Oligonucleotide analogues having modified intersubunit linkages and/or terminal groups

Patent metadata

Field	Value
Publication number	US-10760078-B2
Application number	US-201816225909-A
Country	US
Kind code	B2
Filing date	Dec 19, 2018
Priority date	May 28, 2010
Publication date	Sep 1, 2020
Grant date	Sep 1, 2020

Abstract

Oligonucleotide analogues comprising modified intersubunit linkages and/or modified 3′ and/or 5′-end groups are provided. 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.

First claim

The invention claimed is:

1. A process for preparing an oligomer, wherein the process comprises:
(a) deprotecting the ring nitrogen of a solid-phase-supported morpholino subunit of structure (XXXI);
wherein Formula (XXXI) is

or a salt, stereoisomer or tautomer thereof, wherein;
W is, at each occurrence, independently S or O;
X is, at each occurrence, independently —NR 8 R 9 or —OR 3 ;
Y is, at each occurrence, independently O or -NR 10 ;
R 3 is, at each occurrence, independently hydrogen or C 1 -C 6 alkyl;
R 4 is, at each occurrence, independently hydrogen, methyl, —C(═NH)NH 2 , -Z-L-NHC(═NH)NH 2 or -[C(O)CHR′NH] m H, where Z is carbonyl (C(O)) or a direct bond, R′ is a side chain of a naturally occurring amino acid or a one- or two-carbon homolog thereof, and m is 1 to 6;
R 5 is, at each occurrence, independently hydrogen, methyl or an electron pair;
R 7 is, at each occurrence, independently hydrogen C 1 -C 6 alkyl or C 1 -C 6 alkoxyalkyl;
R 8 is, at each occurrence, independently hydrogen or C 2 -C 12 alkyl;
R 9 is, at each occurrence, independently hydrogen, C 1 -C 12 alkyl, C 1 -C 12 aralkyl or aryl;
R 10 is, at each occurrence, independently hydrogen, C 1 -C 12 alkyl or -LNR 4 R 5 R 7 ;
L is an optional linker up to 18 atoms in length comprising alkyl, alkoxy or alkylamino groups, or combinations thereof;
wherein, R 8 and R 9 may join to form a 5-18 membered mono or bicyclic heterocycle or R 8 , R 9 or R 3 may join with R 10 to form a 5-7 membered heterocycle,
and wherein when X is 4-piperazino, X has the following structure (III):

wherein;
R 11 is, at each occurrence, independently C 2 -C 12 alkyl, C 1 -C 12 aminoalkyl, C 1 -C 12 alkylcarbonyl, aryl, heteroaryl or heterocyclyl;
R is, at each occurrence, independently an electron pair, hydrogen or C 1 -C 12 alkyl;
R 12 is, at each occurrence, independently, hydrogen, C 1 -C 12 alkyl, C 1 -C 12 aminoalkyl, —NH 2 , —CONH 2 , —NR 13 R 14 , —NR 13 R 14 R 15 , C 1 -C 12 alkylcarbonyl, oxo, —CN, trifluoromethyl, amidyl, amidinyl, amidinylalkyl, amidinylalkylcarbonyl guanidinyl, guanidinylalkyl, guanidinylalkylcarbonyl, cholate, deoxycholate, aryl, heteroaryl, heterocycle, —SR 13 or C 1 -C 12 alkoxy, wherein R 13 , R 14 and R 15 are, at each occurrence, independently C 1 -C 12 alkyl;
Z is a linkage to a solid support;
B is a base-pairing moiety; and
PG is C 7 -C 30 aralkyl;
(b) reacting the product of step (a) with a morpholino subunit of structure (XXXI) wherein Z is halo;
(c) repeating n-2 iterations of steps (a) and (b), wherein n is 10 to 40; and
(d) cleaving the product of steps (a), (b), and (c) from the solid-phase support,
wherein the oligomer is an oligomer 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 oligomer can bind in a sequence-specific manner to a target nucleic acid, wherein the intersubunit linkages have the following general structure (I):

or a salt, stereoisomer or tautomer thereof, and wherein each of the intersubunit linkages (I) are independently linkage (A) or linkage (B):
wherein for linkage (A):
W is, at each occurrence, independently S or O;
X is, at each occurrence, independently —N(CH 3 ) 2 , —NR 1 R 2 , —OR 3 or

Y is, at each occurrence, independently O or —NR 2 ;
R 1 is, at each occurrence, independently hydrogen or methyl;
R 2 is, at each occurrence, independently hydrogen or -LNR 4 R 5 R 7 ;
R 3 is, at each occurrence, independently hydrogen or C 1 -C 6 alkyl;
R 4 is, at each occurrence, independently hydrogen, methyl, —C(═NH)NH 2 , -Z-L-NHC(═NH)NH 2 or -[C(O)CHR′NH m ]H, where Z is carbonyl(C(O)) or a direct bond, R′ is a side chain of a naturally occurring amino acid or a one- or two-carbon homolog thereof, and m is 1 to 6;
R 5 is, at each occurrence, independently hydrogen, methyl or an electron pair;
R 6 is, at each occurrence, independently hydrogen or methyl;
R 7 is, at each occurrence, independently hydrogen C 1 -C 6 alkyl or C 1 -C 6 alkoxyalkyl;
L is an optional linker up to 18 atoms in length comprising alkyl, alkoxy or alkylamino groups, or combinations thereof; and
wherein for linkage (B):
W is, at each occurrence, independently S or O;
X is, at each occurrence, independently —NR 8 R 9 or —OR 3 ; and
Y is, at each occurrence, independently O or —NR 10 ,
R 8 is, at each occurrence, independently hydrogen or C 2 -C 12 alkyl;
R 9 is, at each occurrence, independently hydrogen, C 1 -C 12 alkyl, C 1 -C 12 aralkyl or aryl;
R 10 is, at each occurrence, independently hydrogen, C 1 -C 12 alkyl or -LNR 4 R 5 R 7 ;
wherein R 8 and R 9 may join to form a 5-18 membered mono or bicyclic heterocycle or R 8 , R 9 or R 3 may join with R 10 to form a 5-7 membered heterocycle, and wherein when X is 4-piperazinyl, X has the following structure (III):

wherein:
R 11 is, at each occurrence, independently C 7 -C 12 alkyl, C 1 -C 12 aminoalkyl, C 1 -C 12 alkylcarbonyl, wherein alkyl is not substituted with amidinyl or guanidinyl, aryl, heteroaryl or heterocyclyl; and
R is, at each occurrence, independently an electron pair, hydrogen or C 1 -C 12 alkyl; and
R 12 is, at each occurrence, independently, hydrogen, C 1 -C 12 alkyl, C 1 -C 12 aminoalkyl, —NH 2 , —CONH 2 , —NR 13 R 14 , —NR 13 R 14 R 15 , C 1 -C 12 alkylcarbonyl, oxo, —CN, trifluoromethyl, amidyl, amidinyl, amidinylalkyl, amidinylalkylcarbonyl guanidinyl, guanidinylalkyl, guanidinylalkylcarbonyl, cholate, deoxycholate, aryl, heteroaryl, heterocycle, —SR 13 or C 1 -C 12 alkoxy, wherein R 13 , R 14 and R 15 are, at each occurrence, independently C 1 -C 12 alkyl; and
wherein at least one of the intersubunit linkages is linkage (B) wherein: i) R 8 and R 9 join to form a 5-18 membered mono or bicyclic heterocycle; or ii) R 8 , R 9 or R 3 join with R 10 to form a 5-7 membered heterocycle.

2. The process of claim 1 , wherein Z of step (b) is chloro.

3. The process of claim 1 , wherein the PG is trityl or methoxy trityl.

4. The process of 1 , wherein at least one of the intersubunit linkages is linkage (A), and wherein X is —N(CH 3 ) 2 at each occurrence of linkage (A).

5. The process of claim 1 , wherein at least one linkage (B) has the following structure (IV):

wherein Z represents a 5-18 membered mono or bicyclic heterocycle.

6. The process of claim 1 , wherein the oligomer has the following structure (XVII):

or a salt, stereoisomer or tautomer thereof, wherein:
R 17 is, at each occurrence, independently absent, hydrogen or C 1 -C 6 alky

Assignees

• Sarepta Therapeutics Inc

Inventors

• Hanson Gunnar J
• Rudolph Alexander Charles
• Cai Bao Zhong
• Zhou Ming
• Weller Dwight D

Classifications

• Y02P20/55

  Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups · CPC title

• C12N2310/3513

  Protein; Peptide · CPC title

• C12N2310/3233

  Morpholino-type ring · CPC title

• C12N2310/11

  Antisense · CPC title

• C12N15/1131

  against viruses · CPC title