Treatment of pyrroline-5-carboxylate reductase 1 (PYCR1) related disease by inhibition of natural antisense transcript to PYCR1

• US 9,902,995 B2
• Filed: 06/07/2016
• Issued: 02/27/2018
• Est. Priority Date: 02/22/2010
• Status: Expired due to Fees

• Current Assignee: CURNA, Inc. (Opko Health, Inc.)
• Original Assignee: CURNA, Inc. (Opko Health, Inc.)
• Inventors: Collard, Joseph, Khorkova Sherman, Olga
• Primary Examiner(s): Gibbs, Terra C
• Application Number:
  US15/175,633
• Publication Number:
  US 20160289759A1
• Time in Patent Office: 630 Days
• Field of Search: 435 61, 435 911, 435325, 435375
• CPC Class Codes: A61K 31/7088 Compounds having three or more nucleosides or nucleotides
• CPC Class Codes: A61P 1/02 Stomatological preparations, e.g. drugs for caries, aphtae, periodontitis
• 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 1/16 for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
• CPC Class Codes: A61P 11/00 Drugs for disorders of the respiratory system
• CPC Class Codes: A61P 13/02 of urine or of the urinary tract, e.g. urine acidifiers
• CPC Class Codes: A61P 13/08 of the prostate
• CPC Class Codes: A61P 13/10 of the bladder
• CPC Class Codes: A61P 13/12 of the kidneys
• CPC Class Codes: A61P 15/00 Drugs for genital or sexual disorders for disorders of sex hormones A61P5/24; Contraceptives
• 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 19/06 Antigout agents, e.g. antihyperuricemic or uricosuric agents
• CPC Class Codes: A61P 19/08 for bone diseases, e.g. rachitism, Paget's disease
• CPC Class Codes: A61P 19/10 for osteoporosis
• 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 25/04 Centrally acting analgesics, e.g. opioids
• CPC Class Codes: A61P 25/08 : Antiepileptics; Anticonvulsants
• CPC Class Codes: A61P 25/14 : for treating abnormal movements, e.g. chorea, dyskinesia
• CPC Class Codes: A61P 25/16 : Anti-Parkinson drugs
• CPC Class Codes: A61P 25/18 : Antipsychotics, i.e. neuroleptics; Drugs for mania or schizophrenia
• CPC Class Codes: A61P 25/24 : Antidepressants
• 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 27/02 : Ophthalmic agents
• 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 35/00 : Antineoplastic agents
• CPC Class Codes: A61P 35/02 : specific for leukemia
• CPC Class Codes: A61P 43/00 : Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: A61P 5/00 : Drugs for disorders of the endocrine system
• 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 2310/11 : Antisense
• CPC Class Codes: C12N 2310/113 : targeting other non-coding nucleic acids, e.g. antagomirs
• CPC Class Codes: C12N 2310/14 : interfering N.A.
• CPC Class Codes: C12N 2310/315 : Phosphorothioates
• CPC Class Codes: C12N 2320/30 : Special therapeutic applications
• CPC Class Codes: C12Q 1/68 : involving nucleic acids
• CPC Class Codes: C12Q 1/6876 : Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2600/136 : Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/158 : Expression markers
• CPC Class Codes: C12Q 2600/178 : miRNA, siRNA or ncRNA
• CPC Class Codes: C12Y 105/01002 : Pyrroline-5-carboxylate reductase (1.5.1.2)

Abstract

The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of Pyrroline-5-carboxylate reductase 1 (PYCR1), in particular, by targeting natural antisense polynucleotides of Pyrroline-5-carboxylate reductase 1 (PYCR1). The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of PYCR1.

Claims

1. A method of selecting a modified antisense oligonucleotide which can modulate a function of and/or the expression of a Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide in patient cells or tissues in vivo or in vitro comprising:

selecting at least one modified antisense oligonucleotide of 10 to 30 nucleotides in length which is at least 90% complementary to a region of a natural antisense polynucleotide the PYCR1 polynucleotide;

contacting said at least one modified antisense oligonucleotide with said natural antisense polynucleotide to form a hybrid;

measuring the thermal melting point of the hybrid of the at least one modified antisense oligonucleotide with said natural antisense polynucleotide under stringent hybridization conditions;

selecting at least one modified antisense oligonucleotide having binding affinity to said natural antisense polynucleotide based upon the thermal melting point results;

determining the modulation activity of the selected at least one modified antisense oligonucleotide having binding affinity to said natural antisense polynucleotide and

selecting at least one modified antisense oligonucleotide which modulates a function of and/or expression of the PYCR1 polynucleotide wherein the at least one modified antisense oligonucleotide comprises one or more modifications selected from;

at least one modified sugar moiety, at least one modified intemucleoside linkage, at least one modified nucleotide, and combinations thereof.

2. The method according to claim 1 comprising:

contacting said cells or tissues with at least one modified antisense oligonucleotide of 12 to 30 nucleotides in length that targets and specifically hybridizes to a complementary region of a natural antisense polynucleotide of the Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide;

thereby modulating a function of and/or the expression of the Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide in patient cells or tissues in vivo or in vitro.

3. The method of claim 2, wherein a function of and/or the expression of the Pyrroline-5-carboxylate reductase 1 (PYCR1) is increased in vivo or in vitro with respect to a control.

4. The method of claim 2, wherein the at least one modified antisense oligonucleotide targets a natural antisense sequence of a Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide having SEQ ID NO:

2.

5. The method of claim 2, wherein the at least one modified antisense oligonucleotide targets a natural antisense polynucleotide comprising coding and/or non-coding nucleic acid sequences of a Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide.

6. The method of claim 1, wherein the at least one modified antisense oligonucleotide comprises one or more modifications selected from:

at least one modified sugar moiety, at least one modified internucleoside linkage or at least one modified nucleotide.

7. The method of claim 1, wherein the one or more modifications comprise 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 combinations thereof.

8. The method of claim 1, wherein the one or more modifications comprise at least one modified internucleoside linkage selected from:

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

9. The method of claim 6, wherein the one or more modifications comprise at least one modified nucleotide selected from:

a peptide nucleic acid (PNA), a locked nucleic acid (LNA), an arabino-nucleic acid (FANA), an analogue, a derivative, and combinations thereof.

10. The method of claim 1, wherein the at least one modified antisense oligonucleotide comprises at least one oligonucleotide sequence set forth as SEQ ID NOS:

3 to 6.

11. The method according to claim 1 comprising:

contacting said cells or tissues with at least one short interfering RNA (siRNA) oligonucleotide 19 to 30 nucleotides in length, said at least one siRNA oligonucleotide being specific for a natural antisense polynucleotide of a Pyrroline-5-carboxylate reductase 1 (PYCR1) polynucleotide.

12. The method of claim 6, wherein said modified antisense oligonucleotide comprises at least one phosphorothioate internucleotide linkage.

13. The method of claim 6, wherein said modified antisense oligonucleotide comprises a backbone of phosphorothioate internucleotide linkages.

14. The method of claim 6, wherein the modified antisense 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.