WO2008109372A4 - Nucleic acid compounds for inhibiting pdgf gene expression and uses thereof - Google Patents
Nucleic acid compounds for inhibiting pdgf gene expression and uses thereof Download PDFInfo
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- WO2008109372A4 WO2008109372A4 PCT/US2008/055374 US2008055374W WO2008109372A4 WO 2008109372 A4 WO2008109372 A4 WO 2008109372A4 US 2008055374 W US2008055374 W US 2008055374W WO 2008109372 A4 WO2008109372 A4 WO 2008109372A4
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- C12N15/113—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
- C12N15/1138—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 against receptors or cell surface proteins
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- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/10—Type of nucleic acid
- C12N2310/14—Type of nucleic acid interfering N.A.
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Abstract
The present disclosure provides meroduplex ribonucleic acid molecules (mdRNA) capable of decreasing or silencing PDGF 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 PDGF mRNA. In addition, the meroduplex may have at least one uridine substituted with a 5-methyluridine, a nucleoside replaced with a locked nucleic acid, or optionally other modifications, and any combination thereof. Also provided are methods of decreasing expression of a PDGF gene in a cell or in a subject to treat a PDGF -related disease.
Claims
1. A meroduplex ribonucleic acid (mdRNA) molecule that down regulates the expression of a human platelet-derived growth factor (PDGF) mRNA, the mdKNA molecule comprising a first strand of 15 to 40 nucleotides in length that is complementary to any one of PDGFA mRNA as set form in SEQ ID NO: 1158 or 1159, human PDGFB mRNA as set forth in SEQ ID NO: 1544 or 1545, human PDGFC mRNA as set forth in SEQ ID NO:2104, or human PDGFD mRNA as set forth in SEQ ID NO:2396 or 2397, 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.
2. The mdRNA molecule of claim 1 wherein the first strand is 15 to 25 nucleotides in length or 26 to 40 nucleotides in length.
3. The mdRNA molecule of claim 1 wherein the gap comprises from 1 to 10 unpaired nucleotides.
4. The mdRNA molecule of claim 1 wherein the mdRNA molecule comprises at least one 5-methyluridine, 2-thioribothymidine, or 2'-O-methyl-5- methyluridine.
5. The mdRNA molecule of claim 1 wherein the mdRNA molecule comprises at least one locked nucleic acid (LNA) molecule, deoxy nucleotide, G clamp, 21 -sugar modification, modified intemucleoside linkage, or any combination thereof.
6. The mdRNA molecule of claim 1 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.
7. An mdRNA molecule that down regulates the expression of a human PDGF mRNA, the mdRNA molecule comprising a first strand of 15 to 40 nucleotides in length that is complementary to any one of human PDGFA mRNA as set forth in SEQ ID NO: 1158 or 1159, human PDGFB mRNA as set forth in SEQ ID NO: 1544 or 1545, human PDGFC mRNA as set forth in SEQ ID NO.2104, or human PDGFD
85 mRNA as set forth in SEQ ID NO:2396 or 2397, 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, and wherein at least one pyrimidine of the mdRNA molecule is a pyrimidine nucleoside according to Formula I or
wherein:
R1 and R2 are each independently a -H, -OH, -OCH3, -OCH2OCH2CH3, -OCH2CH2OCH3, halogen, substituted or unsubstituted Ci-C10 alkyl, alkoxy, alkoxyalkyl, hydroxyalkyl, carboxyalkyl, alkylsulfonylamino, aminoalkyl, dialkylamino, alkylaminoalkyl, dialkylaminoalkyl, haloalkyl, trifluoromethyl, cycloalkyl, (cycloalkyl)alkyl, substituted or unsubstituted C2-C 10 alkenyl, substituted or unsubstituted -O-allyl, -0-CH2CH=CH2, -0-CH=CHCH3, substituted or unsubstituted C2-C 10 alkynyl, carbamoyl, carbamyl, carboxy, carbonylamino, substituted or unsubstituted aryl, substituted or unsubstituted aralkyl, -NH2, -NO2, -C≡, or heterocyclo group,
R3 and R4 are each independently a hydroxyl, a protected hydroxyl, a phosphate, or an internucleoside linking group, and
R3 and R8 are each independently O or S.
8. The mdRNA molecule of claim 7 wherein the first strand is 15 to 25 nucleotides in length or 26 to 40 nucleotides in length.
9. The mdRNA molecule of claim 7 wherein the gap comprises from 1 to 10 unpaired nucleotides.
86
10. The mdRNA molecule of claim 7 wherein at least one nucleoside is according to Formula I and in which R1 is methyl and R2 is -OH or -O-methyl.
1 1. The mdRNA molecule of claim 7 wherein at least one R2 is selected from the group consisting of 2'-0-(Ci-C5) alkyl, 2'-O-methyl, 2'-OCH2OCH2CH3, 2'-OCH2CH2OCH3, 2'-O-allyl, and fluoro.
12. The mdRNA molecule of claim 7 wherein the mdRNA molecule comprises at least one 5-methyluridine, 2-thioribothymidine, or 2'-O-methyl-5- methyluridine.
13. The mdRNA molecule of claim 7 wherein the mdRNA molecule comprises at Least one locked nucleic acid (LNA) molecule, deoxy nucleotide, G clamp, 2'-sugar modification, modified intemucleoside linkage, or any combination thereof.
14. The mdRNA molecule of claim 7 wherein contains an overhang of one to four nucleotides on at least one 3'-end that is not a part of the gap or the dsRNA molecule has a blunt end on one or both ends of the mdRNA molecule.
15. An mdRNA molecule that down regulates the expression of a human PDGF mRNA, the mdRNA molecule comprising a first strand that is complementary to any one of human PDGFA mRNA as set forth in SEQ ID NO: 1158 or 1159, human PDGFB mRNA as set forth in SEQ ID NO: 1544 or 1545, human PDGFC mRNA as set forth in SEQ ID NO.2104, or human PDGFD mRNA as set forth in SEQ ID NO:2396 or 2397, 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, and wherein the double-stranded regions have a combined length of about 15 base pairs to about 40 base pairs.
16. The mdRNA molecule of claim 15 wherein the first strand i s 15 to 25 nucleotides in length or 26 to 40 nucleotides in length.
17. The mdRNA molecule of claim 15 wherein the gap comprises from 1 to 10 unpaired nucleotides.
87
18. The mdRN A molecule of claim 15 wherein the mdRN A molecule comprises at least one 5-methyluridine, 2-thioribothymidine, or 2'-O-methyl-5- methyluridine.
19. The mdRNA molecule of claim 15 wherein the first strand is 19 to 23 nucleotides in length and is complementary to a human PDGFA nucleic acid sequence as set forth in any one of SEQ ID NOS: 1160-1380, or human PDGFB nucleic acid sequence as set forth in any one of SEQ ID NOS: 1546-1864, human PDGFC nucleic acid sequence as set forth in any one of SEQ ID NOS :2105-2270, or human PDGFD nucleic acid sequence as set forth in any one of SEQ ID NOS.2398-2620.
20. The mdRNA molecule of claim 15 wherein the first strand is 25 to 29 nucleotides in length and is complementary to a human PDGFA nucleic acid sequence as set forth in any one of SEQ ID NOS:1381-1543, or human PDGFB nucleic acid sequence as set forth in any one of SEQ ID NOS: 1865-2103, human PDGFC nucleic acid sequence as set forth in any one of SEQ ID NOS:2271-2395, or human PDGFD nucleic acid sequence as set forth in any one of SEQ ID NOS :2621 -2932.
21. A method for reducing the expression of a human PDGF gene, comprising administering an mdRNA molecule according to any one of claims 1-22 to a cell expressing a human PDGF gene, wherein the mdRNA molecule reduces the expression of the PDGF gene in the cell.
22. The method according to claim 21 wherein the cell is a human cell.
23. Use of an mdRNA as defined in any one of the preceding claims for the manufacture of a medicament for use in the therapy of a hyperproliferative or inflammatory disease.
24. A double-stranded ribonucleic acid (dsRNA) molecule that down regulates the expression of a human platelet-derived growth factor (PDGF) mRNA, the dsRNA molecule comprising a first strand of 26 to 40 nucleotides in length that is complementary to any one of PDGFA mRNA as set forth in SEQ ID NO: 1 158 or
1159, human PDGFB mRNA as set forth in SEQ ID NO: 1544 or 1545. human PDGFC mRNA as set forth in SEQ ID NO:2104, or human PDGFD mRNA as set forth in SEQ ID NO:2396 or 2397, and a second strand that is complementary to the
88 first strand, and wherein upon annealing of the first strand and the second strand the dsRNA has a 3' overhang and a blunt end.
25. The dsRNA molecule of claim 24 wherein the first strand is from 27 to 35 nucleotides in length.
26. The dsRNA molecule of claim 24 wherein the dsRNA molecule comprises at least one 5-methyluridine, 2-thioribothymidine, or 2'-O-methyl-5- methyluridine.
27. The dsRNA molecule of claim 24 wherein the dsRNA molecule comprises at least one locked nucleic acid (LNA) molecule, deoxy nucleotide, G clarnp, 2'-sugar modification, modified internucleoside linkage, or any combination thereof.
28. The dsRNA molecule of claim 24 wherein the 3'-overhang has from one to four nucleotides and is on the first strand.
29. The dsRNA molecule of claim 24 wherein the dsRNA molecule has a S'-teπninal end comprising a hydroxyl or a phosphate.
30. A dsRNA molecule that down regulates the expression of a human PDGF mRNA, the dsRNA molecule comprising a first strand of 26 to 40 nucleotides in length that is complementary to any one of PDGFA mRNA as set forth in SEQ ID NO:1158 or 1159, human PDGFB mRNA as set forth in SEQ ID NO: 1544 or 1545, human PDGFC mRNA as set forth in SEQ ID NO:2104, or human PDGFD mRNA as set forth in SEQ ID NO:2396 or 2397, and a second strand that is complementary to the first strand, and wherein upon annealing of the first strand and the second strand the dsRNA has a 3' overhang and a blunt end, and wherein at least one pyrimidine of the dsRNA molecule comprises a pyrimidine nucleoside according to Formula 1 or II:
R1 and R2 are each independently a -H, -OH, -OCH3, -OCH2OCH2CH3, -OCH2CH2OCH3, halogen, substituted or unsubstituted Ci -C 10 alkyl, alkoxy, alkoxyalkyl, hydroxy alkyl, carboxyalkyl, alkylsulfonylamino, aminoalkyl, dialkylamino, alkylaminoalkyl, dialkylaminoalkyl, haloalkyl, trifluoromethyl, cycloalkyl, (cycloalkyl)alkyls substituted or unsubstituted C2-CiO alkenyl, substituted or unsubstituted -O-allyl, -0-CH2CH=CH2, -0-CH=CHCH3, substituted or unsubstituted C2-C 10 alkynyl, carbamoyl, carbamyl, carboxy, carbonylamino, substituted or unsubstituted aryl, substituted or unsubstituted aralkyl, -NH2, -NO2, -C≡N, or heterocyclo group,
R3 and R4 are each independently a hydroxyl, a protected hydroxyl, a phosphate, or an internucleoside linking group, and
R5 and R8 are each independently O or S.
31. The dsRNA molecule of claim 30 wherein the first strand is from 27 to 35 nucleotides in length.
32. The dsRNA molecule of claim 30 wherein at least one nucleoside is according to Formula I and in which R1 is methyl and R2 is -OH or -O-methyl.
33. The dsRNA molecule of claim 30 wherein at least one R2 is selected from the group consisting of 2'-0-(C1-C5) alkyl, 2'-O-methyl, 2'-OCH2OCH2CH3, 2'-OCH2CH2OCH3, 2'-O-allyl, and 2'-fluoro.
34. The dsRNA molecule of claim 30 wherein the dsRNA molecule comprises at least one 5-methyluridine, 2-thioribothymidi-ie, or 2'-O-methyl-5- methyluridine.
90
35. The dsRNA molecule of claim 30 wherein the dsRNA molecule comprises at least one LNA, deoxy nucleotide, G clamp, 2'-sugar modification, modified intemucleoside linkage, or any combination thereof.
36. The dsRNA molecule of claim 30, wherein the 3'-overhang has from one to four nucleotides and is on the first strand.
37. A method for reducing the expression of a human PDGF gene, comprising administering a dsRNA molecule according to any one of claims 24-36 to a cell expressing a PDGF gene, wherein the dsRNA molecule reduces the expression of the PDGF family gene in the cell.
38. The method according to claim 37 wherein the cell is a human cell.
39. Use of a dsRNA molecule as defined in any one of claims 24-38 for the manufacture of a medicament for use in the therapy of a hyperproliferative or inflammatory disease.
91
Priority Applications (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US12/552,082 US20100105134A1 (en) | 2007-03-02 | 2009-09-01 | Nucleic acid compounds for inhibiting gene expression and uses thereof |
US13/327,545 US20130011922A1 (en) | 2007-03-02 | 2011-12-15 | Nucleic acid compounds for inhibiting gene expression and uses thereof |
Applications Claiming Priority (12)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US93494007P | 2007-03-02 | 2007-03-02 | |
US60/934,940 | 2007-03-02 | ||
US93493007P | 2007-03-16 | 2007-03-16 | |
US60/934,930 | 2007-03-16 | ||
US93492107P | 2007-05-24 | 2007-05-24 | |
US60/934,921 | 2007-05-24 | ||
US93296807P | 2007-05-30 | 2007-05-30 | |
US93296907P | 2007-05-30 | 2007-05-30 | |
US60/932,968 | 2007-05-30 | ||
US60/932,969 | 2007-05-30 | ||
US93296707P | 2007-06-01 | 2007-06-01 | |
US60/932,967 | 2007-06-01 |
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PCT/US2008/055357 Continuation-In-Part WO2008109359A1 (en) | 2007-03-02 | 2008-02-28 | Nucleic acid compounds for inhibiting pdgfr family gene expression and uses thereof |
Related Child Applications (3)
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PCT/US2008/055360 Continuation-In-Part WO2008109361A1 (en) | 2007-03-02 | 2008-02-28 | Nucleic acid compounds for inhibiting erbb family gene expression and uses thereof |
AU2009212920A Division AU2009212920A1 (en) | 2007-03-02 | 2009-09-01 | Nucleic acid compounds for inhibiting gene expression and uses thereof |
US12/552,082 Continuation-In-Part US20100105134A1 (en) | 2007-03-02 | 2009-09-01 | Nucleic acid compounds for inhibiting gene expression and uses thereof |
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WO2008109372A2 WO2008109372A2 (en) | 2008-09-12 |
WO2008109372A3 WO2008109372A3 (en) | 2009-02-26 |
WO2008109372A4 true WO2008109372A4 (en) | 2009-04-30 |
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PCT/US2008/055374 WO2008109372A2 (en) | 2007-03-02 | 2008-02-28 | Nucleic acid compounds for inhibiting pdgf gene expression and uses thereof |
PCT/US2008/055550 WO2008109469A2 (en) | 2007-03-02 | 2008-02-29 | Nucleic acid compounds for inhibiting pcna gene expression and uses thereof |
PCT/US2008/055560 WO2008109474A1 (en) | 2007-03-02 | 2008-02-29 | Nucleic acid compounds for inhibiting fgf2 gene expression and uses thereof |
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PCT/US2008/055550 WO2008109469A2 (en) | 2007-03-02 | 2008-02-29 | Nucleic acid compounds for inhibiting pcna gene expression and uses thereof |
PCT/US2008/055560 WO2008109474A1 (en) | 2007-03-02 | 2008-02-29 | Nucleic acid compounds for inhibiting fgf2 gene expression and uses thereof |
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Families Citing this family (4)
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JP5876637B2 (en) | 2006-10-18 | 2016-03-02 | マリーナ バイオテック,インコーポレイテッド | Nicked or gapped nucleic acid molecules and their use |
CN103597074A (en) * | 2011-06-16 | 2014-02-19 | Isis制药公司 | Antisense modulation of fibroblast growth factor receptor 4 expression |
WO2017134526A1 (en) | 2016-02-02 | 2017-08-10 | Olix Pharmaceuticals, Inc. | Treatment of angiogenesis-associated diseases using rna complexes that target angpt2 and pdgfb |
WO2019002536A1 (en) * | 2017-06-30 | 2019-01-03 | Hummingbird Diagnostics Gmbh | Novel mirna biomarkers and use thereof |
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EP1710307A3 (en) * | 2002-02-20 | 2007-06-06 | Sirna Therapeutics, Inc. | RNA interference mediated inhibition of gene expression using short interfering nucleic acid (siNA) |
AU2003219781A1 (en) * | 2002-02-20 | 2003-09-09 | Sirna Therapeutics, Inc | RNA INTERFERENCE MEDIATED INHIBITION OF PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA) GENE EXPRESSION USING SHORT INTERFERING NUCLEIC ACID (siNA) |
US20080199438A1 (en) * | 2004-03-16 | 2008-08-21 | Dnavec Research Inc. | Methods For Suppressing Tumor Proliferation |
JP2008174450A (en) * | 2005-04-21 | 2008-07-31 | Univ Nihon | Composition for preservation of vascular endothelium |
WO2007056153A2 (en) * | 2005-11-04 | 2007-05-18 | Nastech Pharmaceutical Company Inc. | Peptide-dicer substrate rna conjugates as delivery vehicles for sirna |
US8329888B2 (en) * | 2006-03-23 | 2012-12-11 | Santaris Pharma A/S | Small internally segmented interfering RNA |
JP5876637B2 (en) * | 2006-10-18 | 2016-03-02 | マリーナ バイオテック,インコーポレイテッド | Nicked or gapped nucleic acid molecules and their use |
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- 2008-02-28 WO PCT/US2008/055374 patent/WO2008109372A2/en active Application Filing
- 2008-02-29 WO PCT/US2008/055550 patent/WO2008109469A2/en active Application Filing
- 2008-02-29 WO PCT/US2008/055560 patent/WO2008109474A1/en active Application Filing
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Publication number | Publication date |
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WO2008109469A2 (en) | 2008-09-12 |
WO2008109474B1 (en) | 2008-11-13 |
WO2008109469A4 (en) | 2009-04-09 |
WO2008109469A3 (en) | 2008-12-24 |
WO2008109474A1 (en) | 2008-09-12 |
WO2008109372A2 (en) | 2008-09-12 |
WO2008109372A3 (en) | 2009-02-26 |
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