Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel

Nat Chem Biol. 2017 Oct;13(10):1129-1136. doi: 10.1038/nchembio.2462. Epub 2017 Aug 28.

Abstract

Whereas screening of the small-molecule metabolites produced by most cultivatable microorganisms often results in the rediscovery of known compounds, genome-mining programs allow researchers to harness much greater chemical diversity, and result in the discovery of new molecular scaffolds. Here we report the genome-guided identification of a new antibiotic, klebsazolicin (KLB), from Klebsiella pneumoniae that inhibits the growth of sensitive cells by targeting ribosomes. A ribosomally synthesized post-translationally modified peptide (RiPP), KLB is characterized by the presence of a unique N-terminal amidine ring that is essential for its activity. Biochemical in vitro studies indicate that KLB inhibits ribosomes by interfering with translation elongation. Structural analysis of the ribosome-KLB complex showed that the compound binds in the peptide exit tunnel overlapping with the binding sites of macrolides or streptogramin-B. KLB adopts a compact conformation and largely obstructs the tunnel. Engineered KLB fragments were observed to retain in vitro activity, and thus have the potential to serve as a starting point for the development of new bioactive compounds.

MeSH terms

  • Anti-Bacterial Agents / chemistry
  • Anti-Bacterial Agents / metabolism
  • Anti-Bacterial Agents / pharmacology*
  • Binding Sites / drug effects
  • Cloning, Molecular
  • Klebsiella pneumoniae / chemistry*
  • Klebsiella pneumoniae / metabolism
  • Peptides / chemistry
  • Peptides / metabolism
  • Peptides / pharmacology*
  • Protein Engineering
  • Ribosomes / chemistry*
  • Ribosomes / drug effects*

Substances

  • Anti-Bacterial Agents
  • Peptides
  • klebsazolicin

Associated data

  • PubChem-Substance/340469118