Amidite compound and method for producing polynucleotide using said compound

Patent metadata

Field	Value
Publication number	US-11401296-B2
Application number	US-201917049905-A
Country	US
Kind code	B2
Filing date	Apr 23, 2019
Priority date	Apr 24, 2018
Publication date	Aug 2, 2022
Grant date	Aug 2, 2022

Abstract

The present invention provides an amidite compound represented by formula (1) which enables a synthesis of RNA with high purity, and the method for preparing a polynucleotide by using the same compound. (In the formula (1), wherein R represents the following formula (wherein Ra and Rb are identical to or different from each other and each represents a methyl group, an ethyl group, or a hydrogen atom, with the proviso that Ra and Rb does not represent a hydrogen atom, n is an integer of 1 to 5), and Ba represents a group containing optionally protected nucleobase structure, and G1 and G2 are identical to or different from each other and each represents a protecting group for a hydroxy group, and G3 are identical to or different from each other and each represents an alkyl group.

First claim

The invention claimed is:

1. An amidite compound represented by formula (1):

wherein
R represents a formula:

wherein
R a and R b are identical to or different from each other and each represents a methyl group, an ethyl group, or a hydrogen atom, with the proviso that R a and R b do not represent a hydrogen atom at the same time,
n represents an integer of 1 to 5,

B a represents a group containing optionally-protected nucleobase structure,
G 1 and G 2 are identical to or different from each other and each represents a protecting group for a hydroxy group, and
G 3 are identical to or different from each other and each represents an alkyl group.

2. The amidite compound according to claim 1 wherein R a represents a methyl group or an ethyl group, and R b represents a hydrogen atom.

3. The amidite compound according to claim 1 wherein G 1 represents the following group:

wherein
R 1 , R 2 and R 3 are identical to or different from each other, and each represents a hydrogen atom or an alkoxy group.

4. The amidite compound according to claim 1
wherein G 2 represents the group:

5. The amidite compound according to claim 1 wherein G 3 represents an isopropyl group.

6. A method for preparing a compound containing a polynucleotide structure represented by formula (2):

wherein
B a is identical to or different from each other and each represents a group containing optionally-protected nucleobase structure,
X represents an oxygen atom or a sulfur atom, and
m is a positive integer,

which comprises a step of subjecting the amidite compound according to claim 1 to a solid phase synthesis reaction.

7. The method according to claim 6 wherein the compound containing the polynucleotide structure represented by formula (2) is a compound resulting from the step of reacting a compound represented by formula (3):

wherein
B a is identical to or different from each other and each represents a group containing optionally-protected nucleobase structure,
X represents an oxygen atom or a sulfur atom,
R is identical to or different from each other and each represents a formula:

wherein
R a and R b are identical to or different from each other and each represents a methyl group, an ethyl group, or a hydrogen atom, with the proviso that R a and R b do not represent a hydrogen atom at the same time,
n represents an integer of 1 to 5,

m is a positive integer,

which is resulting from a solid phase synthesis reaction utilizing the amidite compound, with tetraalkylammonium fluoride.

8. The method according to claim 7 wherein R a represents a methyl group or an ethyl group, and R b represents a hydrogen atom.

9. The method according to claim 7 wherein n=1.

10. An ether compound represented by formula (4):

wherein R a , R b and n are the same as defined in claim 1 , and R c represents a C1-C6 alkyl group or a phenyl group.

11. The ether compound according to claim 10 wherein R a represents a methyl group or an ethyl group, R b represents a hydrogen atom, and R c represents a methyl group.

12. The compound according to claim 10 wherein n=1.

13. A method for preparing an ether compound represented by formula (7):

wherein
R a and R b are the same as defined below,

which comprises the steps of:
(a): reacting a compound represented by formula (5):

wherein R a and R b are identical to or different from each other and each represents a methyl group, an ethyl group, or a hydrogen atom, with the proviso that R a and R b do not represent a hydrogen atom at the same time,
with a cyanide ion, and
(b): reacting 3-hydroxyalkylnitrile represented by formula (6):

wherein
R a and R b are the same as defined above,

resulting from step (a), with bis(methylthiomethyl)ether in a solvent in the presence of an oxidizing agent and an acid.

14. The method according to claim 13 wherein R a represents a methyl group or an ethyl group, and R b represents a hydrogen atom.

15. The method according to claim 13 wherein R a represents a methyl group, and R b represents a hydrogen atom.

16. The method according to claim 15 for preparing a compound represented by formula (8):

which comprises the steps of:

A: hydrolyzing 3-aminocrotononitrile,
B: reducing the cyanoacetone obtained by the step A to obtain 3-hydroxybutanenitrile, and
C: reacting the 3-hydroxybutanenitrile obtained by the step B with bis(methylthiomethyl)ether in a solvent in the presence of an oxidizing agent and an acid.

17. A method for preparing a compound represented by formula (10):

wherein
B a , R a , R b , n and G 4 are the same as defined below, which comprises reacting a compound represented by formula (9):

wherein
B a represented a compound containing optionally-protected nucleobase structure, and G 4 represents a protecting group for a hydroxy group,

with a compound represented by formula (4):

wherein
R a and R b are identical to or different from each other and each represents a methyl group, an ethyl group, or a hydrogen atom, with the proviso that R a and R b do not represent a hydrogen atom at the same time,
R c represents a C1-C6 alkyl group or a phenyl group, and
n is an integer of 1 to 4,

in the presence of an oxidizing agent.

18. The method according to claim 17 wherein tetrahydropyran or 4-methyltetrahydropyran is used as a reaction solvent.

19. The method according to claim 17 wherein G 4 represents a group represented by a G 4 -1 or G 4 -2 structure.

20. A method for preparing the compound represented by formula (1) as defined in claim 1 , which comprises further steps of:
deprotecting the compound rep

Assignees

• Sumitomo Chemical Co

Inventors

• Tanaka Yuki
• Saito Tatsuya
• Ihara Hideki

Classifications

• C07H19/10 Primary

  with the saccharide radical esterified by phosphoric or polyphosphoric acids · CPC title

• C07H21/02

  with ribosyl as saccharide radical · CPC title

• C07H19/167

  with ribosyl as the saccharide radical · CPC title

• C07C253/16

  by reaction of cyanides with lactones or compounds containing hydroxy groups or etherified or esterified hydroxy groups · CPC title

• C07F7/1804

  Compounds having Si-O-C linkages (Si-O-acyl linkages C07F7/1896) · CPC title