3′ end caps for RNAi agents for use in RNA interference

Patent metadata

Field	Value
Publication number	US-11008570-B2
Application number	US-201916249128-A
Country	US
Kind code	B2
Filing date	Jan 16, 2019
Priority date	Oct 4, 2013
Publication date	May 18, 2021
Grant date	May 18, 2021

Abstract

The disclosure relates to novel compounds and compositions comprising a RNAi agent comprising a novel compound as a 3′ end cap. The disclosure also relates to processes for making such compositions, and methods and uses of such compositions, e.g., to mediate RNA interference.

First claim

What is claimed is:

1. An RNAi agent of formula Ia:

in which:
X comprises a strand of the RNAi agent;
Y is CH or N;
m is 0 or 1;
p is 1, 2 or 3;
R 3 is hydrogen, 2-(hydroxyl-methyl)-benzyl, 3-(hydroxy-methyl)-benzyl, succinate, or a solid support;
wherein the (CH 2 ) m O—R 3 moiety is attached to the phenyl ring at position 3 or 4;
R 4 is hydrogen;
R 5 is hydrogen; or
R 4 and R 5 , together with the phenyl rings to which R 4 and R 5 are attached, form 6H-benzo[c]chromene.

2. The RNAi agent of claim 1 , wherein X is attached at the 3′ end of a strand of the RNAi agent.

3. The RNAi agent of claim 2 , wherein the strand of the RNAi agent terminates at its 3′ end in a phosphate or modified internucleoside linker, and X is attached at the phosphate or modified internucleoside linker.

4. The RNAi agent of claim 2 , wherein the strand of the RNAi agent terminates at its 3′ end in a phosphate or modified internucleoside linker, the phosphate or modified internucleoside linker being substituted in 5′ to 3′ order with a spacer comprising one of a second phosphate or a modified internucleoside linker, wherein X is attached at the second phosphate or modified internucleoside linker.

5. The RNAi agent of claim 1 selected from:

6. The RNAi agent of claim 1 , wherein the strand of the RNAi agent is a first strand, and X further comprises a second strand.

7. The RNAi agent of claim 1 , wherein a first and/or a second strand of the RNAi agent are no more than about 30 nucleotides long.

8. The RNAi agent of claim 1 , wherein the RNAi agent has 1 or 2 blunt ends.

9. The RNAi agent of claim 1 , wherein the RNAi agent comprises an overhang on at least one 5′ end or 3′ end.

10. The RNAi agent of claim 1 , wherein the RNAi agent comprises a spacer.

11. The RNAi agent of claim 10 , wherein the spacer is a ribitol.

12. The RNAi agent of claim 10 , wherein the spacer is 2′-deoxy-ribitol, diribitol, 2′-methoxyethoxy-ribitol (ribitol with 2′-MOE), C3, C4, C5, C6, or 4-methoxybutane-1,3-diol, or an abasic nucleotide.

13. The RNAi agent of claim 1 , wherein at least one nucleotide of the RNAi agent is modified.

14. The RNAi agent of claim 13 , wherein said at least one modified nucleotide is selected from 2′ alkoxyribonucleotide, 2′ alkoxyalkoxy ribonucleotide, or 2′-fluoro ribonucleotide, 2′-OMe, 2′-MOE, and 2′-H.

15. The RNAi agent of claim 1 , wherein one or more nucleotides is modified or is DNA or is replaced by a peptide nucleic acid (PNA), locked nucleic acid (LNA), morpholino nucleotide, threose nucleic acid (TNA), glycol nucleic acid (GNA) arabinose nucleic acid (ANA), 2′-fluoroarabinose nucleic acid (FANA), cyclohexene nucleic acid (CeNA), anhydrohexitol nucleic acid (HNA), and/or unlocked nucleic acid (UNA); and/or at least one nucleotide comprises a modified internucleoside linker wherein the modified internucleoside linker is selected from phosphorothioate, phosphorodithioate, phosphoramidate, boranophosphonate, an amide linker, and a compound of formula (I)

wherein R 6 is selected from O − , S − , NH 2 , BH 3 , CH 3 , C 1-6 alkyl, C 6-10 aryl, C 1-6 alkoxy and C 6-10 aryl-oxy, wherein C 1-6 alkyl and C 6-10 aryl are unsubstituted or optionally independently substituted with 1 to 3 groups independently selected from halo, hydroxyl and NH 2 ; and R 7 is selected from O, S, NH, or CH 2 .

16. A composition comprising an RNAi agent of claim 1 , and a pharmaceutically acceptable carrier.

17. A method for inhibiting or reducing the level and/or activity of a target gene in a cell, comprising introducing into the cell an RNAi agent of claim 1 .

18. A compound of formula Ia:

in which:
X is H; OH, wherein the hydroxyl group can optionally be functionalized as succinate or attached to a solid support; ODMT; carboxylic acid; the 3′ end of a strand of a RNAi agent; or the 3′ end of a molecule comprising a strand of a RNAi agent, wherein the 3′ end of the strand terminates in a phosphate or modified internucleoside linker and further comprises in 5′ to 3′ order: a spacer, and a second phosphate or modified internucleoside linker;
Y is CH or N;
m is 0 or 1;
p is 1, 2 or 3;
R 3 is hydrogen, 2-(hydroxyl-methyl)-benzyl, 3-(hydroxyl-methyl)-benzyl, succinate, or a solid support;
wherein the (CH 2 ) m O—R 3 moiety is attached to the phenyl ring at position 3 or 4;
R 4 is hydrogen;
R 5 is hydrogen; or
R 4 and R 5 , together with the phenyl rings to which R 4 and R 5 are attached, form 6H-benzo[c]chromene.

19. The compound of claim 18 selected from:

20. A compound selected from:

in which:
X is H; OH, wherein the hydroxyl group can optionally be functionalized as succinate or attached to a solid support; ODMT; carboxylic acid; the 3′ end of a strand of a RNAi agent; or the 3′ end of a molecule comprising a strand of a RNAi agent, wherein the 3′ end of the strand terminates in a phosphate or modified internucleoside linker and further comprises in 5′ to 3′ order: a spacer, and a second phosphate or modified internucleoside linker, and
q is 1 or 2.

Assignees

• Novartis Ag

Inventors

• Baryza Jeremy Lee
• Blommers Marcel
• Fernandez Cesar
• Geno Erin
• Gossert Alvar
• Greenidge Paulette
• Huesken Dieter
• Hunziker Juerg
• Natt Francois Jean-Charles
• Patnaik Anup
• Patterson Andrew
• Rondeau Jean-Michel Rene
• Weiler Jan
• Zhu Meicheng

Classifications

• C07D401/04

  directly linked by a ring-member-to-ring-member bond · CPC title

• C12N2310/344

  Position-specific modifications, e.g. on every purine, at the 3'-end · CPC title

• C07D215/14

  Radicals substituted by oxygen atoms · CPC title

• C12N2320/51

  modulating the chemical stability, e.g. nuclease-resistance · CPC title

• C07D217/14

  other than aralkyl radicals · CPC title