Article ID Journal Published Year Pages File Type
443792 Journal of Molecular Graphics and Modelling 2010 10 Pages PDF
Abstract

Computational docking to nicotinic acetylcholine receptors (nAChRs) and other members of the Cys-loop receptor family is complicated by the flexibility of the so-called C-loop. As observed in the large number of published crystal structures of the acetylcholine binding protein (AChBP), a structural surrogate and homology modeling template for the nAChRs, the conformation of this loop is controlled by the ligand present in the binding pocket. As part of the development of a protocol for unbiased docking to the nAChRs, we here present the results of docking of ligands with known binding modes to an AChBP ensemble with systematic variations in C-loop closure generated via a series of targeted geometry optimizations. We demonstrate the ability to correctly predict binding modes for 12 out of 15 ligands and induced degrees of C-loop closure for 14 out of 15 ligands. Our approach holds a promising potential for structure based drug discovery within nAChRs and related receptors.

Graphical abstract.Figure optionsDownload full-size imageDownload high-quality image (120 K)Download as PowerPoint slideResearch highlights▶ Docking to flexible acetylcholine binding proteins ▶ Ensemble generation through targeted molecular mechanics optimization ▶ Ensemble docking ▶ 83% of experimentally validated binding modes and C-loop closures determined correctly.

Related Topics
Physical Sciences and Engineering Chemistry Physical and Theoretical Chemistry
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