title: Solvation studies of DMP323 and A76928 bound to HIV protease: analysis of water sites using grand canonical Monte Carlo simulations.
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.
authors.affiliation: Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla 92093-0365, USA.
authors.forename: T J
authors.initials: TJ
authors.lastname: Marrone
authors.forename: H
authors.initials: H
authors.lastname: Resat
authors.forename: C N
authors.initials: CN
authors.lastname: Hodge
authors.forename: C H
authors.initials: CH
authors.lastname: Chang
authors.forename: J A
authors.initials: JA
authors.lastname: McCammon
mesh_terms: D000438:Alcohols / Q000737:chemistry*; D001381:Azepines; D016333:HIV Protease / Q000737:chemistry* / Q000648:ultrastructure; D017320:HIV Protease Inhibitors / Q000737:chemistry*; D015497:HIV-1 / Q000201:enzymology; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009010:Monte Carlo Method; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012997:Solvents; D014508:Urea / Q000031:analogs & derivatives* / Q000737:chemistry; D014867:Water
chemical_list: C095534:A 76928; D000438:Alcohols; D001381:Azepines; D017320:HIV Protease Inhibitors; D012997:Solvents; D014867:Water; D014508:Urea; D016333:HIV Protease; C085816:DMP 323