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Research Article

Cytotoxic monastrol derivatives as adjective inhibitors of drug-resistant Eg5: a molecular dynamics perspective

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Received 06 Nov 2023, Accepted 27 Feb 2024, Published online: 07 Mar 2024

References

  • Adasme, M. F., Linnemann, K. L., Bolz, S. N., Kaiser, F., Salentin, S., Haupt, V. J., & Schroeder, M. (2021). PLIP 2021: Expanding the scope of the protein-ligand interaction profiler to DNA and RNA. Nucleic Acids Research, 49(W1), W530–W534. https://doi.org/10.1093/nar/gkab294
  • Aqvist, J., & Marelius, J. (2001). The linear interaction energy method for predicting ligand binding free energies. Combinatorial Chemistry & High Throughput Screening, 4(8), 613–626. https://doi.org/10.2174/1386207013330661
  • Aqvist, J., Medina, C., & Samuelsson, J. E. (1994). A new method for predicting binding affinity in computer-aided drug design. Protein Engineering, 7(3), 385–391. https://doi.org/10.1093/protein/7.3.385
  • Berendsen, H. J. C., Postma, J. P. M., Van Gunsteren, W. F., & Hermans, J. (1981). Interaction models for water in relation to protein hydration. In Pullman, B., (Ed.), Intermolecular forces. The Jerusalem symposia on quantum chemistry and biochemistry (vol. 14). https://doi.org/10.1007/978-94-015-7658-1_21
  • Bohlooli, S., Nejatkhah, N., Sepehri, S., Doostkamel, D., & Razzaghi-Asl, N. (2020). Synthesis and cytotoxicity evaluation of novel cyclic/non-cyclic N-aryl enamino amides against human cancer cell lines. Research in Pharmaceutical Sciences, 15(6), 563–570. https://doi.org/10.4103/1735-5362.301341
  • Bondi, A. (1964). Van der Waals Volumes and Radii. The Journal of Physical Chemistry, 68(3), 441–451. https://doi.org/10.1021/j100785a001
  • Chin, G. M., & Herbst, R. (2006). Induction of apoptosis by monastrol, an inhibitor of the mitotic kinesin Eg5, is independent of the spindle checkpoint. Molecular Cancer Therapeutics, 5(10), 2580–2591. https://doi.org/10.1158/1535-7163.MCT-06-0201
  • Daina, A., & Zoete, V. (2016). A boiled-egg to predict gastrointestinal absorption and brain penetration of small molecules. ChemMedChem. 11(11), 1117–1121. https://doi.org/10.1002/cmdc.201600182
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. https://doi.org/10.1038/srep42717
  • Damjanović, A., Brooks, B. R., & García-Moreno, B. (2011). Conformational relaxation and water penetration coupled to ionization of internal groups in proteins. The Journal of Physical Chemistry. A, 115(16), 4042–4053. https://doi.org/10.1021/jp110373f
  • 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
  • Ertl, P., Rohde, B., & Selzer, P. (2000). Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. Journal of Medicinal Chemistry, 43(20), 3714–3717. https://doi.org/10.1021/jm000942e
  • Frappier, V., Chartier, M., & Najmanovich, R. J. (2015). ENCoM server: Exploring protein conformational space and the effect of mutations on protein function and stability. Nucleic Acids Research, 43(W1), W395–W400. https://doi.org/10.1093/nar/gkv343
  • Guido, B. C., Ramos, L. M., Nolasco, D. O., Nobrega, C. C., Andrade, B. Y., Pic-Taylor, A., Neto, B. A., & Corrêa, J. R. (2015). Impact of kinesin Eg5 inhibition by 3,4-dihydropyrimidin-2(1H)-one derivatives on various breast cancer cell features. BMC Cancer, 15(1), 283. https://doi.org/10.1186/s12885-015-1274-1
  • 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(12), 1463–1472. 10.1002/(SICI)1096-987X(199709)18:12
  • Ittisoponpisan, S., Islam, S. A., Khanna, T., Alhuzimi, E., David, A., & Sternberg, M. J. E. (2019). Can predicted protein 3D structures provide reliable insights into whether missense variants are disease associated? Journal of Molecular Biology, 431(11), 2197–2212. https://doi.org/10.1016/j.jmb.2019.04.009
  • Jin, Q., Huang, F., Wang, X., Zhu, H., Xian, Y., Li, J., Zhang, S., & Ni, Q. (2017). High Eg5 expression predicts poor prognosis in breast cancer. Oncotarget, 8(37), 62208–62216. https://doi.org/10.18632/oncotarget.19215
  • Kaan, H. Y. K., Ulaganathan, V., Hackney, D. D., & Kozielski, F. (2010). An allosteric transition trapped in an intermediate state of a new kinesin-inhibitor complex. The Biochemical Journal, 425(1), 55–60. https://doi.org/10.1042/BJ20091207
  • Kapitein, L. C., Peterman, E., Kwok, B. H., Kim, J. H., Kapoor, T. M., & Schmidt, C. F. (2005). The bipolar mitotic kinesin Eg5 moves on both microtubules that it crosslinks. Nature, 435(7038), 114–118. https://doi.org/10.1038/nature03503
  • King, E., Aitchison, E., Li, H., & Luo, R. (2021). Recent developments in free energy calculations for drug discovery. Frontiers in Molecular Biosciences, 8, 712085. https://doi.org/10.3389/fmolb.2021.712085
  • Luo, L., Parrish, C., Nevins, N., McNulty, D. E., Chaudhari, A. M., Carson, J. D., Sudakin, V., Shaw, A. N., Lehr, R., Zhao, H., Sweitzer, S., Lad, L., Wood, K. W., Sakowicz, R., Annan, R. S., Huang, P. S., Jackson, J. R., Dhanak, D., Copeland, R. A., & Auger, K. R. (2007). ATP-competitive inhibitors of the mitotic kinesin KSP that function via an allosteric mechanism. Nature Chemical Biology, 3(11), 722–726. https://doi.org/10.1038/nchembio.2007.34
  • Malde, A. K., Zuo, L., Breeze, M., Stroet, M., Poger, D., Nair, P. C., Oostenbrink, C., & Mark, A. E. (2011). An Automated force field Topology Builder (ATB) and repository: Version 1.0. Journal of Chemical Theory and Computation, 7(12), 4026–4037. https://doi.org/10.1021/ct200196m
  • Maliga, Z., & Mitchison, T. (2006). Small-molecule and mutational analysis of allosteric Eg5 inhibition by monastrol. BMC Chemical Biology, 6(1), 2. https://doi.org/10.1186/1472-6769-6-2
  • Maliga, Z., & Mitchison, T. J. (2005). Human Eg5 motor domain bound to Mg-ADP and monastrol. https://doi.org/10.2210/pdb2211x2288/pdb
  • Mayer, T. U., Kapoor, T. M., Haggarty, S. J., King, R. W., Schreiber, S. L., & Mitchison, T. (1999). Small molecule inhibitor of mitotic spindle bipolarity identified in a phenotype-based screen. Science (New York, N.Y.), 286(5441), 971–974. https://doi.org/10.1126/science.286.5441.971
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
  • Myers, S. M., & Collins, I. (2016). Recent findings and future directions for interpolar mitotic kinesin inhibitors in cancer therapy. Future Medicinal Chemistry, 8(4), 463–489. https://doi.org/10.4155/fmc.16.5
  • Ogunwa, T. H., Laudadio, E., Galeazzi, R., & Miyanishi, T. (2019). Insights into the molecular mechanisms of Eg5 inhibition by (+)-morelloflavone. Pharmaceuticals (Basel, Switzerland), 12(2), 58. https://doi.org/10.3390/ph12020058
  • 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
  • Prabhavathi, H., Dasegowda, K. R., Renukananda, K. H., Lingaraju, K., & Naika, H. R. (2021). Exploration and evaluation of bioactive phytocompounds against BRCA proteins by in silico approach. Journal of Biomolecular Structure & Dynamics, 39(15), 5471–5485. https://doi.org/10.1080/07391102.2020.1790424
  • Razzaghi-Asl, N., Ebadi, A., Shahabipour, S., & Gholamin, D. (2021). Identification of a potential SARS-CoV2 inhibitor via molecular dynamics simulations and amino acid decomposition analysis. Journal of Biomolecular Structure & Dynamics, 39(17), 6633–6648. https://doi.org/10.1080/07391102.2020.1797536
  • Ricci, A., Gallorini, M., Del Bufalo, D., Cataldi, A., D'Agostino, I., Carradori, S., & Zara, S. (2022). Negative modulation of the angiogenic cascade induced by allosteric kinesin Eg5 inhibitors in a gastric adenocarcinoma in vitro model. Molecules (Basel, Switzerland), 27(3), 957. https://doi.org/10.3390/molecules27030957
  • Rodrigues, C. H., Pires, D. E., & Ascher, D. B. (2018). DynaMut: Predicting the impact of mutations on protein conformation, flexibility and stability. Nucleic Acids Research, 46(W1), W350–W355. https://doi.org/10.1093/nar/gky300
  • Salentin, S., Schreiber, S., Haupt, V. J., Adasme, M. F., & Schroeder, M. (2015). PLIP: Fully automated protein-ligand interaction profiler. Nucleic Acids Research, 43(W1), W443–W447. https://doi.org/10.1093/nar/gkv315
  • Sanner, M. F. (1999). Python: A programming language for software integration and development. Journal of Molecular Graphics & Modelling, 17(1), 57–61. PMID: 10660911
  • Sarli, V., & Giannis, A. (2008). Targeting the kinesin spindle protein: Basic principles and clinical implications. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, 14(23), 7583–7587. https://doi.org/10.1158/1078-0432.CCR-08-0120
  • Sehnal, D., Bittrich, S., Deshpande, M., Svobodová, R., Berka, K., Bazgier, V., Velankar, S., Burley, S. K., Koča, J., & Rose, A. S. (2021). Mol* viewer: Modern web app analysis of large biomolecular structures. Nucleic Acids Research, 49(W1), W431–W437. https://doi.org/10.1093/nar/gkab314
  • Sheth, P. R., Basso, A., Duca, J. S., Lesburg, C. A., Ogas, P., Gray, K., Nale, L., Mannarino, A. F., Prongay, A. J., & Le, H. V. (2009). Thermodynamics of nucleotide and inhibitor binding to wild-type and ispinesib-resistant forms of human kinesin spindle protein. Biochemistry, 48(46), 11045–11055. https://doi.org/10.1021/bi900946r
  • Tavangar, S., Bohlooli, S., & Razzaghi-Asl, N. (2020). Synthesis and cytotoxic effect of a few N-heteroaryl enamino amides and dihydropyrimidinethiones on AGS and MCF-7 human cancer cell lines. Research in Pharmaceutical Sciences, 15(2), 154–163. https://doi.org/10.4103/1735-5362.283815
  • Tcherniuk, S., van Lis, R., Kozielski, F., & Skoufias, D. A. (2010). Mutations in the human kinesin Eg5 that confer resistance to monastrol and S-trityl-L-cysteine in tumor derived cell lines. Biochemical Pharmacology, 79(6), 864–872. https://doi.org/10.1016/j.bcp.2009.11.001
  • Turner, J., Anderson, R., Guo, J., Beraud, C., Fletterick, R., & Sakowicz, R. (2001). Crystal structure of the mitotic spindle kinesin Eg5 reveals a novel conformation of the neck-linker. The Journal of Biological Chemistry, 276(27), 25496–25502. https://doi.org/10.1074/jbc.M100395200
  • Ulaganathan, V., Talapatra, S. K., Rath, O., Pannifer, A., Hackney, D. D., & Kozielski, F. (2013). Structural insights into a unique inhibitor binding pocket in kinesin spindle protein. Journal of the American Chemical Society, 135(6), 2263–2272. https://doi.org/10.1021/ja310377d
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
  • Wildman, S. A., & Crippen, G. N. (1999). Prediction of physicOchemical parameters by atomic contributions. Journal of Chemical Information and Computer Sciences, 39(5), 868–873. https://doi.org/10.1021/ci990307l
  • Wojcik, E. J., Buckley, R. S., Richard, J., Liu, L., Huckaba, T. M., & Kim, S. (2013). Kinesin-5: Cross-bridging mechanism to targeted clinical therapy. Gene, 531(2), 133–149. https://doi.org/10.1016/j.gene.2013.08.004
  • Wu, Z., Peng, Y., Yu, Z., Li, W., Liu, G., & Tang, Y. (2020). NetInfer: A web server for prediction of targets and therapeutic and adverse effects via network-based inference methods. Journal of Chemical Information and Modeling, 60(8), 3687–3691. https://doi.org/10.102/acs.jcim.0c00291
  • Yan, Y., Sardana, V., Xu, B., Homnick, C., Halczenko, W., Buser, C. A., Schaber, M., Hartman, G. D., Huber, H. E., & Kuo, L. C. (2004). Inhibition of a mitotic motor protein: Where, how, and conformational consequences. Journal of Molecular Biology, 335(2), 547–554. https://doi.org/10.1016/j.jmb.2003.10.074
  • Zhang, W. (2011). Exploring the intermediate states of ADP-ATP exchange: A simulation study on Eg5. The Journal of Physical Chemistry. B, 115(5), 784–795. https://doi.org/10.1021/jp107255t
  • Zhang, W., Zhai, L., Lu, W., Boohaker, R. J., Padmalayam, I., & Li, Y. (2016). Discovery of novel allosteric Eg5 inhibitors through structure-based virtual screening. Chemical Biology & Drug Design, 88(2), 178–187. https://doi.org/10.1111/cbdd.12744

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