New approaches for computing ligand-receptor binding kinetics

Curr Opin Struct Biol. 2018 Apr;49:1-10. doi: 10.1016/j.sbi.2017.10.001. Epub 2017 Nov 11.

Abstract

The recent and growing evidence that the efficacy of a drug can be correlated to target binding kinetics has seeded the development of a multitude of novel methods aimed at computing rate constants for receptor-ligand binding processes, as well as gaining an understanding of the binding and unbinding pathways and the determinants of structure-kinetic relationships. These new approaches include various types of enhanced sampling molecular dynamics simulations and the combination of energy-based models with chemometric analysis. We assess these approaches in the light of the varying levels of complexity of protein-ligand binding processes.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Drug Discovery / methods*
  • Humans
  • Kinetics
  • Ligands
  • Molecular Docking Simulation / methods*
  • Molecular Dynamics Simulation*
  • Protein Binding
  • Protein Conformation / drug effects
  • Proteins / chemistry
  • Proteins / metabolism*
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / pharmacology*
  • Thermodynamics*

Substances

  • Ligands
  • Proteins
  • Small Molecule Libraries