Table 1.
The duration times of the unbinding pathways of the inhibitors (ns) with respect to their activity.
Fig 1.
Structure of SARS-Cov-2 Plpro enzyme.
The superimposed crystallographic structures of the apo form (PDB ID: 6W9C), colored in green, and the complexed form of SARS-CoV-2 Plpro in complex with GRL0617 (PDB ID: 7CMD) [34] colored in yellow. The sequence from Thr266 to Gly272 is considered as the BL2 loop.
Fig 2.
The details of the unbinding pathway of GRL0617 in three series of replicas.
(A) The RMSD values of the inhibitor in three replicas (Displayed in Å) and the backbone RMSD values of residues of the BL2 loop in three replicas (Displayed in nm) throughout the simulations. (B) The 2D structure of GRL0617 was obtained from PDB. (C) The Total interaction Energies of the protein-ligand complexes throughout the simulations. (D) The native state of the GRL0617 in the crystallographic conformation and the interactions with the residues of the binding pocket (frame at 0 ns). (E) An intermediate state of GRL0617 in the unbinding pathway where the Tyr268 residue forced the inhibitor to change its native conformation (2nd replica, frame in 68 ns). (F) In another intermediate state, the entire molecule is lifted, and almost all essential bonds and interactions between the ligand and the residues are water-mediated and broken (3rd replica, frame in 85 ns). (G) The unbound state of the inhibitor is entirely free and solvated in the simulation box (1st replica, frame in 100 ns). (H) The free energy landscape (FEL) representation of the unbinding pathway of the GRL0617, replica No 1. (I) The free energy landscape (FEL) representation of the unbinding pathway of the GRL0617, replica No 2. (J) The free energy landscape (FEL) representation of the unbinding pathway of the GRL0617, replica No 3. Letter “N” indicates the native crystallographic conformation.
Fig 3.
The details of the unbinding pathway of PLP_Snyder441 from SARS-CoV-2 Plpro in three series of replicas.
(A) The RMSD values of the inhibitor in three replicas (Displayed in Å) and the backbone RMSD values of residues of the BL2 loop in three replicas (Displayed in nm) throughout the simulations. (B) The 2D structure of PLP_Snyder441 was obtained from PDB. (C) The Total interaction Energies of the protein-ligand complexes throughout the simulations. (D) The bound state of the PLP_Snyder441 in the crystallographic (native) conformation and the interactions with the residues of the binding pocket (frame at 0 ns). (E) An intermediate state of PLP_Snyder441 in the unbinding pathway where the BL2 loop gradually starts to take some distance from the enzyme (1st replica, frame in 150 ns). (F) Another intermediate state where the BL2 loop is entirely flat and the inhibitor is stuck to the residues on the tip of the loop (Tyr268 and the Gln269) and is almost solvated (2nd replica, frame in 55 ns). (G) The unbound state of the inhibitor is entirely free and solvated in the simulation box. (H) The free energy landscape (FEL) representation of the unbinding pathway of the PLP_Snyder441, replica No 1. (I) The free energy landscape (FEL) representation of the unbinding pathway of the PLP_Snyder441, replica No 2. (J) The free energy landscape (FEL) representation of the unbinding pathway of the PLP_Snyder441, replica No 3. Letter “N” indicates the native crystallographic conformation.
Fig 4.
The details of the unbinding pathway of PLP_Snyder495 from SARS-CoV-2 Plpro in three series of replicas.
(A) The RMSD values of the inhibitor in three replicas (Displayed in Å) and the backbone RMSD values of residues of the BL2 loop in three replicas (Displayed in nm) throughout the simulations. (B) The 2D structure of PLP_Snyder495 was obtained from PDB. (C) The Total interaction Energies of the protein-ligand complexes throughout the simulations. (D) The bound state of the PLP_Snyder495 in the crystallographic (native) conformation and the interactions with the residues of the binding pocket (frame at 0 ns). (E) An intermediate state of PLP_Snyder495 in the unbinding pathway where the inhibitor gradually lifted up and out of the binding pocket and made stronger hydrogen bonds with the Glu167 (1st replica, frame in 12 ns). (F) Another intermediate state where the BL2 loop is entirely flat and the inhibitor is stuck to the residues on the tip of the loop (Tyr268 and the Gln269) (3rd replica, frame in 25 ns). (G) The unbound state of the inhibitor is entirely free and solvated in the simulation box. (H) The free energy landscape (FEL) representation of the unbinding pathway of the PLP_Snyder495, replica No 1. (I) The free energy landscape (FEL) representation of the unbinding pathway of the PLP_Snyder495, replica No 2. (J) The free energy landscape (FEL) representation of the unbinding pathway of the PLP_Snyder495, replica No 3. Letter “N” indicates the native crystallographic conformation.
Fig 5.
The details of the unbinding pathway of PLP_Snyder530 from SARS-CoV-2 Plpro in three series of replicas.
(A) The RMSD values of the inhibitor in three replicas (Displayed in Å) and the backbone RMSD values of residues of the BL2 loop in three replicas (Displayed in nm) throughout the simulations. (B) The 2D structure of PLP_Snyder530 was obtained from PDB. (C) The Total interaction Energies of the protein-ligand complexes throughout the simulations. (D) The bound state of the PLP_Snyder530 in the crystallographic (native) conformation and the interactions with the residues of the binding pocket (frame at 0 ns). (E) An intermediate state of PLP_Snyder530 in the unbinding pathway in which the naphthalene moiety had turned and is out of the crystallographic (native) binding conformation (3rd replica, frame in 50 ns). (F) Another intermediate state where the BL2 loop is completely flat and the inhibitor is stuck to the residues on the tip of the loop (Tyr268 and the Gln269) (2nd replica, frame in 60 ns). (G) The unbound state of the inhibitor that is completely free and solvated in the simulation box. (H) The free energy landscape (FEL) representation of the unbinding pathway of the PLP_Snyder530, replica No 1. (I) The free energy landscape (FEL) representation of the unbinding pathway of the PLP_Snyder530 replica No 2. (J) The free energy landscape (FEL) representation of the unbinding pathway of the PLP_Snyder530, replica No 3. Letter “N” indicates the native crystallographic conformation.
Fig 6.
The flexibility of the BL2 loop.
(A) the crystallographic structures of the Plpro are superimposed to compare the flexibility of the BL2 loop and the degree of its opening mechanism. The fully open structure of the BL2 (Black), which was achieved from the unbinding pathways and in the presence of the inhibitor, showed that the distance between the Cα atoms of the Tyr268 on the tip of the BL2 loop in each structure reaches 11.5 Å. (B) the RMSF values of the residues of the Plpro enzyme during the unbinding pathways of the inhibitors and in the apo form of the enzyme, with respect to the important regions of the enzyme.