Compositions comprising reversibly modified oligonucleotides and uses thereof

Patent metadata

Field	Value
Publication number	US-12037358-B2
Application number	US-202217836209-A
Country	US
Kind code	B2
Filing date	Jun 9, 2022
Priority date	Aug 23, 2016
Publication date	Jul 16, 2024
Grant date	Jul 16, 2024

Abstract

Disclosed herein are glutathione-sensitive oligonucleotides and methods of using the same. Any oligonucleotide of interest may be modified with a glutathione-sensitive moiety, including oligonucleotides used for in vivo delivery, such as nucleic acid inhibitor molecules. Typically, the glutathione-sensitive moiety is used to reversibly modify the 2′-carbon of a sugar moiety in one or more nucleotides in the oligonucleotide, although other carbon positions may also be modified with the glutathione-sensitive moiety. Also disclosed are glutathione-sensitive nucleotide and nucleoside monomers, including glutathione-sensitive nucleoside phosphoramidites that can be used, for example, in standard oligonucleotide synthesis methods. In addition, glutathione-sensitive nucleotide and nucleoside monomers without a phosphoramidite can be used therapeutically, for example, as anti-viral agents.

First claim

We claim:

1. A glutathione-sensitive oligonucleotide, wherein the glutathione-sensitive oligonucleotide comprises at least one nucleotide represented by Formula I:

wherein X is O, S, Se or NR′, wherein R′ is hydrogen, halogen, an aliphatic, an aryl, a heteroaryl or a heterocycle;
wherein R 1 , R 2 , R 3 and R 4 are each independently hydrogen, halogen, OH, C 1 -C 6 alkyl, C 1 -C 6 haloalkyl or wherein two of R 1 , R 2 , R 3 and R 4 are taken together to form a 5-8 membered ring, wherein the ring optionally contains a heteroatom;
wherein J is O, S, NR′, CR′R″, wherein each of R′ and R″ is independently hydrogen, halogen, an aliphatic, aryl or heteroaryl;
wherein B is hydrogen, a natural nucleobase, a modified nucleobase or a universal nucleobase;
wherein U 2 is absent or O, S, NR′, or CR′R″, wherein R′ and R″ are each independently hydrogen, an aliphatic, an aryl, a heteroaryl, a heterocycle or a cycloalkyl;
wherein W is hydrogen, a phosphate group, an internucleotide linking group attaching the at least one nucleotide represented by Formula I to a nucleotide or an oligonucleotide, a halogen, OR′, SR′, NR′R″, an aliphatic, an aryl, a heteroaryl, a cycloalkyl, a heterocycle, wherein R′ and R″ are each independently hydrogen, halogen, an aliphatic, an aryl, a heteroaryl, a heterocycle or are taken together to form a heterocyclic ring;
wherein I is absent or O, S, NR′, or CR′R″, wherein R′ and R″ are each independently hydrogen, an aliphatic, an aryl, a heteroaryl, a heterocycle and a cycloalkyl;
wherein U 1 is absent, hydrogen, an internucleotide linking group attaching the at least one nucleotide represented by Formula I to a nucleotide or an oligonucleotide, or O, S, NR′ or CR′R″, wherein R′ and R″ are each independently hydrogen, an aliphatic, an aryl, a heteroaryl, a heterocycle and a cycloalkyl and wherein at least one of U 1 or W is an internucleotide linking group attaching the at least one nucleotide represented by Formula I to a nucleotide or an oligonucleotide and provided that if U 1 is an internucleotide linking group, A is absent;
wherein I and U 1 can be combined to form CR′—CR″ alkyl, CR′—CR″ alkenyl, CR′—CR″ alkynyl, an aliphatic, an aryl, a heteroaryl, a heterocycle or taken together to form cycloalkyl or heterocyclic ring;
wherein A is absent, a hydrogen, a phosphate group, a phosphate mimic or a phosphoramidate; and
wherein L is a glutathione-sensitive moiety selected from a glutathione-sensitive moiety represented by:

wherein Y is O, S, Se, or NR′, wherein R′ is hydrogen, halogen, an aliphatic, an aryl, a heteroaryl, or a heterocycle;
wherein Z is O, S, NR′, or CR′R″, wherein R′ and R″ are each independently hydrogen, halogen, CH 3 , an aliphatic, an aryl, a heteroaryl, a heterocycle, or R′ and R″ are taken together to form a heterocyclic ring;
wherein Z 1 is N or CR′, wherein R′ is hydrogen, halogen, an aliphatic, an aryl, a heteroaryl, a heterocycle;
wherein V is C or SO;
wherein X 2 and X 3 are independently hydrogen, halogen, nitro, amino, acyl, an aliphatic, OR 10 , COR 10 , CO 2 R 10 , or NQ 1 Q 2 ; wherein R 10 is independently hydrogen, an aliphatic, a hydroxyl or alkoxy substituted aliphatic, an arylaliphatic, a hydroxyl or alkoxy substituted aryl, or an alkoxy substituted heterocyclic;
wherein G and E can be each independently absent or CH 2 , CHR′, CR′R″, NH, or NR′, wherein R′ and R″ are each independently hydrogen, halogen, an aliphatic, an aryl, a heteroaryl, a heterocycle or R′ and R″ are taken together to form a heterocyclic ring;
wherein P and Q are taken together to form a disulfide bridge or a sulfonyl group;
wherein P 1 and Q 1 are taken together to form a disulfide bridge or a sulfonyl group or wherein P 1 and Q 1 are each independently a disulfide bridge or a sulfonyl group;
wherein when P 1 and Q 1 form a disulfide bridge, M 1 , M 2 , P 1 , and Q 1 can form a 4-9 membered ring, wherein the ring can be aromatic or cycloalkyl, wherein the aromatic or cycloalkyl ring can optionally contain a heteroatom;
wherein T is an aliphatic, an aryl, or T is a ligand optionally connected via a spacer to P or Q;
wherein T a and T b are each independently absent or CH 3 , an aliphatic, an aryl, a heteroaryl, a heterocycle or a ligand optionally connected via any spacer to P 1 or Q 1 ;
wherein M 1 and M 2 are each independently an aliphatic, an aromatic, a heteroaryl, or a cycloalkyl;
wherein M 3 and M 4 are each independently hydrogen, an aliphatic, an aromatic, a heteroaryl, a cycloalkyl or COOR, wherein R is hydrogen, CH 3 , or an aliphatic, or M 3 and M 4 can be taken to form a 4-9 membered ring, wherein the ring can be aromatic or cycloalkyl, wherein the aromatic or cycloalkyl ring can optionally contain a heteroatom;
wherein K is C, CH, or an aliphatic; and
wherein n is 0-5.

2. The glutathione-sensitive oligonucleotide of claim 1 , wherein:
a) L is represented by Formula II, wherein Y is O; wherein Z is NR′; wherein R′ is hydrogen or an aliphatic; and wherein V is C;
b) L is represented by Formula II, wherein Y is O; wherein Z is NR′; wherein R′ is hydrogen or an aliphatic; wherein V is C; and wherein X 2 and X 3 are independently hydrogen, halogen, nitro or amino;
c) L is represented by Formula III, wherein Y is O, S or NH; wherein Z 1 is N or CH; and wherein V is C;
d) L is represented by Formula III, wherein Y is O, S or NH; wherein Z 1 is N or CH; wherein V is C; and wherein M 1 and M 2 are C 2 to C 6 alkyl or are taken together with P 1 and Q 1 to form a 5-8 membered ring, wherein the ring is cycloalkyl;
e) L is represented by Formula IIIa:

wherein Y is O, S or NH; and wherein Z 1 is N or CR′, wherein R′ is hydrogen, halogen, an aliphatic, an aryl, a heteroaryl, or a heterocycle;
f) L is represented by Formula IIIb:

wherein Y is O, S or NH; and wherein Z 1 is N or CR′, wherein R′ is hydrogen, halogen, an aliphatic, an aryl, a heteroaryl, or a heterocycle; and T a and T b are each independently absent or CH 3 , an aliphatic, an aryl, a heteroaryl, a heterocycle or a ligand optionally connected via spacer to a sulfur atom;
g) L is represented by Formula IIIa(i) or IIIb(i):

h) L is represented by Formula IV, wherein Y is O, S or NH; wherein Z is NH or N—CH 3 ; wherein V is C; and wherein G is CH 2 and E is absent or wherein E is CH 2 and G is absent;
i) L is represented by Formula IV, wherein Y is O, S or NH; wherein Z is NH or N—CH 3 ; wherein V is C; wherein G is CH 2 and E is absent or wherein E is CH 2 and G is absent; and
wherein M 3 and M 4 are independently C 2 to C 6 alkyl or taken together to form a 5-8 membered ring, wherein the ring is cycloalkyl;
j) L is represented by Formula IVa:

wherein Y is O, S, or NH; wherein Z is O, S or NH; wherein R 5 , R 6 , and R 7 are each independently OAcyl, NHR′, NR′, or CR′R″, wherein R′ and R″ are each independently hydrogen, halogen, an aliphatic, an aryl, a heteroaryl, a heterocyclic, or can be taken together to form a heteroc

Assignees

• Dicerna Pharmaceuticals Inc

Inventors

• Wang Weimin
• Krishnamurthy Venkata

Classifications

• C12N2310/314

  Phosphoramidates · CPC title

• C12N2310/141

  MicroRNAs, miRNAs · CPC title

• C12N2310/14

  interfering nucleic acids [NA] · CPC title

• C12N2310/12

  catalytic nucleic acids, e.g. ribozymes · CPC title

• C12N2310/113

  targeting other non-coding nucleic acids, e.g. antagomirs · CPC title