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Development of A. solani β-tubulin models and comparison of docking results for benzo[d]azoles derivatives as potential antifungal agents
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Negi AS, Gautam Y, Alam S, Chanda D, Luqman S, Sarkar J, et al. Natural antitubulin agents: Importance of 3,4,5-trimethoxyphenyl fragment. Bioorg Med Chem. 2015;23:373–89. doi:10.1016/j.bmc.2014.12.027
Ranjan P, Kumar SP, Kari V, Jha PC. Exploration of interac-tion zones of β-tubulin colchicine binding domain of hel-minths and binding mechanism of anthelmintics. Comput Biol Chem. 2017;68:78–91. doi:10.1016/j.compbiolchem.2017.02.008
Davidse LC. Differential binding of methyl benzimidazol-2-yl carbamate to fungal tubulin as a mechanism of resistance to this antimitotic agent in mutant strains of Aspergillus nidulans. J Cell Biol. 1977;72:174–193. doi:10.1083/jcb.72.1.174
Li W, Sun H, Xu S, Zhu Z, Xu J. Tubulin inhibitors targeting the colchicine binding site: A perspective of privileged structures. Future Med Chem. 2017;9:1765–1794. doi:10.4155/fmc-2017-0100
Massarotti A, Coluccia A, Silvestri R, Sorba G, Brancale A. The Tubulin Colchicine Domain: a Molecular Modeling Per-spective. ChemMedChem. 2012;7:33–42. doi:10.1002/cmdc.201100361
Wang Y, Zhang H, Gigant B, Yu Y, Wu Y, Chen X, et al. Struc-tures of a diverse set of colchicine binding site inhibitors in complex with tubulin provide a rationale for drug discovery. FEBS J. 2016;283:102–111. doi:10.1111/febs.13555
Tuna BG, Atalay PB, Kuku G, Acar EE, Kara HK, Yilmaz MD, et al. Enhanced antitumor activity of carbendazim on HeLa cervical cancer cells by aptamer mediated controlled re-lease. RSC Adv. 2019;9:36005–36010. doi:10.1111/febs.13555
Goyal K, Sharma A, Arya R, Sharma R, Gupta GK, Sharma AK. Double Edge Sword Behavior of Carbendazim: A Potent Fun-gicide With Anticancer Therapeutic Properties. Anticancer Agents Med Chem. 2018;18:38–45. doi:10.2174/1871520616666161221113623
Yenjerla M, Cox C, Wilson L, Jordan MA. Carbendazim Inhib-its Cancer Cell Proliferation by Suppressing Microtubule Dynamics. J Pharmacol Exp Ther. 2009;328:390–398. doi:10.1124/jpet.108.143537
Vela-Corcía D, Romero D, de Vicente A, Pérez-García A. Analysis of β-tubulin-carbendazim interaction reveals that binding site for MBC fungicides does not include residues involved in fungicide resistance. Sci Rep. 2018;8:7161. doi:10.1038/s41598-018-25336-5
Xu S, Wang J, Wang H, Bao Y, Li Y, Govindaraju M, et al. Molecular characterization of carbendazim resistance of Fusarium species complex that causes sugarcane pokkah boeng disease. BMC Genomics. 2019;20:115. doi:10.1186/s12864-019-5479-6
Cai M, Lin D, Chen L, Bi Y, Xiao L, Liu X. M233I Mutation in the β-Tubulin of Botrytis cinerea Confers Resistance to Zox-amide. Sci Rep. 2015;5:16881. doi:10.1038/srep16881
Aguayo-Ortiz R, Méndez-Lucio O, Medina-Franco JL, Castillo R, Yépez-Mulia L, Hernández-Luis F, et al. Towards the iden-tification of the binding site of benzimidazoles to β-tubulin of Trichinella spiralis: Insights from computational and ex-perimental data. J Mol Graph Model. 2013;41:12–19. doi:10.1016/j.jmgm.2013.01.007
Aguayo-Ortiz R, Méndez-Lucio O, Romo-Mancillas A, Castillo R, Yépez-Mulia L, Medina-Franco JL, et al. Molecular basis for benzimidazole resistance from a novel β-tubulin binding site model. J Mol Graph Model. 2013;45:26–37. doi:10.1016/j.jmgm.2013.07.008
Wang Y, Zhang H, Gigant B, Yu Y, Wu Y, Chen X, et al. Struc-tures of a diverse set of colchicine binding site inhibitors in complex with tubulin provide a rationale for drug discovery. FEBS J. 2016;283:102–11. doi:10.1111/febs.13555
Trott O, Olson AJ. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31:455–461. doi:10.1002/jcc.21334
Schrödinger Release 2019-2: Maestro, Induced Fit Docking Protocol, MacroModel, Prime; Schrödinger, LLC: New York, NY, 2019.
Obydennov KL, Kalinina TA, Galieva NA, Beryozkina T V., Zhang Y, Fan Z, et al. Synthesis, Fungicidal Activity, and Mo-lecular Docking of 2-Acylamino and 2-Thioacylamino Deriv-atives of 1H-benzo[d]imidazoles as Anti-Tubulin Agents. J Agric Food Chem. 2021;69:12048–12062. doi:10.1021/acs.jafc.1c03325
Berthold MR, Cebron N, Dill F, Gabriel TR, Kötter T, Meinl T, et al. KNIME: The Konstanz Information Miner. 2008. p. 319–326. doi:10.1007/978-3-540-78246-9_38
Sander T, Freyss J, von Korff M, Rufener C. DataWarrior: An Open-Source Program For Chemistry Aware Data Visualiza-tion And Analysis. J Chem Inf Model. 2015;55:460–473. doi:10.1021/ci500588j
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, et al. AutoDock4 and AutoDockTools4: Auto-mated docking with selective receptor flexibility. J Comput Chem. 2009;30:2785–2791. doi:10.1002/jcc.21256
O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. J Cheminform. 2011;3:33. doi:10.1186/1758-2946-3-33
Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018;46:296–303. doi:10.1093/nar/gky427
Voinkov EK, Drokin RA, Fedotov V V., Butorin II, Savateev K V., Lyapustin DN, et al. Azolo[5,1‐c][1,2,4]triazines and Az-oloazapurines: Synthesis, Antimicrobial activity and in sili-co Studies. ChemistrySelect. 2022;7. doi:10.1002/slct.202104253
Tavella D, Ouellette DR, Garofalo R, Zhu K, Xu J, Oloo EO, et al. A novel method for in silico assessment of Methionine oxidation risk in monoclonal antibodies: Improvement over the 2-shell model. PLoS One. 2022;17:e0279689. doi:10.1371/journal.pone.0279689
Lihan M, Lupyan D, Oehme D. Target‐template relationships in protein structure prediction and their effect on the accu-racy of thermostability calculations. Protein Sci. 2023;32. doi:10.1002/pro.4557
Rodriguez Moncivais OJ, Chavez SA, Estrada Jimenez VH, Sun S, Li L, Kirken RA, et al. Structural analysis of janus ty-rosine kinase variants in hematological malignancies: im-plications for drug development and opportunities for novel therapeutic strategies. Int J Mol Sci. 2023;24:14573. doi:10.3390/ijms241914573
Champion C, Gall R, Ries B, Rieder SR, Barros EP, Riniker S. Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases. J Chem Inf Model. 2023;63:7133–47. doi:10.1021/acs.jcim.3c01469
Berman HM. The Protein Data Bank. Nucleic Acids Res. 2000;28:235–242. doi:10.1093/nar/28.1.235
Alhalaweh A, Lou B, Bostrom D, Velaga SP. CCDC 668711: Experimental Crystal Structure Determination. CSD Com-mun. 2007;668711. doi:10.5517/ccqfvb9
Lin Y, Ong YC, Keller S, Karges J, Bouchene R, Manoury E, et al. Synthesis, characterization and antiparasitic activity of organometallic derivatives of the anthelmintic drug al-bendazole. Dalt Trans. 2020;49:6616–6626. doi:10.1039/D0DT01107J
Hiscock JR, Gale PA, Lalaoui N, Light ME, Wells NJ. Benzim-idazole-based anion receptors exhibiting selectivity for lac-tate over pyruvate. Org Biomol Chem. 2012;10:7780. doi:10.1039/c2ob26299a
Beisken S, Meinl T, Wiswedel B, de Figueiredo LF, Berthold M, Steinbeck C. KNIME-CDK: Workflow-driven cheminfor-matics. BMC Bioinformatics. 2013;14:257. doi:10.1039/c2ob26299a
National Center for Biotechnology Information (NCBI)[Internet]. Bethesda (MD): National Library of Medi-cine (US), Na-tional Center for Biotechnology Information. 1988. https://www.ncbi.nlm.nih.gov/
Gui M, Croft JT, Zabeo D, Acharya V, Kollman JM, Burgoyne T, et al. SPACA9 is a lumenal protein of human ciliary sin-glet and doublet microtubules. Proc Natl Acad Sci. 2022;119. doi:10.1073/pnas.2207605119
DOI: https://doi.org/10.15826/chimtech.2024.11.1.04
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