References
- Appleby, T. C., Perry, J. K., Murakami, E., Barauskas, O., Feng, J., Cho, A., Fox, D., Wetmore, D. R., McGrath, M. E., Ray, A. S., Sofia, M. J., Swaminathan, S., & Edwards, T. E. (2015). Viral replication. Structural basis for RNA replication by the hepatitis C virus polymerase. Science (New York, N.Y.), 347(6223), 771–775. https://doi.org/https://doi.org/10.1126/science.1259210
- Arba, M., Wahyudi, S. T., Brunt, D. J., Paradis, N., & Wu, C. (2020). Mechanistic insight on the remdesivir binding to RNA-Dependent RNA polymerase (RdRp) of SARS-cov-2. Computers in Biology and Medicine, 129, 104156. https://doi.org/https://doi.org/10.1016/j.compbiomed.2020.104156
- Baron, S. A., Devaux, C., Colson, P., Raoult, D., & Rolain, J. M. (2020). Teicoplanin: An alternative drug for the treatment of COVID-19? International Journal of Antimicrobial Agents, 55(4), 105944. https://doi.org/https://doi.org/10.1016/j.ijantimicag.2020.105944
- Beigel, J. H., Tomashek, K. M., Dodd, L. E., Mehta, A. K., Zingman, B. S., Kalil, A. C., Hohmann, E., Chu, H. Y., Luetkemeyer, A., Kline, S., Lopez de Castilla, D., Finberg, R. W., Dierberg, K., Tapson, V., Hsieh, L., Patterson, T. F., Paredes, R., Sweeney, D. A., Short, W. R., … Lane, H. C. (2020). Remdesivir for the treatment of Covid-19 - preliminary report. New England Journal of Medicine, 383(19), 1813–1826. https://doi.org/https://doi.org/10.1056/NEJMoa2007764
- Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B., & Lindahl, E. (2010). Implementation of the CHARMM force field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models. Journal of Chemical Theory and Computation, 6(2), 459–466. https://doi.org/https://doi.org/10.1021/ct900549r
- de Vicente, J., Hendricks, R. T., Smith, D. B., Fell, J. B., Fischer, J., Spencer, S. R., Stengel, P. J., Mohr, P., Robinson, J. E., Blake, J. F., Hilgenkamp, R. K., Yee, C., Adjabeng, G., Elworthy, T. R., Li, J., Wang, B., Bamberg, J. T., Harris, S. F., Wong, A., … Farrell, R. (2009). Non-nucleoside inhibitors of HCV polymerase NS5B. Part 4: Structure-based design, synthesis, and biological evaluation of benzo[d]isothiazole-1,1-dioxides. Bioorganic & Medicinal Chemistry Letters, 19(19), 5652–5656. https://doi.org/https://doi.org/10.1016/j.bmcl.2009.08.022
- Diamond, M. S., & Pierson, T. C. (2020). The challenges of vaccine development against a new virus during a pandemic. Cell Host & Microbe, 27(5), 699–703. https://doi.org/https://doi.org/10.1016/j.chom.2020.04.021
- Elfiky, A. A. (2020). Anti-HCV, nucleotide inhibitors, repurposing against COVID-19. Life Sciences, 248, 117477. https://doi.org/https://doi.org/10.1016/j.lfs.2020.117477
- Elfiky, A. A. (2020). Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study. Life Sciences, 253, 117592. https://doi.org/https://doi.org/10.1016/j.lfs.2020.117592
- Elfiky, A. A. (2020). SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: An in silico perspective. Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/https://doi.org/10.1080/07391102.2020.1758790
- 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.
- Furuta, Y., Komeno, T., & Nakamura, T. (2017). Favipiravir (T-705), a broad spectrum inhibitor of viral RNA polymerase. Proceedings of the Japan Academy, Series B, 93(7), 449–463. https://doi.org/https://doi.org/10.2183/pjab.93.027
- 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/https://doi.org/10.1126/science.abb7498
- Gong, P., & Peersen, O. B. (2010). Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America, 107(52), 22505–22510. https://doi.org/https://doi.org/10.1073/pnas.1007626107
- Harrison, C. (2020). Coronavirus puts drug repurposing on the fast track. Nature Biotechnology, 38(4), 379–381. https://doi.org/https://doi.org/10.1038/d41587-020-00003-1
- Hayden, F. G., & Shindo, N. (2019). Influenza virus polymerase inhibitors in clinical development. Current Opinion in Infectious Diseases, 32(2), 176–186. https://doi.org/https://doi.org/10.1097/QCO.0000000000000532
- 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
- Julander, J. G., Siddharthan, V., Evans, J., Taylor, R., Tolbert, K., Apuli, C., Stewart, J., Collins, P., Gebre, M., Neilson, S., Van Wettere, A., Lee, Y.-M., Sheridan, W. P., Morrey, J. D., & Babu, Y. S. (2017). Efficacy of the broad-spectrum antiviral compound BCX4430 against Zika virus in cell culture and in a mouse model. Antiviral Research, 137, 14–22. https://doi.org/https://doi.org/10.1016/j.antiviral.2016.11.003
- Ko, W. C., Rolain, J. M., Lee, N. Y., Chen, P. L., Huang, C. T., Lee, P. I., & Hsueh, P. R. (2020). Arguments in favour of remdesivir for treating SARS-CoV-2 infections. International Journal of Antimicrobial Agents, 55(4), 105933. https://doi.org/https://doi.org/10.1016/j.ijantimicag.2020.105933
- Law, V., Knox, C., Djoumbou, Y., Jewison, T., Guo, A. C., Liu, Y., Maciejewski, A., Arndt, D., Wilson, M., Neveu, V., Tang, A., Gabriel, G., Ly, C., Adamjee, S., Dame, Z. T., Han, B., Zhou, Y., & Wishart, D. S. (2014). DrugBank 4.0: Shedding new light on drug metabolism. Nucleic Acids Research, 42(Database issue), D1091–1097. https://doi.org/https://doi.org/10.1093/nar/gkt1068
- 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
- McDonald, S. M. (2013). RNA synthetic mechanisms employed by diverse families of RNA viruses. Wiley Interdisciplinary Reviews: RNA, 4(4), 351–367. https://doi.org/https://doi.org/10.1002/wrna.1164
- Morishita, T. (2003). Modified velocity scaling scheme for molecular dynamics at constant temperature and/or pressure. Molecular Simulation, 29(1), 63–69. https://doi.org/https://doi.org/10.1080/0892702031000065737
- 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
- Naik, V. R., Munikumar, M., Ramakrishna, U., Srujana, M., Goudar, G., Naresh, P., Kumar, B. N., & Hemalatha, R. (2020). Remdesivir (GS-5734) as a therapeutic option of 2019-nCOV main protease - in silico approach. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/https://doi.org/10.1080/07391102.2020.1781694
- Nguyen, H. L., Thai, N. Q., Truong, D. T., & Li, M. S. (2020). Remdesivir strongly binds to both RNA-dependent RNA polymerase and main protease of SARS-CoV-2: Evidence from molecular simulations. Journal of Physical Chemistry B, 124(50), 11337-11348.
- Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/https://doi.org/10.1063/1.328693
- Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., Smith, J. C., Kasson, P. M., van der Spoel, D., Hess, B., & Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (Oxford, England)), 29(7), 845–854. https://doi.org/https://doi.org/10.1093/bioinformatics/btt055
- R Studio Team. (2018). Integrated development environment for R. RStudio, PBC.
- Remdesivir for Certain Hospitalized COVID-19 Patients. https://www.fda.gov/news-events/press-announcements/fda-approves-first-treatment-covid-19
- Rolain, J. M., Colson, P., & Raoult, D. (2007). Recycling of chloroquine and its hydroxyl analogue to face bacterial, fungal and viral infections in the 21st century. International Journal of Antimicrobial Agents, 30(4), 297–308. https://doi.org/https://doi.org/10.1016/j.ijantimicag.2007.05.015
- Rose, P. W., Prlić, A., Altunkaya, A., Bi, C., Bradley, A. R., Christie, C. H., Costanzo, L. D., Duarte, J. M., Dutta, S., Feng, Z., Green, R. K., Goodsell, D. S., Hudson, B., Kalro, T., Lowe, R., Peisach, E., Randle, C., Rose, A. S., Shao, C., … Burley, S. K. (2017). The RCSB protein data bank: Integrative view of protein, gene and 3D structural information. Nucleic Acids Research, 45(D1), D271–D281. https://doi.org/https://doi.org/10.1093/nar/gkw1000
- 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. (2017). Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses. Science Translational Medicine, 9(396), eaal3653.
- Shu, B., & Gong, P. (2016). Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation. Proceedings of the National Academy of Sciences of the United States of America, 113(28), E4005–4014. https://doi.org/https://doi.org/10.1073/pnas.1602591113
- Standing, J. F. (2020). Response to: Optimizing hydroxychloroquine dosing for patients with COVID-19: An integrative modeling approach for effective drug repurposing: Quantitative clinical pharmacology input to SARS-CoV-2 therapeutics should be based on robust data. Clinical Pharmacology & Therapeutics, 108(1), 11–15.
- Tchesnokov, E. P., Feng, J. Y., Porter, D. P., & Gotte, M. (2019). Mechanism of inhibition of ebola virus RNA-dependent RNA polymerase by Remdesivir. Viruses, 11(4), 326. https://doi.org/https://doi.org/10.3390/v11040326
- 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.21334
- Wakchaure, P. D., Ghosh, S., & Ganguly, B. (2020). Revealing the inhibition mechanism of RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 by Remdesivir and nucleotide analogues: A molecular dynamics simulation study. Journal of Physical Chemistry B, 124(47), 10641–10652. https://doi.org/https://doi.org/10.1021/acs.jpcb.0c06747
- 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
- Wang, Y., Zhang, D., Du, G., Du, R., Zhao, J., Jin, Y., Fu, S., Gao, L., Cheng, Z., Lu, Q., Hu, Y., Luo, G., Wang, K., Lu, Y., Li, H., Wang, S., Ruan, S., Yang, C., Mei, C., … Wang, C. (2020). Remdesivir in adults with severe COVID-19: A randomised, double-blind, placebo-controlled, multicentre trial. Lancet (London, England), 395(10236), 1569–1578. https://doi.org/https://doi.org/10.1016/S0140-6736(20)31022-9
- 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/https://doi.org/10.1038/nature17180
- Warren, T. K., Wells, J., Panchal, R. G., Stuthman, K. S., Garza, N. L., Van Tongeren, S. A., Dong, L., Retterer, C. J., Eaton, B. P., Pegoraro, G., Honnold, S., Bantia, S., Kotian, P., Chen, X., Taubenheim, B. R., Welch, L. S., Minning, D. M., Babu, Y. S., Sheridan, W. P., & Bavari, S. (2014). Protection against filovirus diseases by a novel broad-spectrum nucleoside analogue BCX4430. Nature, 508(7496), 402–405. https://doi.org/https://doi.org/10.1038/nature13027
- Westover, J.B., Mathis, A., Taylor, R., Wandersee L., Bailey, K. W., Sefing, E. J., Hickerson, B. T., Jung, K. H., Sheridan, W.P., & Gowen, B.B. (2018). Galidesivir limits Rift Valley fever virus infection and disease in Syrian golden hamsters. Antiviral Res., 156, 38–45.
- Wishart, D. S., Feunang, Y. D., Guo, A. C., Lo, E. J., Marcu, A., Grant, J. R., Sajed, T., Johnson, D., Li, C., Sayeeda, Z., Assempour, N., Iynkkaran, I., Liu, Y., Maciejewski, A., Gale, N., Wilson, A., Chin, L., Cummings, R., Le, D., … Wilson, M. (2018). DrugBank 5.0: A major update to the DrugBank database for 2018. Nucleic Acids Research, 46(D1), D1074–D1082. https://doi.org/https://doi.org/10.1093/nar/gkx1037
- Wu, J., Wang, H., & Li, B. (2020). Structure-aided ACEI-capped remdesivir-loaded novel PLGA nanoparticles: Toward a computational simulation design for anti-SARS-CoV-2 therapy. Physical Chemistry Chemical Physics, 22(48), 28434–28439.
- Xu, X., Han, M., Li, T., Sun, W., Wang, D., Fu, B., Zhou, Y., Zheng, X., Yang, Y., Li, X., Zhang, X., Pan, A., & Wei, H. (2020). Effective treatment of severe COVID-19 patients with tocilizumab. Proceedings of the National Academy of Sciences of the United States of America, 117(20), 10970–10975. https://doi.org/https://doi.org/10.1073/pnas.2005615117
- Zhang, L., & Zhou, R. (2020). Structural basis of the potential binding mechanism of Remdesivir to SARS-CoV-2 RNA-dependent RNA polymerase. Journal of Physical Chemistry B, 124(32), 6955–6962. https://doi.org/https://doi.org/10.1021/acs.jpcb.0c04198
- Zhou, Y., Hou, Y., Shen, J., Huang, Y., Martin, W., & Cheng, F. (2020). Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discovery, 6, 14. https://doi.org/https://doi.org/10.1038/s41421-020-0153-3
- Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., Niu, P., Zhan, F., Ma, X., Wang, D., Xu, W., Wu, G., Gao, G. F., Tan, W., & China Novel Coronavirus Investigating and Research Team. (2020). A novel coronavirus from patients with pneumonia in China, 2019. The New England Journal of Medicine, 382(8), 727–733. https://doi.org/https://doi.org/10.1056/NEJMoa2001017
- 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