Hydrophobic Pocket of SARS-Cov-2 Spike Glycoprotein are Potential as Binding Pocket

Abstract

Abstract Coronavirus disease 2019 (COVID-19) caused by SARS-Cov-2 was recently spread all over the world. Spike glyprotein of SARS-Cov-2 (SARS-Cov-2 S-glycoprotein) is the main agent for host cell recognition. Finding the potential of binding pocket of S-glycoprotein may help to find the specific anti-coronavirus drug. Here we analysed potential binding pocket of SARS-Cov-2 Spike-glycoprotein which is suitable for anti-SARS-Cov-2. In pursuit this aim, dogsitescorer, site finder, and DEPTH were used for binding pocket prediction. Molecular interaction protein-ligands were performed using MOE 2009.10. Based on pocket prediction by Dogsitescorer, there are seven out of eleven pockets which have druggability score above 0.8. Molecular interaction studies revealed that interaction between six potential pockets and ligands resulted in negative scores at all. Our result shows that pocket_4 and pocket_6 are located on upper of SARS-Cov-2 S-glycoprotein and have big volume, 878.94 and 683.05 (Å3) respectively, yet lower number of hydrogen bond. Hydrophobic pocket zero, three, and five which is located in the middle of S-Glycoprotein have high number of interaction. These suggest that hydrophobicity of pocket and both upper and middle positions of S-Glycoprotein pocket are considered for developing anti-coronavirus drugs. We propose that hydrophobic pocket of SARS-Cov-2 S-glycoprotein is important for drug design.