Screening efficient BH3-mimetics to hBcl-B by means of peptidodynmimetic method

Mol Biosyst. 2013 Apr 5;9(4):700-12. doi: 10.1039/c2mb25195g.

Abstract

The crucial residues of hBaxBH3 peptide for interaction with hBcl-B, an anti-apoptotic protein, were identified using molecular docking studies on the polypeptides and temperature-specific molecular dynamic simulations performed for the protein-peptide complex at near-physiological conditions (pH 7.0, 1 atmospheric pressure and 0.1 M NaCl). The data from the methods were examined by a 'strong residue contacts' filter strategy and the data analyses of the former and latter methods identified 10 (Q52, K57, S60, L63, K64, R65, G67, D68, D71 & S72) and 3 (S60, E61 & K64) crucial residues of the hBaxBH3 peptide for interacting with the protein, respectively. We have herein demonstrated that BH3-chemical mimetics screened using the pharmacophoric residues of hBaxBH3 obtained from the 'peptidodynmimetic method' were superior in terms of ligand efficiencies, bioavailability and pharmacokinetic properties vis-à-vis that of small molecule BH3-mimetics retrieved using the conventional 'peptidomimetic method'. The unique advantages of the 'peptidodynmimetic method' to identify efficient BH3-mimetics for modulating interfaces (composed of a large number of amino acids) of other anti-apoptotic proteins-BH3-only peptides have also been discussed in detail.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Biomimetics* / methods
  • Models, Molecular
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Molecular Mimicry
  • Molecular Sequence Data
  • Mutation
  • Peptide Fragments / chemistry*
  • Peptide Fragments / genetics
  • Protein Conformation
  • Protein Interaction Domains and Motifs
  • Proto-Oncogene Proteins / chemistry*
  • Proto-Oncogene Proteins / genetics
  • Proto-Oncogene Proteins c-bcl-2 / chemistry*
  • Proto-Oncogene Proteins c-bcl-2 / genetics

Substances

  • BCL2-like 10 protein
  • Bax protein (53-86)
  • Peptide Fragments
  • Proto-Oncogene Proteins
  • Proto-Oncogene Proteins c-bcl-2