VEGFR-2-Targeted Semisynthetic Theobromine Derivative: A Computer-Aided Drug Design (CADD) Approach

Angiogenesis plays a pivotal role in tumor progression, and VEGFR-2 is a well-established therapeutic target in cancer treatment. In this study, we report the design, semi-synthesis, and comprehensive evaluation of a novel theobromine-based VEGFR-2 inhibitor, T-1-BHEPA [([Formula: see text]-[Formula: see text]-(4-(1-(2-benzoylhydrazono)ethyl)phenyl)-2-(3,7-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1[Formula: see text]-purin-1-yl)acetamide]. A structure-based computer-aided drug design (CADD) approach was employed, beginning with pharmacophore modeling, followed by in-depth computational validation. The binding affinity of T-1-BHEPA to VEGFR-2 was examined through molecular docking, 400 ns molecular dynamics (MD) simulations, MM-GBSA binding energy calculations, and protein–ligand interaction fingerprinting (ProLIF) interaction analysis, all of which confirmed a strong and stable interaction with the VEGFR-2 active site. DFT calculations indicated T-1-BHEPA’s stability and reactivity. Before semi-synthesis, in silico ADMET evaluations highlighted good solubility, nonhepatotoxicity, low CYP2D6 interaction and noncarcinogenic potential, along with a favorable chronic toxicity profile. Consistent with these predictions, T-1-BHEPA exhibited potent in vitro VEGFR-2 inhibition (IC 50 [Formula: see text] 0.059 ± 0.006 [Formula: see text]M), comparable to sorafenib (IC 50 [Formula: see text] 0.045 ± 0.006 [Formula: see text]M). T-1-BHEPA demonstrated selective cytotoxicity against a panel of cancer cell lines, with pronounced activity against MDA-MB-231 (IC 50 [Formula: see text] 11.64 ± 1.0 [Formula: see text]M), and a high selectivity index (SI > 6.7) over normal WI-38 cells. Cell cycle analysis revealed G2/M phase arrest, while apoptosis assays confirmed significant increases in early and late apoptotic populations. These effects were further supported by molecular markers, including elevated caspase-3, upregulation of Bax and downregulation of Bcl-2, consistent with activation of the intrinsic apoptotic pathway. Overall, T-1-BHEPA represents a rationally designed and biologically validated VEGFR-2 inhibitor with promising anticancer efficacy and safety, warranting further preclinical development.