Bera I, Payghan PV. Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery.
Curr Pharm Des 2020;
25:3339-3349. [PMID:
31480998 DOI:
10.2174/1381612825666190903153043]
[Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/01/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND
Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process.
OBJECTIVE
The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design.
METHOD
This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained.
RESULTS
This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations.
CONCLUSION
The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.
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