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

Future Medicinal Chemistry
Shristi Pawnikar, Yinglong Miao

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.

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Citations

Sep 17, 2020·International Journal of Molecular Sciences·Marcus ConradHeinrich Sticht
Dec 16, 2020·Future Medicinal Chemistry·Harriet Wall
May 15, 2021·Frontiers in Molecular Biosciences·Hung N DoYinglong Miao
Jul 21, 2021·Nucleic Acids Research·Zhichao TangJingxin Wang
Jul 22, 2020·Journal of Chemical Theory and Computation·Yinglong MiaoJinan Wang

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Software Mentioned

CHARMM
CPPTRAJ
Fual
VMD
Plerixafor
GaMD
Anton
CGenFF
AutoDock
PLX

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