Fig. 7
(A) Visualization of docking simulations of inhibitors with the crystal structure of the SARS-CoV-2 3CLpro (PDB ID: 6Y84) using PyMOL. Candesartan (Cnd) is colored blue, eltrombopag (Elt) is orange, amcinonide (B5) is purple, pimozide (B11) is green, nelfinavir (B21) is pink, and lumacaftor (B22) is yellow. 3CLpro was shown in white ribbons, red sticks represent the catalytic amino acids His41 and Cys145. (B) Interaction of inhibitor molecules with the protein shown using LigPlot+. The following inhibitors are depicted: (1) Candesartan (Cnd), (2) Eltrombopag (Elt), (3) Amcinonide (B5), (4) Pimozide (B11), (5) Nelfinavir (B21), (6) Lumacaftor (B22). Nitrogen (N) is shown in blue, oxygen (O) in red, carbon (C) in green, phosphorus (P) in pink, and sulfur (S) in yellow. Phosphorus atoms are highlighted in brick red to indicate hydrophobic residues. Red dashed lines represent hydrophobic interactions, while black lines denote covalent bonds within the chemical structure of the ligand. (C) RMSD analysis of MD simulations. RMSD of Cα atoms of 3CLpro were plotted and labeled as “RMSD of Protein”. RMSD of all atoms of inhibitors in inhibitor-3CLpro simulations were plotted and labeled as “RMSD of Inhibitors”. (D) Interaction frequency of inhibitors with amino acids in the active site of 3CLpro throughout the 100 ns simulation obtained from VMD timeline plugin.
