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Research Articles

Exploring the mechanism of action of podophyllotoxin derivatives through molecular docking, molecular dynamics simulation and MM/PBSA studies

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Pages 8856-8865 | Received 02 Dec 2021, Accepted 15 Oct 2022, Published online: 28 Oct 2022

References

  • Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
  • Ardalani, H., Avan, A., & Ghayour-Mobarhan, M. (2017). Podophyllotoxin: a novel potential natural anticancer agent. Avicenna Journal of Phytomedicine, 7(4), 285–294.
  • Binarová, P., & Tuszynski, J. (2019). Tubulin: Structure, functions and roles in disease. Cells, 8(10), 1294. https://doi.org/10.3390/cells8101294
  • Burden, D. A., & Osheroff, N. (1998). Mechanism of action of eukaryotic topoisomerase II and drugs targeted to the enzyme. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, 1400(1–3), 139–154. https://doi.org/10.1016/S0167-4781(98)00132-8
  • Cooper, G. M. (2000). The cell: a molecular approach (2nd ed). ASM Press.
  • Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
  • Gordaliza, M., Castro, M. A., del Corral, J. M., & Feliciano, A. S. (2000). Antitumor properties of podophyllotoxin and related compounds. Current Pharmaceutical Design, 6(18), 1811–1839. https://doi.org/10.2174/1381612003398582
  • Guerram, M., Jiang, Z.-Z., & Zhang, L.-Y. (2012). Podophyllotoxin, a medicinal agent of plant origin: past, present and future: Podophyllotoxin, a medicinal agent of plant origin: past, present and future. Chinese Journal of Natural Medicines, 10(3), 161–169. https://doi.org/10.3724/SP.J.1009.2012.00161
  • Han, H., Xu, X., Ma, Y., Luo, Y., Wang, Z., Yang, M., Wen, Z., Zhang, Y., Yin, T., Zhao, Q., Lin, H., Lu, G., Yang, R., Wang, X., Qi, J., & Yang, Y. (2020). Discovering podophyllotoxin derivatives as potential anti‐tubulin agents: Design, synthesis and biological evaluation. ChemistrySelect, 5(34), 10526–10536. https://doi.org/10.1002/slct.202002962
  • Huang, J., & MacKerell, A. D. (2013). CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. Journal of Computational Chemistry, 34(25), 2135–2145. https://doi.org/10.1002/jcc.23354
  • Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22(12), 2577–2637. https://doi.org/10.1002/bip.360221211
  • Kittakoop, P. (2015). Anticancer drugs and potential anticancer leads inspired by natural products. Studies in Natural Products Chemistry, 44, 251–307.
  • Kumar, R., & Saran, S. (2018). Structure, molecular dynamics simulation, and docking studies of dictyostelium discoideum and human STRAPs. Journal of Cellular Biochemistry, 119(9), 7177–7191. https://doi.org/10.1002/jcb.26840.
  • Kumari, R., Kumar, R., & Lynn, A, Open Source Drug Discovery Consortium. (2014). Open Source Drug Discovery Consortium, Lynn A. 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
  • Michael, H. (2020). Import and plot Gromacs.xvg data files. Available from https://www.mathworks.com/matlabcentral/fileexchange/70607-import-and-plot-gromacs-xvg-data-files.
  • Mukhtar, E., Adhami, V. M., & Mukhtar, H. (2014). Targeting microtubules by natural agents for cancer therapymicrotubule-targeting agents for cancer chemotherapy. Molecular Cancer Therapeutics, 13(2), 275–284. https://doi.org/10.1158/1535-7163.MCT-13-0791
  • Naik, P. K., Alam, A., Malhotra, A., & Rizvi, O. (2010). Molecular modeling and structure-activity relationship of podophyllotoxin and its congeners. Journal of Biomolecular Screening, 15(5), 528–540. https://doi.org/10.1177/1087057110368994
  • Newman, D. J., Cragg GM, I., & Kingston, D. G. (2008). Natural products as pharmaceuticals and sources for lead structures. The Practice of Medicinal Chemistry [Internet], 159–186. Available from: https://linkinghub.elsevier.com/retrieve/pii/B9780123741943000081 [cited 2020 Aug 6].
  • Nogales, E., Wolf, S. G., & Downing, K. H. (1998). Structure of the αβ tubulin dimer by electron crystallography. Nature, 391(6663), 199–203. https://doi.org/10.1038/34465
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera? A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
  • Shah, Z., Gohar, U. F., Jamshed, I., Mushtaq, A., Mukhtar, H., Zia-UI-Haq, M., Toma, S. I., Manea, R., Moga, M., & Popovici, B. (2021). Podophyllotoxin: History, Recent Advances and Future Prospects. Biomolecules, 11(4), 603. https://doi.org/10.3390/biom11040603
  • Touw, W. G., Baakman, C., Black, J., te Beek, T. A. H., Krieger, E., Joosten, R. P., & Vriend, G. (2015). A series of PDB-related databanks for everyday needs. Nucleic Acids Research, 43(Database issue), D364–D368. https://doi.org/10.1093/nar/gku1028
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
  • Wu, C.-C., Li, T.-K., Farh, L., Lin, L.-Y., Lin, T.-S., Yu, Y.-J., Yen, T.-J., Chiang, C.-W., & Chan, N.-L. (2011). Structural basis of Type II topoisomerase inhibition by the anticancer drug etoposide. Science (New York, N.Y.), 333(6041), 459–462. https://doi.org/10.1126/science.1204117
  • You, Y. (2005). Podophyllotoxin derivatives: Current synthetic approaches for new anticancer agents. Current Pharmaceutical Design, 11(13), 1695–1717. https://doi.org/10.2174/1381612053764724
  • 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

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