Antisense antibacterial method and compound

• US 7,625,873 B2
• Filed: 05/10/2006
• Issued: 12/01/2009
• Est. Priority Date: 07/02/2004
• Status: Expired due to Fees

• Current Assignee: Sarepta Therapeutics, Inc.
• Original Assignee: Avi Biopharma, Inc.
• Inventors: Iversen, Patrick L., Weller, Dwight D., Geller, Bruce L., Deere, Jesse D.
• Primary Examiner(s): ZARA, JANE J
• Application Number:
  US11/432,216
• Publication Number:
  US 20070049542A1
• Time in Patent Office: 1,301 Days
• Field of Search: 435/6, 435/91.1, 435/91.31, 435/471, 514/44, 536/23.1, 536/24.32, 536/24.5
• US Class Current: 514/44.00R
• CPC Class Codes: A61P 31/04 Antibacterial agents
• CPC Class Codes: C07F 9/65583 each of the hetero rings containing nitrogen as ring hetero atom
• CPC Class Codes: C07F 9/65613 containing the ring system (X = CH2, O, S, NH) optionally with an additional double bond and/or substituents, e.g. cephalosporins and analogs
• 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 2310/11 Antisense
• CPC Class Codes: C12N 2310/3145 with the nitrogen in 3' or 5'-position
• CPC Class Codes: C12N 2310/3233 Morpholino-type ring

Abstract

A method and antisense compound for inhibiting the growth of pathogenic bacterial cells are disclosed. The compound contains no more than 12 nucleotide bases and has a targeting nucleic acid sequence of no fewer than 10 bases in length that is complementary to a target sequence containing or within 10 bases, in a downstream direction, of the translational start codon of a bacterial mRNA that encodes a bacterial protein essential for bacterial replication. The compound binds to a target mRNA with a T_m of between 50° to 60° C. The relatively short antisense compounds are substantially more active than conventional antisense compounds having a targeting base sequence of 15 or more bases.

Claims

1. A method of inhibiting the growth of Escherichia coli, Salmonella typhimurium, or Yersinia pestis pathogenic bacterial cells, comprising exposing the bacterial cells to a growth-inhibiting amount of an antisense oligonucleotide compound, composed of morpholino subunits and phosphorus-containing intersubunit linkages joining a morpholino nitrogen of one subunit to a 5′

exocyclic carbon of an adjacent subunit, and having;

(i) no more than 12 nucleotide bases,

(ii) a targeting nucleic acid sequence of no fewer than 10 bases in length that is complementary to a target sequence containing or within 10 bases, in a downstream direction, of the translational start codon in SEQ ID NO;

2; and

(iii) a T_m, when hybridized with the target sequence, between 50°

to 60°

C.;

wherein said morpholino subunits in the oligonucleotide compound are joined by a combination of (a) uncharged phosphorodiamidate linkages, in accordance with structure I,

2. The method of claim 1, wherein X in said uncharged linkages is N(CH₃)₂.

3. The method of claim 1, wherein the oligonucleotide compound to which the cells are exposed has a targeting sequence that is complementary to a target sequence containing the translational start codon of the bacterial mRNA.

4. The method of claim 1, wherein the oligonucleotide compound to which the cells are exposed has a targeting sequence that is complementary to a target sequence that is within 10 bases, in a downstream direction, of the translational start codon of the bacterial mRNA.

5. The method of claim 1, wherein the oligonucleotide compound to which the cells are exposed contains only 11 bases, and its nucleic acid sequence is completely complementary to the mRNA target sequence.

6. The method of claim 1, for use in inhibiting a bacterial Escherichia coli, Salmonella typhimurium, or Yersinia pestis infection in a mammalian subject, wherein said exposing includes administering said compound in a therapeutically effective amount.