Antisense antibacterial method and composition

• US 6,677,153 B2
• Filed: 11/29/2000
• Issued: 01/13/2004
• Est. Priority Date: 11/29/1999
• Status: Expired due to Term

• Current Assignee: Sarepta Therapeutics, Inc.
• Original Assignee: Avi Biopharma, Inc.
• Inventors: Iversen, Patrick L.
• Primary Examiner(s): McGarry, Sean
• Application Number:
  US09/726,774
• Publication Number:
  US 20020082226A1
• Time in Patent Office: 1,140 Days
• Field of Search: 536/23.1, 536/24.1, 536/24.5, 435/320.1, 435/375, 514/44
• US Class Current: 435/375
• 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: A61P 11/00 Drugs for disorders of the respiratory system
• CPC Class Codes: A61P 17/00 Drugs for dermatological disorders
• CPC Class Codes: A61P 31/00 Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
• CPC Class Codes: A61P 31/04 Antibacterial agents
• 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 2310/311 Phosphotriesters
• CPC Class Codes: C12N 2310/312 Phosphonates
• CPC Class Codes: C12N 2310/314 Phosphoramidates
• 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 2310/3233 Morpholino-type ring
• 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

The invention relates to compositions comprising oligomers antisense to bacterial 16S or 23S rRNA and capable of selectively modulating the biological activity thereof, and methods for their use. More particularly, the invention relates to antisense oligomers directed to 16S or 23S rRNA found in one or more particular bacteria, or generally conserved among bacteria in general, and to pharmaceutical compositions and methods of treatment comprising the same.

Claims

1. A method of inhibiting growth of bacteria selected from the group consisting of Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Enterococcus faecium, and Salmonella typhimurium, comprising

contacting said bacteria in vitro with an effective amount of an antisense morpholino oligomer containing from 10 to 40 nucleotide subunits, each of said subunits comprising a morpholino ring supporting a base-pairing moiety effective to bind by Watson-Crick base pairing to a respective nucleotide base, said base-pairing moieties including a targeting nucleic acid sequence at least 10 nucleotides in length which is complementary to a 16S or 23S rRNA nucleic acid sequence of said bacteria, wherein adjacent subunits are joined by uncharged phosphorodiamidate linkages.

2. The method of claim 1, wherein said oligomer is able to hybridize with the bacterial sequence at a T_m substantially greater than 37°

C.

3. The method of claim 1, wherein each linkage is a phosphorodiamidate linkage in accordance with the structure below, where X═

NR₂, R is hydrogen or methyl, Y₁═

O, Z═

O, and P, is a purine or pynmidine base pairing moiety effective to bind, by base specific hydrogen bonding, to a base in a polynucleotide,

4. The method of claim 1, where the antisense oligomer is 25 or fewer bases in length.

5. The method of claim 1, wherein the region of complementarity with the target RNA sequence has a length of 13 to 20 bases.

6. The method of claim 1, wherein the targeting sequence is selected from the group consisting of SEQ ID NOs:

91-92, 102-115, and 121-138.