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Stabilization of Microtubules by Taxane Diterpenoids: Insight from Docking and MD simulations

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Abstract

Microtubules are formed from the molecules of tubulin, whose dynamics is important for many functions in a cell, the most dramatic of which is mitosis. Taxol is known to interact within a specific site on tubulin and also believed to block cell-cycle progression during mitosis by binding to and stabilizing microtubules. Along with the tremendous potential that taxol has shown as an anticancer drug, clinical problems exist with solubility, toxicity, and development of drug resistance. The crystal structure of taxane diterpenoids, namely, 10, 13-deacetyl-abeo-baccatin-IV (I), 5-acetyl-2-deacetoxydecinnamoyl-taxinine-0.29hydrate (II), 7, 9-dideacetyltaxayuntin (III), and Taxawallin-K (IV), are very similar to the taxol molecule. Considerable attention has been given to such molecules whose archetype is taxol but do not posses long aliphatic chains, to be developed as a substitute for taxol with fewer side effects. In the present work, the molecular docking of these taxane diterpenoids has been carried out with the tubulin alpha-beta dimer (1TUB) and refined microtubule structure (1JFF) using Glide-XP, in order to assess the potential of tubulin binding of these cytotoxic agents. Results show that all the ligands dock into the classical taxol binding site of tubulin. Taxol shows the best binding capabilities. On the basis of docking energy and interactions, apart from taxol, molecule II has a better tendency of binding with 1TUB while molecule I shows better binding capability with bovine tubulin 1JFF. To validate the binding capabilities, molecular dynamics (MD) simulations of the best docked complexes of ligands with 1JFF have been carried out for 15.0 ns using DESMOND. Average RMSD variations and time line study of interactions and contacts indicate that these complexes remain stable during the course of the dynamics. However, taxol and molecule II prevail over other taxoids.

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Acknowledgments

U. Yadava is thankful to the Department of Science and Technology, New Delhi, for the financial support through its Fast Track Young Scientist Scheme and University Grants Commission, New Delhi for the award of Raman Fellowship.

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Authors and Affiliations

  1. Department of Physics, DDU Gorakhpur University, Gorakhpur, 273009, India

    Umesh Yadava, Hariom Gupta & Mihir Roychoudhury

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  1. Umesh Yadava
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  2. Hariom Gupta
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  3. Mihir Roychoudhury
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Correspondence to Umesh Yadava.

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Yadava, U., Gupta, H. & Roychoudhury, M. Stabilization of Microtubules by Taxane Diterpenoids: Insight from Docking and MD simulations. J Biol Phys 41, 117–133 (2015). https://doi.org/10.1007/s10867-014-9369-5

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