Table 1.
Top 15 HITs interacting with the 1M17 protein, with the energies ranging between -13.1 to -12.2 kcal/mol. Chemical structures of ligands are given in S1 Table.
Table 2.
Top 15 HITs interacting with the 1XKK protein, with energies ranging between -13.8 to -12.6 kcal/mol. Chemical structures of ligands are given in S2 Table.
Fig 1.
Validating the docking process involves re-docking erlotinib to the EGFR protein (PDB ID: 1M17).
The crystal conformation of the ligand is depicted using red sticks, while the docked pose is illustrated with blue sticks.
Fig 2.
Graphs depicting the Root Mean Square Deviation (RMSD) for complexes (A = 1M17, B = 1XKK) in both ligand-bound and ligand-unbound states.
Table 3.
Average Root Mean Square Deviation values of ligand bound and unbound proteins.
Fig 3.
Graphs depicting the Root Mean Square Fluctuation (RMSF) for complexes (A = 1M17 and B = 1XKK) in both ligand-bound and ligand-unbound states.
Fig 4.
Important residues, loops, and motifs in human EGFR protein and Root Mean Square Fluctuation (RMSF) graph of apo protein.
Fig 5.
The change in distance between the ligands and side chain residues of EGFR proteins.
A) 1M17-Ligand complexes, and B) 1XKK-Ligand complexes, respectively.
Fig 6.
The Anisotropic Network Model (ANM analysis) of the apo EGFR protein (A) and NPA008122 bound EGFR protein (B).
The backbone is shown in tube form and the green arrows indicate the degree of elasticity.
Fig 7.
Buried solvent-accessible surface area (B-SASA) values for 1M17-ATP, 1M17-Erlotinib, 1M17-JFD00243, and 1M17-NPA015124 complexes.
Table 4.
Binding free energies (in kcal/mol) for the 1M17-Ligand and 1XKK-Ligand complexes calculated using MM-PBSA.
Fig 8.
Principal Component Analysis (PCA) of unbound Apo-1M17 and ligand-bound 1M17 proteins.
Fig 9.
Principal Component Analysis (PCA) of unbound Apo-1XKK and ligand-bound 1XKK proteins.
Table 5.
The secondary structure statistics of the minimum-energy basin conformations extracted from the FELs of 1M17 and 1XKK in the absence and presence of screened compounds.
Fig 10.
The FEL plots of 1M17 in the absence (A) and presence of ATP (B), Erlotinib (C), RJC02094 (D), JFD00848 (E), NPA015124 (F), NPA008122 (G), and JFD00243 (H) compounds, respectively.
3-D protein structures individually represent the lowest energy conformation(s) retrieved from FEL.
Fig 11.
The FEL plots of 1XKK in the absence (A) and presence of BTB13627 (B), JFD00243 (C), NPA030938 (D), ZINC000257243713 (E), and ZINC000033088664 (F) compounds, respectively.
3-D protein structures individually represent the lowest energy conformation(s) retrieved from FEL.