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Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
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Statistical analysis of EGFR structures' performance in virtual screening.

Yan Li1, Xiang Li2, Zigang Dong3

  • 1The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA. yanli0208@hi.umn.edu.

Journal of Computer-Aided Molecular Design
|October 19, 2015
PubMed
Summary

This study assesses EGFR structures for identifying true drug inhibitors versus decoys using docking and MM-PBSA. Optimal structures for virtual screening depend on receptor conformation differences, not bound-ligand properties.

Keywords:
EGFR conformationEnrichmentMM-PBSAMolecular dockingReceptor flexibility

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Drug discovery

Background:

  • Epidermal Growth Factor Receptor (EGFR) is a key target in cancer therapy.
  • Virtual screening methods are crucial for identifying potential EGFR inhibitors.
  • The selection of appropriate EGFR structures is vital for successful virtual screening campaigns.

Purpose of the Study:

  • To evaluate the efficacy of different Epidermal Growth Factor Receptor (EGFR) structures in distinguishing true inhibitors from decoys.
  • To determine the impact of receptor conformation and bound state on docking and MM-PBSA performance.
  • To identify optimal EGFR structures and strategies for virtual screening.

Main Methods:

  • Statistical analysis of docking and Molecular Mechanics with the Poisson-Boltzmann Surface Area (MM-PBSA) results.
  • Assessment of enrichment factors for known EGFR inhibitors against decoy compounds.
  • Comparison of performance across various EGFR conformations and bound states.

Main Results:

  • Docking performance is highly sensitive to receptor conformation and bound ligand.
  • Enrichment of true inhibitors correlates better with differences between EGFR structures than with bound-ligand properties.
  • Optimal structures for virtual screening can be selected based on complex information alone.
  • Ensemble docking benefits from a mixed combination of distinct EGFR conformations.
  • MM-PBSA shows consistent performance across various EGFR structures, indicating minimal impact of structure choice on scoring and ranking.

Conclusions:

  • The choice of Epidermal Growth Factor Receptor (EGFR) structure significantly impacts docking performance for virtual screening.
  • Ensemble docking using diverse EGFR conformations is recommended for improved inhibitor identification.
  • Receptor structure selection has a negligible effect on the performance of MM-PBSA for EGFR inhibitor screening.