Oligonucleotides containing N-2 substituted purines

• US 5,587,469 A
• Filed: 08/30/1995
• Issued: 12/24/1996
• Est. Priority Date: 01/11/1990
• Status: Expired due to Term

• Current Assignee: ISIS Pharmaceuticals Incorporated
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Manoharan, Muthiah, Cook, Phillip D., Ramasamy, Kanda S.
• Primary Examiner(s): Wilson, James O.
• Application Number:
  US08/473,450
• Time in Patent Office: 482 Days
• Field of Search: 536/27.6, 536/27.13, 536/22.1, 536/23.1
• US Class Current: 536/23.1
• 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 47/51 the non-active ingredient being a modifying agent
• 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: A61P 31/12 Antivirals
• 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: 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 15/1131 against viruses
• CPC Class Codes: C12N 15/1132 against retroviridae, e.g. HIV
• CPC Class Codes: C12N 15/1133 against herpetoviridae, e.g. HSV
• CPC Class Codes: C12N 15/1135 against oncogenes or tumor suppressor genes
• CPC Class Codes: C12N 15/1137 against enzymes viral enzymes C12N15/1131; receptors C12N15/1138
• CPC Class Codes: C12N 15/1138 against receptors or cell surface proteins
• CPC Class Codes: C12N 2310/3125 Methylphosphonates
• CPC Class Codes: C12N 2310/315 : Phosphorothioates
• CPC Class Codes: C12N 2310/318 : where the PO2 is completely replaced, e.g. MMI or formacetal
• 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 2310/3521 : 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 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: C12Y 113/11012 : Linoleate 13S-lipoxygenase (1.13.11.12)

Abstract

This invention presents novel purine-based compounds for inclusion into oligonucleotides. The compounds of the invention, when incorporated into oligonucleotides are especially useful as "antisense" agents--agents that are capable of specific hybridization with a nucleotide sequence of an RNA. Oligonucleotides are used for a variety of therapeutic and diagnostic purposes, such as treating diseases, regulating gene expression in experimental systems, assaying for RNA and for RNA products through the employment of antisense interactions with such RNA, diagnosing diseases, modulating the production of proteins, and cleaving RNA in site specific fashions. The compounds of the invention include novel heterocyclic bases, nucleosides, and nucleotides. When incorporated into oligonucleotides, the compounds of the invention can be useful for modulating the activity of RNA.

Claims

1. An oligonucleotide having at least one nucleotide of formula:

##STR7## wherein G is CH or N;

X is NH₂ or OH;

Y is RQ or NHRQ, wherein said R is a hydrocarbyl group having from 2 to about 20 carbon atoms; and

Q is H, NH₂, polyalkylamino, hydrazines, hydroxylamines, imidazoles, imidazole amides, alkylimidazoles, tetrazole, triazole, or alkoxy groups; and

Z is ribose, 2'"'"'-O alkyl ribose, or deoxyribose.

3. The compound of claim 1 wherein Q is imidazole, imidazole amide, alkylimidazole, tetrazole, or triazole.

4. The oligonucleotide of claim 1 wherein Q is imidazole, an imidazole amide or an alkylimidazole.

5. The oligonucleotide of claim 1 wherein Y is RQ, said Q is an imidazole.

6. The oligonucleotide of claim 1 wherein Y is NHRQ, said Q is an imidazole.

7. The oligonucleotide of claim 1 wherein G is N;

X is NH₂ ;

Y is NHRQ, said R is a lower alkane; and

Q is an imidazole.

8. The oligonucleotide of claim 7 wherein said R is an alkane having between about 2 to about 4 carbon atoms.

9. The oligonucleotide of claim 7 wherein R is propyl.

10. The oligonucleotide of claim 1 wherein G is N;

X is OH;

Y is NHRQ, said R is a lower alkane; and

Q is an imidazole.

11. The oligonucleotide of claim 10 wherein R is an alkane having between about 2 to about 4 carbon atoms.

12. The oligonucleotide of claim 10 wherein R is propyl.

13. The oligonucleotide of claim 10 wherein R is ethyl.

14. The oligonucleotide of claim 10 wherein R is isobutyryl and Q is a methyl-imidazole.

15. The oligonucleotide of claim 1 wherein G is N;

X is NH₂ ;

Y is NHRQ, said Q is H and R is an alkane having from about 5 to about 20 carbon atoms.

16. The oligonucleotide of claim 1 wherein G is N;

X is OH;

Y is NHRQ, said Q is H and R is an alkane having from about 5 to about 20 carbon atoms.

17. The oligonucleotide of claim 16 wherein R is nonyl.

18. The oligonucleotide of claim 16 wherein R is isobutyrylnonane.

19. The oligonucleotide of claim 1 wherein Y is RQ, said R is a lower alkane;

and Q is an amine, wherein said amine is selected from the group consisting of NH₂, polyalkylamine, hydrazine (--NH--NH--), and hydroxylamine (N--NH--OH).

20. The oligonucleotide of claim 1 wherein Y is NHRQ, said R is a lower alkane;

and Q is an amine, wherein said amine comprises is selected from the group consisting of NH₂, polyalkylamine, hydrazine (--NH--NH--), and hydroxylamine (--NH--OH).

21. The oligonucleotide of claim 1 wherein G is N;

X is NH₂ ;

Y is NHRQ, said R is a lower alkane; and

Q is an amine, wherein said amine is selected from the group consisting of NH₂, polyalkylamine, hydrazine (--NH--NH--), and hydroxylamine (--NH--OH).

22. The compound of claim 21 wherein said amine is NH₂.

23. The oligonucleotide of claim 1 wherein G is N;

X is OH;

Y is NHRQ, said R is a lower alkane; and

Q is an amine, wherein said amine is selected from the group consisting of NH₂, polyalkylamine, hydrazines (--NH--NH--), and hydroxylamines (--NH--OH).

24. The oligonucleotide of claim 23 wherein said amine is NH₂.

25. The oligonucleotide of claim 23 wherein R is hexane and Q is NH₂.

26. The oligonucleotide of claim 1 wherein Y is NHRQ, said Q is an alkoxy group.

27. The oligonucleotide of claim 1 wherein Y is RQ, said Q is an alkoxy group.

28. The oligonucleotide of claim 1 further having a phosphate group at the 3'"'"' position of the ribose or deoxyribose.

29. The oligonucleotide of claim 28 wherein said phosphate is a methylphosphonate, phosphorothioate, phosphoramidite, or a phosphorotriester.

2. An oligonucleotide having at least one nucleotide of formula:

##STR8## wherein G is CH or N;

X is NH₂ or OH;

Y is R-aminoalkylamino or NHR-aminoalkylamino, wherein said R is a hydrocarbyl group having from 2 to about 20 carbon atoms; and

Z is ribose, 2'"'"'-O alkyl ribose, or deoxyribose.