International Journal of Innovative Approaches in Agricultural Research
Abbreviation: IJIAAR | ISSN (Online): 2602-4772 | DOI: 10.29329/ijiaar

Original article | International Journal of Innovative Approaches in Agricultural Research 2021, Vol. 5(3) 269-278

Docking Studies on the Effects of Some Bioactive Compounds from Pistacia atlantica Desf. against Main Protease SARS-CoV2

Taıb Nadjat, Sıtayeb Tayeb, Necmi Beşer & Aıssaouı Nadia

pp. 269 - 278   |  DOI:

Published online: September 30, 2021  |   Number of Views: 8  |  Number of Download: 31


Novel coronavirus which was named later as SARS-CoV2 appeared in Wuhan, China, in the end of December 2019. Actually, no precise drugs are existed and research concerning SARS-CoV2 treatment is deficient. SARS-CoV2 main protease (Mpro) was crystallized by Liu et al. (2020) and represented a crucial drug target. The present work aimed to evaluate some bioactive compounds from Pistacia atlantica as possible SARS-CoV2 Mpro inhibitors, based on molecular docking approach. Molecular docking was carried out using AutoDock Vina software. The results indicated that Beta-Eudesmol, Elemol, Verbenol, Pinocarvone, Myrtenal, Myrtenol and Trans-Carveol have a potential inhibitor activity of SARS-CoV2 Mpro. Nevertheless, further investigations are required to develop and optimize drug process to combat SARS-CoV2.

Keywords: SARS-CoV2, molecular docking, bioactive compounds, Pistacia atlantica

How to Cite this Article?

APA 6th edition
Nadjat, T., Tayeb, S., Beser, N. & Nadia, A. (2021). Docking Studies on the Effects of Some Bioactive Compounds from Pistacia atlantica Desf. against Main Protease SARS-CoV2 . International Journal of Innovative Approaches in Agricultural Research, 5(3), 269-278. doi: 10.29329/ijiaar.2021.378.2

Nadjat, T., Tayeb, S., Beser, N. and Nadia, A. (2021). Docking Studies on the Effects of Some Bioactive Compounds from Pistacia atlantica Desf. against Main Protease SARS-CoV2 . International Journal of Innovative Approaches in Agricultural Research, 5(3), pp. 269-278.

Chicago 16th edition
Nadjat, Taib, Sitayeb Tayeb, Necmi Beser and Aissaoui Nadia (2021). "Docking Studies on the Effects of Some Bioactive Compounds from Pistacia atlantica Desf. against Main Protease SARS-CoV2 ". International Journal of Innovative Approaches in Agricultural Research 5 (3):269-278. doi:10.29329/ijiaar.2021.378.2.

  1. Aanouz, I., Belhassan, A., El-Khatabi, K., Lakhlifi, K., El-ldrissi, M., & Bouachrine, M. 2020. Moroccan Medicinal plants as inhibitors against SARS-CoV-2 main protease: Computational investigations, Journal of Biomolecular Structure and Dynamics. [Google Scholar]
  2. Abdelli, I., Hassani, F., Bekkel Brikci, S., & Ghalem, S. 2020. In silico study the inhibition of Angiotensin converting enzyme 2 receptor of COVID-19 by Ammoides verticillata components harvested from western Algeria. Journal of Biomolecular Structure and Dynamics, (just-accepted), 1-17. [Google Scholar]
  3. Ait Said, S., Fernandez, C., Greff, S., Derridj, A., Gauquelin, T., & Mevy, J., 2011.Interpopulation variability of leaf morpho-anatomical and terpenoid patterns of Pistacia atlantica Desf. Ssp atlantica growng along an aridity gradient in Algeria. Flora-Morphology, Distribution, Functional Ecology of plants, 206(4), 397-405. [Google Scholar]
  4. Anand, K., Ziebuhr, J., Wadhwani, P., Mesters, J. R., & Hilgenfeld, R. 2003. (3CL pro) Structure: Basis for design of Anti-SARS drugs. Science, 300(5626), 1763–1767. [Google Scholar]
  5. Astani, A., Reichling, J., & Schnitzler, P. 2011. Screening for antiviral activities of isolated compounds from essential oils. Evidence-based complementary and alternative medicine. [Google Scholar]
  6. Benhammou, A., Yaacoubi, A., Nibou, L., & Tanouti, B. 2007. Chromium (VI) adsorption from aqueous solution onto Moroccan Al-pillared and cationic surfactant stevensite. Journal of hazardous materials, 140(1-2), 104-109. [Google Scholar]
  7. Benhammou, N., Bekkara, F. A., & Panovska, T. K. 2008. Antioxidant and antimicrobial activities of the Pistacia lentiscus and Pistacia atlantica extracts. African Journal of Pharmacy and Pharmacology, 2(2), 022-028. [Google Scholar]
  8. Benhassaini, H., Benabderrahmane, M., & Chikhi, K. 2003. Contribution à l'évaluation de l'activité antiseptique de l'oléorésine et des huiles essentielles du pistachier de l'Atlas sur certaines sources microbiennes: candida albicans (ATC 20027), candida albicans (ATCC 20032) et saccharomyces cerevisiae. Ethnopharmacologia, 30, 38-46. [Google Scholar]
  9. Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H, Shindyalov I, Bourne P. 2000. The protein data bank. [Google Scholar]
  10. Bobone, S.; Hilsch, M.; Storm, J.; Dunsing, V.; Herrmann, A.; Chiantia, S. 2017.  Phosphatidylserine Lateral Organization Influences the Interaction of Influenza Virus Matrix Protein 1 with Lipid Membranes. [Google Scholar]
  11. 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 and Dynamics, (just-accepted), 1-14. [Google Scholar]
  12. Chang K. O., Y. Kim, S. Lovell, A. D. Rathnayake, and W. C. Groutas,. 2019.  “Antiviral drug discovery: Norovirus proteases and development of inhibitors,”  Viruses, vol. 11, no. 2, pp. 1–14.  [Google Scholar]
  13.  Chen, Y.; Liu, Q.; Guo, D. 2020. Emerging coronaviruses: Genome structure, replication, and pathogenesis.J. Med. [Google Scholar]
  14. Daget P, Godron. M,. 1974. Vocabulaire d’écologie, Paris, Hachette, 275p. [Google Scholar]
  15. DeLano, W. L. 2002. Pymol: An open-source molecular graphics tool. CCP4 News. Protein Crystallography. [Google Scholar]
  16. El Oualidi, J., Ater, M., & Taleb, A. 2004. Conception, essai et évaluation de meilleures pratiques de conservation in situ d’espèces végétales sauvages d’importance économique. Rap. Nat. Proj. Rég. EP/INT0204/GEF. [Google Scholar]
  17. Farhoosh, R., Tavakoli, J., & Khodaparast, M. H. H. 2008. Chemical composition and oxidative stability of kernel oils from two current subspecies of Pistacia atlantica in Iran. Journal of the American Oil Chemists' Society, 85(8), 723. [Google Scholar]
  18. Fatemeh Mahjoub1, Kambiz Akhavan Rezayat2, Mahdi Yousefi3, Masoud Mohebbi4, Roshanak Salari5., 2018. Pistacia atlantica Desf. A review of its traditional uses, phytochemicals and Pharmacology. Journal of Medicine and Life Vol. 11, Issue 3, July-September 2018, pp.180–186 [Google Scholar]
  19. Hamdan, I. I., & Afifi, F. U. 2004. Studies on the in vitro and in vivo hypoglycemic activities of some medicinal plants used in treatment of diabetes in Jordanian traditional medicine. Journal of ethnopharmacology, 93(1), 117-121. [Google Scholar]
  20. Höfer, C.T.; Di Lella, S.; Dahmani, I.; Jungnick, N.; Bordag, N.; Bobone, S.; Huang, Q.; Keller, S.; Herrmann, A.; Chiantia, S. 2019. Structural determinants of the interaction between influenza A virus matrix protein M1 and lipid membranes. Biochim. Biophys. Acta Biomembr. 1861, 1123–1134. [Google Scholar]
  21. Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Yang, H. 2020.  Structure-based drug design, virtual screening and high-throughput screening rapidly identify antiviral leads targeting COVID-19. BioRxiv, 2020.02.26.964882. [Google Scholar]
  22. Jaghoori, M. M., Bleijlevens, B., & Olabarriaga, S. D. 2016. 1001 ways to run AutoDock Vina for virtual screening. Journal of computer-aided molecular design, 30(3), 237-249. [Google Scholar]
  23. Karimi Ali  , Mohmmad Taghi Moradi , Asghar Gafourian. 2020. In Vitro Anti-adenovirus Activity and Antioxidant Potential of Pistacia atlantica Desf. Leaves. Research Journal of Pharmacognosy (RJP) 7(2): 53-60. [Google Scholar]
  24. Konovalov, O., Myagkov, I., Struth, B., & Lohner, K. 2002. Lipid discrimination in phospholipid monolayers by the antimicrobial frog skin peptide PGLa. A synchrotron X-ray grazing incidence and reflectivity study. European Biophysics Journal, 31(6), 428-437. [Google Scholar]
  25. Laskowski, R. A., & Swindells, M. B. 2011. LigPlot+: multiple ligand–protein interaction diagrams for drug discovery. 51 (10), 2778–2786. [Google Scholar]
  26. Liu, Y. W., Huang, C. F., Huang, K. B. and Lee, F. J. 2005. Role for Gcs1p in regulation of Arl1p at trans-Golgi compartments. Mol Biol Cell 16, 4024-33. [Google Scholar]
  27. Mcconkey B, Sobolev V, Edelman M. 1983. The performance of current methods in ligand-protein docking. Curr Sci;83. [Google Scholar]
  28. Medeiros, L.B.P.; Rocha, M.D.S.; Lima, S.G.D.; Júnior, G.R.D.S.; Citó, A.M.D.G.L.; Silva, D.D.; Lopes, J.A.D.; Moura, D.J.; Saffi, J.; Mobin, M.; et al. 2012. Chemical constituents and evaluation of cytotoxic and antifungal activity of Lantana camara essential oils. Rev Bras Farmacogn. 22, 1259–1267. [Google Scholar]
  29. Monjauze, A. 1980. Connaissance du bétoum Pistacia atlantica Desf. [Google Scholar]
  30. N. Aziz, M. Y. Kim, and J. Y. Cho. 2020. Anti-inflammatory effects of luteolin: A revie of in vitro, in vivo, and in silico studies, J. Ethnopharmacol., 225:  342–358. [Google Scholar]
  31. 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 and Dynamics, 1-15. [Google Scholar]
  32. 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. [Google Scholar]
  33. Quézel, P., & Médail, F. 2003. Ecologie et biogéographie des forêts du bassin méditerranéen. Ecology and Biogeography of the forests of the Mediterranean basin. [Google Scholar]
  34. Sandeep, G., Nagasree, K. P., Hanisha, M., & Kumar, M. M. K. 2011. AUDocker LE: A GUI for virtual screening with AUTODOCK Vina. BMC research notes, 4(1), 1-4. [Google Scholar]
  35. Sanner, M. F. 1999. Python: a programming language for software integration and development. J Mol Graph Model, 17(1), 57-61. [Google Scholar]
  36. Subramanian Boopathi, Adolfo B. Poma & Ponmalai Kolandaivel. 2020. Novel [Google Scholar]
  37. 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment, Journal of Biomolecular Structure and Dynamics, [Google Scholar]
  38. Suyash Pant, Meenakshi Singh, V. Ravichandiran, U. S. N. Murty & Hemant Kumar Srivastava. 2020. Peptide-like and small-molecule inhibitors against Covid-19, Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2020.1757510. [Google Scholar]
  39. Topçu, G., Ay, M., Bilici, A., Sarıkürkcü, C., Öztürk, M., & Ulubelen, A. 2007. A new flavone from antioxidant extracts of Pistacia terebinthus. Food Chemistry, 103(3), 816-822. [Google Scholar]
  40. Trott, O., & Olson, A. J. 2010. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. [Google Scholar]
  41. Vieira, P., Morais, S., Bezerra, F., et al. 2014. Chemical composition and antifungal activity of essential oils from Ocimum species. Ind Crop Prod 55:267–71. [Google Scholar]
  42. X. Liu and X.-J. Wang. 2020. “Potential inhibitors against 2019-nCoV coronavirus M protease from clinically. [Google Scholar]
  43. X. Xu, P. Chen, J. Wang, et al. 2020. Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission, Sci. China Life Sci. 63 457e460 [Google Scholar]
  44. Xue, X.; Yu, H.; Yang, H.; Xue, F.; Wu, Z.; Shen, W.; Li, J.; Zhou, Z.; Ding, Y.; Zhao, Q.; et al. 2008. Structures of two coronavirus main proteases: Implications for substrate binding and antiviral drug design. J. Virol., 82, 2515–2527. [Google Scholar]
  45. Yang, H., Yang, M., Ding, Y., Liu, Y., Lou, Z., Zhou, Z., Sun, L., Mo, L., Ye, S., Pang, H., Gao, G. F., Anand, K., Bartlam, M., Hilgenfeld, R., & Rao, Z. 2003. The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proceedings of the National Academy of Sciences, 100(23), 13190–13195. [Google Scholar]
  46. Zhao, Q., Li, S., Xue, F., Zou, Y., Chen, C., Bartlam, M., & Rao, Z. 2008. Structure of the main protease from a Global Infectious Human Coronavirus, HCoV-HKU1. Journal of Virology, 82(17), 8647–8655. [Google Scholar]