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.