# US 8,541,562 B2 · Bridged artificial nucleoside and nucleotide

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- Number: US 8,541,562 B2
- Document ID: US8541562B2
- Status: Granted
- Kind: B2
- Application number: 13/502,611
- Filed: 2010-10-19
- Published: 2012-08-16
- Granted: 2013-09-24
- Earliest claimed: 2009-10-29
- Assignees: Osaka University
- Applicants: Satoshi Obika; Yoshiyuki Hari; Tetsuya Kodama; Aiko Yahara; Masaru Nishida
- Inventors: Satoshi Obika; Yoshiyuki Hari; Tetsuya Kodama; Aiko Yahara; Masaru Nishida
- Web page: https://patentgrep.com/patent/US8541562B2

## CPC

- C07H 19/073: with 2-deoxyribosyl as the saccharide radical
- A61P 43/00: Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
- C07H 19/06: Pyrimidine radicals
- C07H 19/16: Purine radicals
- C07H 19/173: with 2-deoxyribosyl as the saccharide radical
- 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 23/00: Compounds containing boron, silicon or a metal, e.g. chelates or vitamin B12 (esters with inorganic acids C07H11/00)
- C12N 15/111: {General methods applicable to biologically active non-coding nucleic acids}
- C12N 2310/11: Antisense
- C12N 2310/3231: having an additional ring, e.g. LNA, ENA
- C12N 2320/51: modulating the chemical stability, e.g. nuclease-resistance
- 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)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- Y02P: CLIMATE CHANGE MITIGATION TECHNOLOGIES IN THE PRODUCTION OR PROCESSING OF GOODS

## Abstract

It is an object of the present invention to provide a novel molecule for antisense therapies which is not susceptible to nuclease degradation in vivo and has a high binding affinity and specificity for the target mRNAs and which can efficiently regulate expression of specific genes. The novel artificial nucleoside of the present invention has an amide bond introduced into a bridge structure of 2′,4′-BNA/LNA. The oligonucleotide containing the 2′,4′-bridged artificial nucleotide has a binding affinity for a single-stranded RNA comparable to known 2′,4′-BNA/LNA and has an increased nuclease resistance over LNA. Particularly, it is expected to be applied to nucleic acid drugs because of its much stronger binding affinity for single-stranded RNAs than S-oligo's affinity.

## Claims

### Claim 1

A compound represented by the following formula I or formula II or a salt thereof:
wherein,
Base represents a purin-9-yl group or a 2-oxo-1,2-dihydropyrimidin-1-yl group that may have any one or more substituents selected from group α, wherein the group α consists of a hydroxyl group, a hydroxyl group protected with a protecting group for nucleic acid synthesis, linear alkyl groups having 1 to 6 carbon atoms, linear alkoxy groups having 1 to 6 carbon atoms, a mercapto group, a mercapto group protected with a protecting group for nucleic acid synthesis, linear alkylthio groups having 1 to 6 carbon atoms, an amino group, linear alkylamino groups having 1 to 6 carbon atoms, an amino group protected with a protecting group for nucleic acid synthesis and halogen atoms;
R1 represents a hydrogen atom, an alkyl group having 1 to 7 carbon atoms that may be branched or form a cyclic group, an alkenyl group having 2 to 7 carbon atoms that may be branched or form a cyclic group, an aryl group having 3 to 12 carbon atoms that may have any one or more substituents selected from the group α and may contain heteroatoms, an aralkyl group with an aryl moiety having 3 to 12 carbon atoms that may have any one or more substituents selected from the group α and may contain heteroatoms, or a protecting group for an amino group on nucleic acid synthesis;
R2 and R3 represents, each independently, a hydrogen atom, a protecting group for a hydroxyl group on nucleic acid synthesis, an alkyl group having 1 to 7 carbon atoms that may be branched or form a cyclic group, an alkenyl group having 2 to 7 carbon atoms that may be branched or form a cyclic group, an aryl group having 3 to 12 carbon atoms that may have any one or more substituents selected from the group α and may contain heteroatoms, an aralkyl group with an aryl moiety having 3 to 12 carbon atoms that may have any one or more substituents selected from the group α and may contain heteroatoms, an acyl group that may have any one or more substituents selected from the group α, a silyl group that may have any one or more substituents selected from the group α, a phosphate group that may have any one or more substituents selected from the group α, a phosphate group protected with a protecting group for nucleic acid synthesis, —P(R4)R5 (wherein R4 and R5 represent, each independently, a hydroxyl group, a hydroxyl group protected with a protecting group for nucleic acid synthesis, a mercapto group, a mercapto group protected with a protecting group for nucleic acid synthesis, an amino group, an alkoxy group having 1 to 5 carbon atoms, an alkylthio group having 1 to 5 carbon atoms, an cyanoalkoxy group having 1 to 6 carbon atoms or an amino group substituted with an alkyl group having 1 to 6 carbon atoms.);
X represents an oxygen atom, a sulfur atom, an amino group or a methylene group;
m is an integer from 0 to 2; and
n is an integer from 0 to 1.

### Claim 2 (depends on 1)

The compound or salt thereof according to claim 1, wherein the Base in the formula I or formula II is a 6-aminopurin-9-yl group, a 2,6-diaminopurin-9-yl group, a 2-amino-6-chloropurin-9-yl group, a 2-amino-6-fluoropurin-9-yl group, a 2-amino-6-bromopurin-9-yl group, a 2-amino-6-hydroxypurin-9-yl group, a 6-amino-2-methoxypurin-9-yl group, a 6-amino-2-chloropurin-9-yl group, a 6-amino-2-fluoropurin-9-yl group, a 2,6-dimethoxypurin-9-yl group, a 2,6-dichloropurin-9-yl group, a 6-mercaptopurin-9-yl group, a 2-oxo-4-amino-1,2-dihydropyrimidin-1-yl group, a 4-amino-2-oxo-5-fluoro-1,2-dihydropyrimidin-1-yl group, a 4-amino-2-oxo-5-chloro-1,2-dihydropyrimidin-1-yl group, a 2-oxo-4-methoxy-1,2-dihydropyrimidin-1-yl group, a 2-oxo-4-mercapto-1,2-dihydropyrimidin-1-yl group, a 2-oxo-4-hydroxy-1,2-dihydropyrimidin-1-yl group, a 2-oxo-4-hydroxy-5-methyl-1,2-dihydropyrimidin-1-yl group or a 4-amino-5-methyl-2-oxo-1,2-dihydropyrimidin-1-yl group.

### Claim 3 (depends on 1)

The compound or salt thereof according to claim 1, wherein the R1 in the formula I or formula II is a hydrogen atom, a methyl group, an ethyl group, an n-propyl group, an isopropyl group, a phenyl group or a benzyl group.

### Claim 4 (depends on 1)

The compound or salt thereof according to claim 1, wherein the m in the formula I is 0.

### Claim 5 (depends on 1)

The compound or salt thereof according to claim 1, wherein the n in the formula II is 0.

### Claim 6 (depends on 1)

The compound or salt thereof according to claim 1, wherein the Base in the formula I or formula II is a 2-oxo-4-hydroxy-5-methyl-1,2-dihydropyrimidin-1-yl group.

### Claim 7

An oligonucleotide containing at least one nucleoside structure represented by the following formula III or formula IV or pharmacologically acceptable salts thereof:
wherein
Base represents a purin-9-yl group or a 2-oxo-1,2-dihydropyrimidin-1-yl group that may have any one or more substituents selected from group α, wherein the group α consists of a hydroxyl group, a hydroxyl group protected with a protecting group for nucleic acid synthesis, linear alkyl groups having 1 to 6 carbon atoms, linear alkoxy groups having 1 to 6 carbon atoms, a mercapto group, a mercapto group protected with a protecting group for nucleic acid synthesis, linear alkylthio groups having 1 to 6 carbon atoms, an amino group, linear alkylamino groups having 1 to 6 carbon atoms, an amino group protected with a protecting group for nucleic acid synthesis and halogen atoms;
R1 represents a hydrogen atom, an alkyl group having 1 to 7 carbon atoms that may be branched or form a cyclic group, an alkenyl group having 2 to 7 carbon atoms that may be branched or form a cyclic group, an aryl group having 3 to 12 carbon atoms that may have any one or more substituents selected from the group a and may contain heteroatoms, an aralkyl group with an aryl moiety having 3 to 12 carbon atoms that may have any one or more substituents selected from the group α and may contain heteroatoms, or a protecting group for an amino group on nucleic acid synthesis;
X represents an oxygen atom, a sulfur atom, an amino group or a methylene group;
m is an integer from 0 to 2; and
n is an integer from 0 to 1.

### Claim 8 (depends on 2)

The compound or salt thereof according to claim 2, wherein the R1 in the formula I or formula II is a hydrogen atom, a methyl group, an ethyl group, an n-propyl group, an isopropyl group, a phenyl group or a benzyl group.

### Claim 9 (depends on 2)

The compound or salt thereof according to claim 2, wherein the m in the formula I is 0.

### Claim 10 (depends on 3)

The compound or salt thereof according to claim 3, wherein the m in the formula I is 0.

### Claim 11 (depends on 2)

The compound or salt thereof according to claim 2, wherein the n in the formula II is 0.

### Claim 12 (depends on 3)

The compound or salt thereof according to claim 3, wherein the n in the formula II is 0.

### Claim 13 (depends on 2)

The compound or salt thereof according to claim 2, wherein the Base in the formula I or formula II is a 2-oxo-4-hydroxy-5-methyl-1,2-dihydropyrimidin-1-yl group.

### Claim 14 (depends on 3)

The compound or salt thereof according to claim 3, wherein the Base in the formula I or formula II is a 2-oxo-4-hydroxy-5-methyl-1,2-dihydropyrimidin-1-yl group.

### Claim 15 (depends on 4)

The compound or salt thereof according to claim 4, wherein the Base in the formula I or formula II is a 2-oxo-4-hydroxy-5-methyl-1,2-dihydropyrimidin-1-yl group.

### Claim 16 (depends on 5)

The compound or salt thereof according to claim 5, wherein the Base in the formula I or formula II is a 2-oxo-4-hydroxy-5-methyl-1,2-dihydropyrimidin-1-yl group.

### Claim 17 (depends on 8)

The compound or salt thereof according to claim 8, wherein the m in the formula I is 0.

### Claim 18 (depends on 8)

The compound or salt thereof according to claim 8, wherein the n in the formula II is 0.

### Claim 19 (depends on 8)

The compound or salt thereof according to claim 8, wherein the Base in the formula I or formula II is a 2-oxo-4-hydroxy-5-methyl-1,2-dihydropyrimidin-1-yl group.