In silico based unraveling of New Delhi metallo-β-lactamase (NDM-1) inhibitors from natural compounds: a molecular docking and molecular dynamics simulation study

References

• Appadurai, R., & Senapati, S. (2017). How mutations can resist drug binding yet keep HIV-1 protease functional. Biochemistry, 56(23), 2907–2920. doi:10.1021/acs.biochem.7b00139
   PubMed Web of Science ®Google Scholar
• Bebrone, C. (2007). Metallo-beta-lactamases (classification, activity, genetic organization, structure, zinc coordination) and their superfamily. Biochemical Pharmacology, 74(12), 1686–1701. doi:10.1016/j.bcp.2007.05.021
   PubMed Web of Science ®Google Scholar
• Bin Sayeed, M. S., & Ameen, S. S. (2015). Beta-sitosterol: A promising but orphan nutraceutical to fight against cancer. Nutrition and Cancer, 67(8), 1214–1220. doi:10.1080/01635581.2015.1087042
   PubMed Web of Science ®Google Scholar
• Bush, K., & Jacoby, G. A. (2010). Updated functional classification of beta-lactamases. Antimicrobial Agents and Chemotherapy, 54(3), 969–976. doi:10.1128/AAC.01009-09
   PubMed Web of Science ®Google Scholar
• Case, D. A., Darden, T. A., Cheatham, T. E., III, Simmerling, C. L., Wang, J., Duke, R. E., … Kollman, P. A. (2012). Amber 12, University of California, San Francisco
   Google Scholar
• Deng, R. (2007). Therapeutic effects of guggul and its constituent guggulsterone: Cardiovascular benefits. Cardiovascular Drug Reviews, 25(4), 375–390. doi:10.1111/j.1527-3466.2007.00023.x
   PubMed Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics., 103(19), 8577–8593. doi:10.1063/1.470117
   Web of Science ®Google Scholar
• Faheem, M., Rehman, M. T., Danishuddin, M., & Khan, A. U. (2013). Biochemical characterization of CTX-M-15 from Enterobacter cloacae and designing a novel non-beta-lactam-beta-lactamase inhibitor. PLoS One, 8(2), e56926. doi:10.1371/journal.pone.0056926
   PubMed Web of Science ®Google Scholar
• Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D. S., & Olson, A. J. (2016). Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nature Protocols, 11(5), 905–919. doi:10.1038/nprot.2016.051
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2010). How to obtain statistically converged MM/GBSA results. Journal of Computational Chemistry, 31(4), 837–846. doi:10.1002/jcc.21366
   PubMed Web of Science ®Google Scholar
• Groundwater, P. W., Xu, S., Lai, F., Varadi, L., Tan, J., Perry, J. D., & Hibbs, D. E. (2016). New Delhi metallo-beta-lactamase-1: Structure, inhibitors and detection of producers. Future Medicinal Chemistry, 8(9), 993–1012. doi:10.4155/fmc-2016-0015
   PubMed Web of Science ®Google Scholar
• Guo, Y., Wang, J., Niu, G., Shui, W., Sun, Y., Zhou, H., … Rao, Z. (2011). A structural view of the antibiotic degradation enzyme NDM-1 from a superbug. Protein & Cell, 2(5), 384–394. doi:10.1007/s13238-011-1055-9
   PubMed Web of Science ®Google Scholar
• Hall, B. G., & Barlow, M. (2005). Revised Ambler classification of {beta}-lactamases. Journal of Antimicrobial Chemotherapy, 55(6), 1050–1051. doi:10.1093/jac/dki130
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79(2), 926–935. doi:10.1063/1.445869
   Web of Science ®Google Scholar
• Khan, A. U., Maryam, L., & Zarrilli, R. (2017). Structure, Genetics and Worldwide Spread of New Delhi Metallo-β-lactamase (NDM): A threat to public health. BMC Microbiology, 17(1), 101.doi:10.1186/s12866-017-1012-8
   PubMedGoogle Scholar
• Kim, Y., Tesar, C., Mire, J., Jedrzejczak, R., Binkowski, A., Babnigg, G., … Joachimiak, A. (2011). Structure of apo- and monometalated forms of NDM-1–a highly potent carbapenem-hydrolyzing metallo-beta-lactamase. PLoS One, 6(9), e24621. doi:10.1371/journal.pone.0024621
   PubMed Web of Science ®Google Scholar
• King, D., & Strynadka, N. (2011). Crystal structure of New Delhi metallo-beta-lactamase reveals molecular basis for antibiotic resistance. Protein Science, 20(9), 1484–1491. doi:10.1002/pro.697
   PubMed Web of Science ®Google Scholar
• Kupchan, S. M., & Doskotch, R. W. (1962). Tumor Inhibitors. I. Aristolochic Acid, the Active Principle of Aristolochia INDICA. Journal of Medicinal and Pharmaceutical Chemistry, 91, 657–659.
   PubMedGoogle Scholar
• Levy, S. B., & Marshall, B. (2004). Antibacterial resistance worldwide: causes, challenges and responses. Nature Medicine, 10(S12), S122–S129. doi:10.1038/nm1145
   PubMedGoogle Scholar
• Linciano, P., Cendron, L., Gianquinto, E., Spyrakis, F., & Tondi, D. (2018). Ten years with New Delhi Metallo-beta-lactamase-1 (NDM-1): From structural insights to inhibitor design. ACS Infectious Diseases, 5(1), 9–34. doi:10.1021/acsinfecdis.8b00247
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A. (2000). Drug-like properties and the causes of poor solubility and poor permeability. Journal of Pharmacological and Toxicological Methods, 44(1), 235–249.
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A. (2004). Lead- and drug-like compounds: The rule-of-five revolution. Drug Discovery Today: Technologies, 1(4), 337–341. doi:10.1016/j.ddtec.2004.11.007
   PubMedGoogle Scholar
• Michl, J., Ingrouille, M. J., Simmonds, M. S., & Heinrich, M. (2014). Naturally occurring aristolochic acid analogues and their toxicities. Natural Product Reports, 31(5), 676–693. doi:10.1039/c3np70114j
   PubMed Web of Science ®Google Scholar
• Mohan, R., Hammers, H., Bargagna-Mohan, P., Zhan, X., Herbstritt, C., Ruiz, A., … Pribluda, V. (2004). Withaferin A is a potent inhibitor of angiogenesis. Angiogenesis, 7(2), 115–122. doi:10.1007/s10456-004-1026-3
   PubMedGoogle Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. doi:10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Nordmann, P., Boulanger, A. E., & Poirel, L. (2012). NDM-4 metallo-beta-lactamase with increased carbapenemase activity from Escherichia coli. Antimicrobial Agents and Chemotherapy, 56(4), 2184–2186. doi:10.1128/AAC.05961-11
   PubMed Web of Science ®Google Scholar
• Raju, J., & Mehta, R. (2009). Cancer chemopreventive and therapeutic effects of diosgenin, a food saponin. Nutrition and Cancer, 61(1), 27–35. doi:10.1080/01635580802357352
   PubMed Web of Science ®Google Scholar
• Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. doi:10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Shakil, S., Azhar, E. I., Tabrez, S., Kamal, M. A., Jabir, N. R., Abuzenadah, A. M., … Alam, Q. (2011). New Delhi metallo-beta-lactamase (NDM-1): An update. Journal of Chemotherapy, 23(5), 263–265. doi:10.1179/joc.2011.23.5.263
   PubMed Web of Science ®Google Scholar
• Shohat, B., Gitter, S., Abraham, A., & Lavie, D. (1967). Antitumor activity of withaferin A (NSC-101088). Cancer Chemotherapy Reports, 51(5), 271–276.
   PubMedGoogle Scholar
• Skagseth, S., Akhter, S., Paulsen, M. H., Muhammad, Z., Lauksund, S., Samuelsen, Ø., … Bayer, A. (2017). Metallo-beta-lactamase inhibitors by bioisosteric replacement: Preparation, activity and binding. European Journal of Medicinal Chemistry, 135, 159–173. doi:10.1016/j.ejmech.2017.04.035
   PubMed Web of Science ®Google Scholar
• Tang, Y. T., & Marshall, G. R. (2011). Virtual screening for lead discovery. Methods in Molecular Biology (Clifton, N.J.), 716, 1–22. doi:10.1007/978-1-61779-012-6_1
   PubMedGoogle Scholar
• WHO. (2014). Antimicrobial resistance: global report on surveillance. Geneva: World Health Organisation.
   Google Scholar
• WHO. (2015). Global action plan on antimicrobial resistance. Geneva: World Health Organisation.
   Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. doi:10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Yang, H. Y., Chen, P. C., & Wang, J. D. (2014). Chinese herbs containing aristolochic acid associated with renal failure and urothelial carcinoma: a review from epidemiologic observations to causal inference. BioMed Research International, 2014, 1. doi:10.1155/2014/569325
   Google Scholar
• Yong, D., Toleman, M. A., Giske, C. G., Cho, H. S., Sundman, K., Lee, K., & Walsh, T. R. (2009). Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrobial Agents and Chemotherapy, 53(12), 5046–5054. doi:10.1128/AAC.00774-09
   PubMed Web of Science ®Google Scholar
• Zhang, H., & Hao, Q. (2011). Crystal structure of NDM-1 reveals a common beta-lactam hydrolysis mechanism. The FASEB Journal, 25(8), 2574–2582. doi:10.1096/fj.11-184036
   PubMed Web of Science ®Google Scholar