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Computational and Mathematical Methods in Medicine
Volume 2012, Article ID 541594, 11 pages
http://dx.doi.org/10.1155/2012/541594
Research Article

Implication of Crystal Water Molecules in Inhibitor Binding at ALR2 Active Site

Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, Punjab 160 062, S.A.S Nagar, India

Received 23 September 2011; Revised 30 December 2011; Accepted 13 January 2012

Academic Editor: Joti Yasumasa

Copyright © 2012 Hymavati et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Water molecules play a crucial role in mediating the interaction between a ligand and a macromolecule. The solvent environment around such biomolecule controls their structure and plays important role in protein-ligand interactions. An understanding of the nature and role of these water molecules in the active site of a protein could greatly increase the efficiency of rational drug design approaches. We have performed the comparative crystal structure analysis of aldose reductase to understand the role of crystal water in protein-ligand interaction. Molecular dynamics simulation has shown the versatile nature of water molecules in bridge H bonding during interaction. Occupancy and life time of water molecules depend on the type of cocrystallized ligand present in the structure. The information may be useful in rational approach to customize the ligand, and thereby longer occupancy and life time for bridge H-bonding.