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/https://doi.org/10.1016/j.softx.2015.06.001
- Anandakrishnan, R., Aguilar, B., & Onufriev, A. V. (2012). H++ 3.0: Automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Research, 40(Web Server issue), W537–W541. https://doi.org/https://doi.org/10.1093/nar/gks375
- Arooj, M., Sakkiah, S., Cao, G. Ping., & Lee, K. W. (2013). An innovative strategy for dual inhibitor design and its application in dual inhibition of human thymidylate synthase and dihydrofolate reductase enzymes. PLos One, 8(4), e60470. https://doi.org/https://doi.org/10.1371/journal.pone.0060470
- Báez-Santos, Y. M., Barraza, S. J., Wilson, M. W., Agius, M. P., Mielech, A. M., Davis, N. M., Baker, S. C., Larsen, S. D., & Mesecar, A. D. (2014). X-ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-like Proteases. Journal of Medicinal Chemistry, 57(6), 2393–2412. https://doi.org/https://doi.org/10.1021/jm401712t
- Báez-Santos, Y. M., St. John, S. E., & Mesecar, A. D. (2015). The SARS-coronavirus papain-like protease: Structure, function and inhibition by designed antiviral compounds. Antiviral Research, 115, 21–38. https://doi.org/https://doi.org/10.1016/j.antiviral.2014.12.015
- Bienert, S., Waterhouse, A., de Beer, T. A. P., Tauriello, G., Studer, G., Bordoli, L., & Schwede, T. (2017). The Swiss-model repository-new features and functionality. Nucleic Acids Research, 45(D1), D313–D319. https://doi.org/https://doi.org/10.1093/nar/gkw1132
- Blanchard, J. E., Elowe, N. H., Huitema, C., Fortin, P. D., Cechetto, J. D., Eltis, L. D., & Brown, E. D. (2004). High-throughput screening identifies inhibitors of the SARS coronavirus main proteinase. Chemistry & Biology, 11(10), 1445–1453. https://doi.org/https://doi.org/10.1016/j.chembiol.2004.08.011
- Cao, B., Wang, Y., Wen, D., Liu, W. Wang, Jingli, Fan, G., Ruan, L., Song, B., Cai, Y., Wei, M., Li, X., Xia, J., Chen, N., Xiang, J., Yu, T., Bai, T., Xie, X., Zhang, L., … Wang, C. (2020). A trial of lopinavir–ritonavir in adults hospitalized with severe covid-19. New England Journal of Medicine, 382(19), 1787–1799.. https://doi.org/https://doi.org/10.1056/NEJMoa2001282.
- Chen, L., Chen, S., Gui, C., Shen, J., Shen, X., & Jiang, H. (2006). Discovering severe acute respiratory syndrome coronavirus 3CL protease inhibitors: virtual screening, surface plasmon resonance, and fluorescence resonance energy transfer assays. Journal of Biomolecular Screening, 11(8), 915–921. https://doi.org/https://doi.org/10.1177/1087057106293295
- Chen, L.-R., Wang, Y.-C., Lin, Y. W., Chou, S.-Y., Chen, S.-F., Liu, L. T., Wu, Y.-T., Kuo, C.-J., Chen, T. S.-S., & Juang, S.-H. (2005). Synthesis and evaluation of isatin derivatives as effective SARS coronavirus 3CL protease inhibitors. Bioorganic & Medicinal Chemistry Letters, 15(12), 3058–3062. https://doi.org/https://doi.org/10.1016/j.bmcl.2005.04.027
- Cho, J. K., Curtis-Long, M. J., Lee, K. H., Kim, D. W., Ryu, H. W., Yuk, H. J., & Park, K. H. (2013). Geranylated flavonoids displaying SARS-CoV papain-like protease inhibition from the fruits of Paulownia tomentosa. Bioorganic & Medicinal Chemistry, 21(11), 3051–3057. https://doi.org/https://doi.org/10.1016/j.bmc.2013.03.027
- Choy, K.-T., Wong, Y.-L., Kaewpreedee, P., Sia, S. F., Chen, D., Hui, K. P. Y., Chu, D. K. W., Chan, M. C. W., Cheung, P.-H., Huang, X., Peiris, M., & Yen, H.-L. (2020). Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro. Antiviral Research, Antiviral Res, 178, 104786. https://doi.org/https://doi.org/10.1016/j.antiviral.2020.104786 32251767
- Cinatl, J., Morgenstern, B., Bauer, G., Chandra, P., Rabenau, H., & Doerr, H. W. (2003). Glycyrrhizin, an active component of liquorice roots, and replication of SARS-associated coronavirus. The Lancet, 361(9374), 2045–2046. https://doi.org/https://doi.org/10.1016/S0140-6736(03)13615-X
- 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/https://doi.org/10.1038/srep42717
- Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. Methods in Molecular Biology, 1263, 243–250. https://doi.org/https://doi.org/10.1007/978-1-4939-2269-7_19
- Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., & Kollman, P. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry, 24(16), 1999–2012. https://doi.org/https://doi.org/10.1002/jcc.10349
- Fehr, A. R., & Perlman, S. (2015). Coronaviruses: An overview of their replication and pathogenesis. Methods in Molecular Biology (Clifton, N.J.), 1282, 1–23. https://doi.org/https://doi.org/10.1007/978-1-4939-2438-7_1
- Fiore, C., Eisenhut, M., Krausse, R., Ragazzi, E., Pellati, D., Armanini, D., & Bielenberg, J. (2008). Antiviral effects of Glycyrrhiza species. Phytotherapy Research, 22(2), 141–148. https://doi.org/https://doi.org/10.1002/ptr.2295
- Gautret, P., Lagier, J.-C., Parola, P., Hoang, V. T., Meddeb, L., Mailhe, M., Doudier, B., Courjon, J., Giordanengo, V., Vieira, V. E., Dupont, H. T., Honoré, S., Colson, P., Chabrière, E., La Scola, B., Rolain, J.-M., Brouqui, P., & Raoult, D. (2020). Hydroxychloroquine and azithromycin as a treatment of COVID-19: Results of an open-label non-randomized clinical trial. International Journal of Antimicrobial Agents, 105949, 105949. https://doi.org/https://doi.org/10.1016/j.ijantimicag.2020.105949
- Hassan, M. Z., Osman, H., Ali, M. A., & Ahsan, M. J. (2016). Therapeutic potential of coumarins as antiviral agents. European Journal of Medicinal Chemistry, 123, 236–255. https://doi.org/https://doi.org/10.1016/j.ejmech.2016.07.056
- Hoever, G., Baltina, L., Michaelis, M., Kondratenko, R., Baltina, L., Tolstikov, G. A., Doerr, H. W., & Cinatl, J. (2005). Antiviral activity of glycyrrhizic acid derivatives against SARS-coronavirus . Journal of Medicinal Chemistry, 48(4), 1256–1259. https://doi.org/https://doi.org/10.1021/jm0493008
- Huang, C., Wei, P., Fan, K., Liu, Y., & Lai, L. (2004). 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general base mechanism. Biochemistry, 43(15), 4568–4574. https://doi.org/https://doi.org/10.1021/bi036022q
- Ikeda, S., Yazawa, M., & Nishimura, C. (1987). Anti-viral activity and inhibition of topoisomerase by ofloxacin, a new quinolone derivative. Antiviral Research, 8(3), 103–113. https://doi.org/https://doi.org/10.1016/0166-3542(87)90064-7
- Jana, S., & Singh, S. K. (2019). Identification of selective MMP-9 inhibitors through multiple e-pharmacophore, ligand-based pharmacophore, molecular docking, and density functional theory approaches. Journal of Biomolecular Structure & Dynamics, 37(4), 944–965. https://doi.org/https://doi.org/10.1080/07391102.2018.1444510
- Kim, D. W., Seo, K. H., Curtis-Long, M. J., Oh, K. Y., Oh, J.-W., Cho, J. K., Lee, K. H., & Park, K. H. (2014). Phenolic phytochemical displaying SARS-CoV papain-like protease inhibition from the seeds of Psoralea corylifolia. Journal of Enzyme Inhibition and Medicinal Chemistry, 29(1), 59–63. https://doi.org/https://doi.org/10.3109/14756366.2012.753591
- Koes, D. R., & Camacho, C. J. (2012). ZINCPharmer: Pharmacophore search of the ZINC database. Nucleic Acids Research, 40(Web Server issue), W409–W414. https://doi.org/https://doi.org/10.1093/nar/gks378
- 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/https://doi.org/10.1021/ci500020m
- 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/https://doi.org/10.1016/j.febslet.2008.12.059
- 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), 5068. https://doi.org/https://doi.org/10.33011/livecoms.1.1.5068
- Liu, J., Zhu, Y., He, Y., Zhu, H., Gao, Y., Li, Z., Zhu, J., Sun, X., Fang, F., Wen, H., & Li, W. (2020). Combined pharmacophore modeling, 3D-QSAR and docking studies to identify novel HDAC inhibitors using drug repurposing. Journal of Biomolecular Structure & Dynamics, 38(2), 533–547. https://doi.org/https://doi.org/10.1080/07391102.2019.1590241
- Liu, Y.-C., Huang, V., Chao, T.-C., Hsiao, C.-D., Lin, A., Chang, M.-F., & Chow, L.-P. (2005). Screening of drugs by FRET analysis identifies inhibitors of SARS-CoV 3CL protease. Biochemical and Biophysical Research Communications, 333(1), 194–199. https://doi.org/https://doi.org/10.1016/j.bbrc.2005.05.095
- Mackenzie, J. S., Drury, P., Ellis, A., Grein, T., Leitmeyer, K. C., Mardel, S., Merianos, A., Olowokure, B., Roth, C., Slattery, R., Thomson, G., Werker, D., & Ryan, M. (2004). The Who response to SARS and preparations for the future. In Learning from SARS: Preparing for the next disease outbreak. Workshop summary. National Academies Press.
- Manvar, D., Mishra, M., Kumar, S., & Pandey, V. N. (2012). Identification and evaluation of anti hepatitis C virus phytochemicals from Eclipta alba. Journal of Ethnopharmacology, 144(3), 545–554. https://doi.org/https://doi.org/10.1016/j.jep.2012.09.036
- Meagher, K. L., & Carlson, H. A. (2004). Incorporating protein flexibility in structure-based drug discovery: Using HIV-1 protease as a test case. Journal of the American Chemical Society, 126(41), 13276–13281. https://doi.org/https://doi.org/10.1021/ja0469378
- Ménard, R., Khouri, H. E., Plouffe, C., Dupras, R., Ripoll, D., Vernet, T., Tessier, D. C., Lalberté, F., Thomas, D. Y., & Storer, A. C. (1990). A protein engineering study of the role of aspartate 158 in the catalytic mechanism of papain. Biochemistry, 29(28), 6706–6713. https://doi.org/https://doi.org/10.1021/bi00480a021
- Mitra, K., Chadha, A., & Doble, M. (2019). Pharmacophore based approach to screen and evaluate novel Mycobacterium cell division inhibitors targeting FtsZ - A modelling and experimental study. European Journal of Pharmaceutical Sciences: Official Journal of the European Federation for Pharmaceutical Sciences, 135, 103–112. https://doi.org/https://doi.org/10.1016/j.ejps.2019.04.023
- Muramatsu, T., Takemoto, C., Kim, Y.-T., Wang, H., Nishii, W., Terada, T., Shirouzu, M., & Yokoyama, S. (2016). SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity. Proceedings of the National Academy of Sciences of the United States of America, 113(46), 12997–13002. https://doi.org/https://doi.org/10.1073/pnas.1601327113
- Naresh, K. N., Sreekumar, A., & Rajan, S. S. (2015). Structural insights into the interaction between molluscan hemocyanins and phenolic substrates: An in silico study using docking and molecular dynamics. Journal of Molecular Graphics & Modelling, 61, 272–280. https://doi.org/https://doi.org/10.1016/j.jmgm.2015.07.006
- Park, J.-Y., Jeong, H. J., Kim, J. H., Kim, Y. M., Park, S.-J., Kim, D., Park, K. H., Lee, W. S., & Ryu, Y. B. (2012a). Diarylheptanoids from Alnus japonica inhibit papain-like protease of severe acute respiratory syndrome coronavirus. Biological & Pharmaceutical Bulletin, 35(11), 2036–2042. https://doi.org/https://doi.org/10.1248/bpb.b12-00623
- Park, J.-Y., Kim, J. H., Kim, Y. M., Jeong, H. J., Kim, D. W., Park, K. H., Kwon, H.-J., Park, S.-J., Lee, W. S., & Ryu, Y. B. (2012b). Tanshinones as selective and slow-binding inhibitors for SARS-CoV cysteine proteases. Bioorganic & Medicinal Chemistry, 20(19), 5928–5935. https://doi.org/https://doi.org/10.1016/j.bmc.2012.07.038
- Park, J.-Y., Ko, J.-A., Kim, D. W., Kim, Y. M., Kwon, H.-J., Jeong, H. J., Kim, C. Y., Park, K. H., Lee, W. S., & Ryu, Y. B. (2016). Chalcones isolated from Angelica keiskei inhibit cysteine proteases of SARS-CoV. Journal of Enzyme Inhibition and Medicinal Chemistry, 31(1), 23–30. https://doi.org/https://doi.org/10.3109/14756366.2014.1003215
- Park, J.-Y., Yuk, H. J., Ryu, H. W., Lim, S. H., Kim, K. S., Park, K. H., Ryu, Y. B., & Lee, W. S. (2017). Evaluation of polyphenols from Broussonetia papyrifera as coronavirus protease inhibitors. Journal of Enzyme Inhibition and Medicinal Chemistry, 32(1), 504–512. https://doi.org/https://doi.org/10.1080/14756366.2016.1265519
- 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/https://doi.org/10.1002/jcc.20084
- Pillaiyar, T., Manickam, M., Namasivayam, V., Hayashi, Y., & Jung, S.-H. (2016). An overview of severe acute respiratory syndrome-coronavirus (SARS-CoV) 3CL protease inhibitors: Peptidomimetics and small molecule chemotherapy. Journal of Medicinal Chemistry, 59(14), 6595–6628. https://doi.org/https://doi.org/10.1021/acs.jmedchem.5b01461
- Provisional Death Counts for Coronavirus Disease (COVID-19) [WWW Document]. (2020). Retrieved December 4, 2020, from https://www.cdc.gov/nchs/nvss/vsrr/covid19/index.htm.
- Ramajayam, R., Tan, K.-P., Liu, H.-G., & Liang, P.-H. (2010a). Synthesis and evaluation of pyrazolone compounds as SARS-coronavirus 3C-like protease inhibitors. Bioorganic & Medicinal Chemistry, 18(22), 7849–7854. https://doi.org/https://doi.org/10.1016/j.bmc.2010.09.050
- Ramajayam, R., Tan, K.-P., Liu, H.-G., & Liang, P.-H. (2010b). Synthesis, docking studies, and evaluation of pyrimidines as inhibitors of SARS-CoV 3CL protease. Bioorganic & Medicinal Chemistry Letters, 20(12), 3569–3572. https://doi.org/https://doi.org/10.1016/j.bmcl.2010.04.118
- Schneidman-Duhovny, D., Dror, O., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2008). PharmaGist: A webserver for ligand-based pharmacophore detection. Nucleic Acids Research, 36(Web Server issue), W223–W228. https://doi.org/https://doi.org/10.1093/nar/gkn187
- Sekiguchi, J., & Shuman, S. (1997). Novobiocin inhibits vaccinia virus replication by blocking virus assembly. Virology, 235(1), 129–137. https://doi.org/https://doi.org/10.1006/viro.1997.8684
- Sheahan, T. P., Sims, A. C., Leist, S. R., Schäfer, A., Won, J., Brown, A. J., Montgomery, S. A., Hogg, A., Babusis, D., Clarke, M. O., Spahn, J. E., Bauer, L., Sellers, S., Porter, D., Feng, J. Y., Cihlar, T., Jordan, R., Denison, M. R., & Baric, R. S. (2020). Comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against MERS-CoV. Nature Communications, 11, 1–14. https://doi.org/https://doi.org/10.1038/s41467-019-13940-6
- Song, Y. H., Kim, D. W., Curtis-Long, M. J., Yuk, H. J., Wang, Y., Zhuang, N., Lee, K. H., Jeon, K. S., & Park, K. H. (2014). Papain-like protease (PLpro) inhibitory effects of cinnamic amides from Tribulus terrestris fruits. Biological & Pharmaceutical Bulletin, 37(6), 1021–1028. https://doi.org/https://doi.org/10.1248/bpb.b14-00026
- Sousa da Silva, A. W., & Vranken, W. F. (2012). ACPYPE - AnteChamber PYthon Parser interfacE. BMC Research Notes, 5, 367. https://doi.org/https://doi.org/10.1186/1756-0500-5-367
- Thangapandian, S., John, S., Sakkiah, S., & Lee, K. W. (2011). Molecular docking and pharmacophore filtering in the discovery of dual-inhibitors for human leukotriene A4 hydrolase and leukotriene C4 synthase. Journal of Chemical Information and Modeling, 51(1), 33–44. https://doi.org/https://doi.org/10.1021/ci1002813
- Torbeev, V. Y., Raghuraman, H., Mandal, K., Senapati, S., Perozo, E., & Kent, S. B. H. (2009). Dynamics of “flap” structures in three HIV-1 protease/inhibitor complexes probed by total chemical synthesis and pulse-EPR spectroscopy. Journal of the American Chemical Society, 131(3), 884–885. https://doi.org/https://doi.org/10.1021/ja806526z
- Vincent, J.-L., & Taccone, F. S. (2020). Understanding pathways to death in patients with COVID-19. The Lancet. Respiratory Medicine, 8(5), 430–432. https://doi.org/https://doi.org/10.1016/S2213-2600(20)30165-X32272081
- Wahedi, H. M., Ahmad, S., & Abbasi, S. W. (2020). Stilbene-based natural compounds as promising drug candidates against COVID-19. Journal of Biomolecular Structure & Dynamics, 1–10. https://doi.org/https://doi.org/10.1080/07391102.2020.176274332345140
- 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/https://doi.org/10.1016/j.cell.2020.02.058
- Wang, J. (2020). Fast identification of possible drug treatment of coronavirus disease-19 (COVID-19) through computational drug repurposing study. Journal of Chemical Information and Modeling, 60(6), 3277–3286. https://doi.org/https://doi.org/10.1021/acs.jcim.0c00179
- Wang, L., Yang, R., Yuan, B., Liu, Y., & Liu, C. (2015). The antiviral and antimicrobial activities of licorice, a widely-used Chinese herb. Acta Pharmaceutica Sinica B, 5(4), 310–315. https://doi.org/https://doi.org/10.1016/j.apsb.2015.05.005
- WHO. Coronavirus [WWW Document]. (n.d.). Retrieved April 8, 2020, from https://www.who.int/emergencies/diseases/novel-coronavirus-2019
- Woo, P. C. Y., Huang, Y., Lau, S. K. P., & Yuen, K.-Y. (2010). Coronavirus genomics and bioinformatics analysis. Viruses, 2(8), 1804–1820. https://doi.org/https://doi.org/10.3390/v2081803
- Xu, Y., Liu, X., Wang, Y., Zhou, N., Peng, J., Gong, L., Ren, J., Luo, C., Luo, X., Jiang, H., Chen, K., & Zheng, M. (2015). Combinatorial pharmacophore modeling of multidrug and toxin extrusion transporter 1 inhibitors: A theoretical perspective for understanding multiple inhibitory mechanisms. Scientific Reports, 5, 13684–13613. https://doi.org/https://doi.org/10.1038/srep13684
- Yamamoto, N., Matsuyama, S., Hoshino, T., & Yamamoto, N. (2020). Nelfinavir inhibits replication of severe acute respiratory syndrome coronavirus 2 in vitro. BioRxiv. https://doi.org/https://doi.org/10.1101/2020.04.06.026476
- Yamamoto, N., Yang, R., Yoshinaka, Y., Amari, S., Nakano, T., Cinatl, J., Rabenau, H., Doerr, H. W., Hunsmann, G., Otaka, A., Tamamura, H., Fujii, N., & Yamamoto, N. (2004). HIV protease inhibitor nelfinavir inhibits replication of SARS-associated coronavirus. Biochemical and Biophysical Research Communications, 318(3), 719–725. https://doi.org/https://doi.org/10.1016/j.bbrc.2004.04.083
- Yuan, S., Chan, J. F.-W., den-Haan, H., Chik, K. K.-H., Zhang, A. J., Chan, C. C.-S., Poon, V. K.-M., Yip, C. C.-Y., Mak, W. W.-N., Zhu, Z., Zou, Z., Tee, K.-M., Cai, J.-P., Chan, K.-H., de la Peña, J., Pérez-Sánchez, H., Cerón-Carrasco, J. P., & Yuen, K.-Y. (2017). Structure-based discovery of clinically approved drugs as Zika virus NS2B-NS3 protease inhibitors that potently inhibit Zika virus infection in vitro and in vivo. Antiviral Research, 145, 33–43. https://doi.org/https://doi.org/10.1016/j.antiviral.2017.07.007