Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
권호 표지
DOI QR코드

DOI QR Code

Potential of Hanjeli (Coix lacryma-jobi) essential oil in preventing SARS-CoV-2 infection via blocking the Angiotensin Converting Enzyme 2 (ACE2) receptor

  • Diningrat, Diky Setya (Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Medan) ;
  • Sari, Ayu Nirmala (Biology Study Program, Faculty of Science and Technology, UIN Ar-Raniry Banda Aceh) ;
  • Harahap, Novita Sari (Department of Sports Science, Faculty of Sports Science, Universitas Negeri Medan) ;
  • Kusdianti, Kusdianti (Department of Biology, Faculty of Mathematics and Natural Sciences Education, Indonesian University of Education)
  • Received : 2021.09.14
  • Accepted : 2021.12.27
  • Published : 2021.12.31
Download PDF
⟨ Previous Next ⟩

Abstract

Covid-19 is an ongoing pandemic as we speak in 2022. This infectious disease is caused by the SARS-CoV-2 virus, which infects cells by binding to the angiotensin-converting enzyme 2 (ACE2) receptor on the cell surface. Thus, strategies that inhibit the binding of SARS-CoV-2 to the ACE2 receptor can stop this contagion. Hanjeli (Coix lacryma-jobi) essential oil contains many bioactive compounds, including dodecanoic acid; tetradecanoic acid; 7-Amino-8-imino-2-(2-imino-2H-chromen-3-yl); and 1,5,7,10-tetraaza-phen-9-one. These compounds suppress viral replication and may prevent Covid-19. Accordingly, this study assessed whether, these four limonoid compounds can block the ACE2 receptor. To this end, their physicochemical properties were predicted using Lipinski's "rule of five" on the SwissADME website, and their toxicity was assessed using the online tools ProTox and pkCSM. Additionally, their interactions with the ACE2 receptor were predicted via molecular docking using Autodock Vina. All the four compounds satisfied the "rule of five" and tetradecanoic acid was predicted to have a higher affinity than the comparison compound remdesivir and the original ligand of ACE2. Molecular docking results suggested that the compounds from hanjeli essential oil interact with the active site of the ACE2 receptor similarly as the original ligand and remdesivir. In conclusion, hanjeli essential oil contains compounds predicted hinder the interaction of SARS-CoV-2 with the ACE2 receptor. Accordingly, our data may facilitate the development of a phytomedical strategy against SARS-CoV-2 infection.

Keywords

Acknowledgement

The authors thank to the DRPM Kemendikbudristekdikti which has funded this research with the 2021 multi-year basic research scheme numbered DIPA SP DIPA-023.17. The author also expresses appreciation to the research team members from the Department of Biology, Faculty of Mathematics and Natural Sciences, Medan State University; Biology Study Program, Faculty of Science and Technology, UIN Ar-Raniry Banda Aceh; Department of Sports Science, Faculty of Sports Science, State University of Medan; Department of Biology, Faculty of Mathematics and Natural Sciences Education, Indonesian Education University, Bandung.

References

  1. Arwansyah A, Ambarsari L, Sumaryada TI. (2014). Simulasi docking senyawa kurkumin dan analognya sebagai inhibitor reseptor androgen pada kanker prostat. Current Biochemistry 1(1):11-19 https://doi.org/10.29244/cb.1.1.11-19
  2. Bimonte S, Crispo A, Amore A, Celentano E, Cuomo A, Cascella M. (2020). Potential antiviral drugs for SARS-Cov-2 treatment: preclinical findings and ongoing clinical research. In Vivo 34(3 suppl):1597-1602 https://doi.org/10.21873/invivo.11949
  3. Borkotoky S, Banerjee M. (2020). A computational prediction of SARS-CoV-2 structural protein inhibitors from Azadirachta indica (Neem). Journal of Biomolecular Structure and Dynamics, pp. 1-11
  4. Chagas CM, Moss S, Alisaraie L. (2018). Drug metabolites and their effects on the development of adverse reactions: Revisiting lipinski's rule of five. International Journal of Pharmaceutics 549(1-2):133-149 https://doi.org/10.1016/j.ijpharm.2018.07.046
  5. Dahab MA, Hegazy MM, Abbass HS. (2020). Hordatines as a potential inhibitor of COVID-19 main protease and RNA polymerase: an In-Silico approach. Natural Products and Bioprospecting 10(6):453-462 https://doi.org/10.1007/s13659-020-00275-9
  6. Decaro N and Lorusso A. (2020). Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses. Veterinary Microbiology 244:108693 https://doi.org/10.1016/j.vetmic.2020.108693
  7. Diningrat DS, Risfandi M, Harahap NS, Sari AN, Siregar HK. (2020). Phytochemical screening and antibacterial activity coix lacryma-jobi oil. Journal of Plant Biotechnology 47(1):100-106. https://doi.org/10.5010/JPB.2020.47.1.100
  8. Gheblawi M, Wang K, Viveiros A, Nguyen Q, Zhong JC, Turner AJ, Raizada MK, Grant MB, Oudit GY. (2020). Angiotensin-converting enzyme 2: SARS-CoV-2 receptor and regulator of the renin-angiotensin system: celebrating the 20th anniversary of the discovery of ACE2. Circulation Research 126(10):1456-1474 https://doi.org/10.1161/circresaha.120.317015
  9. Goodsell DS, Sanner MF, Olson AJ, Forli S. (2021). The AutoDock suite at 30. Protein Science 30(1):31-43 https://doi.org/10.1002/pro.3934
  10. Helmy YA, Fawzy M, Elaswad A, Sobieh A, Kenney SP, Shehata AA. (2020). The COVID-19 pandemic: a comprehensive review of taxonomy, genetics, epidemiology, diagnosis, treatment, and control. Journal of Clinical Medicine 9(4):1225 https://doi.org/10.3390/jcm9041225
  11. Hussein RK, Elkhair HM. (2021). Molecular docking identification for the efficacy of some zinc complexes with chloroquine and hydroxychloroquine against main protease of COVID-19. Journal of Molecular Structure 1231:129979 https://doi.org/10.1016/j.molstruc.2021.129979
  12. Kanakaveti V, Shanmugam A, Ramakrishnan C, Anoosha P, Sakthivel R, Rayala SK, Gromiha MM. (2020). Computational approaches for identifying potential inhibitors on targeting protein interactions in drug discovery. Advances In Protein Chemistry And Structural Biology 121:25-47 https://doi.org/10.1016/bs.apcsb.2019.11.013
  13. Koulgi S, Vinod J, Mallikarjunachari VNU, Uddhavesh S, Rajendra J. (2020). Remdesivir-bound and ligand-free simulations reveal the probable mechanism of inhibiting the RNA dependent RNA polymerase of severe acute respiratory syndrome coronavirus 2. RSC Advances 10(45):26792-26803 https://doi.org/10.1039/d0ra04743k
  14. Li S, Li S, Disoma C, Zheng R, Zhou M, Razzaq A, Liu P, Zhou Y, Dong Z, Du A, Peng J. (2021). SARS-CoV-2: Mechanism of infection and emerging technologies for future prospects. Reviews in Medical Virology 31(2):e2168.
  15. Lipinski CA. (2004). Lead-and drug-like compounds: the rule-of-five revolution. Drug Discovery Today: Technologies 1(4):337-341 https://doi.org/10.1016/j.ddtec.2004.11.007
  16. Maia EHB, Assis LC, de Oliveira TA, da Silva AM, Taranto AG. (2020). Structure-based virtual screening: from classical to artificial intelligence. Frontiers in Chemistry 8:343 https://doi.org/10.3389/fchem.2020.00343
  17. Muttaqin FZ, Ismail H, Hubbi NM. (2019). Studi molecular docking, molecular dynamic, dan prediksi toksisitas senyawa turunan alkaloid naftiridin sebagai inhibitor protein kasein kinase 2-A pada kanker leukemia. Journal of Pharmacoscript 2(1):49-64 https://doi.org/10.36423/pharmacoscript.v2i1.241
  18. Neldi V, Suharjono S. (2020). Remdesivir: Mechanism and effectiveness for coronavirus disease 2019 (COVID-19). Pharmaceutical Sciences & Research 7(4):5
  19. Ni W, Yang X, Yang D, Bao J, Li R, Xiao Y, Hou C, Wang H, Liu J, Yang D, Xu Y. (2020). Role of angiotensin-converting enzyme 2 (ACE2) in COVID-19. Critical Care 24(1):1-10 https://doi.org/10.1186/s13054-019-2683-3
  20. Patrick G. (2001). Instant notes in medicinal chemistry. BIOS Scientific Publishers Ltd.
  21. Prasetiawati R, Suherman M, Permana B, Rahmawati R. (2021). Molecular docking study of anthocyanidin compounds against Epidermal Growth Factor Receptor (EGFR) as anti-lung cancer. Indonesian Journal of Pharmaceutical Science and Technology 8(1):8-20 https://doi.org/10.24198/ijpst.v8i1.29872
  22. Pratama KF, Fauzi M, Hasanah AN. (2020). Activity screening and structure modification of trigonelline as new anticancer drug for non small cell lung cancer through In Silico. Indonesian Journal of Pharmaceutical Science and Technology 7(3):90-99 https://doi.org/10.24198/ijpst.v7i3.26765
  23. Ren LL, Wang YM, Wu ZQ, Xiang ZC, Guo L, Xu T, Jiang YZ, Xiong Y, Li YJ, Li XW, Li H. (2020). Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study. Chinese Medical Journal 133(9):1015 https://doi.org/10.1097/CM9.0000000000000722
  24. Rothan HA, Byrareddy SN. (2020). The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak. Journal of Autoimmunity 109:102433 https://doi.org/10.1016/j.jaut.2020.102433
  25. Seffernick JT, Lindert S. (2020). Hybrid methods for combined experimental and computational determination of protein structure. The Journal of Chemical Physics 153(24):240901 https://doi.org/10.1063/5.0026025
  26. Setiawan H, Irawan MI. (2017). Kajian pendekatan penempatan ligan pada protein menggunakan algoritma genetika. Jurnal Sains dan Seni ITS 6(2):A68-A72
  27. Suhadi A, Rizarullah R and Feriyani F. (2019). Simulasi docking senyawa aktif daun binahong sebagai inhibitor enzyme aldose reductase. Sel Jurnal Penelitian Kesehatan 6(2):55-65 https://doi.org/10.22435/sel.v6i2.1651
  28. Vaduganathan M, Vardeny O, Michel T, McMurray JJ, Pfeffer MA, Solomon SD. (2020). Renin-angiotensin-aldosterone system inhibitors in patients with Covid-19. New England Journal of Medicine 382(17):1653-1659 https://doi.org/10.1056/nejmsr2005760
  29. Valdes-Tresanco MS, Valdes-Tresanco ME, Valiente PA, Moreno E. (2020). AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4. Biology Direct 15(1):1-12 https://doi.org/10.1186/s13062-019-0257-6
  30. Wan Y, Shang J, Graham R, Baric RS, Li F. (2020). Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. Journal of virology 94(7):e00127-20
  31. Wiese O, Annalise EZ, Tahir SP. (2021). Molecules in pathogenesis: angiotensin converting enzyme 2 (ACE2). Journal of Clinical Pathology 74(5):285-290 https://doi.org/10.1136/jclinpath-2020-206954
  32. World Health Organization (WHO) (2020). Geneva: World Health Organization. https://apps.who.int/iris/bitstream/handle/10665/331865/nCoVsitrep23Apr2020-eng.pdf
  33. Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 367(6483):1260-1263 https://doi.org/10.1126/science.abb2507
  34. Wu A, Peng Y, Huang B, Ding X, Wang X, Niu P, Meng J, Zhu Z, Zhang Z, Wang J, Sheng J. (2020). Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. Cell Host & Microbe 27(3):325-328 https://doi.org/10.1016/j.chom.2020.02.001
  35. Xu X, Chen P, Wang J, Feng J, Zhou H, Li X, Zhong W, Hao P. (2020). Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Science China Life Sciences 63(3):457-460 https://doi.org/10.1007/s11427-020-1637-5
  36. Yang Y, Islam MS, Wang J, Li Y, Chen X (2020). Traditional Chinese medicine in the treatment of patients infected with 2019-new coronavirus (SARS-CoV-2): a review and perspective. International Journal of Biological Sciences 16(10):1708 https://doi.org/10.7150/ijbs.45538
  37. Yin W, Mao C, Luan X, Shen DD, Shen Q, Su H, Wang X, Zhou F, Zhao W, Gao M, Chang S. (2020). Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir. Science 368(6498):1499-1504 https://doi.org/10.1126/science.abc1560
  38. Zhao Z, Tajkhorshid E. (2021). GOLEM: Automated and robust cryo-em-guided ligand docking with explicit water molecules. Biophysical Journal 120(3):290a https://doi.org/10.1016/j.bpj.2020.11.1861
  39. Zheng YY, Ma YT, Zhang JY, Xie X. (2020). COVID-19 and the cardiovascular system. Nature Reviews Cardiology 17(5):259-260 https://doi.org/10.1038/s41569-020-0360-5