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

Protein Science : a Publication of the Protein Society
T J MarroneJ Andrew McCammon

Abstract

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.

References

Mar 1, 1994·Biophysical Journal·V LounnasG N Phillips
Jan 1, 1993·Annual Review of Biochemistry·A Wlodawer, J W Erickson

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Citations

Mar 10, 1999·Biopolymers·M S Madhusudhan, S Vishveshwara
Apr 3, 2007·BMC Structural Biology·Sergei V Rakhmanov, Vsevolod J Makeev
May 30, 2014·Journal of Molecular Modeling·Paulius MikulskisUlf Ryde
Oct 29, 2015·Journal of the American Chemical Society·Gregory A RossJonathan W Essex
May 17, 2005·Biophysical Journal·Monika FuxreiterRoman Osman
May 15, 2018·Current Medicinal Chemistry·Xiao HuAlessandro Contini
Sep 1, 2006·Journal of Chemical Theory and Computation·Joshua A SpeidelMihaly Mezei
Mar 25, 2009·Journal of Chemical Information and Modeling·Matthew ClarkJeffrey S Wiseman

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