Fig 1.
Overview of adenosine deaminase (ADA, PDB code: 1VFL) and the three ligands.
(a) ADA structure. The α12 helix (P159-K171) is colored yellow; the α13 helix is colored red; and the structural gate is colored cyan, which consists of the α7 helix (T57-A73) and residues A183 to I188. (b) The binding pocket of ADA with an open form. (c) The binding pocket of ADA with a closed form. (d) The ligand FR0 (obtained from PDB: 1DNV). (e) The ligand FR2 (obtained from PDB: 1NDW) and (f) the ligand PRH (obtained from PDB: 1KRM) are denoted by sticks and mesh. The surrounding residues are depicted by light orange sticks.
Fig 2.
Chemical structures and LUMO orbits of the three ligands: FR0, FR2, and PRH.
Ki and Egap of the three ligands are annotated.
Fig 3.
Electrostatic potential information of the three ligands: FR0, FR2, and PRH.
Surface area in each electrostatic potential (ESP) ranges on the vdW surface of (a) FR0 (c) FR2 and (e) PRH. ESP-mapped molecular vdW surface of (b) FR0 (d) FR2 and (f) PRH.
Fig 4.
Structural stability of the five systems.
(a) RMSD of C-α (c) radius of gyration (Rg) (e) SASA and (g) RMSF of three systems: ADA, ADA-FR2, and ADA-FR0. (b) RMSD of C-α (d) radius of gyration (f) SASA and (h) RMSF of the two systems: ADA-PRH and ADA (without PRH).
Fig 5.
Conformation change in residues P159 to K171 of the three systems: ADA, ADA-FR2, and ADA-FR0.
(a) Differences in the secondary structures of residues P150 to K171 of the three systems. (b) Probability of P159 to S162 to form a helix. (c) Structure of P159 to K171 (yellow for ADA, red for ADA-FR2, and blue for ADA-FR0). (d) RMSD; (e) Rg; and (f) SASA of P159 to K171 in the 100 ns simulations. (g) Average RMSD; (h) average Rg; and (i) average SASA of P159 to K171.
Fig 6.
(a) Dihedral changes of Pro159 of the three systems. (b) Residues P159 to K171 are shown in cartoon, and Pro159 is shown in sticks. ADA is in cyan; ADA-FR2 is in salmon; and ADA-FR0 is in slate. (c) Distance changes between Phe65 and Pro159 of the three systems in the 100 ns simulations. (d) Distance between Phe65 and Pro159 of the three systems (ADA in cyan, ADA-FR2 in salmon, and ADA-FR0 in slate).
Fig 7.
Conformation change in residues T57 to A73 of the two systems: ADA-PRH and ADA (without PRH).
(a) Differences in the secondary structures (DSSPs) of T57 to A73 between the two systems. (b) Probabilities of L62 to I72 to form a helix. (c) Distance changes between Thr57 and Ile185 in the 100 ns simulations. (d) ADA-PRH complex (left) on the surface, residues T57 to A73, and residues A183 to I188 (right) in a mesh. (e) ADA (without PRH) (left) on the surface, residues T57 to A73, and residues A183 to I188 (right) in a mesh.
Fig 8.
Structure stability of T57 to A73 of the two systems.
(a) RMSD; (b) Rg; and (c) SASA of residues T57 to A73 in the 100 ns simulations. (d) Relative frequencies of RMSD; (e) Rg; and (f) SASA of residues T57 to A73.
Fig 9.
Cation–pi interaction between Arg235 and Phe334.
(a) Arg235 is depicted in a yellow stick; and Phe334 is shown in a magenta stick. (b) The distance between the NH1 atom of Arg235 and the center of the benzene group of Phe334 in the 100 ns simulations.
Fig 10.
Free energy landscape (FEL) and structures of the two most stable structures of the five systems.
The α7 helix is colored cyan; the structural gate is colored cyan, which consist of the α7 helix (T57-A73) and residues A183 to I188. (a) ADA. (b) ADA-FR0 complex. (c) ADA-FR2 complex. (d) ADA-PRH complex. (e) ADA (without PRH).
Table 1.
The probability of PC1 and PC2 during MD simulation.
Table 2.
The probability of H-bond between ADA and FR0 during MD simulation.
Table 3.
The probability of H-bond between ADA and FR2 during MD simulation.
Table 4.
The probability of H-bond between ADA and PRH during MD simulation.
Fig 11.
Computational alanine scanning of the binding site residues in open and closed inhibitor complexes.
Analysis was performed using FoldX approach on the conformational ensembles obtained from the 200 ns MD simulations. Binding free energies and alanine scanning of the binding site residues are shown for ADA-FR0 α-ZOL (a), ADA-FR2 (b), and ADA-PRH (c). Energetic binding hotspots correspond to residues whose alanine scanning results indicate a significant decrease in binding free energy.
Table 5.
Average van der Waals, electrostatic interaction energies and binding free energies between inhibitors and ADA.