Figure 7: Docking analysis of cordycepin with RIG-I structure. (A). Molecular docking programs suggest higher binding probability of cordycepin with respect to ATP binding domain than other domains of RIG-I protein. Docking scores (converted in Z score statistics) obtained from different blind docking programs are displayed in the box plot where the central rectangle spans the first quartile to the third quartile and a segment inside the rectangle shows the median and “whiskers” above and below the box show the locations of the minimum and maximum values. FD_ATP_DM, FD_ATP_DM, PD_ATP_DM, PD_RNA_DM and PD_OTR_DM denote docking results obtained from Patch Dock [27] and Fire Dock [28] when cordycepin is docked at ATP binding domain, RNA binding domain, and others binding domains, respectively. (B). Comparative analysis of ligand binding, represented by ΔG of docking of the cordycepin in absence (-ATP) and presence (+ATP) of ATP with RIG-I structure. Lower the ΔG value higher the probability of stability of binding between the ligand the protein. (C). Comparative analysis of the average GOLD clash score of the cordycepin in absence (-ATP) and presence (+ATP) of ATP with RIG-1 structure. Higher clash score indicates more unfavouredness of the complex is (D). Cartoon representation RIG-I protein structure (PDB ID: 3TMI) where the Rec A-like domain 1 or the ATP binding domain (region: 240-444) is shown in magenta, Rec A-like helicase domain 2 (region: 600-744) in yellow, alpha-helical domain 3 (region: 470-599) in green and the repressor domain (region: 795-923) in grey. The linker (region: 445-469) connecting Rec A-like domain 1 or the ATP binding domain with alpha-helical domain 3 is coloured in blue, while the “V” shape linker (region: 745-794) between Rec A-like helicase domain 2 and repressor domain is coloured in brown. The docked cordycepin is shown in stick representation. Residues within the 5Å of docked cordycepin (PHE 241, LYS 242, PRO 243, ARG 244, TYR 246, GLN 247, VAL 452, VAL 453, GLY 267, CYS 268, GLY 269, LYS 270, THR 271, PHE 272, ARG 732) are highlighted whereas probable hydrogen bonds formed between cordycepin and RIG-I residues are marked by black lines. (E). 293T cells were transfected with pEF-BOS-RIG-I K270A expressing FLAG tagged mutant RIG-I. After 24 h transfected cells were incubated with Cordycepin and Poly-IC. After 10 h of incubation whole cell lysates were prepared, immuno precipitated with anti-FLAG antibody and then precessed for SDSPAGE analysis. Western blotting with anti-MAVS antibody indicate co-precipitating MAVS with FLAG tagged RIG in Cordycepin treated and Poly-IC treated cells in immunoprecipitated fraction and non-immunoprecipitated (INPUT) fractions from the same samples were probed with anti-MAVS (upper panel). Over expression of RIG was confirmed by anti-FLAG antibody (lower panel).