title: Role of Molecular Dynamics and Related Methods in Drug Discovery.
abstract: Molecular dynamics (MD) and related methods are close to becoming routine computational tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and entropic effects. This allows a more accurate estimate of the thermodynamics and kinetics associated with drug-target recognition and binding, as better algorithms and hardware architectures increase their use. Here, we review the theoretical background of MD and enhanced sampling methods, focusing on free-energy perturbation, metadynamics, steered MD, and other methods most consistently used to study drug-target binding. We discuss unbiased MD simulations that nowadays allow the observation of unsupervised ligand-target binding, assessing how these approaches help optimizing target affinity and drug residence time toward improved drug efficacy. Further issues discussed include allosteric modulation and the role of water molecules in ligand binding and optimization. We conclude by calling for more prospective studies to attest to these methods' utility in discovering novel drug candidates.
authors.affiliation: Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia , Via Morego 30, 16163 Genova, Italy.|IAS-5/INM-9 Computational Biomedicine Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany.
authors.forename: Marco
authors.initials: M
authors.lastname: De Vivo
authors.affiliation: Department of Pharmacy and Biotechnology, University of Bologna , Via Belmeloro 6, I-40126 Bologna, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Masetti
authors.affiliation: CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy.|BiKi Technologies srl, Via XX Settembre 33/10, 16121 Genova, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Bottegoni
authors.affiliation: Department of Pharmacy and Biotechnology, University of Bologna , Via Belmeloro 6, I-40126 Bologna, Italy.|CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Cavalli
mesh_terms: D002626:Chemistry, Pharmaceutical; D056004:Molecular Dynamics Simulation