315
Views
1
CrossRef citations to date
0
Altmetric
Research Articles

Identification of SARS-CoV-2 main protease inhibitors from FDA-approved drugs by artificial intelligence-supported activity prediction system

ORCID Icon, , , , , & show all
Pages 1767-1775 | Received 01 Nov 2021, Accepted 26 Dec 2021, Published online: 05 Jan 2022

References

  • Ajeet, A., B., Verma, S. K., & Singh, A. (2020). Docking analysis of 07 anti-HCV drugs with COVID-19 main protease PDB ID: 6LU7. American Journal of Pharmacological Sciences, 8(2), 21–25.
  • Chen, X., Kosoglou, T., Statkevich, P., Kumar, B., Li, J., Dockendorf, M. F., Wang, G., Lowe, R. S., Jiang, J., Liu, H., Wang, Z., Cutler, D. L., & Hu, P. (2014). Pharmacokinetics of vorapaxar and its metabolite following oral administration in healthy Chinese and American subjects. International Journal of Clinical Pharmacology and Therapeutics, 52(10), 889–899. https://doi.org/10.5414/CP202121
  • Dotolo, S., Marabotti, A., Facchiano, A., & Tagliaferri, R. (2021). A review on drug repurposing applicable to COVID-19. Briefings in Bioinformatics, 22(2), 726–741. https://doi.org/10.1093/bib/bbaa288
  • Dowara, H., Dowarah, J., Marak, B. N., Yadav, U. C. S., & Singh, V. P. (2021). Potential drug development and therapeutic approaches for clinical intervention in COVID-19. Bioorganic Chemistry, 114 (105016), 105016–105019.
  • Fu, L., Ye, F., Feng, Y., Yu, F., Wang, Q., Wu, Y., Zhao, C., Sun, H., Huang, B., Niu, P., Song, H., Shi, Y., Li, X., Tan, W., Qi, J., & Gao, G. F. (2020). Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease . Nature Communications, 11(1), 4417–4418. https://doi.org/10.1038/s41467-020-18233-x
  • Gimeno, A., Mestres-Truyol, J., Ojeda-Montes, M. J., Macip, G., Saldivar-Espinoza, B., Cereto-Massagué, A., Pujadas, G., & Garcia-Vallvé, S. (2020). Prediction of novel inhibitors of the main protease (Mpro) of SARS-CoV-2 through consensus docking and drug reposition. International Journal of Molecular Sciences, 21(11), 3793. https:// https://doi.org/10.3390/ijms21113793
  • Gul, S., Ozcan, O., Asar, S., Okyar, A., Barıs, I., & Kavakli, I. H. (2021). In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials. Journal of Biomolecular Structure & Dynamics, 39(17), 6772–6791. https://doi.org/10.1080/07391102.2020.1802346
  • 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.
  • Komatsu, H., Ikeda, K., Tanaka, T., & Matsuzaki, T. (2019a). Development of practical artificial intelligence system for drug discovery and its application to activity prediction of small molecule protein-protein interaction modulators. Journal of Biological Macromolecules, 19(1), 5–19. https://doi.org/10.14533/jbm.19.5
  • Komatsu, H., Tanaka, T., & Matsuzaki, T. (2019b). Efficient drug discovery approach for PPI and ubiquitin-proteasome targets with unique in silico screening and AI-based activity prediction technologies. Medical Science Digest, 45 (4), 225–231.
  • Liu, X., & Wang, X.-J. (2020). Potential inhibitors for 2019-nCoV coronavirus M protease from clinically approved medicines. Journal of Genetics and Genomics = Yi Chuan Xue Bao, 47(2), 119–121.
  • Matsuyama, S., Nao, N., Shirato, K., Kawase, M., Saito, S., Takayama, I., Nagata, N., Sekizuka, T., Katoh, H., Kato, F., Sakata, M., Tahara, M., Kutsuna, N., Ohmagari, N., Kuroda, M., Suzuki, T., Kageyama, T., & Takeda, M. (2020). Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells. Proceedings of the National Academy of Sciences of the United States of America, 117(13), 7001–7003.
  • Merck & Co., Inc. (2021). Merck and Ridgeback’s Molnupiravir, an Oral COVID-19 Antiviral Medicine, Receives First Authorization in the World. News release: November 4, 2021 6:40 am ET. https://www.merck.com/news/merck-and-ridgebacks-molnupiravir-an-oral-covid-19-antiviral-medicine-receives-first-authorization-in-the-world/
  • Milligan, J. C., Zeisner, T. U., Papageorgiou, G., Joshi, D., Soudy, C., Ulferts, R., Wu, M., Lim, C. T., Tan, K. W., Weissmann, F., Canal, B., Fujisawa, R., Deegan, T., Nagaraj, H., Bineva-Todd, G., Basier, C., Curran, J. F., Howell, M., Beale, R., … Diffley, J. F. X. (2021). Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of Nsp5 main protease. Biochemical Journal, 478(13), 2499–2515. https://doi.org/10.1042/BCJ20210197
  • Mody, V., Ho, J., Wills, S., Mawri, A., Lawson, L., Ebert, M. C. C. J. C., Fortin, G. M., Rayalam, S., & Taval, S. (2021). Identification of 3-chymotrypsin like protease (3CLPro) inhibitors as potential anti-SARS-CoV-2 agents. Communications Biology, 4(1), 1–10. https://doi.org/10.1038/s42003-020-01577-x
  • Molavi, Z., Razi, S., Mirmotalebisohi, S. A., Adibi, A., Sameni, M., Karami, F., Niazi, V., Niknam, Z., Aliashrafi, M., Taheri, M., Ghafouri-Fard, S., Jeibouei, S., Mahdian, S., Zali, H., Ranjbar, M. M., & Yazdani, M. (2021). Identification of FDA approved drugs against SARS-CoV-2 RNA dependent RNA polymerase (RdRp) and 3-chymotrypsin-like protease (3CLpro), drug repurposing approach. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie, 138, 111544. https://doi.org/10.1016/j.biopha.2021.111544
  • NS Healthcare Staff Writer. (2021). Pfizer initiates Phase 2/3 study of potential oral Covid-19 drug. https://www.ns-healthcare.com/news/pfizer-study-oral-covid-19-therapy/
  • 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, 33. doi:10.1186/1758-2946-3-33. PMC 3198950. PMID 21982300
  • Paul, A., Sarkar, A., Saha, S., Maji, A., Janah, P., & Maity, T. K. (2021). Synthetic and computational efforts towards the development of peptidomimetics and small-molecule SARS-CoV 3CLpro inhibitors. Bioorganic & Medicinal Chemistry, 46, 116301–116339. https://doi.org/10.1016/j.bmc.2021.116301
  • Pfizer Inc. (2021a). Pfizer Starts Global Phase 2/3 EPIC-PEP Study of Novel COVID-19 Oral Antiviral Candidate for Post-Exposure Prophylaxis in Adults. News: Monday, September 27, 2021 – 06:45 am. https://www.pfizer.com/news/press-release/press-release-detail/pfizer-starts-global-phase-23-epic-pep-study-novel-covid-19
  • Pfizer Inc. (2021b). Pfizer Seeks Emergency Use Authorization for Novel COVID-19 Oral Antiviral Candidate. News: Tuesday, November 16, 2021 – 02:00 pm. https://www.pfizer.com/news/press-release/press-release-detail/pfizer-seeks-emergency-use-authorization-novel-covid-19
  • PubChem. (2021). National Center for Biotechnology Information. National Library of Medicine. National Institutes of Health. https://pubchem.ncbi.nlm.nih.gov/
  • Reiner, Ž., Hatamipour, M., Banach, M., Pirro, M., Al-Rasadi, K., Jamialahmadi, T., Radenkovic, D., Montecucco, F., & Sahebkar, A. (2020). Statins and the Covid-19 main protease: In silico evidence on direct interaction. Archives of Medical Science , 16(3), 490–496. https://doi.org/10.5114/aoms.2020.94655
  • Salasc, F., Lahlali, T., Laurent, E., Rosa-Calatrava, M., & Pizzorno, A. (2021). Treatments for COVID-19: Lessons from 2020 and new therapeutic options. Current Opinion in Pharmacology, 62, 43–59. https://doi.org/10.1016/j.coph.2021.11.002
  • Sato, Y., Kashiwakura, I., Yamaguchi, M., Yoshino, H., Tanaka, T., Ikeda, K., Ye, Z., Komatsu, K., Matsuzaki, T., & Hosoda, M. (2021). Discovery of a novel small-molecule interleukin-6 inhibitor through virtual screening using artificial intelligence. Medicinal Chemistry, 18. https://doi.org/10.2174/1573406418666211116144243
  • Schroedl, S. (2019). Current methods and challenges for deep learning in drug discovery. Drug Discovery Today. Technologies, 32–33, 9–17. https://doi.org/10.1016/j.ddtec.2020.07.003
  • Towey, R. (2021). Fauci says FDA will review Merck’s new Covid treatment ‘as quickly as they possibly can’. https://www.cnbc.com/2021/10/01/fauci-says-fda-will-review-mercks-new-covid-treatment-as-quickly-as-they-possibly-can-.html
  • Verma, D. K., Kapoor, S., Das, S., & Thakur, K. G. (2020). Potential inhibitors of SARS-CoV-2 Main protease (Mpro) identified from the library of FDA approved drugs using molecular docking studies. Preprints (www.preprints.org). https://doi.org/10.20944/preprints202004.0149.v1
  • Wallach, I., Dzamba, M., & Heifets, A. (2015). AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Discovery. arXiv:1510.02855v1 [cs.LG], 1-11. https://arxiv.org/pdf/1510.02855v1.pdf
  • Yasugi, M., Kubota-Koketsu, R., Yamashita, A., Kawashita, N., Du, A., Sasaki, T., Nishimura, M., Misaki, R., Kuhara, M., Boonsathorn, N., Fujiyama, K., Okuno, Y., Nakaya, T., & Ikuta, K. (2013). Human monoclonal antibodies broadly neutralizing against influenza B virus. PLoS Pathogens, 9(2), e1003150.
  • Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science (New York, N.Y.), 368(6489), 409–412.
  • Zheng, L., Chen, Y., Bao, J., He, L., Dong, S., Qi, Y., & Zhang, J. Z. H. (2021). Discovery of novel inhibitors of SARS-CoV-2 main protease. Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/10.1080/07391102.2021.1972041
  • Zheng, C., Shao, W., Chen, X., Zhang, B., Wang, G., & Zhang, Z. (2021). Real-world effectiveness of COVID-19 vaccines: A literature review and meta-analysis. International Journal of Infectious Diseases, 114, 252–260. https://doi.org/10.1016/j.ijid.2021.11.009

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.