Novel Allosteric Sites on Ras for Lead Generation

PLoS One. 2011;6(10):e25711. doi: 10.1371/journal.pone.0025711. Epub 2011 Oct 25.

Abstract

Aberrant Ras activity is a hallmark of diverse cancers and developmental diseases. Unfortunately, conventional efforts to develop effective small molecule Ras inhibitors have met with limited success. We have developed a novel multi-level computational approach to discover potential inhibitors of previously uncharacterized allosteric sites. Our approach couples bioinformatics analysis, advanced molecular simulations, ensemble docking and initial experimental testing of potential inhibitors. Molecular dynamics simulation highlighted conserved allosteric coupling of the nucleotide-binding switch region with distal regions, including loop 7 and helix 5. Bioinformatics methods identified novel transient small molecule binding pockets close to these regions and in the vicinity of the conformationally responsive switch region. Candidate binders for these pockets were selected through ensemble docking of ZINC and NCI compound libraries. Finally, cell-based assays confirmed our hypothesis that the chosen binders can inhibit the downstream signaling activity of Ras. We thus propose that the predicted allosteric sites are viable targets for the development and optimization of new drugs.

Publication types

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

MeSH terms

  • Allosteric Site / drug effects*
  • Cell Line
  • Computational Biology
  • Computer Simulation
  • Drug Design*
  • Humans
  • Models, Molecular
  • Nucleotides / chemistry
  • Nucleotides / metabolism
  • Protein Binding / drug effects
  • Signal Transduction / drug effects
  • Small Molecule Libraries / metabolism
  • ras Proteins / antagonists & inhibitors*
  • ras Proteins / chemistry*
  • ras Proteins / metabolism

Substances

  • Nucleotides
  • Small Molecule Libraries
  • ras Proteins