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Research Articles

BREED based de novo hybridization approach: generating novel T790M/C797S-EGFR tyrosine kinase inhibitors to overcome the problem of mutation and resistance in non small cell lung cancer (NSCLC)

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Pages 2838-2856 | Received 17 Jan 2020, Accepted 07 Apr 2020, Published online: 23 Apr 2020

References

  • Chen, L., Fu, W., Zheng, L., Liu, Z., & Liang, G. (2018). Recent progress of small-molecule epidermal growth factor receptor (EGFR) inhibitors against C797S resistance in non-small cell lung cancer. Journal of Medicinal Chemistry, 61(10), 4290–4300. 10.1021/acs.jmedchem.7b01310
  • Cheng, S., Guo, A., Lu, P., Ma, J., Coleman, M., & Wang, Y. L. (2015). Functional characterization of BTK C481S mutation that confers ibrutinib resistance: Exploration of alternative kinase inhibitors. Leukemia, 29(4), 895–900. 10.1038/leu.2014.263
  • Chen, F., Liu, H., Sun, H., Pan, P., Li, Y., Li, D., & Hou, T. (2016). Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein protein binding free energies and re-rank binding poses generated by protein-protein docking. Physical Chemistry Chemical Physics, 18(32), 22129–22139. 10.1039/C6CP03670H
  • Chuang, J. C., Salahudeen, A. A., & Wakelee, H. A. (2016). Rociletinib, a third generation EGFR tyrosine kinase inhibitor: Current data and future directions. Expert Opinion on Pharmacotherapy., 17(7), 989–993. 10.1517/14656566.2016.1162786
  • Cross, D. A. E., Ashton, S. E., Ghiorghiu, S., Eberlein, C., Nebhan, C. A., Spitzler, P. J., Orme, J. P., Finlay, M. R. V., Ward, R. A., Mellor, M. J., Hughes, G., Rahi, A., Jacobs, V. N., Brewer, M. R., Ichihara, E., Sun, J., Jin, H., Ballard, P., Al-Kadhimi, K., … Pao, W. (2014). AZD9291, an irreversible EGFR TKI, overcomes T790M-mediated resistance to EGFR inhibitors in lung cancer. Cancer Discovery, 4(9), 1046–1061. 10.1158/2159-8290.CD-14-0337
  • Ertl, P., Rohde, B., & Selzer, P. (2000). Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. Journal of Medicinal Chemistry, 43(20), 3714–3717. 10.1021/jm000942e
  • Gohlke, H., & Klebe, G. (2002). Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angewandte Chemie International Edition, 41(15), 2644–2676. 10.1002/1521-3773(20020802)41:15<2644::AID-ANIE2644>3.0.CO;2-O
  • Hedley, P. L., Jørgensen, P., Schlamowitz, S., Wangari, R., Moolman-Smook, J., Brink, P. A., Kanters, J. K., Corfield, V. A., & Christiansen, M. (2009). The genetic basis of long QT and short QT syndromes: A mutation update. Human Mutation, 30(11), 1486–1511. 10.1002/humu.21106
  • Ho, C. M. W., & Marshall, G. R. (1993). SPLICE: A program to assemble partial query solutions from three-dimensional database searches into novel ligands. Journal of Computer-Aided Molecular Design, 7(6), 623–647. 10.1007/BF00125322
  • Hou, T., Li, N., Li, Y., & Wang, W. (2012). Characterization of domain-peptide interaction interface: Prediction of SH3 domain-mediated protein-protein interaction network in yeast by generic structure-based models. Journal of Proteome Research, 11(5), 2982–2995. 10.1021/pr3000688
  • Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods: II. The accuracy of ranking poses generated from docking. Journal of Computational Chemistry, 32(5), 866–877. 10.1002/jcc.21666
  • John, A., Umashankar, V., Krishnakumar, S., & Deepa, P. R. (2015). Comparative modeling and molecular dynamics simulation of substrate binding in human fatty acid synthase: Enoyl reductase and β-Ketoacyl Reductase Catalytic Domains. Genomics & Informatics, 13(1), 15–12. 10.5808/GI.2015.13.1.15
  • Kobayashi, S., Boggon, T. J., Dayaram, T., Jänne, P. A., Kocher, O., Meyerson, M., Johnson, B. E., Eck, M. J., Tenen, D. G., & Halmos, B. (2005). EGFR mutation and resistance of non–small-cell lung cancer to gefitinib. New England Journal of Medicine, 352(8), 786–792. 10.1056/NEJMoa044238
  • Kong, L. L., Ma, R., Yao, M. Y., Yan, X. E., Zhu, S. J., Zhao, P., & Yun, C. H. (2017). Structural pharmacological studies on EGFR T790M/C797S. Biochemical and Biophysical Research Communications., 488(2), 266–272. 10.1016/j.bbrc.2017.04.138
  • Konze, K., Bos, P., Dahlgren, M., Leswing, K., Tubert-Brohman, I., Bortolato, A., Robbason, B., Abel, R., & Bhat, S. (2019). Reaction-based enumeration, active learning, and free energy calculations to rapidly explore synthetically tractable chemical space and optimize potency of cyclin dependent kinase 2 inhibitors. Journal of Chemical Information and Modeling, 59(9), 3782–3793. 10.1021/acs.jcim.9b00367
  • Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1-3), 3–25. 10.1016/S0169-409X(96)00423-1
  • Maemondo, M., Inoue, A., Kobayashi, K., Sugawara, S., Oizumi, S., Isobe, H., Gemma, A., Harada, M., Yoshizawa, H., Kinoshita, I., Fujita, Y., Okinaga, S., Hirano, H., Yoshimori, K., Harada, T., Ogura, T., Ando, M., Miyazawa, H., Tanaka, T., … Nukiwa, T. (2010). Gefitinib or chemotherapy for non–small-cell lung cancer with mutated EGFR. New England Journal of Medicine, 362(25), 2380–2388. 10.1056/NEJMoa0909530
  • Martyna, G. J. (1994). Constant-temperature molecular dynamics with momentum conservation. Physical Review E, 50(4), 3234–3236. 10.1103/PhysRevE.50.3234
  • Mitsudomi, T., Morita, S., Yatabe, Y., Negoro, S., Okamoto, I., Tsurutani, J., Seto, T., Satouchi, M., Tada, H., Hirashima, T., Asami, K., Katakami, N., Takada, M., Yoshioka, H., Shibata, K., Kudoh, S., Shimizu, E., Saito, H., Toyooka, S., Nakagawa, K., & Fukuoka, M. (2010). Gefitinib versus cisplatin plus docetaxel in patients with non-small-cell lung cancer harbouring mutations of the epidermal growth factor receptor (WJTOG3405): An open label, randomised phase 3 trial. Lancet Oncology., 11(2), 121–128. 10.1016/S1470-2045(09)70364-X
  • Mok, T. S., Wu, Y.-L., Thongprasert, S., Yang, C.-H., Chu, D.-T., Saijo, N., Sunpaweravong, P., Han, B., Margono, B., Ichinose, Y., Nishiwaki, Y., Ohe, Y., Yang, J.-J., Chewaskulyong, B., Jiang, H., Duffield, E. L., Watkins, C. L., Armour, A. A., & Fukuoka, M. (2009). Gefitinib or carboplatin–paclitaxel in pulmonary adenocarcinoma. New England Journal of Medicine, 361(10), 947–957. 10.1056/NEJMoa0810699
  • Niederst, M. J., & Engelman, J. A. (2013). Bypass mechanisms of resistance to receptor tyrosine kinase inhibition in lung cancer. Science Signaling, 6(294), re6–re6. 10.1126/scisignal.2004652
  • Ohashi, K., Sequist, L. V., Arcila, M. E., Lovly, C. M., Chen, X., Rudin, C. M., Moran, T., Camidge, D. R., Vnencak-Jones, C. L., Berry, L., Pan, Y., Sasaki, H., Engelman, J. A., Garon, E. B., Dubinett, S. M., Franklin, W. A., Riely, G. J., Sos, M. L., Kris, M. G., … Pao, W. (2013). Characteristics of lung cancers harboring NRAS mutations. Clinical Cancer Research, 19(9), 2584–2591.
  • Pao, W., Miller, V. A., Politi, K. A., Riely, G. J., Somwar, R., Zakowski, M. F., Kris, M. G., & Varmus, H. (2005). Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain. PLoS Medicine, 2(3), e73. 10.1371/journal.pmed.0020073
  • Pierce, A. C., Rao, G., & Bemis, G. W. (2004). BREED: Generating novel inhibitors through hybridization of known ligands. Application to CDK2, P38, and HIV Protease. Journal of Medicinal Chemistry, 47(11), 2768–2775. 10.1021/jm030543u
  • Qin, M., Wang, T., Xu, B., Ma, Z., Jiang, N., Xie, H., Gong, P., & Zhao, Y. (2015). Novel hydrazone moiety-bearing aminopyrimidines as selective inhibitors of epidermal growth factor receptor T790M mutant. European Journal of Medicinal Chemistry., 104, 115–126. 10.1016/j.ejmech.2015.09.031
  • Rosell, R., Carcereny, E., Gervais, R., Vergnenegre, A., Massuti, B., Felip, E., Palmero, R., Garcia-Gomez, R., Pallares, C., Sanchez, J. M., Porta, R., Cobo, M., Garrido, P., Longo, F., Moran, T., Insa, A., De Marinis, F., Corre, R., Bover, I., … Paz-Ares, L. (2012). Erlotinib versus standard chemotherapy as first-line treatment for European patients with advanced EGFR mutation-positive non-small-cell lung cancer (EURTAC): A multicentre, open-label, randomised phase 3 trial. Lancet Oncology., 13(3), 239–246. 10.1016/S1470-2045(11)70393-X
  • Schmitt, S., Kuhn, D., & Klebe, G. (2002). A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology. Journal of Molecular Biology., 323(2), 387–406. 10.1016/S0022-2836(02)00811-2
  • Schuttelkopf, A. W., & Aalten, V. V. (2004). PRODRG: a tool for high throughput crystallography of protein-ligand complexes. Acta Cryst, D, 60, 1355–1363.
  • Sequist, L. V., Yang, J. C.-H., Yamamoto, N., O'Byrne, K., Hirsh, V., Mok, T., Geater, S. L., Orlov, S., Tsai, C.-M., Boyer, M., Su, W.-C., Bennouna, J., Kato, T., Gorbunova, V., Lee, K. H., Shah, R., Massey, D., Zazulina, V., Shahidi, M., & Schuler, M. (2013). Phase III study of afatinib or cisplatin plus pemetrexed in patients with metastatic lung adenocarcinoma with EGFR mutations. Journal of Clinical Oncology, 31(27), 3327–3334. 10.1200/JCO.2012.44.2806
  • Shivani, P., Palmi, M., & Mahesh, C. (2018). Rational approach to identify newer caspase-1 inhibitors using pharmacophore based virtual screening, docking and molecular dynamic simulation studies. J. Mol. Graph Model, 81, 106–115.
  • Shivani, P., Palmi, M., Vishal, R., & Mahesh, C. (2018). Structure-based design, synthesis and evaluation of 2,4-diaminopyrimidine derivatives as novel caspase-1 inhibitors. Bioorganic Chemistry., 78, 258–268.
  • Vistoli, G., Pedretti, A., & Testa, B. (2008). Assessing drug-likeness–what are we missing. Drug Discovery Today, 13(7-8), 285–294. 10.1016/j.drudis.2007.11.007
  • Walter, A. O., Sjin, R. T. T., Haringsma, H. J., Ohashi, K., Sun, J., Lee, K., Dubrovskiy, A., Labenski, M., Zhu, Z., Wang, Z., Sheets, M., St Martin, T., Karp, R., van Kalken, D., Chaturvedi, P., Niu, D., Nacht, M., Petter, R. C., Westlin, W., … Allen, A. (2013). Discovery of a mutant-selective covalent inhibitor of EGFR that overcomes T790M-mediated resistance in NSCLC. Cancer Discovery, 3(12), 1404–1415. 10.1158/2159-8290.CD-13-0314
  • Woyach, J. A., Furman, R. R., Liu, T.-M., Ozer, H. G., Zapatka, M., Ruppert, A. S., Xue, L., Li, D. H.-H., Steggerda, S. M., Versele, M., Dave, S. S., Zhang, J., Yilmaz, A. S., Jaglowski, S. M., Blum, K. A., Lozanski, A., Lozanski, G., James, D. F., Barrientos, J. C., … Byrd, J. C. (2014). Resistance mechanisms for the Bruton's tyrosine kinase inhibitor ibrutinib. New England Journal of Medicine, 370(24), 2286–2294. 10.1056/NEJMoa1400029
  • Zhong, H., Tran, L. M., & Stang, J. L. (2009). Induced-fit docking studies of the active and inactive states of protein tyrosine kinases. Journal of Molecular Graphics and Modelling, 28(4), 336–346. 10.1016/j.jmgm.2009.08.012
  • Zhou, W., Ercan, D., Chen, L., Yun, C.-H., Li, D., Capelletti, M., Cortot, A. B., Chirieac, L., Iacob, R. E., Padera, R., Engen, J. R., Wong, K.-K., Eck, M. J., Gray, N. S., & Jänne, P. A. (2009). Novel mutant-selective EGFR kinase inhibitors against EGFR T790M. Nature, 462(7276), 1070–1074. 10.1038/nature08622
  • Zhu, K., Borrelli, W. K., Greenwood, J. R., Day, T., Abel, R., Farid, R. S., & Harder, E. (2014). Docking covalent inhibitors: a parameter free approach to pose prediction and scoring. Journal of Chemical Information and Modeling, 54(7), 1932–1940. 10.1021/ci500118s

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