Current Computer-Aided Drug Design

Subhash C. Basak
Departments of Chemistry, Biochemistry & Molecular Biology University of Minnesota Duluth
Duluth, MN 55811
USA

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Post-Docking Optimization and Analysis of Protein-Ligand Interactions of Estrogen Receptor Alpha using AMMOS Software

Author(s): Tania Pencheva, Dessislava Jereva, Maria A. Miteva, Ilza Pajeva.

Abstract:

Understanding protein-ligand interactions is a critical step in rational drug design/virtual ligand screening. In this work we applied the AMMOS_ProtLig software for post-docking optimization of estrogen receptor alpha complexes generated after virtual ligand screening protocol. Using MOE software we identified the ligand-receptor interactions in the optimized complexes at different levels of protein flexibility and compared them to the experimentally observed interactions. We analyzed in details the binding sites of three X-ray complexes of the same receptor and identified the key residues for the protein-ligand interactions. The complexes were further processed with AMMOS_ProtLig and the interactions in the predicted poses were compared to those observed in the X-ray structures. The effect of employing different levels of flexibility was analyzed. The results confirmed the AMMOS_ProtLig applicability as a helpful postdocking optimization tool for virtual ligand screening of estrogen receptors.

Keywords: AMMOS, binding site, estrogen receptor, in silico screening, protein flexibility, protein-ligand interactions, ligand, screening, X-ray, Complexes

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Article Details

VOLUME: 9
ISSUE: 1
Year: 2013
Page: [83 - 94]
Pages: 12
DOI: 10.2174/1573409911309010008