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In silico identification of compounds from Nigella sativa seed oil as potential inhibitors of SARS-CoV-2 targets

Duru et al., Bulletin of the National Research Centre, doi:10.1186/s42269-021-00517-x
Mar 2021  
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In Silico study of compounds from Nigella Sativa oil. Authors identify component phytochemicals with gas chromatography-mass spectrometry and analyze binding affinity with SARS-CoV-2 targets. Caryophyllene oxide, α-bergamotene, and β-bisabolene were identified as promising candidates for inhibition.
Duru et al., 12 Mar 2021, peer-reviewed, 3 authors.
In Silico studies are an important part of preclinical research, however results may be very different in vivo.
This PaperNigella SativaAll
In silico identification of compounds from Nigella sativa seed oil as potential inhibitors of SARS-CoV-2 targets
Chidi Edbert Duru, Ijeoma Akunna Duru, Abayomi Emmanuel Adegboyega
Bulletin of the National Research Centre, doi:10.1186/s42269-021-00517-x
Background: The growing number of cases, severity and fatality of the COVID-19 pandemic, coupled with the fact that no cure has been found has made infected individuals especially in Africa, to resort to the consumption of different natural products to alleviate their condition. One of such plant materials that have been consumed to remedy the severity of this viral infection is the oil of Nigella sativa seed commonly called black seed oil. In this study, we extracted and characterized the oil from this seed using gas chromatography coupled to a mass selective detector to identify the component phytochemicals. Site-directed multiligand docking of the identified compounds was performed on SARS-CoV-2 molecular targets-Replicase polyprotein 1a, RNA binding protein of NSP9, ADP ribose phosphatase of NSP3, 3-chymotrypsin-like protease 3CLpro, and RNA-dependent RNA polymerase RDRP, and ACE2-angiotensinconverting enzyme from the Homo sapiens. Results: The binding affinity of caryophyllene oxide was the highest on 3CLpro (− 6.0 kcal/mol), NSP3 (− 6.3 kcal/ mol), NSP9 (− 6.3 kcal/mol), and RDRP (− 6.9 kcal/mol) targets, while α-bergamotene gave the best binding affinity on RPIA (5.7 kcal/mol) target. The binding affinity of β-bisabolene on the ACE2 target (− 8.0 kcal/mol) was almost the same as Remdesivir (− 8.1 kcal/mol). The ADMET properties of these three phytochemicals showed that they are good drug leads for these SARS-CoV-2 receptors. Conclusion: The findings from this study strongly indicate that the reported recovery from COVID-19 infection claimed by patients who consumed black seed oil could be linked to the presence of caryophyllene oxide, α-bergamotene, and β-bisabolene in this natural product.
Abbreviations COVID-19: Coronavirus disease 2019; SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; GC-MS: Gas chromatography-mass spectrometer; MSD: Mass selective detector; NIST: National Institute of Standards and Technology; RP1A: Replicase polyprotein; NSP9: Nonstructural protein 9; NSP3: Nonstructural protein 3; 3CLpro: 3-Chymotrypsin-like protease; RDRP: RNAdependent RNA polymerase; ACE2: Angiotensin-converting enzyme; CASTp: Computed atlas for surface topography of proteins; ADMET: Absorption, distribution, metabolism and elimination and toxicity; FDA: Food and drug administration; TYR : Tyrosine; MET: Methionine; TRP: Tryptophan; ILE: Isoleusine; SER: Serine; ALA: Alanine; PHE: Phenylalanine; THR: Threonine; VAL: Valine; ARG : Arginine; PRO: Proline; LEU: Leucine; HIS: Histidine; ASN: Asparagine; GLY: Glycine; LYS: Lysine; GLU: Glutathione. Authors' contributions CED conceived, designed, and wrote the research, and performed the DFT studies. IAD extracted and characterized the oil sample, and proof-read the manuscript. AEA performed the docking studies and post docking analysis. All authors have approved the manuscript in the present form and gave the permission to submit the manuscript for publication. All authors read and approved the final manuscript. Funding No funds, grants, or other support was received. Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests The authors declare..
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