In silico prediction of SARS-CoV-2 main protease and polymerase inhibitors: 3D-Pharmacophore modelling

References

• Ahmed, S. F., Quadeer, A. A., & McKay, M. R. (2020). Preliminary identification of potential vaccine targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies. Viruses, 12(3), 254–268. https://doi.org/10.3390/v12030254
   PubMed Web of Science ®Google Scholar
• Cao, B., Wang, Y., Wen, D., Liu, W., Wang, J., Fan, G., Ruan, L., Song, B., Cai, Y., Wei, M., Li, X., Xia, J., Chen, N., Xiang, J., Yu, T., Bai, T., Xie, X., Zhang, L., Li, C., … Wang, C. (2020). A Trial of Lopinavir-Ritonavir in Adults Hospitalized with Severe COVID-19. The New England Journal of Medicine, 382(19), 1787–1799. https://doi.org/10.1056/NEJMoa2001282
   PubMed Web of Science ®Google Scholar
• Carlesso, A., Chintha, C., Gorman, A. M., Samali, A., & Eriksson, L. A. (2019). Merits and pitfalls of conventional and covalent docking in identifying new hydroxyl aryl aldehyde like compounds as human IRE1 inhibitors. Scientific Reports, 9(1), 10. https://doi.org/10.1038/s41598-019-39939-z
   PubMedGoogle Scholar
• Chan, J. F. W., Kok, K. H., Zhu, Z., Chu, H., To, K. K. W., Yuan, S., & Yuen, K. Y. (2020). Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerging Microbes & Infections, 9(1), 221–236. https://doi.org/10.1080/22221751.2020.1719902
   PubMed Web of Science ®Google Scholar
• Chan, J. F. W., To, K. K. W., Tse, H., Jin, D. Y., & Yuen, K. Y. (2013). Interspecies transmission and emergence of novel viruses: Lessons from bats and birds. Trends in Microbiology, 21(10), 544–555. https://doi.org/10.1016/j.tim.2013.05.005
   PubMed Web of Science ®Google Scholar
• Chandwani, A., & Shuter, J. (2008). Lopinavir/ritonavir in the treatment of HIV-1 infection: A review. Therapeutics and Clinical Risk Management, 4(5), 1023–1033. https://doi.org/10.2147/tcrm.s3285
   PubMedGoogle Scholar
• Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., Qiu, Y., Wang, J., Liu, Y., Wei, Y., Xia, J., Yu, T., Zhang, X., & Zhang, L. (2020). Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study. Lancet (London, England), 395(10223), 507–513. https://doi.org/10.1016/S0140-6736(20)30211-7
   PubMed Web of Science ®Google Scholar
• Chen, Y., Liu, Q., & Guo, D. (2020). Emerging coronaviruses: Genome structure, replication, and pathogenesis. Journal of Medical Virology, 92(4), 418–423. https://doi.org/10.1002/jmv.25681
   PubMed Web of Science ®Google Scholar
• Elfiky, A. A. (2020). Anti-HCV, nucleotide inhibitors, repurposing against COVID-19. Life Sciences, 248, 117477–117482. https://doi.org/10.1016/j.lfs.2020.117477
   PubMed Web of Science ®Google Scholar
• Elfiky, A. A., & Ismail, A. (2019). Molecular dynamics and docking reveal the potency of novel GTP derivatives against RNA dependent RNA polymerase of genotype 4a HCV. Life Sciences, 238, 116958–116990. https://doi.org/10.1016/j.lfs.2019.116958
   PubMed Web of Science ®Google Scholar
• Enjuanes, L., Almazán, F., Sola, I., & Zuñiga, S. (2006). Biochemical Aspects of Coronavirus Replication and Virus-Host Interaction. Annual Review of Microbiology, 60, 211–230. https://doi.org/10.1146/annurev.micro.60.080805.142157
   PubMed Web of Science ®Google Scholar
• Eynde, J. J. V. (2020). COVID-19: A brief overview of the discovery clinical trial. Pharmaceuticals,13(4), 65–72.
   Google Scholar
• Fauci, A. S., Lane, H. C., & Redfield, R. R. (2020). COVID-19 - Navigating the Uncharted. The New England Journal of Medicine, 382(13), 1268–1269. https://doi.org/10.1056/NEJMe2002387
   PubMed Web of Science ®Google Scholar
• 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, Physical and Biological Sciences, 93(7), 449–463. https://doi.org/10.2183/pjab.93.027
   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
• Haji Agha Bozorgi, A., & Zarghi, A. (2014). Search for the pharmacophore of histone deacetylase inhibitors using pharmacophore query and docking study. Iranian Journal of Pharmaceutical Research : IJPR, 13(4), 1165–1172.
   PubMed Web of Science ®Google Scholar
• Han, B., Martin, R., Xu, S., Parvangada, A., Svarovskaia, E. S., Mo, H., & Dvory-Sobol, H. (2019). Sofosbuvir susceptibility of genotype 1 to 6 HCV from DAA-naïve subjects. Antiviral Research, 170, 104574 https://doi.org/10.1016/j.antiviral.2019.104574
   PubMed Web of Science ®Google Scholar
• Hirashima, S., Suzuki, T., Ishida, T., Noji, S., Yata, S., Ando, I., Komatsu, M., Ikeda, S., & Hashimoto, H. (2006). Benzimidazole derivatives bearing substituted biphenyls as hepatitis C virus NS5B RNA-dependent RNA polymerase inhibitors: Structure-activity relationship studies and identification of a potent and highly selective inhibitor JTK-109. Journal of Medicinal Chemistry, 49(15), 4721–4736. https://doi.org/10.1021/jm060269e
   PubMed Web of Science ®Google Scholar
• 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. https://doi.org/10.1016/j.cell.2020.02.052
   PubMed Web of Science ®Google Scholar
• Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y., Zhang, L., Fan, G., Xu, J., Gu, X., Cheng, Z., Yu, T., Xia, J., Wei, Y., Wu, W., Xie, X., Yin, W., Li, H., Liu, M., … Cao, B. (2020). Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet (London, England), 395(10223), 497–506. https://doi.org/10.1016/S0140-6736(20)30183-5
   PubMed Web of Science ®Google Scholar
• Izquierdo, L., Helle, F., François, C., Castelain, S., Duverlie, G., & Brochot, E. (2014). Simeprevir for the treatment of hepatitis C virus infection. Pharmacogenomics and Personalized Medicine, 7, 241–249. https://doi.org/10.2147/PGPM.S52715
   PubMedGoogle Scholar
• Jasenosky, L. D., Cadena, C., Mire, C. E., Borisevich, V., Haridas, V., Ranjbar, S., Nambu, A., Bavari, S., Soloveva, V., Sadukhan, S., Cassell, G. H., Geisbert, T. W., Hur, S., & Goldfeld, A. E. (2019). The FDA-Approved Oral Drug Nitazoxanide Amplifies Host Antiviral Responses and Inhibits Ebola Virus. iScience, 19, 1279–1290. https://doi.org/10.1016/j.isci.2019.07.003
   PubMed Web of Science ®Google Scholar
• Jia, H. P., Look, D. C., Shi, L., Hickey, M., Pewe, L., Netland, J., Farzan, M., Wohlford-Lenane, C., Perlman, S., & McCray, P. B. (2005). ACE2 Receptor Expression and Severe Acute Respiratory Syndrome Coronavirus Infection Depend on Differentiation of Human Airway Epithelia. Journal of Virology, 79(23), 14614–14621. https://doi.org/10.1128/JVI.79.23.14614-14621.2005
   PubMed Web of Science ®Google Scholar
• Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., … Yang, H. (2020). Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289–293. https://doi.org/10.1038/s41586-020-2223-y
   PubMed Web of Science ®Google Scholar
• Korba, B. E., Elazar, M., Lui, P., Rossignol, J. F., & Glenn, J. S. (2008). Potential for hepatitis C virus resistance to nitazoxanide or tizoxanide. Antimicrobial Agents and Chemotherapy, 52(11), 4069–4071. https://doi.org/10.1128/AAC.00078-08
   PubMed Web of Science ®Google Scholar
• Li, Q., Guan, X., Wu, P., Wang, X., Zhou, L., Tong, Y., Ren, R., Leung, K. S. M., Lau, E. H. Y., Wong, J. Y., Xing, X., Xiang, N., Wu, Y., Li, C., Chen, Q., Li, D., Liu, T., Zhao, J., Liu, M., … Feng, Z. (2020). Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia. The New England Journal of Medicine, 382(13), 1199–1207. https://doi.org/10.1056/NEJMoa2001316
   PubMed Web of Science ®Google Scholar
• Lo, M. K., Jordan, R., Arvey, A., Sudhamsu, J., Shrivastava-Ranjan, P., Hotard, A. L., Flint, M., McMullan, L. K., Siegel, D., Clarke, M. O., Mackman, R. L., Hui, H. C., Perron, M., Ray, A. S., Cihlar, T., Nichol, S. T., & Spiropoulou, C. F. (2017). GS-5734 and its parent nucleoside analog inhibit Filo-, Pneumo-, and Paramyxoviruses. Scientific Reports, 7(1), 1–7. https://doi.org/10.1038/srep43395
   PubMedGoogle Scholar
• Lv, Z., Chu, Y., & Wang, Y. (2015). HIV protease inhibitors: A review of molecular selectivity and toxicity. HIV/AIDS - Res Palliat Care, 7, 95–104.
   Google Scholar
• Macchiagodena, M., Pagliai, M., & Procacci, P. (2020). Inhibition of the main protease 3CL-pro of the coronavirus disease 19 via structure-based ligand design and molecular modeling. Biomolecules (q-bio.BM), 1–28.
   Google Scholar
• Malcolm, B. A., Liu, R., Lahser, F., Agrawal, S., Belanger, B., Butkiewicz, N., Chase, R., Gheyas, F., Hart, A., Hesk, D., Ingravallo, P., Jiang, C., Kong, R., Lu, J., Pichardo, J., Prongay, A., Skelton, A., Tong, X., Venkatraman, S., … Njoroge, F. G. (2006). SCH 503034, a mechanism-based inhibitor of hepatitis C virus NS3 protease, suppresses polyprotein maturation and enhances the antiviral activity of alpha interferon in replicon cells. Antimicrobial Agents and Chemotherapy, 50(3), 1013–1020. https://doi.org/10.1128/AAC.50.3.1013-1020.2006
   PubMed Web of Science ®Google Scholar
• McMullan, L. K., Flint, M., Chakrabarti, A., Guerrero, L., Lo, M. K., Porter, D., Nichol, S. T., Spiropoulou, C. F., & Albariño, C. (2019). Characterisation of infectious Ebola virus from the ongoing outbreak to guide response activities in the Democratic Republic of the Congo: A phylogenetic and in vitro analysis. Lancet Infectious Diseases., 19(9), 1023–1032. https://doi.org/10.1016/S1473-3099(19)30291-9
   PubMed Web of Science ®Google Scholar
• McPhee, F., Sheaffer, A. K., Friborg, J., Hernandez, D., Falk, P., Zhai, G., Levine, S., Chaniewski, S., Yu, F., Barry, D., Chen, C., Lee, M. S., Mosure, K., Sun, L.-Q., Sinz, M., Meanwell, N. A., Colonno, R. J., Knipe, J., & Scola, P. (2012). Preclinical profile and characterization of the hepatitis C virus NS3 protease inhibitor asunaprevir (BMS-650032). Antimicrobial Agents and Chemotherapy, 56(10), 5387–5396. https://doi.org/10.1128/AAC.01186-12
   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 : a European Journal of Chemical Biology, 21(5), 730–738. https://doi.org/10.1002/cbic.202000047
   PubMed Web of Science ®Google Scholar
• Perlman, S., & Netland, J. (2009). Coronaviruses post-SARS: Update on replication and pathogenesis. Nature Reviews. Microbiology, 7(6), 439–450. https://doi.org/10.1038/nrmicro2147
   PubMed Web of Science ®Google Scholar
• Petrosillo, N., Viceconte, G., Ergonul, O., Ippolito, G., & Petersen, E. (2020). COVID-19, SARS and MERS: Are they closely related? Clinical Microbiology and Infection, 26(6), 729–734. https://doi.org/10.1016/j.cmi.2020.03.026
   PubMed Web of Science ®Google Scholar
• Pickett, S. D., Mason, J. S., & McLay, L. M. (1996). Diversity profiling and design using 3D pharmacophores: Pharmacophore-derived queries (PDQ). Journal of Chemical Information and Computer Sciences, 36(6), 1214–1223. https://doi.org/10.1021/ci960039g
   Google Scholar
• Pillaiyar, T., Manickam, M., Namasivayam, V., Hayashi, Y., & Jung, S. H. (2016). An overview of severe acute respiratory syndrome-coronavirus (SARS-CoV) 3CL protease inhibitors: Peptidomimetics and small molecule chemotherapy. Journal of Medicinal Chemistry, 59(14), 6595–6628. https://doi.org/10.1021/acs.jmedchem.5b01461
   PubMed Web of Science ®Google Scholar
• Sayad, B., Sobhani, M., & Khodarahmi, R. (2020). Sofosbuvir as Repurposed Antiviral Drug Against COVID-19: Why Were We Convinced to Evaluate the Drug in a Registered/Approved Clinical Trial? Arch Med Res, 500, 3–5.
   Google Scholar
• Sheahan, T. P., Sims, A. C., Leist, S. R., Schäfer, A., Won, J., Brown, A. J., Montgomery, S. A., Hogg, A., Babusis, D., Clarke, M. O., Spahn, J. E., Bauer, L., Sellers, S., Porter, D., Feng, J. Y., Cihlar, T., Jordan, R., Denison, M. R., & Baric, R. S. (2020). Comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against MERS-CoV. Nature Communications, 11(1), 222–235. https://doi.org/10.1038/s41467-019-13940-6
   PubMed Web of Science ®Google Scholar
• Sidwell, R. W., Bailey, K. W., Wong, M. H., Barnard, D. L., & Smee, D. F. (2005). In vitro and in vivo influenza virus-inhibitory effects of viramidine. Antiviral Research, 68(1), 10–17. https://doi.org/10.1016/j.antiviral.2005.06.003
   PubMed Web of Science ®Google Scholar
• Sinokrot, H., Smerat, T., Najjar, A., & Karaman, R. (2017). Advanced prodrug strategies in nucleoside and non-nucleoside antiviral agents: A review of the recent five years. Molecules, 22, 1736–1754.
   Google Scholar
• Sofia, M. J. (2011). Nucleotide prodrugs for HCV therapy. Antiviral Chemistry & Chemotherapy, 22(1), 23–49. https://doi.org/10.3851/IMP1797
   PubMedGoogle Scholar
• Sofia, M. J., Chang, W., Furman, P. A., Mosley, R. T., & Ross, B. S. (2012). Nucleoside, nucleotide, and non-nucleoside inhibitors of hepatitis C virus NS5B RNA-dependent RNA-polymerase. Journal of Medicinal Chemistry, 55(6), 2481–2531. https://doi.org/10.1021/jm201384j
   PubMed Web of Science ®Google Scholar
• Tang, B., Bragazzi, N. L., Li, Q., Tang, S., Xiao, Y., & Wu, J. (2020). An updated estimation of the risk of transmission of the novel coronavirus (2019-nCov). Infectious Disease Modelling, 5, 248–255. https://doi.org/10.1016/j.idm.2020.02.001
   PubMedGoogle Scholar
• Wei, C., Mook, R. A., Jr. Robert, A., & Premont, R. T. W. (2018). Niclosamide: Beyond an antihelminthic drug. Cellular Signalling, 41, 89–96. https://doi.org/10.1016/j.cellsig.2017.04.001
   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 (New York, N.Y.), 367(6483), 1260–1263. https://doi.org/10.1126/science.abb2507
   PubMed Web of Science ®Google Scholar
• Wyles, D. L., Rodríguez-Torres, M., Lawitz, E., Shiffman, M. L., Pol, S., Herring, R., Massetto, B., Kanwar, B., Trenkle, J. D., & Pang, P. S. (2014). All-Oral Combination of Ledipasvir. Vedroprevir, Tegobuvir, and Ribavirin in Treatment- Naive Patients with Genotype 1 HCV Infection David, 60, 56–64.
   Google Scholar
• Xu, J., Shi, P.-Y., Li, H., & Zhou, J. (2020). Broad Spectrum Antiviral Agent Niclosamide and Its Therapeutic Potential. ACS Infectious Diseases, 6(5), 909–915. https://doi.org/10.1021/acsinfecdis.0c00052
   PubMed Web of Science ®Google Scholar
• Yang, P. L., Gao, M., Lin, K., Liu, Q., & Villareal, V. A. (2011). Anti-HCV drugs in the pipeline. Current Opinion in Virology, 1(6), 607–616. https://doi.org/10.1016/j.coviro.2011.10.019
   PubMed Web of Science ®Google Scholar
• Yao, X., Guo, S., Wu, W., Wang, J., Wu, S., He, S., Wan, Y., Nandakumar, K. S., Chen, X., Sun, N., Zhu, Q., & Liu, S. (2018). Q63, a novel DENV2 RdRp non-nucleoside inhibitor, inhibited DENV2 replication and infection. Journal of Pharmacological Sciences, 138(4), 247–256. https://doi.org/10.1016/j.jphs.2018.06.012
   PubMed Web of Science ®Google Scholar
• Yin, W., Mao, C., Luan, X., Shen, D.-D., Shen, Q., Su, H., Wang, X., Zhou, F., Zhao, W., Gao, M., Chang, S., Xie, Y.-C., Tian, G., Jiang, H.-W., Tao, S.-C., Shen, J., Jiang, Y., Jiang, H., Xu, Y., … Xu, H. E. (2020). Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir. Science (New York, N.Y.), 368(6498), 1499–1504. https://doi.org/10.1126/science.abc1560
   PubMed Web of Science ®Google Scholar
• Zhou, H., Su, X., Lin, L., Zhang, J., Qi, Q., Guo, F., Xu, F., & Yang, B. (2019). Inhibitory effects of antiviral drug candidates on canine parvovirus in f81 cells. Viruses, 11(8), 742–714. https://doi.org/10.3390/v11080742
   Web of Science ®Google Scholar
• 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. (2020). A novel coronavirus from patients with pneumonia in China, 2019. The New England Journal of Medicine, 382(8), 727–733. https://doi.org/10.1056/NEJMoa2001017
   PubMed Web of Science ®Google Scholar