NUCLEIC ACID COMPOUNDS FOR INHIBITING HIF1A GENE EXPRESSION AND USES THEREOF

• US 20100015706A1
• Filed: 02/28/2008
• Published: 01/21/2010
• Est. Priority Date: 03/02/2007
• Status: Abandoned Application

• Current Assignee: Marina Biotech, Inc. (Pentair Plc (Ireland))
• Original Assignee: Mdrna Inc. (Adhera Therapeutics, Inc.)
• Inventors: Quay, Steven C., McSwiggen, James, Ahmadian, Mohammad, Vaish, Narendra K.
• Application Number:
  US12/528,786
• Publication Number:
  US 20100015706A1
• Time in Patent Office: Days
• US Class Current: 435/366
• CPC Class Codes: A61P 15/08 for gonadal disorders or for enhancing fertility, e.g. inducers of ovulation or of spermatogenesis
• 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 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• 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: A61P 9/12 Antihypertensives
• 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 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/3231 having an additional ring, e.g. LNA, ENA
• CPC Class Codes: C12N 2310/53 partially self-complementary or closed

Abstract

The present disclosure provides meroduplex ribonucleic acid molecules (mdRNA) capable of decreasing or silencing HIF1A gene expression. An mdRNA of this disclosure comprises at least three strands that combine to form at least two non-overlapping double-stranded regions separated by a nick or gap wherein one strand is complementary to a HIF1A mRNA. In addition, the meroduplex may have at least one uridine substituted with a 5-methyluridine, a nucleoside is a locked nucleic acid, or optionally other modifications, and any combination thereof. Also provided are methods of decreasing expression of a HIF1A gene in a cell or in a subject to treat a HIF1A-related disease.

Claims

1-39. -39. (canceled)

40. A meroduplex ribonucleic acid (mdRNA) molecule that down regulates the expression of any one of a human hypoxia-inducible factor 1 alpha (HIF1A) mRNA, the mdRNA molecule comprising a first strand of 15 to 40 nucleotides in length that is complementary to the human HIF1A mRNA as set forth in SEQ ID NO:

1158 or 1159, and a second strand and a third strand that is each complementary to non-overlapping regions of the first strand, wherein the second strand and third strand can anneal with the first strand to form at least two double-stranded regions spaced apart by a nick or a gap.

41. The mdRNA molecule of claim 40 wherein the first strand is 15 to 25 nucleotides in length or 26 to 40 nucleotides in length.

42. The mdRNA molecule of claim 40 wherein the gap comprises from 1 to 10 unpaired nucleotides.

43. The mdRNA molecule of claim 40 wherein the double-stranded regions have a combined length of about 15 base pairs to about 40 base pairs.

44. The mdRNA molecule of claim 40 wherein the mdRNA molecule comprises at least one 5-methyluridine, 2-thioribothymidine, or 2′

-O-methyl-5-methyluridine.

45. The mdRNA molecule of claim 40 wherein the mdRNA molecule comprises at least one locked nucleic acid (LNA) molecule, deoxy nucleotide, G clamp, 2′

-sugar modification, modified internucleoside linkage, or any combination thereof.

46. The mdRNA molecule of claim 40 wherein the mdRNA contains an overhang of one to four nucleotides on at least one 3′

-end that is not part of the gap or has a blunt end at one or both ends of the mdRNA.

47. The mdRNA molecule of claim 40 wherein at least one pyrimidine of the mdRNA molecule is a pyrimidine nucleoside according to Formula I or II:

48. The mdRNA molecule of claim 47 wherein at least one nucleoside is according to Formula I and in which R¹ is methyl and R² is —

OH or —

O-methyl.

49. The mdRNA molecule of claim 47 wherein at least one R² is selected from the group consisting of 2′

-O—

(C₁-C₅) alkyl, 2′

-O-methyl, 2′

-OCH₂OCH₂CH₃, 2′

-OCH₂CH₂OCH₃, 2′

-O-allyl, and fluoro.

50. The mdRNA molecule of claim 40 wherein the first strand is 19 to 23 nucleotides in length and is complementary to a human HIF1A nucleic acid sequence as set forth in any one of SEQ ID NOS:

1160-1671.

51. The mdRNA molecule of claim 40 wherein the first strand is 25 to 29 nucleotides in length and is complementary to a human HIF1A nucleic acid sequence as set forth in any one of SEQ ID NOS:

1160-1671.

52. A method for reducing the expression of a human HIF1A gene, comprising administering an mdRNA molecule of claim 40 to a cell expressing a human HIF1A gene, wherein the mdRNA molecule reduces the expression of the human HIF1A gene in the cell.

53. The method according to claim 52 wherein the cell is a human cell.

54. A double-stranded ribonucleic acid (dsRNA) molecule that down regulates the expression of any one of a human hypoxia-inducible factor 1 alpha (HIF1A) mRNA, the mdRNA molecule comprising a first strand of 15 to 40 nucleotides in length that is complementary to the human HIF1A mRNA as set forth in SEQ ID NO:

1158 or 1159, and a second strand that is complementary to the first strand.

55. The dsRNA molecule of claim 54 wherein the first strand is from 15 to 25 nucleotides in length or 26 to 40 nucleotides in length.

56. The dsRNA molecule of claim 54 wherein the dsRNA molecule has a blunt end at one or both ends of the dsRNA.

57. The dsRNA molecule of claim 54 wherein the dsRNA molecule has a 3′

-end overhang of one to four nucleotides at one or both ends of the dsRNA.

58. The dsRNA molecule of claim 54 wherein the dsRNA molecule comprises at least one 5-methyluridine, 2-thioribothymidine, or 2′

-O-methyl-5-methyluridine.

59. The dsRNA molecule of claim 54 wherein the dsRNA molecule comprises at least one locked nucleic acid (LNA) molecule, deoxy nucleotide, G clamp, 2′

-sugar modification, modified internucleoside linkage, or any combination thereof.

60. The dsRNA molecule of claim 54 wherein the dsRNA molecule has a 5′

-terminal end comprising a hydroxyl or a phosphate.

61. The dsRNA molecule of claim 54 wherein at least one pyrimidine of the dsRNA molecule comprises a pyrimidine nucleoside according to Formula I or II:

62. The dsRNA molecule of claim 61 wherein at least one nucleoside is according to Formula I and in which R¹ is methyl and R² is —

OH or —

O-methyl.

63. The dsRNA molecule of claim 61 wherein at least one R² is selected from the group consisting of 2′

-O—

(C₁-C₅) alkyl, 2′

-O-methyl, 2′

-OCH₂OCH₂CH₃, 2′

-OCH₂CH₂OCH₃, 2′

-O-allyl, and 2′

-fluoro.

64. A method for reducing the expression of a human HIF1A gene, comprising administering a dsRNA molecule of claim 54 to a cell expressing a human HIF1A gene, wherein the dsRNA molecule reduces the expression of the human HIF1A gene in the cell.

65. The method according to claim 64 wherein the cell is a human cell.

66. The dsRNA molecule of claim 54 wherein the first strand is 19 to 23 nucleotides in length and is complementary to a human HIF1A nucleic acid sequence as set forth in any one of SEQ ID NOS:

1160-1671.

67. The dsRNA molecule of claim 54 wherein the first strand is 25 to 29 nucleotides in length and is complementary to a human HIF1A nucleic acid sequence as set forth in any one of SEQ ID NOS:

1160-1671.