Molecular Docking Analysis of Rutin Reveals Possible Inhibition of SARS-CoV-2 Vital Proteins

Rahman, Fazlur; Tabrez, Shams; Ali, Rahat; Alqahtani, Ali S.; Ahmed, Mohammad Z.; Rub, Abdur

BACKGROUND AND AIM: The coronavirus disease 2019 (COVID-19), emerged by the end of 2019 in Wuhan, China. It spread and became a public health emergency all over the world by mid of April 2020. Flavonoids are specialized metabolites that have antimicrobial properties including anti-viral activity. Rutin, a medically important flavonoid belongs to one of the best natural antioxidant classes. It contains many pharmaceutical properties such as antiprotozoal, antibacterial, and antiviral. Keeping the antimicrobial potential of rutin in mind, we studied its role in the inhibition of essential proteins of SARS-CoV-2 including main protease (M(pro)), RNA-dependent RNA polymerase (RdRp), papain-like protease (PL(pro)), and spike (S)-protein through different in silico approaches. EXPERIMENTAL PROCEDURE: Molecular docking, inhibition constant, hydrogen bond calculations, and ADMET-properties prediction were performed using different software. RESULTS AND CONCLUSION: Molecular docking study showed that rutin bound effectively with M(pro), RdRp, PL(pro), and S-proteins of SARS-CoV-2. Out of these four proteins, M(pro) exhibited the strongest binding affinity with the least binding energy (-8.9 Kcal/mol) and stabilized through hydrogen bonds with bond lengths ranging from 1.18 Å to 3.17 Å as well as hydrophobic interactions. The predicted ADMET and bioactivity showed its optimal solubility, non-toxic, and non-carcinogenic properties. The values of the predicted inhibitory constant of the rutin with SARS-CoV-2 vital proteins ranged between 5.66 μM to 6.54 μM which suggested its promising drug candidature. This study suggested rutin alone or in combination as a dietary supplement may be used to fight against COVID-19 after detailed in vitro and in vivo studies.