Computational modelling of potential Zn-sensitive non-β-lactam inhibitors of imipenemase-1 (IMP-1)

References

• Aarts, H., & Margolles, A. (2014). Antibiotic resistance genes in food and gut (non pathogenic) bacteria. Bad genes in good bugs. Frontiers in Microbiology, 5, 754–2015. https://doi.org/10.3389/fmicb.2014.00754
   PubMed Web of Science ®Google Scholar
• Arjomandi, K. 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
• Ayipo, Y. O., Ahmad, I., Najib, Y. S., Sheu, S. K., Patel, H., & Mordi, M. N. (2022). Molecular modelling and structure-activity relationship of a natural derivative of o-hydroxybenzoate as a potent inhibitor of dual NSP3 and NSP12 of SARS-CoV-2: in silico study. Journal of Biomolecular Structure and Dynamics, 1–19. https://doi.org/10.1080/07391102.2022.2026818
   PubMed Web of Science ®Google Scholar
• Ayipo, Y. O., Osunniran, W. A., Babamale, H. F., Ayinde, M. O., & Mordi, M. N. (2022). Metalloenzyme mimicry and modulation strategies to conquer antimicrobial resistance: Metal-ligand coordination perspectives. Coordination Chemistry Reviews, 453, 214317. https://doi.org/10.1016/j.ccr.2021.214317
   Web of Science ®Google Scholar
• Ayipo, Y. O., Osunniran, W. A., Badeggi, U. M., Saheed, I. O., Jimoh, A. A., Babamale, H. F., & Olaide, E. O. (2021). Synthesis, characterization and antibacterial study of co(Ii) and cu(ii) complexes of mixed ligands of piperaquine and diclofenac. Journal of the Turkish Chemical Society, Section A: Chemistry, 8(2), 633–650. https://doi.org/10.18596/jotcsa.898523
   Google Scholar
• Ayipo, Y. O., Yahaya, S. N., Babamale, H. F., Ahmad, I., Patel, H., & Mordi, M. N. (2021). β- Carboline alkaloids induce structural plasticity and inhibition of SARS-CoV-2 nsp3 macrodomain more potently than remdesivir metabolite GS-441524: Computational approach. Turkish Journal of Biology, 45(Special Issue 1), 503–517. https://doi.org/10.3906/biy-2106-64
   Google Scholar
• Bahr, G., González, L. J., & Vila, A. J. (2022). Metallo-β-lactamases and a tug-of-war for the available zinc at the host–pathogen interface. Current Opinion in Chemical Biology, 66, 102103. https://doi.org/10.1016/j.cbpa.2021.102103
   PubMed Web of Science ®Google Scholar
• Benet, L. Z., Hosey, C. M., Ursu, O., & Oprea, T. I. (2016). BDDCS, the Rule of 5 and drugability. Advanced Drug Delivery Reviews, 101(6), 89–98. https://doi.org/10.1016/j.addr.2016.05.007
   PubMedGoogle Scholar
• Boyd, S. E., Livermore, D. M., Hooper, D. C., & Hope, W. W. (2020). Metallo-β-lactamases: Structure, function, epidemiology, treatment options, and the development pipeline. Antimicrobial Agents and Chemotherapy, 64(10), 1–20. https://doi.org/10.1128/AAC.00397-20
   Web of Science ®Google Scholar
• Bush, K. (2018). Past and present perspectives on β-lactamases. Antimicrobial Agents and Chemotherapy, 62(10), 1–20. https://doi.org/10.1128/AAC.01076-18
   Web of Science ®Google Scholar
• Cain, R., Brem, J., Zollman, D., McDonough, M. A., Johnson, R. M., Spencer, J., Makena, A., Abboud, M. I., Cahill, S., Lee, S. Y., McHugh, P. J., Schofield, C. J., & Fishwick, C. W. G. (2018). In silico fragment-based design identifies subfamily B1 metallo-β-lactamase inhibitors. Journal of Medicinal Chemistry, 61(3), 1255–1260. https://doi.org/10.1021/acs.jmedchem.7b01728
   PubMed Web of Science ®Google Scholar
• Castro-Alvarez, A., Costa, A. M., & Vilarrasa, J. (2017). The performance of several docking programs at reproducing protein-macrolide-like crystal structures. Molecules, 22(1), 136. https://doi.org/10.3390/molecules22010136
   PubMed Web of Science ®Google Scholar
• CDC. (2019). Antibiotic resistance threats in the United States, 2019. U.S. Department of Health and Human Services, CDC. https://www.cdc.gov/drugresistance/pdf/threats-report/2019-ar-threats-report-508.pdf
   Google Scholar
• Chen, A. Y. (2020). Conversion of metal chelators to selective and potent inhibitors of New Delhi metallo-beta-lactamase [doctoral dissertation]. UC San Diego. https://escholarship.org/uc/item/8xk949p6
   Google Scholar
• Chen, J., Wang, J., & Zhu, W. (2017). Zinc ion-induced conformational changes in new Delphi metallo-β-lactamase 1 probed by molecular dynamics simulations and umbrella sampling. Physical Chemistry Chemical Physics: PCCP, 19(4), 3067–3075. https://doi.org/10.1039/c6cp08105c
   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, 42713–42717. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Diene, S. M., Pinault, L., Keshri, V., Armstrong, N., Khelaifia, S., Chabrière, E., Caetano-Anolles, G., Colson, P., La Scola, B., Rolain, J. M., Pontarotti, P., & Raoult, D. (2019). Human metallo-β-lactamase enzymes degrade penicillin. Scientific Reports, 9(1), 1–7. https://doi.org/10.1038/s41598-019-48723-y
   PubMedGoogle Scholar
• Elekofehinti, O. O., Iwaloye, O., Molehin, O. R., & Famusiwa, C. D. (2021). Identification of lead compounds from large natural product library targeting 3C-like protease of SARS-CoV-2 using E-pharmacophore modelling, QSAR and molecular dynamics simulation. In Silico Pharmacology, 9(1), 1–19. https://doi.org/10.1007/s40203-021-00109-7
   PubMedGoogle Scholar
• Feng, H., Liu, X., Wang, S., Fleming, J., Wang, D. C., & Liu, W. (2017). The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis. Nature Communications, 8(1), 2242. https://doi.org/10.1038/s41467-017-02339-w
   PubMedGoogle Scholar
• González-Bello, C., Rodríguez, D., Pernas, M., Rodríguez, Á., & Colchón, E. (2020). β-lactamase inhibitors to restore the efficacy of antibiotics against superbugs. Journal of Medicinal Chemistry, 63(5), 1859–1881. https://doi.org/10.1021/acs.jmedchem.9b01279
   PubMed Web of Science ®Google Scholar
• Harder, E., Damm, W., Maple, J., Wu, C., Reboul, M., Xiang, J. Y., Wang, L., Lupyan, D., Dahlgren, M. K., Knight, J. L., Kaus, J. W., Cerutti, D. S., Krilov, G., Jorgensen, W. L., Abel, R., & Friesner, R. A. (2016). OPLS3: A force field providing broad coverage of drug-like small molecules and proteins. Journal of Chemical Theory and Computation, 12(1), 281–296. https://doi.org/10.1021/acs.jctc.5b00864
   PubMed Web of Science ®Google Scholar
• Hinchliffe, P., González, M. M., Mojica, M. F., González, J. M., Castillo, V., Saiz, C., Kosmopoulou, M., Tooke, C. L., Llarrull, L. I., Mahler, G., Bonomo, R. A., Vila, A. J., & Spencer, J. (2016). Cross-class metallo-β-lactamase inhibition by bisthiazolidines reveals multiple binding modes. Proceedings of the National Academy of Sciences of the United States of America, 113(26), E3745–E3754. https://doi.org/10.1073/pnas.1601368113
   PubMed Web of Science ®Google Scholar
• Ishii, R., Minagawa, A., Takaku, H., Takagi, M., Nashimoto, M., & Yokoyama, S. (2005). Crystal structure of the tRNA 3′ processing endoribonuclease tRNase Z from Thermotoga maritima. The Journal of Biological Chemistry, 280(14), 14138–14144. https://doi.org/10.1074/jbc.M500355200
   PubMed Web of Science ®Google Scholar
• Iyer, R. N. (2022). β-lactam antibiotics. In Reference module in biomedical sciences. Elsevier Inc. https://doi.org/10.1016/B978-0-12-820472-6.00212-7
   Google Scholar
• Jahan, I., & Nayeem, S. M. (2020). Conformational dynamics of superoxide dismutase (SOD1) in osmolytes: A molecular dynamics simulation study. RSC Advances, 10(46), 27598–27614. https://doi.org/10.1039/D0RA02151B
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118(45), 11225–11236. https://doi.org/10.1021/ja9621760
   Web of Science ®Google Scholar
• Kalibaeva, G., Ferrario, M., & Ciccotti, G. (2003). Constant pressure-constant temperature molecular dynamics: A correct constrained NPT ensemble using the molecular virial. Molecular Physics, 101(6), 765–778. https://doi.org/10.1080/0026897021000044025
   Web of Science ®Google Scholar
• Kang, J. S., Zhang, A. L., Faheem, M., Zhang, C. J., Ai, N., Buynak, J. D., Welsh, W. J., & Oelschlaeger, P. (2018). Virtual screening and experimental testing of B1 metallo-β-lactamase inhibitors. Journal of Chemical Information and Modeling, 58(9), 1902–1914. https://doi.org/10.1021/acs.jcim.8b00133
   PubMed Web of Science ®Google Scholar
• Kar, B., Kundu, C. N., Pati, S., & Bhattacharya, D. (2021). Discovery of phyto-compounds as novel inhibitors against NDM-1 and VIM-1 protein through virtual screening and molecular modelling. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/10.1080/07391102.2021.2019125
   Google Scholar
• Kufareva, I., & Abagyan, R. (2012). Methods of protein structure comparison. Methods in Molecular Biology (Clifton, NJ), 857, 231–257. https://doi.org/10.1007/978-1-61779-588-6_10
   PubMedGoogle Scholar
• Larsson, D. G. J., & Flach, C. F. (2022). Antibiotic resistance in the environment. Nature Reviews. Microbiology, 20(5), 257–269. https://doi.org/10.1038/s41579-021-00649-x
   PubMed Web of Science ®Google Scholar
• Li, S. C. (2013). The difficulty of protein structure alignment under the RMSD. Algorithms for Molecular Biology: AMB, 8(1), 1–9. https://doi.org/10.1186/1748-7188-8-1
   PubMedGoogle Scholar
• Lima, L. M., Silva, B. N. M. d., Barbosa, G., & Barreiro, E. J. (2020). β-lactam antibiotics: An overview from a medicinal chemistry perspective. European Journal of Medicinal Chemistry, 208, 112829. https://doi.org/10.1016/j.ejmech.2020.112829
   PubMed Web of Science ®Google Scholar
• Lisa, M., Palacios, A. R., Aitha, M., González, M. M., Moreno, D. M., Crowder, M. W., Bonomo, R. A., Spencer, J., Tierney, D. L., Llarrull, L. I., & Vila, A. J. (2017). A general reaction mechanism for carbapenem hydrolysis by mononuclear and binuclear metallo-β-lactamases. Nature Communications, 8(1), 1–11. https://doi.org/10.1038/s41467-017-00601-9
   PubMedGoogle Scholar
• Madhavi Sastry, G., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. https://doi.org/10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Martyna, G. J. (1994). Remarks on “Constant-temperature molecular dynamics with momentum conservation”. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 50(4), 3234–3236. https://doi.org/10.1103/physreve.50.3234
   PubMed Web of Science ®Google Scholar
• Mojica, M. F., Rossi, M. A., Vila, A. J., & Bonomo, R. A. (2022). The urgent need for metallo-β-lactamase inhibitors: An unattended global threat. The Lancet. Infectious Diseases, 22(1), e28–e34. https://doi.org/10.1016/S1473-3099(20)30868-9
   PubMed Web of Science ®Google Scholar
• Moreira, J. S., Galvão, D. S., Xavier, C. F. C., Cunha, S., Pita, S. S. R., Reis, J. N., & Freitas, H. F. (2021). Phenotypic and in silico studies for a series of synthetic thiosemicarbazones as New Delhi metallo-beta-lactamase carbapenemase inhibitors. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2021.2001379
   Web of Science ®Google Scholar
• Murray, C. J., 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
• Naderi, M., Lemoine, J. M., Govindaraj, R. G., Kana, O. Z., Feinstein, W. P., & Brylinski, M. (2019). Binding site matching in rational drug design: Algorithms and applications. Briefings in Bioinformatics, 20(6), 2167–2184. https://doi.org/10.1093/bib/bby078
   PubMed Web of Science ®Google Scholar
• Parmar, P., Rao, P., Sharma, A., Shukla, A., & Rawal, R. M. (2021). Meticulous assessment of natural compounds from NPASS database for identifying analogue of GRL0617, the only known inhibitor for SARS ‑ CoV2 papain ‑ like protease (PLpro) using rigorous computational workflow. Molecular Diversity, 26(1), 389–407. https://doi.org/10.1007/s11030-021-10233-3
   PubMed Web of Science ®Google Scholar
• Pawara, R., Ahmad, I., Nayak, D., Wagh, S., Wadkar, A., Ansari, A., Belamkar, S., Surana, S., Nath Kundu, C., Patil, C., & Patel, H. (2021). Novel, selective acrylamide linked quinazolines for the treatment of double mutant EGFR-L858R/T790M Non-Small-Cell lung cancer (NSCLC). Bioorganic Chemistry, 115, 105234. https://doi.org/10.1016/j.bioorg.2021.105234
   PubMed Web of Science ®Google Scholar
• Pettinati, I., Brem, J., Lee, S. Y., McHugh, P. J., & Schofield, C. J. (2016). The chemical biology of human metallo-β-lactamase fold proteins. Trends in Biochemical Sciences, 41(4), 338–355. https://doi.org/10.1016/j.tibs.2015.12.007
   PubMed Web of Science ®Google Scholar
• Pettinati, I., Grzechnik, P., de Almeida, C. R., Brem, J., McDonough, M. A., Dhir, S., Proudfoot, N. J., & Schofield, C. J. (2018). Biosynthesis of histone messenger RNA employs a specific 3’ end endonuclease. eLife, 7, 1–26. https://doi.org/10.7554/eLife.39865
   Web of Science ®Google Scholar
• Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
   PubMed Web of Science ®Google Scholar
• Prieto-Martínez, F. D., López-López, E., Eurídice Juárez-Mercado, K., & Medina-Franco, J. L. (2019). Computational drug design methods—Current and future perspectives. In Silico Drug Design, 3, 19–44. https://doi.org/10.1016/b978-0-12-816125-8.00002-x
   Google Scholar
• Ramírez, D., & Caballero, J. (2018). Is it reliable to take the molecular docking top scoring position as the best solution without considering available structural data? Molecules, 23(5), 1017–1038. https://doi.org/10.3390/molecules23051038
   PubMed Web of Science ®Google Scholar
• Salari-Jazi, A., Mahnam, K., Sadeghi, P., Damavandi, M. S., & Faghri, J. (2021). Discovery of potential inhibitors against New Delhi from natural compounds: In silico‑based methods. Scientific Reports, 11(1), 1–20. https://doi.org/10.1038/s41598-021-82009-6
   PubMed Web of Science ®Google Scholar
• Salimraj, R., Hinchliffe, P., Kosmopoulou, M., Tyrrell, J. M., Brem, J., van Berkel, S. S., Verma, A., Owens, R. J., McDonough, M. A., Walsh, T. R., Schofield, C. J., & Spencer, J. (2019). Crystal structures of VIM-1 complexes explain active site heterogeneity in VIM-class metallo-β-lactamases. The FEBS Journal, 286(1), 169–183. https://doi.org/10.1111/febs.14695
   PubMed Web of Science ®Google Scholar
• Schaenzer, A. J., & Wright, G. D. (2020). Antibiotic resistance by enzymatic modification of antibiotic targets. Trends in Molecular Medicine, 26(8), 768–782. https://doi.org/10.1016/j.molmed.2020.05.001
   PubMed Web of Science ®Google Scholar
• Schrodinger Release 2020-3. (2021). Maestro-Desmond interoperability tools, Schrödinger release 2020-3. D. E. Shaw Research.
   Google Scholar
• Siemann, S., Evanoff, D. P., Marrone, L., Clarke, A. J., Viswanatha, T., & Dmitrienko, G. I. (2002). N-arylsulfonyl hydrazones as inhibitors of IMP-1 metallo-β-lactamase. Antimicrobial Agents and Chemotherapy, 46(8), 2450–2457. https://doi.org/10.1128/AAC.46.8.2450-2457.2002
   PubMed Web of Science ®Google Scholar
• Sliwoski, G., Kothiwale, S., Meiler, J., & Lowe, E. W. (2014). Computational methods in drug discovery. Pharmacological Reviews, 66(1), 334–395. https://doi.org/10.1124/pr.112.007336
   PubMed Web of Science ®Google Scholar
• Softley, C. A., Zak, K. M., Bostock, M. J., Fino, R., Zhou, R. X., Kolonko, M., Mejdi-Nitiu, R., Meyer, H., Sattler, M., & Popowicz, G. M. (2020). Structure and molecular recognition mechanism of IMP-13 metallo-β-lactamase. Antimicrobial Agents and Chemotherapy, 64(6), 0123–20. 10.1128/AAC.00123-20
   PubMed Web of Science ®Google Scholar
• Tan, X., Kim, H. S., Baugh, K., Huang, Y., Kadiyala, N., Wences, M., Singh, N., Wenzler, E., & Bulman, Z. P. (2021). Therapeutic options for metallo-β-lactamaseproducing enterobacterales. Infection and Drug Resistance, 14, 125–142. https://doi.org/10.2147/IDR.S246174
   PubMed Web of Science ®Google Scholar
• Tomar, V., Mazumder, M., Chandra, R., Yang, J., & Sakharkar, M. K. (2018). Small molecule drug design. In Encyclopedia of bioinformatics and computational biology: ABC of bioinformatics (Vol. 1, pp. 741–760). Elsevier. https://doi.org/10.1016/B978-0-12-809633-8.20157-X
   Google Scholar
• Toney, J. H., Hammond, G. G., Fitzgerald, P. M. D., Sharma, N., Balkovec, J. M., Rouen, G. P., Olson, S. H., Hammond, M. L., Greenlee, M. L., & Gao, Y. D. (2001). Succinic acids as potent inhibitors of plasmid-borne IMP-1 metallo-β-lactamase. The Journal of Biological Chemistry, 276(34), 31913–31918. https://doi.org/10.1074/jbc.M104742200
   PubMed Web of Science ®Google Scholar
• Tooke, C. L., Hinchliffe, P., Bragginton, E. C., Colenso, C. K., Hirvonen, V. H. A., Takebayashi, Y., & Spencer, J. (2019). β-lactamases and β-lactamase inhibitors in the 21st century. Journal of Molecular Biology, 431(18), 3472–3500. https://doi.org/10.1016/j.jmb.2019.04.002
   PubMed Web of Science ®Google Scholar
• van Bambeke, F., Mingeot-Leclercq, M.-P., Glupczynski, Y., & Tulkens, P. M. (2017). Mechanisms of action. Infectious Diseases, 2, 1162–1180.e1. https://doi.org/10.1016/b978-0-7020-6285-8.00137-4
   Google Scholar
• van den Akker, F., & Bonomo, R. A. (2018). Exploring additional dimensions of complexity in inhibitor design for serine β-lactamases: Mechanistic and intra- and inter-molecular chemistry approaches. Frontiers in Microbiology, 9, 610–622. https://doi.org/10.3389/fmicb.2018.00622
   PubMed Web of Science ®Google Scholar
• Veber, D. F., Johnson, S. R., Cheng, H., Smith, B. R., Ward, K. W., & Kopple, K. D. (2002). Molecular properties that influence the oral bioavailability of drug candidates. Journal of Medicinal Chemistry, 45(12), 2615–2623. https://doi.org/10.1021/jm020017n
   PubMed Web of Science ®Google Scholar
• Wang, X., Yang, Y., Gao, Y., & Niu, X. (2020). Discovery of the novel inhibitor against New Delhi metallo-β-lactamase based on virtual screening and molecular modelling. International Journal of Molecular Sciences, 21(10), 3567. https://doi.org/10.3390/ijms21103567
   PubMed Web of Science ®Google Scholar
• Yamaguchi, Y., Kato, K., Ichimaru, Y., Jin, W., Sakai, M., Abe, M., Wachino, J. I., Arakawa, Y., Miyagi, Y., Imai, M., Fukuishi, N., Yamagata, Y., Otsuka, M., Fujita, M., & Kurosaki, H. (2021). Crystal structures of metallo-β-lactamase (IMP-1) and Its D120E mutant in complexes with citrate and the inhibitory effect of the benzyl group in citrate monobenzyl ester. Journal of Medicinal Chemistry, 64(14), 10019–10026. https://doi.org/10.1021/acs.jmedchem.1c00308
   PubMed Web of Science ®Google 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
• Yusof, Y. (2015). Design, synthesis and testing of neovel classes of inhibitors against metallo-b-lactamases towards drug leads to combat antibiotic resistance [doctoral thesis]. The University of Queensland. https://espace.library.uq.edu.au/data/UQ_394200/s4276299_final_thesis.pdf?Expires=1490156556&Signature=SLBQCBM-JiIZXqkz1Tpn9kuF3T3KJwtq2tm9WfIxXhy0QFa∼59iw1∼29pxmFto6VqybzpR98u4vpl32Ruvp4SkqE0ZwyS82-wdRH6ScvFs52HxNivgbrBRoPj70y9MqHTIaJZaS6q4ee7sbLvs5uIV0D
   Google Scholar
• Zhang, Y., & Skolnick, J. (2005). TM-align: A protein structure alignment algorithm based on the TM-score. Nucleic Acids Research, 33(7), 2302–2309. https://doi.org/10.1093/nar/gki524
   PubMed Web of Science ®Google Scholar