A new approach used in docking study for predicting the combination drug efficacy in EML4-ALK target of NSCLC

References

• Aier, I., Varadwaj, P. K., & Raj, U (2016). Structural insights into conformational stability of both wild-type and mutant EZH2 receptor. Scientific reports, 6(1), 1–10.
   Google Scholar
• Arnold, K., Bordoli, L., Kopp, J., & Schwede, T. (2006). The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling. Bioinformatics (Oxford, England), 22(2), 195–201. https://doi.org/10.1093/bioinformatics/bti770
   PubMed Web of Science ®Google Scholar
• Awad, M. M., Katayama, R., McTigue, M., Liu, W., Deng, Y.-L., Brooun, A., Friboulet, L., Huang, D., Falk, M. D., Timofeevski, S., Wilner, K. D., Lockerman, E. L., Khan, T. M., Mahmood, S., Gainor, J. F., Digumarthy, S. R., Stone, J. R., Mino-Kenudson, M., Christensen, J. G., … Shaw, A. T. (2013). Acquired resistance to crizotinib from a mutation in CD74–ROS1. The New England Journal of Medicine, 368(25), 2395–2401.
   PubMed Web of Science ®Google Scholar
• Bekker, H., Berendsen, H. J. C., Dijkstra, E. J., Achterop, S., Vondrumen, R., Vanderspoel, D., & Renardus, M. K. R. (1993). Gromacs-a parallel computer for molecular-dynamics simulations. In 4th International Conference on Computational Physics (PC 92), (pp. 252–256). World Scientific Publishing.
   Google Scholar
• Benkert, P., Biasini, M., & Schwede, T. (2011). Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (Oxford, England), 27(3), 343–350.
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J., Postma, J. V., Van Gunsteren, W. F., DiNola, A. R. H. J., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Gallo Cassarino, T., Bertoni, M., Bordoli, L., & Schwede, T. (2014). SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42, W252–W258.
   PubMed Web of Science ®Google Scholar
• Brentnall, T. A. (2005). Management strategies for patients with hereditary pancreatic cancer. Current Treatment Options in Oncology, 6(5), 437–445. https://doi.org/10.1007/s11864-005-0046-6
   PubMedGoogle Scholar
• Brooks, B. R., Brooks, C. L., Mackerell, A. D., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A. R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., … Karplus, M. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30(10), 1545–1614.
   PubMed Web of Science ®Google Scholar
• Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126(1), 014101.
   PubMed Web of Science ®Google Scholar
• Casaluce, F., Sgambato, A., Sacco, P. C., Palazzolo, G., Maione, P., Rossi, A., Ciardiello, F., & Gridelli, C. (2016). Resistance to crizotinib in advanced non-small cell lung cancer (NSCLC) with ALK rearrangement: Mechanisms, treatment strategies and new targeted therapies. Current Clinical Pharmacology, 11(2), 77–87.
   PubMedGoogle Scholar
• Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010). MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica Section D Biological Crystallography, 66(1), 12–21. https://doi.org/10.1107/S0907444909042073
   PubMedGoogle Scholar
• Chen, Z., Fillmore, C. M., Hammerman, P. S., Kim, C. F., & Wong, K. K. (2014). Non-small-cell lung cancers: A heterogeneous set of diseases. Nature Reviews. Cancer, 14(8), 535–546.
   PubMed Web of Science ®Google Scholar
• Cheng, F., Kovács, I. A., & Barabási, A.-L. (2019). Network-based prediction of drug combinations. Nature Communications, 10(1), 1197. https://doi.org/10.1038/s41467-019-09186-x
   PubMed Web of Science ®Google Scholar
• Clarke, S. (1993). Protein methylation. Current Opinion in Cell Biology, 5(6), 977–983. https://doi.org/10.1016/0955-0674(93)90080-a
   PubMed Web of Science ®Google Scholar
• Cruz, C. S. D., Tanoue, L. T., & Matthay, R. A. (2011). Lung cancer: Epidemiology, etiology, and prevention. Clinics in Chest Medicine, 32(4), 605–644. https://doi.org/10.1016/j.ccm.2011.09.001
   PubMed Web of Science ®Google Scholar
• Crystal, A. S., Shaw, A. T., Sequist, L. V., Friboulet, L., Niederst, M. J., Lockerman, E. L., Frias, R. L., Gainor, J. F., Amzallag, A., Greninger, P., Lee, D., Kalsy, A., Gomez-Caraballo, M., Elamine, L., Howe, E., Hur, W., Lifshits, E., Robinson, H. E., Katayama, R., … Engelman, J. A. (2014). Patient-derived models of acquired resistance can identify effective drug combinations for cancer. Science (New York, N.Y.), 346(6216), 1480–1486.
   PubMed Web of Science ®Google Scholar
• Cui, J. J., Tran-Dubé, M., Shen, H., Nambu, M., Kung, P.-P., Pairish, M., Jia, L., Meng, J., Funk, L., Botrous, I., McTigue, M., Grodsky, N., Ryan, K., Padrique, E., Alton, G., Timofeevski, S., Yamazaki, S., Li, Q., Zou, H., … Edwards, M. P. (2011). Structure based drug design of crizotinib (PF-02341066), a potent and selective dual inhibitor of mesenchymal–epithelial transition factor (c-MET) kinase and anaplastic lymphoma kinase (ALK). Journal of Medicinal Chemistry, 54(18), 6342–6363. https://doi.org/10.1021/jm2007613
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅ log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Das, A., Cheng, R. R., Hilbert, M. L., Dixon-Moh, Y. N., Decandio, M., Vandergrift William, A., Banik, N. L., Lindhorst, S. M., Cachia, D., Varma, A. K., Patel, S. J., & Giglio, P. (2015). Synergistic effects of crizotinib and temozolomide in experimental FIG-ROS1 fusion-positive glioblastoma. Cancer Growth and Metastasis, 8, CGM.S32801. https://doi.org/10.4137/CGM.S32801
   Google Scholar
• Di Veroli, G. Y., Fornari, C., Wang, D., Mollard, S., Bramhall, J. L., Richards, F. M., & Jodrell, D. I. (2016). Combenefit: an interactive platform for the analysis and visualization of drug combinations. Bioinformatics (Oxford, England), 32(18), 2866–2868.
   PubMed Web of Science ®Google Scholar
• Diller, D. J., & Merz, K. M. Jr. (2001). High throughput docking for library design and library prioritization. Proteins: Structure, Function, and Genetics, 43(2), 113–124. https://doi.org/10.1002/1097-0134(20010501)43:2<113::AID-PROT1023>3.0.CO;2-T
   PubMed Web of Science ®Google Scholar
• Ettinger, D. S., Akerley, W., Borghaei, H., Chang, A. C., Cheney, R. T., Chirieac, L. R., D’Amico, T. A., Demmy, T. L., Govindan, R., Grannis, F. W., Grant, S. C., Horn, L., Jahan, T. M., Komaki, R., Kong, F.-M S., Kris, M. G., Krug, L. M., Lackner, R. P., Lennes, I. T., … Hughes, M. (2013). Non–small cell lung cancer, version 2.2013. Journal of the National Comprehensive Cancer Network, 11(6), 645–653. https://doi.org/10.6004/jnccn.2013.0084
   PubMed Web of Science ®Google Scholar
• Feig, M., & Brooks, C. L. III. (2004). Recent advances in the development and application of implicit solvent models in biomolecule simulations. Current Opinion in Structural Biology, 14(2), 217–224.
   PubMed Web of Science ®Google Scholar
• Fernandes, C. L., Sachett, L. G., Pol-Fachin, L., & Verli, H. (2010). GROMOS96 43a1 performance in predicting oligosaccharide conformational ensembles within glycoproteins. Carbohydrate Research, 345(5), 663–671.
   PubMed Web of Science ®Google Scholar
• Giles, T. D., Weber, M. A., Basile, J., Gradman, A. H., Bharucha, D. B., Chen, W., & Pattathil, M. (2014). Efficacy and safety of nebivolol and valsartan as fixed-dose combination in hypertension: A randomised, multicentre study. The Lancet, 383(9932), 1889–1898. https://doi.org/10.1016/S0140-6736(14)60614-0
   PubMed Web of Science ®Google Scholar
• Huang, L., Jiang, Y., & Chen, Y. (2017). Predicting drug combination index and simulating the network-regulation dynamics by mathematical modeling of drug-targeted EGFR-ERK signaling pathway. Scientific Reports, 7(1), 40752–40759. https://doi.org/10.1038/srep40752
   PubMedGoogle Scholar
• Hughes, J. P., Rees, S., Kalindjian, S. B., & Philpott, K. L. (2011). Principles of early drug discovery. British Journal of Pharmacology, 162(6), 1239–1249. https://doi.org/10.1111/j.1476-5381.2010.01127.x
   PubMed Web of Science ®Google Scholar
• Hyndman, R. J., & Koehler, A. B. (2006). Another look at measures of forecast accuracy. International Journal of Forecasting, 22(4), 679–688. https://doi.org/10.1016/j.ijforecast.2006.03.001
   Web of Science ®Google Scholar
• Ianevski, A., Timonen, S., Kononov, A., Aittokallio, T., & Giri, A. K. (2020). SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy. PLoS Computational Biology, 16(2), e1007604.
   PubMed Web of Science ®Google Scholar
• Jalily Hasani, H., & Barakat, K. (2017). Homology modeling: An overview of fundamentals and tools. International Review on Modelling and Simulations (IREMOS), 10(2), 129–145. https://doi.org/10.15866/iremos.v10i2.11412
   Google Scholar
• Kanwal, M., Ding, X. J., & Cao, Y. (2017). Familial risk for lung cancer. Oncology Letters, 13(2), 535–542.
   PubMed Web of Science ®Google Scholar
• Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E. (2019). PubChem 2019 update: Improved access to chemical data. Nucleic Acids Research, 47(D1), D1102–D1109. https://doi.org/10.1093/nar/gky1033
   PubMed Web of Science ®Google Scholar
• Lin, C.-H., Chang, T.-T., Sun, M.-F., Chen, H.-Y., Tsai, F.-J., Chang, K.-L., Fisher, M., & Chen, C. Y.-C. (2011). Potent inhibitor design against H1N1 swine influenza: structure-based and molecular dynamics analysis for M2 inhibitors from traditional Chinese medicine database. Journal of Biomolecular Structure & Dynamics, 28(4), 471–482.
   PubMed Web of Science ®Google Scholar
• Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. The Journal of Physical Chemistry A, 105(43), 9954–9960. https://doi.org/10.1021/jp003020w
   Web of Science ®Google Scholar
• Meng, X. Y., Zhang, H. X., Mezei, M., & Cui, M. (2011). Molecular docking: A powerful approach for structure-based drug discovery. Current Computer-Aided Drug Design, 7(2), 146–157. https://doi.org/10.2174/157340911795677602
   PubMed Web of Science ®Google Scholar
• Meng, X. Y., Zhang, H. X., Mezei, M., & Cui, M. (2011). Molecular docking: A powerful approach for structure-based drug discovery. Current Computer-Aided Drug Design, 7(2), 146–157. https://doi.org/10.2174/157340911795677602
   PubMed Web of Science ®Google Scholar
• Nosé, S., & Klein, M. L. (1983). Constant pressure molecular dynamics for molecular systems. Molecular Physics, 50(5), 1055–1076. https://doi.org/10.1080/00268978300102851
   Web of Science ®Google Scholar
• Ou, S.-H I., Govindan, R., Eaton, K. D., Otterson, G. A., Gutierrez, M. E., Mita, A. C., Argiris, A., Brega, N. M., Usari, T., Tan, W., Ho, S. N., & Robert, F. (2017). Phase I results from a study of crizotinib in combination with erlotinib in patients with advanced nonsquamous non–small cell lung cancer. Journal of Thoracic Oncology, 12(1), 145–151.
   PubMed Web of Science ®Google Scholar
• Pagadala, N. S., Syed, K., & Tuszynski, J. (2017). Software for molecular docking: A review. Biophysical Reviews, 9(2), 91–102.
   PubMedGoogle Scholar
• Pang, C. N. I., Gasteiger, E., & Wilkins, M. R. (2010). Identification of arginine-and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications. BMC Genomics, 11(1), 1–16. https://doi.org/10.1186/1471-2164-11-92
   PubMedGoogle Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
   Web of Science ®Google Scholar
• Peng, Y.-H., Shiao, H.-Y., Tu, C.-H., Liu, P.-M., Hsu, J. T.-A., Amancha, P. K., Wu, J.-S., Coumar, M. S., Chen, C.-H., Wang, S.-Y., Lin, W.-H., Sun, H.-Y., Chao, Y.-S., Lyu, P.-C., Hsieh, H.-P., & Wu, S.-Y. (2013). Protein kinase inhibitor design by targeting the Asp-Phe-Gly (DFG) motif: The role of the DFG motif in the design of epidermal growth factor receptor inhibitors. Journal of Medicinal Chemistry, 56(10), 3889–3903.
   PubMed Web of Science ®Google Scholar
• Rao, S. N., Head, M. S., Kulkarni, A., & LaLonde, J. M. (2007). Validation studies of the site-directed docking program LibDock. Journal of Chemical Information and Modeling, 47(6), 2159–2171.
   PubMed Web of Science ®Google Scholar
• Ravikumar, A., Ramakrishnan, C., & Srinivasan, N. (2019). Stereochemical assessment of (φ, ψ) outliers in protein structures using bond geometry-specific ramachandran steric-maps. Structure (London, England: 1993), 27(12), 1875–1884. https://doi.org/10.1016/j.str.2019.09.009
   PubMed Web of Science ®Google Scholar
• Rühle, V. (2007). Berendsen and nose-hoover thermostats. American Journal of Physics, 1–4.
   Google Scholar
• Rühle, V. (2008). Pressure coupling/barostats. Journal Club, 1-5.
   Google Scholar
• Schüttelkopf, A. W., & Van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60(8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Sidorov, P., Naulaerts, S., Ariey-Bonnet, J., Pasquier, E., & Ballester, P. J. (2019). Predicting synergism of cancer drug combinations using NCI-ALMANAC data. Frontiers in Chemistry, 509, 1–13.
   Google Scholar
• Sung, H., Ferlay, J., Siegel, R. L., Laversanne, M., Soerjomataram, I., Jemal, A., & Bray, F. (2021). Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: A Cancer Journal for Clinicians, 71(3), 209–249. https://doi.org/10.3322/caac.21660
   PubMed Web of Science ®Google Scholar
• Tallei, T. E., Fatimawali, A. Y., Idroes, R., Kusumawaty, D., Emran, T. B., Yesiloglu, T. Z., … Celik, I. (2021). An analysis based on molecular docking and molecular dynamics simulation study of bromelain as anti-SARS-CoV-2 variants. Frontiers in Pharmacology, 12, 1-18.
   PubMed Web of Science ®Google Scholar
• Tan, X., Hu, L., Luquette, L. J., Gao, G., Liu, Y., Qu, H., Xi, R., Lu, Z. J., Park, P. J., & Elledge, S. J. (2012). Systematic identification of synergistic drug pairs targeting HIV. Nature Biotechnology, 30(11), 1125–1130.
   PubMed Web of Science ®Google Scholar
• Tirado-Rives, J., & Jorgensen, W. L. (2006). Contribution of conformer focusing to the uncertainty in predicting free energies for protein − ligand binding. Journal of Medicinal Chemistry, 49(20), 5880–5884. https://doi.org/10.1021/jm060763i
   PubMed Web of Science ®Google Scholar
• Torkamannia, A., Omidi, Y., & Ferdousi, R. (2022). A review of machine learning approaches for drug synergy prediction in cancer. Briefings in Bioinformatics, 23(3). https://doi.org/10.1093/bib/bbac075
   Google Scholar
• Wallner, B., & Elofsson, A. (2005). All are not equal: A benchmark of different homology modeling programs. Protein Science, 14(5), 1315–1327. https://doi.org/10.1110/ps.041253405
   PubMed Web of Science ®Google Scholar
• Wang, F., Dai, W., Wang, Y., Shen, M., Chen, K., Cheng, P., Zhang, Y., Wang, C., Li, J., Zheng, Y., Lu, J., Yang, J., Zhu, R., Zhang, H., Zhou, Y., Xu, L., & Guo, C. (2014). The synergistic in vitro and in vivo antitumor effect of combination therapy with salinomycin and 5-fluorouracil against hepatocellular carcinoma. PLoS One, 9(5), e97414. https://doi.org/10.1371/journal.pone.0097414
   PubMed Web of Science ®Google Scholar
• Wang, W., Li, X., Wang, Q., Zhu, X., Zhang, Q., & Du, L. (2018). The acidic pH-induced structural changes in apo-CP43 by spectral methodologies and molecular dynamics simulations. Journal of Molecular Structure, 1152, 177–188. https://doi.org/10.1016/j.molstruc.2017.09.082
   Web of Science ®Google Scholar
• Wang, T., Pickard, A. J., & Gallo, J. M. (2016). Histone methylation by temozolomide; a classic DNA methylating anticancer drug. Anticancer Research, 36(7), 3289–3299.
   PubMed Web of Science ®Google Scholar
• Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303.
   PubMed Web of Science ®Google Scholar
• Young, P. (2014, April). The leapfrog method and other “symplectic” algorithms for integrating newton’s laws of motion. http://young.physics.ucsc.edu/115/leapfrog.pdf.
   Google Scholar
• Younus, S., Vinod Chandra, S. S., & Nair, A. S. S. (2021). Docking and dynamic simulation study of Crizotinib and Temozolomide drug with Glioblastoma and NSCLC target to identify better efficacy of the drug. Future Journal of Pharmaceutical Sciences, 7(1), 1–17. https://doi.org/10.1186/s43094-021-00323-2
   Web of Science ®Google Scholar
• Zheng, W., Sun, W., & Simeonov, A. (2018). Drug repurposing screens and synergistic drug‐combinations for infectious diseases. British Journal of Pharmacology, 175(2), 181–191.
   PubMed Web of Science ®Google Scholar
• Zhou, J., Song, Z., Zhang, R., Liu, R., Wu, Q., Li, J., Tang, X., Xu, B., Ding, J., Han, N., & Huang, Z. (2017). Distinctive molecular and biochemical characteristics of a glycoside hydrolase family 20 β-N-acetylglucosaminidase and salt tolerance. BMC Biotechnology, 17(1), 1–15. https://doi.org/10.1186/s12896-017-0358-1
   PubMedGoogle Scholar