Nigelladine A among Selected Compounds from Nigella sativa Exhibits Propitious Interaction with Omicron Variant of SARS-CoV-2: An In Silico Study
Miraz et al.
, Nigelladine A among Selected Compounds from Nigella sativa Exhibits Propitious Interaction with Omicron..
, International Journal of Clinical Practice, doi:10.1155/2023/9917306
In Silico study of 96 phytochemical compounds of nigella sativa, identifying Nigelladine A as the most promising compound for SARS-CoV-2 inhibition with the highest docking scores for the spike protein and Mpro. Dithymoquinone, kaempferol, Nigelladine B, Nigellidine, and Nigellidine sulphate also showed high docking scores.
Miraz et al., 20 Feb 2023, peer-reviewed, 13 authors.
In Silico studies are an important part of preclinical research, however results may be very different in vivo.
International Journal of Clinical Practice
Volume 2023, Article ID 9917306, 14 pages
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
Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
Department of Pharmacy, Jagannath University, Dhaka 1100, Bangladesh
Preventive Dentistry Department, Orthodontic Division, College of Dentistry, Jouf University, Sakaka 72345, Saudi Arabia
Department of Dental Research Cell, Saveetha Dental College and Hospitals,
Saveetha Institute of Medical and Technical Sciences, Chennai, India
Department of Public Health, Faculty of Allied Health Sciences, Dafodil International University, Dhaka, Bangladesh
Correspondence should be addressed to Sukalyan Kumar Kundu; firstname.lastname@example.org
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
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..
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