U.S. patent application number 12/922322 was filed with the patent office on 2012-02-16 for peptide nucleic acid derivatives with good cell penetration and strong affinity for nucleic acid.
This patent application is currently assigned to CTI BIO. Invention is credited to Shin Chung, Heui-Yeon Kim, Mi-Ran Kim, Jong-Ook Lee, Hyun-Jin Park.
Application Number | 20120040918 12/922322 |
Document ID | / |
Family ID | 41065678 |
Filed Date | 2012-02-16 |
United States Patent
Application |
20120040918 |
Kind Code |
A9 |
Lee; Jong-Ook ; et
al. |
February 16, 2012 |
PEPTIDE NUCLEIC ACID DERIVATIVES WITH GOOD CELL PENETRATION AND
STRONG AFFINITY FOR NUCLEIC ACID
Abstract
The present invention provides a novel class of peptide nucleic
acid derivatives, which show good cell penetration and strong
binding affinity for nucleic acid.
Inventors: |
Lee; Jong-Ook; (Seoul,
KR) ; Chung; Shin; (Gyounggi-do, KR) ; Kim;
Heui-Yeon; (Incheon, KR) ; Park; Hyun-Jin;
(Gyeonggi-do, KR) ; Kim; Mi-Ran; (Gyeonggi-do,
KR) |
Assignee: |
CTI BIO
Seoul
KR
|
Prior
Publication: |
|
Document Identifier |
Publication Date |
|
US 20110178031 A1 |
July 21, 2011 |
|
|
Family ID: |
41065678 |
Appl. No.: |
12/922322 |
Filed: |
March 13, 2009 |
PCT Filed: |
March 13, 2009 |
PCT NO: |
PCT/KR2009/001256 PCKC 00 |
371 Date: |
September 13, 2010 |
Current U.S.
Class: |
514/21.3;
435/375; 514/21.4; 514/21.5; 514/21.6; 514/21.7; 514/21.8; 530/324;
530/325; 530/326; 530/327; 530/328; 530/329; 530/330; 544/276;
544/277; 544/280 |
Current CPC
Class: |
A61P 35/00 20180101;
C07D 473/16 20130101; A61P 31/04 20180101; C07D 473/18 20130101;
C07D 487/04 20130101; C07K 14/003 20130101; A61P 31/12
20180101 |
Class at
Publication: |
514/21.3;
530/330; 514/21.8; 435/375; 544/280; 544/277; 544/276; 530/329;
530/328; 530/327; 530/326; 530/325; 530/324; 514/21.7; 514/21.6;
514/21.5; 514/21.4 |
International
Class: |
A61K 38/16 20060101
A61K038/16; A61K 38/08 20060101 A61K038/08; C12N 5/00 20060101
C12N005/00; C07D 487/04 20060101 C07D487/04; C07D 473/16 20060101
C07D473/16; A61K 38/10 20060101 A61K038/10; A61P 31/12 20060101
A61P031/12; A61P 31/04 20060101 A61P031/04; A61P 35/00 20060101
A61P035/00; C07K 7/08 20060101 C07K007/08; C07K 14/00 20060101
C07K014/00; C07K 7/06 20060101 C07K007/06; C07D 473/18 20060101
C07D473/18 |
Foreign Application Data
Date |
Code |
Application Number |
Mar 14, 2008 |
KR |
10-2008-23658 |
Nov 11, 2008 |
KR |
10-2008-111459 |
Claims
1. A peptide nucleic acid derivative of Formula I or a
pharmaceutically acceptable salt thereof: ##STR00095## wherein, n
is an integer equal to or larger than 5; S.sub.1, S.sub.2, . . . ,
S.sub.n-1, S.sub.n, T.sub.1, T.sub.2, . . . , and T.sub.n
independently represent hydrido, deuterido, substituted or
non-substituted alkyl, or substituted or non-substituted aryl
radical; X and Y independently represent hydrido, deuterido,
hydroxy, substituted or non-substituted alkyloxy, substituted or
non-substituted aryloxy, substituted or non-substituted amino,
substituted or non-substituted alkyl, substituted or
non-substituted acyl, substituted or non-substituted sulfonyl, or
substituted or non-substituted aryl radical; Z represents hydrido,
deuterido, hydroxy, substituted or non-substituted alkyloxy,
substituted or non-substituted aryloxy, substituted or
non-substituted amino, substituted or non-substituted alkyl, or
substituted or non-substituted aryl radical; B.sub.1, B.sub.2, . .
. , B.sub.n-1, and B.sub.n are independently selected from natural
nucleobases including adenine, thymine, guanine, cytosine and
uracil, and unnatural nucleobases; and, at least one of B.sub.1,
B.sub.2, . . . , B.sub.n-1, and B.sub.n independently represents an
unnatural nucleobase with a substituted or non-substituted amino
radical covalently linked to the moiety responsible for its due
nucleobase pairing properties.
2. The peptide nucleic acid derivative according to claim 1 or a
pharmaceutically acceptable salt thereof: wherein, n is an integer
equal to or larger than 5 but smaller than or equal to 30; S.sub.1,
S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1, T.sub.2, . . . ,
T.sub.n-1, and T.sub.n are hydrido radical; X and Y are
independently selected from hydrido, substituted or non-substituted
alkyl, substituted or non-substituted acyl, substituted or
non-substituted sulfonyl, and substituted or non-substituted aryl
radical; Z represents hydrido, hydroxy, substituted or
nonsubstituted alkyloxy, substituted or non-substituted amino,
substituted or non-substituted alkyl, or substituted or
non-substituted aryl radical; B.sub.2, . . . , B.sub.n-1, and
B.sub.n are independently selected from natural nucleobases
including adenine, thymine, guanine, cytosine and uracil, and
unnatural nucleobases; and, at least one of B.sub.1, B.sub.2, . . .
, B.sub.n-1, and B.sub.n is independently selected from unnatural
nucleobases represented by Formula II, Formula III, or Formula IV:
##STR00096## wherein, R.sub.1, R.sub.2, R.sub.3, R.sub.4, R.sub.5
and R.sub.6 are independently selected from substituted or
non-substituted alkyl, hydrido, hydroxy, and substituted or
non-substituted alkyloxy radical; and, L.sub.1, L.sub.2 and L.sub.3
are a covalent linker represented by Formula V connecting a basic
amino group to the moiety responsible for nucleobase pairing
properties: ##STR00097## wherein, Q.sub.1 and Q.sub.m are
substituted or non-substituted methylene (--CH.sub.2--) radical,
and Q.sub.m is directly linked to the basic amino group; Q.sub.2,
Q.sub.3, . . . , and Q.sub.m-1 are independently selected from
substituted or non-substituted methylene, oxygen (--O--), sulfur
(--S--), and substituted or non-substituted amino radical
[--N(H)--, or --N(substituent)-]; and, m is an integer equal to or
larger than 2 but smaller than or equal to 15.
3. The peptide nucleic acid derivative according to claim 2 or a
pharmaceutically acceptable salt thereof: wherein, n is an integer
equal to or larger than 8 but smaller than or equal to 25; S.sub.1,
S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1, T.sub.2, . . . ,
T.sub.n-1, and T.sub.n are hydrido radical; X and Y are
independently selected from hydrido, substituted or non-substituted
alkyl, and substituted or non-substituted acyl radical; Z
represents hydroxy, or substituted or non-substituted amino
radical; B.sub.1, B.sub.2, . . . , B.sub.n-1, and B.sub.n are
independently selected from natural nucleobases including adenine,
thymine, guanine, cytosine and uracil, and unnatural nucleobases;
at least two of B.sub.1, B.sub.2, . . . , B.sub.n-1, and B.sub.n
are independently selected from unnatural nucleobases represented
by Formula II, Formula III, or Formula IV; R.sub.1, R.sub.2,
R.sub.3, R.sub.4, R.sub.5 and R.sub.6 are independently selected
from substituted or non-substituted alkyl, and hydrido radical;
Q.sub.1 and Q.sub.m are substituted or non-substituted methylene
radical, and Q.sub.m is directly linked to the basic amino group;
Q.sub.2, Q.sub.3, . . . , and Q.sub.m-1 are independently selected
from substituted or non-substituted methylene, oxygen, and amino
radical; and, m is an integer equal to or larger than 2 but smaller
than or equal to 12.
4. The peptide nucleic acid derivative according to claim 2 or a
pharmaceutically acceptable salt thereof: wherein, n is an integer
equal to or larger than 10 but smaller than or equal to 25;
S.sub.1, S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1, T.sub.2, . .
. , T.sub.n-1, and T.sub.n are hydrido radical; X and Y are
independently selected from hydrido, and substituted or
non-substituted acyl radical; Z represents hydroxy, alkyloxy, or
substituted or non-substituted amino radical; and, B.sub.1,
B.sub.2, . . . , B.sub.n-1, and B.sub.n are independently selected
from natural nucleobases including adenine, thymine, guanine,
cytosine and uracil, and unnatural nucleobases; at least three of
B.sub.1, B.sub.2, . . . , B.sub.n-1, and B.sub.n are independently
selected from unnatural nucleobases represented by Formula II,
Formula III, or Formula IV; R.sub.1, R.sub.2, R.sub.3, R.sub.4,
R.sub.5 and R.sub.6 are independently selected from substituted or
non-substituted alkyl, and hydrido radical; Q.sub.1 and Q.sub.m are
methylene radical, and Q.sub.m is directly linked to the basic
amino group; Q.sub.2, Q.sub.3, . . . , and Q.sub.m-1 are
independently selected from methylene, oxygen, and amino radical;
and, m is an integer equal to or larger than 2 but smaller than or
equal to 10.
5. The peptide nucleic acid derivative according to claim 2 or a
pharmaceutically acceptable salt thereof: wherein, n is an integer
equal to or larger than 10 but smaller than or equal to 20;
S.sub.1, S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1, T.sub.2, . .
. , T.sub.n-1, and T.sub.n are hydrido radical; X and Y are
independently selected from hydrido, and substituted or
non-substituted acyl radical; Z represents hydroxy, or substituted
or non-substituted amino radical; B.sub.1, B.sub.2, . . . ,
B.sub.n-1, and B.sub.n is independently selected from natural
nucleobases including adenine, thymine, guanine, cytosine and
uracil, and unnatural nucleobases; at least three of B.sub.1,
B.sub.2, . . . , B.sub.n-1, and B.sub.n are independently selected
from unnatural nucleobases represented by Formula II, Formula III,
or Formula IV; R.sub.1, R.sub.3, and R.sub.5 are hydrido radical,
and R.sub.2, R.sub.4, and R.sub.6 independently represent hydrido,
or substituted or non-substituted amidinyl radical; Q.sub.1 and
Q.sub.m are methylene radical, and Q.sub.m is directly linked to
the basic amino group; Q.sub.2, Q.sub.3, . . . , and Q.sub.m-1 are
independently selected from methylene, oxygen, and amino radical;
and, m is an integer equal to or larger than 2 but smaller than or
equal to 10.
6. The peptide nucleic acid derivative according to claim 2 or a
pharmaceutically acceptable salt thereof: wherein, n is an integer
equal to or larger than 10 but smaller than or equal to 20;
S.sub.1, S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1, T.sub.2, . .
. , T.sub.n-1, and T.sub.n are hydrido radical; X and Y are
independently selected from hydrido, and substituted or
non-substituted acyl radical; Z represents hydroxy, or substituted
or non-substituted amino radical; B.sub.1, B.sub.2, . . . ,
B.sub.n-1, and B.sub.n are independently selected from adenine,
thymine, guanine, cytosine, and unnatural nucleobases; at least
three of B.sub.1, B.sub.2, . . . , B.sub.n-1, and B.sub.n are
independently selected from unnatural nucleobases represented by
Formula II, Formula III, or Formula IV; R.sub.1, R.sub.3, and
R.sub.5 are hydrido radical, and R.sub.2, R.sub.4, and R.sub.6
independently represents hydrido or amidinyl radical; Q.sub.1 and
Q.sub.m are methylene radical, and Q.sub.m is directly linked to
the basic amino group; Q.sub.2, Q.sub.3, . . . , and Q.sub.m-1 are
independently selected from methylene, and oxygen radical; and, m
is an integer equal to or larger than 2 but smaller than or equal
to 8.
7. The peptide nucleic acid derivative according to claim 2 or a
pharmaceutically acceptable salt thereof: wherein, n is an integer
equal to or larger than 8 but smaller than or equal to 20; S.sub.1,
S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1, T.sub.2, . . . ,
T.sub.n-1, and T.sub.n are hydrido radical; X is hydrido radical; Y
represents hydrido, or substituted or non-substituted acyl radical;
Z represents hydroxy, or substituted or non-substituted amino
radical; B.sub.1, B.sub.2, . . . , B.sub.n-1, and B.sub.n are
independently selected from adenine, thymine, guanine, cytosine,
and unnatural nucleobases; at least three of B.sub.1, B.sub.2, . .
. , B.sub.n-1, and B.sub.n are independently selected from
unnatural nucleobases represented by Formula II, Formula III, or
Formula IV; R.sub.1, R.sub.3, and R.sub.5 are hydrido radical, and
R.sub.2, R.sub.4, and R.sub.6 independently represent hydrido or
amidinyl radical; L.sub.1 represents
--(CH.sub.2).sub.2--O--(CH.sub.2).sub.2--,
--CH.sub.2--O--(CH.sub.2).sub.2--, or
--CH.sub.2--O--(CH.sub.2).sub.3-- with the right end is directly
linked to the basic amino group; and, L.sub.2 and L.sub.3 are
independently selected from
--(CH.sub.2).sub.2--O--(CH.sub.2).sub.2--,
--(CH.sub.2).sub.3--O--(CH.sub.2).sub.2--,
--(CH.sub.2).sub.2--O--(CH.sub.2).sub.3--, --(CH.sub.2).sub.2--,
--(CH.sub.2).sub.3--, --(CH.sub.2).sub.4--, --(CH.sub.2).sub.5--,
--(CH.sub.2).sub.6--, --(CH.sub.2).sub.7--, and
--(CH.sub.2).sub.8-- with the right end is directly linked to the
basic amino group.
8. A pharmaceutical composition comprising a therapeutically
effective amount of the peptide nucleic acid derivative of claim 1
or a pharmaceutically acceptable salt thereof.
9. A method to use the peptide nucleic acid derivative of claim 1
or a salt thereof for a diagnostic purpose.
10. An in vitro method for modulating cellular protein expression,
said method comprising: administering the peptide nucleic acid
derivative of claim 1; and determining the protein expression level
in a cell.
11. A compound of Formula VI: ##STR00098## wherein, R.sub.7 is
hydrido, N-succinyl, or substituted or non-substituted alkyl
radical; P.sub.1 is selected from hydrido, t-butoxycarbonyl,
(9H-fluoren-9-yl)methoxy-carbonyl, substituted or non-substituted
benzyloxycarbonyl, and substituted or non-substituted arylsulfonyl
radical; P.sub.2 is selected from hydrido, t-butoxycarbonyl,
(9H-fluoren-9-yl)methoxy-carbonyl, substituted or non-substituted
benzyloxycarbonyl, substituted alkyloxycarbonyl, substituted or
non-substituted alkyl, amidinyl,
1,3-bis(t-butoxy-carbonyl)amidinyl,
1,3-bis-(benzyloxycarbonyl)amidinyl radical; and, L.sub.1 is a
linker represented by Formula V: ##STR00099## wherein, Q.sub.1 and
Q.sub.m are substituted or non-substituted methylene radical, and
Q.sub.m is directly linked to the amino radical; Q.sub.2, Q.sub.3,
. . . , and Q.sub.m-1 are independently selected from substituted
or non-substituted methylene, oxygen, sulfur, and substituted or
non-substituted amino radical; and, m is an integer equal to or
larger than 2 but smaller than or equal to 15.
12. A compound of Formula VII: ##STR00100## wherein, R.sub.8 is
hydrido, N-succinyl, or substituted or non-substituted alkyl
radical; P.sub.1 is selected from hydrido, t-butoxycarbonyl,
(9H-fluoren-9-yl)methoxy-carbonyl, substituted or non-substituted
benzyloxycarbonyl, and substituted or non-substituted arylsulfonyl
radical; P.sub.2 is selected from hydrido, t-butoxycarbonyl,
(9H-fluoren-9-yl)methoxy-carbonyl, substituted or non-substituted
benzyloxycarbonyl, substituted alkyloxycarbonyl, substituted or
non-substituted alkyl, amidinyl,
1,3-bis(t-butoxy-carbonyl)amidinyl,
1,3-bis-(benzyl-oxycarbonyl)amidinyl radical; P.sub.3 is selected
from hydrido, t-butoxycarbonyl, (9H-fluoren-9-yl)methoxy-carbonyl,
and substituted or non-substituted benzyloxycarbonyl radical;
P.sub.4 is selected from hydrido, and t-butoxycarbonyl radical;
and, L.sub.2 is a linker represented by Formula V: ##STR00101##
wherein, Q.sub.1 and Q.sub.m are substituted or non-substituted
methylene radical, and Q.sub.m is directly linked to the amino
radical; Q.sub.2, Q.sub.3, . . . , and Q.sub.m-1 are independently
selected from substituted or non-substituted methylene, oxygen,
sulfur, and substituted or non-substituted amino radical; and, m is
an integer equal to or larger than 2 but smaller than or equal to
15.
13. A compound of Formula VIII: ##STR00102## wherein, R.sub.9 is
hydrido, N-succinyl, or substituted or non-substituted alkyl
radical; P.sub.1 is selected from hydrido, t-butoxycarbonyl,
(9H-fluoren-9-yl)methoxy-carbonyl, substituted or non-substituted
benzyloxycarbonyl, and substituted or non-substituted arylsulfonyl
radical; P.sub.2 is selected from hydrido, t-butoxycarbonyl,
(9H-fluoren-9-yl)methoxy-carbonyl, substituted or non-substituted
benzyloxycarbonyl, substituted alkyloxycarbonyl, substituted or
non-substituted alkyl, amidinyl,
1,3-bis(t-butoxy-carbonyl)amidinyl,
1,3-bis-(benzyl-oxycarbonyl)amidinyl radical; and, L.sub.3 is a
linker represented by Formula V: ##STR00103## wherein, Q.sub.1 and
Q.sub.m are substituted or non-substituted methylene radical, and
Q.sub.m is directly linked to the amino radical; Q.sub.2, Q.sub.3,
. . . , and Q.sub.m-1 are independently selected from substituted
or non-substituted methylene, oxygen, sulfur, and substituted or
non-substituted amino radical; and, m is an integer equal to or
larger than 2 but smaller than or equal to 15.
14. A compound of Formula IX: ##STR00104## wherein, R.sub.10 is
hydroxy, substituted or non-substituted alkyloxy, or substituted or
non-substituted amino radical; P.sub.2 is selected from hydrido,
t-butoxycarbonyl, (9H-fluoren-9-yl)methoxy-carbonyl, substituted or
non-substituted benzyloxycarbonyl, substituted alkyloxycarbonyl,
substituted or non-substituted alkyl, amidinyl,
1,3-bis(t-butoxy-carbonyl)amidinyl,
1,3-bis-(benzyloxycarbonyl)amidinyl radical; and, L.sub.1 is a
linker represented by Formula V: ##STR00105## wherein, Q.sub.1 and
Q.sub.m are substituted or non-substituted methylene radical, and
Q.sub.m is directly linked to the amino radical; Q.sub.2, Q.sub.3,
. . . , and Q.sub.m-1 are independently selected from substituted
or non-substituted methylene, oxygen, sulfur, and substituted or
non-substituted amino radical; and, m is an integer equal to or
larger than 2 but smaller than or equal to 15.
15. A compound of Formula X: ##STR00106## wherein, R.sub.11 is
hydroxy, substituted or non-substituted alkyloxy, or substituted or
non-substituted amino radical; P.sub.2 is selected from hydrido,
t-butoxycarbonyl, (9H-fluoren-9-yl)methoxy-carbonyl, substituted or
non-substituted benzyloxycarbonyl, substituted alkyloxycarbonyl,
substituted or non-substituted alkyl, amidinyl,
1,3-bis(t-butoxy-carbonyl)amidinyl,
1,3-bis-(benzyl-oxycarbonyl)amidinyl radical; P.sub.3 is selected
from hydrido, t-butoxycarbonyl, (9H-fluoren-9-yl)methoxy-carbonyl,
and substituted or non-substituted benzyloxycarbonyl radical;
P.sub.4 is selected from hydrido, and t-butoxycarbonyl radical;
and, L.sub.2 is a linker represented by Formula V: ##STR00107##
wherein, Q.sub.1 and Q.sub.m are substituted or non-substituted
methylene radical, and Q.sub.m is directly linked to the amino
radical; Q.sub.2, Q.sub.3, . . . , and Q.sub.m-1 are independently
selected from substituted or non-substituted methylene, oxygen,
sulfur, and substituted or non-substituted amino radical; and, m is
an integer equal to or larger than 2 but smaller than or equal to
15.
16. A compound of Formula XI: ##STR00108## wherein, R.sub.12 is
hydroxy, substituted or non-substituted alkyloxy, or substituted or
non-substituted amino radical; P.sub.2 is selected from hydrido,
t-butoxycarbonyl, (9H-fluoren-9-yl)methoxy-carbonyl, substituted or
non-substituted benzyloxycarbonyl, substituted alkyloxycarbonyl,
substituted or non-substituted alkyl, amidinyl,
1,3-bis(t-butoxy-carbonyl)amidinyl,
1,3-bis-(benzyl-oxycarbonyl)amidinyl radical; and, L.sub.3 is a
linker represented by Formula V: ##STR00109## wherein, Q.sub.1 and
Q.sub.m are substituted or non-substituted methylene radical, and
Q.sub.m is directly linked to the amino radical; Q.sub.2, Q.sub.3,
. . . , and Q.sub.m-1 are independently selected from substituted
or non-substituted methylene, oxygen, sulfur, and substituted or
non-substituted amino radical; and, m is an integer equal to or
larger than 2 but smaller than or equal to 15.
Description
FIELD OF INVENTION
[0001] The present invention relates to peptide nucleic acid
derivatives chemically modified to show good cell penetration and
strong affinity for nucleic acid.
BRIEF DESCRIPTIONS OF DRAWINGS
[0002] FIG. 1 provides HPLC chromatograms before and after
purification of Oligo 17 by reverse phase HPLC.
[0003] FIG. 2 provides a MALDI-TOF mass spectrum for a purified
batch of Oligo 17.
[0004] FIG. 3 provides graphs of absorbance changes with
temperature for Oligo 17 against complementary or mismatch DNA.
[0005] FIGS. 4(a) and 4(b) provide confocal microscopy images (at
63.times. objective) 1, 2, 3 and 24 h after HeLa cells were treated
with Oligo 1 and Oligo 2 at 5 .mu.M, respectively.
[0006] FIGS. 5(a) and 5(b) provide confocal microscopy images (at
63.times. objective) 0.5 and 1 h after MCF-7 cells were treated
with Oligo 6 and Oligo 7 at 2.5 .mu.M, respectively.
[0007] FIGS. 6(a) and 6(b) provide confocal microscopy pictures (at
40.times. objective) 6 or 24 h after HeLa cells were treated with
Oligo 1 and Oligo 6 at 1 .mu.M, respectively.
[0008] FIGS. 7(a) and 7(b) provide confocal microscopy pictures
(40.times. objective) 24 h after JAR cells were treated with Oligo
21 and Oligo 28 at 2 .mu.M, respectively.
[0009] FIGS. 7(c) and 7(d) provide confocal microscopy pictures (at
40.times. objective) 24 h after A549 cells were treated with Oligo
21 and Oligo 28 at 2 .mu.M, respectively.
[0010] FIGS. 7(e) and 7(f) provide confocal microscopy pictures (at
40.times. objective) 12 h after HeLa cells were treated with Oligo
21 and Oligo 28 at 2 .mu.M, respectively.
[0011] FIG. 7(g) provides confocal microscopy pictures (at
40.times. objective) 24 h after HeLa cells were treated with Oligo
21 at 2 .mu.M.
[0012] FIGS. 8(a), 8(b) and 8(c) provide confocal microscopy images
(40.times. objective) 24 h after HeLa, A549, and JAR cells were
treated with 2 .mu.M Oligo 22, respectively.
[0013] FIG. 9 provides western blotting results for JAR cells
treated with 5 .mu.M or 10 .mu.M Oligo 9, 5 .mu.M or 10 .mu.M Oligo
10, cotreatment with the oligomers at 5 .mu.M or 10 .mu.M each, and
blank (no oligomer treatment).
[0014] FIG. 10 is the representative structure for the PNA
oligomers of this invention.
BACKGROUND OF THE INVENTION
[0015] Oligonucleotides have been used for diverse biological
purposes including antisense inhibition of gene expression, PCR
(polymerase chain reaction), diagnostic analysis by gene chips, and
so on. Since oligonucleotides interact in a sequence specific
manner with nucleic acids such as DNA and RNA, they are quite
useful to predictably modulate biological processes involving DNA
or RNA within cell. Unlike small molecule drugs, however,
oligonucleotides do not readily penetrate mammalian cell membrane,
and therefore hardly affect biological processes within cell unless
properly modified or formulated to readily penetrate plasma
membrane.
[0016] Proteins as Drug Targets: Proteins mediate diverse cellular
functions. It would not be surprising to find that most of
currently marketed drugs show therapeutic activity through
modulating functions of protein(s). For example, non-steroidal
anti-inflammatory drug aspirin inhibits enzymes called
cyclooxygenases for its anti-inflammatory activity. Losartan binds
to and antagonize the function of a trans-membrane receptor called
angiotensin II receptor for its antihypertensive activity.
Rosiglitazone selectively activates an intracellular receptor
called peroxisome proliferator-activated receptor .gamma.
(PPAR.gamma.) to elicit its antidiabetic activity. Etanercept is a
fusion protein which binds to a cytokine called tumor necrosis
factor-.alpha. (TNF-.alpha.), and neutralizes the biological
activity of TNF-.alpha. for its anti-rheumatic activity. Herceptin
is a monoclonal antibody to treat breast cancer by selectively
binding to erbB2 over-expressed in certain types of breast cancer
cells.
[0017] Antisense Inhibition of Protein Synthesis: Proteins are
encoded by DNA (2-deoxyribose nucleic acid). In response to
cellular stimulation, DNA is transcribed to produce pre-mRNA
(pre-messenger ribonucleic acid) in the nucleus. The intron
portion(s) of pre-mRNA is enzymatically spliced out yielding mRNA
(messenger ribonucleic acid), which is then translocated to the
cytosolic compartment. In the cytosol, a complex of translational
machinery called ribosome binds to mRNA and carries out the protein
synthesis as it scans the genetic information encoded along the
mRNA. (Biochemistry vol 41, 4503-4510, 2002; Cancer Res. vol 48,
2659-2668, 1988)
[0018] An oligonucleotide binding to mRNA or pre-mRNA in a sequence
specific manner is called antisense oligonucleotide (AO). AO may
tightly bind to an mRNA and inhibit the protein synthesis by
ribosome along the mRNA in the cytosol. AO needs to be present
within cell in order to inhibit the synthesis of its target
protein. AO may tightly bind to a pre-mRNA in the nucleus and
affect the splicing of the pre-mRNA, producing an mRNA of altered
sequence and consequently an altered protein.
##STR00001## ##STR00002##
[0019] Unnatural Oligonucleotides: Oligonucleotides of DNA or RNA
are susceptible to degradation by endogenous nucleases, limiting
their therapeutic utility. To date, many types of unnatural
oligonucleotides have been developed and studied intensively.
(Clin. Exp. Pharmacol. Physiol. vol 33, 533-540, 2006) Some of them
show extended metabolic stability compared to DNA and RNA. Provided
above are chemical structures for some of representative unnatural
oligonucleotides. Such oligonucleotides predictably bind to a
complementary nucleic acid as DNA or RNA does.
[0020] Phosphorothioate oligonucleotide (PTO) is a DNA analog with
one of the backbone phosphate oxygen atoms replaced with sulfur
atom per monomer. Such a small structural change made PTO
comparatively resistant to degradation by nucleases. (Ann. Rev.
Biochem. vol 54, 367-402, 1985)
[0021] Reflecting the structural similarity of PTO and DNA, they
both poorly penetrate cell membrane in most mammalian cell types.
For some types of cells abundantly expressing transporter(s) for
DNA, however, DNA and PTO show good cell penetration. Systemically
administered PTOs are known to readily distribute to the liver and
kidney. (Nucleic Acids Res. vol 25, 3290-3296, 1997)
[0022] In order to facilitate PTO's cell penetration in vitro,
lipofection has been popularly practiced. However, lipofection
physically alters cell membrane, causes cytotoxicity, and therefore
would not be ideal for long term therapeutic use.
[0023] Over the past 20 years, antisense PTOs and variants of PTOs
have been clinically evaluated to treat cancers, immunological
disorders, metabolic diseases, and so on. (Biochemistry vol 41,
4503-4510, 2002; Clin. Exp. Pharmacol. Physiol. vol 33, 533-540,
2006) Many of such antisense drug candidates have not been
successful partly due to PTO's poor cell penetration. In order to
overcome the poor cell penetration, PTO needs to be administered at
high dose for therapeutic activity. However, PTOs are known to be
associated with dose dependent toxicities such as increased
coagulation time, complement activation, tubular nephropathy,
Kupffer cell activation, and immune stimulation including
splenomegaly, lymphoid hyperplasia, mononuclear cell infiltration.
(Clin. Exp. Pharmacol. Physiol. vol 33, 533-540, 2006)
[0024] Many antisense PTOs have been found to show due clinical
activity for diseases with a significant contribution from the
liver or kidney. ISIS-301012 (mipomersen) is a PTO analog which
inhibits the synthesis of apoB-100, a protein involved in LDL
cholesterol transport. Mipomersen manifested due clinical activity
in a certain population of atherosclerosis patients most likely due
to its preferential distribution to the liver.
(www.medscape.com/viewarticle/556073: Accessed on Feb. 19, 2009)
ISIS-113715 is an antisense PTO analog inhibiting the synthesis
protein tyrosine phosphatase 1B (PTP1B), and was found to show
therapeutic activity in type II diabetes patients. (Curr. Opin.
Mol. Ther. vol 6, 331-336, 2004)
[0025] In phosphoroamidite morpholino oligonucleotide (PMO), the
backbone phosphate and 2-deoxyribose of DNA are replaced with
phosphoamidite and morpholine, respectively. (Appl. Microbiol.
Biotechnol. vol 71, 575-586, 2006) While the DNA backbone is
negatively charged, the PMO backbone is not charged. Thus the
binding between PMO and mRNA is free of electrostatic repulsion
between the backbones, and tends to be stronger than that between
DNA and mRNA. Since PMO is structurally very different from DNA,
PMO wouldn't be recognized by the hepatic transporter(s)
recognizing DNA. However, PMO doesn't readily penetrate cell
membrane.
[0026] Peptide nucleic acid (PNA) is a polypeptide with
N-(2-aminoethyl)glycine as the unit backbone, and was discovered by
Nielsen and colleagues. (Science vol 254, 1497-1500, 1991) Like DNA
and RNA, PNA also selectively binds to complementary nucleic acid
[Nature (London) vol 365, 566-568, 1992] Like PMO, the backbone of
PNA is not charged. Thus the binding between PNA and RNA tends to
be stronger than that between DNA and RNA. Since PNA is
structurally markedly different from DNA, PNA wouldn't be
recognized by the hepatic transporter(s) recognizing DNA, and would
show a tissue distribution profile very different from that of DNA
or PTO. However, PNA also poorly penetrates mammalian cell
membrane. (Adv. Drug Delivery Rev. vol 55, 267-280, 2003)
[0027] In locked nucleic acid (LNA), the backbone ribose ring of
RNA is structurally constrained to increase the binding affinity
for RNA or DNA. Thus, LNAs may be regarded as high affinity DNA or
RNA derivatives. (Biochemistry vol 45, 7347-7355, 2006)
[0028] Antisense Mechanisms: Antisense mechanism differs depending
on types of AOs. RNAse H recognizes a duplex of mRNA with DNA, RNA,
or PTO, and degrades the duplex portion of mRNA. Thus, the
antisense activity of PTO is significantly amplified by RNAse H. In
the meantime, RNAse H does not recognize a duplex of mRNA with PMO,
PNA, or LNA. In other words, PMO, PNA and LNA must rely purely on
the steric blocking of mRNA for their antisense activity.
(Biochemistry vol 41, 4501-4510, 2002)
[0029] For oligonucleotides with the same binding affinity for
mRNA, PTO should therefore show stronger antisense activity than
PMO, PNA, and LNA. For steric block AOs such as PMO, PNA, and LNA,
strong affinity for mRNA is desired for antisense activity.
[0030] Antisense Activity of PNA: The binding affinity of PNA for
mRNA would increase as the length of PNA increases to a certain
point. However, the antisense activity of PNA doesn't seem to
always increase to the length of PNA. There were cases that the
antisense activity of PNA reached the maximum activity at 12 to
13-mer and decreases thereafter. (Nucleic acids Res. vol 32,
4893-4902, 2004) On the other hand, optimum antisense activity was
reached with 15 to 18-mer PNAs against a certain mRNA, reflecting
that the structural accessibility of the target binding site of the
mRNA would be important. (Biochemistry vol 40, 53-64, 2001)
[0031] In many cases, PNAs have been reported to inhibit protein
synthesis by ribosome at micromolar level under good cell
penetrating conditions. (Science vol 258, 1481-85, 1992;
Biochemistry vol 40, 7853-7859, 2001; Nucleic acids Res. vol 32,
4893-4902, 2004) However, PNAs targeting a highly accessible
position of mRNA were found to show antisense activity at
sub-micromolar level (Neuropeptides vol 38, 316-324, 2004;
Biochemistry vol 40, 53-64, 2001) or even at sub-nanomolar level
(Nucleic Acids Res. vol 36, 4424-4432, 2008) under good
transfection conditions.
[0032] In addition to targeting a highly accessible site in mRNA,
strong binding affinity of PNA for mRNA would be very required for
good antisense activity. Unlike DNA, PTO, and LNA, the backbone of
PNA is not charged. PNA tends to aggregate and become less suitable
for binding to mRNA as its size increases. It is desired to improve
PNA's binding affinity for mRNA without increasing the length of
PNA. Incorporation of PNA monomers with a point charge would be
beneficial in preventing PNA from aggregating.
[0033] Cell Penetration Strategies for PNA: PNAs do not readily
penetrate cell membrane and tend to show poor antisense activity
unless properly transfected. In early years, the antisense activity
of PNA was assessed by microinjection (Science vol 258, 1481-85,
1992) or electroporation (Biochemistry vol 40, 7853-7859, 2001).
Microinjection and electroporation are invasive and inappropriate
to be applied for therapeutic purposes. In order to improve the
cell penetration, various strategies have been developed. (Adv.
Drug Delivery Rev. vol 55, 267-280, 2003; Curr. Top. Med. Chem. vol
7, 727-737, 2007)
[0034] PNAs have been effectively delivered into cell by covalent
incorporation of cell penetrating peptides (Neuropeptides vol 38,
316-324, 2004), lipofection following duplex formation with a
complementary DNA (Biochemistry vol 40, 53-64, 2001), lipofection
of PNAs with a covalently attached 9-aminoacridine (Nucleic Acids
Res. vol 32, 2695-2706, 2004), lipofection of PNAs with covalently
attached phosphonate anions (Nucleic Acids Res. vol 36, 4424-4432,
2008), and so on. Also cell penetration was improved by attaching
to PNA a lipophilic moiety such as adamantane (Bioconjugate Chem.
vol 10, 965-972, 1999) or amphiphilic group such as tetraphenyl
phosphonium. (Nucleic Acids Res. vol 29, 1852-1863, 2001)
Nevertheless, such a covalent modification is unlikely to increase
the binding affinity for mRNA despite marked improvement in the
cell penetration.
[0035] PNAs with a Covalently Attached CPP: Cell penetrating
peptides (CPPs) are polypeptides showing good cell penetration, and
have multiple positive charges from arginine or lysine residues. To
date many CPPs such as transportan, penetratin, NLS (nuclear
localization signal), and Tat have been discovered. CPPs are known
to efficiently carry a covalently attached cargo into cell. PNAs
with a covalently attached CPP also showed good cell
penetration.
[0036] Although some PNAs with a covalently attached CPP showed
antisense IC.sub.50s around 100 nM (Neuropeptides vol 38, 316-324,
2004), micromolar antisense IC.sub.50s are rather prevalent for
such PNAs.
[0037] PNAs with a covalently linked CPP are composed of two
portions, the hydrophobic PNA domain and the positively charged CPP
domain. Such a PNA tends to aggregate and be trapped in endosomes
within cell, and would not be available for the antisense
inhibition of protein synthesis. (Curr Top. Med. Chem. vol 7,
727-737, 2007; Nucleic Acids Res. vol 33, 6837-6849, 2005)
Furthermore, such a covalently attached CPP hardly increases the
binding affinity of PNA for mRNA.
[0038] PNAs with a Chiral Backbone: There have been attempts to
introduce a chiral substituent on the PNA backbone of
2-aminoethyl-glycine (Aeg). For example, the aqueous solubility of
PNA was significantly improved by incorporating PNA monomer(s) with
a backbone of 2-aminoethyl-lysine in place of Aeg. (Angew. Chem.
Int. Ed. Engl. vol 35, 1939-1941, 1996)
[0039] By introducing the backbone of
L-(2-amino-2-methyl)ethyl-glycine in place of Aeg, the binding
affinity of PNA for DNA and RNA was significantly improved. A
10-mer PNA with all of the backbone of
L-(2-amino-2-methyl)ethyl-glycine in place of 2-aminoethyl-glycine
showed an increase of 19.degree. C. and 10.degree. C. in T.sub.m
against complementary DNA and RNA, respectively. Such an increase
doesn't seem to be proportional to the number of substitution with
L-(2-amino-2-methyl)ethyl-glycine, though. (J. Am. Chem. Soc. vol
128, 10258-10267, 2006)
[0040] GPNA: The cell penetration of PNA was reported to be
markedly improved by incorporating PNA monomers with a backbone of
2-aminoethyl-arginine in place of Aeg. (J. Am. Chem. Soc. vol 125,
6878-6879, 2003) Such PNAs have been termed `GPNA` since they have
guanidinium moiety on the backbone.
[0041] GPNAs with the backbone of 2-aminoethyl-D-arginine were
reported to have stronger affinity for DNA and RNA than the
corresponding GPNAs with that of 2-aminoethyl-L-arginine. (Chem.
Commun. 244-246, 2005) For a 10-mer GPNA with 5 GPNA monomers with
the backbone of 2-aminoethyl-D-arginine there was an increase of
7.degree. C. in T.sub.m (melting temperature) against complementary
DNA compared to the corresponding unmodified PNA. (Bioorg. Med.
Chem. Lett. Vol 16, 4931-4935, 2006)
[0042] A 16-mer antisense GPNA against human EGFR-TK was reported
to show antitumor activity upon ip (intra peritoneal)
administration in athymic nude mice, although the in vitro
antisense activity was not documented for the antisense GPNA in the
prior art. (WO 2008/061091)
PNAs with Modified Nucleobase: Like cases with DNA, nucleobase
modifications have been pursued to improve PNA's affinity for
nucleic acids.
[0043] PNAs with adenine replaced with 2,6-diaminopurine were
evaluated for their affinity for complementary DNA or RNA.
Substitution with 2,6-diaminopurine was found to elicit an increase
of 2.5.about.6.degree. C. in T.sub.m per replacement. (Nucleic
Acids Res. vol 25, 4639-4643, 1997)
##STR00003##
[0044] PNAs with cytosine replaced with
9-(2-aminoethoxy)phenoxazine were evaluated for their affinity for
complementary DNA or RNA. A single substitution with
9-(2-aminoethoxy)phenoxazine elicited an increase of
10.7.about.23.7.degree. C. in T.sub.m, although such an increase
was markedly dependent on the nucleotide sequence. Nucleobase
9-(2-aminopropoxy)phenoxazine also induced a large increase in
T.sub.m. Due to a huge increase in T.sub.m, PNA monomer with either
9-(2-aminoethoxy)-phenoxazine or 9-(2-aminoethoxy)phenoxazine as a
cytosine replacement has been termed `G-clamp`. (Org. Lett. vol 4,
4395-4398, 2002) However, cell penetration data was not reported
for PNAs with G-clamp(s).
[0045] PNAs with cytosine replaced with either
6-{2-(2-aminoethoxy)phenyl}-pyrrolocytosine or
6-{2,6-di(2-aminoethoxy)phenyl}pyrrolocytosine were evaluated for
their affinity for complementary DNA or RNA. A single substitution
with either 6-{2-(2-aminoethoxy)phenyl}pyrrolocytosine or
6-{2,6-di(2-aminoethoxy)-phenyl}pyrrolocytosine increased T.sub.m
by 3.about.11.5.degree. C. (J. Am. Chem. Soc. vol 130, 12574-12575,
2008) However, such PNAs were not evaluated for cell
penetration.
[0046] Other Use of PNAs: By tightly binding to a microRNA, PNA can
inhibit the regulatory function of the microRNA, leading to an
increase in the expression level of the protein(s) directly
regulated by the microRNA. (RNA vol 14, 336-346, 2008) By tightly
binding to a ribonucleoprotein such as telomerase, PNA can modulate
the cellular function of the ribonucleoprotein. (Bioorg. Med. Chem.
Lett. vol 9, 1273-78, 1999) By tightly binding to a certain portion
of a gene in the nucleus, PNA can modulate the transcription level
of the gene. (Biochemistry vol 46, 7581-89, 2007)
[0047] Since PNA tightly binds to DNA and RNA, and sensitively
discriminates a single base pair mismatch, PNA would be suitable
for high fidelity detection of single nucleotide polymorphism
(SNP). Since PNA binds tightly to DNA and RNA with high sequence
specificity, PNA may find various other therapeutic and diagnostic
applications involving DNA or RNA. (FASEB vol 14, 1041-1060,
2000)
SUMMARY OF INVENTION
[0048] The present invention provides a novel class of PNA
oligomers represented by Formula I, or a pharmaceutically
acceptable salt thereof:
##STR00004## [0049] wherein,
[0050] n is an integer equal to or larger than 5;
[0051] S.sub.1, S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1,
T.sub.2, . . . , T.sub.n-1, and T.sub.n independently represent
hydrido, deuterido, substituted or non-substituted alkyl, or
substituted or non-substituted aryl radical;
[0052] X and Y independently represent hydrido, deuterido, hydroxy,
substituted or non-substituted alkyloxy, substituted or
non-substituted aryloxy, substituted or non-substituted amino,
substituted or non-substituted alkyl, substituted or
non-substituted acyl, substituted or non-substituted sulfonyl, or
substituted or non-substituted aryl radical;
[0053] Z represents hydrido, deuterido, hydroxy, substituted or
non-substituted alkyloxy, substituted or non-substituted aryloxy,
substituted or non-substituted amino, substituted or
non-substituted alkyl, or substituted or non-substituted aryl
radical;
[0054] B.sub.1, B.sub.2, . . . , B.sub.n-1, and B.sub.n are
independently selected from natural nucleobases including adenine,
thymine, guanine, cytosine and uracil, and unnatural nucleobases;
and,
[0055] at least one of B.sub.1, B.sub.2, . . . , B.sub.n-1, and
B.sub.n independently represents an unnatural nucleobase with a
substituted or non-substituted amino radical covalently linked to
the moiety responsible for its due nucleobase pairing
properties.
[0056] A PNA oligomer of Formula I shows improved binding affinity
for nucleic acid and cell penetration compared to its corresponding
`unmodified`PNA oligomer. PNA oligomers of this invention are
useful to sequence specifically inhibit or modulate cellular and
physiological functions mediated by nucleic acids or
physiologically active molecules having a nucleic acid domain such
as ribonucleoproteins. Also PNA oligomers of this invention are
useful for diagnostic purposes due to their sequence specific
binding capability for nucleic acids.
DESCRIPTION OF INVENTION
[0057] The present invention provides a novel class of PNA
oligomers represented by Formula I, or a pharmaceutically
acceptable salt thereof:
##STR00005##
[0058] wherein,
[0059] n is an integer equal to or larger than 5;
[0060] S.sub.1, S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1,
T.sub.2, . . . , T.sub.n-1, and T.sub.n independently represent
hydrido, deuterido, substituted or non-substituted alkyl, or
substituted or non-substituted aryl radical;
[0061] X and Y independently represent hydrido, deuterido, hydroxy,
substituted or non-substituted alkyloxy, substituted or
non-substituted aryloxy, substituted or non-substituted amino,
substituted or non-substituted alkyl, substituted or
non-substituted acyl, substituted or non-substituted sulfonyl, or
substituted or non-substituted aryl radical;
[0062] Z represents hydrido, deuterido, hydroxy, substituted or
non-substituted alkyloxy, substituted or non-substituted aryloxy,
substituted or non-substituted amino, substituted or
non-substituted alkyl, or substituted or non-substituted aryl
radical;
[0063] B.sub.1, B.sub.2, . . . , B.sub.n-1, and B.sub.n are
independently selected from natural nucleobases including adenine,
thymine, guanine, cytosine and uracil, and unnatural nucleobases;
and,
[0064] at least one of B.sub.1, B.sub.2, . . . , B.sub.n-1, and
B.sub.n independently represents an unnatural nucleobase with a
substituted or non-substituted amino radical covalently linked to
the moiety responsible for its due nucleobase pairing
properties.
[0065] A PNA oligomer of this invention shows improved cell
penetration and binding to nucleic acid compared to its
corresponding `unmodified` PNA oligomer. In this invention,
`unmodified` PNA oligomer refers to a PNA oligomer of Formula I,
wherein S.sub.1, S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1,
T.sub.2, . . . , T.sub.n-1, and T.sub.n are hydrido radical; and
B.sub.1, B.sub.2, . . . , B.sub.n-1, and B.sub.n are independently
selected from natural nucleobases comprising adenine, thymine,
guanine, and cytosine.
[0066] A PNA oligomer of this invention readily penetrates
mammalian cell membrane, and can affect or alter cellular functions
by sequence specifically binding to a nucleic acid or a
nucleoprotein within cell.
[0067] A PNA oligomer of Formula I can potently inhibit ribosomal
protein synthesis by tightly binding to mRNA. A PNA oligomer of the
present invention can tightly bind to a pre-mRNA and alter the
splicing of the pre-mRNA to mRNA. Further, a PNA oligomer of the
present invention can bind tightly to a microRNA, and inhibit mRNA
degradation induced by the microRNA.
[0068] A PNA oligomer of Formula I can predictably bind to the
nucleic acid domain of a ribonucleoprotein, for example telomerase,
and modulate its physiological function(s). A PNA oligomer of the
present invention can bind to a gene and modulate the transcription
of the gene. A PNA oligomer of Formula I can bind to a viral gene
or its transcript, and inhibit the proliferation of the virus. A
PNA oligomer of this invention can affect cellular functions other
than those described above by sequence specifically binding to a
nucleic acid or a nucleoprotein within mammalian cell. In addition,
a PNA oligomer of the present invention can tightly bind to a
bacterial mRNA, nucleic acid, or gene, and inhibit bacterial
proliferation or alter bacterial biosynthesis profiles.
[0069] A PNA oligomer of this invention is highly sensitive to a
base mismatch in binding to its complementary DNA counterpart, and
would be appropriate for detecting single nucleotide polymorphism
(SNP) with high fidelity. PNA oligomers of the present invention
bind tightly to their complementary DNAs with high sequence
specificity, and may be useful for gene profiling. A PNA oligomer
of Formula I may be useful to probe or locate a nucleic acid
bearing molecule such as telomere within cell if properly tagged
with a chromophore, for example, fluorophore. PNA oligomers of this
invention may be useful for a variety of diagnostic or analytical
purposes other than those detailed above.
[0070] A PNA oligomer of the present invention possesses good
aqueous solubility compared to the corresponding `unmodified` PNA
oligomer, and can be used as dissolved in water, saline, or a
buffer solution. A PNA oligomer of Formula I can be formulated with
a cationic lipid such as lipofectamine. A PNA oligomer of this
invention may be duplexed with a complementary DNA and the
resulting duplex can be formulated with a cationic lipid.
[0071] A PNA oligomer of this invention may be formulated in a
variety of dosage forms including but not limited to injectable
formulation, nasal spray, tablet, granules, hard capsule, soft
capsule, liposomal formulation, oral suspension, transdemal
formulation, and so on.
[0072] A PNA oligomer of the present invention can be administered
to a subject at therapeutically effective doses, which would vary
depending on indication, administration route, dosing schedule,
situations of subject, and so on.
[0073] A PNA oligomer of the present invention can be administered
to a subject by a variety of routes including but not limited to
intravenous injection, subcutaneous injection, intraperitoneal
injection, nasal inhalation, oral administration, transdermal
application, and so on.
[0074] A PNA oligomer of Formula I can be administered to a subject
in combination with a pharmaceutically acceptable adjuvant
including but not limited to citric acid, hydrochloric acid,
tartaric acid, stearic acid, polyethyleneglycol,
polypropyleneglycol, ethanol, sodium bicarbonate, distilled water,
hyaluronic acid, cationic lipid such as lipofectamine, starch,
gelatin, talc, ascorbic acid, olive oil, palm oil, methylcelluose,
titanium oxide, sodium carboxymethylcellulose, sweetener,
preservative, and so on.
[0075] A PNA oligomer of the present invention, depending on the
presence of basic or acidic functional group(s) therein, may be
used as neutralized with an equivalent amount of a pharmaceutically
acceptable acid or base including but not limited to sodium
hydroxide, potassium hydroxide, hydrochloric acid, methanesulfonic
acid, citric acid, and so on.
[0076] Preferred PNA oligomers encompass PNA oligomers of Formula
I, or a pharmaceutically acceptable salt thereof:
[0077] wherein,
[0078] n is an integer equal to or larger than 5 but smaller than
or equal to 30;
[0079] S.sub.1, S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1,
T.sub.2, . . . , T.sub.n-1, and T.sub.n are hydrido radical;
[0080] X and Y are independently selected from hydrido, substituted
or non-substituted alkyl, substituted or non-substituted acyl,
substituted or non-substituted sulfonyl, and substituted or
non-substituted aryl radical;
[0081] Z represents hydrido, hydroxy, substituted or nonsubstituted
alkyloxy, substituted or non-substituted amino, substituted or
non-substituted alkyl, or substituted or non-substituted aryl
radical;
[0082] B.sub.1, B.sub.2, . . . , B.sub.n-1, and B.sub.n are
independently selected from natural nucleobases including adenine,
thymine, guanine, cytosine and uracil, and unnatural nucleobases;
and,
[0083] at least one of B.sub.1, B.sub.2, . . . , B.sub.n-1, and
B.sub.n is independently selected from unnatural nucleobases
represented by Formula II, Formula III, or Formula IV:
##STR00006##
[0084] wherein,
[0085] R.sub.1, R.sub.2, R.sub.3, R.sub.4, R.sub.5 and R.sub.6 are
independently selected from substituted or non-substituted alkyl,
hydrido, hydroxy, and substituted or non-substituted alkyloxy
radical; and,
[0086] L.sub.1, L.sub.2 and L.sub.3 are a covalent linker
represented by Formula V connecting a basic amino group to the
moiety responsible for nucleobase pairing properties:
##STR00007##
[0087] wherein,
[0088] Q.sub.1 and Q.sub.m are substituted or non-substituted
methylene (--CH.sub.2--) radical, and Q.sub.m is directly linked to
the basic amino group;
[0089] Q.sub.2, Q.sub.3, . . . , and Q.sub.m-1 are independently
selected from substituted or non-substituted methylene, oxygen
(--O--), sulfur (--S--), and substituted or non-substituted amino
radical [--N(H)--, or --N(substituent)-]; and,
m is an integer equal to or larger than 2 but smaller than or equal
to 15.
[0090] PNA oligomers of particular interest comprise PNA oligomers
of Formula I, or a pharmaceutically acceptable salt thereof:
[0091] wherein,
[0092] n is an integer equal to or larger than 8 but smaller than
or equal to 25;
[0093] S.sub.1, S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1,
T.sub.2, . . . , T.sub.n-1, and T.sub.n are hydrido radical;
[0094] X and Y are independently selected from hydrido, substituted
or non-substituted alkyl, and substituted or non-substituted acyl
radical;
[0095] Z represents hydroxy, or substituted or non-substituted
amino radical;
[0096] B.sub.1, B.sub.2, . . . , B.sub.n-1, and B.sub.n are
independently selected from natural nucleobases including adenine,
thymine, guanine, cytosine and uracil, and unnatural
nucleobases;
[0097] at least two of B.sub.1, B.sub.2, . . . , B.sub.n-1, and
B.sub.n are independently selected from unnatural nucleobases
represented by Formula II, Formula III, or Formula IV;
[0098] R.sub.1, R.sub.2, R.sub.3, R.sub.4, R.sub.5 and R.sub.6 are
independently selected from substituted or non-substituted alkyl,
and hydrido radical;
[0099] Q.sub.1 and Q.sub.m are substituted or non-substituted
methylene radical, and Q.sub.m is directly linked to the basic
amino group;
[0100] Q.sub.2, Q.sub.3, . . . , and Q.sub.m-1 are independently
selected from substituted or non-substituted methylene, oxygen, and
amino radical; and,
[0101] m is an integer equal to or larger than 2 but smaller than
or equal to 12.
[0102] PNA oligomers of high interest comprise PNA oligomers of
Formula I, or a pharmaceutically acceptable salt thereof:
[0103] wherein,
[0104] n is an integer equal to or larger than 10 but smaller than
or equal to 25;
[0105] S.sub.1, S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1,
T.sub.2, . . . , T.sub.n-1, and T.sub.n are hydrido radical;
[0106] X and Y are independently selected from hydrido, and
substituted or non-substituted acyl radical;
[0107] Z represents hydroxy, alkyloxy, or substituted or
non-substituted amino radical; and,
[0108] B.sub.1, B.sub.2, . . . , B.sub.n-1, and B.sub.n are
independently selected from natural nucleobases including adenine,
thymine, guanine, cytosine and uracil, and unnatural
nucleobases;
[0109] at least three of B.sub.1, B.sub.2, . . . , B.sub.n-1, and
B.sub.n are independently selected from unnatural nucleobases
represented by Formula II, Formula III, or Formula IV;
[0110] R.sub.1, R.sub.2, R.sub.3, R.sub.4, R.sub.5 and R.sub.6 are
independently selected from substituted or non-substituted alkyl,
and hydrido radical;
[0111] Q.sub.1 and Q.sub.m are methylene radical, and Q.sub.m is
directly linked to the basic amino group;
[0112] Q.sub.2, Q.sub.3, . . . , and Q.sub.m-1 are independently
selected from methylene, oxygen, and amino radical; and,
[0113] m is an integer equal to or larger than 2 but smaller than
or equal to 10.
[0114] PNA oligomers of higher interest encompass PNA oligomers of
Formula I, or a pharmaceutically acceptable salt thereof:
[0115] wherein,
[0116] n is an integer equal to or larger than 10 but smaller than
or equal to 20;
[0117] S.sub.1, S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1,
T.sub.2, . . . , T.sub.n-1, and T.sub.n are hydrido radical;
[0118] X and Y are independently selected from hydrido, and
substituted or non-substituted acyl radical;
[0119] Z represents hydroxy, or substituted or non-substituted
amino radical;
[0120] B.sub.1, B.sub.2, . . . , B.sub.n-1, and B.sub.n is
independently selected from natural nucleobases including adenine,
thymine, guanine, cytosine and uracil, and unnatural
nucleobases;
[0121] at least three of B.sub.1, B.sub.2, . . . , B.sub.n-1, and
B.sub.n are independently selected from unnatural nucleobases
represented by Formula II, Formula III, or Formula IV;
[0122] R.sub.1, R.sub.3, and R.sub.5 are hydrido radical, and
R.sub.2, R.sub.4, and R.sub.6 independently represent hydrido, or
substituted or non-substituted amidinyl radical;
[0123] Q.sub.1 and Q.sub.m are methylene radical, and Q.sub.m is
directly linked to the basic amino group;
[0124] Q.sub.2, Q.sub.3, . . . , and Q.sub.m-1 are independently
selected from methylene, oxygen, and amino radical; and,
[0125] m is an integer equal to or larger than 2 but smaller than
or equal to 10.
[0126] PNA oligomers of highest interest comprise PNA oligomers of
Formula I, or a pharmaceutically acceptable salt thereof:
[0127] wherein,
[0128] n is an integer equal to or larger than 10 but smaller than
or equal to 20;
[0129] S.sub.1, S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1,
T.sub.2, . . . , T.sub.n-1, and T.sub.n are hydrido radical;
[0130] X and Y are independently selected from hydrido, and
substituted or non-substituted acyl radical;
[0131] Z represents hydroxy, or substituted or non-substituted
amino radical;
[0132] B.sub.1, B.sub.2, . . . , B.sub.n-1, and B.sub.n are
independently selected from adenine, thymine, guanine, cytosine,
and unnatural nucleobases;
[0133] at least three of B.sub.1, B.sub.2, . . . , B.sub.n-1, and
B.sub.n are independently selected from unnatural nucleobases
represented by Formula II, Formula III, or Formula IV;
[0134] R.sub.1, R.sub.3, and R.sub.5 are hydrido radical, and
R.sub.2, R.sub.4, and R.sub.6 independently represents hydrido or
amidinyl radical;
[0135] Q.sub.1 and Q.sub.m are methylene radical, and Q.sub.m is
directly linked to the basic amino group;
[0136] Q.sub.2, Q.sub.3, . . . , and Q.sub.m-1 are independently
selected from methylene, and oxygen radical; and,
[0137] m is an integer equal to or larger than 2 but smaller than
or equal to 8.
[0138] Specific PNA oligomers of strong interest comprise PNA
oligomers of Formula I, or a pharmaceutically acceptable salt
thereof:
[0139] wherein,
[0140] n is an integer equal to or larger than 8 but smaller than
or equal to 20;
[0141] S.sub.1, S.sub.2, . . . , S.sub.n-1, S.sub.n, T.sub.1,
T.sub.2, . . . , T.sub.n-1, and T.sub.n are hydrido radical;
[0142] X is hydrido radical;
[0143] Y represents hydrido, or substituted or non-substituted acyl
radical;
[0144] Z represents hydroxy, or substituted or non-substituted
amino radical;
[0145] B.sub.1, B.sub.2, . . . , B.sub.n-1, and B.sub.n are
independently selected from adenine, thymine, guanine, cytosine,
and unnatural nucleobases;
[0146] at least three of B.sub.1, B.sub.2, . . . , B.sub.n-1, and
B.sub.n are independently selected from unnatural nucleobases
represented by Formula II, Formula III, or Formula IV;
[0147] R.sub.1, R.sub.3, and R.sub.5 are hydrido radical, and
R.sub.2, R.sub.4, and R.sub.6 independently represent hydrido or
amidinyl radical;
[0148] L.sub.1 represents
--(CH.sub.2).sub.2--O--(CH.sub.2).sub.2--,
--CH.sub.2--O--(CH.sub.2).sub.2--, or
--CH.sub.2--O--(CH.sub.2).sub.3-- with the right end is directly
linked to the basic amino group; and,
[0149] L.sub.2 and L.sub.3 are independently selected from
--(CH.sub.2).sub.2--O--(CH.sub.2).sub.2--,
--(CH.sub.2).sub.3--O--(CH.sub.2).sub.2--,
--(CH.sub.2).sub.2--O--(CH.sub.2).sub.3--, --(CH.sub.2).sub.2--,
--(CH.sub.2).sub.3--, --(CH.sub.2).sub.4--, --(CH.sub.2).sub.5--,
--(CH.sub.2).sub.6--, --(CH.sub.2).sub.7--, and
--(CH.sub.2).sub.8-- with the right end is directly linked to the
basic amino group.
[0150] The above used terms and abbreviations for the PNA oligomers
of this invention are illustrated in the table below.
TABLE-US-00001 Term/ Abbreviation Illustration or definition
oligomer oligonucleotide hydrido single hydrogen atom (-H)
deuterido single deuterium atom (-D) alkyl linear or branched alkyl
radical aryl aromatic group such as phenyl, pyridyl, furyl,
naphthyl, etc methylene --(CH.sub.2)-- acyl '--C(O)--' substituted
with hydrido, alkyl, or aryl radical sulfonyl '--S(O).sub.2--'
substituted with alkyl, or aryl radical alkyloxy 'R--O--' where R
is substituted or non-substituted alkyl radical oxygen '--O--'
sulfur '--S--' amidinyl ##STR00008## cytosine (C) ##STR00009##
thymine (T) ##STR00010## uracil (U) ##STR00011## adenine (A)
##STR00012## guanine (G) ##STR00013##
General Synthetic Procedures
[0151] For characterization of molecules of this invention NMR
spectra were recorded on a Varian Mercury 300 MHz, Bruker Avance
400 MHz, or Varian Inova 500 MHz NMR spectrometer. Either a Bruker
Daltonics Ultraflex MALDI-TOF or an Agilent LC/MS Ion Trap System
was employed for determination of molecular weight. PNA oligomers
were analyzed and purified by C.sub.18-reverse phase HPLC either on
a Hewlett Packard 1050 HPLC or a Shimazu LC-6AD HPLC. Unless noted
otherwise, silica gel was used for chromatographic separation of
small molecules prepared in this invention. Melting point is
reported as uncorrected.
[0152] Unnatural nucleobase derivatives used for the synthesis of
PNA monomers of this invention were prepared according to one of
the methods (Methods A, B, and C) provided below or with minor
modification(s) thereof, unless detailed otherwise in actual
synthetic examples.
[0153] Method A: 6-alkyl-pyrollocytosine derivatives were
synthesized as properly protected according to Scheme 1 or with
minor variation(s) thereof. Such 6-alkyl-pyrollocytosine
derivatives were used to synthesize PNA monomers containing a
nucleobase represented by Formula II as a cytosine equivalent.
[0154] First compound a was deprotonated with NaH and then
alkylated with ethylbromoacetate to obtain compound b. Compound b
was subjected to a palladium catalyzed coupling with a terminal
acetylene derivative, which was in situ annulated to product c
according to the literature. (Nucleosides Nucleotides & Nucleic
Acids vol 22, 1029-1033, 2003)
##STR00014##
[0155] Method B: 2,6-diaminopurine derivatives were synthesized as
properly protected according to Scheme 2 or with minor variation(s)
thereof. Such 2,6-diamino-purine derivatives were used to
synthesize PNA monomers containing a nucleobase represented by
Formula III as an adenine equivalent.
[0156] First 2-haloadenine was reacted with a diamine at high
temperature to obtain compound d, which was then reacted with
Boc.sub.2O to give compound e. Compound e was deprotonated with
NaH, and alkylated with ethylbromoacetate to obtain compound f. The
aromatic amino group of compound f was protected with either Cbz or
Boc group to yield compound g.
##STR00015##
[0157] Method C: N-alkylated guanine derivatives were synthesized
as properly protected according to Scheme 3 or with minor
variations thereof. Such guanine derivatives were used to
synthesize PNA monomers containing a nucleobase represented by
Formula IV as a guanine equivalent.
##STR00016##
[0158] First 2-halohypoxanthine was reacted with a diamine at high
temperature to obtain compound h, which was then reacted with
Boc.sub.2O to give compound i. Compound i was deprotonated with
NaH, and alkylated with ethylbromoacetate to obtain compound j.
[0159] Two types of PNA monomers were synthesized according to
either Method D or Method E to prepare PNA oligomers of Formula I.
PNA oligomers were prepared by Panagene, Inc. (www.panagene.com,
Daejon, South Korea) using PNA monomers of type o of Scheme 4 upon
request of CTI Bio. Alternatively, PNA monomers of type q of Scheme
5 were used in-house for the synthesis of PNA oligomers according
to the method described in the prior art or with minor
modification(s) thereof. (U.S. Pat. No. 6,133,444)
[0160] Method D: PNA monomers with a modified nucleobase were
prepared according to Scheme 4 or with minor variation(s) thereof
as properly protected for the PNA oligomer synthesis method
described in the literature. (Org. Lett. vol 9, 3291-3293, 2006) In
Scheme 4, compound k may correspond to compound c of Scheme 1,
compound g of Scheme 2, or compound j of Scheme 3, however, may not
be necessarily limited to one of those ester compounds.
##STR00017##
[0161] First ester k was subjected to alkaline hydrolysis to afford
acid l, which was then coupled with ethyl
N-[2-{N-(2-benzothiazolinyl)sulfonylamino}ethyl]-glycinate to
obtain compound m. Compound m was mildly hydrolyzed with LiOH to
give acid n, which was cyclized by an EDCI coupling reaction to
obtain modified PNA monomer o. The chemical structure for PNA
monomer o was assumed as in Scheme 4 throughout this invention,
given that such assigned PNA monomers have successfully yielded PNA
oligomers in the literature. (Org. Lett. vol 9, 3291-3293,
2006)
[0162] Method E: Alternatively, PNA monomers with a modified
nucleobase were prepared according to Scheme 5 or with minor
variation(s) thereof as properly protected for the PNA oligomer
synthesis method provided in the prior art. (U.S. Pat. No.
6,133,444) In Scheme 5, compound k may correspond to compound c of
Scheme 1, compound g of Scheme 2, or compound j of Scheme 3,
however, may not be necessarily limited to one of those ester
compounds.
##STR00018##
[0163] First acid l was coupled with ethyl
N-[2-{N-(9H-fluoren-9-yl)amino}ethyl]-glycinate to obtain compound
p by an EDCI coupling reaction. Then compound p was mildly
hydrolyzed with LiOH to obtain PNA monomer q with a modified
nucleobase.
[0164] The following examples contain detailed descriptions of the
preparation methods for compounds of this invention. The detailed
descriptions of these examples are presented for illustrative
purposes only and should not be interpreted as a restriction to the
present invention. Most of these detailed descriptions fall within
the scope, and serve to exemplify the above described GENERAL
SYNTHETIC PROCEDURES which form a part of the invention. The
abbreviations used in the following examples are defined in the
following table.
TABLE-US-00002 Category Denotation .sup.1H NMR Proton nuclear
magnetic resonance. In presenting NMR data, widely accepted
abbreviations were used as follows: s for singlet, d for doublet, t
for triplet, q for quartet, m for multiplet, br for broad, J for
coupling constant, CDCl.sub.3 for deuterated chloroform,
DMSO.sub.d6 for hexa-deuterated DMSO, and so on. MS Mass
spectroscopy. In presenting MS data, popularly accepted
abbreviations were used as follows: MALDI-TOF for matrix assisted
laser desorption ionization time of flight, ESI for electrospray
ionization, MW for molecular weight, (m + 1) for MH.sup.+ ion peak,
(m + 23) for MNa.sup.+ ion peak, etc. Solvents Widely accepted
abbreviations were used for solvents as follows: THF for
tetrahydrofuran, MC for methylene chloride, DMF for
dimethylformamide, EtOH for ethanol, MeOH for methanol, DMSO for
dimethylsulfoxide, EA for ethyl acetate, and so on. Reagents
Popularly accepted abbreviations were used for reagents as follows:
NaH for sodium hydride, HCl for hydrochloric acid, EDCI for
1-ethyl- 3-(3-dimethylaminopropyl)carbodiimide hydrochloride, HOBT
for 1- hydroxy-benzotriazole, Boc for t-butyloxycarbonyl,
Boc.sub.2O for Boc anhydride or di-t-butyl-dicarbonate, Cbz for
benzylozycarbonyl, Fmoc for (9H-fluoren-9-yl)-methoxycarbonyl, Bts
for (benzo[d]thiazole-2- sulfonyl), Bts-Cl for
(benzo-[d]thiazole-2-sulfonyl)chloride, TFA for trifluoroacetic
acid, TEA for triethyl-amine, DIEA for N,N- diisopropylethylamine,
LiOH for lithium hydroxide, Aeg for N-(2- aminoethyl)glycine,
Fmoc-Aeg-OH for N-[2-{(9H-fluoren-9-yl)-
methoxycarbonyl}amino-ethyl]glycine, Fmoc-Aeg-OMe for methyl N-
[2-(Fmoc-amino)ethyl]-glycinate, Fmoc-Aeg-OtBu for t-butyl N-[2-
(Fmoc-amino)ethyl]-glycinate, Fmoc-Aeg-OSu for N-succinyl N-[2-
(Fmoc-amino)-ethyl]-glycinate, HBTU for
O-(benzotriazol-1-yl)-1,1,3,3- tetramethyluranium
hexafluorophosphate, DCC for 1,3-dicyclo- hexylcarbodiimide, and so
on. Others Widely accepted abbreviations were used for
terminologies as follows: mp for melting point, .degree. C. for
degree in Celcius, h for hour, min for minute, g for gram, mg for
milligram, kg for kilogram, l for liter, ml for milliliter, M for
mole/l, compd for compound, aq for aqueous, RT for room
temperature, and so on.
EXAMPLE 1
Preparation of 3-{(t-butoxycarbonyl)amino}-1-propanol (1)
##STR00019##
[0166] To 14 g of 3-amino-1-propanol dissolved in 150 ml THF and
150 ml water, was added drop-wise over 30 min 40.7 g of Boc.sub.2O
dissolved in 100 ml THF. After the reaction mixture was stirred for
24 h, the THF was removed under reduced pressure. The resulting aq
layer was extracted with 200 ml EA, and the organic layer was
washed with 0.5M aq citric acid and with distilled water, and then
dried over anhydrous magnesium sulfate. Magnesium sulfate was
filtered off, and the resulting filtrate was concentrated in vacuo
to give 25 g of compd 1 as a colorless liquid. .sup.1H NMR (400
MHz; CDCl.sub.3): .delta.4.84 (br s, 1H), 3.66 (t, J=5.6 Hz, 2H),
3.28 (q, J=6.0 Hz, 2H), 3.05 (br s, 1H), 1.66 (m, 2H), 1.45 (s,
9H).
EXAMPLE 2
Preparation of ethyl {(N-benzoyl)-5-iodocytosine-1-yl}acetate
(2)
[0167] To a stirred solution of 8.3 g of N-benzoyl-5-iodocytosine
dissolved in 60 ml DMF, was added at 0.degree. C. 1.06 g of 55% NaH
in mineral oil, and the solution was stirred at RT for 2 h. After
2.7 ml ethyl bromoacetate was added to the reaction mixture, the
reaction solution was stirred for another 24 h at RT, which was
followed by removal of the solvent under reduced pressure. The
resulting residue was dissolved and the insoluble material was
filtered off. The filtrate was washed two times with saturated aq
ammonium chloride, dried over anhydrous magnesium sulfate, and
concentrated in vacuo. The resulting residue was purified by column
chromatography (1:1 hexane/EA) to yield 6.5 g of compd 2 (compd b
in Scheme 1) as a yellow solid. mp 154-5.degree. C. .sup.1H NMR
(400 MHz; CDCl.sub.3) .delta. 13.31 (br s, 1H), 8.37 (d, J=7.2 Hz,
2H), 7.69 (s, 1H), 7.55 (t, J=7.4 Hz, 1H), 7.46 (t, J=7.6 Hz, 2H),
4.49 (s, 2H), 4.27 (q, J=7.2 Hz, 2H), 1.32 (t, J=7.2 Hz, 3H).
EXAMPLE 3
Preparation of 3-{3-(t-butoxycarbonylamino)propyloxy}-1-propyne
(3)
##STR00020##
[0169] To 6.5 g of 55% NaH in mineral oil dispersed in 150 ml THF
at 0.degree. C., was added dropwise over 15 min 25 g of compd 1,
and the mixture was stirred for 1 h. After 17.5 ml propargyl
bromide (80% toluene solution) was added drop-wise over 30 min, the
reaction mixture was stirred at RT for 20 h. The reaction was
quenched by slowly adding 250 ml water and THF was removed under
reduced pressure. Then the resulting aq mixture was extracted with
250 ml EA, which was washed 3 times with 250 ml water. The organic
layer was dried over anhydrous magnesium sulfate, and magnesium
sulfate was filtered off. The resulting filtrate was concentrated
in vacuo and subjected to column chromatography (5:1 Hexane/EA) to
afford 22.7 g of compd 3 as a yellow liquid. .sup.1H NMR (400 MHz;
DMSO.sub.d6) .delta. 6.78 (t, J=5.2 Hz, 1H), 4.09 (d, J=2.4 Hz,
2H), 3.43-3.39 (m, 3H), 2.95 (q, J=6.4 Hz, 2H), 1.60 (m, 2H), 1.37
(s, 9H).
EXAMPLE 4
Preparation of 4-{2-(t-butoxycarbonylamino)ethoxy}-1-butyne (4)
##STR00021##
[0171] To 3.8 g of 4-(2-azidoethoxy)-1-butyne dissolved in 17 ml
THF, were added 7.2 g of triphenylphosphine and 0.7 ml water, and
the reaction mixture was stirred for 8 h, which was followed by
removal of the solvent under reduced pressure. Then the resulting
residue was dissolved in 20 ml EA and extracted twice with 10 ml 1M
aq HCl. Aq sodium carbonate was added to the aq layer to adjust pH
to 9.about.10. 5.96 g of Boc.sub.2O dissolved in 15 ml THF was
added to the solution, and the reaction mixture was stirred for 12
h. After THF was removed in vacuo, the resulting solution was
extracted with EA. The organic layer was washed with 0.5M aq citric
acid, and dried over anhydrous magnesium sulfate. The organic layer
was concentrated and purified by column chromatography (9:1
Hexane/EA) to afford 3.4 g of compd 4 as a yellow oil. .sup.1H NMR
(400 MHz; CDCl.sub.3) .delta.4.95 (s, 1H), 3.58 (t, J=6.8 Hz, 2H),
3.53 (t, J=5.0 Hz, 2H), 3.32 (m, 2H), 2.46 (m, 2H), 2.00 (t, J=2.8
Hz, 1H), 1.45 (s, 9H).
EXAMPLE 5
Preparation of 3-{2-(t-butoxycarbonylamino)ethoxy}-1-propyne
(5)
##STR00022##
[0173] 20 g of 2-{(t-butoxycarbonyl)amino}-1-ethanol was reacted
and purified by similarly following the procedure described in
Example 3 to afford 23.7 g of compd 5 as a pale yellow oil. .sup.1H
NMR (400 MHz; DMSO.sub.d6) .delta. 6.81 (t, 1H), 4.11 (d, J=2.4 Hz,
2H), 3.41 (m, 3H), 3.07 (q, J=6.0 Hz, 2H), 1.38 (s, 9H).
EXAMPLE 6
Preparation of
3-[N-{3-(t-butoxycarbonylamino)propyl}-N-(t-butoxy-carbonyl)amino]-1-prop-
yne (6)
##STR00023##
[0175] To a stirred solution of
N-[3-(t-butoxycarbonylamino)propyl]-N-(2-propynyl)amine dissolved
in 83 ml THF and 95 ml water, was added drop-wise 42 g of
Boc.sub.2O at RT. The reaction solution was stirred for 1.5 h, and
concentrated in vacuo. The resulting aq layer was extracted with
EA. The EA layer was washed in series with 0.5M aq citric acid and
brine, dried over anhydrous magnesium sulfate, concentrated under
reduced pressure, and purified by column chromatography (1:1
Hexane/EA) to give 19 g of compd 6 as a yellow oil. .sup.1H NMR
(400 MHz; CDCl.sub.3) .delta. 5.26 (br s, 0.6H), 4.74 (br s, 0.4H),
4.07 (br s, 1H), 3.98 (br s, 1H), 3.40 (t, J=6.4 Hz, 2H), 3.13 (m,
2H), 2.21 (t, 1H), 1.73 (m, 2H), 1.49 (s, 9H), 1.45 (s, 9H).
EXAMPLE 7
Preparation of
3-[2-{2,3-bis(benzyloxycarbonyl)guanidino}-ethoxy]-1-propyne
(7)
##STR00024##
[0177] To a stirred solution of 10.9 g of compd 5 dissolved in 110
ml MC, was added 110 ml TFA at 0.degree. C. drop-wise over 2 h, and
the reaction mixture was stirred for another 3 h. The reaction
solution was concentrated under reduced pressure and the resulting
residue was dissolved in 40 ml MC at 0.degree. C., to which was
added 12.3 ml TEA and then 8.8 g of
1,3-bis(benzyloxycarbonyl)-2-(methylthio)pseudourea at RT. The
reaction solution was stirred for 4 h and washed twice with water.
The organic layer was dried over anhydrous magnesium sulfate,
concentrated in vacuo, and subjected to column chromatography (5:1
hexane/EA) to afford 9.8 g of compd 7 as a white solid. .sup.1H NMR
(400 MHz; DMSO.sub.d6) .delta. 11.72 (s, 1H), 8.58 (s, 1H),
7.40-7.35 (m, 10H), 5.18 (s, 2H), 5.12 (s, 2H), 4.18 (d, 2H),
3.67-3.66 (m, 4H), 2.43 (t, 1H).
EXAMPLE 8
Preparation of
2-{(t-butoxycarbonyl)amino}-1-(2-propynyl-1-oxy)}-(R)-propane
(8)
##STR00025##
[0179] 10.8 g of t-butyl (R)-1-hydroxypropan-2-ylcarbamate was
reacted and purified by similarly following the procedure described
in Example 3 to afford 10.1 g of compd 8 as a yellow oil. .sup.1H
NMR (500 MHz; DMSO.sub.d6) .delta. 6.63 (d, 1H), 4.11 (d, 2H), 3.60
(m, 1H), 3.37-3.33 (m, 2H), 3.26-3.23 (m, 1H), 1.38 (s, 9H), 1.05
(d, 3H).
EXAMPLE 9
Preparation of
N-[2-{2-(t-butoxycarbonyl)aminoethoxy}ethyl]-N-[2-{(3-butynyl)-1-oxy}ethy-
l]-N-(t-butoxycarbonyl)amine (9)
##STR00026##
[0181] To a stirred solution of 5 g of 2-{(3-butynyl)-1-oxy}ethyl
methanesulfonate and 5.32 g of
2-[2-{2-(t-butoxycarbonyl)amino}ethyl-1-oxy]ethylamine in 60 ml
acetonitrile, was added drop-wise 3.6 g of potassium carbonate
dissolved in water at 0.degree. C. The reaction solution was
allowed to slowly warm to RT and stirred for another 24 h, and then
concentrated under reduced pressure. The resulting residue was
dissolved in MC and washed with water. The organic layer was
concentrated and dissolved in 80 ml THF and 80 ml water, to which
was added 8.4 g of Boc.sub.2O dissolved in 50 ml THF. The reaction
mixture was stirred at RT for 16 h, which was followed by removal
of THF in vacuo and extraction with EA. The organic layer was
washed in series with 0.5M aq citric acid, water, and brine. The
organic layer was dried over anhydrous sodium sulfate,
concentrated, and purified by column chromatography (hexane 1:4
EA/hexane) to obtain 2.45 g of compd 9 as a pale yellow oil.
.sup.1H NMR (400 MHz; CDCl.sub.3) .delta. 5.08 (br s, 0.5H), 4.93
(br s, 0.5H), 3.61-3.46 (m, 12H), 3.31 (m, 2H), 2.48 (m, 2H), 1.99
(t, 1H), 1.48 (s, 9H), 1.46 (s, 9H).
EXAMPLE 10
Preparation of ethyl
2-[6-{3-(t-butoxycarbonylamino)propyl-1-oxy}-methyl-2-oxo-2H-pyrrolo[2,3--
d]pyrimidin-3(7H)-yl]acetate (10)
##STR00027##
[0183] To a stirred solution of 6.5 g of compd 2 dissolved in 120
ml DMF, were added in series 580 mg of CuI, 4.2 ml TEA, 9.74 g of
compd 3, and 1.76 g of Pd(PPh.sub.3).sub.4. Then the reaction
mixture was stirred for 24 h at 50.degree. C. with light shielded,
and concentrated under reduced pressure. The resulting residue was
dissolved in 250 ml EtOH and stirred at reflux for 18 h. Then the
solution was concentrated in vacuo and subjected to chromatographic
separation (95:5 EA/EtOH) to obtain 2.3 g of compd 10 as a dark red
foam/solid. .sup.1H NMR (400 MHz; DMSO.sub.d6) .delta. 11.30 (br s,
1H), 8.37 (s, 1H), 6.78 (m, 1H), 6.19 (s, 1H), 4.70 (s, 2H), 4.37
(s, 2H), 4.14 (q, J=7.2 Hz, 2H), 3.42 (t, J=6.4 Hz, 2H), 2.98 (m,
2H), 1.63 (m, 2H), 1.36 (s, 9H), 1.20 (t, J=7.2 Hz, 3H).
EXAMPLE 11
Preparation of
2-[6-{3-(t-butoxycarbonylamino)propyl-1-oxy}methyl-2-oxo-2H-pyrrolo-[2,3--
d]pyrimidin-3(7H)-yl]acetic acid (11)
##STR00028##
[0185] To 3.3 g of compd 10, were added 15 ml THF, 30 ml water, and
then 760 mg LiOH, and the mixture was stirred at RT for 20 min.
After THF was removed under reduced pressure, the resulting aq
solution was washed with diethyl ether. The aq layer was acidified
to pH 3 with 1M aq HCl and extracted with EA. The organic layer was
dried over anhydrous sodium sulfate and concentrated in vacuo to
yield 2.46 g of compd 11 as a white solid. .sup.1H NMR (400 MHz;
DMSO.sub.d6) .delta. 11.05 (s, 1H), 8.16 (s, 1H), 6.79 (t, 1H),
6.12 (s, 1H), 4.35 (s, 2H), 4.23 (s, 2H), 3.41 (t, 2H), 2.97 (q,
J=6.4 Hz, 2H), 1.64 (m, 2H), 1.36 (s, 9H).
EXAMPLE 12
Preparation of ethyl
N-[2-{(benzo[d]thiazole-2-sulfonyl)amino}-ethyl]-N-[2-[6-{3-(t-butoxycarb-
onylamino)propyl-1-oxy}methyl-2-oxo-2H-pyrrolo-[2,3-d]pyrimidin-3(7H)-yl]a-
cetyl]glycinate (12)
##STR00029##
[0187] To 4.0 g of compd 11 and 3.6 g of ethyl
N-[2-{(benzo[d]thiazole-2-sulfonyl)amino}ethyl]glycinate dissolved
in 30 ml DMF, were added at RT 2.42 g of EDCI and 1.70 g of HOBt.
The reaction mixture was stirred for 8 h. After the solvent was
removed in vacuo, the resulting residue was dissolved in MC, and
washed with 1M aq HCl and then with water. The MC layer was
concentrated under reduced pressure and purified by column
chromatography (95:5 MC/MeOH) to obtain 4.6 g of compd 12 as a
yellow foam/solid. .sup.1H NMR (400 MHz; DMSO.sub.d6) .delta. 11.09
(br s, 1H), 8.74 (s, 0.6H), 8.58 (s, 0.4H), 8.27 (m, 1H), 8.20-8.14
(m, 2H), 7.66 (m, 2H), 6.56 (br s, 1H), 6.16 (m, 1H), 4.91 (s,
1.2H), 4.73 (s, 0.8H), 4.38 (s, 2.6H), 4.17 (m, 0.9H), 4.07 (m,
2.5H), 3.67 (m, 1.1H), 3.49-3.44 (m, 4H), 3.26 (m, 0.9H), 3.01 (m,
2H), 1.66 (m, 2H), 1.38 (s, 9H), 1.24 (t, J=7.0 Hz, 1.2H), 1.17 (t,
J=7.0 Hz, 1.8H).
EXAMPLE 13
Preparation of
N-[2-{(benzo[d]thiazole-2-sulfonyl)amino}ethyl]-N-[2-[6-{3-(t-butoxycarbo-
nylamino)propyl-1-oxy}methyl-2-oxo-2H-pyrrolo-[2,3-d]-pyrimidin-3(7H)-yl]a-
cetyl]glycine (13)
##STR00030##
[0189] 4.5 g of compd 12 and 670 mg of LiOH were dispersed in 20 ml
THF and 20 ml water, and stirred at RT for 20 min. THF was removed
in vacuo, and the resulting aq solution was washed with diethyl
ether. The aq layer was acidified to pH 3 with 1M aq HCl, and
extracted with EA. The EA layer was dried over anhydrous sodium
sulfate and concentrated under reduced pressure to afford 4.4 g of
compd 13 as a dark yellow solid. .sup.1H NMR (400 MHz; DMSO.sub.d6)
.delta. 11.32 (br s, 1H), 8.36 (m, 1H), 8.28 (m, 1.6H), 8.22 (s,
0.4H), 7.73 (m, 2H), 6.78 (m, 1H), 6.20 (s, 1H), 4.94 (s, 1.2H),
4.84 (s, 0.8H), 4.52 (s, 0.8H), 4.37 (s, 2H), 4.30 (s, 1.2H), 4.26
(m, 1.2H), 4.07 (m, 2H), 3.87 (m, 0.8H), 3.43 (m, 2H), 2.99 (m,
2H), 1.63 (m, 2H), 1.37 (s, 9H).
EXAMPLE 14
Preparation of
1-{(benzo[d]thiazole-2-sulfonyl)}-2-oxo-4-[6-{3-(t-butoxycarbonylamino)pr-
opyl-1-oxy}methyl-2-oxo-2H-pyrrolo[2,3-d]pyrimidin-3(7H)-yl]acetyl]piperaz-
ine (14)
##STR00031##
[0191] 4.4 g of compd 13 and 1.49 g of EDCI in 50 ml DMF were
stirred at RT for 16 h. After the reaction mixture was concentrated
in vacuo, the resulting residue was dissolved in 50 ml MC. The MC
solution was washed in series with 1M aq HCl and water,
concentrated in vacuo, and then purified by column chromatography
(acetone) to obtain 1.5 g of compd 14 as a brown foam/solid.
.sup.1H NMR (400 MHz; DMSO.sub.d6) .delta. 11.25 (br s, 1H), 8.36
(m, 1H), 8.29 (m, 1H), 8.25 (s, 0.6H), 8.19 (0.4H), 7.72 (m, 2H),
6.78 (t, J=5.2 Hz, 1H), 6.18 (s, 1H), 4.92 (s, 1.2H), 4.82 (s,
0.8H), 4.51 (s, 0.8H), 4.37 (s, 2H), 4.29 (s, 1.2H), 4.23 (m,
1.2H), 4.06 (m, 2H), 3.87 (m, 0.8H), 3.41 (t, J=6.4 Hz, 2H), 2.98
(q, J=6.8 Hz, 2H), 1.62 (m, 2H), 1.36 (s, 9H). MS/ESI (m+23,
MNa.sup.+)=682.2 (observed), MW=659.8
(C.sub.28H.sub.33N.sub.7O.sub.8S.sub.2).
[0192] Starting from acetylene derivatives 4.about.9,
pyrollocytosine derivatives 15.about.20 were prepared by similarly
following the procedure described in Example 10. Spectral and
physical data for compds 15.about.20 are provided in the table
below.
EXAMPLES 15.about.20
Analytical Data for Pyrollocytosine Derivatives 15.about.20
TABLE-US-00003 ##STR00032## [0193] Starting Compd Material X
Spectral & Physical Data 15 4 ##STR00033## .sup.1H NMR (400
MHz; DMSO.sub.d6) .delta. 11.12 (s, 1 H), 8.27 (s, 1 H), 6.79 (t, J
= 5.4 Hz, 1 H), 6.00 (s, 1 H), 4.68 (s, 2 H), 4.14 (q, J = 7.2 Hz,
2 H), 3.65 (t, J = 6.6, 2 H), 3.39 (t, J = 6.2 Hz, 2 H), 3.08 (m, 2
H), 2.78 (t, J = 6.6 Hz, 2 H), 1.37 (s, 9 H), 1.20 (t, J = 7.2 Hz,
3 H). Pale green foam/solid. 16 5 ##STR00034## .sup.1H NMR (400
MHz; DMSO.sub.d6) .delta. 11.35 (s, 1 H), 8.39 (s, 1 H), 6.87 (t, J
= 5.2 Hz, 1 H), 6.21 (s, 1 H), 4.70 (s, 2 H), 4.41 (s, 2 H), 4.15
(q, J = 7.2 Hz, 2 H), 3.43 (m, 2 H), 3.12 (m, 2 H), 1.38 (s, 9 H),
1.21 (t, J = 7.2 Hz, 3 H). Pale yellow foam/solid. 17 6
##STR00035## .sup.1H NMR (400 MHz; DMSO.sub.d6) .delta. 11.20 (br
s, 0.6 H), 8.86 (br s, 0.4 H), 8.57 (s, 0.2 H), 8.35 (s, 0.8 H),
6.83-6.76 (m, 1 H), 6.00 (s, 0.8 H), 5.76 (s, 0.2 H), 4.75 (s, 0.3
H), 4.70 (s, 1.7 H), 4.55 (s, 0.3 H), 4.30 (s, 1.7 H), 4.14 (q, J =
7.2 Hz, 2 H), 3.18 (m, 2 H), 2.90-2.88 (m, 2 H), 1.58 (m, 2 H),
1.40-1.36 (m, 18 H), 1.20 (t, 3 H). Brown foam/solid. 18 7
##STR00036## .sup.1H NMR (400 MHz; DMSO.sub.d6) .delta. 11.57 (s, 1
H), 11.33 (s, 1 H), 8.50 (m, 1 H), 8.37 (s, 1 H), 7.44-7.31 (m, 10
H), 6.22 (s, 1 H), 5.22 (s, 2 H), 5.03 (s, 2 H), 4.70 (s, 2 H),
4.44 (s, 2 H), 4.14 (q, 2 H), 3.57-3.53 (m, 4 H), 1.21 (t, 3 H).
Pale brown solid. 19 8 ##STR00037## .sup.1H NMR (500 MHz;
DMSO.sub.d6) .delta. 11.32 (s, 1 H), 8.38 (s, 1 H), 6.71 (d, 1 H),
6.20 (s, 1 H), 4.70 (s, 2 H), 4.41 (m, 2 H), 4.14 (q, 2 H), 3.65
(m, 1 H), 3.37-3.34 (m, 1 H), 3.26-3.22 (m, 1 H), 1.37 (s, 9 H),
1.20 (t, 3 H), 1.02 (d, 3 H). Pale brown solid. 20 9 ##STR00038##
.sup.1H NMR (500 MHz; DMSO.sub.d6) .delta. 11.13 (s, 1 H), 8.25 (s,
1 H), 6.73 (s, 1 H), 5.99 (s, 1 H), 4.68 (s, 2 H), 4.12 (q, 2 H),
3.67 (t, 2 H), 3.48~3.27 (m, 10 H), 3.04 (q, 2 H), 2.78 (t, 2 H),
1.38 (s, 9 H), 1.36 (s, 1 H), 1.19 (t, 3 H). Brown solid.
[0194] Starting from pyrollocytosine derivatives 15, 16, 17, and
20, modified cytosine PNA monomers 21.about.24 were prepared by
similarly following the procedures described in Examples
11.about.14. Spectral and physical data for compds 21.about.24 are
provided in the table below.
EXAMPLES 21.about.24
Analytical Data for Cytosine PNA Monomers 21.about.24
TABLE-US-00004 ##STR00039## [0195] Starting Compd Material X
Spectral & Physical Data 21 15 ##STR00040## .sup.1H NMR (400
MHz; DMSO.sub.d6) .delta. 11.06 (s, 1 H), 8.36 (m, 1 H), 8.28 (m, 1
H), 8.14 (s, 0.6 H), 8.08 (2, 0.4 H), 7.72 (m, 2 H), 6.78 (t, 1 H),
5.98 (s, 1 H), 4.91 (s, 1.2 H), 4.80 (s, 0.8 H), 4.51 (s, 0.8 H),
4.29 (s, 1.2 H), 4.24 (m, 1.2 H), 4.06 (m, 2 H), 3.86 (m, 0.8 H),
3.64 (t, J = 6.4 Hz, 2 H), 3.38 (t, J = 6.0 Hz, 2 H), 3.07 (m, 2
H), 2.78 (m, 2 H), 1.37 (s, 9 H). MS/ESI (m + 1) = 660.2
(observed), MW = 659.8 (C.sub.28H.sub.33N.sub.7O.sub.8S.sub.2).
Brown foam/solid. 22 16 ##STR00041## .sup.1H NMR (400 MHz;
DMSO.sub.d6) .delta. 11.31 (s, 1 H), 8.36 (m, 1 H), 8.30-8.27 (m,
1.6 H), 8.22 (s, 0.4 H), 7.73 (m, 2 H), 6.87 (t, J = 5.6 Hz, 1 H),
6.20 (m, 1 H), 4.94 (s, 1.2 H), 4.83 (s, 0.8 H), 4.52 (s, 0.7 H),
4.41 (s, 2.1 H), 4.30 (s, 1.1 H), 4.25 (m, 1.2 H), 4.06 (m, 2 H),
3.87 (m, 0.8 H), 3.42 (t, 2 H), 3.12 (m, 2 H), 1.38 (s, 9 H).
MS/ESI (m + 1) = 646.2 (observed), MW = 645.7
(C.sub.27H.sub.31N.sub.7O.sub.8S.sub.2). Red foam/solid. 23 17
##STR00042## .sup.1H NMR (400 MHz; DMSO.sub.d6) .delta. 11.16 (br
s, 1 H), 8.36 (m, 1 H), 8.28 (m, 1 H), 8.21 (s, 0.6 H), 8.15 (s,
0.4 H), 7.73 (m, 2 H), 6.77 (br s, 1 H), 6.00 (br s, 1 H), 4.92 (s,
1.2 H), 4.82 (s, 0.8 H), 4.52 (s, 0.9 H), 4.30 (s, 3.1 H), 4.25 (m,
1.2 H), 4.07 (m, 2 H), 3.87 (m, 0.8 H), 3.19 (m, 2 H), 2.89 (m, 2
H), 1.59 (m, 2 H), 1.41-1.36 (m, 18 H); MS/ESI (m + 23/MNa.sup.+) =
781.3 (observed), MW = 758.9
(C.sub.33H.sub.42N.sub.80.sub.9S.sub.2). Red foam/solid. 24 20
##STR00043## .sup.1H NMR (500 MHz; DMSO.sub.d6) .delta. 11.10 (m, 1
H), 8.35 (m, 1 H), 8.28 (m, 1 H), 8.14 (s, 0.6 H), 8.08 (s, 0.4 H),
7.72 (m, 2 H), 6.76 (m, 1 H), 5.97-5.96 (s, 1 H), 4.90 (s, 1.2 H),
4.80 (s, 0.8 H), 4.51 (s, 0.8 H), 4.29 (s, 1.2 H), 4.25 (t, 1.2 H),
4.08-4.04 (m, 2 H), 3.86 (t, 0.8 H), 3.66 (m, 2 H), 3.47 (m, 2 H),
3.41 (m, 2 H), 3.32-3.30 (m, 4 H), 3.27 (m, 2 H), 3.04 (m, 2 H),
2.77 (m, 2 H), 1.37 (s, 9 H), 1.35 (s, 9 H). MS/ESI (m + 23/MNa*) =
869.3 (observed), MW = 847.0
(C.sub.37H.sub.50N.sub.8O.sub.11S.sub.2). Yellow solid.
EXAMPLE 25
Preparation of 2-{3-(t-butoxycarbonylamino)propyl}amino-adenine
(25)
##STR00044##
[0197] 6.8 g of 2-chloroadenine dissolved in 68 ml
1,3-diaminopropane and 68 ml monomethoxyethanol was stirred at
reflux for 24 h, and the reaction mixture was concentrated in
vacuo. The resulting residue was dissolved in 100 ml THF and 100 ml
water, to which was slowly added 60 g of Boc.sub.2O dissolved in 70
ml THF. The reaction mixture was stirred at RT for 6 h, and then
the organic solvent was removed under reduced pressure. The
resulting aq layer was extracted twice with 100 ml EA. The organic
layer was washed with 0.5M aq citric acid and with brine, and dried
over anhydrous magnesium sulfate. The organic layer was
concentrated under reduced pressure and subjected to
chromatographic separation (1:10 MeOH/MC) to obtain 4.07 g of a
compd protected with two Boc groups. This compound was dissolved in
100 ml MeOH, to which was added slowly 45 ml saturated aq sodium
carbonate. The reaction solution was stirred at 50.degree. C. for 1
h, and then concentrated in vacuo. The resulting residue was
dissolved in 50 ml MeOH and the insoluble material was filtered
off. Then the filtrate was concentrated to afford 3.16 g of compd
25 as a white solid. .sup.1H NMR (400 MHz; DMSO.sub.d6) .delta.
12.11 (br s, 1H), 7.63 (s, 1H), 6.78 (t, 1H), 6.55 (s, 2H), 6.07
(t, 1H), 3.20 (q, 2H), 2.96 (q, 2H), 1.60 (m, 2H), 1.37 (s,
9H).
[0198] Starting from 2-chloroadenine and a proper diamine,
2,6-diaminopurine derivatives 26.about.30 were prepared by
similarly following the procedure described in Example 25. Spectral
and physical data for compounds 26.about.30 are provided in the
table below.
EXAMPLES 26.about.30
Analytical Data for 2,6-diaminopurine Derivatives 26.about.30
TABLE-US-00005 ##STR00045## [0199] Compd Starting Diamine L.sub.2
Spectral & Physical Data 26 ##STR00046## --(CH.sub.2).sub.2--
.sup.1H NMR (400 MHz; DMSO.sub.d5) .delta. 12.20 (br s, 1 H), 7.66
(s, 1 H), 6.84 (t, 1 H), 6.62 (s, 2 H), 6.10 (t, 1 H), 3.25 (q, 2
H), 3.08 (q, 2 H), 1.36 (s, 9 H). Pale yellow solid. 27
##STR00047## --(CH.sub.2).sub.4-- .sup.1H NMR (500MHz; DMSO.sub.d6)
.delta. 12.07 (br s, 1 H), 7.63 (s, 1 H), 6.75 (s, 1 H), 6.50 (s, 2
H), 6.02 (s, 1 H), 3.18 (q, 2 H), 2.91 (q, 2 H), 1.48-1.36 (m, 13
H). Yellowish green solid. 28 ##STR00048## --(CH.sub.2).sub.5--
.sup.1H NMR (400 MHz; DMSO.sub.d6) .delta. 12.14 (br s, 1 H), 7.65
(s, 1 H), 6.77 (t, 1 H), 6.55 (s, 2 H), 6.01 (s, 1 H), 3.17 (m, 2
H), 2.89 (q, 2 H), 1.48 (m, 2 H), 1.41-1.36 (m, 11 H), 1.26 (m, 2
H). Pale yellow solid. 29 ##STR00049## --(CH.sub.2).sub.7-- .sup.1H
NMR (500 MHz; DMSO.sub.d6) .delta. 12.11 (br s, 1 H), 7.64 (s, 1
H), 6.78 (t, J = 5.6 Hz, 1 H), 6.56 (s, 2 H), 6.04 (t, J = 5.5 Hz,
1 H), 3.17 (td, J = 6.3, 6.3 Hz, 2 H), 2.88 (td, J = 6.7, 6.7 Hz, 2
H), 1.49-1.47 (m, 2 H), 1.36-1.31 (m, 11 H), 1.29-1.22 (m, 6 H).
Yellowish green solid. 30 ##STR00050## ##STR00051## .sup.1H NMR
(500 MHz; DMSO.sub.d6) .delta. 12.15 (s, 1 H), 7.64 (s, 1 H), 6.84
(t, 1 H), 6.56 (s, 2 H), 6.05 (t, 1 H), 3.48 (t, 2 H), 3.39-3.34
(m, 4 H), 3.07 (q, 2 H), 1.37 (s, 9 H). Yellow foam.
EXAMPLES 31
Preparation of
2-[2-{2-(t-butoxycarbonylamino)-2-methyl}ethyl]-amino-1H-purin-6(9H)-one
(31)
##STR00052##
[0201] 11 g of 2-chlorohypoxanthine and 4.96 ml 1,2-diaminopropane
(racemic) were dispersed in 33 ml monomethoxyethanol, and stirred
for 24 h at 130.degree. C. The solvent was removed in vacuo, and
the resulting residue was dissolved in 97 ml THF and 97 ml water,
to which was slowly added 22.8 g of Boc.sub.2O dissolved in 64 ml
THF. The reaction mixture was stirred at RT for 6 h, and EA was
added to the solution. The resulting precipitate was collected by
filtration to obtain compd 31 as a grey solid. .sup.1H NMR (500
MHz; DMSO.sub.d6) .delta. 12.42 (s, 1H), 10.44 (br s, 1H), 7.61 (s,
1H), 6.76 (d, 1H), 6.27 (m, 1H), 3.67 (m, 1H), 3.32 (m, 1H), 3.14
(m, 1H), 1.36 (s, 9H), 1.02 (d, 3H).
EXAMPLE 32
Preparation of ethyl
2-[6-amino-2-{3-(t-butoxycarbonylamino)-propyl}amino-9H-purin-9-yl]acetat-
e (32)
##STR00053##
[0203] To a stirred solution of 3.16 g of compd 25 dissolved in 100
ml DMF, was added 480 mg of 55% NaH in mineral oil. The reaction
solution was stirred for 2 h, after which was slowly added 1.98 ml
ethyl bromoacetate. 2 h later, the reaction mixture was
concentrated in vacuo, and purified by column chromatography (1:10
EtOH/EA) to give 2.92 g of diaminopurine analog 32 as a pale yellow
solid. .sup.1H NMR (400 MHz; DMSO.sub.d6) .delta. 7.67 (s, 1H),
6.80 (t, 1H), 6.71 (s, 2H), 6.28 (t, 1H), 4.85 (s, 2H), 4.15 (q,
2H), 3.20 (q, 2H), 2.94 (q, 2H), 1.57 (m, 2H), 1.37 (s, 9H), 1.21
(t, 3H).
EXAMPLE 33
Preparation of ethyl
2-[6-(benzyloxycarbonypamino-2-{3-(t-butoxy-carbonylamino)propyl}amino-9H-
-purin-9-yl]acetate (33)
##STR00054##
[0205] To a stirred solution of 4.68 g of compd 32 dissolved in 100
ml DMF, was added at RT 13.2 g of
N-(benzyloxycarbonyl)-N'-methyl-imidazolium triflate. 12 h later
the reaction mixture was concentrated under reduced pressure, and
subjected to column chromatography (5% MeOH in MC) to yield 5.4 g
of compd 33 as a white solid. .sup.1H NMR (400 MHz; DMSO.sub.d6)
.delta. 10.19 (s, 1H), 7.92 (s, 1H), 7.45-7.33 (m, 5H), 6.88 (t,
1H), 6.77 (t, 1H), 5.18 (s, 2H), 4.94 (s, 2H), 4.16 (q, 2H), 3.25
(q, 2H), 2.95 (q, 2H), 1.60 (m, 2H), 1.36 (s, 9H), 1.21 (t,
3H).
EXAMPLE 34
Preparation of ethyl
N-[2-{2-(benzo[d]thiazole)sulfonyl}amino-ethyl]-N-[2-[6-(benzyloxycarbony-
l)amino-2-{3-(t-butoxycarbonylamino)-propyl}amino-9H-purin-9-yl]acetyl]gly-
cinate (34)
##STR00055##
[0207] 5.4 g of compd 33 and 950 mg of LiOH were dissolved in 40 ml
THF and 40 ml water, and stirred at RT for 1 h. THF was removed in
vacuo, and the resulting aq solution was acidified to pH 3 with 1M
aq HCl, and then extracted with EA. The organic layer was dried
over anhydrous sodium sulfate and concentrated under reduced
pressure. The resulting residue and 2.92 g of ethyl
2-N-[2-{(benzo[d]thiazole-2-sulfonyl)amino}ethyl]glycinate were
dissolved in 240 ml DMF, to which were added at RT 1.95 g of EDCI
and 1.38 g of HOBt. The reaction mixture was stirred for 20 h,
concentrated under reduced pressure, and dissolved in MC. The MC
solution was washed with 1M aq HCl, concentrated in vacuo, and then
purified by column chromatography (5% MeOH/MC) to obtain 2.7 g of
compd 34 as a pale yellow foam. .sup.1H NMR (400 MHz; DMSO.sub.d6)
.delta. 10.18 (m, 1H), 8.97 (br s, 0.6H), 8.80 (br s, 0.4H), 8.28
(d, 1H), 8.18 (m, 1H), 7.80 (s, 0.6H), 7.76 (s, 0.4H), 7.66 (m,
2H), 7.46-7.32 (m, 5H), 6.77 (m, 2H), 5.18 (s, 2H), 5.10 (s, 1.2H),
4.89 (s, 0.8H), 4.45 (s, 0.8H), 4.17 (q, 0.8H), 4.07-4.00 (m,
2.4H), 3.68 (m, 1.2H), 3.47 (m, 1.2H), 3.41 (m, 0.9H), 3.22 (m,
2.7H), 2.94 (m, 2H), 1.59 (m, 2H), 1.36 (s, 9H), 1.31-1.12 (m,
3H).
EXAMPLE 35
Preparation of
1-(benzo[d]thiazole-2-sulfonyl)-2-oxo-4-[[6-(benzyl-oxycarbonyl)amino-2-{-
3-(t-butoxycarbonylamino)propylamino}-9H-purin-9-yl]-acetyl]piperazine
(35)
##STR00056##
[0209] 2.7 g of compd 34 and 340 mg of LiOH were dispersed in 15 ml
THF and 20 ml water, and stirred for 30 min at RT. THF was removed
under reduced pressure. Then the resulting aq layer was acidified
to pH 3 with 1M aq HCl, and extracted with EA. The EA layer was
dried over anhydrous sodium sulfate and concentrated in vacuo to
obtain 2.48 g of a crude product. The crude product and 716 mg of
EDCI dissolved in 70 ml DMF were stirred at RT for 20 h. The
solvent was removed under reduced pressure, and the resulting
residue was dissolved in MC and washed with 1M aq HCl and then with
water. The organic layer was concentrated in vacuo and purified by
column chromatography (acetone) to obtain 1.4 g of compd 35 as a
white foam. .sup.1H NMR (400 MHz; DMSO.sub.d6) .delta. 10.16 (s,
1H), 8.35 (m, 1H), 8.26 (m, 1H), 7.81 (s, 0.6H), 7.77 (s, 0.4H),
7.72 (m, 2H), 7.45-7.31 (m, 5H), 6.78 (m, 2H), 5.18 (s, 2H), 5.12
(s, 1.2H), 5.01 (s, 0.8H), 4.55 (s, 0.8H), 4.29-4.27 (m, 2.4H),
4.09 (m, 2H), 3.88 (m, 0.8H), 3.26 (m, 2H), 2.95 (m, 2H), 1.61 (m,
2H), 1.36 (s, 9H); MS/ESI (m+1)=779.2 (observed), MW=778.9
(C.sub.34H.sub.38N.sub.NO.sub.8S.sub.2).
[0210] Starting from 2,6-diaminopurine derivatives 26.about.30,
modified adenine PNA monomers 36.about.40 were prepared by
similarly following the procedures described in Examples
32.about.35. Spectral and physical data for compds 36.about.40 are
provided in the table below.
EXAMPLES 36.about.40
Analytical Data for Adenine PNA monomers 36.about.40
TABLE-US-00006 ##STR00057## [0211] Starting Compd Material L.sub.2
Spectral & Physical Data 36 26 --(CH.sub.2).sub.2-- .sup.1H NMR
(400 MHz; DMSO.sub.d6) .delta. 10.17 (s, 1 H), 8.36 (m, 1 H), 8.26
(m, 1 H), 7.82 (s, 0.6 H), 7.78 (s, 0.4 H), 7.72 (m, 2 H),
7.45-7.31 (m, 5 H), 6.79 (2 H), 5.18 (s, 2 H), 5.12 (s, 1.2 H),
5.01 (s, 0.8 H), 4.55 (s, 0.8 H), 4.29-4.25 (m, 2.4 H), 4.09 (m, 2
H), 3.87 (m, 0.8 H), 3.29 (m, 2 H), 3.11 (m, 2 H), 1.33 (d, 9 H).
MS/ESI (m + 1) = 765.2 (observed), MW = 764.8
(C.sub.33H.sub.36N.sub.10O.sub.8S.sub.2). White foam. 37 27
--(CH.sub.2).sub.4-- .sup.1H NMR (400 MHz; DMSO.sub.d6) .delta.
10.10 (s, 1 H), 8.36 (m, 1 H), 8.26 (m, 1 H), 7.80 (s, 0.6 H),
7.76- 7.71 (m, 2.4 H), 7.46-7.31 (m, 5 H), 6.81-6.73 (m, 2 H), 5.18
(s, 2 H), 5.12 (s, 1.2 H), 5.01 (s, 0.8 H), 4.55 (s, 0.8 H),
4.30-4.25 (m, 2.4 H), 4.09 (m, 2 H), 3.88 (m, 0.8 H), 3.26 (m, 2
H), 2.90 (m, 2 H), 1.50- 1.36 (m, 13 H); MS/ESI (m + 1) = 793.3
(observed), MW = 792.9 (C.sub.35H.sub.40N.sub.10O.sub.8S.sub.2).
Yellowish red foam/solid. 38 28 --(CH.sub.2).sub.5-- .sup.1H NMR
(400 MHz; DMSO.sub.d6) .delta. 10.09 (s, 1 H), 8.35 (m, 1 H), 8.26
(m, 1 H), 7.80 (s, 0.6 H), 7.76 (s, 0.4 H), 7.74-7.72 (m, 2.0 H),
7.46-7.31 (m, 5 H), 6.79-6.72 (m, 2 H), 5.18 (s, 2 H), 5.12 (s, 1.2
H), 5.01 (s, 0.8 H), 4.56 (s, 0.8 H), 4.30-4.27 (m, 2.4 H), 4.09
(m, 2 H), 3.88 (m, 0.8 H), 3.25 (m, 2 H), 2.89 (m, 2 H), 1.49 (m, 2
H), 1.36 (m, 11 H), 1.25 (m, 2 H); MS/ESI (m + 1) = 807.3
(observed), MW = 806.9 (C.sub.36H.sub.42N.sub.10O.sub.8S.sub.2).
Yellow foam/solid. 39 29 --(CH.sub.2).sub.7-- .sup.1H NMR (500 MHz;
DMSO.sub.d6) .delta. 10.11 (d, J = 3.1 Hz, 1 H), 8.37-8.34 (m, 1
H), 8.28-8.24 (m, 1 H), 7.80 (s, 0.6 H), 7.76 (s, 0.4 Hz),
7.75-7.70 (m, 2 H), 7.75-7.31 (m, 5 H), 6.82-6.74 (m, 2 H), 5.18
(s, 2 H), 5.12 (s, 1.2 H), 5.01 (s, 0.8 H), 4.58 (s, 0.8 H), 4.29
(m, 1.2 H), 4.27 (q, J = 4.9 Hz, 1 H), 4.06-4.03 (m, 2 H), 3.88 (t,
J = 5.2 Hz, 1 H), 3.26- 3.20 (m, 2 H), 2.88-2.85 (m, 2 H),
1.51-1.45 (m, 2 H), 1.39-1.32 (m, 11 H), 1.28-1.15 (m, 6 H). MS/ESI
(m + 1) = 834.8 (observed), MW = 835.0
(C.sub.38H.sub.46N.sub.10O.sub.8S.sub.2). Reddish yellow
foam/solid. 40 30 ##STR00058## .sup.1H NMR (400 MHz; DMSO.sub.d6)
.delta. 10.14 (s, 1 H), 8.35 (m, 1 H), 8.26 (m, 1 H), 7.82 (s, 0.6
H), 7.78 (s, 0.4 H), 7.73 (m, 2 H), 7.46-7.31 (m, 5 H), 6.81- 6.74
(m, 2 H), 5.18 (s, 2 H), 5.13 (s, 1.2 H), 5.02 (s, 0.8 H), 4.55 (s,
0.8 H), 4.30-4.26 (m, 2.4 H), 4.09 (m, 2 H), 3.88 (m, 0.8 H), 3.50
(m, 2 H), 3.43-3.38 (m, 4 H), 3.07 (m, 2 H), 1.36 (s, 9 H); MS/ESI
(m + 1) = 809.3 (observed), MW = 808.9
(C.sub.35H.sub.40N.sub.10O.sub.9S.sub.2). Pale yellow foam.
EXAMPLE 41
Preparation of ethyl
2-[2-[2-{2-(t-butoxycarbonyamino)-2-methyl}ethyl]amino-6-oxo-6,9-dihydro--
1H-purin-2-yl]acetate (41)
##STR00059##
[0213] To a stirred solution of 4.69 g of compd 31 in 47 ml DMF,
was added 790 mg of 55% NaH in mineral oil and the reaction
solution was stirred for 2 h. After 1.85 ml ethyl bromoacetate was
slowly added, the reaction solution was stirred for another 2 h.
The reaction mixture was concentrated in vacuo and purified by
column chromatography (5:95 MeOH/MC) to obtain 5.04 g of compd 41
as a pale yellow solid. .sup.1H NMR (500 MHz; DMSO.sub.d6) .delta.
10.55 (s, 1H), 7.67 (s, 1H), 6.74 (d, 1H), 6.40 (m, 1H), 4.87 (s,
2H), 4.17 (q, 2H), 3.65 (m, 1H), 3.28 (m, 1H), 3.16 (m, 1H), 1.36
(s, 9H), 1.21 (t, 3H), 1.01 (d, 3H).
EXAMPLE 42
Preparation of 2-{2-(t-butoxycarbonylamino)ethoxy}ethylamine
(42)
##STR00060##
[0215] To 146 g of
[2-{2-(t-butoxycarbonylamino)ethoxy}ethyl]methane sulfonate was
dissolved in 500 ml DMF, was added 134 g of sodium azide. The
reaction mixture was stirred at 70.degree. C. for 20 h, and then
concentrated under reduced pressure. The resulting residue was
dissolved in 1,200 ml water and extracted with EA. The organic
layer was dried over anhydrous sodium sulfate and concentrated in
vacuo. The resulting residue was dissolved in 2,000 ml THF, to
which was added 162 g of triphenylphosphine. The reaction mixture
was stirred at RT for 2 h, after which was added 200 ml water. The
reaction mixture was stirred at RT for 18 h and concentrated to 500
ml under reduced pressure. Then the resulting precipitate was
filtered off. The filtrate was further concentrated under reduced
pressure to remove THF, and washed with MC. The aq layer was
concentrated to obtain 86.2 g of compd 42 as a liquid. .sup.1H NMR
(400 MHz; CDCl.sub.3) .delta. 4.96 (br s, 1H), 3.54-3.48 (m, 4H),
3.34 (q, 2H), 2.88 (t, 2H), 1.48-1.46 (m, 11H).
EXAMPLE 43
Preparation of
2-[2-{2-(t-butoxycarbonylamino)-ethoxy}ethyl]amino-1H-purin-6(9H)-one
(43)
##STR00061##
[0217] 6.3 g of compd 42 and 2.0 g of 2-bromohypoxanthine were
dispersed in 55 ml monomethoxyethanol and 17.5 ml water. The
reaction mixture was stirred at reflux for 16 h, and the solvent
was removed under reduced pressure. Then the concentrate was
stirred in 20 ml MC and 10 ml water for 30 min, and the resulting
precipitate was collected by filtration to obtain 2.1 g of compd 43
as a pale yellow solid. .sup.1H NMR (500 MHz; DMSO.sub.d6) .delta.
12.43 (br s, 1H), 10.45 (br s, 1H), 7.89 (s, 0.2H), 7.61 (s, 0.8H),
6.77 (m, 1H), 6.34 (s, 0.8H), 6.12 (s, 0.2H), 3.52 (t, 2H), 3.41
(m, 4H), 3.09 (q, 2H), 1.36 (s, 9H).
EXAMPLE 44
Preparation of
2-[2-[3-(t-butoxycarbonylamino)propyloxy}-ethyl]]-amino-1H-purin-6(9H)-on-
e (44)
##STR00062##
[0219] 2-{3-(t-butoxycarbonylamino)propyloxy}ethylamine and
2-bromohypo-xanthine were reacted by similarly following the
procedure described in Example 43 to yield compound 44 as a white
solid. .sup.1H NMR (500 MHz; DMSO.sub.d6) .delta. 12.43 (br s, 1H),
10.45 (br s 1H), 7.61 (m, 1H), 6.80 (t, 1H), 6.30 (s, 0.7H), 6.08
(s, 0.3H), 3.49 (t, 2H), 3.41 (t, 4H), 2.99 (q, 2H), 1.61 (m, 2H),
1.37 (s, 9H).
EXAMPLE 45
Preparation of
2-{3-(t-butoxycarbonylamino)propyl}amino-1H-purin-6(9H)-one
(45)
##STR00063##
[0221] A mixture of 10 g of chlorohypoxanthine and 19.6 ml
1,3-diaminopropane dispersed in 40 ml monomethoxyethanol was
stirred at 130.degree. C. for 10 h. Then the solvent was removed
under reduced pressure and the resulting residue was dissolved in
150 ml THF and 150 ml water, to which was added slowly 19.2 g of
Boc.sub.2O dissolved in 100 ml THF. The mixture was stirred at RT
for 6 h. After EA was added, the resulting precipitate was
collected by filtration to obtain 6.31 g of compd 45 as a dark
green solid. .sup.1H NMR (400 MHz; DMSO.sub.d6) .delta. 11.13 (br
s, 1H), 7.64 (s, 1H), 6.87 (s, 1H), 6.31 (s, 1H), 3.23 (q, 2H),
2.98 (m, 2H), 1.62 (m, 2H), 1.38 (s, 9H).
[0222] Guanine derivatives 46.about.47 were prepared using a proper
diamine by similarly following the procedure described in Example
45. Spectral and physical data for compds 46.about.47 are provided
in the table below.
EXAMPLES 46.about.47
Analytical Data for Guanine Derivatives 46.about.47
TABLE-US-00007 ##STR00064## [0223] Diamine Compd used n Spectral
& Physical Data 46 Ethylene 2 .sup.1H NMR (500 MHz;
DMSO.sub.d6) .delta. 12.43 diamine (br s, 1 H), 10.61 (br, 1 H),
7.62 (s, 1 H), 6.93 (t, 1 H), 6.32 (s, 1 H), 3.29 (q, 2 H), 3.10
(q, 2 H), 1.37 (s, 9 H). Grey solid. 47 Pentylene 5 .sup.1H NMR
(500 MHz; DMSO.sub.d6) .delta. 12.44 diamine (s, 1 H), 10.35 (s, 1
H), 7.60 (s, 1 H), 6.80 (m, 1 H), 6.29 (m, 1 H), 3.21 (m, 2 H),
2.90 (m, 2 H), 1.49 (m, 2 H), 1.39-1.35 (m, 11 H), 1.27-1.23 (m, 2
H). Pale brown solid.
[0224] Compds 43.about.46 were transformed into compds 48.about.51
by similarly following the procedure described in Example 32.
Spectral and physical data for compounds 48.about.51 are provided
in the table below.
EXAMPLES 48.about.51
Analytical Data for Guanine Derivatives 48.about.51
TABLE-US-00008 ##STR00065## [0225] Starting Compd Material L.sub.3
Spectral & Physical Data 48 43 ##STR00066## .sup.1H NMR (500
MHz; DMSO.sub.d6) .delta. 10.67 (s, 1 H), 7.69 (s, 1 H), 6.78 (m, 1
H), 6.15 (t, 1 H), 4.87 (s, 2 H), 4.15 (q, 2 H), 3.51 (m, 2 H),
3.41 (m, 4 H), 3.10 (m, 2 H), 1.37 (s, 9 H), 1.20 (t, 3 H). White
foam/solid. 49 44 ##STR00067## .sup.1H NMR (500 MHz; DMSO.sub.d6)
.delta. 10.57 (s, 1 H), 7.69 (s, 1 H), 6.79 (m, 1 H), 6.44 (m, 1
H), 4.87 (s, 2 H), 4.16 (q, 2 H), 3.48 (t, 2 H), 3.40 (m, 4 H),
2.99 (q, 2 H), 1.61 (m, 2 H), 1.37 (s, 9 H), 1.21 (t, 3 H). Yellow
foam/solid. 50 45 ##STR00068## .sup.1H NMR (500 MHz; DMSO.sub.d6)
.delta. 10.64 (s, 1 H), 7.68 (s, 1 H), 6.91 (t, 1 H), 6.47 (s, 1
H), 4.88 (s, 2 H), 4.16 (q, 2 H), 3.28 (q, 2 H), 3.08 (q, 2 H),
1.36 (s, 9 H), 1.21 (t, 3 H). Dark red solid. 51 46 ##STR00069##
.sup.1H NMR (400 MHz; DMSO.sub.d6) .delta. 10.44 (br s, 1 H), 7.66
(s, 1 H), 6.77 (m, 1 H), 6.41 (m, 1 H), 4.86 (s, 2 H), 4.16 (q, 2
H), 3.21 (q, 2 H), 2.89 (q, 2 H), 1.48 (m, 2 H), 1.41-1.36 (m, 11
H), 1.28-1.19 (m, 5 H). Dark grey solid.
[0226] Starting from guanine derivatives 48, 49 and 51, modified
guanine PNA monomers 52.about.54 were prepared by similarly
following the procedures described in Examples 34.about.35.
Spectral and physical data for compds 52.about.54 are provided in
the table below.
EXAMPLES 52.about.54
Analytical Data for guanine PNA monomers 52.about.54
TABLE-US-00009 ##STR00070## [0227] Starting Compd Material L.sub.3
Spectral & Physical Data 52 48 ##STR00071## .sup.1H NMR (400
MHz; DMSO.sub.d6) .delta. 10.61 (m, 1 H), 8.36 (m, 1 H), 8.25 (m, 1
H), 7.76-7.65 (m, 3 H), 6.78 (t, 1 H), 6.54 (m, 1 H), 5.07 (s, 1.2
H), 4.96 (s, 0.8 H), 4.54 (s, 0.8 H), 4.30 (s, 1.2 H), 4.25 (m, 1.2
H), 4.07 (m, 2 H), 3.88 (m, 0.8 H), 3.49 (m, 2.4 H), 3.40 (m, 3.6
H), 3.09 (m, 2 H), 1.36 (s, 9 H); MS/ESI (m + 1) = 676.1
(observed), MW = 675.8 (C.sub.27H.sub.33N.sub.9O.sub.8S.sub.2).
Dark brown foam/solid. 53 49 ##STR00072## .sup.1H NMR (400 MHz;
DMSO.sub.d6) .delta. 10.69 (s, 1 H), 8.36 (m, 1 H), 8.25 (m, 1 H),
7.73 (m, 2 H), 7.64-7.60 (m, 1 H), 6.80 (t, 1 H), 6.65 (br s, 1 H),
5.05 (s, 1.2 H), 4.94 (s, 0.8 H), 4.54 (s, 0.8 H), 4.29 (s, 1.2 H),
4.24 (m, 1.2 H), 4.07 (m, 2 H), 3.87 (m, 0.8 H), 3.46~3.39 (m, 6
H), 2.97 (m, 2 H), 1.60 (m, 2 H), 1.36 (s, 9 H); MS/ESI (m + 1) =
689.8 (observed), MW = 689.8
(C.sub.28H.sub.35N.sub.9O.sub.8S.sub.2). Yellow foam/solid. 54 51
##STR00073## .sup.1H NMR (400 MHz; DMSO.sub.d6) .delta. 10.42-10.40
(m, 1 H), 8.37-8.32 (m, 1 H), 8.28-8.25 (m, 1 H), 7.73- 7.70 (m, 2
H), 7.58-7.54 (m, 1 H), 6.76 (t, 1 H), 6.39- 6.38 (m, 1 H), 5.03
(s, 1.2 H), 4.92 (s, 0.8 H), 4.54 (s, 0.8 H), 4.29 (s, 1.2 H), 4.25
(m, 1.2 H), 4.08-4.07 (m, 2 H), 3.87 (m, 0.8 H), 3.18 (m, 2 H),
2.89 (m, 2 H), 1.47 (m, 2 H), 1.40-1.30 (m, 11 H), 1.24 (m, 2 H).
MS/ESI (m + 23/MNa*) = 696.2 (observed), MW = 673.8
(C.sub.28H.sub.35N.sub.9O.sub.7S.sub.2). Red foam/solid.
EXAMPLE 55
Preparation of ethyl
2-[6-amino-2-{2-(t-butoxycarbonyl-amino)ethyl}-amino-9H-purin-9-yl]acetat-
e (55)
##STR00074##
[0229] Compd 55 was prepared from compd 26 by similarly following
the procedure for Example 32. Pale yellow solid. .sup.1H NMR (400
MHz; DMSO.sub.d6) .delta. 7.70 (s, 1H), 6.84 (t, 1H), 6.79 (s, 2H),
6.30 (t, 1H), 4.87 (s, 2H), 4.16 (q, 2H), 3.25 (q, 2H), 3.08 (q,
2H), 1.37 (s, 9H), 1.22 (t, 3H).
EXAMPLE 56
Preparation of ethyl
2-[6-amino-2-[2-{2,3-bis(benzyloxy-carbonyl)guanidino}ethyl]amino-9H-puri-
n-9-yl]acetate (56)
##STR00075##
[0231] To 4.42 g of compd 55 dissolved in 22 ml MC, was slowly
added 22 ml TFA at 0.degree. C., and the solution was stirred for
2.5 h. The reaction solution was concentrated under reduced
pressure, to which was added 100 ml diethyl ether. The resulting
precipitate was collected by filtration to obtain 5.79 g of a pale
brown solid intermediate product. 3.9 g of the intermediate was
dissolved in 39 ml MC, to which was added slowly 6.9 ml TEA at
0.degree. C. The solution was stirred for 15 min at RT, to which
was added 2.48 g of
1,3-bis(benzyloxycarbonyl)-2-(methylthio)pseudourea. Then the
reaction mixture was stirred for another 24 h, and washed with 0.5M
aq HCl. The organic layer was dried over anhydrous magnesium
sulfate and concentrated under reduced pressure to yield 4.58 g of
compd 56 as a pale yellow solid. .sup.1H NMR (500 MHz; DMSO.sub.d6)
.delta. 11.59 (s, 1H), 8.56 (t, 1H), 7.69 (s, 1H), 7.39-7.29 (m,
10H), 6.75 (s, 2H), 6.53 (s, 1H), 5.15 (s, 2H), 5.02 (s, 2H), 4.86
(s, 2H), 4.13 (q, 2H), 3.50 (q, 2H), 3.37 (m, 2H), 1.19 (t,
3H).
EXAMPLE 57
Preparation of ethyl
2-[6-(benzyloxycarbonylamino)-2-[2-{2,3-bis-(benzyloxycarbonyl)guanidino}-
ethyl]amino-9H-purin-9-yl]acetate (57)
##STR00076##
[0233] 4.54 g of compd 56 and 8.22 g of
N-(benzyloxycarbonyl)-N'-methyl-imidazolium triflate were dissolved
in 90 ml DMF, and stirred for 29 h at RT. The solvent was removed
under reduced pressure, and the resulting residue was purified by
column chromatography (1:3 hexane/EA) to afford 3.06 g of compd 57
as a white foam/solid. .sup.1H NMR (500 MHz; DMSO.sub.d6) .delta.
11.60 (s, 1H), 10.25 (s, 1H), 8.57 (t, 1H), 7.95 (s, 1H), 7.45-7.29
(m, 15H), 7.14 (t, 1H), 5.18 (s, 2H), 5.14 (s, 2H), 5.02 (s, 2H),
4.95 (s, 2H), 4.15 (q, 2H), 3.54 (q, 2H), 3.42 (q, 2H), 1.19 (t,
3H).
EXAMPLE 58
Preparation of ethyl
2-[6-amino-2-{4-(t-butoxycarbonyl-amino)butyl}-amino-9H-purin-9-yl]acetat-
e (58)
##STR00077##
[0235] Compd 58 was prepared from compd 27 as a reddish yellow
foam/solid by similarly following the procedure described in
Example 32. .sup.1H NMR (500 MHz; DMSO.sub.d6) .delta. 7.67 (s,
1H), 6.79 (t, 1H), 6.69 (s, 2H), 6.30 (m, 1H), 4.85 (s, 2H), 4.15
(q, 2H), 3.22-3.17 (m, 2H), 2.93-2.89 (m, 2H), 1.45 (m, 2H),
1.40-1.36 (m, 11H), 1.21 (t, 3H).
EXAMPLE 59
Preparation of ethyl
2-[6-(benzyloxycarbonylamino)-2-[4-{2,3-bis-(benzyloxycarbonyl)guanidino}-
butyl]amino-9H-purin-9-yl]acetate (59)
##STR00078##
[0237] Compd 59 was prepared from compd 58 as a pale yellow
foam/solid by similarly following the procedures described in
Examples 56.about.57. .sup.1H NMR (500 MHz; DMSO.sub.d6) .delta.
11.49 (s, 1H), 10.12 (s, 1H), 8.28 (t, 1H), 7.91 (s, 1H), 7.45-7.31
(m, 5H), 6.95 (t, 1H), 5.17 (s, 2H), 4.93 (s, 2H), 4.16 (q, 2H),
3.28 (m, 4H), 1.51 (m, 4H), 1.46 (s, 9H), 1.38 (s, 9H), 1.21 (t,
3H).
EXAMPLE 60
Preparation of ethyl
2-[6-amino-2-{5-(t-butoxycarbonylamino)-pentyl}amino-9H-purin-9-yl]acetat-
e (60)
##STR00079##
[0239] Compd 60 was prepared from compd 28 as a reddish yellow
foam/solid by similarly following the procedure described in
Example 32. .sup.1H NMR (500 MHz; DMSO.sub.d6) .delta. 7.67 (s,
1H), 6.78 (t, 1H), 6.69 (s, 2H), 6.28 (m, 1H), 4.85 (s, 2H), 4.15
(q, 2H), 3.18 (q, 2H), 2.89 (q, 2H), 1.47 (m, 2H), 1.40-1.34 (m,
11H), 1.25 (m, 2H), 1.21 (t, 3H).
EXAMPLE 61
Preparation of ethyl
2-[6-{di-(t-butoxycarbonyl)}amino-2-[5-{(t-butoxycarbonyl)amino}pentyl]am-
ino-9H-purin-9-yl]acetate (61)
##STR00080##
[0241] To 6.98 g of compd 60 dissolved in 100 ml THF, were added
7.95 g of Boc.sub.2O and 186 mg of 4-(N,N-dimethylamino)pyridine,
and the solution was stirred for 10 min. Then the solution was
mixed with 4.62 ml TEA, stirred for 30 min, slowly heated to
50.degree. C., and then stirred for another 24 h at the
temperature. The reaction solution was concentrated in vacuo, and
the resulting residue was dissolved in 170 ml EA and washed in
series with 0.5M aq HCl and water. The organic layer was dried over
anhydrous sodium sulfate, concentrated, and subjected to
chromatographic separation (1:1 hexane/MC.fwdarw.MC) to obtain
compd 61 as a yellow foam/solid. .sup.1H NMR (500 MHz; DMSO.sub.d6)
.delta. 8.05 (s, 1H), 7.23 (t, 1H), 6.77 (t, 1H), 5.00 (s, 2H),
4.19 (q, 2H), 3.25 (q, 2H), 2.91 (q, 2H), 1.53 (m, 2H), 1.40-1.39
(m, 29H), 1.28 (m, 2H), 1.22 (t, 3H).
EXAMPLE 62
Preparation of ethyl
2-[2-[2-{2,3-bis-(benzyloxycarbonyl)-guanidino}ethyl]amino-6-oxo-6,9-dihy-
dro-1H-purin-2-yl]acetate (62)
##STR00081##
[0243] Compd 50 was converted to compd 62 as a white solid by
similarly following the procedure described in Example 57. .sup.1H
NMR (500 MHz; DMSO.sub.d6) .delta. 11.59 (s, 1H), 10.68 (s, 1H),
8.50 (t, 1H), 7.68 (s, 1H), 7.42-7.29 (m, 10H), 6.58 (m, 1H), 5.13
(s, 2H), 5.02 (s, 2H), 4.86 (s, 2H), 4.12 (q, 2H), 3.50 (m, 2H),
3.46 (m, 2H), 1.18 (t, 3H).
EXAMPLE 63
Preparation of
2-[6-(benzyloxycarbonylamino)-2-[2-{2,3-bis-(benzyloxycarbonyl)guanidino}-
ethyl]amino-9H-purin-9-yl]acetic acid (63)
##STR00082##
[0245] To 2.57 g of compd 57 dissolved in 7.1 ml THF and 7.1 ml
water, was added 340 mg of LiOH at 0.degree. C., and the solution
was stirred at RT for 40 min. The reaction solution was acidified
to pH 5-6 with 1N aq HCl at 0.degree. C., and the resulting solid
was collected by filtration to yield 2.33 g of compd 63 as a white
solid. .sup.1H NMR (500 MHz; DMSO.sub.d6) .delta. 11.59 (s, 1H),
10.21 (s, 1H), 8.57 (t, 1H), 7.93 (s, 1H), 7.45-7.28 (m, 15H), 7.12
(t, 1H), 5.17 (s, 2H), 5.13 (s, 2H), 5.02 (s, 2H), 4.83 (s, 2H),
3.53 (q, 2H), 3.42 (q, 2H).
EXAMPLE 64
Preparation of t-butyl
N-[2-{(9H-fluoren-9-yl)methoxycarbonyl-amino}ethyl)]-N-[2-{6-(benzyloxyca-
rbonylamino)-2-[2-{2,3-bis-(benzyloxy-carbonyl)-guanidino}ethyl]amino-9H-p-
urin-9-yl}acetyl]glycinate (64)
##STR00083##
[0247] To 1.6 g of compd 63 dissolved in 30 ml DMF, were added at
0.degree. C. 660 mg of EDCI and 910 mg of Fmoc-Aeg-OtBu. The
reaction solution was stirred for 2 h at RT and then concentrated
under reduced pressure. The resulting residue was dissolved in 50
ml MC and washed with 0.5M aq HCl, and the organic layer was dried
over anhydrous sodium sulfate. Then the organic layer was
concentrated and subjected to chromatographic separation (65:1
MC/MeOH) to obtain 500 mg of compd 64 as a white solid. .sup.1H NMR
(500 MHz; DMSO.sub.d6) .delta. 11.59 (s, 0.4H), 11.58 (s, 0.6H),
10.21 (s, 1H), 8.55 (m, 1H), 7.47-7.28 (m, 20H), 7.06 (br, 1H),
5.17-4.89 (m, 8H), 4.34-4.28 (m, 2.8H), 4.20 (m, 1H), 3.95 (s,
1.2H), 3.52 (m, 3.4H), 3.43 (m, 2.2H), 3.34 (m, 1.7H), 3.12 (m,
0.7H), 1.43 (s, 3H), 1.34 (s, 6H).
EXAMPLE 65
Preparation of
N-[2-{(9H-fluoren-9-yl)methoxycarbonylamino}-ethyl)]-N-[2-{6-(benzyloxyca-
rbonylamino)-2-[2-{2,3-bis(benzyloxycarbonyl)-guanidino}ethyl]amino-9H-pur-
in-9-yl}acetyl]glycine (65)
##STR00084##
[0249] To 460 mg of compd 64 dissolved in 3.6 ml MC, was slowly
added 3.6 ml TFA at 0.degree. C. The reaction solution was stirred
at RT for 3.5 h, and then 50 ml diethyl ether was added. The
resulting precipitate was collected by filtration to yield 430 mg
of compd 65 as a white solid. .sup.1H NMR (400 MHz; DMSO.sub.d6)
.delta. 11.57 (s, 1H), 10.77 (br s, 1H), 8.66 (s, 1H), 8.54 (s,
1H), 7.87 (m, 2H), 7.63 (m, 2H), 7.50-7.28 (m, 21H), 5.26-4.96 (m,
8H), 4.34-4.18 (m, 4H), 4.03 (s, 1H), 3.52-3.36 (m, 7H), 3.13 (m,
1H). MS/ESI (m+1)=1019.4 (observed), MW=1018.0
(C.sub.53H.sub.51N.sub.11O.sub.11).
EXAMPLE 66
Preparation of
N-[2-{(9H-fluoren-9-yl)methoxycarbonylamino}-ethyl)]-N-[2-{6-(benzyloxyca-
rbonylamino)-2-[4-{2,3-bis(benzyloxycarbonyl)-guanidino}-butyl]amino-9H-pu-
rin-9-yl]acetyl}glycine (66)
##STR00085##
[0251] Compd 59 was converted to compd 66 as a white foam/solid by
similarly following the procedures described in Examples
63.about.65. .sup.1H NMR (500 MHz; DMSO.sub.d6) .delta. 12.84 (br
s, 1H), 11.50 (s, 1H), 10.14-10.13 (m, 1H), 8.28 (m, 1H), 7.88 (m,
2H), 7.80-7.77 (m, 1H), 7.68-7.66 (m, 2H), 7.49 (t, 1H), 7.45-7.29
(m, 9H), 6.90 (m, 1H), 5.17 (s, 2H), 5.07 (s, 1.2H), 4.89 (s,
0.8H), 4.35-4.18 (m, 3H), 4.00 (s, 1H), 3.52 (m, 1H), 3.35-3.25 (m,
6H), 3.12 (m, 1H), 1.49 (m, 4H), 1.44 (d, 9H), 1.37 (d, 9H). MS/ESI
(m+1)=978.4 (observed), MW=978.1
(C.sub.49H.sub.59N.sub.11O.sub.11).
EXAMPLE 67
Preparation of
N-[2-{(9H-fluoren-9-yl)methoxycarbonylamino}-ethyl)]-N-[2-[6-[2-{2,3-bis(-
benzyloxycarbonyl)guanidino}ethoxy]methyl-2-oxo-2H-pyrrolo[2,3-d]pyrimidin-
-3(7H)-yl]acetyl]glycine (67)
##STR00086##
[0253] Compd 18 was converted to compd 67 as a pale yellow solid by
similarly following the procedures described in Examples
63.about.65. .sup.1H NMR (500 MHz; DMSO.sub.d6) .delta. 11.99 (br
s, 1H), 11.57 (br, 1H), 8.56 (m, 1H), 8.48-8.45 (m, 1H), 7.89-7.87
(m, 2H), 7.70-7.65 (m, 2H), 7.49-7.26 (m, 15H), 6.36-6.33 (m, 1H),
5.20 (s, 2H), 5.03-5.01 (m, 3.3H), 4.83 (s, 0.7H), 4.49-4.17 (m,
5.7H), 4.01 (m, 1.3H), 3.57-3.11 (m, 8H); MS/ESI (m+1)=899.7
(observed), MW=898.9 (C.sub.47H.sub.46N.sub.8O.sub.11).
EXAMPLE 68
Preparation of
N-[2-{(9H-fluoren-9-yl)methoxycarbonylamino}-ethyl)]-N-{2-[2-{2,3-bis-(be-
nzyloxycarbonyl)guanidino}ethyl]amino-6-oxo-6,9-dihydro-1H-purin-2-yl]acet-
yl}glycine (68)
##STR00087##
[0255] Compd 62 was converted to compd 68 as a white foam/solid by
following the procedures described in Examples 63.about.65. .sup.1H
NMR (500 MHz; DMSO.sub.d6) .delta. 11.58 (s, 1H), 10.88 (s, 1H),
8.51 (m, 1H), 7.93 (m, 1H), 7.87 (m, 2H), 7.64 (m, 2H), 7.47 (t,
1H), 7.41-7.26 (m, 14H), 6.66 (br, 1H), 5.16-4.89 (m, 8H),
4.34-4.18 (m, 3.8H), 4.00 (m, 1.2H), 3.50-3.35 (m, 7H), 3.13 (m,
1H); MS/ESI (m+1)=885.3 (observed), MW=884.9
(C.sub.45H.sub.44N.sub.10O.sub.10).
EXAMPLE 69
Preparation of
2-[6-{2-(t-butoxycarbonylamino)ethoxy}methyl-2-oxo-2H-pyrrolo-[2,3-d]pyri-
midin-3(7H)-yl]acetic acid (69)
##STR00088##
[0257] Compound 16 was hydrolyzed to compound 69 as a pale brown
solid by similarly following the procedure described in Example 11.
.sup.1H NMR (500 MHz; DMSO.sub.d6) .delta. 13.03 (br s, 1H), 11.31
(s, 1H), 8.37 (s, 1H), 6.85 (t, 1H), 6.19 (s, 1H), 4.63 (s, 2H),
4.40 (s, 2H), 3.42 (t, 2H), 3.11 (q, 2H), 1.37 (s, 9H).
EXAMPLE 70
Preparation of methyl
N-[2-{(9H-fluoren-9-yl)methoxycarbonyl-amino}ethyl)]-N-{2-[6-{2-(t-butoxy-
carbonylamino)ethoxy}methyl-2-oxo-2H-pyrrolo-[2,3-d]pyrimidin-3(7H)-yl]ace-
tyl}glycinate (70)
##STR00089##
[0259] 3.6 g of compd 69, 3.6 g of Fmoc-Aeg-OMe, 2.5 g of EDCI 1.73
g of HOBt, and 2.24 ml DIEA were dissolved in 70 ml DMF, and
stirred at RT for 1.5 h. The reaction solvent was removed under
reduced pressure, and the resulting residue was dissolved in 100 ml
MC and washed in series with 1M aq HCl, distilled water, and brine.
The organic layer was dried over anhydrous sodium sulfate,
concentrated in vacuo, and purified by column chromatography (100:2
MC/MeOH) to afford 2.5 g of compd 70 as a yellow foam/solid.
.sup.1H NMR (500 MHz; DMSO.sub.d6) .delta. 11.30 (s, 1H), 8.24 (s,
0.65H), 8.21 (s, 0.35H), 7.89-7.87 (m, 2H), 7.71-7.67 (m, 2H),
7.48-7.25 (m, 5H), 6.87 (t, 1H), 6.17 (s, 0.7H), 6.15 (s, 0.3H),
4.93 (s, 1.3H), 4.74 (s, 0.7H), 4.40-4.39 (m, 2.7H), 4.35-4.21 (m,
3H), 4.08 (s, 1.3H), 3.73 (s, 0.8H), 3.62 (s, 2.2H), 3.51 (t,
1.4H), 3.43-3.30 (m, 3.6H), 3.13-3.10 (m, 3H), 1.37 (s, 9H).
EXAMPLE 71
Preparation of
N-[2-{(9H-fluoren-9-yl)methoxycarbonylamino}-ethyl)]-N-{2-[6-{2-(t-butoxy-
carbonylamino)ethoxy}methyl-2-oxo-2H-pyrrolo-[2,3-d]pyrimidin-3(7H)-yl]ace-
tyl}glycine (71)
##STR00090##
[0261] To 5.0 g of compd 70 dissolved in 75 ml 1:1:1
acetonitrile/acetone/water, was slowly added at 0.degree. C. 28.5
ml 2.5N aq LiOH. The reaction solution was stirred for 10 min and
neutralized with 20% aq citric acid. After the solution pH was
adjusted to 8 with saturated aq sodium bicarbonate, 516 mg of
Fmoc-OSu was added to the solution and the solution was stirred for
2 h at RT. Then the solution was acidified to pH 3 with 20% aq
citric acid and stirred for 90 min at 0.degree. C. The resulting
precipitate was collected by filtration to give 4.0 g of compd 71
as a yellowish green solid. .sup.1H NMR (500 MHz; DMSO.sub.d6)
.delta. 12.02 (br, 1H), 8.51-8.49 (m, 1H), 7.89-7.88 (d, 2H),
7.70-7.50 (m, 2H), 7.49 (t, 1H), 7.42-7.28 (m, 4H), 6.87 (t, 1H),
6.36 (s, 0.7H), 6.33 (s, 0.3H), 5.02 (s, 1.2H), 4.84 (0.8H),
4.43-4.42 (m, 2.4H), 4.34-4.19 (m, 3.2H), 4.01 (s, 1.4H), 3.48 (t,
1.2H), 3.44-3.41 (m, 2.1H), 3.37-3.29 (m, 2H), 3.12-3.10 (m, 2.7H),
1.37 (s, 9H); MS/ESI (m+1)=689.3 (observed), MW=688.7
(C.sub.35H.sub.40N.sub.6O.sub.9).
EXAMPLE 72
Preparation of
N-[2-{(9H-fluoren-9-yl)methoxycarbonylamino}-ethyl)]-N-{2-[5-{(t-butoxyca-
rbonyl)amino}pentyl]amino-6-oxo-6,9-dihydro-1H-purin-2-yl]acetyl}glycine
(72)
##STR00091##
[0263] Compd 51 was converted to compd 72 as a white foam/solid by
similarly following the procedures described in Examples
69.about.71. .sup.1H NMR (500 MHz; DMSO.sub.d6) .delta. 13.01 (br,
1H), 10.52-10.46 (m, 1H), 7.88 (d, 2H), 7.65 (d, 2H), 7.54 (s,
0.5H), 7.50 (s, 0.5H), 7.48 (m, 1H), 7.40 (t, 2H), 7.31 (m, 2H),
6.81 (t, 0.5H), 6.72 (t, 0.5H), 6.52-6.48 (m, 1H), 4.98 (s, 1H),
4.77 (s, 1H), 4.33 (d, 1H), 4.23-4.21 (m, 2H), 4.05 (m, 1H), 3.96
(s, 1H), 3.50 (m, 1H), 3.35 (m, 2H), 3.21 (m, 2H), 3.14 (q, 1H),
2.88 (m, 2H), 1.46 (q, 2H), 1.39-1.35 (m, 11H), 1.23 (m, 2H);
MS/ESI (m+1)=717.4 (observed), MW=716.8
(C.sub.36H.sub.44N.sub.8O.sub.8)
EXAMPLE 73
Preparation of
N-[2-{(9H-fluoren-9-yl)methoxycarbonylamino}-ethyl)]-N-[2-[6-{bis(t-butox-
ycarbonyl)amino}-2-{5-(t-butoxycarbonylamino)-pentyl}amino-9H-purin-9-yl]a-
cetyl]glycine (73)
##STR00092##
[0265] Compd 61 was converted to compd 73 as a white foam/solid by
similarly following the procedures described in Examples
69.about.71. .sup.1H NMR (500 MHz; DMSO.sub.d6) .delta. 12.71 (br
s, 1H), 7.90-7.87 (m, 3H), 7.67 (m, 2H), 7.44-7.39 (m, 3H), 7.31
(m, 2H), 7.07 (m, 1H), 6.69 (m, 1H), 5.11 (s, 1.2H), 4.93 (s,
0.8H), 4.37-4.21 (m, 3.8H), 4.01 (s, 1.2H), 3.52 (m, 1H), 3.36 (m,
2H), 3.23 (m, 2H), 3.13 (m, 1H), 2.88 (m, 2H), 1.49 (m, 2H),
1.38-1.35 (m, 27H), 1.27-1.25 (m, 4H); MS/ESI (m+1)=916.5
(observed), MW=916.0 (C.sub.46H.sub.61N.sub.9O.sub.11).
[0266] Preparation of PNA Oligomers: PNA Monomers o, which were
Synthesized according to Scheme 4, were sent to Panagene, Inc
(www.panagene.com, Daejon, South Korea) to prepare PNA oligomers of
Formula I by Panagene according to the method described in the
literature or with minor modification(s) thereof. (Org. Lett. vol
9, 3291-3293, 2006) PNA oligomers were received from Panagene as
characterized by MALDI-TOF and analyzed by C.sub.18-reverse phase
HPLC. PNA oligomers received from Panagene were used without
further purification.
[0267] PNA monomers q of Scheme 5 were used to synthesize PNA
oligomers of Formula I according to the method disclosed in the
prior art or with minor modification(s) thereof. (U.S. Pat. No.
6,133,444) Those PNA oligomers were purified by C.sub.18-reverse
phase HPLC (aq acetonitrile with 0.1% TFA) and characterized by
MALDI-TOF. FIG. 1 provides HPLC chromatograms before and after
purification of Oligo 17 by reverse phase HPLC. FIG. 2 provides a
MALDI-TOF mass spectrum for a purified batch of Oligo 17. FIGS. 1
and 2 are provided for illustrative purposes only and should not be
interpreted as a restriction to this invention.
[0268] PNA oligomers synthesized for this invention are provided in
Table 1 along with their molecular weight data by MALDI-TOF. Of the
abbreviations used in Table 1, A, T, G, and C refer to unmodified
nucleobase adenine, thymine, guanine, and cytosine, respectively.
Modified nucleobases C(mXn), C(mXn.sub.g), A(mXn), A(m), A(mg), and
G(m) are as defined below Table 1 along with Lys, Fam, L(1), and
L(2). These PNA oligomers are presented for illustrative purposes
only and should not be interpreted as a restriction to the present
invention.
TABLE-US-00010 TABLE 1 PNA oligomers of this invention and mass
spectral data thereof..sup.a Entry Sequence (N .fwdarw. C) MW (m +
1).sup.b Oligo Fam-L(1)L(1)-TGC(1O3)-TAC 4079.0 4078.3 1
(1O3)-TAC(1O3)-TG-Lys-NH.sub.2 Oligo Fam-L(1)L(1)-TGC-TAC-TAC-
3745.6 3745.5 2 TG-Lys-NH.sub.2 Oligo TGC(1O3)-TAC-TAC(1O3)-TG-
3319.4 3318.5 3 Lys-NH.sub.2 Oligo TGC-TAC(1O3)-TAC-TG-Lys-NH.sub.2
3208.3 3208.3 4 Oligo TGC-TAC-TAC-TG-Lys-NH.sub.2 3097.2 3097.8 5
Oligo Fam-L(1)L(1)-TC(1O3)T-CC 6140.1 6141.8 6
(1O3)C-AGC(1O3)-GTG-C(1O3) GC-C(1O3)AT-Lys-NH.sub.2 Oligo
Fam-L(1)L(1)-TCT-CCC-AGC- 5584.4 5583.1 7 GTG-CGC-CAT-Lys-NH.sub.2
Oligo TGC(2O2)-TAC-TAC(2O2)-TG- 3319.4 3318.9 8 Lys-NH.sub.2 Oligo
GC(2O2)A-C(2O2)AT-TTG-C 3553.7 3552.7 9 (2O2)CT-NH.sub.2 Oligo
GC(1O2)A-C(1O2)AT-TTG-C 3511.6 3511.1 10 (1O2)CT-NH.sub.2 Oligo
GCA-CAT-TTG-CCT-Lys-NH.sub.2 3348.3 3345.8 11 Oligo
CA(3)T-A(3)GT-A(3)TA-A(3) 3580.8 3580.9 12 GT-NH.sub.2 Oligo
CA(4)T-A(4)GT-A(4)TA-A(4) 3636.9 3634.9 13 GT-NH.sub.2 Oligo
CA(5)T-A(5)GT-A(5)TA-A(5) 3693.0 3691.5 14 GT-NH.sub.2 Oligo
CA(7)T-A(7)GT-A(7)TA-A(7) 3805.0 3803.4 15 GT-NH.sub.2 Oligo
CAT-AGT-ATA-AGT-Lys-NH.sub.2 3420.3 3418.3 16 Oligo
CA(5)T-A(5)GT-A(5)TA-A(5) 3820.9 3819.8 17 GT-Lys-NH.sub.2 Oligo
CA(2O2)T-A(2O2)GT-A(2O2) 3700.7 3701.4 18 TA-A(2O2)GT-NH.sub.2
Oligo L(1)-TAG(2O3)-CTG(2O3)- 3746.9 3748.9 19 CTG-ATT-Lys-NH.sub.2
Oligo TG(5)G-C(1O2)AA-C(1O2)TG- 3525.6 3523.8 20 A(5)T-Lys-NH.sub.2
Oligo Fam-L(2)-TG(5)G-C(1O2)AA- 3997.0 3996.1 21
C(1O2)TG-A(5)T-Lys-NH.sub.2 Oligo Fam-L(2)-TT-C(1O2)AT-A(5) 4806.9
4806.7 22 GT-A(5)TA-AG(5)T-Lys-NH.sub.2 Oligo
Fam-L(2)L(2)-TC(1O2)A-GA(5) 4084.2 4083.8 23
A-C(1O2)TT-A(5)T-Lys-NH.sub.2 Oligo Fam-L(2)-CA(5)T-A(4.sub.g)GT-A
4348.5 4347.4 24 (4.sub.g)TA(5)-AGT-Lys-NH.sub.2 Oligo
TT-C(1O2.sub.g)AT-A(5)GT-A(5) 4377.4 4375.6 25
TA-AG(5)T-Lys-NH.sub.2 Oligo GC(1N3)A-C(1N3)AT-TTG-C 3550.8 3550.9
26 (1N3)CT-NH.sub.2 Oligo CAT-AGT-ATA-AGT-NH.sub.2 3292.3 3292.5 27
Oligo Fam-L(2)-TGG-CAA-CTG-AT- 3617.5 3616.3 28 Lys-NH.sub.2
.sup.aThe employed abbreviations for monomers are defined as below.
.sup.bObserved ion peak for MH.sup.+ unless noted otherwise.
##STR00093## ##STR00094##
[0269] Binding Affinity for DNA: PNA oligomers of this invention
were evaluated for their binding affinity for DNA by measuring
T.sub.m values as follows.
[0270] 4 .mu.M PNA oligomer and 4 .mu.M DNA were mixed in aq buffer
(pH 7.16, 10 mM sodium phosphate, 100 mM NaCl), and incubated at
90.degree. C. for a few minutes and slowly cooled down to RT. Then
the solution was transferred into a 4 ml quartz cuvette and the
cuvette was tightly sealed. The cuvette was mounted on an Agilent
8453 UV/Visible spectrophotometer and absorbance changes at 260 nm
were recorded with increasing the temperature of the cuvette by
either 0.5 or 1.0.degree. C. per minute. From the absorbance vs
temperature curve, the temperature showing the largest increase
rate in absorbance was read out as the melting temperature T.sub.m
between PNA and DNA. DNAs for T.sub.m measurement were purchased
either from Bioneer, Inc. (www.bioneer.com, Daejon, South Korea) or
from Ahram Biosystems (www.ahrambio.com, Seoul, South Korea), and
used without further purification.
[0271] FIG. 3 provides graphs of absorbance changes with
temperature for Oligo 17 against complementary or mismatch DNA. For
sequences of the mismatch DNAs against Oligo 17, refer to Table 2.
In FIG. 3, there is a transition temperature in each curve, which
was read out as the T.sub.m value for the curve.
[0272] T.sub.m values are provided in Table 2 for PNA oligomers of
this invention. These T.sub.m values are presented for illustrative
purposes only and should not be interpreted as a restriction to
this invention.
TABLE-US-00011 TABLE 2 T.sub.m values between PNA and complementary
or mismatch DNA. DNA Sequence Entry (5' .fwdarw. 3') T.sub.m,
.degree. C. Remark Oligo 5 CAG-TAG-TAG-CA 55 unmodified PNA
oligomer Oligo 3 65 C(1O3) .times. 2 Oligo 4 61 C(1O3) .times. 1
Oligo 8 68 C(2O2) .times. 2 Oligo 10 AGG-CAA-TTG-TGC >85 C(1O2)
.times. 3 Oligo 11 59 unmodified PNA oligomer Oligo 12
ACT-TAT-ACT-ATG 60 A(3) .times. 4 Oligo 13 64 A(4) .times. 4 Oligo
14 69 A(5) .times. 4 Oligo 15 71 A(7) .times. 4 Oligo 18 66 A(2O2)
.times. 4 Oligo 27 55 unmodified PNA oligomer Oligo 16
ACT-TAT-ACT-ATG 56 unmodified PNA oligomer Oligo 17 ACT-TAT-ACT-ATG
72 complementary ACT-TAC-ACT-ATG 61 mismatch (T .fwdarw. C)
ACT-TAA-ACT-ATG 59 mismatch (T .fwdarw. A) ACT-TAG-ACT-ATG 58
mismatch (T .fwdarw. G) Oligo 24 ACT-TAT-ACT-ATG 70 A(5) .times. 2
plus A(4.sub.g) .times. 2 Oligo 20 ATC-AGT-TGC-CA 84 complementary
ATC-ATT-TGC-CA 62 mismatch (G .fwdarw. T) ATC-AAT-TGC-CA 65
mismatch (G .fwdarw. A)
[0273] Replacement of cytosine with an unnatural nucleobase
pyrrolocytosine derivative of this invention markedly increased PNA
oligomer's affinity for complementary DNA. For example, Oligo 10
having three `modified` cytosine `C(1O2)` monomers showed a T.sub.m
exceeding 85.degree. C., while the corresponding `unmodified` Oligo
11 showed a T.sub.m of 58.degree. C. Other modified cytosine
monomers such as `C(1O3)` or `C(2O2)` also significantly increased
PNA oligomer's affinity for complementary DNA, as exemplified with
Oligo 3 and Oligo 8.
[0274] `Modified` adenine nucleobases of this invention also
significantly increased PNA oligomer's affinity for complementary
DNA. For example, Oligo 15 having four `modified` adenine A(7)
monomers showed a T.sub.m of 71.degree. C., which is significantly
higher than the T.sub.m of 55.degree. C. observed with `unmodified`
Oligo 27. Other `modified` adenine monomers such as A(4), and A(5)
also markedly increased affinity for complementary DNA.
[0275] `Modified` PNA monomers of this invention were found to be
quite sensitive to base mismatch. For example, decreases of
11.about.14.degree. C. in T.sub.m were observed with single base
mismatches for an A(5) monomer in Oligo 17. Single base mismatches
for a C(1O2) monomer in Oligo 20 resulted in decreases of
19.about.22.degree. C. in T.sub.m.
[0276] Cell Penetration: In order to evaluate the cell penetration
ability of PNA oligomers of this invention, cancer cells of human
origin were treated with PNA oligomers covalently tagged with
fluorescein. The applied method is provided in brief as
follows.
[0277] To each cover glass (autoclaved) placed in each well of a
24-well plate, were seeded 20,000.about.100,000 cells depending on
the growth rate of the cell line used, and the cells were cultured
at 37.degree. C. and 5% CO.sub.2 for 16 to 24 h. Then the medium
was replaced with 500 .mu.l fresh Opti-MEM medium (with or without
1% FBS), to which was added an aliquot of aq stock solution of a
PNA oligomer covalently tagged with fluorescein. After cells were
cultured for a designated interval, the cells were washed with PBS,
and fixed by incubating in 3.7% or 4% paraformaldehyde. The cells
were thoroughly washed several times with PBS or PBS containing
0.1% Tween-20. Then the cover glass was mounted onto a slide glass
using a drop of mounting solution and sealed with nail polish for
confocal fluorescence microscopy. Fluorescence images were taken
either on a Zeiss LSM 510 confocal microscope (Germany) at
63.times. objective or on a Nikon C1Si confocal microscope at
40.times. objective.
[0278] The cell penetration images in FIGS. 4.about.8 are provided
for illustrative purposes only and should not be interpreted as a
restriction to the present invention.
[0279] In FIGS. 4(a) and 4(b), are provided confocal microscopy
images (at 63.times. objective) 1, 2, 3 and 24 h after HeLa cells
were treated with Oligo 1 and Oligo 2 at 5 .mu.M, respectively
(without FBS). While fluorescence intensity is clear and becomes
intense over 24 h in FIG. 4(a), fluorescence intensity is faint in
FIG. 4(b), indicating that Oligo 1 penetrates HeLa cells
significantly faster than `unmodified` Oligo 2.
[0280] In FIGS. 5(a) and 5(b), are provided confocal microscopy
images (at 63.times. objective) 0.5 and 1 h after MCF-7 cells were
treated with Oligo 6 and Oligo 7 at 2.5 .mu.M, respectively
(without FBS). While fluorescence intensity is clear and becomes
intense over 1 h in FIG. 5(a), fluorescence intensity is faint in
FIG. 5(b), indicating that Oligo 6 penetrates MCF-7 cells
significantly faster than `unmodified` Oligo 7.
[0281] In FIGS. 6(a) and 6(b), are provided confocal microscopy
pictures (at 40.times. objective) 6 or 24 h after HeLa cells were
treated with Oligo 1 and Oligo 6 at 1 .mu.M, respectively (with 1%
FBS). While fluorescence intensity is faint even at 24 h in FIG.
6(a), fluorescence intensity is clear and becomes intense over 24 h
in FIG. 6(b), suggesting that Oligo 6 penetrate HeLa Cells
significantly faster than Oligo 1.
[0282] In FIGS. 7(a) and 7(b), are provided confocal microscopy
pictures (40.times. objective) 24 h after JAR cells were treated
with Oligo 21 and Oligo 28 at 2 .mu.M, respectively (without FBS).
While fluorescence intensity is strong in FIG. 7(a), there is no
significant fluorescence intensity in FIG. 7(b), suggesting that
Oligo 21 penetrate JAR cells significantly faster than `unmodified`
Oligo 28.
[0283] In FIGS. 7(c) and 7(d), are provided confocal microscopy
pictures (at 40.times. objective) 24 h after A549 cells were
treated with Oligo 21 and Oligo 28 at 2 .mu.M, respectively
(without FBS). While fluorescence intensity is strong in FIG. 7(c),
there is no significant fluorescence intensity in FIG. 7(d),
suggesting that Oligo 21 penetrate A549 cells significantly faster
than `unmodified` Oligo 28.
[0284] In FIGS. 7(e) and 7(f), are provided confocal microscopy
pictures (at 40.times. objective) 12 h after HeLa cells were
treated with Oligo 21 and Oligo 28 at 2 .mu.M, respectively
(without FBS). While fluorescence intensity is apparent in FIG.
7(e), there is no significant fluorescence intensity in FIG. 7(f),
suggesting that Oligo 21 penetrate HeLa cells significantly faster
than `unmodified` Oligo 28.
[0285] In FIG. 7(g), are provided confocal microscopy pictures (at
40.times. objective) 24 h after HeLa cells were treated with Oligo
21 at 2 .mu.M (without FBS). Given that the cellular fluorescence
in FIG. 7(g) is significantly stronger than that in FIG. 7(e),
Oligo 21 appears to penetrate over 24 h rather than 12 h.
[0286] FIGS. 8(a), 8(b) and 8(c) provide confocal microscopy images
(40.times. objective) 24 h after HeLa, A549, and JAR cells were
treated with 2 .mu.M Oligo 22, respectively (without FBS). All the
images are associated with fluorescence within cell, indicating
that Oligo 22 possesses good cell penetration in the tested
cells.
ANTISENSE EXAMPLE
[0287] Oligo 9 and Oligo 12 possess the same base sequences as
T1-12 and T5-12, respectively, which were reported to inhibit the
ribosomal synthesis of mdm2 in the literature. (Nucleic Acids Res.
vol 32, 4893-4902, 2004) Oligo 9 and Oligo 12 were evaluated for
their ability to inhibit the ribosomal synthesis of mdm2 in JAR
cells as follows. The following antisense example is presented for
illustrative purposes only and should not be interpreted as a
restriction to the present invention.
[0288] JAR cells (ATCC catalog #HTB-144) were grown in RPMI-1640
medium supplemented with 10% FBS and 1% penicillin-streptomycin at
37.degree. C. and 5% CO.sub.2. Cells were then seeded into each
well of a 12-well plate containing 1 ml of the same medium, and
treated with an aliquot of an aqueous stock solution of Oligo 9 or
Oligo 12 of a designated concentration. Then the cells were
incubated at 37.degree. C. and 5% CO.sub.2 for 15 h.
[0289] The cells in each well were washed with cold PBS and treated
with 80 .mu.l RIPA buffer containing 1% protease inhibitors
cocktail, and the plate was incubated at 4.degree. C. and agitated
slowly for 15 min. The content of each well was scraped out into a
microtube. The microtube was incubated in ice for 10 min and
centrifuged at 10,000 g. The resulting supernatant was collected
and subjected to protein quantification by Bradford assay and
western blot analysis. For electrophoresis, 20 .mu.g of protein was
loaded onto each lane of the gel in a minigel apparatus, separated
and transferred onto a PVDF membrane (0.45.mu., Millipore). The
primary mdm2 antibody used for western blotting was SC-965 (Santa
Cruz Biotechnology).
[0290] FIG. 9 provides western blotting results for JAR cells
treated with 5 .mu.M or 10 .mu.M Oligo 9, 5 .mu.M or 10 .mu.M Oligo
10, cotreatment with the oligomers at 5 .mu.M or 10 .mu.M each, and
blank (no oligomer treatment). In FIG. 9, treatment with Oligo 9 or
Oligo 10, or cotreatment with Oligo 9 and Oligo 10 significantly
inhibited ribosomal synthesis of mdm2 in JAR cells both at 5 .mu.M
and 10 .mu.M.
Sequence CWU 1
1
35111DNAArtificial SequencePNA modified nucleotide 1tgntantant g
11211DNAArtificial SequencePNA modified oligonucleotide 2tgctactact
g 11311DNAArtificial SequencePNA modified oligonucleotide
3tgntactant g 11411DNAArtificial Sequencemodified PNA
oligonucleotide 4tgctantact g 11511DNAArtificial SequencePNA
modified oligonucleotide 5tgctactact g 11618DNAArtificial
SequencePNA modified oligonucleotide 6tntcncagng tgngcnat
18718DNAArtificial SequencePNA modified oligonucleotide 7tctcccagcg
tgcgccat 18811DNAArtificial SequencePNA modified oligonucleotide
8tgntactant g 11912DNAArtificial SequencePNA modified
oligonucleotide 9gnanatttgn ct 121012DNAArtificial SequencePNA
modified oligonucleotide 10gnanatttgn ct 121112DNAArtificial
SequencePNA modified oligonucleotide 11gcacatttgc ct
121212DNAArtificial SequencePNA modified oligonucleotide
12cntngtntan gt 121312DNAArtificial SequencePNA modified
oligonucleotide 13cntngtntan gt 121412DNAArtificial SequencePNA
modified oligonucleotide 14cntngtntan gt 121512DNAArtificial
SequencePNA modified oligonucleotide 15cntngtntan gt
121612DNAArtificial SequencePNA modified oligonucleotide
16catagtataa gt 121712DNAArtificial SequencePNA modified
oligonucleotide 17cntngtntan gt 121812DNAArtificial SequencePNA
modified oligonucleotide 18cntngtntan gt 121912DNAArtificial
SequencePNA modified oligonucleotide 19tanctnctga tt
122011DNAArtificial SequencePNA modified oligonucleotide
20tngnaantgn t 112111DNAArtificial SequencePNA modified
oligonucleotide 21tngnaantgn t 112214DNAArtificial SequencePNA
modified oligonucleotide 22ttnatngtnt aant 142311DNAArtificial
SequencePNA modified oligonucleotide 23tnagnanttn t
112412DNAArtificial SequencePNA modified oligonucleotide
24cntngtntna gt 122514DNAArtificial SequencePNA modified
oligonucleotide 25ttnatngtnt aant 142612DNAArtificial SequencePNA
modified oligonucleotide 26gnanatttgn ct 122712DNAArtificial
SequencePNA modified oligonucleotide 27catagtataa gt
122811DNAArtificial SequencePNA modified oligonucleotide
28tggcaactga t 112911DNAArtificial SequencePNA modified
oligonucleotide 29nagtagtagn a 113012DNAArtificial SequencePNA
modified oligonucleotide 30aggnaattgt gn 123112DNAArtificial
SequencePNA modified oligonucleotide 31ncttntnctn tg
123212DNAArtificial SequencePNA modified oligonucleotide
32acttatacta tg 123312DNAArtificial SequencePNA modified
oligonucleotide 33acttanacta tg 123412DNAArtificial SequencePNA
modified oligonucleotide 34ncttntnctn tg 123511DNAArtificial
SequencePNA modified oligonucleotide 35atcanttgcc a 11
* * * * *