Dual targeting of VEGFR2 and ErbB3 by a novel quinoline derivative E5: Mechanistic insights from DFT, molecular docking and MD simulations.
TL;DR
A novel quinoline derivative, 7-(benzyloxy)-N-(3-chloro-2-fluorophenyl)-6-methoxyquinolin-4-amine (E5), was successfully identified as a potent dual-target inhibitor with favourable dual-target binding potency, highlighting E5 as a promising lead compound that warrants further investigation to address clinical anti-angiogenic therapeutic resistance.
Abstract
Acquired resistance to anti-angiogenic therapy often arises via erb-b2 receptor tyrosine kinase 3 (ErbB3)-mediated compensatory signalling, necessitating dual vascular endothelial growth factor receptor 2 (VEGFR2)/ErbB3 inhibitors that can simultaneously block both pathways to overcome resistance. Herein, we adopted a multi-scale computational strategy integrating density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulations to screen and characterize dual-target candidates from our in-house compound library. A novel quinoline derivative, 7-(benzyloxy)-N-(3-chloro-2-fluorophenyl)-6-methoxyquinolin-4-amine (E5), was successfully identified as a potent dual-target inhibitor with favourable dual-target binding potency. Experimental validation using in vitro kinase assays confirmed that E5 potently inhibits VEGFR2 and ErbB3, with IC50 values of 0.42 μM and 0.04 μM, respectively. Our DFT calculations revealed that E5 adopts a flat conformation (20.05 × 10.61 × 6.02 ų) with balanced electrostatic potential and the lowest LUMO energy (-0.88 eV) among reference compounds, enabling it to adapt to the distinct ATP-binding pockets of VEGFR2 and ErbB3 with different gatekeeper residues. High-precision molecular docking identified target-specific binding modes: van der Waals and hydrophobic interactions dominate in the E5-VEGFR2 association, while ErbB3 engages with E5 via hydrogen bonding to THR768, sulfur-π interaction with CYS721, and π-π stacking with PHE834. 200 ns all-atom MD simulations further confirmed the stability of E5-VEGFR2 and E5-ErbB3 complexes, with MM/PBSA binding free energies of -32.41 kcal/mol (VEGFR2) and -31.22 kcal/mol (ErbB3), both predominantly contributed by van der Waals interactions. This work demonstrates the reliability and efficiency of computational approaches for the rational screening and discovery of dual-target kinase inhibitors, highlighting E5 as a promising lead compound that warrants further investigation to address clinical anti-angiogenic therapeutic resistance.