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Enrichment of virtual hits by progressive shape-matching and docking

Authors
Choi, JiwonHe, NingningKim, NayoungYoon, Sukjoon
Issue Date
Feb-2012
Publisher
ELSEVIER SCIENCE INC
Keywords
Virtual screening; Lead hopping; Docking; Ligand-centric methods; Receptor-centric methods; Principal component analysis
Citation
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, v.32, pp.82 - 88
Journal Title
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
Volume
32
Start Page
82
End Page
88
URI
https://scholarworks.sookmyung.ac.kr/handle/2020.sw.sookmyung/11981
DOI
10.1016/j.jmgm.2011.10.002
ISSN
1093-3263
Abstract
The main applications of virtual chemical screening include the selection of a minimal receptor-relevant subset of a chemical library with a maximal chemical diversity. We have previously reported that the combination of ligand-centric and receptor-centric virtual screening methods may provide a compromise between computational time and accuracy during the hit enrichment process. In the present work, we propose a "progressive distributed docking" method that improves the virtual screening process using an iterative combination of shape-matching and docking steps. Known ligands with low docking scores were used as initial 3D templates for the shape comparisons with the chemical library. Next, new compounds with good template shape matches and low receptor docking scores were selected for the next round of shape searching and docking. The present iterative virtual screening process was tested for enriching Peroxisome proliferator-activated receptor and Phosphoinositide 3-kinase relevant compounds from a selected subset of the chemical libraries. It was demonstrated that the iterative combination improved the lead-hopping practice by improving the chemical diversity in the selected list of virtual hits. (C) 2011 Elsevier Inc. All rights reserved.
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