A molecular docking study of SARS-CoV-2 main protease against phytochemicals of Boerhavia diffusa Linn. for novel COVID-19 drug discovery

• Published in: Virusdisease 2021-03, Vol.32 (1), p.46-54
• Main Authors: Rutwick Surya, U., Praveen, N.
• Format: Article
• Language: English
• Subjects: Amino acids; Biochemistry; Biomedical and Life Sciences; Boerhavia diffusa; Cell Biology; COVID-19; COVID-19 vaccines; Crystal structure; Disease transmission; Drug discovery; Drug therapy; Drugs; Ecdysone; Epidemics; Flavonoids; Hydrogen bonds; Kaempferol; Life Sciences; Ligands; Microbiology; Original; Original Article; Phytochemicals; Protein Structure; Proteinase; Proteinase inhibitors; Proteins; Quercetin; Severe acute respiratory syndrome coronavirus 2; Spatial data; Viruses
• ISSN: 2347-3584; 2347-3517
• DOI: 10.1007/s13337-021-00683-6

SARS-CoV-2, the causative virus of the Corona virus disease that was first recorded in 2019 (COVID-19), has already affected over 110 million people across the world with no clear targeted drug therapy that can be efficiently administered to the wide spread victims. This study tries to discover a novel potential inhibitor to the main protease of the virus, by computer aided drug discovery where various major active phytochemicals of the plant Boerhavia diffusa Linn. namely 2-3-4 beta-Ecdysone, Bioquercetin, Biorobin, Boeravinone J, Boerhavisterol, kaempferol, Liriodendrin, quercetin and trans-caftaric acid were docked to SAR-CoV-2 Main Protease using Molecular docking server. The ligands that showed the least binding energy were Biorobin with  − 8.17 kcal/mol, Bioquercetin with  − 7.97 kcal/mol and Boerhavisterol with  − 6.77 kcal/mol. These binding energies were found to be favorable for an efficient docking and resultant inhibition of the viral main protease. The graphical illustrations and visualizations of the docking were obtained along with inhibition constant, intermolecular energy (total and degenerate), interaction surfaces and HB Plot for all the successfully docked conditions of all the 9 ligands mentioned. Additionally the druglikeness of the top 3 hits namely Bioquercetin, Biorobin and Boeravisterol were tested by ADME studies and Boeravisterol was found to be a suitable candidate obeying the Lipinsky’s rule. Since the main protease of SARS has been reported to possess structural similarity with the main protease of MERS, comparative docking of these ligands were also carried out on the MERS Mpro, however the binding energies for this target was found to be unfavorable for spontaneous binding. From these results, it was concluded that Boerhavia diffusa possess potential therapeutic properties against COVID-19.