325
Views
6
CrossRef citations to date
0
Altmetric
Original Articles

Structural investigations into the binding mode of novel neolignans Cmp10 and Cmp19 microtubule stabilizers by in silico molecular docking, molecular dynamics, and binding free energy calculations

, , , &
Pages 1232-1240 | Received 30 Mar 2015, Accepted 15 Jul 2015, Published online: 01 Sep 2015

References

  • Asthana, S., Shukla, S., Ruggerone, P., & Vargiu, A. V. (2014). Molecular mechanism of viral resistance to a potent non-nucleoside inhibitor unveiled by molecular simulations. Biochemistry, 53, 6941–6953.10.1021/bi500490z
  • Canales, A., Rodríguez-Salarichs, J., Trigili, C., Nieto, L., Coderch, C., Andreu, J. M., … Díaz, J. F. (2011). Insights into the interaction of discodermolide and docetaxel with tubulin. mapping the binding sites of microtubule-stabilizing agents by using an integrated NMR and computational approach. ACS Chemical Biology, 6, 789–799.10.1021/cb200099u
  • 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, 10089–10092.10.1063/1.464397
  • DeLano, W. (2002). The PyMol molecular graphics system, version 0.99. San Carlos, CA: DeLano Scientific.
  • Durham, E., Dorr, B., Woetzel, N., Staritzbichler, R., & Meiler, J. (2009). Solvent accessible surface area approximations for rapid and accurate protein structure prediction. Journal of Molecular Modeling, 15, 1093–1108.10.1007/s00894-009-0454-9
  • Field, J. J., Díaz, J. F., & Miller, J. H. (2013). The binding sites of microtubule-stabilizing agents. Chemistry & Biology, 20, 301–315.
  • Goodsell, D. S., Morris, G. M., & Olson, A. J. (1996). Automated docking of flexible ligands: Applications of autodock. Journal of Molecular Recognition, 9, 1–5.10.1002/(ISSN)1099-1352
  • Hadfield, J. A., Ducki, S., Hirst, N., & McGown, A. T. (2003). Tubulin and microtubules as targets for anticancer drugs. Progress in Cell Cycle Research., 5, 309–325.
  • Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18, 1463–1472.10.1002/(ISSN)1096-987X
  • Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4, 435–447.10.1021/ct700301q
  • Hetényi, C., & van der Spoel, D. (2006). Blind docking of drug-sized compounds to proteins with up to a thousand residues. FEBS Letters, 580, 1447–1450.10.1016/j.febslet.2006.01.074
  • Honore, S., Pasquier, E., & Braguer, D. (2005). Understanding microtubule dynamics for improved cancer therapy. Cellular and Molecular Life Sciences, 62, 3039–3056. (n.d.) http://plasma-gate.weizmann.ac.il/Grace/10.1007/s00018-005-5330-x
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14, 33–38.10.1016/0263-7855(96)00018-5
  • Jordan, A., Hadfield, J. A., Lawrence, N. J., & McGown, A. T. (1998). Tubulin as a target for anticancer drugs: Agents which interact with the mitotic spindle. Medicinal Research Reviews, 18, 259–296.10.1002/(ISSN)1098-1128
  • Kannan, S., Poulsen, A., Yang, H. Y., Ho, M., Ang, S. H., Eldwin, T. S., … Nacro, K. (2015). Probing the binding mechanism of Mnk inhibitors by docking and molecular dynamics simulations. Biochemistry, 54, 32–46.10.1021/bi501261j
  • Keskin, O., Durell, S. R., Bahar, I., Jernigan, R. L., & Covell, D. G. (2002). Relating molecular flexibility to function: A case study of tubulin. Biophysical Journal, 83, 663–680.10.1016/S0006-3495(02)75199-0
  • Kim, K. H., Kim, H. K., Choi, S. U., Moon, E., Kim, S. Y., & Lee, K. R. (2011). Bioactive lignans from the rhizomes of Acorus gramineus. Journal of Natural Products, 74, 2187–2192.10.1021/np200541m
  • Kumar, A., Roy, S., Tripathi, S., & Sharma, A. (2015). Molecular docking based virtual screening of natural compounds as potential BACE1 inhibitors: 3D – QSAR pharmacophore mapping and molecular dynamics analysis. Journal of Biomolecular Structure and Dynamics, 1–11. doi:10.1080/07391102.2015.1022603
  • Kumar, B. S., Singh, A., Kumar, A., Singh, J., Hasanain, M., Singh, A, … Negi, A. S. (2014). Synthesis of neolignans as microtubule stabilizers. Bioorganic & Medicinal Chemistry, 22, 1342–1354.
  • 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, 1951–1962.10.1021/ci500020m
  • Liao, S. Y., Mo, G. Q., Chen, J. C., & Zheng, K. C. (2014). Exploration of the binding mode between (−)-zampanolide and tubulin using docking and molecular dynamics simulation. Journal of Molecular Modeling, 20, 2070. doi:10.1007/s00894-014-2070-6
  • Löwe, J., Li, H., Downing, K. H., & Nogales, E. (2001). Refined structure of αβ-tubulin at 3.5 Å resolution. Journal of Molecular Biology, 313, 1045–1057.10.1006/jmbi.2001.5077
  • Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19, 1639–1662.10.1002/(ISSN)1096-987X
  • Moujir, L., Seca, A. M. L., Silva, A. M. S., López, M. R., Padilla, N., Cavaleiro, J. A. S., & Neto, C. P. (2007). Cytotoxic activity of lignans from Hibiscus cannabinus. Fitoterapia, 78, 385–387.10.1016/j.fitote.2007.03.010
  • Natarajan, K., & Senapati, S. (2012). Understanding the basis of drug resistance of the mutants of αβ-tubulin dimer via molecular dynamics simulations. PLoS ONE, 7, e42351. doi:10.1371/journal.pone.0042351
  • Nogales, E., Whittaker, M., Milligan, R. A., & Downing, K. H. (1999). High-resolution model of the microtubule. Cell, 96, 79–88.10.1016/S0092-8674(00)80961-7
  • Nogales, E., Wolf, S. G., & Downing, K. H. (1998). Structure of the alpha beta tubulin dimer by electron crystallography. Nature, 391, 199–203.10.1038/34465
  • Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327–341.10.1016/0021-9991(77)90098-5
  • Sanchita, Chauhan, R., Soni, G., Sudhamalla, B., & Sharma, A. (2013). Docking and molecular dynamics studies of peptide inhibitors of ornithine decarboxylase: A rate-limiting enzyme for the metabolism of Fusarium solani. Journal of Biomolecular Structure and Dynamics, 31, 874–887.10.1080/07391102.2012.718526
  • Sanner, M. F. (1999). Python: A programming language for software integration and development. Journal of Molecular Graphics & Modelling, 17, 57–61.
  • Schiff, P. B., Fant, J., & Horwitz, S. B. (1979). Promotion of microtubule assembly in vitro by taxol. Nature, 277, 665–667.10.1038/277665a0
  • Schüttelkopf, A. W., & Van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60, 1355–1363.10.1107/S0907444904011679
  • Sui, H., & Downing, K. H. (2010). Structural basis of interprotofilament interaction and lateral deformation of microtubules. Structure, 18, 1022–1031.10.1016/j.str.2010.05.010
  • Tan, H., Wei, K., Bao, J., & Zhou, X. (2013). In silico study on multidrug resistance conferred by I223R/H275Y double mutant neuraminidase. Molecular BioSystems, 9, 2764–2774.10.1039/c3mb70253g
  • 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, 1701–1718.10.1002/(ISSN)1096-987X
  • Vriend, G. (1990). WHAT IF: A molecular modeling and drug design program. Journal of Molecular Graphics, 8, 52–56.10.1016/0263-7855(90)80070-V
  • Xiao, H., Verdier-Pinard, P., Fernandez-Fuentes, N., Burd, B., Angeletti, R., Fiser, A., … Orr, G. A. (2006). Insights into the mechanism of microtubule stabilization by Taxol. Proceedings of the National Academy of Sciences, 103, 10166–10173.10.1073/pnas.0603704103

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.