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Identification of SARS-CoV-2 RNA-dependent RNA polymerase inhibitors from the major phytochemicals of Nigella sativa: An in silico approach.

  • Ahmad Mir, Shabir1
  • Firoz, Ahmad2
  • Alaidarous, Mohammed1, 3
  • Alshehri, Bader1
  • Aziz Bin Dukhyil, Abdul1
  • Banawas, Saeed1, 3, 4
  • Alsagaby, Suliman A1
  • Alturaiki, Wael1
  • Ahmad Bhat, Gulzar5
  • Kashoo, Faizan6
  • Abdel-Hadi, Ahmad M1
  • 1 Department of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi Arabia. , (Saudi Arabia)
  • 2 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Ssaudi Arabia. , (Saudi Arabia)
  • 3 Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia. , (Saudi Arabia)
  • 4 Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA.
  • 5 Department of Clinical Biochemistry, Sher-i-Kashmir Institute of Medical Science, Srinagar, India. , (India)
  • 6 Department of Physical Therapy and Health Rehabilitation, College of Applied Medical Sciences, Majmaah University, Al Majmaah-11952, Saudi Arabia. , (Saudi Arabia)
Published Article
Saudi Journal of Biological Sciences
Publication Date
Sep 08, 2021
DOI: 10.1016/j.sjbs.2021.09.002
PMID: 34518755


The coronavirus disease 2019 (COVID-19), which emerged in December 2019, continues to be a serious health concern worldwide. There is an urgent need to develop effective drugs and vaccines to control the spread of this disease. In the current study, the main phytochemical compounds of Nigella sativa were screened for their binding affinity for the active site of the RNA-dependent RNA polymerase (RdRp) enzyme of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The binding affinity was investigated using molecular docking methods, and the interaction of phytochemicals with the RdRp active site was analyzed and visualized using suitable software. Out of the nine phytochemicals of N. sativa screened in this study, a significant docking score was observed for four compounds, namely α-hederin, dithymoquinone, nigellicine, and nigellidine. Based on the findings of our study, we report that α-hederin, which was found to possess the lowest binding energy (-8.6 kcal/mol) and hence the best binding affinity, is the best inhibitor of RdRp of SARS-CoV-2, among all the compounds screened here. Our results prove that the top four potential phytochemical molecules of N. sativa, especially α-hederin, could be considered for ongoing drug development strategies against SARS-CoV-2. However, further in vitro and in vivo testing are required to confirm the findings of this study. © 2021 The Author(s).

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