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Research Articles

Structure-based virtual screening, molecular docking, and molecular dynamics simulation approaches for identification of new potential inhibitors of class a β-lactamase enzymes

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Pages 5631-5641 | Received 09 Apr 2023, Accepted 14 Jun 2023, Published online: 26 Jun 2023

References

  • Ambler, R. P. (1980). The structure of beta-lactamases. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 289(1036), 321–331. https://doi.org/10.1098/rstb.1980.0049
  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
  • Blush, K., & A., Brandford, P. (2016). Beta-lactam and beta-lactamase inhibitors: An overview. Cold Spring Harbor Perspectives in Medicine, 22, 1–3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968164/pdf/cshperspectmed-ANR-a025247.pdf
  • Bush, K. (2010). Bench-to-bedside review: The role of β-lactamases in antibiotic-resistant Gram-negative infections. Critical Care, 14(3), 224. https://doi.org/10.1186/cc8892
  • Bush, K., & Jacoby, G. A. (2010). Updated functional classification of β MINIREVIEW updated functional classification of ɴʟ -lactamases. Antimicrobial Agents and Chemotherapy, 54(3), 969–976. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2825993&tool=pmcentrez&rendertype=abstract https://doi.org/10.1128/AAC.01009-09
  • Chen, J. (2018). Functional roles of magnesium binding to extracellular signal-regulated kinase 2 explored by molecular dynamics simulations and principal component analysis. Journal of Biomolecular Structure & Dynamics, 36(2), 351–361. https://doi.org/10.1080/07391102.2016.1277783
  • Chen, J., Zeng, Q., Wang, W., Sun, H., & Hu, G. (2022). Decoding the identification mechanism of an SAM-III riboswitch on ligands through multiple independent gaussian-accelerated molecular dynamics simulations. Journal of Chemical Information and Modeling, 62(23), 6118–6132. https://doi.org/10.1021/acs.jcim.2c00961
  • 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, 42717. https://doi.org/10.1038/srep42717
  • Danishuddin, M., & Khan, A. U. (2012). Molecular modeling and docking analysis of Beta-lactamases with inhibitors: A comparative study. In Silico Biology, 11(5), 273–280. https://doi.org/10.3233/ISB-2012-0443
  • 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
  • Drawz, S. M., & Bonomo, R. A. (2010). Three decades of β-lactamase inhibitors. Clinical Microbiology Reviews, 23(1), 160–201. https://doi.org/10.1128/CMR.00037-09
  • Drawz, S. M., Papp-Wallace, K. M., & Bonomo, R. A. (2014). New β-lactamase inhibitors: A therapeutic renaissance in an MDR world. Antimicrobial Agents and Chemotherapy, 58(4), 1835–1846. https://doi.org/10.1128/AAC.00826-13
  • Eberhardt, J., Santos-Martins, D., Tillack, A. F., & Forli, S. (2021). AutoDock Vina 1.2.0: New docking methods, expanded force field, and python bindings. Journal of Chemical Information and Modeling, 61(8), 3891–3898. https://doi.org/10.1021/acs.jcim.1c00203
  • Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
  • Evans, D. J., & Holian, B. L. (1985). The Nose-Hoover thermostat. The Journal of Chemical Physics, 83(8), 4069–4074. https://doi.org/10.1063/1.449071
  • Ghafourian, S., Sadeghifard, N., Soheili, S., & Sekawi, Z. (2015). Extended spectrum beta-lactamases: Definition, classification and epidemiology. Current Issues in Molecular Biology, 17(1), 11–21. https://doi.org/10.21775/cimb.017.011
  • Gulshan, K., Singh, A. K., & Deepak, A. (2023). Structural and functional characterization of RNA dependent RNA polymerase of Macrobrachium rosenbergii nodavirus (MnRdRp). Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2023.2175384
  • 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. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
  • Holten, K. B., & Onusko, E. M. (2000). Appropriate prescribing of oral beta-lactam antibiotics. American Family Physician.
  • Meza, J. C. (2010). Steepest descent. WIREs Computational Statistics, 2(6), 719–722. https://doi.org/10.1002/wics.117
  • Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639–1662. https://doi.org/10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
  • 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
  • Prestinaci, F., Pezzotti, P., & Pantosti, A. (2015). Antimicrobial resistance: A global multifaceted phenomenon. Pathogens and Global Health, 109(7), 309–318. https://doi.org/10.1179/2047773215Y.0000000030
  • Reynolds, C. H., Tounge, B. A., & Bembenek, S. D. (2008). Ligand binding efficiency: Trends, physical basis, and implications. Journal of Medicinal Chemistry, 51(8), 2432–2438. CCC https://doi.org/10.1021/jm701255b
  • Shapiro, A. B., & Gao, N. (2021). Interactions of the diazabicyclooctane serine β-lactamase inhibitor ETX1317 with target enzymes. ACS Infectious Diseases, 7(1), 114–122. https://doi.org/10.1021/acsinfecdis.0c00656
  • Sousa Da Silva, A. W., & Vranken, W. F. (2012). ACPYPE-Antechamber python parser interface. BMC Research Notes, 5, 1–8. https://doi.org/10.1186/1756-0500-5-367
  • 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
  • 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
  • Tooke, C. L., Hinchliffe, P., Lang, P. A., Mulholland, A. J., Brem, J., Schofield, C. J., & Spencer, J. (2019). Molecular basis of class A β-lactamase inhibition by relebactam. Antimicrobial Agents and Chemotherapy, 63(10) https://doi.org/10.1128/AAC.00564-19
  • Toussaint, K. A., & Gallagher, J. C. (2015). β-lactam/β-lactamase inhibitor combinations: From then to now. Annals of Pharmacotherapy, 49(1), 86–98. https://doi.org/10.1177/1060028014556652
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
  • Vázquez-Ucha, J. C., Arca-Suárez, J., Bou, G., & Beceiro, A. (2020). New carbapenemase inhibitors: Clearing the way for the β-lactams. International Journal of Molecular Sciences, 21(23), 9308. https://doi.org/10.3390/ijms21239308
  • Williams, J. D. (1999). β-Lactamases and β-lactamase inhibitors. International Journal of Antimicrobial Agents, 12(SUPPL. 1), S3–S7. https://doi.org/10.1016/S0924-8579(99)00085-0
  • Wong, D., & van Duin, D. (2017). Novel beta-lactamase inhibitors: Unlocking their potential in therapy. Drugs, 77(6), 615–628. https://doi.org/10.1007/s40265-017-0725-1
  • Zhao, T.-T., Lu, X., Yang, X.-H., Wang, L.-M., Li, X., Wang, Z.-C., Gong, H.-B., & Zhu, H.-L. (2012). Synthesis, biological evaluation, and molecular docking studies of 2,6-dinitro-4-(trifluoromethyl)phenoxysalicylaldoxime derivatives as novel antitubulin agents. Bioorganic & Medicinal Chemistry, 20(10), 3233–3241. https://doi.org/10.1016/j.bmc.2012.03.057

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