<p>Due to the blood–brain barrier (BBB), DNA topoisomerase I (Topo I) inhibitors often cause dose-limiting toxicity in glioblastoma (GBM) treatment. Therefore, developing low-toxicity Topo I inhibitors with enhanced BBB permeability holds a significant promise for improving GBM treatment outcomes. In this study, structure-based virtual screening methods combined with biological evaluations successfully identified three potent Topo I inhibitors, which exhibited IC₅₀ values of approximately 25&#xa0;µM against A172 cells. Structural similarity analysis showed that these compounds have novel scaffolds. Compounds F1260-0895 and F2557-0012 exhibited negligible cytotoxicity on HK-2 cells. The most active compound, F2557-0012, directly targets human Topo I. Clonal formation assays and growth inhibition curves demonstrated the sustained inhibitory effects of F2557-0012 on A172 cells. The flow cytometric analysis showed that F2557-0012 effectively inhibits cell proliferation with minimal effect on apoptosis. Molecular dynamic simulations demonstrated that compound F2557-0012 exhibits stable binding to the Topo I-DNA complex. Two new easily synthesized compounds, demonstrating improved BBB permeability and reduced hematotoxicity, were derived from F1260-0895 and F2557-0012 through structural optimization utilizing the OptADMET platform. Molecular docking analyses indicated that the two novel compounds exhibited a significantly stronger interaction with the Topo I-DNA complex. Further investigations are warranted to synthesize optimized compounds and evaluate their anti-GBM activity both in vitro and in vivo.</p> Graphical Abstract <p></p>