# US 12,600,744 B2 · Method for producing oligonucleic acid compound

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- Number: US 12,600,744 B2
- Document ID: US12600744B2
- Status: Granted
- Kind: B2
- Application number: 17/776,356
- Filed: 2020-11-13
- Published: 2023-01-19
- Granted: 2026-04-14
- Earliest claimed: 2019-11-13
- Assignees: Nippon Shinyaku Co., Ltd.
- Applicants: Nippon Shinyaku Co., Ltd.
- Inventors: Yutaro Kotobuki; Koki Kato
- Web page: https://patentgrep.com/patent/US12600744B2

## CPC

- 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
- C07H 21/02: with ribosyl as saccharide radical
- C07H 1/00: Processes for the preparation of sugar derivatives
- C07H 21/04: with deoxyribosyl as saccharide radical
- Y02P 20/55: Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups
- C07H: SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS (derivatives of aldonic or saccharic acids C07C, C07D; aldonic acids, saccharic acids C07C59/105, C07C59/285; cyanohydrins C07C255/16; glycals C07D; compounds of unknown constitution C07G; polysaccharides, derivatives thereof C08B; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification C12N15/00; sugar industry C13)
- Y02P: CLIMATE CHANGE MITIGATION TECHNOLOGIES IN THE PRODUCTION OR PROCESSING OF GOODS

## Abstract

The present invention relates to a method for producing a compound represented by general formula [C-1-1], which comprises: a step for reacting a compound represented by general formula [B-1-1] with a compound represented by general formula [P] to form a compound represented by general formula [B-1-2]; and a step for reacting the compound represented by general formula [B-1-2] with a compound represented by general formula [A-1] to form the compound represented by general formula [C-1-1].

## Claims

### Claim 1

A method for producing a compound of general formula [C-1-1] comprising
Step 1) a compound of general formula [B-1-1]:
wherein
each BP is the same or different and is an optionally protected nucleic acid base,
p is an integer from 1 to 10,
Q1 is a removable group under an acidic condition,
each W is the same or different and is a lone pair of electrons, an oxygen atom or a sulfur atom,
each X is the same or different and is a hydroxyl group protected with a removable group under a neutral condition, 1,1,3,3-tetra(C1-6 alkyl) guanidyl, C1-6 alkoxy, di(C1-6 alkyl)amino, mono(amino-C1-6 alkyl protected with a removable group under a basic condition)amino, di(amino-C1-6 alkyl protected with a removable group under a basic condition)amino, or a substituent having general formula [2]:
wherein
* is a binding position with a phosphorus atom,
a is an integer from 0 to 2,
E is CH2, CH-A1, or N-A2,
A1 is C1-6 alkyl, mono(C1-6 alkyl)amino-C1-6 alkyl protected with a removable group under a basic condition, di(C1-6 alkyl)amino-C1-6 alkyl, tri (C1-6 alkyl) ammonio-C1-6 alkyl, amino protected with a removable group under a basic condition, mono(C1-6 alkyl)amino protected with a removable group under a basic condition, di(C1-6 alkyl)amino, tri (C1-6 alkyl) ammonio, amino substituted with amidino protected with a removable group under a basic condition, or a substituent having general formula [3]:
wherein
* is a binding position with E,
b is an integer from 0 to 2,
c is 0 or 1,
R11 is C1-6 alkyl, and
M is CH2, an oxygen atom, a sulfur atom, or N-(a removable group under a basic condition), and
A2 is C1-6 alkyl, mono(C1-6 alkyl)amino-C1-6 alkyl protected with a removable group under a basic condition, di(C1-6 alkyl)amino-C1-6 alkyl, tri(C1-6 alkyl)ammonio-C1-6 alkyl, a removable group under a basic condition, aryl, or heteroaryl, is reacted with a compound of general formula [P]:
wherein
X is as defined above, and
LG1 and LG2 are independently a leaving group
to form a compound of general formula [B-1-2]:
wherein p, BP, Q1, W, X and LG1 are as defined above, and
Step 2) the compound of general formula [B-1-2] is reacted with a compound of general formula [A-1]:
wherein
BP, W and X are as defined above, and
G is
(1) a silyl substituent,
(2) long-chain alkyl-carbonyl,
(3) benzoyl substituted with 1 to 5 long-chain alkyloxy and/or long-chain alkenyloxy, or
(4) a substituent having the following general formula [7]:
wherein
* is a binding position with T,
Z is
(1) (soluble polymer soluble in an organic solvent)-oxy,
(2) (soluble polymer soluble in an organic solvent)-amino,
(3) long-chain alkyloxy,
(4) a solid phase carrier, or
(5) a substituent having one of the following general formulae [8A] to [8N]:
wherein
* is a binding position with L,
j is an integer from 0 to 4,
k is an integer from 0 to 5,
R8a is a hydrogen atom or C1-6 alkyl,
R8b is the same or different and each is long-chain alkyl,
R8c is the same or different and each is a substituent having one of the following general formulae [9A] to [9E]:
wherein
* is a binding position, and
R9 is long-chain alkyl and/or long-chain alkenyl,
R8d is the same or different and each is a hydrogen atom, a halogen, long-chain alkyl optionally substituted with 1 to 13 halogens, or long-chain alkyloxy optionally substituted with 1 to 13 halogens,
R8e is
(1) long-chain alkyl,
(2) long-chain alkyl-carbonyl, or
(3) benzoyl substituted with 1 to 5 long-chain alkyloxy and/or long-chain alkenyloxy, and
R8f is
(1) long-chain alkyl,
(2) long-chain alkyl-carbonyl, or
(3) long-chain alkenyl-carbonyl, and
L is a substituent having general formula [10]:
wherein
* is a binding position with Z,
** is a binding position with T, and
L1 is an unsubstituted or substituted C2-10 alkylene or an unsubstituted or substituted C6-10 arylene, and
n is an integer from 1 to 50,
T is a single bond or a substituent group having general formula [11]:
wherein
X and W are as defined above,
* is a binding position with **O,
** is a binding position with G, and
q is an integer from 0 to 10,
provided that T is a single bond when G is a silyl substituent,
to form a compound of general formula [C-1-1]:
wherein n, p, BP, Q1, G, T, W, and X are as defined above.

### Claim 2 (depends on 1)

A method for producing a compound of general formula [C-1-1] comprising
Step 1′) a compound of general formula [A-1]:
wherein n, BP, G, T, W, and X are as defined in claim 1,
is reacted with a compound of general formula [P]:
wherein X, LG1 and LG2 are as defined in claim 1,
to form a compound of general formula [A-1-3]:
wherein n, BP, W, X, G, T and LG1 are as defined in claim 1, and
Step 2′) the compound of general formula [A-1-3] is reacted with a compound of general formula [B-1-1]:
wherein p, BP, W, X, and Q1 are as defined in claim 1,
to form a compound of general formula [C-1-1]:
wherein n, p, BP, Q1, G, T, W, and X are as defined above.

### Claim 3 (depends on 1)

The method according to claim 1, wherein the method further comprises a step: the compound of general formula [C-1-1] formed by the method according to claim 1, is treated with an oxidizing agent to form a compound of general formula [C-1]:
wherein n, p, BP, Q1, G, T, W, and X are as defined in claim 1.

### Claim 4 (depends on 1, 3)

The method according to claim 1, wherein the method further comprises a step: a continuous reaction to remove Q1 in situ is carried out by adding a solution containing an acid to a reaction mixture containing the compound [C-1] formed by the method according to claim 3, to form a compound of general formula [E-1]:
wherein n, p, BP, G, T, W, and X are as defined in claim 1.

### Claim 5 (depends on 1)

The method according to claim 1, wherein the method further comprises removing Q1 from the compound [A-1-1]:
wherein n, BP, Q1, G, T, W, and X are as defined in claim 1,
to form a compound of general formula [A-1]:
wherein BP, W, X, G, T and n are as defined above.

### Claim 6 (depends on 1)

The method according to claim 1, wherein
BP is an optionally protected nucleic acid base,
Q1 is a removable group under an acidic condition,
W is a lone pair of electrons, an oxygen atom, or a sulfur atom,
X is di(C1-6 alkyl)amino or selected from among substituents having general formulae [2-1] to [2-8]:
wherein * is a binding position with a phosphorus atom
G is a substituent having general formula [7]:
wherein
* is a binding position with T,
Z is a substituent having one of general formulae [8A] to [8D], [8E], [8G], [8H], [8J], [8K], and [8N]:
wherein
* is a binding position with L,
k is an integer from 0 to 5,
R8a is a hydrogen atom or C1-6 alkyl,
R8b is the same or different and each is long-chain alkyl,
R8c is the same or different and each is a substituent having the following general formula [9A]:
wherein
* is a binding position, and
R9 is long-chain alkyl and/or long-chain alkenyl,
R8d is the same or different and each is a hydrogen atom, a halogen, long-chain alkyl optionally substituted with 1 to 13 halogens, or long-chain alkyloxy optionally substituted with 1 to 13 halogens,
R8e is
(1) long-chain alkyl,
(2) long-chain alkyl-carbonyl, or
(3) benzoyl substituted with 1 to 5 long-chain alkyloxy and/or long-chain alkenyloxy, and
R8f is
(1) long-chain alkyl,
(2) long-chain alkyl-carbonyl, or
(3) long-chain alkenyl-carbonyl, and
L is a substituent having general formula [10]:
wherein
* is a binding position with Z,
** is a binding position with an oxygen atom, and
L1 is an unsubstituted or substituted C2-10 alkylene or an unsubstituted or substituted C6-10 arylene,
T is a single bond or a substituent having the following general formula [11]:
wherein
X and W are as defined above,
* is a binding position with O,
** is a binding position with G, and
q is an integer from 0 to 10, and
n is 1 to 25.

### Claim 7 (depends on 1)

The method according to claim 1, wherein
BP is an optionally protected nucleic acid base,
Q1 is H or a removable group under an acidic condition,
W is an oxygen atom,
X is di(C1-6 alkyl)amino,
G is selected from the group consisting of the formulae:
wherein * is a binding position with T,
T is a single bond,
n is an integer from 1 to 25.

### Claim 8 (depends on 4)

The method according to claim 4, wherein the method comprises removing Q1 from a compound wherein Q1 is trityl, monomethoxytrityl or dimethoxytrityl, and n, BP, W, X, G and T are as defined above,
in the presence of trifluoroacetic acid and 2,2,2-trifluoroethanol, and optionally, triisopropylsilane or ethanol.

### Claim 9 (depends on 1)

The method according to claim 1, wherein the optionally protected nucleic acid base is independently adenine, guanine, hypoxanthine, cytosine, thymine, uracil or a modified base thereof.

### Claim 10 (depends on 1)

The method according to claim 1, wherein the protected nucleic acid base is a nucleic acid base wherein an amino group and/or a hydroxyl group of the nucleic acid base is protected with a protecting group, and
the protecting group of the amino group is independently selected from the group consisting of benzoyl, 4-methoxybenzoyl, acetyl, propionyl, butylyl, isobutylyl, phenylacetyl, phenoxyacetyl, 4-tert-butylphenoxyacetyl, 4-isopropylphenoxyacetyl, and (dimethylamino)methylene, and
the protecting group of the hydroxy group is independently selected from the group consisting of 2-cyanoethyl, 4-nitrophenethyl, phenylsulfonylethyl, methylsulfonylethyl, trimethylsilylethyl, phenyl optionally substituted with 1 to 5 electron-withdrawing groups at any substitutable positions, diphenylcarbamoyl, dimethylcarbamoyl, diethylcarbamoyl, methylphenylcarbamoyl, 1-pyrolidinylcarbamoyl, morpholinocarbamoyl, 4-(tert-butylcarboxy) benzyl, 4-[(dimethylamino) carboxy] benzyl, and 4-(phenylcarboxy)benzyl.

### Claim 11 (depends on 1)

The method according to claim 1, wherein G is selected from the group consisting of the formulae:
wherein * is a binding position with T,
and T is a single bond.

### Claim 12 (depends on 1)

The method according to claim 1, wherein X is di(C1-6 alkyl)amino.

### Claim 13 (depends on 1)

The method according to claim 1, wherein LG1 and LG2 are the same or different and is a halogen.

### Claim 14 (depends on 1)

The method according to claim 1, wherein W is an oxygen atom.

### Claim 15 (depends on 3)

The method according to claim 3, wherein the oxidizing agent is iodine or magnesium monoperoxyphthalate hexahydrate.