溶剂化
分子动力学
药物发现
溶剂模型
化学
计算机科学
药品
纳米技术
组合化学
溶剂
计算化学
材料科学
有机化学
生物
药理学
生物化学
作者
Lucas A. Defelipe,Juan Pablo Arcon,Carlos P. Modenutti,Marcelo A. Martí,Adrián Turjanski,Xavier Barril
出处
期刊:Molecules
[MDPI AG]
日期:2018-12-11
卷期号:23 (12): 3269-3269
被引量:27
标识
DOI:10.3390/molecules23123269
摘要
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.
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