A crystal structure of a dimer of the antibiotic ramoplanin illustrates membrane positioning and a potential Lipid II docking interface

Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13759-64. doi: 10.1073/pnas.0904686106. Epub 2009 Aug 3.

Abstract

The glycodepsipeptide antibiotic ramoplanin A2 is in late stage clinical development for the treatment of infections from Gram-positive pathogens, especially those that are resistant to first line antibiotics such as vancomycin. Ramoplanin A2 achieves its antibacterial effects by interfering with production of the bacterial cell wall; it indirectly inhibits the transglycosylases responsible for peptidoglycan biosynthesis by sequestering their Lipid II substrate. Lipid II recognition and sequestration occur at the interface between the extracellular environment and the bacterial membrane. Therefore, we determined the structure of ramoplanin A2 in an amphipathic environment, using detergents as membrane mimetics, to provide the most physiologically relevant structural context for mechanistic and pharmacological studies. We report here the X-ray crystal structure of ramoplanin A2 at a resolution of 1.4 A. This structure reveals that ramoplanin A2 forms an intimate and highly amphipathic dimer and illustrates the potential means by which it interacts with bacterial target membranes. The structure also suggests a mechanism by which ramoplanin A2 recognizes its Lipid II ligand.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Anti-Bacterial Agents / chemistry*
  • Anti-Bacterial Agents / pharmacology
  • Cell Membrane / drug effects
  • Crystallography, X-Ray / methods
  • Depsipeptides / chemistry*
  • Depsipeptides / pharmacology
  • Dimerization
  • Drug Resistance, Bacterial
  • Gram-Positive Bacteria / metabolism
  • Ligands
  • Lipids / chemistry
  • Microbial Sensitivity Tests
  • Models, Chemical
  • Molecular Conformation
  • Peptides / chemistry
  • Protein Binding

Substances

  • Anti-Bacterial Agents
  • Depsipeptides
  • Ligands
  • Lipids
  • Peptides
  • ramoplanin