Mechanistic insights into Zika virus NS3 helicase inhibition by Epigallocatechin-3-gallate: Supplementary Files

Deepak Kumar; Nitin Sharma; Murali Aarthy; Sanjeev Singh; Rajanish Giri

In-silico studies were carried out on X-Ray crystal structure (PDB ID: 5GJC, resolution 2.2 Ã…) of NS3 helicase bound to ATP-Mn 2+ and crystal structure containing bound ssRNA with PDB ID: 5GJB (1.7 Ã…) . Further, the docking process was initiated by following a series of necessary steps such as protein preparation, receptor grid generation, ligand preparation and finally ligand docking. Protein preparation was carried out by using Protein Preparation wizard in Schrodinger LLC Maestro v11.0. In protein preparation, force field OPLS-2005 was utilized for H-bond network optimization and energy minimization. Cocrystallization artifacts such as missing side chains and loops were filled by using Prime. Protonation states were generated using Epik at pH 7.4. In literature, three crystal water molecules were reported at the substrate binding site, therefore except these water molecules rest were deleted beyond 5 Ã… from the ligand. A receptor grid was generated on the centroid of substrate binding site by picking up the atoms of co-crystallized ligand (ATP) in 5GJC and ssRNA in 5GJB. The length of the grid was kept 20 Ã…. Before final docking step, EGCG molecule was also prepared using LigPrep module of Maestro as described by Sharma et. al. Further, ligand docking was carried out by using extra precision glide (Glide XP) program from Schrodinger (Glide, Version 11). EGCG molecule was docked flexibly at rigid active site on the protein. Final XP dock scores were analyzed for significant interactions with active site residues.