Applications of Molecular Dynamics Simulations in Drug Discovery

Sara AlRawashdeh; Khaled H Barakat

doi:10.1007/978-1-0716-3441-7_7

Applications of Molecular Dynamics Simulations in Drug Discovery

Methods Mol Biol. 2024:2714:127-141. doi: 10.1007/978-1-0716-3441-7_7.

Authors

Sara AlRawashdeh¹, Khaled H Barakat²

Affiliations

¹ Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.
² Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada. kbarakat@ualberta.ca.

PMID: 37676596
DOI: 10.1007/978-1-0716-3441-7_7

Abstract

In the current drug development process, molecular dynamics (MD) simulations have proven to be very useful. This chapter provides an overview of the current applications of MD simulations in drug discovery, from detecting protein druggable sites and validating drug docking outcomes to exploring protein conformations and investigating the influence of mutations on its structure and functions. In addition, this chapter emphasizes various strategies to improve the conformational sampling efficiency in molecular dynamics simulations. With a growing computer power and developments in the production of force fields and MD techniques, the importance of MD simulations in helping the drug development process is projected to rise significantly in the future.

Keywords: Drug discovery; Enhanced sampling; Molecular dynamics simulations; Protein druggability.

Publication types

Review

MeSH terms

Drug Discovery*
Molecular Dynamics Simulation*
Mutation
Protein Conformation