Anti-quorum sensing effects of SidA protein on Escherichia coli receptors: in silico analysis

References

• Adak, S., Upadrasta, L., Kumar, S. P. J., Soni, R., & Banerjee, R. (2011). Quorum quenching – An alternative antimicrobial therapeutics. In A. Mendez-Vilas (Ed.), Proceedings of the International Conference on Antimicrobial Research (pp. 586–593).
   Google Scholar
• Ahmed, A., Li, J., Shiloach, Y., Robbins, J. B., & Szu, S. C. (2006). Safety and immunogenicity of Escherichia coli O157 O-specific polysaccharide conjugate vaccine in 2–5-year-old children. The Journal of Infectious Diseases, 193(4), 515–521. https://doi.org/10.1086/499821
   PubMed Web of Science ®Google Scholar
• Ahmed, M. Z., Muteeb, G., Khan, S., Alqahtani, A. S., Somvanshi, P., Alqahtani, M. S., Ameta, K. L., & Haque, S. (2020). Identifying novel inhibitor of quorum sensing transcriptional regulator (SidA) of Klebsiella pneumoniae through modelling, docking and molecular dynamics simulation. Journal of Biomolecular Structure & Dynamics, 39(10), 3594–3604. https://doi.org/10.1080/07391102.2020.1767209
   PubMed Web of Science ®Google Scholar
• Alam, M. J., & Zurek, L. (2004). Association of Escherichia coli O157:H7 with houseflies on a cattle farm. Applied and Environmental Microbiology, 70(12), 7578–7580. https://doi.org/10.1128/AEM.70.12.7578-7580.2004
   PubMed Web of Science ®Google Scholar
• Azerang, P., Yazdani, M., RayatSanati, K., & Tahghighi, A. (2022). Newly identified COVID-19 drug candidates based on computational strategies. Journal of Computational Biophysics and Chemistry, 21(1), 123–137. https://doi.org/10.1142/S2737416521410039
   Google Scholar
• Badeli, Z. (2022). Investigating the simultaneous effect of LED209 and garlic extract on the expression of genes under the control of sensor kinase QseC in enterohemorrhagic Escherichia coli. Journal of Veterinary Research, 71(1), 41–47.
   Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• BIOVIA (2020). Dassault Systèmes, Biovia Discovery Studio. Dassault Systèmes.
   Google Scholar
• Bodini, S., Manfredini, S., Epp, M., Valentini, S., & Santori, F. (2009). Quorum sensing inhibition activity of garlic extract and p‐coumaric acid. Letters in Applied Microbiology, 49(5), 551–555. https://doi.org/10.1111/j.1472-765X.2009.02704.x
   PubMed Web of Science ®Google Scholar
• Choo, S., Chin, V. K., Wong, E. H., Madhavan, P., Tay, S. T., Yong, P. V. C., & Chong, P. P. (2020). Antimicrobial properties of allicin used alone or in combination with other medications. Folia Microbiologica, 65(3), 451–465. https://doi.org/10.1007/s12223-020-00786-5
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle Mesh Ewald-an N.Log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• DeLano, W. L. (2002). The PyMOL molecular graphics system. Retrieved from http://www.pymol.org/
   Google Scholar
• Donlan, R. M., & Costerton, J. W. (2002). Biofilms: Survival mechanisms of clinically relevant microorganisms. Clinical Microbiology Reviews, 15(2), 167–193. https://doi.org/10.1128/CMR.15.2.167-193.2002
   PubMed Web of Science ®Google Scholar
• Dwivedi, V. P., Bhattacharya, D., Singh, M., Bhaskar, A., Kumar, S., Fatima, S., Sobia, P., Kaer, L. V., & Das, G. (2019). Allicin enhances antimicrobial activity of macrophages during Mycobacterium tuberculosis infection. Journal of Ethnopharmacology, 243, 111634. https://doi.org/10.1016/j.jep.2018.12.008
   PubMed Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smoothparticle mesh Ewald potential. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
   Web of Science ®Google Scholar
• Girish, V. M., Liang, H., Aguilan, J. T., Nosanchuk, J. D., Friedman, J. M., & Nacharaju, P. (2019). Anti-biofilm activity of garlic extract loaded nanoparticles. Nanomedicine: Nanotechnology, Biology, and Medicine, 20, 102009. https://doi.org/10.1016/j.nano.2019.04.012
   PubMed Web of Science ®Google Scholar
• Grabski, H., Ginosyan, S., & Tiratsuyan, S. (2021). Molecular simulations and Markov state modeling reveal inactive form of quorum sensing regulator SidA of Escherichia coli. Journal of IEEE/ACM Transactions on Computational Biology and Bioinformatics, 18(6), 2835–2840. https://doi.org/10.1109/TCBB.2021.3074567
   PubMed Web of Science ®Google Scholar
• 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>3.3.CO;2-L
   Web of Science ®Google Scholar
• Jafari, A., Babajani, A., Sarrami Forooshani, R., Yazdani, M., & Rezaei-Tavirani, M. (2022). Clinical applications and anticancer effects of antimicrobial peptides: From bench to bedside. Frontiers in Oncology, 12, 819563. https://doi.org/10.3389/fonc.2022.819563
   PubMed Web of Science ®Google Scholar
• Kåhrström, C. T. (2013). Entering a post-antibiotic era? Nature Reviews Microbiology, 11(3), 146–146. https://doi.org/10.1038/nrmicro2983
   PubMedGoogle Scholar
• Koh, C. L., Sam, C. K., Yin, W. F., Tan, L. Y., Krishnan, T., Chong, Y. M., & Chan, K. G. (2013). Plant-derived natural products as sources of anti-quorum sensing compounds. Sensors, 13(5), 6217–6228. https://doi.org/10.3390/s130506217
   PubMed Web of Science ®Google 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. https://doi.org/10.1002/jcc.21256 19399780
   PubMed Web of Science ®Google Scholar
• Nayara, S. R., Luana, K. S., Jonatas, L., Juliane, S., César, F., Francinaldo, S., Raí, C., Josivan, S., Lorane, I. S., & Cleydson, B. R. (2014). Computational analysis of physicochemical, pharmacokinetic and toxicological properties of deoxyhypusine synthase inhibitors with antimalarial activity. Computational Molecular Bioscience, 4(4), 47–57.
   Google Scholar
• Nguyen, Y., Nguyen, N. X., Rogers, J. L., Liao, J., MacMillan, J. B., Jiang, Y., & Sperandio, V. (2015). Structural and mechanistic roles of novel chemical ligands on the SidA quorum-sensing transcription regulator. mBio, 6(2), e02429-14. https://doi.org/10.1128/mBio.02429-14
   PubMed Web of Science ®Google Scholar
• Nosé, S. (1984). A unified formulation of the constant temperature molecular dynamics methods. The Journal of Chemical Physics, 81(1), 511–519. https://doi.org/10.1063/1.447334
   Web of Science ®Google Scholar
• Nowdehi, J.,Mosaddegh, E.,Khaksar, S.,Torkzadeh-Mahani, M.,Beihaghi, M., &Yazdani, M. (2024). Synthesis, in silico studies, and in vitro biological evaluation of newly-designed 5-amino-1H-tetrazole-linked 5-fluorouracil analog as a potential antigastric-cancer agent. Journal of Biomolecular Structure & Dynamics, 1–19. https://doi.org/10.1080/07391102.2024.2318480 38385480
   PubMedGoogle Scholar
• Rabbani, S., Krammer, E.-M., Roos, G., Zalewski, A., Preston, R., Eid, S., Zihlmann, P., Prévost, M., Lensink, M. F., Thompson, A., Ernst, B., & Bouckaert, J. (2017). Mutation of Tyr137 of the universal Escherichia coli fimbrial adhesin FimH relaxes the tyrosine gate prior to mannose binding. IUCrJ, 4(Pt 1), 7–23. https://doi.org/10.1107/S2052252516016675
   PubMedGoogle Scholar
• Rahmani Far, S., & Zeighami, H. (2017). Bacterial biofilms. Quarterly Journal of Laboratory and Diagnosis, 37, 27.
   Google Scholar
• Raina, S., De Vizio, D., Odell, M., Clements, M., Vanhulle, S., & Keshavarz, T. (2009). Microbial quorum sensing. A tool or a target for antimicrobial therapy. Biotechnology and Applied Biochemistry, 54(2), 65–84. https://doi.org/10.1042/BA20090072
   PubMedGoogle Scholar
• Rajamanikandan, S., & Srinivasan, P. (2017). Exploring the selectivity of auto-inducer complex with LuxR using molecular docking, mutational studies and molecular dynamics simulations. Journal of Molecular Structure, 1131, 281–293. https://doi.org/10.1016/j.molstruc.2016.11.056
   Web of Science ®Google Scholar
• Ranjbar-Omid, M., Arzanlou, M., Amani, M., Shokri Al-Hashem, S. K., Amir Mozafari, N., & Peeri Doghaheh, H. (2015). Study of the effect of allicin (an active component of garlic) sub-MIC concentrations on biofilm formation by Proteus mirabilis. FEMS Microbiology Letters, 362(9), 1-9. https://doi.org/10.1093/femsle/fnv049
   PubMed Web of Science ®Google Scholar
• Reiter, J., Hübbers, A. M., Albrecht, F., Leichert, L. I. O., & Slusarenko, A. J. (2020). Allicin, a natural antimicrobial defence substance from garlic, inhibits DNA gyrase activity in bacteria. International Journal of Medical Microbiology, 310(1), 151359. https://doi.org/10.1016/j.ijmm.2019.151359
   PubMed Web of Science ®Google Scholar
• Rumbaugh Kendra, P. (2011). Quorum sensing methods and protocols. Humanna Press.
   Google Scholar
• Sivasankar, C., Jha, N. K., Singh, S. R., Murali, A., & Shetty, P. H. (2020). Molecular evaluation of quorum quenching potential of vanillic acid against Yersinia enterocolitica through transcriptomic and in silico analysis. Journal of Medical Microbiology, 69(11), 1319–1331. https://doi.org/10.1099/jmm.0.001261
   PubMed Web of Science ®Google Scholar
• Soto, S. M. (2014). Importance of biofilms in urinary tract infections: New therapeutic approaches. Advances in Biology, 2014, 1–13. https://doi.org/10.1155/2014/543974
   Google Scholar
• Sousa da Silva, A. W., & Vranken, W. F. (2012). ACPYPE – AnteChamber PYthon Parser interfacE. BMC Research Notes, 5(1), 367. https://doi.org/10.1186/1756-0500-5-367
   PubMedGoogle Scholar
• Tedeschi, P.,Nigro, M.,Travagli, A.,Catani, M.,Cavazzini, A.,Merighi, S., &Gessi, S. (2022). Therapeutic Potential of Allicin and Aged Garlic Extract in Alzheimer’s Disease. International Journal of Molecular Sciences, 23(13), 6950.https://doi.org/10.3390/ijms23136950
   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
• 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 16211538
   PubMed Web of Science ®Google Scholar
• Waters, C. M., &Bassler, B. L. (2005). Quorum sensing: cell-to-cell communication in bacteria. Annual Review of Cell and Developmental Biology, 21, 319–346. https://doi.org/10.1146/annurev.cellbio.21.012704.131001 16212498
   PubMed Web of Science ®Google Scholar
• Yazdani, M., Jafari, A., Mahdian, S., Namazi, M., & Gharaghani, S. (2023). Rational approaches to discover SARS-CoV-2/ACE2 interaction inhibitors: Pharmacophore-based virtual screening, molecular docking, molecular dynamics and binding free energy studies. Journal of Molecular Liquids, 375, 121345. https://doi.org/10.1016/j.molliq.2023.121345
   PubMed Web of Science ®Google Scholar
• Zimmerman, K. (1991). All purpose molecular mechanics simulator and energy minimizer. Journal of Computational Chemistry, 12, 310–319.
   Web of Science ®Google Scholar