TY  - JOUR
AU  - De Vivo, Marco
AU  - Masetti, Matteo
AU  - Bottegoni, Giovanni
AU  - Cavalli, Andrea
TI  - Role of Molecular Dynamics and Related Methods in Drug Discovery
JO  - Journal of medicinal chemistry
VL  - 59
IS  - 9
SN  - 1520-4804
CY  - Washington, DC
PB  - ACS
M1  - FZJ-2016-05808
SP  - 4035 - 4061
PY  - 2016
AB  - 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.
LB  - PUB:(DE-HGF)16
UR  - <Go to ISI:>//WOS:000375969200002
C6  - pmid:26807648
DO  - DOI:10.1021/acs.jmedchem.5b01684
UR  - https://juser.fz-juelich.de/record/820516
ER  -