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Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis

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Abstract

FGFR3 kinase mutations are associated with a variety of malignancies, but FGFR3 mutant inhibitors have rarely been studied. Furthermore, the mechanism of pan-FGFR inhibitors resistance caused by kinase domain mutations is still unclear. In this study, we try to explain the mechanism of drug resistance to FGFR3 mutation through global analysis and local analysis based on molecular dynamics simulation, binding free energy analysis, umbrella sampling and community network analysis. The results showed that FGFR3 mutations caused a decrease in the affinity between drugs and FGFR3 kinase, which was consistent with the reported experimental results. Possible mechanisms are that mutations affect drug-protein affinity by altering the environment of residues near the hinge region where the protein binds to the drug, or by affecting the A-loop and interfering with the allosteric communication networks. In conclusion, we systematically elucidated the underlying mechanism of pan-FGFR inhibitor resistance caused by FGFR3 mutation based on molecular dynamics simulation strategy, which provided theoretical guidance for the development of FGFR3 mutant kinase inhibitors.

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Acknowledgements

This work was supported by the Natural Science Foundation of Zhejiang Province, China (Grant No. LGF20B020001); National Natural Science Foundation of China (Grant No. 81402839, 81803580); MOE Key Laboratory of Tumor Molecular Biology (Grant No. 50411651-2020-4) and the Guangdong Basic and Applied Basic Research Foundation (Grant No. 2021A1515011184).

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B.L. is responsible for research performing, data analyzing and paper writing. J.D. and X.W. are responsible data analyzing. Y.L. is responsible for script writing. J.W., Q.C. and W.L. are responsible for research designing and revised paper writing.

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Correspondence to Qian Chen or Wulan Li.

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Liu, B., Ding, J., Liu, Y. et al. Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis. J Comput Aided Mol Des 37, 325–338 (2023). https://doi.org/10.1007/s10822-023-00510-8

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