Development of a potent Bcl-x(L) antagonist based on alpha-helix mimicry

J Am Chem Soc. 2002 Oct 9;124(40):11838-9. doi: 10.1021/ja026861k.

Abstract

The rational design of low-molecular weight ligands that disrupt protein-protein interactions is still a challenging goal in medicinal chemistry. Our approach to this problem involves the design of molecular scaffolds that mimic the surface functionality projected along one face of an alpha-helix. Using a terphenyl scaffold, which in a staggered conformation closely reproduces the projection of functionality on the surface of an alpha-helix, we designed mimics of the pro-apoptotic alpha-helical Bak-peptide as inhibitors of the Bak/Bcl-xL interaction. This led to the development of a potent Bcl-xL antagonist (KD = 114 nM), whose binding affinity for Bcl-xL was assessed by a fluorescence polarization assay. To determine the binding site of the developed inhibitor we used docking studies and an HSQC-NMR experiment with 15N-labeled Bcl-xL protein. These studies suggest that the inhibitor is binding in the same hydrophobic cleft as the Bak- and Bad-peptides.

Publication types

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

MeSH terms

  • Binding Sites
  • Fluorescence Polarization
  • Membrane Proteins / chemistry
  • Membrane Proteins / metabolism
  • Models, Molecular
  • Molecular Mimicry
  • Protein Structure, Secondary
  • Proto-Oncogene Proteins c-bcl-2 / antagonists & inhibitors*
  • Proto-Oncogene Proteins c-bcl-2 / chemistry
  • Proto-Oncogene Proteins c-bcl-2 / metabolism
  • Terphenyl Compounds / chemical synthesis
  • Terphenyl Compounds / chemistry*
  • Terphenyl Compounds / pharmacology
  • bcl-2 Homologous Antagonist-Killer Protein
  • bcl-X Protein

Substances

  • Membrane Proteins
  • Proto-Oncogene Proteins c-bcl-2
  • Terphenyl Compounds
  • bcl-2 Homologous Antagonist-Killer Protein
  • bcl-X Protein