Inhibition of multiple SARS-CoV-2 proteins by an antiviral biomolecule, seselin from Aegle marmelos deciphered using molecular docking analysis

References

• Arul, V., Kumaraguru, S., & Dhananjayan, R. (1999). Effects of ageline and lupeol, the two cardioactive principles isolated from the leaves of Aegle marmelos Corr. Journal of Pharmacy and Pharmacology, 51, 252–252.
   Google Scholar
• Badam, L., Bedekar, S. S., Sonawane, K. B., & Joshi, S. P. (2002). In vitro antiviral activity of bael (Aegle marmelos Corr) upon human coxsackieviruses B1-B6. The Journal of Communicable Diseases, 34(2), 88–99.
   PubMedGoogle Scholar
• Boobis, A., Gundert-Remy, U., Kremers, P., Macheras, P., & Pelkonen, O. (2002). In silico prediction of ADME and pharmacokinetics: Report of an expert meeting organised by COST B15. European Journal of Pharmaceutical Sciences: Official Journal of the European Federation for Pharmaceutical Sciences, 17(4–5), 183–193. https://doi.org/10.1016/S0928-0987(02)00185-9
   PubMed Web of Science ®Google Scholar
• Bugrim, A., Nikolskaya, T., & Nikolsky, Y. (2004). Early prediction of drug metabolism and toxicity: Systems biology approach and modeling. Drug Discovery Today, 9(3), 127–135. https://doi.org/10.1016/S1359-6446(03)02971-4
   PubMed Web of Science ®Google Scholar
• Chadwick, D. J., & Marsh, J. (Eds.). (2008). Ethnobotany and the search for new drugs. Ciba Foundation Symposium (Vol. 185). John Wiley & Sons.
   Google Scholar
• Chou, K. C., Wei, D. Q., Du, Q. S., Sirois, S., & Zhong, W. Z. (2006). Progress in computational approach to drug development against SARS. Current Medicinal Chemistry, 13(27), 3263–3270. https://doi.org/10.2174/092986706778773077
   PubMed Web of Science ®Google Scholar
• Cronin, M. T. (2001). Prediction of drug toxicity. Farmaco (Societa Chimica Italiana: 1989), 56(1–2), 149–151. https://doi.org/10.1016/S0014-827X(01)01018-7
   PubMedGoogle 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
• Dallakyan, S. (2008). PyRx-python prescription v. 0.8, The Scripps Research Institute, 2010.
   Google Scholar
• Elmezayen, A. D., Al-Obaidi, A., Şahin, A. T., & Yelekçi, K. (2020). Drug repurposing for coronavirus (COVID-19): In silico screening of known drugs against coronavirus 3CL hydrolase and protease enzymes. Journal of Biomolecular Structure and Dynamics, 39(8), 2980–2992. https://doi.org/10.1080/07391102.2020.1758791
   PubMed Web of Science ®Google Scholar
• Enmozhi, S. K., Raja, K., Sebastine, I., & Joseph, J. (2020). Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: An in silico approach. Journal of Biomolecular Structure and Dynamics, 39(9), 3092–3098. https://doi.org/10.1080/07391102.2020.1760136
   PubMed Web of Science ®Google Scholar
• Farnsworth, N. R. (1994). Ethnopharmacology and drug development. In Ciba foundation symposium 185‐Ethnobotany and the search for new drugs: Ethnobotany and the Search for New Drugs: Ciba Foundation Symposium. John Wiley & Sons.
   Google Scholar
• Farooq, S. (2005). 555 medicinal plants. Field and laboratory manual (identification with its phytochemical and in vitro studies data. International Book Distributors.
   Google Scholar
• Feng, P., Zhao, L., Guo, F., Zhang, B., Fang, L., Zhan, G., Xu, X., Fang, Q., Liang, Z., & Li, B. (2018). The enhancement of cardiotoxicity that results from inhibiton of CYP 3A4 activity and hERG channel by berberine in combination with statins. Chemico-Biological Interactions, 293, 115–123. https://doi.org/10.1016/j.cbi.2018.07.022
   PubMed Web of Science ®Google Scholar
• Gfeller, D., Grosdidier, A., Wirth, M., Daina, A., Michielin, O., & Zoete, V. (2014). SwissTargetPrediction: A web server for target prediction of bioactive small molecules. Nucleic Acids Research, 42(1), 32–38.
   Google Scholar
• Goren, R., & Tomer, E. (1971). Effects of seselin and coumarin on growth, indoleacetic acid Oxidase, and Peroxidase, with Special Reference to Cucumber (Cucumis sativa L.) Radicles. Plant Physiology, 47(2), 312–316. https://doi.org/10.1104/pp.47.2.312
   PubMed Web of Science ®Google Scholar
• Govindachari, T. R., & Premila, M. S. (1983). Some alkaloids from Aegle marmelos. Phytochemistry, 22(3), 755–757. https://doi.org/10.1016/S0031-9422(00)86977-0
   Web of Science ®Google Scholar
• Gunatilaka, A. A., Kingston, D. G., Wijeratne, E. M., Bandara, B. M., Hofmann, G. A., & Johnson, R. K. (1994). Biological activity of some coumarins from Sri Lankan Rutaceae. Journal of Natural Products, 57(4), 518–520. https://doi.org/10.1021/np50106a013
   PubMed Web of Science ®Google Scholar
• Hadži, D., Kidrič, J., Koller, J., & Mavri, J. (1990). The role of hydrogen bonding in drug-receptor interactions. Journal of Molecular Structure, 237, 139–150. https://doi.org/10.1016/0022-2860(90)80136-8
   Web of Science ®Google Scholar
• Hall, D. C., Jr., & Ji, H. F. (2020). A search for medications to treat COVID-19 via in silico molecular docking models of the SARS-CoV-2 spike glycoprotein and 3CL protease. Travel Medicine and Infectious Disease, 35, 101646. https://doi.org/10.1016/j.tmaid.2020.101646
   PubMed Web of Science ®Google Scholar
• Hofmann, H., & Pöhlmann, S. (2004). Cellular entry of the SARS coronavirus. Trends in Microbiology, 12(10), 466–472. https://doi.org/10.1016/j.tim.2004.08.008
   PubMed Web of Science ®Google Scholar
• Huang, L., Kashiwada, Y., Cosentino, L. M., Fan, S., & Lee, K. H. (1994). 3′,4′-Di-o-(−)-camphanoyl-(+) -ciskhellactone and related compounds: A new class of potent anti-HIV agents. Bioorganic and Medicinal Chemistry Letters, 4(4), 593–598. https://doi.org/10.1016/S0960-894X(01)80161-X
   Web of Science ®Google Scholar
• Huentelman, M. J., Zubcevic, J., Hernandez Prada, J. A., Xiao, X., Dimitrov, D. S., Raizada, M. K., & Ostrov, D. A. (2004). Structure-based discovery of a novel angiotensin-converting enzyme 2 inhibitor. Hypertension, 44(6), 903–906. https://doi.org/10.1161/01.HYP.0000146120.29648.36
   PubMed Web of Science ®Google Scholar
• Jimenez-Garcia, S. N., Vazquez-Cruz, M. A., Guevara-Gonzalez, R. G., Torres-Pacheco, I., Cruz-Hernandez, A., & Feregrino-Perez, A. A. (2013). Current approaches for enhanced expression of secondary metabolites as bioactive compounds in plants for agronomic and human health purposes–a review. Polish Journal of Food and Nutrition Sciences, 63(2), 67–78. https://doi.org/10.2478/v10222-012-0072-6
   Web of Science ®Google Scholar
• Jogalekar, M. P., Veerabathini, A., & Gangadaran, P. (2020). Novel 2019 coronavirus: Genome structure, clinical trials, and outstanding questions. Experimental Biology and Medicine, 245, 964–969. https://doi.org/10.1177/1535370220920540
   Web of Science ®Google Scholar
• Kubinyi, H. (2001). Hydrogen bonding: The last mystery in drug design. In B. Testa, H. van de Waterbeemd, G. Folkers, R. Guy (Eds.), Pharmacokinetic optimization in drug research: Biological, physicochemical, and computational strategies (pp. 513–524). Verlag Helvetica Chimica Acta.
   Google Scholar
• Kumari, R., & Kumar, R. (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
• Kuo, C. J., Liu, H. G., Lo, Y. K., Seong, C. M., Lee, K. I., Jung, Y. S., & Liang, P. H. (2009). Individual and common inhibitors of coronavirus and picornavirus main proteases. FEBS Letters, 583(3), 549–555. https://doi.org/10.1016/j.febslet.2008.12.059
   PubMed Web of Science ®Google Scholar
• Lima, V., Silva, C. B., Mafezoli, J., Bezerra, M. M., Moraes, M. O., Mourao, G. S., Silva, J. N., & Oliveira, M. C. (2006). Antinociceptive activity of the pyranocoumarin seselin in mice. Fitoterapia, 77(7–8), 574–578. https://doi.org/10.1016/j.fitote.2006.09.005
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A. (2004). Lead- and drug-like compounds: The rule-of-five revolution. Drug Discovery Today. Technologies, 1(4), 337–341. https://doi.org/10.1016/j.ddtec.2004.11.007
   PubMedGoogle Scholar
• Liu, X., Shi, D., Zhou, S., Liu, H., Liu, H., & Yao, X. (2018). Molecular dynamics simulations and novel drug discovery. Expert Opinion on Drug Discovery, 13(1), 23–37. https://doi.org/10.1080/17460441.2018.1403419
   PubMed Web of Science ®Google Scholar
• Liu, X., Zhang, B., J. Z., Yang, H., & Rao, Z. (2020). The crystal structure of COVID-19 main protease in complex with an inhibitor N3. RCSB PDB.
   Google Scholar
• Manandhar, M. D., Shoeb, A., Kapil, R. S., & Popli, S. P. (1978). New alkaloids from Aegle marmelos. Phytochemistry, 17(10), 1814–1815. https://doi.org/10.1016/S0031-9422(00)88714-2
   Web of Science ®Google Scholar
• McConkey, B. J., Sobolev, V., & Edelman, M. (2002). The performance of current methods in ligand-protein docking. Current Science, 83(7), 845–855.
   Web of Science ®Google Scholar
• Melnick, J. L. (1984). Enteroviruses. In A. S. Evans (Ed.), Viral infections of humans (pp. 187–251). Springer.
   Google Scholar
• Meng, X. Y., Zhang, H. X., Mezei, M., & Cui, M. (2011). Molecular docking: A powerful approach for structure-based drug discovery. Current Computer-Aided Drug Design, 7(2), 146–157. https://doi.org/10.2174/157340911795677602
   PubMed Web of Science ®Google Scholar
• Mukandiwa, L., Ahmed, A., Eloff, J. N., & Naidoo, V. (2013). Isolation of seselin from Clausena anisata (Rutaceae) leaves and its effects on the feeding and development of Lucilia cuprina larvae may explain its use in ethnoveterinary medicine. Journal of Ethnopharmacology, 150(3), 886–891. https://doi.org/10.1016/j.jep.2013.09.037
   PubMed Web of Science ®Google Scholar
• Mukandiwa, L., Eloff, J. N., & Naidoo, V. (2015). Larvicidal activity of leaf extracts and seselin from Clausena anisata (Rutaceae) against Aedes aegypti. South African Journal of Botany, 100, 169–173. https://doi.org/10.1016/j.sajb.2015.05.016
   Web of Science ®Google Scholar
• Muralidharan, N., Sakthivel, R., Velmurugan, D., & Gromiha, M. M. (2020). Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19. Journal of Biomolecular Structure and Dynamics, 39(7), 2673–2678. https://doi.org/10.1080/07391102.2020.1752802
   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), 33. https://doi.org/10.1186/1758-2946-3-33
   PubMed Web of Science ®Google Scholar
• Ortega, N. C. C., Gonzalez, C. P., Sanchez, M. A. Z., Ramirez, A. B. H., & Gutierrez, S. P. (2007). Antifungal activity of seselin in protecting stored maize from Aspergillus flavus. Asian Journal of Plant Sciences, 6, 712–714.
   Google Scholar
• Parveen, M., Ahmad, F., Malla, A. M., Khan, M. S., Rehman, S. U., Tabish, M., Silva, M. R., & Silva, P. S. (2016). Structure elucidation and DNA binding specificity of natural compounds from Cassia siamea leaves: A biophysical approach. Journal of Photochemistry and Photobiology. B, Biology, 159, 218–288. https://doi.org/10.1016/j.jphotobiol.2016.03.060
   PubMed Web of Science ®Google Scholar
• Pires, D. E., 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
• Rane, J. S., Chatterjee, A., Kumar, A., & Ray, S. (2020). Targeting SARS-CoV-2 spike protein of COVID-19 with naturally occurring phytochemicals: An in-silico study for drug development. Journal of Biomolecular Structure and Dynamics, 1–11. https://doi.org/10.26434/chemrxiv.12094203.v1
   Google Scholar
• Sampangi-Ramaiah, M. H., Vishwakarma, R., & Shaanker, R. U. (2020). Molecular docking analysis of selected natural products from plants for inhibition of SARS-CoV-2 main protease. Current Science, 118(7), 1087–1092.
   Web of Science ®Google Scholar
• Scavone, C., Brusco, S., Bertini, M., Sportiello, L., Rafaniello, C., Zoccoli, A., Berrino, L., Racagni, G., Rossi, F., & Capuano, A. (2020). Current pharmacological treatments for COVID‐19: What’s next? British Journal of Pharmacology, 177(21), 4813–4824. https://doi.org/10.1111/bph.15072
   PubMed Web of Science ®Google Scholar
• Singh, G., Jayadev Magani, S. K., Sharma, R., Bhat, B., Shrivastava, A., Chinthakindi, M., & Singh, A. (2019). Structural, functional and molecular dynamics analysis of cathepsin B gene SNPs associated with tropical calcific pancreatitis, a rare disease of tropics. PeerJ, 7, e7425 https://doi.org/10.7717/peerj.7425
   PubMed Web of Science ®Google Scholar
• Somu, C., Karuppiah, H., & Sundaram, J. (2019). Antiviral activity of seselin from Aegle marmelos against nuclear polyhedrosis virus infection in the larvae of silkworm, Bombyx mori. Journal of Ethnopharmacology, 245, 112155 https://doi.org/10.1016/j.jep.2019.112155
   PubMed Web of Science ®Google Scholar
• Surti, M., Patel, M., Adnan, M., Moin, A., Ashraf, S. A., Siddiqui, A. J., Snoussi, M., Deshpande, S., & Reddy, M. N. (2020). Ilimaquinone (marine sponge metabolite) as a novel inhibitor of SARS-CoV-2 key target proteins in comparison with suggested COVID-19 drugs: Designing, docking and molecular dynamics simulation study. RSC Advances, 10(62), 37707–37720. https://doi.org/10.1039/D0RA06379G
   PubMed Web of Science ®Google Scholar
• Tanaka, H., Ahn, J. W., Katayama, M., Wada, K., Marumo, S., & Osaka, Y. (1985). Isolation of two ovicidal substances against two-spotted spider mite. Agricultural and Biological Chemistry, 49(7), 2189–2190. https://doi.org/10.1271/bbb1961.49.2189
   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
• Ul Qamar, M. T., Alqahtani, S. M., Alamri, M. A., & Chen, L. L. (2020). Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. Journal of Pharmaceutical Analysis, 10(4), 313–319. https://doi.org/10.1016/j.jpha.2020.03.009
   PubMed Web of Science ®Google Scholar
• Wan, Y., Shang, J., Graham, R., Baric, R. S., & Li, F. (2020). Receptor recognition by the novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS coronavirus. Journal of Virology, 94(7), e00127–20. https://doi.org/10.1128/JVI.00127-20
   PubMed Web of Science ®Google Scholar
• Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C. L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science (New York, N.Y.), 367(6483), 1260–1263. https://doi.org/10.1126/science.abb2507
   PubMed Web of Science ®Google Scholar
• Wu, C., Liu, Y., Yang, Y., Zhang, P., Zhong, W., Wang, Y., Wang, Q., Xu, Y., Li, M., Li, X., Zheng, M., & Zheng, M. (2020). Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica B, 10(5), 766–788. https://doi.org/10.1016/j.apsb.2020.02.008
   PubMed Web of Science ®Google Scholar
• Yang, H., Sun, L., Li, W., Liu, G., & Tang, Y. (2018). In silico prediction of chemical toxicity for drug design using machine learning methods and structural alerts. Frontiers in Chemistry, 6, 30.
   PubMed Web of Science ®Google Scholar
• Yunta, M. J. (2017). It is important to compute intramolecular hydrogen bonding in drug design. Am J Model Optim, 5, 24–57.
   Google Scholar
• Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science (New York, N.Y.), 368(6489), 409–412. https://doi.org/10.1126/science.abb3405
   PubMed Web of Science ®Google Scholar
• Zhang, L., Sun, X., & Hilgenfeld, R. (2020). Crystal structure of the free enzyme of the SARS-CoV-2 (2019-nCoV) main protease. RCSB PDB.
   Google Scholar
• Zhang, Y., Zheng, N., Hao, P., Cao, Y., & Zhong, Y. (2005). A molecular docking model of SARS-CoV S1 protein in complex with its receptor, human ACE2. Computational Biology and Chemistry, 29(3), 254–257. https://doi.org/10.1016/j.compbiolchem.2005.04.008
   PubMed Web of Science ®Google Scholar
• Zhu, Y., & Sun, F. (2020). Structure of post fusion core of 2019-nCoV S2 subunit. RCSB PDB.
   Google Scholar