# US 9,752,142 B2 · Gapped oligomeric compounds comprising 5′-modified deoxyribonucleosides in the gap and uses thereof

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- Number: US 9,752,142 B2
- Document ID: US9752142B2
- Status: Granted
- Kind: B2
- Application number: 14/238,094
- Filed: 2012-08-08
- Published: 2014-10-16
- Granted: 2017-09-05
- Earliest claimed: 2011-08-11
- Assignees: Ionis Pharmaceuticals, Inc.
- Applicants: Michael Oestergaard; Thazha P. Prakash; Punit P. Seth; Eric E. Swayze
- Inventors: Michael Oestergaard; Thazha P. Prakash; Punit P. Seth; Eric E. Swayze
- Web page: https://patentgrep.com/patent/US9752142B2

## CPC

- C12N 15/113: Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; {Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing (when used in plants C12N15/8218)}
- C12N 15/111: {General methods applicable to biologically active non-coding nucleic acids}
- C12N 2310/11: Antisense
- C12N 2310/312: Phosphonates
- C12N 2310/3125: Methylphosphonates
- C12N 2310/314: Phosphoramidates
- C12N 2310/315: Phosphorothioates
- C12N 2310/316: Phosphonothioates
- C12N 2310/321: 2'-O-R Modification
- C12N 2310/3231: having an additional ring, e.g. LNA, ENA
- C12N 2310/3341: 5-Methylcytosine
- C12N 2310/341: Gapmers, i.e. of the type ===---===
- C12N 2310/351: Conjugate
- C12N 2320/34: Allele or polymorphism specific uses
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)

## Abstract

The present invention provides gapped oligomeric compounds comprising at least one 5′-substituted P-D-2′-deoxyribonucleoside in the gap region. Certain such gapped oligomeric compounds are useful for hybridizing to a complementary nucleic acid, including but not limited to, nucleic acids in a cell. The oligomeric compounds provided herein have improved properties such as selectivity, potency and improved proinflammatory profile. In certain embodiments, hybridization results in modulation of the amount of activity or expression of the target nucleic acid in a cell.

## Claims

### Claim 1

A gapped oligomeric compound comprising a contiguous sequence of linked monomer subunits having a gap region located between a 5′-region and a 3′-region wherein the 5′ and 3′-regions each, independently, have from 2 to 8 contiguous RNA-like
modified nucleosides that each adopt a 3′-endo conformational geometry when put into an oligomeric compound and wherein the gap region has from 6 to 14 contiguous monomer subunits selected from β-D-2′-deoxyribonucleosides and 5′-substituted β-D-2′-deoxyribonucleosides having Formula I:
wherein independently for each 5′-substituted β-D-2′-deoxyribonucleoside having Formula I:
T1 and T2 are each, independently, an internucleoside linking group linking the 5′-substituted β-D-2′-deoxyribonucleoside having Formula I to the remainder of the gapped oligomeric compound;
Bx is a heterocyclic base moiety;
R1 is C1-C6 alkyl, substituted C1-C6 alkyl, C2-C6 alkenyl, substituted C2-C6 alkenyl, C2-C6 alkynyl or substituted C2-C6 alkynyl; and
wherein said gap region comprises at least one 5′-substituted β-D-2′-deoxyribonucleoside having Formula I and a plurality of β-D-2′-deoxyribonucleosides.

### Claim 2 (depends on 1)

The gapped oligomeric compound of claim 1 wherein each substituted group comprises one or more optionally protected substituent groups independently selected from halogen, OJ1, NJ1J2, ═NJ1, SJ1, N3, CN, OC(=L)J1, OC(=L)NJ1J2 and NJ3C(=L)NJ1J2, wherein each J1, J2 and J3 is, independently, H, C1-C6 alkyl or a protecting group, and L is O, S or NJ1.

### Claim 3 (depends on 1)

The gapped oligomeric compound of claim 1 wherein each R1 is independently selected from C1-C6 alkyl, substituted C1-C6 alkyl, C2-C6 alkenyl and C2-C6 alkynyl.

### Claim 4 (depends on 1)

The gapped oligomeric compound of claim 1 wherein each R1 is independently selected from CH3, CH2CH3, CH2CH2OH, CH2CHCH2 and CHCH2.

### Claim 5 (depends on 1)

The gapped oligomeric compound of claim 1 wherein each R1 is CH3.

### Claim 6 (depends on 1)

The gapped oligomeric compound of claim 1 having only one 5′-substituted β-D-2′-deoxyribonucleoside of Formula I.

### Claim 7 (depends on 1)

The gapped oligomeric compound of claim 1 having only two 5′-substituted β-D-2′-deoxyribonucleosides of Formula I.

### Claim 8 (depends on 1)

The gapped oligomeric compound of claim 1 wherein each 5′-substituted β-D-2′-deoxyribonucleoside has the configuration of Formula Ia:

### Claim 9 (depends on 1)

The gapped oligomeric compound of claim 1 wherein each 5′-substituted β-D-2′-deoxyribonucleoside has the configuration of Formula Ib:

### Claim 10 (depends on 1)

The gapped oligomeric compound of claim 1 wherein each internucleoside linking group that links adjacent monomer subunits is independently selected from a phosphodiester or phosphorothioate internucleoside linking group.

### Claim 11 (depends on 1)

The gapped oligomeric compound of claim 1 wherein each internucleoside linking group that links adjacent monomer subunits is a phosphorothioate internucleoside linking group.

### Claim 12 (depends on 1)

The gapped oligomeric compound of claim 1 wherein each monomer subunit comprises a heterocyclic base moiety independently selected from uracil, thymine, cytosine, 4-N-benzoylcytosine, 5-methylcytosine, 4-N-benzoyl-5-methylcytosine, adenine, 6-N-benzoyladenine, guanine and 2-N-isobutyrylguanine.

### Claim 13 (depends on 1)

The gapped oligomeric compound of claim 1 wherein each modified nucleoside in the 5′ and 3′-regions is independently selected from a bicyclic nucleoside comprising a bicyclic furanosyl sugar moiety or a modified nucleoside comprising a furanosyl sugar moiety having at least one substituent group.

### Claim 14 (depends on 13)

The gapped oligomeric compound of claim 13 comprising one or more 2′-modified nucleosides that each have a 2′-substituent group independently selected from halogen, OCH3, OCH2F, OCHF2, OCF3, OCH2CH3, O(CH2)2F, OCH2CHF2, OCH2CF3, OCH2—CH═CH2, O(CH2)2—OCH3, O(CH2)2—SCH3, O(CH2)2—OCF3, O(CH2)3—N(R3)(R4), O(CH2)2—ON(R3)(R4), O(CH2)2—O(CH2)2—N(R3)(R4), OCH2C(═O)—N(R4)(R4), OCH2C(═O)—N(R5)—(CH2)2—N(R3)(R4) and O(CH2)2—N(R5)—C(═NR6)[N(R3)(R4)] wherein R3, R4, R5 and R6 are each, independently, H or C1-C6 alkyl.

### Claim 15 (depends on 14)

The gapped oligomeric compound of claim 14 wherein each 2′-substituent group is independently selected from F, OCH3, O(CH2)2—OCH3 and OCH2C(═O)—N(H)CH3.

### Claim 16 (depends on 15)

The gapped oligomeric compound of claim 15 wherein each 2′-substituent group is O(CH2)2—OCH3.

### Claim 17 (depends on 13)

The gapped oligomeric compound of claim 13 comprising one or more bicyclic nucleosides wherein each bicyclic nucleoside has a bridging group independently selected from 4′-(CH2)—O-2′, 4′-(CH2)—S-2′, 4′-(CH2)2—O-2′, 4′-CH(CH3)—O-2′, 4′-CH(CH2OCH3)—O-2′, 4′-C(CH3)2—O-2′, 4′-CH2—N(OCH3)-2′, 4′-CH2—O—N(CH3)-2′, 4′-CH2—NCH3—O-2′, 4′-CH2—C(H)(CH3)-2′ and 4′-CH2—C(═CH2)-2′.

### Claim 18 (depends on 17)

The gapped oligomeric compound of claim 17 wherein each bridging group is 4′-CH[(S)—(CH3)]—O-2′.

### Claim 19 (depends on 1)

The gapped oligomeric compound of claim 1 comprising at least two different types of modified nucleosides in the 5′ and 3′-regions comprising at least two different modified ribofuranosyl sugar moieties.

### Claim 20 (depends on 19)

The gapped oligomeric compound of claim 19 wherein the 5′ and 3′-regions include only 4′-CH[(S)—(CH3)]—O-2′ bicyclic nucleosides and 2′-O(CH2)2—OCH3 substituted nucleosides.

### Claim 21 (depends on 1)

The gapped oligomeric compound of claim 1 wherein the modified nucleosides in the 5′ and 3′-regions each have the same modified sugar moiety.

### Claim 22 (depends on 1)

The gapped oligomeric compound of claim 1 wherein the 5′ and 3′-regions each, independently, have from 3 to 6 monomer subunits and the gap region has from 6 to 10 monomer subunits.

### Claim 23 (depends on 1)

A method of inhibiting gene expression comprising contacting one or more cells, a tissue or the animal with the oligomeric compound of claim 1 wherein said oligomeric compound is complementary to a target RNA.

### Claim 24 (depends on 23)

The method of claim 23 wherein said cells are in a human.

### Claim 25 (depends on 23)

The method of claim 23 wherein said target RNA is human mRNA.

### Claim 26 (depends on 23)

The method of claim 23 wherein said target RNA is cleaved thereby inhibiting the function of said target RNA.