Antisense antibacterial method and compound

Abstract

An antibacterial antisense conjugate and method of using the same for treating a bacterial infection in a mammalian host are disclosed. The conjugate includes an antisense oligonucleotide conjugated to a carrier peptide that significantly enhances the antibacterial activity of the oligonucleotide. The antisense oligonucleotide contains 10-20 nucleotide bases and has a targeting nucleic acid sequence 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, where the compound binds to a target mRNA with a T m of between 50° to 60° C. The carrier peptide is an arginine-rich peptide containing between 6 and 12 amino acids.

1 - 22 . (canceled) 
     
     
         23 . A method of treating a bacterial infection in a mammalian host, comprising administering to the host, a therapeutically effective amount of an antisense conjugate composed of:
 (a) a substantially uncharged antisense oligonucleotide having between 10-20 bases and a targeting sequence of at least 10 contiguous bases complementary to a target region of the infecting bacteria's mRNA for acyl carrier protein (acpP), where the target region contains the translational start codon of the bacterial mRNA, or a sequence that is within 20 bases, in a downstream direction, of the translational start codon, thereby to inhibit replication of the bacteria, and   (b) conjugated to the oligonucleotide, a carrier peptide that is (i) represented by the sequence (RXX) n —, where X is an uncharged amino acid selected from the group consisting of alanine, β-alanine, valine, leucine, isoleucine, serine, threonine, phenylalanine, and tryptophan, and n=2 or 3, and (ii) coupled to the oligonucleotide at the peptide's C terminus.   
     
     
         24 . The method of  claim 23 , wherein the carrier peptide has the form (RFF) n . 
     
     
         25 . The method of  claim 24 , wherein the carrier peptide has the form (RFF) n R—. 
     
     
         26 . The method of  claim 23 , wherein the carrier peptide is linked at its C-terminus to the 5′ end of the oligonucleotide through a one- or two-amino acid linker. 
     
     
         27 . The method of  claim 23 , wherein the carrier peptide is linked at its C-terminus to the 3′ end of the oligonucleotide through a one- or two-amino acid linker. 
     
     
         28 . The method of  claim 26 , wherein the linker is AhxβAla, where Ahx is 6-aminohexanoic acid and βAla is β-alanine. 
     
     
         29 . The method of  claim 23 , wherein the oligonucleotide of the conjugate is 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. 
     
     
         30 . The method of  claim 29 , wherein the morpholino subunits in the oligonucleotide are joined by phosphorodiamidate linkages, in accordance with the structure: 
       
         
           
           
               
               
           
         
       
       where Y 1 ═O, Z═O, Pj is a purine or pyrimidine base-pairing moiety effective to bind, by base-specific hydrogen bonding, to a base in a polynucleotide, and X is alkyl, alkoxy, thioalkoxy, amino or alkyl amino, including dialkylamino. 
     
     
         31 . The method of  claim 29 , wherein the oligonucleotide contains 1 positively charged linkage per every 3-10 linkages. 
     
     
         32 . The method of  claim 23 , for treating a gram-negative bacterial infection. 
     
     
         33 . The method of  claim 32 , wherein the gram-negative bacterial infection is a  Burkholderia  infection. 
     
     
         34 . The method of  claim 33 , wherein the  Burkholderia  infection is a  Burkholderia cepacia, Burkholderia mallei , or  Burkholderia pseudomallei  infection. 
     
     
         35 . The method of  claim 34 , wherein the  Burkholderia cepacia  infection is a  Burkholderia multivorans, Burkholderia vietnamiensis, Burkholderia stabilis, Burkholderia cenocepacia , or  Burkholderia ambifaria  infection. 
     
     
         36 . The method of  claim 23 , for treating a gram-positive bacterial infection. 
     
     
         37 . The method of  claim 36 , wherein the gram-positive infection is a  Clostridium  infection.