‘Computational studies on coumestrol-ArlR interaction to target ArlRS signaling cascade involved in MRSA virulence’

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
• Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins, 17(4), 412–425. https://doi.org/10.1002/prot.340170408
   PubMed Web of Science ®Google Scholar
• Anand, U., Jacobo-Herrera, N., Altemimi, A., & Lakhssassi, N. (2019). A comprehensive review on medicinal plants as antimicrobial therapeutics: Potential avenues of biocompatible drug discovery. Metabolites, 9(11), 258. https://doi.org/10.3390/metabo9110258
   PubMed Web of Science ®Google Scholar
• Arip, M., Selvaraja, M., R, M., Tan, L. F., Leong, M. Y., Tan, P. L., Yap, V. L., Chinnapan, S., Tat, N. C., Abdullah, M., K, D., & Jubair, N. (2022). Review on plant-based management in combating antimicrobial resistance-mechanistic perspective. Frontiers in Pharmacology, 13, 879495. https://doi.org/10.3389/fphar.2022.879495
   PubMed Web of Science ®Google Scholar
• Basu, P. (2010). Chapter 5 – gasification theory and modeling of gasifiers. In P. Basu (Ed.), Biomass Gasification and Pyrolysis. Academic Press.
   Google Scholar
• Bera, K., Ghosh, B., & Mukhopadhyay, M. (2022). Functional principal of nanotechnology in clinical research. In Nanomaterials in clinical therapeutics: Synthesis and applications (pp. 33–73). Wiley Online library. https://doi.org/10.1002/9781119857747.ch2
   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. Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, IN., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Bodner, C. C., & Hymowitz, T. (2002). Ethnobotany of Pueraria species, Pueraria (pp. 50–86). CRC Press.
   Google Scholar
• Bourret, R. B. (2010). Receiver domain structure and function in response regulator proteins. Current Opinion in Microbiology, 13(2), 142–149. https://doi.org/10.1016/j.mib.2010.01.015
   PubMed Web of Science ®Google Scholar
• Burgui, S., Gil, C., Solano, C., Lasa, I., & Valle, J. (2018). A systematic evaluation of the two-component systems network reveals that ArlRS is a key regulator of catheter colonization by Staphylococcus aureus. Frontiers in Microbiology, 9, 342. https://doi.org/10.3389/fmicb.2018.00342
   PubMed Web of Science ®Google Scholar
• Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G. V., Christie, C. H., Dalenberg, K., Di Costanzo, L., Duarte, J. M., Dutta, S., Feng, Z., Ganesan, S., Goodsell, D. S., Ghosh, S., Green, R. K., Guranović, V., Guzenko, D., Hudson, B. P., … Zhuravleva, M. (2021). RCSB Protein Data Bank: Powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. Nucleic Acids Research, 49(D1), D437–D451. https://doi.org/10.1093/nar/gkaa1038
   PubMed Web of Science ®Google Scholar
• Cao, Y., & Li, L. (2014). Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model. Bioinformatics (Oxford, England), 30(12), 1674–1680. https://doi.org/10.1093/bioinformatics/btu104
   PubMed Web of Science ®Google Scholar
• Capra, E. J., & Laub, M. T. (2012). The evolution of two-component signal transduction systems. Annual Review of Microbiology, 66, 325–347. https://doi.org/10.1146/annurev-micro-092611-150039
   PubMed Web of Science ®Google Scholar
• Cheng, F., Li, W., Zhou, Y., Shen, J., Wu, Z., Liu, G., Lee, P. W., & Tang, Y. (2012). A comprehensive source and free tool for assessment of chemical ADMET properties. Journal of Chemical Information and Modeling, 52(11), 3099–3105. (). https://doi.org/10.1016/j.molstruc.2017.09.108
   PubMed Web of Science ®Google Scholar
• Cui, T., Tang, S., Liu, C., Li, Z., Zhu, Q., You, J., Si, X., Zhang, F., He, P., Liu, Z., Miao, M., Yang, G., Shen, Q., & Jiang, L. (2018). Three new isoflavones from the Pueraria montana var. lobata (Willd.) and their bioactivities. Natural Product Research, 32(23), 2817–2824. https://doi.org/10.1080/14786419.2017.1385008
   PubMed Web of Science ®Google Scholar
• Cushnie, T. P. T., & Lamb, A. J. (2005). Antimicrobial activity of flavonoids. International Journal of Antimicrobial Agents, 26(5), 343–356. https://doi.org/10.1016/j.ijantimicag.2005.09.002
   PubMed Web of Science ®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, 42717. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Dassault Systemes BIOVIA. (2008). Discovery Studio, Accelrys [2.1]; Dassault Systemes BIOVIA: San Diego, CA, USA.
   Google Scholar
• Deb, S., Reeves, A. A., Hopefl, R., & Bejusca, R. (2021). ADME and pharmacokinetic properties of remdesivir: Its drug interaction potential. Pharmaceuticals, 14(7), 655. https://doi.org/10.3390/ph14070655
   Web of Science ®Google Scholar
• DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on. Protein Crystallography, 40, 82–92.
   Google Scholar
• Dennington, R. (2016). GaussView Version 6. Semichem.
   Google Scholar
• Duke, J. A. (1992). Handbook of phytochemical constituents of GRAS herbs and other economic plants. CRC Press. https://doi.org/10.1201/9780203752623
   Google Scholar
• Fett, W. F., & Osman, S. F. (1982). Inhibition of bacteria by the soybean isoflavonoids glyceollin and coumestrol. Phytopathology, 72(7), 755–760. https://doi.org/10.1094/Phyto-72-755
   Web of Science ®Google Scholar
• Filimonov, D. A., Lagunin, A. A., Gloriozova, T. A., Rudik, A. V., Druzhilovskii, D. S., Pogodin, P. V., & Poroikov, V. V. (2014). Prediction of the biological activity spectra of organic compounds using the PASS online web resource. Chemistry of Heterocyclic Compounds, 50(3), 444–457. https://doi.org/10.1007/s10593-014-1496-1
   Web of Science ®Google Scholar
• Fourches, D., Muratov, E., & Tropsha, A. (2015). Curation of chemogenomics data. Nature Chemical Biology, 11(8), 535. https://doi.org/10.1038/nchembio.1881
   PubMed Web of Science ®Google Scholar
• Fournier, B., & Hooper, D. C. (2000). A new two-component regulatory system involved in adhesion, autolysis, and extracellular proteolytic activity of staphylococcus aureus. Journal of Bacteriology, 182(14), 3955–3964. https://doi.org/10.1128/JB.182.14.3955-3964.2000
   PubMed Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Petersson, G. A., Nakatsuji, H., Li, X., Caricato, M., Marenich, A., Bloino, J., Janesko, B. G., Gomperts, R., Mennucci, B., Hratchian, H. P., Ortiz, J. V., … Fox, D. J. (2016). Gaussian 09, Revision A.02. Gaussian.
   Google Scholar
• Gaulton, A., Hersey, A., Nowotka, M., Bento, A. P., Chambers, J., Mendez, D., Mutowo, P., Atkinson, F., Bellis, L. J., Cibrián-Uhalte, E., Davies, M., Dedman, N., Karlsson, A., Magariños, M. P., Overington, J. P., Papadatos, G., Smit, I., & Leach, A. R. (2017). The ChEMBL database in 2017. Nucleic Acids Research, 45(D1), D945–D954. https://doi.org/10.1093/nar/gkw1074
   PubMed Web of Science ®Google Scholar
• Groisman, E. A. (2016). Feedback control of two-component regulatory systems. Annual Review of Microbiology, 70, 103–124. https://doi.org/10.1146/annurev-micro-102215-095331
   PubMed Web of Science ®Google Scholar
• Havsteen, B. H. (2002). The biochemistry and medical significance of the flavonoids. Pharmacology & Therapeutics, 96(2–3), 67–202. https://doi.org/10.1016/S0163-7258(02)00298-X
   PubMed Web of Science ®Google Scholar
• Heinig, M., & Frishman. (2004). ST RIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Research, 32(suppl_2), W500–W502. https://doi.org/10.1093/nar/gkh429
   PubMedGoogle 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%3C1463::AID-JCC4%3E3.0.CO;2-H
   Web of Science ®Google Scholar
• Hoang, T. X., Trovato, A., Seno, F., Banavar, J. R., & Maritan, A. (2004). Geometry and symmetry presculpt the free-energy landscape of proteins. Proceedings of the National Academy of Sciences of the United States of America, 101(21), 7960–7964. https://doi.org/10.1073/pnas.0402525101
   PubMed Web of Science ®Google Scholar
• Hong, H., Landauer, M. R., Foriska, M. A., & Ledney, G. D. (2006). Antibacterial activity of the soy isoflavone genistein. Journal of Basic Microbiology, 46(4), 329–335. https://doi.org/10.1002/jobm.200510073
   PubMed Web of Science ®Google Scholar
• Hubbard, R. E., & Haider, M. K. (2010). Hydrogen bonds in proteins: Role and strength. ELS. https://doi.org/10.1002/9780470015902.a0003011.pub2
   Google Scholar
• Jencks, W. P. (1981). On the attribution and additivity of binding energies. Proceedings of the National Academy of Sciences of the United States of America, 78(7), 4046–4050. https://doi.org/10.1073/pnas.78.7.4046
   PubMed Web of Science ®Google Scholar
• Jensen, F. (2017). Introduction to computational chemistry. John Wiley & Sons.
   Google Scholar
• Kalescky, R., Zhou, H., Liu, J., & Tao, P. (2016). Rigid residue scan simulations systematically reveal residue entropic roles in protein allostery. PLoS Computational Biology, 12(4), e1004893. https://doi.org/10.1371/journal.pcbi.1004893
   PubMed Web of Science ®Google Scholar
• Kinjo, J.-E. I., Takeshita, T., Abe, Y. O. K. O., Terada, N., Yamashita, H., Yamasaki, M., Takeuchi, K., Murakami, K., Tomimatsu, T., & Nohara, T. (1988). Studies on the constituents of Pueraria lobata. IV: Chemical constituents in the flowers and the leaves. Chemical and Pharmaceutical Bulletin, 36(3), 1174–1179. https://doi.org/10.1248/cpb.36.1174
   Web of Science ®Google Scholar
• Koopmans, T. (1934). Über die Zuordnung von Wellenfunktionen und Eigenwerten zu den einzelnen Elektronen eines Atoms. Physica, 1(1–6), 104–113. https://doi.org/10.1016/S0031-8914(34)90011-2
   Google Scholar
• Kopustinskiene, D. M., Bernatonyte, U., Maslii, Y., Herbina, N., & Bernatoniene, J. (2022). Natural herbal non-opioid topical pain relievers—comparison with traditional therapy. Pharmaceutics, 14(12), 2648. https://doi.org/10.3390/pharmaceutics14122648
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A, Open Source Drug Discovery Consortium. (2014). g_mmpbsa–a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Kurkcuoglu, Z., Koukos, P. I., Citro, N., Trellet, M. E., Rodrigues, J. P. G. L. M., Moreira, I. S., Roel-Touris, J., Melquiond, A. S. J., Geng, C., Schaarschmidt, J., Xue, L. C., Vangone, A., & Bonvin, A. M. J. J. (2018). Performance of HADDOCK and a simple contact-based proteinligand binding affinity predictor in the D3R grand challenge 2. Journal of Computer-Aided Molecular Design, 32(1), 175–185. https://doi.org/10.1007/s10822-017-0049-y
   PubMed Web of Science ®Google Scholar
• Kwiecinski, J. M., Jelani, D. A., Fuentes, E. J., & Horswill, A. R. (2022). Therapeutic inhibition of Staphylococcus aureus ArlRS two-component regulatory system blocks virulence. Antimicrobial Agents and Chemotherapy, 66(7), e00187-22. https://doi.org/10.1128/aac.00187-22
   PubMed Web of Science ®Google Scholar
• Lagunin, A., Stepanchikova, A., Filimonov, D., & Poroikov, V. (2000). PASS: Prediction of activity spectra for biologically active substances. Bioinformatics (Oxford, England), 16(8), 747–748. https://doi.org/10.1093/bioinformatics/16.8.747
   PubMed Web of Science ®Google Scholar
• Lalouckova, K., Mala, L., Marsik, P., & Skrivanova, E. (2021). In vitro antibacterial effect of the methanolic extract of the Korean soybean fermented product doenjang against Staphylococcus aureus. Animals, 11(8), 2319. https://doi.org/10.3390/ani11082
   Web of Science ®Google Scholar
• Lau, C. S. (2005). A glycoside flavonoid in kudzu (Pueraria lobata) identification, quantification, and determination of antioxidant activity. Applied Biochemistry and Biotechnology, 121, 783–794. https://doi.org/10.1007/978-1-59259-991-2_66
   PubMedGoogle Scholar
• Lee, A. S., de Lencastre, H., Garau, J., Kluytmans, J., Malhotra-Kumar, S., Peschel, A., & Harbarth, S. (2018). Methicillin-resistant Staphylococcus aureus. Nature Reviews. Disease Primers, 4, 18033. https://doi.org/10.1038/nrdp.2018.33
   PubMed Web of Science ®Google Scholar
• Lemkul, J. (2019). From proteins to perturbed Hamiltonians: A suite of tutorials for the GROMACS-2018 molecular simulation package [Article V1. 0]. Living Journal of Computational Molecular Science, 1(1), 1–53. https://doi.org/10.33011/livecoms.1.1.5068
   Google Scholar
• Liu, Y., Grimm, M., Dai, W.-T., Hou, M.-C., Xiao, Z.-X., & Cao, Y. (2020). CB-Dock: A web server for cavity detection-guided protein–ligand blind docking. Acta Pharmacologica Sinica, 41(1), 138–144. https://doi.org/10.1038/s41401-019-0228-6
   PubMed Web of Science ®Google Scholar
• 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
   Web of Science ®Google Scholar
• Lu, J., Xie, Y., Tan, Y., Qu, J., Matsuda, H., Yoshikawa, M., & Yuan, D. (2013). Simultaneous Determination of isoflavones, saponins and flavones in Flos Puerariae by ultra performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Chemical & Pharmaceutical Bulletin, 61(9), 941–951. https://doi.org/10.1248/cpb.c13-00271
   PubMed Web of Science ®Google Scholar
• Luong, T. T., & Lee, C. Y. (2006). The arl locus positively regulates Staphylococcus aureus type 5 capsule via an mgrA–dependent pathway. Microbiology (Reading, England), 152(Pt 10), 3123–3131. https://doi.org/10.1099/mic.0.29177-0
   PubMedGoogle Scholar
• Malachowa, N., & DeLeo, F. R. (2010). Mobile genetic elements of Staphylococcus aureus. Cellular and Molecular Life Sciences: CMLS, 67(18), 3057–3071. https://doi.org/10.1007/s00018-010-0389-4
   PubMed Web of Science ®Google Scholar
• Martis, E. A. F., & Coutinho, E. C. (2019). Free energy-based methods to understand drug resistance mutations. In C. G. Mohan (Ed.), Structural bioinformatics: Applications in preclinical drug discovery process. Springer International Publishing.
   Google Scholar
• Memmi, G., Nair, D. R., & Cheung, A. (2012). Role of ArlRS in autolysis in methicillin-sensitive and methicillin-resistant Staphylococcus aureus strains. Journal of Bacteriology, 194(4), 759–767. https://doi.org/10.1128/JB.06261-11
   PubMed Web of Science ®Google Scholar
• Morris, G. M., Huey, R., & Olson, A. J. (2008). Using AutoDock for ligand-receptor docking. Current Protocols in Bioinformatics, 24(1), 8.14.11–8.14.40. https://doi.org/10.1002/0471250953.bi0814s24
   Google Scholar
• Novotny, J. (1991). Protein antigenicity: A thermodynamic approach. Molecular Immunology, 28(3), 201–207. https://doi.org/10.1016/0161-5890(91)90062-o
   PubMed Web of Science ®Google Scholar
• Ong, Z. X., Kannan, B., & Becker, D. L. (2023). Exploiting transposons in the study of Staphylococcus aureus pathogenesis and virulence. Critical Reviews in Microbiology, 49(3), 297–317. https://doi.org/10.1080/1040841X.2022.2052794
   PubMed Web of Science ®Google Scholar
• Ouyang, Z., Zheng, F., Chew, J. Y., Pei, Y., Zhou, J., Wen, K., Han, M., Lemieux, M. J., Hwang, P. M., & Wen, Y. (2019). Deciphering the activation and recognition mechanisms of Staphylococcus aureus response regulator ArlR. Nucleic Acids Research, 47(21), 11418–11429. https://doi.org/10.1093/nar/gkz891
   PubMed Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
   Web of Science ®Google Scholar
• Pendleton, J. N., Gorman, S. P., & Gilmore, B. F. (2013). Clinical relevance of the ESKAPE pathogens. Expert Review of anti-Infective Therapy, 11(3), 297–308. https://doi.org/10.1586/eri.13.12
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF chimera—a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Pires, D. E. V., 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. https://doi.org/10.1021/acs.jmedchem.5b00104
   PubMed Web of Science ®Google Scholar
• Pogodin, P. V., Lagunin, A. A., Filimonov, D. A., & Poroikov, V. V. (2015). PASS targets: Ligand-based multi-target computational system based on a public data and naïve Bayes approach. SAR and QSAR in Environmental Research, 26(10), 783–793. https://doi.org/10.1080/1062936X.2015.1078407
   PubMed Web of Science ®Google Scholar
• Pogodin, P. V., Lagunin, A. A., Rudik, A. V., Filimonov, D. A., Druzhilovskiy, D. S., Nicklaus, M. C., & Poroikov, V. V. (2018). How to achieve better results using PASS-based virtual screening: Case study for kinase inhibitors. Frontiers in Chemistry, 6, 133. https://doi.org/10.3389/fchem.2018.00133
   PubMed Web of Science ®Google Scholar
• Sarker, S. D., & Nahar, L. (2020). Medicinal natural products: A disease-focused approach. Academic Press.
   Google Scholar
• Schüttelkopf, A. W., & Van Aalten, D. M. (2004). PRODRG: A tool for high throughput crystallography of protein–ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Stock, A. M., Robinson, V. L., & Goudreau, P. N. (2000). Two-component signal transduction. Annual Review of Biochemistry, 69, 183–215. https://doi.org/10.1146/annurev.biochem.69.1.183
   PubMed Web of Science ®Google Scholar
• Sukhwal, A., & Sowdhamini, R. (2013). Oligomerisation status and evolutionary conservation of interfaces of protein structural domain superfamilies. Molecular BioSystems, 9(7), 1652–1661. https://doi.org/10.1039/C3MB25484D
   PubMedGoogle Scholar
• Tang, J., Wang, Y., Zhou, H., Ye, Y., Talukdar, M., Fu, Z., Liu, Z., Li, J., Neculai, D., Gao, J., & Huang, H. (2020). Sunitinib inhibits RNase L by destabilizing its active dimer conformation. The Biochemical Journal, 477(17), 3387–3399. https://doi.org/10.1042/BCJ20200260
   PubMed Web of Science ®Google Scholar
• Taylor, T. A., & Unakal, C. G. (2022). Staphylococcus aureus. In StatPearls [Internet]. StatPearls Publishing.
   Google Scholar
• Tong, S. Y. C., Davis, J. S., Eichenberger, E., Holland, T. L., & Fowler, V. G. (2015). Staphylococcus aureus infections: Epidemiology, pathophysiology, clinical manifestations, and management. Clinical Microbiology Reviews, 28(3), 603–661. https://doi.org/10.1128/CMR.00134-14
   PubMed Web of Science ®Google Scholar
• Tripoli, E., Guardia, M. L., Giammanco, S., Majo, D. D., & Giammanco, M. (2007). Citrus flavonoids: Molecular structure, biological activity and nutritional properties: A review. Food Chemistry, 104(2), 466–479. https://doi.org/10.1016/j.foodchem.2006.11.054
   Web of Science ®Google Scholar
• Tungmunnithum, D., Intharuksa, A., & Sasaki, Y. (2020). A promising view of kudzu plant, Pueraria montana var. lobata (Willd.) Sanjappa & Pradeep: Flavonoid phytochemical compounds, taxonomic data, traditional uses and potential biological activities for future cosmetic application. Cosmetics, 7(1), 12. https://doi.org/10.3390/cosmetics7010012
   Google Scholar
• Vangone, A., & Bonvin, A. M. J. J. (2015). Contact-based prediction of binding affinity in protein-protein complexes. eLife, 4, e07454. https://doi.org/10.7554/eLife.07454
   PubMed Web of Science ®Google Scholar
• Vangone, A., Schaarschmidt, J., Koukos, P., Geng, C., Citro, N., Trellet, M. E., Xue, L. C., & Bonvin, A. M. J. J. (2019). Large-scale prediction of binding affinity in protein-small ligand complexes: The PRODIGY-LIG web server. Bioinformatics (Oxford, England), 35(9), 1585–1587. https://doi.org/10.1093/bioinformatics/bty816
   PubMed Web of Science ®Google Scholar
• Vaou, N., Stavropoulou, E., Voidarou, C., Tsigalou, C., & Bezirtzoglou, E. (2021). Towards advances in medicinal plant antimicrobial activity: A review study on challenges and future perspectives. Microorganisms, 9(10), 2041. https://doi.org/10.3390/microorganisms9102041
   PubMed Web of Science ®Google Scholar
• Veber, D. F., Johnson, S. R., Cheng, H.-Y., Smith, B. R., Ward, K. W., & Kopple, K. D. (2002). Molecular properties that influence the oral bioavailability of drug candidates. Journal of Medicinal Chemistry, 45(12), 2615–2623., https://doi.org/10.1021/jm020017n
   PubMed Web of Science ®Google Scholar
• Verma, A. K., Ahmed, S. F., Hossain, M., Bhojiya, A. A., Upadhyay, S. K., Srivastava, A. K., Singh, N., Harina, H., Rahaman, M. M., & Bahadur, N. M. (2022). Unlocking SGK1 inhibitor potential of bis-[1-N, 7-N, pyrazolo tetraethoxyphthalimido {-4-(3, 5-Dimethyl-4-(spiro-3-methylpyazolo)-1, 7-dihydro-1H-dipyrazolo [3, 4-b; 4', 3'-e] pyridin-8-yl)}] p-disubstituted phenyl compounds: A computational study. Journal of Biomolecular Structure and Dynamics, 40(24), 13412–13431. https://doi.org/10.1080/07391102.2021.1988711
   PubMed Web of Science ®Google Scholar
• Walker, J. N., Crosby, H. A., Spaulding, A. R., Salgado-Pabón, W., Malone, C. L., Rosenthal, C. B., Schlievert, P. M., Boyd, J. M., & Horswill, A. R. (2013). The Staphylococcus aureus ArlRS two-component system is a novel regulator of agglutination and pathogenesis. PLoS Pathogens, 9(12), e1003819. https://doi.org/10.1371/journal.ppat.1003819
   PubMed Web of Science ®Google Scholar
• Wen, Y., Ouyang, Z., Devreese, B., He, W., Shao, Y., Lu, W., & Zheng, F. (2017). Crystal structure of master biofilm regulator CsgD regulatory domain reveals an atypical receiver domain. Protein Science: A Publication of the Protein Society, 26(10), 2073–2082. https://onlinelibrary.wiley.com/journal/1469896x https://doi.org/10.1002/pro.3245
   PubMed Web of Science ®Google Scholar
• Wen, Y., Ouyang, Z., Yu, Y., Zhou, X., Pei, Y., Devreese, B., Higgins, P. G., & Zheng, F. (2017). Mechanistic insight into how multidrug resistant Acinetobacter baumannii response regulator AdeR recognizes an intercistronic region. Nucleic Acids Research, 45(16), 9773–9787. https://doi.org/10.1093/nar/gkx624
   PubMed Web of Science ®Google Scholar
• Wertheim, H. F. L., Melles, D. C., Vos, M. C., van Leeuwen, W., van Belkum, A., Verbrugh, H. A., & Nouwen, J. L. (2005). The role of nasal carriage in Staphylococcus aureus infections. The Lancet Infectious Diseases, 5(12), 751–762. https://doi.org/10.1016/S1473-3099(05)70295-4
   PubMed Web of Science ®Google Scholar
• Wu, Z. (2010). Flora of China Vol. 10 (Fabaceae). Science Press and Missouri Botanical Garden Press.
   Google Scholar
• Xie, M., & Schowen, R. L. (1999). Secondary structure and protein deamidation. Journal of Pharmaceutical Sciences, 88(1), 8–13. https://doi.org/10.1021/js9802493
   PubMed Web of Science ®Google Scholar
• Xue, L. C., Rodrigues, J. P., Kastritis, P. L., Bonvin, A. M., & Vangone, A. (2016). PRODIGY: A web-server for predicting the binding affinity in protein-protein complexes. Bioinformatics, 32(23), 3676–3678. https://doi.org/10.1093/bioinformatics/btw514
   PubMed Web of Science ®Google Scholar
• Yildiz, S. C. (2022). Staphylococcus aureus and methicillin resistant Staphylococcus aureus (MRSA) carriage and infections. In Staphylococcal infections-recent advances and perspectives. IntechOpen. https://doi.org/10.5772/intechopen.107138
   Google Scholar
• Zídek, L., Novotny, M. V., & Stone, M. J. (1999). Increased protein backbone conformational entropy upon hydrophobic ligand binding. Nature Structural Biology, 6(12), 1118–1121. https://doi.org/10.1038/70057
   PubMedGoogle Scholar
• Zhang, G., Liu, J., Gao, M., Kong, W., Zhao, Q., Shi, L., & Wang, Q. (2020). Tracing the edible and medicinal plant Pueraria montana and Its products in the marketplace yields subspecies level distinction using DNA barcoding and DNA metabarcoding. Frontiers in Pharmacology, 11, 336. https://doi.org/10.3389/fphar.2020.00336
   PubMed Web of Science ®Google Scholar
• Zhou, Y.-X., Zhang, H., & Peng, C. (2014). Puerarin: A review of pharmacological effects. Phytotherapy Research: PTR, 28(7), 961–975. https://doi.org/10.1002/ptr.5083
   PubMed Web of Science ®Google Scholar