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Protein Science, Vol 7, Issue 3 573-579, Copyright © 1998 by Cold Spring Harbor Laboratory Press

ARTICLE

Solvation studies of DMP323 and A76928 bound to HIV protease: Analysis of water sites using grand canonical Monte Carlo simulations

T. J. MARRONE, H. RESAT, C. N. HODGE, C. H. CHANG and J. A. MCCAMMON
Department of Chemistry and Biochemistry and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365 Present address: Agouron Pharmaceuticals, 3301 North Torrey Pines Court, La Jolla, California 92037.

We examine the water solvation of the complex of the inhibitors DMP323 and A76928 bound to HIV-1 protease through grand canonical Monte Carlo simulations, and demonstrate the ability of this method to reproduce crystal waters and effectively predict water positions not seen in the DMP323 or A76928 structures. The simulation method is useful for identifying structurally important waters that may not be resolved in the crystal structures. It can also be used to identify water positions around a putative drug candidate docked into a binding pocket. Knowledge of these water positions may be useful in designing drugs to utilize them as bridging groups or displace them in the binding pocket. In addition, the method should be useful in finding water sites in homology models of enzymes for which crystal structures are unavailable.
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