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Research Articles

Phytomolecules as potential candidates to intervene the function of E. coli sodium-proton antiporters; Ec-NhaA

, , , ORCID Icon & ORCID Icon
Pages 15598-15609 | Received 27 Oct 2022, Accepted 06 Mar 2023, Published online: 19 Mar 2023

References

  • Abishad, P., Niveditha, P., Unni, V., Vergis, J., Kurkure, N. V., Chaudhari, S., Rawool, D. B., & Barbuddhe, S. B. (2021). In silico molecular docking and in vitro antimicrobial efficacy of phytochemicals against multi-drug-resistant enteroaggregative Escherichia coli and non-typhoidal Salmonella spp. Gut Pathogens, 13(1), 1–11. https://doi.org/10.1186/s13099-021-00443-3
  • Călinescu, O., Danner, E., Böhm, M., Hunte, C., & Fendler, K. (2014). Species differences in bacterial NhaA Na+/H + exchangers. FEBS Letters, 588(17), 3111–3116.
  • Carugo, O., & Pongor, S. (2008). A normalized root‐mean‐spuare distance for comparing protein three‐dimensional structures. Protein Science, 10(7), 1470–1473. https://doi.org/10.1110/ps.690101
  • 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
  • Deisl, C., Simonin, A., Anderegg, M., Albano, G., Kovacs, G., Ackermann, D., Moch, H., Dolci, W., Thorens, B., A. Hediger, M., & Fuster, D. G. (2013). Sodium/hydrogen exchanger NHA2 is critical for insulin secretion in beta-cells. Proceedings of the National Academy of Sciences, 110(24), 10004–10009. https://doi.org/10.1073/pnas.1220009110
  • DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography, 40, 82–92.
  • Durrant, J. D., & McCammon, J. A. (2011). Molecular dynamics simulations and drug discovery. BMC Biology, 9(1), 1–9. https://doi.org/10.1186/1741-7007-9-71
  • Dwivedi, M. (2021). Site-directed mutations reflecting functional and structural properties of Ec-NhaA. Biochimie, 180, 79–89. https://doi.org/10.1016/j.biochi.2020.10.017
  • Dwivedi, M., & Mahendiran, S. (2022). Ubiquitous existence of cation-proton antiporter and its structure-function interplay: A clinical prospect. Current Protein & Peptide Science, 24(1), 43-58. https://doi.org/10.2174/1389203724666221114093235.
  • Dwivedi, M., & Shaw, A. (2021). Implication of cation-proton antiporters (CPA) in human health and diseases causing microorganisms. Biochimie, 182, 85–98. https://doi.org/10.1016/j.biochi.2021.01.004
  • Dwivedi, M., Sukenik, S., Friedler, A., & Padan, E. (2016). The Ec-NhaA antiporter switches from antagonistic to synergistic antiport upon a single point mutation. Scientific Reports, 6, 23339. https://doi.org/10.1038/srep23339
  • Fliegel, L. (2008). Molecular biology of the myocardial Na+/H + exchanger. Journal of Molecular and Cellular Cardiology, 44(2), 228–237. https://doi.org/10.1016/j.yjmcc.2007.11.016
  • Huang, C. Y. T., Kargar, F., Debnath, T., Debnath, B., Valentin, M. D., Synowicki, R., Schoeche, S., Lake, R. K., & Balandin, A. A. (2020). Properties of shape-engineered phoxonic crystals: Brillouin-mandelstam spectroscopy and ellipsometry study. arXiv preprint arXiv:2003.01777.
  • Karmazyn, M. (2013). NHE-1: Still a viable therapeutic target. Journal of Molecular and Cellular Cardiology, 61, 77–82. https://doi.org/10.1016/j.yjmcc.2013.02.006
  • Kondapalli, K. C., Kallay, L. M., Muszelik, M., & Rao, R. (2012). Unconventional chemiosmotic coupling of NHA2, a mammalian Na+/H + antiporter, to a plasma membrane H + gradient. The Journal of Biological Chemistry, 287(43), 36239–36250. https://doi.org/10.1074/jbc.M112.403550
  • Land, H., & Humble, M. S. (2018). YASARA: A tool to obtain structural guidance in biocatalytic investigations. Methods in Molecular Biology (Clifton, N.J.), 1685, 43–67. https://doi.org/10.1007/978-1-4939-7366-8_4
  • Lee, C., Yashiro, S., Dotson, D. L., Uzdavinys, P., Iwata, S., Sansom, M. S., von Ballmoos, C., Beckstein, O., Drew, D., & Cameron, A. D. (2014). Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights. Journal of General Physiology, 144(6), 529–544. https://doi.org/10.1085/jgp.201411219
  • Lee, S. K., Chang, G. S., Lee, I. H., Chung, J. E., Sung, K. Y., & No, K. T. (2004). The PreADME: PC-based program for batch prediction of ADME properties. In EuroQSAR (Vol. 9, pp. 5–10), Istanbul, Turkey.
  • Lee, S. K., Lee, I. H., Kim, H. J., Chang, G. S., Chung, J. E., & No, K. T. (2003). The PreADME Approach: Web-based program for rapid prediction of physico-chemical, drug absorption and drug-like properties. In EuroQSAR 2002 Designing Drugs and Crop Protectants: Processes, Problems and Solutions Blackwell Publishing, 418–420. Massachusetts.
  • Lindorff‐Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side‐chain torsion potentials for the Amber ff99SB protein force field. Proteins: Structure, Function, and Bioinformatics, 78(8), 1950–1958. https://doi.org/10.1002/prot.22711
  • Lobanov, M. Y., Bogatyreva, N. S., & Galzitskaya, O. V. (2008). Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 42(4), 623–628. https://doi.org/10.1134/S0026893308040195
  • Martínez, L. (2015). Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. Plos One, 10(3), e0119264. https://doi.org/10.1371/journal.pone.0119264
  • Michael, C. A., Dominey-Howes, D., & Labbate, M. (2014). The antimicrobial resistance crisis: Causes, consequences, and management. Frontiers in Public Health, 16(2), 145.
  • Mihel, J., Šikić, M., Tomić, S., Jeren, B., & Vlahoviček, K. (2008). PSAIA–protein structure and interaction analyzer. BMC Structural Biology, 8(1), 1–11. https://doi.org/10.1186/1472-6807-8-21
  • Minato, Y., Ghosh, A., Faulkner, W. J., Lind, E. J., Schesser Bartra, S., Plano, G. V., Jarrett, C. O., Hinnebusch, B. J., Winogrodzki, J., Dibrov, P., & Häse, C. C. (2013). Na+/H + antiport is essential for Yersinia pestis virulence. Infection and Immunity, 81(9), 3163–3172. https://doi.org/10.1128/IAI.00071-13
  • Mohanraj, K., Karthikeyan, B. S., Vivek-Ananth, R. P., Chand, R. P. B., Aparna, S. R., Mangalapandi, P., & Samal, A. (2018). IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry And Therapeutics. Scientific Reports, 8(1), 4329. https://doi.org/10.1038/s41598-018-22631-z
  • 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. https://doi.org/10.1002/jcc.21256
  • Mulkidjanian, A. Y., Dibrov, P., & Galperin, M. Y. (2008). The past and present of sodium energetics: May the sodium-motive force be with you. Biochimica et Biophysica Acta, 1777(7–8), 985–992. https://doi.org/10.1016/j.bbabio.2008.04.028
  • Packer, M. (2017). Activation and inhibition of sodium-hydrogen exchanger is a mechanism that links the pathophysiology and treatment of diabetes mellitus with that of heart failure. Circulation, 136(16), 1548–1559.
  • Padan, E. (2008). The enlightening encounter between structure and function in the NhaA Na+–H + antiporter. Trends in Biochemical Sciences, 33(9), 435–443. https://doi.org/10.1016/j.tibs.2008.06.007
  • Padan, E., Bibi, E., Ito, M., & Krulwich, T. A. (2005). Alkaline pH homeostasis in bacteria: New insights. Biochimica et Biophysica Acta, 1717(2), 67–88.
  • Padan, E., Kozachkov, L., Herz, K., & Rimon, A. (2009). NhaA crystal structure: Functional–structural insights. Journal of Experimental Biology, 212(11), 1593–1603. https://doi.org/10.1242/jeb.026708
  • Padan, E., & Landau, M. (2016). Sodium-proton (Na+/H+) antiporters: Properties and roles in health and disease. In The alkali metal ions: Their role for life (Vol. 16, pp. 391–458).
  • Patiño-Ruiz, M., Dwivedi, M., Călinescu, O., Karabel, M., Padan, E., & Fendler, K. (2019). Replacement of Lys-300 with a glutamine in the NhaA Na+/H+ antiporter of Escherichia coli yields a functional electrogenic transporter. The Journal of Biological Chemistry, 294(1), 246–256.
  • Pinner, E., Kotler, Y., Padan, E., & Schuldiner, S. (1993). Physiological role of nhaB, a specific Na+/H + antiporter in Escherichia coli. The Journal of Biological Chemistry, 268(3), 1729–1734.
  • Pires, D. E., 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.
  • Quick, M., Dwivedi, M., & Padan, E. (2021). Insight into the direct interaction of Na+ with NhaA and mechanistic implications. Scientific Reports, 11(1), 7045. https://doi.org/10.1038/s41598-021-86318-8
  • Rost, B., Sander, C., & Schneider, R. (1994). Redefining the goals of protein secondary structure prediction. Journal of Molecular Biology, 235(1), 13–26. https://doi.org/10.1016/S0022-2836(05)80007-5
  • Schrödinger, L., & DeLano, W. (2020). The PyMOL molecular graphics system, version 1.2r3pre. Schrödinger, LLC. http://www.pymol.org/pymol
  • Shaw, D. E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R. O., Eastwood, M. P., Bank, J. A., Jumper, J. M., Salmon, J. K., Shan, Y., & Wriggers, W. (2010). Atomic-level characterization of the structural dynamics of proteins. Science, 330(6002), 341–346.
  • Singer, A. C., Shaw, H., Rhodes, V., & Hart, A. (2016). Review of antimicrobial resistance in the environment and its relevance to environmental regulators. Frontiers in Microbiology, 7(1), 1728.
  • Taglicht, D., Padan, E., & Schuldiner, S. (1993). Proton-sodium stoichiometry of NhaA, an electrogenic antiporter from Escherichia coli. The Journal of Biological Chemistry, 268(8), 5382–5387.
  • Vimont, S., & Berche, P. (2000). NhaA, an Na(+)/H(+) antiporter involved in environmental survival of Vibrio cholerae. Journal of Bacteriology, 182(10), 2937–2944. https://doi.org/10.1128/JB.182.10.2937-2944.2000
  • Waseem, H., Williams, M. R., Jameel, S., & Hashsham, S. A. (2018). Antimicrobial Resistance in the Environment. Water Environment Research, 90(10), 865–884. https://doi.org/10.2175/106143018X15289915807056
  • Yeves, A. D. M., & Ennis, I. L. (2020). Na+/H + exchanger and cardiac hypertrophy. Hipertensión y Riesgo Vascular, 37(1), 22–32. https://doi.org/10.1016/j.hipert.2019.09.002

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