1. The prediction of treatment outcome in NSCLC patients harboring an EGFR exon 20 mutation using molecular modeling.
- Author
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Zwierenga F, Zhang L, Melcr J, Schuuring E, van Veggel BAMH, de Langen AJ, Groen HJM, Groves MR, and van der Wekken AJ
- Subjects
- Humans, Treatment Outcome, Molecular Docking Simulation, Models, Molecular, Prognosis, Carcinoma, Non-Small-Cell Lung genetics, Carcinoma, Non-Small-Cell Lung drug therapy, Carcinoma, Non-Small-Cell Lung pathology, ErbB Receptors genetics, Lung Neoplasms genetics, Lung Neoplasms drug therapy, Lung Neoplasms pathology, Exons genetics, Mutation, Protein Kinase Inhibitors therapeutic use, Molecular Dynamics Simulation
- Abstract
Introduction: The structural effect of uncommon heterogenous in-frame deletion and/or insertion mutations within exon 20 (EGFRex20+) in relation to therapy response is poorly understood. This study aims to elucidate the structural alterations caused by EGFRex20+ mutations and correlate these changes with patient responses., Material and Method: We selected EGFRex20+ mutations from advanced NSCLC patients in the Position20 and AFACET studies for computational analysis. Homology models representing both inactive and active conformations of these mutations were generated using the Swiss-Model server. Molecular docking studies with EGFR-TKIs was conducted using smina, followed by Molecular Dynamic (MD) simulations performed with GROMACS. These computational findings were compared with clinical outcomes to evaluate their potential in predicting patient response., Results: Our docking studies of 29 EGFRex20+ mutations revealed that the binding energies of afatinib, osimertinib, zipalertinib, and sunvozertinib, compared to the wild type, do not significantly impact either TKI's efficacy. MD simulations for eight EGFRex20+ mutations (A763_Y764insFQEA, A767_V769dup, S768_D770dup, D770_N771insG, D770_P772dup, N771_H773dup, H773_V774insY and H773_V774delinsLM) revealed varying degrees of instability. For six variants, predicted activation based on the αC-helix stability and orientation, as well as TKI sensitivity, aligned well with clinical observations from the Position20 and AFACET studies. Two mutations (D770_N771insG and N771_H773dup) predicted as poor to moderate responders, showed minimal activation of the αC-helix region, warranting further investigation., Conclusion: In conclusion, MD simulations can effectively predict patient outcomes by connecting computational results with clinical data and advancing our understanding of EGFR mutations and their therapeutic responses., Competing Interests: Declaration of competing interest JM and MG are employees of Protyon, a spin-out company of the UMCG to provide molecular modeling support for clinical decision-making. ES reports lectures for Bio-Rad, Seracare, Roche, Biocartis, Illumina, Lilly, Janssen Cilag (Johnson&Johnson), AstraZeneca and Agena Bioscience; he is consultant in advisory boards for MSD/Merck, GSK, AstraZeneca, Astellas Pharma, Sysmex, Roche, Novartis, Bayer, BMS, Lilly, Amgen, Illumina, Agena Bioscience, Janssen Cilag (Johnson&Johnson), Sinnovisionlab, Diaceutics, CC Diagnostics and Protyon; and received research grants from Biocartis, Invitae-ArcherDX, AstraZeneca, Agena Bio-science, BMS, Bio-Rad, Roche, Boehringer Ingelheim, CC Diagnostics, SNN/EFRO and Abbott (all paid to UMCG account); and travel reimbursements from Bio-Rad, Abbott, Illumina, Agena Bioscience, Roche, IQNPath and BioRAD. BV has personal fees from Bristol-Myers Squibb, Johnson & Johnson en Astra Zeneca; outside the submitted work. AL reports grants from AstraZeneca, BMS, MSD, Boehringer Ingelheim, and non-financial support from Merck Serono and Roche, all outside the submitted work. AW has grants and personal fees from AstraZeneca, Boehringer Ingelheim, Pfizer, Roche, Takeda, Janssen Cilag, Lilly, Amgen, Merck; outside the submitted work and all institutional payments. All other authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2024
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