Structure-Guided Design and Mechanistic Elucidation of New Chromene Derivatives as Selective Vascular Endothelial...

In this study, a novel series of chromene-based derivatives was rationally designed as potential VEGFR-2 inhibitors based on key structural and pharmacophoric features required for antiangiogenic activity. Accordingly, twelve chromene derivatives (13a-e, 15a-e, and 17a-b) were successfully synthesized and structurally characterized. The synthesized compounds were evaluated in vitro for their cytotoxic activity against human cancer cell lines (MCF-7, HepG-2, and HCT-116), in addition to normal WI-38 and WISH cells. Among the tested compounds, compound 13a demonstrated the most potent and selective antiproliferative activity, exhibiting low micromolar IC₅₀ values and favorable selectivity indices. Enzymatic assays confirmed its VEGFR-2 inhibitory activity (IC₅₀ = 1.666 ± 0.025 µM), comparable to the reference drug sorafenib. Mechanistic investigations revealed that compound 13a effectively inhibited cancer cell migration in a wound healing assay, highlighting its potential antiangiogenic properties. Furthermore, compound 13a induced significant G0/G1 cell cycle arrest in MCF-7 cells and triggered apoptosis, as evidenced by Annexin V/PI staining. To support the experimental findings, Density Functional Theory (DFT) calculations confirmed favorable structural stability and electronic properties. Molecular docking studies demonstrated strong binding interactions within the VEGFR-2 ATP-binding site. These results were further validated by 200 ns molecular dynamics simulations, MM-GBSA binding free energy calculations, Protein-Ligand Interaction Fingerprints (Pro-LIF), Principal Component Analysis of Trajectories (PCA-T), and Free Energy Landscape (FEL) analyses, confirming the dynamic stability and favorable energetics of the VEGFR-2-13a complex. Overall, this integrated experimental and computational study identifies compound 13a as a promising VEGFR-2-targeted anticancer lead warranting further preclinical investigation.