References
- Agrawal, S., & Goel, R. K. (2016). Curcumin and its protective and therapeutic uses. National Journal of Physiology, Pharmacy and Pharmacology, 6(1), 1–8.
- Ahlquist, P., Noueiry, A. O., Lee, W. M., Kushner, D. B., & Dye, B. T. (2003). Host factors in positive-strand RNA virus genome replication. Journal of Virology, 77(15), 8181–8186. https://doi.org/10.1128/jvi.77.15.8181-8186.2003
- Ahmed, S., & Shohael, A. M. (2019). In silico studies of four anthraquinones of Sennaalata l. As potential antifungal compounds. Pharmacology Online, 2, 259–268.
- Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C., & Garry, R. F. (2020). Correspondence: The proximal origin of SARS-CoV-2. Nature Medicine, 26 (4), 450–452. https://doi.org/10.1038/s41591-020-0820-9
- Andres, A., Donovan, S. M., & Kuhlenschmidt, M. S. (2009). Soy isoflavones and virus infections. The Journal of Nutritional Biochemistry, 20(8), 563–569. https://doi.org/10.1016/j.jnutbio.2009.04.004
- Badam, L., Joshi, S. P., & Bedekar, S. S. (1999). In vitro' antiviral activity of neem (Azadirachtaindica. A. Juss) leaf extract against group B coxsackieviruses. The Journal of Communicable Diseases, 31 (2), 79–90.
- Batlle, D., Wysocki, J., & Satchell, K. (2020). Soluble angiotensin-converting enzyme 2: A potential approach for coronavirus infection therapy. Clinical Science, 134(5), 543–545. https://doi.org/10.1042/CS20200163
- Benvenuto, D., Giovanetti, M., Ciccozzi, A., Spoto, S., Angeletti, S., & Ciccozzi, M. (2020). The 2019-new coronavirus epidemic: Evidence for virus evolution. Journal of Medical Virology, 92 (4), 455–459. https://doi.org/10.1002/jmv.25688
- Boopathi, S., Poma, A. B., & Kolandaivel, P. (2020). Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1758788
- Carugo, O., & Pongor, S. (2001). A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Science, 10(7), 1470–1473. https://doi.org/10.1110/ps.690101
- Chatterjee, S. (2020). Understanding the nature of variations in structural sequences coding for coronavirus spike, envelope, membrane and nucleocapsid proteins of SARS-CoV-2. Envelope, membrane and nucleocapsid proteins of SARS-CoV-2. https://ssrn.com/abstract=3562504
- Chen, L., & Hao, G. (2020). The role of angiotensin converting enzyme 2 in coronaviruses/influenza viruses and cardiovascular disease. Cardiovasc Research, 116(12), 1932-1936. https://doi.org/10.1093/cvr/cvaa093.
- Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., Yang, Q., Wang, J., Liu, Y., Wei, Y., Xia, J., Yu, T., Zhang, X., & Zhang, L. (2020). Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study. The Lancet, 395 (10223), 507–513.
- Cheng, F., Li, W., Zhou, Y., Shen, J., Wu, Z., Liu, G., Lee, P. W., & Tang, Y. (2012). admetSAR: 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/10.1021/ci300367a
- Chu, H., Chan, J. F. W., Wang, Y., Yuen, T. T. T., Chai, Y., Hou, Y., Shuai, H., Yang, D., Hu, B., Huang, X., Zhang, X., Cai, J. P., Zhou, J., Yuan, S., Kok, K. H., Wang, K. K., Chan, I. H. E., Yee, Zhang, A. J., … Yuen, K. Y. (2020). Comparative replication and immune activation profiles of SARS-CoV-2 and SARS-CoV in human lungs: An ex vivo study with implications for the pathogenesis of COVID-19. Clinical Infectious Diseases, 71(6), 1400–1409. https://doi.org/10.1093/cid/ciaa410
- Conti, P., Ronconi, G., Caraffa, A. L., Gallenga, C. E., Ross, R., Frydas, I., & Kritas, S. K. (2020). Induction of pro-inflammatory cytokines (IL-1 and IL-6) and lung inflammation by Coronavirus-19 (COVI-19 or SARS-CoV-2): Anti-inflammatory strategies. Journal of Biological Regulators and Homeostatic Agents, 34, 1.
- Cyranoski, D. (2020). Mystery deepens over animal source of coronavirus. Nature, 579 (7797), 18–19. https://doi.org/10.1038/d41586-020-00548-w
- David, L., Olivier, S., Hervé, G., Maria, A. M., & Bruno, O. V. (2008). FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects. BMC Bioinformatics, 9, 396.
- Drwal, M. N., Banerjee, P., Dunkel, M., Wettig, M. R., & Preissner, R. (2014). ProTox: A web server for the in silico prediction of rodent oral toxicity. Nucleic Acids Research, 42(Web Server issue), W53–8. https://doi.org/10.1093/nar/gku401
- Elfiky, A. A. (2020). Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study. Life Sciences, 253, 117592 https://doi.org/10.1016/j.lfs.2020.117592
- Elfiky, A. A. (2020). SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: An in silico perspective. Journal of Biomolecular Structure and Dynamics, 1–9.doi: 10.1080/07391102.2020.1761882
- Fehr, A. R., & Perlman, S. (2015). Coronaviruses: An overview of their replication and pathogenesis. Coronaviruses, 1282, 1–23. https://doi.org/10.1007/978-1-4939-2438-7_1
- Garozzo, A., Timpanaro, R., Stivala, A., Bisignano, G., & Castro, A. (2011). Activity of Melaleuca alternifolia (tea tree) oil on Influenza virus A/PR/8: study on the mechanism of action. Antiviral Research, 89(1), 83–88. https://doi.org/10.1016/j.antiviral.2010.11.010
- Gupta, M. K., Vemula, S., Donde, R., Gouda, G., Behera, L., & Vadde, R. (2020). In silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1751300
- Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series. 41, 95–98.
- Hasan, A., Paray, B. A., Hussain, A., Qadir, F. A., Attar, F., Aziz, F. M., Sharifi, M., Derakhshankhah, H., Rasti, B., & Mehrabi, M. (2020). A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin. Journal of Biomolecular Structure and Dynamics, 22, 1–9.
- Huang, F., Li, Y., Leung, E. L.-H., Liu, X., Liu, K., Wang, Q., Lan, Y., Li, X., Yu, H., Cui, L., Luo, H., & Luo, L. (2020). A review of therapeutic agents and Chinese herbal medicines against SARS-COV-2 (COVID-19). Pharmacological Research, 158, 104929. https://doi.org/10.1016/j.phrs.2020.104929
- Jendele, L., Krivak, R., Skoda, P., Novotny, M., & Hoksza, D. (2019). PrankWeb: A web server for ligand binding site prediction and visualization. Nucleic Acids Research, 47(W1), W345–W349. https://doi.org/10.1093/nar/gkz424
- Jones, D. T. (1999). Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology, 292(2), 195–202. https://doi.org/10.1006/jmbi.1999.3091
- Kaul, T. N., Middleton, E., & Ogra, P. L. (1985). Antiviral effect of flavonoids on human viruses. Journal of Medical Virology, 15(1), 71–79. https://doi.org/10.1002/jmv.1890150110
- Kirchdoerfer, R. N., & Ward, A. B. (2019). Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors. Nature Communications, 10(1), 2342. https://doi.org/10.1038/s41467-019-10280-3
- Krieger, E., Joo, K., Lee, J., Lee, J., Raman, S., Thompson, J., Tyka, M., Baker, D., & Karplus, K. (2009). Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins: Structure, Function, and Bioinformatics, 77 (S9), 114–122.
- Kufareva, I., & Abagyan, R. (2012). Methods of protein structure comparison. Methods in Molecular Biology, 857, 231–257. https://doi.org/10.1007/978-1-61779-588-6_10
- Lai, M. M., & Cavanagh, D. (1997). The molecular biology of coronaviruses. Advances in Virus Research, 48, 1–100.
- Lagorce, D., Sperandio, O., Baell, J. B., Miteva, M. A., & Villoutreix, B. O. (2015). FAF-Drugs3: A web server for compound property calculation and chemical library design. Nucleic Acids Research, 43(W1), W200–W207.
- Lam, A. M., Espiritu, C., Bansal, S., Steuer, H. M. M., Niu, C., Zennou, V., Keilman, M., Zhu, Y., Lan, S., Otto, M. J., & Furman, P. A. (2012). Genotype and subtype profiling of PSI-7977 as a nucleotide inhibitor of hepatitis C virus. Antimicrobial Agents and Chemotherapy, 56(6), 3359–3368. https://doi.org/10.1128/AAC.00054-12
- 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
- Lukas, J., Radoslav, K., Petr, S., Marian, N., & David, H. (2019). Prank Web: A web server for ligand binding site prediction and visualization. Nucleic Acids Research, 47(W1), W345–W349.
- Mair, C. E., Liu, R., Atanasov, A. G., Schmidtke, M., Dirsch, V. M., & Rollinger, J. M. (2016). Antiviral and anti-proliferative in vitro activities of piperamides from black pepper. Planta Medica, 81(S 01), S1–S381.
- Miller, W. A., & Koev, G. (2000). Synthesis of subgenomic RNAs by positive-strand RNA viruses. Virology, 273(1), 1–8. https://doi.org/10.1006/viro.2000.0421
- Moghadamtousi, S. Z., Kadir, H. A., Hassandarvish, P., Tajik, H., Abubakar, S., & Zandi, K. (2014). A Review on antibacterial, antiviral, and antifungal activity of curcumin. BioMed Research International, 2014, 186864. https://doi.org/10.1155/2014/186864
- 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 & Dynamics. https://doi.org/10.1080/07391102.2020.1752802
- Pandit, M., & Latha, N. (2020). In silico studies reveal potential antiviral activity of phytochemicals from medicinal plants for the treatment of COVID-19 infection. Structural Biology Bioinformatics. https://doi.org/10.21203/rs.3.rs-22687/v1
- Perlman, S. (2020). Another decade, another coronavirus. The New England Journal of Medicine, 382(8), 760–762. https://doi.org/10.1056/NEJMe2001126
- Tatar, G., & Turhan, K. (2020). Investigation of N terminal domain of SARS CoV 2 nucleocapsid protein with antiviral compounds based on molecular modeling approach. ScienceOpen. https://doi.org/10.14293/S2199-1006.1.SOR-.PPPT99I.v1
- Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res, 22(22), 4673–4680. https://doi.org/10.1093/nar/22.22.4673
- 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
- Ubani, A., Agwom, F., Shehu, N. Y., Luka, P., Umera, A., Umar, U., Omale, S. N. E., & Aguiyi, J. C. (2020). Molecular docking analysis of some phytochemicals on two SARS-COV-2 targets. https://doi.org/10.1101/2020.03.31.017657.
- Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell, 181(2), 281–292.e6. https://doi.org/10.1016/j.cell.2020.02.058
- Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303. https://doi.org/10.1093/nar/gky427
- Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M., & Barton, G. J. (2009). Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics (Oxford, England)), 25(9), 1189–1191. https://doi.org/10.1093/bioinformatics/btp033
- Woo, P. C., Huang, Y., Lau, S. K., & Yuen, K. Y. (2010). Coronavirus genomics and bioinformatics analysis. Viruses, 2(8), 1804–1820. https://doi.org/10.3390/v2081803
- Yuzhen, Y., & Godzik, A. (2004). FATCAT: A web server for flexible structure comparison and structure similarity searching. Nucleic Acids Research, 32(Web Server issue), W582–W585. https://doi.org/10.1093/nar/gkh430
- Zakaryan, H., Arabyan, E., Oo, A., & Zandi, K. (2017). Flavonoids: Promising natural compounds against viral infections. Archives of Virology, 162(9), 2539–2551. https://doi.org/10.1007/s00705-017-3417-y
- Zhou, P., Yang, X. L., Wang, X. G., Hu, B., Zhang, L., Zhang, W., Si, H., Zhu, Y., Li, B., Huang, C. L., Chen, H. D., Chen, J., Luo, Y., Guo, H., Jiang, R. D., Liu, M. Q., Chen, Y., Shen, X. R., Wang, … Shi, Z. L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270–273.