compositions described herein includes using extended codons
based on frameshift suppression. Four or more base codons can
insert, including but not limited to, one or multiple non-natural
amino acids into the same protein. For example, in the presence of
mutated O-tRNAs, including but not limited to, a special frameshift
suppressor tRNAs, with anticodon loops, for example, with at least
8-10 nt anticodon loops, the four or more base codon is read as
single amino acid. In other embodiments, the anticodon loops can
decode, including but not limited to, at least a four-base codon,
at least a five-base codon, or at least a six-base codon or more.
Since there are 256 possible four-base codons, multiple-non-natural
amino acids can be encoded in the same cell using a four or more
base codon. See, Anderson et al., (2002) Exploring the Limits of
Codon and Anticodon Size, Chemistry and Biology, 9:237-244;
Magliery, (2001) Expanding the Genetic Code: Selection of Efficient
Suppressors of Four-base Codons and Identification of "Shifty"
Four-base Codons with a Library Approach in Escherichia coli, J.
Mol. Biol. 307: 755-769.
[0396] For example, four-base codons have been used to incorporate
non-natural amino acids into proteins using in vitro biosynthetic
methods. See, e.g., Ma et al., (1993) Biochemistry. 32:7939; and
Hohsaka et al., (1999) J. Am. Chem. Soc. 121:34. CGGG and AGGU were
used to simultaneously incorporate 2-naphthylalanine and an NBD
derivative of lysine into streptavidin in vitro with two chemically
acylated frameshift suppressor tRNAs. See, e.g., Hohsaka et al.,
(1999) J. Am. Chem. Soc., 121:12194. In an in vivo study, Moore et
al. examined the ability of tRNALeu derivatives with NCUA
anticodons to suppress UAGN codons (N can be U, A, G, or C), and
found that the quadruplet UAGA can be decoded by a tRNALeu with a
UCUA anticodon with an efficiency of 13 to 26% with little decoding
in the 0 or -1 frame. See, Moore et al., (2000) J. Mol. Biol.
298:195. In one embodiment, extended codons based on rare codons or
nonsense codons can be used in the methods and compositions
described herein, which can reduce missense readthrough and
frameshift suppression at other unwanted sites.
[0397] For a given system, a selector codon can also include one of
the natural three base codons, where the endogenous system does not
use (or rarely uses) the natural base codon. For example, this
includes a system that is lacking a tRNA that recognizes the
natural three base codon, and/or a system where the three base
codon is a rare codon.
[0398] Selector codons optionally include unnatural base pairs.
These unnatural base pairs further expand the existing genetic
alphabet. One extra base pair increases the number of triplet
codons from 64 to 125. Properties of third base pairs include
stable and selective base pairing, efficient enzymatic
incorporation into DNA with high fidelity by a polymerase, and the
efficient continued primer extension after synthesis of the nascent
unnatural base pair. Descriptions of unnatural base pairs which can
be adapted for methods and compositions include, e.g., Hirao, et
al., (2002) An unnatural base pair for incorporating amino acid
analogues into protein, Nature Biotechnology, 20:177-182, and see
also, Wu, Y., et. al. (2002) J. Am. Chem. Soc. 124:14626-14630.
Other relevant publications are listed below.
[0399] For in vivo usage, the unnatural nucleoside is membrane
permeable and is phosphorylated to form the corresponding
triphosphate. In addition, the increased genetic information is
stable and not destroyed by cellular enzymes. Previous efforts by
Benner and others took advantage of hydrogen bonding patterns that
are different from those in canonical Watson-Crick pairs, the most
noteworthy example of which is the iso-C:iso-G pair See, e.g.,
Switzer et al., (1989) J. Am. Chem. Soc. 111:8322; and Piccirilli
et al., (1990) Nature, 343:33; Kool, (2000) Curr. Opin. Chem. Biol.
4:602. These bases in general mispair to some degree with natural
bases and cannot be enzymatically replicated. Kool and co-workers
demonstrated that hydrophobic packing interactions between bases
can replace hydrogen bonding to drive the formation of base pair.
See, Kool, (2000) Curr. Opin. Chem. Biol., 4:602; and Guckian and
Kool, (1998) Angew. Chem. Int. Ed. Engl., 36, 2825. In an effort to
develop an unnatural base pair satisfying all the above
requirements, Schultz, Romesberg and co-workers have systematically
synthesized and studied a series of unnatural hydrophobic bases. A
PICS:PICS self-pair is found to be more stable than natural base
pairs, and can be efficiently incorporated into DNA by Klenow
fragment of Escherichia coli DNA polymerase I (KF). See, e.g.,
McMinn et al., (1999) J. Am. Chem. Soc., 121:11585-6; and Ogawa et
al., (2000) J. Am. Chem. Soc., 122:3274. A 3MN:3MN self-pair can be
synthesized by KF with efficiency and selectivity sufficient for
biological function. See, e.g., Ogawa et al., (2000) J. Am. Chem.
Soc. 122:8803. However, both bases act as a chain terminator for
further replication. A mutant DNA polymerase has been recently
evolved that can be used to replicate the PICS self pair. In
addition, a 7AI.self pair can be replicated. See, e.g., Tae et al.,
(2001) J. Am. Chem. Soc., 123:7439. A novel metallobase pair,
Dipic:Py, has also been developed, which forms a stable pair upon
binding Cu(II). See, Meggers et al., (2000) J. Am. Chem. Soc.
122:10714. Because extended codons and unnatural codons are
intrinsically orthogonal to natural codons, the non-natural amino
acid methods described herein can take advantage of this property
to generate orthogonal tRNAs for them.
[0400] A translational bypassing system can also be used to
incorporate a non-natural amino acid in a desired polypeptide. In a
translational bypassing system, a large sequence is incorporated
into a gene but is not translated into protein. The sequence
contains a structure that serves as a cue to induce the ribosome to
hop over the sequence and resume translation downstream of the
insertion.)
[0401] In certain embodiments, the protein or polypeptide of
interest (or portion thereof) in the methods and/or compositions
described herein is encoded by a nucleic acid. Typically, the
nucleic acid comprises at least one selector codon, at least two
selector codons, at least three selector codons, at least four
selector codons, at least five selector codons, at least six
selector codons, at least seven selector codons, at least eight
selector codons, at least nine selector codons, ten or more
selector codons.
[0402] Genes coding for proteins or polypeptides of interest can be
mutagenized using methods well-known to one of skill in the art and
described herein under "Mutagenesis and Other Molecular Biology
Techniques" to include, for example, one or more selector codon for
the incorporation of a non-natural amino acid. For example, a
nucleic acid for a protein of interest is mutagenized to include
one or more selector codon, providing for the incorporation of the
one or more non-natural amino acids. The methods and compositions
described herein include any such variant, including but not
limited to, mutant, versions of any protein, for example, including
at least one non-natural amino acid. Similarly, the methods and
compositions described herein include corresponding nucleic acids,
i.e., any nucleic acid with one or more selector codon that encodes
one or more non-natural amino acid.
[0403] Nucleic acid molecules encoding a protein of interest,
including by way of example only, GH polypeptide may be readily
mutated to introduce a cysteine at any desired position of the
polypeptide. Cysteine is widely used to introduce reactive
molecules, water soluble polymers, proteins, or a wide variety of
other molecules, onto a protein of interest. Methods suitable for
the incorporation of cysteine into a desired position of a
polypeptide are well known in the art, such as those described in
U.S. Pat. No. 6,608,183, which is incorporated by reference herein,
and standard mutagenesis techniques.
VIII. In Vivo Generation of Polypeptides Comprising Non-Natural
Amino Acids
[0404] The polypeptides described herein can be generated in vivo
using modified tRNA and tRNA synthetases to add to or substitute
amino acids that are not encoded in naturally-occurring
systems.
[0405] Methods for generating tRNAs and tRNA synthetases which use
amino acids that are not encoded in naturally-occurring systems are
described in, e.g., U.S. Pat. No. 7,045,337, entitled "In vivo
incorporation of unnatural amino acids" and U.S. Pat. No.
7,083,970, entitled "Methods and compositions for the production of
orthogonal tRNA-aminoacyl tRNA synthetase pairs" which are
incorporated by reference herein. These methods involve generating
a translational machinery that functions independently of the
synthetases and tRNAs endogenous to the translation system (and are
therefore sometimes referred to as "orthogonal"). In one embodiment
the translation system comprises a polynucleotide encoding the
polypeptide; the polynucleotide can be mRNA that was transcribed
from the corresponding DNA, or the mRNA may arise from, an RNA
viral vector; further the polynucleotide comprises a selector codon
corresponding to the predesignated site of incorporation for the
non-natural amino acid. The translation further comprises a tRNA
comprising the non-natural amino acid, where the tRNA is specific
to the aforementioned selector codon; in further embodiments, the
non-natural amino acid is aminoacylated. In further or additional
embodiments, the translation system comprises an aminoacyl
synthetase specific for the tRNA, and in other or further
embodiments, the translation system comprises an orthogonal tRNA
and an orthogonal aminoacyl tRNA synthetase. In further or
additional embodiments, the translation system comprises at least
one of the following: a plasmid comprising the aforementioned
polynucleotide (typically in the form of DNA), genomic DNA
comprising the aforementioned polynucleotide (typically in the form
of DNA), or genomic DNA into which the aforementioned
polynucleotide has been integrated (in further embodiments, the
integration is stable integration). In further or additional
embodiments of the translation system, the selector codon is
selected from the group consisting of an amber codon, ochre codon,
opal codon, a unique codon, a rare codon, an unnatural codon, a
five-base codon, and a four-base codon. In further or additional
embodiments of the translation system, the tRNA is a suppressor
tRNA. In further or additional embodiments, the non-natural amino
acid polypeptide is synthesized by a ribosome.
[0406] In further or additional embodiments, the translation system
comprises an orthogonal tRNA (O-tRNA) and an orthogonal aminoacyl
tRNA synthetase (Q-RS). Typically, the O--RS preferentially
aminoacylates the O-tRNA with at least one non-natural amino acid
in the translation system and the O-tRNA recognizes at least one
selector codon that is not recognized by other tRNAs in the system.
The translation system thus inserts the non-natural amino acid into
a protein produced in the system, in response to an encoded
selector codon, thereby "substituting" an amino acid into a
position in the encoded polypeptide.
[0407] A wide variety of orthogonal tRNAs and aminoacyl tRNA
synthetases have been described in the art for inserting particular
synthetic amino acids into polypeptides, and are generally suitable
for in the methods described herein to produce the non-natural
amino acid polypeptides described herein. For example,
keto-specific O-tRNA/aminoacyl-tRNA synthetases are described in
Wang, L., et al., Proc. Natl. Acad. Sci. USA 100:56-61 (2003) and
Zhang, Z. et al., Biochem. 42(22):6735-6746 (2003). Exemplary
O--RS, or portions thereof, are encoded by polynucleotide sequences
and include amino acid sequences disclosed in U.S. Patent
Application Publications 2003/0082575 and 2003/0108885, each
incorporated herein by reference. Corresponding O-tRNA molecules
for use with the O--RSs are also described in U.S. Pat. No.
7,045,337, entitled "In vivo incorporation of unnatural amino
acids" and U.S. Pat. No. 7,083,970, entitled "Methods and
compositions for the production of orthogonal tRNA-aminoacyl tRNA
synthetase pairs" which are incorporated by reference herein. In
addition, Mehl et al. in J. Am. Chem. Soc. 2003; 125:935-939 and
Santoro et al. Nature Biotechnology 2002 October; 20:1044-1048,
which are incorporated by reference in their entirety herein,
discuss screening methods and aminoacyl tRNA synthetase and tRNA
molecules for the incorporation of p-aminophenylalanine into
polypeptides.
[0408] Exemplary O-tRNA sequences suitable for use in the methods
described herein include, but are not limited to, nucleotide
sequences SEQ ID NOs: 1-3 as disclosed in U.S. Patent Application
Publication 2003/0108885 (Ser. No. 10/126,931) which is
incorporated by reference herein. Other examples of
O-tRNA/aminoacyl-tRNA synthetase pairs specific to particular
non-natural amino acids are described in U.S. Patent Application
Publication 2003/0082575 (Ser. No. 10/126,927) which is
incorporated by reference herein. O--RS and O-tRNA that incorporate
both keto- and azide-containing amino acids in S. cerevisiae are
described in Chin, J. W., et al., Science 301:964-967 (2003).
[0409] Use of O-tRNA/aminoacyl-tRNA synthetases involves selection
of a specific codon which encodes the non-natural amino acid. While
any codon can be used, it is generally desirable to select a codon
that is rarely or never used in the cell in which the
O-tRNA/aminoacyl-tRNA synthetase is expressed. For example,
exemplary codons include nonsense codon such as stop codons (amber,
ochre, and opal), four or more base codons and other natural
three-base codons that are rarely or unused.
[0410] Specific selector codon(s) can be introduced into
appropriate positions in the polynucleotide coding sequence using
mutagenesis methods known in the art (including but not limited to,
site-specific mutagenesis, cassette mutagenesis, restriction
selection mutagenesis, etc.).
[0411] Methods for generating components of the protein
biosynthetic machinery, such as O--RSs, O-tRNAs, and orthogonal
O-tRNA/O--RS pairs that can be used to incorporate a non-natural
amino acid are described in Wang, L., et al., Science 292: 498-500
(2001); Chin, J. W., et al., J. Am. Chem. Soc. 124:9026-9027
(2002); Zhang, Z. et al., Biochemistry 42: 6735-6746 (2003).
Methods and compositions for the in vivo incorporation of
non-natural amino acids are described in U.S. Patent Application
Publication 2003/0082575 (Ser. No. 10/126,927) which is
incorporated by reference herein. Methods for selecting an
orthogonal tRNA-tRNA synthetase pair for use in in vivo translation
system of an organism are also described in U.S. Pat. No.
7,045,337, entitled "In vivo incorporation of unnatural amino
acids" and U.S. Pat. No. 7,083,970, entitled "Methods and
compositions for the production of orthogonal tRNA-aminoacyl tRNA
synthetase pairs" which are incorporated by reference herein. In
addition PCT Publication No. WO 04/035743 entitled "Site Specific
Incorporation of Keto Amino Acids into proteins, which is
incorporated by reference in its entirety, describes orthogonal RS
and tRNA pairs for the incorporation of keto amino acids. PCT
Publication No. WO 04/094593 entitled "Expanding the Eukaryotic
Genetic Code," which is incorporated by reference herein in its
entirety, describes orthogonal RS and tRNA pairs for the
incorporation of non-naturally encoded amino acids in eukaryotic
host cells.
[0412] Methods for producing at least one recombinant orthogonal
aminoacyl-tRNA synthetase (O--RS) comprise: (a) generating a
library of (optionally mutant) RSs derived from at least one
aminoacyl-tRNA synthetase (RS) from a first organism, including but
not limited to, a prokaryotic organism, such as Mathanococcus
jannaschii, Methanobacterium thermoautotrophicum, Halobacterium,
Escherichia coli, A. fulgidus, P. furiosus, P. horikoshii, A.
pernix, T. thermophilus, or the like, or a eukaryotic organism; (b)
selecting (and/or screening) the library of RSs (optionally mutant
RSs) for members that aminoacylate an orthogonal tRNA (O-tRNA) in
the presence of a non-natural amino acid and a natural amino acid,
thereby providing a pool of active (optionally mutant) RSs; and/or,
(c) selecting (optionally through negative selection) the pool for
active RSs (including but not limited to, mutant RSs) that
preferentially aminoacylate the O-tRNA in the absence of the
non-natural amino acid, thereby providing the at least one
recombinant O--RS; wherein the at least one recombinant O--RS
preferentially aminoacylates the O-tRNA with the non-natural amino
acid.
[0413] In one embodiment, the RS is an inactive RS. The inactive RS
can be generated by mutating an active RS. For example, the
inactive RS can be generated by mutating at least about 1, at least
about 2, at least about 3, at least about 4, at least about 5, at
least about 6, or at least about 10 or more amino acids to
different amino acids, including but not limited to, alanine.
[0414] Libraries of mutant RSs can be generated using various
techniques known in the art, including but not limited to rational
design based on protein three dimensional RS structure, or
mutagenesis of RS nucleotides in a random or rational design
technique. For example, the mutant RSs can be generated by
site-specific mutations, random mutations, diversity generating
recombination mutations, chimeric constructs, rational design and
by other methods described herein or known in the art.
[0415] In one embodiment, selecting (and/or screening) the library
of RSs (optionally mutant RSs) for members that are active,
including but not limited to, that aminoacylate an orthogonal tRNA
(O-tRNA) in the presence of a non-natural amino acid and a natural
amino acid, includes: introducing a positive selection or screening
marker, including but not limited to, an antibiotic resistance
gene, or the like, and the library of (optionally mutant) RSs into
a plurality of cells, wherein the positive selection and/or
screening marker comprises at least one selector codon, including
but not limited to, an amber codon, ochre codon, opal codon, a
unique codon, a rare codon, an unnatural codon, a five-base codon,
and a four-base codon; growing the plurality of cells in the
presence of a selection agent; identifying cells that survive (or
show a specific response) in the presence of the selection and/or
screening agent by suppressing the at least one selector codon in
the positive selection or screening marker, thereby providing a
subset of positively selected cells that contains the pool of
active (optionally mutant) RSs. Optionally, the selection and/or
screening agent concentration can be varied.
[0416] In one aspect, the positive selection marker is a
chloramphenicol acetyltransferase (CAT) gene and the selector codon
is an amber stop codon in the CAT gene. Optionally, the positive
selection marker is a .beta.-lactamase gene and the selector codon
is an amber stop codon in the .beta.-lactamase gene. In another
aspect the positive screening marker comprises a fluorescent or
luminescent screening marker or an affinity based screening marker
(including but not limited to, a cell surface marker).
[0417] In one embodiment, negatively selecting or screening the
pool for active RSs (optionally mutants) that preferentially
aminoacylate the O-tRNA in the absence of the non-natural amino
acid includes: introducing a negative selection or screening marker
with the pool of active (optionally mutant) RSs from the positive
selection or screening into a plurality of cells of a second
organism, wherein the negative selection or screening marker
comprises at least one selector codon (including but not limited
to, an antibiotic resistance gene, including but not limited to, a
chloramphenicol acetyltransferase (CAT) gene); and, identifying
cells that survive or show a specific screening response in a first
medium supplemented with the non-natural amino acid and a screening
or selection agent, but fail to survive or to show the specific
response in a second medium not supplemented with the non-natural
amino acid and the selection or screening agent, thereby providing
surviving cells or screened cells with the at least one recombinant
O--RS. For example, a CAT identification protocol optionally acts
as a positive selection and/or a negative screening in
determination of appropriate O--RS recombinants. For instance, a
pool of clones is optionally replicated on growth plates containing
CAT (which comprises at least one selector codon) either with or
without one or more non-natural amino acid. Colonies growing
exclusively on the plates containing non-natural amino acids are
thus regarded as containing recombinant O--RS. In one aspect, the
concentration of the selection (and/or screening) agent is varied.
In some aspects the first and second organisms are different. Thus,
the first and/or second organism optionally comprises: a
prokaryote, a eukaryote, a mammal, an Escherichia coli, a fungi, a
yeast, an archaebacterium, a eubacterium, a plant, an insect, a
protist, etc. In other embodiments, the screening marker comprises
a fluorescent or luminescent screening marker or an affinity based
screening marker.
[0418] In another embodiment, screening or selecting (including but
not limited to, negatively selecting) the pool for active
(optionally mutant) RSs includes: isolating the pool of active
mutant RSs from the positive selection step (b); introducing a
negative selection or screening marker, wherein the negative
selection or screening marker comprises at least one selector codon
(including but not limited to, a toxic marker gene, including but
not limited to, a ribonuclease barnase gene, comprising at least
one selector-codon), and the pool of active (optionally mutant) RSs
into a plurality of cells of a second organism; and identifying
cells that survive or show a specific screening response in a first
medium not supplemented with the non-natural amino acid, but fail
to survive or show a specific screening response in a second medium
supplemented with the non-natural amino acid, thereby providing
surviving or screened cells with the at least one recombinant
O--RS, wherein the at least one recombinant O--RS is specific for
the non-natural amino acid. In one aspect, the at least one
selector codon comprises about two or more selector codons. Such
embodiments optionally can include wherein the at least one
selector codon comprises two or more selector codons, and wherein
the first and second organism are different (including but not
limited to, each organism is optionally, including but not limited
to, a prokaryote, a eukaryote, a mammal, an Escherichia coli, a
fungi, a yeast, an archaebacteria, a eubacteria, a plant, an
insect, a protist, etc.). Also, some aspects include wherein the
negative selection marker comprises a ribonuclease barnase gene
(which comprises at least one selector codon). Other aspects
include wherein the screening marker optionally comprises a
fluorescent or luminescent screening marker or an affinity based
screening marker. In the embodiments herein, the screenings and/or
selections optionally include variation of the screening and/or
selection stringency.
[0419] In one embodiment, the methods for producing at least one
recombinant orthogonal aminoacyl-tRNA synthetase (O--RS) can
further comprise: (d) isolating the at least one recombinant O--RS;
(e) generating a second set of O--RS (optionally mutated) derived
from the at least one recombinant O--RS; and, (f) repeating steps
(b) and (c) until a mutated O--RS is obtained that comprises an
ability to preferentially aminoacylate the O-tRNA. Optionally,
steps (d)-(f) are repeated, including but not limited to, at least
about two times. In one aspect, the second set of mutated O--RS
derived from at least one recombinant O--RS can be generated by
mutagenesis, including but not limited to, random mutagenesis,
site-specific mutagenesis, recombination or a combination
thereof.
[0420] The stringency of the selection/screening steps, including
but not limited to, the positive selection/screening step (b), the
negative selection/screening step (c) or both the positive and
negative selection/screening steps (b) and (c), in the
above-described methods, optionally includes varying the
selection/screening stringency. In another embodiment, the positive
selection/screening step (b), the negative selection/screening step
(c) or both the positive and negative selection/screening steps (b)
and (c) comprise using a reporter, wherein the reporter is detected
by fluorescence-activated cell sorting (FACS) or wherein the
reporter is detected by luminescence. Optionally, the reporter is
displayed on a cell surface, on a phage display or the like and
selected based upon affinity or catalytic activity involving the
non-natural amino acid or an analogue. In one embodiment, the
mutated synthetase is displayed on a cell surface, on a phage
display or the like.
[0421] Methods for producing a recombinant orthogonal tRNA (O-tRNA)
include: (a) generating a library of mutant tRNAs derived from at
least one tRNA, including but not limited to, a suppressor tRNA,
from a first organism; (b) selecting (including but not limited to,
negatively selecting) or screening the library for (optionally
mutant) tRNAs that are aminoacylated by an aminoacyl-tRNA
synthetase (RS) from a second organism in the absence of a RS from
the first organism, thereby providing a pool of tRNAs (optionally
mutant); and, (c) selecting or screening the pool of tRNAs
(optionally mutant) for members that are aminoacylated by an
introduced orthogonal RS(O--RS), thereby providing at least one
recombinant O-tRNA; wherein the at least one recombinant O-tRNA
recognizes a selector codon and is not efficiency recognized by the
RS from the second organism and is preferentially aminoacylated by
the O--RS. In some embodiments the at least one tRNA is a
suppressor tRNA and/or comprises a unique three base codon of
natural and/or unnatural bases, or is a nonsense codon, a rare
codon, an unnatural codon, a codon comprising at least 4 bases, an
amber codon, an ochre codon, or an opal stop codon. In one
embodiment, the recombinant O-tRNA possesses an improvement of
orthogonality. It will be appreciated that in some embodiments,
O-tRNA is optionally imported into a first organism from a second
organism without the need for modification. In various embodiments,
the first and second organisms are either the same or different and
are optionally chosen from, including but not limited to,
prokaryotes (including but not limited to, Methanococcus
jannaschii, Methanobacterium thermoautotrophicum, Escherichia coli,
Halobacterium, etc.), eukaryotes, mammals, fungi, yeasts,
archaebacteria, eubacteria, plants, insects, protists, etc.
Additionally, the recombinant tRNA is optionally aminoacylated by a
non-natural amino acid, wherein the non-natural amino acid is
biosynthesized in vivo either naturally or through genetic
manipulation. The non-natural amino acid is optionally added to a
growth medium for at least the first or second organism.
[0422] In one aspect, selecting (including but not limited to,
negatively selecting) or screening the library for (optionally
mutant) tRNAs that are aminoacylated by an aminoacyl-tRNA
synthetase (step (b)) includes: introducing a toxic marker gene,
wherein the toxic marker gene comprises at least one of the
selector codons (or a gene that leads to the production of a toxic
or static agent or a gene essential to the organism wherein such
marker gene comprises at least one selector codon) and the library
of (optionally mutant) tRNAs into a plurality of cells from the
second organism; and, selecting surviving cells, wherein the
surviving cells contain the pool of (optionally mutant) tRNAs
comprising at least one orthogonal tRNA or nonfunctional tRNA. For
example, surviving cells can be selected by using a comparison
ratio cell density assay.
[0423] In another aspect, the toxic marker gene can include two or
more selector codons. In another embodiment of the methods, the
toxic marker gene is a ribonuclease barnase gene, where the
ribonuclease barnase gene comprises at least one amber codon.
Optionally, the ribonuclease barnase gene can include two or more
amber codons.
[0424] In one embodiment, selecting or screening the pool of
(optionally mutant) tRNAs for members that are aminoacylated by an
introduced orthogonal RS(O--RS) can include: introducing a positive
selection or screening marker gene, wherein the positive marker
gene comprises a drug resistance gene (including but not limited
to, .beta.-lactamase gene, comprising at least one of the selector
codons, such as at least one amber stop codon) or a gene essential
to the organism, or a gene that leads to detoxification of a toxic
agent, along with the O--RS, and the pool of (optionally mutant)
tRNAs into a plurality of cells from the second organism; and,
identifying surviving or screened cells grown in the presence of a
selection or screening agent, including but not limited to, an
antibiotic, thereby providing a pool of cells possessing the at
least one recombinant tRNA, where the at least recombinant tRNA is
aminoacylated by the O--RS and inserts an amino acid into a
translation product encoded by the positive marker gene, in
response to the at least one selector codons. In another
embodiment, the concentration of the selection and/or screening
agent is varied.
[0425] Methods for generating specific O-tRNA/O--RS pairs are
provided. Methods include: (a) generating a library of mutant tRNAs
derived from at least one tRNA from a first organism; (b)
negatively selecting or screening the library for (optionally
mutant) tRNAs that are aminoacylated by an aminoacyl-tRNA
synthetase (RS) from a second organism in the absence of a RS from
the first organism, thereby providing a pool of (optionally mutant)
tRNAs; (c) selecting or screening the pool of (optionally mutant)
tRNAs for members that are aminoacylated by an introduced
orthogonal RS(O--RS), thereby providing at least one recombinant
O-tRNA. The at least one recombinant O-tRNA recognizes a selector
codon and is not efficiency recognized by the RS from the second
organism and is preferentially aminoacylated by the O--RS. The
method also includes (d) generating a library of (optionally
mutant) RSs derived from at least one aminoacyl-tRNA synthetase
(RS) from a third organism; (e) selecting or screening the library
of mutant RSs for members that preferentially aminoacylate the at
least one recombinant O-tRNA in the presence of a non-natural amino
acid and a natural amino acid, thereby providing a pool of active
(optionally mutant) RSs; and, (f) negatively selecting or screening
the pool for active (optionally mutant) RSs that preferentially
aminoacylate the at least one recombinant O-tRNA in the absence of
the non-natural amino acid, thereby providing the at least one
specific O-tRNA/O--RS pair, wherein the at least one specific
O-tRNA/O--RS pair comprises at least one recombinant O--RS that is
specific for the non-natural amino acid and the at least one
recombinant O-tRNA. Specific O-tRNA/O--RS pairs produced by the
methods are included. For example, the specific O-tRNA/O--RS pair
can include, including but not limited to, a mutRNATyr-mutTyrRS
pair, such as a mutRNATyr-SS12TyrRS pair, a mutRNALeu-mutLeuRS
pair, a mutRNAThr-mutThrRS pair, a mutRNAGlu-mutGluRS pair, or the
like. Additionally, such methods include wherein the first and
third organism are the same (including but not limited to,
Methanococcus jannaschii).
[0426] Methods for selecting an orthogonal tRNA-tRNA synthetase
pair for use in an in vivo translation system of a second organism
are also included in the methods described herein. The methods
include: introducing a marker gene, a tRNA and an aminoacyl-tRNA
synthetase (RS) isolated or derived from a first organism into a
first set of cells from the second organism; introducing the marker
gene and the tRNA into a duplicate cell set from a second organism;
and, selecting for surviving cells in the first set that fail to
survive in the duplicate cell set or screening for cells showing a
specific screening response that fail to give such response in the
duplicate cell set, wherein the first set and the duplicate cell
set are grown in the presence of a selection or screening agent,
wherein the surviving or screened cells comprise the orthogonal
tRNA-tRNA synthetase pair for use in the in the in vivo translation
system of the second organism. In one embodiment, comparing and
selecting or screening includes an in vivo complementation assay.
The concentration of the selection or screening agent can be
varied.
[0427] The organisms described herein comprise a variety of
organism and a variety of combinations. In one embodiment, the
organisms are optionally a prokaryotic organism, including but not
limited to, Methanococcus jannaschii, Methanobacterium
thermoautotrophicum, Halobacterium, Escherichia coli, A. fulgidus,
P. furiosus, P. horikoshii, A. pernix, T. thermophilus, or the
like. Alternatively, the organisms optionally comprise a eukaryotic
organism, including but not limited to, plants (including but not
limited to, complex plants such as monocots, or dicots), algae,
protists, fungi (including but not limited to, yeast, etc), animals
(including but not limited to, mammals, insects, arthropods, etc.),
or the like.
A. Expression in Non-Eukaryotes and Eukaryotes
[0428] The techniques disclosed in this section can be applied to
the expression in non-eukaryotes and eukaryotes of the non-natural
amino acid polypeptides described herein. To obtain high level
expression of a cloned polynucleotide, one typically subclones
polynucleotides encoding a desired polypeptide into an expression
vector that contains a strong promoter to direct transcription, a
transcription/translation terminator, and if for a nucleic acid
encoding a protein, a ribosome binding site for translational
initiation. Suitable bacterial promoters are described in, e.g., in
Sambrook et al. and Ausubel et al.
[0429] Bacterial expression systems for expressing polypeptides are
available in, including but not limited to, E. coli, Bacillus sp.,
Pseudomonas fluorescens, Pseudomonas aeruginosa, Pseudomonas
putida, and Salmonella (Palva et al., Gene 22:229-235 (1983);
Mosbach et al., Nature 302:543-545 (1983). Kits for such expression
systems are commercially available. Eukaryotic expression systems
for mammalian cells, yeast, and insect cells are also commercially
available. In cases where orthogonal tRNAs and aminoacyl tRNA
synthetases (described elsewhere herein) are used to express the
polypeptides, host cells for expression are selected based on their
ability to use the orthogonal components. Exemplary host cells
include Gram-positive bacteria (including but not limited to B.
brevis or B. subtilis, or Streptomyces) and Gram-negative bacteria
(E. coli or Pseudomonas fluorescens, Pseudomonas aeruginosa,
Pseudomonas putida), as well as yeast and other eukaryotic cells.
Cells comprising O-tRNA/O--RS pairs can be used as described
herein.
[0430] A eukaryotic host cell or non-eukaryotic host cell as
described herein provides the ability to synthesize polypeptides
which comprise non-natural amino acids in large useful quantities.
In one aspect, the composition optionally includes, but is not
limited to, at least 10 micrograms, at least 50 micrograms, at
least 75 micrograms, at least 100 micrograms, at least 200
micrograms, at least 250 micrograms, at least 500 micrograms, at
least 1 milligram, at least 10 milligrams, at least 100 milligrams,
at least one gram, or more of the polypeptides that comprises a
non-natural amino acid, or an amount that can be achieved with in
vivo polypeptide production methods (details on recombinant protein
production and purification are provided herein). In another
aspect, the protein is optionally present in the composition at a
concentration of, including but not limited to, at least 10
micrograms of polypeptide per liter, at least 50 micrograms of
polypeptide per liter, at least 75 micrograms of polypeptide per
liter, at least 100 micrograms of polypeptide per liter, at least
200 micrograms of polypeptide per liter, at least 250 micrograms of
polypeptide per liter, at least 500 micrograms of polypeptide per
liter, at least 1 milligram of polypeptide per liter, or at least
10 milligrams of polypeptide per liter or more, in, including but
not limited to, a cell lysate, a buffer, a pharmaceutical buffer,
or other liquid suspension (including but not limited to, in a
volume of, anywhere from about 1 nl to about 100 L or more). The
production of large quantities (including but not limited to,
greater that that typically possible with other methods, including
but not limited to, in vitro translation) of a protein in a
eukaryotic cell including at least one non-natural amino acid is a
feature of the methods, techniques and compositions described
herein.
[0431] A eukaryotic host cell or non-eukaryotic host cell as
described herein provides the ability to biosynthesize proteins
that comprise non-natural amino acids in large useful quantities.
For example, proteins comprising a non-natural amino acid can be
produced at a concentration of, including but not limited to, at
least 10 .mu.g/liter, at least 50 .mu.g/liter, at least 75
.mu.g/liter, at least 100 .mu.g/liter, at least 200 .mu.g/liter, at
least 250 .mu.g/liter, or at least 500 .mu.g/liter, at least 1
mg/liter, at least 2 mg/liter, at least 3 mg/liter, at least 4
mg/liter, at least 5 mg/liter, at least 6 mg/liter, at least 7
mg/liter, at least 8 mg/liter, at least 9 mg/liter, at least 10
mg/liter, at least 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300,
400, 500, 600, 700, 800, 900 mg/liter, 1 g/liter, 5 g/liter, 10
g/liter or more of protein in a cell extract, cell lysate, culture
medium, a buffer, and/or the like.
I. Expression Systems, Culture, and Isolation
[0432] The techniques disclosed in this section can be applied to
the expression systems, culture and isolation of the non-natural
amino acid polypeptides described herein. Non-natural amino acid
polypeptides may be expressed in any number of suitable expression
systems including, but not limited to, yeast, insect cells,
mammalian cells, and bacteria. A description of exemplary
expression systems is provided herein.
[0433] Yeast As used herein, the term "yeast" includes any of the
various yeasts capable of expressing a gene encoding the
non-natural amino acid polypeptide. Such yeasts include, but are
not limited to, ascosporogenous yeasts (Endomycetales),
basidiosporogenous yeasts and yeasts belonging to the Fungi
imperfecti (Blastomycetes) group. The ascosporogenous yeasts are
divided into two families, Spermophthoraceae and
Saccharomycetaceae. The latter is comprised of four subfamilies,
Schizosaccharomycoideae (e.g., genus Schizosaccharomyces),
Nadsonioideae, Lipomycoideae and Saccharomycoideae (e.g., genera
Pichia, Kluyveromyces and Saccharomyces). The basidiosporogenous
yeasts include the genera Leucosporidium, Rhodosporidium,
Sporidioholus, Filobasidium, and Filobasidiella. Yeasts belonging
to the Fungi Imperfecti (Blastomycetes) group are divided into two
families, Sporobolomycetaceae (e.g., genera Sporobolomyces and
Bullera) and Cryptococcaceae (e.g., genus Candida).
[0434] In certain embodiments, the species within the genera
Pichia, Kluyveromyces, Saccharomyces, Schizosaccharomyces,
Hansenula, Torulopsis, and Candida, including, but not limited to,
P. pastoris, P. guillerimondii, S. cerevisiae, S. carlsbergensis,
S. diastaticus, S. douglasii, S. kluyveri, S, norbensis, S.
oviformis, K. lactis, K. fragilis, C. albicans, C. maltosa, and H.
polymorpha are used in the methods, techniques and compositions
described herein.
[0435] The selection of suitable yeast for expression of the
non-natural amino acid polypeptide is within the skill of one of
ordinary skill in the art. In selecting yeast hosts for expression,
suitable hosts may include, but are not limited to, those shown to
have, by way of example, good secretion capacity, low proteolytic
activity, and overall robustness. Yeast are generally available
from a variety of sources including, but not limited to, the Yeast
Genetic Stock Center, Department of Biophysics and Medical Physics,
University of California (Berkeley, Calif.), and the American Type
Culture Collection ("ATCC") (Manassas, Va.).
[0436] The term "yeast host" or "yeast host cell" includes yeast
that can be, or has been, used as a recipient for recombinant
vectors or other transfer DNA. The term includes the progeny of the
original yeast host cell that has received the recombinant vectors
or other transfer DNA. It is understood that the progeny of a
single parental cell may not necessarily be completely identical in
morphology or in genomic or total DNA complement to the original
parent, due to accidental or deliberate mutation. Progeny of the
parental cell that are sufficiently similar to the parent to be
characterized by the relevant property, such as the presence of a
nucleotide sequence encoding a non-natural amino acid polypeptide,
are included in the progeny intended by this definition.
[0437] Expression and transformation vectors, including
extrachromosomal replicons or integrating vectors, have been
developed for transformation into many yeast hosts. For example,
expression vectors have been developed for S. cerevisiae (Sikorski
et al., Genetics (1998) 122:19; Ito et al., J. Bacteriol. (1983)
153:163; Hinnen et al., Proc. Natl. Acad. Sci. USA (1978) 75:1929);
C. albicans (Kurtz et al., Mol. Cell. Biol. (1986) 6:142); C.
maltosa (Kunze et al., 1. Basic Microbiol. (1985) 25:141); H.
polymorpha (Gleeson et al.; J. Gen. Microbiol. (1986) 132:3459;
Roggenkamp et al., Mol. Gen. Genet. (1986) 202:302); K. fragilis
(Das et al., J. Bacteriol. (1984) 158:1165); K. lactis (De
Louvencourt et al., J. Bacteriol. (1983) 154:737; Van den Berg et
al., Bio/Technology (1990) 8:135); P. guillerimondii (Kunze et al.,
J. Basic Microbiol. (1985) 25:141); P. pastoris (U.S. Pat. Nos.
5,324,639; 4,929,555; and 4,837,148; Cregg et al., Mol. Cell. Biol.
(1985) 5:3376); Schizosaccharomyces pombe (Beach et al., Nature
(1982) 300:706); A. nidulans (Ballance et al., Biochem. Biophys.
Res. Commun. (1983) 1.12:284-89; Tilburn et al., Gene (1983)
26:205-221; and Yelton et al., Proc. Natl. Acad. Sci. USA (1984)
81:1470-74); A. niger (Kelly and Hynes, EMBO J. (1985) 4:475-479);
T. reesia (EP 0 244 234); and filamentous fungi such as, e.g.,
Neurospora, Penicillium, Tolypocladium (WO 91/00357), each herein
incorporated by reference in their entirety.
[0438] Control sequences for yeast vectors include, but are not
limited to, promoter regions from genes such as alcohol
dehydrogenase (ADH) (EP 0 284 044); enolase; glucokinase;
glucose-6-phosphate isomerase;
glyceraldehyde-3-phosphate-dehydrogenase (GAP or GAPDH);
hexokinase; phosphofructokinase; 3-phosphoglycerate mutase; and
pyruvate kinase (PyK) (EP 0 329 203). The yeast PHO5 gene, encoding
acid phosphatase, also may provide useful promoter sequences
(Miyanohara et al., PROC. NATL. ACAD. SCI. USA (1983) 80:1). Other
suitable promoter sequences for use with yeast hosts may include
the promoters for 3-phosphoglycerate kinase (Hitzeman et al., J.
BIOL. CHEM. (1980) 255:12073); and other glycolytic enzymes, such
as pyruvate decarboxylase, triosephosphate isomerase, and
phosphoglucose isomerase (Holland et al., BIOCHEMISTRY (1978)
17:4900; Hess et al., J. ADV. ENZYME REG. (1969) 7:149). Inducible
yeast promoters having the additional advantage of transcription
controlled by growth conditions may include the promoter regions
for alcohol dehydrogenase 2; isocytochrome C; acid phosphatase;
metallothionein; glyceraldehyde-3-phosphate dehydrogenase;
degradative enzymes associated with nitrogen metabolism; and
enzymes responsible for maltose and galactose utilization. Suitable
vectors and promoters for use in yeast expression are further
described in EP 0 073 657.
[0439] Yeast enhancers also may be used with yeast promoters. In
addition, synthetic promoters may also function as yeast promoters.
By way of example, the upstream activating sequences (UAS) of a
yeast promoter may be joined with the transcription activation
region of another yeast promoter, creating a synthetic hybrid
promoter. Examples of such hybrid promoters include the ADH
regulatory sequence linked to the GAP transcription activation
region. See U.S. Pat. Nos. 4,880,734 and 4,876,197, which are
incorporated by reference herein in their entirety. Other examples
of hybrid promoters include promoters that consist of the
regulatory sequences of the ADH2, GAL4, GAL10, or PHO5 genes,
combined with the transcriptional activation region of a glycolytic
enzyme gene such as GAP or PyK. See EP 0 164 556. Furthermore, a
yeast promoter may include naturally occurring promoters of
non-yeast origin that have the ability to bind yeast RNA polymerase
and initiate transcription.
[0440] Other control elements that may comprise part of the yeast
expression vectors include terminators, for example, from GAPDH or
the enolase genes (Holland et al., J. BIOL. CHEM. (1981) 256:1385).
In addition, the origin of replication from the 2.mu. plasmid
origin is suitable for yeast. A suitable selection gene for use in
yeast is the trp1 gene present in the yeast plasmid. See Tschumper
et al., GENE (1980) 10:157; Kingsman et al., GENE (1979) 7:141. The
trp1 gene provides a selection marker for a mutant strain of yeast
lacking the ability to grow in tryptophan. Similarly,
Leu2-deficient yeast strains (ATCC 20,622 or 38,626) are
complemented by known plasmids bearing the Leu2 gene.
[0441] Methods of introducing exogenous DNA into yeast hosts
include, but are not limited to, either the transformation of
spheroplasts or of intact yeast host cells treated with alkali
cations. By way of example, transformation of yeast can be carried
out according to the method described in Hsiao et al., PROC. NATL.
ACAD. SCI. USA (1979) 76:3829 and Van Solingen et al., J. BACT.
(1977) 130:946. However, other methods for introducing
[0442] DNA into cells such as by nuclear injection,
electroporation, or protoplast fusion may also be used as described
generally in SAMBROOK ET AL., MOLECULAR CLOING: A LAB. MANUAL
(2001). Yeast host cells may then be cultured using standard
techniques known to those of ordinary skill in the art.
[0443] Other methods for expressing heterologous proteins in yeast
host cells are well known to those of ordinary skill in the art.
See generally U.S. Patent Publication No. 20020055169, U.S. Pat.
Nos. 6,361,969; 6,312,923; 6,183,985; 6,083,723; 6,017,731;
5,674,706; 5,629,203; 5,602,034; and 5,089,398; U.S. Reexamined
Pat. Nos. RE37,343 and RE35,749; PCT Published Patent Applications
WO 99/07862; WO 98/37208; and WO 98/26080; European Patent
Applications EP 0 946 736; EP 0 732 403; EP 0 480 480; WO 90/10277;
EP 0 340 986; EP 0 329 203; EP 0 324 274; and EP 0 164 556. See
also Gellissen et al., ANTONIE VAN LEEUWENHOEK (1992)
62(1-2):79-93; Romanos et al., YEAST (1992) 8(6):423-488; Goeddel,
METHODS IN ENZYMOLOGY (1990) 185:3-7, each incorporated by
reference herein in its entirety.
[0444] The yeast host strains may be grown in fermentors during the
amplification stage using standard feed batch fermentation methods.
The fermentation methods may be adapted to account for differences
in a particular yeast host's carbon utilization pathway or mode of
expression control. By way of example, fermentation of a
Saccharomyces yeast host may require a single glucose feed, complex
nitrogen source (e.g., casein hydrolysates), and multiple vitamin
supplementation, whereas, the methylotrophic yeast P. pastoris may
require glycerol, methanol, and trace mineral feeds, but only
simple ammonium (nitrogen) salts for optimal growth and expression.
See, e.g., U.S. Pat. No. 5,324,639; Elliott et al., J. PROTEIN
CHEM. (1990) 9:95; and Fieschko et al., BIOTECH. BIOENG. (1987)
29:1113, each incorporated by reference herein in its entirety.
[0445] Such fermentation methods, however, may have certain common
features independent of the yeast host strain employed. By way of
example, a growth limiting nutrient, typically carbon, may be added
to the fermentor during the amplification phase to allow maximal
growth. In addition, fermentation methods generally employ a
fermentation medium designed to contain adequate amounts of carbon,
nitrogen, basal salts, phosphorus, and other minor nutrients
(vitamins, trace minerals and salts, etc.). Examples of
fermentation media suitable for use with Pichia are described in
U.S. Pat. Nos. 5,324,639 and 5,231,178, each incorporated by
reference herein in its entirety.
[0446] Baculovirus-Infected Insect Cells The term "insect host" or
"insect host cell" refers to an insect that can be, or has been,
used as a recipient for recombinant vectors or other transfer DNA.
The term includes the progeny of the original insect host cell that
has been transfected. It is understood that the progeny of a single
parental cell may not necessarily be completely identical in
morphology or in genomic or total DNA complement to the original
parent, due to accidental or deliberate mutation. Progeny of the
parental cell that are sufficiently similar to the parent to be
characterized by the relevant property, such as the presence of a
nucleotide sequence encoding a non-natural amino acid polypeptide,
are included in the progeny intended by this definition.
[0447] The selection of suitable insect cells for expression of a
polypeptide is well known to those of ordinary skill in the art.
Several insect species are well described in the art and are
commercially available including, but not limited to, Aedes
aegypti, Bombyx mori, Drosophila melanogaster, Spodoptera
frugiperda, and Trichoplusia ni. In selecting insect hosts for
expression, suitable hosts may include, but are not limited to,
those shown to have, inter alia, good secretion capacity, low
proteolytic activity, and overall robustness. Insect are generally
available from a variety of sources including, but not limited to,
the Insect Genetic Stock Center, Department of Biophysics and
Medical Physics, University of California (Berkeley, Calif.); and
the American Type Culture Collection ("ATCC") (Manassas, Va.).
[0448] Generally, the components of a baculovirus-infected insect
expression system include a transfer vector, usually a bacterial
plasmid, which contains both a fragment of the baculovirus genome,
and a convenient restriction site for insertion of the heterologous
gene to be expressed; a wild type baculovirus with a sequence
homologous to the baculovirus-specific fragment in the transfer
vector (this allows for the homologous recombination of the
heterologous gene in to the baculovirus genome); and appropriate
insect host cells and growth media. The materials, methods and
techniques used in constructing vectors, transfecting cells,
picking plaques, growing cells in culture, and the like are known
in the art and manuals are available describing these
techniques.
[0449] After inserting the heterologous gene into the transfer
vector, the vector and the wild type viral genome are transfected
into an insect host cell where the vector and viral genome
recombine. The packaged recombinant virus is expressed and
recombinant plaques are identified and purified. Materials and
methods for baculovirus/insect cell expression systems are
commercially available in kit form from, for example, Invitrogen
Corp. (Carlsbad, Calif.). These techniques are described in SUMMERS
AND SMITH, TEXAS AGRICULTURAL EXPERIMENT STATION BULLETIN No. 1555
(1987), herein incorporated by reference. See also, RICHARDSON, 39
METHODS IN MOLECULAR BIOLOGY: BACULOVIRUS EXPRESSION PROTOCOLS
(1995); AUSUBEL ET AL., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY
16.9-16.11 (1994); KING AND POSSEE, THE BACULOVIRUS SYSTEM: A
LABORATORY GUIDE (1992); and O'REILLY ET AL., BACULOVIRUS
EXPRESSION VECTORS: A LABORATORY MANUAL (1992).
[0450] The production of various heterologous proteins using
baculovirus/insect cell expression systems is described in the
following references and such techniques can be adapted to produce
the non-natural amino acid polypeptides described herein. See,
e.g., U.S. Pat. Nos. 6,368,825; 6,342,216; 6,338,846; 6,261,805;
6,245,528, 6,225,060; 6,183,987; 6,168,932; 6,126,944; 6,096,304;
6,013,433; 5,965,393; 5,939,285; 5,891,676; 5,871,986; 5,861,279;
5,858,368; 5,843,733; 5,762,939; 5,753,220; 5,605,827; 5,583,023;
5,571,709; 5,516,657; 5,290,686; WO02/06305; WO01/90390;
WO01/27301; WO01/05956; WO00/55345; WO00/20032 WO99/51721; WO
99/45130; WO 99/31257; WO 99/10515; WO 99/09193; WO 97/26332; WO
96/29400; WO 96/25496; WO 96/06161; WO 95/20672; WO 93/03173; WO
92/16619; WO 92/02628; WO 92/01801; WO 90/14428; WO 90/10078; WO
90/02566; WO 90/02186; WO 90/01556; WO 89/01038; WO 89/01037; WO
88/07082., each incorporated by reference herein in its
entirety.
[0451] Vectors that are useful in baculovirus/insect cell
expression systems are known include, but are not limited to,
insect expression and transfer vectors derived from the baculovirus
Autographa californica nuclear polyhedrosis virus (AcNPV), which is
a helper-independent, viral expression vector. Viral expression
vectors derived from this system usually use the strong viral
polyhedrin gene promoter to drive expression of heterologous genes.
See generally, O'Reilly ET AL., BACULOVIRUS EXPRESSION VECTORS: A
LABORATORY MANUAL (1992).
[0452] Prior to inserting the foreign gene into the baculovirus
genome, the above-described components, comprising a promoter,
leader (if desired), coding sequence of interest, and transcription
termination sequence, are typically assembled into an intermediate
transplacement construct (transfer vector). Intermediate
transplacement constructs are often maintained in a replicon, such
as an extra chromosomal element (e.g., plasmids) capable of stable
maintenance in a host, such as bacteria. The replicon will have a
replication system, thus allowing it to be maintained in a suitable
host for cloning and amplification. More specifically, the plasmid
may contain the polyhedrin polyadenylation signal (Miller, ANN.
REV. MICROBIOL. (1988) 42:177) and a prokaryotic
ampicillin-resistance (amp) gene and origin of replication for
selection and propagation in E. coli.
[0453] One commonly used transfer vector for introducing foreign
genes into AcNPV is pAc373. Many other vectors, known to those of
skill in the art, have also been designed including, for example,
pVL985, which alters the polyhedrin start codon from ATG to ATT,
and which introduces a BamHI cloning site 32 base pairs downstream
from the ATT. See Luckow and Summers, VIROLOGY 170:31 (1989). Other
commercially available vectors include, for example,
PBlueBac4.5/V5-His; pBlueBacHis2; pMelBac; pBlueBac4.5 (Invitrogen
Corp., Carlsbad, Calif.).
[0454] After insertion of the heterologous gene, the transfer
vector and wild type baculoviral genome are co-transfected into an
insect cell host. Illustrative methods for introducing heterologous
DNA into the desired site in the baculovirus virus are described in
SUMMERS AND SMITH, TEXAS AGRICULTURAL EXPERIMENT STATION BULLETIN
No. 1555 (1987); Smith et al., MOL. CELL. BIOL. (1983) 3:2156;
Luckow and Summers, VIROLOGY (1989) 170:31. By way of example, the
insertion can be into a gene such as the polyhedrin gene, by
homologous double crossover recombination; insertion can also be
into a restriction enzyme site engineered into the desired
baculovirus gene. See Miller et al., BIOESSAYS (1989) 11(4):91.
[0455] Transfection may be accomplished by electroporation using
methods described in TROTTER AND WOOD, 39 METHODS IN MOLECULAR
BIOLOGY (1995); Mann and King, J. GEN. VIROL. (1989) 70:3501.
Alternatively, liposomes may be used to transfect the insect cells
with the recombinant expression vector and the baculovirus. See,
e.g., Liebman et al., BIOTECHNIQUES (1999) 26(1):36; Graves et al.,
BIOCHEMISTRY (1998) 37:6050; Nomura et al., J. BIOL. CHEM. (1998)
273(22):13570; Schmidt et al., PROTEIN EXPRESSION AND PURIFICATION
(1998) 12:323; Siffert et al., NATURE GENETICS (1998) 18:45;
TILKINS ET AL., CELL BIOLOGY: A LABORATORY HANDBOOK 145-154 (1998);
Cai et al., PROTEIN EXPRESSION AND PURIFICATION (1997) 10:263;
Dolphin et al., NATURE GENETICS (1997) 17:491; Kost et al., GENE
(1997) 190:139; Jakobsson et al., J. BIOL. CHEM. (1996) 271:22203;
Rowles et al., J. BIOL. CHEM. (1996) 271(37):22376; Reverey et al.,
J. BIOL. CHEM. (1996) 271(39):23607-10; Stanley et al., J. BIOL.
CHEM. (1995) 270:4121; Sisk et al., J. VIROL. (1994) 68(2):766; and
Peng et al., BIOTECHNIQUES (1993) 14(2):274. Commercially available
liposomes include, for example, Cellfectin.RTM. and Lipofectin.RTM.
(Invitrogen, Corp., Carlsbad, Calif.). In addition, calcium
phosphate transfection may be used. See TROTTER AND WOOD, 39
METHODS IN MOLECULAR BIOLOGY (1995); Kitts, NAR (1990) 18(19):5667;
and Mann and King, J. GEN. VIROL. (1989) 70:3501.
[0456] Baculovirus expression vectors usually contain a baculovirus
promoter. A baculovirus promoter is any DNA sequence capable of
binding a baculovirus RNA polymerase and initiating the downstream
(3') transcription of a coding sequence (e.g., structural gene)
into mRNA. A promoter will have a transcription initiation region
which is usually placed proximal to the 5' end of the coding
sequence. This transcription initiation region typically includes
an RNA polymerase binding site and a transcription initiation site.
A baculovirus promoter may also have a second domain called an
enhancer, which, if present, is usually distal to the structural
gene. Moreover, expression may be either regulated or
constitutive.
[0457] Structural genes, abundantly transcribed at late times in
the infection cycle, provide particularly useful promoter
sequences. Examples include sequences derived from the gene
encoding the viral polyhedron protein (FRIESEN ET AL., The
Regulation of Baculovirus Gene Expression in THE MOLECULAR BIOLOGY
OF BACULOVIRUSES (1986); EP 0 127 839 and 0 155 476) and the gene
encoding the p10 protein (Vlak et al., J. GEN. VIROL. (1988)
69:765.
[0458] The newly formed baculovirus expression vector is packaged
into an infectious recombinant baculovirus and subsequently grown
plaques may be purified by techniques such as those described in
Miller et al., BIOESSAYS (1989)11(4):91; SUMMERS AND SMITH, TEXAS
AGRICULTURAL EXPERIMENT STATION BULLETIN No. 1555 (1987).
[0459] Recombinant baculovirus expression vectors have been
developed for infection into several insect cells. For example,
recombinant baculoviruses have been developed for, inter alia,
Aedes aegypti (ATCC No. CCL-125), Bombyx mori (ATCC No. CRL-8910),
Drosophila melanogaster (ATCC No. 1963), Spodoptera frugiperda, and
Trichoplusia ni. See Wright, NATURE (1986) 321:718; Carbonell et
al., J. VIROL. (1985) 56:153; Smith et al., MOL. CELL. BIOL. (1983)
3:2156. See generally, Fraser et al., IN VITRO CELL. DEV. BIOL.
(1989) 25:225. More specifically, the cell lines used for
baculovirus expression vector systems commonly include, but are not
limited to, Sf9 (Spodoptera frugiperda) (ATCC No. CRL-1711), Sf21
(Spodoptera frugiperda) (Invitrogen Corp., Cat. No. 11497-013
(Carlsbad, Calif.)), Tri-368 (Trichopulsia ni), and High-Five.TM.
BTI-TN-5B1-4 (Trichopulsia ni).
[0460] Cells and culture media are commercially available for both
direct and fusion expression of heterologous polypeptides in a
baculovirus/expression.
[0461] E. Coli, Pseudomonas, and other Prokaryotes: Bacterial
expression techniques are well known in the art. A wide variety of
vectors are available for use in bacterial hosts. The vectors may
be single copy or low or high multicopy vectors. Vectors may serve
for cloning and/or expression. In view of the ample literature
concerning vectors, commercial availability of many vectors, and
even manuals describing vectors and their restriction maps and
characteristics, no extensive discussion is required here. As is
well-known, the vectors normally involve markers allowing for
selection, which markers may provide for cytotoxic agent
resistance, prototrophy or immunity. Frequently, a plurality of
markers are present, which provide for different
characteristics.
[0462] A bacterial promoter is any DNA sequence capable of binding
bacterial RNA polymerase and initiating the downstream (3'')
transcription of a coding sequence (e.g. structural gene) into
mRNA. A promoter will have a transcription initiation region which
is usually placed proximal to the 5' end of the coding sequence.
This transcription initiation region typically includes an RNA
polymerase binding site and a transcription initiation site. A
bacterial promoter may also have a second domain called an
operator, that may overlap an adjacent RNA polymerase binding site
at which RNA synthesis begins. The operator permits negative
regulated (inducible) transcription, as a gene repressor protein
may bind the operator and thereby inhibit transcription of a
specific gene. Constitutive expression may occur in the absence of
negative regulatory elements, such as the operator. In addition,
positive regulation may be achieved by a gene activator protein
binding sequence, which; if present is usually proximal (5') to the
RNA polymerase binding sequence. An example of a gene activator
protein is the catabolite activator protein (CAP), which helps
initiate transcription of the lac operon in Escherichia coli (E.
coli) [Raibaud et al., ANNU. REV. GENET. (1984) 18:173]. Regulated
expression may therefore be either positive or negative, thereby
either enhancing or reducing transcription.
[0463] Sequences encoding metabolic pathway enzymes provide
particularly useful promoter sequences. Examples include promoter
sequences derived from sugar metabolizing enzymes, such as
galactose, lactose (lac) [Chang et al., NATURE (1977) 198:1056],
and maltose. Additional examples include promoter sequences derived
from biosynthetic enzymes such as tryptophan (trp) [Goeddel et al.,
NUC. ACIDS RES. (1980) 8:4057; Yelverton et al., NUCL. ACIDS RES.
(1981) 9:731; U.S. Pat. No. 4,738,921; IFNPub. Nos. 036 776 and 121
775], each is herein incorporated by reference in its entirety. The
.beta.-galactosidase (bla) promoter system [Weissmann (1981) "The
cloning of interferon and other mistakes." In Interferon 3 (Ed. I.
Gresser)], bacteriophage lambda PL [Shimatake et al., NATURE (1981)
292:128] and T5 [U.S. Pat. No. 4,689,406], each is herein
incorporated by reference in its entirety promoter systems also
provide useful promoter sequences. Preferred methods encompassed
herein utilize strong promoters, such as the T7 promoter to induce
polypeptide production at high levels. Examples of such vectors
include, but are not limited to, the pET29 series from Novagen, and
the pPOP vectors described in WO99/05297, which is herein
incorporated by reference in its entirety. Such expression systems
produce high levels of polypeptide in the host without compromising
host cell viability or growth parameters.
[0464] In addition, synthetic promoters which do not occur in
nature also function as bacterial promoters. For example,
transcription activation sequences of one bacterial or
bacteriophage promoter may be joined with the operon sequences of
another bacterial or bacteriophage promoter, creating a synthetic
hybrid promoter [U.S. Pat. No. 4,551,433, which is herein
incorporated by reference in its entirety]. For example, the tac
promoter is a hybrid trp-lac promoter comprised of both trp
promoter and lac operon sequences that is regulated by the lac
repressor [Amann et al., GENE (1983) 25:167; de Boer et al., PROC.
NATL. ACAD. SCI. (1983) 80:21]. Furthermore, a bacterial promoter
can include naturally occurring promoters of non-bacterial origin
that have the ability to bind bacterial RNA polymerase and initiate
transcription. A naturally occurring promoter of non-bacterial
origin can also be coupled with a compatible RNA polymerase to
produce high levels of expression of some genes in prokaryotes. The
bacteriophage T7 RNA polymerase/promoter system is an example of a
coupled promoter system [Studier et al., J. MOL. BIOL. (1986)
189:113; Tabor et al., Proc Natl. Acad. Sci. (1985) 82:1074]. In
addition, a hybrid promoter can also be comprised of a
bacteriophage promoter and an E. coli operator region (IFNPub. No.
267 851).
[0465] In addition to a functioning promoter sequence, an efficient
ribosome binding site is also useful for the expression of foreign
genes in prokaryotes. In E. coli, the ribosome binding site is
called the Shine-Dalgarno (SD) sequence and includes an initiation
codon (ATG) and a sequence 3-9 nucleotides in length located 3-11
nucleotides upstream of the initiation codon [Shine et al., NATURE
(1975) 254:34]. The SD sequence is thought to promote binding of
mRNA to the ribosome by the pairing of bases between the SD
sequence and the 3' and of E. coli 16S rRNA [Steitz et al. "Genetic
signals and nucleotide sequences in messenger RNA", In Biological
Regulation and Development: Gene Expression (Ed. R. F. Goldberger,
1979)]. To express eukaryotic genes and prokaryotic genes with weak
ribosome-binding site [Sambrook et al. "Expression of cloned genes
in Escherichia coli", Molecular Cloning: A Laboratory Manual,
1989].
[0466] The term "bacterial host" or "bacterial host cell" refers to
a bacterial that can be, or has been, used as a recipient for
recombinant vectors or other transfer DNA. The term includes the
progeny of the original bacterial host cell that has been
transfected. It is understood that the progeny of a single parental
cell may not necessarily be completely identical in morphology or
in genomic or total DNA complement to the original parent, due to
accidental or deliberate mutation. Progeny of the parental cell
that are sufficiently similar to the parent to be characterized by
the relevant property, such as the presence of a nucleotide
sequence encoding a polypeptide, are included in the progeny
intended by this definition.
[0467] The selection of suitable host bacteria for expression of a
polypeptide is well known to those of ordinary skill in the art. In
selecting bacterial hosts for expression, suitable hosts may
include those shown to have, inter alia, good inclusion body
formation capacity, low proteolytic activity, good secretion
capacity, good soluble protein production capability, and overall
robustness. Bacterial hosts are generally available from a variety
of sources including, but not limited to, the Bacterial Genetic
Stock Center, Department of Biophysics and Medical Physics,
University of California (Berkeley, Calif.); and the American Type
Culture Collection ("ATCC") (Manassas, Va.).
Industrial/pharmaceutical fermentation generally use bacterial
derived from K strains (e.g. W3110) or from bacteria derived from B
strains (e.g. BL21). These strains are particularly useful because
their growth parameters are extremely well known and robust. In
addition, these strains are non-pathogenic, which is commercially
important for safety and environmental reasons. In one embodiment
of the methods described and encompassed herein, the E. coli host
includes, but is not limited to, strains of BL21, DH10B, or
derivatives thereof. In another embodiment of the methods described
and encompassed herein, the E. coli host is a protease minus strain
including, but not limited to, OMP- and LON-. In another
embodiment, the bacterial host is a species of Pseudomonas, such a
P. fluorescens, P. aeruginosa, and P. putida. An example of a
Pseudomonas strain is P. fluorescens biovar I, strain MB101 (Dow
Chemical).
[0468] Once a recombinant host cell strain has been established
(i.e., the expression construct has been introduced into the host
cell and host cells with the proper expression construct are
isolated), the recombinant host cell strain is cultured under
conditions appropriate for production of polypeptides. The method
of culture of the recombinant host cell strain will be dependent on
the nature of the expression construct utilized and the identity of
the host cell. Recombinant host strains are normally cultured using
methods that are well known to the art. Recombinant host cells are
typically cultured in liquid medium containing assimilatable
sources of carbon, nitrogen, and inorganic salts and, optionally,
containing vitamins, amino acids, growth factors, and other
proteinaceous culture supplements well known to the art. Liquid
media for culture of host cells may optionally contain antibiotics
or anti-fungals to prevent the growth of undesirable microorganisms
and/or compounds including, but not limited to, antibiotics to
select for host cells containing the expression vector.
[0469] Recombinant host cells may be cultured in batch or
continuous formats, with either cell harvesting (in the case where
the polypeptide accumulates intracellularly) or harvesting of
culture supernatant in either batch or continuous formats. For
production in prokaryotic host cells, batch culture and cell
harvest are preferred.
[0470] In one embodiment, the non-natural amino acid polypeptides
described herein are purified after expression in recombinant
systems. The polypeptides may be purified from host cells or
culture medium by a variety of methods known to the art. Normally,
many polypeptides produced in bacterial host cells may be poorly
soluble or insoluble (in the form of inclusion bodies). In one
embodiment, amino acid substitutions may readily be made in the
polypeptides that are selected for the purpose of increasing the
solubility of the recombinantly produced polypeptide utilizing the
methods disclosed herein as well as those known in the art. In the
case of insoluble polypeptide, the polypeptide may be collected
from host cell lysates by centrifugation or filtering and may
further be followed by homogenization of the cells. In the case of
poorly soluble polypeptide, compounds including, but not limited
to, polyethylene imine (PEI) may be added to induce the
precipitation of partially soluble polypeptide. The precipitated
protein may then be conveniently collected by centrifugation or
filtering. Recombinant host cells may be disrupted or homogenized
to release the inclusion bodies from within the cells using a
variety of methods well known to those of ordinary skill in the
art. Host cell disruption or homogenization may be performed using
well known techniques including, but not limited to, enzymatic cell
disruption, sonication, dounce homogenization, or high pressure
release disruption. In one embodiment of the methods described and
encompassed herein, the high pressure release technique is used to
disrupt the E. coli host cells to release the inclusion bodies of
the polypeptides. When handling inclusion bodies of polypeptides,
it is advantageous to minimize the homogenization time on
repetitions in order to maximize the yield of inclusion bodies
without loss due to factors such as solubilization, mechanical
shearing or proteolysis.
[0471] Insoluble or precipitated polypeptides may then be
solubilized using any of a number of suitable solubilization agents
known to the art. By way of example, the polypeptides are
solubilized with urea or guanidine hydrochloride. The volume of the
solubilized polypeptides should be minimized so that large batches
may be produced using conveniently manageable batch sizes. This
factor may be significant in a large-scale commercial setting where
the recombinant host may be grown in batches that are thousands of
liters in volume. In addition, when manufacturing polypeptides in a
large-scale commercial setting, in particular for human
pharmaceutical uses, the avoidance of harsh chemicals that can
damage the machinery and container, or the protein product itself,
should be avoided, if possible. It has been shown in the methods
described and encompassed herein that the milder denaturing agent
urea can be used to solubilize the polypeptide inclusion bodies in
place of the harsher denaturing agent guanidine hydrochloride. The
use of urea significantly reduces the risk of damage to stainless
steel equipment utilized in the manufacturing and purification
process of a polypeptide while efficiently solubilizing the
polypeptide inclusion bodies.
[0472] In the case of soluble polypeptides, the peptides may be
secreted into the periplasmic space or into the culture medium. In
addition, soluble peptides may be present in the cytoplasm of the
host cells. The soluble peptide may be concentrated prior to
performing purification steps. Standard techniques, including but
not limited to those described herein, may be used to concentrate
soluble peptide from, by way of example, cell lysates or culture
medium. In addition, standard techniques, including but not limited
to those described herein, may be used to disrupt host cells and
release soluble peptide from the cytoplasm or periplasmic space of
the host cells.
[0473] When the polypeptide is produced as a fusion protein, the
fusion sequence is preferably removed. Removal of a fusion sequence
may be accomplished by methods including, but not limited to,
enzymatic or chemical cleavage. Enzymatic removal of fusion
sequences may be accomplished using methods well known to those in
the art. The choice of enzyme for removal of the fusion sequence
will be determined by the identity of the fusion, and the reaction
conditions will be specified by the choice of enzyme. Chemical
cleavage may be accomplished using reagents, including but not
limited to, cyanogen bromide, TEV protease, and other reagents. The
cleaved polypeptide is optionally purified from the cleaved fusion
sequence by well known methods. Such methods will be determined by
the identity and properties of the fusion sequence and the
polypeptide. Methods for purification may include, but are not
limited to, size-exclusion chromatography, hydrophobic interaction
chromatography, ion-exchange chromatography or dialysis or any
combination thereof.
[0474] The polypeptide is also optionally purified to remove DNA
from the protein solution. DNA may be removed by any suitable
method known to the art, including, but not limited to,
precipitation or ion exchange chromatography. In one embodiment,
DNA is removed by precipitation with a nucleic acid precipitating
agent, such as, but not limited to, protamine sulfate. The
polypeptide may be separated from the precipitated DNA using
standard well known methods including, but not limited to,
centrifugation or filtration. Removal of host nucleic acid
molecules is an important factor in a setting where the polypeptide
is to be used to treat humans and the methods described herein
reduce host cell DNA to pharmaceutically acceptable levels.
[0475] Methods for small-scale or large-scale fermentation may also
be used in protein expression, including but not limited to,
fermentors, shake flasks, fluidized bed bioreactors, hollow fiber
bioreactors, roller bottle culture systems, and stirred tank
bioreactor systems. Each of these methods can be performed in a
batch, fed-batch, or continuous mode process.
[0476] Human forms of the non-natural amino acid polypeptides
described herein can generally be recovered using methods standard
in the art. For example, culture medium or cell lysate can be
centrifuged or filtered to remove cellular debris. The supernatant
may be concentrated or diluted to a desired volume or diafiltered
into a suitable buffer to condition the preparation for further
purification. Further purification of the non-natural amino acid
polypeptides described herein include, but are not limited to,
separating deamidated and clipped forms of a polypeptide variant
from the corresponding intact form.
[0477] Any of the following exemplary procedures can be employed
for purification of a non-natural amino acid polypeptide described
herein: affinity chromatography; anion- or cation-exchange
chromatography (using, including but not limited to, DEAE
SEPHAROSE); chromatography on silica; reverse phase HPLC; gel
filtration (using, including but not limited to, SEPHADEX G-75);
hydrophobic interaction chromatography; size-exclusion
chromatography, metal-chelate chromatography;
ultrafiltration/diafiltration; ethanol precipitation; ammonium
sulfate precipitation; chromatofocusing; displacement
chromatography; electrophoretic procedures (including but not
limited to preparative isoelectric focusing), differential
solubility (including but not limited to ammonium sulfate
precipitation), SDS-PAGE, or extraction.
[0478] Polypeptides encompassed within the methods and compositions
described herein, including but not limited to, polypeptides
comprising non-natural amino acids, antibodies to polypeptides
comprising non-natural amino acids, binding partners for
polypeptides comprising non-natural amino acids, etc., may be
purified, either partially or substantially to homogeneity,
according to standard procedures known to and used by those of
skill in the art. Accordingly, polypeptides described herein may be
recovered and purified by any of a number of methods well known in
the art, including but not limited to, ammonium sulfate or ethanol
precipitation, acid or base extraction, column chromatography,
affinity column chromatography, anion or cation exchange
chromatography, phosphocellulose chromatography, hydrophobic
interaction chromatography, hydroxylapatite chromatography, lectin
chromatography, gel electrophoresis and any combination thereof.
Protein refolding steps can be used, as desired, in making
correctly folded mature proteins. High performance liquid
chromatography (HPLC), affinity chromatography or other suitable
methods can be employed in final purification steps where high
purity is desired. In one embodiment; antibodies made against
non-natural amino acids (or polypeptides comprising non-natural
amino acids) are used as purification reagents, including but not
limited to, for affinity-based purification of polypeptides
comprising one or more non-natural amino acid(s). Once purified,
partially or to homogeneity, as desired, the polypeptides are
optionally used for a wide variety of utilities, including but not
limited to, as assay components, therapeutics, prophylaxis,
diagnostics, research reagents, and/or as immunogens for antibody
production.
[0479] In addition to other references noted herein, a variety of
purification/protein folding methods are well known in the art,
including, but not limited to, those set forth in R. Scopes,
Protein Purification, Springer-Verlag, N.Y. (1982); Deutscher,
Methods in Enzymology Vol. 182: Guide to Protein Purification,
Academic Press, Inc. N.Y. (1990); Sandana (1997) Bioseparation of
Proteins, Academic Press, Inc.; Bollag et al. (1996) Protein
Methods, 2nd Edition Wiley-Liss, NY; Walker (1996) The Protein
Protocols Handbook Humana Press, NJ, Harris and Angal (1990)
Protein Purification Applications: A Practical Approach IRL Press
at Oxford, Oxford, England; Harris and Angal Protein Purification
Methods: A Practical Approach IRL Press at Oxford, Oxford, England;
Scopes (1993) Protein Purification Principles and Practice 3rd
Edition Springer Verlag, NY; Janson and Ryden (1998) Protein
Purification: Principles. High Resolution Methods and Applications,
Second Edition Wiley-VCH, NY; and Walker (1998) Protein Protocols
on CD-ROM Humana Press, NJ; and the references cited therein.
[0480] One advantage of producing polypeptides comprising at least
one non-natural amino acid in a eukaryotic host cell or
non-eukaryotic host cell is that typically the polypeptides will be
folded in their native conformations. However, in certain
embodiments of the methods and compositions described herein, after
synthesis, expression and/or purification, polypeptides can possess
a conformation different from the desired conformations of the
relevant polypeptides. In one aspect of the methods and
compositions described herein, the expressed protein is optionally
denatured and then renatured. This optional denaturation and
renaturation is accomplished utilizing methods known in the art,
including but not limited to, by adding a chaperonin to the
polypeptide of interest, and by solubilizing the proteins in a
chaotropic agent including, but not limited to, guanidine HCl, and
utilizing protein disulfide isomerase.
[0481] In general, it is occasionally desirable to denature and
reduce expressed polypeptides and then to cause the polypeptides to
re-fold into the preferred conformation. By way of example, such
re-folding may be accomplished with the addition guanidine, urea,
DTT, DTE, and/or a chaperonin to a translation product of interest.
Methods of reducing, denaturing and renaturing proteins are well
known to those of skill in the art (see, the references above, and
Debinski, et al. (1993) J. Biol. Chem., 268: 14065-14070; Kreitman
and Pastan (1993) Bioconjug. Chem., 4: 581-585; and Buchner, et
al., (1992) Anal. Biochem., 205: 263-270). Debinski, et al., for
example, describe the denaturation and reduction of inclusion body
proteins in guanidine-DTE. The proteins can be refolded in a redox
buffer containing, including but not limited to, oxidized
glutathione and L-arginine. Refolding reagents can be flowed or
otherwise moved into contact with the one or more polypeptide or
other expression product, or vice-versa.
[0482] In the case of prokaryotic production of a non-natural amino
acid polypeptide, the polypeptide thus produced may be misfolded
and thus lacks or has reduced biological activity. The bioactivity
of the protein may be restored by "refolding". In one embodiment, a
misfolded polypeptide is refolded by solubilizing (where the
polypeptide is also insoluble), unfolding and reducing the
polypeptide chain using, by way of example, one or more chaotropic
agents (including, but not limited to, urea and/or guanidine) and a
reducing agent capable of reducing disulfide bonds (including, but
not limited to, dithiothreitol, DTT or 2-mercaptoethanol, 2-ME). At
a moderate concentration of chaotrope, an oxidizing agent is then
added (e.g., oxygen, cystine or cystamine), which allows the
reformation of disulfide bonds. An unfolded or misfolded
polypeptide may be refolded using standard methods known in the
art, such as those described in U.S. Pat. Nos. 4,511,502,
4,511,503, and 4,512,922, each of which is herein incorporated by
reference in its entirety. The polypeptide may also be cofolded
with other proteins to form heterodimers or heteromultimers. After
refolding or cofolding, the polypeptide may be further
purified.
[0483] Purification of non-natural amino acid polypeptides may be
accomplished using a variety of techniques, including but not
limited those described herein, by way of example hydrophobic
interaction chromatography, size exclusion chromatography, ion
exchange chromatography, reverse-phase high performance liquid
chromatography, affinity chromatography, and the like or any
combination thereof. Additional purification may also include a
step of drying or precipitation of the purified protein.
[0484] After purification, the non-natural amino acid polypeptides
may be exchanged into different buffers and/or concentrated by any
of a variety of methods known to the art, including, but not
limited to, diafiltration and dialysis. hGH that is provided as a
single purified protein may be subject to aggregation and
precipitation. In certain embodiments the purified non-natural
amino acid polypeptides may be at least 90% pure (as measured by
reverse phase high performance liquid chromatography, RP-HPLC, or
sodium dodecyl sulfate-polyacrylamide gel electrophoresis,
SDS-PAGE). In certain other embodiments the purified non-natural
amino acid polypeptides may be at least 95% pure, or at least 98%
pure, or at least 99% or greater purity. Regardless of the exact
numerical value of the purity of the non-natural amino acid
polypeptides, the non-natural amino acid polypeptides is
sufficiently pure for use as a pharmaceutical product or for
further processing, including but not limited to, conjugation with
a water soluble polymer such as PEG.
[0485] In certain embodiments the non-natural amino acid
polypeptides molecules may be used as therapeutic agents in the
absence of other active ingredients or proteins (other than
excipients, carriers, and stabilizers, serum albumin and the like),
and in certain embodiments the non-natural amino acid polypeptides
molecules they may be complexed with another polypeptide or a
polymer.
2. Purification of Non-Natural Amino Acid Polypeptides
[0486] General Purification Methods The techniques disclosed in
this section can be applied to the general purification of the
non-natural amino acid polypeptides described herein. Any one of a
variety of isolation steps may be performed on the cell lysate
extract, culture medium, inclusion bodies, periplasmic space of the
host cells, cytoplasm of the host cells, or other material
comprising the desired polypeptide or on any polypeptide mixtures
resulting from any isolation steps including, but not limited to,
affinity chromatography, ion exchange chromatography, hydrophobic
interaction chromatography, gel filtration chromatography, high
performance liquid chromatography ("HPLC"), reversed phase-HPLC
("RP-HPLC"), expanded bed adsorption, or any combination and/or
repetition thereof and in any appropriate order.
[0487] Equipment and other necessary materials used in performing
the techniques described herein are commercially available. Pumps,
fraction collectors, monitors, recorders, and entire systems are
available from, for example, Applied Biosystems (Foster City,
Calif.), Bio-Rad Laboratories, Inc. (Hercules, Calif.), and
Amersham Biosciences, Inc. (Piscataway, N.J.). Chromatographic
materials including, but not limited to, exchange matrix materials,
media, and buffers are also available from such companies.
[0488] Equilibration, and other steps in the column chromatography
processes described herein such as washing and elution, may be more
rapidly accomplished using specialized equipment such as a pump.
Commercially available pumps include, but are not limited to,
HILOAD.RTM. Pump P-50, Peristaltic Pump P-1, Pump P-901, and Pump
P-903 (Amersham Biosciences, Piscataway, N.J.).
[0489] Examples of fraction collectors include RediFrac Fraction
Collector, FRAC-100 and FRAC-200 Fraction Collectors, and
SUPERFRAC.RTM. Fraction Collector (Amersham Biosciences,
Piscataway, N.J.). Mixers are also available to form pH and linear
concentration gradients. Commercially available mixers include
Gradient Mixer GM-1 and In-Line Mixers (Amersham Biosciences,
Piscataway, N.J.).
[0490] The chromatographic process may be monitored using any
commercially available monitor. Such monitors may be used to gather
information like UV, fluorescence, pH, and conductivity. Examples
of detectors include Monitor UV-1, UVICOR.RTM. S II, Monitor UV-M
II, Monitor UV-900, Monitor UPC-900, Monitor pH/C-900, and
Conductivity Monitor (Amersham Biosciences, Piscataway, N.J.).
Indeed, entire systems are commercially available including the
various AKTA.RTM. systems from Amersham Biosciences (Piscataway,
N.J.).
[0491] In one embodiment of the methods and compositions described
herein, for example, the polypeptide may be reduced and denatured
by first denaturing the resultant purified polypeptide in urea,
followed by dilution into TRIS buffer containing a reducing agent
(such as DTT) at a suitable pH. In another embodiment, the
polypeptide is denatured in urea in a concentration range of
between about 2 M to about 9 M, followed by dilution in TRIS buffer
at a pH in the range of about 5.0 to about 8.0. The refolding
mixture of this embodiment may then be incubated. In one
embodiment, the refolding mixture is incubated at room temperature
for four to twenty-four hours. The reduced and denatured
polypeptide mixture may then be further isolated or purified.
[0492] As stated herein, the pH of the first polypeptide mixture
may be adjusted prior to performing any subsequent isolation steps.
In addition, the first polypeptide mixture or any subsequent
mixture thereof may be concentrated using techniques known in the
art. Moreover, the elution buffer comprising the first polypeptide
mixture or any subsequent mixture thereof may be exchanged for a
buffer suitable for the next isolation step using techniques well
known to those of ordinary skill in the art.
[0493] Ion Exchange Chromatography The techniques disclosed in this
section can be applied to the ion-chromatography of the non-natural
amino acid polypeptides described herein. In one embodiment, and as
an optional, additional step, ion exchange chromatography may be
performed on the first polypeptide mixture. See generally ION
EXCHANGE CHROMATOGRAPHY: PRINCIPLES AND METHODS (Cat. No.
18-1114-21, Amersham Biosciences (Piscataway, N.J.)). Commercially
available ion exchange columns include HITRAP.RTM., HIPREP.RTM.,
and HILOAD.RTM. Columns (Amersham Biosciences, Piscataway, N.J.).
Such columns utilize strong anion exchangers such as Q
SEPHAROSE.RTM. Fast Flow, Q SEPHAROSE.RTM. High Performance, and Q
SEPHAROSE.RTM. XL; strong cation exchangers such as SP
SEPHAROSE.RTM. High Performance, SP SEPHAROSE.RTM. Fast Flow, and
SP SEPHAROSE.RTM. XL; weak anion exchangers such as DEAE
SEPHAROSE.RTM. Fast Flow; and weak cation exchangers such as CM
SEPHAROSE.RTM. Fast. Flow (Amersham Biosciences, Piscataway, N.J.).
Anion or cation exchange column chromatography may be performed on
the polypeptide at any stage of the purification process to isolate
substantially purified polypeptide. The cation exchange
chromatography step may be performed using any suitable cation
exchange matrix. Cation exchange matrices include, but are not
limited to, fibrous, porous, non-porous, microgranular, beaded, or
cross-linked cation exchange matrix materials. Such cation exchange
matrix materials include, but are not limited to, cellulose,
agarose, dextran, polyacrylate, polyvinyl, polystyrene, silica,
polyether, or composites of any of the foregoing. Following
adsorption of the polypeptide to the cation exchanger matrix,
substantially purified polypeptide may be eluted by contacting the
matrix with a buffer having a sufficiently high pH or ionic
strength to displace the polypeptide from the matrix. Suitable
buffers for use in high pH elution of substantially purified
polypeptide include, but are not limited to, citrate, phosphate,
formate, acetate, HEPES, and MES buffers ranging in concentration
from at least about 5 mM to at least about 100 mM.
[0494] Reverse-Phase Chromatography The techniques disclosed in
this section can be applied to the reverse-phase chromatography of
the non-natural amino acid polypeptides described herein. RP-HPLC
may be performed to purify proteins following suitable protocols
that are known to those of ordinary skill in the art. See, e.g.
Pearson et al., ANAL BIOCHEM. (1982) 124:217-230 (1982); Rivier et
al., J. CHROM. (1983) 268:112-119; Kunitani et al., J. CHROM.
(1986) 359:391-402. RP-HPLC may be performed on the polypeptide to
isolate substantially purified polypeptide. In this regard, silica
derivatized resins with alkyl functionalities with a wide variety
of lengths, including, but not limited to, at least about C.sub.3
to at least about C.sub.30, at least about C.sub.3 to at least
about C.sub.20, or at least about C.sub.3 to at least about
C.sub.18, resins may be used. Alternatively, a polymeric resin may
be used. For example, TosoHaas Amberchrome CG1000sd resin may be
used, which is a styrene polymer resin. Cyano or polymeric resins
with a wide variety of alkyl chain lengths may also be used.
Furthermore, the RP-HPLC column may be washed with a solvent such
as ethanol. A suitable elution buffer containing an ion pairing
agent and an organic modifier such as methanol, isopropanol,
tetrahydrofuran, acetonitrile or ethanol, may be used to elute the
polypeptide from the RP-HPLC column. The most commonly used ion
pairing agents include, but are not limited to, acetic acid, formic
acid, perchloric acid, phosphoric acid, trifluoroacetic acid,
heptafluorobutyric acid, triethylamine, tetramethylammonium,
tetrabutylammonium, triethylammonium acetate. Elution may be
performed using one or more gradients or isocratic conditions, with
gradient conditions preferred to reduce the separation time and to
decrease peak width. Another method involves the use of two
gradients with different solvent concentration ranges. Examples of
suitable elution buffers for use herein may include, but are not
limited to, ammonium acetate and acetonitrile solutions.
[0495] Hydrophobic Interaction Chromatography Purification
Techniques The techniques disclosed in this section can be applied
to the hydrophobic interaction chromatography purification of the
non-natural amino acid polypeptides described herein. Hydrophobic
interaction chromatography (HIC) may be performed on the
polypeptide. See generally HYDROPHOBIC INTERACTION CHROMATOGRAPHY
HANDBOOK: PRINCIPLES AND METHODS (Cat. No. 18-1020-90, Amersham
Biosciences (Piscataway, N.J.) which is incorporated by reference
herein. Suitable HIC matrices may include, but are not limited to,
alkyl- or aryl-substituted matrices, such as butyl-, hexyl-, octyl-
or phenyl-substituted matrices including agarose, cross-linked
agarose, sepharose, cellulose, silica, dextran, polystyrene,
poly(methacrylate) matrices, and mixed mode resins, including but
not limited to, a polyethyleneamine resin or a butyl- or
phenyl-substituted poly(methacrylate) matrix. Commercially
available sources for hydrophobic interaction column chromatography
include, but are not limited to, HITRAP.RTM., HIPREP.RTM., and
HILOAD.RTM. columns (Amersham Biosciences, Piscataway, N.J.).
Briefly, prior to loading, the HIC column may be equilibrated using
standard buffers known to those of ordinary skill in the art, such
as an acetic acid/sodium chloride solution or HEPES containing
ammonium sulfate. Ammonium sulfate may be used as the buffer for
loading the HIC column. After loading the polypeptide, the column
may then washed using standard buffers and conditions to remove
unwanted materials but retaining the polypeptide on the HIC column.
The polypeptide may be eluted with about 3 to about 10 column
volumes of a standard buffer, such as a HEPES buffer containing
EDTA and lower ammonium sulfate concentration than the
equilibrating buffer, or an acetic acid/sodium chloride buffer,
among others. A decreasing linear salt gradient using, for example,
a gradient of potassium phosphate, may also be used to elute the
polypeptide molecules. The eluant may then be concentrated, for
example, by filtration such as diafiltration or ultrafiltration.
Diafiltration may be utilized to remove the salt used to elute
polypeptide.
[0496] Other Purification Techniques The techniques disclosed in
this section can be applied to other purification techniques of the
non-natural amino acid polypeptides described herein. Yet another
isolation step using, for example, gel filtration (GEL FILTRATION:
PRINCIPLES AND METHODS (Cat. No. 18-1022-18, Amersham Biosciences,
Piscataway, N.J., which is herein incorporated by reference in its
entirety), hydroxyapatite chromatography (suitable matrices
include, but are not limited to, HA-Ultrogel, High Resolution
(Calbiochem), CHT Ceramic Hydroxyapatite (BioRad), Bio-Gel
HTP-Hydroxyapatite (BioRad)), HPLC, expanded bed adsorption,
ultrafiltration, diafiltration, lyophilization, and the like, may
be performed on the first polypeptide mixture or any subsequent
mixture thereof, to remove any excess salts and to replace the
buffer with a suitable buffer for the next isolation step or even
formulation of the final drug product. The yield of polypeptide,
including substantially purified polypeptide, may be monitored at
each step described herein using various techniques, including but
not limited to those described herein. Such techniques may also
used to assess the yield of substantially purified polypeptide
following the last isolation step. By way of example, the yield of
polypeptide may be monitored using any of several reverse phase
high pressure liquid chromatography columns, having a variety of
alkyl chain lengths such as cyano RP-HPLC, C.sub.18RP-HPLC; as well
as cation exchange HPLC and gel filtration HPLC.
[0497] In certain embodiments, the yield of polypeptide after each
purification step may be at least about 30%, at least about 35%, at
least about 40%, at least about 45%, at least about 50%, at least
about 55%, at least about 60%, at least about 65%, at least about
70%, at least about 75%, at least about 80%, at least about 85%, at
least about 90%, at least about 91%, at least about 92%, at least
about 93%, at least about 94%, at least about 95%, at least about
96%, at least about 97%, at least about 98%, at least about 99%, at
least about 99.9%, or at least about 99.99%, of the polypeptide in
the starting material for each purification step.
[0498] Purity may be determined using standard techniques, such as
SDS-PAGE, or by measuring polypeptide using Western blot and ELISA
assays. For example, polyclonal antibodies may be generated against
proteins isolated from negative control yeast fermentation and the
cation exchange recovery. The antibodies may also be used to probe
for the presence of contaminating host cell proteins.
[0499] RP-HPLC material Vydac C4 (Vydac) consists of silica gel
particles, the surfaces of which carry C4-alkyl chains. The
separation of polypeptide from the proteinaceous impurities is
based on differences in the strength of hydrophobic interactions.
Elution is performed with an acetonitrile gradient in diluted
trifluoroacetic acid. Preparative HPLC is performed using a
stainless steel column (filled with 2.8 to 3.2 liter of Vydac C4
silicagel). The Hydroxyapatite Ultrogel eluate is acidified by
adding trifluoroacetic acid and loaded onto the Vydac C4 column.
For washing and elution an acetonitrile gradient in diluted
trifluoroacetic acid is used. Fractions are collected and
immediately neutralized with phosphate buffer. The polypeptide
fractions which are within the IPC limits are pooled.
[0500] DEAE Sepharose (Pharmacia) material consists of
diethylaminoethyl (DEAE)-groups which are covalently bound to the
surface of Sepharose beads. The binding of polypeptide to the DEAE
groups is mediated by ionic interactions. Acetonitrile and
trifluoroacetic acid pass through the column without being
retained. After these substances have been washed off, trace
impurities are removed by washing the column with acetate buffer at
a low pH. Then the column is washed with neutral phosphate buffer
and polypeptide is eluted with a buffer with increased ionic
strength. The column is packed with DEAE Sepharose fast flow. The
column volume is adjusted to assure a polypeptide load in the range
of 3-10 mg polypeptide/ml gel. The column is washed with water and
equilibration buffer (sodium/potassium phosphate). The pooled
fractions of the HPLC eluate are loaded and the column is washed
with equilibration buffer. Then the column is washed with washing
buffer (sodium acetate buffer) followed by washing with
equilibration buffer. Subsequently, polypeptide is eluted from the
column with elution buffer (sodium chloride, sodium/potassium
phosphate) and collected in a single fraction in accordance with
the master elution profile. The eluate of the DEAE Sepharose column
is adjusted to the specified conductivity. The resulting drug
substance is sterile filtered into Teflon bottles and stored at
-70.degree. C.
[0501] Additional methods include, but are not limited to, steps to
remove endotoxins. Endotoxins are lipopolysaccharides (LPSs) which
are located on the outer membrane of Gram-negative host cells, such
as, for example, Escherichia coli. Methods for reducing endotoxin
levels include, but are not limited to, purification techniques
using silica supports, glass powder or hydroxyapatite,
reverse-phase, affinity, size-exclusion, anion-exchange
chromatography, hydrophobic interaction chromatography, a
combination of these methods, and the like. Modifications or
additional methods may be required to remove contaminants such as
co-migrating proteins from the polypeptide of interest. Methods for
measuring endotoxin levels are known to one of ordinary skill in
the art and include, but are not limited to, Limulus Amebocyte
Lysate (LAL) assays.
[0502] Additional methods and procedures include, but are not
limited to, SDS-PAGE coupled with protein staining methods,
immunoblotting, matrix assisted laser desorption/ionization-mass
spectrometry (MALDI-MS), liquid chromatography/mass spectrometry,
isoelectric focusing, analytical anion exchange, chromatofocusing,
and circular dichroism
[0503] In certain embodiments the non-natural amino acids described
herein may be biosynthetically incorporated into polypeptides,
thereby making non-natural amino acid polypeptides. In other
embodiments, such amino acids are incorporated at a specific site
within the polypeptide. In other embodiments, such amino acids
incorporated into the polypeptide using a translation system. In
other embodiments, such translation systems comprise: (i) a
polynucleotide encoding the polypeptide, wherein the polynucleotide
comprises a selector codon corresponding to the pre-designated site
of incorporation of the above amino acids, and (ii) a tRNA
comprising the amino acid, wherein the tRNA is specific to the
selector codon. In other embodiments of such translation systems,
the polynucleotide is mRNA produced in the translation system. In
other embodiments of such translation systems, the translation
system comprises a plasmid or a phage comprising the
polynucleotide. In other embodiments of such translation systems,
the translation system comprises genomic DNA comprising the
polynucleotide. In other embodiments of such translation systems,
the polynucleotide is stably integrated into the genomic DNA. In
other embodiments of such translation systems, the translation
system comprises tRNA specific for a selector codon selected from
the group consisting of an amber codon, ochre codon, opal codon, a
unique codon, a rare codon, an unnatural codon, a five-base codon,
and a four-base codon. In other embodiments of such translation
systems, the tRNA is a suppressor tRNA. In other embodiments of
such translation systems, the translation system comprises a tRNA
that is aminoacylated to the amino acids above. In other
embodiments of such translation systems, the translation system
comprises an aminoacyl synthetase specific for the tRNA. In other
embodiments of such translation systems, the translation system
comprises an orthogonal tRNA and an orthogonal aminoacyl tRNA
synthetase. In other embodiments of such translation systems, the
polypeptide is synthesized by a ribosome, and in further
embodiments the translation system is an in vivo translation system
comprising a cell selected from the group consisting of a bacterial
cell, archeaebacterial cell, and eukaryotic cell. In other
embodiments the cell is an Escherichia coli cell, yeast cell, a
cell from a species of Pseudomonas, mammalian cell, plant cell, or
an insect cell. In other embodiments of such translation systems,
the translation system is an in vitro translation system comprising
cellular extract from a bacterial cell, archeaebacterial cell, or
eukaryotic cell. In other embodiments, the cellular extract is from
an Escherichia coli cell, a cell from a species of Pseudomonas,
yeast cell, mammalian cell, plant cell, or an insect cell. In other
embodiments at least a portion of the polypeptide is synthesized by
solid phase or solution phase peptide synthesis, or a combination
thereof, while in other embodiments further comprise ligating the
polypeptide to another polypeptide. In other embodiments the
non-natural amino acids described herein may be biosynthetically
incorporated into polypeptides, wherein the polypeptide is a
protein homologous to a therapeutic protein selected from the group
consisting of: alpha-1 antitrypsin, angiostatin, antihemolytic
factor, antibody, apolipoprotein, apoprotein, atrial natriuretic
factor, atrial natriuretic polypeptide, atrial peptide, C-X-C
chemokine, T39765, NAP-2, ENA-78, gro-a, gro-b, gro-c, IP-10,
GCP-2, NAP-4, SDF-1, PF4, MIG, calcitonin, c-kit ligand, cytokine,
CC chemokine, monocyte chemoattractant protein-1, monocyte
chemoattractant protein-2, monocyte chemoattractant protein-3,
monocyte inflammatory protein-1 alpha, monocyte inflammatory
protein-i beta, RANTES, 1309, R83915, R91733, HCC1, T58847, D31065,
T64262, CD40, CD40 ligand, c-kit ligand, collagen, colony
stimulating factor (CSF), complement factor 5a, complement
inhibitor, complement receptor 1, cytokine, epithelial neutrophil
activating peptide-78, MIP-16, MCP-1, epidermal growth factor
(EGF), epithelial neutrophil activating peptide, erythropoietin
(EPO), exfoliating toxin, Factor IX, Factor VII, Factor VIII,
Factor X, fibroblast growth factor (FGF), fibrinogen, fibronectin,
four-helical bundle protein, G-CSF, glp-1, GM-CSF,
glucocerebrosidase, gonadotropin, growth factor, growth factor
receptor, grf, hedgehog protein, hemoglobin, hepatocyte growth
factor (hGF), hirudin, human growth hormone (hGH), human serum
albumin, ICAM-1, ICAM-1 receptor, LFA-1, LFA-1 receptor, insulin,
insulin-like growth factor (IGF), IGF-I, IGF-II, interferon (IFN),
IFN-alpha, IFN-beta, IFN-gamma, any interferon-like molecule or
member of the IFN family, interleukin (IL), IL-1, IL-2, IL-3, IL-4,
IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, keratinocyte
growth factor (KGF), lactoferrin, leukemia inhibitory factor,
luciferase, neurturin, neutrophil inhibitory factor (NIF),
oncostatin M, osteogenic protein, oncogene product, paracitonin,
parathyroid hormone, PD-ECSF, PDGF, peptide hormone, pleiotropin,
protein A, protein G, pth, pyrogenic exotoxin A, pyrogenic exotoxin
B, pyrogenic exotoxin C, pyy, relaxin, renin, SCF, small
biosynthetic protein, soluble complement receptor I, soluble I-CAM
1, soluble interleukin receptor, soluble TNF receptor, somatomedin,
somatostatin, somatotropin, streptokinase, superantigens,
staphylococcal enterotoxin, SEA, SEB, SEC1, SEC2, SEC3, SED, SEE,
steroid hormone receptor, superoxide dismutase, toxic
shock-syndrome toxin, thymosin alpha 1, tissue plasminogen
activator, tumor growth factor (TGF), tumor necrosis factor, tumor
necrosis factor alpha, tumor necrosis factor beta, tumor necrosis
factor receptor (TNFR), VLA-4 protein, VCAM-1 protein, vascular
endothelial growth factor (VEGF), urokinase, mos, ras, raf, met,
p53, tat, fos, myc, jun, myb, rel, estrogen receptor, progesterone
receptor, testosterone receptor, aldosterone receptor, LDL
receptor, and corticosterone.
B. In Vivo Post-Translational Modifications
[0504] By producing proteins or polypeptides of interest with at
least one non-natural amino acid in eukaryotic cells, such
polypeptides may include eukaryotic post-translational
modifications. In certain embodiments, a protein includes at least
one non-natural amino acid and at least one post-translational
modification that is made in vivo by a eukaryotic cell, where the
post-translational modification is not made by a prokaryotic cell.
By way of example, the post-translation modification includes, but
is not limited to, acetylation, acylation, lipid-modification,
palmitoylation, palmitate addition, phosphorylation,
glycolipid-linkage modification, glycosylation, and the like. In
one aspect, the post-translational modification includes attachment
of an oligosaccharide (including but not limited to,
(GlcNAc-Man).sub.2-Man-GlcNAc-GlcNAc)) to an asparagine by a
GlcNAc-asparagine linkage. See Table 1 which lists some examples of
N-linked oligosaccharides of eukaryotic proteins (additional
residues can also be present, which are not shown). In another
aspect, the post-translational modification includes attachment of
an oligosaccharide (including but not limited to, Gal-GalNAc,
Gal-GlcNAc, etc.) to a serine or threonine by a GalNAc-serine or
GalNAc-threonine linkage, or a GlcNAc-serine or a GlcNAc-threonine
linkage.
TABLE-US-00002 TABLE 1 Examples of oligosaccharides through
GLCNAC-linkage Type Base Structure HIGH-MANNOSE ##STR00049## HYBRID
##STR00050## COMPLEX ##STR00051## XYLOSE ##STR00052##
[0505] In yet another aspect, the post-translation modification
includes proteolytic processing of precursors (including but not
limited to; calcitonin precursor, calcitonin gene-related peptide
precursor, preproparathyroid hormone, preproinsulin, proinsulin,
prepro-opiomelanocortin, pro-opiomelanocortin and the like),
assembly into a multisubunit protein or macromolecular assembly,
translation to another site in the cell (including but not limited
to, to organelles, such as the endoplasmic reticulum, the golgi
apparatus, the nucleus, lysosomes, peroxisomes, mitochondria,
chloroplasts, vacuoles, etc., or through the secretory pathway). In
certain embodiments, the protein comprises a secretion or
localization sequence, an epitope tag, a FLAG tag, a polyhistidine
tag, a GST fusion, or the like.
[0506] One advantage of a non-natural amino acid is that it
presents additional chemical moieties that can be used to add
additional molecules. These modifications can be made in vivo in a
eukaryotic or non-eukaryotic cell, or in vitro. Thus, in certain
embodiments, the post-translational modification is through the
non-natural amino acid. For example, the post-translational
modification can be through a nucleophilic-electrophilic reaction.
Most reactions currently used for the selective modification of
proteins involve covalent bond formation between nucleophilic and
electrophilic reaction partners, including but not limited to the
reaction of .alpha.-haloketones with histidine or cysteine side
chains. Selectivity in these cases is determined by the number and
accessibility of the nucleophilic residues in the protein. In
polypeptides described herein or produced using the methods
described herein, other more selective reactions can be used,
including, but not limited to, the reaction of a non-natural
keto-amino acid with hydrazides or aminooxy compounds, in vitro and
in vivo. See, e.g., Cornish, et al., (1996) J. Am. Chem. Soc.,
118:8150-8151; Mahal, et al., (1997) Science, 276:1125-1128; Wang,
et al., (2001) Science 292:498-500; Chin, et al., (2002) J. Am.
Chem. Soc. 124:9026-9027; Chin, et al., (2002) Proc. Natl. Acad.
Sci., 99:11020-11024; Wang, et al., (2003) Proc. Natl. Acad. Sci.,
100:56-61; Zhang, et al., (2003) Biochemistry. 42:6735-6746; and,
Chin, et al., (2003) Science, 301:964-7. This allows the selective
labeling of virtually any protein with a host of reagents including
fluorophores, crosslinking agents, saccharide derivatives and
cytotoxic molecules. See also, U.S. Pat. No. 6,927,042 entitled
"Glycoprotein synthesis" filed Jan. 16, 2003, which is incorporated
by reference herein. Post-translational modifications, including
but not limited to, through an azido amino acid, can also made
through the Staudinger ligation (including but not limited to, with
triarylphosphine reagents). See, e.g., Kiick et al., (2002)
Incorporation of azides into recombinant proteins for
chemoselective modification by the Staudinger ligtation, PNAS
99:19-24.
IX. Alternate Systems for Producing Non-Natural Amino Acid
Polypeptides
[0507] Several strategies have been employed to introduce
non-natural amino acids into proteins in non-recombinant host
cells, mutagenized host cells, or in cell-free systems. The
alternate systems disclosed in this section can be applied to
production of the non-natural amino acid. By way of example,
derivatization of amino acids with reactive side-chains such as
Lys, Cys and Tyr resulted in the conversion of lysine to
N.sup.2-acetyl-lysine. Chemical synthesis also provides a
straightforward method to incorporate non-natural amino acids. With
the recent development of enzymatic ligation and native chemical
ligation of peptide fragments, it is possible to make larger
proteins. See, e.g., P. E. Dawson and S. B. H. Kent, Annu. Rev.
Biochem., 69:923 (2000). Chemical peptide ligation and native
chemical ligation are described in U.S. Pat. No. 6,184,344, U.S.
Patent Publication No. 2004/0138412, U.S. Patent Publication No.
2003/0208046, WO 02/098902, and WO 03/042235, which are herein
incorporated by reference in their entirety. A general in vitro
biosynthetic method in which a suppressor tRNA chemically acylated
with the desired non-natural amino acid is added to an in vitro
extract capable of supporting protein biosynthesis, has been used
to site-specifically incorporate over 100 non-natural amino acids
into a variety of proteins of virtually any size. See, e.g., V. W.
Cornish, D. Mendel and P. G. Schultz, Angew. Chem. Int. Ed. Engl.,
1995, 34:621 (1995); C. J. Noren, S. J. Anthony-Cahill, M. C.
Griffith, P. G. Schultz, A general method for site-specific
incorporation of unnatural amino acids into proteins, Science 244
182-188 (1989); and, J. D. Bain, C. G. Glabe, T. A. Dix, A. R.
Chamberlin, E. S. Diala, Biosynthetic site-specific incorporation
of a non-natural amino acid into a polypeptide, J. Am. Chem. Soc.
111 8013-8014 (1989). A broad range of functional groups has been
introduced into proteins for studies of protein stability, protein
folding, enzyme mechanism, and signal transduction.
[0508] An in vivo method, termed selective pressure incorporation,
was developed to exploit the promiscuity of wild-type synthetases.
See, e.g., N. Budisa, C. Minks, S. Alefelder, W. Wenger, F. M.
Dong, L. Moroder and R. Huber, FASEB J., 13:41 (1999). An
auxotrophic strain, in which the relevant metabolic pathway
supplying the cell with a particular natural amino acid is switched
off, is grown in minimal media containing limited concentrations of
the natural amino acid, while transcription of the target gene is
repressed. At the onset of a stationary growth phase, the natural
amino acid is depleted and replaced with the non-natural amino acid
analog. Induction of expression of the recombinant protein results
in the accumulation of a protein containing the non-natural analog.
For example, using this strategy, o, m and p-fluorophenylalanines
have been incorporated into proteins, and exhibit two
characteristic shoulders in the UV spectrum which can be easily
identified, see, e.g., C. Minks, R. Huber, L. Moroder and N.
Budisa, Anal. Biochem., 284:29 (2000); trifluoromethionine has been
used to replace methionine in bacteriophage T4 lysozyme to study
its interaction with chitooligosaccharide ligands by .sup.19F NMR,
see, e.g. H. Duewel, E. Daub, V. Robinson and J. F. Honek,
Biochemistry, 36:3404 (1997); and trifluoroleucine has been
incorporated in place of leucine, resulting in increased thermal
and chemical stability of a leucine-zipper protein. See, e.g., Y.
Tang, G. Ghirlanda, W. A. Petka, T. Nakajima, W. F. DeGrado and D.
A. Tirrell, Angew. Chem. Int. Ed. Engl., 40:1494 (2001). Moreover,
selenomethionine and telluromethionine are incorporated into
various recombinant proteins to facilitate the solution of phases
in X-ray crystallography. See, e.g. W. A. Hendrickson, J. R. Horton
and D. M. Lemaster, EMBO J. 9:1665 (1990), J. O. Boles, K.
Lewinski, M. Kunkle, J. D. Odom, B. Dunlap, L. Lebioda and M.
Hatada, Nat. Struct. Biol., 1:283 (1994); N. Budisa, B. Steipe, P.
Demange, C. Eckerskorn, J. Kellermann and R. Huber, Eur. J.
Biochem., 230:788 (1995); and, N. Budisa, W. Karnbrock, S.
Steinbacher, A. Humm, L. Prade, T. Neuefeind, L. Moroder and R.
Huber, J. Mol. Biol., 270:616 (1997). Methionine analogs with
alkene or alkyne functionalities have also been incorporated
efficiently, allowing for additional modification of proteins by
chemical means. See, e.g., J. C. M. van Hest and D. A. Tirrell,
FEBS Lett., 428:68 (1998); J. C. M. van Hest, K. L. Kiick and D. A.
Tirrell, J. Am. Chem. Soc., 122:1282 (2000); and, K. L. Kiick and
D. A. Tirrell, Tetrahedron, 56:9487 (2000); U.S. Pat. No.
6,586,207; U.S. Patent Publication 2002/0042097, which are herein
incorporated by reference in their entirety.
[0509] The success of this method depends on the recognition of the
non-natural amino acid analogs by aminoacyl-tRNA synthetases,
which, in general, require high selectivity to insure the fidelity
of protein translation. One way to expand the scope of this method
is to relax the substrate specificity of aminoacyl-tRNA
synthetases, which has been achieved in a limited number of cases.
By way of example only, replacement of Ala.sup.294 by Gly in
Escherichia coli phenylalanyl-tRNA synthetase (PheRS) increases the
size of substrate binding pocket, and results in the acylation of
tRNAPhe by p-Cl-phenylalanine (p-Cl-Phe). See, M. Ibba, P. Kast and
H. Hennecke, Biochemistry, 33:7107 (1994). An Escherichia coli
strain harboring this mutant PheRS allows the incorporation of
p-Cl-phenylalanine or p-Br-phenylalanine in place of phenylalanine.
See, e.g. M. Ibba and H. Hennecke, FEBS Lett., 364:272 (1995); and,
N. Sharma, R. Furter, P. Kast and D. A. Tirrell, FEBS Lett., 467:37
(2000). Similarly, a point mutation Phe130Ser near the amino acid
binding site of Escherichia coli tyrosyl-tRNA synthetase was shown
to allow azatyrosine to be incorporated more efficiently than
tyrosine. See, F. Hamano-Takaku, T. Iwama, S. Saito-Yano, K.
Takaku, Y. Monden, M. Kitabatake, D. Soil and S. Nishimura, J.
Biol. Chem., 275:40324 (2000).
[0510] Another strategy to incorporate non-natural amino acids into
proteins in vivo is to modify synthetases that have proofreading
mechanisms. These synthetases cannot discriminate and therefore
activate amino acids that are structurally similar to the cognate
natural amino acids. This error is corrected at a separate site,
which deacylates the mischarged amino acid from the tRNA to
maintain the fidelity of protein translation. If the proofreading
activity of the synthetase is disabled, structural analogs that are
misactivated may escape the editing function and be incorporated.
This approach has been demonstrated recently with the valyl-tRNA
synthetase (ValRS). See, V. Doring, H. D. Mootz, L. A. Nangle, T.
L. Hendrickson, V. de Crecy-Lagard, P. Schimmel and P. Marliere,
Science, 292:501 (2001). ValRS can misaminoacylate tRNAVal with
Cys, Thr, or aminobutyrate (Abu); these noncognate amino acids are
subsequently hydrolyzed by the editing domain. After random
mutagenesis of the Escherichia coli chromosome, a mutant
Escherichia coli strain was selected that has a mutation in the
editing site of ValRS. This edit-defective ValRS incorrectly
charges tRNAVal with Cys. Because Abu sterically resembles Cys
(--SH group of Cys is replaced with --CH3 in Abu), the mutant ValRS
also incorporates Abu into proteins when this mutant Escherichia
coli strain is grown in the presence of Abu. Mass spectrometric
analysis shows that about 24% of valines are replaced by Abu at
each valine position in the native protein.
[0511] Solid-phase synthesis and semisynthetic methods have also
allowed for the synthesis of a number of proteins containing novel
amino acids. For example, see the following publications and
references cited within, which are as follows: Crick, F. H. C.,
Barrett, L. Brenner, S. Watts-Tobin, R. General nature of the
genetic code for proteins. Nature, 192:1227-1232 (1961); Kaiser, E.
T. Synthetic approaches to biologically active peptides and
proteins including enyzmes, Acc Chem Res, 22:47-54 (1989);
Nakatsuka, T., Sasaki, T., Kaiser, E. T. Peptide segment coupling
catalyzed by the semisynthetic enzyme thiosubtilisin, J Am Chem
Soc, 109:3808-3810 (1987); Schnolzer, M., Kent, S B H. Constructing
proteins by dovetailing unprotected synthetic peptides:
backbone-engineered HIV protease, Science, 256(5054):221-225
(1992); Chaiken, I. M. Semisynthetic peptides and proteins, CRC
Crit Rev Biochem, 11(3):255-301 (1981); Offord, R. E. Protein
engineering by chemical means? Protein Eng. 1(3):151-157 (1987);
and, Jackson, D. Y., Burnier, J., Quan, C., Stanley, M., Tom, J.,
Wells, J. A. A Designed Peptide Ligase for Total Synthesis of
Ribonuclease A with Unnatural Catalytic Residues, Science,
266(5183):243 (1994).
[0512] Chemical modification has been used to introduce a variety
of non-natural side chains, including cofactors, spin labels and
oligonucleotides into proteins in vitro. See, e.g. Corey, D. R.,
Schultz, P. G. Generation of a hybrid sequence-specific
single-stranded deoxyribonuclease, Science, 238(4832):1401-1403
(1987); Kaiser, E. T., Lawrence D. S., Rokita, S. E. The chemical
modification of enzymatic specificity, Annu. Rev Biochem,
54:565-595 (1985); Kaiser, E. T., Lawrence, D. S. Chemical mutation
of enzyme active sites, Science, 226(4674):505-511 (1984); Neet, K.
E., Nanci A, Koshland, D. E. Properties of thiol-subtilisin, J
Biol. Chem, 243(24):6392-6401 (1968); Polgar, L. (ed.)., M. L.
Bender, A new enzyme containing a synthetically formed active site.
Thiol-subtilisin. J. Am Chem Soc, 88:3153-3154 (1966); and,
Pollack, S. J., Nakayama, G. Schultz, P. G. Introduction of
nucleophiles and spectroscopic probes into antibody combining
sites, Science, 224(4881):1038-1040 (1988).
[0513] Alternatively, biosynthetic methods that employ chemically
modified aminoacyl-tRNAs have been used to incorporate several
biophysical probes into proteins synthesized in vitro. See the
following publications and references cited within: Brunner, J. New
Photolabeling and crosslinking methods, Annu. Rev Biochem, 483-514
(1993); and, Krieg, U. C., Walter, P., Hohnson, A. E.
Photocrosslinking of the signal sequence of nascent preprolactin of
the 54-kilodalton polypeptide of the signal recognition particle,
Proc. Natl. Acad. Sci. 8604-8608 (1986).
[0514] Previously, it has been shown that non-natural amino acids
can be site-specifically incorporated into proteins in vitro by the
addition of chemically aminoacylated suppressor tRNAs to protein
synthesis reactions programmed with a gene containing a desired
amber nonsense mutation. Using these approaches, one can substitute
a number of the common twenty amino acids with close structural
homologues, e.g., fluorophenylalanine for phenylalanine, using
strains auxotrophic for a particular amino acid. See, e.g. Noren,
C. J., Anthony-Cahill, Griffith, M. C., Schultz, P. G. A general
method for site-specific incorporation of unnatural amino acids
into proteins, Science, 244: 182-188 (1989); M. W. Nowak, et al.,
Science 268:439-42 (1995); Bain, J. D., Glabe, C. G., Dix, T. A.,
Chamberlin, A. R., Diala, E. S. Biosynthetic site-specific
Incorporation of a non-natural amino acid into a polypeptide, J. Am
Chem Soc, 111:8013-8014 (1989); N. Budisa et al., FASEB J. 13:41-51
(1999); Ellman, J. A., Mendel, D., Anthony-Cahill, S., Noren, C.
J., Schultz, P. G. Biosynthetic method for introducing unnatural
amino acids site-specifically into proteins, Methods in Enz., vol.
202, 301-06 (199); and, Mendel, D., Cornish, V. W. & Schultz,
P. G. Site-Directed Mutagenesis with an Expanded Genetic Code, Annu
Rev Biophys. Biomol Struct. 24, 435-62 (1995).
[0515] For example, a suppressor tRNA was prepared that recognized
the stop codon UAG and was chemically aminoacylated with a
non-natural amino acid. Conventional site-directed mutagenesis was
used to introduce the stop codon TAG, at the site of interest in
the protein gene. See, e.g. Sayers, J. R., Schmidt, W. Eckstein, F.
5', 3' Exonuclease in phosphorothioate-based
oligonucleotide-directed mutagenesis, Nucleic Acids Res, 791-802
(1988). When the acylated suppressor tRNA and the mutant gene were
combined in an in vitro transcription/translation system, the
non-natural amino acid was incorporated in response to the UAG
codon which gave a protein containing that amino acid at the
specified position. Experiments using [.sup.3H]-Phe and experiments
with .alpha.-hydroxy acids demonstrated that only the desired amino
acid is incorporated at the position specified by the UAG codon and
that this amino acid is not incorporated at any other site in the
protein. See, e.g. Noren, et al, supra; Kobayashi et al., (2003)
Nature Structural Biology 10(6):425-432; and, Ellman, J. A.,
Mendel, D., Schultz, P. G. Site-specific incorporation of novel
backbone structures into proteins, Science, 197-200 (1992):
[0516] Microinjection techniques have also been used to incorporate
non-natural amino acids into proteins. See, e.g., M. W. Nowak, P.
C. Kearney, J. R. Sampson, M. E. Saks, C. G. Labarca, S. K.
Silverman, W. G. Zhong, J. Thorson, J. N. Abelson, N. Davidson, P.
G. Schultz, D. A. Dougherty and H. A. Lester, Science 268:439
(1995); and, D. A. Dougherty, Curr. Opin. Chem. Biol., 4:645
(2000). A Xenopus oocyte was coinjected with two RNA species made
in vitro: an mRNA encoding the target protein with a UAG stop codon
at the amino acid position of interest and an amber suppressor tRNA
aminoacylated with the desired non-natural amino acid. The
translational machinery of the oocyte then inserts the non-natural
amino acid at the position specified by UAG. This method has
allowed in vivo structure-function studies of integral membrane
proteins, which are generally not amenable to in vitro expression
systems. Examples include the incorporation of a fluorescent amino
acid into tachykinin neurokinin-2 receptor to measure distances by
fluorescence resonance energy transfer, see, e.g., G. Turcatti, K.
Nemeth, M. D. Edgerton, U. Meseth, F. Talabot, M. Peitsch, J.
Knowles, H. Vogel and A. Chollet, J. Biol. Chem., 271:19991 (1996);
the incorporation of biotinylated amino acids to identify
surface-exposed residues in ion channels, see, e.g., J. P.
Gallivan, H. A. Lester and D. A. Dougherty, Chem. Biol., 4:739
(1997); the use of caged tyrosine analogs to monitor conformational
changes in an ion channel in real time, see, e.g., J. C. Miller, S.
K. Silverman, P. M. England, D. A. Dougherty and H. A. Lester,
Neuron, 20:619 (1998); and, the use of alpha hydroxy amino acids to
change ion channel backbones for probing their gating mechanisms.
See, e.g. P. M. England, Y. Zhang, D. A. Dougherty and H. A.
Lester, Cell, 96:89 (1999); and, T. Lu, A. Y. Ting, J. Mainland, L.
Y. Jan, P. G. Schultz and J. Yang, Nat. Neurosci., 4:239
(2001).
[0517] The ability to incorporate non-natural amino acids directly
into proteins in vivo offers a wide variety of advantages including
but not limited to high yields of mutant proteins, technical ease,
the potential to study the mutant proteins in cells or possibly in
living organisms and the use of these mutant proteins in
therapeutic treatments. The ability to include non-natural amino
acids with various sizes, acidities, nucleophilicities,
hydrophobicities, and other properties into proteins can greatly
expand our ability to rationally and systematically manipulate the
structures of proteins, both to probe protein function and create
new proteins or organisms with novel properties.
[0518] In one attempt to site-specifically incorporate para-F-Phe,
a yeast amber suppressor tRNAPheCUA/phenylalanyl-tRNA synthetase
pair was used in a p-F-Phe resistant, Phe auxotrophic Escherichia
coli strain. See, e.g., R. Furter, Protein Sci., 7:419 (1998).
[0519] It may also be possible to obtain expression of a desired
polynucleotide using a cell-free (in-vitro) translational system.
Translation systems may be cellular or cell-free, and may be
prokaryotic or eukaryotic. Cellular translation systems include,
but are not limited to, whole cell preparations such as
permeabilized cells or cell cultures wherein a desired nucleic acid
sequence can be transcribed to mRNA and the mRNA translated.
Cell-free translation systems are commercially available and many
different types and systems are well-known. Examples of cell-free
systems include, but are not limited to, prokaryotic lysates such
as Escherichia coli lysates, and eukaryotic lysates such as wheat
germ extracts, insect cell lysates, rabbit reticulocyte lysates,
rabbit oocyte lysates and human cell lysates. Eukaryotic extracts
or lysates may be preferred when the resulting protein is
glycosylated, phosphorylated or otherwise modified because many
such modifications are only possible in eukaryotic systems. Some of
these extracts and lysates are available commercially (Promega;
Madison, Wis.; Stratagene; La Jolla, Calif.; Amersham; Arlington
Heights, Ill.; GIBCO/BRL; Grand Island, N.Y.). Membranous extracts,
such as the canine pancreatic extracts containing microsomal
membranes, are also available which are useful for translating
secretory proteins. In these systems, which can include either mRNA
as a template (in-vitro translation) or DNA as a template (combined
in-vitro transcription and translation), the in vitro synthesis is
directed by the ribosomes. Considerable effort has been applied to
the development of cell-free protein expression systems. See, e.g.,
Kim, D.-M. and J. R. Swartz, Biotechnology and Bioengineering, 74
:309-316 (2001); Kim, D.-M. and J. R. Swartz, Biotechnology
Letters, 22, 1537-1542, (2000); Kim, D.-M., and J. R. Swartz,
Biotechnology Progress, 16, 385-390, (2000); Kim, D.-M., and J. R.
Swartz, Biotechnology and Bioengineering, 66, 180-188, (1999); and
Patnaik, R. and J. R. Swartz, Biotechniques 24, 862-868, (1998);
U.S. Pat. No. 6,337,191; U.S. Patent Publication No. 2002/0081660;
WO 00/55353; WO 90/05785, which are incorporated by reference
herein. Another approach that may be applied to the expression of
polypeptides comprising a non-natural amino acid include the
mRNA-peptide fusion technique. See, e.g., R. Roberts and J.
Szostak, Proc. Natl Acad. Sci. (USA) 94 12297-12302 (1997); A.
Frankel, et al., Chemistry & Biology 10, 1043-1050 (2003). In
this approach, an mRNA template linked to puromycin is translated
into peptide on the ribosome. If one or more tRNA molecules has
been modified, non-natural amino acids can be incorporated into the
peptide as well. After the last mRNA codon has been read, puromycin
captures the C-terminus of the peptide. If the resulting
mRNA-peptide conjugate is found to have interesting properties in
an in vitro assay, its identity can be easily revealed from the
mRNA sequence. In this way, one may screen libraries of
polypeptides comprising one or more non-natural amino acids to
identify polypeptides having desired properties. More recently, in
vitro ribosome translations with purified components have been
reported that permit the synthesis of peptides substituted with
non-natural amino acids. See, e.g., A. Forster et al., Proc. Natl
Acad. Sci. (USA) 100 6353 (2003).
[0520] Reconstituted translation systems may also be used. Mixtures
of purified translation factors have also been used successfully to
translate mRNA into protein as well as combinations of lysates or
lysates supplemented with purified translation factors such as
initiation factor-1 (IF-1), IF-2, IF-3, elongation factor T
(EF-Tu), or termination factors. Cell-free systems may also be
coupled transcription/translation systems wherein DNA is introduced
to the system, transcribed into mRNA and the mRNA translated as
described in Current Protocols in Molecular Biology (F. M. Ausubel
et al. editors, Wiley Interscience, 1993), which is hereby
specifically incorporated by reference. RNA transcribed in
eukaryotic transcription system may be in the form of heteronuclear
RNA (hnRNA) or 5'-end caps (7-methyl guanosine) and 3'-end poly A
tailed mature mRNA, which can be an advantage in certain
translation systems. For example, capped mRNAs are translated with
high efficiency in the reticulocyte lysate system.
[0521] A tRNA may be aminoacylated with a desired amino acid by any
method or technique, including but not limited to, chemical or
enzymatic aminoacylation.
[0522] Aminoacylation may be accomplished by aminoacyl tRNA
synthetases or by other enzymatic molecules, including but not
limited to, ribozymes. The term "ribozyme" is interchangeable with
"catalytic RNA." Cech and coworkers (Cech, 1987, Science,
236:1532-1539; McCorkle et al., 1987, Concepts Biochem. 64:221-226)
demonstrated the presence of naturally occurring RNAs that can act
as catalysts (ribozymes). However, although these natural RNA
catalysts have only been shown to act on ribonucleic acid
substrates for cleavage and splicing, the recent development of
artificial evolution of ribozymes has expanded the repertoire of
catalysis to various chemical reactions. Studies have identified
RNA molecules that can catalyze aminoacyl-RNA bonds on their own
(2')3'-termini (Illangakekare et al., 1995 Science 267:643-647),
and an RNA molecule which can transfer an amino acid from one RNA
molecule to another (Lohse et al., 1996, Nature 381:442-444).
[0523] U.S. Patent Application Publication 2003/0228593, which is
incorporated by reference herein, describes methods to construct
ribozymes and their use in aminoacylation of tRNAs with naturally
encoded and non-naturally encoded amino acids.
Substrate-immobilized forms of enzymatic molecules that can
aminoacylate tRNAs, including but not limited to, ribozymes, may
enable efficient affinity purification of the aminoacylated
products. Examples of suitable substrates include agarose,
sepharose, and magnetic beads. The production and use of a
substrate-immobilized form of ribozyme for aminoacylation is
described in Chemistry and Biology 2003, 10:1077-1084 and U.S.
Patent Application Publication 2003/0228593, which are incorporated
by reference herein.
[0524] Chemical aminoacylation methods include, but are not limited
to, those introduced by Hecht and coworkers (Hecht, S. M. Acc.
Chem. Res. 1992, 25, 545; Heckler, T. G.; Roesser, J. R.; Xu, C.;
Chang, P.; Hecht, S. M. Biochemistry 1988, 27, 7254; Hecht, S. M.;
Alford, B. L.; Kuroda, Y.; Kitano, S. J. Biol. Chem. 1978, 253,
4517) and by Schultz, Chamberlin, Dougherty and others (Cornish, V.
W.; Mendel, D.; Schultz, P. G. Angew. Chem. Int. Ed. Engl. 1995,
34, 621; Robertson, S. A.; Ellman, J. A.; Schultz, P. G. J. Am.
Chem. Soc. 1991, 113, 2722; Noren, C. J.; Anthony-Cahill, S. J.;
Griffith, M. C.; Schultz, P. G. Science 1989, 244, 182; Bain, J.
D.; Glabe, C. G.; Dix, T. A.; Chamberlin, A. R. J. Am. Chem. Soc.
1989, 111, 8013; Bain, J. D. et al. Nature 1992, 356, 537;
Gallivan, J. P.; Lester, H. A.; Dougherty, D. A. Chem. Biol. 1997,
4, 740; Turcatti, et al. J. Biol. Chem. 1996, 271, 19991; Nowak, M.
W. et al. Science, 1995, 268, 439; Saks, M. E. et al. J. Biol.
Chem. 1996, 271, 23169; Hohsaka, T. et al. J. Am. Chem. Soc. 1999,
121, 34), which are incorporated by reference herein, to avoid the
use of synthetases in aminoacylation. Such methods or other
chemical aminoacylation methods may be used to aminoacylate tRNA
molecules.
[0525] Methods for generating catalytic RNA may involve generating
separate pools of randomized ribozyme sequences, performing
directed evolution on the pools, screening the pools for desirable
aminoacylation activity, and selecting sequences of those ribozymes
exhibiting desired aminoacylation activity.
[0526] Ribozymes can comprise motifs and/or regions that facilitate
acylation activity, such as a GGU motif and a U-rich region. For
example, it has been reported that U-rich regions can facilitate
recognition of an amino acid substrate, and a GGU-motif can form
base pairs with the 3' termini of a tRNA. In combination, the GGU
and motif and U-rich region facilitate simultaneous recognition of
both the amino acid and tRNA simultaneously, and thereby facilitate
aminoacylation of the 3' terminus of the tRNA.
[0527] Ribozymes can be generated by in vitro selection using a
partially randomized r24mini conjugated with tRNAAsnCCCG, followed
by systematic engineering of a consensus sequence found in the
active clones. An exemplary ribozyme obtained by this method is
termed "Fx3 ribozyme" and is described in U.S. Pub. App. No.
2003/0228593, the contents of which is incorporated by reference
herein, acts as a versatile catalyst for the synthesis of various
aminoacyl-tRNAs charged with cognate non-natural amino acids.
[0528] Immobilization on a substrate may be used to enable
efficient affinity purification of the aminoacylated tRNAs.
Examples of suitable substrates include, but are not limited to,
agarose, sepharose, and magnetic beads. Ribozymes can be
immobilized on resins by taking advantage of the chemical structure
of RNA, such as the 3'-cis-diol on the ribose of RNA can be
oxidized with periodate to yield the corresponding dialdehyde to
facilitate immobilization of the RNA on the resin. Various types of
resins can be used including inexpensive hydrazide resins wherein
reductive amination makes the interaction between the resin and the
ribozyme an irreversible linkage. Synthesis of aminoacyl-tRNAs can
be significantly facilitated by this on-column aminoacylation
technique. Kourouklis et al. Methods 2005; 36:2394 describe a
column-based aminoacylation system.
[0529] Isolation of the aminoacylated tRNAs can be accomplished in
a variety of ways. One suitable method is to elute the
aminoacylated tRNAs from a column with a buffer such as a sodium
acetate solution with 10 mM EDTA, a buffer containing 50 mM
N-(2-hydroxyethyl)piperazine-N'-(3-propanesulfonic acid), 12.5 mM
KCl, pH 7.0, 10 mM EDTA, or simply an EDTA buffered water (pH
7.0).
[0530] The aminoacylated tRNAs can be added to translation
reactions in order to incorporate the amino acid with which the
tRNA was aminoacylated in a position of choice in a polypeptide
made by the translation reaction. Examples of translation systems
in which the aminoacylated tRNAs of the present invention may be
used include, but are not limited to cell lysates. Cell lysates
provide reaction components necessary for in vitro translation of a
polypeptide from an input mRNA. Examples of such reaction
components include but are not limited to ribosomal proteins, rRNA,
amino acids, tRNAs, GTP, ATP, translation initiation and elongation
factors and additional factors associated with translation.
Additionally, translation systems may be batch translations or
compartmentalized translation. Batch translation systems combine
reaction components in a single compartment while compartmentalized
translation systems separate the translation reaction components
from reaction products that can inhibit the translation efficiency.
Such translation systems are available commercially.
[0531] Further, a coupled transcription/translation system may be
used. Coupled transcription/translation systems allow for both
transcription of an input DNA into a corresponding mRNA, which is
in turn translated by the reaction components. An example of a
commercially available coupled transcription/translation is the
Rapid Translation System (RTS, Roche Inc.). The system includes a
mixture containing E. coli lysate for providing translational
components such as ribosomes and translation factors. Additionally,
an RNA polymerase is included for the transcription of the input
DNA into an mRNA template for use in translation. RTS can use
compartmentalization of the reaction components by way of a
membrane interposed between reaction compartments, including a
supply/waste compartment and a transcription/translation
compartment.
[0532] Aminoacylation of tRNA may be performed by other agents,
including but not limited to, transferases, polymerases, catalytic
antibodies, multi-functional proteins, and the like.
[0533] Stephan in Scientist 2005 Oct. 10; pages 30-33 describes
additional methods to incorporate non-naturally encoded amino acids
into proteins. Lu et al. in Mol Cell. 2001 October; 8(4):759-69
describe a method in which a protein is chemically ligated to a
synthetic peptide containing unnatural amino acids (expressed
protein ligation).
X. Post-Translational Modifications of Non-Natural Amino Acid
Components of a Polypeptide
[0534] Methods, compositions, techniques and strategies have been
developed to site-specifically incorporate non-natural amino acids
during the in vivo translation of proteins. By incorporating a
non-natural amino acid with a sidechain chemistry that is
orthogonal to those of the naturally-occurring amino acids, this
technology makes possible the site-specific derivatization of
recombinant proteins. As a result, a major advantage of the
methods, compositions, techniques and strategies described herein
is that derivatized proteins can now be prepared as defined
homogeneous products. However, the methods, compositions, reaction
mixtures, techniques and strategies described herein are not
limited to non-natural amino acid polypeptides formed by in vivo
protein translation techniques, but includes non-natural amino acid
polypeptides formed by any technique, including by way of example
only in vitro techniques, expressed protein ligation, chemical
synthesis, ribozyme-based techniques (see, e.g., section herein
entitled "Expression in Alternate Systems").
[0535] The ability to incorporate non-natural amino acids into
recombinant proteins broadly expands the chemistries which may be
implemented for post-translational derivatization, wherein such
derivatization occurs either in vivo or in vitro. More
specifically, protein derivatization utilizing the reductive
alkylation or reductive amination reactions between a carbonyl
containing compound, such as, by way of example, aldehydes, and an
aromatic amine to form an alkylated amine, including a secondary
amine or a tertiary amine, linkage on a non-natural amino acid
portion of a polypeptide offers several advantages. First, the
naturally occurring amino acids (a) do not contain aromatic amine
groups that can react with carbonyl groups to form alkylated
aromatic amines, thereby creating secondary amine or tertiary amine
linkages, and (b) aromatic amine groups can react with carbonyl
containing groups to form alkylated amines, including secondary
amines or tertiary amines, and thus reagents designed to form such
alkylated amines will react site-specifically with the non-natural
amino acid component of the polypeptide (assuming of course that
the non-natural amino acid and the corresponding reagent have been
designed to form alkylated amines and the corresponding amine
linkage). Such site specific derivatization is illustrated in FIGS.
19-34, wherein the sidechain containing an aromatic amine is
preferentially reductively alkylated over sidechains containing
protonated amines or imidizole moieties. Second, such alkylated
aromatic amines have amine linkages which are stable under
biological conditions, suggesting that proteins derivatized by such
linkages are valid candidates for therapeutic applications. Third,
the stability of such amine linkage can be manipulated based on the
identity (i.e., the functional groups and/or structure) of the
non-natural amino acid to which the linkage has been formed. In
some embodiments, the alkylated amine, including a secondary amine
or a tertiary amine, linkage to the non-natural amino acid
polypeptide has a decomposition half life less than one hour, in
other embodiments less than 1 day, in other embodiments less than 2
days, in other embodiments less than 1 week and in other
embodiments more than 1 week. In yet other embodiments, the
resulting alkylated amine, including a secondary amine or a
tertiary amine, is stable for at least four weeks under biological
conditions. In yet other embodiments, the resulting alkylated
amine, including a secondary amine or a tertiary amine, is stable
for at least three weeks under biological conditions. In yet other
embodiments, the resulting alkylated amine, including a secondary
amine or a tertiary amine, is stable for at least two weeks under
biological conditions. In yet other embodiments, the resulting
alkylated amine, including a secondary amine or a tertiary amine,
is stable for at least one week under biological conditions. In
other embodiments the resulting alkylated amine, including a
secondary amine or a tertiary amine, linkage is stable for at least
6 days under biological conditions. In other embodiments the
resulting alkylated amine, including a secondary amine or a
tertiary amine, linkage is stable for at least 5 days under
biological conditions. In other embodiments the resulting alkylated
amine, including a secondary amine or a tertiary amine, linkage is
stable for at least 4 days under biological conditions. In other
embodiments the resulting alkylated amine, including a secondary
amine or a tertiary amine, linkage is stable for at least 3 days
under biological conditions. In other embodiments the resulting
alkylated amine, including a secondary amine or a tertiary amine,
linkage is stable for at least 2 days under biological conditions.
In other embodiments the resulting alkylated amine, including a
secondary amine or a tertiary amine, linkage is stable for at least
1 day under biological conditions. In other embodiments the
resulting alkylated amine, including a secondary amine or a
tertiary amine, linkage is stable for up to 24 hours under
biological conditions. In other embodiments the resulting alkylated
amine, including a secondary amine or a tertiary amine, linkage is
stable for up to 12 hours under biological conditions. In other
embodiments the resulting alkylated amine, including a secondary
amine or a tertiary amine, linkage is stable for up to 6 hours
under biological conditions. In other embodiments the resulting
alkylated amine, including a secondary amine or a tertiary amine,
linkage is stable for up to 3 hours under biological conditions. In
other embodiments the resulting alkylated amine, including a
secondary amine or a tertiary amine, linkage is stable for up to 2
hours under biological conditions. In other embodiments the
resulting alkylated amine, including a secondary amine or a
tertiary amine, linkage is stable for up to 1 hour under biological
conditions. In yet other embodiments, the resulting alkylated
amine, including a secondary amine or a tertiary amine, is stable
for at least two weeks under mildly acidic conditions, in other
embodiments the resulting alkylated amine, including a secondary
amine or a tertiary amine, linkage is stable for at least 5 days
under mildly acidic conditions. In other embodiments, the
non-natural amino acid polypeptide is stable for at least 1 day in
a pH between about 2 and about 8; in other embodiments, from a pH
of about 2 to about 6; in other embodiment, in a pH of about 2 to
about 4. In other embodiments, the non-natural amino acid
polypeptide is stable for at least 1 day in a pH between about 6
and about 10; in other embodiments, from a pH of about 4 to about
8; in other embodiment, in a pH of about 4 to about 10. In other
embodiments, the non-natural amino acid polypeptide is stable for
at least 1 day in a pH between about 2 and about 5; in other
embodiments, from a pH of about 3 to about 7; in other embodiment,
in a pH of about 3 to about 10. In other embodiments, using the
strategies, methods, compositions and techniques described herein,
the synthesis of alkylated amine, including secondary amine or
tertiary amine linkages to a non-natural amino acid polypeptide,
may vary to alter the decomposition half-life to the needs required
(e.g., for a therapeutic use such as sustained release, or a
diagnostic use, commercial products, or an industrial use or a
military use).
[0536] The non-natural amino acid polypeptides described above are
useful for, including but not limited to, novel therapeutics,
diagnostics, catalytic enzymes, industrial enzymes, binding
proteins (including but not limited to, antibodies and antibody
fragments), and including but not limited to, the study of protein
structure and function. See, e.g., Dougherty, (2000) Unnatural
Amino Acids as Probes of Protein Structure and Function, Current
Opinion in Chemical Biology. 4:645-652. Other uses for the
non-natural amino acid polypeptides described above include, by way
of example only, assay-based, cosmetic, plant biology,
environmental, energy-production, and/or military uses. However,
the non-natural amino acid polypeptides described above can undergo
further modifications so as to incorporate new or modified
functionalities, including manipulating the therapeutic
effectiveness of the polypeptide, improving the safety profile of
the polypeptide, adjusting the pharmacokinetics, pharmacologics
and/or pharmacodynamics of the polypeptide (e.g., increasing water
solubility, bioavailability, increasing serum half-life, increasing
therapeutic half-life, modulating immunogenicity, modulating
biological activity, or extending the circulation time), providing
additional functionality to the polypeptide, incorporating a tag,
label or detectable signal into the polypeptide, easing the
isolation properties of the polypeptide, and any combination of the
aforementioned modifications.
[0537] The methods, compositions, strategies and techniques
described herein are not limited to a particular type, class or
family of polypeptides or proteins. Indeed, virtually any
polypeptides may include at least one non-natural amino acids
described herein. By way of example only, the polypeptide can be
homologous to a therapeutic protein selected from the group
consisting of: alpha-1 antitrypsin, angiostatin, antihemolytic
factor, antibody, apolipoprotein, apoprotein, atrial natriuretic
factor, atrial natriuretic polypeptide, atrial peptide, C-X-C
chemokine, T39765, NAP-2, ENA-78, gro-a, gro-b, gro-c, IP-10,
GCP-2, NAP-4, SDF-1, PF4, MIG, calcitonin, c-kit ligand, cytokine,
CC chemokine, monocyte chemoattractant protein-1, monocyte
chemoattractant protein-2, monocyte chemoattractant protein-3,
monocyte inflammatory protein-1 alpha, monocyte inflammatory
protein-i beta, RANTES, 1309, R83915, R91733, HCC1, T58847, D31065,
T64262, CD40, CD40 ligand, c-kit ligand, collagen, colony
stimulating factor (CSF), complement factor 5a, complement
inhibitor, complement receptor 1, cytokine, epithelial neutrophil
activating peptide-78, MIP-16, MCP-1, epidermal growth factor
(EGF), epithelial neutrophil activating peptide, erythropoietin
(EPO), exfoliating toxin, Factor IX, Factor VII, Factor VIII,
Factor X, fibroblast growth factor (FGF), fibrinogen, fibronectin,
four-helical bundle protein, G-CSF, glp-1, GM-CSF,
glucocerebrosidase, gonadotropin, growth factor, growth factor
receptor, grf, hedgehog protein, hemoglobin, hepatocyte growth
factor (hGF), hirudin, human growth hormone (hGH), human serum
albumin, ICAM-1, ICAM-1 receptor, LFA-1, LFA-1 receptor, insulin,
insulin-like growth factor (IGF), IGF-I, IGF-II, interferon (IFN),
IFN-alpha, IFN-beta, IFN-gamma, any interferon-like molecule or
member of the IFN family, interleukin (IL), IL-1, IL-2, IL-3, IL-4,
IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, keratinocyte
growth factor (KGF), lactoferrin, leukemia inhibitory factor,
luciferase, neurturin, neutrophil inhibitory factor (NIF),
oncostatin M, osteogenic protein, oncogene product, paracitonin,
parathyroid hormone, PD-ECSF, PDGF, peptide hormone, pleiotropin,
protein A, protein G, pth, pyrogenic exotoxin A, pyrogenic exotoxin
B, pyrogenic exotoxin C, pyy, relaxin, renin, SCF, small
biosynthetic protein, soluble complement receptor I, soluble I-CAM
1, soluble interleukin receptor, soluble TNF receptor, somatomedin,
somatostatin, somatotropin, streptokinase, superantigens,
staphylococcal enterotoxin, SEA, SEB, SEC1, SEC2, SEC3, SED, SEE,
steroid hormone receptor, superoxide dismutase, toxic shock
syndrome toxin, thymosin alpha 1, tissue plasminogen activator,
tumor growth factor (TGF), tumor necrosis factor, tumor necrosis
factor alpha, tumor necrosis factor beta, tumor necrosis factor
receptor (TNFR), VLA-4 protein, VCAM-1 protein, vascular
endothelial growth factor (VEGF), urokinase, mos, ras, raf, met,
p53, tat, fos, myc, jun, myb, rel, estrogen receptor, progesterone
receptor, testosterone receptor, aldosterone receptor, LDL
receptor, and corticosterone. The non-natural amino acid
polypeptide may also be homologous to any polypeptide member of the
growth hormone supergene family.
[0538] Such modifications include the incorporation of further
functionality onto the non-natural amino acid component of the
polypeptide, including but not limited to, a label; a dye; a
polymer; a water-soluble polymer; a derivative of polyethylene
glycol; a photocrosslinker; a cytotoxic compound; a drug; an
affinity label; a photoaffinity label; a reactive compound; a
resin; a second protein or polypeptide or polypeptide analog; an
antibody or antibody fragment; a metal chelator; a cofactor; a
fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an
antisense polynucleotide; a saccharide, a water-soluble dendrimer,
a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a
fluorophore, a metal-containing moiety; a radioactive moiety; a
novel functional group; a group that covalently or noncovalently
interacts with other molecules; a photocaged moiety; an actinic
radiation excitable moiety; a ligand; a photoisomerizable moiety;
biotin; a biotin analogue; a moiety incorporating a heavy atom; a
chemically cleavable group; a photocleavable group; an elongated
side chain; a carbon-linked sugar; a redox-active agent; an amino
thioacid; a toxic moiety; an isotopically labeled moiety; a
biophysical probe; a phosphorescent group; a chemiluminescent
group; an electron dense group; a magnetic group; an intercalating
group; a chromophore; an energy transfer agent; a biologically
active agent; a detectable label; a small molecule; an inhibitory
ribonucleic acid; a radionucleotide; a neutron-capture agent; a
derivative of biotin; quantum dot(s); a nanotransmitter; a
radiotransmitter; an abzyme, an activated complex activator, a
virus, an adjuvant, an aglycan, an allergan, an angiostatin, an
antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a
shuttle vector, a macromolecule, a mimotope, a receptor, a reverse
micelle, and any combination thereof.
[0539] Thus, by way of example only, a non-natural amino acid
polypeptide containing any one of the following amino acids may be
further modified using the methods and compositions described
herein:
(a)
##STR00053##
wherein: is selected from the group consisting of a monocyclic aryl
ring, a bicyclic aryl ring, a multicyclic aryl ring, a monocyclic
heteroaryl ring, a bicyclic heteroaryl ring, and a multicyclic
heteroaryl ring; [0540] A is independently CR.sub.a, or N; [0541] B
is independently CR.sub.a, N, O, or S; each R.sub.a is
independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; and n is 0, 1, 2, 3, 4, 5, or 6; [0542] R.sub.1 is
H, an amino protecting group, resin, amino acid, polypeptide, or
polynucleotide; and [0543] R.sub.2 is OH, an ester protecting
group, resin, amino acid, polypeptide, or polynucleotide; [0544]
each of R.sub.3 and R.sub.4 is independently H, halogen, lower
alkyl, or substituted lower alkyl, or R.sub.3 and R.sub.4 or two
R.sub.3 groups optionally form a cycloalkyl or a heterocycloalkyl;
[0545] M is H or --CH.sub.2R.sub.5; or the M-N--C(R.sub.5) moiety
may form a 4 to 7 membered ring structure; [0546] R.sub.5 is alkyl,
substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0547] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N--CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; [0548]
or R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; and [0549] each R' is independently H, alkyl, or
substituted alkyl. Such non-natural amino acids include, but are
not limited to, the amino acids with the following structures:
##STR00054##
[0549] wherein, each A' is independently selected from CR.sub.a, N,
or
##STR00055##
and up to two A' may be
##STR00056##
[0550] with the remaining A' selected from CR.sub.a, or N. [0551]
In addition, such non-natural amino acids include, but are not
limited to, the amino acids with the following structures:
##STR00057##
[0551] wherein; G is an amine protecting group, including, but not
limited to,
##STR00058##
wherein:
##STR00059##
is selected from the group consisting of a monocyclic aryl ring, a
bicyclic aryl ring, a multicyclic aryl ring, a monocyclic
heteroaryl ring, a bicyclic heteroaryl ring, and a multicyclic
heteroaryl ring; [0552] A is independently CR.sub.a, or N; [0553] B
is independently CR.sub.a, N, O, or S; [0554] each R.sub.a is
independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; and n is 0, 1, 2, 3, 4, 5, or 6; [0555] R.sub.1 is
H, an amino protecting group, resin, amino acid, polypeptide, or
polynucleotide; and [0556] R.sub.2 is OH, an ester protecting
group, resin, amino acid, polypeptide, or polynucleotide; [0557]
each of R.sub.3 and R.sub.4 is independently H, halogen, lower
alkyl, or substituted lower alkyl, or R.sub.3 and R.sub.4 or two
R.sub.3 groups optionally form a cycloalkyl or a heterocycloalkyl;
[0558] Y is --NH--NH.sub.2, --NH--NHR', --CR'.dbd.NR', --NO.sub.2,
or --N.sub.3, and [0559] each R' is independently H, alkyl, or
substituted alkyl. [0560] In addition, such non-natural amino acids
include, but are not limited to, the amino acids with the following
structures:
##STR00060##
[0560] wherein:
##STR00061##
is selected from the group consisting of a monocyclic aryl ring, a
bicyclic aryl ring, a multicyclic aryl ring, a monocyclic
heteroaryl ring, a bicyclic heteroaryl ring, and a multicyclic
heteroaryl ring; [0561] A is independently CR.sub.a, or N; [0562] B
is independently CR.sub.a, N, O, or S; [0563] each R.sub.a is
independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; and n is 0, 1, 2, 3, 4, 5, or 6; [0564] R.sub.1 is
H, an amino protecting group, resin, amino acid, polypeptide, or
polynucleotide; and [0565] R.sub.2 is OH, an ester protecting
group, resin, amino acid, polypeptide, or polynucleotide; [0566]
each of R.sub.3 and R.sub.4 is independently H, halogen, lower
alkyl, or substituted lower alkyl, or R.sub.3 and R.sub.4 or two
R.sub.3 groups optionally form a cycloalkyl or a heterocycloalkyl;
[0567] M is H or --CH.sub.2R.sub.5; or the M-N--C(R.sub.5) moiety
may form a 4 to 7 membered ring structure; [0568] R.sub.5 is alkyl,
substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0569] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof, and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; [0570]
or R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; and [0571] each R' is independently H, alkyl, or
substituted alkyl. Such non-natural amino acids include, but are
not limited to, the amino acids with the following structures:
##STR00062##
[0571] wherein, each A' is independently selected from CR.sub.a, N,
or
##STR00063##
and up to two A' may be
##STR00064##
[0572] with the remaining A' selected from CR.sub.a, or N.
##STR00065##
wherein: [0573] L is optional, and when present is lower alkylene,
substituted lower alkylene, lower cycloalkylene, substituted lower
cycloalkylene, lower alkenylene, substituted lower alkenylene,
alkynylene, lower heteroalkylene, substituted heteroalkylene, lower
heterocycloalkylene, substituted lower heterocycloalkylene,
arylene, substituted arylene, heteroarylene, substituted
heteroarylene, alkarylene, substituted alkarylene, aralkylene, or
substituted aralkylene; [0574] Q is optional, and when present is a
linker selected from the group consisting of lower alkylene,
substituted lower alkylene, lower alkenylene, substituted lower
alkenylene, lower heteroalkylene, substituted lower heteroalkylene,
--O-(alkylene or substituted alkylene)-, --S-(alkylene or
substituted alkylene)-, where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(O)-(alkylene
or substituted alkylene)-, --C(S)-(alkylene or substituted
alkylene)-, --NR'-(alkylene or substituted alkylene)-,
--CON(R'')-(alkylene or substituted alkylene)-, --CSN(R')-(alkylene
or substituted alkylene)-, --N(R')CO-(alkylene or substituted
alkylene)-, and where each R' is independently H, alkyl, or
substituted alkyl; [0575] R.sub.1 is H, an amino protecting group,
resin, amino acid, polypeptide, or polynucleotide; and [0576]
R.sub.2 is OH, an ester protecting group, resin, amino acid,
polypeptide, or polynucleotide; [0577] each of R.sub.3 and R.sub.4
is independently H, halogen, lower alkyl, or substituted lower
alkyl, or R.sub.3 and R.sub.4 or two R.sub.3 groups optionally form
a cycloalkyl or a heterocycloalkyl; [0578] each R.sub.a is
independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; [0579] R.sub.6 is a protected aldehyde or a masked
aldehyde, wherein the protecting group includes, but is not limited
to,
##STR00066##
[0579] where each X.sub.1 is independently selected from the group
consisting of --O--, --S--, --N(H)--, --N(R)--, --N(Ac)--, and
--N(OMe)-; X.sub.2 is --OR, --OAc, --SR, --N(R).sub.2, --N(R)(Ac),
--N(R)(OMe), or N.sub.3, and where each R' and R is independently
H, alkyl, or substituted alkyl;
##STR00067##
wherein: [0580] L is optional, and when present is lower alkylene,
substituted lower alkylene, lower cycloalkylene, substituted lower
cycloalkylene, lower alkenylene, substituted lower alkenylene,
alkynylene; lower heteroalkylene, substituted heteroalkylene, lower
heterocycloalkylene, substituted lower heterocycloalkylene,
arylene, substituted arylene, heteroarylene, substituted
heteroarylene, alkarylene, substituted alkarylene, aralkylene, or
substituted aralkylene; [0581] Q is optional, and when present is a
linker selected from the group consisting of lower alkylene,
substituted lower alkylene, lower alkenylene, substituted lower
alkenylene, lower heteroalkylene, substituted lower heteroalkylene,
--O--, --O-(alkylene or substituted alkylene)-, --S--,
--S-(alkylene or substituted alkylene)-, --S(O).sub.k-- where k is
1, 2, or 3, --S(O).sub.k(alkylene or substituted alkylene)-,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --N(R')--,
--NR'-(alkylene or substituted alkylene)-, --C(O)N(R')--,
--CON(R'')-(alkylene or substituted alkylene)-, --CSN(R'')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO--,
--N(R')CO-(alkylene or substituted alkylene)-, --N(R')C(O)O--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R'')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R'').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--, where
each R' is independently H, alkyl, or substituted alkyl; [0582]
R.sub.1 is H, an amino protecting group, resin, amino acid,
polypeptide, or polynucleotide; and [0583] R.sub.2 is OH, an ester
protecting group, resin, amino acid, polypeptide, or
polynucleotide; [0584] each of R.sub.3 and R.sub.4 is independently
H, halogen, lower alkyl, or substituted lower alkyl, or R.sub.3 and
R.sub.4 or two R.sub.3 groups optionally form a cycloalkyl or a
heterocycloalkyl; [0585] each R.sub.a is independently selected
from the group consisting of H, halogen, alkyl, --NO.sub.2, --CN,
substituted alkyl, --N(R').sub.2, --C(O).sub.kR',
--C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where k is 1, 2, or
3; n is 0, 1, 2, 3, 4, 5, or 6; [0586] M is H or --CH.sub.2R.sub.5;
[0587] R.sub.5 is alkyl, substituted alkyl, alkenyl, substituted
alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy,
alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide,
substituted polyalkylene oxide, cycloalkyl, substituted cycloalkyl,
aryl, substituted aryl, heteroaryl, substituted heteroaryl,
heterocycle, substituted heterocycle, alkaryl, substituted alkaryl,
aralkyl, substituted aralkyl, --C(O)R'', --C(O)OR'',
--C(O)N(R'').sub.2, --C(O)NHCH(R'').sub.2, -(alkylene or
substituted alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0588] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; [0589]
or R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; [0590] each R' is independently H, alkyl, or
substituted alkyl;
##STR00068##
[0590] is selected from the group consisting of a monocyclic aryl
ring, a bicyclic aryl ring, a multicyclic aryl ring, a monocyclic
heteroaryl ring, a bicyclic heteroaryl ring, and a multicyclic
heteroaryl ring; [0591] A is independently CR.sub.a, or N; and
[0592] B is independently CR.sub.a, N, O, or S.
[0593] In one aspect of the methods and compositions described
herein are compositions that include at least one polypeptide with
at least one, including but not limited to, at least two, at least
three, at least four, at least five, at least six, at least seven,
at least eight, at least nine, or at least ten or more non-natural
amino acids that have been post-translationally modified. The
post-translationally-modified non-natural amino acids can be the
same or different, including but not limited to, there can be 1, 2,
3, 4, 5, 6, 7, 8, 9, 10 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or
more different sites in the protein that comprise 1, 2, 3, 4, 5, 6,
7, 8, 9, 10, 11, 12, 13; 14, 15, 16, 17, 18, 19, 20, or more
different post-translationally-modified non-natural amino acids. In
another aspect, a composition includes a polypeptide with at least
one, but fewer than all, of a particular amino acid present in the
polypeptide is substituted with the post-translationally-modified
non-natural amino acid. For a given polypeptide with more than one
post-translationally-modified non-natural amino acids, the
post-translationally-modified non-natural amino acids can be
identical or different (including but not limited to, the
polypeptide can include two or more different types of
post-translationally-modified non-natural amino acids, or can
include two of the same post-translationally-modified non-natural
amino acid). For a given polypeptide with more than two
post-translationally-modified non-natural amino acids, the
post-translationally-modified non-natural amino acids can be the
same, different or a combination of a multiple
post-translationally-modified non-natural amino acid of the same
kind with at least one different post-translationally-modified
non-natural amino acid.
A. Methods for Post-Translationally Modifying Non-Natural Amino
Acid Polypeptides using a Single Post-Translational Modification
Step: Reductive Alkylation Reactions of Aromatic Amine-Containing
Non-Natural Amino Acids with Carbonyl-Containing Reagents
[0594] The sidechains of the naturally occurring amino acids lack
highly nucleophilic sites. Therefore, the incorporation of a
non-natural amino acid with a nucleophilic-containing sidechain,
including, by way of example only, an amino acid containing an
aromatic amine group or a substituted aromatic amine group, makes
possible the site-specific alkylation of this sidechain via
nucleophilic addition to a carbonyl containing reagent, including
an aldehyde-containing reagent, followed by a reduction reaction.
This reductive alkylation reaction generates an amine linkage,
including secondary and tertiary amines.
[0595] The methods for derivatizing and/or further modifying may be
conducted with naturally generated polypeptides or chemically
synthesized polypeptides that has been purified prior to the
reductive alkylation step or after the reductive alkylation step.
In addition, the methods for derivatizing and/or further modifying
may be conducted with on synthetic polymers, polysaccharides, or
polynucleotides which have been purified before or after such
modifications.
[0596] Post-translational modification of polypeptides based upon
reductive alkylation of an aromatic amine-containing polypeptide
with an aldehyde-containing reagent has distinct advantages. First,
aromatic amines can be reductively alkylated with
carbonyl-containing compounds, including aldehydes, and ketones, in
a pH range of about 4 to about 10 (and in further embodiments in a
pH range of about 4 to about 7) with a reducing agent, such as
NaBCNH.sub.3, to generate secondary or tertiary amine linkages.
Other reducing agents which may be used include, but are not
limited to, TCEP, Na.sub.2S, Na.sub.2S.sub.2O.sub.4, LiAlH.sub.4,
B.sub.2H.sub.6, and NaBH.sub.4. Second, under these reaction
conditions the chemistry is selective for non-natural amino acids
as the sidechains of naturally occurring amino acids are
unreactive. This allows for site-specific derivatization of
polypeptides which have incorporated non-natural amino acids
containing aromatic amine moieties or protected aldehyde moieties,
including, by way of example, recombinant proteins. Such
derivatized polypeptides and proteins can thereby be prepared as
defined homogeneous products. Third, the mild conditions needed to
effect the reaction of an aromatic amine moiety on an amino acid,
which has been incorporated into a polypeptide, with an
aldehyde-containing reagent generally do not irreversibly destroy
the tertiary structure of the polypeptide (excepting, of course,
where the purpose of the reaction is to destroy such tertiary
structure). Similarly, the mild conditions needed to effect the
reaction of an aldehyde moiety on an amino acid, which has been
incorporated into a polypeptide and deprotected, with an aromatic
amine-containing reagent generally do not irreversibly destroy the
tertiary structure of the polypeptide (excepting, of course, where
the purpose of the reaction is to destroy such tertiary structure).
Fourth, the reaction occurs rapidly at room temperature, which
allows the use of many types of polypeptides or reagents that would
otherwise be unstable at higher temperatures. Fifth, the reaction
occurs readily is aqueous conditions, again allowing use of
polypeptides and reagents incompatible (to any extent) with
non-aqueous solutions. Six, the reaction occurs readily even when
the ratio of polypeptide or amino acid to reagent is
stoichiometric, stoichiometric-like, or near-stoichiometric, so
that it is unnecessary to add excess reagent or polypeptide to
obtain a useful amount of reaction product Seventh, the resulting
amine can be produced regioselectively and/or regiospecifically,
depending upon the design of the amine and carbonyl-portions of the
reactants. Finally, the reductive alkylation of aromatic amines
with aldehyde-containing reagents, and the reductive amination of
aldehydes with aromatic amine containing reagents, generates amine,
including secondary and tertiary amine, linkages which are stable
under biological conditions.
[0597] By way of example only, the following non-natural amino
acids may be reductively alkylated with aldehyde-containing
reagents described herein,
##STR00069##
wherein:
##STR00070##
is selected from the group consisting of a monocyclic aryl ring, a
bicyclic aryl ring, a multicyclic aryl ring, a monocyclic
heteroaryl ring, a bicyclic heteroaryl ring, and a multicyclic
heteroaryl ring; [0598] A is independently CR.sub.a, or N; [0599] B
is independently CR.sub.a, N, O, or S; [0600] each R.sub.a is
independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; and n is 0, 1, 2, 3, 4, 5, or 6; [0601] R.sub.1 is
H, an amino protecting group, resin, amino acid, polypeptide, or
polynucleotide; and [0602] R.sub.2 is OH, an ester protecting
group, resin, amino acid, polypeptide, or polynucleotide; [0603]
each of R.sub.3 and R.sub.4 is independently H, halogen, lower
alkyl, or substituted lower alkyl, or R.sub.3 and R.sub.4 or two
R.sub.3 groups optionally form a cycloalkyl or a heterocycloalkyl;
[0604] M is H or --CH.sub.2R.sub.5, or the M-N--C(R.sub.5) moiety
may form a 4 to 7 membered ring structure; [0605] R.sub.5 is alkyl,
substituted alkyl, alkenyl; substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0606] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-,
--N(R.sub.1)CO-(alkylene or substituted alkylene)-, --N(R')C(O)O--,
-(alkylene or substituted alkylene)-O--N.dbd.CR'--, -(alkylene or
substituted alkylene)-C(O)NR'-(alkylene or substituted alkylene)-,
-(alkylene or substituted alkylene)-S(O).sub.k-(alkylene or
substituted alkylene)-S--, -(alkylene or substituted
alkylene)-S--S--, --S(O).sub.kN(R')--, --N(R')C(O)N(R')--,
--N(R')C(S)N(R')--, --N(R')S(O).sub.kN(R')--, --N(R')--N.dbd.,
--C(R').dbd.N--, --C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; [0607]
or R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; and [0608] each R' is independently H, alkyl, or
substituted alkyl. Such non-natural amino acids include, but are
not limited to, the amino acids with the following structures:
##STR00071##
[0608] wherein, each A' is independently selected from CR.sub.a, N,
or
##STR00072##
and up to two A' may be
##STR00073##
[0609] with the remaining A' selected from CR.sub.a, or N. [0610]
In addition, such non-natural amino acids include, but are not
limited to, the amino acids with the following structures:
##STR00074##
[0610] wherein; G is an amine protecting group, including, but not
limited to,
##STR00075##
wherein:
##STR00076##
is selected from the group consisting of a monocyclic aryl ring, a
bicyclic aryl ring, a multicyclic aryl ring, a monocyclic
heteroaryl ring, a bicyclic heteroaryl ring, and a multicyclic
heteroaryl ring; [0611] A is independently CR.sub.a, or N; [0612] B
is independently CR.sub.a, N, O, or S; [0613] each R.sub.a is
independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; and n is 0, 1, 2, 3, 4, 5, or 6; [0614] R.sub.1 is
H, an amino protecting group, resin, amino acid, polypeptide, or
polynucleotide; and [0615] R.sub.2 is OH, an ester protecting
group, resin, amino acid, polypeptide, or polynucleotide; [0616]
each of R.sub.3 and R.sub.4 is independently H, halogen, lower
alkyl, or substituted lower alkyl, or R.sub.3 and R.sub.4 or two
R.sub.3 groups optionally form a cycloalkyl or a heterocycloalkyl;
[0617] M is H or --CH.sub.2R.sub.5; or the M-N--C(R.sub.5) moiety
may form a 4 to 7 membered ring structure; [0618] R.sub.5 is alkyl,
substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0619] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; [0620]
or R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; and [0621] each R' is independently H, alkyl, or
substituted alkyl. Such non-natural amino acids include, but are
not limited to, the amino acids with the following structures:
##STR00077##
[0621] wherein, each A' is independently selected from CR.sub.a, N,
or
##STR00078##
and up to two A' may be
##STR00079##
[0622] with the remaining A' selected from CR.sub.a, or N. Such
reductive alkylation reactions post-translationally modify aromatic
amine-containing non-natural amino acid polypeptides into
non-natural amino acid polypeptides which contain mono-alkylated or
di-alkylated aromatic amine-containing non-natural amino acids.
[0623] The types of polypeptides that comprise such aromatic
amine-containing non-natural amino acids is practically unlimited
as long as the aromatic amine-containing non-natural amino acid is
located on the polypeptide so that the aldehyde-containing reagent
can react with the aromatic amine group and not create a resulting
modified non-natural amino acid that destroys the tertiary
structure of the polypeptide (excepting, of course, if such
destruction is the purpose of the reaction).
[0624] By way of example only, the carbonyl-containing reagents
that are reactive with the aromatic amine-containing non-natural
amino acids described herein, and which can also be used to further
modify aromatic amine-containing non-natural amino acid
polypeptides, include aldehyde-containing compounds with the
following structure,
##STR00080##
wherein; [0625] R.sub.5 is alkyl, substituted alkyl, alkenyl,
substituted alkenyl, alkynyl, substituted alkynyl, alkoxy,
substituted alkoxy, alkylalkoxy, substituted alkylalkoxy,
polyalkylene oxide, substituted polyalkylene oxide, cycloalkyl,
substituted cycloalkyl, aryl, substituted aryl, heteroaryl,
substituted heteroaryl, heterocycle, substituted heterocycle,
alkaryl, substituted alkaryl, aralkyl, substituted aralkyl,
--C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2, --C(O)NHCH(R'').sub.2,
-(alkylene or substituted alkylene)-N(R'').sub.2, -(alkenylene or
substituted alkenylene)-N(R'').sub.2, -(alkylene or substituted
alkylene)-(aryl or substituted aryl), -(alkenylene or substituted
alkenylene)-(aryl or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0626] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof, and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; each
R' is independently H, alkyl, or substituted alkyl.
[0627] In addition, by way of example only, the carbonyl-containing
reagents that are reactive with the aromatic amine-containing
non-natural amino acids described herein and which can be used to
further modify aromatic amine-containing non-natural amino acid
polypeptides, are dicarbonyl-containing compounds, including
diketones, ketoaldehydes and dialdehydes, with the following
structures,
##STR00081##
wherein; [0628] each R.sub.1 is independently selected from H,
optionally substituted alkyl, optionally substituted alkene,
optionally substituted alkyne, optionally substituted cycloalkyl,
optionally substituted heterocycle, optionally substituted aryl, or
optionally substituted heteroaryl; [0629] R.sub.5 is alkylene,
substituted alkylene, alkenylene, substituted alkenylene,
alkynylene, substituted alkynylene, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkylene, substituted cycloalkylene,
arylene, substituted arylene, heteroarylene, substituted
heteroarylene, heterocycloalkylene, substituted
heterocycloalkylene, --C(O)R''--, --C(O)OR''--, --C(O)N(R'')--,
-(alkylene or substituted alkylene)-N(R'')--, --(alkenylene or
substituted alkenylene)-N(R'')--, -(alkylene or substituted
alkylene)-ON(R'')--, -(alkylene or substituted
alkylene)-C(O)SR''--, wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, substituted alkylene, alkenylene, substituted
alkenylene, alkynylene, substituted alkynylene, aryl, substituted
aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted
heterocycle, alkaryl, substituted alkaryl, aralkyl, or substituted
aralkyl; [0630] or R.sub.5 is L-X, where, X is a selected from the
group consisting of a label; a dye; a polymer; a water-soluble
polymer; a derivative of polyethylene glycol; a photocrosslinker; a
cytotoxic compound; a drug; an affinity label; a photoaffinity
label; a reactive compound; a resin; a second protein or
polypeptide or polypeptide analog; an antibody or antibody
fragment; a metal chelator; a cofactor; a fatty acid; a
carbohydrate; a polynucleotide; a DNA; a RNA; an antisense
polynucleotide; a saccharide, a water-soluble dendrimer, a
cyclodextrin, a biomaterial; a nanoparticle; a spin label; a
fluorophore, a metal-containing moiety; a radioactive moiety; a
novel functional group; a group that covalently or noncovalently
interacts with other molecules; a photocaged moiety; an actinic
radiation excitable moiety; a ligand; a photoisomerizable moiety;
biotin; a biotin analogue; a moiety incorporating a heavy atom; a
chemically cleavable group; a photocleavable group; an elongated
side chain; a carbon-linked sugar; a redox-active agent; an amino
thioacid; a toxic moiety; an isotopically labeled moiety; a
biophysical probe; a phosphorescent group; a chemiluminescent
group; an electron dense group; a magnetic group; an intercalating
group; a chromophore; an energy transfer agent; a biologically
active agent; a detectable label; a small molecule; an inhibitory
ribonucleic acid; a radionucleotide; a neutron-capture agent; a
derivative of biotin; quantum dot(s); a nanotransmitter; a
radiotransmitter; an abzyme, an activated complex activator, a
virus, an adjuvant, an aglycan, an allergan, an angiostatin, an
antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a
shuttle vector, a macromolecule, a mimotope, a receptor, a reverse
micelle, and any combination thereof; and L is optional, and when
present is a linker selected from the group consisting of alkylene,
substituted alkylene, alkenylene, substituted alkenylene, --O--,
--O-(alkylene or substituted alkylene)-, -(alkylene or substituted
alkylene)-O--, --C(O)--, --C(O)-(alkylene or substituted
alkylene)-, -(alkylene or substituted alkylene)-C(O)--,
--C(O)N(R')--, --C(O)N(R')-(alkylene or substituted alkylene)-,
-(alkylene or substituted alkylene)-C(O)N(R'), --OC(O)N(R')--,
--OC(O)N(R')-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-OC(O)N(R')--, --N(R')C(O)--,
--NR'C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-NR'C(O)--, --S--, --S-(alkylene or
substituted alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; each
R' is independently H, alkyl, or substituted alkyl; n is 1, 2, or
3.
[0631] The types of carbonyl-containing reagents which can react
with aromatic amine-containing non-natural amino acids is
practically unlimited as long as the aromatic amine-containing
non-natural amino acid is located on the polypeptide so that the
carbonyl-containing reagent can react with the aromatic amine group
and not create a resulting modified non-natural amino acid that
destroys the tertiary structure of the polypeptide (excepting, of
course, if such destruction is the purpose of the reaction). Such
carbonyl-containing reagents include, but are not limited to,
reagents containing at least one aldehyde moiety and reagents
containing at least two aldehyde moieties.
[0632] Additionally, the reaction between an aldehyde moiety and an
aromatic amine moiety is facile and such reductive alkylation
reactions have at least one of the following characteristics: (i)
occurs in a pH range of about 4 to about 7, (ii) generates an amine
linkage which is stable under biological conditions; (iii) is
site-specific; (iv) does not irreversibly destroy the tertiary
structure of a polypeptide; (v) occurs rapidly at room temperature;
(vi) occurs readily is aqueous conditions; (vii) occurs readily
when the ratio of the non-natural amino acid comprising the
aromatic amine moiety to the aldehyde-containing reactant is
stoichiometric, stoichiometric-like or near stoichiometric; and
(viii) is regioselective and/or regiospecific. The orthogonal
nature of the reductive alkylation reactions results in the
regioselectivity and/or regiospecificity, thereby allowing for site
specific post-translational modification of non-natural amino acid
polypeptides without affecting other amino acids in polypeptide
containing the non-natural amino acid(s).
[0633] Illustrative embodiments of methods for reductively
alkylating an aromatic amine-containing non-natural amino acid in a
polypeptide are presented in FIGS. 20-34. Certain embodiments,
include a single reductive alkylation of an aromatic
amine-containing non-natural amino acid on a polypeptide with a
carbonyl-containing reagent, including an aldehyde-containing
reagent, producing a secondary amine moiety, whereas other
embodiments include two reductive alkylations of an aromatic
amine-containing non-natural amino acid on a polypeptide with a
carbonyl-containing reagent, including an aldehyde-containing
reagent, producing a tertiary amine moiety. Additionally, certain
embodiments include a single reductive alkylation of an aromatic
amine-containing non-natural amino acid on a polypeptide with a
reagent containing at least two carbonyl groups, thereby producing
a secondary amine moiety. Still other embodiments include double
reductive alkylations of an aromatic amine-containing non-natural
amino acid on a polypeptide with a reagent containing at least two
carbonyl groups, thereby producing a tertiary amine moiety. In
these illustrative embodiments, an aldehyde-containing reagent is
added to a buffered solution (pH of about 4 to about 7) of an
aromatic amine-containing non-natural amino acid polypeptide and a
reducing agent such as, by way of example only, sodium
cyanoborohydride. The reaction proceeds at ambient temperature, and
the resulting alkylated aromatic amine-containing non-natural amino
acid polypeptide may be purified by HPLC, FPLC or size-exclusion
chromatography.
[0634] In other embodiments, multiple linker chemistries can react
site-specifically with an aromatic amine-containing non-natural
amino acid polypeptide. In one embodiment, the linker methods
described herein utilize linkers containing the carbonyl
functionality, including an aldehyde functionality, on at least one
linker termini (mono, bi- or multi-functional). The reductive
alkylation of an aromatic amine-containing polypeptide with an
aldehyde-derivatized linker generates a stable amine linkage. Bi-
and/or multi-functional linkers, also known as heterofunctional
linkers (e.g., carbonyl, including an aldehyde, with one, or more,
other linking chemistries) allow the site-specific connection of
different molecules (e.g., other polypeptides, polynucleic acids,
polymers or small molecules) to the non-natural amino acid
polypeptide, while mono-functional linkers, also known as
homofunctional linkers (carbonyl-substituted, including aldehyde
substituted, on all termini) facilitate the site-specific dimer- or
oligomerization of the aromatic amine non-natural amino acid
polypeptide. By combining this linker strategy with the in vivo
translation technology described herein, it becomes possible to
specify the three-dimensional structures of chemically-elaborated
proteins.
B. Methods for Post-Translationally Modifying Non-Natural Amino
Acid Polypeptides Using Two Post-Translational Modification Steps:
Formation of Aromatic Amine-Containing Non-Natural Amino Acids
Followed by Reductive Alkylation Reactions of Aromatic
Amine-Containing Non-Natural Amino Acids with Carbonyl-Containing
Reagents
[0635] Aromatic amine-containing amino acids can be translationally
incorporated into polypeptides prior to reductive alkylation with
carbonyl-containing reagents, including aldehyde-containing
reagents. Alternatively, precursors of aromatic amine-containing
amino acids, such as amino acids containing substituted aromatic
moieties, can be translationally incorporated into polypeptides and
subsequently transformed into aromatic amine-containing amino acids
prior to reductive alkylation with carbonyl-containing reagents.
The latter method involves two post-translational modifications,
whereas the former involves only a single post-translational
modification. The methods for derivatizing and/or further modifying
may be conducted with naturally generated polypeptides or
chemically synthesized polypeptides which may be purified prior to,
or after, these modification methods. In addition, the methods for
derivatizing and/or further modifying may be conducted with on
synthetic polymers, polysaccharides, or polynucleotides which may
be purified prior to, or after, these modification methods.
[0636] By way of example only, the following non-natural amino
acids can be reduced to generate aromatic amine-containing amino
acids,
##STR00082##
wherein:
##STR00083##
is selected from the group consisting of a monocyclic aryl ring, a
bicyclic aryl ring, a multicyclic aryl ring, a monocyclic
heteroaryl ring, a bicyclic heteroaryl ring, and a multicyclic
heteroaryl ring; [0637] A is independently CR.sub.a, or N; [0638] B
is independently CR.sub.a, N, O, or S; [0639] each R.sub.a is
independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; and n is 0, 1, 2, 3, 4, 5, or 6; [0640] R.sub.1 is
H, an amino protecting group, resin, amino acid, polypeptide, or
polynucleotide; and [0641] R.sub.2 is OH, an ester protecting
group, resin, amino acid, polypeptide, or polynucleotide; [0642]
each of R.sub.3 and R.sub.4 is independently H, halogen, lower
alkyl, or substituted lower alkyl, or R.sub.3 and R.sub.4 or two
R.sub.3 groups optionally form a cycloalkyl or a heterocycloalkyl;
[0643] Y is --NH--NH.sub.2, --NH--NHR', --CR'.dbd.NR', --NO.sub.2,
or --N.sub.3, and [0644] each R' is independently H, alkyl, or
substituted alkyl. Such non-natural amino acids include, but are
not limited to, the amino acids with the following structure:
##STR00084##
[0645] Illustrative embodiments for reductively generating an
aromatic amine-containing non-natural amino acid on a natural
polypeptide, synthetic polymer, polysaccharide, polynucleotide or
chemically synthesized polypeptide are presented in FIGS. 14 and
15. Certain embodiments include reduction of imine substituents
into aromatic primary amine-containing non-natural amino acids,
imine substituents into aromatic secondary amine-containing
non-natural amino acids, reduction of hydrazine amine substituents
into aromatic primary amine-containing non-natural amino acids,
reduction of hydrazine amine substituents into aromatic secondary
amine-containing non-natural amino acids, reduction of
nitro-substituents into aromatic primary amine-containing
non-natural amino acids, and reduction of azido-substituents into
aromatic primary amine-containing non-natural amino acids. In these
illustrative embodiments, substituted aromatic moieties are reduced
in a buffered solution (pH of about 4 to about 7), and the reducing
agents used includes, but is not limited to, TCEP, Na.sub.2S,
Na.sub.2S.sub.2O.sub.4, LiAlH.sub.4, B.sub.2H.sub.6, NaBH.sub.4 or
NaBCNH.sub.3. The reaction proceeds at ambient temperature and the
resulting aromatic amine-containing non-natural amino acid natural
polypeptide, synthetic polymer, polysaccharide, polynucleotide or
chemically synthesized polypeptide may be purified by HPLC, FPLC or
size-exclusion chromatography.
[0646] Reductive alkylation of such aromatic amine-containing amino
acid generated from the reduction of substituted aromatic
moiety-containing amino acids is as described in section A: Methods
for Post-Translationally Modifying Non-Natural Amino Acid
Polypeptides using a Single Post-Translational Modification Step:
Reductive Alkylation Reactions of Aromatic Amine-Containing
Non-Natural Amino Acids with Aldehyde-Containing Reagents.
Illustrative embodiments of reductive alkylation of aromatic
amine-containing amino acid generated by reductions of a protected
(or masked) amine is presented in FIGS. 15 and 34. The reductive
alkylation step follows the first post-translational step which
reductively generates aromatic amine-containing non-natural amino
acids on polypeptides The reductive alkylations are the second
post-translationally reactions which thereby modify aromatic
amine-containing non-natural amino acid polypeptides into
non-natural amino acid polypeptides with alkylated aromatic
amine-containing non-natural amino acids. Such post-translational
modifications or post incorporation modifications may also be
applied to aromatic amine containing amino acids incorporated into
on synthetic polymers, polysaccharides, polynucleotides or
chemically synthesized polypeptides.
[0647] The types of polypeptides that comprise such aromatic
amine-containing non-natural amino acids is practically unlimited
as long as the aromatic amine-containing non-natural amino acid is
located on the polypeptide so that the carbonyl-containing reagent,
including aldehyde-containing reagents, can react with the aromatic
amine group and not create a resulting modified non-natural amino
acid that destroys the tertiary structure of the polypeptide
(excepting, of course, if such destruction is the purpose of the
reaction).
[0648] By way of example only, the aldehyde-containing reagents
that are reactive with the aromatic amine-containing non-natural
amino acids described herein, and can also be used to further
modify aromatic amine-containing non-natural amino acid
polypeptides are compounds with the following structure,
##STR00085##
wherein; [0649] R.sub.5 is alkyl, substituted alkyl, alkenyl,
substituted alkenyl, alkynyl, substituted alkynyl, alkoxy,
substituted alkoxy, alkylalkoxy, substituted alkylalkoxy,
polyalkylene oxide, substituted polyalkylene oxide, cycloalkyl,
substituted cycloalkyl, aryl, substituted aryl, heteroaryl,
substituted heteroaryl, heterocycle, substituted heterocycle,
alkaryl, substituted alkaryl, aralkyl, substituted aralkyl,
--C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2, --C(O)NHCH(R'').sub.2,
-(alkylene or substituted alkylene)-N(R'').sub.2, -(alkenylene or
substituted alkenylene)-N(R'').sub.2, -(alkylene or substituted
alkylene)-(aryl or substituted aryl), -(alkenylene or substituted
alkenylene)-(aryl or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0650] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-,-(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; each
R' is independently H, alkyl, or substituted alkyl.
[0651] In addition, by way of example only, the carbonyl-containing
reagents that are reactive with the aromatic amine-containing
non-natural amino acids described herein and which can be used to
further modify aromatic amine-containing non-natural amino acid
polypeptides, are dicarbonyl-containing compounds, including
diketones, ketoaldehydes and dialdehydes, with the following
structures,
##STR00086##
wherein; [0652] each R.sub.1 is independently selected from H,
optionally substituted alkyl, optionally substituted alkene,
optionally substituted alkyne, optionally substituted cycloalkyl,
optionally substituted heterocycle, optionally substituted aryl, or
optionally substituted heteroaryl; [0653] R.sub.5 is alkylene,
substituted alkylene, alkenylene, substituted alkenylene,
alkynylene, substituted alkynylene, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkylene, substituted cycloalkylene,
arylene, substituted arylene, heteroarylene, substituted
heteroarylene, heterocycloalkylene, substituted
heterocycloalkylene, --C(O)R''--, --C(O)OR''--, --C(O)N(R'')--,
-(alkylene or substituted alkylene)-N(R'')--, -(alkenylene or
substituted alkenylene)-N(R'')--, -(alkylene or substituted
alkylene)-ON(R'')--, -(alkylene or substituted
alkylene)-C(O)SR''--, wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, substituted alkylene, alkenylene, substituted
alkenylene, alkynylene, substituted alkynylene, aryl, substituted
aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted
heterocycle, alkaryl, substituted alkaryl, aralkyl, or substituted
aralkyl; [0654] or R.sub.5 is L-X, where, X is a selected from the
group consisting of a label; a dye; a polymer; a water-soluble
polymer; a derivative of polyethylene glycol; a photocrosslinker; a
cytotoxic compound; a drug; an affinity label; a photoaffinity
label; a reactive compound; a resin; a second protein or
polypeptide or polypeptide analog; an antibody or antibody
fragment; a metal chelator; a cofactor; a fatty acid; a
carbohydrate; a polynucleotide; a DNA; a RNA; an antisense
polynucleotide; a saccharide, a water-soluble dendrimer, a
cyclodextrin, a biomaterial; a nanoparticle; a spin label; a
fluorophore, a metal-containing moiety; a radioactive moiety; a
novel functional group; a group that covalently or noncovalently
interacts with other molecules; a photocaged moiety; an actinic
radiation excitable moiety; a ligand; a photoisomerizable moiety;
biotin; a biotin analogue; a moiety incorporating a heavy atom; a
chemically cleavable group; a photocleavable group; an elongated
side chain; a carbon-linked sugar; a redox-active agent; an amino
thioacid; a toxic moiety; an isotopically labeled moiety; a
biophysical probe; a phosphorescent group; a chemiluminescent
group; an electron dense group; a magnetic group; an intercalating
group; a chromophore; an energy transfer agent; a biologically
active agent; a detectable label; a small molecule; an inhibitory
ribonucleic acid; a radionucleotide; a neutron-capture agent; a
derivative of biotin; quantum dot(s); a nanotransmitter; a
radiotransmitter; an abzyme, an activated complex activator, a
virus, an adjuvant, an aglycan, an allergan, an angiostatin, an
antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a
shuttle vector, a macromolecule, a mimotope, a receptor, a reverse
micelle, and any combination thereof; and L is optional, and when
present is a linker selected from the group consisting of alkylene,
substituted alkylene, alkenylene, substituted alkenylene, --O--,
--O-(alkylene or substituted alkylene)-, -(alkylene or substituted
alkylene)-O--, --C(O)--, --C(O)-(alkylene or substituted
alkylene)-, -(alkylene or substituted alkylene)-C(O)--,
--C(O)N(R')--, --C(O)N(R')-(alkylene or substituted alkylene)-,
-(alkylene or substituted alkylene)-C(O)N(R'), --OC(O)N(R')--,
--OC(O)N(R')-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-OC(O)N(R')--, --N(R')C(O)--,
--NR'C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-NR'C(O)--, --S--, --S-(alkylene or
substituted alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; each
R' is independently H, alkyl, or substituted alkyl; n is 1, 2, or
3.
[0655] The types of carbonyl-containing reagents which can react
with aromatic amine-containing non-natural amino acids is
practically unlimited as long as the aromatic amine-containing
non-natural amino acid is located on the polypeptide so that the
carbonyl-containing reagent, including aldehyde-containing
reagents, can react with the aromatic amine group and not create a
resulting modified non-natural amino acid that destroys the
tertiary structure of the polypeptide (excepting, of course, if
such destruction is the purpose of the reaction). Such
carbonyl-containing reagents include, but are not limited to,
reagents containing at least one carbonyl moiety and/or reagents
containing at least two carbonyl moieties.
[0656] Additionally, the reaction between an carbonyl moiety, by
way of example only an aldehyde moiety, and an aromatic amine
moiety is facile and such reductive alkylation reactions have at
least one of the following characteristics: (i) occurs in a pH
range of about 4 to about 7, (ii) generates an amine linkage which
is stable under biological conditions; (iii) is site-specific; (iv)
does not irreversibly destroy the tertiary structure of a
polypeptide; (v) occurs rapidly at room temperature; (vi) occurs
readily is aqueous conditions; (vii) occurs readily when the ratio
of the non-natural amino acid comprising the aromatic amine moiety
to the aldehyde-containing reactant is stoichiometric,
stoichiometric-like or near stoichiometric; and (viii) is
regioselective and/or regiospecific. The orthogonal nature of the
reductive alkylation reactions results in the regioselectivity
and/or regiospecificity, thereby allowing for site specific
post-translational modification of non-natural amino acid
polypeptides without affecting other amino acids in the non-natural
amino acid polypeptide.
[0657] Certain embodiments, include a single reductive alkylation
of the aromatic amine moiety with a carbonyl-containing reagent
producing a secondary amine moiety, whereas other embodiments
include two reductive alkylations of the aromatic amine moiety with
two carbonyl-containing reagents producing a tertiary amine moiety.
The carbonyl-containing reagents in this embodiment may be
identical or different. Additionally, certain embodiments include a
single reductive alkylation of the aromatic amine moiety with a
reagent containing at least two carbonyl groups, thereby producing
a secondary amine moiety. Still other embodiments include two
reductive alkylations, also referred to as double reductive
alkylation, of the aromatic amine moiety with a reagent containing
at least two carbonyl groups, thereby producing a cyclic, tertiary
amine moiety. In these illustrative embodiments, the
carbonyl-containing reagent is added to a buffered solution (pH of
about 4 to about 7) of the aromatic amine-containing non-natural
amino acid on a natural polypeptide, synthetic polymer,
polysaccharide, polynucleotide or chemically synthesized
polypeptide and a reducing agent such as, by way of example only,
NaBCNH.sub.3, TCEP, Na.sub.2S, Na.sub.2S.sub.2O.sub.4, LiAlH.sub.4,
B.sub.2H.sub.6, and NaBH.sub.4. The reaction proceeds at ambient
temperature and the resulting alkylated aromatic amine-containing
non-natural amino acid polypeptide may be purified by HPLC, FPLC or
size-exclusion chromatography.
[0658] In other embodiments, multiple linker chemistries can react
site-specifically with an aromatic amine-containing non-natural
amino acid polypeptide. In one embodiment, the linker methods
described herein utilize linkers containing the carbonyl
functionality, including aldehyde functionality, on at least one
linker termini (mono, bi- or multi-functional). The reductive
alkylation of a carbonyl-derivatized linker with an aromatic
amine-containing polypeptide generates a stable amine linkage. Bi-
and/or multi-functional linkers, also known as heterofunctional
linkers (e.g., aldehyde with one, or more, other linking
chemistries) allow the site-specific connection of different
molecules (e.g., other polypeptides, polynucleic acids, polymers or
small molecules) to the non-natural amino acid polypeptide, while
mono-functional linkers, also known as homofunctional linkers (e.g.
aldehyde-substituted on all termini) facilitate the site-specific
dimer- or oligomerization of the aromatic amine non-natural amino
acid polypeptide. By combining this linker strategy with the in
vivo translation technology described herein, it becomes possible
to specify the three-dimensional structures of
chemically-elaborated polypeptides.
C. Methods for Post-Translationally Modifying Non-Natural Amino
Acid Polypeptides using a Two Post-Translational Modification
Steps: Deprotection of Protected Aldehyde-Containing Non-Natural
Amino Acids Followed by Reductive Amination of the
Aldehyde-Containing Non-Natural Amino Acids with Aromatic
Amine-Containing Reagents
[0659] The incorporation of non-natural amino acids with masked or
protected electrophilic-containing sidechain, into polypeptides
allows for site-specific reductive amination of the sidechains.
Such non-natural amino acids include masked or protected carbonyl
groups, such as, by way of example only, amino acids containing
masked aldehyde groups or protected aldehyde groups, and wherein
the site-specific reductive amination is accomplished, upon
unmasking or deprotection of the aldehyde, via nucleophilic
addition of an aromatic amine to the available aldehyde-containing
sidechain. This reductive amination reaction generates an amine
linkage, including secondary and tertiary amines. The methods for
derivatizing and/or further modifying may be conducted with
naturally generated polypeptides or chemically synthesized
polypeptides which have been purified prior to the reductive
amination step or after the reductive amination step. In addition,
the methods for derivatizing and/or further modifying may be
conducted with on synthetic polymers, polysaccharides, or
polynucleotides which may be purified prior to, or after, these
modification methods.
[0660] By way of example only, the following non-natural amino
acids are the type of masked/protected aldehyde moiety-containing
amino acids which may be incorporated into polypeptides, then
unmasked/deprotected prior to reductively aminated the available
aldehyde containing sidechain to generate an amine linkage.
##STR00087##
wherein: [0661] L is optional, and when present is lower alkylene,
substituted lower alkylene, lower cycloalkylene, substituted lower
cycloalkylene, lower alkenylene, substituted lower alkenylene,
alkynylene, lower heteroalkylene, substituted heteroalkylene, lower
heterocycloalkylene, substituted lower heterocycloalkylene,
arylene, substituted arylene, heteroarylene, substituted
heteroarylene, alkarylene, substituted alkarylene, aralkylene, or
substituted aralkylene; [0662] Q is optional, and when present is a
linker selected from the group consisting of lower alkylene,
substituted lower alkylene, lower alkenylene, substituted lower
alkenylene, lower heteroalkylene, substituted lower heteroalkylene,
--O-(alkylene or substituted alkylene)-, --S-(alkylene or
substituted alkylene)-, where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(O)-(alkylene
or substituted alkylene)-, --C(S)-(alkylene or substituted
alkylene)-, --NR'-(alkylene or substituted alkylene)-,
--CON(R'')-(alkylene or substituted alkylene)-, --CSN(R')-(alkylene
or substituted alkylene)-, --N(R')CO-(alkylene or substituted
alkylene)-, and where each R' is independently H, alkyl, or
substituted alkyl; [0663] R.sub.1 is H, an amino protecting group,
resin, amino acid, polypeptide, or polynucleotide; and [0664]
R.sub.2 is OH, an ester protecting group, resin, amino acid,
polypeptide, or polynucleotide; [0665] each of R.sub.3 and R.sub.4
is independently H, halogen, lower alkyl, or substituted lower
alkyl, or R.sub.3 and R.sub.4 or two R.sub.3 groups optionally form
a cycloalkyl or a heterocycloalkyl; [0666] each R.sub.a is
independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; [0667] R.sub.6 is a protected aldehyde or a masked
aldehyde, wherein the protecting group includes, but is not limited
to,
##STR00088##
[0667] where each X.sub.1 is independently selected from the group
consisting of --O--, --S--, --N(H)--, --N(R)--, --N(Ac)--, and
--N(OMe)-; X.sub.2 is --OR, --OAc, --SR, --N(R).sub.2, --N(R)(Ac),
--N(R)(OMe), or N.sub.3, and where each R' and R is independently
H, alkyl, or substituted alkyl. Such non-natural amino acids may
also be in the form of a salt, or may be incorporated into a
non-natural amino acid polypeptide, polymer, or a polynucleotide.
Such non-natural amino acids may also be incorporated into a
non-natural amino acid polypeptide and then post-translationally
modified by deprotecting to form an aldehyde group "in-situ"
followed by reductive amination of the aldehyde with an aromatic
amine containing reagent. In addition, non-natural amino acids
having the structure of Formula (E) may also be incorporated into a
polymer or a polynucleotide and are deprotecting to form an
aldehyde group "in-situ" followed by reductive amination of the
aldehyde with an aromatic amine containing reagent.
[0668] By way of example only, the aromatic amine-containing
reagents which are reactive with the unmasked/deprotected
aldehyde-containing non-natural amino acids described herein are
compounds with the following structure:
##STR00089##
wherein,
##STR00090##
is selected from the group consisting of a monocyclic aryl ring, a
bicyclic aryl ring, a multicyclic aryl ring, a monocyclic
heteroaryl ring, a bicyclic heteroaryl ring, and a multicyclic
heteroaryl ring; [0669] A is independently CR.sub.a, or N; [0670] B
is independently CR.sub.a, N, O, or S; [0671] each R.sub.a is
independently selected from the group consisting of H, halogen,
alkyl, --NO.sub.2, --CN, substituted alkyl, --N(R').sub.2,
--C(O).sub.kR', --C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where
k is 1, 2, or 3; n is 0, 1, 2, 3, 4, 5, or 6; [0672] M is H or
--CH.sub.2R.sub.5; [0673] R.sub.5 is alkyl, substituted alkyl,
alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy,
substituted alkoxy, alkylalkoxy, substituted alkylalkoxy,
polyalkylene oxide, substituted polyalkylene oxide, cycloalkyl,
substituted cycloalkyl, aryl, substituted aryl, heteroaryl,
substituted heteroaryl, heterocycle, substituted heterocycle,
alkaryl, substituted alkaryl, aralkyl, substituted aralkyl,
--C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2, --C(O)NHCH(R'').sub.2,
-(alkylene or substituted alkylene)-N(R'').sub.2, -(alkenylene or
substituted alkenylene)-N(R'').sub.2, -(alkylene or substituted
alkylene)-(aryl or substituted aryl), -(alkenylene or substituted
alkenylene)-(aryl or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0674] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O)-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; each
R' is independently H, alkyl, or substituted alkyl. Such reagents
include compounds having the following structures,
##STR00091##
[0674] These compounds may also be used to further modify
aldehyde-containing non-natural amino acid polypeptides (naturally
or chemically synthesized), synthetic polymers, polysaccharides, or
polynucleotides.
[0675] These reductive amination reactions post-translationally
modify unmasked/deprotected aldehyde-containing non-natural amino
acid polypeptides into non-natural amino acid polypeptides which
contain aromatic amine-containing non-natural amino acid. The types
of polypeptides that comprise such aromatic amine-containing
non-natural amino acids is practically unlimited as long as the
unmasked/deprotected aldehyde-containing non-natural amino acid is
located on the polypeptide such that the aromatic amine-containing
reagent can react with the available aldehyde group and not create
a resulting modified non-natural amino acid that destroys the
tertiary structure of the polypeptide (excepting, of course, if
such destruction is the purpose of the reaction).
[0676] Additionally, the reaction between an aldehyde moiety and an
aromatic amine moiety is facile and such reductive amination
reactions have at least one of the following characteristics: (i)
occurs in a pH range of about 4 to about 7, (ii) generates an amine
linkage which is stable under biological conditions; (iii) is
site-specific; (iv) does not irreversibly destroy the tertiary
structure of a polypeptide; (v) occurs rapidly at room temperature;
(vi) occurs readily is aqueous conditions; (vii) occurs readily
when the ratio of the non-natural amino acid comprising the
aldehyde moiety to the aromatic amine-containing reactant is
stoichiometric, stoichiometric-like or near stoichiometric; and
(viii) is regioselective and/or regiospecific. The orthogonal
nature of the reductive amination reactions results in the
regioselectivity and/or regiospecificity, thereby allowing for site
specific post-translational modification of non-natural amino acid
polypeptides without affecting other amino acids in the non-natural
amino acid polypeptide.
[0677] An illustrative embodiment of reductively aminating an
unmasked or deprotected aldehyde-containing non-natural amino acid
on a polypeptide is presented in FIG. 18. In addition, certain
embodiments include a single reductive amination of an unmasked or
deprotected aldehyde-containing non-natural amino acid on a
polypeptide with an aromatic amine-containing reagent, thereby
producing a secondary amine moiety. Additionally, certain
embodiments include a reductive amination of a carbonyl-containing
non-natural amino acid on a polypeptide, in which the carbonyl
moiety contains at least two unmasked or deprotected aldehyde
groups, with an aromatic amine-containing reagent, thereby
producing a cyclic tertiary amine moiety. Still other embodiments
include two reductive aminations of an unmasked or deprotected
aldehyde-containing non-natural amino acid on a polypeptide
containing at least two aldehyde groups, with two identical or two
different aromatic amine-containing reagents thereby producing two
secondary amine moieties. In these illustrative embodiments, an
aromatic amine-containing reagent is added to a buffered solution
(pH of about 4 to about 7) of an unmasked or deprotected
aldehyde-containing non-natural amino acid polypeptide and a
reducing agent such as, by way of example only, TCEP, Na.sub.2S,
Na.sub.2S.sub.2O.sub.4, LiAlH.sub.4, B.sub.2H.sub.6, NaBH.sub.4 or
NaBCNH.sub.3. The reaction proceeds at ambient temperature and the
resulting aminated aldehyde-containing non-natural amino acid
polypeptide may be purified by HPLC, FPLC or size-exclusion
chromatography.
[0678] In other embodiments, multiple linker chemistries can react
site-specifically with an unmasked or deprotected
aldehyde-containing non-natural amino acid polypeptide. In one
embodiment, the linker methods described herein utilize linkers
containing the aromatic amine functionality on at least one linker
termini (mono, bi- or multi-functional). The reductive amination of
an aromatic amine-derivatized linker with an unmasked or
deprotected aldehyde-containing polypeptide generates a stable
amine linkage. Bi- and/or multi-functional linkers, also known as
heterofunctional linkers (e.g., aromatic amine with one, or more,
other linking chemistries) allow the site-specific connection of
different molecules (e.g., other polypeptides, polynucleic acids,
polymers or small molecules) to the non-natural amino acid
polypeptide, while mono-functional linkers, also known as
homofunctional linkers (aromatic amine-substituted on all termini)
facilitate the site-specific dimer- or oligomerization of the
unmasked or deprotected aldehyde-containing non-natural amino acid
polypeptide. By combining this linker strategy with the in vivo
translation technology described herein, it becomes possible to
specify the three-dimensional structures of chemically-elaborated
proteins.
D. Example of Adding Functionality Macromolecular Polymers Coupled
to Non-Natural Amino Acid Polypeptides
[0679] Various modifications to the non-natural amino acid
polypeptides described herein can be effected using the
compositions, methods, techniques and strategies described herein.
These modifications include the incorporation of further
functionality onto the non-natural amino acid component of the
polypeptide, including but not limited to, a label; a dye; a
polymer; a water-soluble polymer; a derivative of polyethylene
glycol; a photocrosslinker; a cytotoxic compound; a drug; an
affinity label; a photoaffinity label; a reactive compound; a
resin; a second protein or polypeptide or polypeptide analog; an
antibody or antibody fragment; a metal chelator; a cofactor; a
fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an
antisense polynucleotide; a saccharide, a water-soluble dendrimer,
a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a
fluorophore, a metal-containing moiety; a radioactive moiety; a
novel functional group; a group that covalently or noncovalently
interacts with other molecules; a photocaged moiety; an actinic
radiation excitable moiety; a ligand; a photoisomerizable moiety;
biotin; a biotin analogue; a moiety incorporating a heavy atom; a
chemically cleavable group; a photocleavable group; an elongated
side chain; a carbon-linked sugar; a redox-active agent; an amino
thioacid; a toxic moiety; an isotopically labeled moiety; a
biophysical probe; a phosphorescent group; a chemiluminescent
group; an electron dense group; a magnetic group; an intercalating
group; a chromophore; an energy transfer agent; a biologically
active agent; a detectable label; a small molecule; an inhibitory
ribonucleic acid; a radionucleotide; a neutron-capture agent; a
derivative of biotin; quantum dot(s); a nanotransmitter; a
radiotransmitter; an abzyme, an activated complex activator, a
virus, an adjuvant, an aglycan, an allergan, an angiostatin, an
antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a
shuttle vector, a macromolecule, a mimotope, a receptor, a reverse
micelle, and any combination thereof. As an illustrative,
non-limiting example of the compositions, methods, techniques and
strategies described herein, the following description will focus
on adding macromolecular polymers to the non-natural amino acid
polypeptide with the understanding that the compositions, methods,
techniques and strategies described thereto are also applicable
(with appropriate modifications, if necessary and for which one of
skill in the art could make with the disclosures herein) to adding
other functionalities, including but not limited to those listed
above.
[0680] A wide variety of macromolecular polymers and other
molecules can be linked to the non-natural amino acid polypeptides
described herein to modulate biological properties of the
non-natural amino acid polypeptide (or the corresponding natural
amino acid polypeptide), and/or provide new biological properties
to the non-natural amino acid polypeptide (or the corresponding
natural amino acid polypeptide). These macromolecular polymers can
be linked to the non-natural amino acid polypeptide via the
non-natural amino acid, or any functional substituent of the
non-natural amino acid, or any substituent or functional group
added to the non-natural amino acid.
[0681] Water soluble polymers can be coupled to the non-natural
amino acids incorporated into polypeptides (natural or synthetic),
polynucleotides, poly saccharides or synthetic polymers. The water
soluble polymers may be coupled via a non-natural amino acid
incorporated in the polypeptide or any functional group or
substituent of a non-natural amino acid, or any functional group or
substituent added to a non-natural amino acid. In some cases, the
non-natural amino acid polypeptides described herein comprise one
or more non-natural amino acid(s) linked to water soluble polymers
and one or more naturally-occurring amino acids coupled to water
soluble polymers. Covalent attachment of hydrophilic polymers to a
biologically active molecule represents one approach to increasing
water solubility (such as in a physiological environment),
bioavailability, increasing serum half-life, increasing therapeutic
half-life, modulating immunogenicity, modulating biological
activity, or extending the circulation time of the biologically
active molecule, including proteins, peptides, and particularly
hydrophobic molecules. Additional important features of such
hydrophilic polymers may include biocompatibility, lack of
toxicity, and lack of immunogenicity. For therapeutic use of the
end-product preparation, a pharmaceutically acceptable polymer may
be used.
[0682] Examples of hydrophilic polymers include, but are not
limited to, polyalkyl ethers and alkoxy-capped analogs thereof
(e.g., polyoxyethylene glycol, polyoxyethylene/propylene glycol,
and methoxy or ethoxy-capped analogs thereof, especially
polyoxyethylene glycol, the latter is also known as polyethylene
glycol or PEG); polyvinylpyrrolidones; polyvinylalkyl ethers;
polyoxazolines, polyalkyl oxazolines and polyhydroxyalkyl
oxazolines; polyacrylamides, polyalkyl acrylamides, and
polyhydroxyalkyl acrylamides (e.g., polyhydroxypropylmethacrylamide
and derivatives thereof); polyhydroxyalkyl acrylates; polysialic
acids and analogs thereof; hydrophilic peptide sequences;
polysaccharides and their derivatives, including dextran and
dextran derivatives, e.g., carboxymethyldextran, dextran sulfates,
aminodextran; cellulose and its derivatives, e.g., carboxymethyl
cellulose, hydroxyalkyl celluloses; chitin and its derivatives,
e.g., chitosan, succinyl chitosan, carboxymethylchitin,
carboxymethylchitosan; hyaluronic acid and its derivatives;
starches; alginates; chondroitin sulfate; albumin; pullulan and
carboxymethyl pullulan; polyaminoacids and derivatives thereof,
e.g., polyglutamic acids, polylysines, polyaspartic acids,
polyaspartamides; maleic anhydride copolymers such as: styrene
maleic anhydride copolymer, divinylethyl ether maleic anhydride
copolymer; polyvinyl alcohols; copolymers thereof; terpolymers
thereof; mixtures thereof; and derivatives of the foregoing. The
water soluble polymer may be any structural form including but not
limited to linear, forked or branched. In some embodiments, polymer
backbones that are water-soluble, with from about 2 to about 300
termini, are particularly useful. Multifunctional polymer
derivatives include, but are not limited to, linear polymers having
two termini, each terminus being bonded to a functional group which
may be the same or different. In some embodiments, the water
polymer comprises a poly(ethylene glycol) moiety. The molecular
weight of the polymer may be of a wide range, including but not
limited to, between about 100 Da and about 100,000 Da or more. The
molecular weight of the polymer may be between about 100 Da and
about 100,000 Da, including but not limited to, 100,000 Da, 95,000
Da, 90,000 Da, 85,000 Da, 80,000 Da, 75,000 Da, 70,000 Da, 65,000
Da, 60,000 Da, 55,000 Da, 50,000 Da, 45,000 Da, 40,000 Da, 35,000
Da, 30,000 Da, 25,000 Da, 20,000 Da, 15,000 Da, 10,000 Da, 9,000
Da, 8,000 Da, 7,000 Da, 6,000 Da, 5,000 Da, 4,000 Da, 3,000 Da,
2,000 Da, 1,000 Da, 900 Da, 800 Da, 700 Da, 600 Da, 500 Da, 400 Da,
300 Da, 200 Da, and 100 Da. In some embodiments, the molecular
weight of the polymer is between about 100 Da and about 50,000' Da.
In some embodiments, the molecular weight of the polymer is between
about 100 Da and about 40,000 Da. In some embodiments, the
molecular weight of the polymer is between about 1,000 Da and about
40,000 Da. In some embodiments, the molecular weight of the polymer
is between about 5,000 Da and about 40,000 Da. In some embodiments,
the molecular weight of the polymer is between about 10,000 Da and
about 40,000 Da. In some embodiments, the poly(ethylene glycol)
molecule is a branched polymer. The molecular weight of the
branched chain PEG may be between about 1,000 Da and about 100,000
Da, including but not limited to, 100,000 Da, 95,000 Da, 90,000 Da,
85,000 Da, 80,000 Da, 75,000 Da, 70,000 Da, 65,000 Da, 60,000 Da,
55,000 Da, 50,000 Da, 45,000 Da, 40,000 Da, 35,000 Da, 30,000 Da,
25,000 Da, 20,000 Da, 15,000 Da, 10,000 Da, 9,000 Da, 8,000 Da,
7,000 Da, 6,000 Da, 5,000 Da, 4,000 Da, 3,000 Da, 2,000 Da, and
1,000 Da. In some embodiments, the molecular weight of the branched
chain PEG is between about 1,000 Da and about 50,000 Da. In some
embodiments, the molecular weight of the branched chain PEG is
between about 1,000 Da and about 40,000 Da. In some embodiments,
the molecular weight of the branched chain PEG is between about
5,000 Da and about 40,000 Da. In some embodiments, the molecular
weight of the branched chain PEG is between about 5,000 Da and
about 20,000 Da. Those of ordinary skill in the art will recognize
that the foregoing list for substantially water soluble backbones
is by no means exhaustive and is merely illustrative, and that all
polymeric materials having the qualities described above are
contemplated as being suitable for use in methods and compositions
described herein.
[0683] As described above, one example of a hydrophilic polymer is
poly(ethylene glycol), abbreviated PEG, which has been used
extensively in pharmaceuticals, on artificial implants, and in
other applications where biocompatibility, lack of toxicity, and
lack of immunogenicity are of importance. The polymer:polypeptide
embodiments described herein will use PEG as an example hydrophilic
polymer with the understanding that other hydrophilic polymers may
be similarly utilized in such embodiments.
[0684] PEG is a well-known, water soluble polymer that is
commercially available or can be prepared by ring-opening
polymerization of ethylene glycol according to methods well known
in the art (Sandler and Karo, Polymer Synthesis, Academic Press,
New York, Vol. 3, pages 138-161). PEG is typically clear,
colorless, odorless, soluble in water, stable to heat, inert to
many chemical agents, does not hydrolyze or deteriorate, and is
generally non-toxic. Poly(ethylene glycol) is considered to be
biocompatible, which is to say that PEG is capable of coexistence
with living tissues or organisms without causing harm. More
specifically, PEG is substantially non-immunogenic, which is to say
that PEG does not tend to produce an immune response in the body.
When attached to a molecule having some desirable function in the
body, such as a biologically active agent, the PEG tends to mask
the agent and can reduce or eliminate any immune response so that
an organism can tolerate the presence of the agent. PEG conjugates
tend not to produce a substantial immune response or cause clotting
or other undesirable effects.
[0685] The term "PEG" is used broadly to encompass any polyethylene
glycol molecule, without regard to size or to modification at an
end of the PEG, and can be represented as linked to a non-natural
amino acid polypeptide by the formula:
XO--(CH.sub.2CH.sub.2O).sub.nCH.sub.2CH.sub.2--Y
where n is 2 to 10,000 and X is H or a terminal modification,
including but not limited to, a C.sub.1-4 alkyl, a protecting
group, or a terminal functional group. The term PEG includes, but
is not limited to, poly(ethylene glycol) in any of its forms,
including bifunctional PEG, multiarmed PEG, derivatized PEG, forked
PEG, branched PEG (with each chain having a molecular weight of
from about 1 kDa to about 100 kDa, from about 1 kDa to about 50
kDa, or from about 1 kDa to about 20 kDa), pendent PEG (i.e. PEG or
related polymers having one or more functional groups pendent to
the polymer backbone), or PEG with degradable linkages therein. In
one embodiment, PEG in which n is from about 20 to about 2000 is
suitable for use in the methods and compositions described herein.
In some embodiments, the water polymer comprises a poly(ethylene
glycol) moiety. The molecular weight of the polymer may be of a
wide range, including but not limited to, between about 100 Da and
about 100,000 Da or more. The molecular weight of the polymer may
be between about 100 Da and about 100,000 Da, including but not
limited to, 100,000 Da, 95,000 Da, 90,000 Da, 85,000 Da, 80,000 Da,
75,000 Da, 70,000 Da, 65,000 Da, 60,000 Da, 55,000 Da, 50,000 Da,
45,000 Da, 40,000 Da, 35,000 Da, 30,000 Da, 25,000 Da, 20,000 Da,
15,000 Da, 10,000 Da, 9,000 Da, 8,000 Da, 7,000 Da, 6,000 Da, 5,000
Da, 4,000 Da, 3,000 Da, 2,000 Da, 1,000 Da, 900 Da, 800 Da, 700 Da,
600 Da, 500 Da, 400 Da, 300 Da, 200 Da, and 100 Da. In some
embodiments, the molecular weight of the polymer is between about
100 Da and about 50,000 Da. In some embodiments, the molecular
weight of the polymer is between about 100 Da and about 40,000 Da.
In some embodiments, the molecular weight of the polymer is between
about 1,000 Da and about 40,000 Da. In some embodiments, the
molecular weight of the polymer is between about 5,000 Da and about
40,000 Da. In some embodiments, the molecular weight of the polymer
is between about 10,000 Da and about 40,000 Da. In some
embodiments, the poly(ethylene glycol) molecule is a branched
polymer. The molecular weight of the branched chain PEG may be
between about 1,000 Da and about 100,000 Da, including but not
limited to, 100,000 Da, 95,000 Da, 90,000 Da, 85,000 Da, 80,000 Da,
75,000 Da, 70,000 Da, 65,000 Da, 60,000 Da, 55,000 Da, 50,000 Da,
45,000 Da, 40,000 Da, 35,000 Da, 30,000 Da, 25,000 Da, 20,000 Da,
15,000 Da, 10,000 Da, 9,000 Da, 8,000 Da, 7,000 Da, 6,000 Da, 5,000
Da, 4,000 Da, 3,000 Da, 2,000 Da, and 1,000 Da. In some
embodiments, the molecular weight of the branched chain PEG is
between about 1,000 Da and about 50,000 Da. In some embodiments,
the molecular weight of the branched chain PEG is between about
1,000 Da and about 40,000 Da. In some embodiments, the molecular
weight of the branched chain PEG is between about 5,000 Da and
about 40,000 Da. In some embodiments, the molecular weight of the
branched chain PEG is between about 5,000 Da and about 20,000 Da. A
wide range of PEG molecules are described in, including but not
limited to, the Shearwater Polymers, Inc. catalog, Nektar
Therapeutics catalog, incorporated herein by reference.
[0686] Specific examples of terminal functional groups in the
literature include, but are not limited to, N-succinimidyl
carbonate (see e.g., U.S. Pat. Nos. 5,281,698, 5,468,478), amine
(see, e.g., Buckmann et al. Makromol. Chem. 182:1379 (1981),
Zalipsky et al. Eur. Polym. J. 19:1177 (1983)), hydrazide (See,
e.g., Andresz et al. Makromol. Chem. 179:301 (1978)), succinimidyl
propionate and succinimidyl butanoate (see, e.g., Olson et al. in
Poly(ethylene glycol) Chemistry & Biological Applications, pp
170-181, Harris & Zalipsky Eds., ACS, Washington, D.C., 1997;
see also U.S. Pat. No. 5,672,662), succinimidyl succinate (See,
e.g., Abuchowski et al. Cancer Biochem. Biophys. 7:175 (1984) and
Joppich et al. Makromol. Chem. 180:1381 (1979), succinimidyl ester
(see, e.g., U.S. Pat. No. 4,670,417), benzotriazole carbonate (see,
e.g., U.S. Pat. No. 5,650,234), glycidyl ether (see, e.g., Pitha et
al. Eur. J Biochem. 94:11 (1979), Elling et al., Biotech. Appl.
Biochem. 13:354 (1991), oxycarbonylimidazole (see, e.g., Beauchamp,
et al., Anal. Biochem. 131:25 (1983), Tondelli et al. J. Controlled
Release 1:251 (1985)), p-nitrophenyl carbonate (see, e.g.,
Veronese, et al., Appl. Biochem. Biotech., 11: 141 (1985); and
Sartore et al., Appl. Biochem. Biotech., 27:45 (1991)), aldehyde
(see, e.g., Harris et al. J. Polym. Sci. Chem. Ed. 22:341 (1984),
U.S. Pat. No. 5,824,784, U.S. Pat. No. 5,252,714), maleimide (see,
e.g., Goodson et al. Bio/Technology 8:343 (1990), Romani et al. in
Chemistry of Peptides and Proteins 2:29 (1984)), and Kogan,
Synthetic Comm. 22:2417 (1992)), orthopyridyldisulfide (see, e.g.,
Woghiren, et al. Bioconj. Chem. 4:314 (1993)), acrylol (see, e.g.,
Sawhney et al., Macromolecules, 26:581 (1993)), vinylsulfone (see,
e.g., U.S. Pat. No. 5,900,461). All of the above references and
patents are incorporated herein by reference.
[0687] In some cases, a PEG terminates on one end with hydroxy or
methoxy, i.e., X is H or CH.sub.3 ("methoxy PEG"). Alternatively,
the PEG can terminate with a reactive group, thereby forming a
bifunctional polymer. Typical reactive groups can include those
reactive groups that are commonly used to react with the functional
groups found in the 20 common amino acids (including but not
limited to, maleimide groups, activated carbonates (including but
not limited to, p-nitrophenyl ester); activated esters (including
but not limited to, N-hydroxysuccinimide, p-nitrophenyl ester) and
aldehydes) as well as functional groups that are inert to the 20
common amino acids but that react specifically with complementary
functional groups present in non-natural amino acids (including but
not limited to, aromatic amine groups).
[0688] It is noted that the other end of the PEG, which is shown in
the above formula by Y, will attach either directly or indirectly
to a polypeptide (synthetic or natural), polynucleotide,
polysaccharide or synthetic polymer via a non-natural amino acid.
When Y is an aldehyde group, then the aldehyde-containing PEG
reagent can react with an aromatic amine-containing non-natural
amino acid in a polypeptide to form a PEG group linked to the
polypeptide via an amine linkage. Examples of appropriate reaction
conditions, purification methods and reagents are described
throughout this specification and the accompanying Figures. FIG. 35
presents a schematic illustrating the comparison between N-terminal
PEGylation and PEGylation based on reductive alkylation of aromatic
amine moieties on amino acids which have been incorporated into
peptides. The figure illustrates that under the reaction conditions
used the PEGylation of a natural peptide is only easily achieved at
the terminal amine, whereas under the reaction conditions used for
PEGylation of non-natural peptides with incorporated non-natural
amino acids containing aromatic moieties may be achieved at the
site of incorporation of the non-natural amino acid into the
sequence, without any reaction at the protonated terminal amine.
The site of PEGylation depends on the site of incorporation of the
non-natural amino acid containing the aromatic amine moiety. Such a
site may be a terminal site, or it may be at any site within the
peptide sequence.
[0689] By way of example only and not as a limitation on the types
or classes of PEG reagents that may be used with the compositions,
methods, techniques and strategies described herein, FIG. 36
presents illustrative examples of aldehyde-containing PEG reagents
that can react with aromatic amine-containing non-natural amino
acid polypeptides to form non-natural amino acid polypeptides
linked to the PEG group via an amine linkage. Also presented in
FIG. 36 are examples of branched aldehyde-containing PEG reagents
that can react with aromatic amine-containing non-natural amino
acid polypeptides to form non-natural amino acid polypeptides
linked to PEG groups.
[0690] Heterobifunctional derivatives are also particularly useful
when it is desired to attach different molecules to each terminus
of the PEG polymer. In some embodiments, one end of the PEG
contains an aldehyde moiety which can react with an aromatic amine
group present in a non-natural amino acid to form an amine linkage
between the PEG and the peptide, while the other end of the PEG
contains other functionality which may undergo further reaction by
treatment with an appropriate agent. By way of example such
functionality may be an amine group available to act as a
nucleophile on a variety of electrophiles, including carbonyl
containing reagents.
[0691] Thus, in some embodiments, the polypeptide comprising the
non-natural amino acid is linked to a water soluble polymer, such
as polyethylene glycol (PEG), via the side chain of the non-natural
amino acid. The non-natural amino acid methods and compositions
described herein provide a highly efficient method for the
selective modification of proteins with PEG derivatives, which
involves the selective incorporation of non-natural amino acids,
including but not limited to, those amino acids containing
functional groups or substituents not found in the 20 naturally
incorporated amino acids, into proteins in response to a selector
codon and the subsequent modification of those amino acids with a
suitably reactive PEG derivative. Known chemistry methodologies of
a wide variety are suitable for use with the non-natural amino acid
methods and compositions described herein to incorporate a water
soluble polymer into the protein.
[0692] The polymer backbone can be linear or branched. Branched
polymer backbones are generally known in the art. Typically, a
branched polymer has a central branch core moiety and a plurality
of linear polymer chains linked to the central branch core. PEG is
used in branched forms that can be prepared by addition of ethylene
oxide to various polyols, such as glycerol, glycerol oligomers,
pentaerythritol and sorbitol. The central branch moiety can also be
derived from several amino acids, such as lysine. The branched
poly(ethylene glycol) can be represented in general form as
R(--PEG-OH).sub.m in which R is derived from a core moiety, such as
glycerol, glycerol oligomers, or pentaerythritol, and m represents
the number of arms. Multi-armed PEG molecules, such as those
described in U.S. Pat. Nos. 5,932,462 5,643,575; 5,229,490;
4,289,872; U.S. Pat. Appl. 2003/0143596; WO 96/21469; and WO
93/21259, each of which is incorporated by reference herein in its
entirety, can also be used as the polymer backbone.
[0693] Branched PEG can also be in the form of a forked PEG
represented by PEG(-YCHZ.sub.2).sub.n, where Y is a linking group
and Z is an activated terminal group linked to CH by a chain of
atoms of defined length. Yet another branched form, the pendant
PEG, has reactive groups, such as carboxyl, along the PEG backbone
rather than at the end of PEG chains. FIG. 36 shows non-limiting
examples of branched aldehyde-containing PEG reagents used in the
methods described herein.
[0694] In addition to these forms of PEG, the polymer can also be
prepared with weak or degradable linkages in the backbone. For
example, PEG can be prepared with ester linkages in the polymer
backbone that are subject to hydrolysis. As shown below, this
hydrolysis results in cleavage of the polymer into fragments of
lower molecular weight:
--PEG-CO.sub.2--PEG-+H.sub.2O.fwdarw.PEG-CO.sub.2H+HO-PEG-
It is understood by those skilled in the art that the term
poly(ethylene glycol) or PEG represents or includes all the forms
known in the art including but not limited to those disclosed
herein. The molecular weight of the polymer may be of a wide range,
including but not limited to, between about 100 Da and about
100,000 Da or more. The molecular weight of the polymer may be
between about 100 Da and about 100,000 Da, including but not
limited to, 100,000 Da, 95,000 Da, 90,000 Da, 85,000 Da, 80,000 Da,
75,000 Da, 70,000 Da, 65,000 Da, 60,000 Da, 55,000 Da, 50,000 Da,
45,000 Da, 40,000 Da, 35,000 Da, 30,000 Da, 25,000 Da, 20,000 Da,
15,000 Da, 10,000 Da, 9,000 Da, 8,000 Da, 7,000 Da, 6,000 Da, 5,000
Da, 4,000 Da, 3,000 Da, 2,000 Da, 1,000 Da, 900 Da, 800 Da, 700 Da,
600 Da, 500 Da, 400 Da, 300 Da, 200 Da, and 100 Da. In some
embodiments, the molecular weight of the polymer is between about
100 Da and about 50,000 Da. In some embodiments, the molecular
weight of the polymer is between about 100 Da and about 40,000 Da.
In some embodiments, the molecular weight of the polymer is between
about 11,000 Da and about 40,000 Da. In some embodiments, the
molecular weight of the polymer is between about 5,000 Da and about
40,000 Da. In some embodiments, the molecular weight of the polymer
is between about 10,000 Da and about 40,000 Da.
[0695] In order to maximize the desired properties of PEG, the
total molecular weight and hydration state of the PEG polymer or
polymers attached to the biologically active molecule must be
sufficiently high to impart the advantageous characteristics
typically associated with PEG polymer attachment, such as increased
water solubility and circulating half life, while not adversely
impacting the bioactivity of the parent molecule.
[0696] The methods and compositions described herein may be used to
produce substantially homogenous preparations of polymer:protein
conjugates. "Substantially homogenous" as used herein means that
polymer:protein conjugate molecules are observed to be greater than
half of the total protein. The polymer:protein conjugate has
biological activity and the present "substantially homogenous"
PEGylated polypeptide preparations provided herein are those which
are homogenous enough to display the advantages of a homogenous
preparation, e.g., ease in clinical application in predictability
of lot to lot pharmacokinetics.
[0697] One may also choose to prepare a mixture of polymer:protein
conjugate molecules, and the advantage provided herein is that one
may select the proportion of mono-polymer:protein conjugate to
include in the mixture. Thus, if desired, one may prepare a mixture
of various proteins with various numbers of polymer moieties
attached (i.e., di-, tri-, tetra-, etc.) and combine said
conjugates with the mono-polymer:protein conjugate prepared using
the methods described herein, and have a mixture with a
predetermined proportion of mono-polymer:protein conjugates.
[0698] The proportion of polyethylene glycol molecules to protein
molecules will vary, as will their concentrations in the reaction
mixture. In general, the optimum ratio (in terms of efficiency of
reaction in that there is minimal excess unreacted protein or
polymer) may be determined by the molecular weight of the
polyethylene glycol selected and on the number of available
reactive groups available. As relates to molecular weight,
typically the higher the molecular weight of the polymer, the fewer
number of polymer molecules which may be attached to the protein.
Similarly, branching of the polymer should be taken into account
when optimizing these parameters. Generally, the higher the
molecular weight (or the more branches) the higher the
polymer:protein ratio.
[0699] As used herein, and when contemplating hydrophilic
polymer:polypeptide/protein conjugates, the term "therapeutically
effective amount" further refers to an amount which gives the
desired benefit to a patient. The amount will vary from one
individual to another and will depend upon a number of factors,
including the overall physical condition of the patient and the
underlying condition to be treated. A therapeutically effective
amount of the present compositions may be readily ascertained by
one skilled in the art using publicly available materials and
procedures.
[0700] The number of water soluble polymers linked to a modified or
unmodified non-natural amino acid polypeptide (i.e., the extent of
PEGylation or glycosylation) described herein can be adjusted to
provide an altered (including but not limited to, increased or
decreased) pharmacologic, pharmacokinetic or pharmacodynamic
characteristic such as in vivo half-life. In some embodiments, the
half-life of the polypeptide is increased at least about 10, 20,
30, 40, 50, 60, 70, 80, 90 percent, two fold, five-fold, 10-fold,
50-fold, or at least about 100-fold over an unmodified
polypeptide.
[0701] In one embodiment, a polypeptide comprising an aromatic
amine-containing non-natural amino acid is modified with a PEG
derivative that contains a terminal aldehyde moiety that is linked
directly to the PEG backbone. In another embodiment, a polypeptide
comprising an aromatic amine-containing non-natural amino acid is
modified with a branched PEG derivative that contains a terminal
aldehyde moiety, with each chain of the branched PEG having a MW
ranging from about 1040 kDa and, in other embodiments, from about
5-20 kDa.
[0702] In some embodiments, the aldehyde-terminal PEG derivative
will have the structure:
RO--(CH.sub.2CH.sub.2O).sub.n--O--(CH.sub.2).sub.m--CH.sub.2--NH--CH.sub-
.2--C(O)H
where R is a simple alkyl (methyl, ethyl, propyl, etc.), m is 2-10
and n is 100-1,000 (i.e., average molecular weight is between 5-40
kDa). The molecular weight of the polymer may be of a wide range,
including but not limited to, between about 100 Da and about
100,000 Da or more. The molecular weight of the polymer may be
between about 100 Da and about 100,000 Da, including but not
limited to, 100,000 Da, 95,000 Da, 90,000 Da, 85,000 Da, 80,000 Da,
75,000 Da, 70,000 Da, 65,000 Da, 60,000 Da, 55,000 Da, 50,000 Da,
45,000 Da, 40,000 Da, 35,000 Da, 30,000 Da, 25,000 Da, 20,000 Da,
15,000 Da, 10,000 Da, 9,000 Da, 8,000 Da, 7,000 Da, 6,000 Da, 5,000
Da, 4,000 Da, 3,000 Da, 2,000 Da, 1,000 Da, 900 Da, 800 Da, 700 Da,
600 Da, 500 Da, 400 Da, 300 Da, 200 Da, and 100 Da. In some
embodiments, the molecular weight of the polymer is between about
100 Da and about 50,000 Da. In some embodiments, the molecular
weight of the polymer is between about 100 Da and about 40,000 Da.
In some embodiments, the molecular weight of the polymer is between
about 1,000 Da and about 40,000 Da. In some embodiments, the
molecular weight of the polymer is between about 5,000 Da and about
40,000 Da. In some embodiments, the molecular weight of the polymer
is between about 10,000 Da and about 40,000 Da.
[0703] In another embodiment, a polypeptide comprising a aromatic
amine amino acid is modified with a branched PEG derivative that
contains a terminal aldehyde moiety thus forming an amine bond with
each chain of the branched PEG having a MW ranging from about 1040
kDa and, in other embodiments, from about 5-20 kDa. The molecular
weight of the branched chain PEG may be between about 1,000 Da and
about 100,000 Da, including but not limited to, 100,000 Da, 95,000
Da, 90,000 Da, 85,000 Da, 80,000 Da, 75,000 Da, 70,000 Da, 65,000
Da, 60,000 Da, 55,000 Da, 50,000 Da, 45,000 Da, 40,000 Da, 35,000
Da, 30,000 Da, 25,000 Da, 20,000 Da, 15,000 Da, 10,000 Da, 9,000
Da, 8,000 Da, 7,000 Da, 6,000 Da, 5,000 Da, 4,000 Da, 3,000 Da,
2,000 Da, and 1,000 Da. In some embodiments, the molecular weight
of the branched chain PEG is between about 1,000 Da and about
50,000 Da. In some embodiments, the molecular weight of the
branched chain PEG is between about 1,000 Da and about 40,000 Da.
In some embodiments, the molecular weight of the branched chain PEG
is between about 5,000 Da and about 40,000 Da. In some embodiments,
the molecular weight of the branched chain PEG is between about
5,000 Da and about 20,000 Da.
[0704] Several reviews and monographs on the functionalization and
conjugation of PEG are available. See, for example, Harris,
Macromol. Chem. Phys. C25: 325-373 (1985); Scouten, Methods in
Enzymology 135: 30-65 (1987); Wong et al, Enzyme Microb. Technol.
14: 866-874 (1992); Delgado et al., Critical Reviews in Therapeutic
Drug Carrier Systems 9: 249-304 (1992); Zalipsky, Bioconjugate
Chem. 6: 150-165 (1995).
[0705] Methods for activation of polymers can also be found in WO
94/17039, U.S. Pat. No. 5,324,844, WO 94/18247, WO 94/04193, U.S.
Pat. No. 5,219,564, U.S. Pat. No. 5,122,614, WO 90/13540, U.S. Pat.
No. 5,281,698, and WO 93/15189, and for conjugation between
activated polymers and enzymes including but not limited to
Coagulation Factor VIII (WO 94/15625), haemoglobin (WO 94/09027),
oxygen carrying molecule (U.S. Pat. No. 4,412,989), ribonuclease
and superoxide dismutase (Veronese at al., App. Biochem. Biotech.
11: 141-52 (1985)), all of which are herein incorporated by
reference in their entirety.
[0706] If necessary, the PEGylated non-natural amino acid
polypeptides described herein obtained from the hydrophobic
chromatography can be purified further by one or more procedures
known to those skilled in the art including, but are not limited
to, affinity chromatography; anion- or cation-exchange
chromatography (using, including but not limited to, DEAE
SEPHAROSE); chromatography on silica; reverse phase HPLC; gel
filtration (using, including but not limited to, SEPHADEX G-75);
hydrophobic interaction chromatography; size-exclusion
chromatography, metal-chelate chromatography;
ultrafiltration/diafiltration; ethanol precipitation; ammonium
sulfate precipitation; chromatofocusing; displacement
chromatography; electrophoretic procedures (including but not
limited to preparative isoelectric focusing), differential
solubility (including but not limited to ammonium sulfate
precipitation), or extraction. Apparent molecular weight may be
estimated by GPC by comparison to globular protein standards
(Preneta A Z, PROTEIN PURIFICATION METHODS, A PRACTICAL APPROACH
(Harris & Angal, Eds.) IRL Press 1989, 293-306). The purity of
the non-natural amino acid polypeptide:PEG conjugate can be
assessed by proteolytic degradation (including but not limited to,
trypsin cleavage) followed by mass spectrometry analysis. Pepinsky
R B., et al., J. Pharmcol. & Exp. Ther. 297(3):1059-66
(2001).
[0707] PEGylation of natural polypeptides by reductive alkylation
of the terminal amine moiety requires more time than that required
for PEGylation of an aromatic amine moiety on a non-natural amino
acid. Additionally, the latter PEGylation method is site specific
and may occur at any site in the polypeptide where the non-natural
amino acid has been incorporated. FIG. 37 shows the PEGylation of a
terminal amine of a peptide MT-9 using stoichiometric or near
stoichiometric ratios, at pH 5, requires at least twelve hours for
about 50% PEGylation to occur. In contrast, FIG. 38 shows is a
non-limiting example of the PEGylation of a peptide which contains
an amino acid containing an aromatic amine moiety, including but
not limited to pAF2 (p-amino-phenylalanine). In FIG. 38 the peptide
MT-9 is near complete PEGylation with 20 k PEG aldehyde or 40 k PEG
aldehyde in stoichiometric or near stoichiometric ratios, at pH 4,
after reacting for about one hour.
[0708] This demonstrates the beneficial characteristics of
PEGylation using reductive alkylation of an amino acid containing
an aromatic amine moiety, such as selectivity (only PEGylation at
the aromatic amine containing amino acid); fast reaction time
(about one hour versus twelve hours); stoichiometric or near
stoichiometric ratios rather than an excess of PEG aldehyde reagent
(thereby using less reagent); and specificity (in contrast to only
N-terminal PEGylation, PEGylation via reductive alkylation of an
amino acid containing an aromatic amine moiety may occur at any
anywhere in the peptide sequence).
[0709] A non-limiting example of the PEGylation of hGH ("human
growth hormone") is shown in FIG. 39, wherein the tyrosine residue
at position 35 of the hGH protein has been translationally replaced
with an amino acid containing an aromatic amine moiety, including
but not limited to pAF2 (p-amino-phenylalanine), which is then
reductively alkylated with a PEG containing an aldehyde moiety.
Also shown in FIG. 39 is a non-limiting example of the PEGylation
of IFN.alpha., wherein an amino acid containing an aromatic amine
moiety, including but not limited to pAF2, is incorporated into the
IFN.alpha. sequence and is subsequently reductively alkylated with
a branched PEG containing an aldehyde moiety.
[0710] A water soluble polymer linked to a non-natural amino acid
of a polypeptide described herein can be further derivatized or
substituted without limitation.
E. Further Examples of Modifications Using Site-Specific
Derivatization
[0711] A non-limiting example of the selective, site-specific
derivatization of polypeptides/proteins is shown in FIGS. 20-34,
wherein reductive alkylation of the aromatic amine moiety,
including but not limited to pAF2 (p-amino-phenylalanine), occurs
preferentially over other sidechain groups such as, by way of
example lysine, or any end group derivatization. Such selective,
site-specific derivatization may allow for modification of
polypeptides/proteins to design agonists and/or antagonists, site
specific pegylation of polypeptides/proteins, prodrug design,
polypeptide/protein glycosylation, polypeptide/protein
dimerization, small molecule drug conjugates of
polypeptides/proteins, and small molecule drug conjugates of
antibodies.
F. Enhancing Affinity for Serum Albumin
[0712] Various molecules can also be fused to the non-natural amino
acid polypeptides described herein to modulate the half-life in
serum. In some embodiments, molecules are linked or fused to the
modified or unmodified non-natural amino acid polypeptides
described herein to enhance affinity for endogenous serum albumin
in an animal.
[0713] For example, in some cases, a recombinant fusion of a
polypeptide and an albumin binding sequence is made. Exemplary
albumin binding sequences include, but are not limited to, the
albumin binding domain from streptococcal protein G (see. e.g.,
Makrides et al., J. Pharmacol. Exp. Ther. 277:534-542 (1996) and
Sjolander et al., J. Immunol. Methods 201:115-123 (1997)), or
albumin-binding peptides such as those described in, e.g., Dennis,
et al., J. Biol. Chem. 277:35035-35043 (2002).
[0714] In other embodiments, the modified or unmodified non-natural
amino acid polypeptides described herein are acylated with fatty
acids. In some cases, the fatty acids promote binding to serum
albumin. See, e.g., Kurtzhals, et al., Biochem. J. 312:725-731
(1995).
[0715] In other embodiments, the modified or unmodified non-natural
amino acid polypeptides described herein are fused directly with
serum albumin (including but not limited to, human serum albumin).
Those of skill in the art will recognize that a wide variety of
other molecules can also be linked to non-natural amino acid
polypeptides, modified or unmodified, as described herein, to
modulate binding to serum albumin or other serum components.
G. Glycosylation of Non-Natural Amino Acid Polypeptides Described
Herein
[0716] The methods and compositions described herein include
polypeptides incorporating one or more non-natural amino acids
bearing saccharide residues. The saccharide residues may be either
natural (including but not limited to, N-acetylglucosamine) or
non-natural (including but not limited to, 3-fluorogalactose). The
saccharides may be linked to the non-natural amino acids either by
an N- or O-linked glycosidic linkage (including but not limited to,
N-acetylgalactose-L-serine) or a non-natural linkage (including but
not limited to, a heterocycle, including a nitrogen-containing
heterocycle, linkage or the corresponding C- or S-linked
glycoside). The saccharide (including but not limited to, glycosyl)
moieties can be added to the non-natural amino acid polypeptides
either in vivo or in vitro. In some embodiments, a polypeptide
comprising an aromatic amine-containing non-natural amino acid is
modified with a saccharide derivatized with an aldehyde group to
generate the corresponding glycosylated polypeptide linked via an
amine linkage. In other embodiments, a polypeptide comprising a
protected aldehyde-containing non-natural amino acid which, upon
deprotection, is modified with a saccharide derivatized with an
aromatic amine group to generate the corresponding glycosylated
polypeptide linked via an amine linkage. Once attached to the
non-natural amino acid, the saccharide may be further elaborated by
treatment with glycosyltransferases and other enzymes to generate
an oligosaccharide bound to the non-natural amino acid polypeptide.
See, e.g., H. Liu, et al. J. Am. Chem. Soc. 125: 1702-1703
(2003).
H. Use of Linking Groups and Applications, Including Polypeptide
Dimers and Multimers
[0717] In addition to adding functionality directly to the
non-natural amino acid polypeptide, the non-natural amino acid
portion of the polypeptide may first be modified with a
multifunctional (e.g., bi-, tri, tetra-) linker molecule that then
subsequently is further modified. That is, at least one end of the
multifunctional linker molecule reacts with at least one
non-natural amino acid in a polypeptide and at least one other end
of the multifunctional linker is available for further
functionalization. If all ends of the multifunctional linker are
identical, then (depending upon the stoichiometric conditions)
homomultimers of the non-natural amino acid polypeptide may be
formed. If the ends of the multifunctional linker have distinct
chemical reactivities, then at least one end of the multifunctional
linker group will be bound to the non-natural amino acid
polypeptide and the other end can subsequently react with a
different functionality, including by way of example only: a label;
a dye; a polymer; a water-soluble polymer; a derivative of
polyethylene glycol; a photocrosslinker; a cytotoxic compound; a
drug; an affinity label; a photoaffinity label; a reactive
compound; a resin; a second protein or polypeptide or polypeptide
analog; an antibody or antibody fragment; a metal chelator; a
cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a
RNA; an antisense polynucleotide; a saccharide, a water-soluble
dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin
label; a fluorophore, a metal-containing moiety; a radioactive
moiety; a novel functional group; a group that covalently or
noncovalently interacts with other molecules; a photocaged moiety;
an actinic radiation excitable moiety; a ligand; a
photoisomerizable moiety; biotin; a biotin analogue; a moiety
incorporating a heavy atom; a chemically cleavable group; a
photocleavable group; an elongated side chain; a carbon-linked
sugar; a redox-active agent; an amino thioacid; a toxic moiety; an
isotopically labeled moiety; a biophysical probe; a phosphorescent
group; a chemiluminescent group; an electron dense group; a
magnetic group; an intercalating group; a chromophore; an energy
transfer agent; a biologically active agent; a detectable label; a
small molecule; an inhibitory ribonucleic acid; a radionucleotide;
a neutron-capture agent; a derivative of biotin; quantum dot(s); a
nanotransmitter; a radiotransmitter; an abzyme, an activated
complex activator, a virus, an adjuvant, an aglycan, an allergan,
an angiostatin, an antihormone, an antioxidant, an aptamer, a guide
RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a
receptor, a reverse micelle, and any combination thereof.
[0718] The multifunctional linker group has the general
structure:
##STR00092##
wherein: [0719] each X is an aldehyde or an aromatic amine; [0720]
each L is independently selected from the group consisting of
alkylene, substituted alkylene, alkenylene, substituted alkenylene,
--O--, --O-(alkylene or substituted alkylene)-, --S--,
--S-(alkylene or substituted alkylene)-, --S(O).sub.k-- where k is
1, 2, or 3, --S(O).sub.k(alkylene or substituted alkylene)-,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --N(R')--,
--NR'-(alkylene or substituted alkylene)-, --C(O)N(R')--,
--CON(R')-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)NR'C(O)O-(alkylene or substituted alkylene)-,
--O--CON(R')-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, --N(R')C(O)O-(alkylene
or substituted alkylene)-, --S(O).sub.kN(R')--, --N(R')C(O)N(R')--,
--N(R')C(O)N(R')-(alkylene or substituted alkylene)-,
--N(R')C(S)N(R')--, --N(R')S(O).sub.kN(R')--, --N(R')--N.dbd.,
--C(R').dbd.N--, --C(R').dbd.N--N(R')--, --C(R')--N--N--,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; [0721]
wherein R' is independently H, alkyl, or substituted alkyl; [0722]
L.sub.1 is optional, and when present, is
--C(R').sub.p--NR'--C(O)O-(alkylene or substituted alkylene)- where
[0723] p is 0, 1, or 2; [0724] W is an aldehyde or an aromatic
amine; and n is 1 to 3.
[0725] The methods and compositions described herein also provide
for polypeptide combinations, such as homodimers, heterodimers,
homomultimers, or heteromultimers (i.e., trimers, tetramers, etc.).
By way of example only, the following description focuses on the GH
supergene family members, however, the methods, techniques and
compositions described in this section can be applied to virtually
any other polypeptide which can provide benefit in the form of
dimers and multimers, including by way of example only: alpha-1
antitrypsin, angiostatin, antihemolytic factor, antibody,
apolipoprotein, apoprotein, atrial natriuretic factor, atrial
natriuretic polypeptide, atrial peptide, C-X-C chemokine, T39765,
NAP-2, ENA-78, gro-a, gro-b, gro-c, IP-10, GCP-2, NAP-4, SDF-1,
PF4, MIG, calcitonin, c-kit ligand, cytokine, CC chemokine,
monocyte chemoattractant protein-1, monocyte chemoattractant
protein-2, monocyte chemoattractant protein-3, monocyte
inflammatory protein-1 alpha, monocyte inflammatory protein-i beta,
RANTES, 1309, R83915, R91733, HCC1, T58847, D31065, T64262, CD40,
CD40 ligand, c-kit ligand, collagen, colony stimulating factor
(CSF), complement factor 5a, complement inhibitor, complement
receptor 1, cytokine, epithelial neutrophil activating peptide-78,
MIP-16, MCP-1, epidermal growth factor (EGF), epithelial neutrophil
activating peptide, erythropoietin (EPO), exfoliating toxin, Factor
IX, Factor VII, Factor VIII, Factor X, fibroblast growth factor
(FGF), fibrinogen, fibronectin, four-helical bundle protein, G-CSF,
glp-1, GM-CSF, glucocerebrosidase, gonadotropin, growth factor,
growth factor receptor, grf, hedgehog protein, hemoglobin,
hepatocyte growth factor (hGF), hirudin, human growth hormone
(hGH), human serum albumin, ICAM-1, ICAM-1 receptor, LFA-1, LFA-1
receptor, insulin, insulin-like growth factor (IGF), IGF-I, IGF-II,
interferon (IFN), IFN-alpha, IFN-beta, IFN-gamma, any
interferon-like molecule or member of the IFN family, interleukin
(IL), IL-1, IL-2, IL-3, IL4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10,
IL-11, IL-12, keratinocyte growth factor (KGF), lactoferrin,
leukemia inhibitory factor, luciferase, neurturin, neutrophil
inhibitory factor (NIF), oncostatin M, osteogenic protein, oncogene
product, paracitonin, parathyroid hormone, PD-ECSF, PDGF, peptide
hormone, pleiotropin, protein A, protein G, pth, pyrogenic exotoxin
A, pyrogenic exotoxin B, pyrogenic exotoxin C, pyy, relaxin, renin,
SCF, small biosynthetic protein, soluble complement receptor I,
soluble I-CAM 1, soluble interleukin receptor, soluble TNF
receptor, somatomedin, somatostatin, somatotropin, streptokinase,
superantigens, staphylococcal enterotoxin, SEA, SEB, SEC1, SEC2,
SEC3, SED, SEE, steroid hormone receptor, superoxide dismutase,
toxic shock syndrome toxin, thymosin alpha 1, tissue plasminogen
activator, tumor growth factor (TGF), tumor necrosis factor, tumor
necrosis factor alpha, tumor necrosis factor beta, tumor necrosis
factor receptor (TNFR), VLA-4 protein, VCAM-1 protein, vascular
endothelial growth factor (VEGF), urokinase, mos, ras, raf, met,
p53, tat, fos, myc, jun, myb, rel, estrogen receptor, progesterone
receptor, testosterone receptor, aldosterone receptor, LDL
receptor, and corticosterone.
[0726] Thus, encompassed within the methods, techniques and
compositions described herein are a GH supergene family member
polypeptide containing one or more non-natural amino acids bound to
another GH supergene family member or variant thereof or any other
polypeptide that is a non-GH supergene family member or variant
thereof, either directly to the polypeptide backbone or via a
linker. Due to its increased molecular weight compared to monomers,
the GH supergene family member dimer or multimer conjugates may
exhibit new or desirable properties, including but not limited to
different pharmacological, pharmacokinetic, pharmacodynamic,
modulated therapeutic half-life, or modulated plasma half-life
relative to the monomeric GH supergene family member. In some
embodiments, the GH supergene family member dimers described herein
will modulate the dimerization of the GH supergene family member
receptor. In other embodiments, the GH supergene family member
dimers or multimers described herein will act as a GH supergene
family member receptor antagonist, agonist, or modulator.
[0727] In some embodiments, the GH supergene family member
polypeptides are linked directly, including but not limited to, via
an Asn-Lys amide linkage or Cys-Cys disulfide linkage. In some
embodiments, the linked GH supergene family member polypeptides,
and/or the linked non-GH supergene family member, will comprise
different non-natural amino acids to facilitate dimerization,
including but not limited to, a first GH supergene family member,
and/or the linked non-GH supergene family member, polypeptide
comprising an aromatic amine-containing non-natural amino acid
conjugated to a second GH supergene family member polypeptide
comprising a aldehyde-containing non-natural amino acid and the
polypeptides are reacted via reductive alkylation, forming an amine
linkage between the two.
[0728] Alternatively, the two GH supergene family member
polypeptides, and/or the linked non-GH supergene family members,
are linked via a linker. Any hetero- or homo-bifunctional linker
can be used to link the two GH supergene family members, and/or the
linked non-GH supergene family member, polypeptides, which can have
the same or different primary sequence. In some cases, the linker
used to tether the GH supergene family member, and/or the linked
non-GH supergene family member, polypeptides together can be a
bifunctional PEG reagent.
[0729] In some embodiments, the methods and compositions described
herein provide for water-soluble bifunctional linkers that have a
dumbbell structure that includes: a) aldehyde-containing moiety on
at least a first end of a polymer backbone; and b) at least a
second functional group on a second end of the polymer backbone.
The second functional group can be the same or different as the
first functional group. The second functional group, in some
embodiments, is not reactive with the first functional group. The
methods and compositions described herein provide, in some
embodiments, water-soluble compounds that comprise at least one arm
of a branched molecular structure. For example, the branched
molecular structure can be dendritic.
[0730] In some embodiments, the methods and compositions described
herein provide multimers comprising one or more GH supergene family
member formed by reactions with water soluble activated polymers
that have the structure:
R--(CH.sub.2CH.sub.2O).sub.n--O--(CH.sub.2).sub.m--X
wherein n is from about 5 to about 3,000, m is 2-10, X can be a
carbonyl (including an aldehyde)-containing moiety, and R is a
capping group, a functional group, or a leaving group that can be
the same or different as X. R can be, for example, a functional
group selected from the group consisting of hydroxyl, protected
hydroxyl, alkoxyl, N-hydroxysuccinimidyl ester, 1-benzotriazolyl
ester, N-hydroxysuccinimidyl carbonate, 1-benzotriazolyl carbonate,
acetal, aldehyde, aldehyde hydrates, alkenyl, acrylate,
methacrylate, acrylamide, active sulfone, amine, aminooxy,
protected amine, hydrazide, protected hydrazide, protected thiol,
carboxylic acid, protected carboxylic acid, isocyanate,
isothiocyanate, maleimide, vinylsulfone, dithiopyridine,
vinylpyridine, iodoacetamide, epoxide, glyoxals, diones, mesylates,
tosylates, and tresylate, alkene, and ketone.
I. Example of Adding Functionality: Easing the Isolation Properties
of a Polypeptide
[0731] A naturally-occurring or non-natural amino acid polypeptide
may be difficult to isolate from a sample for a number of reasons,
including but not limited to the solubility or binding
characteristics of the polypeptide. For example, in the preparation
of a polypeptide for therapeutic use, such a polypeptide may be
isolated from a recombinant system that has been engineered to
overproduce the polypeptide. However, because of the solubility or
binding characteristics of the polypeptide, achieving a desired
level of purity often proves difficult. The methods, compositions,
techniques and strategies described herein provide a solution to
this situation.
[0732] Using the methods, compositions, techniques and strategies
described herein, one of skill in the art can produce an alkylated
amine-containing non-natural amino acid polypeptide that is
homologous to the desired polypeptide, wherein the alkylated
amine-containing non-natural amino acid polypeptide has improved
isolation characteristics. In one embodiment, a homologous
non-natural amino acid polypeptide is produced biosynthetically. In
a further or additional embodiment, the non-natural amino acid has
incorporated into its structure one of the non-natural amino acids
described herein. In a further or additional embodiment, the
non-natural amino acid is incorporated at a terminal or internal
position and is further incorporated site specifically.
[0733] In one embodiment, the resulting non-natural amino acid, as
produced biosynthetically, already has the desired improved
isolation characteristics. In further or additional embodiments,
the non-natural amino acid comprises an amine linkage to a group
that provides the improved isolation characteristics. In further or
additional embodiments, the non-natural amino acid is further
modified to form an alkylated amine-containing non-natural amino
acid polypeptide, wherein the modification provides an amine
linkage to a group that provides the improved isolation
characteristics. In some embodiments, such a group is directly
linked to the non-natural amino acid, and in other embodiments,
such a group is linked via a linker group to the non-natural amino
acid. In certain embodiments, such a group is connected to the
non-natural amino acid by a single chemical reaction, in other
embodiments a series of chemical reactions is required to connect
such a group to the non-natural amino acid. Preferably, the group
imparting improved isolation characteristics is linked site
specifically to the non-natural amino acid in the non-natural amino
acid polypeptide and is not linked to a naturally occurring amino
acid under the reaction conditions utilized.
[0734] In further or additional embodiments the resulting
non-natural amino acid polypeptide is homologous to the GH
supergene family members, however, the methods, techniques and
compositions described in this section can be applied to virtually
any other polypeptide which can benefit from improved isolation
characteristics, including by way of example only: alpha-1
antitrypsin, angiostatin, antihemolytic factor, antibody,
apolipoprotein, apoprotein, atrial natriuretic factor, atrial
natriuretic polypeptide, atrial peptide, C-X-C chemokine, T39765,
NAP-2, ENA-78, gro-a, gro-b, gro-c, IP-10, GCP-2, NAP-4, SDF-1,
PF4, MIG, calcitonin, c-kit ligand, cytokine, CC chemokine,
monocyte chemoattractant protein-1, monocyte chemoattractant
protein-2, monocyte chemoattractant protein-3, monocyte
inflammatory protein-1 alpha, monocyte inflammatory protein-i beta,
RANTES, 1309, R83915, R91733, HCC1, T58847, D31065, T64262, CD40,
CD40 ligand, c-kit ligand, collagen, colony stimulating factor
(CSF), complement factor 5a, complement inhibitor, complement
receptor 1, cytokine, epithelial neutrophil activating peptide-78,
MIP-16, MCP-1, epidermal growth factor (EGF), epithelial neutrophil
activating peptide, erythropoietin (EPO), exfoliating toxin, Factor
IX, Factor VII, Factor VIII, Factor X, fibroblast growth factor
(FGF), fibrinogen, fibronectin, four-helical bundle protein, G-CSF,
glp-1, GM-CSF, glucocerebrosidase, gonadotropin, growth factor,
growth factor receptor, grf, hedgehog protein, hemoglobin,
hepatocyte growth factor (hGF), hirudin, human growth hormone
(hGH), human serum albumin, ICAM-1, ICAM-1 receptor, LFA-1, LFA-1
receptor, insulin, insulin-like growth factor (IGF), IGF-I, IGF-II,
interferon (IFN), IFN-alpha, IFN-beta, IFN-gamma, any
interferon-like molecule or member of the IFN family, interleukin
(IL), IL-1, IL-2, IL-3, IL4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10,
IL-1, IL-12, keratinocyte growth factor (KGF), lactoferrin,
leukemia inhibitory factor, luciferase, neurturin, neutrophil
inhibitory factor (NIF), oncostatin M, osteogenic protein, oncogene
product, paracitonin, parathyroid hormone, PD-ECSF, PDGF, peptide
hormone, pleiotropin, protein A, protein G, pth, pyrogenic exotoxin
A, pyrogenic exotoxin B, pyrogenic exotoxin C, pyy, relaxin, renin,
SCF, small biosynthetic protein, soluble complement receptor I,
soluble I-CAM 1, soluble interleukin receptor, soluble TNF
receptor, somatomedin, somatostatin, somatotropin, streptokinase,
superantigens, staphylococcal enterotoxin, SEA, SEB, SEC1, SEC2,
SEC3, SED, SEE, steroid hormone receptor, superoxide dismutase,
toxic shock syndrome toxin, thymosin alpha 1, tissue plasminogen
activator, tumor growth factor (TGF), tumor necrosis factor, tumor
necrosis factor alpha, tumor necrosis factor beta, tumor necrosis
factor receptor (TNFR), VLA-4 protein, VCAM-1 protein, vascular
endothelial growth factor (VEGF), urokinase, mos, ras, raf, met,
p53, tat, fos, myc, jun, myb, rel, estrogen receptor, progesterone
receptor, testosterone receptor, aldosterone receptor, LDL
receptor, and corticosterone.
[0735] In further or additional embodiments, the group imparting
improved isolation characteristics improves the water solubility of
the polypeptide; in other embodiments, the group improves the
binding properties of the polypeptide; in other embodiments, the
group provides new binding properties to the polypeptide
(including, by way of example only, a biotin group or a
biotin-binding group). In embodiments wherein the group improves
the water solubility of the polypeptide, the group is selected from
the water soluble polymers described herein, including by way of
example only, any of the PEG polymer groups described herein.
J. Example of Adding Functionality: Detecting the Presence of a
Polypeptide
[0736] A naturally-occurring or non-natural amino acid polypeptide
may be difficult to detect in a sample (including an in vivo sample
and an in vitro sample) for a number of reasons, including but not
limited to the lack of a reagent or label that can readily bind to
the polypeptide. The methods, compositions, techniques and
strategies described herein provide a solution to this
situation.
[0737] Using the methods, compositions, techniques and strategies
described herein, one of skill in the art can produce an alkylated
amine-containing non-natural amino acid polypeptide that is
homologous to the desired polypeptide, wherein the alkylated
amine-containing non-natural amino acid polypeptide allows the
detection of the polypeptide in an in vivo sample and an in vitro
sample. In one embodiment, a homologous non-natural amino acid
polypeptide is produced biosynthetically. In a further or
additional embodiment, the non-natural amino acid has incorporated
into its structure one of the non-natural amino acids described
herein. In a further or additional embodiment, the non-natural
amino acid is incorporated at a terminal or internal position and
is further incorporated site specifically.
[0738] In one embodiment, the resulting non-natural amino acid, as
produced biosynthetically, already has the desired detection
characteristics. In further or additional embodiments, the
non-natural amino acid comprises an amine linkage to a group that
provides the improved detection characteristics. In further or
additional embodiments, the non-natural amino acid is further
modified to form an alkylated amine-containing non-natural amino
acid polypeptide, wherein the modification provides an amine
linkage to a group that provides the improved detection
characteristics. In some embodiments, such a group is directly
linked to the non-natural amino acid, and in other embodiments,
such a group is linked via a linker group to the non-natural amino
acid. In certain embodiments, such a group is connected to the
non-natural amino acid by a single chemical reaction, in other
embodiments a series of chemical reactions is required to connect
such a group to the non-natural amino acid. Preferably, the group
imparting improved detection characteristics is linked site
specifically to the non-natural amino acid in the non-natural amino
acid polypeptide and is not linked to a naturally occurring amino
acid under the reaction conditions utilized.
[0739] In further or additional embodiments the resulting
non-natural amino acid polypeptide is homologous to the GH
supergene family members, however, the methods, techniques and
compositions described in this section can be applied to virtually
any other polypeptide which needs to be detected in an in vivo
sample and an in vitro sample, including by way of example only:
alpha-1 antitrypsin, angiostatin, antihemolytic factor, antibody,
apolipoprotein, apoprotein, atrial natriuretic factor, atrial
natriuretic polypeptide, atrial peptide, C-X-C chemokine, T39765,
NAP-2, ENA-78, gro-a, gro-b, gro-c, IP-10, GCP-2, NAP-4, SDF-1,
PF4, MIG, calcitonin, c-kit ligand, cytokine, CC chemokine,
monocyte chemoattractant protein-1, monocyte chemoattractant
protein-2, monocyte chemoattractant protein-3, monocyte
inflammatory protein-1 alpha, monocyte inflammatory protein-i beta,
RANTES, 1309, R83915, R91733, HCC1, T58847, D31065, T64262, CD40,
CD40 ligand, c-kit ligand, collagen, colony stimulating factor
(CSF), complement factor 5a, complement inhibitor, complement
receptor 1, cytokine, epithelial neutrophil activating peptide-78,
MIP-16, MCP-1, epidermal growth factor (EGF), epithelial neutrophil
activating peptide, erythropoietin (EPO), exfoliating toxin, Factor
IX, Factor VII, Factor VIII, Factor X, fibroblast growth factor
(FGF), fibrinogen, fibronectin, four-helical bundle protein, G-CSF,
glp-1, GM-CSF, glucocerebrosidase, gonadotropin, growth factor,
growth factor receptor, grf, hedgehog protein, hemoglobin,
hepatocyte growth factor (hGF), hirudin, human growth hormone
(hGH), human serum albumin, ICAM-1, ICAM-1 receptor, LFA-1, LFA-1
receptor, insulin, insulin-like growth factor (IGF), IGF-I, IGF-II,
interferon (IFN), IFN-alpha, IFN-beta, IFN-gamma, any
interferon-like molecule or member of the IFN family, interleukin
(IL), IL-1, IL-2, IL-3, IL4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10,
IL-11, IL-12, keratinocyte growth factor (KGF), lactoferrin,
leukemia inhibitory factor, luciferase, neurturin, neutrophil
inhibitory factor (NIF), oncostatin M, osteogenic protein, oncogene
product, paracitonin, parathyroid hormone, PD-ECSF, PDGF, peptide
hormone, pleiotropin, protein A, protein G, pth, pyrogenic exotoxin
A, pyrogenic exotoxin B, pyrogenic exotoxin C, pyy, relaxin, renin,
SCF, small biosynthetic protein, soluble complement receptor I,
soluble I-CAM 1, soluble interleukin receptor, soluble TNF
receptor, somatomedin, somatostatin, somatotropin, streptokinase,
superantigens, staphylococcal enterotoxin, SEA, SEB, SEC1, SEC2,
SEC3, SED, SEE, steroid hormone receptor, superoxide dismutase,
toxic shock syndrome toxin, thymosin alpha 1, tissue plasminogen
activator, tumor growth factor (TGF), tumor necrosis factor, tumor
necrosis factor alpha, tumor necrosis factor beta, tumor necrosis
factor receptor (TNFR), VLA4 protein, VCAM-1 protein, vascular
endothelial growth factor (VEGF), urokinase, mos, ras, raf, met,
p53, tat, fos, myc, jun, myb, rel, estrogen receptor, progesterone
receptor, testosterone receptor, aldosterone receptor, LDL
receptor, and corticosterone.
[0740] In further or additional embodiments, the group imparting
improved detection characteristics is selected from the group
consisting of a label; a dye; an affinity label; a photoaffinity
label; a spin label; a fluorophore; a radioactive moiety; a moiety
incorporating a heavy atom; an isotopically labeled moiety; a
biophysical probe; a phosphorescent group; a chemiluminescent
group; an electron dense group; a magnetic group; a chromophore; an
energy transfer agent; a detectable label; and any combination of
the above.
K. Example of Adding Functionality: Improving the Therapeutic
Properties of a Polypeptide
[0741] A naturally-occurring or non-natural amino acid polypeptide
will be able to provide a certain therapeutic benefit to a patient
with a particular disorder, disease or condition. Such a
therapeutic benefit will depend upon a number of factors, including
by way of example only: the safety profile of the polypeptide, and
the pharmacokinetics, pharmacologics and/or pharmacodynamics of the
polypeptide (e.g., water solubility, bioavailability, serum
half-life, therapeutic half-life, immunogenicity, biological
activity, or circulation time). In addition, it may be advantageous
to provide additional functionality to the polypeptide, such as an
attached cytotoxic compound or drug, or it may be desirable to
attach additional polypeptides to form the homo- and
heteromultimers described herein. Such modifications preferably do
not destroy the activity and/or tertiary structure of the original
polypeptide. The methods, compositions, techniques and strategies
described herein provide solutions to these issues.
[0742] Using the methods, compositions, techniques and strategies
described herein, one of skill in the art can produce an alkylated
amine-containing non-natural amino acid polypeptide that is
homologous to the desired polypeptide, wherein the alkylated
amine-containing non-natural amino acid polypeptide has improved
therapeutic characteristics. In one embodiment, a homologous
non-natural amino acid polypeptide is produced biosynthetically. In
a further or additional embodiment, the non-natural amino acid has
incorporated into its structure one of the non-natural amino acids
described herein. In a further or additional embodiment, the
non-natural amino acid is incorporated at a terminal or internal
position and is further incorporated site specifically.
[0743] In one embodiment, the resulting non-natural amino acid, as
produced biosynthetically, already has the desired improved
therapeutic characteristics. In further or additional embodiments,
the non-natural amino acid comprises an amine linkage to a group
that provides the improved therapeutic characteristics. In further
or additional embodiments, the non-natural amino acid is further
modified to form an alkylated amine-containing non-natural amino
acid polypeptide, wherein the modification provides an amine
linkage to a group that provides the improved therapeutic
characteristics. In some embodiments, such a group is directly
linked to the non-natural amino acid, and in other embodiments,
such a group is linked via a linker group to the non-natural amino
acid. In certain embodiments, such a group is connected to the
non-natural amino acid by a single chemical reaction, in other
embodiments a series of chemical reactions is required to connect
such a group to the non-natural amino acid. Preferably, the group
imparting improved therapeutic characteristics is linked site
specifically to the non-natural amino acid in the non-natural amino
acid polypeptide and is not linked to a naturally occurring amino
acid under the reaction conditions utilized.
[0744] In further or additional embodiments the resulting
non-natural amino acid polypeptide is homologous to the GH
supergene family members, however, the methods, techniques and
compositions described in this section can be applied to virtually
any other polypeptide which can benefit from improved therapeutic
characteristics, including by way of example only: alpha-1
antitrypsin, angiostatin, antihemolytic factor, antibody,
apolipoprotein, apoprotein, atrial natriuretic factor, atrial
natriuretic polypeptide, atrial peptide, C-X-C chemokine, T39765,
NAP-2, ENA-78, gro-a, gro-b, gro-c, IP-10, GCP-2, NAP-4, SDF-1,
PF4, MIG, calcitonin, c-kit ligand, cytokine, CC chemokine,
monocyte chemoattractant protein-1, monocyte chemoattractant
protein-2, monocyte chemoattractant protein-3, monocyte
inflammatory protein-1 alpha, monocyte inflammatory protein-i beta,
RANTES, 1309, R83915, R91733, HCC1, T58847, D31065, T64262, CD40,
CD40 ligand, c-kit ligand, collagen, colony stimulating factor
(CSF), complement factor 5a, complement inhibitor, complement
receptor 1, cytokine, epithelial neutrophil activating peptide-78,
MIP-16, MCP-1, epidermal growth factor (EGF), epithelial neutrophil
activating peptide, erythropoietin (EPO), exfoliating toxin, Factor
IX, Factor VII, Factor VIII, Factor X, fibroblast growth factor
(FGF), fibrinogen, fibronectin, four-helical bundle protein, G-CSF,
glp-1, GM-CSF, glucocerebrosidase, gonadotropin, growth factor,
growth factor receptor, grf, hedgehog protein, hemoglobin,
hepatocyte growth factor (hGF), hirudin, human growth hormone
(hGH), human serum albumin, ICAM-1, ICAM-1 receptor, LFA-1, LFA-1
receptor, insulin, insulin-like growth factor (IGF), IGF-I, IGF-II,
interferon (IFN), IFN-alpha, IFN-beta, IFN-gamma, any
interferon-like molecule or member of the IFN family, interleukin
(IL), IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10,
IL-11, IL-12, keratinocyte growth factor (KGF), lactoferrin,
leukemia inhibitory factor, luciferase, neurturin, neutrophil
inhibitory factor (NIF), oncostatin M, osteogenic protein, oncogene
product, paracitonin, parathyroid hormone, PD-ECSF, PDGF, peptide
hormone, pleiotropin, protein A, protein G, pth, pyrogenic exotoxin
A, pyrogenic exotoxin B, pyrogenic exotoxin C, pyy, relaxin, renin,
SCF, small biosynthetic protein, soluble complement receptor I,
soluble I-CAM 1, soluble interleukin receptor, soluble TNF
receptor, somatomedin, somatostatin, somatotropin, streptokinase,
superantigens, staphylococcal enterotoxin, SEA, SEB, SEC1, SEC2,
SEC3, SED, SEE, steroid hormone receptor, superoxide dismutase,
toxic shock syndrome toxin, thymosin alpha 1, tissue plasminogen
activator, tumor growth factor (TGF), tumor necrosis factor, tumor
necrosis factor alpha, tumor necrosis factor beta, tumor necrosis
factor receptor (TNFR), VLA-4 protein, VCAM-1 protein, vascular
endothelial growth factor (VEGF), urokinase, mos, ras, raf, met,
p53, tat, fos, myc, jun, myb, rel, estrogen receptor, progesterone
receptor, testosterone receptor, aldosterone receptor, LDL
receptor, and corticosterone.
[0745] In further or additional embodiments, the group imparting
improved therapeutic characteristics improves the water solubility
of the polypeptide; in other embodiments, the group improves the
binding properties of the polypeptide; in other embodiments, the
group provides new binding properties to the polypeptide
(including, by way of example only, a biotin group or a
biotin-binding group). In embodiments wherein the group improves
the water solubility of the polypeptide, the group is selected from
the water soluble polymers described herein, including by way of
example only the PEG polymer groups. In further or additional
embodiments the group is a cytotoxic compound, whereas in other
embodiments the group is a drug. In further embodiments the linked
drug or cytotoxic compound can be cleaved from the non-natural
amino acid polypeptide so as to deliver the drug or cytotoxic
compound to a desired therapeutic location. In other embodiments,
the group is a second polypeptide, including by way of example, an
alkylated amine-containing non-natural amino acid polypeptide,
further including by way of example, a polypeptide that has the
same amino acid structure as the first non-natural amino acid
polypeptide.
[0746] In further or additional embodiments, the alkylated
amine-containing non-natural amino acid polypeptide is a modified
alkylated amine-containing non-natural amino acid polypeptide. In
further or additional embodiments, the alkylated amine-containing
non-natural amino acid polypeptide increases the bioavailability of
the polypeptide relative to the homologous naturally-occurring
amino acid polypeptide. In further or additional embodiments, the
alkylated amine-containing non-natural amino acid polypeptide
increases the safety profile of the polypeptide relative to the
homologous naturally-occurring amino acid polypeptide. In further
or additional embodiments, the alkylated amine-containing
non-natural amino acid polypeptide increases the water solubility
of the polypeptide relative to the homologous naturally-occurring
amino acid polypeptide. In further or additional embodiments, the
alkylated amine-containing non-natural amino acid polypeptide
increases the therapeutic half-life of the polypeptide relative to
the homologous naturally-occurring amino acid polypeptide. In
further or additional embodiments, the alkylated amine-containing
non-natural amino acid polypeptide increases the serum half-life of
the polypeptide relative to the homologous naturally-occurring
amino acid polypeptide. In further or additional embodiments, the
alkylated amine-containing non-natural amino acid polypeptide
extends the circulation time of the polypeptide relative to the
homologous naturally-occurring amino acid polypeptide. In further
or additional embodiments, the alkylated amine-containing
non-natural amino acid polypeptide modulates the biological
activity of the polypeptide relative to the homologous
naturally-occurring amino acid polypeptide. In further or
additional-embodiments, the alkylated amine-containing non-natural
amino acid polypeptide modulates the immunogenicity of the
polypeptide relative to the homologous naturally-occurring amino
acid polypeptide.
XI. Therapeutic Uses of Modified Polypeptides
[0747] For convenience, the "modified or unmodified" non-natural
polypeptides described in this section have been described
generically and/or with specific examples. However, the "modified
or unmodified" non-natural polypeptides described in this section
should not be limited to just the generic descriptions or specific
example provided in this section, but rather the "modified or
unmodified" non-natural polypeptides described in this section
apply equally well to all "modified or unmodified" non-natural
polypeptides comprising at least one amino acid which falls within
the scope of Formulas (A)-(E) and (I)-(XVI), including any
sub-formulas or specific compounds that fall within the scope of
Formulas (A)-(E) and (I)-(XVI) that are described in the
specification, claims and figures herein.
[0748] The modified or unmodified non-natural amino acid
polypeptides described herein, including homo- and hetero-multimers
thereof find multiple uses, including but not limited to:
therapeutic, diagnostic, assay-based, industrial, cosmetic, plant
biology, environmental, energy-production, and/or military uses. As
a non-limiting illustration, the following therapeutic uses of
modified or unmodified non-natural amino acid polypeptides are
provided.
[0749] The modified or unmodified non-natural amino acid
polypeptides described herein are useful for treating a wide range
of disorders, conditions, or diseases. Administration of the
modified or unmodified non-natural amino acid polypeptide products
described herein results in any of the activities demonstrated by
commercially available polypeptide preparations in humans. Average
quantities of the modified or unmodified non-natural amino acid
polypeptide product may vary and in particular should be based upon
the recommendations and prescription of a qualified physician. The
exact amount of the modified or unmodified non-natural amino acid
polypeptide is a matter of preference subject to such factors as
the exact type of condition being treated, the condition of the
patient being treated, as well as the other ingredients in the
composition. The amount to be given may be readily determined by
one skilled in the art based upon therapy with the modified or
unmodified non-natural amino acid polypeptide.
A. Administration and Pharmaceutical Compositions
[0750] The "modified or unmodified" non-natural amino acid
polypeptides described herein, including homo- and hetero-multimers
thereof find multiple uses, including but not limited to:
therapeutic, diagnostic, assay-based, industrial, cosmetic, plant
biology, environmental, energy-production, and/or military uses. As
a non-limiting illustration, the following therapeutic uses of
"modified or unmodified" non-natural amino acid polypeptides are
provided.
[0751] The "modified or unmodified" non-natural amino acid
polypeptides described herein are useful for treating a wide range
of disorders. Administration of the "modified or unmodified"
non-natural amino acid polypeptide products described herein
results in any of the activities demonstrated by commercially
available polypeptide preparations in humans. Average quantities of
the "modified or unmodified" non-natural amino acid polypeptide
product may vary and in particular should be based upon the
recommendations and prescription of a qualified physician. The
exact amount of the "modified or unmodified" non-natural amino acid
polypeptide is a matter of preference subject to such factors as
the exact type of condition being treated, the condition of the
patient being treated, as well as the other ingredients in the
composition. The amount to be given may be readily determined by
one skilled in the art based upon therapy with the "modified or
unmodified" non-natural amino acid polypeptide.
[0752] The non-natural amino acid polypeptides, modified or
unmodified, as described herein (including but not limited to,
synthetases, proteins comprising one or more non-natural amino
acid, etc.) are optionally employed for therapeutic uses, including
but not limited to, in combination with a suitable pharmaceutical
carrier. Such compositions, for example, comprise a therapeutically
effective amount of the non-natural amino acid polypeptides,
modified or unmodified, as described herein, and a pharmaceutically
acceptable carrier or excipient. Such a carrier or excipient
includes, but is not limited to, saline, buffered saline, dextrose,
water, glycerol, ethanol, and/or combinations thereof. The
formulation is made to suit the mode of administration. In general,
methods of administering proteins are well known in the art and can
be applied to administration of the non-natural amino acid
polypeptides, modified or unmodified, as described herein.
[0753] Therapeutic compositions comprising one or more of the
non-natural amino acid polypeptides, modified or unmodified, as
described herein are optionally tested in one or more appropriate
in vitro and/or in vivo animal models of disease, to confirm
efficacy, tissue metabolism, and to estimate dosages, according to
methods well known in the art. In particular, dosages can be
initially determined by activity, stability or other suitable
measures of non-natural to natural amino acid homologues (including
but not limited to, comparison of a polypeptide modified to include
one or more non-natural amino acids to a natural amino acid
polypeptide), i.e., in a relevant assay.
[0754] Administration is by any of the routes normally used for
introducing a molecule into ultimate contact with blood or tissue
cells. The non-natural amino acid polypeptides, modified or
unmodified, as described herein, are administered in any suitable
manner, optionally with one or more pharmaceutically acceptable
carriers. Suitable methods of administering the non-natural amino
acid polypeptides, modified or unmodified, as described herein, to
a patient are available, and, although more than one route can be
used to administer a particular composition, a particular route can
often provide a more immediate and more effective action or
reaction than another route.
[0755] Pharmaceutically acceptable carriers are determined in part
by the particular composition being administered, as well as by the
particular method used to administer the composition. Accordingly,
there is a wide variety of suitable formulations of pharmaceutical
compositions described herein.
[0756] The non-natural amino acid polypeptides described herein and
compositions comprising such polypeptides may be administered by
any conventional route suitable for proteins or peptides,
including, but not limited to parenterally, e.g. injections
including, but not limited to, subcutaneously or intravenously or
any other form of injections or infusions. Polypeptide
pharmaceutical compositions comprising non-natural amino acid
polypeptides described herein, may be administered by a number of
routes including, but not limited to oral, intravenous,
intraperitoneal, intramuscular, transdermal, subcutaneous, topical,
sublingual, or rectal means. Compositions comprising non-natural
amino acid polypeptides, modified or unmodified, as described
herein, can also be administered via liposomes. Such administration
routes and appropriate formulations are generally known to those of
skill in the art. The non-natural amino acid polypeptides described
herein, may be used alone or in combination with other suitable
components, including but not limited to, a pharmaceutical
carrier.
[0757] The non-natural amino acid polypeptides, modified or
unmodified, as described herein, alone or in combination with other
suitable components, can also be made into aerosol formulations
(i.e., they can be "nebulized") to be administered via inhalation.
Aerosol formulations can be placed into pressurized acceptable
propellants, such as dichlorodifluoromethane, propane, nitrogen,
and the like.
[0758] Formulations suitable for parenteral administration, such
as, for example, by intraarticular (in the joints), intravenous,
intramuscular, intradermal, intraperitoneal, and subcutaneous
routes, include aqueous and non-aqueous, isotonic sterile injection
solutions, which can contain antioxidants, buffers, bacteriostats,
and solutes that render the formulation isotonic with the blood of
the intended recipient, and aqueous and non-aqueous sterile
suspensions that can include suspending agents, solubilizers,
thickening agents, stabilizers, and preservatives. The formulations
of packaged nucleic acid can be presented in unit-dose or
multi-dose sealed containers, such as ampules and vials.
[0759] Parenteral administration and intravenous administration are
preferred methods of administration. In particular, the routes of
administration already in use for natural amino acid homologue
therapeutics (including but not limited to, those typically used
for EPO, IFN, GH, G-CSF, GM-CSF, IFNs, interleukins, antibodies,
and/or any other pharmaceutically delivered protein), along with
formulations in current use, provide preferred routes of
administration and formulation for the non-natural amino acid
polypeptides, modified or unmodified, as described herein.
[0760] The dose administered to a patient, in the context
compositions and methods described herein, is sufficient to have a
beneficial therapeutic response in the patient over time. The dose
is determined by the efficacy of the particular formulation, and
the activity, stability or serum half-life of the non-natural amino
acid polypeptides, modified or unmodified, employed and the
condition of the patient, as well as the body weight or surface
area of the patient to be treated. The size of the dose is also
determined by the existence, nature, and extent of any adverse
side-effects that accompany the administration of a particular
formulation, or the like in a particular patient.
[0761] In determining the effective amount of the formulation to be
administered in the treatment or prophylaxis of disease (including
but not limited to, cancers, inherited diseases, diabetes, AIDS, or
the like), the physician evaluates circulating plasma levels,
formulation toxicities, progression of the disease, and/or where
relevant, the production of anti-non-natural amino acid polypeptide
antibodies.
[0762] The dose administered, for example, to a 70 kilogram
patient, is typically in the range equivalent to dosages of
currently-used therapeutic proteins, adjusted for the altered
activity or serum half-life of the relevant composition. The
pharmaceutical formulations described herein can supplement
treatment conditions by any known conventional therapy, including
antibody administration, vaccine administration, administration of
cytotoxic agents, natural amino acid polypeptides, nucleic acids,
nucleotide analogues, biologic response modifiers, and the
like.
[0763] For administration, the pharmaceutical formulations
described herein are administered at a rate determined by the LD-50
or ED-50 of the relevant formulation, and/or observation of any
side-effects of the non-natural amino acid polypeptides, modified
or unmodified, at various concentrations, including but not limited
to, as applied to the mass and overall health of the patient.
Administration can be accomplished via single or divided doses.
[0764] If a patient undergoing infusion of a formulation develops
fevers, chills, or muscle aches, he/she receives the appropriate
dose of aspirin, ibuprofen, acetaminophen or other pain/fever
controlling drug. Patients who experience reactions to the infusion
such as fever, muscle aches, and chills are premedicated 30 minutes
prior to the future infusions with either aspirin, acetaminophen,
or, including but not limited to, diphenhydramine. Meperidine is
used for more severe chills and muscle aches that do not quickly
respond to antipyretics and antihistamines. Cell infusion is slowed
or discontinued depending upon the severity of the reaction.
[0765] Non-natural amino acid polypeptides, modified or unmodified,
as described herein, can be administered directly to a mammalian
subject. Administration is by any of the routes normally used for
introducing a polypeptide to a subject. The non-natural amino acid
polypeptides, modified or unmodified, as described herein, include
those suitable for oral, rectal, topical, inhalation (including but
not limited to, via an aerosol), buccal (including but not limited
to, sub-lingual), vaginal, parenteral (including but not limited
to, subcutaneous, intramuscular, intradermal, intraarticular,
intrapleural, intraperitoneal, intracerebral, intraarterial, or
intravenous), topical (i.e., both skin and mucosal surfaces,
including airway surfaces) and transdermal administration, although
the most suitable route in any given case will depend on the nature
and severity of the condition being treated. Administration can be
either local or systemic. The formulations can be presented in
unit-dose or multi-dose sealed containers, such as ampoules and
vials. The non-natural amino acid polypeptides, modified or
unmodified, as described herein, can be prepared in a mixture in a
unit dosage injectable form (including but not limited to,
solution, suspension, or emulsion) with a pharmaceutically
acceptable carrier. The non-natural amino acid polypeptides,
modified or unmodified, as described herein, can also be
administered by continuous infusion (using, including but not
limited to, minipumps such as osmotic pumps), single bolus or
slow-release depot formulations.
[0766] Formulations suitable for administration include aqueous and
non-aqueous solutions, isotonic sterile solutions, which can
contain antioxidants, buffers, bacteriostats, and solutes that
render the formulation isotonic, and aqueous and non-aqueous
sterile suspensions that can include suspending agents,
solubilizers, thickening agents, stabilizers, and preservatives.
Solutions and suspensions can be prepared from sterile powders,
granules, and tablets of the kind previously described.
[0767] Freeze-drying is a commonly employed technique for
presenting proteins which serves to remove water from the protein
preparation of interest. Freeze-drying, or lyophilization, is a
process by which the material to be dried is first frozen and then
the ice or frozen solvent is removed by sublimation in a vacuum
environment. An excipient may be included in pre-lyophilized
formulations to enhance stability during the freeze-drying process
and/or to improve stability of the lyophilized product upon
storage. Pikal, M. Biopharm. 3(9)26-30 (1990) and Arakawa et al.
Pharm. Res. 8(3):285-291 (1991).
[0768] The spray drying of pharmaceuticals is also known to those
of ordinary skill in the art. For example, see Broadhead, J. et
al., "The Spray Drying of Pharmaceuticals," in Drug Dev. Ind.
Pharm, 18 (11 & 12), 1169-1206 (1992). In addition to small
molecule pharmaceuticals, a variety of biological materials have
been spray dried and these include: enzymes, sera, plasma,
micro-organisms and yeasts. Spray drying is a useful technique
because it can convert a liquid pharmaceutical preparation into a
fine, dustless or agglomerated powder in a one-step process. The
basic technique comprises the following four steps: a) atomization
of the feed solution into a spray; b) spray-air contact; c) drying
of the spray; and d) separation of the dried product from the
drying air. U.S. Pat. Nos. 6,235,710 and 6,001,800, which are
herein incorporated by reference in their entirety, describe the
preparation of recombinant erythropoietin by spray drying.
[0769] The pharmaceutical compositions described herein may
comprise a pharmaceutically acceptable carrier, excipient or
stabilizer. Pharmaceutically acceptable carriers are determined in
part by the particular composition being administered, as well as
by the particular method used to administer the composition.
Accordingly, there is a wide variety of suitable formulations of
pharmaceutical compositions (including optional pharmaceutically
acceptable carriers, excipients, or stabilizers) for the
non-natural amino acid polypeptides, modified or unmodified,
described herein, (see, for example, in Remington: The Science and
Practice of Pharmacy, Nineteenth Ed (Easton, Pa.: Mack Publishing
Company, 1995); Hoover, John E., Remington's Pharmaceutical
Sciences, Mack Publishing Co., Easton, Pa. 1975; Liberman, H. A.
and Lachman, L., Eds., Pharmaceutical Dosage Forms, Marcel Decker,
New York, N.Y., 1980; and Pharmaceutical Dosage Forms and Drug
Delivery Systems, Seventh Ed. (Lippincott Williams & Wilkins,
1999)). Suitable carriers include buffers containing succinate,
phosphate, borate, HEPES, citrate, imidazole, acetate, bicarbonate,
and other organic acids; antioxidants including but not limited to,
ascorbic acid; low molecular weight polypeptides including but not
limited to those less than about 10 residues; proteins, including
but not limited to, serum albumin, gelatin, or immunoglobulins;
hydrophilic polymers including but not limited to,
polyvinylpyrrolidone; amino acids including but not limited to,
glycine, glutamine, asparagine, arginine, histidine or histidine
derivatives, methionine, glutamate, or lysine; monosaccharides,
disaccharides, and other carbohydrates, including but not limited
to, trehalose, sucrose, glucose, mannose, or dextrins; chelating
agents including but not limited to, EDTA and edentate disodium;
divalent metal ions including but not limited to, zinc, cobalt, or
copper; sugar alcohols including but not limited to, mannitol or
sorbitol; salt-forming counter ions including but not limited to,
sodium; and/or nonionic surfactants, including but not limited to
Tween.TM. (including but not limited to, Tween 80 (polysorbate 80)
and Tween 20 (polysorbate 20), Pluronics.TM. and other pluronic
acids, including but not limited to, and other pluronic acids,
including but not limited to, pluronic acid F68 (poloxamer 188), or
PEG. Suitable surfactants include for example but are not limited
to polyethers based upon poly(ethylene oxide)-poly(propylene
oxide)-poly(ethylene oxide), i.e., (PEO-PPO-PEO), or poly(propylene
oxide)-poly(ethylene oxide)-poly(propylene oxide), i.e.,
(PPO-PEO-PPO), or a combination thereof. PEO-PPO-PEO and
PPO-PEO-PPO are commercially available under the trade names
Pluronics.TM., R-Pluronics.TM., Tetronics.TM. and R-Tetronics.TM.
(BASF Wyandotte Corp., Wyandotte, Mich.) and are further described
in U.S. Pat. No. 4,820,352 incorporated herein in its entirety by
reference. Other ethylene/polypropylene block polymers may be
suitable surfactants. A surfactant or a combination of surfactants
may be used to stabilize PEGylated non-natural amino acid
polypeptides against one or more stresses including but not limited
to stress that results from agitation. Some of the above may be
referred to as "bulking agents." Some may also be referred to as
"tonicity modifiers." Antimicrobial preservatives may also be
applied for product stability and antimicrobial effectiveness;
suitable preservatives include but are not limited to, benzyl
alcohol, benzalkonium chloride, metacresol, methyl/propyl parabene,
cresol, and phenol, or a combination thereof.
[0770] The non-natural amino acid polypeptides, modified or
unmodified, as described herein, including those linked to water
soluble polymers such as PEG can also be administered by or as part
of sustained-release systems. Sustained-release compositions
include, including but not limited to, semi-permeable polymer
matrices in the form of shaped articles, including but not limited
to, films, or microcapsules. Sustained-release matrices include
from biocompatible materials such as poly(2-hydroxyethyl
methacrylate) (Langer et al., J. Biomed. Mater. Res., 15: 267-277
(1981); Langer, Chem. Tech., 12: 98-105 (1982), ethylene vinyl
acetate (Langer et al., supra) or poly-D-(-)-3-hydroxybutyric acid
(EP 133,988), polylactides (polylactic acid) (U.S. Pat. No.
3,773,919; EP 58,481), polyglycolide (polymer of glycolic acid),
polylactide co-glycolide (copolymers of lactic acid and glycolic
acid) polyanhydrides, copolymers of L-glutamic acid and
gamma-ethyl-L-glutamate (U. Sidman et al., Biopolymers, 22, 547-556
(1983), poly(ortho)esters, polypeptides, hyaluronic acid, collagen,
chondroitin sulfate, carboxylic acids, fatty acids, phospholipids,
polysaccharides, nucleic acids, polyamino acids, amino acids such
as phenylalanine, tyrosine, isoleucine, polynucleotides, polyvinyl
propylene, polyvinylpyrrolidone and silicone. Sustained-release
compositions also include a liposomally entrapped compound.
Liposomes containing the compound are prepared by methods known per
se: DE 3,218,121; Eppstein et al., Proc. Natl. Acad. Sci. U.S.A.,
82: 3688-3692 (1985); Hwang et al., Proc. Natl. Acad. Sci. U.S.A.,
77: 40304034 (1980); EP 52,322; EP 36,676; EP 143,949; Japanese
Pat. Appln. 83-118008; U.S. Pat. Nos. 4,485,045, 4,619,794,
5,021,234, and 4,544,545; and EP 102,324.
[0771] Liposomally entrapped polypeptides can be prepared by
methods described in, e.g., DE 3,218,121; Eppstein et al., Proc.
Natl. Acad. Sci. U.S.A., 82: 3688-3692 (1985); Hwang et al., Proc.
Natl. Acad. Sci. U.S.A., 77: 4030-4034 (1980); EP 52,322; EP
36,676; EP 143,949; Japanese Pat. Appln. 83-118008; U.S. Pat. Nos.
4,485,045, 4,619,794, 5,021,234, and 4,544,545; and EP 102,324.
Composition and size of liposomes are well known or able to be
readily determined empirically by one skilled in the art. Some
examples of liposomes as described in, e.g., Park J W, et al.,
Proc. Natl. Acad. Sci. USA 92:1327-1331 (1995); Lasic D and
Papahadjopoulos D (eds): MEDICAL APPLICATIONS OF LIPOSOMES (1998);
Drummond D C, et al., Liposomal drug delivery systems for cancer
therapy, in Teicher B (ed): CANCER DRUG DISCOVERY AND DEVELOPMENT
(2002); Park J W, et al., Clin. Cancer Res. 8:1172-1181 (2002);
Nielsen U B, et al., Biochim. Biophys. Acta 1591(1-3):109-118
(2002); Mamot C, et al., Cancer Res. 63: 3154-3161 (2003).
[0772] The dose administered to a patient in the context of the
compositions, formulations and methods described herein, should be
sufficient to cause a beneficial response in the subject over time.
Generally, the total pharmaceutically effective amount of the
non-natural amino acid polypeptides, modified or unmodified, as
described herein, administered parenterally per dose is in the
range of about 0.01 .mu.g/kg/day to about 100 .mu.g/kg, or about
0.05 mg/kg to about 1 mg/kg, of patient body weight, although this
is subject to therapeutic discretion. The frequency of dosing is
also subject to therapeutic discretion, and may be more frequent or
less frequent than the commercially available products approved for
use in humans. Generally, a polymer:polypeptide conjugate,
including by way of example only, a PEGylated polypeptide, as
described herein, can be administered by any of the routes of
administration described above.
[0773] In some embodiments is a method for treating a disorder,
condition or disease comprising administering a therapeutically
effective amount of a polypeptide comprising at least one
non-natural amino acid selected from the group consisting of:
##STR00093## [0774] wherein each R.sub.a is independently selected
from the group consisting of H, halogen, alkyl, --NO.sub.2, --CN,
substituted alkyl, --N(R').sub.2, --C(O).sub.kR',
--C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where k is 1, 2, or
3; [0775] M is H or --CH.sub.2R.sub.5; or the M-N--C(R.sub.5)
moiety may form a 4 to 7 membered ring structure; [0776] R.sub.1 is
H, an amino protecting group, resin, amino acid, polypeptide, or
polynucleotide; [0777] R.sub.2 is OH, an ester protecting group,
resin, amino acid, polypeptide, or polynucleotide; [0778] R.sub.5
is alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR, -(alkylene or substituted alkylene)-S--S-(aryl or
substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0779] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-, --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R').dbd.N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and --C(R').sub.2--N(R')--N(R')--; [0780]
or R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; and [0781] each R' is independently H, alkyl, or
substituted alkyl with a proviso that when R.sub.1 is H then
R.sub.2 is not OH, or when R.sub.2 is OH then R.sub.1 is not H.
[0782] In other embodiments is a method for treating a disorder,
condition or disease, further comprising administering a
pharmaceutically acceptable carrier with the therapeutically
effective amount of the polypeptide. In further embodiments is a
method for treating a disorder, condition or disease, wherein
R.sub.1 and R.sub.2 are both polypeptides. In some embodiments is a
method for treating a disorder, condition or disease, wherein X is
a water-soluble polymer. In other embodiments is a method for
treating a disorder, condition or disease, wherein X is a
derivative of polyethylene glycol. In a further embodiment is a
method for treating a disorder, condition or disease, wherein X is
a cytotoxic compound.
In some embodiments is a method for treating a disorder, condition
or disease, wherein X is a drug.
[0783] In some embodiments is a method for treating a disorder,
condition or disease, wherein X is a second polypeptide. In other
embodiments is a method for treating a disorder, condition or
disease, wherein the second polypeptide is a peptide containing a
non-natural amino acid polypeptide.
[0784] In some embodiments is a method for treating a disorder,
condition or disease, wherein the polypeptide is a protein
homologous to a therapeutic protein selected from the group
consisting of: alpha-1 antitrypsin, angiostatin, antihemolytic
factor, antibody, antibody fragment, apolipoprotein, apoprotein,
atrial natriuretic factor, atrial natriuretic polypeptide, atrial
peptide, C-X-C chemokine, T39765, NAP-2, ENA-78, gro-a, gro-b,
gro-c, IP-10, GCP-2, NAP-4, SDF-1, PF4, MIG, calcitonin, c-kit
ligand, cytokine, CC chemokine, monocyte chemoattractant protein-1,
monocyte chemoattractant protein-2, monocyte chemoattractant
protein-3, monocyte inflammatory protein-1 alpha, monocyte
inflammatory protein-i beta, RANTES, 1309, R83915, R91733, HCC1,
T58847, D31065, T64262, CD40, CD40 ligand, c-kit ligand, collagen,
colony stimulating factor (CSF), complement factor 5a, complement
inhibitor, complement receptor 1, cytokine, epithelial neutrophil
activating peptide-78, MIP-16, MCP-1, epidermal growth factor
(EGF), epithelial neutrophil activating peptide, erythropoietin
(EPO), exfoliating toxin, Factor IX, Factor VII, Factor VIII;
Factor X, fibroblast growth factor (FGF), fibrinogen, fibronectin,
four-helical bundle protein, G-CSF, glp-1, GM-CSF,
glucocerebrosidase, gonadotropin, growth factor, growth factor
receptor, grf, hedgehog protein, hemoglobin, hepatocyte growth
factor (hGF), hirudin, human growth hormone (hGH), human serum
albumin, ICAM-1, ICAM-1 receptor, LFA-1, LFA-1 receptor, insulin,
insulin-like growth factor (IGF), IGF-I, IGF-II, interferon (IFN),
IFN-alpha, IFN-beta, IFN-gamma, interleukin (IL), IL-1, IL-2, IL-3,
IL4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12,
keratinocyte growth factor (KGF), lactoferrin, leukemia inhibitory
factor, luciferase, neurturin, neutrophil inhibitory factor (NIF),
oncostatin M, osteogenic protein, oncogene product, paracitonin,
parathyroid hormone, PD-ECSF, PDGF, peptide hormone, pleiotropin,
protein A, protein G, pth, pyrogenic exotoxin A, pyrogenic exotoxin
B, pyrogenic exotoxin C, pyy, relaxin, renin, SCF, small
biosynthetic protein, soluble complement receptor I, soluble I-CAM
1, soluble interleukin receptor, soluble TNF receptor, somatomedin,
somatostatin, somatotropin, streptokinase, superantigens,
staphylococcal enterotoxin, SEA, SEB, SEC1, SEC2, SEC3, SED, SEE,
steroid hormone receptor, superoxide dismutase, toxic shock
syndrome toxin, thymosin alpha 1, tissue plasminogen activator,
tumor growth factor (TGF), tumor necrosis factor, tumor necrosis
factor alpha, tumor necrosis factor beta, tumor necrosis factor
receptor (TNFR), VLA4 protein, VCAM-1 protein, vascular endothelial
growth factor (VEGF), urokinase, mos, ras, raf, met, p53, tat, fos,
myc, jun, myb, rel, estrogen receptor, progesterone receptor,
testosterone receptor, aldosterone receptor, LDL receptor, and
corticosterone.
[0785] In other embodiments is a method for treating a disorder,
condition or disease, wherein the at least one non-natural amino
acid is incorporated at a specific site within the polypeptide. In
some embodiments is a method for treating a disorder, condition or
disease, wherein the polypeptide is synthesized by a ribosome. In
some embodiments is a method for treating a disorder, condition or
disease, wherein the polypeptide comprising at least one
non-natural amino acid is stable in aqueous solution for at least 1
month. In other embodiments is a method for treating a disorder,
condition or disease, wherein the polypeptide comprising at least
one non-natural amino acid is stable for at least 2 weeks. In some
embodiments is a method for treating a disorder, condition or
disease, wherein the polypeptide comprising at least one
non-natural amino acid is stable for at least 5 days.
[0786] In a further embodiment is a method for detecting the
presence of a polypeptide in a patient, the method comprising
administering an effective amount of a homologous non-natural amino
acid polypeptide comprising at least one non-natural amino acid
selected from the group consisting of:
##STR00094## [0787] wherein each R.sub.a is independently selected
from the group consisting of H, halogen, alkyl, --NO.sub.2, --CN,
substituted alkyl, --N(R').sub.2, --C(O).sub.kR',
--C(O)N(R').sub.2, --OR', and --S(O).sub.kR', where k is 1, 2, or
3; [0788] M is H or --CH.sub.2R.sub.5; or the M-N--C(R.sub.5)
moiety may form a 4 to 7 membered ring structure; [0789] R.sub.1 is
H, an amino protecting group, resin, amino acid, polypeptide, or
polynucleotide; [0790] R.sub.2 is OH, an ester protecting group,
resin, amino acid, polypeptide, or polynucleotide; [0791] R.sub.5
is alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,
substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy,
substituted alkylalkoxy, polyalkylene oxide, substituted
polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl,
substituted aryl, heteroaryl, substituted heteroaryl, heterocycle,
substituted heterocycle, alkaryl, substituted alkaryl, aralkyl,
substituted aralkyl, --C(O)R'', --C(O)OR'', --C(O)N(R'').sub.2,
--C(O)NHCH(R'').sub.2, -(alkylene or substituted
alkylene)-N(R'').sub.2, -(alkenylene or substituted
alkenylene)-N(R'').sub.2, -(alkylene or substituted alkylene)-(aryl
or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl
or substituted aryl), -(alkylene or substituted
alkylene)-ON(R'').sub.2, -(alkylene or substituted
alkylene)-C(O)SR'', -(alkylene or substituted alkylene)-S--S-(aryl
or substituted aryl), wherein each R'' is independently hydrogen,
alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy,
substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted
heteroaryl, heterocycle, substituted heterocycle, alkaryl,
substituted alkaryl, aralkyl, substituted aralkyl, or --C(O)OR';
[0792] or R.sub.5 is L-X, where, X is a selected from the group
consisting of a label; a dye; a polymer; a water-soluble polymer; a
derivative of polyethylene glycol; a photocrosslinker; a cytotoxic
compound; a drug; an affinity label; a photoaffinity label; a
reactive compound; a resin; a second protein or polypeptide or
polypeptide analog; an antibody or antibody fragment; a metal
chelator; a cofactor; a fatty acid; a carbohydrate; a
polynucleotide; a DNA; a RNA; an antisense polynucleotide; a
saccharide, a water-soluble dendrimer, a cyclodextrin, a
biomaterial; a nanoparticle; a spin label; a fluorophore, a
metal-containing moiety; a radioactive moiety; a novel functional
group; a group that covalently or noncovalently interacts with
other molecules; a photocaged moiety; an actinic radiation
excitable moiety; a ligand; a photoisomerizable moiety; biotin; a
biotin analogue; a moiety incorporating a heavy atom; a chemically
cleavable group; a photocleavable group; an elongated side chain; a
carbon-linked sugar; a redox-active agent; an amino thioacid; a
toxic moiety; an isotopically labeled moiety; a biophysical probe;
a phosphorescent group; a chemiluminescent group; an electron dense
group; a magnetic group; an intercalating group; a chromophore; an
energy transfer agent; a biologically active agent; a detectable
label; a small molecule; an inhibitory ribonucleic acid; a
radionucleotide; a neutron-capture agent; a derivative of biotin;
quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme,
an activated complex activator, a virus, an adjuvant, an aglycan,
an allergan, an angiostatin, an antihormone, an antioxidant, an
aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule,
a mimotope, a receptor, a reverse micelle, and any combination
thereof; and L is optional, and when present is a linker selected
from the group consisting of alkylene, substituted alkylene,
alkenylene, substituted alkenylene, --O--, --O-(alkylene or
substituted alkylene)-, -(alkylene or substituted alkylene)-O--,
--C(O)--, --C(O)-(alkylene or substituted alkylene)-, -(alkylene or
substituted alkylene)-C(O)--, --C(O)N(R')--, --C(O)N(R')-(alkylene
or substituted alkylene)-, -(alkylene or substituted
alkylene)-C(O)N(R'), --OC(O)N(R')--, --OC(O)N(R')-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-OC(O)N(R')--, --N(R')C(O)--, --NR'C(O)-(alkylene or
substituted alkylene)-, -(alkylene or substituted
alkylene)-NR'C(O)--, --S--, --S-(alkylene or substituted
alkylene)-, --S(O).sub.k-- where k is 1, 2, or 3,
--S(O).sub.k(alkylene or substituted alkylene)-, --C(S)--,
--C(S)-(alkylene or substituted alkylene)-, --CSN(R')--,
--CSN(R')-(alkylene or substituted alkylene)-; --N(R')CO-(alkylene
or substituted alkylene)-, --N(R')C(O)O--, -(alkylene or
substituted alkylene)-O--N.dbd.CR'--, -(alkylene or substituted
alkylene)-C(O)NR'-(alkylene or substituted alkylene)-, -(alkylene
or substituted alkylene)-S(O).sub.k-(alkylene or substituted
alkylene)-S--, -(alkylene or substituted alkylene)-S--S--,
--S(O).sub.kN(R')--, --N(R')C(O)N(R')--, --N(R')C(S)N(R')--,
--N(R')S(O).sub.kN(R')--, --N(R')--N.dbd., --C(R').dbd.N--,
--C(R')--N--N(R')--, --C(R').dbd.N--N.dbd.,
--C(R').sub.2--N.dbd.N--, and C(R').sub.2--N(R')--N(R')--; [0793]
or R.sub.5 and any R.sub.a optionally form a cycloalkyl or a
heterocycloalkyl; [0794] each R' is independently H, alkyl, or
substituted alkyl; and with a proviso that when R.sub.1 is H then
R.sub.2 is not OH, or when R.sub.2 is OH then R.sub.1 is not H.
[0795] In other embodiments is a method for detecting the presence
of a polypeptide in a patient wherein the at least one non-natural
acid is incorporated at a specific site within the polypeptide. In
some embodiments is a method for detecting the presence of a
polypeptide in a patient, wherein the non-natural amino acid is
incorporated using a translation system. In some embodiments is a
method for detecting the presence of a polypeptide in a patient,
wherein the non-natural amino acid is incorporated into the
polypeptide using a translation system and a post translation
modification system. In other embodiments is a method for detecting
the presence of a polypeptide in a patient, wherein the at least
one non-natural amino acid is stable in aqueous solution for at
least 1 month. In some embodiments is a method for detecting the
presence of a polypeptide in a patient, wherein the at least one
non-natural amino acid is stable for at least 2 weeks. In other
embodiments is a method for detecting the presence of a polypeptide
in a patient, wherein the at least one non-natural amino acid is
stable for at least 5 days.
[0796] In some embodiments is a method for detecting the presence
of a polypeptide in a patient, wherein the polypeptide is a protein
homologous to a therapeutic protein selected from the group
consisting of: alpha-1 antitrypsin, angiostatin, antihemolytic
factor, antibody, apolipoprotein, apoprotein, atrial natriuretic
factor, atrial natriuretic polypeptide, atrial peptide, C-X-C
chemokine, T39765, NAP-2, ENA-78, gro-a, gro-b, gro-c, IP-10,
GCP-2, NAP-4, SDF-1, PF4, MIG, calcitonin, c-kit ligand, cytokine,
CC chemokine, monocyte chemoattractant protein-1, monocyte
chemoattractant protein-2, monocyte chemoattractant protein-3,
monocyte inflammatory protein-1 alpha, monocyte inflammatory
protein-i beta, RANTES, 1309, R83915, R91733, HCC1, T58847, D31065,
T64262, CD40, CD40 ligand, c-kit ligand, collagen, colony
stimulating factor (CSF), complement factor 5a, complement
inhibitor, complement receptor 1, cytokine, epithelial neutrophil
activating peptide-78, MIP-16, MCP-1, epidermal growth factor
(EGF), epithelial neutrophil activating peptide, erythropoietin
(EPO), exfoliating toxin, Factor IX, Factor VII, Factor VIII,
Factor X, fibroblast growth factor (FGF), fibrinogen, fibronectin,
four-helical bundle protein, G-CSF, glp-1, GM-CSF,
glucocerebrosidase, gonadotropin, growth factor, growth factor
receptor, grf, hedgehog protein, hemoglobin, hepatocyte growth
factor (hGF), hirudin, human growth hormone (hGH), human serum
albumin, ICAM-1, ICAM-1 receptor, LFA-1, LFA-1 receptor, insulin,
insulin-like growth factor (IGF), IGF-I, IGF-II, interferon (IFN),
IFN-alpha, IFN-beta, IFN-gamma, interleukin (IL), IL-1, IL-2, IL-3,
IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12,
keratinocyte growth factor (KGF), lactoferrin, leukemia inhibitory
factor, luciferase, neurturin, neutrophil inhibitory factor (NIF),
oncostatin M, osteogenic protein, oncogene product, paracitonin,
parathyroid hormone, PD-ECSF, PDGF, peptide hormone, pleiotropin,
protein A, protein G, pth, pyrogenic exotoxin A, pyrogenic exotoxin
B, pyrogenic exotoxin C, pyy, relaxin, renin, SCF, small
biosynthetic protein, soluble complement receptor I, soluble I-CAM
1, soluble interleukin receptor, soluble TNF receptor, somatomedin,
somatostatin, somatotropin, streptokinase, superantigens,
staphylococcal enterotoxin, SEA, SEB, SEC1, SEC2, SEC3, SED, SEE,
steroid hormone receptor, superoxide dismutase, toxic shock
syndrome toxin, thymosin alpha 1, tissue plasminogen activator,
tumor growth factor (TGF), tumor necrosis factor, tumor necrosis
factor alpha, tumor necrosis factor beta, tumor necrosis factor
receptor (TNFR), VLA4 protein, VCAM-1 protein, vascular endothelial
growth factor (VEGF), urokinase, mos, ras, raf, met, p53, tat, fos,
myc, jun, myb, rel, estrogen receptor, progesterone receptor,
testosterone receptor, aldosterone receptor, LDL receptor, and
corticosterone.
EXAMPLES
[0797] The following examples describe methods for synthesis of
aromatic amine containing amino acids.
Example 1a
Synthesis of 3-chloro-4-amino-phenylalanine
[0798] 3-chloro-4-amino-phenylalanine was synthesized according to
the method in FIG. 11.
Example 1b
Synthesis of 3-iodo-4-amino-phenylalanine
[0799] 3-iodo-4-amino-phenylalanine was synthesized according to
the method in FIG. 11.
Example 1c
Synthesis of 3-methoxy-4-amino-phenylalanine
[0800] 3-methoxy-4-amino-phenylalanine was synthesized according to
the method in FIG. 12.
Example 1d
Synthesis of 3-fluoro-4-amino-phenylalanine
[0801] 3-fluoro-4-amino-phenylalanine was synthesized according to
the method in FIG. 12.
Example 1e: Synthesis of N-methyl-p-amino-phenylalanine
[0802] N-methyl-p-amino-phenyalanine was synthesized according to
the method in FIG. 13.
Example 1f
Synthesis of N-ethyl-R-amino-phenylalanine
[0803] N-ethyl-p-amino-phenylalanine was synthesized according to
the method in FIG. 13.
[0804] The following examples describe methods for cloning and
expression of a modified polypeptide followed by post-translational
modification
Example 2
PEGylation of hGH
[0805] This example details cloning and expression of a modified
polypeptide in E. coli. An introduced translation system that
comprises an orthogonal tRNA (O-tRNA) and an orthogonal aminoacyl
tRNA synthetase (O--RS) is used to express the polypeptide
containing a non-natural amino acid. The O--RS preferentially
aminoacylates the O-tRNA with a non-natural amino acid. In turn the
translation system inserts the non-natural amino acid into the
polypeptide, in response to an encoded selector codon. The
transformation of E. coli with plasmids containing the modified
gene and the orthogonal aminoacyl tRNA synthetase/tRNA pair
(specific for the desired non-natural amino acid) allows the
site-specific incorporation of non-natural amino acid into the
polypeptide. The transformed E. coli, grown at 37.degree. C. in
media containing between 0.01-100 mM of the particular non-natural
amino acid, expresses modified polypeptide with high fidelity and
efficiency. The His-tagged polypeptide containing a non-natural
amino acid is produced by the E. coli host cells as inclusion
bodies or aggregates. The aggregates are solubilized and affinity
purified under denaturing conditions in 6M guanidine HCl. Refolding
is performed by dialysis at 4.degree. C. overnight in 50 mM
TRIS-HCl, pH8.0, 40 .mu.M CuSO.sub.4, and 2% (w/v) Sarkosyl. The
material is then dialyzed against 20 mM TRIS-HCl, pH 8.0, 100 mM
NaCl, 2 mM CaCl.sub.2, followed by removal of the His-tag. See
Boissel et al., (1993) 268:15983-93. Methods for purification of
polypeptides are well known in the art and are confirmed by
SDS-PAGE, Western Blot analyses, or electrospray-ionization ion
trap mass spectrometry and the like.
[0806] By way of example, hGH polypeptide with p-aminophenylalanine
substituted for the tyrosine at position 35 (H6-hGH Y35pAF2) was
generated in E. coli cells using constructs that encode for hGH,
and an orthogonal tRNA synthetase-orthogonal tRNA pair for the
non-natural amino acid. The expressed protein was purified using
IMAC and IEX chromatography. The protein was dialyzed into 10 mM
Sodium Phosphate, 20 g/L glycine, 5 g/L mannitol, pH 7.0 and was
then concentrated to 350 uM. The pH of the sample was adjusted to
pH 4.0 using 10% acetic acid. Post translational modification of
H6-hGH Y35pAF2 was demonstrated by the pegylation of H6-hGH Y35pAF2
by reductive alkylation of the p-aminophenylalanine with various
PEG-aldehydes. A non-limiting procedure for such pegylation is
outlined in FIG. 39 and is described herein as follows: 100 ul
PEGylation reactions were set-up using 20K, 30K, and 40K PEG
aldehyde. The PEG aldehyde was in 20 mM acetate buffer at pH 4.0.
Each reaction had a 1:1 molar ratio of PEG to protein, and a 5:1
molar ratio of NaCNBH.sub.3 solubilized in DMF:protein. The
reactions were incubated at either 4 degrees or at room temperature
and were analyzed by SDS-PAGE after 3, 4, 6 and 16 hrs. Gel
electrophoresis of the resulting peptides are shown in the FIG.
40
[0807] The following examples describe methods for modification of
polypeptides by post-translational modification as shown in FIGS.
20-34, wherein X is p-aminophenylalanine.
Example 3a
Reductive Alkylations of Reduced Urotensin-II (UT-II-SH) with
Propionaldehyde and Benzaldehyde
[0808] A mixture of 3 equivalents of NaBCNH.sub.3 at pH 4 was added
to a mixture of 0.25 mM propionaldehyde (or 0.25 mM benzaldehyde)
and 0.25 mM reduced urotensin and allowed to react for 2 hours.
Analysis of the product mixture was by HPLC with the following
conditions: 0-50% B (A, 0.05% TFA in water; B, 60% acetonitrile and
0.05% TFA in water), flow rate: 1.5 mL/min; column: Zorbax Extend
C18, 3.5 m, 4.6.times.50 mm.
Example 3b
Reductive Alkylations of Urotensin-II (UT-II) with Propionaldehyde
and Benzaldehyde
[0809] A mixture of 3 equivalents of NaBCNH.sub.3 at pH 4 was added
to a mixture of 0.25 mM propionaldehyde (or 0.25 mM benzaldehyde)
and 0.25 mM urotensin and allowed to react for 2 hours. Analysis of
the product mixture was by HPLC with the following conditions:
5-60% B (A, 0.05% TFA in water; B, 60% acetonitrile and 0.05% TFA
in water), flow rate: 1.5 mL/min; column: Zorbax Extend C18, 3.5 m,
4.6.times.50 mm.
Example 3c
Reductive Alkylations of Peptide XT-8 with Propionaldehyde,
Benzaldehyde, Isobutaldehyde and Pivalaldehyde
[0810] A mixture of 3 equivalents of NaBCNH.sub.3 at pH 4 was added
to a mixture of 0.25 mM propionaldehyde (or 0.25 mM benzaldehyde,
or 0.25 mM isobutaldehyde or 0.25 mM pivalaldehyde) and 0.25 mM
XT-8 were allowed to react for 2 hours. Analysis of the product
mixture was by HPLC with the following conditions: 5-60% B (A,
0.05% TFA in water; B, 60% acetonitrile and 0.05% TFA in water),
flow rate: 1.5 mL/min; column: Zorbax Extend C18, 3.5 m,
4.6.times.50 mm.
Example 3d
Reductive Alkylations of Peptide SXT-9 with Propionaldehyde,
Benzaldehyde, Isobutaldehyde and Pivalaldehyde
[0811] A mixture of 3 equivalents of NaBCNH.sub.3 at pH 4 was added
to a mixture of 0.25 mM propionaldehyde (or 0.25 mM benzaldehyde,
or 0.25 mM isobutaldehyde or 0.25 mM pivalaldehyde) and 0.25 mM
SXT-9 were allowed to react for 2 hours. Analysis of the product
mixture was by HPLC with the following conditions: 5-60% B (A,
0.05% TFA in water; B, 60% acetonitrile and 0.05% TFA in water),
flow rate: 1.5 mL/min; column: Zorbax Extend C18, 3.5 m,
4.6.times.50 mm.
Example 3e
Reductive Alkylations of Peptide HXT-9 with Propionaldehyde,
Benzaldehyde Isobutaldehyde and Pivalaldehyde
[0812] A mixture of 3 equivalents of NaBCNH.sub.3 at pH 4 was added
to a mixture of 0.25 mM propionaldehyde (or 0.25 mM benzaldehyde,
or 0.25 mM isobutaldehyde or 0.25 mM pivalaldehyde) and 0.25 mM
HXT-9 were allowed to react for 2 hours. Analysis of the product
mixture was by HPLC with the following conditions: 5-60% B (A,
0.05% TFA in water; B, 60% acetonitrile and 0.05% TFA in water),
flow rate: 1.5 mL/min; column: Zorbax Extend C18, 3.5 m,
4.6.times.50 mm.
Example 3f
Reductive Alkylations of Peptide WXT-9 with Propionaldehyde,
Benzaldehyde, and Isobutaldehyde
[0813] A mixture of 3 equivalents of NaBCNH.sub.3 at pH 4 was added
to a mixture of 0.25 mM propionaldehyde (or 0.25 mM benzaldehyde,
or 0.25 mM isobutaldehyde) and 0.25 mM WXT-9 were allowed to react
for 2 hours. Analysis of the product mixture was by HPLC with the
following conditions: 5-60% B (A, 0.05% TFA in water; B, 60%
acetonitrile and 0.05% TFA in water), flow rate: 1.5 mL/min;
column: Zorbax Extend C18, 3.5 m, 4.6.times.50 mm.
Example 3g
Reductive Alkylations of Peptide NXT-9 with Propionaldehyde, and
Benzaldehyde
[0814] A mixture of 3 equivalents of NaBCNH.sub.3 at pH 4 was added
to a mixture of 0.25 mM propionaldehyde (or 0.25 mM benzaldehyde)
and 0.25 mM NXT-9 were allowed to react for 2 hours. Analysis of
the product mixture was by HPLC with the following conditions:
5-60% B (A, 0.05% TFA in water; B, 60% acetonitrile and 0.05% TFA
in water), flow rate: 1.5 mL/min; column: Zorbax Extend C18, 3.5 m,
4.6.times.50 mm.
Example 3h
Reductive Alkylations of Peptide RXT-10 with Propionaldehyde or
Benzaldehyde
[0815] A mixture of 3 equivalents of NaBCNH.sub.3 at pH 4 was added
to a mixture of 0.25 mM propionaldehyde (or 0.25 mM benzaldehyde)
and 0.25 mM RXT-10 were allowed to react for 2 hours. Analysis of
the product mixture was by HPLC with the following conditions:
5-60% B (A, 0.05% TFA in water; B, 60% acetonitrile and 0.05% TFA
in water), flow rate: 1.5 mL/min; column: Zorbax Extend C18, 3.5 m,
4.6.times.50 mm.
Example 31
Reductive Alkylations of Peptide AXT-11 with Propionaldehyde or
Benzaldehyde
[0816] A mixture of 3 equivalents of NaBCNH.sub.3 at pH 4 was added
to a mixture of 0.25 mM propionaldehyde (or 0.25 mM benzaldehyde)
and 0.25 mM AXT-11 were allowed to react for 2 hours. Analysis of
the product mixture was by HPLC with the following conditions:
5-60% B (A, 0.05% TFA in water; B, 60% acetonitrile and 0.05% TFA
in water), flow rate: 1.5 mL/min; column: Zorbax Extend C18, 3.5 m,
4.6.times.50 mm.
Example 3j
Reductive alkylations of peptide AXT-11 with 3-phenylpropanal,
2-phenylacetaldehyde, or cinnamaldehyde
[0817] A mixture of 3 equivalents of NaBCNH.sub.3 at pH 4 was added
to a mixture of 0.25 mM 3-phenylpropanal (or 0.25 mM
2-phenylacetaldehyde or 0.25 mM cinnamaldehyde) and 0.25 mM AXT-11
were allowed to react for 5 hours. Analysis of the product mixture
was by HPLC with the following conditions: 5-60% B (A, 0.05% TFA in
water; B, 60% acetonitrile and 0.05% TFA in water), flow rate: 1.5
mL/min; column: Zorbax Extend C18, 3.5 m, 4.6.times.50 mm.
Example 3k
Reductive alkylations of peptide AXT-11 with
1H-imidazole-5-carbaldehyde, thiophene-2-carbaldehyde,
picolinaldehyde, or quinoline-4-carbaldehyde
[0818] A mixture of 3 equivalents of NaBCNH.sub.3 at pH 4 was added
to a mixture of 0.25 mM of 1H-imidazole-5-carbaldehyde (or 0.25 mM
thiophene-2-carbaldehyde, or 0.25 mM picolinaldehyde, or 0.25 mM
quinoline-4-carbaldehyde) and 0.25 mM AXT-11 were allowed to react
for 5 hours. Analysis of the product mixture was by HPLC with the
following conditions: 5-60% B (A, 0.05% TFA in water; B, 60%
acetonitrile and 0.05% TFA in water), flow rate: 1.5 mL/min;
column: Zorbax Extend C18, 3.5 m, 4.6.times.50 mm.
Example 31
Reductive alkylations of peptide AXT-11 with benzaldehyde,
1-phenylbutane-1,3-dione, or a mixture of benzaldehyde and
1-phenylbutane-1,3-dione
[0819] A mixture of 3 equivalents of NaBCNH.sub.3 at pH 4 was added
to a mixture of 0.20 mM of benzaldehyde, (or 0.20 mM
1-phenylbutane-1,3-dione, or a mixture of 0.20 mM benzaldehyde and
0.20 mM 1-phenylbutane-1,3-dione) and 0.20 mM AXT-11 were allowed
to react for 2 hours. Analysis of the product mixture was by HPLC
with the following conditions: 5-60% B (A, 0.05% TFA in water; B,
60% acetonitrile and 0.05% TFA in water), flow rate: 1.5 mL/min;
column: Zorbax Extend C18, 3.5 m, 4.6.times.50 mm.
Example 3m
Reductive alkylations of peptide NXT-9 with benzaldehyde,
1-phenylpropane-1,2-dione, or a mixture of benzaldehyde and
1-phenylpropane-1,2-dione
[0820] A mixture of 3 equivalents of NaBCNH.sub.3 at pH 4 was added
to a mixture of 0.20 mM of benzaldehyde, (or 0.20 mM
1-phenylpropane-1,2-dione, or a mixture of 0.20 mM benzaldehyde and
0.20 mM 1-phenylpropane-1,2-dione) and 0.20 mM NXT-9 were allowed
to react for 2 hours. Analysis of the product mixture was by HPLC
with the following conditions: 5-60% B (A, 0.05% TFA in water; B,
60% acetonitrile and 0.05% TFA in water), flow rate: 1.5 mL/min;
column: Zorbax Extend C18, 3.5 m, 4.6.times.50 mm.
Example 3n
Reductive alkylations of peptide MXT-9 with benzaldehyde,
acetophenone, a mixture of benzaldehyde and acetophenone, a mixture
of benzaldehyde and 1,2-propionaldehyde, or a mixture of
benzaldehyde and butan-2-one
[0821] A mixture of 3 equivalents of NaBCNH.sub.3 at pH 4 was added
to a mixture of 0.20 mM of benzaldehyde, (or 0.20 mM acetophenone,
or a mixture of 0.20 mM benzaldehyde and 0.20 mM acetophenone, or a
mixture of 0.20 mM benzaldehyde and 0.20 mM propionaldehyde, or a
mixture of 0.20 mM benzaldehyde and 0.20 mM butan-2-one) and 0.20
mM MXT-9 were allowed to react for 2 hours. Analysis of the product
mixture was by HPLC with the following conditions: 5-60% B (A,
0.05% TFA in water; B, 60% acetonitrile and 0.05% TFA in water),
flow rate: 1.5 mL/min; column: Zorbax Extend C18, 3.5 m,
4.6.times.50 mm.
Example 3o
Reduction of Peptide MXT-9-N.sub.3 Followed by Reductive
Alkylations of Peptide MXT-9-NH.sub.2 with propionaldehyde or
benzaldehyde
[0822] A mixture of MXT-9-N.sub.3 was reduced with TCEP giving the
peptide MXT-9-NH.sub.2. A mixture of 3 equivalents of NaBCNH.sub.3
at pH 4 was added to a mixture of 0.20 mM of propionaldehyde, (or
0.20 mM benzaldehyde) and 0.20 mM MXT-9-NH.sub.2 were allowed to
react for 1 hour. Analysis of the product mixture was by HPLC with
the following conditions: 5-60% B (A, 0.05% TFA in water; B, 60%
acetonitrile and 0.05% TFA in water), flow rate: 1.5 mL/min;
column: Zorbax Extend C18, 3.5 m, 4.6.times.50 mm.
[0823] The following examples describe methods to measure and
compare the in vitro and in vivo activity of a modified
therapeutically active non-natural amino acid polypeptide to the in
vitro and in vivo activity of a therapeutically active natural
amino acid polypeptide.
Example 4
Measurement of Non-Natural Amino Acid Polypeptide Activity and
Affinity
[0824] This example details the measurement of non-natural amino
acid polypeptide activity and affinity of non-natural amino acid
polypeptides for their receptor, binding partner, or ligand.
[0825] Protein for the non-natural amino acid polypeptide receptor,
binding partner, or ligand is expressed and isolated according to
methods known to those of ordinary skill in the art. The
Biocore.TM. system is used to analyze the binding of non-natural
amino acid polypeptide to its receptor. Similarly, a binding
partner or ligand may be used in this assay.
[0826] Approximately 600-800 RUs of soluble receptor is immobilized
on a Biacore.TM. CM5 chip, using a standard amine-coupling
procedure, as recommended by the manufacturer. Various
concentrations of wild type or (modified) non-natural amino acid
polypeptide in HBS-EP buffer (Biacore.TM., Pharmacia) are injected
over the surface at a flow rate of 40 .mu.l/min for 4-5 minutes,
and dissociation was monitored for 15 minutes post-injection. The
surface is regenerated by a 15 second pulse of 4.5M MgCl.sub.2.
Only a minimal loss of binding affinity (1-5%) is observed after at
least 100 regeneration cycles. A reference cell with no receptor
immobilized is used to subtract any buffer bulk effects and
non-specific binding.
[0827] Kinetic binding data obtained from (modified) non-natural
amino acid polypeptide titration experiments is processed with
BiaEvaluation 4.1 software (BIACORE.TM.). Equilibrium dissociation
constants (Kd) are calculated as ratios of individual rate
constants (k.sub.off/k.sub.on).
[0828] Stable Cell Lines are established expressing receptor,
binding partner, or ligand for the non-natural amino acid
polypeptide. Cells are electroporated with a construct that
containing the receptor, binding partner, or ligand cDNA.
Transfected cells are allowed to recover for 48 hours before
cloning. Receptor, binding partner, or ligand expressing
transfectants are identified by surface staining with antibody
against the receptor and are analyzed on a FACS Array (BD
Biosciences, San Diego, Calif.). Stably transfected cell clones are
established upon further rounds of repeated subcloning of desired
transfectants. Such cells are used in cell binding assays.
[0829] Cells (3.times.10.sup.6) are incubated in duplicate in
PBS/1% BSA (100 .mu.l) in the absence or presence of various
concentrations (volume: 10 .mu.l) of unlabeled natural amino acid
polypeptide or a negative control polypeptide and in the presence
of .sup.125I-(modified) non-natural amino acid polypeptide (approx.
100,000 cpm or 1 ng) at 0.degree. C. for 90 minutes (total volume:
120 .mu.l). Cells are then resuspended and layered over 200 .mu.l
ice cold FCS in a 350 .mu.l plastic centrifuge tube and centrifuged
(1000 g; 1 minute). The pellet is collected by cutting off the end
of the tube and pellet and supernatant counted separately in a
gamma counter (Packard).
[0830] Specific binding (cpm) is determined as total binding in the
absence of a competitor (mean of duplicates) minus non-specific
binding. The non-specific binding is measured for each of the cell
types used. Experiments are run on separate days using the same
preparation of .sup.125I-(modified) non-natural amino acid
polypeptide and should display internal consistency.
.sup.125I-(modified) non-natural amino acid polypeptide
demonstrates binding to the receptor, binding protein, or
ligand-producing cells. The binding is inhibited in a dose
dependent manner by unlabeled natural amino acid polypeptide, but
not by a negative control polypeptide.
Example 5
In Vivo Studies of Modified Therapeutically Active Non-Natural
Amino Acid Polypeptide
[0831] Modified therapeutically active non-natural amino acid
polypeptide, therapeutically active natural amino acid polypeptide
and buffer solution are administered to mice or rats. The results
will show superior activity and prolonged half life of the modified
therapeutically active non-natural amino acid polypeptide of in
comparison to that for therapeutically active natural amino acid
polypeptide.
Example 6
Measurement of the In Vivo Half-Life of Conjugated and
Non-Conjugated Modified Therapeutically Active Non-Natural Amino
Acid Polypeptide and Variants Thereof
[0832] All animal experimentation is conducted in an AAALAC
accredited facility and under protocols approved by the
Institutional Animal Care and Use Committee of St. Louis
University. Rats are housed individually in cages in rooms with a
12-hour light/dark cycle. Animals are provided access to certified
Purina rodent chow 5001 and water ad libitum.
Example 7
Pharmacokinetic Studies
[0833] The quality of each modified therapeutically active
non-natural amino acid polypeptide are evaluated by three assays
before entering animal experiments. The purity of the modified
therapeutically active non-natural amino acid polypeptide are
examined by running a 4-12% acrylamide NuPAGE Bis-Tris gel with MES
SDS running buffer under non-reducing conditions (Invitrogen,
Carlsbad, Calif.). The gels are stained with Coomassie blue. The
modified therapeutically active non-natural amino acid polypeptide
band is greater than 95% pure based on densitometry scan. The
endotoxin level in each modified therapeutically active non-natural
amino acid polypeptide is tested by a kinetic LAL assay using the
KTA.sup.2 kit from Charles River Laboratories (Wilmington, Mass.),
and is less than 5 EU per dose. The biological activity of the
modified therapeutically active non-natural amino acid polypeptide
is assessed with the cell assays that characterize bioactivity of
the polypeptide.
[0834] Pharmacokinetic properties of modified therapeutically
active non-natural amino acid polypeptide compounds are compared to
each other and to therapeutically active natural amino acid
polypeptide in male Sprague-Dawley rats (261-425 g) obtained from
Charles River Laboratories. Catheters are surgically installed into
the carotid artery for blood collection. Following successful
catheter installation, animals are assigned to treatment groups
(three to six per group) prior to dosing. Animals are dosed
subcutaneously with 1 mg/kg of compound in a dose volume of
0.41-0.55 ml/kg. Blood samples are collected at various time points
via the indwelling catheter and into EDTA-coated microfuge tubes.
Plasma is collected after centrifugation, and stored at -80.degree.
C. until analysis. Compound concentrations are measured using
antibody sandwich ELISA kits from either BioSource International
(Camarillo, Calif.) or Diagnostic Systems Laboratories (Webster,
Tex.). Concentrations are calculated using standards corresponding
to the analog that is dosed. Pharmacokinetic parameters are
estimated using the modeling program WinNonlin (Pharsight, version
4.1). Noncompartmental analysis with linear-up/log-down trapezoidal
integration is used, and concentration data is uniformly weighted.
The data is then plotted to obtain Cmax: maximum concentration;
terminal .sub.t1/2: terminal half-life; AUC.sub.0->inf: area
under the concentration-time curve extrapolated to infinity; MRT:
mean residence time; Cl/f: apparent total, plasma clearance; and
Vz/f: apparent volume of distribution during terminal phase.
Example 8
Pharmacodynamic Studies
[0835] Male Sprague-Dawley rats are obtained from Charles River
Laboratories. Animals are allowed to acclimate for a period of
three weeks, during which time biological characteristics
associated with the natural amino acid polypeptide are monitored.
Animals with an acceptable level of change in these biological
characteristics are randomized to treatment groups. Rats are
administered either a bolus dose or daily dose subcutaneously of
the modified non-natural amino acid polypeptide. Throughout the
study rats are daily and sequentially anesthetized, bled, and dosed
(when applicable) and the correlating biological characteristics
are measured. Blood is collected from the orbital sinus using a
heparinized capillary tube and placed into an EDTA coated microfuge
tube. Plasma is isolated by centrifugation and stored at
-80.degree. C. until analysis. The plasma concentrations following
a single subcutaneous dose in the rats are obtained.
Example 9
Human Clinical Trial of the Safety and/or Efficacy of Modified
Therapeutically Active Non-Natural Amino acid Polypeptide
[0836] Objective To compare the safety and pharmacokinetics of
subcutaneously administered a modified therapeutically active,
non-natural amino acid polypeptide to the safety and
pharmacokinetics of a therapeutically active natural amino acid
polypeptide.
[0837] Patients Eighteen healthy volunteers ranging between 20-40
years of age and weighing between 60-90 kg are enrolled in the
study. The subjects will have no clinically significant abnormal
laboratory values for hematology or serum chemistry, and a negative
urine toxicology screen, HIV screen, and hepatitis B surface
antigen. They should not have any evidence of the following:
hypertension; a history of any primary hematologic disease; history
of significant hepatic, renal, cardiovascular, gastrointestinal,
genitourinary, metabolic, neurologic disease; a history of anemia
or seizure disorder; a known sensitivity to bacterial or
mammalian-derived products, PEG, or human serum albumin; habitual
and heavy consumer to beverages containing caffeine; participation
in any other clinical trial or had blood transfused or donated
within 30 days of study entry; had exposure to a therapeutically
active natural amino acid polypeptide within three months of study
entry; had an illness within seven days of study entry; and have
significant abnormalities on the pre-study physical examination or
the clinical laboratory evaluations within 14 days of study entry.
All subjects are evaluable for safety and all blood collections for
pharmacokinetic analysis are collected as scheduled. All studies
are performed with institutional ethics committee approval and
patient consent.
[0838] Study Design This will be a Phase I, single-center,
open-label, randomized, two-period crossover study in healthy male
volunteers. Eighteen subjects are randomly assigned to one of two
treatment sequence groups (nine subjects/group). A therapeutically
active natural amino acid polypeptide is administered over two
separate dosing periods as a bolus s.c. injection in the upper
thigh using equivalent doses of the modified therapeutically active
non-natural amino acid polypeptide. Additional dosing, dosing
frequency, or other parameter as desired, may be added to the study
by including additional groups of subjects. Each dosing period is
separated by a 14-day washout period. Subjects are confined to the
study center at least 12 hours prior to and 72 hours following
dosing for each of the two dosing periods, but not between dosing
periods. Additional groups of subjects may be added if there are to
be additional dosing, frequency, or other parameter, to be tested
for the modified therapeutically active non-natural amino acid
polypeptide as well.
[0839] Blood Sampling Serial blood is drawn by direct vein puncture
before and after administration of modified therapeutically active
non-natural amino acid polypeptide or therapeutically active
natural amino acid polypeptide. Venous blood samples (5 mL) for
determination of serum modified therapeutically active non-natural
amino acid polypeptide or therapeutically active natural amino acid
polypeptide concentrations are obtained at about 30, 20, and 10
minutes prior to dosing (3 baseline samples) and at approximately
the following times after dosing: 30 minutes and at 1, 2, 5, 8, 12,
15, 18, 24, 30, 36, 48, 60 and 72 hours. Each serum sample is
divided into two aliquots. All serum samples are stored at
-20.degree. C. Serum samples are shipped on dry ice. Fasting
clinical laboratory tests (hematology, serum chemistry, and
urinalysis) are performed immediately prior to the initial dose on
day 1, the morning of day 4, immediately prior to dosing on day 16,
and the morning of day 19.
[0840] Bioanalytical Methods An ELISA kit procedure (Diagnostic
Systems Laboratory [DSL], Webster Tex.), is used for the
determination of serum concentrations.
[0841] Safety Determinations Vital signs are recorded immediately
prior to each dosing (Days 1 and 16), and at 6, 24, 48, and 72
hours after each dosing. Safety determinations are based on the
incidence and type of adverse events and the changes in clinical
laboratory tests from baseline. In addition, changes from pre-study
in vital sign measurements, including blood pressure, and physical
examination results are evaluated.
[0842] Data Analysis Post-dose serum concentration values are
corrected for pre-dose baseline concentrations by subtracting from
each of the post-dose values the mean baseline concentration
determined from averaging the levels from the three samples
collected at 30, 20, and 10 minutes before dosing. Pre-dose serum
concentrations are not included in the calculation of the mean
value if they are below the quantification level of the assay.
Pharmacokinetic parameters are determined from serum concentration
data corrected for baseline concentrations. Pharmacokinetic
parameters are calculated by model independent methods on a Digital
Equipment Corporation VAX 8600 computer system using the latest
version of the BIOAVL software. The following pharmacokinetics
parameters are determined: peak serum concentration (C.sub.max);
time to peak serum concentration (t.sub.max); area under the
concentration-time curve (AUC) from time zero to the last blood
sampling time (AUC.sub.0-72) calculated with the use of the linear
trapezoidal rule; and terminal elimination half-life (t.sub.1/2),
computed from the elimination rate constant. The elimination rate
constant is estimated by linear regression of consecutive data
points in the terminal linear region of the log-linear
concentration-time plot. The mean, standard deviation (SD), and
coefficient of variation (CV) of the pharmacokinetic parameters are
calculated for each treatment. The ratio of the parameter means
(preserved formulation/non-preserved formulation) is
calculated.
[0843] Safety Results The incidence of adverse events is equally
distributed across the treatment groups. There are no clinically
significant changes from baseline or pre-study clinical laboratory
tests or blood pressures, and no notable changes from pre-study in
physical examination results and vital sign measurements. The
safety profiles for the two treatment groups should appear
similar.
[0844] Pharmacokinetic Results Mean serum modified therapeutically
active non-natural amino acid polypeptide or therapeutically active
natural amino acid polypeptide concentration-time profiles
(uncorrected for baseline levels) in all 18 subjects after
receiving a single dose of modified therapeutically active
non-natural amino acid polypeptide or therapeutically active
natural amino acid polypeptide are compared at each time point
measured. All subjects should have pre-dose baseline concentrations
within the normal physiologic range. Pharmacokinetic parameters are
determined from serum data corrected for pre-dose mean baseline
concentrations and the C.sub.max and t.sub.max are determined. The
mean t.sub.max for the therapeutically active natural amino acid
polypeptide is significantly shorter than the t.sub.max for the
modified therapeutically active non-natural amino acid polypeptide.
Terminal half-life values are significantly shorter for the
therapeutically active natural amino acid polypeptide compared with
the terminal half-life for the modified therapeutically active
non-natural amino acid polypeptide.
[0845] Although the present study is conducted in healthy male
subjects, similar absorption characteristics and safety profiles
would be anticipated in other patient populations; such as male or
female patients with cancer or chronic renal failure, pediatric
renal failure patients, patients in autologous predeposit programs,
or patients scheduled for elective surgery.
[0846] In conclusion, subcutaneously administered single doses of
modified therapeutically active non-natural amino acid polypeptide
will be safe and well tolerated by healthy male subjects. Based on
a comparative incidence of adverse events, clinical laboratory
values, vital signs, and physical examination results, the safety
profiles of the modified therapeutically active non-natural amino
acid polypeptide and the therapeutically active natural amino acid
polypeptide will be equivalent. The modified therapeutically active
non-natural amino acid polypeptide potentially provides large
clinical utility to patients and health care providers.
[0847] It is understood that the examples and embodiments described
herein are for illustrative purposes only and that various
modifications or changes in light thereof will be suggested to
persons skilled in the art and are to be included within the spirit
and purview of this application and scope of the appended claims.
All publications, patents, and patent applications cited herein are
hereby incorporated by reference in their entirety for all
purposes.
TABLE-US-00003 SEQUENCE LISTING Protein, nucleic acid, SEQ ID
Sequence Notes tRNA or RS 1 CCGGCGGTAGTTCAGCAGGGCAGAACGGCGGACTCTA
M. jannaschii tRNA AATCCGCATGGCGCTGGTTCAAATCCGGCCCGCCGGA
mtRNA.sub.CUA.sup.Tyr CCA 2 CCCAGGGTAGCCAAGCTGGGCCAACGGCGACGGACTC
HLAD03; an tRNA TAAATCCGTTCTCGTAGGAGTTCGAGGGTTCGAATCC optimized
amber CTTCCCTGGGACCA supressor tRNA 3
GCGAGGGTAGCCAAGCTCGGCCAACGGCGACGGACTT HL325A; an tRNA
CCTAATCCGTTCTCGTAGGAGTTCGAGGGTTCGAATC optimized AGGA
CCTCCCCTCGCACCA frameshift supressor tRNA 4
MDEFEMIKRNTSEIISEEELREVLKKDEKSAGIGFEP Aminoacyl tRNA RS
SGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLN synthetase for the
QKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSTFQLD incorporation of p-
KDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAE azido-L-
VIYPIMQVNTYYYLGVDVAVGGMEQRKIHMLARELLP phenylalanine
KKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEI
RAKIKKAYCPAGVVEGNPLMEIAKYFLEYPLTIKRPE
KFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELI KILEPIRKRL p-Az-PheRS(6) 5
MDEFEMIKRNTSEIISEEELREVLKKDEKAAIGFEPS Aminoacyl tRNA RS
GKIHLLGHYLQIKKMIDLQNAGFDIIILLADLHAYLN synthetase for the
QKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSSFQLD incorporation of p-
KDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAE benzoyl-L-
VIYPIMQVNTSHYLGVDVAVGGMEQRKIHMLARELLP phenylalanine
KKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEI
RAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPE
KFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELI KILEPIRKRL p-BpaRS(1) 6
MDEFEMIKRNTSEIISEEELREVLKKDEKAATGFEPS Aminoacyl tRMA RS
GKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLNQ synthetase for the
KGELDEIRKIGDYNKKVFEAMGLKAKYVYGSPFQLDK incorporation of
DYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEV propargyl-
IYPIMQVNAIYLAVDVAVGGMEQRKIHMLARELLPKK phenylalanine
VVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRA
KIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKF
GGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKI LEPIRKRL Propargyl-PheRS 7
MDEFE MIKRN TSEII SEEEL REVLK KDEKS Aminoacyl tRNA RS AAIGF EPSGK
IHLGH YLQIK KMIDL QNAGF synthetase for the DIIIL LADLH AYLNQ KGELD
EIRKI GDYNK incorporation of KVFEA MGLKA KYVYG SPFQL DKDYT LNVYR
propargyl- LALKT TLKRA RRSME LIARE DENPK VAEVI phenylalanine RS
YPIMQ VNIPY LPVD VAVGG MEQRK IHMLA RELLP KKVVC IHNPV LTGLD GEGKM
SSSKG NFIAV DDSPE EIRAK IKKAY CPAGV VEGNP IMEIA KYFLE YPLTI KRPEK
FGGDL TVNSY EELES LFKNK ELHPM DLKNA VAEEL IKILE PIRKR L
Propargyl-PheRS 8 MDEFE MIKRN TSEII SEEEL REVLK KDEKS Aminoacyl
tRNA RS AAIGF EPSGK IHLGH YLQIK KMIDL QNAGF synthetase for the
DIIIL LADLH AYLNQ KGELD EIRKI GDYNK incorporation of KVFEA MGLKA
KYVYG SKFQL DKDYT LNVYR propargyl- LALKT TLKRA RRSME LIARE DENPK
VAEVI phenylalanine RS YPIMQ VNAIY LAVD VAVGG MEQRK IHMLA RELLP
KKVVC IHNPV LTGLD GEGKM SSSKG NFIAV DDSPE EIRAK IKKAY CPAGV VEGNP
IMEIA KYFLE YPLTI KRPEK FGGDL TVNSY EELES LFKNK ELHPM DLKNA VAEEL
IKILE PIRKR L Propargyl-PheRS 9
MDEFEMIKRNTSEIISEEELREVLKKDEKSATIGFEP Aminoacyl tRNA RS
SGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLN synthetase for the
QKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSNFQLD incorporation of p-
KDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAE azido-
VIYPIMQVNPLHYQGVDVAVGGMEQRKIHMLARELLP phenylalanine
KKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEI
RAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPE
KFGGDKTVNSYEELESLFKNKELHPMDLKNAVAEELI KILEPIRKRL p-Az-PheRS(1) 10
MDEFEMIKRNTSEIISEEELREVLKKDEKSATIGFEP Aminoacyl tRNA RS
SGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLN synthetase for the
QKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSSFQLD incorporation of p-
KDYTLNVYRLALKTTLKARRSMELIAREDENPKVAEV azido-
IYPIMQVNPLHYQGVDVAVGGMEQRKIHMLARELLPK phenylalanine
KVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIR
AKIKKAYCPAGVVEGNPIMEIAKYFLYPLTIKRPEKF
GGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKI LEPIRKRL p-Az-PheRS(3) 11
MDEFEMIKRNTSEIISEEELREVLKKDEKSALIGFEP Aminoacyl tRNA RS
SGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLN synthetase for the
QKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSTFQLD incorporation of p-
KDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAE azido-
VIYPIMQVNPVHYQGVDVAVGGMEQRKIHMLARELLP phenylalanine
KKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEI
RAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPE
KFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELI KILEPIRKRL p-Az-PheRS(4) 12
MDEFEMIKRNTSEIISEEELREVLKKDEKSALIGFEP Aminoacyl tRNA RS
SGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLN synthetase for the
QKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSTFQLD incorporation of p-
KDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAE azido-
VIYPIMQVNPSHYQGVDVAVGGMEQRKIHMLARELLP phenylalanine
KKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEI
RAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPE
KFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELI KILEPIRKRL p-Az-PheRS(2) 13
MDEFEMIKRNTSEIISEEELREVLKKDEKSALIGFEP Aminoacyl tRNA RS
SGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLN synthetase for the
QKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSTFQLD incorporation of p-
KDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAE azido-
VIYPIMQVGCHYRGVDVAVGGMEQRKIHMLARELLP phenylalanine
KKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEI
RAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPE
KFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELI KILEPIRKRL (LW1) 14
MDEFEMIKRNTSEIISEEELREVLKKDEKSALIGFEP Aminoacyl tRNA RS
SGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLN synthetase for the
QKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSTFQLD incorporation of p-
KDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAE azido-
VIYPIMQVNGTHYRGVDVAVGGMEQRKIHMLARELLP phenylalanine
KKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEI
RAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPE
KFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELI KILEPIRKRL (LW5) 15
MDEFEMIKRNTSEIISEEELREVLKKDEKSALIGFEP Aminoacyl tRNA RS
SGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLN synthetase for the
QKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSTFQLD incorporation of p-
KDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAE azido-
VIYPIMQVNGGHYLGVDVAVGGMEQRKIHMLARELLP phenylalanine
KKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEI
RAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPE
KFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELI KILEPIRKRL (LW6) 16
MDEFEMIKRNTSEIISEEELREVLKKDEKSALIGFEP Aminoacyl tRNA RS
SGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLN synthetase for the
QKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSTFQLD incorporation of p-
KDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAE azido-
VIYPIMQVNVIHYDGVDVAVGGMEQRKIHMLARELLP phenylalanine
KKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEI
RAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPE
KFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELI KILEPIRKRL (AzPheRS-5) 17
MDEFEMIKRNTSEIISEEELREVLKKDEKSALIGFEP Aminoacyl tRNA RS
SGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLN synthetase for the
QKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSTFQLD incorporation of p-
KDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAE azido-
VIYPIMQVNTYYYLGVDVAVGGMEQRKIHMLARELLP phenylalanine
KKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEI
RAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPE
KFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELI KILEPIRKRL (AzPheRS-6)
Sequence CWU 1
1
26177DNAMethanococcus jannaschii 1ccggcggtag ttcagcaggg cagaacggcg
gactctaaat ccgcatggcg ctggttcaaa 60tccggcccgc cggacca
77288DNAArtificial SequenceDescription of Artificial Sequence
Synthetic nucleotide sequence 2cccagggtag ccaagctcgg ccaacggcga
cggactctaa atccgttctc gtaggagttc 60gagggttcga atcccttccc tgggacca
88389DNAArtificial SequenceDescription of Artificial Sequence
Synthetic nucleotide sequence 3gcgagggtag ccaagctcgg ccaacggcga
cggacttcct aatccgttct cgtaggagtt 60cgagggttcg aatccctccc ctcgcacca
894306PRTArtificial SequenceDescription of Artificial Sequence
Synthetic amino acid sequence 4Met Asp Glu Phe Glu Met Ile Lys Arg
Asn Thr Ser Glu Ile Ile Ser1 5 10 15Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ser Ala Gly20 25 30Ile Gly Phe Glu Pro Ser Gly
Lys Ile His Leu Gly His Tyr Leu Gln35 40 45Ile Lys Lys Met Ile Asp
Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile50 55 60Leu Leu Ala Asp Leu
His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp65 70 75 80Glu Ile Arg
Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met85 90 95Gly Leu
Lys Ala Lys Tyr Val Tyr Gly Ser Thr Phe Gln Leu Asp Lys100 105
110Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu
Lys115 120 125Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp
Glu Asn Pro130 135 140Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln
Val Asn Thr Tyr Tyr145 150 155 160Tyr Leu Gly Val Asp Val Ala Val
Gly Gly Met Glu Gln Arg Lys Ile165 170 175His Met Leu Ala Arg Glu
Leu Leu Pro Lys Lys Val Val Cys Ile His180 185 190Asn Pro Val Leu
Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser195 200 205Lys Gly
Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala210 215
220Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn
Pro225 230 235 240Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro
Leu Thr Ile Lys245 250 255Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr
Val Asn Ser Tyr Glu Glu260 265 270Leu Glu Ser Leu Phe Lys Asn Lys
Glu Leu His Pro Met Asp Leu Lys275 280 285Asn Ala Val Ala Glu Glu
Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys290 295 300Arg
Leu3055306PRTArtificial SequenceDescription of Artificial Sequence
Synthetic amino acid sequence 5Met Asp Glu Phe Glu Met Ile Lys Arg
Asn Thr Ser Glu Ile Ile Ser1 5 10 15Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ser Ala Gly20 25 30Ile Gly Phe Glu Pro Ser Gly
Lys Ile His Leu Gly His Tyr Leu Gln35 40 45Ile Lys Lys Met Ile Asp
Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile50 55 60Leu Leu Ala Asp Leu
His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp65 70 75 80Glu Ile Arg
Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met85 90 95Gly Leu
Lys Ala Lys Tyr Val Tyr Gly Ser Ser Phe Gln Leu Asp Lys100 105
110Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu
Lys115 120 125Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp
Glu Asn Pro130 135 140Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln
Val Asn Thr Ser His145 150 155 160Tyr Leu Gly Val Asp Val Ala Val
Gly Gly Met Glu Gln Arg Lys Ile165 170 175His Met Leu Ala Arg Glu
Leu Leu Pro Lys Lys Val Val Cys Ile His180 185 190Asn Pro Val Leu
Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser195 200 205Lys Gly
Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala210 215
220Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn
Pro225 230 235 240Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro
Leu Thr Ile Lys245 250 255Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr
Val Asn Ser Tyr Glu Glu260 265 270Leu Glu Ser Leu Phe Lys Asn Lys
Glu Leu His Pro Met Asp Leu Lys275 280 285Asn Ala Val Ala Glu Glu
Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys290 295 300Arg
Leu3056304PRTArtificial SequenceDescription of Artificial Sequence
Synthetic amino acid sequence 6Met Asp Glu Phe Glu Met Ile Lys Arg
Asn Thr Ser Glu Ile Ile Ser1 5 10 15Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ala Ala Ile20 25 30Gly Phe Glu Pro Ser Gly Lys
Ile His Leu Gly His Tyr Leu Gln Ile35 40 45Lys Lys Met Ile Asp Leu
Gln Asn Ala Gly Phe Asp Ile Ile Ile Leu50 55 60Leu Ala Asp Leu His
Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp Glu65 70 75 80Ile Arg Lys
Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met Gly85 90 95Leu Lys
Ala Lys Tyr Val Tyr Gly Ser Pro Phe Gln Leu Asp Lys Asp100 105
110Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys
Arg115 120 125Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu
Asn Pro Lys130 135 140Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val
Asn Ala Ile Tyr Leu145 150 155 160Ala Val Asp Val Ala Val Gly Gly
Met Glu Gln Arg Lys Ile His Met165 170 175Leu Ala Arg Glu Leu Leu
Pro Lys Lys Val Val Cys Ile His Asn Pro180 185 190Val Leu Thr Gly
Leu Asp Gly Glu Gly Lys Met Ser Ser Ser Lys Gly195 200 205Asn Phe
Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala Lys Ile210 215
220Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn Pro Ile
Met225 230 235 240Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro Leu Thr
Ile Lys Arg Pro245 250 255Glu Lys Phe Gly Gly Asp Leu Thr Val Asn
Ser Tyr Glu Glu Leu Glu260 265 270Ser Leu Phe Lys Asn Lys Glu Leu
His Pro Met Asp Leu Lys Asn Ala275 280 285Val Ala Glu Glu Leu Ile
Lys Ile Leu Glu Pro Ile Arg Lys Arg Leu290 295 3007305PRTArtificial
SequenceDescription of Artificial Sequence Synthetic amino acid
sequence 7Met Asp Glu Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile
Ile Ser1 5 10 15Glu Glu Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys
Ser Ala Ala20 25 30Ile Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly
His Tyr Leu Gln35 40 45Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly
Phe Asp Ile Ile Ile50 55 60Leu Leu Ala Asp Leu His Ala Tyr Leu Asn
Gln Lys Gly Glu Leu Asp65 70 75 80Glu Ile Arg Lys Ile Gly Asp Tyr
Asn Lys Lys Val Phe Glu Ala Met85 90 95Gly Leu Lys Ala Lys Tyr Val
Tyr Gly Ser Pro Phe Gln Leu Asp Lys100 105 110Asp Tyr Thr Leu Asn
Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu Lys115 120 125Arg Ala Arg
Arg Ser Met Glu Leu Ile Ala Arg Glu Asp Glu Asn Pro130 135 140Lys
Val Ala Glu Val Ile Tyr Pro Ile Met Gln Val Asn Ile Pro Tyr145 150
155 160Leu Pro Val Asp Val Ala Val Gly Gly Met Glu Gln Arg Lys Ile
His165 170 175Met Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val Cys
Ile His Asn180 185 190Pro Val Leu Thr Gly Leu Asp Gly Glu Gly Lys
Met Ser Ser Ser Lys195 200 205Gly Asn Phe Ile Ala Val Asp Asp Ser
Pro Glu Glu Ile Arg Ala Lys210 215 220Ile Lys Lys Ala Tyr Cys Pro
Ala Gly Val Val Glu Gly Asn Pro Ile225 230 235 240Met Glu Ile Ala
Lys Tyr Phe Leu Glu Tyr Pro Leu Thr Ile Lys Arg245 250 255Pro Glu
Lys Phe Gly Gly Asp Leu Thr Val Asn Ser Tyr Glu Glu Leu260 265
270Glu Ser Leu Phe Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys
Asn275 280 285Ala Val Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile
Arg Lys Arg290 295 300Leu3058305PRTArtificial SequenceDescription
of Artificial Sequence Synthetic amino acid sequence 8Met Asp Glu
Phe Glu Met Ile Lys Arg Asn Thr Ser Glu Ile Ile Ser1 5 10 15Glu Glu
Glu Leu Arg Glu Val Leu Lys Lys Asp Glu Lys Ser Ala Ala20 25 30Ile
Gly Phe Glu Pro Ser Gly Lys Ile His Leu Gly His Tyr Leu Gln35 40
45Ile Lys Lys Met Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile50
55 60Leu Leu Ala Asp Leu His Ala Tyr Leu Asn Gln Lys Gly Glu Leu
Asp65 70 75 80Glu Ile Arg Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe
Glu Ala Met85 90 95Gly Leu Lys Ala Lys Tyr Val Tyr Gly Ser Lys Phe
Gln Leu Asp Lys100 105 110Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala
Leu Lys Thr Thr Leu Lys115 120 125Arg Ala Arg Arg Ser Met Glu Leu
Ile Ala Arg Glu Asp Glu Asn Pro130 135 140Lys Val Ala Glu Val Ile
Tyr Pro Ile Met Gln Val Asn Ala Ile Tyr145 150 155 160Leu Ala Val
Asp Val Ala Val Gly Gly Met Glu Gln Arg Lys Ile His165 170 175Met
Leu Ala Arg Glu Leu Leu Pro Lys Lys Val Val Cys Ile His Asn180 185
190Pro Val Leu Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser
Lys195 200 205Gly Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile
Arg Ala Lys210 215 220Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val
Glu Gly Asn Pro Ile225 230 235 240Met Glu Ile Ala Lys Tyr Phe Leu
Glu Tyr Pro Leu Thr Ile Lys Arg245 250 255Pro Glu Lys Phe Gly Gly
Asp Leu Thr Val Asn Ser Tyr Glu Glu Leu260 265 270Glu Ser Leu Phe
Lys Asn Lys Glu Leu His Pro Met Asp Leu Lys Asn275 280 285Ala Val
Ala Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys Arg290 295
300Leu3059306PRTArtificial SequenceDescription of Artificial
Sequence Synthetic amino acid sequence 9Met Asp Glu Phe Glu Met Ile
Lys Arg Asn Thr Ser Glu Ile Ile Ser1 5 10 15Glu Glu Glu Leu Arg Glu
Val Leu Lys Lys Asp Glu Lys Ser Ala Thr20 25 30Ile Gly Phe Glu Pro
Ser Gly Lys Ile His Leu Gly His Tyr Leu Gln35 40 45Ile Lys Lys Met
Ile Asp Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile50 55 60Leu Leu Ala
Asp Leu His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp65 70 75 80Glu
Ile Arg Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met85 90
95Gly Leu Lys Ala Lys Tyr Val Tyr Gly Ser Asn Phe Gln Leu Asp
Lys100 105 110Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr
Thr Leu Lys115 120 125Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg
Glu Asp Glu Asn Pro130 135 140Lys Val Ala Glu Val Ile Tyr Pro Ile
Met Gln Val Asn Pro Leu His145 150 155 160Tyr Gln Gly Val Asp Val
Ala Val Gly Gly Met Glu Gln Arg Lys Ile165 170 175His Met Leu Ala
Arg Glu Leu Leu Pro Lys Lys Val Val Cys Ile His180 185 190Asn Pro
Val Leu Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser195 200
205Lys Gly Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg
Ala210 215 220Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu
Gly Asn Pro225 230 235 240Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu
Tyr Pro Leu Thr Ile Lys245 250 255Arg Pro Glu Lys Phe Gly Gly Asp
Leu Thr Val Asn Ser Tyr Glu Glu260 265 270Leu Glu Ser Leu Phe Lys
Asn Lys Glu Leu His Pro Met Asp Leu Lys275 280 285Asn Ala Val Ala
Glu Glu Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys290 295 300Arg
Leu30510306PRTArtificial SequenceDescription of Artificial Sequence
Synthetic amino acid sequence 10Met Asp Glu Phe Glu Met Ile Lys Arg
Asn Thr Ser Glu Ile Ile Ser1 5 10 15Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ser Ala Thr20 25 30Ile Gly Phe Glu Pro Ser Gly
Lys Ile His Leu Gly His Tyr Leu Gln35 40 45Ile Lys Lys Met Ile Asp
Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile50 55 60Leu Leu Ala Asp Leu
His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp65 70 75 80Glu Ile Arg
Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met85 90 95Gly Leu
Lys Ala Lys Tyr Val Tyr Gly Ser Ser Phe Gln Leu Asp Lys100 105
110Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu
Lys115 120 125Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp
Glu Asn Pro130 135 140Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln
Val Asn Pro Leu His145 150 155 160Tyr Gln Gly Val Asp Val Ala Val
Gly Gly Met Glu Gln Arg Lys Ile165 170 175His Met Leu Ala Arg Glu
Leu Leu Pro Lys Lys Val Val Cys Ile His180 185 190Asn Pro Val Leu
Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser195 200 205Lys Gly
Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala210 215
220Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn
Pro225 230 235 240Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro
Leu Thr Ile Lys245 250 255Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr
Val Asn Ser Tyr Glu Glu260 265 270Leu Glu Ser Leu Phe Lys Asn Lys
Glu Leu His Pro Met Asp Leu Lys275 280 285Asn Ala Val Ala Glu Glu
Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys290 295 300Arg
Leu30511306PRTArtificial SequenceDescription of Artificial Sequence
Synthetic amino acid sequence 11Met Asp Glu Phe Glu Met Ile Lys Arg
Asn Thr Ser Glu Ile Ile Ser1 5 10 15Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ser Ala Leu20 25 30Ile Gly Phe Glu Pro Ser Gly
Lys Ile His Leu Gly His Tyr Leu Gln35 40 45Ile Lys Lys Met Ile Asp
Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile50 55 60Leu Leu Ala Asp Leu
His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp65 70 75 80Glu Ile Arg
Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met85 90 95Gly Leu
Lys Ala Lys Tyr Val Tyr Gly Ser Thr Phe Gln Leu Asp Lys100 105
110Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu
Lys115 120 125Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp
Glu Asn Pro130 135 140Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln
Val Asn Pro Val His145 150 155 160Tyr Gln Gly Val Asp Val Ala Val
Gly Gly Met Glu Gln Arg Lys Ile165 170 175His Met Leu Ala Arg Glu
Leu Leu Pro Lys Lys Val Val Cys Ile His180 185 190Asn Pro Val Leu
Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser195 200 205Lys Gly
Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala210 215
220Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn
Pro225 230 235 240Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro
Leu Thr Ile Lys245 250 255Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr
Val Asn Ser Tyr Glu Glu260 265 270Leu Glu Ser Leu Phe Lys Asn Lys
Glu Leu His Pro Met Asp Leu Lys275 280 285Asn Ala Val Ala Glu Glu
Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys290 295 300Arg
Leu30512306PRTArtificial SequenceDescription of Artificial
Sequence
Synthetic amino acid sequence 12Met Asp Glu Phe Glu Met Ile Lys Arg
Asn Thr Ser Glu Ile Ile Ser1 5 10 15Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ser Ala Thr20 25 30Ile Gly Phe Glu Pro Ser Gly
Lys Ile His Leu Gly His Tyr Leu Gln35 40 45Ile Lys Lys Met Ile Asp
Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile50 55 60Leu Leu Ala Asp Leu
His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp65 70 75 80Glu Ile Arg
Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met85 90 95Gly Leu
Lys Ala Lys Tyr Val Tyr Gly Ser Ser Phe Gln Leu Asp Lys100 105
110Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu
Lys115 120 125Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp
Glu Asn Pro130 135 140Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln
Val Asn Pro Ser His145 150 155 160Tyr Gln Gly Val Asp Val Ala Val
Gly Gly Met Glu Gln Arg Lys Ile165 170 175His Met Leu Ala Arg Glu
Leu Leu Pro Lys Lys Val Val Cys Ile His180 185 190Asn Pro Val Leu
Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser195 200 205Lys Gly
Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala210 215
220Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn
Pro225 230 235 240Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro
Leu Thr Ile Lys245 250 255Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr
Val Asn Ser Tyr Glu Glu260 265 270Leu Glu Ser Leu Phe Lys Asn Lys
Glu Leu His Pro Met Asp Leu Lys275 280 285Asn Ala Val Ala Glu Glu
Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys290 295 300Arg
Leu30513306PRTArtificial SequenceDescription of Artificial Sequence
Synthetic amino acid sequence 13Met Asp Glu Phe Glu Met Ile Lys Arg
Asn Thr Ser Glu Ile Ile Ser1 5 10 15Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ser Ala Leu20 25 30Ile Gly Phe Glu Pro Ser Gly
Lys Ile His Leu Gly His Tyr Leu Gln35 40 45Ile Lys Lys Met Ile Asp
Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile50 55 60Leu Leu Ala Asp Leu
His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp65 70 75 80Glu Ile Arg
Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met85 90 95Gly Leu
Lys Ala Lys Tyr Val Tyr Gly Ser Glu Phe Gln Leu Asp Lys100 105
110Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu
Lys115 120 125Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp
Glu Asn Pro130 135 140Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln
Val Asn Gly Cys His145 150 155 160Tyr Arg Gly Val Asp Val Ala Val
Gly Gly Met Glu Gln Arg Lys Ile165 170 175His Met Leu Ala Arg Glu
Leu Leu Pro Lys Lys Val Val Cys Ile His180 185 190Asn Pro Val Leu
Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser195 200 205Lys Gly
Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala210 215
220Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn
Pro225 230 235 240Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro
Leu Thr Ile Lys245 250 255Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr
Val Asn Ser Tyr Glu Glu260 265 270Leu Glu Ser Leu Phe Lys Asn Lys
Glu Leu His Pro Met Asp Leu Lys275 280 285Asn Ala Val Ala Glu Glu
Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys290 295 300Arg
Leu30514306PRTArtificial SequenceDescription of Artificial Sequence
Synthetic amino acid sequence 14Met Asp Glu Phe Glu Met Ile Lys Arg
Asn Thr Ser Glu Ile Ile Ser1 5 10 15Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ser Ala Leu20 25 30Ile Gly Phe Glu Pro Ser Gly
Lys Ile His Leu Gly His Tyr Leu Gln35 40 45Ile Lys Lys Met Ile Asp
Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile50 55 60Leu Leu Ala Asp Leu
His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp65 70 75 80Glu Ile Arg
Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met85 90 95Gly Leu
Lys Ala Lys Tyr Val Tyr Gly Ser Glu Phe Gln Leu Asp Lys100 105
110Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu
Lys115 120 125Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp
Glu Asn Pro130 135 140Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln
Val Asn Gly Thr His145 150 155 160Tyr Arg Gly Val Asp Val Ala Val
Gly Gly Met Glu Gln Arg Lys Ile165 170 175His Met Leu Ala Arg Glu
Leu Leu Pro Lys Lys Val Val Cys Ile His180 185 190Asn Pro Val Leu
Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser195 200 205Lys Gly
Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala210 215
220Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn
Pro225 230 235 240Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro
Leu Thr Ile Lys245 250 255Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr
Val Asn Ser Tyr Glu Glu260 265 270Leu Glu Ser Leu Phe Lys Asn Lys
Glu Leu His Pro Met Asp Leu Lys275 280 285Asn Ala Val Ala Glu Glu
Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys290 295 300Arg
Leu30515306PRTArtificial SequenceDescription of Artificial Sequence
Synthetic amino acid sequence 15Met Asp Glu Phe Glu Met Ile Lys Arg
Asn Thr Ser Glu Ile Ile Ser1 5 10 15Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ser Ala Ala20 25 30Ile Gly Phe Glu Pro Ser Gly
Lys Ile His Leu Gly His Tyr Leu Gln35 40 45Ile Lys Lys Met Ile Asp
Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile50 55 60Leu Leu Ala Asp Leu
His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp65 70 75 80Glu Ile Arg
Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met85 90 95Gly Leu
Lys Ala Lys Tyr Val Tyr Gly Ser Glu Phe Gln Leu Asp Lys100 105
110Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu
Lys115 120 125Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp
Glu Asn Pro130 135 140Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln
Val Asn Gly Gly His145 150 155 160Tyr Leu Gly Val Asp Val Ile Val
Gly Gly Met Glu Gln Arg Lys Ile165 170 175His Met Leu Ala Arg Glu
Leu Leu Pro Lys Lys Val Val Cys Ile His180 185 190Asn Pro Val Leu
Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser195 200 205Lys Gly
Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala210 215
220Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn
Pro225 230 235 240Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro
Leu Thr Ile Lys245 250 255Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr
Val Asn Ser Tyr Glu Glu260 265 270Leu Glu Ser Leu Phe Lys Asn Lys
Glu Leu His Pro Met Asp Leu Lys275 280 285Asn Ala Val Ala Glu Glu
Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys290 295 300Arg
Leu30516306PRTArtificial SequenceDescription of Artificial Sequence
Synthetic amino acid sequence 16Met Asp Glu Phe Glu Met Ile Lys Arg
Asn Thr Ser Glu Ile Ile Ser1 5 10 15Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ser Ala Ala20 25 30Ile Gly Phe Glu Pro Ser Gly
Lys Ile His Leu Gly His Tyr Leu Gln35 40 45Ile Lys Lys Met Ile Asp
Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile50 55 60Leu Leu Ala Asp Leu
His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp65 70 75 80Glu Ile Arg
Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met85 90 95Gly Leu
Lys Ala Lys Tyr Val Tyr Gly Ser Arg Phe Gln Leu Asp Lys100 105
110Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu
Lys115 120 125Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp
Glu Asn Pro130 135 140Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln
Val Asn Val Ile His145 150 155 160Tyr Asp Gly Val Asp Val Ala Val
Gly Gly Met Glu Gln Arg Lys Ile165 170 175His Met Leu Ala Arg Glu
Leu Leu Pro Lys Lys Val Val Cys Ile His180 185 190Asn Pro Val Leu
Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser195 200 205Lys Gly
Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala210 215
220Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn
Pro225 230 235 240Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro
Leu Thr Ile Lys245 250 255Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr
Val Asn Ser Tyr Glu Glu260 265 270Leu Glu Ser Leu Phe Lys Asn Lys
Glu Leu His Pro Met Asp Leu Lys275 280 285Asn Ala Val Ala Glu Glu
Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys290 295 300Arg
Leu30517306PRTArtificial SequenceDescription of Artificial Sequence
Synthetic amino acid sequence 17Met Asp Glu Phe Glu Met Ile Lys Arg
Asn Thr Ser Glu Ile Ile Ser1 5 10 15Glu Glu Glu Leu Arg Glu Val Leu
Lys Lys Asp Glu Lys Ser Ala Gly20 25 30Ile Gly Phe Glu Pro Ser Gly
Lys Ile His Leu Gly His Tyr Leu Gln35 40 45Ile Lys Lys Met Ile Asp
Leu Gln Asn Ala Gly Phe Asp Ile Ile Ile50 55 60Leu Leu Ala Asp Leu
His Ala Tyr Leu Asn Gln Lys Gly Glu Leu Asp65 70 75 80Glu Ile Arg
Lys Ile Gly Asp Tyr Asn Lys Lys Val Phe Glu Ala Met85 90 95Gly Leu
Lys Ala Lys Tyr Val Tyr Gly Ser Thr Phe Gln Leu Asp Lys100 105
110Asp Tyr Thr Leu Asn Val Tyr Arg Leu Ala Leu Lys Thr Thr Leu
Lys115 120 125Arg Ala Arg Arg Ser Met Glu Leu Ile Ala Arg Glu Asp
Glu Asn Pro130 135 140Lys Val Ala Glu Val Ile Tyr Pro Ile Met Gln
Val Asn Thr Tyr Tyr145 150 155 160Tyr Leu Gly Val Asp Val Ala Val
Gly Gly Met Glu Gln Arg Lys Ile165 170 175His Met Leu Ala Arg Glu
Leu Leu Pro Lys Lys Val Val Cys Ile His180 185 190Asn Pro Val Leu
Thr Gly Leu Asp Gly Glu Gly Lys Met Ser Ser Ser195 200 205Lys Gly
Asn Phe Ile Ala Val Asp Asp Ser Pro Glu Glu Ile Arg Ala210 215
220Lys Ile Lys Lys Ala Tyr Cys Pro Ala Gly Val Val Glu Gly Asn
Pro225 230 235 240Ile Met Glu Ile Ala Lys Tyr Phe Leu Glu Tyr Pro
Leu Thr Ile Lys245 250 255Arg Pro Glu Lys Phe Gly Gly Asp Leu Thr
Val Asn Ser Tyr Glu Glu260 265 270Leu Glu Ser Leu Phe Lys Asn Lys
Glu Leu His Pro Met Asp Leu Lys275 280 285Asn Ala Val Ala Glu Glu
Leu Ile Lys Ile Leu Glu Pro Ile Arg Lys290 295 300Arg
Leu3051811PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 18Glu Thr Pro Asp Cys Xaa Trp Lys Tyr Cys Val1 5
10199PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 19Ser Xaa Cys Tyr His Lys Trp Cys Thr1
5209PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 20His Xaa Cys Tyr His Lys Trp Cys Thr1
5219PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 21Trp Xaa Cys Tyr His Lys Trp Cys Thr1
5229PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 22Asn Xaa Cys Tyr His Lys Trp Cys Thr1
52310PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 23Arg Asn Xaa Cys Tyr His Lys Trp Cys Thr1 5
102411PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 24Ala Arg Asn Xaa Cys Tyr His Lys Trp Cys Thr1 5
102510PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 25Ala Arg Xaa Cys Tyr His Lys Trp Cys Thr1 5
10269PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 26Asn Xaa Cys Tyr His Lys Trp Cys Thr1 5
* * * * *
References