Identification of novel metallo-β-lactamases inhibitors using ligand-based pharmacophore modelling and structure-based virtual screening

References

• Aarjane, M., Slassi, S., Ghaleb, A., Tazi, B., & Amine, A. (2021). Synthesis, biological evaluation, molecular docking and in silico ADMET screening studies of novel isoxazoline derivatives from acridone. Arabian Journal of Chemistry, 14(4), 103057. https://doi.org/10.1016/j.arabjc.2021.103057
   Web of Science ®Google Scholar
• Brem, J., van Berkel, S. S., Zollman, D., Lee, S. Y., Gileadi, O., McHugh, P. J., Walsh, T. R., McDonough, M. A., & Schofield, C. J. (2016). Structural basis of metallo-β-lactamase inhibition by captopril stereoisomers. Antimicrobial Agents and Chemotherapy, 60(1), 142–150. https://doi.org/10.1128/AAC.01335-15
   PubMed Web of Science ®Google Scholar
• Chen, C., & Yang, K. (2020). Ruthenium complexes as prospective inhibitors of metallo-β-lactamases to reverse carbapenem resistance. Dalton Transactions, 49(40), 14099–14105. https://doi.org/10.1039/d0dt02430a
   PubMed Web of Science ®Google Scholar
• Docquier, J. D., & Mangani, S. (2018). An update on β-lactamase inhibitor discovery and development. Drug Resistance Updates, 36, 13–29. https://doi.org/10.1016/j.drup.2017.11.002
   PubMed Web of Science ®Google Scholar
• Eiamphungporn, W., Schaduangrat, N., Malik, A. A., & Nantasenamat, C. (2018). Tackling the antibiotic resistance caused by class A β-lactamases through the use of β-lactamase inhibitory protein. International Journal of Molecular Sciences, 19(8), 2222. https://doi.org/10.3390/ijms19082222
   PubMed Web of Science ®Google Scholar
• F Mojica, M., A Bonomo, R., & Fast, W. (2016). B1-metallo-β-lactamases: Where do we stand? Current Drug Targets, 17(9), 1029–1050. https://doi.org/10.2174/1389450116666151001105622
   PubMed Web of Science ®Google Scholar
• Gavara, L., Sevaille, L., De Luca, F., Mercuri, P., Bebrone, C., Feller, G., Legru, A., Cerboni, G., Tanfoni, S., Baud, D., Cutolo, G., Bestgen, B., Chelini, G., Verdirosa, F., Sannio, F., Pozzi, C., Benvenuti, M., Kwapien, K., Fischer, M., … Hernandez, J.-F. (2020). 4-Amino-1,2,4-triazole-3-thione-derived Schiff bases as metallo-β-lactamase inhibitors. European Journal of Medicinal Chemistry, 208, 112720. https://doi.org/10.1016/j.ejmech.2020.112720
   PubMed Web of Science ®Google Scholar
• Hou, C. F. D., Liu, J. W., Collyer, C., Mitić, N., Pedroso, M. M., Schenk, G., & Ollis, D. L. (2017). Insights into an evolutionary strategy leading to antibiotic resistance. Scientific Reports, 7(1), 40357. https://doi.org/10.1038/srep40357
   PubMedGoogle Scholar
• Ju, L. C., Cheng, Z., Fast, W., Bonomo, R. A., & Crowder, M. W. (2018). The continuing challenge of metallo-β-lactamase inhibition: Mechanism matters. Trends in Pharmacological Sciences, 39(7), 635–647. https://doi.org/10.1016/j.tips.2018.03.007
   PubMed Web of Science ®Google Scholar
• Khaldan, A., Bouamrane, S., El-Mernissi, R., Maghat, H., Ajana, M. A., Sbai, A., Bouachrine, M., & Lakhlifi, T. (2021). 3D-QSAR modeling, molecular docking and ADMET properties of benzothiazole derivatives as α-glucosidase inhibitors. Materials Today: Proceedings, 45, 7643–7652. https://doi.org/10.1016/j.matpr.2021.03.114
   Google Scholar
• Khalili Arjomandi, O., Kavoosi, M., & Adibi, H. (2019). Synthesis and enzyme-based evaluation of analogues L-tyrosine thiol carboxylic acid inhibitor of metallo-β-lactamase IMP-1. Journal of Enzyme Inhibition and Medicinal Chemistry, 34(1), 1414–1425. https://doi.org/10.1080/14756366.2019.1651314
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A. (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
• Kurz, J. L., Pedroso, M. M., Richard, E., McGeary, R. P., & Schenk, G. (2023). Inhibitors for metallo-β-lactamases from the B1 and B3 subgroups provide an avenue to combat a major mechanism of antibiotic resistance. Bioorganic & Medicinal Chemistry Letters, 92, 129387. https://doi.org/10.1016/j.bmcl.2023.129387
   PubMed Web of Science ®Google Scholar
• Lagorce, D., Bouslama, L., Becot, J., Miteva, M. A., & Villoutreix, B. O. (2017). FAF-Drugs4: Free ADME-tox filtering computations for chemical biology and early stages drug discovery. Bioinformatics, 33(22), 3658–3660. https://doi.org/10.1093/bioinformatics/btx491
   PubMed Web of Science ®Google Scholar
• Li, N., Xu, Y., Xia, Q., Bai, C., Wang, T., Wang, L., He, D., Xie, N., Li, L., Wang, J., Zhou, H.-G., Xu, F., Yang, C., Zhang, Q., Yin, Z., Guo, Y., & Chen, Y. (2014). Simplified captopril analogues as NDM-1 inhibitors. Bioorganic & Medicinal Chemistry Letters, 24(1), 386–389. https://doi.org/10.1016/j.bmcl.2013.10.068
   PubMed Web of Science ®Google Scholar
• López-López, E., Naveja, J. J., & Medina-Franco, J. L. (2019). DataWarrior: An evaluation of the open-source drug discovery tool. Expert Opinion on Drug Discovery, 14(4), 335–341. https://doi.org/10.1080/17460441.2019.1581170
   PubMed Web of Science ®Google Scholar
• McGeary, R. P., Tan, D. T., & Schenk, G. (2017). Progress toward inhibitors of metallo-β-lactamases. Future Medicinal Chemistry, 9(7), 673–691. https://doi.org/10.4155/fmc-2017-0007
   PubMed Web of Science ®Google Scholar
• Murray, C. J. L., Ikuta, K. S., Sharara, F., Swetschinski, L., Robles Aguilar, G., Gray, A., Han, C., Bisignano, C., Rao, P., Wool, E., Johnson, S. C., Browne, A. J., Chipeta, M. G., Fell, F., Hackett, S., Haines-Woodhouse, G., Kashef Hamadani, B. H., Kumaran, E. A. P., McManigal, B., … Naghavi, M. (2022). Global burden of bacterial antimicrobial resistance in 2019: A systematic analysis. The Lancet, 399(10325), 629–655. https://doi.org/10.1016/S0140-6736(21)02724-0
   PubMed Web of Science ®Google Scholar
• Nagar, P. R., Gajjar, N. D., & Dhameliya, T. M. (2021). In search of SARS CoV-2 replication inhibitors: Virtual screening, molecular dynamics simulations and ADMET analysis. Journal of Molecular Structure, 1246, 131190. https://doi.org/10.1016/j.molstruc.2021.131190
   PubMed Web of Science ®Google Scholar
• O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. https://doi.org/10.1186/1758-2946-3-33
   PubMed Web of Science ®Google Scholar
• Palacios, A. R., Rossi, M. A., Mahler, G. S., & Vila, A. J. (2020). Metallo-β-lactamase inhibitors inspired on snapshots from the catalytic mechanism. Biomolecules, 10(6), 854. https://doi.org/10.3390/biom10060854
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Robert, X., & Gouet, P. (2014). Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research, 42(Web Server issue), W320–W324. https://doi.org/10.1093/nar/gku316
   PubMed Web of Science ®Google Scholar
• Schüttelkopf, A. W., & Van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Shaaban, M. M., Ragab, H. M., Akaji, K., McGeary, R. P., Bekhit, A.-E A., Hussein, W. M., Kurz, J. L., Elwakil, B. H., Bekhit, S. A., Ibrahim, T. M., Mahran, M. A., & Bekhit, A. A. (2020). Design, synthesis, biological evaluation and in silico studies of certain aryl sulfonyl hydrazones conjugated with 1,3-diaryl pyrazoles as potent metallo-β-lactamase inhibitors. Bioorganic Chemistry, 105, 104386. https://doi.org/10.1016/j.bioorg.2020.104386
   PubMed Web of Science ®Google Scholar
• Shi, C., Chen, J., Kang, X., Shen, X., Lao, X., & Zheng, H. (2019). Approaches for the discovery of metallo‐β‐lactamase inhibitors: A review. Chemical Biology & Drug Design, 94(2), 1427–1440. https://doi.org/10.1111/cbdd.13526
   PubMed Web of Science ®Google Scholar
• Somboro, A. M., Osei Sekyere, J., Amoako, D. G., Essack, S. Y., & Bester, L. A. (2018). Diversity and proliferation of metallo-β-lactamases: A clarion call for clinically effective metallo-β-lactamase inhibitors. Applied and Environmental Microbiology, 84(18), e00698-18. https://doi.org/10.1128/AEM.00698-18
   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
• Sunseri, J., & Koes, D. R. (2016). Pharmit: Interactive exploration of chemical space. Nucleic Acids Research, 44(W1), W442–W448. https://doi.org/10.1093/nar/gkw287
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Trotter, A. J., Aydin, A., Strinden, M. J., & O'Grady, J. (2019). Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance. Current Opinion in Microbiology, 51, 39–45. https://doi.org/10.1016/j.mib.2019.03.001
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, 8(2), 127–134. https://doi.org/10.1093/protein/8.2.127
   PubMedGoogle Scholar
• Yan, Y. H., Li, G., & Li, G. B. (2020). Principles and current strategies targeting metallo‐β‐lactamase mediated antibacterial resistance. Medicinal Research Reviews, 40(5), 1558–1592. https://doi.org/10.1002/med.21665
   PubMed Web of Science ®Google Scholar