Remdesivir analogs against SARS-CoV-2 RNA-dependent RNA polymerase 

References

• Adams, M. J. (2004). Chemometrics in Analytical Spectroscopy. Royal Society of Chemistry. https://doi.org/10.1039/9781847550484
   Google Scholar
• Agostini, M. L., Andres, E. L., Sims, A. C., Graham, R. L., Sheahan, T. P., Lu, X., Smith, E. C., Case, J. B., Feng, J. Y., Jordan, R., Ray, A. S., Cihlar, T., Siegel, D., Mackman, R. L., Clarke, M. O., Baric, R. S., & Denison, M. R. (2018). Coronavirus susceptibility to the antiviral remdesivir (GS-5734) is mediated by the viral polymerase and the proofreading exoribonuclease. mBio, 9(2), e00221-18. https://doi.org/10.1128/mBio.00221-18
   PubMed Web of Science ®Google Scholar
• Ahmed, S., Islam, N., Shahinozzaman, M., Fakayode, S. O., Afrin, N., & Halim, M. A. (2021). Virtual screening, molecular dynamics, density functional theory and quantitative structure activity relationship studies to design peroxisome proliferator-activated receptor-γ agonists as anti-diabetic drugs. Journal of Biomolecular Structure & Dynamics, 39(2), 728–742. https://doi.org/10.1080/07391102.2020.1714482
   PubMed Web of Science ®Google Scholar
• Ahmed, S., Mahtarin, R., Ahmed, S. S., Akter, S., Islam, M. S., Mamun, A. A., Islam, R., Hossain, M. N., Ali, M. A., Sultana, M. U. C., Parves, M. R., Ullah, M. O., & Halim, M. A. (2020). Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 0(0), 1–16. https://doi.org/10.1080/07391102.2020.1796804
   Google Scholar
• Alam, S., & Khan, F. (2017). 3D-QSAR studies on maslinic acid analogs for anticancer activity against breast cancer cell line MCF-7. Scientific Reports, 7(1), 6019. https://doi.org/10.1038/s41598-017-06131-0
   PubMed Web of Science ®Google Scholar
• Benkert, P., Biasini, M., & Schwede, T. (2011). Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (Oxford, England), 27(3), 343–350. https://doi.org/10.1093/bioinformatics/btq662
   PubMed Web of Science ®Google Scholar
• Berhanu, W. M., Pillai, G. G., Oliferenko, A. A., & Katritzky, A. R. (2012). Quantitative structure-activity/property relationships: The ubiquitous links between cause and effect. ChemPlusChem, 77(7), 507–517. https://doi.org/10.1002/cplu.201200038
   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
   PubMedGoogle 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
• Bibi, S., & Sakata, K. (2016). Current status of computer-aided drug design for type 2 diabetes. Current Computer Aided-Drug Design, 12(2), 167–177. https://doi.org/10.2174/1573409912666160426120709
   Web of Science ®Google Scholar
• Bikadi, Z., & Hazai, E. (2009). Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. Journal of Cheminformatics, 1(1), 15. https://doi.org/10.1186/1758-2946-1-15
   PubMed Web of Science ®Google Scholar
• Bimonte, S., Crispo, A., Amore, A., Celentano, E., Cuomo, A., & Cascella, M. (2020). Potential antiviral drugs for SARS-Cov-2 treatment: Preclinical findings and ongoing clinical research. In Vivo (Athens, Greece), 34(3 Suppl), 1597–1602. https://doi.org/10.21873/invivo.11949
   PubMedGoogle Scholar
• Borbone, N., Piccialli, G., Roviello, G. N., & Oliviero, G. (2021). Nucleoside analogs and nucleoside precursors as drugs in the fight against SARS-CoV-2 and other coronaviruses. Molecules (Molecules), 26(4), 986. https://doi.org/10.3390/molecules26040986
   PubMed Web of Science ®Google Scholar
• Brown, A. J., Won, J. J., Graham, R. L., Dinnon, K. H., Sims, A. C., Feng, J. Y., Cihlar, T., Denison, M. R., Baric, R. S., & Sheahan, T. P. (2019). Broad spectrum antiviral remdesivir inhibits human endemic and zoonotic deltacoronaviruses with a highly divergent RNA dependent RNA polymerase. Antiviral Research, 169, 104541. https://doi.org/10.1016/j.antiviral.2019.104541
   PubMed Web of Science ®Google Scholar
• Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Di Costanzo, L., Christie, C., Dalenberg, K., Duarte, J. M., Dutta, S., Feng, Z., Ghosh, S., Goodsell, D. S., Green, R. K., Guranovic, V., Guzenko, D., Hudson, B. P., Kalro, T., Liang, Y., … Zardecki, C. (2019). RCSB Protein Data Bank: Biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. Nucleic Acids Research, 47(D1), D464–D474. https://doi.org/10.1093/nar/gky1004
   PubMed Web of Science ®Google Scholar
• Chan, J. F.-W., Yuan, S., Kok, K.-H., To, K. K.-W., Chu, H., Yang, J., Xing, F., Liu, J., Yip, C. C.-Y., Poon, R. W.-S., Tsoi, H.-W., Lo, S. K.-F., Chan, K.-H., Poon, V. K.-M., Chan, W.-M., Ip, J. D., Cai, J.-P., Cheng, V. C.-C., Chen, H., Hui, C. K.-M., & Yuen, K.-Y. (2020). A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: A study of a family cluster. Lancet (London, England), 395(10223), 514–523. https://doi.org/10.1016/S0140-6736(20)30154-9
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Cho, A., Zhang, L., Xu, J., Lee, R., Butler, T., Metobo, S., Aktoudianakis, V., Lew, W., Ye, H., Clarke, M., Doerffler, E., Byun, D., Wang, T., Babusis, D., Carey, A. C., German, P., Sauer, D., Zhong, W., Rossi, S., … Kim, C. U. (2014). Discovery of the first C-nucleoside HCV polymerase inhibitor (GS-6620) with demonstrated antiviral response in HCV infected patients. Journal of Medicinal Chemistry, 57(5), 1812–1825. https://doi.org/10.1021/jm400201a
   PubMed Web of Science ®Google Scholar
• Choong, Y. S., Tye, G. J., & Lim, T. S. (2013). Minireview: Applied structural bioinformatics in proteomics. The Protein Journal, 32(7), 505–511. https://doi.org/10.1007/s10930-013-9514-1
   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(January), 42713–42717. https://doi.org/10.1038/srep42717
   PubMedGoogle Scholar
• De Benedetti, P. G., & Fanelli, F. (2010). Computational quantum chemistry and adaptive ligand modeling in mechanistic QSAR. Drug Discovery Today, 15(19–20), 859–866. https://doi.org/10.1016/j.drudis.2010.08.003
   PubMed Web of Science ®Google Scholar
• De Jong, S. (1990). Multivariate calibration, H. Martens and T. Naes, Wiley, New York, 1989. ISBN 0 471 90979 3. Price: £75.00, US$138.00. No. of pages: 504. Journal of Chemometrics, 4(6), 441–441. https://doi.org/10.1002/cem.1180040607
   Google Scholar
• Dickson, C. J., Madej, B. D., Skjevik, Å. A., Betz, R. M., Teigen, K., Gould, I. R., & Walker, R. C. (2014). Lipid14: The amber lipid force field. Journal of Chemical Theory and Computation, 10(2), 865–879. https://doi.org/10.1021/ct4010307
   PubMed Web of Science ®Google Scholar
• Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang, L. P., Simmonett, A. C., Harrigan, M. P., Stern, C. D., Wiewiora, R. P., Brooks, B. R., & Pande, V. S. (2017). OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLOS Computational Biology, 13(7), e1005659. https://doi.org/10.1371/journal.pcbi.1005659
   PubMed Web of Science ®Google Scholar
• Fakayode, S. O., Busch, K. W., & Busch, M. A. (2009). Chemometric approach to chiral recognition using molecular spectroscopy. In Encyclopedia of Analytical Chemistry. John Wiley & Sons, Ltd. https://doi.org/10.1002/9780470027318.a9082
   Google Scholar
• Fakayode, S. O., Mitchell, B. S., & Pollard, D. A. (2014). Determination of boiling point of petrochemicals by gas chromatography-mass spectrometry and multivariate regression analysis of structural activity relationship. Talanta, 126, 151–156. https://doi.org/10.1016/j.talanta.2014.03.037
   PubMed Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., & Petersson, G. A. (2009). Gaussian 09, A.02. Gaussian, Inc. 111
   Google Scholar
• Funar-Timofei, S., Borota, A., & Crisan, L. (2017). Combined molecular docking and QSAR study of fused heterocyclic herbicide inhibitors of D1 protein in photosystem II of plants. Molecular Diversity, 21(2), 437–454. https://doi.org/10.1007/s11030-017-9735-x
   PubMed Web of Science ®Google Scholar
• Gao, Y., Yan, L., Huang, Y., Liu, F., Zhao, Y., Cao, L., Wang, T., Sun, Q., Ming, Z., Zhang, L., Ge, J., Zheng, L., Zhang, Y., Wang, H., Zhu, Y., Zhu, C., Hu, T., Hua, T., Zhang, B., … Rao, Z. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science (New York, N.Y.), 368(6492), 779–782. https://doi.org/10.1126/science.abb7498
   PubMed Web of Science ®Google Scholar
• Geraghty, R. J., Aliota, M. T., & Bonnac, L. F. (2021). Broad-spectrum antiviral strategies and nucleoside analogues. Viruses, 13(4), 667. https://doi.org/10.3390/v13040667
   PubMed Web of Science ®Google Scholar
• Hashemian, S. M., Farhadi, T., & Velayati, A. A A. (2020). A review on remdesivir: A possible promising agent for the treatment of COVID-19. Drug Design, Development and Therapy, 14, 3215–3222. https://doi.org/10.2147/DDDT.S261154
   PubMed Web of Science ®Google Scholar
• Hernandez, M., Liang Gan, G., Linvill, K., Dukatz, C., Feng, J., & Bhisetti, G. (2019). A quantum-inspired method for three-dimensional ligand-based virtual screening. Journal of Chemical Information and Modeling, 59(10), 4475–4485. https://doi.org/10.1021/acs.jcim.9b00195
   PubMed Web of Science ®Google Scholar
• Hillen, H. S., Kokic, G., Farnung, L., Dienemann, C., Tegunov, D., & Cramer, P. (2020). Structure of replicating SARS-CoV-2 polymerase. Nature, 584(7819), 154–156. https://doi.org/10.1038/s41586-020-2368-8
   PubMed Web of Science ®Google Scholar
• Kamer, G., & Argos, P. (1984). Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Research, 12(18), 7269–7282. https://doi.org/10.1093/nar/12.18.7269
   PubMed Web of Science ®Google Scholar
• Khadka, S., Yuchi, A., Shrestha, D. B., Budhathoki, P., Al-Subari, S. M. M., Ziad Alhouzani, T. M., & Anwar Butt, I. (2020). Repurposing drugs for COVID-19: An approach for treatment in the pandemic. Alternative Therapies in Health and Medicine, 26(S2), 100–107.
   PubMedGoogle Scholar
• Khan, S., Attar, F., Bloukh, S. H., Sharifi, M., Nabi, F., Bai, Q., Khan, R. H., & Falahati, M. (2021). A review on the interaction of nucleoside analogues with SARS-CoV-2 RNA dependent RNA polymerase. International Journal of Biological Macromolecules, 181, 605–611. https://doi.org/10.1016/j.ijbiomac.2021.03.112
   PubMed Web of Science ®Google Scholar
• 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), 1–9. https://doi.org/10.1038/s41467-019-10280-3
   PubMedGoogle Scholar
• Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., & Cheatham, T. E. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33(12), 889–897. https://doi.org/10.1021/ar000033j
   PubMed Web of Science ®Google Scholar
• Krieger, E., Darden, T., Nabuurs, S. B., Finkelstein, A., & Vriend, G. (2004). Making optimal use of empirical energy functions: Force-field parameterization in crystal space. Proteins, 57(4), 678–683. https://doi.org/10.1002/prot.20251
   PubMed Web of Science ®Google Scholar
• Krivov, G. G., Shapovalov, M. V., & Dunbrack, R. L. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins, 77(4), 778–795. https://doi.org/10.1002/prot.22488
   PubMed Web of Science ®Google Scholar
• Kurkcuoglu, Z., Koukos, P. I., Citro, N., Trellet, M. E., Rodrigues, J. P. G. L. M., Moreira, I. S., Roel-Touris, J., Melquiond, A. S. J., Geng, C., Schaarschmidt, J., Xue, L. C., Vangone, A., & Bonvin, A. M. J. J. (2018). Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. Journal of Computer-Aided Molecular Design, 32(1), 175–185. https://doi.org/10.1007/s10822-017-0049-y
   PubMed Web of Science ®Google Scholar
• Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L., & Wang, X. (2020). Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature, 581(7807), 215–220. https://doi.org/10.1038/s41586-020-2180-5
   PubMed Web of Science ®Google Scholar
• Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., Bi, Y., Ma, X., Zhan, F., Wang, L., Hu, T., Zhou, H., Hu, Z., Zhou, W., Zhao, L., … Tan, W. (2020). Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding. Lancet (London, England), 395(10224), 565–574. https://doi.org/10.1016/S0140-6736(20)30251-8
   PubMed Web of Science ®Google Scholar
• Mackerell, A. D., Feig, M., & Brooks, C. L. (2004). Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. Journal of Computational Chemistry, 25(11), 1400–1415. https://doi.org/10.1002/jcc.20065
   PubMed Web of Science ®Google Scholar
• Martinez, M. A. (2020). Clinical trials of repurposed antivirals for SARS-CoV-2. Antimicrobial Agents and Chemotherapy, 64(9), 1–19. https://doi.org/10.1128/AAC.01101-20
   Web of Science ®Google Scholar
• Mazanetz, M. P. (2013). Quantum mechanical applications in drug discovery. In L. Dormer (Ed.), In silico drug discovery and design (pp. 64–79). Future Medicine. https://doi.org/10.4155/EBO.13.291
   Google Scholar
• Mercorelli, B., Palù, G., & Loregian, A. (2018). Drug repurposing for viral infectious diseases: How far are we?. Trends in microbiology, 26(10), 865–876. https://doi.org/10.1016/j.tim.2018.04.004
   PubMed Web of Science ®Google Scholar
• Onawole, A. T., Sulaiman, K. O., Kolapo, T. U., Akinde, F. O., & Adegoke, R. O. (2020). COVID-19: CADD to the rescue. Virus Research, 285, 198022. https://doi.org/10.1016/j.virusres.2020.198022
   PubMed Web of Science ®Google Scholar
• Pack, S. (1991). Factor analysis in chemistry, (2nd edition), E. R. Malinowski, Wiley-Interscience, 1991. ISBN 0-471-53009-3. Price £43.70. Journal of Chemometrics, 5(6), 545. https://doi.org/10.1002/cem.1180050607
   Google Scholar
• Parvathaneni, V., & Gupta, V. (2020). Utilizing drug repurposing against COVID-19 - Efficacy, limitations, and challenges. Life Science, 259, 118275. https://doi.org/10.1016/j.lfs.2020.118275
   PubMed Web of Science ®Google Scholar
• Peng, R. D. (2015). R programming for data science, 109–116.
   Google Scholar
• Pruijssers, A. J., George, A. S., Schäfer, A., Leist, S. R., Gralinksi, L. E., Dinnon, K. H., Yount, B. L., Agostini, M. L., Stevens, L. J., Chappell, J. D., Lu, X., Hughes, T. M., Gully, K., Martinez, D. R., Brown, A. J., Graham, R. L., Perry, J. K., Du Pont, V., Pitts, J., … Sheahan, T. P. (2020). Remdesivir inhibits SARS-CoV-2 in human lung cells and chimeric SARS-CoV expressing the SARS-CoV-2 RNA polymerase in mice. Cell Reports, 32(3), 107940. https://doi.org/10.1016/j.celrep.2020.107940
   PubMed Web of Science ®Google Scholar
• Rstudio Team. (2019). RStudio: Integrated development for R. RStudio, Inc. https://doi.org/10.1007/978-3-642-20966-6
   Google Scholar
• 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/10.1038/s41586-020-2179-y
   PubMed Web of Science ®Google Scholar
• Shanmugam, A., Muralidharan, N., Velmurugan, D., & Gromiha, M. M. (2020). Therapeutic targets and computational approaches on drug development for COVID-19. Current Topics in Medicinal Chemistry, 20(24), 2210–2220. https://doi.org/10.2174/1568026620666200710105507
   PubMed Web of Science ®Google Scholar
• Shannon, A., Le, N. T. T., Selisko, B., Eydoux, C., Alvarez, K., Guillemot, J. C., Decroly, E., Peersen, O., Ferron, F., & Canard, B. (2020). Remdesivir and SARS-CoV-2: Structural requirements at both nsp12 RdRp and nsp14 Exonuclease active-sites. Antiviral Research, 178, 104793. https://doi.org/10.1016/j.antiviral.2020.104793
   PubMed Web of Science ®Google Scholar
• Sheahan, T. P., Sims, A. C., & Graham, R. L. (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
• Shi, Y., Shuai, L., Wen, Z., Wang, C., Yan, Y., Jiao, Z., Guo, F., Fu, Z. F., Chen, H., Bu, Z., & Peng, G. (2021). The preclinical inhibitor GS441524 in combination with GC376 efficaciously inhibited the proliferation of SARS-CoV-2 in the mouse respiratory tract. Emerging Microbes & Infections, 10(1), 481–492. https://doi.org/10.1080/22221751.2021.1899770
   PubMed Web of Science ®Google Scholar
• Siegel, D., Hui, H. C., Doerffler, E., Clarke, M. O., Chun, K., Zhang, L., Neville, S., Carra, E., Lew, W., Ross, B., Wang, Q., Wolfe, L., Jordan, R., Soloveva, V., Knox, J., Perry, J., Perron, M., Stray, K. M., Barauskas, O., … Mackman, R. L. (2017). Discovery and synthesis of a phosphoramidate prodrug of a pyrrolo[2,1-f][triazin-4-amino] adenine c-nucleoside (gs-5734) for the treatment of ebola and emerging viruses. Journal of Medicinal Chemistry, 60(5), 1648–1661. https://doi.org/10.1021/acs.jmedchem.6b01594
   PubMed Web of Science ®Google Scholar
• Skariyachan, S., Gopal, D., Chakrabarti, S., & Kempanna, P. (2020). Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID- 19. The COVID-19 resource centre is hosted on Elsevier Connect, the company ’ s public news and information. January.
   Google Scholar
• Studer, G., Tauriello, G., Bienert, S., Biasini, M., Johner, N., & Schwede, T. (2021). ProMod3—A versatile homology modelling toolbox. PLOS Computational Biology, 17(1), e1008667. https://doi.org/10.1371/journal.pcbi.1008667
   PubMed Web of Science ®Google Scholar
• Subissi, L., Posthuma, C. C., Collet, A., Zevenhoven-Dobbe, J. C., Gorbalenya, A. E., Decroly, E., Snijder, E. J., Canard, B., & Imbert, I. (2014). One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities. Proceedings of the National Academy of Sciences of the United States of America, 111(37), E3900–E3909. https://doi.org/10.1073/pnas.1323705111
   PubMed Web of Science ®Google Scholar
• Susnow, R. G., & Dixon, S. L. (2003). Use of robust classification techniques for the prediction of human cytochrome P450 2D6 inhibition. Journal of Chemical Information and Computer Sciences, 43(4), 1308–1315. https://doi.org/10.1021/ci030283p
   PubMedGoogle 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
• Uzunova, K., Filipova, E., Pavlova, V., & Vekov, T. (2020). Insights into antiviral mechanisms of remdesivir, lopinavir/ritonavir and chloroquine/hydroxychloroquine affecting the new SARS-CoV-2. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie, 131(August), 110668. https://doi.org/10.1016/j.biopha.2020.110668
   PubMedGoogle Scholar
• Vangone, A., Schaarschmidt, J., Koukos, P., Geng, C., Citro, N., Trellet, M. E., Xue, L. C., & Bonvin, A. M. J. J. (2019). Large-scale prediction of binding affinity in protein-small ligand complexes: The PRODIGY-LIG web server. Bioinformatics (Oxford, England), 35(9), 1585–1587. https://doi.org/10.1093/bioinformatics/bty816
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Wang, Q., Wu, J., Wang, H., Gao, Y., Liu, Q., Mu, A., Ji, W., Yan, L., Zhu, Y., Zhu, C., Fang, X., Yang, X., Huang, Y., Gao, H., Liu, F., Ge, J., Sun, Q., Yang, X., Xu, W., … Rao, Z. (2020). Structural basis for RNA replication by the SARS-CoV-2 polymerase. Cell, 182(2), 417–428.e13. https://doi.org/10.1016/j.cell.2020.05.034
   PubMed Web of Science ®Google Scholar
• 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 Res, 46(W1), W296–W303. https://doi.org/10.1093/nar/gky427
   PubMed Web of Science ®Google Scholar
• Wickham, H. (2009). ggplot2: Elegant graphics for data analysis. Springer-Verlag. https://doi.org/10.1007/978-0-387-98141-3
   Google Scholar
• Wold, S., Esbensen, K., & Geladi, P. (1987). Principal component analysis. Chemometrics and Intelligent Laboratory Systems, 2(1–3), 37–52. https://doi.org/10.1016/0169-7439(87)80084-9
   Web of Science ®Google Scholar
• Woo, H., & Roux, B. (2005). Calculation of absolute protein–ligand binding free. Proceedings of the National Academy of Sciences, 102(19), 6825–6830. https://doi.org/10.1073/pnas.0409005102
   PubMed Web of Science ®Google Scholar
• 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, 367(6483), 1260–1263. https://doi.org/10.1126/science.abb2507
   PubMed Web of Science ®Google Scholar
• Xue, L. C., Rodrigues, J. P., Kastritis, P. L., Bonvin, A. M., & Vangone, A. (2016). PRODIGY: A web server for predicting the binding affinity of protein-protein complexes. Bioinformatics (Oxford, England), 32(23), 3676–3678. https://doi.org/10.1093/bioinformatics/btw514
   PubMed Web of Science ®Google Scholar
• 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/10.1126/science.abb2762
   PubMed Web of Science ®Google Scholar
• Ye, Z.-W., Yuan, S., Chan, J. F.-W., Zhang, A. J., Yu, C.-Y., Ong, C. P., Yang, D., Chan, C. C.-Y., Tang, K., Cao, J., Poon, V. K.-M., Chan, C. C.-S., Cai, J.-P., Chu, H., Yuen, K.-Y., & Jin, D.-Y. (2021). Beneficial effect of combinational methylprednisolone and remdesivir in hamster model of SARS-CoV-2 infection. Emerging Microbes & Infections, 10(1), 291–304. https://doi.org/10.1080/22221751.2021.1885998
   PubMed Web of Science ®Google Scholar
• Yesudhas, D., Srivastava, A., & Gromiha, M. M. (2021). COVID-19 outbreak: History, mechanism, transmission, structural studies and therapeutics. Infection, 49(2), 199–213. https://doi.org/10.1007/s15010-020-01516-2
   PubMed Web of Science ®Google Scholar
• Yin, W., Luan, X., Li, Z., Zhou, Z., Wang, Q., Gao, M., Wang, X., Zhou, F., Shi, J., You, E., Liu, M., Wang, Q., Jiang, Y., Jiang, H., Xiao, G., Zhang, L., Yu, X., Zhang, S., & Eric Xu, H. (2021). Structural basis for inhibition of the SARS-CoV-2 RNA polymerase by suramin. Nature Structural & Molecular Biology, 28(3), 319–325. https://doi.org/10.1038/s41594-021-00570-0
   PubMed Web of Science ®Google Scholar
• Yu, C. H. (2009). Book Review: Creswell, J., & Plano Clark, V. (2007). Designing and conducting mixed methods research. Thousand Oaks, CA: Sage. Organizational Research Methods, 12(4), 801–804. https://doi.org/10.1177/1094428108318066
   Web of Science ®Google Scholar
• Zhang, W. F., Stephen, P., Stephen, P., Thériault, J. F., Wang, R., & Lin, S. X. (2020). Novel coronavirus polymerase and nucleotidyl-transferase structures: Potential to target new outbreaks. The Journal of Physical Chemistry Letters, 11(11), 4430–4435. https://doi.org/10.1021/acs.jpclett.0c00571
   PubMed Web of Science ®Google Scholar