A Molecular Docking Study against COVID-19 Protease with a Pomegranate Phyto-Constituents 'Urolithin' and Other Repurposing Drugs: From a Supplement to Ailment
Varish Ahmad *
Health Information Technology Department, Faculty of Applied Studies, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
*Author to whom correspondence should be addressed.
Abstract
Aim: We conducted an in silico study on Urolithin and different antimicrobial agents targeting virus protease and peptidase.
Methodology: The docking study was completed by using docking tools. Drug compounds and COVID-19 receptor molecules were prepared, docking was performed and interaction was visualized through Discovery Studio visualizer.
Results: Urolithin A has interacted against peptidase (PDB ID:2GTB) with binding energy -6.93 kcal/mol and against protease (PDB ID:6LU7) with the binding energy -5.46 kcal/mol, while Urolithin B has interacted to peptidase (PDB ID:2GTB) with binding energy -6.74 kcal/mol and with protease it interacted with a binding energy -4.67 kcal/mol. The antimicrobial agent Ofloxacin was found to interact against protease (PDB ID:6LU7) with a binding energy -6.84 kcal/mol and against protease (PDB:6LU7) with a binding energy -8.00 kcal/mol.
Conclusion: The most common interacting amino acids of target enzymes of the virus with studied drugs were His41, His164, Met165, Glu166, Gln189. From the docking studies, it is observed that Ofloxacin and Urolithin have the potential to inhibit the virus protease as well as peptidase significantly and these could prevent the entry of the virus to the inside of the host cell. Thus, further antiviral research on these antimicrobial agents and Urolithin could be helpful to control the COVID-19 disease.
Keywords: Antimicrobial agents, urolithin, antiviral, SARS-CoV-2, protease