Method for the synthesis of phosphorus atom modified nucleic acids

• US 9,695,211 B2
• Filed: 05/27/2016
• Issued: 07/04/2017
• Est. Priority Date: 12/02/2008
• Status: Active Grant

• Current Assignee: WAVE Life Sciences Ltd.
• Original Assignee: Wave Life Sciences Japan, Inc.
• Inventors: Wada, Takeshi, Shimizu, Mamoru
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US15/167,583
• Publication Number:
  US 20160347780A1
• Time in Patent Office: 403 Days
• Field of Search: 536 231, 536 24, 536 3, 536 253
• CPC Class Codes: C07H 1/00 Processes for the preparation of sugar derivatives
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids

Abstract

Described herein are methods of syntheses of phosphorous atom-modified nucleic acids comprising chiral X-phosphonate moieties. The methods described herein provide backbone-modified nucleic acids in high diasteteomeric purity via an asymmetric reaction of an achiral molecule comprising a chemically stable H-phosphonate moiety with a nucleoside/nucleotide.

Claims

1. A method for a synthesis of a nucleic acid comprising a chiral X-phosphonate moiety comprising:

reacting a molecule comprising an achiral H-phosphonate moiety, a chiral reagent, and a nucleoside comprising a 5′

-OH moiety to form a condensed intermediate; and

converting the condensed intermediate to the nucleic acid comprising a chiral X-phosphonate moiety;

wherein;

the nucleic acid comprising a chiral X-phosphonate moiety is a compound of Formula 1;

2. The method of claim 1, wherein the molecule comprising an achiral H-phosphonate moiety is a compound of Formula 2:

3. The method of claim 2, wherein the chiral reagent is a compound of Formula 3:

4. The method of claim 3, wherein the nucleoside comprising a 5′

-OH moiety is a compound of Formula 4;

5. The method of claim 4, wherein the step of converting the condensed intermediate to a compound of Formula 1 comprises:

capping the condensed intermediate and modifying the capped condensed intermediate to produce a compound of Formula 5;

6. The method of claim 5, wherein in each of formulae 3-5, G¹, G², and G³ are independently hydrogen, alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, hetaryl, or aryl, and G⁴ and G⁵ are taken together to form a saturated or partially unsaturated heteroatom-containing ring of up to about 20 ring atoms which is monocyclic or polycyclic, fused or unfused.

7. The method of claim 6, wherein G⁴ and G⁵ are taken together to form a saturated 5-membered saturated ring containing one nitrogen atom.

8. The method of claim 7, wherein one of G¹ and G² is alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, hetaryl, or aryl.

9. The method of claim 8, wherein the other of G¹ and G² is alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, hetaryl, or aryl.

10. The method of claim 8, wherein the other of G¹ and G² is hydrogen.

11. The method of claim 9, wherein G³ is hydrogen.

12. The method of claim 11, wherein the chiral reagent of formula 3 is

13. The method of claim 10, wherein G³ is hydrogen.

14. The method of claim 13, wherein the chiral reagent of formula 3 is

15. The method of claim 6, further comprising providing an activating reagent.

16. The method of claim 15, wherein the activating reagent is imidazole, 4,5-dicyanoimidazole (DCI), 4,5-dichloroimidazole, 1-phenylimidazolium triflate (PhIMT), benzimidazolium triflate (BIT), benztriazole, 3-nitro-1,2,4-triazole (NT), tetrazole, 5-ethylthiotetrazole, 5-(4-nitrophenyl)tetrazole, N-cyanomethylpyrrolidinium triflate (CMPT), N-cyanomethylpiperidinium triflate, or N-cyanomethyldimethylammonium triflate.

17. The method of claim 5, wherein R^a is substituted or unsubstituted trityl or substituted silyl.

18. The method of claim 17, wherein R^b is substituted or unsubstituted methyl ether.

19. The method of claim 18, wherein R³ is a linking moiety connected to a solid support or a linking moiety connected to a nucleic acid.

20. The method of claim 5, wherein n is about 10 to about 200.

21. The method of claim 1, wherein at least one R² is —

OMe.