122
Views
1
CrossRef citations to date
0
Altmetric
Research Articles

Computational identification of new TKI as potential noncovalent reversible EGFRL858R/T790M inhibitors: VHTS, molecular docking, DFT study and molecular dynamic simulation

ORCID Icon, , , , , & show all
Pages 4870-4887 | Received 12 Dec 2022, Accepted 05 Jun 2023, Published online: 22 Jun 2023

References

  • Abdallah, S. M.-B., & Hirsh, V. (2018). Irreversible tyrosine kinase inhibition of epidermal growth factor receptor with afatinib in EGFR activating mutation-positive advanced non-small-cell lung cancer. Current Oncology (Toronto, Ont.), 25(Suppl 1), S9–S17. https://doi.org/10.3747/co.25.3732
  • Abdelli, F., Jellali, K., Anguita, E., González-Muñoz, M., Villalobo, E., Madroñal, I., Alcalde, J., Ben Ali, M., Elloumi-Mseddi, J., Jemel, I., Tebar, F., Enrich, C., Aifa, S., & Villalobo, A. (2021). The role of the calmodulin-binding and calmodulin-like domains of the epidermal growth factor receptor in tyrosine kinase activation. Journal of Cellular Physiology, 236(7), 4997–5011. https://doi.org/10.1002/jcp.30205
  • Aifa, S., Frikha, F., Miled, N., Johansen, K., Lundström, I., & Svensson, S. P. S. (2006). Phosphorylation of Thr654 but not Thr669 within the juxtamembrane domain of the EGF receptor inhibits calmodulin binding. Biochemical and Biophysical Research Communications, 347(2), 381–387. https://doi.org/10.1016/j.bbrc.2006.05.200
  • Benet, L. Z., Hosey, C. M., Ursu, O., & Oprea, T. I. (2016). BDDCS, the rule of 5 and drugability. Advanced Drug Delivery Reviews, 101, 89–98. https://doi.org/10.1016/j.addr.2016.05.007
  • Cao, Y., Charisi, A., Cheng, L.-C., Jiang, T., & Girke, T. (2008). ChemmineR: A compound mining framework for R. Bioinformatics (Oxford, England), 24(15), 1733–1734. https://doi.org/10.1093/bioinformatics/btn307
  • Chico, L. K., Van Eldik, L. J., & Watterson, D. M. (2009). Targeting protein kinases in central nervous system disorders. Nature Reviews. Drug Discovery, 8(11), 892–909. https://doi.org/10.1038/nrd2999
  • Cortot, A. B., & Jänne, P. A. (2014). Molecular mechanisms of resistance in epidermal growth factor receptor-mutant lung adenocarcinomas. European Respiratory Review : An Official Journal of the European Respiratory Society, 23(133), 356–366. https://doi.org/10.1183/09059180.00004614
  • Doak, B. C., & Kihlberg, J. (2017). Drug discovery beyond the rule of 5 - Opportunities and challenges. Expert Opinion on Drug Discovery, 12(2), 115–119. https://doi.org/10.1080/17460441.2017.1264385
  • Guan, L., Yang, H., Cai, Y., Sun, L., Di, P., Li, W., Liu, G., & Tang, Y. (2019). ADMET-score – A comprehensive scoring function for evaluation of chemical drug-likeness. MedChemComm, 10(1), 148–157. https://doi.org/10.1039/C8MD00472B
  • Ito, T., Nagashima, H., Akiyama, M., Utsumi, Y., Sato, H., Chiba, S., Sugai, M., Ube, K., Mori, Y., Watanabe, K., Fukuhara, T., & Maemondo, M. (2022). Treatment with immune checkpoint inhibitors after EGFR-TKIs in EGFR-mutated lung cancer. Thoracic Cancer, 13(3), 386–393. https://doi.org/10.1111/1759-7714.14267
  • Jänne, P. A., Engelman, J. A., & Johnson, B. E. (2005). Epidermal growth factor receptor mutations in non–small-cell lung cancer: Implications for treatment and tumor biology. Journal of Clinical Oncology, 23(14), 3227–3234. https://doi.org/10.1200/JCO.2005.09.985
  • Joshi, T., Sharma, P., Joshi, T., & Chandra, S. (2020). In silico screening of anti- inflammatory compounds from Lichen by targeting cyclooxygenase-2. Journal of Biomolecular Structure & Dynamics, 38(12), 3544–3562. https://doi.org/10.1080/07391102.2019.1664328
  • Karlsen, E.-A., Kahler, S., Tefay, J., Joseph, S. R., & Simpson, F. (2021). Epidermal growth factor receptor expression and resistance patterns to targeted therapy in non-small cell lung cancer: A review. Cells, 10(5), 1206. https://doi.org/10.3390/cells10051206
  • Kim, T. E., & Murren, J. R. (2002). Erlotinib OSI/Roche/Genentech. Current Opinion in Investigational Drugs (London, England : 2000), 3(9), 1385–1395.
  • Kocher, F., Lunger, F., Seeber, A., Amann, A., Pircher, A., Hilbe, W., & Fiegl, M. (2016). Incidental diagnosis of asymptomatic non-small-cell lung cancer: A registry-based analysis. Clinical Lung Cancer, 17(1), 62–67.e1. https://doi.org/10.1016/j.cllc.2015.08.006
  • Liam, C.-K. (2019). The role of osimertinib in epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer. Journal of Thoracic Disease, 11(Suppl 3), S448–S452. https://doi.org/10.21037/jtd.2018.11.45
  • Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 46(1-3), 3–26. https://doi.org/10.1016/s0169-409x(00)00129-0
  • Maione, P., Sacco, P. C., Sgambato, A., Casaluce, F., Rossi, A., & Gridelli, C. (2015). Overcoming resistance to targeted therapies in NSCLC: Current approaches and clinical application. Therapeutic Advances in Medical Oncology, 7(5), 263–273. https://doi.org/10.1177/1758834015595048
  • Markóczy, Z., Sárosi, V., Kudaba, I., Gálffy, G., Turay, Ü. Y., Demirkazik, A., Purkalne, G., Somfay, A., Pápai-Székely, Z., Rásó, E., & Ostoros, G. (2018). Erlotinib as single agent first line treatment in locally advanced or metastatic activating EGFR mutation-positive lung adenocarcinoma (CEETAC): An open-label, non-randomized, multicenter, phase IV clinical trial. BMC Cancer, 18(1), 598. https://doi.org/10.1186/s12885-018-4283-z
  • Mathew, M. P., Tan, E., Saeui, C. T., Bovonratwet, P., Liu, L., Bhattacharya, R., & Yarema, K. J. (2015). Metabolic glycoengineering sensitizes drug-resistant pancreatic cancer cells to tyrosine kinase inhibitors erlotinib and gefitinib. Bioorganic & Medicinal Chemistry Letters, 25(6), 1223–1227. https://doi.org/10.1016/j.bmcl.2015.01.060
  • Osoegawa, A., Yamaguchi, M., Nakamura, T., Morinaga, R., Tanaka, K., Kashiwabara, K., Miura, T., Suetsugu, T., Harada, T., Asoh, T., Taguchi, K., Nabeshima, K., Kishimoto, J., Sakai, K., Nishio, K., & Sugio, K. (2021). High incidence of C797S mutation in patients with long treatment history of EGFR tyrosine kinase inhibitors including osimertinib. JTO Clinical and Research Reports, 2(7), 100191. https://doi.org/10.1016/j.jtocrr.2021.100191
  • Piergies, N., Paluszkiewicz, C., & Kwiatek, W. M. (2019). Vibrational fingerprint of Erlotinib: FTIR, RS, and DFT Studies. Journal of Spectroscopy, 2019, e9191328–10. https://doi.org/10.1155/2019/9191328
  • Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., Smith, J. C., Kasson, P. M., van der Spoel, D., Hess, B., & Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (Oxford, England), 29(7), 845–854. https://doi.org/10.1093/bioinformatics/btt055
  • Rhodes, G., & Rhodes, G. (2006). Chapter 9 - Other diffraction methods. In Crystallography Made Crystal Clear (Third Edition), Complementary Science. Academic Press. pp. 211–235. https://doi.org/10.1016/B978-012587073-3/50011-8
  • Schettino, C., Bareschino, M. A., Ricci, V., & Ciardiello, F. (2008). Erlotinib: An EGF receptor tyrosine kinase inhibitor in non-small-cell lung cancer treatment. Expert Review of Respiratory Medicine, 2(2), 167–178. https://doi.org/10.1586/17476348.2.2.167
  • Sevvanthi, S., Muthu, S., Raja, M., Aayisha, S., & Janani, S. (2020). PES, molecular structure, spectroscopic (FT-IR, FT-Raman), electronic (UV-Vis, HOMO-LUMO), quantum chemical and biological (docking) studies on a potent membrane permeable inhibitor: Dibenzoxepine derivative. Heliyon, 6(8), e04724. https://doi.org/10.1016/j.heliyon.2020.e04724
  • Song, Z., Ge, Y., Wang, C., Huang, S., Shu, X., Liu, K., Zhou, Y., & Ma, X. (2016). Challenges and perspectives on the development of small-molecule EGFR inhibitors against T790M-mediated resistance in non-small-cell lung cancer. Journal of Medicinal Chemistry, 59(14), 6580–6594. https://doi.org/10.1021/acs.jmedchem.5b00840
  • Spaans, J. N., & Goss, G. D. (2014). Trials to overcome drug resistance to EGFR and ALK targeted therapies - past, present, and future. Frontiers in Oncology, 4, 233. https://doi.org/10.3389/fonc.2014.00233
  • Tiseo, M., Bartolotti, M., Gelsomino, F., & Bordi, P. (2010). Emerging role of gefitinib in the treatment of non-small-cell lung cancer (NSCLC). Drug Design, Development and Therapy, 4, 81–98. https://doi.org/10.2147/dddt.s6594
  • Tsubata, Y., Tanino, R., & Isobe, T. (2021). Current therapeutic strategies and prospects for EGFR mutation-positive lung cancer based on the mechanisms underlying drug resistance. Cells, 10(11), 3192. https://doi.org/10.3390/cells10113192
  • Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., & MacKerell, A. D. (2010). CHARMM General Force Field (CGenFF): A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. Journal of Computational Chemistry, 31(4), 671–690. https://doi.org/10.1002/jcc.21367
  • Yadava, U., Gupta, H., & Roychoudhury, M. (2012). A comparison of crystallographic and DFT optimized geometries on two taxane diterpenoids and docking studies with phospholipase A2. Medicinal Chemistry Research, 21(9), 2162–2168. https://doi.org/10.1007/s00044-011-9724-z
  • Yang, C., Zhang, Y., Zeng, X., Chen, H., Chen, Y., Yang, D., Shen, Z., Wang, X., Liu, X., Xiong, M., Chen, H., & Huang, K. (2021). Kidney injury molecule-1 is a potential receptor for SARS-CoV-2. Journal of Molecular Cell Biology, 13(3), 185–196. https://doi.org/10.1093/jmcb/mjab003
  • Yang, T., Li, Z., Chen, Y., Feng, D., Wang, G., Fu, Z., Ding, X., Tan, X., Zhao, J., Luo, X., Chen, K., Jiang, H., & Zheng, M. (2021). DrugSpaceX: A large screenable and synthetically tractable database extending drug space. Nucleic Acids Research, 49(D1), D1170–D1178. https://doi.org/10.1093/nar/gkaa920
  • Yong-Feng, Z., Mei-Shan, W., Chuan-Lu, Y., Mei-Zhong, M., Wei-Xiu, P., & Rong-Cai, M. (2008). Ab initio calculations of the ionization spectrum of SO2. Chinese Physics B, 17(11), 4163.
  • Yuan, M., Huang, L.-L., Chen, J.-H., Wu, J., & Xu, Q. (2019). The emerging treatment landscape of targeted therapy in non-small-cell lung cancer. Signal Transduction and Targeted Therapy, 4(1), 61. https://doi.org/10.1038/s41392-019-0099-9
  • Zhang, W., Lei, P., Dong, X., & Xu, C. (2014). The new concepts on overcoming drug resistance in lung cancer. Drug Design, Development and Therapy, 8, 735–744. https://doi.org/10.2147/DDDT.S60672
  • Zhang, X., Gureasko, J., Shen, K., Cole, P. A., & Kuriyan, J. (2006). An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor. Cell, 125(6), 1137–1149. https://doi.org/10.1016/j.cell.2006.05.013
  • Zhao, L., Wang, Z., Du, H., Chen, S., & Wang, P. (2021). Lung adenocarcinoma patient harboring EGFR-KDD achieve durable response to Afatinib: A case report and literature review. Frontiers in Oncology, 11, 605853. https://doi.org/10.3389/fonc.2021.605853
  • Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. (2011). SwissParam: A fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 32(11), 2359–2368. https://doi.org/10.1002/jcc.21816

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.