Structure-based identification of potential natural compound inhibitors targeting bacterial cytoskeleton protein FtsZ from Acinetobacter baumannii by computational studies

References

• Araya, G., Benites, J., Reyes, J. S., Marcoleta, A. E., Valderrama, J. A., Lagos, R., & Monasterio, O. (2019). Inhibition of Escherichia coli and Bacillus subtilis FtsZ polymerization and Bacillus subtilis growth by dihydroxynaphtyl aryl ketones. Frontiers in Microbiology, 10, 1225. https://doi.org/10.3389/fmicb.2019.01225
   PubMed Web of Science ®Google Scholar
• Aylett, C. H., Izoré, T., Amos, L. A., & Löwe, J. (2013). Structure of the Tubulin/FtsZ-like protein TubZ from Pseudomonas bacteriophage ΦkZ. Journal of Molecular Biology, 425(12), 2164–2173. https://doi.org/10.1016/j.jmb.2013.03.019
   PubMed Web of Science ®Google Scholar
• Ballu, S., Itteboina, R., Sivan, S. K., & Manga, V. (2018a). Structural insights of Staphylococcus Aureus FtsZ inhibitors through molecular docking, 3D-QSAR and molecular dynamics simulations. Journal of Receptor and Signal Transduction Research, 38(1), 61–70. https://doi.org/10.1080/10799893.2018.1426607
   PubMed Web of Science ®Google Scholar
• Bi, E., & Lutkenhaus, J. (1991). FtsZ ring structure associated with division in Escherichia Coli. Nature, 354(6349), 161–164. https://doi.org/10.1038/354161a0
   PubMed Web of Science ®Google Scholar
• Blaauwen, T. D., Hamoen, L. W., & Levin, P. A. (2017). The Divisome at 25: The road ahead. Current Opinion in Microbiology, 36, 85–94. https://doi.org/10.1016/j.mib.2017.01.007
   PubMed Web of Science ®Google Scholar
• Boucher, H. W., Talbot, G. H., Bradley, J. S., Edwards, J. E., Gilbert, D., Rice, L. B., Scheld, M., Spellberg, B., & Bartlett, J. (2009). Bad bugs, no drugs: No ESKAPE! An update from the Infectious Diseases Society of America. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 48(1), 1–12. https://doi.org/10.1086/595011
   PubMed Web of Science ®Google Scholar
• Bowers, K. J., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., et al. (2006). “Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters.” in Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, SC’06. https://doi.org/10.1145/1188455.1188544
   Google Scholar
• Cheng, F., Li, W., Zhou, Y., Shen, J., Wu, Z., Liu, G., Lee, P. W., & Tang, Y. (2012). AdmetSAR: A comprehensive source and free tool for assessment of chemical ADMET properties. Journal of Chemical Information and Modeling, 52(11), 3099–3105. https://doi.org/10.1021/ci300367a
   PubMed Web of Science ®Google Scholar
• Corbin, B. D., Wang, Y., Beuria, T. K., & Margolin, W. (2007). Interaction between cell division proteins FtsE and FtsZ. Journal of Bacteriology, 189(8), 3026–3035. https://doi.org/10.1128/JB.01581-06
   PubMed Web of Science ®Google Scholar
• Cossio-Pérez, R., Palma, J., & Pierdominici-Sottile, G. (2017). Consistent principal component modes from molecular dynamics simulations of proteins. Journal of Chemical Information and Modeling, 57(4), 826–834. https://doi.org/10.1021/acs.jcim.6b00646
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Domadia, P. N., Bhunia, A., Sivaraman, J., Swarup, S., & Dasgupta, D. (2008). Berberine targets assembly of Escherichia coli cell division protein FtsZ. Biochemistry, 47(10), 3225–3234. https://doi.org/10.1021/bi7018546
   PubMed Web of Science ®Google Scholar
• Fang, Z., Ban, L., Li, Y., Yuan, W., Liu, Z., Liu, T., Li, X., Wong, K.-Y., Lu, Y., Sun, N., & Yao, X. (2018). A Quinoline-based FtsZ inhibitor for the study of antimicrobial activity and synergistic effects with β-Lactam antibiotics. Journal of Pharmacological Sciences, 137(3), 283–289. https://doi.org/10.1016/j.jphs.2018.07.005
   PubMed Web of Science ®Google Scholar
• Gordon, N. C., & Wareham, D. W. (2010). Multidrug-resistant Acinetobacter Baumannii: Mechanisms of virulence and resistance. International Journal of Antimicrobial Agents, 35(3), 219–226. https://doi.org/10.1016/j.ijantimicag.2009.10.024
   PubMed Web of Science ®Google Scholar
• Gunsteren, W. F. V., & Berendsen, H. J. (1988). A leap-frog algorithm for stochastic dynamics. Molecular Simulation, 1(3), 173–185. https://doi.org/10.1080/08927028808080941
   Web of Science ®Google Scholar
• Gurnani, M., Chauhan, A., Ranjan, A., Singh Tuli, H., Alkhanani, M. F., Haque, S., Dhama, K., Lal, R., & Jindal, T. (2022). Filamentous thermosensitive mutant Z: An appealing target for emerging pathogens and a Trek on its natural inhibitors. Biology, 11(5), 624. https://doi.org/10.3390/biology11050624
   PubMedGoogle Scholar
• Han, H., Wang, Z., Li, T., Teng, D., Mao, R., Hao, Y., Yang, N., Wang, X., & Wang, J. (2021). Recent progress of bacterial FtsZ inhibitors with a focus on peptides. The FEBS Journal, 288(4), 1091–1106. https://doi.org/10.1111/febs.15489
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Ke, Q., Gong, X., Liao, S., Duan, C., & Li, L. (2022). Effects of thermostats/barostats on physical properties of liquids by molecular dynamics simulations. Journal of Molecular Liquids, 365, 120116. https://doi.org/10.1016/j.molliq.2022.120116
   Web of Science ®Google Scholar
• Kim, Y. J., Kim, S. I., Kim, Y. R., Hong, K. W., Wie, S. H., Park, Y. J., Jeong, H., & Kang, M. W. (2012). Carbapenem-resistant Acinetobacter Baumannii: Diversity of resistant mechanisms and risk factors for infection. Epidemiology and Infection, 140(1), 137–145. https://doi.org/10.1017/S0950268811000744
   PubMed Web of Science ®Google Scholar
• Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., & Cheatham, T. E. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33(12), 889–897. https://doi.org/10.1021/ar000033j
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A, Open Source Drug Discovery Consortium. (2014). 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
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. https://doi.org/10.1021/ci200227u
   PubMed Web of Science ®Google Scholar
• Lin, L., Tan, B., Pantapalangkoor, P., Ho, T., Hujer, A. M., Taracila, M. A., Bonomo, R. A., & Spellberg, B. (2013). Acinetobacter Baumannii ROmpA vaccine dose alters immune polarization and immunodominant epitopes. Vaccine, 31(2), 313–318. https://doi.org/10.1016/j.vaccine.2012.11.008
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 64, 4–17. https://doi.org/10.1016/j.addr.2012.09.019
   Web of Science ®Google Scholar
• Lu, C., Wu, C., Ghoreishi, D., Chen, W., Wang, L., Damm, W., Ross, G. A., Dahlgren, M. K., Russell, E., Von Bargen, C. D., Abel, R., Friesner, R. A., & Harder, E. D. (2021). OPLS4: Improving force field accuracy on challenging regimes of chemical space. Journal of Chemical Theory and Computation, 17(7), 4291–4300. https://doi.org/10.1021/acs.jctc.1c00302
   PubMed Web of Science ®Google Scholar
• Matsui, T., Yamane, J., Mogi, N., Yamaguchi, H., Takemoto, H., Yao, M., & Tanaka, I. (2012). Structural reorganization of the bacterial cell-division protein FtsZ from Staphylococcus Aureus. Acta Crystallographica. Section D, Biological Crystallography, 68(Pt 9), 1175–1188. https://doi.org/10.1107/S0907444912022640
   PubMedGoogle Scholar
• McConnell, M. J., Actis, L., & Pachón, J. (2013). Acinetobacter Baumannii: Human infections, factors contributing to pathogenesis and animal models. FEMS Microbiology Reviews, 37(2), 130–155. https://doi.org/10.1111/j.1574-6976.2012.00344.x
   PubMed Web of Science ®Google Scholar
• Miller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.Py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. https://doi.org/10.1021/ct300418h
   PubMed Web of Science ®Google Scholar
• Sass, P., & Brötz-Oesterhelt, H. (2013). Bacterial cell division as a target for new antibiotics. Current Opinion in Microbiology, 16(5), 522–530. https://doi.org/10.1016/j.mib.2013.07.006
   PubMed Web of Science ®Google Scholar
• Schmid, N., Eichenberger, A. P., Choutko, A., Riniker, S., Winger, M., Mark, A. E., & Van Gunsteren, W. F. (2011). Definition and testing of the GROMOS force-field versions 54A7 and 54B7. European Biophysics Journal, 40(7), 843–856. https://doi.org/10.1007/s00249-011-0700-9
   PubMed Web of Science ®Google Scholar
• Seeliger, D., & De Groot, B. L. (2010). Ligand docking and binding site analysis with PyMOL and Autodock/Vina. Journal of Computer-Aided Molecular Design, 24(5), 417–422. https://doi.org/10.1007/s10822-010-9352-6
   PubMed Web of Science ®Google Scholar
• Sharma, A., Vora, J., Patel, D., Sinha, S., Jha, P. C., & Shrivastava, N. (2022). Identification of natural inhibitors against prime targets of SARS-CoV-2 using molecular docking, molecular dynamics simulation and MM-PBSA approaches. Journal of Biomolecular Structure & Dynamics, 40(7), 3296–3311. https://doi.org/10.1080/07391102.2020.1846624
   PubMed Web of Science ®Google Scholar
• Sterling, T., & Irwin, J. J. (2015). ZINC 15 - Ligand discovery for everyone. Journal of Chemical Information and Modeling, 55(11), 2324–2337. https://doi.org/10.1021/acs.jcim.5b00559
   PubMed Web of Science ®Google Scholar
• Tan, C. M., Therien, A. G., Lu, J., Lee, S. H., Caron, A., Gill, C. J., Lebeau-Jacob, C., Benton-Perdomo, L., Monteiro, J. M., Pereira, P. M., Elsen, N. L., Wu, J., Deschamps, K., Petcu, M., Wong, S., Daigneault, E., Kramer, S., Liang, L., Maxwell, E., … Roemer, T. (2012). Restoring methicillin-resistant Staphylococcus Aureus susceptibility to β-Lactam antibiotics. Science Translational Medicine, 4(126), 126ra35. https://doi.org/10.1126/scitranslmed.3003592
   PubMed Web of Science ®Google Scholar
• Vemula, D., Maddi, D. R., & Bhandari, V. (2023). Homology modeling, virtual screening, molecular docking, and dynamics studies for discovering Staphylococcus Epidermidis FtsZ inhibitors. Frontiers in Molecular Biosciences, 10, 1087676. https://doi.org/10.3389/fmolb.2023.1087676
   PubMed Web of Science ®Google Scholar
• Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303. https://doi.org/10.1093/nar/gky427
   PubMed Web of Science ®Google Scholar
• Whitley, K. D., Jukes, C., Tregidgo, N., Karinou, E., Almada, P., Cesbron, Y., Henriques, R., Dekker, C., & Holden, S. (2021). FtsZ treadmilling is essential for Z-ring condensation and septal constriction initiation in Bacillus Subtilis cell division. Nature Communications, 12(1), 2448. https://doi.org/10.1038/s41467-021-22526-0
   PubMed Web of Science ®Google Scholar