Treatment of lipid transport and metabolism gene related diseases by inhibition of natural antisense transcript to a lipid transport and metabolism gene

• US 10,604,755 B2
• Filed: 07/31/2015
• Issued: 03/31/2020
• Est. Priority Date: 05/06/2009
• Status: Active Grant

• Current Assignee: CURNA, Inc. (Opko Health, Inc.)
• Original Assignee: CURNA, Inc. (Opko Health, Inc.)
• Inventors: Collard, Joseph, Khorkova Sherman, Olga, Coito, Carlos
• Primary Examiner(s): Schnizer, Richard A
• Application Number:
  US14/814,895
• Publication Number:
  US 20160024505A1
• Time in Patent Office: 1,705 Days
• Field of Search: None
• CPC Class Codes: A61K 31/713 Double-stranded nucleic acids or oligonucleotides
• CPC Class Codes: A61K 48/00 Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
• CPC Class Codes: A61P 1/04 for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
• CPC Class Codes: A61P 11/00 Drugs for disorders of the respiratory system
• CPC Class Codes: A61P 11/06 Antiasthmatics
• CPC Class Codes: A61P 13/10 of the bladder
• CPC Class Codes: A61P 13/12 of the kidneys
• CPC Class Codes: A61P 17/00 Drugs for dermatological disorders
• CPC Class Codes: A61P 17/06 Antipsoriatics
• CPC Class Codes: A61P 19/00 Drugs for skeletal disorders
• CPC Class Codes: A61P 19/02 for joint disorders, e.g. arthritis, arthrosis
• CPC Class Codes: A61P 21/00 Drugs for disorders of the muscular or neuromuscular system
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 25/28 for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
• CPC Class Codes: A61P 25/30 for treating abuse or dependence
• CPC Class Codes: A61P 27/06 Antiglaucoma agents or miotics
• 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 3/00 Drugs for disorders of the metabolism of the blood or the extracellular fluid A61P7/00
• CPC Class Codes: A61P 3/04 Anorexiants; Antiobesity agents
• CPC Class Codes: A61P 3/06 Antihyperlipidemics
• CPC Class Codes: A61P 3/10 : for hyperglycaemia, e.g. antidiabetics
• CPC Class Codes: A61P 31/00 : Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
• CPC Class Codes: A61P 31/04 : Antibacterial agents
• CPC Class Codes: A61P 33/00 : Antiparasitic agents
• CPC Class Codes: A61P 35/00 : Antineoplastic agents
• CPC Class Codes: A61P 37/00 : Drugs for immunological or allergic disorders
• CPC Class Codes: A61P 37/02 : Immunomodulators
• CPC Class Codes: A61P 37/06 : Immunosuppressants, e.g. drugs for graft rejection
• CPC Class Codes: A61P 37/08 : Antiallergic agents antiasthmatic agents A61P11/06; ophthalmic antiallergics A61P27/14
• CPC Class Codes: A61P 43/00 : Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: A61P 5/14 : of the thyroid hormones, e.g. T3, T4
• CPC Class Codes: A61P 9/00 : Drugs for disorders of the cardiovascular system
• CPC Class Codes: A61P 9/10 : for treating ischaemic or atherosclerotic diseases, e.g. antianginal drugs, coronary vasodilators, drugs for myocardial infarction, retinopathy, cerebrovascula insufficiency, renal arteriosclerosis
• 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 15/1137 : against enzymes viral enzymes C12N15/1131; receptors C12N15/1138
• CPC Class Codes: C12N 15/1138 : against receptors or cell surface proteins
• CPC Class Codes: C12N 2310/11 : Antisense
• CPC Class Codes: C12N 2310/14 : interfering N.A.
• CPC Class Codes: C12N 2310/313 : Phosphorodithioates
• CPC Class Codes: C12N 2310/314 : Phosphoramidates
• CPC Class Codes: C12N 2310/315 : Phosphorothioates
• CPC Class Codes: C12N 2310/321 : 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 : 2'-R Modification
• CPC Class Codes: C12Y 203/01043 : Phosphatidylcholine-sterol O-acyltransferase (2.3.1.43), i.e. lecithin-cholesterol acyltransferase or LCAT

Abstract

The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of a Lipid transport and metabolism gene, in particular, by targeting natural antisense polynucleotides of a Lipid transport and metabolism gene. The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of a Lipid transport and metabolism genes.

Claims

1. A compound comprising a single stranded synthetic, modified antisense RNA oligonucleotide of 19 to 21 nucleotides in length or an optionally modified double stranded siRNA comprising an oligonucleotide of 19 to 30 nucleotides in length wherein said modifications are selected from:

at least one modified sugar moiety;

at least one modified internucleotide linkage;

at least one modified nucleotide, and combinations thereof;

wherein said siRNA oligonucleotide and said single stranded antisense RNA oligonucleotide are each 100% complementary with and specifically hybridize to a target region of a natural antisense polynucleotide of a lipid transport and metabolism gene that is an ABCA1 polynucleotide wherein said natural antisense polynucleotide is SEQ ID NO;

8, and where the antisense RNA oligonucleotide and the siRNA oligonucleotide upregulate the function and/or expression of the ABCA1 polynucleotide in vivo or in vitro as compared to a normal control, and wherein the target region in SEQ ID NO;

8 consists of nucleotides 1-245 and 799-1169, and further wherein the siRNA oligonucleotide and the single stranded oligonucleotide comprise a nucleobase sequence selected from the group consisting of SEQ ID NOS;

27, 28, 29, 31, 32, 33, 35, 38, and 39 wherein each thymine base may be replaced by a uracil base.

2. The siRNA oligonucleotide or single stranded antisense RNA oligonucleotide of claim 1 comprising at least one modified internucleotide linkage selected from the group consisting of phosphorothioate, alkylphosphonate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, carboxymethyl ester, and combinations thereof.

3. The siRNA oligonucleotide or single stranded antisense RNA oligonucleotide of claim 1 comprising at least one phosphorothioate internucleotide linkage.

4. The siRNA oligonucleotide or single stranded antisense RNA oligonucleotide of claim 1 comprising a backbone of phosphorothioate internucleotide linkages.

5. The siRNA oligonucleotide or single stranded antisense RNA oligonucleotide of claim 1 comprising at least one modified nucleotide selected from:

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

6. The siRNA oligonucleotide or single stranded antisense RNA oligonucleotide of claim 1 comprising a plurality of modified internucleotide linkages selected from:

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

7. The siRNA oligonucleotide or single stranded antisense RNA oligonucleotide of claim 1 comprising a plurality of modifications selected from peptide nucleic acids, locked nucleic acids (LNAs), analogues thereof, derivatives thereof, and a combination thereof.

8. The siRNA oligonucleotide or single stranded antisense RNA oligonucleotide of claim 1 comprising 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.

9. The siRNA oligonucleotide or single stranded antisense RNA 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.

10. A single stranded antisense oligonucleotide comprising a non-naturally occurring modified nucleotide wherein the nucleobase sequence of the oligonucleotide consists of a nucleobase sequence selected from the group consisting of SEQ ID NOS:

27, 28, 29, 31, 32, 33, 35, 38, 39, wherein each thymine base may be replaced with a uracil base.

11. A double stranded RNA oligonucleotide of 19 to 30 nucleotides in length comprising the nucleobase sequence of SEQ ID NO:

23 or 24.

12. A pharmaceutical composition comprising a double-stranded or single stranded antisense oligonucleotide of 19 to 30 nucleotides in length and a pharmaceutically acceptable excipient, wherein the double-stranded or single stranded oligonucleotide comprises a non-naturally occurring nucleotide modification and the nucleobase sequence of any one of SEQ ID NOS;

23, 24, 27, 28, 29, 31, 32, 33, 35, 38 and 39, wherein each thymine base may be replaced by a uracil base.

13. The composition of claim 12, wherein the nucleobase sequence of the single stranded antisense oligonucleotide is selected from the nucleobase sequence of any one of SEQ ID NOS:

27, 28, 29, 31, 32, 33, 35, 38 and 39, wherein each thymine base may be replaced by a uracil base.

14. The composition of claim 12, wherein the double-stranded or single stranded antisense oligonucleotide comprises the nucleobase sequence of SEQ ID NO:

23 or SEQ ID NO;

24.

15. The composition of claim 12, wherein the double-stranded or single stranded antisense oligonucleotide comprises one or more modifications selected from:

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