Analysis and prediction pathways of natural products and their cytotoxicity against HeLa cell line protein using docking, molecular dynamics and ADMET

References

• Abotaleb, M., Samuel, S., Varghese, E., Varghese, S., Kubatka, P., Liskova, A., & Büsselberg, D. (2018). Flavonoids in cancer and apoptosis. Cancers (Basel), 11(1), 28. https://doi.org/10.3390/cancers11010028
   PubMed Web of Science ®Google Scholar
• Ah, A., & Yi, A. (2019). In silico pharmacokinetics and molecular docking studies of lead compounds derived from Diospyros mespiliformis. PharmaTutor, 7(3), 31–37. https://doi.org/10.29161/PT.v7.i3.2019.31
   Google Scholar
• Al-Jumaili MHA, Al hdeethi MKY. Study of Selected Flavonoid Structures and Their Potential Activity as Breast Anticancer Agents. Cancer Informatics. January 2021. 10.1177/11769351211055160
   Google Scholar
• Amin, M. L. (2013). P-glycoprotein inhibition for optimal drug delivery. Drug Target Insights, 7, 27–34. 10.4137/2FDTI.S12519.
   PubMedGoogle Scholar
• Arct, J., & Pytkowska, K. (2008). Flavonoids as components of biologically active cosmeceuticals. Clinics in Dermatology, 26(4), 347–357. https://doi.org/10.1016/j.clindermatol.2008.01.004
   PubMed Web of Science ®Google Scholar
• Ashwini, S., Varkey, S. P., & Shantaram, M. (2017). In silico docking of polyphenolic compounds against caspase 3-HeLa cell line protein. International Journal of Drug Development and Research, 9, 28–32.
   Google Scholar
• Bickerton, G. R., Paolini, G. V., Besnard, J., Muresan, S., & Hopkins, A. L. (2012). Quantifying the chemical beauty of drugs. Nature Chemistry, 4(2), 90–98. https://doi.org/10.1038/nchem.1243
   PubMed Web of Science ®Google Scholar
• Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126(1), 014101. https://doi.org/10.1063/1.2408420
   PubMed Web of Science ®Google Scholar
• Chtita, S., Belhassan, A., Bakhouch, M., Taourati, A. I., Aouidate, A., Belaidi, S., Moutaabbid, M., Belaaouad, S., Bouachrine, M., & Lakhlifi, T. (2021). QSAR study of unsymmetrical aromatic disulfides as potent avian SARS-CoV main protease inhibitors using quantum chemical descriptors and statistical methods. Chemometrics and Intelligent Laboratory Systems: An International Journal Sponsored by the Chemometrics Society, 210, 104266. https://doi.org/10.1016/j.chemolab.2021.104266
   PubMed Web of Science ®Google Scholar
• Danley, D. E., Baima, E. T., Mansour, M., Fennell, K. F., Chrunyk, B. A., Mueller, J. P., Liu, S., & Qiu, X. (2015). Discovery and structural characterization of an allosteric inhibitor of bacterial cis-prenyltransferase. Protein Science: A Publication of the Protein Society, 24(1), 20–26. https://doi.org/10.2210/pdb4Q9M/pdb
   PubMed Web of Science ®Google Scholar
• Elokely, K. M., & Doerksen, R. J. (2013). Docking challenge: Protein sampling and molecular docking performance . Journal of Chemical Information and Modeling, 53(8), 1934–1945. https://doi.org/10.1021/ci400040d
   PubMed Web of Science ®Google Scholar
• Fouedjou, R. T., Chtita, S., Bakhouch, M., Belaidi, S., Ouassaf, M., Djoumbissie, L. A., Tapondjou, L. A., & Abul Qais, F. (2021). Cameroonian medicinal plants as potential candidates of SARS-CoV-2 inhibitors. Journal of Biomolecular Structure and Dynamics, 1–15. https://doi.org/10.1080/07391102.2021.1914170
   Google Scholar
• Greenwood, J. R., Calkins, D., Sullivan, A. P., & Shelley, J. C. (2010). Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution. Journal of Computer-Aided Molecular Design, 24(6–7), 591–604. https://doi.org/10.1007/s10822-010-9349-1
   PubMed Web of Science ®Google Scholar
• Hayashi, T., Sawa, K., Kawasaki, M., Arisawa, M., Shimizu, M., & Morita, N. (1988). Inhibition of cow's milk xanthine oxidase by flavonoids. Journal of Natural Products, 51(2), 345–348. https://doi.org/10.1021/np50056a030
   PubMed Web of Science ®Google Scholar
• Herrera, E., Jiménez, R., Aruoma, O. I., Hercberg, S., Sánchez‐García, I., & Fraga, C. (2009). Aspects of antioxidants foods and supplements in health and disease. Nutrition Reviews, 67(1), S140–S144. https://doi.org/10.1111/j.1753-4887.2009.00177.x
   PubMedGoogle Scholar
• Hollman, P. H., & Katan, M. B. (1999). Dietary flavonoids: Intake, health effects and bioavailability. Food and Chemical Toxicology: An International Journal Published for the British Industrial Biological Research Association, 37(9–10), 937–942. https://doi.org/10.1016/S0278-6915(99)00079-4
   PubMed Web of Science ®Google Scholar
• Hwang, J., Youn, K., Ji, Y., Lee, S., Lim, G., Lee, J., Ho, C.-T., Leem, S.-H., & Jun, M. (2020). Biological and computational studies for dual cholinesterases inhibitory effect of zerumbone. Nutrients, 12(5), 1215. https://doi.org/10.3390/nu12051215
   PubMed Web of Science ®Google Scholar
• Kang, N. J., Shin, S. H., Lee, H. J., & Lee, K. W. (2011). Polyphenols as small molecular inhibitors of signaling cascades in carcinogenesis. Pharmacology & Therapeutics, 130(3), 310–324. https://doi.org/10.1016/j.pharmthera.2011.02.004
   PubMed Web of Science ®Google Scholar
• Kelly, E. H., Anthony, R. T., & Dennis, J. B. (2002). Flavonoid antioxidants: chemistry, metabolism and structure-activity relationships. Journal of Nutritional Biochemistry, 13(10), 572–584.
   PubMed Web of Science ®Google Scholar
• Khoo, B. Y., Chua, S. L., & Balaram, P. (2010). Apoptotic effects of chrysin in human cancer cell lines. International Journal of Molecular Sciences, 11(5), 2188–2199. https://doi.org/10.3390/ijms11052188
   PubMed Web of Science ®Google Scholar
• Kidd, P. S., Llugany, M., Poschenrieder, C., Gunse, B., & Barcelo, J. (2001). The role of root exudates in aluminium resistance and silicon-induced amelioration of aluminium toxicity in three varieties of maize (Zea mays L.). Journal of Experimental Botany, 52, 1339–1352.
   PubMed Web of Science ®Google Scholar
• Krych, J., & Gebicka, L. (2013). Catalase is inhibited by flavonoids. International Journal of Biological Macromolecules, 58, 148–153. https://doi.org/10.1016/j.ijbiomac.2013.03.070
   PubMed Web of Science ®Google Scholar
• Kuhn, B. M., Geisler, M., Bigler, L., & Ringli, C. (2011). Flavonols accumulate asymmetrically and affect auxin transport in Arabidopsis. Plant Physiology, 156(2), 585–595. https://doi.org/10.1104/pp.111.175976
   PubMed Web of Science ®Google Scholar
• Kumar, S., Mishra, A., & Pandey, A. K. (2013). Antioxidant mediatedprotective effect of Parthenium hysterophorus against oxidativedamage using in vitro models. BMC Complementary andAlternative Medicine, 13, 120.
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A. (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
• Kurniawan, F., Miura, Y., Kartasasmita, R. E., Yoshioka, N., Mutalib, A., & Tjahjono, D. H. (2018). In silico study, synthesis, and cytotoxic activities of porphyrin derivatives. Pharmaceuticals, 11(1), 8. https://doi.org/10.3390/ph11010008
   Web of Science ®Google Scholar
• Lewis, D. R., Ramirez, M. V., Miller, N. D., Vallabhaneni, P., Ray, W. K., Helm, R. F., Winkel, B. S., & Muday, G. K. (2011). Auxin and ethylene induce flavonol accumulation through distinct transcriptional networks. Plant Physiology, 156(1), 144–164. https://doi.org/10.1104/pp.111.172502
   PubMed Web of Science ®Google Scholar
• Lutz, M., & Zureta, A. (2009). Relación entre la alimentación y la salud del consumidor en aspectos nutricionales y saludables de los productos de panificación. Universidad de Velparaíso, 17.
   Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Małkiewicz, M. A., Szarmach, A., Sabisz, A., Cubała, W. J., Szurowska, E., & Winklewski, P. J. (2019). Blood-brain barrier permeability and physical exercise. Journal of Neuroinflammation, 16(1), 15. https://doi.org/10.1186/s12974-019-1403-x.
   PubMedGoogle Scholar
• Ouassaf, M., Belaidi, S., Al Mogren, M. M., Chtita, S., Khan, S., & Htar, T. (2021). Combined docking methods and molecular dynamics to identify effective antiviral 2, 5-diaminobenzophenonederivatives against SARS-CoV-2. Journal of King Saud University. Science, 33(2), 101352. https://doi.org/10.1016/j.jksus.2021.101352
   PubMed Web of Science ®Google Scholar
• Park, K., & Cho, A. E. (2017). Using reverse docking to identify potential targets for ginsenosides. Journal of Ginseng Research.
   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
• Procházková, D., Bousová, I., & Wilhelmová, N. (2011). Antioxidant and prooxidant properties of flavonoids. Fitoterapia, 82(4), 513–523. https://doi.org/10.1016/j.fitote.2011.01.018
   PubMed Web of Science ®Google Scholar
• Rakers, C., Schwerdtfeger, S.-M., Mortier, J., Duwe, S., Wolff, T., Wolber, G., & Melzig, M. F. (2014). Inhibitory potency of flavonoid derivatives on influenza virus neuraminidase. Bioorganic & Medicinal Chemistry Letters, 24(17), 4312–4317. https://doi.org/10.1016/j.bmcl.2014.07.010
   PubMed Web of Science ®Google Scholar
• Rath, B., Abul Qais, F., Patro, R., Mohapatra, S., & Sharma, T. (2021). Design, synthesis and molecular modeling studies of novel mesalamine linked coumarin for treatment of inflammatory bowel disease. Bioorganic & Medicinal Chemistry Letters, 41, 128029. https://doi.org/10.1016/j.bmcl.2021.128029
   PubMed Web of Science ®Google Scholar
• Rolo-Naranjo, A., Codorniu-Hernandez, E., & Ferro, N. (2010). Quantum chemical associations ligand-residue: Their role to predict flavonoid binding sites in proteins. Journal of Chemical Information and Modeling, 50(5), 924–933. https://doi.org/10.1021/ci900358z
   PubMed Web of Science ®Google Scholar
• Schrödinger LLC. (2011). Suite 2011: Glide, version 5.7. Schrödinger LLC.
   Google Scholar
• Siddiqui, S., Ameen, F., Jahan, I., Nayeem, S. M., & Tabish, M. (2019). A comprehensive spectroscopic and computational investigation on the binding of the anti-asthmatic drug triamcinolone with serum albumin. New Journal of Chemistry, 43(10), 4137–4151. https://doi.org/10.1039/C8NJ05486J
   Web of Science ®Google Scholar
• Siddiqui, S., Ameen, F., Kausar, T., Nayeem, S. M., Ur Rehman, S., & Tabish, M. (2021). Biophysical insight into the binding mechanism of doxofylline to bovine serum albumin: An in vitro and in silico approach. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 249, 119296. https://doi.org/10.1016/j.saa.2020.119296
   PubMed Web of Science ®Google Scholar
• Sousa Da Silva, A. W., & Vranken, W. F. (2012). ACPYPE - AnteChamber PYthon Parser interfacE. BMC Research Notes, 5, 367. https://doi.org/10.1186/1756-0500-5-367.
   PubMedGoogle Scholar
• Watanabe, R., Esaki, T., Kawashima, H., Natsume-Kitatani, Y., Nagao, C., Ohashi, R., & Mizuguchi, K. (2018). Predicting fraction unbound in human plasma from chemical structure: Improved accuracy in the low value ranges. Molecular Pharmaceutics, 15(11), 5302–5311. https://doi.org/10.1021/acs.molpharmaceut.8b00785
   PubMed Web of Science ®Google Scholar
• Williams, R., Spencer, J., & Rice-Evans, C. (2004). Flavonoids: Antioxidants or signalling molecules? Free radic. Free Radical Biology & Medicine, 36(7), 838–849. https://doi.org/10.1016/j.freeradbiomed.2004.01.001
   PubMed Web of Science ®Google Scholar
• Zhang, X., Huang, H., Zhao, X., Lv, Q., Sun, C., Li, X., & Chen, K. (2015). Effects of flavonoids-rich Chinese bayberry (Myrica rubra Sieb. et Zucc.) pulp extracts on glucose consumption in human HepG2 cells. Journal of Functional Foods, 14, 144–153. https://doi.org/10.1016/j.jff.2015.01.030
   Web of Science ®Google Scholar