An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study

References

• Aanouz, I., Belhassan, A., El Khatabi, K., Lakhlifi, T., El Idrissi, M., & Bouachrine, M. (2020). Moroccan medicinal plants as inhibitors of COVID-19: Computational investigations. Journal of Biomolecular Structure & Dynamics. https://doi.org/10.1080/07391102.2020.1758790
   Google Scholar
• Akinboye, E. S., & Bakare, O. (2011). Biological activities of emetine. Open Natural Products Journal, 4, 8–15. https://doi.org/10.2174/1874848101104010008
   Google Scholar
• Arthur, D. E., & Uzairu, A. (2019). Molecular docking studies on the interaction of NCI anticancer analogues with human Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit. Journal of King Saud University - Science, 31(4), 1151–1166. https://doi.org/10.1016/j.jksus.2019.01.011
   Web of Science ®Google Scholar
• Biovia, D. S. (2019). Discovery studio visualizer, 2019. Dassault Systèmes, (v19.1.0.15350).
   Google Scholar
• 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 & Dynamics. https://doi.org/10.1080/07391102.2020.1758788
   Google Scholar
• Coronavirus (COVID-19) events as they happen. (2020). https://www.who.int/emergencies/diseases/novel-coronavirus-2019/events-as-they-happen
   Google Scholar
• Cory, H., Passarelli, S., Szeto, J., Tamez, M., & Mattei, J. (2018). The role of polyphenols in human health and food systems: A mini-review. Frontiers in Nutrition, 5. https://doi.org/10.3389/fnut.2018.00087
   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(1). https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• De Clercq, E., & Li, G. (2016). Approved antiviral drugs over the past 50 years. Clinical Microbiology Reviews, 29(3), 695–747. https://doi.org/10.1128/CMR.00102-15
   PubMed Web of Science ®Google Scholar
• Elfiky, A. A., & Azzam, E. B. (2020). Novel Guanosine Derivatives against MERS CoV polymerase: An in silico perspective. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1758789
   Google Scholar
• Elmezayen, A. D., Al-Obaidi, A., Şahin, A. T., & Yelekçi, K. (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. https://doi.org/10.1080/07391102.2020.1758791
   Web of Science ®Google Scholar
• Enayatkhani, M., Hasaniazad, M., Faezi, S., Guklani, H., Davoodian, P., Ahmadi, N., Einakian, M. A., Karmostaji, A., Ahmadi, K. (2020). Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: An in silico study. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1756411
   PubMed Web of Science ®Google Scholar
• Fitchett, J. R., Head, M. G., Cooke, M. K., Wurie, F. B., & Atun, R. (2014). Funding infectious disease research: A systematic analysis of UK research investments by funders 1997-2010. PLoS One, 9(8), e105722. https://doi.org/10.1371/journal.pone.0105722
   PubMed Web of Science ®Google Scholar
• Ganeshpurkar, A., & Saluja, A. K. (2017). The pharmacological potential of rutin. Saudi Pharmaceutical Journal, 25(2), 149–164. https://doi.org/10.1016/j.jsps.2016.04.025
   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, 105949. https://doi.org/10.1016/j.ijantimicag.2020.105949
   PubMed Web of Science ®Google Scholar
• Grosdidier, A., Zoete, V., & Michielin, O. (2011). SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Research, 39(suppl), W270–7. https://doi.org/10.1093/nar/gkr366
   PubMedGoogle Scholar
• Gupta, M. K., Vemula, S., Donde, R., Gouda, G., Behera, L., & Vadde, R. (2020). In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1751300
   Google Scholar
• Hasan, A., Paray, B. A., Hussain, A., Qadir, F. A., Attar, F., Aziz, F. M., Sharifi, M., Derakhshankhah, H., Rasti, B., Mehrabi, M., Shahpasand, K., Saboury, A. A., & Falahati, M. (2020). A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1754293
   Google Scholar
• Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., … Yang, H. (2020). Structure of Mpro from COVID-19 virus and discovery of its inhibitors. BioRxiv, https://doi.org/10.1101/2020.02.26.964882
   Google Scholar
• Jo, S., Kim, S., Shin, D. H., & Kim, M. S. (2020). Inhibition of SARS-CoV 3CL protease by flavonoids. Journal of Enzyme Inhibition and Medicinal Chemistry, 35(1), 145–151. https://doi.org/10.1080/14756366.2019.1690480
   PubMed Web of Science ®Google Scholar
• Khaerunnisa, S., Kurniawan, H., Awaluddin, R., Suhartati, S. (2020). Potential Inhibitor of COVID-19 Main Protease (M pro) from Several Medicinal Plant Compounds by Molecular Docking Study. Preprints (Www.Preprints.Org) | NOT PEER-REVIEWED | Posted: 13 March 2020, https://doi.org/10.20944/Preprints202003.0226.V1 (March), 1–14.
   Google Scholar
• Khan, R. J., Jha, R. K., Amera, G., Jain, M., Singh, E., Pathak, A., … Singh, A. K. (2020). Targeting SARS-CoV-2: A systematic drug repurposing approach to identify promising inhibitors against 3C-like Proteinase and 2’-O-RiboseMethyltransferase. Journal of Biomolecular Structure & Dynamics, 1–40. https://doi.org/10.1080/07391102.2020.1753577
   Web of Science ®Google Scholar
• Khan, S. A., Zia, K., Ashraf, S., Uddin, R., & Ul-Haq, Z. (2020). Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1751298
   Web of Science ®Google Scholar
• Law, G. L., Tisoncik-Go, J., Korth, M. J., & Katze, M. G. (2013). Drug repurposing: A better approach for infectious disease drug discovery? Current Opinion in Immunology, 25(5), 588–592. https://doi.org/10.1016/j.coi.2013.08.004
   PubMed Web of Science ®Google Scholar
• Lu, H. (2020). Drug treatment options for the 2019-new coronavirus (2019-nCoV). BioScience Trends, 14(1), 69–71. https://doi.org/10.5582/bst.2020.01020
   PubMed Web of Science ®Google Scholar
• Lu, H., Stratton, C. W., & Tang, Y. (2020). Outbreak of pneumonia of unknown etiology in Wuhan, China: The mystery and the miracle. Journal of Medical Virology, 92(4), 401–402. https://doi.org/10.1002/jmv.25678
   PubMed Web of Science ®Google Scholar
• Morse, J. S., Lalonde, T., Xu, S., & Liu, W. R. (2020). Learning from the Past: Possible urgent prevention and treatment options for severe acute respiratory infections caused by 2019‐nCoV. ChemBioChem., 21(5), 730–738. https://doi.org/10.1002/cbic.202000047
   PubMed Web of Science ®Google Scholar
• Muralidharan, N., Sakthivel, R., Velmurugan, D., & Gromiha, M. M. (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. https://doi.org/10.1080/07391102.2020.1752802
   PubMed Web of Science ®Google Scholar
• Owen, C. D., Lukacik, P., Strain-Damerell, C. M., Douangamath, A., Powell, A. J., Fearon, D., Brandao-Neto, J., Crawshaw, A. D., Aragao, D., Williams, M., Flaig, R., Hall, D. R., McAuley, K. E., Mazzorana, M., Stuart, D. I., von Delft, F., & Walsh, M. A. (2020). COVID-19 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, SARS-CoV-2). RCSB Protein Data Bank (PDB) ID, 6Y84, 3–7. https://doi.org/10.2210/pdb6Y84
   Google Scholar
• Panic, G., Duthaler, U., Speich, B., & Keiser, J. (2014). Repurposing drugs for the treatment and control of helminth infections. International Journal for Parasitology: Drugs and Drug Resistance, 4(3), 185–200. https://doi.org/10.1016/j.ijpddr.2014.07.002
   PubMed Web of Science ®Google Scholar
• Pant, S., Singh, M., Ravichandiran, V., Murty, U. S. N., & Srivastava, H. K. (2020). Peptide-like and small-molecule inhibitors against Covid-19. Journal of Biomolecular Structure & Dynamics. https://doi.org/10.1080/07391102.2020.1757510
   Google Scholar
• Park, K. (2019). A review of computational drug repurposing. Translational and Clinical Pharmacology, 27(2), 59–63. https://doi.org/10.12793/tcp.2019.27.2.59
   PubMedGoogle Scholar
• Parvez, M. K., Tabish Rehman, M., Alam, P., Al-Dosari, M. S., Alqasoumi, S. I., & Alajmi, M. F. (2019). Plant-derived antiviral drugs as novel hepatitis B virus inhibitors: Cell culture and molecular docking study. Saudi Pharmaceutical Journal, 27(3), 389–400. https://doi.org/10.1016/j.jsps.2018.12.008
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Sarma, P., Sekhar, N., Prajapat, M., Avti, P., Kaur, H., Kumar, S., … Medhi, B. (2020). In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain). Journal of Biomolecular Structure & Dynamics. https://doi.org/10.1080/07391102.2020.1753580
   Google Scholar
• Schrodinger LLC. (2017). The PyMOL Molecular Graphics System, Version 2.0, Schrödinger, LLC.
   Google Scholar
• Thayil, S. M., & Thyagarajan, S. P. (2016). Pa-9: A flavonoid extracted from plectranthus amboinicus inhibits HIV-1 protease. International Journal of Pharmacognosy and Phytochemical Research, 8(6), 1020–1024.
   Google Scholar
• Thompson, M. A. (2004). Molecular docking using ArgusLab, an efficient shape-based search algorithm and the AScore scoring function [Paper presentation].ACS Meeting.
   Google Scholar
• Thuy, B. T. P., My, T. T. A., Hai, N. T. T., Hieu, L. T., Hoa, T. T., Thi Phuong Loan, H., Triet, N. T., Anh, T. T. V., Quy, P. T., Tat, P. V., Hue, N. V., Quang, D. T., Trung, N. T., Tung, V. T., Huynh, L. K., & Nhung, N. T. A. (2020). Investigation into SARS-CoV-2 resistance of compounds in garlic essential oil. ACS Omega, 5(14), 8312–8320. https://doi.org/10.1021/acsomega.0c00772
   PubMed Web of Science ®Google Scholar
• Vardakas, K. Z., Michalopoulos, A., & Falagas, M. E. (2005). Fluconazole versus itraconazole for antifungal prophylaxis in neutropenic patients with haematological malignancies: A meta-analysis of randomised-controlled trials. British Journal of Haematology, 131(1), 22–28. https://doi.org/10.1111/j.1365-2141.2005.05727.x
   PubMed Web of Science ®Google 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. Cell Research, 30(3), 269–271. https://doi.org/10.1038/s41422-020-0282-0
   PubMed Web of Science ®Google Scholar
• Wang, Y., Fan, G., Salam, A., Horby, P., Hayden, F. G., Chen, C., Pan, J., Zheng, J., Lu, B., Guo, L., Wang, C., & Cao, B. (2020). Comparative effectiveness of combined favipiravir and oseltamivir therapy versus oseltamivir monotherapy in critically ill patients with influenza virus infection. The Journal of Infectious Diseases, 221(10), 1688–1698. https://doi.org/10.1093/infdis/jiz656
   PubMed Web of Science ®Google Scholar
• Wu, Y.-S., Lin, W.-H., T.-A.Hsu, J., & Hsieh, H.-P. (2006). Antiviral drug discovery against SARS-CoV. Current Medicinal Chemistry, 13(17), 2003–2020. https://doi.org/10.2174/092986706777584988
   PubMed Web of Science ®Google Scholar
• Xu, Z., Peng, C., Shi, Y., Zhu, Z., Mu, K., Wang, X., & Zhu, W. (2020). Nelfinavir was predicted to be a potential inhibitor of 2019-nCov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation. BioRxiv, p. 2020.01.27.921627. https://doi.org/10.1101/2020.01.27.921627
   Google Scholar
• Zakaryan, H., Arabyan, E., Oo, A., & Zandi, K. (2017). Flavonoids: Promising natural compounds against viral infections. Archives of Virology, 162(9), 2539–2551. https://doi.org/10.1007/s00705-017-3417-y
   PubMed Web of Science ®Google Scholar
• Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., … Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science, eabb3405. https://doi.org/10.1126/science.abb3405
   Google Scholar