WO2008109368A4 - Nucleic acid compounds for inhibiting vegfr gene expression and uses thereof - Google Patents
Nucleic acid compounds for inhibiting vegfr gene expression and uses thereof Download PDFInfo
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- WO2008109368A4 WO2008109368A4 PCT/US2008/055370 US2008055370W WO2008109368A4 WO 2008109368 A4 WO2008109368 A4 WO 2008109368A4 US 2008055370 W US2008055370 W US 2008055370W WO 2008109368 A4 WO2008109368 A4 WO 2008109368A4
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- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
- 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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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P35/00—Antineoplastic agents
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- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/10—Type of nucleic acid
- C12N2310/11—Antisense
- C12N2310/111—Antisense spanning the whole gene, or a large part of it
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- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/30—Chemical structure
- C12N2310/32—Chemical structure of the sugar
- C12N2310/321—2'-O-R Modification
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- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/30—Chemical structure
- C12N2310/32—Chemical structure of the sugar
- C12N2310/323—Chemical structure of the sugar modified ring structure
- C12N2310/3231—Chemical structure of the sugar modified ring structure having an additional ring, e.g. LNA, ENA
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- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/30—Chemical structure
- C12N2310/33—Chemical structure of the base
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/50—Physical structure
- C12N2310/53—Physical structure partially self-complementary or closed
Abstract
The present disclosure provides meroduplex ribonucleic acid molecules (mdRNA) capable of decreasing or silencing VEGFR (e.g., FLTl, KDR, FLT4) 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 FLTl, KDR, or FLT4 mRNA. In addition, the meroduplex may have at least one uridine that is a 5-methyluridine, a locked nucleic acid, or optionally other modifications, and any combination thereof. Also provided are methods of decreasing expression of a VEGFR gene in a cell or in a subject to treat a VEGFR-related disease.
Claims
1. A meroduplex ribonucleic acid (mdRNA) molecule that down regulates? the expression of any one of a human FMS-like tyrosine kinase 1 (FLTl) rnRNA, human Kinase Insert Domain Receptor (KDR) mRNA, human FMS-like tyrosine kinase 4 (FLT4) mRNA, comprising a first strand of 15 to 40 nucleotides in length that is complementary to a portion of any one of a human FLTl mRNA as set forth in SEQ ID NO: 1158 or 1159, human KDR mRNA as set forth in SEQ ID NO:2468, or human FLT4 mRNA as set forth in SEQ ID NO:3036 or 3037, 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-thioribothyrnidine, 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, 2'-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 FLTl mRNA, human KDR mRNA, human FLT4 mRNA, the mdRNA molecule comprising a first strand of 15 to 40 nucleotides in length that is complementary to any one of human FLTl mRNA as set forth in SEQ ID NO:1158 or 1159, human
84 BCDR mRNA as set forth in SEQ ID NO:2468, or human FLT4 mRNA as set forth in SEQ ID NO:3036 or 3037, 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 II:
wherein:
R1 and R2 are each independently a -H, -OH, -OCH3, -OCH2OCH2CH3, -OCH2CH2OCH3, halogen, substituted or unsubstituted C1-C10 alkyl, alkoxy, alkoxyalkyl, hydroxyalkyl, carboxyalkyl, alkylsulfonylarnino, aminoalkyl, dialkylamino, alkylaminoalkyl, dialkylaminoalkyl, haloalkyl, trifluoromethyl, cycloalkyl, (cycloalkyl)alkyl, substituted or unsubstituted C2-C1O alkenyl, substituted or unsubstituted -O-allyl, -0-CH2CH=CH2, -0-CH=CHCH3, substituted or unsubstituted C2-C10 alkynyl, carbamoyl, carbamyl, carboxy, carbonylamino, substituted or unsubstituted aryl, substituted or unsubstituted aralkyl, -NH2, -NO2, -O=, or heterocyclo group,
R3 and R4 are each independently a hydroxy!, a protected hydroxyl, a phosphate, or an inteπuicleoside linking group, and
R5 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 fiom 1 to 10 unpaired nucleotides.
85
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.
11. 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 rndRNA 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 ciamp, 2'-sugar modification, modified internucleoside 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 FLTl mRNA, human KDRmRNA, human FLT4 mRNA, the mdRNA molecule comprising a first strand of 15 to 40 nucleotides in length that is complementary to any one of human FLTl mRNA as set forth in SEQ ID NO:1158 or 1159, human KDR mRNA as set forth in SEQ ID NO:2468, or human FLT4 mRNA as set forth in SEQ ID NO:3036 or 3037, 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 is 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.
86
18. The mdRNA molecule of claim 15 wherein the radRNA molecule comprises at least one 5-methyluridine, 2-thioribothymidine, or 2'-O-methyl-5- methyhαridine.
19. The mdRNA molecule of claim 15 wherein the first strand is 19 to 23 nucleotides in length and is complementary to a human FLTl nucleic acid sequence as set forth in any one of SEQ ID NOS: 1160-1796, or human KDR nucleic acid sequence as set forth in any one of SEQ ID NOS:2469-2792, or human FLT4 nucleic acid sequence as set forth in any one of SEQ ID NOS:3038-3391.
20. The mdRNA molecule of claim 15 wherein the first strand is 25 to 29 nucleotides in length and is complementary to to a human FLTl nucleic acid sequence as set forth in any one of SEQ ID NOS: 1797-2467, or human KDR nucleic acid sequence as set forth in any one of SEQ ID NOS:2793-3035, or human FLT4 nucleic acid sequence as set forth in any one of SEQ ID NOS:3392-3656.
21. A method for reducing the expression of a human FLTl , KDR, or FLT4 gene, comprising administering an mdRNA molecule according to any one of claims 1-20 to a cell expressing a human FLTl, KDR, or FLT4 gene, wherein the mdRNA molecule reduces the expression of the human FLTl, KDR, or FLT4 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 any one of a human FMS-like tyrosine kinase 1 (FLTl) mRNA, human Kinase Insert Domain Receptor (KDR) niRNA, human FMS-like tyrosine kinase 4 (FLT4) mRNA, the dsRNA molecule comprising a first strand of 26 to 40 nucleotides in length that is complementary to a portion of any one of a human FLTl mRNA as set forth in SEQ ID NO:1158 or 1159, human KDR mRNA as set forth in SEQ ID NO:2468, or human FLT4 mRNA as set forth in SEQ ID NO.-3036 or 3037, and a second strand that is complementary to the first strand, and wherein upon
87 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 clamp, 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 5'-terminal end comprising a hydroxyl or a phosphate.
30. A dsRNA molecule that down regulates the expression a human FLTl mRNA, human KDR mRNA, or human FLT4 mRNA, the dsRNA molecule comprising a first strand of 26 to 40 nucleotides in length that is complementary to a portion of any one of a human FLTl mRNA as set forth in SEQ ID NO:1158 or 1159, human KDR mRNA as set forth in SEQ ID NO:2468, or human FLT4 mRNA as set forth in SEQ ID NO:3036 or 3037, 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 I or II:
88 
wherein;
R1 and R2 are each independently a -H, -OH, -OCH3, -OCH2OCH2CH3, -OCH2CH2OCH3, halogen, substituted or unsubstituted Ci-Cio alkyl, alkoxy, alkoxyalkyl, hydroxyalkyl, carboxyalkyl, alkylsulfonylamino, aminoalkyl, dialkylamino, alkylaminoalkyl, dialkylaminoalkyl, haloalkyl, trifiuoromethyl, 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-C1O 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 Rs 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 1 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 firomthe group consisting of 2'-0-(Ci-C5) alkyl, 2'-O-methyl, 2'-OCH2OCH2CH3. 2'-OCH2CH2OCH3, 2'-O-allyl5 and 2'-fluoro.
34. The dsRNA molecule of claim 30 wherein the dsRNA molecule comprises at least one 5-methyluridine, 2-thioribothymidine, or 2'-O-methyl-5- methyluridine.
89
35. The dsRNA molecule of claim 30 wherein the dsRNA molecule comprises at least one LNA, deoxy nucleotide, G clamp, 2'-sugar modification, modified internucleoside 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 FLTl , KDR, or FLT4 gene, comprising administering a dsRNA molecule according to any one of claims 24-36 to a cell expressing a human FLTl, KDR, or FLT4 gene, wherein the dsRNA molecule reduces the expression of the human FLTl5 KDR, or FLT4 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.
90
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 (10)
| 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 | ||
| US93494107P | 2007-04-13 | 2007-04-13 | |
| US60/934,941 | 2007-04-13 | ||
| US93493207P | 2007-04-20 | 2007-04-20 | |
| US93493307P | 2007-04-20 | 2007-04-20 | |
| US60/934,933 | 2007-04-20 | ||
| US60/934,932 | 2007-04-20 |
Related Parent Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/US2008/055362 Continuation-In-Part WO2008109362A1 (en) | 2007-03-02 | 2008-02-28 | Nucleic acid compounds for inhibiting vegf gene expression and uses thereof |
Related Child Applications (3)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/US2008/055371 Continuation-In-Part WO2008109369A2 (en) | 2007-03-02 | 2008-02-28 | Nucleic acid compounds for inhibiting tnf 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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| Publication Number | Publication Date |
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| WO2008109368A2 WO2008109368A2 (en) | 2008-09-12 |
| WO2008109368A3 WO2008109368A3 (en) | 2008-12-11 |
| WO2008109368A4 true WO2008109368A4 (en) | 2009-01-29 |
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Families Citing this family (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CA2666657A1 (en) | 2006-10-18 | 2008-04-24 | Nastech Pharmaceutical Company Inc. | Nicked or gapped nucleic acid molecules and uses thereof |
| WO2019005926A1 (en) * | 2017-06-27 | 2019-01-03 | Massachusetts Eye And Ear Infirmary | Aav-crispr/cas9 genome editing of vegfr2 for treating ocular diseases |
Family Cites Families (6)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20050148530A1 (en) * | 2002-02-20 | 2005-07-07 | Sirna Therapeutics, Inc. | RNA interference mediated inhibition of vascular endothelial growth factor and vascular endothelial growth factor receptor gene expression using short interfering nucleic acid (siNA) |
| WO2003070910A2 (en) * | 2002-02-20 | 2003-08-28 | Ribozyme Pharmaceuticals, Incorporated | INHIBITION OF VASCULAR ENDOTHELIAL GROWTH FACTOR (VEGF) AND VEGF RECEPTOR GENE EXPRESSION USING SHORT INTERFERING NUCLEIC ACID (siNA) |
| US20050136437A1 (en) * | 2003-08-25 | 2005-06-23 | Nastech Pharmaceutical Company Inc. | Nanoparticles for delivery of nucleic acids and stable double-stranded RNA |
| AU2006311912A1 (en) * | 2005-11-04 | 2007-05-18 | Mdrna, Inc. | Peptide-dicer substrate RNA conjugates as delivery vehicles for siRNA |
| AU2007229161B2 (en) * | 2006-03-23 | 2012-07-12 | Roche Innovation Center Copenhagen A/S | Small internally segmented interfering RNA |
| CA2666657A1 (en) * | 2006-10-18 | 2008-04-24 | Nastech Pharmaceutical Company Inc. | Nicked or gapped nucleic acid molecules and uses thereof |
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| Publication number | Publication date |
|---|---|
| WO2008109368A3 (en) | 2008-12-11 |
| WO2008109368A2 (en) | 2008-09-12 |
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