# US 2021/0340534 A1 · Mixed Tricyclo-DNA, 2'-Modified RNA Oligonucleotide Compositions and Uses Thereof

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- Number: US 2021/0340534 A1
- Document ID: US20210340534A1
- Status: Published application
- Kind: A1
- Application number: 17/206,038
- Filed: 2021-03-18
- Published: 2021-11-04
- Earliest claimed: 2016-09-23
- Assignees: Synthena AG
- Applicants: Synthena AG
- Inventors: Wolfgang Andreas Renner; Branislav Dugovic
- Web page: https://patentgrep.com/patent/US20210340534A1

## 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)}
- A61K 31/7088: Compounds having three or more nucleosides or nucleotides
- A61P 21/00: Drugs for disorders of the muscular or neuromuscular system
- C12N 2310/313: Phosphorodithioates
- C12N 2310/314: Phosphoramidates
- C12N 2310/315: Phosphorothioates
- C12N 2310/321: 2'-O-R Modification
- C12N 2310/322: 2'-R Modification
- C12N 2310/3231: having an additional ring, e.g. LNA, ENA
- C12N 2310/3341: 5-Methylcytosine
- C12N 2310/533: having a mismatch or nick in at least one of the strands
- C12N 2320/33: Alteration of splicing
- C12N 2320/52: modulating the physical stability, e.g. GC-content
- C12N 2320/53: reducing unwanted side-effects
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS

## Abstract

In some embodiments, disclosed herein are oligomeric compounds which include one or more tricyclo-deoxyribonucleic acid (tc-DNA) nucleosides and one or more 2′-modified ribonucleic acid (2′-modified-RNA) nucleosides, and which optionally also include one or more non-nucleotides, each of which is joined by a plurality of internucleoside linkages, including pharmaceutical compositions and methods of using the pharmaceutical compositions for the treatment of diseases including Duchenne muscular dystrophy treatment of familial dysautonomia, spinal muscular atrophy, ataxia telangiectasia, congenital disorder of glycosylation, fronto-temporal dementia, Parkinsonism linked to chromosome 17, Niemann-Pick disease type C. neurofibromatosis type 1, neurofibromatosis type 2, megalencephalic leukoencephalopathy with subcortical cysts type 1. Pelizaeus-Merzbacher disease, Pompe disease, myotonic dystrophy type 2 (DM2 or proximal myotonic myopathy), and myotonic dystrophy type 1 (DM1 or Steinert disease).

## Claims

### Claim 1

An oligomeric compound comprising:
one or more tricyclo-deoxyribonucleic acid (tc-DNA) nucleosides and one or more 2′-modified ribonucleic acid (2′-modified-RNA) nucleosides, and optionally including one or more non-nucleosides;
which are joined by a plurality of internucleoside linkages.

### Claim 2 (depends on 1)

The oligomeric compound of claim 1, comprising from about 10 to about 20 nucleotides.

### Claim 3 (depends on 1, 2)

The oligomeric compound of any one of claim 1 to claim 2, wherein the melting temperature (Tm) of the oligomeric compound is at least 50° C.

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

The oligomeric compound of any one of claim 1 to claim 3, wherein the one or more 2′-modified-RNA nucleosides are incorporated in positions such that self-complementary binding under physiological conditions is prevented.

### Claim 5 (depends on 1, 4)

The oligomeric compound of any one of claim 1 to claim 4, wherein the oligomeric compound is a monomer as determined by non-denaturing gel electrophoresis.

### Claim 6 (depends on 1, 5)

The oligomeric compound of any one of claim 1 to claim 5, wherein the oligomeric compound exhibits a monomer to multimer ratio of at least 100 to 1 as determined by size-exclusion chromatography.

### Claim 7 (depends on 1, 6)

The oligomeric compound of any one of claim 1 to claim 6, wherein the C3 percentage determined in a complement assay in an in vitro serum is at least 55% (relative to non-activated complement at 100%), wherein the in vitro serum is selected from the group consisting of human, monkey, dog, mouse, and rat serum.

### Claim 8 (depends on 1, 7)

The oligomeric compound of any one of claim 1 to claim 7, wherein the oligomeric compound is not toxic in an animal model at a dose that would be equivalent to a therapeutically effective dose in a human, wherein the animal model is a mouse model or a primate model.

### Claim 9 (depends on 1, 8)

The oligomeric compound of any one of claim 1 to claim 8, wherein the one or more 2′-modified-RNA nucleosides are incorporated in at least one position that forms self-complementary Watson-Crick base pairs.

### Claim 10 (depends on 1, 9)

The oligomeric compound of any one of claim 1 to claim 9, wherein the one or more 2′-modified-RNA nucleosides are incorporated in at least two adjacent positions that form self-complementary Watson-Crick base pairs.

### Claim 11 (depends on 1, 10)

The oligomeric compound of any one of claim 1 to claim 10, wherein the one or more 2′-modified-RNA nucleosides are incorporated at three or more adjacent positions that form self-complementary Watson-Crick base pairs.

### Claim 12 (depends on 1, 11)

The oligomeric compound of any one of claim 1 to claim 11, wherein the oligomeric compound does not contain a direct tc-DNA to tc-DNA phosphorothioate internucleoside linkage.

### Claim 13 (depends on 1, 12)

The oligomeric compound of any one of claim 1 to claim 12, which is complementary to a target sequence.

### Claim 14 (depends on 1, 13)

The oligomeric compound of any one of claim 1 to claim 13, wherein the one or more 2′-modified-RNA nucleosides are 2′-O-methyl-RNA nucleosides.

### Claim 15 (depends on 1, 13)

The oligomeric compound of any one of claim 1 to claim 13, wherein the one or more 2′-modified-RNA nucleosides are 2′-fluoro-RNA nucleosides.

### Claim 16 (depends on 1, 13)

The oligomeric compound of any one of claim 1 to claim 13, wherein the one or more 2′-modified-RNA nucleosides are locked nucleic acid RNA nucleosides.

### Claim 17 (depends on 1, 16)

The oligomeric compound of any one of claim 1 to claim 16, wherein each of the plurality of internucloside linkages is independently selected from a phosphorothioate linkage, a phosphorodithioate linkage, and a phosphorodiester linkage, a phosphotriester linkage, an aminoalkylphosphotriester linkage, a methyl phosphonate linkage, an alkyl phosphonate linkage, a 5′-alkylene phosphonate linkage, a phosphonate linkage, a phosphinate linkage, a phosphoramidate linkage, an 3′-aminophosphoramidate linkage, an aminoalkyl phosphoramidate linkage, a thionophosphoramidate linkage, a thionoalkylphosphonate linkage, a thionoalkylphosphotriester linkage, a selenophosphate linkage, or a boranophosphate linkage.

### Claim 18 (depends on 1, 16)

The oligomeric compound of any one of claim 1 to claim 16, wherein the internucloside linkages comprise a plurality of phosphorothioate linkages and a plurality of phosphorodiester linkages.

### Claim 19 (depends on 18)

The oligomeric compound of claim 18, wherein no more than 50% of the plurality of internucleoside linkages are phosphorothioate linkages.

### Claim 20 (depends on 18)

The oligomeric compound of claim 18, wherein no more than 33% of the plurality of internucleoside linkages are phosphorothioate linkages.

### Claim 21 (depends on 18)

The oligomeric compound of claim 18, wherein no more than 25% of the plurality of internucleoside linkages are phosphorothioate linkages.

### Claim 22 (depends on 18)

The oligomeric compound of claim 18, wherein at least 50% of the plurality of internucleoside linkages are phosphorodiester linkages.

### Claim 23 (depends on 18)

The oligomeric compound of claim 18, wherein at least 66% of the plurality of internucleoside linkages are phosphorodiester linkages.

### Claim 24 (depends on 18)

The oligomeric compound of claim 18, wherein at least 75% of the plurality of internucleoside linkages are phosphorodiester linkages.

### Claim 25 (depends on 1, 24)

The oligomeric compound of any one of claim 1 to claim 24 wherein the oligomeric compound comprises a sequence selected from the group consisting of:
(SEQ ID NO: 43)
5′-A*a*G*a*u*g*GCATTTCTA-3′,
(SEQ ID NO: 44)
5′-AAGATGGCA*u*T*u*C*u*A-3′,
(SEQ ID NO: 45)
5′-GAAGATGGCA*u*u*u*c*T-3′,
(SEQ ID NO: 46)
5′-AGGAAGATGGCA*u*u*u*c*u*A-3′,
(SEQ ID NO: 47)
5′-AGGAAGATGG*c*a*u*u*u*CTA-3′,
(SEQ ID NO: 48)
5′-AGGAAGATGG*c*a*u*u*u*c*u*A-3′,
(SEQ ID NO: 49)
5′-A*a*G*a*u*g*GCATTTCTAGTT-3′,
(SEQ ID NO: 50)
5′-A*a*g*a*u*g*GCATTTCTAGTT-3′,
(SEQ ID NO: 51)
5′-AA*g*a*u*g*GCATTTCTAGTT-3′,
(SEQ ID NO: 52)
5′-AGGAAG*a*u*g*GCATTTCTA-3′,
(SEQ ID NO: 53)
5′-AGGA*a*g*a*u*g*GCATTTCTA-3′,
(SEQ ID NO: 54)
5′-GGA*a*g*a*u*g*GCATTTCTA-3′,
(SEQ ID NO: 55)
5′-GGA*a*g*a*u*g*GCATTTCT-3′,
(SEQ ID NO: 56)
5′-AGGAA*g*a*u*g*g*CATTTCTA-3′,
(SEQ ID NO: 57)
5′-AGGA*a*g*a*u*g*g*CATTTCTA-3′,
(SEQ ID NO: 58)
5′-AGGAAGATGG*c*a*u*u*u*c*u-3′,
(SEQ ID NO: 59)
5′-a*g*a*u*g*GCATTTCTAGTT-3′,
(SEQ ID NO: 60)
5′-AGGAAGATGG*c*a*u*u*u*c*u-3′,
(SEQ ID NO: 61)
5′-s*s*AAGAuGGCATTTCTA-3′,
(SEQ ID NO: 62)
5′-s*s*s*s*AAGAuGGCATTTCTA-3′,
(SEQ ID NO: 63)
5′-s*s*s*s*s*s*AAGAuGGCATTTCTA-3′,
(SEQ ID NO: 64)
5′-s*s*s*s*s*s*s*s*AAGAuGGCATTTCTA-3′,
(SEQ ID NO: 65)
5′-s*s*s*s*s*s*s*s*s*s*AAGAuGGCATTTCTA-3′,
(SEQ ID NO: 66)
5′-A*A*G*A*T*G*G*C*A*u*T*T*C*T*A-3′,
(SEQ ID NO: 67)
5′-A*A*G*A*T*G*G*C*a*T*T*T*C*T*A-3′,
(SEQ ID NO: 88)
5′-C*A*T*C*C*T*G*G*A*G*T*T*C*C*T-3′,
(SEQ ID NO: 89)
5′-C*A*T*C*C*T*G*g*A*G*T*T*C*C*T-3′,
(SEQ ID NO: 90)
5′-G*C*C*A*T*C*C*T*G*G*A*G*T*T*C-3′,
(SEQ ID NO: 91)
5′-G*C*C*A*T*C*C*T*G*g*A*G*T*T*C-3′,
(SEQ ID NO: 92)
5′-C*C*G*C*T*G*C*C*C*A*A*T*G*C*C-3′,
(SEQ ID NO: 93)
5′-T*G*C*C*G*C*T*G*C*C*C*A*A*T*G-3′,
(SEQ ID NO: 94)
5′-C*T*G*G*A*G*T*T*C*C*T*G*T*A*A-3′,
(SEQ ID NO: 95)
5′-C*T*G*g*A*G*T*T*C*C*T*G*T*A*A-3′
(SEQ ID NO: 96)
5′-T*C*C*T*G*G*A*G*T*T*C*C*T*G*T-3′,
(SEQ ID NO: 97)
5′-T*C*C*T*G*g*A*G*T*T*C*C*T*G*T-3′
(SEQ ID NO: 98)
5′-A*C*T*T*C*A*T*C*C*C*A*C*T*G*A-3′
(SEQ ID NO: 99)
5′-A*C*T*T*c*A*T*C*C*C*A*C*T*G*A-3′,
(SEQ ID NO: 100)
5′-A*T*T*T*C*A*T*T*C*A*A*C*T*G*T-3′,
(SEQ ID NO: 101)
5′-G*T*G*T*T*C*T*T*G*T*A*C*T*T*C-3′,
(SEQ ID NO: 102)
5′-G*T*G*T*T*C*T*T*G*T*a*C*T*T*C-3′,
(SEQ ID NO: 103)
5′-C*T*G*A*A*G*G*T*G*T*T*C*T*T*G-3′,
(SEQ ID NO: 104)
5′-C*T*G*A*a*G*G*T*G*T*T*C*T*T*G-3′,
(SEQ ID NO: 105)
5′-C*T*C*C*G*G*T*T*C*T*G*A*A*G*G-3′,
(SEQ ID NO: 106)
5′-C*T*C*C*G*G*T*T*c*T*G*A*A*G*G-3′,
(SEQ ID NO: 107)
5′-T*T*G*A*A*T*C*C*T*T*T*A*A*C*A-3′,
(SEQ ID NO: 108)
5′-T*T*G*A*A*T*C*C*T*u*T*A*A*C*A-3′,
(SEQ ID NO: 109)
5′-C*T*T*T*C*A*T*A*A*T*G*C*T*G*G-3′,
(SEQ ID NO: 110)
5′-C*T*T*T*C*a*T*A*A*T*G*C*T*G*G-3′,
and
(SEQ ID NO: 111)
5′-C*T*T*T*C*A*T*A*A*u*G*C*T*G*G-3′,
wherein an * between two nucleosides indicates a phosphorothioate, the absence of an * between two nucleosides indicates a phosphorodiester, the capitalized letters A, C, G, and T indicate tc-DNA nucleosides; the lowercase letters a, u, g, and t indicate 2′-O-methyl-RNA nucleosides, the nucleobase at all C positions is 5-methylcytosine, the nucleobase at all c positions is cytosine, and s represents a —O—CH2—CH2—CH2—O— (1,3-propanediol) non-nucleoside.

### Claim 26 (depends on 1, 25)

A pharmaceutical composition comprising an oligonucleotide molecule according to any one of claim 1 to claim 25.

### Claim 27 (depends on 26)

The pharmaceutical composition of claim 26, for use in the treatment of a neuromuscular or musculoskeletal disease.

### Claim 28 (depends on 27)

The use of claim 27, wherein the neuromuscular or musculoskeletal disease is selected from the group consisting of Duchenne muscular dystrophy, familial dysautonomia, spinal muscular atrophy, ataxia telangiectasia, congenital disorder of glycosylation, fronto-temporal dementia, Parkinsonism linked to chromosome 17, Niemann-Pick disease type C, neurofibromatosis type 1, neurofibromatosis type 2, megalencephalic leukoencephalopathy with subcortical cysts type 1, Pelizaeus-Merzbacher disease, Pompe disease, myotonic dystrophy type 2 (DM2), and myotonic dystrophy type 1 (DM1).

### Claim 29 (depends on 26)

A method for treating a neuromuscular or musculoskeletal disease comprising the step of administering to a patient a therapeutically effective dose of the pharmaceutical composition of claim 26.

### Claim 30 (depends on 29)

The method of claim 29, wherein the neuromuscular or musculoskeletal disease is selected from the group consisting of Duchenne muscular dystrophy, familial dysautonomia, spinal muscular atrophy, ataxia telangiectasia, congenital disorder of glycosylation, fronto-temporal dementia, Parkinsonism linked to chromosome 17, Niemann-Pick disease type C, neurofibromatosis type 1, neurofibromatosis type 2, megalencephalic leukoencephalopathy with subcortical cysts type 1, Pelizaeus-Merzbacher disease, Pompe disease, myotonic dystrophy type 2 (DM2), and myotonic dystrophy type 1 (DM1).