2026-04-04T06:49:10Zhttps://recercat.cat/oai/requestoai:recercat.cat:2445/1580582025-12-05T14:12:49Zcom_2072_1057col_2072_478815col_2072_478917
RECERCAT
author
Defelipe, Lucas A.
author
Arcon, Juan Pablo
author
Modenutti, Carlos P.
author
Martí, Marcelo A.
author
Turjanski,Adrián G.
author
Barril Alonso, Xavier
2020-04-29T14:31:08Z2020-04-29T14:31:08Z2018-12-112020-04-29T14:31:09Z
Simulations of molecular dynamics (MD) are playing an increasingly important role in structure-based drug discovery (SBDD). Here we review the use of MD for proteins in aqueous solvation, organic/aqueous mixed solvents (MDmix) and with small ligands, to the classic SBDD problems: Binding mode and binding free energy predictions. The simulation of proteins in their condensed state reveals solvent structures and preferential interaction sites (hot spots) on the protein surface. The information provided by water and its cosolvents can be used very effectively to understand protein ligand recognition and to improve the predictive capability of well-established methods such as molecular docking. The application of MD simulations to the study of the association of proteins with drug-like compounds is currently only possible for specific cases, as it remains computationally very expensive and labor intensive. MDmix simulations on the other hand, can be used systematically to address some of the common tasks in SBDD. With the advent of new tools and faster computers we expect to see an increase in the application of mixed solvent MD simulations to a plethora of protein targets to identify new drug candidates.
cc-by (c) Defelipe, Lucas A. et al., 2018 http://creativecommons.org/licenses/by/3.0/es info:eu-repo/semantics/openAccess
Dinàmica molecular
Disseny de medicaments
Medicaments peptídics
Molecular dynamics
Drug design
Peptide drugs
Solvents to Fragments to Drugs: MD Applications in Drug Design
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion