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The Role of Water Molecules in Computational Drug Design

[ Vol. 10 , Issue. 1 ]

Author(s):

Stephanie B.A. de Beer, Nico P.E. Vermeulen and Chris Oostenbrink   Pages 55 - 66 ( 12 )

Abstract:


Although water molecules are small and only consist of two different atom types, they play various roles in cellular systems. This review discusses their influence on the binding process between biomacromolecular targets and small molecule ligands and how this influence can be modeled in computational drug design approaches. Both the structure and the thermodynamics of active site waters will be discussed as these influence the binding process significantly. Structurally conserved waters cannot always be determined experimentally and if observed, it is not clear if they will be replaced upon ligand binding, even if sufficient space is available. Methods to predict the presence of water in protein-ligand complexes will be reviewed. Subsequently, we will discuss methods to include water in computational drug research. Either as an additional factor in automated docking experiments, or explicitly in detailed molecular dynamics simulations, the effect of water on the quality of the simulations is significant, but not easily predicted. The most detailed calculations involve estimates of the free energy contribution of water molecules to protein-ligand complexes. These calculations are computationally demanding, but give insight in the versatility and importance of water in ligand binding.

Keywords:

Molecular docking, molecular dynamics simulation, free energy calculation, water bridges

Affiliation:

Leiden-Amsterdam Center for Drug Research, Section of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.



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