Understanding Drug Binding Mechanisms: Insights from Molecular Dynamics Simulations

EasyChair Preprint 12006

Abstract

Molecular dynamics (MD) simulations have emerged as a powerful tool for elucidating the intricate mechanisms underlying drug binding to their target molecules. In this review, we provide an overview of recent advancements in the application of MD simulations to probe drug-binding mechanisms at the atomic level. We discuss the methodology involved in setting up MD simulations of drug-target complexes, including the selection of force fields and simulation parameters. Furthermore, we highlight case studies where MD simulations have provided valuable insights into the dynamic behavior of drug molecules within their binding pockets, the role of water molecules in mediating drug-target interactions, and the conformational changes induced upon drug binding. Additionally, we discuss challenges and limitations associated with MD simulations, such as the need for an accurate representation of the solvent environment and the computational cost of simulating long timescales. Finally, we discuss future directions in the field, including the integration of MD simulations with experimental techniques to validate and refine computational models of drug binding. Overall, MD simulations offer a detailed and atomistic understanding of drug-target interactions, which can aid in the rational design of novel therapeutics with improved efficacy and selectivity.

Keyphrases: Computational drug, Drug binding mechanisms, molecular dynamics simulations

@booklet{EasyChair:12006,
  author    = {Mehmet Ayaz and James Henry},
  title     = {Understanding Drug Binding Mechanisms: Insights from Molecular Dynamics Simulations},
  howpublished = {EasyChair Preprint 12006},
  year      = {EasyChair, 2024}}