Post-synthetic orthogonal amidation plus metal catalyzed azide-alkyne cycloaddition click chemistry on siRNA

Patent metadata

Field	Value
Publication number	US-10550385-B2
Application number	US-201314652359-A
Country	US
Kind code	B2
Filing date	Dec 18, 2013
Priority date	Dec 20, 2012
Publication date	Feb 4, 2020
Grant date	Feb 4, 2020

Abstract

This invention relates to a process for introducing two or more 2′-modifications into an RNA, wherein the RNA has a 2′-O substituent containing an alkyl ester functional group on one or more ribose rings of a strand and a 2′-O substituent containing an alkyne functional groups on one or more ribose rings on the same strand. The process comprises a) adding an amine compound to the RNA to form amidation reactions with the alkyl ester functional groups; b) dissolving the modified RNA from step (a) in a solvent to form a solution; and c) adding an organic azide and a copper or ruthenium catalyst to the solution obtained in step (b) to form 2′-azide-alkyne cycloaddition reaction products with the alkyne functional groups.

First claim

What is claimed is:

1. A process for introducing two or more 2′-modifications into an RNA, wherein the RNA has a 2′-O substituent containing an alkyl ester functional group at the 2′-position on one or more ribose rings of a strand and a 2′-O substituent containing an alkyne functional group at the 2′-position on one or more ribose rings on the same strand, comprising: a) adding an amine compound to the RNA to form amidation reaction products with the alkyl ester functional groups; b) dissolving the modified RNA from step (a) in a solvent to form a solution; and c) adding an organic azide and a copper or ruthenium catalyst to the solution obtained in step (b) to form 2′-azide-alkyne cycloaddition reaction products with the alkyne functional groups.

2. The process of claim 1 , further comprising:
prior to step (a), preparing the RNA from solid-phase synthesis, thereby attaching the RNA to a solid support; and
cleaving the modified RNA from step (a) from its solid support with methylamine, prior to being dissolved in the solvent in step (b).

3. The process of claim 1 , wherein the alkyl ester functional group is methyl ester.

4. The process of claim 1 , wherein the amine compound in step a) is a primary amine.

5. The process of claim 4 , wherein the amine compound is pentylamine.

6. The process of claim 1 , wherein the reaction in step a) is carried out at room temperature.

7. The process of claim 1 , wherein the organic azide of step c) is GalNAc azide or a protected GalNAc azide.

8. The process of claim 7 , wherein the organic azide is acylated GalNAc azide, and wherein the process further comprises deacylation after the cycloaddition reaction is complete to remove the acyl protecting groups.

9. The process of claim 1 , wherein the solvent of step (b) is aqueous CH 3 CN containing 20% CH 3 CN.

10. The process of claim 1 , wherein the copper catalyst of step (c) is Cu(I) with a suitable ligand to stabilize the Cu(I) oxidation state.

11. The process of claim 1 , wherein step (c) is performed at a temperature of between 20° C. to 100° C. for 0.5 to 18 hours.

12. The process of claim 1 , wherein the RNA has a 2′-O substituent containing an alkyl ester functional group at the 2′-position on 5 ribose rings and a 2′-O substituent containing an alkyne functional group at the 2′-position on 5 other ribose rings on the same strand.

13. The process of claim 12 , wherein the 5 ribose rings with the alkyl ester functional groups are modified with amidation reactions and the 5 ribose rings with the alkyne functional groups are modified with azide-alkyne cycloaddition reactions.

14. The process of claim 13 , wherein the RNA is an Apo B passenger strand having a sequence of A, B, C or D (SEQ ID NOs: 2, 3, 4, or 5).

15. The process of claim 14 , wherein the RNA is an Apo B passenger strand having a sequence of C (SEQ ID NO: 4).

16. The process of claim 14 , further comprising, after the 2′-modifications, duplexing the modified passenger strand with a guide strand to form a double stranded RNA.

17. A process for introducing 2′-modifications into an siRNA, wherein the siRNA has a 2′-O substituent containing a methyl ester functional group at the 2′-position on 5 ribose rings on a strand and a 2′-O substituent containing an alkyne functional group at the 2′-position on 5 other ribose rings on the same strand, comprising: a) adding a primary amine compound to the siRNA to form amides via 2′-amidation reactions with all ester functional groups; b) dissolving the modified siRNA from step (a) in a solvent to form a solution; and c) adding an organic azide and a copper or ruthenium catalyst to the solution obtained in the previous step to form triazoles via 2′-azide-alkyne cycloaddition reactions with all alkyne functional groups.

18. The process of claim 17 , further comprising:
prior to step (a), preparing the siRNA from solid-phase synthesis, thereby attaching the siRNA to a solid support; and
cleaving the modified siRNA from step (a) from its solid support with methylamine, prior to being dissolved in the solvent in step (b).

19. The process of claim 1 , wherein the alkyl ester functional group of the RNA has the structure of

wherein R is C 1-20 alkyl, and B is a nucleobase.

Assignees

• Sirna Therapeutics Inc

Inventors

• Zewge Daniel
• Copeland Gregory T
• Li Zhen
• Armstrong Joseph D

Classifications

• C12N2330/30

  chemically synthesised · CPC title

• A61K31/712

  Nucleic acids or oligonucleotides having modified sugars, i.e. other than ribose or 2'-deoxyribose · CPC title

• C12N15/111

  General methods applicable to biologically active non-coding nucleic acids · CPC title

• C12N2310/332

  Abasic residue · CPC title

• C12N2310/317

  with an inverted bond, e.g. a cap structure · CPC title