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Research Article

Molecular docking and molecular dynamics simulations reveal the clinical resistance of the gatekeeper mutation V564F of FGFR2 against Infigratinib

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Article: 2264521 | Received 12 Jun 2023, Accepted 12 Sep 2023, Published online: 05 Oct 2023

References

  • Katoh M. Therapeutics targeting FGF signaling network in human diseases. Trends Pharmacol Sci. 2016;37(12):1–14. doi: 10.1016/j.tips.2016.10.003.
  • Chen H, Ma J, Li W, et al. A molecular brake in the kinase hinge region regulates the activity of receptor tyrosine kinases. Mol Cell. 2007;27(5):717–730. doi: 10.1016/j.molcel.2007.06.028.
  • Huang Z, Marsiglia WM, Basu Roy U, et al. Two FGF receptor kinase molecules act in concert to recruit and transphosphorylate phospholipase Cγ. Mol Cell. 2016;61(1):98–110. doi: 10.1016/j.molcel.2015.11.010.
  • Li C, Dai Y, Kong X, et al. Structural optimization of fibroblast growth factor receptor inhibitors for treating solid tumors. J Med Chem. 2023;66(5):3226–3249. doi: 10.1021/acs.jmedchem.2c01507.
  • Turner LD, Trinh CH, Hubball RA, et al. From fragment to lead: de novo design and development toward a selective FGFR2 inhibitor. J Med Chem. 2022;65(2):1481–1504. doi: 10.1021/acs.jmedchem.1c01163.
  • Ryu S, Nam Y, Kim N, et al. Identification of pyridinyltriazine derivatives as potent panFGFR inhibitors against gatekeeper mutants for overcoming drug resistance. J Med Chem. 2022;65(8):6017–6038. doi: 10.1021/acs.jmedchem.1c01776.
  • Guagnano V, Furet P, Spanka C, et al. Discovery of 3-(2,6-Dichloro-3,5-dimethoxy-phenyl)-1-{6-[4-(4-ethyl- piperazin-1-yl)-phenylamino]-pyrimidin-4-yl}-1-methyl-urea (NVP-BGJ398), a potent and selective inhibitor of the fibroblast growth factor receptor family of receptor tyrosine kinase. J Med Chem. 2011;54(20):7066–7083. doi: 10.1021/jm2006222.
  • Roskoski R. Properties of FDA-approved small molecule protein kinase inhibitors: a 2022 update. Pharmacol Res. 2022;175:106037.
  • Kang C. Infigratinib: first approval. Drugs. 2021;81(11):1355–1360. doi: 10.1007/s40265-021-01567-1.
  • Nogova L, Sequist LV, Garcia JMP, et al. Evaluation of BGJ398, a fibroblast growth factor receptor 1-3 kinase inhibitor, in patientswith advanced solid tumors harboring genetic alterations in fibroblast growth factor receptors: results of a global phase I, dose-escalation and dose-expansion study. J Clin Oncol. 2017;35(2):157–165. doi: 10.1200/JCO.2016.67.2048.
  • Silverman IM, Hollebecque A, Friboulet L, et al. Clinicogenomic analysis of FGFR2-rearranged cholangiocarcinoma identifies correlates of response and mechanisms of resistance to pemigatinib. Cancer Discov. 2021;11(2):326–339. doi: 10.1158/2159-8290.CD-20-0766.
  • Goyal L, Saha SK, Liu LY, et al. Polyclonal secondary FGFR2 mutations drive acquired resistance to FGFR inhibition in patients with FGFR2 fusion-positive cholangiocarcinoma. Cancer Discov. 2017;7(3):252–263. doi: 10.1158/2159-8290.CD-16-1000.
  • Eathiraj S, Palma R, Hirschi M, et al. A novel mode of protein kinase inhibition exploiting hydrophobic motifs of autoinhibited kinases: discovery of ATP-independent inhibitors of fibroblast growth factor receptor. J Biol Chem. 2011;286(23):20677–20687. doi: 10.1074/jbc.M110.213736.
  • Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera - A visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–1612. doi: 10.1002/jcc.20084.
  • Salomon-Ferrer R, Case DA, Walker RC. An overview of the Amber biomolecular simulation package. WIREs Comput Mol Sci. 2013;3(2):198–210. doi: 10.1002/wcms.1121.
  • Bayly CI, Cieplak P, Cornell WD, et al. A Well-Behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem. 1993;97(40):10269–10280. doi: 10.1021/j100142a004.
  • Maier JA, Martinez C, Kasavajhala K, et al. ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theory Comput. 2015;11(8):3696–3713. doi: 10.1021/acs.jctc.5b00255.
  • Wang J, Wolf RM, Caldwell JW, et al. Development and testing of a general amber force field. J Comput Chem. 2004;25(9):1157–1174. doi: 10.1002/jcc.20035.
  • Jorgensen WL, Chandrasekhar J, Madura JD, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79(2):926–935. doi: 10.1063/1.445869.
  • Darden T, York D, Pedersen L. Particle mesh Ewald: an N.long(N)method for Ewald sums in large systems. J Chem Phys. 1993;98(12):10089–10092. doi: 10.1063/1.464397.
  • Ryckaert J-P, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-Alkanes. J Comput Phys. 1977;23(3):327–341. doi: 10.1016/0021-9991(77)90098-5.
  • Wang E, Sun H, Wang J, et al. End-Point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design. Chem Rev. 2019;119(16):9478–9508. doi: 10.1021/acs.chemrev.9b00055.
  • Li M, Wang Y, Fan J, et al. Mechanistic insights into the long-range allosteric regulation of KRAS via neurofibromatosis type 1 (NF1) scaffold upon SPRED1 loading. J Mol Biol. 2022;434(17):167730. doi: 10.1016/j.jmb.2022.167730.
  • Cao S, Jiang X, Tan C, et al. How does nintedanib overcome cancer drug-resistant mutation of RET protein-tyrosine kinase: insights from molecular dynamics simulations. J Mol Model. 2021;27(11):337. doi: 10.1007/s00894-021-04964-1.
  • Zhang H, Chu G, Wang G, et al. Mechanistic understanding of the palmitoylation of go protein in the allosteric regulation of adhesion receptor GPR97. Pharmaceutics. 2022;14(9):1856. doi: 10.3390/pharmaceutics14091856.
  • Qi X, Li G, Liu J, et al. Structural and energetic insights into the selective inhibition of PKMYT1 against WEE1. J Biomol Struct Dyn. 2023;:1–9. doi: 10.1080/07391102.2023.2225106.
  • Li X, Wang C, Peng T, et al. Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6. Comput Struct Biotechnol J. 2021;19:6108–6124. doi: 10.1016/j.csbj.2021.11.010.
  • Lu S, Chen Y, Wei J, et al. Mechanism of allosteric activation of SIRT6 revealed by the action of rationally designed activators. Acta Pharm Sin B. 2021;11(5):1355–1361. doi: 10.1016/j.apsb.2020.09.010.
  • Morris GM, Ruth H, Lindstrom W, et al. Software news and updates AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785–2791. doi: 10.1002/jcc.21256.
  • Ni D, Wei J, He X, et al. Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy. Chem Sci. 2020;12(1):464–476. doi: 10.1039/d0sc05131d.
  • Lu S, He X, Yang Z, et al. Activation pathway of a G protein-coupled receptor uncovers conformational intermediates as targets for allosteric drug design. Nat Commun. 2021;12(1):4721. doi: 10.1038/s41467-021-25020-9.
  • Lu S, Ni D, Wang C, et al. Deactivation pathway of ras GTPase underlies conformational substates as targets for drug design. ACS Catal. 2019;9(8):7188–7196. doi: 10.1021/acscatal.9b02556.
  • Wang Y, Ji D, Lei C, et al. Mechanistic insights into the effect of phosphorylation on RAS conformational dynamics and its interactions with cell signaling proteins. Comput Struct Biotechnol J. 2021;19:1184–1199. doi: 10.1016/j.csbj.2021.01.044.
  • Qiu Y, Yin X, Li X, et al. Untangling dual-targeting therapeutic mechanism of epidermal growth factor receptor (EGFR) based on reversed allosteric communication. Pharmaceutics. 2021;13(5):747. doi: 10.3390/pharmaceutics13050747.
  • Ji M, Chai Z, Chen J, et al. Insights into the allosteric effect of SENP1 Q597A mutation on the hydrolytic reaction of SUMO1 via an integrated computational study. Molecules. 2022;27(13):4149. doi: 10.3390/molecules27134149.
  • Chen J, Zhang S, Wang W, et al. Mutation-induced impacts on the switch transformations of the GDP- and GTP-bound K-Ras: insights from multiple replica Gaussian accelerated molecular dynamics and free energy analysis. J Chem Inf Model. 2021;61(4):1954–1969. doi: 10.1021/acs.jcim.0c01470.
  • Chen J, Zeng Q, Wang W, et al. Decoding the identification mechanism of an SAM-II riboswitch on ligands through multiple independent Gaussian-accelerated molecular dynamics simulations. J Chem Inf Model. 2022;62(23):6118–6132. doi: 10.1021/acs.jcim.2c00961.
  • Shi Y, Cao S, Ni D, et al. The role of conformational dynamics and allostery in the control of distinct efficacies of agonists to the glucocorticoid receptor. Front Mol Biosci. 2022;9:933676. doi: 10.3389/fmolb.2022.933676.
  • Zhuang H, Fan J, Li M, et al. Mechanistic insights into the clinical Y96D mutation with acquired resistance to AMG510 in the KRASG12C. Front Oncol. 2022;12:915512. doi: 10.3389/fonc.2022.915512.
  • He X, Huang N, Qiu Y, et al. Conformational selection mechanism provides structural insights into the optimization of APC-Asef inhibitors. Molecules. 2021;26(4):962. doi: 10.3390/molecules26040962.
  • Zhuang H, Ji D, Fan J, et al. Mechanistic insights into the protection effect of Argonaute-RNA complex on the HCV genome. Biomolecules. 2022;12(11):1631. doi: 10.3390/biom12111631.
  • Roe DR, Cheatham TE. PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput. 2013;9(7):3084–3095. doi: 10.1021/ct400341p.
  • Hu MT, Ma WC, Wang JH, et al. Mechanistic insights into the allosteric mechanism of ZAP-70 induced by the hot spot W165C mutation. J Biomol Struct Dyn. 2023;:1–10. doi: 10.1080/07391102.2023.2240421.
  • Zheng G, Xu S, Liu W, et al. Deciphering the resistance mechanism of RET kinase mutant against vandetenib and nintedanib using molecular dynamics simulations. J Exp Nanosci. 2021;16(1):278–293. doi: 10.1080/17458080.2021.1970141.