References
- Anand, K., Ziebuhr, J., Wadhwani, P., Mesters, J. R., & Hilgenfeld, R. (2003). Coronavirus main proteinase (3CLpro) structure: Basis for design of anti-SARS drugs. Science (New York, N.Y.), 300(5626), 1763–1767. https://doi.org/https://doi.org/10.1126/science.1085658
- Baker, N. A., Sept, D., Joseph, S., Holst, M. J., & McCammon, J. A. (2001). Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences of the United States of America, 98(18), 10037–10041. https://doi.org/https://doi.org/10.1073/pnas.181342398
- Bienert, S., Waterhouse, A., de Beer, T. A., 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
- Chan, J. F., Yao, Y., Yeung, M. L., Deng, W., Bao, L., Jia, L., Li, F., Xiao, C., Gao, H., Yu, P., Cai, J. P., Chu, H., Zhou, J., Chen, H., Qin, C., & Yuen, K. Y. (2015). Treatment with lopinavir/ritonavir or interferon-beta1b improves outcome of MERS-CoV infection in a nonhuman primate model of common marmoset. Journal of Infectious Diseases, 212(12), 1904–1913. https://doi.org/https://doi.org/10.1093/infdis/jiv392
- Chan, K. S., Lai, S. T., Chu, C. M., Tsui, E., Tam, C. Y., Wong, M. M., Tse, M. W., Que, T. L., Peiris, J. S., Sung, J., Wong, V. C., & Yuen, K. Y. (2003). Treatment of severe acute respiratory syndrome with lopinavir/ritonavir: A multicentre retrospective matched cohort study. Hong Kong Medical Journal, 9, 399–406.
- Chen, F., Chan, K. H., Jiang, Y., Kao, R. Y., Lu, H. T., Fan, K. W., Cheng, V. C., Tsui, W. H., Hung, I. F., Lee, T. S., Guan, Y., Peiris, J. S., & Yuen, K. Y. (2004). In vitro susceptibility of 10 clinical isolates of SARS coronavirus to selected antiviral compounds. Journal of Clinical Virology: The Official Publication of the Pan American Society for Clinical Virology, 31(1), 69–75. https://doi.org/https://doi.org/10.1016/j.jcv.2004.03.003
- Chu, C. M., Cheng, V. C., Hung, I. F., Wong, M. M., Chan, K. H., Chan, K. S., Kao, R. Y., Poon, L. L., Wong, C. L., Guan, Y., Peiris, J. S., Yuen, K. Y., & Group, H. U. S. S. (2004). Role of lopinavir/ritonavir in the treatment of SARS: Initial virological and clinical findings. Thorax, 59(3), 252–256. https://doi.org/https://doi.org/10.1136/thorax.2003.012658
- Colson, P., Rolain, J. M., Lagier, J. C., Brouqui, P., & Raoult, D. (2020). Chloroquine and hydroxychloroquine as available weapons to fight COVID-19. International Journal of Antimicrobial Agents, 55(4), 105932. https://doi.org/https://doi.org/10.1016/j.ijantimicag.2020.105932
- Cui, J., Li, F., & Shi, Z. L. (2019). Origin and evolution of pathogenic coronaviruses. Nature Reviews. Microbiology, 17(3), 181–192. https://doi.org/https://doi.org/10.1038/s41579-018-0118-9
- de Wit, E., van Doremalen, N., Falzarano, D., & Munster, V. J. (2016). SARS and MERS: Recent insights into emerging coronaviruses. Nature Reviews. Microbiology, 14(8), 523–534. https://doi.org/https://doi.org/10.1038/nrmicro.2016.81
- Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38, 27-38. https://doi.org/https://doi.org/10.1016/0263-7855(96)00018-5
- Kumari, R., Kumar, R., Open Source Drug Discovery, C., & 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/https://doi.org/10.1021/ci500020m
- Lee, C. C., Kuo, C. J., Hsu, M. F., Liang, P. H., Fang, J. M., Shie, J. J., & Wang, A. H. (2007). Structural basis of mercury- and zinc-conjugated complexes as SARS-CoV 3C-like protease inhibitors. FEBS Letters, 581(28), 5454–5458. https://doi.org/https://doi.org/10.1016/j.febslet.2007.10.048
- Letko, M., Marzi, A., & Munster, V. (2020). Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses. Nature Microbiology, 5(4), 562–569. https://doi.org/https://doi.org/10.1038/s41564-020-0688-y
- Li, G., & De Clercq, E. (2020). Therapeutic options for the 2019 novel coronavirus (2019-nCoV). Nature Reviews Drug Discovery, 19(3), 149–150. https://doi.org/https://doi.org/10.1038/d41573-020-00016-0
- Liu, W., Morse, J. S., Lalonde, T., & Xu, S. (2020). Learning from the past: Possible urgent prevention and treatment options for severe acute respiratory infections caused by 2019-nCoV. Chembiochem: A European Journal of Chemical Biology, 21(5), 730–738. https://doi.org/https://doi.org/10.1002/cbic.202000047
- Perlman, S., & Netland, J. (2009). Coronaviruses post-SARS: Update on replication and pathogenesis. Nature Reviews. Microbiology, 7(6), 439–450. https://doi.org/https://doi.org/10.1038/nrmicro2147
- 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
- Sterling, T., & Irwin, J. J. (2015). ZINC 15 – ligand discovery for everyone. Journal of Chemical Information and Modeling, 55(11), 2324–2337. https://doi.org/https://doi.org/10.1021/acs.jcim.5b00559
- Touret, F., & de Lamballerie, X. (2020). Of chloroquine and COVID-19. Antiviral Research, 177, 104762. https://doi.org/https://doi.org/10.1016/j.antiviral.2020.104762
- Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/https://doi.org/10.1002/jcc.20291
- Wang, M., Cao, R., Zhang, L., Yang, X., Liu, J., Xu, M., Shi, Z., Hu, Z., Zhong, W., & Xiao, G. (2020). Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Research, 30(3), 269–271. https://doi.org/https://doi.org/10.1038/s41422-020-0282-0
- 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/https://doi.org/10.1093/nar/gky427
- Zhang, N., & Zhao, H. (2016). Enriching screening libraries with bioactive fragment space. Bioorganic & Medicinal Chemistry Letters, 26(15), 3594–3597. https://doi.org/https://doi.org/10.1016/j.bmcl.2016.06.013
- Zhao, H., & Caflisch, A. (2014). Discovery of dual ZAP70 and Syk kinases inhibitors by docking into a rare C-helix-out conformation of Syk. Bioorganic & Medicinal Chemistry Letters, 24(6), 1523–1527. https://doi.org/https://doi.org/10.1016/j.bmcl.2014.01.083
- Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. (2011). SwissParam: A fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 32(11), 2359–2368. https://doi.org/https://doi.org/10.1002/jcc.21816
- Zumla, A., Chan, J. F., Azhar, E. I., Hui, D. S., & Yuen, K. Y. (2016). Coronaviruses – drug discovery and therapeutic options. Nature Reviews. Drug Discovery, 15(5), 327–347. https://doi.org/https://doi.org/10.1038/nrd.2015.37