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Promising inhibitors against main protease of SARS CoV-2 from medicinal plants: In silico identification Cover

Promising inhibitors against main protease of SARS CoV-2 from medicinal plants: In silico identification

Open Access
|Dec 2021

References

  1. A. Rahimi, A. Mirzazadeh and S. Tavakolpour, Genetics and genomics of SARS CoV-2: A review of the literature with the special focus on genetic diversity and SARS CoV-2 genome detection, Genomics 113 (2021) 1221–1232; https://doi.org/10.1016/j.ygeno.2020.09.05910.1016/j.ygeno.2020.09.059752524333007398
  2. Y. A. Helmy, M. Fawzy, A. Elaswad, A. Sobieh, S. P. Kenney and A. A. Shehata, The COVID-19 pandemic: A comprehensive review of taxonomy, genetics, epidemiology, diagnosis, treatment, and control, J. Clin. Med. 9 (2020) Article ID 1225; https://doi.org/10.3390/jcm904122510.3390/jcm9041225723057832344679
  3. D. E. Gordon, G. M. Jang, M. Bouhaddou, J. Xu, K. Obernier, K. M. White, M. J. O’Meara, V. V. Rezelj, J. Z. Guo, D. L. Swaney, T. A. Tummino, R. Hüttenhain, R. M. Kaake, A. L. Richards, B. Tutuncuoglu, H. Foussard, J. Batra, K. Haas, M. Modak, M. Kim, P. Haas, B. J. Polacco, H. Braberg, J. M. Fabius, M. Eckhardt, M. Soucheray, M. J. Bennett, M. Cakir, M. J. McGregor, Q. Li, B. Meyer, F. Roesch, T. Vallet, A. Mac Kain, L. Miorin, E. Moreno, Z. Z. Chi Naing, Y. Zhou, S. Peng, Y. Shi, Z. Zhang, W. Shen, I. T. Kirby, J. E. Melnyk, J. S. Chorba, K. Lou, S. A. Dai, I. Barrio-Hernandez, D. Memon, C. Hernandez-Armenta, J. Lyu, C. J. P. Mathy, T. Perica, K. B. Pilla, S. J. Ganesan, D. J. Saltzberg, R. Rakesh, X. Liu, S. B. Rosenthal, L. Calviello, S. Venkataramanan, J. Liboy-Lugo, Y. Lin, X.-P. Huang, Y. F. Liu, S. A. Wankowicz, M. Bohn, M. Safari, F. S. Ugur, C. Koh, N. S. Savar, Q. D. Tran, D. Shengjuler, S. J. Fletcher, M. C. O’Neal, Y. Cai, J. C. J. Chang, D. J. Broadhurst, S. Klippsten, P. P. Sharp, N. A. Wenzell, D. Kuzuoglu-Ozturk, H.-Y. Wang, R. Trenker, J. M. Young, D. A. Cavero, J. Hiatt, T. L. Roth, U. Rathore, A. Subramanian, J. Noack, M. Hubert, R. M. Stroud, A. D. Frankel, O. S. Rosenberg, K. A. Verba, D. A. Agard, M. Ott, M. Emerman, N. Jura, M. von Zastrow, E. Verdin, A. Ashworth, O. Schwartz, C. d’Enfert, S. Mukherjee, M. Jacobson, H. S. Malik, D. G. Fujimori, T. Ideker, C. S. Craik, S. N. Floor, J. S. Fraser, J. D. Gross, A. Sali, B. L. Roth, D. Ruggero, J. Taunton, T. Kortemme, P. Beltrao, M. Vignuzzi, A. García-Sastre, K. M. Shokat, B. K. Shoichet, N. J. Krogan, A SARS-CoV-2 protein interaction map reveals targets for drug repurposing, Nature 583 (2020) 459–468; https://doi.org/10.1038/s41586-020-2286-910.1038/s41586-020-2286-9743103032353859
  4. J.-S. Kim, J. Jang, J. Kim, Y. Chung, C. Yoo and M. Han, Genome-wide identification and characterization of point mutations in the SARS CoV-2 genome, Osong Public Health Res. Perspect. 11 (2020) 101–111; https://doi.org/10.24171/j.phrp.2020.11.310.24171/j.phrp.2020.11.3.05
  5. M. Rastogi, N. Pandey, A. Shukla and S. K. Singh, SARS coronavirus 2:From genome to infectome, Respir. Res. 21 (2020) Article ID 318; https://doi.org/10.1186/s12931-020-01581-z10.1186/s12931-020-01581-z770617533261606
  6. Q. Li, X. Guan, P. Wu, X. Wang, L. Zhou, Y. Tong, R. Ren, K. Leung, E. Lau, J. Wong, X. Xing, N. Xiang, Y. Wu, C. Li, Q. Chen, D. Li, T. Liu, J. Zhao, M. Liu, W. Tu and Z. Feng, Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia, N. Engl. J. Med. 382 (2020) 1199–1207; https://doi.org/10.1056/NEJMoa200131610.1056/NEJMoa2001316712148431995857
  7. COVID-19 Vaccine & Therapeutics Tracker; https://biorender.com/covid-vaccine-tracker; last access date August 5, 2021
  8. A. N. M. Alamgir, Pharmacognostical Botany: Classification of Medicinal and Aromatic Plants (Maps), in Pharmacognostical Botany, Botanical Taxonomy, Morphology, and Anatomy of Drug Plants, in Therapeutic Use of Medicinal Plants and Their Extracts, Vol. 1, Springer International Publishing AG, Cham (Switzerland), 2017, pp. 177–293.10.1007/978-3-319-63862-1_6
  9. O. Ebenezer, M. A. Jordaan, N. Damoyi and M. Shapi, Discovery of potential inhibitors for RNA-dependent RNA polymerase of norovirus: Virtual screening, and molecular dynamics, Int. J. Mol. Sci. 22 (2021) Article ID 171 (24 pages); https://doi.org/10.3390/ijms2201017110.3390/ijms22010171779572733375298
  10. O. Ebenezer, O. Bodede, P. Awolade, M. A. Jordaan, R. E. Ogunsakin and M. Shapi, Medicinal plants with anti-SARS-CoV activity repurposing for treatment of COVID-19 infection: A systematic review and meta-analysis, Acta Pharm. 72 (2022) 199–224; https://doi.org/10.2478/acph-2022-002110.2478/acph-2022-0021
  11. Y. H. Song, D. W. Kim, M. J. Curtis-Long, H. J. Yuk, Y. Wang, N. Zhuang, K. H. Lee, K. S. Jeon and K. H. Park, Papain-like protease (PLpro) inhibitory effects of cinnamic amides from Tribulus terrestris fruits, Biol. Pharm. Bull. 37 (2014) 1021–1028; https://doi.org/10.1248/bpb.b14-0002610.1248/bpb.b14-0002624882413
  12. C.-W. Lin, F.-J. Tsai, C.-H. Tsai, C.-C. Lai, L. Wan, T.-Y. Ho, C.-C. Hsieh and P.-D. L. Chao, Anti-SARS coronavirus 3C-like protease effects of Isatis indigotica root and plant-derived phenolic compounds, Antiviral Res. 68 (2005) 36–42; https://doi.org/10.1016/j.antiviral.2005.07.00210.1016/j.antiviral.2005.07.002711432116115693
  13. Y. Park, H. Kim, M. Kim, J. Jeong, W. Kim, H. Park, J. Kwon, J. Park, S. Lee and B Ryu, Tanshinones as selective and slow-binding inhibitorsFor SARS CoV cysteine proteases, Bioorg. Med. Chem. 20 (2012) 5928–5935; https://doi.org/10.1016/j.bmc.2012.07.0310.1016/j.bmc.2012.07.038
  14. Y. Park, H. Kim, M. Kim, J. Jeong, W. Kim, H. Park, J. Kwon, J. Park, S. Lee and B. Ryu, Chalcones isolated from Angelica keiskei inhibit cysteine proteases of SARS CoV, J. Enzyme Inhib. Med. Chem. 31 (2016) 23–30; https://doi.org/10.3109/14756366.2014.100321510.3109/14756366.2014.100321525683083
  15. S. Jo, S. Kim, H. Shin and S. Kim, Inhibition of SARS CoV 3CL protease byFlavonoids, J. Enzyme Inhib. Med. Chem. 35 (2020) 145–151; https://doi.org/10.1080/14756366.2019.169048010.1080/14756366.2019.1690480688243431724441
  16. B. Ryu, H. Jeong, H. Kim, M. Kim, Y. Park, D. Kim, T. Nguyen, J. Park, S. Chang, H. Park, C. Rho and S. Lee, Biflavonoids from Torreya nucifera displaying SARS CoV 3CL(pro) inhibition, Bioorg. Med. Chem. 18 (2010) 7940–7947; https://doi.org/10.1016/j.bmc.2010.09.0351710.1016/j.bmc.2010.09.035
  17. W. Kim, H. Seo, J. Curtis-Long, Y. Oh, W. Oh, K. Cho, H. Lee and H. Park, Phenolic phytochemical displaying SARS CoV papain-like protease inhibition from the seeds of Psoralea corylifolia, J. Enzyme Inhib. Med. Chem. 29 (2014) 59–63; https://doi.org/10.3109/14756366.2012.7535911810.3109/14756366.2012.753591
  18. J.-Y. Park, H. J. Jeong, J. H. Kim, Y. M. Kim, S.-J. Park, D. Kim, K. H. Park, W. S. Lee and Y. B. Ryu, Diarylheptanoids from Alnus japonica inhibit papain-like protease of severe acute respiratory syndrome coronavirus, Biol. Pharm. Bull. 35 (2012) 2036–2042; https://doi.org/10.1248/bpb.b12-0062310.1248/bpb.b12-0062322971649
  19. B. Ryu, J. Park, M. Kim, Y. Lee, D. Seo, S. Chang, H. Park, C. Rhoand and S. Lee, SARS CoV 3CLpro inhibitory effects of quinone-methide triterpenes from Tripterygium regelii, Bioorg. Med. Chem. Lett. 20 (2010) 1873–1876; https://doi.org/10.1016/j.bmcl.2010.01.1522010.1016/j.bmcl.2010.01.152
  20. N. Chen, P. Lin, K. Huang, C. Chen, P. Hsieh, H. Liang and T. Hsu, Inhibition of SARS CoV 3C-like protease activity by theaflavin-3,3’-digallate (TF3), Evid. Based Complement. Alternat. Med. 2 (2005) 209–215; https://doi.org/10.1093/ecam/neh08110.1093/ecam/neh081114219315937562
  21. J. Cho, J. Curtis-Long, H. Lee, D. Kim, W. Ryu, J. Yuk and H. Park, Geranylated Flavonoids displaying SARS CoV papain-like protease inhibition from the fruits of Paulownia tomentosa, Bioorg. Med. Chem. 21 (2013) 3051–3057; https://doi.org/10.1016/j.bmc.2013.03.0272210.1016/j.bmc.2013.03.027
  22. C.-C. Wen, Y.-H. Kuo, J.-T. Jan, P.-H. Liang, S.-Y. Wang, H.-G. Liu, C.-K. Lee, S.-T. Chang, C.-J. Kuo, S.-S. Lee, C.-C. Hou, P.-W. Hsiao, S.-C. Chien, L.-F. Shyur and N. S. Yang, Specific plant terpenoids and lignoids possess potent antiviral activities against severe acute respiratory syndrome coronavirus, J. Med. Chem. 50 (2007) 4087–4095; https://doi.org/10.1021/jm070295s10.1021/jm070295s17663539
  23. Z. Jin, X. Du, Y. Xu, Y. Deng, M. Liu, Y. Zhao, B. Zhang, X. Li, L. Zhang, C. Peng, Y. Duan, J. Yu, L. Wang, K. Yang, F. Liu, R. Jiang, X. Yang, T. You, X. Liu, X. Yang, F. Bai, H. Liu, X. Liu, L. W. Guddat, W. Xu, G. Xiao, C. Qin, Z. Shi, H. Jiang, Z. Rao and H. Yang, Structure of MproFrom SARS-CoV-2 and discovery of its inhibitors, Nature 582 (2020) 289–293; https://doi.org/10.1038/s41586-020-2223-y10.1038/s41586-020-2223-y32272481
  24. A. Jordaan, O. Ebenezer, N. Damoyi and M. Shapi, Virtual screening, molecular docking studies and DFT calculations of FDA approved compounds similar to the non-nucleoside reverse transcriptase inhibitor (NNRTI) efavirenz, Heliyon 6 (2020) e04642; https://doi.org/10.1016/j.heliyon.2020.e046422510.1016/j.heliyon.2020.e04642
  25. O. Trott and J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoringFunction, efficient optimization, and multithreading, J. Comput. Chem. 31 (2010) 455–461; https://doi.org/10.1002/jcc.2133410.1002/jcc.21334304164119499576
  26. A. Daina, O. Michielin and V. Zoete, SwissADME: aFree web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistryFriendliness of small molecules, Sci. Rep. 7 (2017) Article ID 42717; https://doi.org/10.1038/srep4271710.1038/srep42717533560028256516
DOI: https://doi.org/10.2478/acph-2022-0020 | Journal eISSN: 1846-9558 | Journal ISSN: 1330-0075
Language: English
Page range: 159 - 169
Accepted on: Sep 13, 2021
Published on: Dec 30, 2021
Published by: Croatian Pharmaceutical Society
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year
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© 2021 OLUWAKEMI EBENEZER, MICHAEL SHAPI, published by Croatian Pharmaceutical Society
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.