Oligoribonucleotides with enzymatic activity

• US 6,617,438 B1
• Filed: 12/30/1999
• Issued: 09/09/2003
• Est. Priority Date: 11/05/1997
• Status: Expired due to Term

• Current Assignee: Sirna Therapeutics, Inc. (Alnylam Pharmaceuticals Incorporated)
• Original Assignee: Sirna Therapeutics, Inc. (Alnylam Pharmaceuticals Incorporated)
• Inventors: Burgin, Alex B., Beigelman, Leonid, Zinnen, Shawn, Sweedler, David, Matulic-Adamic, Jasenka, Karpeisky, Alexander, Beaudry, Amber
• Primary Examiner(s): Wilson, James O.
• Assistant Examiner(s): CRANE, LAWRENCE E
• Application Number:
  US09/476,387
• Time in Patent Office: 1,349 Days
• Field of Search: 536/23.1, 536/25.1, 536/25.3, 536/24.5, 514/44, 435/91.1, 435/194, 435/199, 435/325
• 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: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• 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: 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 15/1135 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 2310/111 spanning the whole gene, or a large part of it
• CPC Class Codes: C12N 2310/12 catalytic nucleic acids, e.g. ribozymes
• CPC Class Codes: C12N 2310/121 Hammerhead
• CPC Class Codes: C12N 2310/122 Hairpin
• CPC Class Codes: C12N 2310/18 acting by a non-sequence specific mechanism other than C12N2310/16 or C12N2310/17
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/317 with an inverted bond, e.g. a cap structure
• CPC Class Codes: C12N 2310/318 where the PO2 is completely replaced, e.g. MMI or formacetal
• 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 2310/332 : Abasic residue
• CPC Class Codes: C12N 2310/345 : having at least two different backbone modifications
• CPC Class Codes: C12N 2310/346 : having a combination of backbone and sugar modifications
• CPC Class Codes: C12N 2310/3521 : Methyl
• CPC Class Codes: C12N 2310/3523 : Allyl
• CPC Class Codes: C12P 19/30 : Nucleotides
• CPC Class Codes: C12P 19/305 : Pyrimidine nucleotides
• CPC Class Codes: C12Y 204/02001 : Purine-nucleoside phosphorylase (2.4.2.1)
• CPC Class Codes: C12Y 207/01037 : Protein kinase (2.7.1.37) C12Y207/11001, C12Y207/11008 - C12Y207/11013, C12Y207/11021, C12Y207/11022, C12Y207/11024, C12Y207/11025, C12Y207/1103, C12Y207/12001 take precedence
• CPC Class Codes: C12Y 207/07049 : RNA-directed DNA polymerase (2.7.7.49), i.e. telomerase or reverse-transcriptase
• CPC Class Codes: C12Y 301/03048 : Protein-tyrosine-phosphatase (3.1.3.48)

Abstract

Novel nucleotide triphosphates, methods of synthesis and process of incorporating these nucleotide triphosphates into oligonucleotides, and isolation of novel nucleic acid catalysts (e.g., ribozymes) are disclosed. Also, described are the use of novel enzymatic nucleic acid molecules to inhibit HER2/neu/ErbB2 gene expression and their applications in human therapy.

Claims

1. An enzymatic nucleic acid molecule having formula III namely:

wherein each X, Y, and Z represents independently a nucleotide which may be the same or different;

q is an integer selected from the group consisting of 4, 5, 6, 7, 8, 9, 10, 11, 12, and 15;

n is an integer ranging from 1 to 10;

o is an integer ranging from 3-100;

Z′

is a nucleotide complementary to Z;

each X(q) and X(o) are oligonucleotides which are of sufficient length to stably interact independently with a target nucleic acid sequence;

W is a linker ranging from 2 to 70 nucleotides in length or may be a non-nucleotide linker;

A, U, G, and C represent nucleotides;

C is 2′

-amino; and

_represents a chemical bond or chemical linkage.

2. The nucleic acid of claim 1, wherein n is selected from the group consisting of 2, 3, 4, 5, 6, and 7.

3. The nucleic acid of claim 1, wherein o is selected from the group consisting of 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, and 15.

4. The enzymatic nucleic acid molecule of claim 1, wherein q and o are of the same length.

5. The enzymatic nucleic acid molecule of claim 1, wherein q and o are of different length.

6. The nucleic acid of claim 1, wherein the target nucleic acid sequence is selected from the group consisting of an RNA, DNA and RNA/DNA mixed polymer.

7. The nucleic acid of claim 1, wherein said chemical linkage is selected from the group consisting of phosphate ester linkage, amide linkage, phosphorothioate, and phosphorodithioate.

8. The enzymatic nucleic acid molecule of claim 1, wherein said enzymatic nucleic acid molecule is chemically synthesized.

9. The enzymatic nucleic acid molecule of claim 1, wherein said enzymatic nucleic acid molecule comprises at least one ribonucleotide.

10. The enzymatic nucleic acid molecule of claim 1, wherein said enzymatic nucleic acid molecule comprises no ribonucleotide residues.

11. The enzymatic nucleic acid molecule of claim 1, wherein said enzymatic nucleic acid molecule comprises at least one 2-amino modification.

12. The enzymatic nucleic acid molecule of claim 1, wherein said enzymatic nucleic acid molecule comprises at least three phosphorothioate modifications.

13. The enzymatic nucleic acid molecule of claim 12, wherein said phosphorothioate modification is at the 5′

-end of said enzymatic nucleic acid molecule.

14. The enzymatic nucleic acid molecule of claim 1, wherein said enzymatic nucleic acid molecule comprises a 5′

-cap or a 3′

-cap or both a 5′

-cap and a 3′

-cap.

15. The enzymatic nucleic acid molecule of claim 14, wherein said 5-cap is phosphorothioate modification.

16. The enzymatic nucleic acid molecule of claim 14, wherein said 3′

-cap is an inverted abasic moiety.

17. The enzymatic nucleic acid molecule of claim 1, wherein said nucleic acid molecule has an endonuclease activity to cleave RNA of HER2 gene.

18. The enzymatic nucleic acid molecule of claim 17, wherein said nucleic acid molecule comprises sequences complementary to any of substrate sequences defined as sequence ID Nos. 85-193 and 310-894.

19. The enzymatic nucleic acid molecule of claim 17, wherein said nucleic acid molecule comprises any of ribozyme sequences defined as sequence ID Nos. 194-309 and 895-1479.

20. The enzymatic nucleic acid molecule of claim 17, wherein said enzymatic nucleic acid molecule comprises a substrate binding region which has between 5 and 30 nucleotides complementary to the RNA.

21. The enzymatic nucleic acid molecule of claim 17, wherein said enzymatic nucleic acid molecule comprises a substrate binding region which has between 7 and 12 nucleotides complementary to the RNA.

22. A composition comprising the enzymatic nucleic acid molecule of claim 1, and a pharmaceutically acceptable carrier.

23. A composition comprising the enzymatic nucleic acid molecule of claim 17, and a pharmaceutically acceptable carrier.

24. The enzymatic nucleic acid molecule of claim 17, wherein said enzymatic nucleic acid molecule comprises at least one sugar modification.

25. The enzymatic nucleic acid molecule of claim 17, wherein said enzymatic nucleic acid molecule comprises at least one nucleic acid base modification.

26. The enzymatic nucleic acid molecule of claim 17, wherein said enzymatic nucleic acid molecule comprises at least one phosphate backbone modification.

27. The enzymatic nucleic acid molecule of claim 17, wherein said phosphate backbone modification is selected from the group consisting of phosphorothioate, phosphorodithioate and amide.