Discovery and validation of pyrrolopyrimidine-based VEGFR2 inhibitors targeting tumor angiogenesis via structure-based virtual screening, quantum chemical analysis, and in vitro assays

Tumor angiogenesis, largely driven by VEGFR2 signalling, is a critical hallmark of cancer progression. In this study, we employed a structure-based virtual screening approach of pyrrolopyrimidine analogs from a natural product database, combined with density functional theory (DFT), molecular docking, and molecular dynamics (1 μs) simulations, to identify potential VEGFR2 inhibitors. Binding free energy (MM-GBSA) calculations were used to refine candidate selection. Three top-ranking compounds, CNP0279613, CNP0102100, and CNP0004587, were identified, with CNP0279613 showing the most favourable stability and binding affinity. Biophysical validation using isothermal titration calorimetry confirmed strong binding of CNP0279613 to VEGFR2, while in vitro MTT assays in HUVEC cells demonstrated its superior anti-angiogenic activity compared to the other candidates. Notably, its inhibitory effect was comparable to that of Ramucirumab, an FDA-approved VEGFR2 inhibitor. Together, these computational and experimental findings highlight CNP0279613 as a promising lead scaffold for the development of next-generation anti-angiogenic therapies and warrant further optimization and in vivo evaluation.