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The Challenge of Considering Receptor Flexibility in Ligand Docking and Virtual Screening

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Computational ligand docking and screening is widely employed throughout the pharmaceutical industry to speed up the drug discovery process and identify drug candidates from very large pools of virtual compound libraries. When a ligand interacts with a receptor a number of structural changes within the ligand binding site might occur. It is therefore critical for these methods to accurately predict, or otherwise take into account the receptor flexibility upon ligand binding. This flexibility within the binding pocket explains why a diverse range of ligand sizes and shapes can sometimes bind to the same receptor pocket. This observation supersedes the notion that ligand-receptor interaction is a purely 'lock and key' mechanism. The capability to correctly predict molecular interactions is critical for computer-aided molecular design technology. In this review, we discuss biological cases of receptor flexibility upon ligand binding that can range from 'large-scale' movement of loops to single 'gate-keeper' amino acid movements. In addition, we provide further evidence that rigid receptor docking alone will more than likely fail in the drug-discovery process. We then discuss computational methods, which have been developed to mimic flexibility within the binding pocket and predict ligand-receptor interactions. Early flexible receptor docking methods used 'soft-potential docking' and rotamer libraries. More recently methods have focused on constructing an ensemble of structures generated by a variety of means including X-ray crystallography, NMR, Monte Carlo sampling, Normal Modes-based methods and Molecular Dynamics. It is evident that methods that ignore receptor flexibility can result in poorly docked solutions and therefore the challenge is to develop computational methods, which can accurately and efficiently predict this phenomenon.
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Keywords: computer-aided drug discovery; ligand docking; molecular dynamics; monte carlo; multiple receptor conformations; receptor flexibility; scoring; virtual screening

Document Type: Review Article

Affiliations: Molsoft LLC, 3366 N. Torrey Pines Ct, Suite. 300, La Jolla, CA 92037, USA.

Publication date: October 1, 2005

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  • Current Computer-Aided Drug Design aims to publish all the latest developments in drug design based on computational techniques. The field of computer-aided drug design has had extensive impact in the area of drug design. Current Computer-Aided Drug Design is an essential journal for all medicinal chemists who wish to be kept informed and up-to-date with all the latest and important developments in computer-aided methodologies and their applications in drug discovery. Each issue contains a series of timely, in-depth reviews written by leaders in the field, covering a range of computational techniques for drug design, screening, ADME studies, etc., providing excellent rationales for drug development.
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