NZ624961B2 - Functionally-modified oligonucleotides and subunits thereof - Google Patents
Functionally-modified oligonucleotides and subunits thereof Download PDFInfo
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- NZ624961B2 NZ624961B2 NZ624961A NZ62496112A NZ624961B2 NZ 624961 B2 NZ624961 B2 NZ 624961B2 NZ 624961 A NZ624961 A NZ 624961A NZ 62496112 A NZ62496112 A NZ 62496112A NZ 624961 B2 NZ624961 B2 NZ 624961B2
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- New Zealand
- Prior art keywords
- alkylene
- compound
- arylene
- och
- cnh
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- XDWXRAYGALQIFG-UHFFFAOYSA-L zinc;propanoate Chemical compound [Zn+2].CCC([O-])=O.CCC([O-])=O XDWXRAYGALQIFG-UHFFFAOYSA-L 0.000 description 1
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Classifications
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- C07D413/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing two hetero rings
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- C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic System
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- C07F9/65583—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom containing at least two different or differently substituted hetero rings neither condensed among themselves nor condensed with a common carbocyclic ring or ring system each of the hetero rings containing nitrogen as ring hetero atom
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- C07F9/6561—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom containing systems of two or more relevant hetero rings condensed among themselves or condensed with a common carbocyclic ring or ring system, with or without other non-condensed hetero rings
- C07F9/65616—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom containing systems of two or more relevant hetero rings condensed among themselves or condensed with a common carbocyclic ring or ring system, with or without other non-condensed hetero rings containing the ring system having three or more than three double bonds between ring members or between ring members and non-ring members, e.g. purine or analogs
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- C07F9/02—Phosphorus compounds
- C07F9/547—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom
- C07F9/6564—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom having phosphorus atoms, with or without nitrogen, oxygen, sulfur, selenium or tellurium atoms, as ring hetero atoms
- C07F9/6581—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom having phosphorus atoms, with or without nitrogen, oxygen, sulfur, selenium or tellurium atoms, as ring hetero atoms having phosphorus and nitrogen atoms with or without oxygen or sulfur atoms, as ring hetero atoms
- C07F9/6584—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom having phosphorus atoms, with or without nitrogen, oxygen, sulfur, selenium or tellurium atoms, as ring hetero atoms having phosphorus and nitrogen atoms with or without oxygen or sulfur atoms, as ring hetero atoms having one phosphorus atom as ring hetero atom
- C07F9/65842—Cyclic amide derivatives of acids of phosphorus, in which one nitrogen atom belongs to the ring
- C07F9/65846—Cyclic amide derivatives of acids of phosphorus, in which one nitrogen atom belongs to the ring the phosphorus atom being part of a six-membered ring which may be condensed with another ring system
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- C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
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- C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
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- C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
- C12N15/1131—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against viruses
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Abstract
Disclosed herein are functionally-modified oligonucleotide analogues of formula I where the substituents are as defined herein, comprising modified intersubunit linkages and/or modified 3' and/or 5'-end groups. The disclosed compounds are useful for the treatment of diseases where inhibition of protein expression or correction of aberrant mRNA splice products produces beneficial therapeutic effects. ein expression or correction of aberrant mRNA splice products produces beneficial therapeutic effects.
Description
FUNCTIONALLY-MODIFIED OLIGONUCLEOTIDES AND SUBUNITS
THEREOF
STATEMENT REGARDING SEQUENCE LISTING
The sequence listing associated with this application is provided in text format in lieu of
a paper copy, and is hereby incorporated by reference into the specification. The name
of the text file containing the sequence listing is
120178_498WO_SEQUENCE_LISTING.txt. The text file is about 13 KB, was created
on November 15, 2012, and is being submitted electronically via EFS-web.
BACKGROUND OF THE INVENTION
Technical Field
The present invention is generally related to oligonucleotide compounds
(oligomers) useful as antisense compounds, and more particularly to oligomer
compounds comprising modified intersubunit linkages and/or terminal groups, and the
use of such oligomer compounds in antisense applications.
Description of the Related Art
Antisense oligomers are generally designed to bind in a sequence
specific manner to DNA or RNA regions and alter the expression of disease-causing
proteins. Requirements for successful implementation of antisense therapeutics include
(a) stability in vivo, (b) sufficient membrane permeability and cellular uptake, and (c) a
good balance of binding affinity and sequence specificity. Many oligonucleotide
analogues have been developed in which the phosphodiester linkages of native DNA
are replaced by other linkages that are resistant to nuclease degradation (see, e.g.,
Barawkar, D.A. et al., Proc. Na't’l Acad. Sci. USA 95(19):11047-52 (1998);
Linkletter,B.A. et al., Nucleic Acids Res. 29(11):2370-6 (2001); Micklefield, J., Curr,
Med, Chem, 8(10):1157-79 (2001)). Antisense oligonucleotides having other various
backbone modifications have also been prepared (Crooke, S.T., Antisense Drug
Technology: Principles, Strategies, and Applications, New York, Marcel Dekker
(2001); Micklefield, J., Curr, Med, Chem, 8(10):1157-79 (2001); Crooke, S.T.,
Antisense Drug Technology, Boca Raton, CRC Press (2008)). In addition,
oligonucleotides have been modified by peptide conjugation in order to enhance
cellular uptake (Moulton, H.M. et al., Bioconjug Chem 15(2):290-9 (2004); Nelson,
M.H. et al., Bioconjug. Chem. 16(4):959-66 (2005); Moulton, H.M.et al., Biochim
Biophys Acta (2010)).
The performance of such nucleic acid analogues as antisense or antigene
drugs has been hampered by certain characteristics of the various analogues. For
example, analogues with negatively charged linkages, including phosphorothioate-
linked analogues, suffer from considerable electrostatic repulsion between the negative
charges of the oligomer and the DNA or RNA target. The phosphorothioates also
exhibit non-specific binding to other cellular components such as proteins. These
attributes limit the therapeutic effectiveness of antisense oligomers comprised of native
RNA, native DNA, and negatively charged analogues (Crooke, S.T., Antisense Drug
Technology: Principles, Strategies, and Applications, New York, Marcel Dekker
(2001); Crooke, S.T., Antisense Drug Technology, Boca Raton, CRC Press (2008)).
The nonionic methylphosphonate-linked oligonucleotide analogues can be transported
into cells by passive diffusion and/or fluid phase endocytosis, but their use is hampered
by stereoisomeric complexity and poor solubility (Crooke, S.T., Antisense Drug
Technology: Principles, Strategies, and Applications, New York, Marcel Dekker
(2001); Micklefield, J., Curr, Med, Chem, 8(10):1157-79 (2001)).
Several groups have reported the synthesis of positively charged
oligonucleotides (Bailey, C.P. et al.. Nucleic Acids Res. 26(21):4860-7 (1998);
Micklefield, J., Curr, Med, Chem, 8(10):1157-79 (2001); Egli, M. et al., Biochemistry
44(25):9045-57 (2005)). For example, a class of guanidinium linked nucleosides
(designated DNG), formed by replacement of the phosphate linkages in DNA and RNA
by achiral guanidino groups, has been reported (Dempcy, R.O. et al., Proc. Nat’l Acad.
Sci. USA 91(17):7864-8 (1994); Dempcy, R.O. et al., Proc. Nat’l Acad. Sci. USA
93(9):4326-30 (1996); Barawkar, D.A. et al., Proc. Na't’l Acad. Sci. USA
95(19):11047-52 (1998); Linkletter, B.A. et al., Nucleic Acids Res. 29(11):2370-6
(2001)). Oligomers linked with positively charged methylated thiourea linkages have
also been reported (Arya, D.P. et al., Proc. Nat’l Acad. Sci U S A 96(8): 4384-9 (1999)).
Replacement of some of these linkages with neutral urea linkages has been reported to
reduce the tendency of such positively charged oligomers towards non-sequence-
specific binding (Linkletter, B.A. et al., Bioorg. Med. Chem. 8(8):1893-901 (2000)).
Morpholino oligomers containing (1-piperazino) phosphinylideneoxy and (1-(4-(w-
guanidino-alkanoyl))-piperazino) phosphinylideneoxy linkages have been described
previously (see e.g., WO2008036127).
Although significant progress has been made, there remains a need in the
art for oligonucleotide analogues with improved antisense or antigene performance.
Such improved antisense or antigene performance includes; stronger affinity for DNA
and RNA without compromising sequence selectivity; improved pharmacokinetics and
tissue distribution; improved cellular delivery and reliable and controllable in vivo
distribution.
BRIEF SUMMARY OF THE INVENTION
It is an object tof the invention to provide compounds that address these
issues and provide improvements over existing antisense molecules in the art; and/or to
provide the public with a useful choice. Modification of the intersubunit linkages
and/or conjugation of terminal moieties to the 5’ and/or 3’ terminus of an
oligonucleotide analogue, for example a morpholino oligonucleotide, results in an
antisense oligomer having superior properties. For example, in certain embodiments
the disclosed oligomers have enhanced cell delivery, potency, and/or tissue distribution
compared to other oligonucleotide analogues and/or can be effectively delivered to the
target organs. These superior properties give rise to favorable therapeutic indices,
reduced clinical dosing, and lower cost of goods.
In one embodiment, described herein are compounds comprising a
backbone, the backbone comprising a sequence of morpholino ring structures joined by
intersubunit linkages, the intersubunit linkages joining a 3’-end of one morpholino ring
structure to a 5’-end of an adjacent morpholino ring structure, wherein each morpholino
ring structure is bound to a base-pairing moiety, such that the compound can bind in a
sequence-specific manner to a target nucleic acid.
In one aspect is a compound having the structure of Formula (I):
W P X
or a salt or isomer thereof,
wherein:
n is an integer from 1 to 50;
G is halogen, OH, alkoxy, OSO (alkyl), OSO (aryl), or ;
each B is an independently selected base pair moiety;
10
each Y is independently O or NR ; optionally, R and X8e are bonded
together form a ring;
each W is independently S or O;
11 15 11 15 16 11 12 17
Z is -(L )-(R ), -(L )-(L )-(R ), or –(L )-(L )-(R ) ;
L is selected from:
23 23 1 1
O 23 23
O R R
23 23
P P N R N
O L O
a) ; b) ; c) O L ;
23 23 23 23
23 23
R R R R
23 23
24 24
O N N N N
1 1 1 1 1
d) R R ; e) ; f) R R ; g) ;
23 23
O CH O 23 23
O H O
R R 3
23 23 R R
O N O N
h) O ; i) H ; j) H ; or
k) –C(R ) O-;
wherein L is selected from:
p p p
NN N N
a) ; b) ; c) ;
d) ; or e) ;
L is a linker cleaveable under biological conditions selected from:
a) –(C -C alkylene)-OC(O)O-CH O-;
1 10 2
b) –C(O)-(C -C alkylene)-OC(O)O-CH O-;
1 10 2
c) –C(O)-(CH=CH)-C(O)O-CH O-;
d) –(C -C alkylene)-S-S-CH CH O-; or
1 10 2 2
e) –C(O)–(C -C alkylene)-S-S-CH CH O-;
1 10 2 2
L is divalent radical selected from C -C alkylene, C -C
1 30 3 8
cycloalkylene, C -C arylene, -(C -C arylene)-(C -C alkylene)-, –(C -C alkylene)-
6 30 6 30 1 30 1 30
C(=O)-, –(C -C alkoxy)-C(=O)-, -(3-18 membered heteroalkylene)-C(=O)-, –(C -C
2 30 3 8
cycloalkylene)-C(=O)-, -(C -C cycloalkylene)-(C -C alkylene)-C(=O)-, -(C -C
3 8 1 30 1 30
alkylene) (C -C cycloalkylene)-C(=O)-, -(C -C arylene)-C(=O)-, -(C -C arylene)-
3 8 6 30 6 30
(C -C alkylene)-C(=O)-, -(C -C alkylene)-(C -C arylene)-C(=O)-, -(C -C
1 30 1 30 6 30 1 30
alkylene)-O-C(=O)-, -(C -C cycloalkylene)-O-C(=O)-, -(C -C arylene)-O-C(=O)-, -
3 8 7 30
(C -C arylene)-(C -C alkylene)-O-C(=O)-, -(C -C arylene)-(C -C alkylene)-O-
6 30 1 30 6 30 1 30
21 22
C(=O)-, -C(=O)OR , or -P(=O)(R ) ;
12 13
R is an electron pair, with the provision that if R is C -C alkyl, then
1 30
R is an electron pair, an N-oxide, or C -C alkyl;
13
each R and R is independently selected from hydrogen, a cell-
penetrating peptide, a natural or non-natural amino acid, guanidinyl, amidinyl,
heterocyclyl, C -C alkyl, C -C cycloalkyl; C -C aryl, C -C aralkyl, C -C
1 30 3 8 6 30 7 30 1 30
alkylcarbonyl, C -C cycloalkylcarbonyl, C -C cycloalkylalkylcarbonyl, C -C
3 8 3 8 6 30
arylcarbonyl, C -C aralkylcarbonyl, C -C alkyloxycarbonyl, C -C
7 30 1 30 3 8
cycloalkyloxycarbonyl, C -C aryloxycarbonyl, C -C aralkyloxycarbonyl,
7 30 8 30
21 21 22
-C(=O)OR , -C(=O)NHR , or -P(=O)(R ) ;
R is independently selected from a cell-penetrating peptide, a natural or
non-natural amino acid, guanidinyl, amidinyl, heterocyclyl, C -C alkyl, C -C
1 30 3 8
cycloalkyl; C -C aryl, C -C aralkyl, C -C alkylcarbonyl, C -C cycloalkylcarbonyl,
6 30 7 30 1 30 3 8
C -C cycloalkylalkylcarbonyl, C -C arylcarbonyl, C -C aralkylcarbonyl, C -C
3 8 6 30 7 30 2 30
alkyloxycarbonyl, C -C cycloalkyloxycarbonyl, C -C aryloxycarbonyl, C -C
3 8 7 30 8 30
21 21
aralkyloxycarbonyl, 3-18 membered alkoxyalkylcarbonyl, -SO R , -C(=O)OR ,
-P(=O)(OH) or -P(=O)(R ) ;
R is a solid support matrix suitable for solid phase synthesis of
oligonucleotides;
R is a drug, protein or toxin;
each R is independently C -C alkyl, or a 3-18 membered alkoxyalkyl
1 30
group;
each R is independently an C -C aryloxy;
6 12
23 23
each R is independently H or C –C alkyl; or optionally two R
groups join to form a 3- to 8-membered ring;
R is a C –C alkylene;
Q is independently selected from X1, X2, X3, X4, X5, X6, X7, or X8;
each X is independently selected from X1, X2, X3, X4, X5, X6, X7, or
X8 with the provision that at least one X is not X1;
wherein
X1 is N(CH ) ;
X2 is selected from:
a) -O-alkylene-CO H;
b) -O-alkylene-CHN ;
c) -N(R )-alkylene-CO H;
d) -N(R )-alkylene-CHN ;
e) -L1-CO-alkylene-CO H;
f) -L1-CO-alkylene-CHN ;
g) -L1-CO-alkenylene-CO H;
h) -L1-CO-alkenylene-CHN ;
i) -L1-CO-arylene-CO H;
j) -L1-CO-arylene-CHN ;
k) -L1-CONH-alkylene-CO H;
l) -L1-CONH-alkylene-CHN ;
m) -L1-CONH-arylene-CO H;
n) -L1-CONH-arylene-CHN ;
o) -L1-SO -alkylene-CO H;
p) -L1-SO -alkylene-CHN ;
q) -L1-SO -arylene-CO H;
r) -L1-SO -arylene-CHN ;
s) -L1-alkylene-CO H;
t) -L1-alkylene-CHN ;
u) -L1-arylene-CO H;
v) -L1-arylene-CHN ; and
w) a protected form of any of the above X2 groups;
X3 is selected from:
a) –L1-alkyl;
b) –L1-heterocyclyl;
c) -O-alkylene-CNH-NH ;
d) -N(R )-alkylene-CNH-NH ;
e) -L1-CNH-NH ;
f) -L1-alkylene-CNH-NH ;
g) -L1-arylene-CNH-NH ;
h) -L1-CO-alkylene-CNH-NH ;
i) -L1-CO-alkenylene-CNH-NH ;
j) -L1-CO-arylene-CNH-NH ;
k) -L1-CONH-alkylene-CNH-NH ;
l) -L1-CONH-arylene-CNH-NH ;
m) -L1-SO -alkylene-CNH-NH ;
n) -L1-SO -arylene-CNH-NH ;
o) -O-alkylene-N(R ) ;
p) -N(R )-alkylene-N(R ) ;
q) -L1-N(R ) ;
r) -L1-alkylene-N(R ) ;
s) -L1-arylene-N(R ) ;
t) -L1-CO-alkylene-N(R ) ;
u) -L1-CO-alkenylene-N(R ) ;
v) -L1-CO-arylene-N(R ) ;
w) -L1-CONH-alkylene-N(R ) ;
x) -L1-CONH-arylene-N(R ) ;
y) -L1-SO -alkylene-N(R ) ;
z) -O-alkylene-N(R ) ;
aa) -N(R )-alkylene-N(R ) ;
bb) -L1-N(R ) ;
cc) -L1-alkylene-N(R ) ;
dd) -L1-arylene-N(R ) ;
ee) -L1-CO-alkylene-N(R ) ;
ff) -L1-CO-alkenylene-N(R ) ;
gg) -L1-CO-arylene-N(R ) ;
hh) -L1-CONH-alkylene-N(R ) ;
ii) -L1-CONH-arylene-N(R ) ;
jj) -L1-SO -alkylene-N(R ) ;
kk) -O-alkylene-heterocyclyl;
ll) -N(R )-alkylene-heterocyclyl;
mm) -L1-alkylene-heterocyclyl;
nn) -L1-arylene-heterocyclyl;
oo) -L1-CO-alkylene-heterocyclyl;
pp) -L1-CO-alkenylene-heterocyclyl;
qq) -L1-CO-arylene-heterocyclyl;
rr) -L1-CONH-alkylene-heterocyclyl;
ss) -L1-CONH-arylene-heterocyclyl;
tt) -L1-SO -alkylene-heterocyclyl;
uu) -O-alkylene-N(O)(R ) ;
vv) -N(R )-alkylene- N(O)(R ) ;
ww) -L1- N(O)(R ) ;
xx) -L1-alkylene- N(O)(R ) ;
yy) -L1-arylene- N(O)(R ) ;
zz) -L1-CO-alkylene- N(O)(R ) ;
aaa) -L1-CO-alkenylene- N(O)(R ) ;
bbb) -L1-CO-arylene- N(O)(R ) ;
ccc) -L1-CONH-alkylene- N(O)(R ) ;
ddd) -L1-CONH-arylene- N(O)(R ) ;
eee) -L1-SO -alkylene- N(O)(R ) ;
fff) -O-alkylene-NH-CNH-NH ;
ggg) -N(R )-alkylene-NH-CNH-NH ;
hhh) -L1-NH-CNH-NH ;
iii) -L1-alkylene-NH-CNH-NH ;
jjj) -L1-arylene-NH-CNH-NH ;
kkk) -L1-CO-alkylene-NH-CNH-NH ;
lll) -L1-CO-alkenylene-NH-CNH-NH ;
mmm) -L1-CO-arylene-NH-CNH-NH ;
nnn) -L1-CONH-alkylene-NH-CNH-NH ;
ooo) -L1-CONH-arylene-NH-CNH-NH ;
ppp) -L1-SO -alkylene-NH-CNH-NH ;
qqq) -L1-SO -arylene-NH-CNH-NH ; and
rrr) a protected form of any of the above X3 groups;
with the provision that if X1 is present as N(CH ) and X7 is present as
3 2,
piperidinyl, then X3 is not or
X4 is selected from:
a) -O-alkylene-aryl;
b) -N(R )-aryl;
c) -N(R )-alkylene-aryl;
d) -L1-CO-alkylene-aryl;
e) -L1-CO-alkenylene-aryl;
f) -L1-CO-arylene-aryl;
g) -L1-CONH-alkylene-aryl;
h) -L1-CONH-arylene-aryl;
i) -L1-SO -alkylene-aryl;
j) -L1-SO -arylene-aryl;
k) -L1-alkylene-aryl;
l) -L1-arylene-aryl;
m) -N(R )-alkylene-N(R )-aryl;
n) -N(R )-alkylene-N(R )CO-aryl;
o) -N(R )-alkylene-N(R )SO -aryl;
p) -N(R )-alkylene-N(R )CH -aryl;
q) –L1-aryl;
r) -L1-CO-aryl;
s) -L1-SO -aryl;
t) -L1-alkylene-P(aryl) ;
u) -L1-CO-alkylene-P(aryl) ;
v) -L1-SO -alkylene-P(aryl) ; and
w) a protected form of any of the above X4 groups;
X5 is selected from:
a) -O-alkylene-heteroaryl;
b) -N(R )-alkylene-heteroaryl;
c) -L1-CO-alkylene-heteroaryl;
d) -L1-CO-alkenylene-heteroaryl;
e) -L1-CO-arylene-heteroaryl;
f) -L1-CONH-alkylene-heteroaryl;
g) -L1-CONH-arylene-heteroaryl;
h) -L1-SO -alkylene-heteroaryl;
i) -L1-SO -arylene-heteroaryl;
j) -L1-alkylene-heteroaryl;
k) -L1-arylene-heteroaryl;
l) -N(R )-alkylene-N(R )-hereroaryl;
m) -N(R )-alkylene-N(R )CO-hereroaryl;
n) -N(R )-alkylene-N(R )SO -hereroaryl;
o) -N(R )-alkylene-N(R )CH -hereroaryl;
p) -L1-heteroaryl; and
q) a protected form of any of the above X5 groups;
X6 is selected from:
a) -O-alkylene-(OCH CH ) OH;
2 2 m
b) -O-alkylene-(OCH CH ) OCH ;
2 2 m 3
c) -N(R )-alkylene-(OCH CH ) OH;
2 2 m
d) -N(R )-alkylene-(OCH CH ) OCH ;
2 2 m 3
e) -N(R )-arylene-(OCH CH ) OH;
2 2 m
f) -N(R )-arylene-(OCH CH ) OCH ;
2 2 m 3
g) -L1-alkylene-(OCH CH ) OH;
2 2 m
h) -L1-CO-alkylene-(OCH CH ) OH;
2 2 m
i) -L1-CO-alkylene-(OCH CH ) OCH ;
2 2 m 3
j) -L1-SO -alkylene-(OCH CH ) OH;
2 2 2 m
k) -L1-SO -alkylene-(OCH CH ) OCH ;
2 2 2 m 3
l) -L1-CO-arylene-(OCH CH ) OH;
2 2 m
m) -L1-CO-arylene-(OCH CH ) OCH ;
2 2 m 3
n) -L1-SO -arylene-(OCH CH ) OH;
2 2 2 m
o) -L1-SO -arylene-(OCH CH ) OCH ;
2 2 2 m 3
p) -L1-CO-(OCH CH ) OH;
2 2 m
q) -L1-CO-(OCH CH ) OCH ;
2 2 m 3
r) -N(R )-(dibenzocrown-6);
s) an aza-crown ether; and
t) a protected form of any of the above X6 groups;
X7 is selected from:
a) -heterocyclyl;
b) -N(R )(R )
c) -L1-hydrogen;
d) -L1-alkyl;
e) -L1-CO-alkyl;
f) -L1-CONH-alkyl;
g) -L1-CON(alkyl)-alkyl;
h) -L1-SO -alkyl;and
i) a protected form of any of the above X7 groups;
with the provision that if X1 is present as N(CH ) , and X3 is present
O NH
as or , then X7 is not
piperdinyl;
X8 is selected from:
a) -L1-CA;
b) -L1-dCA;
c) -L1-COCH (R )
d) -L1-COCH(R )NHCO -alkyl;
5 10
e) -OR , wherein R and R together form a ring;
f) a protected form of any of the above X8 groups;
each R is independently hydrogen, alkyl, or a cell-penetrating peptide;
each R is independently C -C alkyl or optionally when two R are C -C
1 12 1 12
alkyl, two R are joined to form a heterocyclic ring;
each R is independently C -C alkyl, alkenyl, or alkynyl;
2 18
each R is independently hydrogen, alkyl, hydroxyalkyl, sulfhydrylalkyl, or
arylalkyl;
each R is independently C -C alkyl;
1 12
each R is independently hydrogen or C -C alkyl;
1 12
L1 is selected from:
NN N O
q q q
a) ; b) ; c) ;
d) ; e) ;
1 4 1 5 2
Q L L Q
f) , and
g) ;
wherein
1 2 6
each Q and Q are each selected from a bond, -O- or -N(R )-;
each E is independently selected from optionally substituted aryl or
optionally substituted heteroaryl;
each E is independently an optionally substituted nitrogen containing
heteroaryl;
each L and L are each independently a bond, optionally substituted C -
C alkyl, or optionally substituted heteroalkyl; and
m, p, q, s, and t are each independently 1-4;
wherein if the X group proximal to the 3' terminus is:
, , , ,
or , then at least one other X group is not X1, and
wherein the compound is not of the formula:
Also described is a method of inhibiting production of a protein, the
method comprising exposing a nucleic acid encoding the protein to an oligomer of the
present disclosure.
Also described is a method of treating a disease in a subject, the method
comprising administering a therapeutically effective amount of an oligomer. Methods
of making the oligomers and methods for their use are also described.
These and other aspects of the invention will be apparent upon reference
to the following detailed description. To this end, various references are set forth herein
which describe in more detail certain background information, procedures, compounds
and/or compositions, and are each hereby incorporated by reference in their entirety.
INCORPORATION BY REFERENCE
All publications, patents, and patent applications mentioned in this
specification are herein incorporated by reference to the same extent as if each
individual publication, patent, or patent application was specifically and individually
indicated to be incorporated by reference.
BRIEF DESCRIPTION OF THE DRAWINGS
The novel features of the invention are set forth with particularity in the
appended claims. A better understanding of the features and advantages of the present
invention will be obtained by reference to the following detailed description that sets
forth illustrative embodiments, in which the principles of the invention are utilized, and
the accompanying drawings of which:
Figure 1 illustrates preparation of a linker for solid-phase synthesis;
Figure 2 illustrates preparation of a solid support for oligomer synthesis;
Figure 3 illustrates solid phase synthesis of oligomers; and
Figure 4 illustrates cleavage of oligomer from solid support.
DETAILED DESCRIPTION OF THE INVENTION
Definitions
In the following description, certain specific details are set forth in order
to provide a thorough understanding of various embodiments. However, one skilled in
the art will understand that the invention may be practiced without these details. In
other instances, well-known structures have not been shown or described in detail to
avoid unnecessarily obscuring descriptions of the embodiments. Unless the context
requires otherwise, throughout the specification and claims which follow, the word
“comprise” and variations thereof, such as, “comprises” and “comprising” are to be
construed in an open, inclusive sense, that is, as “including, but not limited to.”
Further, headings provided herein are for convenience only and do not interpret the
scope or meaning of the claimed invention.
Reference throughout this specification to “one embodiment” or “an
embodiment” means that a particular feature, structure or characteristic described in
connection with the embodiment is included in at least one embodiment. Thus, the
appearances of the phrases “in one embodiment” or “in an embodiment” in various
places throughout this specification are not necessarily all referring to the same
embodiment. Furthermore, the particular features, structures, or characteristics may be
combined in any suitable manner in one or more embodiments. Also, as used in this
specification and the appended claims, the singular forms “a,” “an,” and “the” include
plural referents unless the content clearly dictates otherwise. It should also be noted
that the term “or” is generally employed in its sense including “and/or” unless the
content clearly dictates otherwise.
The terms below, as used herein, have the following meanings, unless
indicated otherwise:
“Amino” refers to the -NH radical.
“Cyano” or “nitrile” refers to the -CN radical.
“Hydroxy” or “hydroxyl” refers to the -OH radical.
“Imino” refers to the =NH substituent.
“Guanidinyl” refers to the –NHC(=NH)NH substituent.
“Amidinyl” refers to the –C(=NH)NH substituent.
“Nitro” refers to the -NO radical.
“Oxo” refers to the =O substituent.
“Thioxo” refers to the =S substituent.
“Cholate” or “CA” refers to the following structure:
HO OH
“Deoxycholate” or “dCA” refers to the following structure:
“Alkyl” refers to a straight or branched hydrocarbon chain radical which
is saturated or unsaturated (i.e., contains one or more double and/or triple bonds),
having from one to thirty carbon atoms, and which is attached to the rest of the
molecule by a single bond. Alkyls comprising any number of carbon atoms from 1 to
are included. An alkyl comprising up to 30 carbon atoms is refered to as a C -C
1 30
alkyl, likewise, for example, an alkyl comprising up to 12 carbon atoms is a C -C
1 12
alkyl. Alkyls (and other moieties defined herein) comprising other numbers of carbon
atoms are represented similarily. Alkyl groups include, but are not limited to, C -C
1 30
alkyl, C -C alkyl, C -C alkyl, C -C alkyl, C -C alkyl, C -C alkyl, C -C alkyl, C -
1 20 1 15 1 10 1 8 1 6 1 4 1
C alkyl, C -C alkyl, C -C alkyl, C -C alkyl and C -C alkyl. Representative alkyl
3 1 2 2 8 3 8 4 8
groups include, but are not limited to, methyl, ethyl, n-propyl, 1-methylethyl
(iso-propyl), n-butyl, i-butyl, s-butyl, n-pentyl, 1,1-dimethylethyl (t-butyl),
3-methylhexyl, 2-methylhexyl, ethenyl, propenyl, butenyl, pentenyl,
penta-1,4-dienyl, ethynyl, propynyl, butynyl, butynyl, pentynyl, hexynyl, and the
like. Unless stated otherwise specifically in the specification, an alkyl group may be
optionally substituted as described below.
“Alkylene” or “alkylene chain” refers to a straight or branched divalent
hydrocarbon chain linking the rest of the molecule to a radical group. Alkylenes may
be saturated or unsaturated (i.e., contains one or more double and/or triple bonds).
Representative alkylenes include, but are not limited to, C -C alkylene, C -C
1 12 1 8
alkylene, C -C alkylene, C -C alkylene, C -C alkylene, C -C alkylene, C alkylene.
1 6 1 4 1 3 1 2 1
Representative alkylene groups include, but are not limited to, methylene, ethylene,
propylene, n-butylene, ethenylene, propenylene, n-butenylene, propynylene,
n-butynylene, and the like. The alkylene chain is attached to the rest of the molecule
through a single or double bond and to the radical group through a single or double
bond. The points of attachment of the alkylene chain to the rest of the molecule and to
the radical group can be through one carbon or any two carbons within the chain.
Unless stated otherwise specifically in the specification, an alkylene chain may be
optionally substituted as described below.
“Alkoxy” refers to a radical of the formula -OR where R is an alkyl
radical as defined. Unless stated otherwise specifically in the specification, an alkoxy
group may be optionally substituted as described below.
“Alkoxyalkyl” refers to a radical of the formula -R OR where R is an
b a a
alkyl radical as defined and where R is an alkylene radical as defined. Unless stated
otherwise specifically in the specification, an alkoxyalkyl group may be optionally
substituted as described below.
“Alkoxyalkylcarbonyl” refers to a radical of the formula –C(=O)R OR
where R is an alkyl radical as defined and where R is an alkylene radical as defined.
Unless stated otherwise specifically in the specification, an alkoxyalkylcarbonyl group
may be optionally substituted as described below.
“Alkylcarbonyl” refers to a radical of the formula –C(=O)R where R is
an alkyl radical as defined above. Unless stated otherwise specifically in the
specification, an alkylcarbonyl group may be optionally substituted as described below.
“Alkyloxycarbonyl” refers to a radical of the formula –C(=O)OR where
R is an alkyl radical as defined. Unless stated otherwise specifically in the
specification, an alkyloxycarbonyl group may be optionally substituted as described
below. Representative alkyloxycarbonyl groups include, but are not limited to –
C(=O)OCH CHOH, –C(=O)OCH CH OCH CHOH, –
2 2 2 2 2 2
C(=O)OCH CH OCH CH OCH CHOH, -C(=O)OCH CH OCH, –
2 2 2 2 2 2 2 2 3
C(=O)OCH CH OCH CH OCH , or –C(=O)OCH CH OCH CH OCH CH OCH .
2 2 2 2 3 2 2 2 2 2 2 3
“Heteroalkylene” refers to an alkylene radical as described above where
one or more carbon atoms of the alkylene is replaced with a O, N or S atom. Unless
stated otherwise specifically in the specification, the heteroalkylene group may be
optionally substituted as described below. Representative heteroalkylene groups
include, but are not limited to -OCH CHO-, –OCH CH OCH CHO-, or –
2 2 2 2 2 2
OCH CH OCH CH OCH CH O-.
2 2 2 2 2 2
“Alkylamino” refers to a radical of the formula -NHR or -NR R where
a a a
each R is, independently, an alkyl radical as defined above. Unless stated otherwise
specifically in the specification, an alkylamino group may be optionally substituted as
described below.
“Amidyl” refers to a radical of the formula –N(H)C(=O)-R where R is
an alkyl or aryl radical as defined herein. Unless stated otherwise specifically in the
specification, an amidyl group may be optionally substituted as described below.
“Amidinylalkyl” refers a radical of the formula -R -C(=NH)NH where
R is an alkylene radical as defined above. Unless stated otherwise specifically in the
specification, an amidinylalkyl group may be optionally substituted as described below.
“Amidinylalkylcarbonyl” refers a radical of the formula –
C(=O)R -C(=NH)NH where R is an alkylene radical as defined above. Unless stated
b 2 b
otherwise specifically in the specification, an amidinylalkylcarbonyl group may be
optionally substituted as described below.
“Aminoalkyl” refers to a radical of the formula -R -NR R where R is
b a a b
an alkylene radical as defined above, and each R is independently a hydrogen or an
alkyl radical.
“Thioalkyl” refers to a radical of the formula -SR where R is an alkyl
radical as defined above. Unless stated otherwise specifically in the specification, a
thioalkyl group may be optionally substituted.
“Aryl” refers to a radical derived from a hydrocarbon ring system
comprising hydrogen, 6 to 30 carbon atoms and at least one aromatic ring. The aryl
radical may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may
include fused or bridged ring systems. Aryl radicals include, but are not limited to, aryl
radicals derived from the hydrocarbon ring systems of aceanthrylene, acenaphthylene,
acephenanthrylene, anthracene, azulene, benzene, chrysene, fluoranthene, fluorene, as-
indacene, s-indacene, indane, indene, naphthalene, phenalene, phenanthrene, pleiadene,
pyrene, and triphenylene. Unless stated otherwise specifically in the specification, the
term “aryl” or the prefix “ar-“ (such as in “aralkyl”) is meant to include aryl radicals
that are optionally substituted.
“Aralkyl” refers to a radical of the formula -R -R where R is an
b c b
alkylene chain as defined above and R is one or more aryl radicals as defined above.
Examples of aralkyl include, but are not limited to, benzyl, diphenylmethyl, trityl and
the like. Unless stated otherwise specifically in the specification, an aralkyl group may
be optionally substituted.
“Arylcarbonyl” refers to a radical of the formula -C(=O)R where R is
one or more aryl radicals as defined above, for example, phenyl. Unless stated
otherwise specifically in the specification, an arylcarbonyl group may be optionally
substituted.
“Aryloxycarbonyl” refers to a radical of the formula -C(=O)OR where
R is one or more aryl radicals as defined above, for example, phenyl. Unless stated
otherwise specifically in the specification, an aryloxycarbonyl group may be optionally
substituted.
“Aralkylcarbonyl” refers to a radical of the formula -C(=O)R -R where
R is an alkylene chain as defined above and R is one or more aryl radicals as defined
above, for example, phenyl. Unless stated otherwise specifically in the specification, an
aralkylcarbonyl group may be optionally substituted.
“Aralkyloxycarbonyl” refers to a radical of the formula -C(=O)OR -R
where R is an alkylene chain as defined above and R is one or more aryl radicals as
defined above, for example, phenyl. Unless stated otherwise specifically in the
specification, an aralkyloxycarbonyl group may be optionally substituted.
“Aryloxy” refers to a radical of the formula -OR where R is one or
more aryl radicals as defined above, for example, phenyl. Unless stated otherwise
specifically in the specification, an arylcarbonyl group may be optionally substituted.
“Cycloalkyl” refers to a stable, non-aromatic, monocyclic or polycyclic
carbocyclic ring, which may include fused or bridged ring systems, which is saturated or
unsaturated, and attached to the rest of the molecule by a single bond. Representative
cycloalkyls include, but are not limited to, cycloaklyls having from three to fifteen
carbon atoms, from three to ten carbon atoms, from three to eight carbon atoms, from
three to six carbon atoms, from three to five carbon atoms, or three to four carbon
atoms. Monocyclic cyclcoalkyl radicals include, for example, cyclopropyl, cyclobutyl,
cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl. Polycyclic radicals include, for
example, adamantyl, norbornyl, decalinyl, and 7,7-dimethyl-bicyclo[2.2.1]heptanyl.
Unless otherwise stated specifically in the specification, a cycloalkyl group may be
optionally substituted.
“Cycloalkylalkyl” refers to a radical of the formula -R R where R is an
b d b
alkylene chain as defined above and R is a cycloalkyl radical as defined above. Unless
stated otherwise specifically in the specification, a cycloalkylalkyl group may be
optionally substituted.
“Cycloalkylcarbonyl” refers to a radical of the formula –C(=O)R where
R is a cycloalkyl radical as defined above. Unless stated otherwise specifically in the
specification, a cycloalkylcarbonyl group may be optionally substituted.
Cycloalkyloxycarbonyl” refers to a radical of the formula –C(=O)OR
where R is a cycloalkyl radical as defined above. Unless stated otherwise specifically
in the specification, a cycloalkyloxycarbonyl group may be optionally substituted.
“Fused” refers to any ring structure described herein which is fused to an
existing ring structure. When the fused ring is a heterocyclyl ring or a heteroaryl ring,
any carbon atom on the existing ring structure which becomes part of the fused
heterocyclyl ring or the fused heteroaryl ring may be replaced with a nitrogen atom.
“Guanidinylalkyl” refers a radical of the formula -R -NHC(=NH)NH
where R is an alkylene radical as defined above. Unless stated otherwise specifically
in the specification, a guanidinylalkyl group may be optionally substituted as described
below.
“Guanidinylalkylcarbonyl” refers a radical of the formula
-C(=O)R -NHC(=NH)NH where R is an alkylene radical as defined above. Unless
b 2 b
stated otherwise specifically in the specification, a guanidinylalkylcarbonyl group may
be optionally substituted as described below.
“Halo” or “halogen” refers to bromo, chloro, fluoro or iodo.
“Haloalkyl” refers to an alkyl radical, as defined above, that is
substituted by one or more halo radicals, as defined above, e.g., trifluoromethyl,
difluoromethyl, fluoromethyl, trichloromethyl, 2,2,2-trifluoroethyl, 1,2-difluoroethyl,
3-bromofluoropropyl, 1,2-dibromoethyl, and the like. Unless stated otherwise
specifically in the specification, a haloalkyl group may be optionally substituted.
“Perhalo” or “perfluoro” refers to a moiety in which each hydrogen atom
has been replaced by a halo atom or fluorine atom, respectively.
“Heterocyclyl” or “heterocyclic ring” refers to a stable 3- to
24-membered non-aromatic ring radical comprising 2 to 23 carbon atoms and from one
to 8 heteroatoms selected from the group consisting of nitrogen, oxygen, phosphorous
and sulfur. Unless stated otherwise specifically in the specification, the heterocyclyl
radical may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may
include fused or bridged ring systems; and the nitrogen, carbon or sulfur atoms in the
heterocyclyl radical may be optionally oxidized; the nitrogen atom may be optionally
quaternized; and the heterocyclyl radical may be partially or fully saturated. Examples
of such heterocyclyl radicals include, but are not limited to, dioxolanyl,
thienyl[1,3]dithianyl, decahydroisoquinolyl, imidazolinyl, imidazolidinyl,
isothiazolidinyl, isoxazolidinyl, morpholinyl, octahydroindolyl, octahydroisoindolyl,
2-oxopiperazinyl, 2-oxopiperidinyl, 2-oxopyrrolidinyl, oxazolidinyl, piperidinyl,
piperazinyl, 4-piperidonyl, pyrrolidinyl, pyrazolidinyl, quinuclidinyl, thiazolidinyl,
tetrahydrofuryl, trithianyl, tetrahydropyranyl, thiomorpholinyl, thiamorpholinyl,
1-oxo-thiomorpholinyl, 1,1-dioxo-thiomorpholinyl, 12-crown-4, 15-crown-5, 18-
crown-6, 21-crown-7, azacrown-6, diazacrown-6, azacrown-7, and diaza-
21-crown-7. Unless stated otherwise specifically in the specification, a heterocyclyl
group may be optionally substituted.
“Heteroaryl” refers to a 5- to 14-membered ring system radical
comprising hydrogen atoms, one to thirteen carbon atoms, one to six heteroatoms
selected from the group consisting of nitrogen, oxygen, phosphorous and sulfur, and at
least one aromatic ring. For purposes of this invention, the heteroaryl radical may be a
monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or
bridged ring systems; and the nitrogen, carbon or sulfur atoms in the heteroaryl radical
may be optionally oxidized; the nitrogen atom may be optionally quaternized.
Examples include, but are not limited to, azepinyl, acridinyl, benzimidazolyl,
benzothiazolyl, benzindolyl, benzodioxolyl, benzofuranyl, benzooxazolyl,
benzothiazolyl, benzothiadiazolyl, benzo[b][1,4]dioxepinyl, 1,4-benzodioxanyl,
benzonaphthofuranyl, benzoxazolyl, benzodioxolyl, benzodioxinyl, benzopyranyl,
benzopyranonyl, benzofuranyl, benzofuranonyl, benzothienyl (benzothiophenyl),
benzotriazolyl, benzo[4,6]imidazo[1,2-a]pyridinyl, carbazolyl, cinnolinyl,
dibenzofuranyl, dibenzothiophenyl, furanyl, furanonyl, isothiazolyl, imidazolyl,
indazolyl, indolyl, indazolyl, isoindolyl, indolinyl, isoindolinyl, isoquinolyl, indolizinyl,
isoxazolyl, naphthyridinyl, oxadiazolyl, 2-oxoazepinyl, oxazolyl, oxiranyl, 1-
oxidopyridinyl, 1-oxidopyrimidinyl, 1-oxidopyrazinyl, 1-oxidopyridazinyl,
1-phenyl-1H-pyrrolyl, phenazinyl, phenothiazinyl, phenoxazinyl, phthalazinyl,
pteridinyl, purinyl, pyrrolyl, pyrazolyl, pyridinyl, pyrazinyl, pyrimidinyl, pyridazinyl,
quinazolinyl, quinoxalinyl, quinolinyl, quinuclidinyl, isoquinolinyl,
tetrahydroquinolinyl, thiazolyl, thiadiazolyl, triazolyl, tetrazolyl, triazinyl, and
thiophenyl (i.e., thienyl). Unless stated otherwise specifically in the specification, a
heteroaryl group may be optionally substituted.
All the above groups may be either substituted or unsubstituted. The
term “substituted” as used herein means any of the above groups (i.e., alkyl, alkylene,
alkoxy, alkoxyalkyl, alkylcarbonyl, alkyloxycarbonyl,alkylamino, amidyl,
amidinylalkyl, amidinylalkylcarbonyl, aminoalkyl, aryl, aralkyl, arylcarbonyl,
aryloxycarbonyl, aralkylcarbonyl, aralkyloxycarbonyl, aryloxy, cycloalkyl,
cycloalkylalkyl, cycloalkylcarbonyl, cycloalkylalkylcarbonyl, cycloalkyloxycarbonyl,
guanidinylalkyl, guanidinylalkylcarbonyl, haloalkyl, heterocyclyl and/or heteroaryl),
may be further functionalized wherein at least one hydrogen atom is replaced by a bond
to a non-hydrogen atom substituent. Unless stated specifically in the specification, a
substituted group may include one or more substituents selected from: oxo, -CO H,
nitrile, nitro, hydroxyl, thiooxy, alkyl, alkylene, alkoxy, alkoxyalkyl, alkylcarbonyl,
alkyloxycarbonyl, aryl, aralkyl, arylcarbonyl, aryloxycarbonyl, aralkylcarbonyl,
aralkyloxycarbonyl, aryloxy, cycloalkyl, cycloalkylalkyl, cycloalkylcarbonyl,
cycloalkylalkylcarbonyl, cycloalkyloxycarbonyl, heterocyclyl, heteroaryl,
dialkylamines, arylamines, alkylarylamines, diarylamines, trialkylammonium (-N R ),
N-oxides, imides, and enamines; a silicon atom in groups such as trialkylsilyl groups,
dialkylarylsilyl groups, alkyldiarylsilyl groups, triarylsilyl groups, perfluoroalkyl or
perfluoroalkoxy, for example, trifluoromethyl or trifluoromethoxy. “Substituted” also
means any of the above groups in which one or more hydrogen atoms are replaced by a
higher-order bond (e.g., a double- or triple-bond) to a heteroatom such as oxygen in
oxo, carbonyl, carboxyl, and ester groups; and nitrogen in groups such as imines,
oximes, hydrazones, and nitriles. For example, “substituted” includes any of the above
groups in which one or more hydrogen atoms are replaced with -NR C(=O)NR R ,
g g h
-NR C(=O)OR , -NR SO R , -OC(=O)NR R , -OR , -SR , -SOR , -SO R , -OSO R ,
g h g 2 h g h g g g 2 g 2 g
-SO OR , =NSO R , and -SO NR R . “Substituted” also means any of the above
2 g 2 g 2 g h
groups in which one or more hydrogen atoms are replaced with -C(=O)R , -C(=O)OR ,
-CH SO R , -CH SO NR R , -SH, -SR or -SSR . In the foregoing, R and R are the
2 2 g 2 2 g h g g g h
same or different and independently hydrogen, alkyl, alkoxy, alkylamino, thioalkyl,
aryl, aralkyl, cycloalkyl, cycloalkylalkyl, haloalkyl, heterocyclyl, N-heterocyclyl,
heterocyclylalkyl, heteroaryl, N-heteroaryl and/or heteroarylalkyl. In addition, each of
the foregoing substituents may also be optionally substituted with one or more of the
above substituents. Furthermore, any of the above groups may be substituted to include
one or more internal oxygen or sulfur atoms. For example, an alkyl group may be
substituted with one or more internal oxygen atoms to form an ether or polyether group.
Similarily, an alkyl group may be substituted with one or more internal sulfur atoms to
form a thioether, disulfide, etc. Amidyl moieties may be substituted with up to 2 halo
atoms, while other groups above may be substituted with one or more halo atoms. With
the exception of alkyl groups, all other groups may also be substituted with amino or
monoalklyamino. With the exception of alkyl and alkylcarbonyl groups, all other
groups may also be substituted with guanidinyl or amidynyl. Optional substitutents for
any of the above groups also include arylphosphoryl, for example -R P(Ar) wherein Ra
is an alkylene and Ar is aryl moiety, for example phenyl.
The terms “antisense oligomer” or “antisense compound” are used
interchangeably and refer to a sequence of subunits, each having a base carried on a
backbone subunit composed of ribose or other pentose sugar or morpholino group, and
where the backbone groups are linked by intersubunit linkages that allow the bases in
the compound to hybridize to a target sequence in a nucleic acid (typically an RNA) by
Watson-Crick base pairing, to form a nucleic acid:oligomer heteroduplex within the
target sequence. The oligomer may have exact sequence complementarity to the target
sequence or near complementarity. Such antisense oligomers are designed to block or
inhibit translation of the mRNA containing the target sequence, and may be said to be
“directed to” a sequence with which it hybridizes.
A “morpholino oligomer” or “PMO” refers to a polymeric molecule
having a backbone which supports bases capable of hydrogen bonding to typical
polynucleotides, wherein the polymer lacks a pentose sugar backbone moiety, and more
specifically a ribose backbone linked by phosphodiester bonds which is typical of
nucleotides and nucleosides, but instead contains a ring nitrogen with coupling through
the ring nitrogen. An exemplary”morpholino” oligomer comprises morpholino subunit
structures linked together by (thio)phosphoramidate or (thio)phosphorodiamidate
linkages, joining the morpholino nitrogen of one subunit to the 5' exocyclic carbon of
an adjacent subunit, each subunit comprising a purine or pyrimidine base-pairing
moiety effective to bind, by base-specific hydrogen bonding, to a base in a
polynucleotide. Morpholino oligomers (including antisense oligomers) are detailed, for
example, in U.S. Pat. Nos. 5,698,685; 5,217,866; 5,142,047; 5,034,506; 5,166,315;
,185,444; 5,521,063; 5,506,337 and pending US patent applications 12/271,036;
12/271,040; and PCT publication number WO/2009/064471 all of which are
incorporated herein by reference in their entirety.
“PMO+” refers to phosphorodiamidate morpholino oligomers comprising
any number of (1-piperazino)phosphinylideneoxy, (1-(4-(w-guanidino-alkanoyl))-
piperazino)phosphinylideneoxy linkages that have been described previously (see e.g.,
PCT publication WO/2008/036127 which is incorporated herein by reference in its
entirety.
“PMO-X”refers to phosphorodiamidate morpholino oligomers disclosed
herein.
A “phosphoramidate” group comprises phosphorus having three attached
oxygen atoms and one attached nitrogen atom, while a “phosphorodiamidate” group
comprises phosphorus having two attached oxygen atoms and two attached nitrogen
atoms.
“Thiophosphoramidate” or “thiophosphorodiamidate” linkages are
phosphoramidate or phosphorodiamidate linkages, respectively, wherein one oxygen
atom, typically the oxygen pendant to the backbone, is replaced with sulfur.
“Intersubunit linkage” refers to the linkage connecting two morpholino
subunits.
“Charged”, “uncharged”, “cationic” and “anionic” as used herein refer to
the predominant state of a chemical moiety at near-neutral pH, e.g., about 6 to 8. For
example, the term may refer to the predominant state of the chemical moiety at
physiological pH, that is, about 7.4.
“Lower alkyl” refers to an alkyl radical of one to six carbon atoms, as
exemplified by methyl, ethyl, n-butyl, i-butyl, t-butyl, isoamyl, n-pentyl, and isopentyl.
In certain embodiments, a “lower alkyl” group has one to four carbon atoms. In other
embodiments a “lower alkyl” group has one to two carbon atoms; i.e. methyl or ethyl.
Analogously, “lower alkenyl” refers to an alkenyl radical of two to six, preferably three
or four, carbon atoms, as exemplified by allyl and butenyl.
A “non-interfering” substituent is one that does not adversely affect the
ability of an antisense oligomer as described herein to bind to its intended target. Such
substituents include small and/or relatively non-polar groups such as methyl, ethyl,
methoxy, ethoxy, or fluoro.
An oligonucleotide or antisense oligomer “specifically hybridizes” to a
target polynucleotide if the oligomer hybridizes to the target under physiological
conditions, with a Tm greater than 37 °C, greater than 45 C, preferably at least 50 C,
and typically 60 C-80 C or higher. The “Tm” of an oligomer is the temperature at
which 50% hybridizes to a complementary polynucleotide. Tm is determined under
standard conditions in physiological saline, as described, for example, in Miyada et al.,
Methods Enzymol. 154:94-107 (1987). Such hybridization may occur with “near” or
“substantial” complementary of the antisense oligomer to the target sequence, as well as
with exact complementarity.
Polynucleotides are described as “complementary” to one another when
hybridization occurs in an antiparallel configuration between two single-stranded
polynucleotides. Complementarity (the degree that one polynucleotide is
complementary with another) is quantifiable in terms of the proportion of bases in
opposing strands that are expected to form hydrogen bonds with each other, according
to generally accepted base-pairing rules.
A first sequence is an “antisense sequence” with respect to a second
sequence if a polynucleotide whose sequence is the first sequence specifically binds to,
or specifically hybridizes with, the second polynucleotide sequence under physiological
conditions.
The term “targeting sequence” is the sequence in the oligonucleotide
analog that is complementary (meaning, in addition, substantially complementary) to
the target sequence in the RNA genome. The entire sequence, or only a portion, of the
analog compound may be complementary to the target sequence. For example, in an
analog having 20 bases, only 12-14 may be targeting sequences. Typically, the
targeting sequence is formed of contiguous bases in the analog, but may alternatively be
formed of non-contiguous sequences that when placed together, e.g., from opposite
ends of the analog, constitute sequence that spans the target sequence.
Target and targeting sequences are described as “complementary” to one
another when hybridization occurs in an antiparallel configuration. A targeting
sequence may have “near” or “substantial” complementarity to the target sequence and
still function for the purpose of the presently described methods, that is, still be
“complementary.” Preferably, the oligonucleotide analog compounds employed in the
presently described methods have at most one mismatch with the target sequence out of
nucleotides, and preferably at most one mismatch out of 20. Alternatively, the
antisense oligomers employed have at least 90% sequence homology, and preferably at
least 95% sequence homology, with the exemplary targeting sequences as designated
herein. For purposes of complementary binding to an RNA target, and as discussed
below, a guanine base may be complementary to either a cytosineor uracil RNA base.
A “heteroduplex” refers to a duplex between an oligonculeotide analog
and the complementary portion of a target RNA. A “nuclease-resistant heteroduplex”
refers to a heteroduplex formed by the binding of an antisense oligomer to its
complementary target, such that the heteroduplex is substantially resistant to in vivo
degradation by intracellular and extracellular nucleases, such as RNAse H, which are
capable of cutting double-stranded RNA/RNA or RNA/DNA complexes.
An agent is “actively taken up by mammalian cells” when the agent can
enter the cell by a mechanism other than passive diffusion across the cell membrane.
The agent may be transported, for example, by “active transport”, referring to transport
of agents across a mammalian cell membrane by e.g. an ATP-dependent transport
mechanism, or by “facilitated transport”, referring to transport of antisense agents
across the cell membrane by a transport mechanism that requires binding of the agent to
a transport protein, which then facilitates passage of the bound agent across the
membrane.
The terms “modulating expression” and/or “antisense activity” refer to
the ability of an antisense oligomer to either enhance or, more typically, reduce the
expression of a given protein, by interfering with the expression or translation of RNA.
In the case of reduced protein expression, the antisense oligomer may directly block
expression of a given gene, or contribute to the accelerated breakdown of the RNA
transcribed from that gene. Morpholino oligomers as described herein are believed to
act via the former (steric blocking) mechanism. Preferred antisense targets for steric
blocking oligomers include the ATG start codon region, splice sites, regions closely
adjacent to splice sites, and 5'-untranslated region of mRNA, although other regions
have been successfully targeted using morpholino oligomers.
An “amino acid subunit” is preferably an a-amino acid residue (–CO-
CHR-NH-); it may also be a b- or other amino acid residue (e.g. -CO-CH CHR-NH-),
where R is an amino acid side chain.
The term “naturally occurring amino acid” refers to an amino acid
present in proteins found in nature. The term “non-natural amino acids” refers to those
amino acids not present in proteins found in nature; examples include beta-alanine ( β-
Ala) and 6-aminohexanoic acid (Ahx).
An “effective amount” or “therapeutically effective amount” refers to an
amount of antisense oligomer administered to a mammalian subject, either as a single
dose or as part of a series of doses, which is effective to produce a desired therapeutic
effect, typically by inhibiting translation of a selected target nucleic acid sequence.
“Treatment” of an individual (e.g. a mammal, such as a human) or a cell
is any type of intervention used in an attempt to alter the natural course of the individual
or cell. Treatment includes, but is not limited to, administration of a pharmaceutical
composition, and may be performed either prophylactically or subsequent to the
initiation of a pathologic event or contact with an etiologic agent.
A "tautomer" refers to a proton shift from one atom of a molecule to
another atom of the same molecule. The compounds presented herein may exist as
tautomers. Tautomers are compounds that are interconvertible by migration of a
hydrogen atom, accompanied by a switch of a single bond and adjacent double bond. In
bonding arrangements where tautomerization is possible, a chemical equilibrium of the
tautomers will exist. All tautomeric forms of the compounds disclosed herein are
contemplated. The exact ratio of the tautomers depends on several factors, including
temperature, solvent, and pH. Some examples of tautomeric interconversions include:
OH O O OH
O OH
NH NH
NH NH
N NH
N N HN N
Antisense Oligomers
A. Oligomers with Modified Intersubunit Linkages
As noted above, one embodiment of the present disclosure is directed to
oligomers comprising novel intersubunit linkages. In some embodiments, the
oligomers have higher affinity for DNA and RNA than do the corresponding
unmodified oligomers and demonstrate improved cell delivery, potency, and/or tissue
distribution properties compared to oligomers having other intersubunit linkages. The
structural features and properties of the various linkage types and oligomers are
described in more detail in the following discussion.
Applicants have found that enhancement of antisense activity,
biodistribution and/or other desirable properties can be optimized by preparing
oligomers having various intersubunit linkages. In one aspect is a compound having the
structure of Formula (I):
W P X
or a salt or isomer thereof,
wherein:
n is an integer from 1 to 50;
G is halogen, OH, alkoxy, OSO (alkyl), OSO (aryl), or ;
each B is an independently selected base pair moiety;
10
each Y is independently O or NR ; optionally, R and X8e are bonded
together form a ring;
each W is independently S or O;
11 15 11 15 16 11 12 17
Z is -(L )-(R ), -(L )-(L )-(R ), or –(L )-(L )-(R ) ;
L is selected from:
23 23
23 23
O R R
23 23
P P N R N
O L O
Q Q O L
a) ; b) ; c) ;
23 23 23 23
23 23
O R R R R
23 23
O N N N
1 1 13 1
L R R R
d) R R ; e) ; f) ; g) ;
23 23
23 23
O CH O
O H O
23 23 R R 3 R R
h) O ; i) ; j) ; or
k) –C(R ) O-;
wherein L is selected from:
p p p
NN N N
a) ; b) ; c) ;
d) ; or e) ;
L is a linker cleaveable under biological conditions selected from:
a) –(C -C alkylene)-OC(O)O-CH O-;
1 10 2
b) –C(O)-(C -C alkylene)-OC(O)O-CH O-;
1 10 2
c) –C(O)-(CH=CH)-C(O)O-CH O-;
d) –(C -C alkylene)-S-S-CH CH O-; or
1 10 2 2
e) –C(O)–(C -C alkylene)-S-S-CH CH O-;
1 10 2 2
L is divalent radical selected from C -C alkylene, C -C
1 30 3 8
cycloalkylene, C -C arylene, -(C -C arylene)-(C -C alkylene)-, –(C -C alkylene)-
6 30 6 30 1 30 1 30
C(=O)-, –(C -C alkoxy)-C(=O)-, -(3-18 membered heteroalkylene)-C(=O)-, –(C -C
2 30 3 8
cycloalkylene)-C(=O)-, -(C -C cycloalkylene)-(C -C alkylene)-C(=O)-, -(C -C
3 8 1 30 1 30
alkylene) (C -C cycloalkylene)-C(=O)-, -(C -C arylene)-C(=O)-, -(C -C arylene)-
3 8 6 30 6 30
(C -C alkylene)-C(=O)-, -(C -C alkylene)-(C -C arylene)-C(=O)-, -(C -C
1 30 1 30 6 30 1 30
alkylene)-O-C(=O)-, -(C -C cycloalkylene)-O-C(=O)-, -(C -C arylene)-O-C(=O)-, -
3 8 7 30
(C -C arylene)-(C -C alkylene)-O-C(=O)-, -(C -C arylene)-(C -C alkylene)-O-
6 30 1 30 6 30 1 30
21 22
C(=O)-, -C(=O)OR , or -P(=O)(R ) ;
12 13
R is an electron pair, with the provision that if R is C -C alkyl, then
1 30
R is an electron pair, an N-oxide, or C -C alkyl;
13
each R and R is independently selected from hydrogen, a cell-
penetrating peptide, a natural or non-natural amino acid, guanidinyl, amidinyl,
heterocyclyl, C -C alkyl, C -C cycloalkyl; C -C aryl, C -C aralkyl, C -C
1 30 3 8 6 30 7 30 1 30
alkylcarbonyl, C -C cycloalkylcarbonyl, C -C cycloalkylalkylcarbonyl, C -C
3 8 3 8 6 30
arylcarbonyl, C -C aralkylcarbonyl, C -C alkyloxycarbonyl, C -C
7 30 1 30 3 8
cycloalkyloxycarbonyl, C -C aryloxycarbonyl, C -C aralkyloxycarbonyl,
7 30 8 30
21 21 22
-C(=O)OR , -C(=O)NHR , or -P(=O)(R ) ;
R is independently selected from a cell-penetrating peptide, a natural or
non-natural amino acid, guanidinyl, amidinyl, heterocyclyl, C -C alkyl, C -C
1 30 3 8
cycloalkyl; C -C aryl, C -C aralkyl, C -C alkylcarbonyl, C -C cycloalkylcarbonyl,
6 30 7 30 1 30 3 8
C -C cycloalkylalkylcarbonyl, C -C arylcarbonyl, C -C aralkylcarbonyl, C -C
3 8 6 30 7 30 2 30
alkyloxycarbonyl, C -C cycloalkyloxycarbonyl, C -C aryloxycarbonyl, C -C
3 8 7 30 8 30
21 21
aralkyloxycarbonyl, 3-18 membered alkoxyalkylcarbonyl, -SO R , -C(=O)OR ,
-P(=O)(OH) or -P(=O)(R ) ;
R is a solid support matrix suitable for solid phase synthesis of
oligonucleotides;
R is a drug, protein or toxin;
each R is independently C -C alkyl, or a 3-18 membered alkoxyalkyl
1 30
group;
each R is independently an C -C aryloxy;
6 12
23 23
each R is independently H or C –C alkyl; or optionally two R
groups join to form a 3- to 8-membered ring;
R is a C –C alkylene;
Q is independently selected from X1, X2, X3, X4, X5, X6, X7, or X8;
xeach X is independently selected from X1, X2, X3, X4, X5, X6, X7, or X8
with the provision that at least one X is not X1;
wherein
X1 is N(CH ) ;
X2 is selected from:
a) -O-alkylene-CO H;
b) -O-alkylene-CHN ;
c) -N(R )-alkylene-CO H;
d) -N(R )-alkylene-CHN ;
e) -L1-CO-alkylene-CO H;
f) -L1-CO-alkylene-CHN ;
g) -L1-CO-alkenylene-CO H;
h) -L1-CO-alkenylene-CHN ;
i) -L1-CO-arylene-CO H;
j) -L1-CO-arylene-CHN ;
k) -L1-CONH-alkylene-CO H;
l) -L1-CONH-alkylene-CHN ;
m) -L1-CONH-arylene-CO H;
n) -L1-CONH-arylene-CHN ;
o) -L1-SO -alkylene-CO H;
p) -L1-SO -alkylene-CHN ;
q) -L1-SO -arylene-CO H;
r) -L1-SO -arylene-CHN ;
s) -L1-alkylene-CO H;
t) -L1-alkylene-CHN ;
u) -L1-arylene-CO H;
v) -L1-arylene-CHN ; and
w) a protected form of any of the above X2 groups;
X3 is selected from:
a) –L1-alkyl;
b) –L1-heterocyclyl;
c) -O-alkylene-CNH-NH ;
d) -N(R )-alkylene-CNH-NH ;
e) -L1-CNH-NH ;
f) -L1-alkylene-CNH-NH ;
g) -L1-arylene-CNH-NH ;
h) -L1-CO-alkylene-CNH-NH ;
i) -L1-CO-alkenylene-CNH-NH ;
j) -L1-CO-arylene-CNH-NH ;
k) -L1-CONH-alkylene-CNH-NH ;
l) -L1-CONH-arylene-CNH-NH ;
m) -L1-SO -alkylene-CNH-NH ;
n) -L1-SO -arylene-CNH-NH ;
o) -O-alkylene-N(R ) ;
p) -N(R )-alkylene-N(R ) ;
q) -L1-N(R ) ;
r) -L1-alkylene-N(R ) ;
s) -L1-arylene-N(R ) ;
t) -L1-CO-alkylene-N(R ) ;
u) -L1-CO-alkenylene-N(R ) ;
v) -L1-CO-arylene-N(R ) ;
w) -L1-CONH-alkylene-N(R ) ;
x) -L1-CONH-arylene-N(R ) ;
y) -L1-SO -alkylene-N(R ) ;
z) -O-alkylene-N(R ) ;
aa) -N(R )-alkylene-N(R ) ;
bb) -L1-N(R ) ;
cc) -L1-alkylene-N(R ) ;
dd) -L1-arylene-N(R ) ;
ee) -L1-CO-alkylene-N(R ) ;
ff) -L1-CO-alkenylene-N(R ) ;
gg) -L1-CO-arylene-N(R ) ;
hh) -L1-CONH-alkylene-N(R ) ;
ii) -L1-CONH-arylene-N(R ) ;
jj) -L1-SO -alkylene-N(R ) ;
kk) -O-alkylene-heterocyclyl;
ll) -N(R )-alkylene-heterocyclyl;
mm) -L1-alkylene-heterocyclyl;
nn) -L1-arylene-heterocyclyl;
oo) -L1-CO-alkylene-heterocyclyl;
pp) -L1-CO-alkenylene-heterocyclyl;
qq) -L1-CO-arylene-heterocyclyl;
rr) -L1-CONH-alkylene-heterocyclyl;
ss) -L1-CONH-arylene-heterocyclyl;
tt) -L1-SO -alkylene-heterocyclyl;
uu) -O-alkylene-N(O)(R ) ;
vv) -N(R )-alkylene- N(O)(R ) ;
ww) -L1- N(O)(R ) ;
xx) -L1-alkylene- N(O)(R ) ;
yy) -L1-arylene- N(O)(R ) ;
zz) -L1-CO-alkylene- N(O)(R ) ;
aaa) -L1-CO-alkenylene- N(O)(R ) ;
bbb) -L1-CO-arylene- N(O)(R ) ;
ccc) -L1-CONH-alkylene- N(O)(R ) ;
ddd) -L1-CONH-arylene- N(O)(R ) ;
eee) -L1-SO -alkylene- N(O)(R ) ;
fff) -O-alkylene-NH-CNH-NH ;
ggg) -N(R )-alkylene-NH-CNH-NH ;
hhh) -L1-NH-CNH-NH ;
iii) -L1-alkylene-NH-CNH-NH ;
jjj) -L1-arylene-NH-CNH-NH ;
kkk) -L1-CO-alkylene-NH-CNH-NH ;
lll) -L1-CO-alkenylene-NH-CNH-NH ;
mmm) -L1-CO-arylene-NH-CNH-NH ;
nnn) -L1-CONH-alkylene-NH-CNH-NH ;
ooo) -L1-CONH-arylene-NH-CNH-NH ;
ppp) -L1-SO -alkylene-NH-CNH-NH ;
qqq) -L1-SO -arylene-NH-CNH-NH ; and
rrr) a protected form of any of the above X3 groups;
with the provision that if X1 is present as N(CH ) and X7 is present as
3 2,
piperidinyl, then X3 is not or
X4 is selected from:
a) -O-alkylene-aryl;
b) -N(R )-aryl;
c) -N(R )-alkylene-aryl;
d) -L1-CO-alkylene-aryl;
e) -L1-CO-alkenylene-aryl;
f) -L1-CO-arylene-aryl;
g) -L1-CONH-alkylene-aryl;
h) -L1-CONH-arylene-aryl;
i) -L1-SO -alkylene-aryl;
j) -L1-SO -arylene-aryl;
k) -L1-alkylene-aryl;
l) -L1-arylene-aryl;
m) -N(R )-alkylene-N(R )-aryl;
n) -N(R )-alkylene-N(R )CO-aryl;
o) -N(R )-alkylene-N(R )SO -aryl;
p) -N(R )-alkylene-N(R )CH -aryl;
q) –L1-aryl;
r) -L1-CO-aryl;
s) -L1-SO -aryl;
t) -L1-alkylene-P(aryl) ;
u) -L1-CO-alkylene-P(aryl) ;
v) -L1-SO -alkylene-P(aryl) ; and
w) a protected form of any of the above X4 groups;
X5 is selected from:
a) -O-alkylene-heteroaryl;
b) -N(R )-alkylene-heteroaryl;
c) -L1-CO-alkylene-heteroaryl;
d) -L1-CO-alkenylene-heteroaryl;
e) -L1-CO-arylene-heteroaryl;
f) -L1-CONH-alkylene-heteroaryl;
g) -L1-CONH-arylene-heteroaryl;
h) -L1-SO -alkylene-heteroaryl;
i) -L1-SO -arylene-heteroaryl;
j) -L1-alkylene-heteroaryl;
k) -L1-arylene-heteroaryl;
l) -N(R )-alkylene-N(R )-hereroaryl;
m) -N(R )-alkylene-N(R )CO-hereroaryl;
n) -N(R )-alkylene-N(R )SO -hereroaryl;
o) -N(R )-alkylene-N(R )CH -hereroaryl;
p) -L1-heteroaryl; and
q) a protected form of any of the above X5 groups;
X6 is selected from:
a) -O-alkylene-(OCH CH ) OH;
2 2 m
b) -O-alkylene-(OCH CH ) OCH ;
2 2 m 3
c) -N(R )-alkylene-(OCH CH ) OH;
2 2 m
d) -N(R )-alkylene-(OCH CH ) OCH ;
2 2 m 3
e) -N(R )-arylene-(OCH CH ) OH;
2 2 m
f) -N(R )-arylene-(OCH CH ) OCH ;
2 2 m 3
g) -L1-alkylene-(OCH CH ) OH;
2 2 m
h) -L1-CO-alkylene-(OCH CH ) OH;
2 2 m
i) -L1-CO-alkylene-(OCH CH ) OCH ;
2 2 m 3
j) -L1-SO -alkylene-(OCH CH ) OH;
2 2 2 m
k) -L1-SO -alkylene-(OCH CH ) OCH ;
2 2 2 m 3
l) -L1-CO-arylene-(OCH CH ) OH;
2 2 m
m) -L1-CO-arylene-(OCH CH ) OCH ;
2 2 m 3
n) -L1-SO -arylene-(OCH CH ) OH;
2 2 2 m
o) -L1-SO -arylene-(OCH CH ) OCH ;
2 2 2 m 3
p) -L1-CO-(OCH CH ) OH;
2 2 m
q) -L1-CO-(OCH CH ) OCH ;
2 2 m 3
r) -N(R )-(dibenzocrown-6);
s) an aza-crown ether; and
t) a protected form of any of the above X6 groups;
X7 is selected from:
a) -heterocyclyl;
b) -N(R )(R )
c) -L1-hydrogen;
d) -L1-alkyl;
e) -L1-CO-alkyl;
f) -L1-CONH-alkyl;
g) -L1-CON(alkyl)-alkyl;
h) -L1-SO -alkyl;and
i) a protected form of any of the above X7 groups;
with the provision that if X1 is present as N(CH ) , and X3 is present
O NH
as or , then X7 is not
piperdinyl;
X8 is selected from:
a) -L1-CA;
b) -L1-dCA;
c) -L1-COCH (R )
d) -L1-COCH(R )NHCO -alkyl;
5 10
e) -OR , wherein R and R together form a ring;
f) a protected form of any of the above X8 groups;
each R is independently hydrogen, alkyl, or a cell-penetrating peptide;
each R is independently C -C alkyl or optionally when two R are C -
1 12 1
C alkyl, two R are joined to form a heterocyclic ring;
each R is independently C -C alkyl, alkenyl, or alkynyl;
2 18
each R is independently hydrogen, alkyl, hydroxyalkyl, sulfhydrylalkyl,
or arylalkyl;
each R is independently C -C alkyl;
1 12
each R is independently hydrogen or C -C alkyl;
1 12
L1 is selected from:
p p p
NN N N
a) ; b) ; c) ;
d) ; e) ;
1 4 5 2
Q L L Q
f) , and
g) ;
wherein
1 2 6
each Q and Q are each selected from a bond, -O- or -N(R )-;
each E is independently selected from optionally substituted aryl or
optionally substituted heteroaryl;
each E is independently an optionally substituted nitrogen containing
heteroaryl;
each L and L are each independently a bond, optionally substituted C -
C alkyl, or optionally substituted heteroalkyl; and
m, p, q, s, and t are each independently 1-4.
11 15
In some embodiments of Formula (I), Z is -(L )-(R ). In other
11 15 16 5 12 17
embodiments, Z is -(L )-(L )-(R ). In another embodiments, Z is -(L )-(R ). In a
further embodiment of Formula (I), each Y is independently O, NH, or NR . In a
further embodiment of the aforementioned embodiments, each W is O. In yet a further
embodiment, each R is independently hydrogen or alkyl. In a further embodiment,
each R is independently C -C alkyl. In yet a further embodiment, each X is
1 12
independently selected from X1, X2, X3, X4, X5, X6, X7, or X8.
11
In one embodiment is a compound of Formula (I), wherein Z is -(L )-
10 1
(R ), each Y is independently O, NH, or NR , each W is O, each R is independently
hydrogen or alkyl, each R is independently C -C alkyl, each X is independently
1 12
selected from X1, X2, X3, X4, X5, X6, X7, or X8 and n is an integer from 1 to 35.
In another embodiment is a compound of Formula (I), wherein n is 1, Z
11 15 10 1
is -(L )-(R ), each Y is independently O, NH, or NR , each W is O, each R is
independently hydrogen or alkyl, each R is independently C -C alkyl, and X is
1 12
selected from X2, X3, X4, X5, X6, X7, or X8. In some embodiments of Formula (I)
wherein n is 1, G is halogen. In another embodiment, W is O. In another embodiment,
13 13
Y is O. In another embodiment, R is aralkyl. In another embodiment R is an
optionally substituted triphenylmethyl group.
In some embodiments is a compound of Formula (I), wherein n is 1, G
is halogen, W is O, Y is O, R is an optionally substituted triphenylmethyl group, and
X is X2. In some embodiments is a compound of Formula (I), wherein n is 1, G is
halogen, W is O, Y is O, R is an optionally substituted triphenylmethyl group, and X
is X3. In some embodiments is a compound of Formula (I), wherein n is 1, G is
halogen, W is O, Y is O, R is an optionally substituted triphenylmethyl group, and X
is X4. In some embodiments is a compound of Formula (I), wherein n is 1, G is
halogen, W is O, Y is O, R is an optionally substituted triphenylmethyl group, and X
is X5. In some embodiments is a compound of Formula (I), wherein n is 1, G is
halogen, W is O, Y is O, R is an optionally substituted triphenylmethyl group, and X
is X6. In some embodiments is a compound of Formula (I), wherein n is 1, G is
halogen, W is O, Y is O, R is an optionally substituted triphenylmethyl group, and X
is X7. In some embodiments is a compound of Formula (I), wherein n is 1, G is
halogen, W is O, Y is O, R is an optionally substituted triphenylmethyl group, and X
is X8.
In another embodiment is a compound of Formula (I) wherein G is -
13 15 16 5
(L )-(L )-(R ). In another embodiment is a compound of Formula (I) wherein G is -
13 15 5 13
(L )-(R ). In another embodiment is a compound of Formula (I) wherein G is -(L )-
12 17
(L )-(R ).
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35 and G is . In another embodiment is a compound of
Formula (I) wherein n is an integer from 1 to 35 and W is O. In another embodiment is
a compound of Formula (I) wherein n is an integer from 1 to 35 and Y is O. In another
embodiment is a compound of Formula (I) wherein n is an integer from 1 to 35, G is
, each W is O, each Y is O, and each X is independently selected from X1,
X2, X3, X4, X5, X6, X7, or X8.
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, and at least one X
is X2. In some embodiments, at least one X2 is selected from -O-alkylene-CO H, -O-
alkylene-CHN, -N(R )-alkylene-COH, and -N(R )-alkylene-CHN. In some
4 2 4
embodiments, at least one X2 is -O-alkylene-CO H. In some embodiments, at least one
X2 is -O-alkylene-CHN . In some embodiments, at least one X2 is -N(R )-alkylene-
CO H. In some embodiments, at least one X2 is -N(R )-alkylene-CHN . In some
embodiments, at least one X2 is selected from -O-alkylene-CO H, -O-alkylene-CHN , -
N(R )-alkylene-CO H, and -N(R )-alkylene-CHN , wherein -alkylene- is -CH -, -
2 4 2
CH CH -, or -CH CH CH -. In further embodiments, at least one X2 is selected from -
2 2 2 2 2
N(H)CH CO H, -N(CH )CH CO H, -N(CH CH )CH CO H, -N(H)CH CH CO H, and
2 2 3 2 2 2 3 2 2 2 2 2
-N(CH )CH CH CO H. In some embodiments, at least one X2 is -N(H)CH CO H. In
3 2 2 2 2 2
some embodiments, at least one X2 is -N(CH )CH CO H. In some embodiments, at
3 2 2
least one X2 is -N(CH CH )CH CO H. In some embodiments, at least one X2 is -
2 3 2 2
N(H)CH CH CO H. In some embodiments, at least one X2 is -N(CH )CH CH CO H.
2 2 2 3 2 2 2
In further embodiments, at least one X2 is selected from -L1-CO-alkylene-CO H, -L1-
CO-alkylene-CHN , -L1-CO-alkenylene-CO H, -L1-CO-alkenylene-CHN , -L1-CO-
4 2 4
arylene-CO H, and -L1-CO-arylene-CHN . In some embodiments, at least one X2 is -
L1-CO-alkylene-CO H. In some embodiments, at least one X2 is -L1-CO-alkylene-
CHN . In some embodiments, at least one X2 is -L1-CO-alkenylene-CO H. In some
embodiments, at least one X2 is -L1-CO-alkenylene-CHN . In some embodiments, at
least one X2 is -L1-CO-arylene-CO H. In some embodiments at least one X2 is L1-
CO-arylene-CHN . In further embodiments, at least one X2 is selected from -L1-CO-
alkylene-COH, -L1-CO-alkylene-CHN, -L1-CO-alkenylene-COH, -L1-CO-
2 4 2
alkenylene-CHN , -L1-CO-arylene-CO H, and -L1-CO-arylene-CHN , wherein L1 is
4 2 4
. In yet further embodiments, at least one X2 is selected from -L1-
CO-alkylene-COH, -L1-CO-alkylene-CHN, -L1-CO-alkenylene-COH, -L1-CO-
2 4 2
alkenylene-CHN , -L1-CO-arylene-CO H, and -L1-CO-arylene-CHN , wherein L1 is
4 2 4
and -alkylene- is -CH -, -CH CH -, or -CH CH CH -. In another
2 2 2 2 2 2
embodiment, at least one X2 is selected from -L1-CO-alkylene-CO H, -L1-CO-
alkylene-CHN, -L1-CO-alkenylene-COH, -L1-CO-alkenylene-CHN, -L1-CO-
4 2 4
arylene-CO H, and -L1-CO-arylene-CHN , wherein L1 is . In
another embodiment, at least one X2 is selected from -L1-CO-alkylene-CO H, -L1-CO-
alkylene-CHN, -L1-CO-alkenylene-COH, -L1-CO-alkenylene-CHN, -L1-CO-
4 2 4
arylene-CO H, and -L1-CO-arylene-CHN , wherein L1 is and -
alkylene- is -CH -, -CH CH -, or -CH CH CH -.
2 2 2 2 2 2
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is X2
NN NN
and X2 is selected from: , OH,
OH OH
, and . In some
embodiments, at least one X2 is . In some embodiments, at
least one X2 is . In some embodiments, at least one X2
is . In some embodiments, at least one X2 is
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is X2
and X2 is selected from: O , N ,
N NH
N NH N
, and . In some
embodiments, at least one X2 is . In some embodiments, at
least one X2 is N . In some embodiments, at least one X2 is
N NH
. In some embodiments, at least one X2 is
N NH
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X2, and X2 is selected from -L1-CONH-alkylene-CO H, -L1-CONH-alkylene-CHN , -
L1-CONH-arylene-CO H, and -L1-CONH-arylene-CHN . In some embodiments, X2
is -L1-CONH-alkylene-CO H. In some embodiments, X2 is -L1-CONH-alkylene-
CHN. In some embodiments, X2 is -L1-CONH-arylene-COH. In some
embodiments, X2 is -L1-CONH-arylene-CHN . In another embodiment, X2 is selected
from -L1-CONH-alkylene-COH, -L1-CONH-alkylene-CHN, -L1-CONH-arylene-
CO H, and -L1-CONH-arylene-CHN , wherein L1 is . In another
embodiment, X2 is selected from -L1-CONH-alkylene-CO H, -L1-CONH-alkylene-
CHN, -L1-CONH-arylene-COH, and -L1-CONH-arylene-CHN, wherein L1 is
4 2 4
and -alkylene- is -CH -, -CH CH -, or -CH CH CH -. In another
2 2 2 2 2 2
embodiment, X2 is selected from -L1-CONH-alkylene-CO H, -L1-CONH-alkylene-
CHN, -L1-CONH-arylene-COH, and -L1-CONH-arylene-CHN, wherein L1 is
4 2 4
. In another embodiment, X2 is selected from -L1-CONH-alkylene-
COH, -L1-CONH-alkylene-CHN, -L1-CONH-arylene-COH, and -L1-CONH-
2 4 2
arylene-CHN , wherein L1 is and -alkylene- is -CH -, -CH CH -, or
4 2 2 2
-CH CH CH -.
2 2 2
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is X2
NN NN
HN HN O
O OH
and X2 is selected from: , ,
NH O
N N N N
, and . In some
embodiments, at least one X2 is O . In some embodiments, at
HN O
least one X2 is . In some embodiments, at least one X2
NH O
is . In some embodiments, at least one X2 is
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X2, and X2 is selected from -L1-SO -alkylene-CO H, -L1-SO -alkylene-CHN , -L1-
2 2 2 4
SO -arylene-CO H, and -L1-SO -arylene-CHN . In some embodiments, X2 is -L1-
2 2 2 4
SO -alkylene-CO H. In some embodiments, X2 is L1-SO -alkylene-CHN . In some
2 2 2 4
embodiments, X2 is -L1-SO -arylene-CO H. In some embodiments, X2 is -L1-SO -
2 2 2
arylene-CHN . In another embodiment, X2 is selected from -L1-SO -alkylene-CO H,
4 2 2
-L1-SO -alkylene-CHN , -L1-SO -arylene-CO H, and -L1-SO -arylene-CHN , wherein
2 4 2 2 2 4
L1 is . In another embodiment, X2 is selected from -L1-SO -
alkylene-COH, -L1-SO -alkylene-CHN, -L1-SO -arylene-COH, and -L1-SO -
2 2 4 2 2 2
arylene-CHN , wherein L1 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is X2
NN S
NN S
and X2 is selected from: O , N ,
NN S NN S
OH N
N NH N NH N
N NH N NH
, and . In some embodiments,
NN S
at least one X2 is O . In some embodiments, at least one X2 is
NN S
. In some embodiments, at least one X2 is
NN S
. In some embodiments, at least one X2 is
NN S
N . In some embodiments, at least one X2 is
N NH
. In some embodiments, at least one X2 is
N NH N
. In some embodiments, at least one X2 is
N NH
. In some embodiments, at least one X2 is
N NH
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X2, and X2 is selected from -L1-alkylene-CO H, -L1-alkylene-CHN , -L1-arylene-
CO H, and -L1-arylene-CHN . In some embodiments, X2 is -L1-alkylene-CO H. In
2 4 2
some embodiments, X2 is -L1-alkylene-CHN . In some embodiments, X2 is -L1-
arylene-COH. In some embodiments, X2 is -L1-arylene-CHN. In some
embodiments, X2 is selected from -L1-alkylene-CO H, -L1-alkylene-CHN , -L1-
arylene-CO H, and -L1-arylene-CHN . In another embodiment, X2 is selected from
-L1-alkylene-CO H, -L1-alkylene-CHN , -L1-arylene-CO H, and -L1-arylene-CHN ,
2 4 2 4
wherein L1 is . In another embodiment, X2 is selected from -L1-
alkylene-COH, -L1-alkylene-CHN, -L1-arylene-COH, and -L1-arylene-CHN ,
2 4 2 4
wherein L1 is and -alkylene- is -CH -, -CH CH -, or -CH CH CH -.
2 2 2 2 2 2
In another embodiment, X2 is selected from -L1-alkylene-CO H, -L1-alkylene-CHN , -
L1-arylene-CO H, and -L1-arylene-CHN , wherein L1 is . In another
embodiment, X2 is selected from -L1-alkylene-COH, -L1-alkylene-CHN, -L1-
arylene-CO H, and -L1-arylene-CHN , wherein L1 is and -alkylene-
is -CH -, -CH CH -, or -CH CH CH -.
2 2 2 2 2 2
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is X2
NN NN O
O OH
and X2 is selected from: , ,
N NH
N NH O
O , , , and
. In some embodiments, at least one X2 is
. In some embodiments, at least one X2 is
NN O
. In some embodiments, at least one X2 is
. In some embodiments, at least one X2 is
N NH O
. In some embodiments, at least one X2 is
N NH
. In some embodiments, at least one X2 is
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is X2
and X2 is selected from:
NN NN
OH N
N NH
N NH
, and . In some embodiments, at
least one X2 is OH. In some embodiments, at least one X2 is
. In some embodiments, at least one X2 is
N NH
. In some embodiments, at least one X2 is
N NH
In any of the aforementioned embodiments of Formula (I) wherein at
least one X is X2 is another embodiment wherein n is an integer from 30-35. In further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is X2, n is an integer from 25-29. In further embodiments of the aforementioned
embodiments of Formula (I) wherein at least one X is X2, n is an integer from 20-24.
In further embodiments of any of the aforementioned embodiments of Formula (I)
wherein at least one X is X2, n is an integer from 15-19. In further embodiments of the
aforementioned embodiments of Formula (I) wherein at least one X is X2, n is an
integer from 10-14. In further embodiments of the aforementioned embodiments of
Formula (I) wherein at least one X is X2, n is an integer from 5-9. In yet further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is X2, n is an integer from 1-4.
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, and at least one X
is X3. In further embodiments at least one X3 is selected from -L1-alkyl and -L1-
heterocyclyl. In some embodiments at least one X3 is -L1-alkyl. In yet another
embodiment, at least one X3 is -L1-alkyl and L1 is . In another
embodiment, at least one X3 is -L1-alkyl and L1 is . In another
embodiment, at least one X3 is -L1-alkyl and L1 is . In a further
embodiment of the aforementioned embodiments wherein at least one X is X3, alkyl is
methyl, ethyl, propyl, and isopropyl. In another embodiment, alkyl is CF . In another
embodiment, alkyl is CN.
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is X3
NN NN NN
and X3 is selected from: , , ,
NCF NCN NN
, , and . In some embodiments, at least
one X is X3 and X3 is . In some embodiments, at least one X is X3 and
X3 is . In some embodiments, at least one X is X3 and X3 is
. In some embodiments, at least one X is X3 and X3 is
. In some embodiments, at least one X is X3 and X3 is
NCN NN
. In some embodiments, at least one X is X3 and X3 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X3, and X3 is -L1-heterocyclyl. In yet another embodiment, at least one X3 is -L1-
heterocyclyl and L1 is . In another embodiment, at least one X3 is -
L1-heterocyclyl and L1 is . In another embodiment, at least one X3
is -L1-heterocyclyl and L1 is . In another embodiment of the
aforementioned embodiments wherein at least one X is X3, heterocyclyl is pyrrolidine,
tetrahydrofuran, piperidine, morpholine, piperazine, pyrrole, furan, thiophene, pyrazole,
imidazole, oxazole, isoxazole, pyridine, and pyrimidine. In a further embodiment,
heterocyclyl is pyrrolidine. In a further embodiment, heterocyclyl is piperidine. In a
further embodiment, heterocyclyl is morpholine. In a further embodiment, heterocyclyl
is piperazine. In a further embodiment, heterocyclyl is pyridine. In a further
embodiment, heterocyclyl is pyrimidine.
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is X3
NN N N
and X3 is selected from: , ,
NN NH NN N N N O
, , and . In some
embodiments, at least one X is X3 and X3 is . In some
embodiments, at least one X is X3 and X3 is . In some
NN NH
embodiments, at least one X is X3 and X3 is . In some
NN N
embodiments, at least one X is X3 and X3 is . In some
N N O
embodiments, at least one X is X3 and X3 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X3, and X3 is selected from -O-alkylene-CNH-NH , -N(R )-alkylene-CNH-NH , -O-
1 1 1 2 1 2
alkylene-N(R ) , -N(R )-alkylene-N(R ) , -O-alkylene-N(R ) , -N(R )-alkylene-N(R ) ,
2 2 3 3
-O-alkylene-heterocyclyl, -N(R)-alkylene-heterocyclyl, -O-alkylene-N(O)(R ), -
1 2 1
N(R )-alkylene-N(O)(R ), -O-alkylene-NH-CNH-NH, and -N(R )-alkylene-NH-
CNH-NH . In a further embodiment, at least one X3 is selected from -O-alkylene-
1 1 1 1
CNH-NH , -N(R )-alkylene-CNH-NH , -O-alkylene-N(R ) , -N(R )-alkylene-N(R ) , -
2 2 2 2
2 1 2 1
O-alkylene-N(R ) , -N(R )-alkylene-N(R ) , -O-alkylene-heterocyclyl, -N(R )-alkylene-
2 1 2
heterocyclyl, -O-alkylene-N(O)(R ), -N(R )-alkylene-N(O)(R ), -O-alkylene-NH-
CNH-NH , and -N(R )-alkylene-NH-CNH-NH wherein -alkylene- is -CH CH - or -
2 2 2 2
CH CH CH -. In a further embodiment, at least one X3 is selected from -O-alkylene-
2 2 2
CNH-NH, -O-alkylene-N(R ), -O-alkylene-N(R ), -O-alkylene-heterocyclyl, -O-
2 2 3
alkylene-N(O)(R ) , and -O-alkylene-NH-CNH-NH . In yet a further embodiment, at
1 1 1
least one X3 is selected from -N(R )-alkylene-CNH-NH , -N(R )-alkylene-N(R ) , -
1 2 1 1 2
N(R )-alkylene-N(R ) , -N(R )-alkylene-heterocyclyl, -N(R )-alkylene-N(O)(R ) , and -
N(R )-alkylene-NH-CNH-NH wherein -alkylene- is -CH CH - or -CH CH CH -. In
2 2 2 2 2 2
some of the above embodiments, at least one X3 is -O-alkylene-CNH-NH . In some of
the above embodiments, at least one X3 is -N(R )-alkylene-CNH-NH . In some of the
above embodiments, at least one X3 is -O-alkylene-N(R ) . In some of the above
embodiments, at least one X3 is -N(R )-alkylene-N(R ) . In some of the above
embodiments, at least one X3 is -O-alkylene-N(R ). In some of the above
embodiments, at least one X3 is -N(R )-alkylene-N(R ) . In some of the above
embodiments, at least one X3 is -O-alkylene-heterocyclyl. In some of the above
embodiments, at least one X3 is -N(R )-alkylene-heterocyclyl. In some of the above
embodiments, at least one X3 is -O-alkylene-N(O)(R ) ,. In some of the above
embodiments, at least one X3 is -N(R )-alkylene-N(O)(R ) . In some of the above
embodiments, at least one X3 is -O-alkylene-NH-CNH-NH . In some of the above
embodiments, at least one X3 is -N(R )-alkylene-NH-CNH-NH .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is X3
and X3 is selected from and . In some embodiments, at
least one X is X3 and X3 is . In some embodiments, at least one X is X3
and X3 is . In further embodiments, at least one X is X3 and X3 is
N N N
selected from , , , ,
N N N
N N N
, , and . In some
embodiments, at least one X is X3 and X3 is . In some embodiments, at
least one X is X3 and X3 is . In some embodiments, at least one X is X3
and X3 is . In some embodiments, at least one X is X3 and X3 is
. In some embodiments, at least one X is X3 and X3 is .
In some embodiments, at least one X is X3 and X3 is . In some
embodiments, at least one X is X3 and X3 is . In some embodiments,
at least one X is X3 and X3 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X3, and X3 is selected from -L1-CNH-NH , -L1-alkylene-CNH-NH , -L1-arylene-
1 1 2
CNH-NH, -L1-alkylene-N(R ), -L1-arylene-N(R ), -L1-alkylene-N(R ), -L1-
2 2 2 3
arylene-N(R ), -L1-alkylene-heterocyclyl, -L1-arylene-heterocyclyl, -L1-alkylene-
N(O)(R ) , -L1-arylene-N(O)(R ) , -L1-alkylene-NH-CNH-NH , and -L1-arylene-NH-
2 2 2
CNH-NH . In a further embodiment, at least one X3 is selected from -L1-arylene-
CNH-NH, -L1-arylene-N(R ), -L1-arylene-N(R ), -L1-arylene-heterocyclyl, -L1-
2 2 3
arylene-N(O)(R ) , and -L1-arylene-NH-CNH-NH . In some embodiments, at least one
X3 is -L1-arylene-CNH-NH . In some embodiments, at least one X3 is -L1-arylene-
N(R ) . In some embodiments, at least one X3 is -L1-arylene-N(R ) . In some
embodiments, at least one X3 is -L1-arylene-heterocyclyl. In some embodiments, at
least one X3 is -L1-arylene-N(O)(R ) . In some embodiments, at least one X3 is -L1-
arylene-NH-CNH-NH . In a further embodiment of the aforementioned embodiments,
L1 is . In yet a further embodiment of the aforementioned
embodiments, L1 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X3, and X3 is selected from -L1-CNH-NH , -L1-alkylene-CNH-NH , -L1-alkylene-
1 2 2
N(R ) , -L1-alkylene-N(R ) , -L1-alkylene-heterocyclyl, -L1-alkylene-N(O)(R ) , and -
2 3 2
L1-alkylene-NH-CNH-NH . In a further embodiment, at least one X3 is selected from
-L1-CNH-NH , -L1-alkylene-CNH-NH , and -L1-alkylene-NH-CNH-NH . In yet a
2 2 2
further embodiment, at least one X3 is selected from -L1-alkylene-N(R ) , -L1-
alkylene-N(R ) , -L1-alkylene-heterocyclyl, and -L1-alkylene-N(O)(R ) . In some
embodiments, at least one X3 is -L1-CNH-NH . In some embodiments, at least one X3
is -L1-alkylene-CNH-NH . In some embodiments, at least one X3 is -L1-alkylene-NH-
CNH-NH . In some embodiments, at least one X3 is -L1-alkylene-N(R ) . In some
embodiments, at least one X3 is -L1-alkylene-N(R ) . In some embodiments, at least
one X3 is -L1-alkylene-heterocyclyl. In some embodiments, at least one X3 is -L1-
alkylene-N(O)(R ) . In a further embodiment of the aforementioned embodiments, L1
is . In another embodiment of the aforementioned embodiments, L1 is
. In yet a further embodiment of the aforementioned embodiments, -
alkylene- is -CH CH - or -CH CH CH -. In some embodiments of the aforementioned
2 2 2 2 2
embodiments, -alkylene- is -CH CH -. In some embodiments of the aforementioned
embodiments, -alkylene- is -CH CH CH -.
2 2 2
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is X3
and X3 is selected from and . In some
embodiments, at least one X3 is . In some embodiments, at least
one X3 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is X3
and X3 is selected from , ,
N NH
N NH N NH
N NH
NH NH
, , , and
. In some embodiments, at least one X3 is
. In some embodiments, at least one X3 is
. In some embodiments, at least one X3 is
. In some embodiments, at least one X3 is
. In some embodiments, at least one X3 is
HN . In some embodiments, at least one X3 is
. In some embodiments, at least one X3 is
N NH
. In some embodiments, at least one X3 is
N NH
. In some embodiments, at least one X3 is
N NH
. In some embodiments, at least one X3 is
N NH
. In some embodiments, at least one X3 is
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X3, and X3 is selected from -L1-CO-alkylene-CNH-NH , -L1-CO-alkenylene-CNH-
NH, -L1-CO-arylene-CNH-NH, -L1-CONH-alkylene-CNH-NH, -L1-CONH-
2 2 2
arylene-CNH-NH, -L1-SO -alkylene-CNH-NH, -L1-SO -arylene-CNH-NH, -L1-
2 2 2 2 2
1 1 1
CO-alkylene-N(R ) , -L1-CO-alkenylene-N(R ) , -L1-CO-arylene-N(R ) , -L1-CONH-
2 2 2
1 1 1
alkylene-N(R ), -L1-CONH-arylene-N(R ), -L1-SO -alkylene-N(R ), -L1-CO-
2 2 2 2
2 2 2
alkylene-N(R ), -L1-CO-alkenylene-N(R ), -L1-CO-arylene-N(R ), -L1-CONH-
3 3 3
2 2 2
alkylene-N(R ), -L1-CONH-arylene-N(R ), -L1-SO -alkylene-N(R ), -L1-CO-
3 3 2 3
alkylene-heterocyclyl, -L1-CO-alkenylene-heterocyclyl, -L1-CO-arylene-heterocyclyl, -
L1-CONH-alkylene-heterocyclyl, -L1-CONH-arylene-heterocyclyl, -L1-SO -alkylene-
heterocyclyl, -L1-CO-alkylene-N(O)(R ), -L1-CO-alkenylene-N(O)(R ), -L1-CO-
2 2 2
arylene-N(O)(R ) , -L1-CONH-alkylene-N(O)(R ) , -L1-CONH-arylene-N(O)(R ) , -
2 2 2
L1-SO -alkylene-N(O)(R ), -L1-CO-alkylene-NH-CNH-NH, -L1-CO-alkenylene-
2 2 2
NH-CNH-NH , -L1-CO-arylene-NH-CNH-NH , -L1-CONH-alkylene-NH-CNH-NH , -
2 2 2
L1-CONH-arylene-NH-CNH-NH, -L1-SO -alkylene-NH-CNH-NH, and -L1-SO -
2 2 2 2
arylene-NH-CNH-NH . In a further embodiment, at least one X3 is selected from -L1-
CO-arylene-CNH-NH , -L1-CONH-arylene-CNH-NH , -L1-SO -arylene-CNH-NH , -
2 2 2 2
1 1 2
L1-CO-arylene-N(R ), -L1-CONH-arylene-N(R ), -L1-CO-arylene-N(R ), -L1-
2 2 3
CONH-arylene-N(R ) , -L1-CO-arylene-heterocyclyl, -L1-CONH-arylene-heterocyclyl,
-L1-CO-arylene-N(O)(R ) , -L1-CONH-arylene-N(O)(R ) , -L1-CO-arylene-NH-CNH-
NH , -L1-CONH-arylene-NH-CNH-NH , and -L1-SO -arylene-NH-CNH-NH . In
2 2 2 2
some embodiments, at least one X3 is -L1-CO-arylene-CNH-NH. In some
embodiments, at least one X3 is -L1-CONH-arylene-CNH-NH . In some embodiments,
at least one X3 is -L1-SO -arylene-CNH-NH . In some embodiments, at least one X3 is
-L1-CO-arylene-N(R ) . In some embodiments, at least one X3 is -L1-CONH-arylene-
N(R ) . In some embodiments, at least one X3 is -L1-CO-arylene-N(R ) . In some
embodiments, at least one X3 is -L1-CONH-arylene-N(R ) . In some embodiments, at
least one X3 is -L1-CO-arylene-heterocyclyl. In some embodiments, at least one X3 is -
L1-CONH-arylene-heterocyclyl. In some embodiments, at least one X3 is -L1-CO-
arylene-N(O)(R ) . In some embodiments, at least one X3 is -L1-CONH-arylene-
N(O)(R ) . In some embodiments, at least one X3 is -L1-CO-arylene-NH-CNH-NH .
In some embodiments, at least one X3 is -L1-CONH-arylene-NH-CNH-NH . In some
embodiments, at least one X3 is -L1-SO -arylene-NH-CNH-NH . In a further
embodiment of the aforementioned embodiments, L1 is . In another
embodiment of the aforementioned embodiments, L1 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is X3
and X3 is selected from and
. In some embodiments, at least one X3
is . In some embodiments, at least one X3 is
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X3, and X3 is selected from -L1-CO-alkylene-CNH-NH , -L1-CO-alkenylene-CNH-
NH , -L1-CONH-alkylene-CNH-NH , -L1-SO -alkylene-CNH-NH , -L1-CO-alkylene-
2 2 2 2
1 1 1
N(R ), -L1-CO-alkenylene-N(R ), -L1-CONH-alkylene-N(R ), -L1-SO -alkylene-
2 2 2 2
1 2 2
N(R ), -L1-CO-alkylene-N(R ), -L1-CO-alkenylene-N(R ), -L1-CONH-alkylene-
2 3 3
N(R ) , -L1-SO -alkylene-N(R ) , -L1-CO-alkylene-heterocyclyl, -L1-CO-alkenylene-
3 2 3
heterocyclyl, -L1-CONH-alkylene-heterocyclyl, -L1-SO -alkylene-heterocyclyl, -L1-
CO-alkylene-N(O)(R ), -L1-CO-alkenylene-N(O)(R ), -L1-CONH-alkylene-
N(O)(R ), -L1-SO -alkylene-N(O)(R ), -L1-CO-alkylene-NH-CNH-NH, -L1-CO-
2 2 2 2
alkenylene-NH-CNH-NH, -L1-CONH-alkylene-NH-CNH-NH, and -L1-SO -
2 2 2
alkylene-NH-CNH-NH . In a further embodiment, at least one X3 is selected from -L1-
SO -alkylene-CNH-NH, -L1-SO -alkylene-N(R ), -L1-SO -alkylene-N(R ), -L1-
2 2 2 2 2 3
SO -alkylene-heterocyclyl, -L1-SO -alkylene-N(O)(R ) , and -L1-SO -alkylene-NH-
2 2 2 2
CNH-NH . In some embodiments, at least one X3 is -L1-SO -alkylene-CNH-NH . In
2 2 2
some embodiments, at least one X3 is -L1-SO -alkylene-N(R ). In some
embodiments, at least one X3 is -L1-SO -alkylene-N(R ) . In some embodiments, at
least one X3 is -L1-SO -alkylene-heterocyclyl. In some embodiments, at least one X3
is -L1-SO -alkylene-N(O)(R ) . In some embodiments, at least one X3 is -L1-SO -
2 2 2
alkylene-NH-CNH-NH . In a further embodiment of the aforementioned embodiments,
L1 is . In another embodiment of the aforementioned embodiments,
L1 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X3, and X3 is selected from -L1-CO-alkylene-CNH-NH , -L1-CO-alkenylene-CNH-
NH , -L1-CONH-alkylene-CNH-NH , -L1-CO-alkylene-N(R ) , -L1-CO-alkenylene-
2 2 2
1 1 2
N(R ), -L1-CONH-alkylene-N(R ), -L1-CO-alkylene-N(R ), -L1-CO-alkenylene-
2 2 3
N(R ), -L1-CONH-alkylene-N(R ), -L1-CO-alkylene-heterocyclyl, -L1-CO-
alkenylene-heterocyclyl, -L1-CONH-alkylene-heterocyclyl, -L1-CO-alkylene-
2 2 2
N(O)(R ) , -L1-CO-alkenylene-N(O)(R ) , -L1-CONH-alkylene-N(O)(R ) , -L1-CO-
2 2 2
alkylene-NH-CNH-NH , -L1-CO-alkenylene-NH-CNH-NH , and -L1-CONH-alkylene-
NH-CNH-NH . In a further embodiment, at least one X3 is selected from -L1-CO-
alkenylene-CNH-NH, -L1-CO-alkenylene-N(R ), -L1-CO-alkenylene-N(R ), -L1-
2 2 3
CO-alkenylene-heterocyclyl, -L1-CO-alkenylene-N(O)(R ) , and -L1-CO-alkenylene-
NH-CNH-NH . In some embodiments, at least one X3 is -L1-CO-alkenylene-CNH-
NH . In some embodiments, at least one X3 is -L1-CO-alkenylene-N(R ) . In some
embodiments, at least one X3 is -L1-CO-alkenylene-N(R ) . In some embodiments, at
least one X3 is -L1-CO-alkenylene-heterocyclyl. In some embodiments, at least one X3
is -L1-CO-alkenylene-N(O)(R ) . In some embodiments, at least one X3 is -L1-CO-
alkenylene-NH-CNH-NH. In a further embodiment of the aforementioned
embodiments, L1 is . In another embodiment of the aforementioned
embodiments, L1 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X3, and X3 is selected from -L1-CO-alkylene-CNH-NH , -L1-CONH-alkylene-CNH-
1 1 2
NH , -L1-CO-alkylene-N(R ) , -L1-CONH-alkylene-N(R ) , -L1-CO-alkylene-N(R ) ,
2 2 2 3
-L1-CONH-alkylene-N(R ), -L1-CO-alkylene-heterocyclyl, -L1-CONH-alkylene-
heterocyclyl, -L1-CO-alkylene-N(O)(R ), -L1-CONH-alkylene-N(O)(R ), -L1-CO-
alkylene-NH-CNH-NH, and -L1-CONH-alkylene-NH-CNH-NH. In a further
embodiment, at least one X3 is selected from -L1-CO-alkylene-CNH-NH , -L1-CO-
alkylene-N(R ), -L1-CO-alkylene-N(R ), -L1-CO-alkylene-heterocyclyl, -L1-CO-
alkylene-N(O)(R ) , and -L1-CO-alkylene-NH-CNH-NH . In some embodiments, at
least one X3 is -L1-CO-alkylene-CNH-NH . In some embodiments, at least one X3 is -
L1-CO-alkylene-N(R ) . In some embodiments, at least one X3 is -L1-CO-alkylene-
N(R ) . In some embodiments, at least one X3 is -L1-CO-alkylene-heterocyclyl. In
some embodiments, at least one X3 is -L1-CO-alkylene-N(O)(R ). In some
embodiments, at least one X3 is -L1-CO-alkylene-NH-CNH-NH . In a further
embodiment of the aforementioned embodiments, L1 is . In another
embodiment of the aforementioned embodiments, L1 is . In yet a
further embodiment of the aforementioned embodiments, -alkylene- is -CH -, -
CH CH -, -CH CH CH -, -CH CH CH CH -, and -CH CH CH CH CH -. In some
2 2 2 2 2 2 2 2 2 2 2 2 2 2
embodiments of the aforementioned embodiments, -alkylene- is -CH -. In some
embodiments of the aforementioned embodiments, -alkylene- is -CH CH -. In some
embodiments of the aforementioned embodiments, -alkylene- is -CH CH CH -. In
2 2 2
some embodiments of the aforementioned embodiments, -alkylene- is -
CH CH CH CH -. In some embodiments of the aforementioned embodiments, -
2 2 2 2
alkylene- is -CH CH CH CH CH -.
2 2 2 2 2
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is X3
H N +
and X3 is selected from NH and
N NH
. In some embodiments, at least one X3
H N +
is NH . In some embodiments, at least one X3 is
N NH
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X3, and X3 is selected from -L1-CO-alkylene-CNH-NH , -L1-CONH-alkylene-CNH-
1 1 2
NH , -L1-CO-alkylene-N(R ) , -L1-CONH-alkylene-N(R ) , -L1-CO-alkylene-N(R ) ,
2 2 2 3
-L1-CONH-alkylene-N(R ), -L1-CO-alkylene-heterocyclyl, -L1-CONH-alkylene-
heterocyclyl, -L1-CO-alkylene-N(O)(R ), -L1-CONH-alkylene-N(O)(R ), -L1-CO-
alkylene-NH-CNH-NH, and -L1-CONH-alkylene-NH-CNH-NH. In a further
embodiment, at least one X3 is selected from -L1-CO-alkylene-CNH-NH , -L1-CO-
alkylene-N(R ), -L1-CO-alkylene-N(R ), -L1-CO-alkylene-heterocyclyl, -L1-CO-
alkylene-N(O)(R ) , and -L1-CO-alkylene-NH-CNH-NH . In some embodiments, at
least one X3 is -L1-CO-alkylene-CNH-NH . In some embodiments, at least one X3 is -
L1-CO-alkylene-N(R ) . In some embodiments, at least one X3 is -L1-CO-alkenylene-
N(R ) . In some embodiments, at least one X3 is -L1-CO-alkenylene-heterocyclyl. In
some embodiments, at least one X3 is -L1-CO-alkenylene-N(O)(R ) . In some
embodiments, at least one X3 is -L1-CO-alkenylene-NH-CNH-NH . In a further
embodiment of the aforementioned embodiments, L1 is . In another
embodiment of the aforementioned embodiments, L1 is . In yet a
further embodiment of the aforementioned embodiments, -alkylene- is -CH CH -, -
CH CH CH -, -CH CH CH CH -, and -CH CH CH CH CH -. In some embodiments
2 2 2 2 2 2 2 2 2 2 2 2
of the aforementioned embodiments, -alkylene- is -CH CH -. In some embodiments of
the aforementioned embodiments, -alkylene- is -CH CH CH -. In some embodiments
2 2 2
of the aforementioned embodiments, -alkylene- is -CH CH CH CH-. In some
2 2 2 2
embodiments of the aforementioned embodiments, -alkylene- is -CH CH CH CH CH -
2 2 2 2 2
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
1 2 2
X3, and X3 is selected from -L1-N(R ) , -L1-N(R ) , -L1-N(O)(R ) , and -L1-NH-
2 3 2
CNH-NH. In some embodiments, at least one X3 is -L1-N(R ). In some
embodiments, at least one X3 is -L1-N(R ) . In some embodiments, at least one X3 is -
L1-N(O)(R ) . In some embodiments, at least one X3 is -L1-NH-CNH-NH . In further
NNH NNH
embodiments at least one X3 is selected from: , ,
NNH NNH NN NN
, , , and . In some
embodiments, at least one X3 is . In some embodiments, at least one
NNH NNH
X3 is . In some embodiments, at least one X3 is . In
some embodiments, at least one X3 is . In some embodiments, at
least one X3 is . In some embodiments, at least one X3 is
. In yet further embodiments at least one X3 is selected from
NN NN
and . In some embodiments, at least one X3 is
NN NN
. In some embodiments, at least one X3 is .
In any of the aforementioned embodiments of Formula (I) wherein at
least one X is X3 is another embodiment wherein n is an integer from 30-35. In further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is X3, n is an integer from 25-29. In further embodiments of the aforementioned
embodiments of Formula (I) wherein at least one X is X3, n is an integer from 20-24.
In further embodiments of any of the aforementioned embodiments of Formula (I)
wherein at least one X is X3, n is an integer from 15-19. In further embodiments of the
aforementioned embodiments of Formula (I) wherein at least one X is X3, n is an
integer from 10-14. In further embodiments of the aforementioned embodiments of
Formula (I) wherein at least one X is X3, n is an integer from 5-9. In yet further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is X3, n is an integer from 1-4.
In another embodiment the X3 group is provided in a protected form. In
another embodiment the protected form comprises a protected nitrogen. In another
embodiment the protected nitrogen is protected with a trifluoroacetyl group.
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, and at least one X
is X4. In further embodiments at least one X4 is selected from -O-alkylene-aryl, -
1 1 1 1 1
N(R)-aryl, -N(R)-alkylene-aryl, -N(R )-alkylene-N(R)-aryl, -N(R )-alkylene-
1 1 1 1 1
N(R )CO-aryl, -N(R )-alkylene-N(R )SO-aryl, and -N(R )-alkylene-N(R )CH -aryl.
In a further embodiment, at least one X4 is -O-alkylene-aryl.
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
1 1 1
X4, and at least one X4 is selected from -N(R )-aryl, -N(R )-alkylene-aryl, -N(R )-
1 1 1 1 1
alkylene-N(R)-aryl, -N(R )-alkylene-N(R)CO-aryl, -N(R )-alkylene-N(R )SO -aryl,
and -N(R )-alkylene-N(R )CH -aryl. In a further embodiment, at least one X4 is -
N(R )-aryl. In yet a further embodiment, at least one X4 is and .
In some embodiments, at least one X4 is . In some embodiments, at least one
X4 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X4, and at least one X4 is -N(R )-alkylene-aryl. In further embodiments, -alkylene- is -
CH -, -CH(CH )-, -CH CH -, and -CH CH CH -. In some embodiments, -alkylene- is -
2 3 2 2 2 2 2
CH -. In some embodiments, -alkylene- is -CH(CH )-. In some embodiments, -
alkylene- is -CH CH -. In some embodiments, -alkylene- is -CH CH CH -. In a
2 2 2 2 2
further embodiment, at least one X4 is selected from:
, , , ,
, , , and . In some
embodiments, at least one X4 is . In some embodiments, at least one X4
is . In some embodiments, at least one X4 is . In some
embodiments, at least one X4 is . In some embodiments, at least one X4
is . In some embodiments, at least one X4 is . In some
embodiments, at least one X4 is . In some embodiments, at least one
X4 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
1 1 1
X4, and at least one X4 is selected from -N(R )-alkylene-N(R )-aryl, and -N(R )-
alkylene-N(R )CH -aryl. In some embodiments, at least one X4 is -N(R )-alkylene-
1 1 1
N(R )-aryl. In some embodiments, at least one X4 is -N(R )-alkylene-N(R )CH -aryl.
In further embodiments, at least one X4 is selected from and
. In some embodiments, at least one X4 is . In
some embodiments, at least one X4 is . In yet a further
embodiment, at least one X4 is selected from -N(R )-alkylene-N(R )CO-aryl and -
N(R )-alkylene-N(R )SO -aryl. In further embodiments, at least one X4 is selected
from and . In some embodiments, at least one
X4 is . In some embodiments, at least one X4 is
. In a further embodiment of the aforementioned embodiments, -
alkylene- is selected from -CH CH-, -CH CH CH-, -CH CH CH CH-, and -
2 2 2 2 2 2 2 2 2
CH CH CH CH CH -. In some embodiments of the aforementioned embodiments, -
2 2 2 2 2
alkylene- is -CH CH -. In some embodiments of the aforementioned embodiments, -
alkylene- is -CH CH CH -. In some embodiments of the aforementioned embodiments,
2 2 2
-alkylene- is -CH CH CH CH-. In some embodiments of the aforementioned
2 2 2 2
embodiments, -alkylene- is -CH CH CH CH CH -.
2 2 2 2 2
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X4, and at least one X4 is selected from -L1-CO-alkylene-aryl, -L1-CO-alkenylene-
aryl, -L1-CO-arylene-aryl, -L1-CONH-alkylene-aryl, -L1-CONH-arylene-aryl, -L1-
SO -alkylene-aryl, -L1-SO -arylene-aryl, -L1-CO-aryl, -L1-SO -aryl, -L1-CO-alkylene-
2 2 2
P(aryl) , and -L1-SO -alkylene-P(aryl) . In a further embodiment, at least one X4 is -
3 2 3
L1-SO -alkylene-P(aryl) . In a further embodiment, at least one X4 is -L1-CO-
alkylene-P(aryl) . In a further embodiment, at least one X4 is selected from -L1-CO-
alkylene-aryl, -L1-CO-alkenylene-aryl, -L1-CO-arylene-aryl, -L1-CONH-alkylene-aryl,
-L1-CONH-arylene-aryl, -L1-SO -alkylene-aryl, -L1-SO -arylene-aryl, -L1-CO-aryl,
and -L1-SO -aryl. In a further embodiment, at least one X4 is selected from -L1-SO -
alkylene-aryl, -L1-SO -arylene-aryl, and -L1-SO -aryl. In some embodiments, at least
one X4 is -L1-SO -alkylene-aryl. In some embodiments, at least one X4 is -L1-SO -
arylene-aryl. In some embodiments, at least one X4 is -L1-SO -aryl. In yet a further
embodiment, at least one X4 is selected from -L1-CO-alkylene-aryl, -L1-CO-
alkenylene-aryl, -L1-CO-arylene-aryl, -L1-CONH-alkylene-aryl, -L1-CONH-arylene-
aryl, and -L1-CO-aryl. In a further embodiment, at least one X4 is selected from -L1-
CONH-alkylene-aryl and -L1-CONH-arylene-aryl. In some embodiments, at least one
X4 is -L1-CONH-alkylene-aryl. In some embodiments, at least one X4 is -L1-CONH-
arylene-aryl. In yet a further embodiment, at least one X4 is selected from -L1-CO-
alkylene-aryl, -L1-CO-alkenylene-aryl, -L1-CO-arylene-aryl, and -L1-CO-aryl. In
some embodiments, at least one X4 is -L1-CO-alkylene-aryl. In some embodiments, at
least one X4 is -L1-CO-alkenylene-aryl. In some embodiments, at least one X4 is -L1-
CO-arylene-aryl. In some embodiments, at least one X4 is -L1-CO-aryl. In a further
embodiment of the aforementioned embodiments, L1 is . In another
embodiment of the aforementioned embodiments, L1 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X4, and X4 is selected from and
N NH
. In some embodiments, at least one X4
is . In some embodiments, at least one X4 is
N NH
. In a further embodiment, at least one X4 is
NN S
N NH
selected from and . In some
NN S
embodiments, at least one X4 is . In some embodiments, at least
N NH
one X4 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X4, and X4 is selected from:
NN NN
, ,
NN O
N NH
N NH
N NH
N NH N NH
N NH
N NH
N NH
N NH
Cl , and Cl .
In some embodiments, at least one X4 is .
In some embodiments, at least one X4 is . In some
embodiments, at least one X4 is . In some
embodiments, at least one X4 is . In some embodiments,
at least one X4 is . In some embodiments, at least
one X4 is . In some embodiments, at least one X4 is
. In some embodiments, at least one X4
is . In some embodiments, at least one X4 is
. In some embodiments, at least one X4
N NH
is . In some embodiments, at least one X4 is
N NH
. In some embodiments, at least one X4 is
N NH
. In some embodiments, at least one X4
N NH
is . In some embodiments, at least one X4 is
N NH
. In some embodiments, at least one X4
N NH
is . In some embodiments, at least one X4 is
N NH
. In some embodiments, at least one X4
N NH
is . In some embodiments, at least one X4 is
N NH
. In a further embodiment, at least one X4 is
N NH
selected from , , and
N NH
. In some embodiments, at least one X4 is
. In some embodiments, at least one X4
N NH
is O . In some embodiments, at least one X4 is
N NH
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X4, and at least one X4 is selected from -L1-alkylene-aryl, -L1-arylene-aryl, -L1-aryl,
and -L1-alkylene-P(aryl) . In some embodiments, at least one X4 is -L1-alkylene-aryl.
In some embodiments, at least one X4 is -L1-arylene-aryl. In some embodiments, at
least one X4 is -L1-aryl. In some embodiments, at least one X4 is -L1-alkylene-
P(aryl). In a further embodiment, at least one X4 is selected from
N NH
NN NO
, , and . In some
embodiments, at least one X4 is . In some embodiments, at least
one X4 is . In some embodiments, at least one X4 is
N NH
In any of the aforementioned embodiments of Formula (I) wherein at
least one X is X4 is another embodiment wherein n is an integer from 30-35. In further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is X4, n is an integer from 25-29. In further embodiments of the aforementioned
embodiments of Formula (I) wherein at least one X is X4, n is an integer from 20-24.
In further embodiments of any of the aforementioned embodiments of Formula (I)
wherein at least one X is X4, n is an integer from 15-19. In further embodiments of the
aforementioned embodiments of Formula (I) wherein at least one X is X4, n is an
integer from 10-14. In further embodiments of the aforementioned embodiments of
Formula (I) wherein at least one X is X4, n is an integer from 5-9. In yet further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is X4, n is an integer from 1-4.
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, and at least one X
is X5. In further embodiments at least one X5 is selected from -O-alkylene-heteroaryl,
1 1 1 1
-N(R)-alkylene-heteroaryl, -N(R )-alkylene-N(R)-heteroaryl, -N(R )-alkylene-
1 1 1 1
N(R)CO-heteroaryl, -N(R )-alkylene-N(R )SO-heteroaryl, and -N(R )-alkylene-
N(R )CH -heteroaryl. In yet further embodiments, at least one X5 is selected from -
1 1 1 1
N(R)-alkylene-heteroaryl, -N(R )-alkylene-N(R)-heteroaryl, -N(R )-alkylene-
1 1 1 1
N(R)CO-heteroaryl, -N(R )-alkylene-N(R )SO-heteroaryl, and -N(R )-alkylene-
N(R )CH -heteroaryl.
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X5, and at least one X5 is -N(R )-alkylene-heteroaryl. In a further embodiment, at least
one X5 is -O-alkylene-heteroaryl. In yet further embodiments, -alkylene- is -CH -, -
CH(CH )-, -CH CH -, and -CH CH CH -. In some embodiments, -alkylene- is -CH -.
3 2 2 2 2 2 2
In some embodiments, -alkylene- is -CH(CH )-. In some embodiments, -alkylene- is -
CH CH -. In some embodiments, -alkylene- is -CH CH CH
2 2 2 2 2
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X5, and at least one X5 is selected from -N(R )-alkylene-heteroaryl, -N(R )-aylkylene-
1 1 1 1 1
N(R)-heteroaryl, -N(R )-alkylene-N(R)CO-heteroaryl, -N(R )-alkylene-N(R )SO -
heteroaryl, and -N(R )-alkylene-N(R )CH -heteroaryl. In some embodiments, at least
one X5 is -N(R )-alkylene-heteroaryl,. In some embodiments, at least one X5 is -
1 1 1
N(R )-alkylene-N(R )-heteroaryl. In some embodiments, at least one X5 is -N(R )-
alkylene-N(R )CO-heteroaryl. In some embodiments, at least one X5 is -N(R )-
alkylene-N(R )SO -heteroaryl. In some embodiments, at least one X5 is -N(R )-
alkylene-N(R )CH-heteroaryl. In a further embodiment of the aforementioned
embodiments, -alkylene- is selected from -CH CH -, -CH CH CH -, -CH CH CH CH -
2 2 2 2 2 2 2 2 2
, and -CH CH CH CH CH-. In some embodiments of the aforementioned
2 2 2 2 2
embodiments, -alkylene- is -CH CH -. In some embodiments of the aforementioned
embodiments, -alkylene- is -CH CH CH-. In some embodiments of the
2 2 2
aforementioned embodiments, -alkylene- is -CH CH CH CH -. In some embodiments
2 2 2 2
of the aforementioned embodiments, -alkylene- is -CH CH CH CH CH -.
2 2 2 2 2
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X5, and at least one X5 is selected from -L1-heteroaryl, -L1-alkylene-heteroaryl, -L1-
arylene-heteroaryl, -L1-CO-alkylene-heteroaryl, -L1-CO-alkenylene-heteroaryl, -L1-
CO-arylene-heteroaryl, -L1-CONH-alkylene-heteroaryl, -L1-CONH-arylene-heteroaryl,
-L1-SO -alkylene-heteroaryl, -L1-SO -arylene-heteroaryl. In a further embodiment at
least one X5 is selected from -L1-SO -alkylene-heteroaryl and -L1-SO -arylene-
heteroaryl. In some embodiments, at least one X5 is -L1-SO -alkylene-heteroaryl. In
some embodiments, at least one X5 is -L1-SO -arylene-heteroaryl. In a further
embodiment at least one X5 is selected from -L1-CONH-alkylene-heteroaryl and -L1-
CONH-arylene-heteroaryl. In some embodiments, at least one X5 is -L1-CONH-
alkylene-heteroaryl. In some embodiments, at least one X5 is -L1-CONH-arylene-
heteroaryl. In a further embodiment at least one X5 is selected from -L1-CO-alkylene-
heteroaryl, -L1-CO-alkenylene-heteroaryl, and -L1-CO-arylene-heteroaryl. In some
embodiments, at least one X5 is -L1-CO-alkylene-heteroaryl. In some embodiments, at
least one X5 is -L1-CO-alkenylene-heteroaryl. In some embodiments, at least one X5
is -L1-CO-alkenylene-heteroaryl. In a further embodiment of the aforementioned
embodiments, L1 is . In another embodiment of the aforementioned
embodiments, L1 is . In yet a further embodiment of the
aforementioned embodiments, -alkylene- is selected from -CH -, -CH(CH )-, -CH CH -
2 3 2 2
, and -CH CH CH -. In some embodiments of the aforementioned embodiments, -
2 2 2
alkylene- is -CH -. In some embodiments of the aforementioned embodiments, -
alkylene- is -CH(CH )-. In some embodiments of the aforementioned embodiments, -
alkylene- is -CH CH -. In some embodiments of the aforementioned embodiments, -
alkylene- is -CH CH CH -. In some embodiments, at least one X5 is -L1-heteroaryl.
2 2 2
In a further embodiment, at least one X5 is selected from ,
N NH N NH N NH
N , N , and N . In some
embodiments, at least one X is X5 and X5 is . In some
N NH
embodiments at least one X5 is N . In some embodiments at least one
N NH
X5 is N . In some embodiments at least one X5 is
N NH
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X5, and at least one X5 is selected from -L1-alkylene-heteroaryl and -L1-arylene-
heteroaryl. In some embodiments at least one X5 is -L1-arylene-heteroaryl. In some
embodiments at least one X5 is -L1-alkylene-heteroaryl. In a further embodiment, at
least one X5 is selected from ,
NN NN NN
N , N , and N . In some
embodiments at least one X5 is . In some embodiments at least one
X5 is N . In some embodiments at least one X5 is
N. In some embodiments at least one X5 is
In any of the aforementioned embodiments of Formula (I) wherein at
least one X is X5 is another embodiment wherein n is an integer from 30-35. In further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is X5, n is an integer from 25-29. In further embodiments of the aforementioned
embodiments of Formula (I) wherein at least one X is X5, n is an integer from 20-24.
In further embodiments of any of the aforementioned embodiments of Formula (I)
wherein at least one X is X5, n is an integer from 15-19. In further embodiments of the
aforementioned embodiments of Formula (I) wherein at least one X is X5, n is an
integer from 10-14. In further embodiments of the aforementioned embodiments of
Formula (I) wherein at least one X is X5, n is an integer from 5-9. In yet further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is X5, n is an integer from 1-4.
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, and at least one X
is X6. In further embodiments at least one X6 is selected from -O-alkylene-
O(CH CH ) OH, -O-alkylene-O(CH CH ) OCH , -N(R )-alkylene-O(CH CH ) OH, -
2 2 m 2 2 m 3 2 2 m
1 1 1
N(R )-alkylene-O(CH CH ) OCH, -N(R )-arylene-O(CH CH ) OH, and -N(R )-
2 2 m 3 2 2 m
arylene-O(CH CH ) OCH . In further embodiments, at least one X6 is selected from -
2 2 m 3
O-alkylene-O(CH CH )OH and -O-alkylene-O(CH CH ) OCH. In some
2 2 m 2 2 m 3
embodiments, at least one X6 is -O-alkylene-O(CH CH ) OH. In some embodiments,
2 2 m
at least one X6 is -O-alkylene-O(CH CH ) OCH . In further embodiments, at least one
2 2 m 3
X6 is selected from -N(R )-alkylene-O(CH CH )OH, -N(R )-alkylene-
2 2 m
O(CH CH ) OCH, -N(R )-arylene-O(CH CH )OH, and -N(R )-arylene-
2 2 m 3 2 2 m
O(CH CH ) OCH . In yet further embodiments, at least one X6 is selected from -
2 2 m 3
N(R )-alkylene-O(CH CH ) OH and -N(R )-alkylene-O(CH CH ) OCH . In some
2 2 m 2 2 m 3
embodiments, at least one X6 is -N(R )-alkylene-O(CH CH ) OH. In some
2 2 m
embodiments, at least one X6 is -N(R )-alkylene-O(CH CH ) OCH . In further
2 2 m 3
embodiments, at least one X6 is selected from -N(R )-arylene-O(CH CH ) OH and -
2 2 m
N(R )-arylene-O(CH CH ) OCH . In some embodiments, at least one X6 is -N(R )-
2 2 m 3
arylene-O(CH CH ) OH. In some embodiments, at least one X6 is -N(R )-arylene-
2 2 m
O(CH CH ) OCH . In yet a further embodiment of the aforementioned embodiments, -
2 2 m 3
alkylene- is selected from -CH CH-, -CH CH CH-, -CH CH CH CH-, and -
2 2 2 2 2 2 2 2 2
CH CH CH CH CH -. In some embodiments of the aforementioned embodiments, -
2 2 2 2 2
alkylene- is -CH CH -. In some embodiments of the aforementioned embodiments, -
alkylene- is -CH CH CH -. In some embodiments of the aforementioned embodiments,
2 2 2
-alkylene- is -CH CH CH CH-. In some embodiments of the aforementioned
2 2 2 2
embodiments, -alkylene- is -CH CH CH CH -.
2 2 2 2
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X6, and X6 is selected from -L1-alkylene-(OCH CH ) OH, -L1-CO-alkylene-
2 2 m
O(CH CH )OH, -L1-CO-alkylene-O(CH CH ) OCH, -L1-SO -alkylene-
2 2 m 2 2 m 3 2
O(CH CH )OH, -L1-SO -alkylene-O(CH CH ) OCH, -L1-CO-arylene-
2 2 m 2 2 2 m 3
O(CH CH )OH, -L1-CO-arylene-O(CH CH ) OCH, -L1-SO -arylene-
2 2 m 2 2 m 3 2
O(CH CH ) OH, and -L1-SO -arylene-O(CH CH ) OCH . In a further embodiment,
2 2 m 2 2 2 m 3
at least one X6 is selected from -L1-SO -alkylene-O(CH CH ) OH, -L1-SO -alkylene-
2 2 2 m 2
O(CH CH ) OCH, -L1-SO -arylene-O(CH CH )OH, and -L1-SO -arylene-
2 2 m 3 2 2 2 m 2
O(CH CH ) OCH . In yet a further embodiment, at least one X6 is selected from -L1-
2 2 m 3
SO -alkylene-O(CH CH ) OH and -L1-SO -alkylene-O(CH CH ) OCH . In some
2 2 2 m 2 2 2 m 3
embodiments, at least one X6 is -L1-SO -alkylene-O(CH CH ) OH. In some
2 2 2 m
embodiments, at least one X6 is -L1-SO -alkylene-O(CH CH ) OCH . In a further
2 2 2 m 3
embodiment, at least one X6 is selected from -L1-SO -arylene-O(CH CH ) OH and -
2 2 2 m
L1-SO -arylene-O(CH CH ) OCH . In some embodiments, at least one X6 is -L1-
2 2 2 m 3
SO -arylene-O(CH CH ) OH. In some embodiments, at least one X6 is -L1-SO -
2 2 2 m 2
arylene-O(CH CH ) OCH . In a further embodiment, at least one X6 is selected from -
2 2 m 3
L1-alkylene-(OCH CH ) OH, -L1-CO-alkylene-O(CH CH ) OH, -L1-CO-alkylene-
2 2 m 2 2 m
O(CH CH ) OCH, -L1-CO-arylene-O(CH CH )OH, and -L1-CO-arylene-
2 2 m 3 2 2 m
O(CH CH ) OCH. In some embodiments, at least one X6 is -L1-alkylene-
2 2 m 3
(OCH CH ) OH. In yet a further embodiment, at least one X6 is selected from -L1-
2 2 m
CO-alkylene-O(CH CH ) OH and -L1-CO-alkylene-O(CH CH ) OCH. In some
2 2 m 2 2 m 3
embodiments, at least one X6 is -L1-CO-alkylene-O(CH CH ) OH. In some
2 2 m
embodiments, at least one X6 is -L1-CO-alkylene-O(CH CH ) OCH . In a further
2 2 m 3
embodiment, at least one X6 is selected from -L1-CO-arylene-O(CH CH ) OH and -
2 2 m
L1-CO-arylene-O(CH CH ) OCH . In some embodiments, at least one X6 is -L1-CO-
2 2 m 3
arylene-O(CH CH ) OH. In some embodiments, at least one X6 is -L1-CO-arylene-
2 2 m
O(CH CH ) OCH . In a further embodiment of the aforementioned embodiments, L1
2 2 m 3
is . In another embodiment of the aforementioned embodiments, L1 is
. In yet a further embodiment of the aforementioned embodiments, -
alkylene- is selected from -CH CH-, -CH CH CH-, -CH CH CH CH-, and -
2 2 2 2 2 2 2 2 2
CH CH CH CH CH -. In some embodiments of the aforementioned embodiments, -
2 2 2 2 2
alkylene- is -CH CH -. In some embodiments of the aforementioned embodiments, -
alkylene- is -CH CH CH -. In some embodiments of the aforementioned embodiments,
2 2 2
-alkylene- is -CH CH CH CH-. In some embodiments of the aforementioned
2 2 2 2
embodiments, -alkylene- is -CH CH CH CH CH -. In some embodiments of the
2 2 2 2 2
aforementioned embodiments, m is 1. In some embodiments of the aforementioned
embodiments, m is 2. In some embodiments of the aforementioned embodiments, m is
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X6, and at least one X6 is selected from -L1-alkylene-(OCH CH ) OH. In some
2 2 m
NN O
embodiments, at least one X6 is . In some
embodiments, at least one X6 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X6, and X6 is selected from -L1-CO-O(CH CH ) OH and -L1-CO-O(CH CH ) OCH .
2 2 m 2 2 m 3
In a further embodiment, at least one X6 is -L1-CO-O(CH CH ) OH. In yet a further
2 2 m
embodiment, at least one X6 is -L1-CO-O(CH CH ) OCH .
2 2 m 3
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is X6
and X6 is selected from -N(R )-(dibenzocrown-6) and an aza-crown ether. In some
embodiments, at least one X6 is -N(R )-(dibenzocrown-6). In some embodiments,
at least one X6 is an aza-crown ether. In further embodiments, at least one X is X6 and
X6 is selected from:
, , and
. In some embodiments, at least one X6 is
. In some embodiments, at least one X6 is
. In some embodiments, at least one X6 is
In any of the aforementioned embodiments of Formula (I) wherein at
least one X is X6 is another embodiment wherein n is an integer from 30-35. In further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is X6, n is an integer from 25-29. In further embodiments of the aforementioned
embodiments of Formula (I) wherein at least one X is X6, n is an integer from 20-24.
In further embodiments of any of the aforementioned embodiments of Formula (I)
wherein at least one X is X6, n is an integer from 15-19. In further embodiments of the
aforementioned embodiments of Formula (I) wherein at least one X is X6, n is an
integer from 10-14. In further embodiments of the aforementioned embodiments of
Formula (I) wherein at least one X is X6, n is an integer from 5-9. In yet further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is X6, n is an integer from 1-4.
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, and at least one X
is X7. In a further embodiment, at least one X7 is a heterocycle. In a further
embodiment, at least one X is X7 and X7 is selected from:
NO NNH N N O
, , , , ,
, and . In some embodiments, at least one X7 is
NO NNH
. In some embodiments, at least one X7 is . In some
embodiments, at least one X7 is . In some embodiments, at least one X7 is
. In some embodiments, at least one X7 is O . In some
embodiments, at least one X7 is . In some embodiments, at least one X7 is
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X7, and at least one X7 is -N(R )(R ). In a further embodiment, at least one X7 is
selected from: , ,
, , , , and
. In some embodiments, at least one X7 is . In some
embodiments, at least one X7 is . In some embodiments, at least one X7 is
. In some embodiments, at least one X7 is . In some
embodiments, at least one X7 is . In some embodiments, at
least one X7 is . In some embodiments, at least one X7 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X7, and at least one X7 is -N(R )(R ). In a further embodiment, at least one X7 is
selected from -L1-CO-alkyl, -L1-CONH-alkyl, -L1-CON(alkyl)-alkyl, and -L1-SO -
alkyl. In a further embodiment, at least one X7 is -L1-CO-alkyl. In a further
embodiment, at least one X7 is -L1-CONH-alkyl. In a further embodiment, at least one
X7 is -L1-CON(alkyl)-alkyl. In a further embodiment, at least one X7 is -L1-SO -
alkyl.
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X7, and at least one X7 is selected from: , ,
N NH
, , O ,
N NH N N
N N N NH
CF CF
O O O O
, , , ,
, and . In some embodiments, at least one X7 is
. In some embodiments, at least one X7 is . In
some embodiments, at least one X7 is . In some embodiments, at
least one X7 is . In some embodiments, at least one X7 is
N NH
N NH
O . In some embodiments, at least one X7 is O . In
some embodiments, at least one X7 is . In some embodiments, at
least one X7 is . In some embodiments, at least one X7 is
N NH N N
. In some embodiments, at least one X7 is .
In some embodiments, at least one X7 is .
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, at least one X is
X7, and at least one X7 is -N(R )(R ). In a further embodiment, at least one X7 is
selected from: HS , , and
HS . In some embodiments, at least one X7 is
. In some embodiments, at least one X7 is
. In some embodiments, at least one X7 is
In any of the aforementioned embodiments of Formula (I) wherein at
least one X is X7 is another embodiment wherein n is an integer from 30-35. In further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is X7, n is an integer from 25-29. In further embodiments of the aforementioned
embodiments of Formula (I) wherein at least one X is X7, n is an integer from 20-24.
In further embodiments of any of the aforementioned embodiments of Formula (I)
wherein at least one X is X7, n is an integer from 15-19. In further embodiments of the
aforementioned embodiments of Formula (I) wherein at least one X is X7, n is an
integer from 10-14. In further embodiments of the aforementioned embodiments of
Formula (I) wherein at least one X is X7, n is an integer from 5-9. In yet further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is X7, n is an integer from 1-4.
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, each Y is O, and at least one X
is X8. In a further embodiment, at least one X8 is -L1-CA. In a further embodiment, at
least one X8 is -L1-dCA. In a further embodiment, at least one X8 is selected from -
L1-COCH (R ) and -L1-COCH(R )NHCO -alkyl. In some embodiments, at least one
X8 is -L1-COCH (R). In some embodiments, at least one X8 is -L1-
COCH(R )NHCO -alkyl.
In another embodiment is a compound of Formula (I) wherein n is an
integer from 1 to 35, G is , each W is O, at least one Y is NR , at least
5 10
one X is X8, at least one X8 is -OR , and R and R together form a ring. In a further
embodiment, the ring formed is selected from: , , and
O N O N
. In some embodiments, the ring formed is . In some
embodiments, the ring formed is . In some embodiments, the ring formed
is .
In any of the aforementioned embodiments of Formula (I) wherein at
least one X is X8 is another embodiment wherein n is an integer from 30-35. In further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is X8, n is an integer from 25-29. In further embodiments of the aforementioned
embodiments of Formula (I) wherein at least one X is X8, n is an integer from 20-24.
In further embodiments of any of the aforementioned embodiments of Formula (I)
wherein at least one X is X8, n is an integer from 15-19. In further embodiments of the
aforementioned embodiments of Formula (I) wherein at least one X is X8, n is an
integer from 10-14. In further embodiments of the aforementioned embodiments of
Formula (I) wherein at least one X is X8, n is an integer from 5-9. In yet further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is X8, n is an integer from 1-4.
In another embodiment is the compound of Formula (I) wherein L1 is
NN N N
selected from: , ,
p p p
N O N
q t q
, , and .
In another embodiment is the compound of Formula (I) wherein L1 is
In another embodiment is the compound of Formula (I) wherein L1 is
wherein p is 2 and q is 2. In another embodiment is the compound
wherein p is 3 and q is 2.
In another embodiment is the compound of Formula (I) wherein L1 is
In another embodiment is the compound of Formula (I) wherein L1 is
wherein p is 1 and q is 2. In another embodiment is the
compound wherein p is 2 and q is 2. In another embodiment is the compound wherein p
is 3 and q is 2.
In another embodiment is the compound of Formula (I) wherein L1
1 4 5 2
Q L L Q
is .
In another embodiment is the compound of Formula (I) wherein L1
1 4 5 2
Q L E L Q
is wherein Q is -N(R )-.
In another embodiment is the compound of Formula (I) wherein L1
1 4 5 2
Q L E L Q
is wherein Q is -N(R )-.
In another embodiment is the compound of Formula (I) wherein L1
1 4 1 5 2
Q L L Q
is wherein E is phenyl.
In another embodiment is the compound of Formula (I) wherein L1
1 4 1 5 2
Q L L Q
is wherein E is heteroaryl.
In another embodiment is the compound of Formula (I) wherein L1
is .
In another embodiment is the compound of Formula (I) wherein L1
is wherein Q is -N(R )-.
In another embodiment is the compound of Formula (I) wherein L1
is wherein E is pyrrolyl. In another embodiment is the compound
of Formula (I) wherein E is imidazolyl. In another embodiment is the compound of
Formula (I) wherein E is triazinyl. In another embodiment is the compound of Formula
(I) wherein E is imidazolyl.
In another embodiment is the compound of Formula (I) wherein W is O,
and Y is NH.
In another embodiment is the compound of Formula (I) wherein W is O,
and Y is NR . In another embodiment is the compound of Formula (I) wherein W is O,
10
and Y is NR , wherein R and X8e together form a ring. In another embodiment is the
compound of Formula (I) wherein R and X8e together for a structure selected from
O P O P O P O
N N N
, , or .
In another embodiment is the compound of Formula (I), wherein L is
23 23
. In another embodiment is the compound of Formula (I), wherein
23 23
O R R
P N R N
L is . In another embodiment is the compound of Formula
23 23
O R R
P N R N
11 24
(I), wherein L is and R is a C -C alkylene. In another
embodiment is the compound of Formula (I), wherein L is
23 23
O R R
P N R N
24 1
and wherein R is ethylene or propylene, and R is hydrogen
or methyl.
In another embodiment is the compound of Formula (I), wherein L is
23 23
O H O
. In another embodiment is the compound of Formula (I),
23 23
O H O
11 4
wherein L is and R is hydrogen or methyl. In another
23 23
O CH O
R R 3
embodiment is the compound of Formula (I), wherein L is H .
In another embodiment is the compound of Formula (I), wherein L is
. In another embodiment is the compound of Formula (I), wherein
L is and wherein p is 2, and q is 2. In another embodiment is the
compound of Formula (I), wherein L is and wherein p is 2, and
q is 3. In another embodiment is the compound of Formula (I), wherein L is
. In another embodiment is the compound of Formula (I),
wherein L is , p and q are independently selected from 1 or 2,
6 13
and R is CH . In another embodiment is the compound of Formula (I), wherein L is
. In another embodiment is the compound of Formula (I),
wherein L is , and p, q, s and t are independently
selected from 1 or 2. In another embodiment is the compound of Formula (I), wherein
Q is X1. In another embodiment is the compound of Formula (I), wherein R is
hydrogen, methyl or both R groups together form a cyclopropyl, cyclobutyl,
cyclopentyl or cyclohexyl ring. In another embodiment is the compound of Formula (I),
wherein R is hydrogen or methyl.
In another embodiment is the compound of Formula (I), wherein Q is
X2. In another embodiment is the compound of Formula (I), wherein Q is X3. In
another embodiment is the compound of Formula (I), wherein Q is X4. In another
embodiment is the compound of Formula (I), wherein Q is X5. In another embodiment
is the compound of Formula (I), wherein Q is X6. In another embodiment is the
compound of Formula (I), wherein Q is X7. In another embodiment is the compound of
Formula (I), wherein Q is X8.
In another embodiment is the compound of Formula (I), wherein Z is –
C(R ) OP(=O)(OH) . In another embodiment is the compound of Formula (I), wherein
R is hydrogen.
In another embodiment is the compound of Formula (I), wherein Z is -
11 15 15
(L )-(R ) and the R is C -C alkyl, C -C alkylcarbonyl, C -C alkyloxycarbonyl,
1 30 1 30 2 30
or a 3-18 membered alkoxyalkylcarbonyl. In another embodiment is the compound of
11 15 15
Formula (I), wherein Z is -(L )-(R ) and the R is a C -C alkyloxycarbonyl. In
2 30
11 15
another embodiment is the compound of Formula (I), wherein Z is -(L )-(R ) and the
R is selected from -C(=O)OCH CHOH, –C(=O)OCH CH OCH CHOH, or –
2 2 2 2 2 2
C(=O)OCH CH OCH CH OCH CH OH. In another embodiment is the compound of
2 2 2 2 2 2
11 15 15
Formula (I), wherein Z is -(L )-(R) and the R is –
C(=O)OCH CH OCH CH OCH CH OH.
2 2 2 2 2 2
In another embodiment is the compound of Formula (I), wherein Z is -
11 15 15
(L )-(R ) and the R is a cell-penetrating peptide. In another embodiment is the
compound of Formula (I), wherein R is a cell-penetrating peptide and the cell-
penetrating peptide is linked through a aminohexanoic acid-derived linker. In another
embodiment is the compound of Formula (I), wherein R is a cell-penetrating peptide
and the cell-penetrating peptide is linked through a aminohexanoic acid-derived linker
comprising the structure: O L .
In another embodiment is the compound of Formula (I), wherein Z is
selected from:
O P N N O OH
O P N N O O
O O OH
H C CH H C CH
3 3 3 3
O P N
O OH
H C CH
or 3 3 .
In another embodiment is the compound of Formula (I), wherein Z is
O P N N O O
O OH
H C CH
In another embodiment is the compound of Formula (I), wherein Z is -
11 15 16
(L )-(L )-(R ).
In another embodiment is the compound of Formula (I), wherein L is
23 23
. In another embodiment is the compound of Formula (I), wherein
23 23
O R R
P N R N
L is . In another embodiment is the compound of Formula
23 23
O R R
P N R N
11 24
(I), wherein L is and R is a C -C alkylene. In another
embodiment is the compound of Formula (I), wherein L is
23 23
O R R
P N R N
24 1
and wherein R is ethylene or propylene, and R is hydrogen
or methyl.
In another embodiment is the compound of Formula (I), wherein L is
23 23
O H O
. In another embodiment is the compound of Formula (I),
23 23
O H O
11 4
wherein L is and R is hydrogen or methyl. In another
23 23
O CH O
R R 3
embodiment is the compound of Formula (I), wherein L is .
In another embodiment is the compound of Formula (I), wherein L is
. In another embodiment is the compound of Formula (I), wherein
L is and wherein p is 2, and q is 2. In another embodiment is the
compound of Formula (I), wherein L is and wherein p is 2, and
q is 3. In another embodiment is the compound of Formula (I), wherein L is
. In another embodiment is the compound of Formula (I),
wherein L is , p and q are independently selected from 1 or 2,
6 13
and R is CH . In another embodiment is the compound of Formula (I), wherein L is
. In another embodiment is the compound of Formula (I),
13 q
wherein L is , and p, q, s and t are independently
selected from 1 or 2. In another embodiment is the compound of Formula (I), wherein
Q is X1. In another embodiment is the compound of Formula (I), wherein R is
hydrogen, methyl or both R groups together form a cyclopropyl, cyclobutyl,
cyclopentyl or cyclohexyl ring. In another embodiment is the compound of Formula (I),
wherein R is hydrogen or methyl.
In another embodiment is the compound of Formula (I), wherein Q is
X2. In another embodiment is the compound of Formula (I), wherein Q is X3. In
another embodiment is the compound of Formula (I), wherein Q is X4. In another
embodiment is the compound of Formula (I), wherein Q is X5. In another embodiment
is the compound of Formula (I), wherein Q is X6. In another embodiment is the
compound of Formula (I), wherein Q is X7. In another embodiment is the compound of
Formula (I), wherein Q is X8.
In another embodiment is the compound of Formula (I), wherein Z is -
11 15 16 15
(L )-(L )-(R ), and L is selected from –(C -C alkylene)-C(=O)-, or -(C -C
1 30 2 30
alkoxy)-C(=O)-. In another embodiment is the compound of Formula (I), wherein Z is
11 15 16 15
-(L )-(L )-(R ), and L is selected from -(C -C alkoxy)-C(=O)-.
2 30
In another embodiment is the compound of Formula (I), wherein Z is -
11 15 16
(L )-(L )-(R) and is represented by the structure:
NHCO Et
Q PO
wherein group A is aminomethyl polystyrene resin.
In another embodiment is the compound of Formula (I), wherein Z is -
11 15 16 16
(L )-(L )-(R) and R is represented by the
NHCO Et
N O S
structure: wherein group
A is aminomethyl polystyrene resin.
In another embodiment is the compound of Formula (I), wherein Z is -
11 15 16 15
(L )-(L )-(R ) and L is represented by the structure: .
In another embodiment is the compound of Formula (I) wherein R is an
electron pair.
In another embodiment is the compound of Formula (I) wherein R is a
C -C alkyl and R is a C -C alkyl. In another embodiment is the compound of
1 30 1 6
13 12
Formula (I) wherein R is a methyl group and R is a methyl group.
In another embodiment is the compound of Formula (I) wherein R is
hydrogen.
In another embodiment is the compound of Formula (I) wherein R is
C -C alkyl. In another embodiment is the compound of Formula (I) wherein R is C -
1 30 1
C alkyl. In another embodiment is the compound of Formula (I) wherein R is C -C
1 6
alkyl. In another embodiment is the compound of Formula (I) wherein R is selected
from prenyl, geranyl, farnesyl or geranylgeranyl.
In another embodiment is the compound of Formula (I) wherein R is a
cell-penetrating peptide.
In another embodiment is the compound of Formula (I) wherein R is a
guanidinyl or amidinyl group.
In another embodiment is the compound of Formula (I) wherein R is a
C -C cycloalkyl.
In another embodiment is the compound of Formula (I) wherein R is a
C -C alkylcarbonyl. In another embodiment is the compound of Formula (I) wherein
1 30
R is a C -C alkylcarbonyl. In another embodiment is the compound of Formula (I)
1 15
wherein R is a C -C alkylcarbonyl. In another embodiment is the compound of
1 10
Formula (I) wherein R is a C -C alkylcarbonyl. In another embodiment is the
compound of Formula (I) wherein R is a C -C alkylcarbonyl. In another embodiment
is the compound of Formula (I) wherein R is a C -C alkylcarbonyl. In another
embodiment is the compound of Formula (I) wherein R is a C -C alkylcarbonyl. In
another embodiment is the compound of Formula (I) wherein R is a C alkylcarbonyl.
In another embodiment is the compound of Formula (I) wherein R is CH CO-.
In another embodiment is the compound of Formula (I) wherein R is a
C -C alkylcarbonyl. In another embodiment is the compound of Formula (I) wherein
1 15
R is a C -C alkyloxycarbonyl. In another embodiment is the compound of Formula
1 30
(I) wherein R is a C -C alkyloxycarbonyl. In another embodiment is the compound
1 10
of Formula (I) wherein R is a C -C alkyloxycarbonyl. In another embodiment is the
compound of Formula (I) wherein R is a C -C alkyloxycarbonyl. In another
embodiment is the compound of Formula (I) wherein R is a C alkyloxycarbonyl. In
another embodiment is the compound of Formula (I) wherein R is a CH OCO-. In
another embodiment is the compound of Formula (I) wherein R is a -
C(=O)OCH CHOH, –C(=O)OCH CH OCH CHOH, or –
2 2 2 2 2 2
C(=O)OCH CH OCH CH OCH CH OH.
2 2 2 2 2 2
In another embodiment is the compound of Formula (I) wherein R is
-C(=O)NHR . In another embodiment is the compound of Formula (I) wherein wherein
13 21 21
R is -C(=O)NHR and R is methyl.
Table 1 provides, by way of example only, representative linkages for
compounds of Formula (I)
Table 1. Representative Intersubunit Linkages (X-groups)
W P X
No. X
2 NNH
4 NN
No. X
8 O N
NO
N NH
No. X
NNH
16 NN
17 NNH
NN
21 NN
22 NN
N NH
No. X
N NH
28 N N
NN O
No. X
N NH
N NH
N NH
O CF
N NH
No. X
N NH
N NH
N NH
N NH
50 NN
No. X
51 N O
52 N
53 N
54 NCF
55 NCN
56 N N O
57 NN
59 NN
60 NN NH
No. X
62 O
67 NN
NN CA
CA=cholate
NN dCA
dCA=deoxycholate
No. X
N NH
73 -N(H)CH CO H
74 -N(CH )CH CO H
3 2 2
75 -N(CH CH )CH CO H
2 3 2 2
76 -N(H)CH CH CO H,
2 2 2
77 -N(CH )CH CH CO H
3 2 2 2
78 O
No. X
N NH
N NH
83 HN
HN O
85 NH O
NN S
No. X
NN S
NN S
89 O
NN S
N NH
N NH N
N NH
N NH
No. X
NN O
N NH O
N NH
100 O
101 NN
N NH
No. X
N NH
105 NN N
107 N
114 N
115 N
No. X
N NH
N NH
N NH
No. X
N NH
N NH
130 NNH
132 NN
No. X
NN S
No. X
N NH
N NH
N NH
N NH
N NH
No. X
155 OH
NN O
157 N
158 NN
N NH
No. X
N NH
N NH
N NH
N NH
B. Oligomers with Modified Terminal Groups
As noted above, the present disclosure also provides an oligomer
comprising modified terminal groups. Applicants have found that modification of the
3’ and/or 5’ end of the oligomer with various chemical moieties provides beneficial
therapeutic properties (e.g., enhanced cell delivery, potency, and/or tissue distribution,
etc.) to the oligomers. In various embodiments, the modified terminal groups comprise
a hydrophobic moiety, while in other embodiments the modified terminal groups
comprise a hydrophilic moiety. The modified terminal groups may be present with or
without the linkages described above. For example, in some embodiments, the
oligomers comprise one or more modified terminal group and modified intersubunit
linkages. Combinations of modified terminal groups and modified linkages also provide
favorable therapeutic properties to the oligomers. In some embodiments the modified
terminal group is a peptide transporter as described herein.
In another embodiment is the compound of Formula (I), wherein L is
23 23
. In another embodiment is the compound of Formula (I), wherein L is
23 23
O R R
P N R N
Q . In another embodiment is the compound of Formula (I),
23 23
O R R
P N R N
11 24
wherein L is and R is a C -C alkylene. In another
23 23
O R R
P N R N
embodiment is the compound of Formula (I), wherein L is and
24 1
wherein R is ethylene or propylene, and R is hydrogen or methyl.
In another embodiment is the compound of Formula (I), wherein L is
23 23
O H O
. In another embodiment is the compound of Formula (I),
23 23
O H O
11 4
wherein L is and R is hydrogen or methyl. In another
23 23
O CH O
R R 3
embodiment is the compound of Formula (I), wherein L is H .
In another embodiment is the compound of Formula (I), wherein L is
. In another embodiment is the compound of Formula (I), wherein
L is and wherein p is 2, and q is 2. In another embodiment is the
compound of Formula (I), wherein L is and wherein p is 2, and
q is 3. In another embodiment is the compound of Formula (I), wherein L is
. In another embodiment is the compound of Formula (I),
wherein L is , p and q are independently selected from 1 or 2,
6 13
and R is CH . In another embodiment is the compound of Formula (I), wherein L is
. In another embodiment is the compound of Formula (I),
13 q
wherein L is , and p, q, s and t are independently
selected from 1 or 2. In another embodiment is the compound of Formula (I), wherein
1 23
R is methyl. In another embodiment is the compound of Formula (I), wherein R is
hydrogen, methyl or both R groups together form a cyclopropyl, cyclobutyl,
cyclopentyl or cyclohexyl ring. In another embodiment is the compound of Formula (I),
wherein R is hydrogen or methyl.
In another embodiment is the compound of Formula (I), wherein Z is –
C(R ) OP(=O)(OH) . In another embodiment is the compound of Formula (I), wherein
R is hydrogen.
In another embodiment is the compound of Formula (I), wherein Z is -
11 15 15
(L )-(R ) and the R is C -C alkyl, C -C alkylcarbonyl, C -C alkyloxycarbonyl,
1 30 1 30 2 30
or a 3-18 membered alkoxyalkylcarbonyl. In another embodiment is the compound of
11 15 15
Formula (I), wherein Z is -(L )-(R ) and the R is a C -C alkyloxycarbonyl. In
2 30
11 15
another embodiment is the compound of Formula (I), wherein Z is -(L )-(R ) and the
R is selected from -C(=O)OCH CHOH, –C(=O)OCH CH OCH CHOH, or –
2 2 2 2 2 2
C(=O)OCH CH OCH CH OCH CH OH. In another embodiment is the compound of
2 2 2 2 2 2
11 15 15
Formula (I), wherein Z is -(L )-(R) and the R is –
C(=O)OCH CH OCH CH OCH CH OH.
2 2 2 2 2 2
In another embodiment is the compound of Formula (I), wherein Z is
selected from:
O P N N O OH
H C CH
3 3 ,
O P N N O O
O OH
H C CH
, or
O P N
O OH
H C CH
3 3 .
In another embodiment is the compound of Formula (I), wherein Z is
O P N N O O
O OH
H C CH
3 3 .
In another embodiment is the compound of Formula (I) wherein R is an
electron pair.
In another embodiment is the compound of Formula (I) wherein R is a
C1-C30 alkyl and R is a C1-C6 alkyl. In another embodiment is the compound of
13 12
Formula (I) wherein R is a methyl group and R is a methyl group.
In another embodiment is the compound of Formula (I) wherein R is
hydrogen.
In another embodiment is the compound of Formula (I) wherein R is
C1-C30 alkyl. In another embodiment is the compound of Formula (I) wherein R is C1-
C10 alkyl. In another embodiment is the compound of Formula (I) wherein R is C1-C6
alkyl. In another embodiment is the compound of Formula (I) wherein R is selected
from prenyl, geranyl, farnesyl or geranylgeranyl.
In another embodiment is the compound of Formula (I) wherein R is a
cell-penetrating peptide.
In another embodiment is the compound of Formula (I) wherein R is a
guanidinyl or amidinyl group.
In another embodiment is the compound of Formula (I) wherein R is a
C -C cycloalkyl.
In another embodiment is the compound of Formula (I) wherein R is a
C -C alkylcarbonyl. In another embodiment is the compound of Formula (I) wherein
1 30
R is a C -C alkylcarbonyl. In another embodiment is the compound of Formula (I)
1 15
wherein R is a C -C alkylcarbonyl. In another embodiment is the compound of
1 10
Formula (I) wherein R is a C -C alkylcarbonyl. In another embodiment is the
compound of Formula (I) wherein R is a C -C alkylcarbonyl. In another embodiment
is the compound of Formula (I) wherein R is a C -C alkylcarbonyl. In another
embodiment is the compound of Formula (I) wherein R is a C -C alkylcarbonyl. In
another embodiment is the compound of Formula (I) wherein R is a C alkylcarbonyl.
In another embodiment is the compound of Formula (I) wherein R is CH CO-.
In another embodiment is the compound of Formula (I) wherein R is a
C -C alkylcarbonyl. In another embodiment is the compound of Formula (I) wherein
1 15
R is a C -C alkyloxycarbonyl. In another embodiment is the compound of Formula
1 30
(I) wherein R is a C -C alkyloxycarbonyl. In another embodiment is the compound
1 10
of Formula (I) wherein R is a C -C alkyloxycarbonyl. In another embodiment is the
compound of Formula (I) wherein R is a C -C alkyloxycarbonyl. In another
embodiment is the compound of Formula (I) wherein R is a C alkyloxycarbonyl. In
another embodiment is the compound of Formula (I) wherein R is a CH OCO-. In
another embodiment is the compound of Formula (I) wherein R is a –
C(O)CH CH CO H. In another embodiment is the compound of Formula (I) wherein
2 2 2
R is a -C(=O)OCH CHOH, –C(=O)OCH CH OCH CHOH, or –
2 2 2 2 2 2
C(=O)OCH CH OCH CH OCH CH OH.
2 2 2 2 2 2
In another embodiment is the compound of Formula (I) wherein R is
-C(=O)NHR . In another embodiment is the compound of Formula (I) wherein wherein
13 21 21
R is -C(=O)NHR and R is methyl.
In some other embodiments, only the 3’ terminus of the oligomer is
conjugated to one of the groups noted above. In some other embodiments, only the 5’
terminus of the oligomer is conjugated to one of the groups noted above. In other
embodiments, both the 3’ and 5’ termini comprise one of the groups noted above. The
terminal group for either the 5’ terminus, the 3’ terminus, or both, may be selected from
any one of the groups noted above or any of the specific groups illustrated in Table 2.
Table 2. Representative Terminal Groups
No. Name Structure
1 Trimethoxybenzoyl
2 9-fluorene-carboxyl
3 4-carbazolylbenzoyl
4 4-indazolylonebenzoyl
No. Name Structure
Farnesyl
6 Geranyl
7 Prenyl
8 Diphenylacetyl
9 Chlorodiphenylacetyl
Hydroxydiphenylacetyl
No. Name Structure
11 4,4-Diphenyl-butionyl
3,3,3-Triphenyl-
propionyl
13 Triphenylacetyl
14 Trityl (Tr)
No. Name Structure
Methoxytrityl
(MeOTr)
Methylsuccinimidyl-
cyclohexoyl
17 Thioacetyl
18 COCH CH SSPy
19 Guanidinyl
Trimethylglycine
21 Lauroyl
Triethyleneglycoloyl
(EG3)
No. Name Structure
23 Succinicacetyl
24 Diphenylphosphoryl
Piperidinyl
26 Tritylpiperidinyl
27 Boc- Piperidinyl
28 Hexynyl
No. Name Structure
29 5-carboxyfluorescein
Benzhydryl
31 p-Chlorobenzhydryl
32 Piperazinyl (pip)
33 Triphenylphos
No. Name Structure
34 Acetamide CH CO-
Methylurea CH NHCO-
1. Peptide Transporters
In some embodiments, the subject oligomer is conjugated to a peptide
transporter moiety, for example a cell-penetrating peptide transport moiety, which is
effective to enhance transport of the oligomer into cells. For example, in some
embodiments the peptide transporter moiety is an arginine-rich peptide. In further
embodiments, the transport moiety is attached to either the 5’ or 3’ terminus of the
oligomer. When such peptide is conjugated to either termini, the opposite termini is
then available for further conjugation to a modified terminal group as described herein.
In some embodiments of the foregoing, the peptide transport moiety
comprises 6 to 16 subunits selected from X’ subunits, Y’ subunits, and Z’ subunits,
where
(a) each X’ subunit independently represents lysine, arginine or an
arginine analog, said analog being a cationic a-amino acid comprising a side chain of
33 34 33 34 35 34
the structure R N=C(NH )R , where R is H or R; R is R , NH , NHR, or NR ,
where R is lower alkyl or lower alkenyl and may further include oxygen or nitrogen;
33 34
R and R may together form a ring; and the side chain is linked to said amino acid via
33 34
R or R ;
(b) each Y’ subunit independently represents a neutral amino acid
-C(O)-(CHR) -NH-, where n is 2 to 7 and each R is independently H or methyl; and
(c) each Z’ subunit independently represents an a-amino acid having
a neutral aralkyl side chain;
wherein the peptide comprises a sequence represented by one of
(X’Y’X’) (X’Y’) and (X’Z’Z’) , where p is 2 to 5 and m is 2 to 8.
p, m, p
In selected embodiments, for each X’, the side chain moiety is guanidyl,
as in the amino acid subunit arginine (Arg). In further embodiments, each Y’ is
-CO-(CH ) CHR-NH-, where n is 2 to 7 and R is H. For example, when n is 5 and R is
2 n-
H, Y’ is a 6-aminohexanoic acid subunit, abbreviated herein as Ahx; when n is 2 and R
is H, Y’ is a b-alanine subunit.
In certain embodiments, peptides of this type include those comprising
arginine dimers alternating with single Y’ subunits, where Y’ is Ahx. Examples
include peptides having the formula (RY’R) or the formula (RRY’) where Y’ is Ahx.
p p,
In one embodiment, Y’ is a 6-aminohexanoic acid subunit, R is arginine and p is 4.
In a further embodiment, each Z’ is phenylalanine, and m is 3 or 4.
In some embodiments, the conjugated peptide is linked to a terminus of
the oligomer via a linker Ahx-B, where Ahx is a 6-aminohexanoic acid subunit and B is
a b-alanine subunit.
In selected embodiments, for each X’, the side chain moiety is
independently selected from the group consisting of guanidyl (HN=C(NH )NH-),
amidinyl (HN=C(NH)C-), 2-aminodihydropyrimidyl, 2-aminotetrahydropyrimidyl,
2-aminopyridinyl, and 2-aminopyrimidonyl, and it is preferably selected from guanidyl
and amidinyl . In one embodiment, the side chain moiety is guanidyl, as in the amino
acid subunit arginine (Arg).
In some embodiments, the Y’ subunits are either contiguous, in that no
X’ subunits intervene between Y’ subunits, or interspersed singly between X’ subunits.
However, in some embodiments the linking subunit may be between Y’ subunits. In
one embodiment, the Y’ subunits are at a terminus of the peptide transporter; in other
embodiments, they are flanked by X’ subunits. In further embodiments, each Y’ is
-CO-(CH ) CHR-NH-, where n is 2 to 7 and R is H. For example, when n is 5 and R is
2 n-
H, Y’ is a 6-aminohexanoic acid subunit, abbreviated herein as Ahx. In selected
embodiments of this group, each X’ comprises a guanidyl side chain moiety, as in an
arginine subunit. Exemplary peptides of this type include those comprising arginine
dimers alternating with single Y’ subunits, where Y’ is preferably Ahx. Examples
include peptides having the formula (RY’R) or the formula (RRY’) where Y’ is
4 4,
preferably Ahx. In some embodiments, the nucleic acid analog is linked to a terminal
Y’ subunit, preferably at the C-terminus. In other embodiments, the linker is of the
structure AhxB, where Ahx is a 6-aminohexanoic acid subunit and B is a b-alanine
subunit.
The peptide transport moieties as described above have been shown to
greatly enhance cell entry of attached oligomers, relative to uptake of the oligomer in
the absence of the attached transport moiety, and relative to uptake by an attached
transport moiety lacking the hydrophobic subunits Y’. Such enhanced uptake may be
evidenced by at least a two-fold increase, or in other embodiments a four-fold increase,
in the uptake of the compound into mammalian cells relative to uptake of the agent by
an attached transport moiety lacking the hydrophobic subunits Y’. In some
embodiments, uptake is enhanced at least twenty fold or at least forty fold, relative to
the unconjugated compound.
A further benefit of the peptide transport moiety is its expected ability to
stabilize a duplex between an antisense oligomer and its target nucleic acid sequence.
While not wishing to be bound by theory, this ability to stabilize a duplex may result
from the electrostatic interaction between the positively charged transport moiety and
the negatively charged nucleic acid. In some embodiments, the number of charged
subunits in the transporter is less than 14, as noted above, or in other embodiments
between 8 and 11, since too high a number of charged subunits may lead to a reduction
in sequence specificity.
Exemplary arginine-rich cell-penetrating peptide transporters are given
below in Table 3.
Table 3. Arginine-Rich Cell-Penetrating Peptide Transporters
Name Sequence (Amino to Carboxy Terminus, 5’ SEQ
to 3’) ID NO
(RFF) ; CP0407 1
3 N-RFFRFFRFFAhxbAla-COOH
RTR 2
N-RTRTRFLRRTAhxbAla-COOH
RFFR 3
N-RFFRFFRFFRAhxbAla-COOH
KTR 4
N-KTRTKFLKKTAhxbAla-COOH
KFF 5
N-KFFKFFKFFAhxbAla-COOH
KFFK 6
N-KFFKFFKFFKAhxbAla-COOH
(RFF) 7
2 N-RFFRFFAhxbAla-COOH
(RFF)2R 8
N-RFFRFFRAhxbAla-COOH
RAhx 9
N-RAhxAhxRAhxAhxRAhxAhxbAla -COOH
(RAhxR)4; P007 10
N-RAhxRRAhxRRAhxRRAhxRAhxbAla -
rTat RRRQRRKKRC 11
R9F2 RRRRRRRRRFFC
(RRAhx)4B 13
RRAhxRRAhxRRAhxRRAhxbAla
(RAhxR) AhxB; 14
4 RAhxRRAhxRRAhxRRAhxRAhxbAla
(AhxRR)4AhxB 15
AhxRRAhxRRAhxRRAhxRRAhxbAla
(RAhx) B 16
6 RAhxRAhxRAhxRAhxRAhxRAhxbAla
(RAhx)8B
RAhxRAhxRAhxRAhxRAhxRAhxRAhxbAla
(RAhxR)5AhxB 18
RAhxRRAhxRRAhxRRAhxRRAhxRAhxbAla
(RAhxRRBR) Ah 19
2 RAhxRRbAla RRAhxRRbAlaRAhxbAla
R4G RRRRG 20
RG RRRRRG 21
R6G RRRRRRG
R7G RRRRRRRG 23
RG RRRRRRRRG 24
R5GR4G RRRRRGRRRRG 25
R F RG RRRRRFFRRRRG 26
2 4
Tat-G RKKRRQRRRG
rTat-G RRRQRRKKRG 28
(RAhxR G ) RAhxRRGGRAhxRGG 29
2 2 2
(RAhxR3Ahx)2G RAhxRRRAhxRAhxRRRG 30
RP RRRRP 31
R5P RRRRRP
R6P RRRRRRP 33
RP RRRRRRRP 34
R8P RRRRRRRRP 35
bAla = beta-alanine; Ahx = 6-aminohexanoic acid
In some embodiments is a compound of Formula (I) wherein Z is –
11 12 17 17
(L )-(L )-(R ) and R is a drug, protein or toxin. In some embodiments is a
compound of Formula (I) wherein L is a linker cleaveable under biological conditions.
In some embodiments is a compound of Formula (I) wherein L is selected from:
a) –(C -C alkylene)-OC(O)O-CH O-;
1 10 2
b) –C(O)-(C -C alkylene)-OC(O)O-CH O-;
1 10 2
c) –C(O)-(CH=CH)-C(O)O-CH O-;
d) –(C -C alkylene)-S-S-CH CH O-; or
1 10 2 2
e) –C(O)–(C -C alkylene)-S-S-CH CH O-.
1 10 2 2
In some embodiments is a compound of Formula (I) wherein R is a
DNA-binding protein. In some embodiments is a compound of Formula (I) wherein R
is a transcription factor. In some embodiments is a compound of Formula (I) wherein
R is a zinc finger protein. In some embodiments is a compound of Formula (I)
wherein R is a drug, protein or toxin selected from the listing provided in Table 4.
Table 4.
ANTIANDROGEN
Bicalutamide, Bifluranol, Cioteronel, Cyproterone, Delmadinone
Acetate, Flutamide, Nilutamide, Osaterone, Oxendolone
ANTIBACTERIAL (ANTIBIOTICS)
Aminoglycosides
Amikacin, Arbekacin, Bambermycins, Butirosin, Dibekacin,
Dihydrostreptomycin, Fortimicins, Gentarnicin, Isepamicin, Kanamycin,
Micronomicin, Neomycin, Netilmicin, Paromomycin, Ribostamycin, Sisomicin,
Spectinomycin, Streptomycin, Tobramycin, Trospectomycin
Amphenicols
Azidamfenicol, Chloramphenicol, Thiamphenicol
Ansamycins
Rifamide, Rifampin, Rifamycin SV, Rifapentine, Rifaximin
β-Lactams
Carbacephems
Loracarbef
Carbapenems
Biapenem, Ertapenem, Fropenem, Imipenem, Meropenem, Panipenem
Cephalosporins
Cefaclor, Cefadroxil, Cefamandole, Cefatrizine, Cefazedone, Cefazolin,
Cefcapene Pivoxil, Cefclidin, Cefdinir, Cefditoren, Cefepime, Cefetamet, Cefixime,
Cefmenoxime, Cefodizime, Cefonicid, Cefoperazone, Ceforanide, Cefoselis,
Cefotaxime, Cefotiam, Cefozopran, Cefpimizole, Cefpiramide, Cefpirome,
Cefpodoximc Proxetil, Cefprozil, Cefroxadine, Cefsulodin, Ceftazidime, Cefteram,
Ceftezole, Ceftibuten, Ceftizoxime, Ceftriaxone, Cefuroxime, Cefuzonam, Cephacetrile
Sodium, Cephalexin, Cephaloglycin, Cephaloridine, Cephalosporin C, Cephalothin,
Cephapirin Sodium, Cephradine, Pivcefalexin
Cephamycins
Cefbuperazone, Cefmetazole, Cefminox, Cefotetan, Cefoxitin
Monobactams
Aztreonam, Carumonam, Tigemonam
Oxacephems
Flomoxef, Moxalactam
Penicillins
Amdinocillin, Amdinocillin Pivoxil, Amoxicillin, Ampicillin, Apalcillin,
Aspoxicillin, Azidocillin, Azlocillin, Bacampicillin, Carbenicillin, Carindacillin,
Clometocillin, Cloxacillin, Cyclacillin, Dicloxacillin, Epicillin, Fenbenicillin,
Floxacillin, Hetacillin, Lenampicillin, Metampicillin, Methicillin Sodium, Mezlocillin,
Nafcillin, Oxacillin, Penamecillin, Penethamate Hydriodide, Penicillin G, Penicillin G
Benzathine, Penicillin G Procaine, Penicillin N, Penicillin O, Penicillin V,
Penimepicycline, Phenethicillin Potassium, Piperacillin, Pivampicillin, Propicillin,
Quinacillin, Sulbenicillin, Sultamicillin, Talampicillin, Temocillin, Ticarcillin
Other
Ritipenem
Lincosamides
Clindamycin, Lincomycin
Macrolides
Azithromycin, Carbomycin, Clarithromycin, Dirithromycin,
Erythromycin, Erythromycin Acistrate, Erythromycin Estolate, Erythromycin
Glucoheptonate, Erythromycin Lactobionate, Erythromycin Propionate, Erythromycin
Stearate, Josamycin, Leucomycins, Midecamycins, Miokamycin, Oleandomycin,
Primycin, Rokitamycin, Rosaramicin, Roxithromycin, Spiramycin, Telithromycin,
Troleandomycin
Polypeptides
Amphomycin, Bacitracin, Bacitracin Zinc, Capreomycin, Colistin,
Enduracidin, Enviomycin, Fusafungine, Gramicidin(s), Gramicidin S, Polymyxin,
Quinupristin, Ristocetin, Teicoplanin, Thiostrepton, Tuberactinomycin, Tyrocidine,
Tyrothricin, Vancomycin, Viomycin
Tetracyclines
Chlortetracycline, Clomocycline, Demeclocycline, Doxycycline,
Guamecycline, Lymecycline, Meclocycline, Methacycline, Minocycline,
Oxytetracycline, Penimepicycline, Pipacycline, Rolitetracycline, Sancycline,
Tetracycline
Others
Cycloserine, Dalfopristin, Mupirocin, Pristinamycin, Virginiamycin
ANTIBACTERIAL (SYNTHETIC)
2,4-Diaminopyrimidines
Brodimoprim, Tetroxoprim, Trimethoprim, Nitrofurans
Furaltadone, Furazolium Chloride, Nifuratel, Nifurfoline, Nifurpirinol,
Nifurprazine, Nifurtoinol, Nitrofurantoin, Oxazolidinones
Linezolid
Quinolones and Analogs
Balofloxacin, Cinoxacin, Ciprofloxacin, Clinafloxacin, Enoxacin,
Fleroxacin, Flumequine, Gatifloxacin, Gemifloxacin, Grepafloxacin, Lomefloxacin,
Miloxacin, Moxifloxacin, Nadifloxacin, Nalidixic Acid, Norfloxacin, Ofloxacin,
Oxolinic Acid, Pazufloxacin, Pefloxacin, Pipemidic Acid, Piromidic Acid, Rosoxacin,
Rufloxacih, Sitafloxacin, Sparfloxacin, Tosufloxacin, Trovafloxacin
Sulfonamides
Acetyl Sulfamethoxypyrazine, Chloramine-B, Chloramine-T,
Dichloramine T, N -Formylsulfisomidine, N - β-D-Glucosylsulfanilamide, Mafenide,
Noprylsulfamide, Phthalylsulfacetamide, Phthalylsulfathiazole, Salazosulfadimidine,
Succinylsulfathiazole, Sulfabenzamide, Sulfacetamide, Sulfachlorpyridazine,
Sulfachrysoidine, Sulfacytine, Sulfadiazine, Sulfadicramide, Sulfadimethoxine,
Sulfadoxine, Sulfaethidole, Sulfaguanidine, Sulfaguanole, Sulfalene, Sulfaloxic Acid,
Sulfamerazine, Sulfameter, Sulfamethazine, Sulfamethizole, Sulfamethomidine,
Sulfamethoxazole, Sulfamethoxypyridazine, Sulfametrole, Sulfamidochrysoidine,
Sulfamoxole, Sulfanilamide, 4-Sulfanilamidosalicylic Acid, N -Sulfanilylsulfanilamide,
Sulfanilylurea, N-SulfaniIyl-3,4-xylamide, Sulfaperine, Sulfaphenazole, Sulfaproxyline,
Sulfapyrazine, Sulfapyridine, Sulfasomizole, Sulfasymazine, Sulfathiazole,
Sulfathiourea, Sulfisomidine, Sulfisoxazole
Sulfones
Acedapsone, Acediasulfone, Acetosulfone Sodium, Dapsone,
Diathymosulfone, Glucosulfone Sodium, Solasulfone, Succisulfone, Sulfanilic Acid, p-
Sulfanilylbenzylamine, Sulfoxone Sodium, Thiazolsulfone
Others
Clofoctol, Hexedine, Methenamine, Metronidazole, Nitroxoline,
Pexiganan, Taurolidine, Xibornol
ANTIBACTERIAL (LEPROSTATIC)
Acedapsone, Acetosulfone Sodium, Qofazimine, Dapsone,
Diathymosulfone, Glucosulfone Sodium, Hydnocarpic Acid, Solasulfone, Succisulfone,
Sulfoxone Sodium
ANTIBACTERIAL (TUBERCULOSTATIC)
p-Aminosalicylic Acid, p-Aminosalicylic Acid Hydrazide, Benzoylpas,
-Bromosalicylhydroxamic Acid, Capreomycin, Clofazimine, Cyacetacide,
Cycloserine, Dihydrostreptomycin, Enviomycin, Ethambutol, Ethionamide, Furonazide,
Glyconiazide, Isoniazid, Morphazinamide, Opiniazide, Phenyl Aminosalicylate,
Protionamide, Pyrazinamide, Rifabutin, Rifalazil, Rifampin, Rifapentine, Salinazid,
Streptomycin, Streptonicozid, Sulfoniazide, Thiacetazone, Tiocarlide,
Tuberactinomycin, Tubercidin, Viomycin, Dimethazan, Fencamine, Indalpine,
Indeloxazine Hydrochloride, Nefopam, Nomifensine, Oxitriptan see 4873 Oxypertine,
Paroxetine, Sertraline, Thiazesim, Trazodone
Hydrazides/Hydrazines
Iproclozide, Iproniazid, Isocarboxazid, Nialamide, Octamoxin,
Phenelzine
Phenyloxazolidinones
Befloxatone, Toloxatone
Pyrrolidones
Cotinine
Tetracydics
Maprotiline, Metralindole, Mianserin, Mirtazapine
Tricyclics
Adinazolam, Amineptine, Amitriptyline, Amitriptylinoxide, Amoxapine,
Butriptyline, Clomipramine, Demexiptiline, Desipramine, Dibenzepin, Dimetaciine,
Dothiepin, Doxepin, Fluacizine, Imipramine, Imipramine N-Oxide, Iprindole,
Lofepramine, Melitracen, Metapramine, Nortriptyline, Noxiptilin, Opipramol,
Pizotyline, Propizepine, Protriptyline, Quinupramine, Tianeptine, Trimipramine
Others
Adrafinil, Bupropion, Butacetin, Dioxadrol, Duloxetine, Etoperidone,
Femoxetine, Fenpentadiol, Fluoxetine, Fluvoxamine, Hematoporphyrin, Hypericin,
Levophacetoperane, Medifoxamine, Milnacipran, Minaprine, Moclobemide,
Nefazodone, Oxaflozane, Piberaline, Prolintane, Pyrisuccideanol, Reboxetine,
Ritanserin, Roxindole, Rubidium Chloride, Sulphide, Tandospirone, Thozalinone,
Tofenacin, Tranylcypromine, Tryptophan, Venlafaxine, Viloxazine, Zimeldine
ANTIDIABETIC
Biguanides
Buformin, Metformin, Phenformin
Hormones/Analogs
Amylin, Insulin, Insulin Aspart, Insulin Glargine, Insulin Lispro,
Pramlintide
Sulfonylurea Derivatives
Acetohexamide, Carbutamide, Chlorpropamide, Glibomuride,
Gliclazide, Glimepiride, Glipizide, Gliquidone, Glisoxepid, Glyburide, Glybuthiazol(e),
Glybuzole, Glyhexamide, Glymidine, Glypinamide, Phenbutamide, Tolazamide,
Tolbutamide, Tolcyclamide
Thiazolidinediones
Pioglitazone, Rosiglitazone, Troglitazone
Others
Acarbose, Calcium Mesoxalate, Miglitol, Nateglinide, Repaglinide,
Voglibose
ANTIESTROGEN
Centchroman, Delmadinone Acetate, Tamoxifen, Toremifene
ANTIFUNGAL (ANTIBIOTICS)
Polyenes
Amphotericin B, Candicidin, Dermostatin, Filipin, Fungichrornin,
Hachimycin, Hamycin, Lucensomycin, Klepartricin, Natamycin, Nystatin, Pecilocin,
Perimycin
Others
Azaserine, Caspofungin, Griseofulvin, Ohgomycins, Pyrrolnitrin,
Siccanin, Tubercidin, Viridin
ANTIFUNGAL (SYNTHETIC)
Allylamines
Butenafine, Naftifine, Terbinafine
Imidazoles
Bifonazole, Butoconazole, Chlordantoin, Chlormidazole, Cloconazole,
Clotrimazole, Econazole, Enilconazole, Fenticonazole, Flutrimazole, Isoconazole,
Ketoconazole, Lanoconazole, Miconazole, Neticonazole, Omoconazole, Oxiconazole
Nitrate, Sertaconazole, Sulconazole, Tioconazole
Thiocarbamates
Liranaftate, Tolciclate, Tolindate, Tolnaftate, Triazoles Fluconazole,
Itraconazole, Posaconazole, Saperconazole, Terconazole, Voriconazole
Others
Acrisorcin, Amorolfine, Biphenamine, Bromosalicylchloranilide,
Buclosamide, Calcium Propionate, Chlorphenesin, Ciclopirox, Cloxyquin,
Coparaffinate, Diamthazole Dihydrochloride, Exalamide, Flucytosine, Hexetidine,
Loflucarban, Nifuratel, Potassium Iodide, Propionic Acid, Pyrithione, Salicylanilide,
Sodium Propionate, Sulbentine, Tenonitrozole, Triacetin, Undecylenic Acid, Zinc
Propionate
ANTIGONADOTROPIN
Danazol, Gestrinone, Paroxypropione
ANTINEOPLASTIC
Alkaloids
9-Aminocamptothecin, Docetaxel, Ecteinascidins, Etoposide, Irinotecan,
Paclitaxel, Rubitecan, Teniposide, Topotecan, Vinblastine, Vincristine, Vindesine
Alkylating Agents
Alkyl Sulfonates
Busulfan, Improsulfan, Piposulfan
Aziridines
Carboquone, Uredepa
Ethylenimines and Methylmelamines
Altretamine, Triethylenemelamine, Triethylenephosphoramide,
Triethylenethiophosphoramide
Nitrogen Mustards
Chlorambucil, Chlornaphazine, Cyclophosphamide, Estramustine,
Ifosfamide, Mechlorethamine, Mechlorethamine Oxide Hydrochloride, Melphalan,
Novembichin, Perfosfamide, Phenesterine, Prednimustine, Trichlonnethine,
Trofosfamide, Uracil Mustard
Nitrosoureas
Carmustine, Chlorozotocin, Fotemustine, Lomustine, Nimustine,
Ranimustine
Others
Dacarbazine, Mannomustine, Mitobronitol, Mitolactol, Pipobroman,
Temozolomide
Antibiotics and Analogs
Aclacinomycins, Anthramycin, Azaserine, Bleomycins, Cactinomycin,
Carubicin, Chromomycins, Dactinomycin, Daunorubicin, 6-Diazooxo-L-norleucine,
Doxorubicin, Epirubicin, Idarubicin, Menogaril, Mitomycins, Mycophenolic Acid,
Nogalamycin, Olivomycins, Peplomycin, Pirarubicin, Plicamycin, Porfiromycin,
Puromycin, Streptonigrin, Streptozocin, TNP-470, Tubercidin, Valrubicin, Zinostatin,
Zorobicin
Antimetabolites
Folk Acid Analogs/Antagonists
Denopterin, Edatrexate, Methotrexate, Nolatrexed, Pemetrexed,
Piritrexim, Pteropterin, Raltitrexed, Trimetrexate
Purine Analogs
Cladribine, Fludarabine, 6-Mercaptopurine, Thiamiprine, Thioguanine,
Tiazofurin
Pyrimidine Analogs
Ancitabine, Azacitidine, 6-Azauridine, Capecitabine, Carmofur,
Cytarabine, Decitabine, Doxifluridine, Emitefur, Enocitabine, Floxuridine,
Fluorouracil, Gemcitabine, Tegafur
Enzymes
L-Asparaginase, Ranpirnase
Immunomodulators
Bropirimine, Interferon- α, Interferon- γ, Interleukin-2, Lentinan,
Propagermanium, PSK , Roquinimex, Sizofiran, Ubenimex
Immunotoxins
Denileukin Diftitox
Monoclonal Antibodies
Alemtuzumab, Edrecolomab, Gemtuzumab Ozogamicin, Ibritumomab
Tiuxetan, Rituximab, Tositumomab I, Trastuzumab
Platinum Complexes
Carbopiatin, Cisplatin, Lobaplatin, Miboplatin, Oxaliplatin
Others
Amsacrine, Arsenic Trioxide, Bisantrene, Defosfamide, Demecoline,
Diaziquone, Eflornithine, Elliptinium Acetate, Etoglucid, Fenretinide, Flavopridol,
Gallium Nitrate, Hydroxyurea, Imatinib, Liarozole, Lonidamine, Miltefosine,
Mitoguazone, Mitoxantrone, Mopidamol, Nictracrine, Pentostatin, Phenamet,
Podophyllinic Acid 2-Ethylhy-drazide, Procarbazine, Razoxane, Sobuzoxane,
Spirogermanium, Tenuazonic Acid, Tirapazamine, Triaziquone, Urethan
ANTINEOPLASTIC (HORMONAL)
Androgens
Calusterone, Dromostanolone, Epitiostanol, Mepitiostane, Testolactone
Antiadrenals
Aminoglutethimide, Mitotane, Trilostane
Antiandrogens
Bicalutamide, Flutamide, Nilutamide
Antiestrogens
Droloxifenc, Idoxifene, Tamoxifen, Torcmifene
Antiprogestins
Onapristone
Aromatase Inhibitors
Aminoglutethimide, Anastrozole, Exemestane, Fadrozole, Formestane,
Letrozole, Vorozole
Estrogens
Diethylstilbestrol, Fosfestrol, Hexestrol, Polyestradiol Phosphate
LH-RH Analogs
Buserelin, Cetrorelix, Goserelin, Leuprolide, Triptorelin
Progestogens
Chlormadinone Acetate, Medroxyprogesterone, Megestrol Acetate,
Melengestrol
Retinoids and Analogs
Alitretinoin, Bexarotene, Mofarotene
Somatostatin Analog
Lanreotide
ANTINEOPLASTIC (PHOTOSENSITIZER)
Porfimer Sodium, Temoporfin, Tin Ethyl Etiopurpurin
ANTINEOPLASTIC (RADIATION SOURCE)
Americium, Chromic Phosphate, Radioactive, Cobalt, Gold,
Radioactive, Colloidal, Ibritumomab Tiuxetan, I-Ethiodized Oil Iobenguane,
Radium, Radon, Samarium Sm Lexidronam, Sodium Iodide, Radioactive, Sodium
Phosphate, Radioactive, Strontium Chloride, Radioactive, Tositumomab I
ANTINEOPLASTIC ADJUNCT
Antimetastatic Agent
Batimastat, Prinomastat
Chemomodulator
Eniluracil
Chemosensitizer
Biricodar, Valspodar
Radioprotective
Amifostine
Radiosensitjzer
Broxuridine, Etanidazole, RSR-13
Uroprotective
Mesna
ANTINEUTROPENIC
Granulocyte Colony-Stimulating Factor, Granulocyte-Macrophage
Colony-Stimulating Factor, Interleukin-3
ANTEPHEOCHROMOCYTOMA
Metyrosine, Phenoxybenzamine, Phentolamine
ANTIPNEUMOCYSTIC
Atovaquone, Eflornithine, Pentamidine, Sulfamethoxazole
ANTIPROGESTIN
Onapristone
ANTIPROSTATIC HYPERTROPHY
Doxazosin, Dutasteride, Epristeride, Finasteride, Gestonorone Caproate,
Mepartricin, Osaterone, Oxendolone, Tamsulosin, Terazosin
ANTIPROTOZOAL (CRYPTOSPO-RIDIUM)
Nitazoxanide
ANTIPROTOZOAL (LEISHMANIA)
Ethylstibamine, Hydroxystilbamidine, N-Methylglucamine,
Pentamidine, Sodium Stibogluconate see 707 Stilbamidine, Urea Stibamine
ANTIPROTOZOAL (TOXO-PLASMA)
Pyrimethamine
ANTIPROTOZOAL (TRICHO-MONAS)
Acetarsone, Aminitrozole, Anisomycin, Azanidazole, Furazolidone,
Hachimycin, Lauroguadine, Mepartricin, Metronidazole, Nifuratel, Nifuroxime,
Nimorazole, Secnidazole, Silver Picrate, Tenonitrozole, Tinidazole
ANTIPROTOZOAL (TRYPANO-SOMA)
Benznidazole, Eflomithine, Melarsoprol, Nifurtimox, Oxophenarsine
Hydrochloride, Pentamidine, Propamidine, Puromycjn, Quinapyramine, Stilbamidine,
Suramin Sodium, Trypan Red, Tryparsamidc
ANTIVIRAL
Monoclonal Antibodies
Palivizumab
Peptidomimetics
Amprenavir, Indinavir, Lopinavir, Nelfinavir, Ritonavir, Saquinavir
Polynucleotides
Ampligen, Fomivirsen
Purines/Pyrimidinones
Abacavir, Acyclovir, Adefovir, Cidofovir, Cytarabine, Didanosine,
Dideoxyadenosine, Edoxudine, Emtricitabine, Famciclovir, Floxuridine, Ganciclovir,
Idoxuridine, Inosine Pranobex, Lamivudine, MADU, Penciclovir, Sorivudine,
Stavudine, Tenofovir, Trifluridine, Valacyclovir, Valganciclovir, Vidarabine,
Zalcitabine, Zidovudine
Sialic Acid Analogs
Oseltamivir, Zanamivir
Others
Acemannan, Acetylleucine Monoethanolamine, Amantadine,
Amidinomycin, Atevirdine, Capravirine, Delavirdine, n-Docosanol, Efavirenz,
Foscamet Sodium, Interferon-", Interferon-$, Interferon-y, Kethoxal, Lysozyme,
Methisazone, Moroxydine, Nevirapine, Pentafiiside, Pleconaril, Podophyllotoxin,
Ribavirin, Rimantadine, Stallimycin, Statolon, Tremacamra, Tromantadine
AROMATASE INHIBITORS
Aminoglutethimide, Anastrozole, Exemestane, Fadrozole, Formestane,
Letrozole, Vorozole
DIAGNOSTIC AID (MRI CONTRAST AGENT)
Ferumoxides, Ferumoxsil, Gadobenate Dimeglumine, Gadobutrol,
Gadodiamide, Gadopentetic Acid, Gadoteridol, Gadoversetamide, Gadoxetic Acid,
Mangafodipir, MS-325, Perflubron
DIAGNOSTIC AID (RADIOACTIVE IMAGING AGENT)
Arcitumomab Complex with Tc, Butedronic Acid Complex, Capromab
Pendetide, Depreotide Complex with Tc, Disofenin Complex with Tc, Exametazime
131 123
Complex with Tc, Fludeoxyglucose F18, o-Iodohippurate Sodium I, Iofetamine I
GLUCOCORTOCOID
21-Acetoxypregnenolone, Alclometasone, Algestone, Amcinonide,
Beclomethasone, Betamethasone, Budesonide, Chloroprednisone, Ciclesonide,
Clobetasol, Clobetasone, Clocortolone, Cloprednol, Corticosterone, Cortisone,
Cortivazol, Deflazacort,
Prednisolone Sodium Phosphate, Prednisone, Prednival, Prednylidene,
Rimexolone, Tixocortol, Triamcinolone, Triamcinolone Acetonide, Triamcinolone
Benetonide, Triamcinolone Hexacetonide
GROWTH HORMONE ANTAGONIST/INHIBITOR
Octreotide, Pegvisomant, Somatostatin
GROWTH HORMONE RELEASING FACTOR
Sermorelin
GROWTH STIMULANT
Somatotropin
REVERSE TRANSCRIPTASE INHIBITOR
Abacavir, Atevirdine, Capravirine, Delavirdine, Didanosine,
Dideoxyadenosine, Efavirenz, Emtricitabine, Foscarnet Sodium, Lamivudine,
Nevirapine, Stavudine, Suramin Sodium, Tenofovir, Zalcitabine, Zidovudine
TOPOISOMERASEI INHIBITOR
9-Aminocamptothecin, Irinotecan, Topotecan
TOPOISOMERASE II INHIBITOR
Daunorubicin, Doxorubicin, Etoposide, Sobuzoxane, Teniposide
C. Properties of the Oligomers
As noted above, the present disclosure is directed to oligomer
comprising various modifications which impart desirable properties (e.g., increased
antisense activity) to the oligomers. In certain embodiments, the oligomer comprises a
backbone comprising a sequence of morpholino ring structures joined by intersubunit
linkages, the intersubunit linkages joining a 3’-end of one morpholino ring structure to a
’-end of an adjacent morpholino ring structure, wherein each morpholino ring structure
is bound to a base-pairing moiety, such that the oligomer can bind in a sequence-
specific manner to a target nucleic acid. The morpholino ring structures may have the
following structure (i):
wherein B is, at each occurrence, independently a base-pairing moiety.
Each morpholino ring structure supports a base pairing moiety (Pi), to
form a sequence of base pairing moieties which is typically designed to hybridize to a
selected antisense target in a cell or in a subject being treated. The base pairing moiety
may be a purine or pyrimidine found in native DNA or RNA (A, G, C, T, or U) or an
analog, such as hypoxanthine (the base component of the nucleoside inosine) or 5-
methyl cytosine. Analog bases that confer improved binding affinity to the oligomer
can also be utilized. Exemplary analogs in this regard include C5-propynyl-modifed
pyrimidines, 9-(aminoethoxy)phenoxazine (G-clamp) and the like.
Further examples of base pairing moieties include, but are not limited to, uracil,
thymine, adenine, cytosine, and guanine having their respective amino groups protected by acyl
protecting groups, 2-fluorouracil, 2-fluorocytosine, 5-bromouracil, 5-iodouracil, 2,6-
diaminopurine, azacytosine, pyrimidine analogs such as pseudoisocytosine and pseudouracil
and other modified nucleobases such as 8-substituted purines, xanthine, or hypoxanthine (the
latter two being the natural degradation products). The modified nucleobases disclosed in Chiu
and Rana, RNA, 2003, 9, 1034-1048, Limbach et al. Nucleic Acids Research, 1994, 22,
2183-2196 and Revankar and Rao, Comprehensive Natural Products Chemistry, vol. 7,
313, are also contemplated.
Further examples of base pairing moieties include, but are not limited to,
expanded-size nucleobases in which one or more benzene rings has been added.
Nucleic base replacements described in the Glen Research catalog
(www.glenresearch.com); Krueger AT et al, Acc. Chem. Res., 2007, 40, 141-150; Kool,
ET, Acc. Chem. Res., 2002, 35, 936-943; Benner S.A., et al., Nat. Rev. Genet., 2005, 6,
553-543; Romesberg, F.E., et al., Curr. Opin. Chem. Biol., 2003, 7, 723-733; Hirao, I.,
Curr. Opin. Chem. Biol., 2006, 10, 622-627, are contemplated as useful for the
synthesis of the oligomers described herein. Some examples of these expanded-size
nucleobases are shown below:
HN NH
As noted above, the oligomer may be modified, in accordance with an
aspect of the invention, to include one or more X2-X8 groups. In some embodiments, a
compound of Formula I contains at least one X3-X8 group and no X2 group. In some
embodiments, a compound of Formula I contains at least one X2, X4, X5, X6, X7, or
X8 group and no X3 group. In some embodiments, a compound of Formula I contains
at least one X2, X3, X5, X6, X7, or X8 group and no X4 group. In some embodiments,
a compound of Formula I contains at least one X2, X3, X4, X6, X7, or X8 group and no
X5 group. In some embodiments, a compound of Formula I contains at least one X2,
X3, X4, X5, X7, or X8 group and no X6 group. In some embodiments, a compound of
Formula I contains at least one X2, X3, X4, X5, X6, or X8 group and no X7 group. In
some embodiments, a compound of Formula I contains at least one X2-X7 group and
no X8 group. In some embodiments is a compound of Formula I wherein X is not
H N +
NH . In some embodiments is a compound of Formula I
wherein R is acetyl and X is not . In some
embodiments is a compound of Formula I wherein X is not
. In some embodiments is a compound of Formula I
H N +
wherein R is acetyl and X is not NH . In some
embodiments is a compound of Formula I wherein X is not
2. In some embodiments is a compound of Formula I
wherein R is acetyl and X is not . In some
embodiments is a compound of Formula I wherein X is not
. In some embodiments is a compound
of Formula I wherein R is acetyl and X is not
. In some embodiments is a compound
of Formula I wherein X is not . In some embodiments is a
compound of Formula I wherein R is acetyl and X is not . In some
embodiments is a compound of Formula I wherein X is not . In some
embodiments is a compound of Formula I wherein R is acetyl and X is not
. In some embodiments is a compound of Formula I wherein X is not
. In some embodiments is a compound of Formula I wherein R is
acetyl and X is not . In some embodiments is a compound of Formula I
wherein X is not . In some embodiments is a compound of Formula
13 CF
I wherein R is acetyl and X is not . In some embodiments is a
compound of Formula I wherein X is not . In some
embodiments is a compound of Formula I wherein R is acetyl and X is not
. In some embodiments is a compound of Formula I
NHhxARhxARNHAc
wherein X is not . In some embodiments is a
compound of Formula I wherein R is acetyl and X is not
NHhxARhxARNHAc
In some embodiments is a compound of Formula I wherein each X group
is independently selected as described above with the provision that if the X group on
the phosphorous linkage proximal to the 3’ terminus is
NH 2
, , ,
, , ,
NHhxARhxARNHAc
or ,
then at least one other X group is not X1.
In some embodiments is a compound of Formula I wherein each X group
is independently selected as described above with the provision that if the X group on
the phosphorous linkage proximal to the 3’ terminus is
NH 2
, , ,
3 NH
, , ,
NHhxARhxARNHAc
or ,
then at least two other X groups are not X1.
In some embodiments is a compound of Formula I wherein each X group
is independently selected as described above with the provision that if the X group on
the phosphorous linkage proximal to the 3’ terminus is
NH 2
, , ,
, , ,
NHhxARhxARNHAc
or ,
then at least three other X groups are not X1.
In some embodiments is a compound of Formula I wherein each X group
is independently selected as described above with the provision that if the X group on
the phosphorous linkage proximal to the 3’ terminus is
NH 2
, , ,
3 NH
, , ,
NHhxARhxARNHAc
or ,
then all other X groups are not X1.
In some embodiments is a compound of Formula I wherein each X group
is independently selected as described above with the provision that if X1 is present as
N(CH ), and X3 is present as or
, then X7 is not piperdinyl.
In some embodiments is a compound of Formula I wherein each X group
is independently selected as described above with the provision that if X1 is present as
N(CH ) and X7 is present as piperidinyl, then X3 is not
3 2,
H N H N
O or NH .
In some embodiments, a compound of Formula I contains one X2-X8
group per every 2-5 X1 groups. In some embodiments, a compound of Formula I
contains 3-5 X2-X8 groups per every 10 X1 groups. In some embodiments, a
compound of Formula I contains 3-5 X2-X8 groups per every 10 X1 groups. In some
embodiments, a compound of Formula I contains 100% X2-X8 groups. In some
embodiments, a compound of Formula I contains 95-100% X2-X8 groups. In some
embodiments, a compound of Formula I contains 90-95% X2-X8 groups. In some
embodiments, a compound of Formula I contains 85-90% X2-X8 groups. In some
embodiments, a compound of Formula I contains 80-85% X2-X8 groups. In some
embodiments, a compound of Formula I contains 75-80% X2-X8 groups. In some
embodiments, a compound of Formula I contains 70-75% X2-X8 groups. In some
embodiments, a compound of Formula I contains 65-70% X2-X8 groups. In some
embodiments, a compound of Formula I contains 60-65% X2-X8 groups. In some
embodiments, a compound of Formula I contains 55-60% X2-X8 groups. In some
embodiments, a compound of Formula I contains 50-55% X2-X8 groups. In some
embodiments, a compound of Formula I contains 45-50% X2-X8 groups. In some
embodiments, a compound of Formula I contains 40-45% X2-X8 groups. In some
embodiments, a compound of Formula I contains 35-40% X2-X8 groups. In some
embodiments, a compound of Formula I contains 30-35% X2-X8 groups. In some
embodiments, a compound of Formula I contains 25-30% X2-X8 groups. In some
embodiments, a compound of Formula I contains 20-25% X2-X8 groups. In some
embodiments, a compound of Formula I contains 15-20% X2-X8 groups. In some
embodiments, a compound of Formula I contains 10-15% X2-X8 groups. In some
embodiments, a compound of Formula I contains 5-10% X2-X8 groups. In some
embodiments, a compound of Formula I contains less than 5% X2-X8 groups.
In some embodiments is a compound of Formula I wherein the X1
groups and the X2-X8 groups are interspersed along the backbone. In some
embodiments is a compound of Formula I wherein the X1 groups and the X2-X8 groups
have a strictly alternating pattern along the backbone. In some embodiments is a
compound of Formula I wherein the X1 groups and the X2-X8 groups do not have a
strictly alternating pattern along the backbone. In some embodiments is a compound of
Formula I having blocks of X1 groups and blocks of X2-X8 groups. In some
embodiments is a compound of Formula I having a central block of X1 groups flanked
by blocks of X2-X8 groups. In some embodiments is a compound of Formula I having
a central block of X2-X8 groups flanked by blocks of X1 groups.
In any of the aforementioned embodiments of Formula (I) wherein at
least one X is selected from X2-X8 is another embodiment wherein n is an integer from
-35. In further embodiments of the aforementioned embodiments of Formula (I)
wherein at least one X is selected from X2-X8, n is an integer from 25-29. In further
embodiments of the aforementioned embodiments of Formula (I) wherein at least one X
is selected from X2-X8, n is an integer from 20-24. In further embodiments of any of
the aforementioned embodiments of Formula (I) wherein at least one X is selected from
X2-X8, n is an integer from 15-19. In further embodiments of the aforementioned
embodiments of Formula (I) wherein at least one X is selected from X2-X8, n is an
integer from 10-14. In further embodiments of the aforementioned embodiments of
Formula (I) wherein at least one X is selected from X2-X8, n is an integer from 5-9. In
yet further embodiments of the aforementioned embodiments of Formula (I) wherein at
least one X is selected from X2-X8, n is an integer from 1-4.
In any of the aforementioned embodiments of Formula (I) wherein n is
an integer from 30-35 is another embodiment wherein one X is X2-X8. In any of the
aforementioned embodiments of Formula (I) wherein n is an integer from 30-35 is
another embodiment wherein two X are independently selected from X2-X8. In any of
the aforementioned embodiments of Formula (I) wherein n is an integer from 30-35 is
another embodiment wherein three X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 30-35
is another embodiment wherein four X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 30-35
is another embodiment wherein five X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 30-35
is another embodiment wherein six X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 30-35
is another embodiment wherein seven X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 30-
is another embodiment wherein eight X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 30-
is another embodiment wherein nine X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 30-
is another embodiment wherein ten X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 30-
is another embodiment wherein eleven X are independently selected from X2-X8.
In any of the aforementioned embodiments of Formula (I) wherein n is an integer from
-35 is another embodiment wherein twelve X are independently selected from X2-
X8. In any of the aforementioned embodiments of Formula (I) wherein n is an integer
from 30-35 is another embodiment wherein thirteen X are independently selected from
X2-X8. In any of the aforementioned embodiments of Formula (I) wherein n is an
integer from 30-35 is another embodiment wherein fourteen X are independently
selected from X2-X8. In any of the aforementioned embodiments of Formula (I)
wherein n is an integer from 30-35 is another embodiment wherein fifteen X are
independently selected from X2-X8. In any of the aforementioned embodiments of
Formula (I) wherein n is an integer from 30-35 is another embodiment wherein sixteen
X are independently selected from X2-X8. In any of the aforementioned embodiments
of Formula (I) wherein n is an integer from 30-35 is another embodiment wherein
seventeen X are independently selected from X2-X8. In any of the aforementioned
embodiments of Formula (I) wherein n is an integer from 30-35 is another embodiment
wherein eighteen X are independently selected from X2-X8. In any of the
aforementioned embodiments of Formula (I) wherein n is an integer from 30-35 is
another embodiment wherein nineteen X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 30-
is another embodiment wherein twenty X are independently selected from X2-X8.
In any of the aforementioned embodiments of Formula (I) wherein n is
an integer from 25-30 is another embodiment wherein one X is X2-X8. In any of the
aforementioned embodiments of Formula (I) wherein n is an integer from 25-30 is
another embodiment wherein two X are independently selected from X2-X8. In any of
the aforementioned embodiments of Formula (I) wherein n is an integer from 25-30 is
another embodiment wherein three X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 25-30
is another embodiment wherein four X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 25-30
is another embodiment wherein five X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 25-30
is another embodiment wherein six X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 25-30
is another embodiment wherein seven X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 25-
is another embodiment wherein eight X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 25-
is another embodiment wherein nine X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 25-
is another embodiment wherein ten X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 25-
is another embodiment wherein eleven X are independently selected from X2-X8.
In any of the aforementioned embodiments of Formula (I) wherein n is an integer from
-30 is another embodiment wherein twelve X are independently selected from X2-
X8. In any of the aforementioned embodiments of Formula (I) wherein n is an integer
from 25-30 is another embodiment wherein thirteen X are independently selected from
X2-X8. In any of the aforementioned embodiments of Formula (I) wherein n is an
integer from 25-30 is another embodiment wherein fourteen X are independently
selected from X2-X8. In any of the aforementioned embodiments of Formula (I)
wherein n is an integer from 25-30 is another embodiment wherein fifteen X are
independently selected from X2-X8. In any of the aforementioned embodiments of
Formula (I) wherein n is an integer 25-30 is another embodiment wherein sixteen X are
independently selected from X2-X8. In any of the aforementioned embodiments of
Formula (I) wherein n is an integer from 25-30 is another embodiment wherein
seventeen X are independently selected from X2-X8. In any of the aforementioned
embodiments of Formula (I) wherein n is an integer from 25-30 is another embodiment
wherein eighteen X are independently selected from X2-X8. In any of the
aforementioned embodiments of Formula (I) wherein n is an integer from 25-30 is
another embodiment wherein nineteen X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 25-
is another embodiment wherein twenty X are independently selected from X2-X8.
In any of the aforementioned embodiments of Formula (I) wherein n is
an integer from 20-25 is another embodiment wherein one X is X2-X8. In any of the
aforementioned embodiments of Formula (I) wherein n is an integer from 20-25 is
another embodiment wherein two X are independently selected from X2-X8. In any of
the aforementioned embodiments of Formula (I) wherein n is an integer from 20-25 is
another embodiment wherein three X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 20-25
is another embodiment wherein four X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 20-25
is another embodiment wherein five X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 20-25
is another embodiment wherein six X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 20-25
is another embodiment wherein seven X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 20-
is another embodiment wherein eight X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 20-
is another embodiment wherein nine X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 20-
is another embodiment wherein ten X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 20-
is another embodiment wherein eleven X are independently selected from X2-X8.
In any of the aforementioned embodiments of Formula (I) wherein n is an integer from
-25 is another embodiment wherein twelve X are independently selected from X2-
X8. In any of the aforementioned embodiments of Formula (I) wherein n is an integer
from 20-25 is another embodiment wherein thirteen X are independently selected from
X2-X8. In any of the aforementioned embodiments of Formula (I) wherein n is an
integer from 20-25 is another embodiment wherein fourteen X are independently
selected from X2-X8. In any of the aforementioned embodiments of Formula (I)
wherein n is an integer from 20-25 is another embodiment wherein fifteen X are
independently selected from X2-X8. In any of the aforementioned embodiments of
Formula (I) wherein n is an integer 20-25 is another embodiment wherein sixteen X are
independently selected from X2-X8. In any of the aforementioned embodiments of
Formula (I) wherein n is an integer from 20-25 is another embodiment wherein
seventeen X are independently selected from X2-X8. In any of the aforementioned
embodiments of Formula (I) wherein n is an integer from 20-25 is another embodiment
wherein eighteen X are independently selected from X2-X8. In any of the
aforementioned embodiments of Formula (I) wherein n is an integer from 20-25 is
another embodiment wherein nineteen X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 20-
is another embodiment wherein twenty X are independently selected from X2-X8.
In any of the aforementioned embodiments of Formula (I) wherein n is
an integer from 15-20 is another embodiment wherein one X is X2-X8. In any of the
aforementioned embodiments of Formula (I) wherein n is an integer from 15-20 is
another embodiment wherein two X are independently selected from X2-X8. In any of
the aforementioned embodiments of Formula (I) wherein n is an integer from 15-20 is
another embodiment wherein three X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 15-20
is another embodiment wherein four X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 15-20
is another embodiment wherein five X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 15-20
is another embodiment wherein six X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 15-20
is another embodiment wherein seven X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 15-
is another embodiment wherein eight X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 15-
is another embodiment wherein nine X are independently selected 15-20 is another
embodiment wherein ten X are independently selected from X2-X8. In any of the
aforementioned embodiments of Formula (I) wherein n is an integer from 15-20 is
another embodiment wherein eleven X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 15-20
is another embodiment wherein twelve X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 15-
is another embodiment wherein thirteen X are independently selected from X2-X8.
In any of the aforementioned embodiments of Formula (I) wherein n is an integer from
-20 is another embodiment wherein fourteen X are independently selected from X2-
X8. In any of the aforementioned embodiments of Formula (I) wherein n is an integer
from 15-20 is another embodiment wherein fifteen X are independently selected from
X2-X8. In any of the aforementioned embodiments of Formula (I) wherein n is an
integer 16-20 is another embodiment wherein sixteen X are independently selected
from X2-X8. In any of the aforementioned embodiments of Formula (I) wherein n is an
integer from 17-20 is another embodiment wherein seventeen X are independently
selected from X2-X8. In any of the aforementioned embodiments of Formula (I)
wherein n is an integer from 18-20 is another embodiment wherein eighteen X are
independently selected from X2-X8. In any of the aforementioned embodiments of
Formula (I) wherein n is an integer from 19-20 is another embodiment wherein nineteen
X are independently selected from X2-X8. In any of the aforementioned embodiments
of Formula (I) wherein n is 20 is another embodiment wherein twenty X are
independently selected from X2-X8.
In any of the aforementioned embodiments of Formula (I) wherein n is
an integer from 10-15 is another embodiment wherein one X is X2-X8. In any of the
aforementioned embodiments of Formula (I) wherein n is an integer from 10-15 is
another embodiment wherein two X are independently selected from X2-X8. In any of
the aforementioned embodiments of Formula (I) wherein n is an integer from 10-15 is
another embodiment wherein three X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 10-15
is another embodiment wherein four X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 10-15
is another embodiment wherein five X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 10-15
is another embodiment wherein six X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 10-15
is another embodiment wherein seven X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 10-
is another embodiment wherein eight X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 10-
is another embodiment wherein nine X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 10-
is another embodiment wherein ten X are independently selected from X2-X8. In
any of the aforementioned embodiments of Formula (I) wherein n is an integer from 11-
is another embodiment wherein eleven X are independently selected from X2-X8.
In any of the aforementioned embodiments of Formula (I) wherein n is an integer from
12-15 is another embodiment wherein twelve X are independently selected from X2-
X8. In any of the aforementioned embodiments of Formula (I) wherein n is an integer
from 13-15 is another embodiment wherein thirteen X are independently selected from
X2-X8. In any of the aforementioned embodiments of Formula (I) wherein n is an
integer from 14-15 is another embodiment wherein fourteen X are independently
selected from X2-X8. In any of the aforementioned embodiments of Formula (I)
wherein n is 15 is another embodiment wherein fifteen X are independently selected
from X2-X8.
In any of the aforementioned embodiments of Formula (I) wherein n is
an integer from 5-10 is another embodiment wherein one X is X2-X8. In any of the
aforementioned embodiments of Formula (I) wherein n is an integer from 5-10 is
another embodiment wherein two X are independently selected from X2-X8. In any of
the aforementioned embodiments of Formula (I) wherein n is an integer from 5-10 is
another embodiment wherein three X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 5-10 is
another embodiment wherein four X are independently selected from X2-X8. In any of
the aforementioned embodiments of Formula (I) wherein n is an integer from 5-10 is
another embodiment wherein five X are independently selected from X2-X8. In any of
the aforementioned embodiments of Formula (I) wherein n is an integer from 6-10 is
another embodiment wherein six X are independently selected from X2-X8. In any of
the aforementioned embodiments of Formula (I) wherein n is an integer from 7-10 is
another embodiment wherein seven X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 8-10 is
another embodiment wherein eight X are independently selected from X2-X8. In any
of the aforementioned embodiments of Formula (I) wherein n is an integer from 9-10 is
another embodiment wherein nine X are independently selected from X2-X8. In any of
the aforementioned embodiments of Formula (I) wherein n is 10 is another embodiment
wherein ten X are independently selected from X2-X8.
In any of the aforementioned embodiments of Formula (I) wherein n is
an integer from 1-5 is another embodiment wherein one X is X2-X8. In any of the
aforementioned embodiments of Formula (I) wherein n is an integer from 2-5 is another
embodiment wherein two X are independently selected from X2-X8. In any of the
aforementioned embodiments of Formula (I) wherein n is an integer from 3-5 is another
embodiment wherein three X are independently selected from X2-X8. In any of the
aforementioned embodiments of Formula (I) wherein n is an integer from 4-5 is another
embodiment wherein four X are independently selected from X2-X8. In any of the
aforementioned embodiments of Formula (I) wherein n is 5 is another embodiment
wherein five X are independently selected from X2-X8.
In some embodiments for antisense applications, the oligomer may be
100% complementary to the nucleic acid target sequence, or it may include mismatches,
e.g., to accommodate variants, as long as a heteroduplex formed between the oligomer
and nucleic acid target sequence is sufficiently stable to withstand the action of cellular
nucleases and other modes of degradation which may occur in vivo. Mismatches, if
present, are less destabilizing toward the end regions of the hybrid duplex than in the
middle. The number of mismatches allowed will depend on the length of the oligomer,
the percentage of G:C base pairs in the duplex, and the position of the mismatch(es) in
the duplex, according to well understood principles of duplex stability. Although such
an antisense oligomer is not necessarily 100% complementary to the nucleic acid target
sequence, it is effective to stably and specifically bind to the target sequence, such that
a biological activity of the nucleic acid target, e.g., expression of encoded protein(s), is
modulated.
The stability of the duplex formed between an oligomer and the target
sequence is a function of the binding T and the susceptibility of the duplex to cellular
enzymatic cleavage. The T of an antisense compound with respect to complementary-
sequence RNA may be measured by conventional methods, such as those described by
Hames et al., Nucleic Acid Hybridization, IRL Press, 1985, pp.107-108 or as described
in Miyada C.G. and Wallace R.B., 1987, Oligonucleotide hybridization techniques,
Methods Enzymol. Vol. 154 pp. 94-107.
In some embodiments, each antisense oligomer has a binding T , with
respect to a complementary-sequence RNA, of greater than body temperature or in
other embodiments greater than 50°C. In other embodiments T 's are in the range 60-
80°C or greater. According to well known principles, the T of an oligomer compound,
with respect to a complementary-based RNA hybrid, can be increased by increasing the
ratio of C:G paired bases in the duplex, and/or by increasing the length (in base pairs)
of the heteroduplex. At the same time, for purposes of optimizing cellular uptake, it
may be advantageous to limit the size of the oligomer. For this reason, compounds that
show high T (50°C or greater) at a length of 20 bases or less are generally preferred
over those requiring greater than 20 bases for high T values. For some applications,
longer oligomers, for example longer than 20 bases may have certain advantages. For
example, in certain embodiments longer oligomers may find particular utility for use in
exon skippin or splice modulation.
The targeting sequence bases may be normal DNA bases or analogues
thereof, e.g., uracil and inosine that are capable of Watson-Crick base pairing to target-
sequence RNA bases.
The oligomers may also incorporate guanine bases in place of adenine
when the target nucleotide is a uracil residue. This is useful when the target sequence
varies across different viral species and the variation at any given nucleotide residue is
either cytosine or uracil. By utilizing guanine in the targeting oligomer at the position
of variability, the well-known ability of guanine to base pair with uracil (termed C/U:G
base pairing) can be exploited. By incorporating guanine at these locations, a single
oligomer can effectively target a wider range of RNA target variability.
The compounds (e.g., oligomers, intersubunit linkages, terminal groups)
may exist in different isomeric forms, for example structural isomers (e.g., tautomers).
With regard to stereoisomers, the compounds may have chiral centers and may occur as
racemates, enantiomerically enriched mixtures, individual enantiomers, mixture or
diastereomers or individual diastereomers. All such isomeric forms are included within
the present invention, including mixtures thereof. The compounds may also possess
axial chirality which may result in atropisomers. Furthermore, some of the crystalline
forms of the compounds may exist as polymorphs, which are included in the present
invention. In addition, some of the compounds may also form solvates with water or
other organic solvents. Such solvates are similarly included within the scope of this
invention.
The oligomers described herein may be used in methods of inhibiting
production of a protein or replication of a virus. Accordingly, in one embodiment a
nucleic acid encoding such a protein is exposed to an oligomer as disclosed herein. In
further embodiments of the foregoing, the antisense oligomer comprises either a 5’ or 3’
modified terminal group or combinations thereof, as disclosed herein, and the base
pairing moieties B form a sequence effective to hybridize to a portion of the nucleic
acid at a location effective to inhibit production of the protein. In one embodiment, the
location is an ATG start codon region of an mRNA, a splice site of a pre-mRNA, or a
viral target sequence as described below.
In one embodiment, the oligomer has a T with respect to binding to the
target sequence of greater than about 50 C, and it is taken up by mammalian cells or
bacterial cells. In another embodiment, the oligomer may be conjugated to a transport
moiety, for example an arginine-rich peptide, as described herein to facilitate such
uptake. In another embodiment, the terminal modifications described herein can
function as a transport moiety to facilitate uptake by mammalian and/or bacterial cells.
The preparation and properties of morpholino oligomers is described in
more detail below and in U.S. Patent No. 5,185,444 and WO/2009/064471, each of
which is hereby incorporated by reference in their entirety.
D. Formulation and Administration of the Oligomers
The present disclosure also describes for formulation and delivery of the
disclosed oligomer. Accordingly, in one embodiment the present disclosure is directed
to a composition comprising an oligomer as disclosed herein and a pharmaceutically
acceptable vehicle.
Effective delivery of the antisense oligomer to the target nucleic acid is
an important aspect of treatment. Routes of antisense oligomer delivery include, but are
not limited to, various systemic routes, including oral and parenteral routes, e.g.,
intravenous, subcutaneous, intraperitoneal, and intramuscular, as well as inhalation,
transdermal and topical delivery. The appropriate route may be determined by one of
skill in the art, as appropriate to the condition of the subject under treatment. For
example, an appropriate route for delivery of an antisense oligomer in the treatment of a
viral infection of the skin is topical delivery, while delivery of a antisense oligomer for
the treatment of a viral respiratory infection is by inhalation. The oligomer may also be
delivered directly to the site of viral infection, or to the bloodstream.
The antisense oligomer may be administered in any convenient vehicle
which is physiologically and/or pharmaceutically acceptable. Such a composition may
include any of a variety of standard pharmaceutically acceptable carriers employed by
those of ordinary skill in the art. Examples include, but are not limited to, saline,
phosphate buffered saline (PBS), water, aqueous ethanol, emulsions, such as oil/water
emulsions or triglyceride emulsions, tablets and capsules. The choice of suitable
physiologically acceptable carrier will vary dependent upon the chosen mode of
administration.
The compounds (e.g., oligomers) of the present invention may generally
be utilized as the free acid or free base. Alternatively, the compounds of this invention
may be used in the form of acid or base addition salts. Acid addition salts of the free
amino compounds of the present invention may be prepared by methods well known in
the art, and may be formed from organic and inorganic acids. Suitable organic acids
include maleic, fumaric, benzoic, ascorbic, succinic, methanesulfonic, acetic,
trifluoroacetic, oxalic, propionic, tartaric, salicylic, citric, gluconic, lactic, mandelic,
cinnamic, aspartic, stearic, palmitic, glycolic, glutamic, and benzenesulfonic acids.
Suitable inorganic acids include hydrochloric, hydrobromic, sulfuric, phosphoric, and
nitric acids. Base addition salts included those salts that form with the carboxylate
anion and include salts formed with organic and inorganic cations such as those chosen
from the alkali and alkaline earth metals (for example, lithium, sodium, potassium,
magnesium, barium and calcium), as well as the ammonium ion and substituted
derivatives thereof (for example, dibenzylammonium, benzylammonium, 2-
hydroxyethylammonium, and the like). Thus, the term “pharmaceutically acceptable
salt” of structure (I) is intended to encompass any and all acceptable salt forms.
In addition, prodrugs are also included within the context of this
invention. Prodrugs are any covalently bonded carriers that release a compound of
structure (I) in vivo when such prodrug is administered to a patient. Prodrugs are
generally prepared by modifying functional groups in a way such that the modification
is cleaved, either by routine manipulation or in vivo, yielding the parent compound.
Prodrugs include, for example, compounds of this invention wherein hydroxy, amine or
sulfhydryl groups are bonded to any group that, when administered to a patient, cleaves
to form the hydroxy, amine or sulfhydryl groups. Thus, representative examples of
prodrugs include (but are not limited to) acetate, formate and benzoate derivatives of
alcohol and amine functional groups of the compounds of structure (I). Further, in the
case of a carboxylic acid (-COOH), esters may be employed, such as methyl esters,
ethyl esters, and the like.
In some instances, liposomes may be employed to facilitate uptake of the
antisense oligonucleotide into cells. (See, e.g., Williams, S.A., Leukemia 10(12):1980-
1989, 1996; Lappalainen et al., Antiviral Res. 23:119, 1994; Uhlmann et al., antisense
oligonucleotides: a new therapeutic principle, Chemical Reviews, Volume 90, No. 4,
pages 544-584, 1990; Gregoriadis, G., Chapter 14, Liposomes, Drug Carriers in
Biology and Medicine, pp. 287-341, Academic Press, 1979). Hydrogels may also be
used as vehicles for antisense oligomer administration, for example, as described in WO
93/01286. Alternatively, the oligonucleotides may be administered in microspheres or
microparticles. (See, e.g., Wu, G.Y. and Wu, C.H., J. Biol. Chem. 262:4429-4432,
1987). Alternatively, the use of gas-filled microbubbles complexed with the antisense
oligomers can enhance delivery to target tissues, as described in US Patent No.
6,245,747. Sustained release compositions may also be used. These may include
semipermeable polymeric matrices in the form of shaped articles such as films or
microcapsules.
In one embodiment, antisense inhibition is effective in treating infection
of a host animal by a virus, by contacting a cell infected with the virus with an antisense
agent effective to inhibit the replication of the specific virus. The antisense agent is
administered to a mammalian subject, e.g., human or domestic animal, infected with a
given virus, in a suitable pharmaceutical carrier. It is contemplated that the antisense
oligonucleotide arrests the growth of the RNA virus in the host. The RNA virus may be
decreased in number or eliminated with little or no detrimental effect on the normal
growth or development of the host.
In one aspect of the method, the subject is a human subject, e.g., a
patient diagnosed as having a localized or systemic viral infection. The condition of a
patient may also dictate prophylactic administration of an antisense oligomer of the
invention, e.g. in the case of a patient who (1) is immunocompromised; (2) is a burn
victim; (3) has an indwelling catheter; or (4) is about to undergo or has recently
undergone surgery. In one preferred embodiment, the oligomer is a
phosphorodiamidate morpholino oligomer, contained in a pharmaceutically acceptable
carrier, and is delivered orally. In another preferred embodiment, the oligomer is a
phosphorodiamidate morpholino oligomer, contained in a pharmaceutically acceptable
carrier, and is delivered intravenously (i.v.).
In another application of the method, the subject is a livestock animal,
e.g., a chicken, turkey, pig, cow or goat, etc, and the treatment is either prophylactic or
therapeutic. The invention also includes a livestock and poultry food composition
containing a food grain supplemented with a subtherapeutic amount of an antiviral
antisense compound of the type described above. Also contemplated is, in a method of
feeding livestock and poultry with a food grain supplemented with subtherapeutic levels
of an antiviral, an improvement in which the food grain is supplemented with a
subtherapeutic amount of an antiviral oligonucleotide composition as described above.
In one embodiment, the antisense compound is administered in an
amount and manner effective to result in a peak blood concentration of at least 200-400
nM antisense oligomer. Typically, one or more doses of antisense oligomer are
administered, generally at regular intervals, for a period of about one to two weeks.
Preferred doses for oral administration are from about 1-1000 mg oligomer per 70 kg.
In some cases, doses of greater than 1000 mg oligomer/patient may be necessary. For
i.v. administration, preferred doses are from about 0.5 mg to 1000 mg oligomer per 70
kg. The antisense oligomer may be administered at regular intervals for a short time
period, e.g., daily for two weeks or less. However, in some cases the oligomer is
administered intermittently over a longer period of time. Administration may be
followed by, or concurrent with, administration of an antibiotic or other therapeutic
treatment. The treatment regimen may be adjusted (dose, frequency, route, etc.) as
indicated, based on the results of immunoassays, other biochemical tests and
physiological examination of the subject under treatment.
An effective in vivo treatment regimen using the antisense
oligonucleotides of the invention may vary according to the duration, dose, frequency
and route of administration, as well as the condition of the subject under treatment (i.e.,
prophylactic administration versus administration in response to localized or systemic
infection). Accordingly, such in vivo therapy will often require monitoring by tests
appropriate to the particular type of viral infection under treatment, and corresponding
adjustments in the dose or treatment regimen, in order to achieve an optimal therapeutic
outcome. Treatment may be monitored, e.g., by general indicators of disease and/or
infection, such as complete blood count (CBC), nucleic acid detection methods,
immunodiagnostic tests, viral culture, or detection of heteroduplex.
The efficacy of an in vivo administered antiviral antisense oligomer of
the invention in inhibiting or eliminating the growth of one or more types of RNA virus
may be determined from biological samples (tissue, blood, urine etc.) taken from a
subject prior to, during and subsequent to administration of the antisense oligomer.
Assays of such samples include (1) monitoring the presence or absence of heteroduplex
formation with target and non-target sequences, using procedures known to those
skilled in the art, e.g., an electrophoretic gel mobility assay; (2) monitoring the amount
of viral protein production, as determined by standard techniques such as ELISA or
Western blotting, or (3) measuring the effect on viral titer, e.g. by the method of
Spearman-Karber. (See, for example, Pari, G.S. et al., Antimicrob. Agents and
Chemotherapy 39(5):1157-1161, 1995; Anderson, K.P. et al., Antimicrob. Agents and
Chemotherapy 40(9):2004-2011, 1996, Cottral, G.E. (ed) in: Manual of Standard
Methods for Veterinary Microbiology, pp. 60-93, 1978).
In some embodiments, the oligomer is actively taken up by mammalian
cells. In further embodiments, the oligomer may be conjugated to a transport moiety
(e.g., transport peptide) as described herein to facilitate such uptake.
E. Preparation of the Oligomers
The morpholino subunits, the modified intersubunit linkages and
oligomers comprising the same can be prepared as described in the examples and in
U.S. Patent Nos. 5,185,444 and 7,943,762 which are hereby incorporated by reference
in their entirety. The morpholino subunits can be prepared according to the following
general Reaction Scheme I.
Reaction Scheme 1. Preparation of Morpholino Subunits
1. NaIO ,MeoH(aq)
4 HO
2. (NH ) B O
4 2 4 7
3. Borane-triethylamine +
4. Methanolic acid (p-TsOH
or HCl)
HO H H
X P Cl
X P O
Referring to Reaction Scheme 1, wherein B represents a base pairing
moiety and PG represents a protecting group, the morpholino subunits may be prepared
from the corresponding ribinucleoside (1) as shown. The morpholino subunit (2) may
be optionally protected by reaction with a suitable protecting group precursor, for
example trityl chloride. The 3’ protecting group is generally removed during solid-state
oligomer synthesis as described in more detail below. The base pairing poiety may be
suitable protected for sold phase oligomer synthesis. Suitable protecting groups include
benzoyl for adenine and cytosine, phenylacetyl for guanine, and pivaloyloxymethyl for
hypoxanthine (I). The pivaloyloxymethyl group can be introduced onto the N1 position
of the hypoxanthine heterocyclic base. Although an unprotected hypoxanthine subunit,
may be employed, yields in activation reactions are far superior when the base is
protected. Other suitable protecting groups include those disclosed in co-pending U.S.
Application No. 12/271,040, which is hereby incorporated by reference in its entirety.
Reaction of 3 with the activated phosphorous compound 4, results in
morpholino subunints having the desired linkage moiety 5. Compounds of structure 4
can be prepared using any number of methods known to those of skill in the art. For
example, such compounds may be prepared by reaction of the corresponding amine and
phosphorous oxychloride. In this regard, the amine starting material can be prepared
using any method known in the art, for example those methods described in the
Examples and in U.S. Patent No. 7,943,762.
Compounds of structure 5 can be used in solid-phase automated
oligomer synthesis for preparation of oligomers comprising the intersubunit linkages.
Such methods are well known in the art. Briefly, a compound of structure 5 may be
modified at the 5’ end to contain a linker to a solid support. For example, compound 5
11 15
may be linked to a solid support by a linker comprising L and L . An exemplary
method is demonstrated in Figures 1 and 2. Once supported, the protecting group (e.g.,
trityl) is removed and the free amine is reacted with an activated phosphorous moiety of
a second compound of structure 5. This sequence is repeated untilthe desired length
oligo is obtained. The protecting group in the termina 5’ end may either be removed or
left on if a 5’-modification is desired. The oligo can be removed from the solid support
using any number of methods, for example treatment with DTT followed by ammonium
hydroxide as depicted in Figure 3.
The preparation of modified morpholino subunits and morpholino
oligomers are described in more detail in the Examples. The morpholino oligomers
containing any number of modified linkages may be prepared using methods described
herein, methods known in the art and/or described by reference herein. Also described
in the examples are global modifications of morpholino oligomers prepared as
previously described (see e.g., PCT publication WO2008036127).
The term "protecting group" refers to chemical moieties that block some
or all reactive moieties of a compound and prevent such moieties from participating in
chemical reactions until the protective group is removed, for example, those moieties
listed and described in T.W. Greene, P.G.M. Wuts, Protective Groups in Organic
Synthesis, 3rd ed. John Wiley & Sons (1999). It may be advantageous, where different
protecting groups are employed, that each (different) protective group be removable by
a different means. Protective groups that are cleaved under totally disparate reaction
conditions allow differential removal of such protecting groups. For example,
protective groups can be removed by acid, base, and hydrogenolysis. Groups such as
trityl, dimethoxytrityl, acetal and tert-butyldimethylsilyl are acid labile and may be used
to protect carboxy and hydroxy reactive moieties in the presence of amino groups
protected with Cbz groups, which are removable by hydrogenolysis, and Fmoc groups,
which are base labile. Carboxylic acid moieties may be blocked with base labile groups
such as, without limitation, methyl, or ethyl, and hydroxy reactive moieties may be
blocked with base labile groups such as acetyl in the presence of amines blocked with
acid labile groups such as tert-butyl carbamate or with carbamates that are both acid
and base stable but hydrolytically removable.
Carboxylic acid and hydroxy reactive moieties may also be blocked with
hydrolytically removable protective groups such as the benzyl group, while amine
groups may be blocked with base labile groups such as Fmoc. A particulary useful
amine protecting group for the synthesis of compounds of Formula (I) is the
trifluoroacetamide. Carboxylic acid reactive moieties may be blocked with oxidatively-
removable protective groups such as 2,4-dimethoxybenzyl, while co-existing amino
groups may be blocked with fluoride labile silyl carbamates.
Allyl blocking groups are useful in the presence of acid- and base-
protecting groups since the former are stable and can be subsequently removed by metal
or pi-acid catalysts. For example, an allyl-blocked carboxylic acid can be deprotected
with a palladium(0)-catalyzed reaction in the presence of acid labile t-butyl carbamate
or base-labile acetate amine protecting groups. Yet another form of protecting group is
a resin to which a compound or intermediate may be attached. As long as the residue is
attached to the resin, that functional group is blocked and cannot react. Once released
from the resin, the functional group is available to react.
Typical blocking/protecting groups are known in the art and include, but
are not limited to the following moieties:
H C CH
CH O
H C Si
Allyl Bn PMB TBDMS Me
H C CH
H C O
H C O H C
CH O
Alloc Cbz TEOC BOC
H C Ph H C
Ph O
t-butyl trityl acetyl
FMOC
F. Antisense Activity of the Oligomers
RNAi
RNA interference (RNAi) is a method of modulating gene expression.
RNAi is a naturally occurring process. RNAi can also be induced by delivery of
exogenous RNA sequences.
Naturally occurring RNAi is initiated by the recognition of double-
stranded RNA sequences (dsRNA) by an RNase III enzyme (e.g., Dicer), followed by
cleavage of the dsRNA into short fragments of ~20 nucleotides called small interfering
RNAs (siRNAs). Dicer is an RNase III enzyme with ATPase/RNA helicase, a DUF283
(Domain of unknown function) domain, a PAZ (Piwi, Argonaut and Zwille) domain
which can bind the characteristic two-base 3' overhangs of microRNA (miRNA) and
siRNA, two catalytic RNase III domains (RIIIa and RIIIb), and a C-terminal double-
stranded RNA-binding domain (dsRBD). Following cleavage, each siRNA molecule is
unwound into two single-stranded RNA sequences (ssRNAs). One strand, the
passenger, is degraded. The other stand, the guide, is incorporated into the RNA-
induced silencing complex (RISC). RISC is a ribonucleoprotein complex containing
members of the Argonaute (Ago) family of proteins. Argonaute proteins have
endonuclease activity. RNAi occurs when the guide strand base binds to a
complementary RNA sequence (for example, mRNA or pre-mRNA). The binding of
the guide sequence induces cleavage of the guide sequence and the complementary
sequence by Argonaute.
RNAi can also be initiated by the introduction of exogenous RNA
sequences, for example siRNA sequences, miRNA sequences, and antisense
oligonucleotides. Antisense oligonucleotides (AONs) are single-stranded
oligonucleotides that are complementary to a target pre-mRNA or mRNA sequence.
Once contacted with the complementary sequence, the AON will bind to the
complementary sequence by Watson-Crick base-pair binding. In certain instances, an
exogenous AON enters a cell. The AON binds to a complementary RNA sequence
(e.g., pre-mRNA or mRNA), and the binding of the antisense sequence molecule
induces cleavage of the complementary RNA sequence (e.g., by RNase-H).
Alternatively, AONs can be designed so that their binding does not
induce cleavage of the complementary RNA strand, but instead disrupts processing of
pre-mRNA (e.g., splicing, capping, polyadenylation), or changes or prevents the
translation of mRNA sequences (e.g., by sterically interfering with the binding of one or
more enzymes). For example, generating an AON as a morpholino results in an AON
that does not support RNase-H mediated cleavage of the complementary strand.
Instead, the binding of the morpholino AON to a target pre-mRNA sequence results in a
stable complex that can (a) disrupt the ability of the splicesome to splice the pre-mRNA
(e.g., by blocking a splice acceptor site or a splice donor site), (b) disrupt capping the
pre-mRNA, or (c) disrupt poly-adenylation of the pre-mRNA (e.g., by blocking the
binding site for CPSF, CstF, or CFI).
The present disclosure provides a method of inhibiting or altering
expression of a target nucleic acid sequence, the method comprising exposing a nucleic
acid encoding the protein to an oligomer as disclosed herein. Accordingly, in one
embodiment a target nucleic acid sequence is exposed to an antisense oligomer as
described herein, or in other embodiments 10% to 50% such modified linkages, as
disclosed herein, where the base pairing moieties Pi form a sequence effective to
hybridize to a portion of the target nucleic acid sequence at a location effective to
inhibit or alter expression of the target nucleic acid sequence. The oligomer may target,
for example, an ATG start codon region of an mRNA, a splice site of a pre-mRNA, or a
viral target sequence as described below. In another embodiment, the method
comprises exposing a target nucleic acid sequence to an antisense oligomer comprising
at least one terminal modification. In another embodiment, the method comprises
exposing a target nucleic acid sequence to an antisense oligomer comprising a peptide
transporter moiety.
In another embodiment, the disclosure provides a method of enhancing
antisense activity of an oligomer having a sequence of morpholino subunits, joined by
intersubunit linkages, supporting base-pairing moieties, the method comprises
modifying an oligomer as described herein to contain at least one of the modified
terminal groups, at least one intersubunit linkage wherein X does not equal X1 or
combinations thereof.
In some embodiments, enhancement of antisense activity may be
evidenced by:
(i) a decrease in expression of a target nucleic acid sequence,
relative to that provided by a corresponding unmodified oligomer, or
(ii) an increase in expression of a target nucleic acid sequence,
relative to that provided by a corresponding unmodified oligomer. Assays suitable for
measurement of these effects are described further below. In one embodiment,
modification provides this activity in a cell-free translation assay, a splice correction
translation assay in cell culture, or a splice correction gain of function animal model
system as described herein. In one embodiment, activity is enhanced by a factor of at
least two, at least five or at least ten.
Described below are various exemplary applications of the oligomers of
the invention including antimicrobrial (e.g., antivirals and antibacterials) applications,
treatment by altering gene expression, cancer treatment, and treatment ofinflammatory,
cardiovascular, and metabolic disorders. This description is not meant to limit the
invention in any way but serves to exemplify the range of diseases and disorders that
can be addressed using oligomers comprising the modified intersubunit linkages
described herein.
Antisense oligonucleotides have been used as antimicrobial drugs (e.g.,
antivirals and antibacterials). In some embodiments, a compound of Formula (I) as
disclosed herein is used as an antiviral drug. In some embodiments, a compound of
Formula (I) as disclosed herein is used to inhibit the expression of virally-encoded
proteins. In some embodiments, inhibiting the expression of virally-encoded proteins
treats a viral infection. In some embodiments, the oligomers can be used in methods of
inhibiting in a mammalian host cell, replication of an infecting RNA virus having a
single-stranded, positive-sense genome. The method includes administering to the
infected host cells, a virus-inhibitory amount of an oligomer as described herein, having
a targeting sequence of at least 12 subunits that is complementary to a target nucleic
acid sequence of the virus. The compound may be administered to a mammalian subject
infected with the virus, or at risk of infection with the virus. In some embodiments, the
target sequence encodes a polyprotein containing non-structural proteins such as
polymerases, helicases and proteases. In some embodiments, the target sites include
targets that are conserved between a variety of viral isolates. Other favored sites include
the IRES (internal ribosome entry site), transactivation protein binding sites, and sites
of initiation of replication.
In some embodiments, a compound of Formula (I) as disclosed herein is
used as an antibacterial drug. In some embodiments, a compound of Formula (I) as
disclosed herein inhibits the expression of a bacterial virulence factor (e.g., a toxin or a
protein that inhibits a host immune response). In some embodiments, inhibiting the
expression of a bacterial virulence factor treats a bacterial infection.
In some embodiments, a compound of Formula (I) as disclosed herein is
used treat a disease or disorder (e.g., cancer, inflammatory, metabolic, neurological,
cardiovascular) by altering the expression of a gene. In some embodiments, a
compound of Formula (I) as disclosed herein is used treat a disease or disorder
characterized by undesired or excessive expression of a gene. For example, disorders
characterized by undesired angiogenesis may be treated by using a compound of
Formula (I) as disclosed herein to inhibit the expression of VEGF or any other gene
implicated in angiogenesis. In some embodiments, disorders characterized by mutated
(e.g., non-functional) gene products are treated by a compound of Formula (I) as
disclosed herein. For example, Duchenne Muscular Dystrophy (DMD) is characterized
by somatic mutations that lead to truncated and non-functional dystrophin. Antisense
oligonucleotides have been used to alter the splicing of mutant dystrophin pre-mRNA
such that a truncated but functional dystrophin protein is produced.
In some embodiments, a compound of Formula (I) as disclosed herein is
used treat a cancer. In some embodiments, a compound of Formula (I) as disclosed
herein is used to decrease the expression of a gene that inhibits apoptosis, inhibits cell
adhesion, promotes angiogenesis, promotes cell proliferation, promotes cell growth, or
participates in DNA repair. For example, some cancers are associated with the over-
expression of anti-apoptotic genes. Inhibiting the expression of these genes by use of a
compound of Formula (I) as disclosed herein may result in an increase in apoptosis of
cancer cells or an increased sensitivity to chemotherapeutic agents.
In some embodiments, a compound of Formula (I) as disclosed herein is
used treat an inflammatory disorder. In some embodiments, a compound of Formula (I)
as disclosed herein is used to decrease the expression of cytokines or cell surface
molecules involved in chemotaxis. For example, autoimmune disorders are associated
with the undesired and excessive immune cell migration. Inhibiting the expression of
cytokines or cell surface molecules associated with chemotaxis may result in a decrease
in immune cell migration and inflammation.
In some embodiments, a compound of Formula (I) as disclosed herein is
used treat a cardiovascular disorder. In some embodiments, a compound of Formula (I)
as disclosed herein is used to inhibit the expression of lipoproteins, or inhibit the
expression of proteins or enzymes that decrease the levels of cardioprotective molecules
(e.g., HDL).
In some embodiments, a compound of Formula (I) as disclosed herein is
used treat a metabolic disorder. In some embodiments, a compound of Formula (I) as
disclosed herein is used to inhibit the expression of gene products that lead to decreased
insulin sensitivity or decreased metabolic rates.
In some embodiments, a compound of Formula (I) as disclosed herein is
used treat a neurological disorder. In some embodiments, a compound of Formula (I) as
disclosed herein is used to inhibit the expression of gene products that lead to decreased
neural transmission (e.g., gene products that decrease myelin).
In some embodiments, a compound of Formula (I) as disclosed herein is
used to modulate expression of nuclear hormone receptors (NHR) from the nuclear
hormone receptor superfamily (NHRSF). Examples of particular NHRs include
glucocorticoid receptor (GR), progesterone receptor (PR) and androgen receptor (AR).
In certain embodiments, the antisense oligonucleotides and agents described herein lead
to increased expression of ligand-independent or other selected forms of the receptors,
and decreased expression of their inactive forms.
NHR modulators may be useful in treating NHR-associated diseases,
including diseases associated with the expression products of genes whose transcription
is stimulated or repressed by NHRs. Compounds that antagonize transactivation can be
useful in treating metabolic diseases associated with increased levels of glucocorticoid,
such as diabetes, osteoporosis and glaucoma, among others. Also, compounds that
agonize transactivation can be useful in treating metabolic diseases associated with a
deficiency in a nuclear hormone receptor.
Modifications
The function of an antisense oligonucleotide is dependent on both the
sequence of the AON and the chemical structure of the AON. Various modifications
may be made by adding moieties to or replacing portions of the nucleotides not
involved in Watson-Crick base-pair binding. Modifications to the chemical structure
can affect the affinity, stability, solubility, toxicity, and stability of the AON.
Different modifications may increase the affinity of the AON for the
complementary sequence. They may also decrease affinity for non-complementary
sequences. Changes to the charge or chirality of a backbone may also affect affinity.
Modifications may increase resistance to undesired degradation by
nucleases. Modifications may also increase or decrease the affinity of the AON for
RNase H. For example, morpholino oligonucleotides and peptide nucleic acids (PNAs)
do not activate RNase H.
Modifications may be designed such that they increase the size of the
AON such that it is not readily filtered by the glomerulus. For example, PEGylation of
an AON increases the size of an AON such that renal filtration is reduced.
Modifications can increase the ability of the AON to bind to plasma proteins in vivo
such that they are not rapidly filtered from the blood.
The toxicity of the AON can also be affected by modifications to the
chemical structure of the AON. Where it is desirable, toxicity may be increased by
certain modifications (e.g., when using the AON as an antimicrobial). Alternatively,
toxicity may be decreased by certain modifications. Phosphorodithioate analogs have
increased toxicity as compared to other analogs.
Further, modifications to the chemical structure of AONs may result in
the AON being directed to specific tissues, organs, or cells. An AON can be directed to
a specific tissue by modifying the AON such that it recognizes tissue-specific proteins
expressed by the cells of the targeted tissues. The conjugation of a ligand may target an
AON to a specific cell. For example, an AON may be conjugated to a ligand that
recognizes and binds to a specific receptor only found on specific cells (e.g.,
hepatocytes). The AON/ligand conjugate bonds to the receptor and accesses the cell by
receptor-mediated endocytosis. Conjugating cholesterol to an AON may target the
AON to the liver. Further, modifications that promote cell/tissue-specific uptake include
the conjugation of polymers, carbohydrate- or peptide-labeled nanoparticles, or
liposomes capable of recognizing cell-specific proteins.
Modifications to the chemical structure may also enhance the ability of
the AON to enter a cell. In certain instances, conjugating lipids to an AON may
increase cellular uptake. Additional conjugates may include protein transduction signals
and nuclear localization signals.
Additionally, AONs may be modified to carry cargo. Therapeutic or
prophylactic agents may be conjugated to AONs. For example, an AON targeting a
cancer cell may further comprise a known chemotherapeutic agent or an AON targeting
a bacterial cell may be conjugated to an antibacterial agent. Labels may also be
conjugated to AONs, for example so that proper targeting may be monitored or progress
of treatment may be monitored. AONs may be conjugated to radiolabels, contrast
agents (e.g., gadolinium), or fluorophores.
Modifications to the chemical structure of the AON may also affect the
method of administering the AON. Modifications may promote transdermal or
transmucosal penetration such that the AON may be administered topically (e.g., as a
nasal spray, ear drop, eye drop, oral spray). As discussed above, modifications may
increase resistance to renal filtration such that the AON may be administered
parenterally. Modifications may result in an AON that may be orally administered by
increasing the AON’s resistance to degradation by the acidic environment of the
stomach or the basic environment of the intestines.
In certain instances, varying the modifications to individual nucleotides
may result in an increase in desirable properties or a decrease in undesirable properties.
EXAMPLES
I. Chemical Synthesis
Unless otherwise noted, all chemicals were obtained from Sigma-
Aldrich-Fluka. Benzoyl adenosine, benzoyl cytidine, and phenylacetyl guanosine were
obtained from Carbosynth Limited, UK.
Synthesis of PMO, PMO+, PPMO and PMO containing further linkage
modifications as described herein was done using methods known in the art and
described in pending U.S. applications Nos. 12/271,036 and 12/271,040 and PCT
publication number WO/2009/064471, which are hereby incorporated by reference in
their entirety.
PMO with a 3’ trityl modification are synthesized essentially as
described in PCT publication number WO/2009/064471 with the exception that the
detritylation step is omitted.
Procedure A for the preparation of activated subunits
Cl P Cl
O N NH
X H X P
X P Cl
Cl O
To a stirred solution of 6 (1 eq) in dichloromethane was added POCl
(1.1 eq), followed by diisopropylethylamine (3 eq) at 0 C, cooled by an ice-bath. After
minutes, the ice-bath was removed and the solution was allowed to warm to room
temperature for one hour. Upon reaction completion, the reaction solution was diluted
with dichloromethane, washed with 10% aqueous citric acid three times. After drying
over MgSO , the organic layer was passed through a plug of silica gel and concentrated
in vacuo. The resulting phosphoroamidodichloride (4) was used directly for the next
step without further purification.
To a solution of the phosphoroamidodichloride (4) (1 eq), 2,6-lutidine (1
eq) in dichloromethane was added Mo(Tr)T (7) (0.5eq)/ dichloromethane solution,
followed by N-methylimidazole (0.2 eq). The reaction stirred at room temperature
overnight. Upon reaction completion, the reaction solution was diluted with
dichloromethane, and washed with 10% aqueous citric acid three times. After drying
over MgSO , the organic layer was filtered, then concentrated. The product (8) was
purified by silica gel chromatography (eluting with a gradient of ethyl acetate/hexanes),
and then stored at -20 C. The structure was confirmed by LCMS analysis.
Procedure B for the preparation of activated subunits
Cl P Cl
O N NH
O N NH O N NH
Cl 6
Cl P O XPO
Cl O
Cl O
7 9 8
To a solution of POCl (1.1eq) in dichloromethane was added 2,6-
lutidine (2eq), followed by dropwise addition of Mo(Tr)T (7) (1eq)/ dichloromethane
solution at 0 C. After 1 hour, the reaction solution was diluted with dichloromethane,
and quickly washed three times with 10% aqueous citric acid. The desired
phosphodichloridate (9) was obtained after drying over MgSO and evaporation of
solvent.
To a solution of the phosphodichloridate (1eq) in dichloromethane was
added 6 (1eq)/ dichloromethane dropwise to the solution at 0 C. After 15 minutes, the
reaction mixture was allowed to warm to room temperature for about an hour. Upon
reaction completion, the product (8) as a white solid was collected by precipitation with
the addition of hexanes, followed by filtration. The product was stored at -20 C after
drying under vacuum. The structure was confirmed by LCMS analysis.
EXAMPLE 1:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL PHOSPHORODICHLORIDATE
To a cooled (ice/water bath) DCM solution (20 mL) of phosphorus
oxychloride (2.12 mL, 22.7 mmol) was added dropwise 2,6-lutidine (4.82 mL, 41.4
mmol) then a DCM solution (20 mL) Mo(Tr)T (2) (10.0 g, 20.7 mmol) was added
dropwise over 15 min (int. temp. 0-10 C) then bath was removed a stirring continued at
ambient temperature for 20 min. The reaction was washed with citric acid solution (40
mL x 3, 10 % w/v aq), dried (MgSO ), filtered and concentrated to a white foam (9.79
g) then used directly for the following procedure.
EXAMPLE 2:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-(DIMETHYLAMINO)PIPERIDINYL)PHOSPHONOCHLORIDATE
O N NH
N N P O
To a cooled (ice/water bath) DCM solution (5 mL) of the
dichlorophosphate from example 1 (5.00 g, 5.00 mmol) was added a DCM solution (5
mL) of the piperidine (0.61 g, 4.76 mmol) dropwise then the bath was removed and
stirring continued at ambient temperature for 30 min.. The reaction was loaded directly
onto column. Chromatography [SiO column (40 g), DCM/EtOH eluant (gradient 1:0
to 1:1)] to afford the title compound (2.5 g) as a white foam. ESI/MS calcd. for 1-(4-
nitrophenyl)piperazine derivative C H N O P 862.4, found m/z = 863.6 (M+1).
46 55 8 7
EXAMPLE 3:
1-(1-(CHLORO((6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHOXY)PHOSPHORYL)PIPERIDINYL)
METHYLPYRROLIDINIUM CHLORIDE
The title compound was synthesized in a manner analogous to that
described in Example 2 to afford the title compound (0.6 g) as a white solid. ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 903.4, found m/z =
49 60 8 7
903.7 (M+).
EXAMPLE 4:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL (4-METHYLPIPERAZINYL)PHOSPHONOCHLORIDATE
To a cooled (ice/water bath) DCM solution(10 mL) of phosphorus
oxychloride (1.02 mL, 11.0 mmol) was added dropwise 2,6-lutidine (3.49 mL, 29.9
mmol) then a DCM solution (10 mL) of methyl piperazine (1.00 g, 10.0 mmol) was
added dropwise and stirring continued for 1 h. A DCM solution (10 mL) of Mo(Tr)T
(2) (4.82, 10.0 mmol) and NMI (79 μL, 1.0 mmol) was added and stirred 4 h then
loaded directly onto column. Chromatography [SiO column (80 g), DCM/Acetone
with 2% TEA eluant (gradient 1:0 to 0:1)] to afford the title compound (0.8 g) as a
white foam. ESI/MS calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P
43 48 7 8
834.4, found m/z = 835.5 (M+1).
EXAMPLE 5:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL MORPHOLINOPHOSPHONOCHLORIDATE
To a cooled solution (ice/water bath) of phosphorus oxychloride (19.1
mL, 205 mmol) in DCM (410 mL) was added dropwise 2,6-lutidine (54.2 mL, 465
mmol) then Mo(Tr)T (2) (90.0 g, 186 mmol) portionwise over 15 min (int. temp. 0-10
C) and stirred. After 5 min, a DCM solution (205 mL) of morpholine (17.9 mL, 205
mmol) was added dropwise over 15 min (int. temp. 0-8 C) and stirred. After 15 min,
additional DCM solution (10 mL) of morpholine (0.500 mL) was added, stirred 5 min
then washed with citric acid solution (300 mL x 3, 10 % w/v aq), dried (MgSO ),
filtered and concentrated to a viscous oil which was loaded directly onto column.
Chromatography [SiO column (330 g), hexanes/EtOAc eluant (gradient 1:0 to 0:1)] to
afford the title compound (78.5 g, 65% yield) as a white foam. ESI/MS calcd. for 1-(4-
nitrophenyl)piperazine derivative C H N O P 821.3, found m/z = 844.4 (M+Na).
43 48 7 8
EXAMPLE 6:
(9-((2R,6S)(((CHLORO(MORPHOLINO)PHOSPHORYL)OXY)METHYL)
TRITYLMORPHOLINYL)OXO-6,9-DIHYDRO-1H-PURINYL)METHYL PIVALATE
The title compound was synthesized in a manner analogous to that
described in Example 5 to afford the title compound (6.35 g, 79% yield) as a white
foam. ESI/MS calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 945.4,
49 56 9 9
found m/z = 1891.9 (2M+1).
EXAMPLE 7:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL (4-ETHYLPIPERAZINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in Example 5 to afford the title compound (11.5 g) as a white foam. ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 848.4, found m/z =
45 53 8 7
849.7 (M+1).
EXAMPLE 8:
((2S,6R)(6-BENZAMIDO-9H-PURINYL)TRITYLMORPHOLINYL)METHYL (4-
ETHYLPIPERAZINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in Example 5 to afford the title compound (4.5 g) as a white foam. ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 961.4, found m/z =
52 56 11 6
962.8 (M+1).
EXAMPLE 9:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL (4-ISOPROPYLPIPERAZIN
YL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in Example 5 to afford the title compound (3.5 g) as a white foam. ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 862.4, found m/z =
46 55 8 7
863.7 (M+1).
EXAMPLE 10:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL METHYL(2-(2,2,2-
TRIFLUOROACETAMIDO)ETHYL)PHOSPHORAMIDOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in Example 5 to afford the title compound (1.0 g) as a white foam. ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H F N O P 904.3, found m/z =
44 48 3 8 8
903.7 (M-1).
EXAMPLE 11:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL METHYL(2-(2,2,2-TRIFLUORO-N-
METHYLACETAMIDO)ETHYL)PHOSPHORAMIDOCHLORIDATE
TFAHN N P O
O NNH
The title compound was synthesized in a manner analogous to that
described in Example 5 to afford the title compound (1.8 g) as a white foam. ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H F N O P 918.3, found m/z =
45 50 3 8 8
1836.6 (2M+).
EXAMPLE 12:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL (4-(2,2,2-TRIFLUOROACETAMIDO)PIPERIDIN
YL)PHOSPHONOCHLORIDATE
To a cooled solution (ice/water bath) of phosphorus oxychloride (17.7
mL, 190 mmol) in DCM (190 mL) was added dropwise 2,6-lutidine (101 mL, 864
mmol) then Mo(Tr)T (2) (83.5 g, 173 mmol) portionwise over 15 min (int. temp. 0-10
C) and stirred. After 30 min, the piperidine (48.9 g, ~190 mmol) was added dropwise
over 15 min (int. temp. 0-8 C) and stirred. After 1h, DIPEA (50 mL) was added
dropwise (int. temp. 0-10 C) and stirred 1h. The reaction was washed with citric acid
solution (500 mL x 3, 10 % w/v aq), dried (MgSO ), filtered and concentrated to a
viscous oil which was loaded directly onto column. Chromatography [SiO column
(330 g), hexanes/EtOAc eluant (gradient 1:0 to 0:1)] to afford the title compound (91.3
g, 70% yield) as a white foam. ESI/MS calcd. for 1-(4-nitrophenyl)piperazine
derivative C H N O P 930.9, found m/z = 954.4 (M+Na).
43 48 7 8
Examples 13-37 were prepared via procedure A described above.
EXAMPLE 13:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-(1-(2,2,2-TRIFLUOROACETYL)PIPERIDINYL)PIPERAZIN
YL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (1.09 g, 23% yield). ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H F N O P 998.41, found m/z =
51 58 3 8 8
997.5 (M-1).
EXAMPLE 14:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-MORPHOLINOPIPERIDINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (0.98 g, 84% yield). ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 904.40, found m/z =
48 57 8 8
903.5 (M-1).
EXAMPLE 15:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL BIS(3-(2,2,2-TRIFLUOROACETAMIDO)PROPYL)PHOSPHORAMIDOCHLORIDATE
TFAHN
O N NH
N P O
TFAHN
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (7.52 g). ESI/MS calcd. for 1-(4-
nitrophenyl)piperazine derivative C H F N O P 1057.37, found m/z = 1056.4 (M-1).
49 54 6 9 9
EXAMPLE 16:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL METHYL(6,7,9,10,17,18,20,21-
OCTAHYDRODIBENZO[B,K][1,4,7,10,13,16]HEXAOXACYCLOOCTADECIN
YL)PHOSPHORAMIDOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (0.30 g). ESI/MS calcd. for
C H ClN O P 952.32, found m/z = 951 (M-1).
50 56 4 11
EXAMPLE 17:
(6-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tritylmorpholinyl)methyl
1,4,7,10-tetraoxaazacyclopentadecanylphosphonochloridate
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (4.26 g, 25% yield). ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 953.41, found m/z =
49 60 7 11
952.7 (M-1).
EXAMPLE 18:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL 1,4,7,10,13-PENTAOXAAZACYCLOOCTADECAN
YLPHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (1.11 g, 18% yield). ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 997.44, found m/z =
51 64 7 12
996.6 (M-1).
EXAMPLE 19:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-OXOPIPERIDINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (1.03 g, 14% yield). ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 833.33, found m/z =
44 48 7 8
832.4 (M-1).
EXAMPLE 20:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (OCTAHYDROISOQUINOLIN-2(1H)-YL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (4.87 g, 32% yield). ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 873.40, found m/z =
48 56 7 7
872.7 (M-1).
EXAMPLE 21:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-(TRIFLUOROMETHYL)PIPERIDINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (1.59 g, 42% yield). ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H F N O P 887.34, found m/z =
45 49 3 7 7
886.6 (M-1).
EXAMPLE 22:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-(4-NITROPHENYL)PIPERAZINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (2.27 g, 24% yield). ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 941.36, found m/z =
49 52 9 9
940.7 (M-1).
EXAMPLE 23:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-ACETYL-1,4-DIAZEPANYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (6.08 g, 20% yield). ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 876.37, found m/z =
46 53 8 8
875.9 (M-1).
EXAMPLE 24:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-ACETYLPIPERAZINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (3.30 g, 20% yield). ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 862.36, found m/z =
45 51 8 8
861.7 (M-1).
EXAMPLE 25:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-CYANOPIPERIDINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (0.84 g, 25% yield). ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 844.35, found m/z =
45 49 8 7
843.6 (M-1).
EXAMPLE 26:
(6-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)
tritylmorpholinyl)methyl hexynyl(methyl)phosphoramidochloridate
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (0.53 g). ESI/MS calcd. for
C H ClN O P 674.24, found m/z = 673 (M-1).
36 40 4 5
EXAMPLE 27:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL HEXENYL(METHYL)PHOSPHORAMIDOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (1.58 g). ESI/MS calcd. for
C H ClN O P 676.26, found m/z = 675 (M-1).
36 42 4 5
EXAMPLE 28:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-([1,1'-BIPHENYL]YLCARBOXAMIDO)PIPERIDIN
YL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (2.78 g). ESI/MS calcd. for
C H ClN O P 843.30, found m/z = 842 (M-1).
47 47 5 6
EXAMPLE 29:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-(3-CYANOBENZAMIDO)PIPERIDINYL)PHOSPHONOCHLORIDATE
O N NH
HN N P
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (4.89 g). ESI/MS calcd. for
C H ClN O P 792.26, found m/z = 793 (M-1).
42 42 6 6
EXAMPLE 30:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL [1,4'-BIPIPERIDIN]-1'-YLPHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (0.83 g). ESI/MS calcd. for
C H ClN O P 731.30, found m/z =730 (M-1).
39 47 5 5
EXAMPLE 31:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-(2',4'-DIMETHOXY-[1,1'-BIPHENYL]YLCARBOXAMIDO)PIPERIDIN
YL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (0.34 g). ESI/MS calcd. for
C H ClN O P 903.32, found m/z = 902 (M-1).
49 51 5 8
EXAMPLE 32:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL BUTENYL(METHYL)PHOSPHORAMIDOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (0.66 g). ESI/MS calcd. for
C H ClN O P 648.23, found m/z = 671 (M+Na).
34 38 4 5
EXAMPLE 33:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-(2',3'-DIMETHOXY-[1,1'-BIPHENYL]YLCARBOXAMIDO)PIPERIDIN
YL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (0.62 g). ESI/MS calcd. for
C H ClN O P 903.32, found m/z = 902 (M-1).
49 51 5 8
EXAMPLE 34:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-(3'-(TRIFLUOROMETHOXY)-[1,1'-BIPHENYL]
YLCARBOXAMIDO)PIPERIDINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (0.44 g). ESI/MS calcd. for
C H ClF N O P 927.28, found m/z = 926 (M-1).
48 46 3 5 7
EXAMPLE 35:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-(4'-(TRIFLUOROMETHOXY)-[1,1'-BIPHENYL]
YLCARBOXAMIDO)PIPERIDINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (0.51 g). ESI/MS calcd. for
C H ClF N O P 927.28, found m/z = 926 (M-1).
48 46 3 5 7
EXAMPLE 36:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-(4'-CHLORO-3'-(TRIFLUOROMETHYL)-[1,1'-BIPHENYL]
YLCARBOXAMIDO)PIPERIDINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (0.56 g). ESI/MS calcd. for
C H Cl F N O P 945.24, found m/z = 944 (M-1).
48 45 2 3 5 6
EXAMPLE 37:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-(3',5'-DICHLORO-[1,1'-BIPHENYL]YLCARBOXAMIDO)PIPERIDIN
YL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (0.42 g). ESI/MS calcd. for
C H Cl N O P 911.22, found m/z = 910 (M-1).
47 45 3 5 6
Examples 38-40 were prepared via procedure B described above.
EXAMPLE 38:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-(PYRIMIDINYL)PIPERAZINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure B to afford the title compound (3.13 g, 24% yield). ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 898.37, found m/z =
47 51 10 7
897.7 (M-1).
EXAMPLE 39:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-(2-(DIMETHYLAMINO)ETHYL)PIPERAZINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure B to afford the title compound (1.0 g, 79% yield). ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 891.42, found m/z =
47 58 9 7
890.8 (M-1).
EXAMPLE 40:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-PHENYLPIPERAZINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure B to afford the title compound (0.72g, 67% yield). ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 896.38, found m/z =
49 53 8 7
895.6 (M-1).
The activated subunits of the foregoing examples can be modified by
incorporating A, G, and C nucleobases by applying procedure A and substituting the
appropriate A, G, and C morpholino derivatives for Mo(Tr)T. The structures of suitably
protected A, G, and C morpholinos are shown in Examples 41-51.
EXAMPLE 41:
N-(9-(6-(HYDROXYMETHYL)TRITYLMORPHOLINYL)-9H-PURINYL)BENZAMIDE
(PROTECTED A)
EXAMPLE 42:
9-(6-(HYDROXYMETHYL)TRITYLMORPHOLINYL)(2-PHENYLACETAMIDO)-9H-
PURINYL PIVALATE (PROTECTED G)
EXAMPLE 43:
N-(1-(6-(HYDROXYMETHYL)TRITYLMORPHOLINYL)OXO-1,2-
DIHYDROPYRIMIDINYL)BENZAMIDE (PROTECTED C)
EXAMPLE 44:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL (4-(2,2,2-TRIFLUORO-N-METHYLACETAMIDO)PIPERIDIN
YL)PHOSPHONOCHLORIDATE
EXAMPLE 45:
(6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHYL METHYL(3-(2,2,2-TRIFLUORO-N-
METHYLACETAMIDO)PROPYL)PHOSPHORAMIDOCHLORIDATE
EXAMPLE 46:
(6-(6-BENZAMIDO-9H-PURINYL)TRITYLMORPHOLINYL)METHYL
MORPHOLINOPHOSPHONOCHLORIDATE
The title compound was synthesized to afford the title compound (10.81
g). ESI/MS calcd. for C H ClN O P 763.24, found m/z = 762 (M-1).
40 39 7 5
EXAMPLE 47:
(6-(6-BENZAMIDO-9H-PURINYL)TRITYLMORPHOLINYL)METHYL (4-
ACETYLPIPERAZINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized to afford the title compound (8.67
g). ESI/MS calcd. for C H ClN O P 804.27, found m/z = 803 (M-1).
42 42 8 5
EXAMPLE 48:
9-(6-(((CHLORO(MORPHOLINO)PHOSPHORYL)OXY)METHYL)TRITYLMORPHOLINYL)-
2-(2-PHENYLACETAMIDO)-9H-PURINYL PIVALATE
The title compound was synthesized to afford the title compound (9.88
g). ESI/MS calcd. for C H ClN O P 983.35, found m/z = 985 (M-1).
53 55 7 8
EXAMPLE 49:
9-(6-((((4-ACETYLPIPERAZINYL)CHLOROPHOSPHORYL)OXY)METHYL)
TRITYLMORPHOLINYL)(2-PHENYLACETAMIDO)-9H-PURINYL PIVALATE
The title compound was synthesized to afford the title compound (8.40
g). ESI/MS calcd. for C H ClN O P 1024.38, found m/z = 1023 (M-1).
55 58 8 8
EXAMPLE 50:
(6-(4-BENZAMIDOOXOPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLINYL)METHYL (4-
ACETYLPIPERAZINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized to afford the title compound (6.36
g). ESI/MS calcd. for C H ClN O P 780.26, found m/z =779 (M-1).
41 42 6 6
EXAMPLE 51:
(6-(4-BENZAMIDOOXOPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLINYL)METHYL
MORPHOLINOPHOSPHONOCHLORIDATE
O N N
N P O
The title compound was synthesized to afford the title compound (10.29
g). ESI/MS calcd. for C H ClN O P 739.23, found m/z =738 (M-1).
39 39 5 6
EXAMPLE 52:
((2S,6R)(6-BENZAMIDO-9H-PURINYL)TRITYLMORPHOLINYL)METHYL (4-
(2,2,2-TRIFLUOROACETAMIDO)PIPERIDINYL)PHOSPHONOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title compound (15.4 g, 66% yield) as a white
solid. ESI/MS calcd. for 1-(4-nitrophenyl)piperazine derivative C H F N O P
53 53 3 11 7
1043.4, found m/z = 1042.5 (M-1).
EXAMPLE 53:
(R)-METHYL(1-PHENYLETHYL)PHOSPHORAMIDIC DICHLORIDE
To a cooled (ice/water bath) solution of phosphorus oxychloride (2.83
mL, 30.3 mmol) in DCM (30 mL) was added sequentially, dropwise, and with stirring
2,6-lutidine (7.06 mL, 60.6 mmol) and a DCM solution of (R)-(+)-N,a-
dimethylbenzylamine (3.73 g, 27.6 mmol). After 5 minutes, the bath was removed and
reaction mixture allowed to warm to ambient temperature. After 1 hour, the reaction
solution was washed with a citric acid solution (50 mL x 3, 10 % w/v aq), dried
(MgSO ), filtered through SiO and concentrated to provide the title compound (3.80 g)
as a white foam. ESI/MS calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P
19 25 4 4
404.2, found m/z = 403.1 (M-1).
EXAMPLE 54:
(S)-METHYL(1-PHENYLETHYL)PHOSPHORAMIDIC DICHLORIDE
The title compound was synthesized in a manner analogous to that
described in Example 53 to afford the title compound (3.95 g) as a white foam. ESI/MS
calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 404.2, found m/z =
19 25 4 4
403.1 (M-1).
EXAMPLE 55:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL METHYL((R)
PHENYLETHYL)PHOSPHORAMIDOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title chlorophosphoroamidate (4.46 g, 28% yield)
as a white solid. ESI/MS calcd. for C H ClN O P 698.2, found m/z = 697.3 (M-1).
38 40 4 5
EXAMPLE 56:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL METHYL((S)
PHENYLETHYL)PHOSPHORAMIDOCHLORIDATE
The title compound was synthesized in a manner analogous to that
described in procedure A to afford the title chlorophosphoroamidate (4.65 g, 23% yield)
as a white solid. ESI/MS calcd. for C H ClN O P 698.2, found m/z = 697.3 (M-1).
38 40 4 5
EXAMPLE 57:
(4-(PYRROLIDINYL)PIPERIDINYL)PHOSPHONIC DICHLORIDE HYDROCHLORIDE
To a cooled (ice/water bath) solution of phosphorus oxychloride (5.70
mL, 55.6 mmol) in DCM (30 mL) was added 2,6-lutidine (19.4 mL, 167 mmol) and a
DCM solution (30 mL) of 4-(1-pyrrolidinyl)-piperidine (8.58 g, 55.6 mmol) and stirred
for 1hour. The suspension was filtered and solid washed with excess diethyl ether to
afford the title pyrrolidine (17.7 g, 91% yield) as a white solid. ESI/MS calcd. for 1-(4-
nitrophenyl)piperazine derivative C H N O P 423.2, found m/z = 422.2 (M-1).
19 30 5 4
EXAMPLE 58:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL (4-(PYRROLIDINYL)PIPERIDIN
YL)PHOSPHONOCHLORIDATE HYDROCHLORIDE
To a stirred, cooled (ice/water bath) solution of the
dichlorophosphoramidate from Example 57 (17.7 g, 50.6 mmol) in DCM (100 mL) was
added a DCM solution (100 mL) of Mo(Tr)T (2) (24.5 g, 50.6 mmol), 2,6-Lutidine
(17.7 mL, 152 mmol), and 1-methylimidazole (0.401 mL, 5.06 mmol) dropwise over 10
minutes. The bath was allowed to warm to ambient temperature as suspension was
stirred. After 6 hours, the suspension was poured onto diethyl ether (1 L), stirred 15
minutes, filtered and solid washed with additional ether to afford a white solid (45.4 g).
The crude product was purified by chromatography [SiO column (120 gram),
DCM/MeOH eluant (gradient 1:0 to 6:4)], and the combined fractions were poured onto
diethyl ether (2.5 L), stirred 15 min, filtered, and the resulting solid washed with
additional ether to afford the title compound (23.1 g, 60 % yield) as a white solid.
ESI/MS calcd. for 1-(4-nitrophenyl)piperazine derivative C H N O P 888.4, found
48 57 8 7
m/z = 887.6 (M-1).
EXAMPLE 59:
3-(TERT-BUTYLDISULFANYL)(ISOBUTOXYCARBONYLAMINO)PROPANOIC ACID
S OH
To S-tert-butylmercapto-L-cysteine (10g, 47.8mmol) in CH CN (40mL)
was added K CO (16.5g, 119.5mmol) in H O (20mL). After stirring for 15 minutes,
2 3 2
iso-butyl chloroformate (9.4mL, 72mmol) was injected slowly. The reaction was allowe
to run for 3 hours. The white solid was filtered through Celite; the filtrate was
concentrated to remove CH CN. The residue was dissolved in ethyl acetate (200mL),
washed with 1N HCl (40ml X 3), brine (40 X 1), dried over Na SO . The title
compound was obtained after chromatography (5% MeOH/DCM).
EXAMPLE 60:
TERT-BUTYL 4-(3-(TERT-BUTYLDISULFANYL)
(ISOBUTOXYCARBONYLAMINO)PROPANAMIDO)PIPERIDINECARBOXYLATE
S NBoc
To the acid from Example 59 (6.98g, 22.6mmol) in DMF (50ml was
added HATU (8.58g, 22.6mmol). After 30 min, Hunig base (4.71ml, 27.1mmol) and 1-
Bocamino piperidine (5.43g, 27.1mmol) were added to the mixture. The reaction
was continued stirring at RT for another 3h. DMF was removed at high vacuum, the
crude residue was dissolved in EtAc (300ml), washed with H O (50ml X 3). The title
compound was obtained after ISCO purification (5% MeOH/DCM).
EXAMPLE 61:
ISOBUTYL 3-(ISOPROPYLDISULFANYL)OXO(PIPERIDINYLAMINO)PROPAN
YLCARBAMATE
S NH
To the compound from Example 60 (7.085g, 18.12mmol) was added
30ml of 4M HCl/Dioxane. The reaction was completed after 2h at RT. The title
compound was used for the next step without further purification.
EXAMPLE 62:
ISOBUTYL 3-(TERT-BUTYLDISULFANYL)(1-(DICHLOROPHOSPHORYL)PIPERIDIN
YLAMINO)OXOPROPANYLCARBAMATE
S N P O
O Cl
To the compound from Example 61 (7.746g, 18.12mmol) in DCM
(200ml) at -78 °C was slowly injected POCl (1.69ml, 18.12mmol) under Ar, followed
by the addition of Et N (7.58ml, 54.36mmol). The reaction was stirred at RT for 5h,
concentrated to remove excess base and solvent. The title compound was given as white
solid after ISCO purification (50% EtAc/Hexane).
EXAMPLE 63:
ISOBUTYL 3-(TERT-BUTYLDISULFANYL)(1-(CHLORO(((2S,6R)(5-METHYL-2,4-
DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TRITYLMORPHOLIN
YL)METHOXY)PHOSPHORYL)PIPERIDIN
YLAMINO)OXOPROPANYLCARBAMATE
To 1-((2R,6S)(hydroxymethyl)tritylmorpholinyl)
methylpyrimidine-2,4(1H,3H)-dione (moT(Tr)) (5.576g, 10.98mmol) in DCM (100ml)
at 0 C, was added lutidine (1.92ml, 16.47mmol) and DMAP (669mg, 5.5mmol),
followed by the addition of the compound from Example 62 (6.13g, 12.08mmol). The
reaction was left stirring at RT for 18h. The title compound was obtained after ISCO
purification (50% EtAc/Hexane).
EXAMPLE 64:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLIN
YL)METHYL HEXYL(METHYL)PHOSPHORAMIDOCHLORIDATE
A DCM (80ml) solution of N-hydroxylmethylamine (4.85ml, 32mmol)
was cooled down to -78 C under N2. A solution of phosphoryl chloride (2.98ml,
32mmol) in DCM (10ml), followed by a solution of Et N (4.46ml, 32mmol) in DCM
(10ml), was added slowly. The stirring was continued while the reaction was allowed
to warm to RT overnight. The desired phosphoramidodichloride was given as clear oil
after ISCO purification (20% EtAc/Hexane).
To moT(Tr) (2) (5.10g, 10.54mmol) in DCM (100ml) at 0 C, was added
lutidine (3.68ml, 31.6mmol) and DMAP (642mg, 5.27mmol), followed by the addition
of the phosphoramidodichloride (4.89g, 21.08mmol). The reaction was left stirring at
RT for 18h. The title compound was obtained after ISCO purification (50%
EtOAc/Hexane).
EXAMPLE 65:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL DODECYL(METHYL)PHOSPHORAMIDOCHLORIDATE
The title compound was prepared according to the general procedures
described in Examples 53 and 55.
EXAMPLE 66:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL MORPHOLINOPHOSPHONOCHLORIDATE
The title compound was prepared according to the general procedures
described in Examples 53 and 55.
EXAMPLE 67:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL (S)(METHOXYMETHYL)PYRROLIDIN
YLPHOSPHONOCHLORIDATE
The title compound was prepared according to the general procedures
described in Examples 53 and 55.
EXAMPLE 68:
((2S,6R)(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)
TRITYLMORPHOLINYL)METHYL 4-(3,4,5-TRIMETHOXYBENZAMIDO)PIPERIDIN
YLPHOSPHONOCHLORIDATE
Boc O
N NBoc
MeO N NH
O N P O
MeO N
MeO N N P O
H MeO
O NNH
To 1-Bocpiperidine (1g, 5mmol) in DCM (20ml) was added Hunig
base (1.74ml, 10mmol), followed by the addition of 3,4,5-trimethoxybenzoyl chloride
(1.38g, 6mmol). The reaction was run at RT for 3h, concentrated to remove solvent and
excess base. The residue was dissolved in EtAc (100ml), washed with 0.05N HCl (3 X
15ml), sat. NaHCO (2 X 15ml), dried over Na SO . Product (10) was obtained after
3 2 4
ISCO purification (5% MeOH/DCM).
To 10 was added 15ml of 4N HCl/Dioxane, reaction was terminated
after 4h. 11 was obtained as white solid.
A DCM (20ml) solution of 11 (1.23g, 4.18mmol) was cooled down to -
78 C under N . A solution of phosphoryl chloride (0.39ml, 4.18mmol) in DCM (2ml),
followed by a solution of Et N (0.583ml, 4.18mmol) in DCM (2ml), was added slowly.
The stirring was continued while the reaction was allowed to warm to RT overnight.
The desired product (12) was obtained after ISCO purification (50% EtAc/Hexane).
To moT(Tr) (1.933g, 4.0mmol) in DCM (20ml) at 0 C, was added
lutidine (0.93ml, 8mmol) and DMAP (49mg, 0.4mmol), followed by the addition of 12
(1.647g, 4mmol). The reaction was left stirring at RT for 18h. The desired product (13)
was obtained after ISCO purification (50% EtAc/Hexane).
EXAMPLE 69:
SYNTHESIS OF CYCLOPHOSPHORAMIDE CONTAINING SUBUNIT
O NNH
O O OH NH
O NNH OH HN
S O NNH
DCM N Substitution
Ph Ph
Ph Ph
Ph Ph
Tosylation
Activation
POCl3
714 DIEA
P O NNH
Ph Ph
The moT subunit (7) (25 g) was suspended in DCM (175 ml) and NMI
(N-methylimidazole, 5.94 g, 1.4 eq.) was added to obtain a clear solution. Tosyl
chloride was added to the reaction mixture, and the reaction progress was monitored by
TLC until done (about 2 hours). An aqueous workup was performed by washing with
0.5 M citric acid buffer (pH=5), followed by brine. The organic layer was separated
and dried over Na2SO4. Solvent was removed with a rotavaporator to obtain the crude
product (14) which was used in the next step without further purification.
The moT Tosylate (14) was mixed with propanolamine (1g/10 ml). The
reaction mixture was then placed in an oven at 45 °C overnight followed by dilution
with DCM (10 ml). An aqueous workup was performed by washing with 0.5 M citric
acid buffer (pH=5), followed by brine. The organic layer was separated and dried over
Na SO . Solvent was removed with a rotavaporator to obtain the crude product (15)
The curde product was analyzed by NMR and HPLC and determined to be ready for the
next step without further purification.
The crude product (15) was dissolved in DCM (2.5 ml DCM/g, 1 eq.)
and mixed with DIEA (3 eq.). This solution was cooled with dry ice-acetone and
POCl was added dropwise (1.5 eq.). The resultant mixture was stirred at room
temperature overnight. An aqueous workup was performed by washing with 0.5 M
citric acid buffer (pH=5), followed by brine. The organic layer was separated and dried
over Na SO . Solvent was removed with a rotavaporator to obtain the crude product as
a yellowish solid. The crude product was purified by silica gel chromatography (crude
product/silica=1 to 5 ratio, gradient DCM to 50% EA/DCM), and fractions were pooled
according to TLC analysis. Solvent was removed to obtain the desired product (16) as a
mixture of diastereomers. The purified product was analyzed by HPLC (NPP quench)
and NMR (H-1 and P-31 ).
The diastereomeric mixture was separated according to the following
procedure. The mixture (2.6 g) was dissolved in DCM. This sample was loaded on a
RediSepRf column (80 g normal phase made by Teledyne Isco) and eluted with 10%
EA/DCM to 50% EA/DCM over 20 minutes. Fractions were collected and analyzed by
TLC. Fractions were pooled according to TLC analysis, and solvent was removed with
a rotavaporator at room temperature. The diastereomeric ratio of ther pooled fractions
was determined by P-31 NMR and NPP-TFA analysis. If needed, the above procedure
was repeated until the diastereomeric ratio reached 97%.
EXAMPLE 70:
GLOBAL CHOLIC ACID MODIFICATION
OH O OH
O O B
NH -H O
O 3 2
N DMSO
+ 500 ul
19 18 20
Cholic acid (17) (12 g, 29.4 mmol), N-hydroxysuccinimide (4.0 g,34.8
mmol), EDCI (5.6 g, 29.3 mmol), and DMAP (1 g, 8.2 mmol) were charged to a round
bottom flask. DCM (400 ml) and THF (40 ml) were added to dissolve. The reaction
mixture was stirred at room temperature overnight. Water (400 ml) was then added to
the reaction mixture, the organic layer separated and washed with water (2X 400 ml),
followed by sat. NaHCO (300 ml) and brine (300 ml). The organic layer was then
dried over Na SO . Solvent was removed with rotavaporator to obtain a white solid.
The crude product (18) was dissolved in chloroform (100 ml) and precipitated into
heptane (1000 ml). The solid was collected by filtration, analyzed by HPLC and NMR
and used without further purification.
Compound 19 (20 mg, 2.8 mmol) was weighed into a vial (4 ml) and
dissolved in DMSO (500 ul). The activated cholate ester (18) (13 mg, 25 mmol) was
added to the reaction mixture according to the ratio of two equivalent of active ester per
modification site followed by stirring at room temperature overnight. Reaction progress
was determined by MALDI and HPLC (C-18 or SAX).
After the reaction was complete (as determined by disappearance of 19),
1ml of concentrated ammonia was added to the reaction mixture once the reaction is
complete. The reaction vial was then placed in an oven (45 C) overnight (18 hours)
followed by cooling to room temperature and dilution with 1% ammonia in water (10
ml). This sample was loaded on to an SPE column (2 cm), and the vial rinsed with 1%
ammonia solution (2X 2ml). The SPE column was washed with 1% ammonia in water
(3X 6ml), and the product eluted with 45% acetonitrile in 1% ammonia in water (6 ml).
Fractions containing oligomer were identified by UV optical density measurement.
Product (20) was isolated by lyophilization. Purity and identity were determined by
MALDI and HPLC (C-18 and/or SAX).
This same procedure is applicable to deoxycholic acid activation and
conjugation to 19.
EXAMPLE 71:
GLOBAL GUANIDINYLATION
Compound 19 (25 mg, 2.8 mmol) was weighed into a vial (6 ml). 1H-
Pyrozolecarboxamidine chloride (15 mg, 102 mmol) and potassium carbonate (20
mg, 0.15 mmol) were added to the vial. Water was added (500 ul), and the reaction
mixture was stirred at room temperature overnight (about 18 hours). Reaction
completion was determined by MALDI.
Once complete, the reaction was diluted with 1% ammonia in water (10
ml) and loaded on to an SPE column (2 cm). The vial was rinsed with 1% ammonia
solution (2X 2ml), and the SPE column was washed with 1% ammonia in water (3X
6ml). Product was eluted with 45% acetonitrile in 1% ammonia in water (6 ml).
Fractions containing oligomer were identified by UV optical density measurement.
Product was isolated by lyophilization. Purity and identity were determined by MALDI
and HPLC (C-18 and/or SAX).
EXAMPLE 72:
GLOBAL THIOACETYL MODIFICATION
O O O
DMSO
500 ul
Ammonolysis
Compound 19 (20 mg, 2.3 mmol) was weighed in to a vial (4 ml) and
dissolved in DMSO (500 ul). N-succinimidyl-S-acetylthioacetate (SATA) (21) (7 mg,
28 mmol) was added to the reaction mixture, and it was allowed to stir at room
temperature overnight. Reaction progress was monitored by MALDI and HPLC.
Once complete, 1% ammonia in water was added to the reaction
mixture, and it was stirred at room temperature for 2 hours. This solution was loaded
on to an SPE column (2 cm). The vial was rinsed with 1% ammonia solution (2X 2ml),
and the SPE column was washed with 1% ammonia in water (3X 6ml). Product (23)
was eluted with 45% acetonitrile in 1% ammonia in water (6 ml). Fractions containing
oligomer were identified by UV optical density measurement. Product was isolated by
lyophilization. Purity and identity were determined by MALDI and HPLC (C-18
and/or SAX).
EXAMPLE 73:
GLOBAL SUCCINIC ACID MODIFICATION
O O B
O B NH -H O
O O DMSO 3 2
500 ul
19 O
Compound 19 (32 mg, 3.7 mmol) was weighed in to a vial (4 ml) and
dissolved in DMSO (500 ul). N-ethyl morpholino (12 mg, 100 mmol) and succinic
anhydride (10 mg, 100 mmol) were added to the reaction mixture, and it was allowed to
stir at room temperature overnight. Reaction progress was monitored by MALDI and
HPLC.
Once complete, 1% ammonia in water was added to the reaction
mixture, and it was stirred at room temperature for 2 hours. This solution was loaded
on to an SPE column (2 cm). The vial was rinsed with 1% ammonia solution (2X 2ml),
and the SPE column was washed with 1% ammonia in water (3X 6ml). Product (24)
was eluted with 45% acetonitrile in 1% ammonia in water (6 ml). Fractions containing
oligomer were identified by UV optical density measurement. Product was isolated by
lyophilization. Purity and identity were determined by MALDI and HPLC (C-18
and/or SAX).
The above procedure is applicable to glutartic acid (glutaric anhydride)
and tetramethyleneglutaric acid (tetramethyleneglutaric anhydride) modification of
compound 19 as well.
EXAMPLE 74:
PREPARATION OF AN OLIGONUCLEOTIDE ANALOGUE COMPRISING A MODIFIED
TERMINAL GROUP
To a solution of a 25-mer PMO containing a free 3’-end (27.7 mg, 3.226
mmol) in DMSO (300mL) was added farnesyl bromide(1.75ml, 6.452 mmol) and
diisopropylethylamine (2.24 mL, 12.9 mmol). The reaction mixture was stirred at room
temperature for 5 hours. The crude reaction mixture was diluted with 10 mL of 1%
aqueous NH OH, and then loaded onto a 2 mL Amberchrome CG300M column. The
column was then rinsed with 3 column volumes of water, and the product was eluted
with 6 mL of 1:1 acetonitrile and water (v/v). The solution was then lyophilized to
obtain the title compound as a white solid.
EXAMPLE 75:
PREPARATION OF MORPHOLINO OLIGOMERS
Preparation of trityl piperazine phenyl carbamate 1b (see Figure 1): To a
cooled suspension of compound 1a in dichloromethane (6 mL/g 11) was added a
solution of potassium carbonate (3.2 eq) in water (4 mL/g potassium carbonate). To
this two-phase mixture was slowly added a solution of phenyl chloroformate (1.03 eq)
in dichloromethane (2 g/g phenyl chloroformate). The reaction mixture was warmed to
ºC. Upon reaction completion (1-2 hr), the layers were separated. The organic layer
was washed with water, and dried over anhydrous potassium carbonate. The product
1b was isolated by crystallization from acetonitrile. Yield = 80%
Preparation of carbamate alcohol 1c: Sodium hydride (1.2 eq) was
suspended in 1-methylpyrrolidinone (32 mL/g sodium hydride). To this suspension
were added triethylene glycol (10.0 eq) and compound 1b (1.0 eq). The resulting slurry
was heated to 95 ºC. Upon reaction completion (1-2 hr), the mixture was cooled to 20
ºC. To this mixture was added 30% dichloromethane/methyl tert-butyl ether (v:v) and
water. The product-containing organic layer was washed successively with aqueous
NaOH, aqueous succinic acid, and saturated aqueous sodium chloride. The product 1c
was isolated by crystallization from dichloromethane/methyl tert-butyl ether/heptane.
Yield = 90%.
Preparation of Tail acid 1d: To a solution of compound 1c in
tetrahydrofuran (7 mL/g 36) was added succinic anhydride (2.0 eq) and DMAP (0.5 eq).
The mixture was heated to 50 ºC. Upon reaction completion (5 hr), the mixture was
cooled to 20 ºC and adjusted to pH 8.5 with aqueous NaHCO3. Methyl tert-butyl ether
was added, and the product was extracted into the aqueous layer. Dichloromethane was
added, and the mixture was adjusted to pH 3 with aqueous citric acid. The product-
containing organic layer was washed with a mixture of pH=3 citrate buffer and
saturated aqueous sodium chloride. This dichloromethane solution of 1d was used
without isolation in the preparation of compound 1e.
Preparation of 1e: To the solution of compound 1d was added N-
hydroxynorbornene-2,3-dicarboxylic acid imide (HONB) (1.02 eq), 4-
dimethylaminopyridine (DMAP) (0.34 eq), and then 1-(3-dimethylaminopropyl)-N'-
ethylcarbodiimide hydrochloride (EDC) (1.1 eq). The mixture was heated to 55 ºC.
Upon reaction completion (4-5 hr), the mixture was cooled to 20 ºC and washed
successively with 1:1 0.2 M citric acid/brine and brine. The dichloromethane solution
underwent solvent exchange to acetone and then to N,N-dimethylformamide, and the
product was isolated by precipitation from acetone/ N,N-dimethylformamide into
saturated aqueous sodium chloride. The crude product was reslurried several times in
water to remove residual N,N-dimethylformamide and salts. Yield = 70% of 1e from
compound 1c. Introduction of the activated “Tail” onto the disulfide anchor-resin was
performed in NMP by the procedure used for incorporation of the subunits during solid
phase synthesis.
Preparation of the Solid Support for Synthesis of Morpholino Oligomers
(see Figure 2): This procedure was performed in a silanized, jacketed peptide vessel
(custom made by ChemGlass, NJ, USA) with a coarse porosity (40-60 µm) glass frit,
overhead stirrer, and 3-way Teflon stopcock to allow N2 to bubble up through the frit or
a vacuum extraction. Temperature control was achieved in the reaction vessel by a
circulating water bath.
The resin treatment/wash steps in the following procedure consist of two
basic operations: resin fluidization and solvent/solution extraction. For resin
fluidization, the stopcock was positioned to allow N2 flow up through the frit and the
specified resin treatment/wash was added to the reactor and allowed to permeate and
completely wet the resin. Mixing was then started and the resin slurry mixed for the
specified time. For solvent/solution extraction, mixing and N2 flow were stopped and
the vacuum pump was started and then the stopcock was positioned to allow evacuation
of resin treatment/wash to waste. All resin treatment/wash volumes were 15 mL/g of
resin unless noted otherwise.
To aminomethylpolystyrene resin (100-200 mesh; ~1.0 mmol/g N2
substitution; 75 g, 1 eq, Polymer Labs, UK, part #1464-X799) in a silanized, jacketed
peptide vessel was added 1-methylpyrrolidinone (NMP; 20 ml/g resin) and the resin
was allowed to swell with mixing for 1-2 hr. Following evacuation of the swell solvent,
the resin was washed with dichloromethane (2 x 1-2 min), 5% diisopropylethylamine in
% isopropanol/dichloromethane (2 x 3-4 min) and dichloromethane (2 x 1-2 min).
After evacuation of the final wash, the resin was fluidized with a solution of disulfide
anchor 2a in 1-methylpyrrolidinone (0.17 M; 15 mL/g resin, ~2.5 eq) and the
resin/reagent mixture was heated at 45 °C for 60 hr. On reaction completion, heating
was discontinued and the anchor solution was evacuated and the resin washed with 1-
methylpyrrolidinone (4 x 3-4 min) and dichloromethane (6 x 1-2 min). The resin
was treated with a solution of 10% (v/v) diethyl dicarbonate in dichloromethane (16
mL/g; 2 x 5-6 min) and then washed with dichloromethane (6 x 1-2 min). The resin 2b
was dried under a N2 stream for 1-3 hr and then under vacuum to constant weight (±
2%). Yield: 110-150% of the original resin weight.
Determination of the Loading of Aminomethylpolystyrene-disulfide
resin: The loading of the resin (number of potentially available reactive sites) is
determined by a spectrometric assay for the number of triphenylmethyl (trityl) groups
per gram of resin.
A known weight of dried resin (25 ± 3 mg) is transferred to a silanized
ml volumetric flask and ~5 mL of 2% (v/v) trifluoroacetic acid in dichloromethane is
added. The contents are mixed by gentle swirling and then allowed to stand for 30 min.
The volume is brought up to 25 mL with additional 2% (v/v) trifluoroacetic acid in
dichloromethane and the contents thoroughly mixed. Using a positive displacement
pipette, an aliquot of the trityl-containing solution (500 μL) is transferred to a 10 mL
volumetric flask and the volume brought up to 10 mL with methanesulfonic acid.
The trityl cation content in the final solution is measured by UV
absorbance at 431.7 nm and the resin loading calculated in trityl groups per gram resin
( μmol/g) using the appropriate volumes, dilutions, extinction coefficient ( ε: 41 μmol-
1cm-1) and resin weight. The assay is performed in triplicate and an average loading
calculated.
The resin loading procedure in this example will provide resin with a
loading of approximately 500 μmol/g. A loading of 300-400 in μmol/g was obtained if
the disulfide anchor incorporation step is performed for 24 hr at room temperature.
Tail loading: Using the same setup and volumes as for the preparation of
aminomethylpolystyrene-disulfide resin, the Tail can be introduced into the molecule.
For the coupling step, a solution of 1e (0.2 M) in NMP containing 4-ethylmorpholine
(NEM, 0.4 M) was used instead of the disulfide anchor solution. After 2 hr at 45 °C,
the resin 2b was washed twice with 5% diisopropylethylamine in 25%
isopropanol/dichloromethane and once with DCM. To the resin was added a solution of
benzoic anhydride (0.4 M) and NEM (0.4 M). After 25 min, the reactor jacket was
cooled to room temperature, and the resin washed twice with 5% diisopropylethylamine
in 25% isopropanol/dichloromethane and eight times with DCM. The resin 2c was
filtered and dried under high vacuum. The loading for resin 2c is defined to be the
loading of the original aminomethylpolystyrene-disulfide resin 2b used in the Tail
loading.
Solid Phase Synthesis: Morpholino Oligomers were prepared on a
Gilson AMS-422 Automated Peptide Synthesizer in 2 mL Gilson polypropylene
reaction columns (Part # 3980270). An aluminum block with channels for water flow
was placed around the columns as they sat on the synthesizer. The AMS-422 will
alternatively add reagent/wash solutions, hold for a specified time, and evacuate the
columns using vacuum.
For oligomers in the range up to about 25 subunits in length,
aminomethylpolystyrene-disulfide resin with loading near 500 μmol/g of resin is
preferred. For larger oligomers, aminomethylpolystyrene-disulfide resin with loading
of 300-400 μmol/g of resin is preferred. If a molecule with 5’-Tail is desired, resin that
has been loaded with Tail is chosen with the same loading guidelines.
The following reagent solutions were prepared:
Detritylation Solution: 10% Cyanoacetic Acid (w/v) in 4:1
dichloromethane/acetonitrile; Neutralization Solution: 5% Diisopropylethylamine in
3:1 dichloromethane/isopropanol; Coupling Solution: 0.18 M (or 0.24 M for oligomers
having grown longer than 20 subunits) activated Morpholino Subunit of the desired
base and linkage type and 0.4 M N ethylmorpholine, in 1,3-dimethylimidazolidinone.
Dichloromethane (DCM) was used as a transitional wash separating the different
reagent solution washes.
On the synthesizer, with the block set to 42 °C, to each column
containing 30 mg of aminomethylpolystyrene-disulfide resin (or Tail resin) was added 2
mL of 1-methylpyrrolidinone and allowed to sit at room temperature for 30 min.
After washing with 2 times 2 mL of dichloromethane, the following synthesis cycle was
employed:
Step Volume Delivery Hold time
Detritylation 1.5 mL Manifold 15 seconds
Detritylation 1.5 mL Manifold 15 seconds
Detritylation 1.5 mL Manifold 15 seconds
Detritylation 1.5 mL Manifold 15 seconds
Detritylation 1.5 mL Manifold 15 seconds
Detritylation 1.5 mL Manifold 15 seconds
Detritylation 1.5 mL Manifold 15 seconds
DCM 1.5 mL Manifold 30 seconds
Step Volume Delivery Hold time
Neutralization 1.5 mL Manifold 30 seconds
Neutralization 1.5 mL Manifold 30 seconds
Neutralization 1.5 mL Manifold 30 seconds
Neutralization 1.5 mL Manifold 30 seconds
Neutralization 1.5 mL Manifold 30 seconds
Neutralization 1.5 mL Manifold 30 seconds
DCM 1.5 mL Manifold 30 seconds
Coupling 350 uL – 500 uL Syringe 40 minutes
DCM 1.5 mL Manifold 30 seconds
Neutralization 1.5 mL Manifold 30 seconds
Neutralization 1.5 mL Manifold 30 seconds
DCM 1.5 mL Manifold 30 seconds
DCM 1.5 mL Manifold 30 seconds
DCM 1.5 mL Manifold 30 seconds
The sequences of the individual oligomers were programmed into the
synthesizer so that each column receives the proper coupling solution (A,C,G,T,I) in the
proper sequence. When the oligomer in a column had completed incorporation of its
final subunit, the column was removed from the block and a final cycle performed
manually with a coupling solution comprised of 4-methoxytriphenylmethyl chloride
(0.32 M in DMI) containing 0.89 M 4-ethylmorpholine.
Cleavage from the resin and removal of bases and backbone protecting
groups: After methoxytritylation, the resin was washed 8 times with 2 mL 1-methyl
pyrrolidinone. One mL of a cleavage solution consisting of 0.1 M 1,4-dithiothreitol
(DTT) and 0.73 M triethylamine in 1-methylpyrrolidinone was added, the column
capped, and allowed to sit at room temperature for 30 min. After that time, the solution
was drained into a 12 mL Wheaton vial. The greatly shrunken resin was washed twice
with 300 µL of cleavage solution. To the solution was added 4.0 mL conc aqueous
ammonia (stored at -20 °C), the vial capped tightly (with Teflon lined screw cap), and
the mixture swirled to mix the solution. The vial was placed in a 45 °C oven for 16-24
hr to effect cleavage of base and backbone protecting groups.
Initial Oligomer Isolation: The vialed ammonolysis solution was
removed from the oven and allowed to cool to room temperature. The solution was
diluted with 20 mL of 0.28% aqueous ammonia and passed through a 2.5x10 cm
column containing Macroprep HQ resin (BioRad). A salt gradient (A: 0.28% ammonia
with B: 1 M sodium chloride in 0.28% ammonia; 0-100% B in 60 min) was used to
elute the methoxytrityl containing peak. The combined fractions were pooled and
further processed depending on the desired product.
Demethoxytritylation of Morpholino Oligomers: The pooled fractions
from the Macroprep purification were treated with 1 M H3PO4 to lower the pH to 2.5.
After initial mixing, the samples sat at room temperature for 4 min, at which time they
are neutralized to pH 10-11 with 2.8% ammonia/water. The products were purified by
solid phase extraction (SPE).
Amberchrome CG-300M (Rohm and Haas; Philadelphia, PA) (3 mL) is
packed into 20 mL fritted columns (BioRad Econo-Pac Chromatography Columns
(732-1011)) and the resin rinsed with 3 mL of the following: 0.28% NH4OH/80%
acetonitrile; 0.5M NaOH/20%ethanol; water; 50 mM H3PO4/80% acetonitrile;
water; 0.5 NaOH/20% ethanol; water; 0.28% NH4OH.
The solution from the demethoxytritylation was loaded onto the column
and the resin rinsed three times with 3-6 mL 0.28% aqueous ammonia. A Wheaton vial
(12 mL) was placed under the column and the product eluted by two washes with 2 mL
of 45% acetonitrile in 0.28% aqueous ammonia. The solutions were frozen in dry ice
and the vials placed in a freeze dryer to produce a fluffy white powder. The samples
were dissolved in water, filtered through a 0.22 micron filter (Pall Life Sciences,
Acrodisc 25 mm syringe filter, with a 0.2 micron HT Tuffryn membrane) using a
syringe and the Optical Density (OD) was measured on a UV spectrophotometer to
determine the OD units of oligomer present, as well as dispense sample for analysis.
The solutions were then placed back in Wheaton vials for lyophilization.
Analysis of Morpholino Oligomers: MALDI-TOF mass spectrometry
was used to determine the composition of fractions in purifications as well as provide
evidence for identity (molecular weight) of the oligomers. Samples were run following
dilution with solution of 3,5-dimethoxyhydroxycinnamic acid (sinapinic acid), 3,4,5-
trihydoxyacetophenone (THAP) or alpha-cyanohydoxycinnamic acid (HCCA) as
matrices.
Cation exchange (SCX) HPLC was performed using a Dionex ProPac
SCX-10, 4x250mm column (Dionex Corporation; Sunnyvale, CA) using 25 mM pH=5
sodium acetate 25% acetonitrile (Buffer A) and 25 mM pH=5 sodium acetate 25%
acetonitrile 1.5 M potassium chloride (buffer B) (Gradient 10-100% B in 15 min) or 25
mM KH2PO4 25% acetonitrile at pH=3.5 (buffer A) and 25 mM KH2PO4 25%
acetonitrile at pH=3.5 with 1.5 M potassium chloride (buffer B) (Gradient 0-35% B in
min). The former system was used for positively charged oligomers that do not have
a peptide attached, while the latter was used for peptide conjugates.
Purification of Morpholino Oligomers by Cation Exchange
Chromatography: The sample is dissolved in 20 mM sodium acetate, pH=4.5 (buffer A)
and applied to a column of Source 30 cation exchange resin (GE Healthcare) and eluted
with a gradient of 0.5 M sodium chloride in 20 mM sodium acetate and 40%
acetonitrile, pH=4.5 (buffer B). The pooled fractions containing product are neutralized
with conc aqueous ammonia and applied to an Amberchrome SPE column. The
product is eluted, frozen, and lyophilized as above.
I. BIOLOGICAL EVALUATION
EXAMPLE 1:
TREATMENT OF INFLUENZA A VIRUS INFECTED CELLS
A series of PMO containing various modified intersubunit linkages was
prepared and used to treat influenza A virus-infected cells in culture. The PMO and
PMO containing the modified intersubunit linkages of the present inventions were all
designed to target the viral M1/M2 segment at the AUG start codon and have one of
two base sequences. Inhibition of influenza A virus replication by antisense targeting
of multiple sites within the M1/M2 segment is described in US Appn. No. 12/945,081
which is incorporated herein by reference in its entirety. In addition to inhibition of
translation by targeting the common M1/M2 AUG start site, splice donor and splice
acceptor sites can also be targeted using compounds of the invention.
An alveolar murine macrophage cell line (ATCC; AMJ2-C11) was
infected at 0.1 MOI with H1N1 (strain PR8) and 1 hour post-infection test compound
was added. Cells were incubated at 35 degrees C overnight. Viral supernatant was then
taken and incubated with VNAR protease to release viral RNA. HA RNA was
quantified by quantitative real-time PCR (qRT-PCR). Cells were washed, fixed, and
permeabilized. M1 and M2 proteins were then probed with monoclonal antibodies for
min at 37 degrees C. Cells were washed and anti-mouse IgG conjugated with Alexa
646 was added for 15 min at room temperature. M1 and M2 were then assayed by flow
cytometry. To determine M1 and M2 protein levels, the percent of M1 or M2 positive
cells was multiplied by the mean flourescent intensity of M1 or M2. Each sample was
then divided by the untreated control to generate the percent of M1 or M2 compared to
untreated scramble controls.
A reduction in viral M2 protein levels from cells treated with various
compounds of the disclosure was observed. The flow cytometry method described
above was used to determine relative M2 protein expression after treatment at 60
micromolar. The compounds of the disclosure inhibited the production of the M2
protein to varying degrees.
EXAMPLE 2:
TREATMENT OF INFLUENZA A VIRUS INFECTED MICE IN VIVO
Additional experiments in support of the invention were performed using
Balb/c mice infected with the PR8 strain of influenza A. Mice were infected with 3.5
TCID via an intranasal inoculation after being treated 4 hours prior with various
compound of the invention disclosed herein. In some experiments an additional dose of
test compound was administered at 96hr post-infection. All doses consisted of 100
micrograms of test compound in 50 microliters of PBS and were administered by
intranasal insufflation. The weight of the animals were monitored daily and was used
as a clinical endpoint for antiviral drug activity. At day 7 post-infection the animals
were sacrificed and lungs were harvested for viral load determinations using the qRT-
PCR method described in Example 1.
TCID determinations were made using half-log serial dilutions of the
lung homogenates and plated onto AMJ-C12 macrophage cells. After 24hr at 35
degrees C, the media was changed and incubated for an additional 72h at 35 degrees C.
50 mL of a solution of 0.5% chicken RBC in PBS was added and incubated for 1h at 4
degrees C. Hemagglutination pattern was read and TCID were calculated using the
Reed and Muench method. TCID50 values were then normalized to input tissue
weight.
The compounds of the invention as disclosed herein show increased
antiviral activity and decreased weight loss compared to a PMOplus compound after
H1N1 infection. Balb/c mice (n = 4) were infected with H1N1 and given a single 100
microgram dose of test compound 4 hours prior to infection. Mice were weighed daily
and percent weight loss was determined from pre-infection weight. Lungs were
harvested day 7 post-infection and assayed for viral load by TCID . Results are
presented as the fold increase in antiviral activity over naked PMO. This experiment
shows approximately 50-fold increased antiviral activity of two PMO-X compounds
compared to un-modified PMO and approximately 10-fold higher activity compared to
a PMOplus compound.
The various embodiments described above can be combined to provide
further embodiments. All of the U.S. patents, U.S. patent application publications, U.S.
patent applications, foreign patents, foreign patent applications and non-patent
publications referred to in this specification and/or listed in the Application Data Sheet,
are incorporated herein by reference, in their entirety. Aspects of the embodiments can
be modified, if necessary to employ concepts of the various patents, applications and
publications to provide yet further embodiments. These and other changes can be made
to the embodiments in light of the above-detailed description. In general, in the
following claims, the terms used should not be construed to limit the claims to the
specific embodiments disclosed in the specification and the claims, but should be
construed to include all possible embodiments along with the full scope of equivalents
to which such claims are entitled. Accordingly, the claims are not limited by the
disclosure.
While preferred embodiments of the present invention have been shown
and described herein, it will be obvious to those skilled in the art that such embodiments
are provided by way of example only. Numerous variations, changes, and substitutions
will now occur to those skilled in the art without departing from the invention. It
should be understood that various alternatives to the embodiments of the invention
described herein may be employed in practicing the invention. It is intended that the
following claims define the scope of the invention and that methods and structures
within the scope of these claims and their equivalents be covered thereby.
The present application claims the benefit under 35 U.S.C. §119(e) of
U.S. Provisional Patent Application No. 61/561,806 filed on November 18, 2011; which
application is incorporated herein by reference in its entirety.
In the description in this specification reference may be made to subject
matter that is not within the scope of the claims of the current application. That subject
matter should be readily identifiable by a person skilled in the art and may assist in
putting into practice the invention as defined in the claims of this application.
Claims (281)
1. A compound having the structure of Formula (I): W P X or a salt or isomer thereof, wherein: n is an integer from 1 to 50; G is halogen, OH, alkoxy, OSO (alkyl), OSO (aryl), or ; each B is an independently selected base pair moiety; 10 10 each Y is independently O or NR ; optionally, R and X8e are bonded together form a ring; each W is independently S or O; 5 11 15 11 15 16 11 12 17 Z is -(L )-(R ), -(L )-(L )-(R ), or –(L )-(L )-(R ) ; L is selected from: 23 23 23 23 R R O R R P P N R N a) ; b) ; c) 23 23 23 23 23 23 23 23 24 24 O N N 1 1 1 1 R R R R d) ; e) ; f) ; g) 23 23 23 23 O CH O R R 3 23 23 h) O ; i) H ; j) 23 23 O H O ; or k) –C(R ) O-; wherein L is selected from: NN N N a) ; b) ; c) d) ; or e) ; L is a linker cleaveable under biological conditions selected from: a) –(C -C alkylene)-OC(O)O-CH O-; 1 10 2 b) –C(O)-(C -C alkylene)-OC(O)O-CH O-; 1 10 2 c) –C(O)-(CH=CH)-C(O)O-CH O-; d) –(C -C alkylene)-S-S-CH CH O-; or 1 10 2 2 e) –C(O)–(C -C alkylene)-S-S-CH CH O-; 1 10 2 2 L is divalent radical selected from C -C alkylene, C -C cycloalkylene, 1 30 3 8 C -C arylene, -(C -C arylene)-(C -C alkylene)-, –(C -C alkylene)-C(=O)-, –(C - 6 30 6 30 1 30 1 30 2 C alkoxy)-C(=O)-, -(3-18 membered heteroalkylene)-C(=O)-, –(C -C cycloalkylene)- 30 3 8 C(=O)-, -(C -C cycloalkylene)-(C -C alkylene)-C(=O)-, -(C -C alkylene) (C -C 3 8 1 30 1 30 3 8 cycloalkylene)-C(=O)-, -(C -C arylene)-C(=O)-, -(C -C arylene)-(C -C alkylene)- 6 30 6 30 1 30 C(=O)-, -(C -C alkylene)-(C -C arylene)-C(=O)-, -(C -C alkylene)-O-C(=O)-, -(C - 1 30 6 30 1 30 3 C cycloalkylene)-O-C(=O)-, -(C -C arylene)-O-C(=O)-, -(C -C arylene)-(C -C 8 7 30 6 30 1 30 alkylene)-O-C(=O)-, -(C -C arylene)-(C -C alkylene)-O-C(=O)-, -C(=O)OR , or 6 30 1 30 -P(=O)(R ) ; 12 13 R is an electron pair, with the provision that if R is C -C alkyl, then 1 30 R is an electron pair, an N-oxide, or C -C alkyl; 10 13 each R and R is independently selected from hydrogen, a cell- penetrating peptide, a natural or non-natural amino acid, guanidinyl, amidinyl, heterocyclyl, C -C alkyl, C -C cycloalkyl; C -C aryl, C -C aralkyl, C -C 1 30 3 8 6 30 7 30 1 30 alkylcarbonyl, C -C cycloalkylcarbonyl, C -C cycloalkylalkylcarbonyl, C -C 3 8 3 8 6 30 arylcarbonyl, C -C aralkylcarbonyl, C -C alkyloxycarbonyl, C -C 7 30 1 30 3 8 cycloalkyloxycarbonyl, C -C aryloxycarbonyl, C -C aralkyloxycarbonyl, 7 30 8 30 21 21 22 -C(=O)OR , -C(=O)NHR , or -P(=O)(R ) ; R is independently selected from a cell-penetrating peptide, a natural or non-natural amino acid, guanidinyl, amidinyl, heterocyclyl, C -C alkyl, C -C 1 30 3 8 cycloalkyl; C -C aryl, C -C aralkyl, C -C alkylcarbonyl, C -C cycloalkylcarbonyl, 6 30 7 30 1 30 3 8 C -C cycloalkylalkylcarbonyl, C -C arylcarbonyl, C -C aralkylcarbonyl, C -C 3 8 6 30 7 30 2 30 alkyloxycarbonyl, C -C cycloalkyloxycarbonyl, C -C aryloxycarbonyl, C -C 3 8 7 30 8 30 21 21 aralkyloxycarbonyl, 3-18 membered alkoxyalkylcarbonyl, -SO R , -C(=O)OR , -P(=O)(OH) or -P(=O)(R ) ; R is a solid support matrix suitable for solid phase synthesis of oligonucleotides; R is a drug, protein or toxin; each R is independently C -C alkyl, or a 3-18 membered alkoxyalkyl 1 30 group; each R is independently an C -C aryloxy; 6 12 23 23 each R is independently H or C –C alkyl; or optionally two R groups join to form a 3- to 8-membered ring; R is a C –C alkylene; Q is independently selected from X1, X2, X3, X4, X5, X6, X7, or X8; each X is independently selected from X1, X2, X3, X4, X5, X6, X7, or X8 with the provision that at least one X is not X1; wherein X1 is N(CH ) ; X2 is selected from: a) -O-alkylene-CO H; b) -O-alkylene-CHN ; c) -N(R )-alkylene-CO H; d) -N(R )-alkylene-CHN ; e) -L1-CO-alkylene-CO H; f) -L1-CO-alkylene-CHN ; g) -L1-CO-alkenylene-CO H; h) -L1-CO-alkenylene-CHN ; i) -L1-CO-arylene-CO H; j) -L1-CO-arylene-CHN ; k) -L1-CONH-alkylene-CO H; l) -L1-CONH-alkylene-CHN ; m) -L1-CONH-arylene-CO H; n) -L1-CONH-arylene-CHN ; o) -L1-SO -alkylene-CO H; p) -L1-SO -alkylene-CHN ; q) -L1-SO -arylene-CO H; r) -L1-SO -arylene-CHN ; s) -L1-alkylene-CO H; t) -L1-alkylene-CHN ; u) -L1-arylene-CO H; v) -L1-arylene-CHN ; and w) a protected form of any of the above X2 groups; X3 is selected from: a) –L1-alkyl; b) –L1-heterocyclyl; c) -O-alkylene-CNH-NH ; d) -N(R )-alkylene-CNH-NH ; e) -L1-CNH-NH ; f) -L1-alkylene-CNH-NH ; g) -L1-arylene-CNH-NH ; h) -L1-CO-alkylene-CNH-NH ; i) -L1-CO-alkenylene-CNH-NH ; j) -L1-CO-arylene-CNH-NH ; k) -L1-CONH-alkylene-CNH-NH ; l) -L1-CONH-arylene-CNH-NH ; m) -L1-SO -alkylene-CNH-NH ; n) -L1-SO -arylene-CNH-NH ; o) -O-alkylene-N(R ) ; p) -N(R )-alkylene-N(R ) ; q) -L1-N(R ) ; r) -L1-alkylene-N(R ) ; s) -L1-arylene-N(R ) ; t) -L1-CO-alkylene-N(R ) ; u) -L1-CO-alkenylene-N(R ) ; v) -L1-CO-arylene-N(R ) ; w) -L1-CONH-alkylene-N(R ) ; x) -L1-CONH-arylene-N(R ) ; y) -L1-SO -alkylene-N(R ) ; z) -O-alkylene-N(R ) ; aa) -N(R )-alkylene-N(R ) ; bb) -L1-N(R ) ; cc) -L1-alkylene-N(R ) ; dd) -L1-arylene-N(R ) ; ee) -L1-CO-alkylene-N(R ) ; ff) -L1-CO-alkenylene-N(R ) ; gg) -L1-CO-arylene-N(R ) ; hh) -L1-CONH-alkylene-N(R ) ; ii) -L1-CONH-arylene-N(R ) ; jj) -L1-SO -alkylene-N(R ) ; kk) -O-alkylene-heterocyclyl; ll) -N(R )-alkylene-heterocyclyl; mm) -L1-alkylene-heterocyclyl; nn) -L1-arylene-heterocyclyl; oo) -L1-CO-alkylene-heterocyclyl; pp) -L1-CO-alkenylene-heterocyclyl; qq) -L1-CO-arylene-heterocyclyl; rr) -L1-CONH-alkylene-heterocyclyl; ss) -L1-CONH-arylene-heterocyclyl; tt) -L1-SO -alkylene-heterocyclyl; uu) -O-alkylene-N(O)(R ) ; vv) -N(R )-alkylene- N(O)(R ) ; ww) -L1- N(O)(R ) ; xx) -L1-alkylene- N(O)(R ) ; yy) -L1-arylene- N(O)(R ) ; zz) -L1-CO-alkylene- N(O)(R ) ; aaa) -L1-CO-alkenylene- N(O)(R ) ; bbb) -L1-CO-arylene- N(O)(R ) ; ccc) -L1-CONH-alkylene- N(O)(R ) ; ddd) -L1-CONH-arylene- N(O)(R ) ; eee) -L1-SO -alkylene- N(O)(R ) ; fff) -O-alkylene-NH-CNH-NH ; ggg) -N(R )-alkylene-NH-CNH-NH ; hhh) -L1-NH-CNH-NH ; iii) -L1-alkylene-NH-CNH-NH ; jjj) -L1-arylene-NH-CNH-NH ; kkk) -L1-CO-alkylene-NH-CNH-NH ; lll) -L1-CO-alkenylene-NH-CNH-NH ; mmm) -L1-CO-arylene-NH-CNH-NH ; nnn) -L1-CONH-alkylene-NH-CNH-NH ; ooo) -L1-CONH-arylene-NH-CNH-NH ; ppp) -L1-SO -alkylene-NH-CNH-NH ; qqq) -L1-SO -arylene-NH-CNH-NH ; and rrr) a protected form of any of the above X3 groups; with the provision that if X1 is present as N(CH ) and X7 is present as 3 2, piperidinyl, then X3 is not or X4 is selected from: a) -O-alkylene-aryl; b) -N(R )-aryl; c) -N(R )-alkylene-aryl; d) -L1-CO-alkylene-aryl; e) -L1-CO-alkenylene-aryl; f) -L1-CO-arylene-aryl; g) -L1-CONH-alkylene-aryl; h) -L1-CONH-arylene-aryl; i) -L1-SO -alkylene-aryl; j) -L1-SO -arylene-aryl; k) -L1-alkylene-aryl; l) -L1-arylene-aryl; m) -N(R )-alkylene-N(R )-aryl; n) -N(R )-alkylene-N(R )CO-aryl; o) -N(R )-alkylene-N(R )SO -aryl; p) -N(R )-alkylene-N(R )CH -aryl; q) –L1-aryl; r) -L1-CO-aryl; s) -L1-SO -aryl; t) -L1-alkylene-P(aryl) ; u) -L1-CO-alkylene-P(aryl) ; v) -L1-SO -alkylene-P(aryl) ; and w) a protected form of any of the above X4 groups; X5 is selected from: a) -O-alkylene-heteroaryl; b) -N(R )-alkylene-heteroaryl; c) -L1-CO-alkylene-heteroaryl; d) -L1-CO-alkenylene-heteroaryl; e) -L1-CO-arylene-heteroaryl; f) -L1-CONH-alkylene-heteroaryl; g) -L1-CONH-arylene-heteroaryl; h) -L1-SO -alkylene-heteroaryl; i) -L1-SO -arylene-heteroaryl; j) -L1-alkylene-heteroaryl; k) -L1-arylene-heteroaryl; l) -N(R )-alkylene-N(R )-hereroaryl; m) -N(R )-alkylene-N(R )CO-hereroaryl; n) -N(R )-alkylene-N(R )SO -hereroaryl; o) -N(R )-alkylene-N(R )CH -hereroaryl; p) -L1-heteroaryl; and q) a protected form of any of the above X5 groups; X6 is selected from: a) -O-alkylene-(OCH CH ) OH; 2 2 m b) -O-alkylene-(OCH CH ) OCH ; 2 2 m 3 c) -N(R )-alkylene-(OCH CH ) OH; 2 2 m d) -N(R )-alkylene-(OCH CH ) OCH ; 2 2 m 3 e) -N(R )-arylene-(OCH CH ) OH; 2 2 m f) -N(R )-arylene-(OCH CH ) OCH ; 2 2 m 3 g) -L1-alkylene-(OCH CH ) OH; 2 2 m h) -L1-CO-alkylene-(OCH CH ) OH; 2 2 m i) -L1-CO-alkylene-(OCH CH ) OCH ; 2 2 m 3 j) -L1-SO -alkylene-(OCH CH ) OH; 2 2 2 m k) -L1-SO -alkylene-(OCH CH ) OCH ; 2 2 2 m 3 l) -L1-CO-arylene-(OCH CH ) OH; 2 2 m m) -L1-CO-arylene-(OCH CH ) OCH ; 2 2 m 3 n) -L1-SO -arylene-(OCH CH ) OH; 2 2 2 m o) -L1-SO -arylene-(OCH CH ) OCH ; 2 2 2 m 3 p) -L1-CO-(OCH CH ) OH; 2 2 m q) -L1-CO-(OCH CH ) OCH ; 2 2 m 3 r) -N(R )-(dibenzocrown-6); s) an aza-crown ether; and t) a protected form of any of the above X6 groups; X7 is selected from: a) -heterocyclyl; b) -N(R )(R ) c) -L1-hydrogen; d) -L1-alkyl; e) -L1-CO-alkyl; f) -L1-CONH-alkyl; g) -L1-CON(alkyl)-alkyl; h) -L1-SO -alkyl;and i) a protected form of any of the above X7 groups; with the provision that if X1 is present as N(CH ) , and X3 is present O NH as or , then X7 is not piperdinyl; X8 is selected from: a) -L1-cholate; b) -L1-deoxycholate; c) -L1-COCH (R ) d) -L1-COCH(R )NHCO -alkyl; 5 5 10 e) -OR , wherein R and R together form a ring; f) a protected form of any of the above X8 groups; each R is independently hydrogen, alkyl, or a cell-penetrating peptide; each R is independently C -C alkyl or optionally when two R are C - 1 12 1 C alkyl, two R are joined to form a heterocyclic ring; each R is independently C -C alkyl, alkenyl, or alkynyl; 2 18 each R is independently hydrogen, alkyl, hydroxyalkyl, sulfhydrylalkyl, or arylalkyl; each R is independently C -C alkyl; 1 12 each R is independently hydrogen or C -C alkyl; 1 12 L1 is selected from: NN N N q q q a) ; b) ; c) ; d) ; e) ; 1 4 5 2 Q L E L Q f) , and g) ; wherein 1 2 6 each Q and Q are each selected from a bond, -O- or -N(R )-; each E is independently selected from optionally substituted aryl or optionally substituted heteroaryl; each E is independently an optionally substituted nitrogen containing heteroaryl; each L and L are each independently a bond, optionally substituted C - C alkyl, or optionally substituted heteroalkyl; and m, p, q, s, and t are each independently 1-4; wherein if the X group proximal to the 3' terminus is: , , , , , , or , then at least one other X group is not X1, and wherein the compound is not of the formula: 5 11 15 12
2. The compound of claim 1, wherein Z is -(L )-(R ) or -(L )- (R ). 5 11 15 11
3. The compound of claim 1, wherein Z is -(L )-(R ) or -(L )- 15 16 (L )-(R ). 5 11 15
4. The compound of claim 1, wherein Z is -(L )-(R ).
5. The compound of claim 1, wherein each Y is independently O, NH, or NR .
6. The compound of claim 1, wherein each W is O.
7. The compound of claim 1, wherein each R is independently hydrogen or alkyl.
8. The compound of claim 1, wherein each R is independently C - C alkyl.
9. The compound of claim 1, wherein each X is independently selected from X1, X2, X3, X4, X5, X6, X7, or X8. 5 11 15
10. The compound of claim 1, wherein Z is -(L )-(R ); each Y is 10 1 independently O, NH, or NR ; each W is O; each R is independently hydrogen or alkyl; each R is independently C -C alkyl; and each X is independently selected from X1, 1 12 X2, X3, X4, X5, X6, X7, or X8.
11. The compound as in any one of claims 1-10, wherein n is 1.
12. The compound of claim 11, wherein G is halogen.
13. The compound as claim 11 or claim 12, wherein W is O.
14. The compound as in any one of claims 11-13, wherein Y is O.
15. The comxpound of claim 14, wherein R is H.
16. The compound of claim 15, wherein R is aralkyl.
17. The compound of claim 16, wherein R is an optionally substituted triphenylmethyl group.
18. The compound of claim 17, wherein X is X2.
19. The compound of claim 17, wherein X is X3.
20. The compound of claim 17, wherein X is X4.
21. The compound of claim 17, wherein X is X5.
22. The compound of claim 17, wherein X is X6.
23. The compound of claim 17, wherein X is X7.
24. The compound of claim 17, wherein X is X8
25. The compound as in any one of claims 1-10, wherein n is an integer from 1 to 40.
26. The compound as in any one of claims 1-10, wherein n is an integer from 1 to 35.
27. The compound of claim 26, wherein G is .
28. The compound of claim 26 or claim 27, wherein each W is O.
29. The compound as in any one of claims 26-28, wherein each Y is
30. The compound of claim 29, wherein at least one X is X2.
31. The compound of claim 30, wherein at least one X2 is selected from -O-alkylene-COH, -O-alkylene-CHN, -N(R )-alkylene-COH, and -N(R )- 2 4 2 alkylene-CHN .
32. The compound of claim 31, wherein -alkylene- is -CH -, - CH CH -, or -CH CH CH -. 2 2 2 2 2
33. The compound of claim 32, wherein at least one X2 is selected from: -N(H)CH COH, -N(CH )CH COH, -N(CH CH )CH COH, - 2 2 3 2 2 2 3 2 2 N(H)CH CH CO H, and -N(CH )CH CH CO H. 2 2 2 3 2 2 2
34. The compound of claim 30, wherein at least one X2 is selected from -L1-CO-alkylene-CO H, -L1-CO-alkylene-CHN , -L1-CO-alkenylene-CO H, -L1- 2 4 2 CO-alkenylene-CHN , -L1-CO-arylene-CO H, and -L1-CO-arylene-CHN . 4 2 4
35. The compound of claim 34, wherein L1 is selected from: NN N N and .
36. The compound of claim 34 or claim 35, wherein -alkylene- is - CH -, -CH CH -, or -CH CH CH -. 2 2 2 2 2 2
37. The compound of claim 36, wherein at least one X2 is selected from: NN NN , OH, OH OH , and .
38. The compound of claim 35, wherein at least one X2 is selected from: O , N , N NH N NH , and .
39. The compound of claim 30, wherein at least one X2 is selected from -L1-CONH-alkylene-COH, -L1-CONH-alkylene-CHN, -L1-CONH-arylene- CO H, and -L1-CONH-arylene-CHN .
40. The compound of claim 39, wherein L1 is selected from: and .
41. The compound of claim 39 or claim 40, wherein -alkylene- is - CH -, -CH CH -, or -CH CH CH -. 2 2 2 2 2 2
42. The compound of claim 41, wherein at least one X2 is selected from: NN NN HN HN O O OH NH O , and .
43. The compound of claim 30, wherein at least one X2 is selected from -L1-SO -alkylene-CO H, -L1-SO -alkylene-CHN , -L1-SO -arylene-CO H, and - 2 2 2 4 2 2 L1-SO -arylene-CHN .
44. The compound of claim 43, wherein L1 is selected from: NN N N and .
45. The compound of claim 44, wherein at least one X2 is selected from: NN S NN S NN S O , N , , NN S N NH N NH N N NH N NH , and .
46. The compound of claim 30, wherein at least one X2 is selected from -L1-alkylene-CO H, -L1-alkylene-CHN , -L1-arylene-CO H, and -L1-arylene- 2 4 2 CHN .
47. The compound of claim 46, wherein L1 is selected from: NN N N and .
48. The compound of claim 46 or claim 47, wherein -alkylene- is - CH -, -CH CH -, or -CH CH CH -. 2 2 2 2 2 2
49. The compound of claim 48, wherein at least one X2 is selected from: NN NN O OH OH O OH , , O , O OH N NH N N N NH O , , and .
50. The compound of claim 47, wherein at least one X2 is selected from: NN NN OH, N , N NH N NH , and .
51. The compound of claim 29, wherein at least one X is X3.
52. The compound of claim 51, wherein at least one X3 is selected from -L1-alkyl and -L1-heterocyclyl.
53. The compound of claim 52, wherein L1 is selected from: NN N N , , and .
54. The compound of claim 53, wherein at least one X3 is -L1-alkyl.
55. The compound of claim 54, wherein at least one X3 is selected from: NN NN NN , , , NCF NCN NN , , and .
56. The compound of claim 53, wherein at least one X3 is -L1- heterocyclyl.
57. The compound of claim 56, wherein at least one X3 is selected from: NN N N NN NH , , , NN N N N O , and .
58. The compound of claim 51, wherein at least one X3 is selected 1 1 1 from -O-alkylene-CNH-NH , -N(R )-alkylene-CNH-NH , -O-alkylene-N(R ) , -N(R )- 2 2 2 1 2 1 2 alkylene-N(R ) , -O-alkylene-N(R ) , -N(R )-alkylene-N(R ) , -O-alkylene-heterocyclyl, 2 3 3 1 2 1 2 -N(R )-alkylene-heterocyclyl, -O-alkylene-N(O)(R ) , -N(R )-alkylene-N(O)(R ) , -O- alkylene-NH-CNH-NH , and -N(R )-alkylene-NH-CNH-NH .
59. The compound of claim 58, wherein -alkylene- is -CH CH -, or - CH CH CH -. 2 2 2
60. The compound of claim 58 or claim 59, wherein at least one X3 is selected from -O-alkylene-CNH-NH, -O-alkylene-N(R ), -O-alkylene-N(R ), -O- 2 2 3 alkylene-heterocyclyl, -O-alkylene-N(O)(R ) , and -O-alkylene-NH-CNH-NH .
61. The compound of claim 60, wherein at least one X3 is selected from: and .
62. The compound of claim 58 or claim 59, wherein at least one X3 is 1 1 1 1 selected from -N(R )-alkylene-CNH-NH, -N(R )-alkylene-N(R ), -N(R )-alkylene- 2 1 1 2 1 N(R ) , -N(R )-alkylene-heterocyclyl, -N(R )-alkylene-N(O)(R ) , and -N(R )-alkylene- NH-CNH-NH .
63. The compound of claim 62, wherein at least one X3 is selected from: N N N , , , , , , and .
64. The compound of claim 51, wherein at least one X3 is selected from -L1-CNH-NH , -L1-alkylene-CNH-NH , -L1-arylene-CNH-NH , -L1-alkylene- 2 2 2 1 1 2 2 N(R ), -L1-arylene-N(R ), -L1-alkylene-N(R ), -L1-arylene-N(R ), -L1-alkylene- 2 2 3 3 heterocyclyl, -L1-arylene-heterocyclyl, -L1-alkylene-N(O)(R ) , -L1-arylene-N(O)(R ) , -L1-alkylene-NH-CNH-NH , and -L1-arylene-NH-CNH-NH .
65. The compound of claim 64, wherein L1 is selected from: and .
66. The compound of claim 64 or claim 65, wherein at least one X3 is selected from -L1-arylene-CNH-NH , -L1-arylene-N(R ) , -L1-arylene-N(R ) , -L1- 2 2 3 arylene-heterocyclyl, -L1-arylene-N(O)(R ) , and -L1-arylene-NH-CNH-NH .
67. The compound of claim 64 or claim 65, wherein at least one X3 is selected from -L1-CNH-NH, -L1-alkylene-CNH-NH, -L1-alkylene-N(R ), -L1- 2 2 2 alkylene-N(R ) , -L1-alkylene-heterocyclyl, -L1-alkylene-N(O)(R ) , and -L1-alkylene- NH-CNH-NH .
68. The compound of claim 67, wherein at least one X3 is -L1-CNH- NH .
69. The compound of claim 68, wherein at least one X3 is selected from: and .
70. The compound of claim 67, wherein at least one X3 is selected from -L1-alkylene-N(R ), -L1-alkylene-N(R ), -L1-alkylene-heterocyclyl, -L1- alkylene-N(O)(R ) , -L1-alkylene-CNH-NH , and -L1-alkylene-NH-CNH-NH . 2 2 2
71. The compound of claim 70, wherein -alkylene- is -CH CH - or - CH CH CH -. 2 2 2
72. The compound of claim 71, wherein at least one X3 is selected from: N NH N NH N NH N NH NH NH , , , and
73. The compound of claim 51, wherein at least one X3 is selected from -L1-CO-alkylene-CNH-NH, -L1-CO-alkenylene-CNH-NH, -L1-CO-arylene- CNH-NH , -L1-CONH-alkylene-CNH-NH , -L1-CONH-arylene-CNH-NH , -L1-SO - 2 2 2 2 alkylene-CNH-NH, -L1-SO -arylene-CNH-NH, -L1-CO-alkylene-N(R ), -L1-CO- 2 2 2 2 1 1 1 alkenylene-N(R ) , -L1-CO-arylene-N(R ) , -L1-CONH-alkylene-N(R ) , -L1-CONH- 2 2 2 1 1 2 arylene-N(R ) , -L1-SO -alkylene-N(R ) , -L1-CO-alkylene-N(R ) , -L1-CO-alkenylene- 2 2 2 3 2 2 2 N(R ), -L1-CO-arylene-N(R ), -L1-CONH-alkylene-N(R ), -L1-CONH-arylene- 3 3 3 N(R ) , -L1-SO -alkylene-N(R ) , -L1-CO-alkylene-heterocyclyl, -L1-CO-alkenylene- 3 2 3 heterocyclyl, -L1-CO-arylene-heterocyclyl, -L1-CONH-alkylene-heterocyclyl, -L1- CONH-arylene-heterocyclyl, -L1-SO-alkylene-heterocyclyl, -L1-CO-alkylene- 2 2 2 N(O)(R ), -L1-CO-alkenylene-N(O)(R ), -L1-CO-arylene-N(O)(R ), -L1-CONH- 2 2 2 2 2 2 alkylene-N(O)(R ) , -L1-CONH-arylene-N(O)(R ) , -L1-SO -alkylene-N(O)(R ) , -L1- 2 2 2 2 CO-alkylene-NH-CNH-NH , -L1-CO-alkenylene-NH-CNH-NH , -L1-CO-arylene-NH- CNH-NH , -L1-CONH-alkylene-NH-CNH-NH , -L1-CONH-arylene-NH-CNH-NH , - 2 2 2 L1-SO -alkylene-NH-CNH-NH , and -L1-SO -arylene-NH-CNH-NH . 2 2 2 2
74. The compound of claim 73, wherein L1 is selected from: NN N N and .
75. The compound of claim 73 or claim 74, wherein at least one X3 is selected from -L1-CO-arylene-CNH-NH, -L1-CONH-arylene-CNH-NH, -L1-SO - 2 2 2 arylene-CNH-NH, -L1-CO-arylene-N(R ), -L1-CONH-arylene-N(R ), -L1-CO- 2 2 2 arylene-N(R ) , -L1-CONH-arylene-N(R ) , -L1-CO-arylene-heterocyclyl, -L1-CONH- arylene-heterocyclyl, -L1-CO-arylene-N(O)(R ) , -L1-CONH-arylene-N(O)(R ) , -L1- CO-arylene-NH-CNH-NH , -L1-CONH-arylene-NH-CNH-NH , and -L1-SO -arylene- 2 2 2 NH-CNH-NH .
76. The compound of claim 75, wherein at least one X3 is selected from: and .
77. The compound of claim 73 or claim 74, wherein at least one X3 is selected from -L1-CO-alkylene-CNH-NH , -L1-CO-alkenylene-CNH-NH , -L1-CONH- alkylene-CNH-NH, -L1-SO -alkylene-CNH-NH, -L1-CO-alkylene-N(R ), -L1-CO- 2 2 2 2 1 1 1 alkenylene-N(R ), -L1-CONH-alkylene-N(R ), -L1-SO -alkylene-N(R ), -L1-CO- 2 2 2 2 2 2 2 alkylene-N(R ), -L1-CO-alkenylene-N(R ), -L1-CONH-alkylene-N(R ), -L1-SO - 3 3 3 2 alkylene-N(R ) , -L1-CO-alkylene-heterocyclyl, -L1-CO-alkenylene-heterocyclyl, -L1- CONH-alkylene-heterocyclyl, -L1-SO-alkylene-heterocyclyl, -L1-CO-alkylene- 2 2 2 N(O)(R ), -L1-CO-alkenylene-N(O)(R ), -L1-CONH-alkylene-N(O)(R ), -L1-SO - 2 2 2 2 alkylene-N(O)(R ), -L1-CO-alkylene-NH-CNH-NH, -L1-CO-alkenylene-NH-CNH- NH , -L1-CONH-alkylene-NH-CNH-NH , and -L1-SO -alkylene-NH-CNH-NH . 2 2 2 2
78. The compound of claim 77, wherein at least one X3 is selected from -L1-SO -alkylene-CNH-NH , -L1-SO -alkylene-N(R ) , -L1-SO -alkylene-N(R ) , 2 2 2 2 2 3 -L1-SO-alkylene-heterocyclyl, -L1-SO -alkylene-N(O)(R ), and -L1-SO -alkylene- 2 2 2 2 NH-CNH-NH .
79. The compound of claim 77, wherein at least one X3 is selected from -L1-CO-alkylene-CNH-NH , -L1-CO-alkenylene-CNH-NH , -L1-CONH-alkylene- CNH-NH , -L1-CO-alkylene-N(R ) , -L1-CO-alkenylene-N(R ) , -L1-CONH-alkylene- 2 2 2 1 2 2 N(R ), -L1-CO-alkylene-N(R ), -L1-CO-alkenylene-N(R ), -L1-CONH-alkylene- 2 3 3 N(R ), -L1-CO-alkylene-heterocyclyl, -L1-CO-alkenylene-heterocyclyl, -L1-CONH- alkylene-heterocyclyl, -L1-CO-alkylene-N(O)(R ) , -L1-CO-alkenylene-N(O)(R ) , -L1- CONH-alkylene-N(O)(R ) , -L1-CO-alkylene-NH-CNH-NH , -L1-CO-alkenylene-NH- CNH-NH , and -L1-CONH-alkylene-NH-CNH-NH .
80. The compound of claim 79, wherein at least one X3 is selected from -L1-CO-alkenylene-CNH-NH , -L1-CO-alkenylene-N(R ) , -L1-CO-alkenylene- N(R ) , -L1-CO-alkenylene-heterocyclyl, -L1-CO-alkenylene-N(O)(R ) , and -L1-CO- alkenylene-NH-CNH-NH .
81. The compound of claim 79, wherein at least one X3 is selected from -L1-CO-alkylene-CNH-NH , -L1-CONH-alkylene-CNH-NH , -L1-CO-alkylene- 1 1 2 N(R ), -L1-CONH-alkylene-N(R ), -L1-CO-alkylene-N(R ), -L1-CONH-alkylene- 2 2 3 N(R ), -L1-CO-alkylene-heterocyclyl, -L1-CONH-alkylene-heterocyclyl, -L1-CO- alkylene-N(O)(R ) , -L1-CONH-alkylene-N(O)(R ) , -L1-CO-alkylene-NH-CNH-NH , 2 2 2 and -L1-CONH-alkylene-NH-CNH-NH .
82. The compound of claim 81, wherein at least one X3 is selected from -L1-CO-alkylene-CNH-NH , -L1-CO-alkylene-N(R ) , -L1-CO-alkylene-N(R ) , - 2 2 3 L1-CO-alkylene-heterocyclyl, -L1-CO-alkylene-N(O)(R ) , and -L1-CO-alkylene-NH- CNH-NH .
83. The compound of claim 82, wherein -alkylene- is -CH -, - CH CH -, -CH CH CH -, -CH CH CH CH -, or -CH CH CH CH CH -. 2 2 2 2 2 2 2 2 2 2 2 2 2 2
84. The compound of claim 83, wherein at least one X3 is selected from: N NH H N 2 NH 2 and .
85. The compound of claim 81, wherein at least one X3 is selected from -L1-CONH-alkylene-CNH-NH, -L1-CONH-alkylene-N(R ), -L1-CONH- alkylene-N(R ) , -L1-CONH-alkylene-heterocyclyl, -L1-CONH-alkylene-N(O)(R ) , and -L1-CONH-alkylene-NH-CNH-NH .
86. The compound of claim 85, wherein -alkylene- is -CH CH -, - CH CH CH -, CH CH CH CH -, or -CH CH CH CH CH -. 2 2 2 2 2 2 2 2 2 2 2 2
87. The compound of claim 51, wherein at least one X3 is selected 1 2 2 from -L1-N(R ) , -L1-N(R ) , -L1-N(O)(R ) , and -L1-NH-CNH-NH . 2 3 2 2
88. The compound of claim 87, wherein at least one X3 is -L1-N(R ) .
89. The compound of claim 88, wherein at least one X3 is selected from: NNH NNH NNH , , , , and .
90. The compound of claim 87, wherein at least one X3 is -L1-N(R ) .
91. The compound of claim 90, wherein at least one X3 is selected from: NN NN and .
92. The compound of claim 29, wherein at least one X is X4.
93. The compound of claim 92, wherein at least one X4 is selected 1 1 1 1 from -O-alkylene-aryl, -N(R )-aryl, -N(R )-alkylene-aryl, -N(R )-alkylene-N(R )-aryl, - 1 1 1 1 1 N(R )-alkylene-N(R)CO-aryl, -N(R )-alkylene-N(R )SO-aryl, and -N(R )-alkylene- N(R )CH -aryl.
94. The compound of claim 93, wherein at least one X4 is selected 1 1 1 1 1 from -N(R )-aryl, -N(R )-alkylene-aryl, -N(R )-alkylene-N(R )-aryl, -N(R )-alkylene- 1 1 1 1 1 N(R )CO-aryl, -N(R )-alkylene-N(R )SO -aryl, and -N(R )-alkylene-N(R )CH -aryl.
95. The compound of claim 94, wherein at least one X4 is -N(R )-aryl.
96. The compound of claim 95, wherein at least one X4 is selected from: and .
97. The compound of claim 94, wherein at least one X4 is -N(R )- alkylene-aryl.
98. The compound of claim 97, wherein -alkylene- is -CH -, -C(CH )- , -CH CH -, or -CH CH CH -. 2 2 2 2 2
99. The compound of claim 98, wherein at least one X4 is selected from: N N N N , , , , , , , and .
100. The compound of claim 94, wherein -alkylene- is -CH CH -, - CH CH CH -, CH CH CH CH -, or -CH CH CH CH CH -. 2 2 2 2 2 2 2 2 2 2 2 2
101. The compound of claim 94 or claim 100, wherein at least one X4 1 1 1 1 is selected from -N(R )-alkylene-N(R )-aryl, and -N(R )-alkylene-N(R )CH -aryl.
102. The compound of claim 101, wherein at least one X4 is selected from: and .
103. The compound of claim 94 or claim 100, wherein at least one X4 1 1 1 1 is selected from -N(R )-alkylene-N(R )CO-aryl and -N(R )-alkylene-N(R )SO -aryl.
104. The compound of claim 103, wherein at least one X4 is selected from: and .
105. The compound of claim 92, wherein at least one X4 is selected from -L1-CO-alkylene-aryl, -L1-CO-alkenylene-aryl, -L1-CO-arylene-aryl, -L1-CONH- alkylene-aryl, -L1-CONH-arylene-aryl, -L1-SO -alkylene-aryl, -L1-SO -arylene-aryl, - L1-CO-aryl, -L1-SO -aryl, -L1-CO-alkylene-P(aryl) , and -L1-SO -alkylene-P(aryl) . 2 3 2 3
106. The compound of claim 105, wherein L1 is selected from: NN N N and .
107. The compound of claim 105 or claim 106, wherein at least one X4 is -L1-CO-alkylene-P(aryl) .
108. The compound of claim 107, wherein at least one X4 is selected from: N NH and .
109. The compound of claim 105 or claim 106, wherein at least one X4 is -L1-SO -alkylene-P(aryl) .
110. The compound of claim 105 or 106, wherein at least one X4 is selected from -L1-CO-alkylene-aryl, -L1-CO-alkenylene-aryl, -L1-CO-arylene-aryl, -L1- CONH-alkylene-aryl, -L1-CONH-arylene-aryl, -L1-SO -alkylene-aryl, -L1-SO -arylene- aryl, -L1-CO-aryl, and -L1-SO -aryl.
111. The compound of claim 110, wherein at least one X4 is selected from -L1-SO -alkylene-aryl, -L1-SO -arylene-aryl, and -L1-SO -aryl. 2 2 2
112. The compound of claim 111, wherein at least one X4 is selected from: NN S N NH and .
113. The compound of claim 110, wherein at least one X4 is selected from -L1-CO-alkylene-aryl, -L1-CO-alkenylene-aryl, -L1-CO-arylene-aryl, -L1-CONH- alkylene-aryl, -L1-CONH-arylene-aryl, and -L1-CO-aryl.
114. The compound of claim 113, wherein at least one X4 is selected from -L1-CONH-alkylene-aryl and -L1-CONH-arylene-aryl.
115. The compound of claim 113, wherein at least one X4 is selected from -L1-CO-alkylene-aryl, -L1-CO-alkenylene-aryl, -L1-CO-arylene-aryl, and -L1-CO- aryl.
116. The compound of claim 115, wherein at least one X4 is -L1-CO- arylene-aryl.
117. The compound of claim 116, wherein at least one X4 is selected from: NN NN O NN O N NH N NH N NH N NH N NH N NH N NH O CF N NH N NH Cl Cl , and .
118. The compound of claim 115, wherein at least one X4 is -L1-CO- aryl.
119. The compound of claim 117, wherein at least one X4 is selected from: N NH N NH , , and .
120. The compound of claim 92, wherein at least one X4 is selected from -L1-alkylene-aryl, -L1-arylene-aryl, -L1-aryl, and -L1-alkylene-P(aryl) .
121. The compound of claim 120, wherein L1 is selected from: NN N N and .
122. The compound of claim 120 or claim 121, wherein at least one X4 is -L1-alkylene-aryl.
123. The compound of claim 120 or claim 121, wherein at least one X4 is -L1-arylene-aryl.
124. The compound of claim 120 or claim 121, wherein at least one X4 is -L1-aryl.
125. The compound of claim 124, wherein at least one X4 is selected from: N NH NN NN , , and .
126. The compound of claim 120 or claim 121, wherein at least one X4 is -L1-alkylene-P(aryl) .
127. The compound of claim 29, wherein at least one X is X5.
128. The compound of claim 127, wherein at least one X5 is selected 1 1 1 from -O-alkylene-heteroaryl, -N(R)-alkylene-heteroaryl, -N(R )-alkylene-N(R )- 1 1 1 1 heteroaryl, -N(R )-alkylene-N(R )CO-heteroaryl, -N(R )-alkylene-N(R )SO -heteroaryl, and -N(R )-alkylene-N(R )CH -heteroaryl.
129. The compound of claim 128, wherein at least one X5 is -N(R )- alkylene-heteroaryl.
130. The compound of claim 129, wherein -alkylene- is -CH -, - C(CH )-, -CH CH -, or -CH CH CH -. 3 2 2 2 2 2
131. The compound of claim 128, wherein at least one X5 is selected 1 1 1 1 from -N(R)-alkylene-heteroaryl, -N(R )-alkylene-N(R)-heteroaryl, -N(R )-alkylene- 1 1 1 1 N(R)CO-heteroaryl, -N(R )-alkylene-N(R )SO-heteroaryl, and -N(R )-alkylene- N(R )CH -heteroaryl.
132. The compound of claim 131, wherein -alkylene- is -CH CH -, - CH CH CH -, CH CH CH CH -, or -CH CH CH CH CH -. 2 2 2 2 2 2 2 2 2 2 2 2
133. The compound of claim 131 or claim 132, wherein at least one X5 1 1 1 is selected from -N(R )-alkylene-heteroaryl, -N(R )-alkylene-N(R )-heteroaryl, and - N(R )-alkylene-N(R )CH -heteroaryl.
134. The compound of claim 131 or claim 132, wherein at least one X5 1 1 1 1 is selected from -N(R )-alkylene-N(R )CO-heteroaryl and -N(R )-alkylene-N(R )SO - heteroaryl.
135. The compound of claim 127, wherein at least one X5 is selected from -L1-heteroaryl, -L1-alkylene-heteroaryl, -L1-arylene-heteroaryl, -L1-CO-alkylene- heteroaryl, -L1-CO-alkenylene-heteroaryl, -L1-CO-arylene-heteroaryl, -L1-CONH- alkylene-heteroaryl, -L1-CONH-arylene-heteroaryl, -L1-SO -alkylene-heteroaryl, -L1- SO -arylene-heteroaryl.
136. The compound of claim 135, wherein L1 is selected from: NN N N , , and .
137. The compound of claim 135 or claim 136, wherein -alkylene- is - CH -, -C(CH )-, -CH CH -, or -CH CH CH -. 2 3 2 2 2 2 2
138. The compound of claim 135 or claim 136, wherein at least one X5 is -L1-heteroaryl.
139. The compound of claim 138, wherein at least one X5 is selected from: N NH N NH , N , N , and N NH
140. The compound as in any one of claims 135-137, wherein at least one X5 is selected from -L1-SO -alkylene-heteroaryl and -L1-SO -arylene-heteroaryl.
141. The compound as in any one of claims 135-137, wherein at least one X5 is selected from -L1-CONH-alkylene-heteroaryl and -L1-CONH-arylene- heteroaryl.
142. The compound as in any one of claims 135-137, wherein at least one X5 is selected from -L1-CO-alkylene-heteroaryl, -L1-CO-alkenylene-heteroaryl, and -L1-CO-arylene-heteroaryl.
143. The compound as in any one of claims 135-137, wherein at least one X5 is selected from -L1-alkylene-heteroaryl and -L1-arylene-heteroaryl.
144. The compound of claim 143, wherein at least one X5 is selected from: NN NN , N , N , and
145. The compound of claim 29, wherein at least one X is X6.
146. The compound of claim 145, wherein at least one X6 is selected from -O-alkylene-(OCH CH ) OH, -O-alkylene-(OCH CH ) OCH , -N(R )-alkylene- 2 2 m 2 2 m 3 (OCH CH ) OH, -N(R )-alkylene-(OCH CH ) OCH , -N(R )-arylene-(OCH CH ) OH, 2 2 m 2 2 m 3 2 2 m and -N(R )-arylene-(OCH CH ) OCH . 2 2 m 3
147. The compound of claim 146, wherein -alkylene- is -CH CH -, - CH CH CH -, -CH CH CH CH -, or -CH CH CH CH CH -. 2 2 2 2 2 2 2 2 2 2 2 2
148. The compound of claim 146 or claim 147, wherein at least one X6 is selected from -O-alkylene-(OCH CH ) OH and -O-alkylene-(OCH CH ) OCH . 2 2 m 2 2 m 3
149. The compound of claim 146 or claim 147, wherein at least one X6 is selected from -N(R )-alkylene-(OCH CH ) OH, -N(R )-alkylene-(OCH CH ) OCH , 2 2 m 2 2 m 3 -N(R )-arylene-(OCH CH ) OH, and -N(R )-arylene-(OCH CH ) OCH . 2 2 m 2 2 m 3
150. The compound of claim 149, wherein at least one X6 is selected from -N(R )-alkylene-(OCH CH ) OH and -N(R )-alkylene-(OCH CH ) OCH . 2 2 m 2 2 m 3
151. The compound of claim 149, wherein at least one X6 is selected from -N(R )-arylene-(OCH CH ) OH, and -N(R )-arylene-(OCH CH ) OCH . 2 2 m 2 2 m 3
152. The compound of claim 145, wherein at least one X6 is selected from -L1-alkylene-(OCH CH ) OH, -L1-CO-alkylene-(OCH CH ) OCH, -L1-SO - 2 2 m 2 2 m 3 2 alkylene-(OCH CH )OH, -L1-SO -alkylene-(OCH CH ) OCH, -L1-CO-arylene- 2 2 m 2 2 2 m 3 (OCH CH )OH, -L1-CO-arylene-(OCH CH ) OCH, -L1-SO -arylene- 2 2 m 2 2 m 3 2 (OCH CH ) OH, and -L1-SO -arylene-(OCH CH ) OCH . 2 2 m 2 2 2 m 3
153. The compound of claim 152, wherein L1 is selected from: NN N N and .
154. The compound of claim 152 or claim 153, wherein -alkylene- is - CH CH -, -CH CH CH -, -CH CH CH CH -, or -CH CH CH CH CH -. 2 2 2 2 2 2 2 2 2 2 2 2 2 2
155. The compound as in any one of claims 152-154, wherein at least one X6 is -L1-alkylene-(OCH CH ) OH. 2 2 m
156. The compound of claim 155, wherein at least one X6 is selected from: NN O O OH
157. The compound as in any one of claims 152-154, wherein at least one X6 is selected from -L1-SO -alkylene-(OCH CH ) OH, -L1-SO -alkylene- 2 2 2 m 2 (OCH CH ) OCH, -L1-SO -arylene-(OCH CH )OH, and -L1-SO -arylene- 2 2 m 3 2 2 2 m 2 (OCH CH ) OCH . 2 2 m 3
158. The compound of claim 157, wherein at least one X6 is selected from -L1-SO -alkylene-(OCH CH ) OH and -L1-SO -alkylene-(OCH CH ) OCH . 2 2 2 m 2 2 2 m 3
159. The compound of claim 157, wherein at least one X6 is selected from -L1-SO -arylene-(OCH CH ) OH and -L1-SO -arylene-(OCH CH ) OCH . 2 2 2 m 2 2 2 m 3
160. The compound as in any one of claims 152-154, wherein at least one X6 is selected from -L1-CO-alkylene-(OCH CH ) OH, -L1-CO-alkylene- 2 2 m (OCH CH ) OCH, -L1-CO-arylene-(OCH CH )OH, and -L1-CO-arylene- 2 2 m 3 2 2 m (OCH CH ) OCH . 2 2 m 3
161. The compound of claim 160, wherein at least one X6 is selected from -L1-CO-alkylene-(OCH CH ) OH and -L1-CO-alkylene-(OCH CH ) OCH . 2 2 m 2 2 m 3
162. The compound of claim 160, wherein at least one X6 is selected from -L1-CO-arylene-(OCH CH ) OH, and -L1-CO-arylene-(OCH CH ) OCH . 2 2 m 2 2 m 3
163. The compound of claim 145, wherein at least one X6 is selected from -L1-CO-(OCH CH ) OH and -L1-CO-(OCH CH ) OCH . 2 2 m 2 2 m 3
164. The compound of claim 145, wherein at least one X6 is selected from -N(R )-(dibenzocrown-6) and an aza-crown ether.
165. The compound of claim 164, wherein at least one X6 is selected from: , , and .
166. The compound of claim 29, wherein at least one X is X7.
167. The compound of claim 166, wherein at least one X7 is heterocycle.
168. The compound of claim 167, wherein at least one X7 is selected from: NO NNH N N O , , , , O , , and .
169. The compound of claim 166, wherein at least one X7 is - N(R )(R ).
170. The compound of claim 169, wherein at least one X7 is selected from: , , , , , , and .
171. The compound of claim 166, wherein at least one X7 is selected from -L1-CO-alkyl, -L1-CONH-alkyl, -L1-CON(alkyl)-alkyl, and -L1-SO -alkyl.
172. The compound of claim 171, wherein L1 is selected from: and .
173. The compound of claim 171 or claim 172, wherein at least one X7 is -L1-CO-alkyl.
174. The compound of claim 173, wherein at least one X7 is selected from: NN NN , , , , N NH N N N NH N N CF CF O , O , O , O , N NH N N O , O , and .
175. The compound of claim 171 or claim 172, wherein at least one X7 is -L1-SO -alkyl.
176. The compound of claim 29, wherein at least one X is X8.
177. The compound of claim 176, wherein at least one X8 is -L1-CA.
178. The compound of claim 177, wherein at least one X8 is selected from: N NH NN CA and CA.
179. The compound of claim 176, wherein at least one X8 is -L1-dCA.
180. The compound of claim 179, wherein at least one X8 is selected from: N NH NN dCA and dCA .
181. The compound of claim 176, wherein at least one X8 is selected from -L1-COCH (R ) and -L1-COCH(R )NHCO -alkyl.
182. The compound of claim 181, wherein L1 is selected from: and .
183. The compound of claim 182, wherein at least one X8 is selected from: HS , HS , and HS .
184. The compound of claim 28, wherein at least one X is X8; X8 is - 5 10 5 10 OR ; and Y is NR ; wherein R and R together form a ring.
185. The compound of claim 184, wherein at least one X8 is selected from: O O O P P P O N O N O N , , and .
186. The compound of claim 1, wherein L1 is selected from: q q q , , , , and .
187. The compound of claim 186, wherein L1 is .
188. The compound of claim 187, wherein p is 2 and q is 2.
189. The compound of claim 187, wherein p is 3 and q is 2.
190. The compound of claim 1, wherein L1 is .
191. The compound of claim 190, wherein p is 1 and q is 2.
192. The compound of claim 190, wherein p is 2 and q is 2.
193. The compound of claim 190, wherein p is 3 and q is 2.
194. The compound of claim 1, wherein L1 1 4 5 2 Q L E L Q is .
195. The compound of claim 194, wherein Q is -N(R )-.
196. The compound of claim 194, wherein Q is -N(R )-.
197. The compound of claim 194, wherein E is phenyl.
198. The compound of claim 194, wherein E is heteroaryl.
199. The compound of claim 1, wherein L1 is .
200. The compound of claim 199, wherein Q is -N(R )-.
201. The compound of claim 199, wherein E is pyrrolyl.
202. The compound of claim 199, wherein E is imidazolyl.
203. The compound of claim 199, wherein E is triazinyl.
204. The compound of claim 199, wherein E is imidazolyl.
205. The compound of claim 1, wherein W is O, and Y is NH.
206. The compound of claim 1, wherein W is O, and Y is NR .
207. The compound of claim 1, wherein W is O, and Y is NR , wherein R and X8e together form a ring.
208. The compound of claim 207, wherein R and X8e together for a O P O P O P O N N N structure selected from , , or . 23 23
209. The compound of claim 2, 3, or 4, wherein L is .
210. The compound of claim 2, 3, or 4, wherein L is 23 23 O R R P N R N
211. The compound of claim 2, 3, or 4, wherein L is 23 23 O H O
212. The compound of claim 2, 3, or 4, wherein L is 23 23 O CH O R R 3
213. The compound of claim 209, wherein L is .
214. The compound of claim 209, wherein L is
215. The compound of claim 209, wherein L is
216. The compound of claim 213 wherein p is 2, and q is 2.
217. The compound of claim 213 wherein p is 2, and q is 3.
218. The compound of claim 214 wherein p and q are independently selected from 1 or 2, and R is CH .
219. The compound of claim 215 wherein p, q, s and t are independently selected from 1 or 2.
220. The compound of claim 210, wherein R is a C -C alkylene.
221. The compound of claim 210, wherein R is ethylene or propylene, and R is hydrogen or methyl.
222. The compound of claim 211, wherein R is hydrogen or methyl.
223. The compound of any of claims 209 to 222, wherein Q is X1.
224. The compound of any of claims 209 to 223, wherein R is hydrogen, methyl or both R groups together form a cyclopropyl, cyclobutyl, cyclopentyl or cyclohexyl ring.
225. The compound of any of claims 209 to 223, wherein R is hydrogen or methyl. 5 23
226. The compound of claim 4, wherein Z is –C(R ) OP(=O)(OH) .
227. The compound of claim 226, wherein R is hydrogen.
228. The compound of claim 4, wherein R is C -C alkyl, C -C 1 30 1 30 alkylcarbonyl, C -C alkyloxycarbonyl, or a 3-18 membered alkoxyalkylcarbonyl. 2 30
229. The compound of claim 228, wherein R is a C -C 2 30 alkyloxycarbonyl.
230. The compound of claim 229, wherein the C -C alkyloxycarbonyl 2 30 is selected from -C(=O)OCH CHOH, –C(=O)OCH CH OCH CHOH, or – 2 2 2 2 2 2 C(=O)OCH CH OCH CH OCH CH OH. 2 2 2 2 2 2
231. The compound of claim 229, wherein the C -C alkyloxycarbonyl 2 30 is –C(=O)OCH CH OCH CH OCH CH OH. 2 2 2 2 2 2
232. The compound of claim 4, wherein Z is selected from: O P N N O OH O P N N O O O O OH H C CH H C CH 3 3 3 3 , , or O P N O OH H C CH 3 3 .
233. The compound of claim 232, wherein Z is O P N N O O O OH H C CH 5 11 15 16
234. The compound of claim 3, wherein Z is -(L )-(L )-(R ). 23 23
235. The compound of claim 234, wherein L is .
236. The compound of claim 234, wherein L is 23 23 O R R P N R N
237. The compound of claim 234, wherein L is 23 23 O H O
238. The compound of claim 234, wherein L is 23 23 O CH O R R 3
239. The compound of claim 235, wherein L is .
240. The compound of claim 235, wherein L is
241. The compound of claim 235, wherein L is
242. The compound of claim 239 wherein p is 2, and q is 2.
243. The compound of claim 239 wherein p is 2, and q is 3.
244. The compound of claim 240 wherein p and q are independently selected from 1 or 2, and R is CH .
245. The compound of claim 241 wherein p, q, s and t are independently selected from 1 or 2.
246. The compound of claim 235, wherein R is a C -C alkylene.
247. The compound of claim 236, wherein R is ethylene or propylene, and R is hydrogen or methyl.
248. The compound of claim 237 , wherein R is hydrogen or methyl.
249. The compound of any of claims 235 to 248, wherein Q is X1.
250. The compound of any of claims 235 to 249, wherein R is hydrogen, methyl or both R groups together form a cyclopropyl, cyclobutyl, cyclopentyl or cyclohexyl ring.
251. The compound of any of claims 235 to 249, wherein R is hydrogen or methyl.
252. The compound of claim 234, wherein L is selected from -(3-18 membered heteroalkylene)-C(=O)-, –(C1-C30 alkylene)-C(=O)-, –(C1-C30 alkylene)- C(=O)-, or -(C -C alkoxy)-C(=O)-. 2 30
253. The compound of claim 252, wherein L15 is selected from -(3-18 membered heteroalkylene)-C(=O)-, or-(C2-C30 alkoxy)-C(=O)-.
254. The compound of claim 234, wherein Z is NHCO Et Q PO wherein group A is aminomethyl polystyrene resin.
255. The compound of claim 1, wherein R is an electron pair. 13 12
256. The compound of claim 1, wherein R is a C -C alkyl and R is 1 30 a C -C alkyl. 13 12
257. The compound of claim 1, wherein R is a methyl group and R is a methyl group.
258. The compound of claim 255, wherein R is hydrogen.
259. The compound of claim 255, wherein R is a C -C alkyl. 1 30
260. The compound of claim 259, wherein R is C -C alkyl. 1 10
261. The compound of claim 259, wherein R is C -C alkyl.
262. The compound of claim 259, wherein R is selected from prenyl, geranyl, farnesyl or geranylgeranyl.
263. The compound of claim 255, wherein R is a cell-penetrating peptide.
264. The compound of claim 255, wherein R is a guanidinyl or amidinyl group.
265. The compound of claim 255, wherein R is a C -C cycloalkyl.
266. The compound of claim 255, wherein R is a C -C 1 30 alkylcarbonyl.
267. The compound of claim 255, wherein R is a C -C 1 15 alkylcarbonyl.
268. The compound of claim 255, wherein R is a C -C 1 10 alkylcarbonyl.
269. The compound of claim 255, wherein R is a C -C alkylcarbonyl.
270. The compound of claim 255, wherein R is a C -C alkylcarbonyl.
271. The compound of claim 255, wherein R is a C -C alkylcarbonyl.
272. The compound of claim 255, wherein R is a C -C alkylcarbonyl.
273. The compound of claim 255, wherein R is a C alkylcarbonyl.
274. The compound of claim 255, wherein R is CH CO-.
275. The compound of claim 255, wherein R is a C -C 1 15 alkylcarbonyl.
276. The compound of claim 255, wherein R is a C -C 1 30 alkyloxycarbonyl.
277. The compound of claim 255, wherein R is a C -C 1 10 alkyloxycarbonyl.
278. The compound of claim 255, wherein R is a C -C alkyloxycarbonyl.
279. The compound of claim 255, wherein R is a C -C alkyloxycarbonyl.
280. The compound of claim 255, wherein R is a C alkyloxycarbonyl.
281. The compound of claim 255, wherein R is a CH OCO-.
Priority Applications (1)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
NZ724064A NZ724064B2 (en) | 2011-11-18 | 2012-11-15 | Functionally-modified oligonucleotides and subunits thereof |
Applications Claiming Priority (3)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US201161561806P | 2011-11-18 | 2011-11-18 | |
US61/561,806 | 2011-11-18 | ||
PCT/US2012/065350 WO2013074834A1 (en) | 2011-11-18 | 2012-11-15 | Functionally-modified oligonucleotides and subunits thereof |
Publications (2)
Publication Number | Publication Date |
---|---|
NZ624961A NZ624961A (en) | 2016-09-30 |
NZ624961B2 true NZ624961B2 (en) | 2017-01-05 |
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