Phylogenic analysis of coronavirus genome and molecular studies on potential anti-COVID-19 agents from selected FDA-approved drugs

References

• Benkert, P., Künzli, M., & Schwede, T. (2009). QMEAN server for protein model quality estimation. Nucleic Acids Research, 37(suppl_2), W510–W514. https://doi.org/10.1093/nar/gkp322
   PubMed Web of Science ®Google Scholar
• Benkert, P., Tosatto, S. C. E., & Schomburg, D. (2008). QMEAN: A comprehensive scoring function for model quality assessment. Proteins: Structure, Function, and Bioinformatics, 71(1), 261–277. https://doi.org/10.1002/prot.21715
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., & Schwede, T. (2017). Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports, 7(1), 1-15. https://doi.org/10.1038/s41598-017-09654-8
   Google Scholar
• Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Cassarino, T. G., Bertoni, M., Bordoli, L., & Schwede, T. (2014). SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42(W1), W252–W258. https://doi.org/10.1093/nar/gku340
   PubMed Web of Science ®Google Scholar
• Biot, C., Daher, W., Chavain, N., Fandeur, T., Khalife, J., Dive, D., & De Clercq, E. (2006). Design and synthesis of hydroxyferroquine derivatives with antimalarial and antiviral activities. Journal of Medicinal Chemistry, 49(9), 2845–2849. https://doi.org/10.1021/jm0601856
   PubMed Web of Science ®Google Scholar
• Bordoli, L., Kiefer, F., Arnold, K., Benkert, P., Battey, J., & Schwede, T. (2009). Protein structure homology modeling using SWISS-MODEL workspace. Nature Protocols, 4(1), 1–13. https://doi.org/10.1038/nprot.2008.197
   PubMed Web of Science ®Google Scholar
• Bowie, J. U., Lüthy, R., & Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional stucture. Science, 253(5016), 164–170. https://doi.org/10.1126/science.1853201
   PubMed Web of Science ®Google Scholar
• Chan, J. F. W., To, K. K. W., Chen, H., & Yuen, K. Y. (2015). Cross-species transmission and emergence of novel viruses from birds. Current Opinion in Virology, 10, 63–69. https://doi.org/10.1016/j.coviro.2015.01.006
   PubMed Web of Science ®Google Scholar
• Chang, C. K., Hou, M. H., Chang, C. F., Hsiao, C. D., & Huang, T. H. (2014). The SARS coronavirus nucleocapsid protein - Forms and functions. Antiviral Research, 103, 39–50. https://doi.org/10.1016/j.antiviral.2013.12.009
   PubMed Web of Science ®Google Scholar
• Chikhale, R. V., Gurav, S. S., Patil, R. B., Sinha, S. K., Prasad, S. K., Shakya, A., Shrivastava, S. K., Gurav, N. S., & Prasad, R. S. (2020). Sars-cov-2 host entry and replication inhibitors from Indian ginseng: An in-silico approach. Journal of Biomolecular Structure and Dynamics, 1–12. https://doi.org/10.1080/07391102.2020.1778539
   Google Scholar
• Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science : a Publication of the Protein Society, 2(9), 1511–1519. https://doi.org/10.1002/pro.5560020916
   PubMed Web of Science ®Google Scholar
• Daina, A., & Zoete, V. (2016). A BOILED-Egg To Predict Gastrointestinal Absorption and Brain Penetration of Small Molecules . ChemMedChem., 11(11), 1117–1121. https://doi.org/10.1002/cmdc.201600182
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2014). ILOGP: A simple, robust, and efficient description of n-octanol/water partition coefficient for drug design using the GB/SA approach. Journal of Chemical Information and Modeling, 54(12), 3284–3301. https://doi.org/10.1021/ci500467k
   PubMed Web of Science ®Google 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
• Drosten, C., Günther, S., Preiser, W., van der Werf, S., Brodt, H.-R., Becker, S., Rabenau, H., Panning, M., Kolesnikova, L., Fouchier, R. A. M., Berger, A., Burguière, A.-M., Cinatl, J., Eickmann, M., Escriou, N., Grywna, K., Kramme, S., Manuguerra, J.-C., Müller, S., … Doerr, H. W. (2003). Identification of a novel coronavirus in patients with severe acute respiratory syndrome. New England Journal of Medicine, 348(20), 1967–1976. https://doi.org/10.1056/NEJMoa030747
   PubMedGoogle Scholar
• Edgar, R. C. (2004). MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113 https://doi.org/10.1186/1471-2105-5-113
   PubMed Web of Science ®Google Scholar
• Fan, H. H., Wang, L. Q., Liu, W. L., An, X. P., Liu, Z. D., He, X. Q., Song, L. H., & Tong, Y. G. (2020). Repurposing of clinically approved drugs for treatment of coronavirus disease 2019 in a 2019-novel coronavirus-related coronavirus model. Chinese Medical Journal, 133(9), 1051–1056. https://doi.org/10.1097/CM9.0000000000000797
   PubMed Web of Science ®Google Scholar
• 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, 56(1), 105949. https://doi.org/10.1016/j.ijantimicag.2020.105949
   PubMed Web of Science ®Google Scholar
• Grosdidier, A., Zoete, V., & Michielin, O. (2011). Fast docking using the CHARMM force field with EADock DSS. J Comput Chem, 32(10), 2149–2159. https://doi.org/10.1002/jcc.21797
   PubMed Web of Science ®Google Scholar
• Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G. R. (2012). Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics, 4(1), 17 https://doi.org/10.1186/1758-2946-4-17
   PubMed Web of Science ®Google Scholar
• Kabalak, P. A., & Esenkaya, A. (2016). Severe pneumonia treated succesfully with levofloxacin and oseltamivir during flu epidemic. Turk Thorac J, 17(2), 84–87. https://doi.org/10.5578/ttj.17.2.018
   PubMed Web of Science ®Google Scholar
• Kolesnikova, L., Slenczka, W., Brodt, H.-R., Klenk, H.-D., & Becker, S. (2003). Electron microscopy in diagnostics of SARS case. Microscopy and Microanalysis, 9(S03), 438–439. https://doi.org/10.1017/S1431927603035104
   Google Scholar
• Krieger, E., Nabuurs, S. B., & Vriend, G. (2003). Homology modeling. In Methods of biochemical analysis. https://doi.org/10.1007/3-540-29623-9_5500
   Google Scholar
• Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., Consortium, O. S. D. D., & 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/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Langereis, M. A., Zeng, Q., Heesters, B., Huizinga, E. G., & de Groot, R. J. (2012). The murine coronavirus hemagglutinin-esterase receptor-binding site: A major shift in ligand specificity through modest changes in architecture. PLoS Pathogens, 8 (1), e1002492.  https://doi.org/10.1371/journal.ppat.1002492
   Google Scholar
• Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Lau, S. K. P., Woo, P. C. Y., Li, K. S. M., Tsang, A. K. L., Fan, R. Y. Y., Luk, H. K. H., Cai, J.-P., Chan, K.-H., Zheng, B.-J., Wang, M., & Yuen, K.-Y. (2015). Discovery of a Novel Coronavirus, China Rattus Coronavirus HKU24, from Norway Rats Supports the Murine Origin of Betacoronavirus 1 and Has Implications for the Ancestor of Betacoronavirus Lineage A. Journal of Virology, 89(6), 3076-3092. https://doi.org/10.1128/jvi.02420-14
   Google Scholar
• Li, F. (2016). Structure, Function, and Evolution of Coronavirus Spike Proteins. Annual Review of Virology, 3(1), 237–261. https://doi.org/10.1146/annurev-virology-110615-042301
   PubMed Web of Science ®Google Scholar
• Li, F., Goila-Gaur, R., Salzwedel, K., Kilgore, N. R., Reddick, M., Matallana, C., Castillo, A., Zoumplis, D., Martin, D. E., Orenstein, J. M., Allaway, G. P., Freed, E. O., & Wild, C. T. (2003). PA-457: A potent HIV inhibitor that disrupts core condensation by targeting a late step in Gag processing. Proceedings of the National Academy of Sciences of the United States of America, 100(23), 13555–13560. https://doi.org/10.1073/pnas.2234683100
   PubMed Web of Science ®Google Scholar
• Lindahl, Abraham, Hess, & van der Spoel, (2021). GROMACS 2020.5 Source code, 1(6). https://doi.org/10.5281/ZENODO.4420785
   Google Scholar
• Lipinski, C. A. (2000). Drug-like properties and the causes of poor solubility and poor permeability. Journal of Pharmacological and Toxicological Methods, 44(1), 235–249. https://doi.org/10.1016/S1056-8719(00)00107-6
   PubMed Web of Science ®Google Scholar
• Lüthy, R., Bowie, J. U., & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356(6364), 83–85. https://doi.org/10.1038/356083a0
   PubMed Web of Science ®Google Scholar
• Marmor, M. F., Kellner, U., Lai, T. Y. Y., Melles, R. B., Mieler, W. F., & Lum, F. (2016). Recommendations on Screening for Chloroquine and Hydroxychloroquine Retinopathy (2016 Revision). Ophthalmology, 123(6), 1386–1394. https://doi.org/10.1016/j.ophtha.2016.01.058
   PubMed Web of Science ®Google Scholar
• Masters, P. S. (2006). The Molecular Biology of Coronaviruses. Advances in Virus Research, 66, 193-292. https://doi.org/10.1016/S0065-3527(06)66005-3
   Google Scholar
• McBride, R., van Zyl, M., & Fielding, B. C. (2014). The coronavirus nucleocapsid is a multifunctional protein. Viruses, 6(8), 2991–3018. In https://doi.org/10.3390/v6082991
   PubMed Web of Science ®Google Scholar
• Mortola, E., & Roy, P. (2004). Efficient assembly and release of SARS coronavirus-like particles by a heterologous expression system. FEBS Letters, 576(1-2), 174–178. https://doi.org/10.1016/j.febslet.2004.09.009
   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
• Pawar, A. Y. (2020). Combating Devastating COVID -19 by Drug Repurposing. International Journal of Antimicrobial Agents, 56(2), 105984. https://doi.org/10.1016/j.ijantimicag.2020.105984
   PubMed Web of Science ®Google Scholar
• Sander, T., Freyss, J., Von Korff, M., Reich, J. R., & Rufener, C. (2009). OSIRIS, an entirely in-house developed drug discovery informatics system. Journal of Chemical Information and Modeling, 49(2), 232–246. https://doi.org/10.1021/ci800305f
   PubMed Web of Science ®Google Scholar
• Sheahan, T. P., Sims, A. C., Graham, R. L., Menachery, V. D., Gralinski, L. E., Case, J. B., Leist, S. R., Pyrc, K., Feng, J. Y., Trantcheva, I., Bannister, R., Park, Y., Babusis, D., Clarke, M. O., Mackman, R. L., Spahn, J. E., Palmiotti, C. A., Siegel, D., Ray, A. S., … Baric, R. S. (2017). Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses. Science Translational Medicine, 9(396), eaal3653. https://doi.org/10.1126/scitranslmed.aal3653
   PubMed Web of Science ®Google Scholar
• Sippl, M. J. (1993). Recognition of errors in three‐dimensional structures of proteins. Proteins: Structure, Function, and Genetics, 17(4), 355–362. https://doi.org/10.1002/prot.340170404
   PubMed Web of Science ®Google Scholar
• Sunseri, J., & Koes, D. R. (2016). Pharmit: Interactive exploration of chemical space. Nucleic Acids Research, 44(W1), W442–W448. https://doi.org/10.1093/nar/gkw287
   PubMed Web of Science ®Google Scholar
• Tan, K. P., Nguyen, T. B., Patel, S., Varadarajan, R., & Madhusudhan, M. S. (2013). Depth: A web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins. Nucleic Acids Research, 41(W1), W314–W321. https://doi.org/10.1093/nar/gkt503
   PubMed Web of Science ®Google Scholar
• Tan, K. P., Varadarajan, R., & Madhusudhan, M. S. (2011). DEPTH: A web server to compute depth and predict small-molecule binding cavities in proteins. Nucleic Acids Research, 39(suppl_2), W242–W248. https://doi.org/10.1093/nar/gkr356
   PubMedGoogle Scholar
• Tian, W., Chen, C., Lei, X., Zhao, J., & Liang, J. (2018). CASTp 3.0: Computed atlas of surface topography of proteins. Nucleic Acids Research, 46(W1), W363–W367. https://doi.org/10.1093/nar/gky473
   PubMed Web of Science ®Google Scholar
• Toh, S., Holbrook-Smith, D., Stogios, P. J., Onopriyenko, O., Lumba, S., Tsuchiya, Y., Savchenko, A., & McCourt, P. (2015). Structure-function analysis identifies highly sensitive strigolactone receptors in Striga. Science (New York, N.Y.), 350(6257), 203–207. https://doi.org/10.1126/science.aac9476
   PubMed Web of Science ®Google Scholar
• Touret, F., Gilles, M., Barral, K., Nougairède, A., Decroly, E., Lamballerie, X. d., & Coutard, B. (2020). In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication. BioRxiv, https://doi.org/10.1101/2020.04.03.023846
   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
• Van Gunsteren, W. F., Billeter, S. R., Eising, A. A., Hunenberger, P. H., Krüger, P., Mark, A. E., Scott, W. R. P., Tironi, I. G., Hünenberger, P. H., & Huenenberger, P. H. (1996). The GROMOS96 manual and user guide.
   Google Scholar
• Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., & Mackerell, A. D. Jr, (2009). CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. Journal of Computational Chemistry, 31(4), 671–690.
   Web of Science ®Google Scholar
• Walls, A. C., Tortorici, M. A., Snijder, J., Xiong, X., Bosch, B. J., Rey, F. A., Veesler, D. (2017). Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion. Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.1708727114
   Google Scholar
• Wang, C., Zheng, X., Gai, W., Zhao, Y., Wang, H., Wang, H., Feng, N., Chi, H., Qiu, B., Li, N., Wang, T., Gao, Y., Yang, S., & Xia, X. (2017). MERS-CoV virus-like particles produced in insect cells induce specific humoural and cellular imminity in rhesus macaques. Oncotarget, 8(8), 12686–12694. https://doi.org/10.18632/oncotarget.8475
   PubMedGoogle Scholar
• 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. In Cell Research. https://doi.org/10.1038/s41422-020-0282-0
   Google Scholar
• Warren, T. K., Jordan, R., Lo, M. K., Ray, A. S., Mackman, R. L., Soloveva, V., Siegel, D., Perron, M., Bannister, R., Hui, H. C., Larson, N., Strickley, R., Wells, J., Stuthman, K. S., Van Tongeren, S. A., Garza, N. L., Donnelly, G., Shurtleff, A. C., Retterer, C. J., … Bavari, S. (2016). Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys. Nature, 531(7594), 381–385. https://doi.org/10.1038/nature17180
   PubMed Web of Science ®Google Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server), W407–W410. https://doi.org/10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• World Health Organization (2021). Coronavirus disease (COVID-19) Weekly Epidemiological Update. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports
   Google Scholar
• Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., Yuan, M.-L., Zhang, Y.-L., Dai, F.-H., Liu, Y., Wang, Q.-M., Zheng, J.-J., Xu, L., Holmes, E. C., & Zhang, Y.-Z. (2020). A new coronavirus associated with human respiratory disease in China. Nature, 579(7798), 265–269. https://doi.org/10.1038/s41586-020-2008-3
   PubMed Web of Science ®Google Scholar
• Yang, L.-Q., Sang, P., Tao, Y., Fu, Y.-X., Zhang, K.-Q., Xie, Y.-H., & Liu, S.-Q. (2014). Protein dynamics and motions in relation to their functions: Several case studies and the underlying mechanisms. Journal of Biomolecular Structure & Dynamics, 32(3), 372–393. https://doi.org/10.1080/07391102.2013.770372
   PubMed Web of Science ®Google Scholar
• Zeng, Q., Langereis, M. A., Van Vliet, A. L. W., Huizinga, E. G., De Groot, R. J. (2008). Structure of coronavirus hemagglutinin-esterase offers insight into corona and influenza virus evolution. Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.0800502105
   Google Scholar