Modelling of AgrA inhibitors to combat anti-microbial resistance in Staphylococcus aureus

References

• Bezar, I. F., Mashruwala, A. A., Boyd, J. M., & Stock, A. M. (2019). Drug-like fragments inhibit agr-mediated virulence expression in Staphylococcus aureus. Scientific Reports, 9(1), 1–14. https://doi.org/10.1038/s41598-019-42853-z
   PubMedGoogle Scholar
• Boz, E., & Stein, M. (2021). Accurate receptor-ligand binding free energies from fast qm conformational chemical space sampling. International Journal of Molecular Sciences, 22(6), 3078. https://doi.org/10.3390/ijms22063078
   PubMed Web of Science ®Google Scholar
• Chemmugil, P., Lakshmi, P. T. V., & Annamalai, A. (2019). A multidisciplinary study to evaluate the anti-quorum sensing ability of phyto-compounds in Ruellia patula Jacq. Avicenna Journal of Medical Biotechnology, 11(1), 48.
   PubMedGoogle Scholar
• Chen, J., Wang, B., Lu, Y., Guo, Y., Sun, J., Wei, B., Zhang, H., & Wang, H. (2019). Quorum sensing inhibitors from marine microorganisms and their synthetic derivatives. Marine Drugs, 17(2), 80. https://doi.org/10.3390/md17020080
   PubMed Web of Science ®Google Scholar
• Diniz, R. C., Soares, L. W., & Nascimento da Silva, L. C. (2018). Virtual screening for the development of new effective compounds against Staphylococcus aureus. Current Medicinal Chemistry, 25(42), 5975–5985. https://doi.org/10.2174/0929867325666180327105842
   PubMed Web of Science ®Google Scholar
• Figueroa, M., Jarmusch, A. K., Raja, H. A., El-Elimat, T., Kavanaugh, J. S., Horswill, A. R., Cooks, R. G., Cech, N. B., & Oberlies, N. H. (2014). Polyhydroxyanthraquinones as quorum sensing inhibitors from the guttates of Penicillium restrictum and their analysis by desorption electrospray ionization mass spectrometry. Journal of Natural Products, 77(6), 1351–1358. https://doi.org/10.1021/np5000704
   PubMed Web of Science ®Google Scholar
• Gilson, M. K., Liu, T., Baitaluk, M., Nicola, G., Hwang, L., & Chong, J. (2016). BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Research, 44(D1), D1045–D1053. https://doi.org/10.1093/nar/gkv1072
   PubMed Web of Science ®Google Scholar
• Gordon, C. P., Williams, P., & Chan, W. C. (2013). Attenuating Staphylococcus aureus virulence gene regulation: A medicinal chemistry perspective. Journal of Medicinal Chemistry, 56(4), 1389–1404. https://doi.org/10.1021/jm3014635
   PubMed Web of Science ®Google Scholar
• Güner, O. F. (2000). Pharmacophore perception, development, and use in drug design: Internat’l University Line.
   Google Scholar
• Horswill, A. R., & Gordon, C. P. (2020). Structure–activity relationship studies of small molecule modulators of the staphylococcal accessory gene regulator. Journal of Medicinal Chemistry, 63(6), 2705–2730. https://doi.org/10.1021/acs.jmedchem.9b00798
   PubMed Web of Science ®Google Scholar
• Ibrahim, Y. M., Abouwarda, A. M., Nasr, T., Omar, F. A., & Bondock, S. (2020). Antibacterial and anti-quorum sensing activities of a substituted thiazole derivative against methicillin-resistant Staphylococcus aureus and other multidrug-resistant bacteria. Microbial Pathogenesis, 149, 104500. https://doi.org/10.1016/j.micpath.2020.104500
   PubMed Web of Science ®Google Scholar
• Igarashi, Y., Yamamoto, K., Fukuda, T., Shojima, A., Nakayama, J., Carro, L., & Trujillo, M. E. (2015). Arthroamide, a cyclic depsipeptide with quorum sensing inhibitory activity from Arthrobacter sp. Journal of Natural Products, 78(11), 2827–2831. https://doi.org/10.1021/acs.jnatprod.5b00540
   PubMed Web of Science ®Google Scholar
• Kar, S., & Roy, K. (2013). How far can virtual screening take us in drug discovery? Expert Opinion on Drug Discovery, 8(3), 245–261. https://doi.org/10.1517/17460441.2013.761204
   PubMed Web of Science ®Google Scholar
• Khodaverdian, V., Pesho, M., Truitt, B., Bollinger, L., Patel, P., Nithianantham, S., Yu, G., Delaney, E., Jankowsky, E., & Shoham, M. (2013). Discovery of antivirulence agents against methicillin-resistant Staphylococcus aureus. Antimicrobial Agents and Chemotherapy, 57(8), 3645–3652. https://doi.org/10.1128/AAC.00269-13
   PubMed Web of Science ®Google Scholar
• Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E. (2021). PubChem in 2021: New data content and improved web interfaces. Nucleic Acids Research, 49(D1), D1388–D1395. https://doi.org/10.1093/nar/gkaa971
   PubMed Web of Science ®Google 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 (Basel, Switzerland), 13(5), 6217–6228. 8) https://doi.org/10.3390/s130506217
   PubMed Web of Science ®Google Scholar
• Maltarollo, V. G., Kronenberger, T., Espinoza, G. Z., Oliveira, P. R., & Honorio, K. M. (2019). Advances with support vector machines for novel drug discovery. Expert Opinion on Drug Discovery, 14(1), 23–33. https://doi.org/10.1080/17460441.2019.1549033
   PubMed Web of Science ®Google Scholar
• Mysinger, M. M., Carchia, M., Irwin, J. J., & Shoichet, B. K. (2012). Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. Journal of Medicinal Chemistry, 55(14), 6582–6594. https://doi.org/10.1021/jm300687e
   PubMed Web of Science ®Google Scholar
• O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 1–14. https://doi.org/10.1186/1758-2946-3-33
   PubMed Web of Science ®Google Scholar
• Palaniappan, B., Solomon, A. P., & David Raj, C. (2021). Targeting AgrA quorum sensing regulator by bumetanide attenuates virulence in Staphylococcus aureus–A drug repurposing approach. Life Sciences, 273, 119306. https://doi.org/10.1016/j.lfs.2021.119306
   PubMed Web of Science ®Google Scholar
• Pawar, S. S., & Rohane, S. H. (2021). Review on discovery studio: An important tool for molecular docking. Asian Journal of Research in Chemistry, 14(1), 1–3. https://doi.org/10.5958/0974-4150.2021.00014.6
   Google Scholar
• Sadiq, S., Rana, N. F., Zahid, M. A., Zargaham, M. K., Tanweer, T., Batool, A., Naeem, A., Nawaz, A., Muneer, Z., Siddiqi, A. R., & Rizwan-Ur-Rehman. (2020). Virtual screening of FDA-approved drugs against LasR of Pseudomonas aeruginosa for antibiofilm potential. Molecules, 25(16), 3723. https://doi.org/10.3390/molecules25163723
   PubMedGoogle Scholar
• Seidel, T., Bryant, S. D., Ibis, G., Poli, G., & Langer, T. (2017). 3D Pharmacophore Modeling Techniques in Computer-Aided Molecular Design Using Ligand Scout. In A. Varnek (Ed.)., Tutorials in Chemoinformatics. https://doi.org/10.1002/9781119161110.ch20
   Google Scholar
• Seidel, T., Ibis, G., Bendix, F., & Wolber, G. (2010). Strategies for 3D pharmacophore-based virtual screening. Drug Discovery Today: Technologies, 7(4), e221–e8. https://doi.org/10.1016/j.ddtec.2010.11.004
   Google Scholar
• Seidel, T., Schuetz, D. A., Garon, A., & Langer, T. (2019). The pharmacophore concept and its applications in computer-aided drug design. Progress in the Chemistry of Organic Natural Products, 110, 99–141.
   PubMedGoogle Scholar
• Shen J, Zhang W, Fang H, Perkins R, Tong W, Hong H, editors (2013). Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes. In BMC bioinformatics. Springer. https://doi.org/10.1186/1471-2105-14-S14-S6
   Google Scholar
• Shivakumar, D., Williams, J., Wu, Y., Damm, W., Shelley, J., & Sherman, W. (2010). Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. Journal of Chemical Theory and Computation, 6(5), 1509–1519. https://doi.org/10.1021/ct900587b
   PubMed Web of Science ®Google Scholar
• Silva, L. N., Zimmer, K. R., Macedo, A. J., & Trentin, D. S. (2016). Plant natural products targeting bacterial virulence factors. Chemical Reviews, 116(16), 9162–9236. 9) https://doi.org/10.1021/acs.chemrev.6b00184
   PubMed Web of Science ®Google Scholar
• Sully, E. K., Malachowa, N., Elmore, B. O., Alexander, S. M., Femling, J. K., Gray, B. M., DeLeo, F. R., Otto, M., Cheung, A. L., Edwards, B. S., Sklar, L. A., Horswill, A. R., Hall, P. R., & Gresham, H. D. (2014). Selective chemical inhibition of agr quorum sensing in Staphylococcus aureus promotes host defense with minimal impact on resistance. PLoS Pathogens, 10(6), e1004174. https://doi.org/10.1371/journal.ppat.1004174
   PubMed Web of Science ®Google Scholar
• Tan, L., Li, S. R., Jiang, B., Hu, X. M., & Li, S. (2018). Therapeutic targeting of the Staphylococcus aureus accessory gene regulator (agr) system. Frontiers in Microbiology, 9, 55. https://doi.org/10.3389/fmicb.2018.00055
   PubMed Web of Science ®Google Scholar
• Tharmalingam, N., Khader, R., Fuchs, B. B., & Mylonakis, E. (2019). The anti-virulence efficacy of 4-(1, 3-dimethyl-2, 3-dihydro-1h-benzimidazol-2-yl) phenol against methicillin-resistant Staphylococcus aureus. Frontiers in Microbiology, 10, 1557. https://doi.org/10.3389/fmicb.2019.01557
   PubMed Web of Science ®Google Scholar
• Triballeau, N., Acher, F., Brabet, I., Pin, J.-P., & Bertrand, H.-O. (2005). Virtual screening workflow development guided by the “receiver operating characteristic” curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4. Journal of Medicinal Chemistry, 48(7), 2534–2547. https://doi.org/10.1021/jm049092j
   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.
   PubMed Web of Science ®Google Scholar
• Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S., & Weiner, P. (1984). A new force field for molecular mechanical simulation of nucleic acids and proteins. Journal of the American Chemical Society, 106(3), 765–784. https://doi.org/10.1021/ja00315a051
   Web of Science ®Google Scholar
• Wu, S. C., Liu, F., Zhu, K., & Shen, J. Z. (2019). Natural products that target virulence factors in antibiotic-resistant Staphylococcus aureus. Journal of Agricultural and Food Chemistry, 67(48), 13195–13211. https://doi.org/10.1021/acs.jafc.9b05595
   PubMed Web of Science ®Google Scholar