TREATMENT OF FRATAXIN (FXN) RELATED DISEASES BY INHIBITION OF NATURAL ANTISENSE TRANSCRIPT TO FXN

• US 20170145414A1
• Filed: 02/02/2017
• Published: 05/25/2017
• Est. Priority Date: 06/09/2011
• Status: Active Grant

• Current Assignee: CURNA, Inc. (Opko Health, Inc.)
• Original Assignee: CURNA, Inc. (Opko Health, Inc.)
• Inventors: Khorkova Sherman, Olga, COLLARD, Joseph
• Granted Patent: US 9,902,959 B2
• Time in Patent Office: Days
• CPC Class Codes: A61K 31/711 Natural deoxyribonucleic acids, i.e. containing only 2'-deoxyriboses attached to adenine, guanine, cytosine or thymine and having 3'-5' phosphodiester links
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 29/00 Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 37/02 Immunomodulators
• CPC Class Codes: A61P 39/06 Free radical scavengers or antioxidants
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: 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
• CPC Class Codes: C12N 2310/11 Antisense
• CPC Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/32 of the sugar
• CPC Class Codes: C12Q 1/68 involving nucleic acids

Abstract

The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of Frataxin (FXN), in particular, by targeting natural antisense polynucleotides of Frataxin (FXN). The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of FXN.

Claims

1. A synthetic, modified oligonucleotide of 10 to 30 nucleotides in length comprising at least one modification wherein the at least one modification is selected from:

at least one modified sugar moiety;

at least one modified internucleotide linkage;

at least one modified nucleotide, and combinations thereof;

wherein said oligonucleotide is an winsome compound, which specifically hybridizes to a natural antisense polynucleotide of a Frataxin (FXN) polynucleotide and apregulates the function and/or expression of a Frataxin (FXN) gene in vivo or in vitro as compared to a normal control.

2. The oligonucleotide according to claim 1 wherein said oligonucleotide is 12 to 30 nucleotides in length and the natural antisense polynucleotide is selected from SEQ ID NO:

2.

3. The oligonucleotide of claim 1, wherein the at least one modification comprises an internucleotide linkage selected from the group consisting of:

phosphorothioate, alkylphosphonate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, carboxymethyl ester, and combinations thereof.

4. The oligonucleotide of claim 1, wherein said oligonucleotide comprises at least one phosphorothioate internucleotide linkage.

5. The oligonucleotide of claim 1, wherein said oligonucleotide comprises a backbone of phosphorothioate internueleotide linkages.

6. The oligonucleotide of claim 1, wherein the oligonucleotide comprises at least one modified nucleotide, said modified nucleotide selected from:

a peptide nucleic acid, a locked nucleic acid (LNA), analogue, derivative, and a combination thereof.

7. The oligonucleotide of claim 1, wherein the oligonucleotide comprises a plurality of modifications, wherein said modifications comprise modified nucleotides selected from:

phosphorothioate, alkylphosphonate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, carboxymethyl ester, and a combination thereof.

8. The oligonucleotide of claim 1, wherein the oligonucleotide comprises a plurality of modifications, wherein said modifications comprise modified nucleotides selected from:

peptide nucleic acids, locked nucleic acids (LNA), analogues, derivatives, and a combination thereof.

9. The oligonucleotide of claim 1, wherein the oligonucleotide comprises at least one modified sugar moiety selected from:

a 2′

-O-methoxyethyl modified sugar moiety, a 2′

-methoxy modified sugar moiety, a 2′

-O-alkyl modified sugar moiety, a bicyclic sugar moiety, and a combination thereof.

10. The oligonucleotide of claim 1, wherein the oligonucleotide comprises a plurality of modifications, wherein said modifications comprise modified sugar moieties selected from:

a 2′

-O-methoxyethyl modified sugar moiety, a 2′

-methoxy modified sugar moiety, a 2′

-O-alkyl modified sugar moiety, a bicyclic sugar moiety, and a combination thereof.

11. The oligonucleotide of claim 1, wherein the oligonucleotide comprises the sequences set forth as SEQ ID NOS:

3 to 6.

12. A pharmaceutical composition comprising one or more oligonucleotides specific for one or more Frataxin (FXN) polynucleotides according to claim 1 and a pharmaceutically acceptable excipient.

13. The composition of claim 12, wherein the oligonucleotides have at least about 90% sequence identity as compared to any one of the nucleotide sequences set forth as SEQ ID NOS:

3 to 6.

14. The composition of claim 12, wherein the oligonucleotides comprise nucleotide sequences set forth as SEQ ID NOS:

3 to 6.

15. The composition of claim 12, wherein the oligonucleotides set forth as SEQ ID NOS:

3 to 6 comprise one or more modifications or substitutions selected from the group consisting of phosphorothionte, LNA and 2′

-OMe.

16. The composition of claim 12, wherein the one or more modifications are selected from:

phosphorothioate, methylphosphonate, peptide nucleic acid, locked nucleic acid (LNA) molecules, and combinations thereof.

17. A method of identifying and selecting at least one oligonucleotide selective for a natural antisense transcript of a FXN gene as a selected target polynucleotide for in vivo administration comprising:

identifying at least one oligonucleotide comprising at least five consecutive nucleotides which are at least partially complementary to as polynucleotide that is antisense to the selected target polynucleotide;

measuring the thermal melting point of a hybrid of an antisense oligonucleotide and the target polynucleotide or the polynucleotide that is antisense to the selected target polynucleotide under stringent hybridization conditions; and

selecting at least one oligonucleotide for in vivo administration based on the information obtained.