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; Rashid Saif; Muhammad  Hassan Raza; Muhammad  Osama Zafar; Saeeda  Zia; Mehwish  Shafiq; Tuba  Ahmad; Iram  Anjum

doi:10.54393/pbmj.v6i3.853

Authors

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

DOI:

https://doi.org/10.54393/pbmj.v6i3.853

Keywords:

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

Abstract

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.

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