Exploring the interaction between epidermal growth factor receptor tyrosine kinase and some of the synthesized inhibitors using combination of in-silico and in-vitro cytotoxicity methods

Abstract

Quinazoline derivatives are potent inhibitors of human epidermal growth factor receptor (EGFR) as anticancer agents. In this study, the cytotoxic effects of a new series of synthesized quinazoline derivatives were evaluated using MTT assay against MCF-7 and HT-29 cell lines. Using molecular docking, the binding modes of all compounds were analyzed at the binding site of EGFR. Based on the results, the compounds L1, L2, L4, L5, L6, L7, L10, L15, and L18 may be promising EGFR inhibitors based on docking score and hydrogen bonds. Consistent with the experimental data, Met769 is recognized as a key residue in the binding of potential inhibitors. According to the MTT cytotoxicity assays, Lipinski's rule of five (RO5), absorption, distribution, metabolism, excretion, and toxicity (ADMET) parameters, and docking studies, three compounds L4, L15, and L10 with IC₅₀ values of 80, 60, and 1 μM against the MCF-7 were selected for further comparative assessments. The dynamics of free EGFR, and selected ligand-EGFR complexes were investigated using molecular dynamics (MD) simulation studies. The results indicated that the three compounds bound to EGFR active site in a stable manner during the simulation through the formation of new hydrogen bonds with Phe699, Leu694, Gly700, Lys721, Met769, Arg817, and Asp831 with the superiority of compound L15. These features can promote future drug candidate designing to produce better derivatives in the search for the anticancer agents.

Keywords: 4(3H)-quinazolinones; 4-Anilinoquinazoline; EGFR; Molecular docking; Molecular dynamics simulation.

Fig. 1

Analysis plots of the protein backbone and ligands structures for free epidermal growth factor receptor (EGFR), complex 1, 2, and 3 during 40 ns molecular dynamic simulation; A, the root mean square deviations (RMSD) plot; B, root mean square fluctuation (RMSF) plot; C, radius of gyration (Rg) plot; D, solvent accessible surface (SASA) plot.

Fig. 2

Analysis plots of the complexes 1, 2, and 3 during 40 ns molecular dynamic simulation; A, Minumum distance plot between hinge region residue Met769 and ligand; B, number of contacts plot of the hinge region residue Met769 and ligand; The H-bonding distribution plot vs time for C, L4-epidermal growth factor receptor (EGFR); D, L15-EGFR; and E, L10-EGFR.

Fig. 3

Schematic interaction resulting from LigPlot and VMD softwares for selected three compounds L4 (A and D), L15 (B and E), and L10 (C and F) after molecular dynamic simulations. In parts A, B, and C, the compounds exposure is blue-highlighted and hydrogen bonding is in green. Hydrophobic interactions are presented by red color. The hinge region residue Met769 is in green in D-F.