Compositions and methods for modulating RNA

• US 6,610,663 B2
• Filed: 10/10/2001
• Issued: 08/26/2003
• Est. Priority Date: 01/11/1990
• Status: Expired due to Fees

• Current Assignee: ISIS Pharmaceuticals Incorporated
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Griffey, Richard, Bruice, Thomas, Guinosso, Charles John, Cook, Phillip Dan, Kawasaki, Andrew Mamoru
• Primary Examiner(s): FREDMAN, JEFFREY NORMAN
• Application Number:
  US09/974,326
• Publication Number:
  US 20020160972A1
• Time in Patent Office: 685 Days
• Field of Search: 536/23.1, 536/24.5, 536/221, 514/44, 435/6
• US Class Current: 514/44.00A
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• 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: C07H 19/04 Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 19/16 Purine radicals
• CPC Class Codes: C07H 19/20 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C07H 23/00 Compounds containing boron, silicon, or a metal, e.g. chelates, vitamin B12 esters with inorganic acids C07H11/00; metal salts, see parent compounds
• CPC Class Codes: C07J 43/003 not condensed
• CPC Class Codes: C07K 14/005 from viruses
• 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 2310/3125 Methylphosphonates
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/32 of the sugar
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/33 of the base
• CPC Class Codes: C12N 2310/333 Modified A
• CPC Class Codes: C12N 2310/336 : Modified G
• CPC Class Codes: C12N 2310/3511 : intercalating or cleaving agent
• CPC Class Codes: C12N 2310/3521 : Methyl
• CPC Class Codes: C12N 2310/3523 : Allyl
• CPC Class Codes: C12N 2310/3527 : Other alkyl chain
• CPC Class Codes: C12N 2310/3531 : Hydrogen
• CPC Class Codes: C12N 2310/3533 : Halogen
• CPC Class Codes: C12N 2740/16322 : New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12N 9/0069 : acting on single donors with incorporation of molecular oxygen, i.e. oxygenases (1.13)
• CPC Class Codes: C12Q 1/68 : involving nucleic acids
• CPC Class Codes: C12Q 1/6813 : Hybridisation assays
• CPC Class Codes: C12Y 113/11012 : Linoleate 13S-lipoxygenase (1.13.11.12)

Abstract

Compositions and methods for modulating the activity of RNA are disclosed. In accordance with preferred embodiments, antisense compositions are prepared comprising targeting and reactive portions. The reactive portions preferably comprise one or two imidazole functionalities conjugated to the targeting oligonucleotide via linkers with or without intervening intercalating moieties. Therapeutics, diagnostics and research methods also are disclosed, as are synthetic nucleosides and nucleoside fragments that can be elaborated into oligonucleotides.

Claims

1. A method for modulating the activity of RNA, comprising contacting said RNA with a composition comprising:

a targeting portion specifically hybridizable with a preselected nucleotide sequence of the RNA; and

a portion which is capable of cleaving a phosphodiester bond in said RNA and which comprises a compound of the structure;

4. The method of claim 1, wherein said —

G₂—

G₃ has one of the structures;

wherein;

R_A is aryl, substituted aryl, or nitrogen heterocyclic;

R_C is H, O⁻

, COO⁻

, OR_G, NH₂, C(R_G)(R_H)(R_I), N(R_G)(R_H)(R_I), Cl, Br, F, CF₃, SR_G, NHC(O)R_G, OC(O)R_G, NO, nitrogen heterocyclic or another electron donating group;

R_D is (CH₂)_q;

R_E is H, (CH₂)_n—

R_J, or a chemical functional group comprising R_J;

R_F is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl or C₂-C₂₀ alkynyl, aryl, or cycloalkyl;

R_G, R_H, and R_I are, independently, H, C₁-C₁₀ alkyl, or substituted alkyl;

R_J is H, nitrogen heterocyclic, a positively charged group, or a phosphoryl hydrogen bond donating group;

R_K is alkyl, acyl or acyl-alkyl;

Z is NH₂ or CH₂;

R_L is H or OH;

n is from about 1 to about 5; and

q is from about 0 to about 5.

2. A method for modulating the activity of RNA, comprising contacting said RNA with a composition comprising:

a targeting portion specifically hybridizable with a preselected nucleotide sequence of the RNA; and

a portion which is capable of intercalating with and cleaving said RNA and which comprises a compound of the structure;

5. The method of claim 2 wherein said —

G₂—

G₃ has one of the structures;

wherein;

R_A is aryl, substituted aryl, or nitrogen heterocyclic;

R_C is H, O⁻

, COO⁻

, OR_G, NH₂, C(R_G)(R_H)(R_I), N(R_G)(R_H) (R_I), Cl, Br, F, CF₃, SR_G, NHC(O)R_G, OC(O)R_G, NO, nitrogen heterocyclic or another electron donating group;

R_D is (CH₂)q;

R_E is H, (CH₂)_n—

R_J, or a chemical functional group comprising R_J;

R_F is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl or C₂-C₂₀ alkynyl, aryl, or cycloallcyl;

R_G, R_H, and R_I are, independently, H, C₁-C₁₀ alkyl, or substituted alkyl;

R_J is H, nitrogen heterocyclic, a positively charged group, or a phosphoryl hydrogen bond donating group;

R_K is alkyl, acyl or acyl-alkyl;

Z is NH₂ or CH₂;

R_L is H or OH;

n is from about 1 to about 5; and

q is from about 0 to about 5.

3. A method for modulating the activity of RNA, comprising contacting said RNA with with a composition comprising:

a targeting portion specifically hybridizable with a preselected nucleotide sequence of the RNA; and

a ribofuranosyl nucleotide which bears at its 2′

site a reactive portion capable of intercalating and cleaving RNA.

6. The method of claim 3 wherein said —

G₂—

G₃ has one of the structures;

wherein;

R_A is aryl, substituted aryl, or nitrogen heterocyclic;

R_C is H, O⁻

, COO⁻

, OR_G, NH₂, C(R_G)(R_H) (R_I), N(R_G)(R_H)(R_I), Cl, Br, F, CF₃, SR_G, NHC(O)R_G, OC(O)R_G, NO, nitrogen heterocyclic or another electron donating group;

R_D is (CH₂)q;

R_E is H, (CH₂)_n—

R_J, or a chemical functional group comprising R_J;

R_F is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl or C₂-C₂₀ alkynyl, aryl, or cycloalkyl;

R_G, R_H, and R_I are, independently, H, C₁-C₁₀ alkyl, or substituted alkyl;

R_J is H, nitrogen heterocyclic, a positively charged group, or a phosphoryl hydrogen bond donating group;

R_K is alkyl, acyl or acyl-alkyl;

Z is NH₂ or CH₂;

R_L is H or OH;

n is from about 1 to about 5; and

q is from about 0 to about 5.