Computational Prediction of Cymbopogon Citratus Compounds as Promising Inhibitors of Main Protease of SARS-CoV-2

Computational Prediction of Cymbopogon Citratus Compounds


  • Tuba Ahmad Department of Biochemistry, Kinnaird College for Women, Lahore, Pakistan
  • Rashid Saif Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan
  • Muhammad Hassan Raza Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan
  • Muhammad Osama Zafar Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan
  • Saeeda Zia Department of Sciences and Humanities, National University of Computer and Emerging Sciences, Lahore, Pakistan
  • Mehwish Shafiq Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan
  • Laraib Ali Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan
  • Hooria Younas Department of Biochemistry, Kinnaird College for Women, Lahore, Pakistan



SARS-CoV-2, Main Protease, COVID-19, MOE, Molecular Docking, MDS Analysis


There is a dire need to develop any antiviral therapy for the treatment of SARS-CoV-2. Objective: To investigate the potential therapeutic drug agents from Cymbopogon citratus compounds against the main-protease (Mpro) of SARS-CoV-2. Methods: Initial screening was carried out using molecular docking, dynamic simulation followed by ADMET profiling and Lipinski’s physiochemical parameters for prediction of drug likeliness. MOE/PyRx was used for docking before determining the stability of the best complexes through NAMD/VMD softwares. Moreover, SwissADME and admetSAR web-based tools were used for drug likeliness of the best complexes. Results: Out of total 50 compounds, 11 presented the lowest binding energies which includes tannic acid, isoorientin, swertiajaponin, chlorogenic acid, cymbopogonol, warfarin, citral diethyl acetal, citral acetate, luteolin, kaempferol and cianidanol with binding energies of -8.12, -7.38, -7.33, -6.88, -6.48, -6.32, -6.31, -6.18, -6.18, -6.13 and -6.02, respectively. Current studies show isoorientin, chlorogenic acid and tannic acid as the promising drug agents using RMSD, Hbond, heatmap graphs. Conclusion: Further in-vivo experiments are suggested to ascertain the medicinal use of these potential inhibitors against COVID-19.


Pal M, Berhanu G, Desalegn C, Kandi V. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): an update. Cureus. 2020 Mar; 12(3): e7423. doi: 10.7759/cureus.7423.

Malik YS, Sircar S, Bhat S, Sharun K, Dhama K, Dadar M, et al. Emerging novel coronavirus (2019-nCoV)—current scenario, evolutionary perspective based on genome analysis and recent developments. Veterinary Quarterly. 2020 Jan; 40(1): 68-76. doi: 10.1080/01652176.2020.1727993.

Pachetti M, Marini B, Benedetti F, Giudici F, Mauro E, Storici P, et al. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. Journal of Translational Medicine. 2020 Dec; 18: 1-9. doi: 10.1186/s12967-020-02344-6.

Harrison AG, Lin T, Wang P. Mechanisms of SARS-CoV-2 transmission and pathogenesis. Trends in Immunology. 2020 Dec; 41(12): 1100-15. doi: 10.1016/

Peiris JS, Lai ST, Poon LL, Guan Y, Yam LY, Lim W, et al. Coronavirus as a possible cause of severe acute respiratory syndrome. The Lancet. 2003 Apr; 361(9366): 1319-25. doi: 10.1016/S0140-6736(03)13077-2.

Chellapandi P and Saranya S. Genomics insights of SARS-CoV-2 (COVID-19) into target-based drug discovery. Medicinal Chemistry Research. 2020 Oct; 29(10): 1777-91. doi: 10.1007/s00044-020-02610-8.

Jin Z, Du X, Xu Y, Deng Y, Liu M, Zhao Y, et al. Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature. 2020 Jun; 582(7811): 289-93. doi: 10.1038/s41586-020-2223-y.

Chatterjee S, Maity A, Chowdhury S, Islam MA, Muttinini RK, Sen D. In silico analysis and identification of promising hits against 2019 novel coronavirus 3C-like main protease enzyme. Journal of Biomolecular Structure and Dynamics. 2021 Sep; 39(14): 5290-303. doi: 10.1080/07391102.2020.1787228.

Shi J and Song J. The catalysis of the SARS 3C‐like protease is under extensive regulation by its extra domain. The FEBS Journal. 2006 Mar; 273(5): 1035-45. doi: 10.1111/j.1742-4658.2006.05130.x.

Nashed NT, Kneller DW, Coates L, Ghirlando R, Aniana A, Kovalevsky A, et al. Autoprocessing and oxyanion loop reorganization upon GC373 and nirmatrelvir binding of monomeric SARS-CoV-2 main protease catalytic domain. Communications Biology. 2022 Sep; 5(1): 976. doi: 10.1038/s42003-022-03910-y.

Asif M and Khodadadi E. Medicinal uses and chemistry of flavonoid contents of some common edible tropical plants. Archives of Advances in Biosciences. 2013 Jun; 4(3): 119-138. doi: 10.22037/jps.v4i3.4648.

Sepúlveda-Arias JC, Veloza LA, Escobar LM, Orozco LM, Lopera IA. Anti-inflammatory effects of the main constituents and epoxides derived from the essential oils obtained from Tagetes lucida, Cymbopogon citratus, Lippia alba and Eucalyptus citriodora. Journal of Essential Oil Research. 2013 Jun; 25(3): 186-93. doi: 10.1080/10412905.2012.751556.

Ranitha M, Nour AH, Sulaiman ZA, Nour AH. A comparative study of lemongrass (Cymbopogon Citratus) essential oil extracted by microwave-assisted hydrodistillation (MAHD) and conventional hydrodistillation (HD) Method. International Journal of Chemical Engineering and Applications. 2014 Apr; 5(2): 104. doi: 10.7763/IJCEA.2014.V5.360.

Zakaryan H, Arabyan E, Oo A, Zandi K. Flavonoids: promising natural compounds against viral infections. Archives of Virology. 2017 Sep; 162: 2539-51. doi: 10.1007/s00705-017-3417-y.

Pinto ZT, Sánchez FF, Santos AR, Amaral AC, Ferreira JL, Escalona-Arranz JC, et al. Chemical composition and insecticidal activity of Cymbopogon citratus essential oil from Cuba and Brazil against housefly. Revista Brasileira de Parasitologia Veterinária. 2015 Jan; 24: 36-44. doi: 10.1590/S1984-29612015006.

Fokom R, Adamou S, Essono D, Ngwasiri DP, Eke P, Mofor CT, et al. Growth, essential oil content, chemical composition and antioxidant properties of lemongrass as affected by harvest period and arbuscular mycorrhizal fungi in field conditions. Industrial Crops and Products. 2019 Oct; 138: 111477. doi: 10.1016/j.indcrop.2019.111477.

Akande IS, Samuel TA, Agbazue U, Olowolagba BL. Comparative proximate analysis of ethanolic and water extracts of Cymbopogon citratus (lemon grass) and four tea brands. Plant Sciences Research. 2011; 3(4): 29-35. doi: 10.3923/psres.2011.29.35.

Dias R, de Azevedo J, Walter F. Molecular docking algorithms. Current Drug Targets. 2008 Dec; 9(12): 1040-7. doi: 10.2174/138945008786949432.

Saif R, Raza MH, Rehman T, Zafar MO, Zia S, Qureshi AR. Molecular docking and dynamic simulation of Olea europaea and Curcuma Longa compounds as potential drug agents for targeting Main-Protease of SARS-nCoV2. ChemRxiv. 2021: 1-22. doi: 10.26434/chemrxiv.13246739.

Okimoto N, Futatsugi N, Fuji H, Suenaga A, Morimoto G, Yanai R, et al. High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations. PLoS Computational Biology. 2009 Oct; 5(10): e1000528. doi: 10.1371/journal.pcbi.1000528.


DOI: 10.54393/fbt.v2i01.23
Published: 2022-06-30

How to Cite

Ahmad, T., Saif, R., Hassan Raza, M., Osama Zafar, M., Zia, S., Shafiq, M., Ali, L., & Younas, H. (2022). Computational Prediction of Cymbopogon Citratus Compounds as Promising Inhibitors of Main Protease of SARS-CoV-2: Computational Prediction of Cymbopogon Citratus Compounds. Futuristic Biotechnology, 2(01), 20–25.



Orginal Articles