Investigating Ligand Binding Mechanisms Through Molecular Dynamics Simulations

EasyChair Preprint 12156

Abstract

Understanding the mechanisms underlying ligand binding to biological macromolecules is crucial for drug design and development. Molecular dynamics (MD) simulations have emerged as powerful tools for investigating the dynamic behavior of biomolecular systems at an atomic level. In this study, we employed MD simulations to explore the binding mechanisms of ligands to their target proteins. First, we performed extensive MD simulations of the apo-protein and ligand-bound protein to characterize their structural dynamics and identify key regions involved in ligand recognition. By analyzing the trajectories, we observed conformational changes in the protein upon ligand binding, including the reorganization of binding pockets and the formation of hydrogen bonds and hydrophobic interactions between the ligand and protein residues. Our study highlights the utility of MD simulations in unraveling the complex mechanisms of ligand binding and provides valuable insights for rational drug design strategies. Through a detailed analysis of protein-ligand interactions at the atomic level, we aim to contribute to the development of novel therapeutics targeting various biological processes.

Keyphrases: ligand binding, molecular dynamics simulations, protein-ligand interactions

@booklet{EasyChair:12156,
  author    = {James Henry and Bilal Ahmed},
  title     = {Investigating Ligand Binding Mechanisms Through Molecular Dynamics Simulations},
  howpublished = {EasyChair Preprint 12156},
  year      = {EasyChair, 2024}}