Pathway and mechanism of drug binding to chemokine receptors revealed by accelerated molecular simulations

Future Med Chem. 2020 Jul;12(13):1213-1225. doi: 10.4155/fmc-2020-0044. Epub 2020 Jun 9.

Abstract

Background: Chemokine GPCRs play key roles in biology and medicine. Particularly, CXCR4 promotes cancer metastasis and facilitate HIV entry into host cells. Plerixafor (PLX) is a CXCR4 drug, but the pathway and binding site of PLX in CXCR4 remain unknown. Results & methodology: We have performed molecular docking and all-atom simulations using Gaussian accelerated molecular dynamics (GaMD), which are consistent with previous mutation experiments, suggesting that PLX binds to the orthosteric site of CXCR4 as an antagonist. The GaMD simulations further revealed an intermediate allosteric binding site at the extracellular mouth of CXCR4. Conclusion: The newly identified allosteric site can be targeted for novel drug design targeting CXCR4 and other chemokine receptors.

Keywords: GPCRs; Gaussian accelerated molecular dynamics; HIV; chemokine receptors; drug binding; plerixafor.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Anti-HIV Agents / chemistry*
  • Anti-HIV Agents / pharmacology
  • Benzylamines / chemistry*
  • Benzylamines / pharmacology
  • Binding Sites / drug effects
  • Cyclams / chemistry*
  • Cyclams / pharmacology
  • Humans
  • Molecular Docking Simulation*
  • Molecular Dynamics Simulation*
  • Molecular Structure
  • Receptors, CXCR4 / antagonists & inhibitors
  • Receptors, CXCR4 / chemistry*

Substances

  • Anti-HIV Agents
  • Benzylamines
  • CXCR4 protein, human
  • Cyclams
  • Receptors, CXCR4
  • plerixafor