Homology modeling and Molecular docking
The crystal structure of TMPRSS2 is not available, hence the homology model structure was created from the amino acid sequence of TMPRSS2 with catalytic domain was retrieved from the UniprotKB (Uniprot Accession O15393) using Schrodinger homology modeling interface[23]; in which, Hepsin structure (PDB: 5CE1) was used as a template, based on the sequence similarity (BLAST).[24] Finally, the modeled structure was optimized and refined by protein preparation wizard.[25]. The structure was validated with the Ramachandran plot (Figure 1S).[ 26]
To understand the binding affinity and the intermolecular interaction of chosen three drug molecules camostat, nafamostat and Leupeptin[16,18-21] with the active site amino acids of the TMPRSS2, the molecular docking has been performed. In prior to the docking simulation, the three drug molecules were prepared by theLigprep module of Schrodinger software[27]Further, these molecules were docked with the TMPRSS2 by extra precision mode (XP) incorporated in the induced fit docking (IFD) method. The IFD resulted in different conformations for each ligand-TMPRSS2 complex. Based on the top score with the lowest energy conformation and intermolecular interactions, the ligand-TMPRSS2 complex was selected for each case and used for further study. PyMOLsoftware[28] was used to analyze the intermolecular interactions between ligand and protein for the individual complex.