Abstract: Hindawi International Journal of Clinical Practice Volume 2023, Article ID 9917306, 14 pages https://doi.org/10.1155/2023/9917306 Research Article Nigelladine A among Selected Compounds from Nigella sativa Exhibits Propitious Interaction with Omicron Variant of SARSCoV-2: An In Silico Study Md Mehedy Hasan Miraz ,1 Md Aff Ullah,1 Abdullah Al Nayem,1 Brototi Chakrobortty,1 Sanjoy Deb,1 Anee Laskar,1 Nishita Umaya Tithi,1 Nilay Saha,1 Anita Rani Chowdhury ,1,2 K. M. Khairul Alam,1 Tania Binte Wahed,1 Mohammad Khursheed Alam ,3,4,5 and Sukalyan Kumar Kundu 1 1 Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh Department of Pharmacy, Jagannath University, Dhaka 1100, Bangladesh 3 Preventive Dentistry Department, Orthodontic Division, College of Dentistry, Jouf University, Sakaka 72345, Saudi Arabia 4 Department of Dental Research Cell, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, India 5 Department of Public Health, Faculty of Allied Health Sciences, Dafodil International University, Dhaka, Bangladesh 2 Correspondence should be addressed to Sukalyan Kumar Kundu; skkbd415@juniv.edu Received 5 January 2023; Revised 17 January 2023; Accepted 3 February 2023; Published 20 February 2023 Academic Editor: Pier P. Sainaghi Copyright © 2023 Md Mehedy Hasan Miraz et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. COVID-19 has been a threat to the entire world for more than two years since its outbreak in December 2019 in Wuhan city of China. SARS-CoV-2, the causative agent, had been reported to mutate over time exposing new variants. To date, no impeccable cure for the disease has been unveiled. Tis study outlines an extensive in silico approach to scrutinize certain phytochemical compounds of Nigella sativa (mainly the black cumin seeds) targeting the spike protein and the main protease (Mpro) enzyme of the Omicron variant of SARS-CoV-2. Te objective of this study is to investigate the extracted compounds with a view to developing a potential inhibitor against the concerned SARS-CoV-2 variant. Te investigation contemplates drug-likeness analysis, molecular docking study, ADME and toxicity prediction, and molecular dynamics simulation which have been executed to elucidate diferent phytochemical and pharmacological properties of the tested compounds. Based on drug-likeness parameters, a total of 96 phytochemical compounds from N. sativa have been screened in the study. Interestingly, Nigelladine A among the compounds exhibited the highest docking score with both the targets with the same binding afnity which is −7.8 kcal/mol. However, dithymoquinone, kaempferol, Nigelladine B, Nigellidine, and Nigellidine sulphate showed mentionable docking scores. Molecular dynamics up to 100 nanoseconds were simulated under GROMOS96 43a1 force feld for the protein-ligand complexes exhibiting the top-docking score. Te root mean square deviations (RMSD), root mean square fuctuations (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and the number of hydrogen bonds have been evaluated during the simulation. From the fndings, the present study suggests that Nigelladine A showed the most promising results among the selected molecules. Tis framework, however, interprets only a group of..