# US 2021/0340536 A1 · 2' fana modified foxp3 antisense oligonucleotides and methods of use thereof

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- Number: US 2021/0340536 A1
- Document ID: US20210340536A1
- Status: Published application
- Kind: A1
- Application number: 17/279,542
- Filed: 2019-09-25
- Published: 2021-11-04
- Earliest claimed: 2018-09-26
- Assignees: AUM LifeTech, Inc; The Children's Hospital of Philadelphia
- Applicants: AUM Lifetech, Inc.; The Children's Hospital of Philadelphia
- Inventors: Veenu Aishwarya; Wayne W. Hancock
- Web page: https://patentgrep.com/patent/US20210340536A1

## 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
- A61K 45/06: Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
- A61N 5/10: X-ray therapy; Gamma-ray therapy; Particle-irradiation therapy (A61N5/01 takes precedence)
- A61P 35/00: Antineoplastic agents
- C12N 2310/11: Antisense
- C12N 2310/315: Phosphorothioates
- C12N 2310/32: of the sugar
- C12N 2310/322: 2'-R Modification
- C12N 2310/341: Gapmers, i.e. of the type ===---===
- 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)
- A61N: ELECTROTHERAPY; MAGNETOTHERAPY; RADIATION THERAPY; ULTRASOUND THERAPY (measurement of bioelectric currents A61B; surgical instruments, devices or methods for transferring non-mechanical forms of energy to or from the body A61B18/00; anaesthetic apparatus in general A61M; incandescent lamps H01K; infrared radiators for heating H05B)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS

## Abstract

The present invention is directed to hybrid chimera antisense oligonucleotides including deoxyribonucleotide and 2′-deoxy-2′-fluoro-β-D-arabinonucleotide which binds to a Foxp3 mRNA, and to methods of use thereof. The methods include the use for reducing expression level of Foxp3 gene, increasing anti-tumor activity, and treating cancer in a subject.

## Claims

### Claim at position 1

1-38. (canceled)

### Claim 39

A modified antisense oligonucleotide (AON) comprising at least one 2′-deoxy-2′-fluoro-β-D-arabinonucleotide (2′-FANA modified nucleotide), wherein the AON binds to a Foxp3 mRNA.

### Claim 40 (depends on 39)

The AON of claim 39, which is a hybrid chimera AON comprising at least one 2′-FANA modified nucleotide and at least one unmodified deoxyribonucleotide, wherein the AON is a 2′-FANA AON.

### Claim 41 (depends on 40)

The AON of claim 40, wherein the 2′-FANA modified nucleotides are positioned according to any of Formulas 1-16.

### Claim 42 (depends on 40)

The AON of claim 40, wherein internucleotide linkages between nucleotides of the 2′-FANA modified nucleotides are selected from the group consisting of phosphodiester bonds, phosphotriester bonds, phosphorothioate bonds (5′O—P(S)O—3O—, 5′S—P(O)(—3′—O—, and 5′O—P(O)O—3′S—), phosphorodithioate bonds, Rp-phosphorothioate bonds, Sp-phosphorothioate bonds, boranophosphate bonds, methylene bonds(methylimino), amide bonds (3′—CH2—CO—NH—5′ and 3′—CH2—NH—CO—5′), methylphosphonate bonds, 3′-thioformacetal bonds, (3′S—CH2—O5′), amide bonds (3′CH2—C(O)NH—5′), phosphoramidate groups, and a combination thereof.

### Claim 43 (depends on 40)

The AON of claim 40, wherein the 2′-FANA AON comprises from about 0 to about 20 2′-deoxy-2′-fluoro-β-D-arabinonucleotide at the 5′-end and from about 0 to about 20 2′-deoxy-2′-fluoro-β-D-arabinonucleotide at the 3′-end, flanking a sequence comprising from about 0 to about 20 deoxyribonucleotide residues.

### Claim 44 (depends on 41)

The AON of claim 41, wherein the 2′-FANA AON comprises at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25, successive nucleotides of SEQ ID NOs: 1-9, SEQ ID NOs: 11-19, SEQ ID NOs: 21-29, SEQ ID NOs: 31-138, SEQ ID NOs: 139-192, SEQ ID NOs: 193-302, or a sequence complimentary thereto.

### Claim 45

A pharmaceutical composition comprising a modified antisense oligonucleotide (AON) comprising at least one 2′-deoxy-2′-fluoro-β-D-arabinonucleotide (2′-FANA modified nucleotide) and a pharmaceutically acceptable carrier, wherein the AON binds to a Foxp3 mRNA.

### Claim 46 (depends on 45)

The composition of claim 45, wherein the AON is a hybrid chimera AON comprising at least one 2′-FANA modified nucleotide and at least one unmodified deoxyribonucleotide, and wherein the AON is a 2′-FANA AON.

### Claim 47 (depends on 46)

The composition of claim 46, wherein the 2′-FANA AON comprises from about 0 to about 20 2′-deoxy-2′-fluoro-β-D-arabinonucleotide at the 5′-end and from about 0 to about 20 2′-deoxy-2′-fluoro-β-D-arabinonucleotide at the 3′-end, flanking a sequence comprising from about 0 to about 20 deoxyribonucleotide residues.

### Claim 48 (depends on 47)

The composition of claim 47, wherein the 2′-FANA AON comprises at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25, successive nucleotides of SEQ ID NOs: 1-9, SEQ ID NOs: 11-19, SEQ ID NOs: 21-29, SEQ ID NOs: 31-138, SEQ ID NOs: 139-192, SEQ ID NOs: 193-302, or a sequence complimentary thereto.

### Claim 49

A method of treating cancer in a subject in need thereof comprising administering to the subject at least one antisense oligonucleotide (AON), wherein the AON binds to a Foxp3 mRNA, and wherein the AON comprises at least one 2′-deoxy-2′-fluoro-β-D-arabinonucleotide (2′-FANA modified nucleotide), thereby treating the cancer.

### Claim 50 (depends on 49)

The method of claim 49, wherein the AON reduces expression level of a Foxp3 gene.

### Claim 51 (depends on 49)

The method of claim 49, wherein the AON is a hybrid chimera AON comprising at least one 2′-FANA modified nucleotide and at least one unmodified deoxyribonucleotide, and wherein the AON is a 2′-FANA AON.

### Claim 52 (depends on 51)

The method of claim 51, wherein the 2′-FANA AON comprises at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25, successive nucleotides of SEQ ID NOs: 1-9, SEQ ID NOs: 11-19, SEQ ID NOs: 21-29, SEQ ID NOs: 31-138, SEQ ID NOs: 139-192, SEQ ID NOs: 193-302, or a sequence complimentary thereto.

### Claim 53 (depends on 51)

The method of claim 51, wherein the 2′-FANA AON increases anti-tumor immunity in the subject.

### Claim 54 (depends on 51)

The method of claim 51, wherein the 2′-FANA AON decreases the activity of a regulatory T cell (Treg) and/or increases the activity of an immune cell.

### Claim 55 (depends on 49)

The method of claim 49, further comprising administering an immunotherapeutic agent, a chemotherapeutic agent and/or a radiotherapy.

### Claim 56 (depends on 55)

The method of claim 55, wherein the immunotherapeutic agent and/or chemotherapeutic agent is selected from the group consisting of a checkpoint inhibitor, vaccine, chimeric antigen receptor (CAR)-T cell therapy, anti-PD-1 antibody (Nivolumab or Pembrolizumab), anti-PD-L1 antibody (Atezolizumab, Avelumab or Durvalumab) and a combination thereof.

### Claim 57 (depends on 55)

The method of claim 55, wherein the immunotherapeutic agent, chemotherapeutic agent and/or radiotherapy is administered prior to, simultaneously with, or after the administration of the AON.

### Claim 58 (depends on 49)

The method of claim 49, wherein the cancer is selected from the group consisting of breast, liver, ovarian, pancreatic, lung cancer, melanoma and glioblastoma.