Methods for identifying antiviral oligonucleotides

• US 20040170959A1
• Filed: 09/12/2003
• Published: 09/02/2004
• Est. Priority Date: 09/13/2002
• Status: Abandoned Application

• Current Assignee: Replicor Inc.
• Original Assignee: Replicor Inc.
• Inventors: Juteau, Jean-Marc, Vaillant, Andrew
• Application Number:
  US10/661,355
• Publication Number:
  US 20040170959A1
• Time in Patent Office: Days
• US Class Current: 435/5
• CPC Class Codes: A61K 2300/00 Mixtures or combinations of active ingredients, wherein at least one active ingredient is fully defined in groups A61K31/00 - A61K41/00
• CPC Class Codes: A61K 31/7088 Compounds having three or more nucleosides or nucleotides
• 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 45/06 Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 25/28 for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
• CPC Class Codes: A61P 31/12 Antivirals
• CPC Class Codes: A61P 31/14 for RNA viruses
• CPC Class Codes: A61P 31/16 for influenza or rhinoviruses
• CPC Class Codes: A61P 31/18 for HIV
• CPC Class Codes: A61P 31/20 for DNA viruses
• CPC Class Codes: A61P 31/22 for herpes viruses
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C12N 15/11 DNA or RNA fragments; Modified forms thereof DNA or RNA not used in recombinant technology, C07H21/00; Non-coding nucleic acids having a biological activity
• CPC Class Codes: C12N 15/115 Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith ; Nucleic acids binding to non-nucleic acids, e.g. aptamers
• CPC Class Codes: C12N 2310/3125 Methylphosphonates
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/351 Conjugate
• CPC Class Codes: C12N 2310/3521 Methyl
• CPC Class Codes: Y02A 50/30 : Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Abstract

Random sequence oligonucleotides that have antiviral activity are described, along with their use as antiviral agents. In many cases, the oligonucleotides are greater than 40 nucleotides in length. Also described are methods for the prophylaxis or treatment of a viral infection in a human or animal, and a method for the prophylaxis treatment of cancer caused by oncoviruses in a human or animal. The methods typically involve administering to a human or animal in need of such treatment, a pharmacologically acceptable, therapeutically effective amount of at least oligonucleotide that does not act by a sequence complementary mode of action.

Claims

1. A method of screening to identify a compound that alters binding of an oligonucleotide to at least one viral component, said method comprising

in separate reactions, contacting said oligonucleotide with said viral component in the presence and absence of a compound to be screened;

and

determining whether a difference occurs in binding of said oligonucleotide to said viral component in the presence of said compound compared to in the absence of said compound, the presence of said difference being indicative of said compound altering the binding of said oligonucleotide to said viral component.

2. The method of claim 1, wherein said compound is a small molecule.

3. The method of claim 1, wherein at least 1000 compounds are screened.

4. The method of claim 1, wherein at least 10,000 compounds are screened.

5. The method of claim 1, wherein said viral component is from a DNA virus.

6. The method of claim 1, wherein said viral component is from a RNA virus.

7. The method of claim 1, wherein said viral component is from HIV.

8. The method of claim 1, wherein said viral component is from HSV.

9. The method of claim 1, wherein said viral component is from RSV.

10. The method of claim 1, wherein said oligonucleotide is at least 2 nucleotides in length.

11. The method of claim 1, wherein said oligonucleotide is at least 5 nucleotides in length.

12. The method of claim 1, wherein said oligonucleotide is at least 10 nucleotides in length.

13. The method of claim 1, wherein said oligonucleotide is at least 15 nucleotides in length.

14. The method of claim 1, wherein said oligonucleotide is at least 20 nucleotides in length.

15. The method of claim 1, wherein said oligonucleotide is at least 30 nucleotides in length.

16. The method of claim 1, wherein said oligonucleotide is at least 40 nucleotides in length.

17. The method of claim 1, wherein said oligonucleotide is at least 80 nucleotides in length.

18. A novel antiviral compound identified by the method of claim 1.

19. A method for purifying oligonucleotides binding to at least one viral component from a pool of oligonucleotides comprising:

contacting said pool with at least one viral component;

displacing bound oligonucleotides of said pool from said component; and

collecting displaced oligonucleotides.

20. The method of claim 19, further comprising sequencing, and testing antiviral activity of collected displaced oligonucleotides.

21. The method of claim 19, wherein said viral component is bound to a solid phase medium.

22. The method of claim 20, wherein said displaced oligonucleotides are further chemically modified oligonucleotides.

31. An antiviral oligonucleotide preparation comprising one or more oligonucleotides identified using a method of claim 19 or 23, wherein said oligonucleotides in said oligonucleotide preparation exhibit higher mean binding affinity with one or more of said viral components than the mean binding affinity of oligonucleotides in the initial oligonucleotide pool.

32. The antiviral oligonucleotide preparation of claim 31, wherein the mean binding affinity of said oligonucleotides is at least two-fold greater than the mean binding affinity of oligonucleotides in the initial oligonucleotide pool.

23. A method for enriching oligonucleotides from a pool of oligonucleotides binding to at least one viral component, comprising:

contacting said pool with at least one viral component; and

amplifying oligonucleotides bound to said viral components to provide an enriched oligonucleotide pool.

24. The method of claim 23, wherein said contacting and amplifying are performed at least one additional time using said enriched oligonucleotide pool as the pool of oligonucleotides, thereby providing at least one further enriched oligonucleotide pool.

25. The method of claim 23, further comprising sequencing and testing antiviral activity of oligonucleotides in said enriched oligonucleotide pool.

26. The method of claim 24, further comprising sequencing and testing antiviral activity of oligonucleotides in at least one further enriched oligonucleotide pool.

27. The method of claim 23, wherein the oligonucleotides in said enriched oligonucleotide pool exhibit higher mean binding affinity with one or more of said viral components than the mean binding affinity of oligonucleotides in the initial pool of oligonucleotides.

28. The method of claim 26, wherein said oligonucleotides are further chemically modified.

29. The method of claim 23, further comprising selecting at least one oligonucleotide from said enriched oligonucleotide pool.

30. The method of claim 29, wherein said selecting comprises eliminating oligonucleotides from said enriched oligonucleotide pool having sequences identical to a sequence from the virus or viruses from which said viral components are derived.