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J Med Chem. 2006 Dec 14;49(25):7427-39.

Protein-ligand binding affinity predictions by implicit solvent simulations: a tool for lead optimization?

Author information

1
School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom.

Abstract

Continuum electrostatics is combined with rigorous free-energy calculations in an effort to deliver a reliable and efficient method for in silico lead optimization. The methodology is tested by calculation of the relative binding free energies of a set of inhibitors of neuraminidase, cyclooxygenase2, and cyclin-dependent kinase 2. The calculated free energies are compared to the results obtained with explicit solvent simulations and empirical scoring functions. For cyclooxygenase2, deficiencies in the continuum electrostatics theory are identified and corrected with a modified simulation protocol. For neuraminidase, it is shown that a continuum representation of the solvent leads to markedly different protein-ligand interactions compared to the explicit solvent simulations, and a reconciliation of the two protocols is problematic. Cyclin-dependent kinase 2 proves more challenging, and none of the methods employed in this study yield high quality predictions. Despite the differences observed, for these systems, the use of an implicit solvent framework to predict the ranking of congeneric inhibitors to a protein is shown to be faster, as accurate or more accurate than the explicit solvent protocol, and superior to empirical scoring schemes.

PMID:
17149872
DOI:
10.1021/jm061021s
[Indexed for MEDLINE]

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