Docking and molecular dynamics studies of human ezrin protein with a modelled SARS-CoV-2 endodomain and their interaction with potential invasion inhibitors

Human ezrin protein interacts with SARS-CoV S endodomain and restricts virus fusion, entry, and early events of infection. In general, their binding strength and their structural stability determines their successful entry into the host cells. However, the binding affinity of these two endodomains with the ezrin protein has been elusive due to a paucity of knowledge on the 3D structure. This study modelled the endodomains of both SARS-CoV-1 and SARS-CoV-2 and then docked these models with human ezrin protein. This study establishes that the modelled endodomains of both SARS-CoV-1 and SARS-Cov-2 consisted of three disulphide bridges for self-stabilization. Protein-protein docking listed four salt bridges with a higher buried surface area between ezrin-SARS-CoV-1 endodomain compared to that of ezrin-SARS-CoV-2 with six salt bridges with lower buried surface area. Molecular simulation of the ezrin-SARS-CoV-1 endodomain showed better structural stability with lower Root Mean Square Deviation score compared to that of ezrin-SARS-CoV-2 endodomain due to the substitution of alanine with cysteine residue. Protein-ligand docking studies confirmed better ezrin-drug interaction for quercetin, minocycline, calcifediol, calcitriol, selamectin, ivermectin and ergocalciferol. However, protein–ligand simulation confirmed strong drug-protein interaction during simulation for all the above-listed drugs except for ergocalciferol which could not establish its interaction with the protein during simulation. Strong drug binding within the active site pocket therefore restricts the interaction of viral endodomain and simultaneously stabilizes the ezrin protein. Furthermore, the higher stability between the ezrin after their interaction with the drug moiety could restrict the virus fusion and the infection. This study provides a basis for further development of these drug molecules to clinical trials aiming to identify potential drug molecules which can treat COVID-19 infection.