References
- Aanouz, I., Belhassan, A., & El-Khatabi, K. (2020). Moroccan medicinal plants as inhibitors against SARS-CoV-2 main protease: Computational investigations. Journal of Biomolecular Structure and Dynamics, 1–9.
- Adeoye, A. O., Oso, B. J., & Olaoye, I. F. (2020). Repurposing of chloroquine and some clinically approved antiviral drugs as effective therapeutics to prevent cellular entry and replication of coronavirus. Journal of Biomolecular Structure and Dynamics, 1–14.
- Al-Tawfiq, J. A., & Memish, Z. A. (2014). Middle East respiratory syndrome coronavirus: Transmission and phylogenetic evolution. Trends in Microbiology, 22(10), 573–579. https://doi.org/https://doi.org/10.1016/j.tim.2014.08.001
- Bertram, S., Heurich, A., Lavender, H., Gierer, S., Danisch, S., Perin, P., Lucas, J. M., Nelson, P. S., Pöhlmann, S., & Soilleux, E. J. (2012). Influenza and SARS-coronavirus activating proteases TMPRSS2 and HAT are expressed at multiple sites in human respiratory and gastrointestinal tracts. PloS One, 7(4), e35876. https://doi.org/https://doi.org/10.1371/journal.pone.0035876
- Bolles, M., Donaldson, E., & Baric, R. (2011). SARS-CoV and emergent coronaviruses: Viral determinants of interspecies transmission. Current Opinion in Virology, 1(6), 624–634. https://doi.org/https://doi.org/10.1016/j.coviro.2011.10.012
- 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, 1–14.
- Brooks, B. R., Brooks, C. L., Mackerell, A. D., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A. R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., … Karplus, M. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30(10), 1545–1614. https://doi.org/https://doi.org/10.1002/jcc.21287
- Cabeça, T. K., Granato, C., & Bellei, N. (2013). Epidemiological and clinical features of human coronavirus infections among different subsets of patients. Influenza and Other Respiratory Viruses, 7(6), 1040–1047. https://doi.org/https://doi.org/10.1111/irv.12101
- Case, D., Belfon, K., & Ben-Shalom, I. (2020). AMBER 2020.
- 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/https://doi.org/10.1021/ci300367a
- Dhama, K., Karthik, K., Khandia, R., Munjal, A., Tiwari, R., Rana, R., Khurana, S. K., Ullah, S., Khan, R. U., Alagawany, M., & Farag, M. R. (2018). Medicinal and therapeutic potential of herbs and plant metabolites/extracts countering viral pathogens-current knowledge and future prospects. Current Drug Metabolism, 19(3), 236–263. https://doi.org/https://doi.org/10.2174/1389200219666180129145252
- Elmezayen, A. D., Al-Obaidi, A., & Şahin, A. T. (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, 1–12.
- Gallagher, T. M., & Buchmeier, M. J. (2001). Coronavirus spike proteins in viral entry and pathogenesis. Virology, 279(2), 371–374. https://doi.org/https://doi.org/10.1006/viro.2000.0757
- Gaunt, E. R. R., Hardie, A., Claas, E. C. C. J., Simmonds, P., & Templeton, K. E. E. (2010). Epidemiology and clinical presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 3 years using a novel multiplex real-time PCR method. Journal of Clinical Microbiology, 48(8), 2940–2947. https://doi.org/https://doi.org/10.1128/JCM.00636-10
- Glowacka, I., Bertram, S., Müller, M. A., Allen, P., Soilleux, E., Pfefferle, S., Steffen, I., Tsegaye, T. S., He, Y., Gnirss, K., Niemeyer, D., Schneider, H., Drosten, C., & Pöhlmann, S. (2011). Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response. Journal of Virology, 85(9), 4122–4134. https://doi.org/https://doi.org/10.1128/JVI.02232-10
- Gorbalenya, A. E., Baker, S. C., & Baric, R. S. (2020). The species Severe acute respiratory syndrome-related coronavirus: Classifying 2019-nCoV and naming it SARS-CoV-2. Nature Microbiology 5(4), 536–544.
- Gyebi, A. G., Ogunro, B. O., Adegunloye, P. A., Ogunyemi, M. O., & Afolabi, O. S. (2020). Potential inhibitors of Coronavirus 3-Chymotrypsin-Like Protease (3CLpro): An in silico screening of alkaloids and terpenoids from African medicinal plants. Journal of Biomolecular Structure and Dynamics, (in press) https://doi.org/https://doi.org/10.1080/7391102.2021764868
- Heurich, A., Hofmann-Winkler, H., Gierer, S., Liepold, T., Jahn, O., & Pöhlmann, S. (2014). TMPRSS2 and ADAM17 cleave ACE2 differentially and only proteolysis by TMPRSS2 augments entry driven by the severe acute respiratory syndrome coronavirus spike protein. Journal of Virology, 88(2), 1293–1307. https://doi.org/https://doi.org/10.1128/JVI.02202-13
- Hendaus, M. A. (2020). Remdesivir in the treatment of Coronavirus Disease 2019 (COVID-19): A simplified summary. Journal of Biomolecular Structure and Dynamics, 1–10.
- Hoffmann, M., Kleine-Weber, H., Schroeder, S., Krüger, N., Herrler, T., Erichsen, S., Schiergens, T. S., Herrler, G., Wu, N.-H., Nitsche, A., Müller, M. A., Drosten, C., & Pöhlmann, S. (2020). SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell, 181(2), 271–280.e8. https://doi.org/https://doi.org/10.1016/j.cell.2020.02.052
- Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/https://doi.org/10.1016/0263-7855(96)00018-5
- Imai, Y., Kuba, K., Rao, S., Huan, Y., Guo, F., Guan, B., Yang, P., Sarao, R., Wada, T., Leong-Poi, H., Crackower, M. A., Fukamizu, A., Hui, C.-C., Hein, L., Uhlig, S., Slutsky, A. S., Jiang, C., & Penninger, J. M. (2005). Angiotensin-converting enzyme 2 protects from severe acute lung failure. Nature, 436(7047), 112–116. https://doi.org/https://doi.org/10.1038/nature03712
- Kawase, M., Shirato, K., van der Hoek, L., Taguchi, F., & Matsuyama, S. (2012). Simultaneous treatment of human bronchial epithelial cells with serine and cysteine protease inhibitors prevents severe acute respiratory syndrome coronavirus entry. Journal of Virology, 86(12), 6537–6545. https://doi.org/https://doi.org/10.1128/JVI.00094-12
- Khan, R. J., Jha, R. K., & Amera, G. (2020). Targeting SARS-Cov-2: A systematic drug repurposing approach to identify promising inhibitors against 3C-like proteinase and 2'-O-ribose methyltransferase. Journal of Biomolecular Structure and Dynamics, 1–40.
- Kuba, K., Imai, Y., Rao, S., Gao, H., Guo, F., Guan, B., Huan, Y., Yang, P., Zhang, Y., Deng, W., Bao, L., Zhang, B., Liu, G., Wang, Z., Chappell, M., Liu, Y., Zheng, D., Leibbrandt, A., Wada, T., … Penninger, J. M. (2005). A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury. Nature Medicine, 11(8), 875–879. https://doi.org/https://doi.org/10.1038/nm1267
- Kudi, A. C., & Myint, S. H. (1999). Antiviral activity of some Nigerian medicinal plant extracts. Journal of Ethnopharmacology, 68(1–3), 289–294. https://doi.org/https://doi.org/10.1016/S0378-8741(99)00049-5
- Kyrieleis, O. J. P., Huber, R., Ong, E., Oehler, R., Hunter, M., Madison, E. L., & Jacob, U. (2007). Crystal structure of the catalytic domain of DESC1, a new member of the type II transmembrane serine proteinase family. The FEBS Journal, 274(8), 2148–2160. https://doi.org/https://doi.org/10.1111/j.1742-4658.2007.05756.x
- Lee, J., Cheng, X., Swails, J. M., Yeom, M. S., Eastman, P. K., Lemkul, J. A., Wei, S., Buckner, J., Jeong, J. C., Qi, Y., Jo, S., Pande, V. S., Case, D. A., Brooks, C. L., MacKerell, A. D., Klauda, J. B., & Im, W. (2016). CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. Journal of Chemical Theory and Computation, 12(1), 405–413. https://doi.org/https://doi.org/10.1021/acs.jctc.5b00935
- 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), 562–568. https://doi.org/https://doi.org/10.1038/s41564-020-0688-y
- Li, F., Li, W., Farzan, M., & Harrison, S. C. (2005). Structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science (New York, N.Y.), 309(5742), 1864–1868. https://doi.org/https://doi.org/10.1126/science.1116480
- Li, W., Moore, M. J., Vasilieva, N., Sui, J., Wong, S. K., Berne, M. A., Somasundaran, M., Sullivan, J. L., Luzuriaga, K., Greenough, T. C., Choe, H., & Farzan, M. (2003). Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature, 426(6965), 450–454. https://doi.org/https://doi.org/10.1038/nature02145
- Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1–3), 3–25. https://doi.org/https://doi.org/10.1016/S0169-409X(96)00423-1
- Lobo-Galo, N., Terrazas-López, M., & Martínez-Martínez, A. (2020). FDA-approved thiol-reacting drugs that potentially bind into the SARS-CoV-2 main protease, essential for viral replication. Journal of Biomolecular Structure and Dynamics, 1–12.
- Lu, R., Yu, X., Wang, W., Duan, X., Zhang, L., Zhou, W., Xu, J., Xu, L., Hu, Q., Lu, J., Ruan, L., Wang, Z., & Tan, W. (2012). Characterization of human coronavirus etiology in Chinese adults with acute upper respiratory tract infection by real-time RT-PCR assays. PloS One., 7(6), e38638. https://doi.org/https://doi.org/10.1371/journal.pone.0038638
- Meyer, J. J. M., Afolayan, A. J., Taylor, M. B., & Erasmus, D. (1997). Antiviral activity of galangin isolated from the aerial parts of Helichrysum aureonitens. Journal of Ethnopharmacology, 56(2), 165–169. https://doi.org/https://doi.org/10.1016/S0378-8741(97)01514-6
- Miller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. https://doi.org/https://doi.org/10.1021/ct300418h
- Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/https://doi.org/10.1002/jcc.21256
- Muralidharan, N., Sakthivel, R., & Velmurugan, D. (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, 1–7.
- 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/https://doi.org/10.1186/1758-2946-3-33
- Ogbole, O. O., Akinleye, T. E., Segun, P. A., Faleye, T. C., & Adeniji, A. J. (2018). In vitro antiviral activity of twenty-seven medicinal plant extracts from Southwest Nigeria against three serotypes of echoviruses. Virology Journal, 15(1), 110. https://doi.org/https://doi.org/10.1186/s12985-018-1022-7
- Paules, C. I., Marston, H. D., & Fauci, A. S. (2020). Coronavirus infections-more than just the common cold. JAMA, 323(8), 707–708. https://doi.org/https://doi.org/10.1001/jama.2020.0757
- Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781–1802. https://doi.org/https://doi.org/10.1002/jcc.20289
- Salentin, S., Schreiber, S., Haupt, V. J., Adasme, M. F., & Schroeder, M. (2015). PLIP: Fully automated protein-ligand interaction profiler. Nucleic Acids Research, 43(W1), W443–W447. https://doi.org/https://doi.org/10.1093/nar/gkv315
- Sánchez-Linares, I., Pérez-Sánchez, H., Cecilia, J. M., & García, J. M. (2012). High-Throughput parallel blind virtual screening using BINDSURF. BMC Bioinformatics, 13(Suppl 14), S13. https://doi.org/https://doi.org/10.1186/1471-2105-13-S14-S13
- Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., Geng, Q., Auerbach, A., & Li, F. (2020). Structural basis of receptor recognition by SARS-CoV-2. Nature, 581(7807), 221–224. https://doi.org/https://doi.org/10.1038/s41586-020-2179-y
- Shulla, A., Heald-Sargent, T., Subramanya, G., Zhao, J., Perlman, S., & Gallagher, T. (2011). A transmembrane serine protease is linked to the severe acute respiratory syndrome coronavirus receptor and activates virus entry. Journal of Virology, 85(2), 873–882. https://doi.org/https://doi.org/10.1128/JVI.02062-10
- Simmons, G., Zmora, P., Gierer, S., Heurich, A., & Pöhlmann, S. (2013). Proteolytic activation of the SARS-coronavirus spike protein: Cutting enzymes at the cutting edge of antiviral research. Antiviral Research, 100(3), 605–614. https://doi.org/https://doi.org/10.1016/j.antiviral.2013.09.028
- Song, W., Gui, M., Wang, X., & Xiang, Y. (2018). Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2. PLoS Pathogens, 14(8), e1007236. https://doi.org/https://doi.org/10.1371/journal.ppat.1007236
- Tong, T. R. (2009). Drug targets in severe acute respiratory syndrome (SARS) virus and other coronavirus infections. Infectious Disorder Drug Targets, 9(2), 223–245. https://doi.org/https://doi.org/10.2174/187152609787847659
- Towler, P., Staker, B., Prasad, S., Menon, S., Tang, J., Parsons, T., Ryan, D., Fisher, M., Williams, D., Dales, N., Patane, M., & Pantoliano, M. (2004). ACE2 X-ray structures reveal a large hinge-bending motion important for inhibitor binding and catalysis. The Journal of Biological Chemistry, 279(17), 17996–18007. https://doi.org/https://doi.org/10.1074/jbc.M311191200
- 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/https://doi.org/10.1002/jcc
- Tubiana, T., Carvaillo, J.-C., Boulard, Y., & Bressanelli, S. (2018). TTClust: A versatile molecular simulation trajectory clustering program with graphical summaries. Journal of Chemical Information and Modeling, 58(11), 2178–2182. https://doi.org/https://doi.org/10.1021/acs.jcim.8b00512
- 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), 281–212. https://doi.org/https://doi.org/10.1016/j.cell.2020.02.058
- Walsh, E. E., Shin, J. H., & Falsey, A. R. (2013). Clinical impact of human coronaviruses 229E and OC43 infection in diverse adult populations. The Journal of Infectious Diseases, 208(10), 1634–1642. https://doi.org/https://doi.org/10.1093/infdis/jit393
- Wan, Y., Shang, J., Graham, R., Baric, R. S., Ralph, 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. https://doi.org/https://doi.org/10.1128/JVI.00127-20
- WHO (2020). Report of the WHO-China joint mission on coronavirus disease 2019 (COVID-19). https://www.who.int/docs/default-source/coronaviruse/who-china-joint-mission-on-covid-19-final-report.pdf
- 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/https://doi.org/10.1126/science.aax0902
- Wu, K., Peng, G., Wilken, M., Geraghty, R. J., & Li, F. (2012). Mechanisms of host receptor adaptation by severe acute respiratory syndrome coronavirus. The Journal of Biological Chemistry, 287(12), 8904–8911. https://doi.org/https://doi.org/10.1074/jbc.M111.325803
- Xia, S., Liu, M., Wang, C., Xu, W., Lan, Q., Feng, S., Qi, F., Bao, L., Du, L., Liu, S., Qin, C., Sun, F., Shi, Z., Zhu, Y., Jiang, S., & Lu, L. (2020). Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion . Cell Research, 30(4), 343–355. https://doi.org/https://doi.org/10.1038/s41422-020-0305-x
- Xu, X., Chen, P., Wang, J., Feng, J., Zhou, H., Li, X., Zhong, W., & Hao, P. (2020). Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Science China: Life Sciences, 63(3), 457–460. https://doi.org/https://doi.org/10.1007/s11427-020-1637-5
- Yamamoto, M., Matsuyama, S., Li, X., Takeda, M., Kawaguchi, Y., Inoue, J. I., & Matsuda, Z. (2016). Identification of nafamostat as a potent inhibitor of middle east respiratory syndrome Coronavirus s protein-mediated membrane fusion using the split-protein-based cell-cell fusion assay. Antimicrobial Agents and Chemotherapy, 60(11), 6532–6539. https://doi.org/https://doi.org/10.1128/AAC.01043-16
- Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., & Zhou, Q. (2020). Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science (New York, N.Y.), 367(6485), 1444–1448. https://doi.org/https://doi.org/10.1126/science.abb2762
- Yuan, Y., Cao, D., Zhang, Y., Ma, J., Qi, J., Wang, Q., Lu, G., Wu, Y., Yan, J., Shi, Y., Zhang, X., & Gao, G. F. (2017). Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains. Nature Communications, 8(1), 1–9. https://doi.org/https://doi.org/10.1038/ncomms15092
- Zhang, H., Penninger, J. M., Li, Y., Zhong, N., & Slutsky, A. S. (2020). Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: Molecular mechanisms and potential therapeutic target. Intensive Care Medicine, 46(4), 586–585. https://doi.org/https://doi.org/10.1007/s00134-020-05985-9
- Zhao, Y., Zhao, Z., Wang, Y., Zhou, Y., Ma, Y., & Zuo, W. (2020). Single-cell RNA expression profiling of ACE2, the putative receptor of Wuhan 2019-nCov. BioRxiv, https://doi.org/https://doi.org/10.1101/2020.01.26.919985
- Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., 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, X., … Shi, Z.-L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270–274. https://doi.org/https://doi.org/10.1038/s41586-020-2012-7
- Zhou, Y., Vedantham, P., Lu, K., Agudelo, J., Carrion, R., Nunneley, J. W., Barnard, D., Pöhlmann, S., McKerrow, J. H., Renslo, A. R., & Simmons, G. (2015). Protease inhibitors targeting coronavirus and filovirus entry. Antiviral Research, 116, 76–84. https://doi.org/https://doi.org/10.1016/j.antiviral.2015.01.011