Molecular Docking Analysis of Phytochemical Thymoquinone as a Therapeutic Agent on SARS-Cov-2 Envelope Protein

Abstract

The sudden outbreak due to severe acute respiratory syndrome coronavirus 2 (SARS- Cov-2) is responsible for causing acute, highly dreadful coronavirus disease (COVID‐19). The pore-forming proteins in the SARS- CoV-2 envelope protein employ amphipathic α-helix for pore formation. The pore openings are essential for the transport of ions, toxins, and viroporin activity. Moreover, there is an insurgence to identify lead compounds to target the novel coronavirus for therapeutic purposes. Therefore in the present study, the SARS CoV-2 envelope protein sequence was analyzed, constructed the three-dimensional homology model, and screened against the bioactive phytochemical Thymoquinone (TQ). Molecular docking was performed between the modeled E protein and TQ to study protein-ligand interactions using ArgusLab 4.0. The investigation revealed that the modeled E protein contains a single α-amphipathic helix identified for the first time across the Amino-terminal region of the transmembrane domain may contribute to pore formation of small membrane proteins. Molecular docking results showed the promising inhibitory potential of the ligand TQ and the binding free energy of the bound complex was found to be -9.01 kcal/mol. The in silico approach has explicitly demonstrated the significant inhibitory effects of the ligand TQ. Therefore it may be used effectively as an antagonist against the SARS- CoV-2 infection owing to its outstanding pharmacological properties.