Table 1.
Protein structure quality information as given by the SWISS-MODEL structure assessment tool.
Fig 1.
The 3D-surface of Evasin-1’s predicted ligand binding site (left) along with the pharmacophores used in the screening of ligands in Pharmit (right).
Positive electrostatic center is colored blue, hydrophobic centers are green, and hydrogen donor center is white.
Table 2.
Binding site prediction of the Cavity module.
Fig 2.
Superimposition of the top 50 ligand hits generated from the ZINC database.
Fig 3.
The 3D rendition, and the 2D and 3D interaction diagram of ZINC8856727 with Evasin-1.
Fig 4.
A. MD simulation trajectory analysis of Root Mean Square Divisions (RMSD) of ZINC8856727 bound with 3FPR, i.e. Evasin-1 100 ns time frame in triplicate displayed: R1 (replicate 1) RMSD plot of ZINC8856727 bound 3FPR (red) with control 3FPR (light green); R2 (replicate 2) RMSD plot of ZINC8856727 bound 3FPR (dark maroon) with control 3FPR (juniper green); R3 (replicate 3) RMSD plot of ZINC8856727 bound 3FPR (yellow) with control 3FPR (cyan) B. MD simulation trajectory analysis of Root Mean Square Fluctuations (RMSF) of ZINC8856727 bound with 3FPR, i.e. Evasin-1 100 ns time frame in triplicate displayed: R1 (replicate 1) RMSF plot of ZINC8856727 bound 3FPR (red) with control 3FPR (black); R2 (replicate 2) RMSF plot of ZINC8856727 bound 3FPR (munsell yellow) with control 3FPR (sap green); R3 (replicate 3) RMSF plot of ZINC8856727 bound 3FPR (munsell yellow) with control 3FPR (cyan blue); C. MD simulation trajectory analysis of Radius of gyration (Rg) of ZINC8856727 bound with 3FPR, i.e. Evasin-1 100 ns time frame in triplicate displayed: R1 (replicate 1) Rg plot of ZINC8856727 bound 3FPR (red) with control 3FPR (light green); R2 (replicate 2) Rg plot of ZINC8856727 bound 3FPR (porcelain) with control 3FPR (dark green); R3 (replicate 3) Rg plot of ZINC8856727 bound 3FPR (black) with control 3FPR (Prussian blue) D. MD simulation trajectory analysis of Hydrogen Bonding (H-Bonds) of ZINC0 = 8856727 bound with 3FPR, i.e. Evasin-1 100 ns time frame in triplicate displayed: R1 (replicate 1) H-Bond plot of ZINC8856727 bound 3FPR (red); R2 (replicate 2) H-Bond plot of ZINC8856727 bound 3FPR (black); R3 (replicate 3) H-Bond plot of ZINC8856727 bound 3FPR (light green) E. Stepwise trajectory analysis for every 25 ns displaying the protein and ligand conformation during 100 ns of simulation of Evasin-1-ZINC8856727 complex. F Free Energy Landscape displaying the achievement of global minima (ΔG, kJ/mol) of 3FPR in presence of ZINC8856727 with respect to their RMSD (nm) and Radius of gyration (Rg, nm). G. MMGBSA trajectory (0 ns, before simulation and 100 ns, after simulation) exhibited conformational changes of ZINC8856727 upon binding with the protein Evasin 1 (PDB I.D. 3FPR). The arrows indicating the overall positional variation (movement and pose) of ZINC08856727 at the binding site cavity.
Table 3.
The average root mean square deviation, radius of gyration, hydrogen bonding.
Table 4.
Binding energy calculation of ZINC8856727 with Evasin-1 and non-bonded interaction energies from MM-GBSA trajectories.
Fig 5.
Principal component analysis of the Evasin-1-ZINC8856727 complex showing a stable configuration throughout the 100 ns run.
Fig 6.
Energy plot of protein Evasin-1 and ZINC8856727 complex system during the entire simulation event of 100 ns.
The total energy (dark green), van der Waal’s energy (cyan) and coulomb energy (red) of the entire system indicating the stability of the individual systems bound to ZINC8856727 molecule.