# US 10,865,414 B2 · Modulators of DNM2 expression

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- Number: US 10,865,414 B2
- Document ID: US10865414B2
- Status: Granted
- Kind: B2
- Application number: 16/248,549
- Filed: 2019-01-15
- Published: 2019-08-08
- Granted: 2020-12-15
- Earliest claimed: 2018-01-15
- Assignees: Ionis Pharmaceuticals, Inc.
- Applicants: Ionis Pharmaceuticals, Inc.
- Inventors: Susan M. Freier
- Web page: https://patentgrep.com/patent/US10865414B2

## CPC

- C12N 15/1137: {against enzymes (viral enzymes C12N15/1131; receptors C12N15/1138)}
- 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 2310/11: Antisense
- C12N 2310/14: interfering nucleic acids [NA]
- C12N 2310/315: Phosphorothioates
- C12N 2310/3231: having an additional ring, e.g. LNA, ENA
- C12N 2310/334: Modified C
- C12N 2310/3341: 5-Methylcytosine
- C12N 2310/341: Gapmers, i.e. of the type ===---===
- C12N 2310/346: having a combination of backbone and sugar modifications
- C12N 2310/351: Conjugate
- C12N 2320/35: based on a specific dosage / administration regimen
- 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 embodiments provide methods, compounds, and compositions useful for inhibiting DNM2 expression, which may be useful for treating, preventing, or ameliorating a disease associated with DNM2.

## Claims

### Claim 1

A compound comprising a modified oligonucleotide consisting of 16 to 20 linked nucleosides and having a nucleobase sequence comprising at least 14 contiguous nucleobases of SEQ ID NO: 2879 or SEQ ID NO: 2123, wherein the modified oligonucleotide comprises at least one of a modified internucleoside linkage and a modified sugar moiety.

### Claim 2 (depends on 1)

The compound of claim 1, wherein the nucleobase sequence comprises SEQ ID NO: 2879.

### Claim 3 (depends on 1)

The compound of claim 1, wherein the nucleobase sequence comprises SEQ ID NO: 2123.

### Claim 4 (depends on 1)

The compound of claim 1, wherein the nucleobase sequence is SEQ ID NO: 2879 or 2123.

### Claim 5 (depends on 1)

The compound of claim 1, wherein the modified oligonucleotide comprises:
a gap segment consisting of 8-12 linked 2′-deoxynucleosides;
a 5′ wing segment consisting of 1-7 linked nucleosides; and
a 3′ wing segment consisting of 1-7 linked nucleosides;
wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein the terminal nucleoside of each wing segment comprises a modified sugar.

### Claim 6 (depends on 1)

The compound of claim 1, wherein the modified oligonucleotide comprises:
a gap segment consisting of 10 linked 2′-deoxynucleosides;
a 5′ wing segment consisting of 3 linked nucleosides; and
a 3′ wing segment consisting of 3 linked nucleosides;
wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of each wing segment comprises a cEt sugar moiety; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.

### Claim 7 (depends on 1)

The compound of claim 1, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

### Claim 8 (depends on 1)

The compound of claim 1, wherein the modified sugar moiety is a bicyclic sugar.

### Claim 9 (depends on 8)

The compound of claim 8, wherein the bicyclic sugar is selected from the group consisting of LNA, ENA, and cEt.

### Claim 10 (depends on 1)

The compound of claim 1, wherein the modified oligonucleotide comprises at least one 5-methylcytosine.

### Claim 11 (depends on 1)

The compound of claim 1, wherein the modified oligonucleotide is single-stranded.

### Claim 12 (depends on 1)

The compound of claim 1, wherein the compound is a double-stranded compound.

### Claim 13 (depends on 1)

The compound of claim 1, comprising a conjugate group.

### Claim 14 (depends on 13)

The compound of claim 13, wherein the compound consists of the modified oligonucleotide and the conjugate group.

### Claim 15

A modified oligonucleotide according to the following formula: Gks Tks Tks Tds Ads Tds Tds Ads Tds Ads Gds Gds Gds mCks Tks Tk; wherein,
A=an adenine nucleobase,
mC=a 5-methylcytosine nucleobase,
G=a guanine nucleobase,
T=a thymine nucleobase,
k=a cEt sugar moiety,
d=a 2′-deoxyribosyl sugar moiety, and
s=a phosphorothioate internucleoside linkage.

### Claim 16

A modified oligonucleotide, wherein the anion form of the modified oligonucleotide has the following chemical structure:

### Claim 17 (depends on 16)

The modified oligonucleotide of claim 16, wherein the modified oligonucleotide is a salt.

### Claim 18 (depends on 17)

The modified oligonucleotide of claim 17, wherein the cation of the salt is a sodium or a potassium.

### Claim 19 (depends on 1)

A chirally enriched population of the compound of claim 1, wherein the population is enriched for compounds having a modified oligonucleotide comprising at least one particular phosphorothioate internucleoside linkage having a particular stereochemical configuration.

### Claim 20 (depends on 16)

A pharmaceutical composition comprising the modified oligonucleotide of claim 16, and at least one pharmaceutically acceptable diluent or carrier.

### Claim 21 (depends on 1)

A method of treating, preventing, or ameliorating centronuclear myopathy, Duchenne Muscular Dystrophy, or Charcot-Marie Tooth disease, the method comprising administering the compound of claim 1 to a subject with a mutation in at least one gene selected from among MTM1, BIN1, and DNM2.

### Claim 22

An in vitro method of inhibiting expression of DNM2 in a cell comprising contacting the cell with compound comprising a single-stranded modified oligonucleotide that is 100% complementary to exon 10, intron 1, intron 11, intron 12, intron 13, intron 14, or the 3′-UTR of a DNM2 nucleic acid transcript, thereby inhibiting expression of DNM2 in the cell.

### Claim 23 (depends on 22)

The in vitro method of claim 22, wherein the modified oligonucleotide consists of 16 to 20 linked nucleosides and has a nucleobase sequence comprising at least 14 contiguous nucleobases of SEQ ID NO: 2879 or SEQ ID NO: 2123, wherein the modified oligonucleotide comprises at least one of a modified internucleoside linkage and a modified sugar moiety.

### Claim 24 (depends on 22)

The in vitro method of claim 22, wherein the modified oligonucleotide is according to the following formula: Gks Tks Tks Tds Ads Tds Tds Ads Tds Ads Gds Gds Gds mCks Tks Tk; wherein,
A=an adenine nucleobase,
mC=a 5-methylcytosine nucleobase,
G=a guanine nucleobase,
T=a thymine nucleobase,
k=a cEt sugar moiety,
d=a 2′-deoxyribosyl sugar moiety, and
s=a phosphorothioate internucleoside linkage.

### Claim 25 (depends on 22)

The in vitro method of claim 22, wherein the anion form of the modified oligonucleotide has the following chemical structure:

### Claim 26 (depends on 22)

The in vitro method of claim 22, wherein the modified oligonucleotide has the following chemical structure:
or a salt thereof.

### Claim 27 (depends on 22)

The in vitro method of claim 22, wherein the modified oligonucleotide has the following chemical structure:

### Claim 28 (depends on 20)

The pharmaceutical composition of claim 20, wherein the pharmaceutically acceptable diluent is phosphate buffered saline.

### Claim 29 (depends on 15)

A chirally enriched population of the modified oligonucleotide of claim 15, wherein the population is enriched for modified oligonucleotides comprising at least one particular phosphorothioate internucleoside linkage having a particular stereochemical configuration.

### Claim 30 (depends on 16)

A chirally enriched population of the modified oligonucleotide of claim 16, wherein the population is enriched for modified oligonucleotides comprising at least one particular phosphorothioate internucleoside linkage having a particular stereochemical configuration.

### Claim 31 (depends on 15)

A pharmaceutical composition comprising the modified oligonucleotide of claim 15, and at least one pharmaceutically acceptable diluent or carrier.

### Claim 32 (depends on 31)

The pharmaceutical composition of claim 31, wherein the pharmaceutically acceptable diluent is phosphate buffered saline.

### Claim 33 (depends on 15)

A method of treating or ameliorating centronuclear myopathy, Duchenne Muscular Dystrophy, or Charcot-Marie Tooth disease, the method comprising administering the modified oligonucleotide of claim 15 to a subject with a mutation in at least one gene selected from among MTM1, BIN1, and DNM2.

### Claim 34 (depends on 16)

A method of treating or ameliorating centronuclear myopathy, Duchenne Muscular Dystrophy, or Charcot-Marie Tooth disease, the method comprising administering the modified oligonucleotide of claim 16 to a subject with a mutation in at least one gene selected from among MTM1, BIN1, and DNM2.

### Claim 35 (depends on 15)

The modified oligonucleotide of claim 15, comprising the modified oligonucleotide covalently linked to a conjugate group.

### Claim 36

A modified oligonucleotide according to the following chemical structure:
or a salt thereof.

### Claim 37 (depends on 36)

The modified oligonucleotide of claim 36, which is the sodium salt or the potassium salt.

### Claim 38 (depends on 36)

A chirally enriched population of the modified oligonucleotide of claim 36, wherein the population is enriched for modified oligonucleotides comprising at least one particular phosphorothioate internucleoside linkage having a particular stereochemical configuration.

### Claim 39 (depends on 36)

A pharmaceutical composition comprising the modified oligonucleotide of claim 36 and at least one pharmaceutically acceptable diluent or carrier.

### Claim 40 (depends on 39)

The pharmaceutical composition of claim 39, wherein the pharmaceutically acceptable diluent is phosphate buffered saline.

### Claim 41 (depends on 36)

A method of treating or ameliorating centronuclear myopathy, Duchenne Muscular Dystrophy, or Charcot-Marie Tooth disease, the method comprising administering the modified oligonucleotide of claim 36 to a subject with a mutation in at least one gene selected from among MTM1, BIN1, and DNM2.

### Claim 42

A modified oligonucleotide according to the following chemical structure:

### Claim 43 (depends on 42)

A chirally enriched population of the modified oligonucleotide of claim 42, wherein the population is enriched for modified oligonucleotides comprising at least one particular phosphorothioate internucleoside linkage having a particular stereochemical configuration.

### Claim 44 (depends on 42)

A pharmaceutical composition comprising the modified oligonucleotide of claim 42 and at least one pharmaceutically acceptable diluent or carrier.

### Claim 45 (depends on 44)

The pharmaceutical composition of claim 44, wherein the pharmaceutically acceptable diluent is phosphate buffered saline.

### Claim 46 (depends on 42)

A method of treating or ameliorating centronuclear myopathy, Duchenne Muscular Dystrophy, or Charcot-Marie Tooth disease, the method comprising administering the modified oligonucleotide of claim 42 to a subject with a mutation in at least one gene selected from among MTM1, BIN1, and DNM2.

### Claim 47 (depends on 32)

The pharmaceutical composition of claim 32, consisting essentially of the modified oligonucleotide and phosphate buffered saline.

### Claim 48 (depends on 40)

The pharmaceutical composition of claim 40, consisting essentially of the modified oligonucleotide and phosphate buffered saline.

### Claim 49 (depends on 45)

The pharmaceutical composition of claim 45, consisting essentially of the modified oligonucleotide and phosphate buffered saline.