Figure 3 | Scientific Reports

Figure 3

From: In silico structural elucidation of RNA-dependent RNA polymerase towards the identification of potential Crimean-Congo Hemorrhagic Fever Virus inhibitors

Figure 3

Per-residue energy distribution-based pharmacophore model. (A) MD simulated conformations of ribavirin (salmon), arbidol (grey) and favipiravir (orange) in sticks, inside the predicted binding pocket of CCHFV-RdRp. The arrangement of motifs and colors are same as in Fig. 2A. (B) Root Mean Square Deviation (RMSD) of CCHFV-RdRp complexed with all three reported drugs with distinctive colors are highlighted over a period of 10 ns simulations, while, Root Mean Square Fluctuation (RMSF) of all residues during MD simulation are highlighted below. (C) Pharmacophoric features projected within the predicted target site of bound ligand with H-bond donors (HBDs) and H-bond acceptors (HBAs) are highlighted in green and red spheres, respectively. Hydrophobic centers are in yellow and exclusion volume spheres are highlighted in grey. (D) 2D interaction plot for all three reported drugs complexed with RdRp. (E) Per-residue decomposition analysis performed with Amber 16 are presented in bar chart for highly contributing residues of predicted binding site of CCHFV-RdRp.

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