Figure 8

MD simulation trajectory analysis from 100 ns time frame in triplicate displayed (A) R1 (replicate 1) RMSD plots of DAPH⁺Cl⁻ bound M^pro (red), nsp2 (green) and nsp7-nsp8 (blue), R2 (replicate 2) RMSD plots of DAPH⁺Cl⁻ bound M^pro (purple), nsp2 (orange) and nsp7-nsp8 (dark red), R3 (replicate 3) RMSD plots of DAPH⁺Cl⁻ bound M^pro (black), nsp2 (yellow) and nsp7-nsp8 (parrot green); (B) [Replicate (1, 2, 3), left panel]: RMSF plots of DAPH⁺Cl⁻ bound M^pro, [replicate (1, 2, 3), middle panel]: RMSF plots of DAPH⁺Cl⁻ bound nsp2, and [replicate (1, 2, 3), right panel]: RMSF plots of DAPH⁺Cl⁻ bound nsp7-nsp8. The RMSF plots of three replicates coded color (red, R1), (black R2) and (green R3). The Y axis scales were adjusted to display the individual replicate plots; (C) R1 (replicate 1) Radius of gyration (Rg) plots of DAPH + Cl⁻ bound M^pro (red), nsp2 (green) and nsp7-nsp8 (blue), R2 (replicate 2) Radius of gyration (Rg) plots of DAPH⁺Cl⁻ bound M^pro (purple), nsp2 (orange) and nsp7-nsp8 (dark red), R3 (replicate 3) Radius of gyration (Rg) plots of DAPH⁺Cl⁻ bound M^pro (black), nsp2 (yellow) and nsp7-nsp8 (parrot green); (D) Binding SASA in the presence (black) and absence (red) of DAPH⁺Cl⁻ with M^pro (left panel), nsp2 (middle panel) and nsp7-nsp8 (right panel). Lowering of SASA (black) signify the binding of ligand to the respective proteins.