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In Silico Inhibition Potential of Artemisinin Derivatives Against SARS-CoV-2 Main Protease

Year 2021, , 809 - 816, 31.05.2021
https://doi.org/10.31202/ecjse.894617

Abstract

The outbreak of COVID-19 caused by the SARS-CoV-2 virus has recently become a pandemic and affected millions worldwide. The natural compounds obtained from medicinal plants have been proven to be the source of many treatments throughout history. Efforts to combat Sars-CoV-2 generally focused on repositioning drugs or finding treatments with natural compounds and have been rapidly ongoing. Main protease (Mpro) is a vital protein of SARS-CoV-2 and an important target of drug research. The present study evaluated seven artemisinin derivatives: Artemisinin, Artemether, Arteether, Artesunate, Dihydroartemisinic acid Dihydroartemisinin and Artemisinic Acid. For this purpose, the molecular docking study was carried out to investigate the potency of artemisinin derivatives against the SARS-CoV-2 Mpro. As a result, Artesunate, Dihydroartemisinic acid and dihydroartemisinin had promising results in Mpro inhibition with the binding energies between -8.42 and -9.35 kcal/mol.

Thanks

The numerical calculations reported in this paper were partially performed at TUBITAK ULAKBIM, High Performance, and Grid Computing Center (TRUBA resources).

References

  • Referans1. Emirik, M. Potential therapeutic effect of turmeric contents against SARS-CoV-2 compared with experimental COVID-19 therapies: in silico study. J. Biomol. Struct. Dyn. 2020, doi:10.1080/07391102.2020.1835719.
  • Referans2. Islam, M.T.; Sarkar, C.; El-Kersh, D.M.; Jamaddar, S.; Uddin, S.J.; Shilpi, J.A.; Mubarak, M.S. Natural products and their derivatives against coronavirus: A review of the non-clinical and pre-clinical data. Phyther. Res. 2020, 34, 2471–2492, doi:10.1002/ptr.6700.
  • Referans3. Wangkheirakpam, S. Traditional and Folk Medicine as a Target for Drug Discovery. In; Mandal, S.C., Mandal, V., Konishi, T.B.T.-N.P. and D.D., Eds.; Elsevier, 2018; pp. 29–56 ISBN 978-0-08-102081-4.
  • Referans4. Ganjhu, R.K.; Mudgal, P.P.; Maity, H.; Dowarha, D.; Devadiga, S.; Nag, S.; Arunkumar, G. Herbal plants and plant preparations as remedial approach for viral diseases. VirusDisease 2015, 26, 225–236, doi:10.1007/s13337-015-0276-6.
  • Referans5. Akbaş, M.N.; Akçakaya, A. COVID-19 ve Fitoterapi. Bezmialem Sci. 2020, 8, 428–437, doi:10.14235/bas.galenos.2020.4962.
  • Referans6. Din, M.; Ali, F.; Waris, A.; Zia, F.; Ali, M. Phytotherapeutic options for the treatment of COVID-19: A concise viewpoint. Phyther. Res. 2020, 34, 2431–2437, doi:10.1002/ptr.6786.
  • Referans7. Antonelli, M.; Donelli, D.; Maggini, V.; Firenzuoli, F. Phytotherapic compounds against coronaviruses: Possible streams for future research. Phyther. Res. 2020, 34, 1469–1470, doi:10.1002/ptr.6712.
  • Referans8. Boozari, M.; Hosseinzadeh, H. Natural products for COVID-19 prevention and treatment regarding to previous coronavirus infections and novel studies. Phyther. Res. 2020, 1–13, doi:10.1002/ptr.6873.
  • Referans9. Derosa, G.; Maffioli, P.; D’Angelo, A.; Di Pierro, F. A role for quercetin in coronavirus disease 2019 (COVID-19). Phyther. Res. 2020, 1–7, doi:10.1002/ptr.6887.
  • Referans10. Rahman, F.; Tabrez, S.; Ali, R.; Alqahtani, A.S.; Ahmed, M.Z.; Rub, A. Journal of Traditional and Complementary Medicine Molecular docking analysis of rutin reveals possible inhibition of SARS-CoV-2 vital proteins. J. Tradit. Chinese Med. Sci. 2021, 11, 173–179, doi:10.1016/j.jtcme.2021.01.006.
  • Referans11. Scavone, C.; Brusco, S.; Bertini, M.; Sportiello, L.; Rafaniello, C.; Zoccoli, A.; Berrino, L.; Racagni, G.; Rossi, F.; Capuano, A. Current pharmacological treatments for COVID-19: What’s next? Br. J. Pharmacol. 2020, 177, 4813–4824, doi:10.1111/bph.15072.
  • Referans12. Singh, E.; Khan, R.J.; Jha, R.K.; Amera, G.M.; Jain, M.; Singh, R.P.; Muthukumaran, J.; Singh, A.K. A comprehensive review on promising anti-viral therapeutic candidates identified against main protease from SARS-CoV-2 through various computational methods. J. Genet. Eng. Biotechnol. 2020, 18, doi:10.1186/s43141-020-00085-z.
  • Referans13. Boras, B.; Jones, R.M.; Anson, B.J.; Arenson, D.; Aschenbrenner, L.; Bakowski, M.A.; Beutler, N.; Binder, J.; Chen, E.; Eng, H.; et al. Discovery of a Novel Inhibitor of Coronavirus 3CL Protease as a Clinical Candidate for the Potential Treatment of COVID-19. bioRxiv Prepr. Serv. Biol. 2020, doi:10.1101/2020.09.12.293498.
  • Referans14. Qu, J.; Li, G.; Wang, J.; Huang, G.H.J.; Chen, Y.; Qu, Q.; Qiong, X.C. Comparative effectiveness of Lopinavir / Ritonavir-based regimens in COVID-19. 2021, 203–210, doi:10.1111/1440-1681.13425.
  • Referans15. Tahir ul Qamar, M.; Alqahtani, S.M.; Alamri, M.A.; Chen, L.L. Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. J. Pharm. Anal. 2020, 10, 313–319, doi:10.1016/j.jpha.2020.03.009.
  • Referans16. Yang, H.; Yang, M.; Ding, Y.; Liu, Y.; Lou, Z.; Zhou, Z.; Sun, L.; Mo, L.; Ye, S.; Pang, H.; et al. The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 13190–13195, doi:10.1073/pnas.1835675100.
  • Referans17. Sehailia, M.; Chemat, S. Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19. J. Biomol. Struct. Dyn. 2020, 0, 1–11, doi:10.1080/07391102.2020.1796809.
  • Referans18. Haq, F.U.; Roman, M.; Ahmad, K.; Rahman, S.U.; Shah, S.M.A.; Suleman, N.; Ullah, S.; Ahmad, I.; Ullah, W. Artemisia annua: Trials are needed for COVID-19. Phyther. Res. 2020, 34, 2423–2424, doi:10.1002/ptr.6733.
  • Referans19. Castilho, P.C.; Gouveia, S.C.; Rodrigues, A.I. Quantification of artemisinin in Artemisia annua extracts by 1H-NMR. Phytochem. Anal. 2008, 19, 329–334, doi:10.1002/pca.1053.
  • Referans20. D’alessandro, S.; Scaccabarozzi, D.; Signorini, L.; Perego, F.; Ilboudo, D.P.; Ferrante, P.; Delbue, S. The use of antimalarial drugs against viral infection. Microorganisms 2020, 8, 1–26, doi:10.3390/microorganisms8010085.
  • Referans21. Gendrot, M.; Duflot, I.; Boxberger, M.; Delandre, O.; Jardot, P.; Le Bideau, M.; Andreani, J.; Fonta, I.; Mosnier, J.; Rolland, C.; et al. Antimalarial artemisinin-based combination therapies (ACT) and COVID-19 in Africa: In vitro inhibition of SARS-CoV-2 replication by mefloquine-artesunate. Int. J. Infect. Dis. 2020, 99, 437–440, doi:10.1016/j.ijid.2020.08.032.
  • Referans22. Schrödinger Release 2018-4: Maestro, Schrödinger, LLC 2018.
  • Referans23. Salentin, S.; Schreiber, S.; Haupt, V.J.; Adasme, M.F.; Schroeder, M. PLIP: Fully automated protein-ligand interaction profiler. Nucleic Acids Res. 2015, 43, W443–W447, doi:10.1093/nar/gkv315.
  • Referans24. Jin, Z.; Du, X.; Xu, Y.; Deng, Y.; Liu, M.; Zhao, Y.; Zhang, B.; Li, X.; Zhang, L.; Peng, C.; et al. Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature 2020, 582, 289–293, doi:10.1038/s41586-020-2223-y.
  • Referans25. Schrödinger Release 2018-4: Protein Preparation Wizard; Epik, Schrödinger, LLC, New York, NY, 2016; Impact, Schrödinger, LLC, New York, NY, 2016; Prime, Schrödinger, LLC, New York, NY, 2018.
  • Referans26. Schrödinger Release 2018-1: Induced Fit Docking protocol; Glide, Schrödinger, LLC, New York, NY, 2016; Prime, Schrödinger, LLC 2018.
  • Referans27. Harder, E.; Damm, W.; Maple, J.; Wu, C.; Reboul, M.; Xiang, J.Y.; Wang, L.; Lupyan, D.; Dahlgren, M.K.; Knight, J.L.; et al. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. J. Chem. Theory Comput. 2016, 12, 281–296, doi:10.1021/acs.jctc.5b00864.
  • Referans28. Jacobson, M.P.; Pincus, D.L.; Rapp, C.S.; Day, T.J.F.; Honig, B.; Shaw, D.E.; Friesner, R.A. “A Hierarchical Approach to All-Atom Protein Loop Prediction,.” Proteins Struct. Funct. Bioinforma. 2004, 55, 351–367.

Artemisinin Türevi Bileşiklerin Sars-CoV-2 Ana Proteaz Proteinine Karşı In Silico İnhibisyon Potansiyeli

Year 2021, , 809 - 816, 31.05.2021
https://doi.org/10.31202/ecjse.894617

Abstract

SARS-CoV-2 virüsünün neden olduğu COVID-19 salgını son zamanlarda bir salgın haline geldi ve dünya çapında milyonlarca insanı etkiledi. Şifalı bitkilerden elde edilen doğal bileşiklerin, tarih boyunca birçok tedavinin kaynağı olduğu kanıtlanmıştır. Sars-CoV-2 ile mücadele çabaları genellikle ilaçları yeniden konumlandırmaya veya doğal bileşiklerle tedaviler bulmaya odaklandı ve hızla devam ediyor. Ana proteaz (Mpro), SARS-CoV-2'nin hayati bir proteinidir ve ilaç araştırmalarının önemli bir hedefidir. Bu çalışmada, Artemisinin, Artemether, Arteether, Artesunate, Dihydroartemisinic acid, Dihydroartemisinin ve Artemisinic Acid olmak üzere 7 artemisinin türevinin değerlendirilmesi amaçlanmıştır. Bu amaçla, artemisinin türevlerinin SARS-CoV-2 Mpro'ya karşı potansiyelini araştırmak için Moleküler Docking çalışması yapılmıştır. Sonuçta Artesunate, Dihydroartemisinic acid ve Dihydroartemisinin, -8.42 ile -9.35 kcal/mol arasında bağlanma enerjisi ile Mpro inhibisyonu açısından umut verici sonuçlar ortaya çıkarmıştır.

References

  • Referans1. Emirik, M. Potential therapeutic effect of turmeric contents against SARS-CoV-2 compared with experimental COVID-19 therapies: in silico study. J. Biomol. Struct. Dyn. 2020, doi:10.1080/07391102.2020.1835719.
  • Referans2. Islam, M.T.; Sarkar, C.; El-Kersh, D.M.; Jamaddar, S.; Uddin, S.J.; Shilpi, J.A.; Mubarak, M.S. Natural products and their derivatives against coronavirus: A review of the non-clinical and pre-clinical data. Phyther. Res. 2020, 34, 2471–2492, doi:10.1002/ptr.6700.
  • Referans3. Wangkheirakpam, S. Traditional and Folk Medicine as a Target for Drug Discovery. In; Mandal, S.C., Mandal, V., Konishi, T.B.T.-N.P. and D.D., Eds.; Elsevier, 2018; pp. 29–56 ISBN 978-0-08-102081-4.
  • Referans4. Ganjhu, R.K.; Mudgal, P.P.; Maity, H.; Dowarha, D.; Devadiga, S.; Nag, S.; Arunkumar, G. Herbal plants and plant preparations as remedial approach for viral diseases. VirusDisease 2015, 26, 225–236, doi:10.1007/s13337-015-0276-6.
  • Referans5. Akbaş, M.N.; Akçakaya, A. COVID-19 ve Fitoterapi. Bezmialem Sci. 2020, 8, 428–437, doi:10.14235/bas.galenos.2020.4962.
  • Referans6. Din, M.; Ali, F.; Waris, A.; Zia, F.; Ali, M. Phytotherapeutic options for the treatment of COVID-19: A concise viewpoint. Phyther. Res. 2020, 34, 2431–2437, doi:10.1002/ptr.6786.
  • Referans7. Antonelli, M.; Donelli, D.; Maggini, V.; Firenzuoli, F. Phytotherapic compounds against coronaviruses: Possible streams for future research. Phyther. Res. 2020, 34, 1469–1470, doi:10.1002/ptr.6712.
  • Referans8. Boozari, M.; Hosseinzadeh, H. Natural products for COVID-19 prevention and treatment regarding to previous coronavirus infections and novel studies. Phyther. Res. 2020, 1–13, doi:10.1002/ptr.6873.
  • Referans9. Derosa, G.; Maffioli, P.; D’Angelo, A.; Di Pierro, F. A role for quercetin in coronavirus disease 2019 (COVID-19). Phyther. Res. 2020, 1–7, doi:10.1002/ptr.6887.
  • Referans10. Rahman, F.; Tabrez, S.; Ali, R.; Alqahtani, A.S.; Ahmed, M.Z.; Rub, A. Journal of Traditional and Complementary Medicine Molecular docking analysis of rutin reveals possible inhibition of SARS-CoV-2 vital proteins. J. Tradit. Chinese Med. Sci. 2021, 11, 173–179, doi:10.1016/j.jtcme.2021.01.006.
  • Referans11. Scavone, C.; Brusco, S.; Bertini, M.; Sportiello, L.; Rafaniello, C.; Zoccoli, A.; Berrino, L.; Racagni, G.; Rossi, F.; Capuano, A. Current pharmacological treatments for COVID-19: What’s next? Br. J. Pharmacol. 2020, 177, 4813–4824, doi:10.1111/bph.15072.
  • Referans12. Singh, E.; Khan, R.J.; Jha, R.K.; Amera, G.M.; Jain, M.; Singh, R.P.; Muthukumaran, J.; Singh, A.K. A comprehensive review on promising anti-viral therapeutic candidates identified against main protease from SARS-CoV-2 through various computational methods. J. Genet. Eng. Biotechnol. 2020, 18, doi:10.1186/s43141-020-00085-z.
  • Referans13. Boras, B.; Jones, R.M.; Anson, B.J.; Arenson, D.; Aschenbrenner, L.; Bakowski, M.A.; Beutler, N.; Binder, J.; Chen, E.; Eng, H.; et al. Discovery of a Novel Inhibitor of Coronavirus 3CL Protease as a Clinical Candidate for the Potential Treatment of COVID-19. bioRxiv Prepr. Serv. Biol. 2020, doi:10.1101/2020.09.12.293498.
  • Referans14. Qu, J.; Li, G.; Wang, J.; Huang, G.H.J.; Chen, Y.; Qu, Q.; Qiong, X.C. Comparative effectiveness of Lopinavir / Ritonavir-based regimens in COVID-19. 2021, 203–210, doi:10.1111/1440-1681.13425.
  • Referans15. Tahir ul Qamar, M.; Alqahtani, S.M.; Alamri, M.A.; Chen, L.L. Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. J. Pharm. Anal. 2020, 10, 313–319, doi:10.1016/j.jpha.2020.03.009.
  • Referans16. Yang, H.; Yang, M.; Ding, Y.; Liu, Y.; Lou, Z.; Zhou, Z.; Sun, L.; Mo, L.; Ye, S.; Pang, H.; et al. The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 13190–13195, doi:10.1073/pnas.1835675100.
  • Referans17. Sehailia, M.; Chemat, S. Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19. J. Biomol. Struct. Dyn. 2020, 0, 1–11, doi:10.1080/07391102.2020.1796809.
  • Referans18. Haq, F.U.; Roman, M.; Ahmad, K.; Rahman, S.U.; Shah, S.M.A.; Suleman, N.; Ullah, S.; Ahmad, I.; Ullah, W. Artemisia annua: Trials are needed for COVID-19. Phyther. Res. 2020, 34, 2423–2424, doi:10.1002/ptr.6733.
  • Referans19. Castilho, P.C.; Gouveia, S.C.; Rodrigues, A.I. Quantification of artemisinin in Artemisia annua extracts by 1H-NMR. Phytochem. Anal. 2008, 19, 329–334, doi:10.1002/pca.1053.
  • Referans20. D’alessandro, S.; Scaccabarozzi, D.; Signorini, L.; Perego, F.; Ilboudo, D.P.; Ferrante, P.; Delbue, S. The use of antimalarial drugs against viral infection. Microorganisms 2020, 8, 1–26, doi:10.3390/microorganisms8010085.
  • Referans21. Gendrot, M.; Duflot, I.; Boxberger, M.; Delandre, O.; Jardot, P.; Le Bideau, M.; Andreani, J.; Fonta, I.; Mosnier, J.; Rolland, C.; et al. Antimalarial artemisinin-based combination therapies (ACT) and COVID-19 in Africa: In vitro inhibition of SARS-CoV-2 replication by mefloquine-artesunate. Int. J. Infect. Dis. 2020, 99, 437–440, doi:10.1016/j.ijid.2020.08.032.
  • Referans22. Schrödinger Release 2018-4: Maestro, Schrödinger, LLC 2018.
  • Referans23. Salentin, S.; Schreiber, S.; Haupt, V.J.; Adasme, M.F.; Schroeder, M. PLIP: Fully automated protein-ligand interaction profiler. Nucleic Acids Res. 2015, 43, W443–W447, doi:10.1093/nar/gkv315.
  • Referans24. Jin, Z.; Du, X.; Xu, Y.; Deng, Y.; Liu, M.; Zhao, Y.; Zhang, B.; Li, X.; Zhang, L.; Peng, C.; et al. Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature 2020, 582, 289–293, doi:10.1038/s41586-020-2223-y.
  • Referans25. Schrödinger Release 2018-4: Protein Preparation Wizard; Epik, Schrödinger, LLC, New York, NY, 2016; Impact, Schrödinger, LLC, New York, NY, 2016; Prime, Schrödinger, LLC, New York, NY, 2018.
  • Referans26. Schrödinger Release 2018-1: Induced Fit Docking protocol; Glide, Schrödinger, LLC, New York, NY, 2016; Prime, Schrödinger, LLC 2018.
  • Referans27. Harder, E.; Damm, W.; Maple, J.; Wu, C.; Reboul, M.; Xiang, J.Y.; Wang, L.; Lupyan, D.; Dahlgren, M.K.; Knight, J.L.; et al. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. J. Chem. Theory Comput. 2016, 12, 281–296, doi:10.1021/acs.jctc.5b00864.
  • Referans28. Jacobson, M.P.; Pincus, D.L.; Rapp, C.S.; Day, T.J.F.; Honig, B.; Shaw, D.E.; Friesner, R.A. “A Hierarchical Approach to All-Atom Protein Loop Prediction,.” Proteins Struct. Funct. Bioinforma. 2004, 55, 351–367.
There are 28 citations in total.

Details

Primary Language English
Subjects Engineering
Journal Section Makaleler
Authors

Mustafa Emirik 0000-0001-9489-9093

Publication Date May 31, 2021
Submission Date March 10, 2021
Acceptance Date April 2, 2021
Published in Issue Year 2021

Cite

IEEE M. Emirik, “In Silico Inhibition Potential of Artemisinin Derivatives Against SARS-CoV-2 Main Protease”, ECJSE, vol. 8, no. 2, pp. 809–816, 2021, doi: 10.31202/ecjse.894617.