Atomistic Models for Free Energy Evaluation of Drug Binding to Membrane Proteins
Authors: Durdagi, S.; Zhao, C.; E. Cuervo, J.; Y. Noskov, S.
Source: Current Medicinal Chemistry, Volume 18, Number 17, June 2011 , pp. 2601-2611(11)
Publisher: Bentham Science Publishers
Abstract:The binding of various molecules to integral membrane proteins with optimal affinity and specificity is central to normal function of cell. While membrane proteins represent about one third of the whole cell proteome, they are a majority of common drug targets. The quest for the development of computational models capable of accurate evaluation of binding affinities, decomposition of the binding into its principal components and thus mapping molecular mechanisms of binding remains one of the main goals of modern computational biophysics and related drug development. The primary scope of this review will be on the recent extension of computational methods for the study of drug binding to membrane proteins. Several examples of such applications will be provided ranging from secondary transporters to voltage gated channels. In this mini-review, we will provide a short summary on the breadth of different methods for binding affinity evaluation. These methods include molecular docking with docking scoring functions, molecular dynamics (MD) simulations combined with post-processing analysis using Molecular Mechanics/Poisson Boltzmann (Generalized Born) Surface Area (MM/PB(GB)SA), as well as direct evaluation of free energies from Free Energy Perturbation (FEP) with constraining schemes, and Potential of Mean Force (PMF) computations. We will compare advantages and shortcomings of popular techniques and provide discussion on the integrative strategies for drug development aimed at targeting membrane proteins.
Keywords: Ligand binding; MM/PBSA; free energy computation; free energy perturbation; lead optimization; membrane protein; molecular docking; molecular simulation; rational drug design; scoring function
Document Type: Research Article
Publication date: June 1, 2011
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