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Research Articles

Drug repurposing combined with MM/PBSA based validation strategies towards MEK inhibitors screening

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Pages 12392-12403 | Received 10 Nov 2020, Accepted 16 Aug 2021, Published online: 30 Aug 2021

References

  • Abdel-Hamid, M. K., & McCluskey, A. (2014). In silico docking, molecular dynamics and binding energy insights into the bolinaquinone-clathrin terminal domain binding site. Molecules, 19(5), 6609–6622. https://doi.org/10.3390/molecules19056609
  • Adasme-Carreño, F., Muñoz-Gutierrez, C., Caballero, J., & Alzate-Morales, J. H. (2014). Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: The protein kinase case. Physical Chemistry Chemical Physics: PCCP, 16(27), 14047–14058. https://doi.org/10.1039/c4cp01378f
  • Ali, S., Khan, F. I., Mohammad, T., Lan, D., Hassan, M. I., & Wang, Y. (2019). Identification and Evaluation of Inhibitors of Lipase from Malassezia restricta using Virtual High-Throughput Screening and Molecular Dynamics Studies. International Journal of Molecular Sciences, 20(4), 884. https://doi.org/10.3390/ijms20040884
  • Barcellos, M. P., Santos, C. B., Federico, L. B., Almeida, P. F. D., da Silva, C. H. D. P., & Taft, C. A. (2019). Pharmacophore and structure-based drug design, molecular dynamics and admet/tox studies to design novel potential pad4 inhibitors. Journal of Biomolecular Structure & Dynamics, 37(4), 966–981. https://doi.org/10.1080/07391102.2018.1444511
  • Berendsen, H. J., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1–3), 43–56. https://doi.org/10.1016/0010-4655(95)00042-E
  • Borkotoky, S., Meena, C. K., & Murali, A. (2016). Interaction analysis of T7 RNA polymerase with heparin and its low molecular weight derivatives–An in silico approach. Bioinformatics and Biology Insights, 10, 155–166. https://doi.org/10.4137/BBI.S40427
  • Carbonell, T., & Freire, E. (2005). Binding thermodynamics of statins to HMG-CoA reductase. Biochemistry, 44(35), 11741–11748. https://doi.org/10.1021/bi050905v
  • Cloete, R., Akurugu, W. A., Werely, C. J., van Helden, P. D., & Christoffels, A. (2017). Structural and functional effects of nucleotide variation on the human TB drug metabolizing enzyme arylamine N-acetyltransferase 1. Journal of Molecular Graphics & Modelling, 75, 330–339. https://doi.org/10.1016/j.jmgm.2017.04.026
  • David, C. C., & Jacobs, D. J. (2014). Principal component analysis: A method for determining the essential dynamics of proteins. In Protein dynamics (pp. 193–226). Humana Press.
  • de Gooijer, M. C., Zhang, P., Weijer, R., Buil, L. C., Beijnen, J. H., & van Tellingen, O. (2018). The impact of P-glycoprotein and breast cancer resistance protein on the brain pharmacokinetics and pharmacodynamics of a panel of MEK inhibitors. International Journal of Cancer, 142(2), 381–391. https://doi.org/10.1002/ijc.31052
  • Dixon, S. L., Smondyrev, A. M., Knoll, E. H., Rao, S. N., Shaw, D. E., & Friesner, R. A. (2006). PHASE: A new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. Journal of Computer-Aided Molecular Design, 20(10–11), 647–671. https://doi.org/10.1007/s10822-006-9087-6
  • Du, J., Sun, H., Xi, L., Li, J., Yang, Y., Liu, H., & Yao, X. (2011). Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM-GBSA calculation. Journal of Computational Chemistry, 32(13), 2800–2809. https://doi.org/10.1002/jcc.21859
  • El Khoury, L., Santos-Martins, D., Sasmal, S., Eberhardt, J., Bianco, G., Ambrosio, F. A., Solis-Vasquez, L., Koch, A., Forli, S., & Mobley, D. L. (2019). Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4. Journal of Computer-Aided Molecular Design, 33(12), 1011–1020. https://doi.org/10.1007/s10822-019-00240-w
  • Freeman, A. K., Ritt, D. A., & Morrison, D. K. (2013). Effects of Raf dimerization and its inhibition on normal and disease-associated Raf signaling. Molecular Cell, 49(4), 751–758. https://doi.org/10.1016/j.molcel.2012.12.018
  • Frémin, C., & Meloche, S. (2010). From basic research to clinical development of MEK1/2 inhibitors for cancer therapy. Journal of Hematology & Oncology, 3(1), 1–11. https://doi.org/10.1186/1756-8722-3-8
  • Fusani, L., Palmer, D. S., Somers, D. O., & Wall, I. D. (2020). Exploring ligand stability in protein crystal structures using binding pose metadynamics. Journal of Chemical Information and Modeling, 60(3), 1528–1539. https://doi.org/10.1021/acs.jcim.9b00843
  • Greenfield, D. A., Schmidt, H. R., Skiba, M. A., Mandler, M. D., Anderson, J. R., Sliz, P., & Kruse, A. C. (2020). Virtual screening for ligand discovery at the σ1 receptor. ACS Medicinal Chemistry Letters, 11(8), 1555–1561. https://doi.org/10.1021/acsmedchemlett.9b00314
  • Halgren, T. A. (2009). Identifying and characterizing binding sites and assessing druggability. Journal of Chemical Information and Modeling, 49(2), 377–389. https://doi.org/10.1021/ci800324m
  • Heigener, D. F., Gandara, D. R., & Reck, M. (2015). Targeting of MEK in lung cancer therapeutics. The Lancet. Respiratory Medicine, 3(4), 319–327. https://doi.org/10.1016/S2213-2600(15)00026-0
  • Infante, J. R., Fecher, L. A., Falchook, G. S., Nallapareddy, S., Gordon, M. S., Becerra, C., DeMarini, D. J., Cox, D. S., Xu, Y., Morris, S. R., Peddareddigari, V. G. R., Le, N. T., Hart, L., Bendell, J. C., Eckhardt, G., Kurzrock, R., Flaherty, K., Burris, H. A., & Messersmith, W. A. (2012). Safety, pharmacokinetic, pharmacodynamic, and efficacy data for the oral MEK inhibitor trametinib: A phase 1 dose-escalation trial. The Lancet. Oncology, 13(8), 773–781. https://doi.org/10.1016/S1470-2045(12)70270-X
  • Ioakimidis, L., Thoukydidis, L., Mirza, A., Naeem, S., & Reynisson, J. (2008). Benchmarking the reliability of QikProp. Correlation between experimental and predicted values. QSAR & Combinatorial Science, 27(4), 445–456. https://doi.org/10.1002/qsar.200730051
  • James, N., & Ramanathan, K. (2018). Ligand-based pharmacophore screening strategy: A pragmatic approach for targeting HER proteins. Applied Biochemistry and Biotechnology, 186(1), 85–108. https://doi.org/10.1007/s12010-018-2724-4
  • Jana, S., & Singh, S. K. (2019). Identification of selective MMP-9 inhibitors through multiple e-pharmacophore, ligand-based pharmacophore, molecular docking, and density functional theory approaches. Journal of Biomolecular Structure & Dynamics, 37(4), 944–965. https://doi.org/10.1080/07391102.2018.1444510
  • Janne, P. A., Shaw, A. T., Pereira, J. R., Jeannin, G., Vansteenkiste, J., Barrios, C. H., … Smith, I. C. (2012). Phase II double-blind, randomized study of selumetinib (SEL) plus docetaxel (DOC) versus DOC plus placebo as second-line treatment for advanced KRAS mutant non-small cell lung cancer (NSCLC).
  • Ji, H., Wang, Z., Perera, S. A., Li, D., Liang, M.-C., Zaghlul, S., McNamara, K., Chen, L., Albert, M., Sun, Y., Al-Hashem, R., Chirieac, L. R., Padera, R., Bronson, R. T., Thomas, R. K., Garraway, L. A., Jänne, P. A., Johnson, B. E., Chin, L., & Wong, K.-K. (2007). Mutations in BRAF and KRAS converge on activation of the mitogen-activated protein kinase pathway in lung cancer mouse models. Cancer Research, 67(10), 4933–4939. https://doi.org/10.1158/0008-5472.CAN-06-4592
  • Karthikeyan, M., & Vyas, R. (2014). Chemoinformatics approach for the design and screening of focused virtual libraries. In Practical cheminformatics (pp. 93–131) New Delhi: Springer. https://doi.org/10.1007/978-81-322-1780-0_2
  • Kim, C., & Giaccone, G. (2018). MEK inhibitors under development for treatment of non-small-cell lung cancer. Expert Opinion on Investigational Drugs, 27(1), 17–30. https://doi.org/10.1080/13543784.2018.1415324
  • Kumari, R., Kumar, R., Open Source Drug Discovery Consortium, & Lynn, A. (2014). g_mmpbsa - A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
  • Londhe, A. M., Gadhe, C. G., Lim, S. M., & Pae, A. N. (2019). Investigation of molecular details of Keap1-Nrf2 inhibitors using molecular dynamics and umbrella sampling techniques. Molecules, 24(22), 4085–4107. https://doi.org/10.3390/molecules24224085
  • Mandal, R., Becker, S., & Strebhardt, K. (2016). Stamping out RAF and MEK1/2 to inhibit the ERK1/2 pathway: An emerging threat to anticancer therapy. Oncogene, 35(20), 2547–2561. https://doi.org/10.1038/onc.2015.329
  • Midha, A., Dearden, S., & McCormack, R. (2015). EGFR mutation incidence in non-small-cell lung cancer of adenocarcinoma histology: A systematic review and global map by ethnicity (mutMapII). American Journal of Cancer Research, 5(9), 2892–2911.
  • Mobley, D. L., & Gilson, M. K. (2017). Predicting binding free energies: Frontiers and benchmarks. Annual Review of Biophysics, 46, 531–558. https://doi.org/10.1146/annurev-biophys-070816-033654
  • Murteira, S., Ghezaiel, Z., Karray, S., & Lamure, M. (2013). Drug reformulations and repositioning in pharmaceutical industry and its impact on market access: Reassessment of nomenclature. Journal of Market Access & Health Policy, 1(1), 21131. https://doi.org/10.3402/jmahp.v1i0.21131
  • Nakae, S., Kitamura, M., Shirai, T., & Tada, T. (2014). 3W8Q: Structure of the human mitogen-activated protein kinase kinase 1 (MEK1). Protein Data Bank.
  • Natarajan, P., Priyadarshini, V., Pradhan, D., Manne, M., Swargam, S., Kanipakam, H., Bhuma, V., & Amineni, U. (2016). E-pharmacophore-based virtual screening to identify GSK-3β inhibitors. Journal of Receptor and Signal Transduction Research, 36(5), 445–458. https://doi.org/10.3109/10799893.2015.1122043
  • Pawar, V. S., Lokwani, D. K., Bhandari, S. V., Bothara, K. G., Chitre, T. S., Devale, T. L., Modhave, N. S., & Parikh, J. K. (2011). Design, docking study and ADME prediction of Isatin derivatives as anti-HIV agents. Medicinal Chemistry Research, 20(3), 370–380. https://doi.org/10.1007/s00044-010-9329-y
  • Pradhan, R., Singhvi, G., Dubey, S. K., Gupta, G., & Dua, K. (2019). MAPK pathway: A potential target for the treatment of non-small-cell lung carcinoma.
  • QikProp, S. (2015). LLC.
  • Raquel-Cunha, A., Cardoso-Carneiro, D., Reis, R. M., & Martinho, O. (2019). Current status of Raf Kinase Inhibitor Protein (RKIP) in lung cancer: Behind RTK signaling. Cells, 8(5), 442. https://doi.org/10.3390/cells8050442
  • Rohini, K., Ramanathan, K., & Shanthi, V. (2019). Multi-dimensional screening strategy for drug repurposing with statistical framework - A new road to influenza drug discovery. Cell Biochemistry and Biophysics, 77(4), 319–333. https://doi.org/10.1007/s12013-019-00887-0
  • Ruben, A. J., Kiso, Y., & Freire, E. (2006). Overcoming roadblocks in lead optimization: A thermodynamic perspective. Chemical Biology & Drug Design, 67(1), 2–4. https://doi.org/10.1111/j.1747-0285.2005.00314.x
  • Sarver, R. W., Peevers, J., Cody, W. L., Ciske, F. L., Dyer, J., Emerson, S. D., Hagadorn, J. C., Holsworth, D. D., Jalaie, M., Kaufman, M., Mastronardi, M., McConnell, P., Powell, N. A., Quin, J., Van Huis, C. A., Zhang, E., & Mochalkin, I. (2007). Binding thermodynamics of substituted diaminopyrimidine renin inhibitors. Analytical Biochemistry, 360(1), 30–40. https://doi.org/10.1016/j.ab.2006.10.017
  • 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
  • Shan, C., Li, H., Zhang, Y., Li, Y., Chen, Y., & He, W. (2019). Binding interactions of epididymal protease inhibitor and semenogelin-1: A homology modeling, docking and molecular dynamics simulation study. PeerJ., 7, e7329. https://doi.org/10.7717/peerj.7329
  • Singh, G., Jayadev Magani, S. K., Sharma, R., Bhat, B., Shrivastava, A., Chinthakindi, M., & Singh, A. (2019). Structural, functional and molecular dynamics analysis of cathepsin B gene SNPs associated with tropical calcific pancreatitis, a rare disease of tropics. PeerJ., 7, e7425. https://doi.org/10.7717/peerj.7425
  • Singh, K. D., & Muthusamy, K. (2013). Molecular modeling, quantum polarized ligand docking and structure-based 3D-QSAR analysis of the imidazole series as dual AT(1) and ET(A) receptor antagonists. Acta Pharmacologica Sinica, 34(12), 1592–1606. https://doi.org/10.1038/aps.2013.129
  • Sneha, P., Thirumal Kumar, D., George Priya Doss, C., Siva, R., & Zayed, H. (2017). Determining the role of missense mutations in the POU domain of HNF1A that reduce the DNA-binding affinity: A computational approach. PLoS One, 12(4), e0174953. https://doi.org/10.1371/journal.pone.0174953
  • Ton, A. T., Gentile, F., Hsing, M., Ban, F., & Cherkasov, A. (2020). Rapid identification of potential inhibitors of SARS‐CoV‐2 main protease by deep docking of 1.3 billion compounds. Molecular Informatics, 39(8), 2000028. https://doi.org/10.1002/minf.202000028
  • Wishart, D. S., Feunang, Y. D., Guo, A. C., Lo, E. J., Marcu, A., Grant, J. R., Sajed, T., Johnson, D., Li, C., Sayeeda, Z., Assempour, N., Iynkkaran, I., Liu, Y., Maciejewski, A., Gale, N., Wilson, A., Chin, L., Cummings, R., Le, D., … Wilson, M. (2018). DrugBank 5.0: A major update to the DrugBank database for 2018. Nucleic Acids Research, 46(D1), D1074–D1082. https://doi.org/10.1093/nar/gkx1037
  • Yadav, R., Imran, M., Dhamija, P., Suchal, K., & Handu, S. (2020). Virtual screening and dynamics of potential inhibitors targeting RNA binding domain of nucleocapsid phosphoprotein from SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 39, 1–16.
  • Yaeger, R., & Corcoran, R. B. (2019). Targeting alterations in the RAF-MEK Pathway. Cancer Discovery, 9(3), 329–341. https://doi.org/10.1158/2159-8290.CD-18-1321
  • Zacharias, N., & Dougherty, D. A. (2002). Cation-pi interactions in ligand recognition and catalysis. Trends in Pharmacological Sciences, 23(6), 281–287. https://doi.org/10.1016/s0165-6147(02)02027-8

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