Elucidating novel antibacterial compounds from the NPASS database against the FimH lectin domain for the treatment of urinary tract infections: an in-silico study

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Behzadi, P., Urbán, E., Matuz, M., Benkő, R., & Gajdács, M. (2021). The role of gram-negative bacteria in urinary tract infections: Current concepts and therapeutic options. In Advances in experimental medicine and biology (vol. 1323, pp. 35–69). Springer. https://doi.org/10.1007/5584_2020_566
   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
• Bouffier, L., & Sojic, N. (2019). Chapter 1. Introduction and overview of electrogenerated chemiluminescence. In Analytical electrogenerated chemiluminescence: from fundamentals to bioassays (pp. 1–28). The Royal Society of Chemistry. https://doi.org/10.1039/9781788015776-00001
   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(1), 42717. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. Methods in Molecular Biology (Clifton, N.J.), 1263, 243–250. https://doi.org/10.1007/978-1-4939-2269-7_19
   PubMedGoogle Scholar
• Debnath, S., & Sen, D. (2021). Mushrooms are potential foods against cancer: Identified by molecular docking and molecular dynamics simulation. Natural Product Research, 1–6. https://doi.org/10.1080/14786419.2021.1912041
   Google Scholar
• Delaney, J. S. (2004). ESOL: Estimating aqueous solubility directly from molecular structure. Journal of Chemical Information and Computer Sciences, 44(3), 1000–1005. https://doi.org/10.1021/ci034243x
   PubMedGoogle Scholar
• Elber, R., Ruymgaart, A. P., & Hess, B. (2011). SHAKE parallelization. The European Physical Journal. Special Topics, 200(1), 211–223. https://doi.org/10.1140/epjst/e2011-01525-9.
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Ghose, A. K., Viswanadhan, V. N., & Wendoloski, J. J. (1999). A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. Journal of Combinatorial Chemistry, 1(1), 55–68. https://doi.org/10.1021/cc9800071
   PubMedGoogle Scholar
• Gupta, S., Kumar, P., Rathi, B., Verma, V., Dhanda, R. S., Devi, P., & Yadav, M. (2021). Targeting of Uropathogenic Escherichia coli papG gene using CRISPR-dot nanocomplex reduced virulence of UPEC. Scientific Reports, 11(1), 17801. https://doi.org/10.1038/s41598-021-97224-4.
   PubMed Web of Science ®Google Scholar
• Huang, J., & MacKerell, A. D. (2013). CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. Journal of Computational Chemistry, 34(25), 2135–2145. https://doi.org/10.1002/jcc.23354
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–27–28. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Kalas, V., Hibbing, M. E., Maddirala, A. R., Chugani, R., Pinkner, J. S., Mydock-McGrane, L. K., Conover, M. S., Janetka, J. W., & Hultgren, S. J. (2018). Structure-based discovery of glycomimetic FmlH ligands as inhibitors of bacterial adhesion during urinary tract infection. Proceedings of the National Academy of Sciences, 115(12), E2819–E2828. https://doi.org/10.1073/pnas.1720140115
   PubMed Web of Science ®Google Scholar
• Kundu, A., Sen, D., & Chatterjee, T. K. (2010). In-vivo antimalarial study of PITC2 of Pluchea indica (L.) less against Plasmodium berghei and Plasmodium yolli model. Pharmacologyonline, 3, 817–823. https://pharmacologyonline.silae.it/files/archives/2010/vol3/77.Kumar.pdf
   Google Scholar
• Laskowski, R. A., Jabłońska, J., Pravda, L., Vařeková, R. S., & Thornton, J. M. (2018). PDBsum: Structural summaries of PDB entries. Protein Science, 27(1), 129–134. https://doi.org/10.1002/pro.3289
   PubMed Web of Science ®Google Scholar
• Lee, D. S., Lee, S.-J., & Choe, H.-S. (2018). Community-acquired urinary tract infection by Escherichia coli in the era of antibiotic resistance. BioMed Research International, 2018, 7656752–7656714. https://doi.org/10.1155/2018/7656752
   PubMed Web of Science ®Google Scholar
• Lee, J. H., Subhadra, B., Son, Y.-J., Kim, D. H., Park, H. S., Kim, J. M., Koo, S. H., Oh, M. H., Kim, H.-J., & Choi, C. H. (2016). Phylogenetic group distributions, virulence factors and antimicrobial resistance properties of uropathogenic Escherichia coli strains isolated from patients with urinary tract infections in South Korea. Letters in Applied Microbiology, 62(1), 84–90. https://doi.org/10.1111/lam.12517
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 46(1–3), 3–26. https://doi.org/10.1016/s0169-409x(00)00129-0
   PubMed Web of Science ®Google Scholar
• Liu, J., Li, D., & Liu, X. (2016). A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat. The Journal of Chemical Physics, 145(2), 024103. https://doi.org/10.1063/1.4954990
   PubMed Web of Science ®Google Scholar
• Maddirala, A. R., Klein, R., Pinkner, J. S., Kalas, V., Hultgren, S. J., & Janetka, J. W. (2019). Biphenyl Gal and GalNAc FmlH lectin antagonists of uropathogenic E. coli (UPEC): Optimization through iterative rational drug design. Journal of Medicinal Chemistry, 62(2), 467–479. https://doi.org/10.1021/acs.jmedchem.8b01561
   PubMed Web of Science ®Google Scholar
• Marcon, J., Schubert, S., Stief, C. G., & Magistro, G. (2019). In vitro efficacy of phytotherapeutics suggested for prevention and therapy of urinary tract infections. Infection, 47(6), 937–944. https://doi.org/10.1007/s15010-019-01315-4
   PubMed Web of Science ®Google Scholar
• Meiers, J., Siebs, E., Zahorska, E., & Titz, A. (2019). Lectin antagonists in infection, immunity, and inflammation. Current Opinion in Chemical Biology, 53, 51–67. https://doi.org/10.1016/j.cbpa.2019.07.005
   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
   PubMed Web of Science ®Google Scholar
• Neese, F. (2012). The ORCA program system. WIREs Computational Molecular Science, 2(1), 73–78. https://doi.org/10.1002/wcms.81
   Google Scholar
• Neese, F., Wennmohs, F., Becker, U., & Riplinger, C. (2020). The ORCA quantum chemistry program package. The Journal of Chemical Physics, 152(22), 224108. https://doi.org/10.1063/5.0004608
   PubMed Web of Science ®Google Scholar
• O’Boyle, N., Banck, M., James, C., Morley, C., Vandermeersch, T., & Hutchison, G. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. https://doi.org/10.1186/1758-2946-3-33
   PubMed Web of Science ®Google Scholar
• O’Rourke, K., & Cadieux, P. A. (2019). Pathogenic Mechanisms of Uropathogens. In The role of bacteria in urology (pp. 23–39). Springer International Publishing. https://doi.org/10.1007/978-3-030-17542-9_3
   Google Scholar
• Rezatofighi, S. E., Mirzarazi, M., & Salehi, M. (2021). Virulence genes and phylogenetic groups of uropathogenic Escherichia coli isolates from patients with urinary tract infection and uninfected control subjects: A case-control study. BMC Infectious Diseases, 21(1), 361. https://doi.org/10.1186/s12879-021-06036-4
   PubMed Web of Science ®Google Scholar
• Rios, A. C., Moutinho, C. G., Pinto, F. C., Del Fiol, F. S., Jozala, A., Chaud, M. V., Vila, M. M. D. C., Teixeira, J. A., & Balcão, V. M. (2016). Alternatives to overcoming bacterial resistances: State-of-the-art. Microbiological Research, 191, 51–80. https://doi.org/10.1016/j.micres.2016.04.008
   PubMed Web of Science ®Google Scholar
• Ruiz-Morales, Y. (2002). HOMO − LUMO Gap as an index of molecular size and structure for polycyclic aromatic hydrocarbons (PAHs) and asphaltenes: A theoretical study. The Journal of Physical Chemistry A, 106(46), 11283–11308. https://doi.org/10.1021/jp021152e
   Web of Science ®Google Scholar
• Sarshar, M., Behzadi, P., Ambrosi, C., Zagaglia, C., Palamara, A. T., & Scribano, D. (2020). FimH and anti-adhesive therapeutics: A disarming strategy against uropathogens. Antibiotics (Basel, Switzerland), 9(7). https://doi.org/10.3390/antibiotics9070397
   Google Scholar
• Sauer, M. M., Jakob, R. P., Luber, T., Canonica, F., Navarra, G., Ernst, B., Unverzagt, C., Maier, T., & Glockshuber, R. (2019). Binding of the bacterial adhesin fimh to its natural, multivalent high-mannose type glycan targets. Journal of the American Chemical Society, 141(2), 936–944. https://doi.org/10.1021/jacs.8b10736
   PubMed Web of Science ®Google Scholar
• Schrödinger, L. (2021). The {PyMOL} molecular graphics system, version 2.5.
   Google Scholar
• Sen, D., Bhaumik, S., Debnath, P., & Debnath, S. (2021). Potentiality of Moringa oleifera against SARS-CoV-2: Identified by a rational computer aided drug design method. Journal of Biomolecular Structure & Dynamics, 1–18. https://doi.org/10.1080/07391102.2021.1898475
   Google Scholar
• Sintsova, A., Frick-Cheng, A. E., Smith, S., Pirani, A., Subashchandrabose, S., Snitkin, E. S., & Mobley, H. (2019). Genetically diverse uropathogenic Escherichia coli adopt a common transcriptional program in patients with UTIs. eLife, 8 https://doi.org/10.7554/eLife.49748
   Google Scholar
• Spaulding, C., & Hultgren, S. (2016). Adhesive pili in UTI pathogenesis and drug development. Pathogens, 5(1), 30. https://doi.org/10.3390/pathogens5010030
   PubMed Web of Science ®Google Scholar
• Spaulding, C. N., Klein, R. D., Ruer, S., Kau, A. L., Schreiber, H. L., Cusumano, Z. T., Dodson, K. W., Pinkner, J. S., Fremont, D. H., Janetka, J. W., Remaut, H., Gordon, J. I., & Hultgren, S. J. (2017). Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist. Nature, 546(7659), 528–532. https://doi.org/10.1038/nature22972
   PubMed Web of Science ®Google Scholar
• Sure, R., Brandenburg, J. G., & Grimme, S. (2016). Small atomic orbital basis set first-principles quantum chemical methods for large molecular and periodic systems: A critical analysis of error sources. ChemistryOpen, 5(2), 94–109. https://doi.org/10.1002/open.201500192
   PubMed Web of Science ®Google Scholar
• Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). gmx_MMPBSA: A new tool to perform end-state free energy calculations with GROMACS. Journal of Chemical Theory and Computation, 17(10), 6281–6291. https://doi.org/10.1021/acs.jctc.1c00645
   PubMed Web of Science ®Google Scholar
• Vivas, R., Barbosa, A. A. T., Dolabela, S. S., & Jain, S. (2019). Multidrug-resistant bacteria and alternative methods to control them: An overview. Microbial Drug Resistance (Larchmont, N.Y.), 25(6), 890–908. https://doi.org/10.1089/mdr.2018.0319
   PubMed Web of Science ®Google Scholar
• WHO. (2020). Antibiotic resistance. WHO. https://www.who.int/news-room/fact-sheets/detail/antibiotic-resistance.
   Google Scholar
• Zapién-Chavarría, K. A., Plascencia-Terrazas, A., Venegas-Ortega, M. G., Varillas-Torres, M., Rivera-Chavira, B. E., Adame-Gallegos, J. R., González-Rangel, M. O., & Nevárez-Moorillón, G. V. (2019). Susceptibility of multidrug-resistant and biofilm-forming uropathogens to mexican oregano essential oil. Antibiotics (Basel, Switzerland), 8(4) https://doi.org/10.3390/antibiotics8040186
   Google Scholar