Computational Prediction of Nigella sativa Compounds as Potential Drug Agents for Targeting Spike Protein of SARS-CoV-2

Computational Prediction of N. sativa Compounds as Potential Drug Agents


  • Laraib Ali Department of Biotechnology, 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
  • Tuba Ahmad Department of Biochemistry, Kinnaird College for Women, Lahore, Pakistan
  • Iram Anjum Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan



SARS-CoV-2, Spike Protein, COVID-19, MOE, Molecular Docking, MDS Analysis


SARS-CoV-2 was first identified in Wuhan, China in December 2019 and has rapidly devastated worldwide. The lack of approved therapeutic drugs has intensified the global situation, so researchers are seeking potential treatments using regular drug agents and traditional herbs as well. Objectives: To identify new therapeutic agents from Nigella sativa against spike protein (PDB ID: 7BZ5) of SARS-CoV-2. Methods: The 46 compounds from N. sativa were docked with spike protein using Molecular Operating Environment (MOE) software and compared with commercially available anti-viral drugs e.g., Arbidol, Favipiravir, Remdesivir, Nelfinavir, Chloroquine, Hydroxychloroquine. The Molecular Dynamic Simulation (MDS) analysis was also applied to determine ligand-protein complex stability. Furthermore, the pharmacological properties of compounds were also analyzed using AdmetSAR and SwissADME. Results: Out of its total 46 ligands, 8 compounds i.e., Methyl stearate, Eicosadienoic acid, Oleic acid, Stearic acid, Linoleic acid, Myristoleic acid, Palmitic acid, and Farnesol were selected for further analysis based on their minimum binding energy ranges from -7.45 to -7.07 kcal/mol. The docking scores of N. sativa phytocompounds were similar to drugs taken as control. Moreover, post simulation analysis of Methyl stearate complex predicted the most stable conformer. Conclusions: Further, in-vivo experiments are suggested to validate the medicinal use of Methyl stearate as potential inhibitors against spike protein of SARS-CoV-2.


Gorbalenya AE, Baker SC, Baric RS, de Groot RJ, Drosten C, Gulyaeva AA, et al. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nature Microbiology. 2020 Apr; 5(4): 536-44. doi: 10.1038/s41564-020-0695-z.

Ng Y, Li Z, Chua YX, Chaw WL, Zhao Z, Er B, et al. Evaluation of the effectiveness of surveillance and containment measures for the first 100 patients with COVID-19 in Singapore—January 2–February 29, 2020. Morbidity and Mortality Weekly Report. 2020 Mar; 69(11): 307. doi: 10.15585/mmwr.mm6911e1.

Kamble P, Daulatabad V, John N, John J. Synopsis of symptoms of COVID-19 during second wave of the pandemic in India. Hormone Molecular Biology and Clinical Investigation. 2021 Dec; 43(1): 97-104. doi: 10.1515/hmbci-2021-0043.

Cvetković VM, Nikolić N, Radovanović Nenadić U, Öcal A, K. Noji E, Zečević M. Preparedness and preventive behaviors for a pandemic disaster caused by COVID-19 in Serbia. International Journal of Environmental Research and Public Health. 2020 Jun; 17(11): 4124. doi: 10.3390/ijerph17114124.

Coutard B, Valle C, De Lamballerie X, Canard B, Seidah NG, Decroly E. The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade. Antiviral Research. 2020 Apr; 176: 104742. doi: 10.1016/j.jare.2020.03.005.

Shereen MA, Khan S, Kazmi A, Bashir N, Siddique R. COVID-19 infection: Emergence, transmission, and characteristics of human coronaviruses. Journal of Advanced Research. 2020 Jul; 24: 91-8. doi: 10.1016/j.jare.2020.03.005.

Li X, Geng M, Peng Y, Meng L, Lu S. Molecular immune pathogenesis and diagnosis of COVID-19. Journal of Pharmaceutical Analysis. 2020 Apr; 10(2): 102-8. doi: 10.1016/j.jpha.2020.03.001.

Gyebi GA, Adegunloye AP, Ibrahim IM, Ogunyemi OM, Afolabi SO, Ogunro OB. Prevention of SARS-CoV-2 cell entry: insight from in silico interaction of drug-like alkaloids with spike glycoprotein, human ACE2, and TMPRSS2. Journal of Biomolecular Structure and Dynamics. 2022 Mar; 40(5): 2121-45. doi: 10.1080/07391102.2020.1835726.

Shajahan A, Supekar NT, Gleinich AS, Azadi P. Deducing the N-and O-glycosylation profile of the spike protein of novel coronavirus SARS-CoV-2. Glycobiology. 2020 Dec; 30(12): 981-8. doi: 10.1093/glycob/cwaa042.

Li X, Luk HKH, Lau SKP, Woo PCY. Human Coronaviruses: General Features. Reference Module in Biomedical Sciences. 2019: B978-0-12-801238-3.95704-0. doi: 10.1016/B978-0-12-801238-3.95704-0.

Yang H and Rao Z. Structural biology of SARS-CoV-2 and implications for therapeutic development. Nature Reviews Microbiology. 2021 Nov; 19(11): 685-700. doi: 10.1038/s41579-021-00630-8.

Iqbal Yatoo M, Hamid Z, Parray OR, Wani AH, Ul Haq A, Saxena A, et al. COVID-19-Recent advancements in identifying novel vaccine candidates and current status of upcoming SARS-CoV-2 vaccines. Human Vaccines & Immunotherapeutics. 2020 Dec; 16(12): 2891-904. doi: 10.1080/21645515.2020.1788310.

Sytar O, Brestic M, Hajihashemi S, Skalicky M, Kubeš J, Lamilla-Tamayo L, et al. COVID-19 prophylaxis efforts based on natural antiviral plant extracts and their compounds. Molecules. 2021 Jan; 26(3): 727. doi: 10.3390/molecules26030727.

Imran M, Khan SA, Alshammari MK, Alkhaldi SM, Alshammari FN, Kamal M, et al. Nigella sativa L. and COVID-19: A glance at the anti-COVID-19 chemical constituents, clinical trials, inventions, and patent literature. Molecules. 2022 Apr; 27(9): 2750. doi: 10.3390/molecules27092750.

Bouchentouf S and Missoum N. Identification of Compounds from Nigella Sativa as New Potential Inhibitors of 2019 Novel Coronasvirus (Covid-19): Molecular Docking Study. 2020 Apr: 1-12. doi: 10.26434/chemrxiv.12055716.v1.

Dias R and de Azevedo WF Jr. Molecular docking algorithms. Currents Drug Targets. 2008 Dec; 9(12): 1040-7. doi: 10.2174/138945008786949432.

Yin J, Li C, Ye C, Ruan Z, Liang Y, Li Y, et al. Advances in the development of therapeutic strategies against COVID-19 and perspectives in the drug design for emerging SARS-CoV-2 variants. Computational and Structural Biotechnology Journal. 2022 Jan; 20: 824-837. doi: 10.1016/j.csbj.2022.01.026.

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. Biological and Medicinal Chemistry. 2021 Mar: 1-22. doi: 10.26434/chemrxiv.13246739.v2.

Saif R, Zafar MO, Raza MH, Zia S, Qureshi AR. Computational prediction of Carica papaya phytocompounds as potential drug agent against RdRp and spike protein of SARS-nCoV2 by molecular docking and dynamics simulation approaches. Research Square. 2022 Aug. doi: 10.21203/

Naqvi AA, Mohammad T, Hasan GM, Hassan M. Advancements in docking and molecular dynamics simulations towards ligand-receptor interactions and structure-function relationships. Current Topics in Medicinal Chemistry. 2018 Aug; 18(20): 1755-68. doi: 10.2174/1568026618666181025114157.


DOI: 10.54393/pbmj.v6i3.853
Published: 2023-03-31

How to Cite

Ali, L. ., Saif, R., Hassan Raza, M. ., Osama Zafar, M. ., Zia, S. ., Shafiq, M. ., Ahmad, T. ., & Anjum, I. . (2023). Computational Prediction of Nigella sativa Compounds as Potential Drug Agents for Targeting Spike Protein of SARS-CoV-2: Computational Prediction of N. sativa Compounds as Potential Drug Agents . Pakistan BioMedical Journal, 6(3), 18–23.



Original Article