Structure-Based Virtual Screening Identifies Novel Small-Molecule Inhibitors Targeting the Endonuclease Active Site of APE1

Abstract Apurinic/apyrimidinic endonuclease 1 (APE1) is a key enzyme in the base excision repair (BER) pathway, and its aberrant overexpression is closely associated with poor prognosis, enhanced invasiveness, and therapeutic resistance in multiple cancers, making it an attractive anticancer drug target. In this study, a systematic structure-based virtual screening workflow was established using the crystal structure of the APE1 endonuclease active pocket (PDB ID: 7TC2) to screen approximately 1.529 million small molecules collected from the DrugBank, TargetMol, Specs, and ChemDiv databases. Through multi-step filtering involving drug-likeness evaluation, molecular docking, interaction fingerprint (IFP) screening, conformational strain energy assessment, and MM/GBSA binding free energy calculations, a set of potential APE1 inhibitor candidates was identified. Representative hit compounds from different databases were further subjected to binding mode analysis and 100 ns molecular dynamics simulations. The results showed that these candidate compounds formed stable hydrogen-bonding and hydrophobic interactions with key residues in the APE1 active site. Among them, DB02187 and T9286 outperformed the reference ligand in multiple dimensions, including complex stability, per-residue energy contribution, and free energy landscape profiles. In contrast, although HIT107168463 exhibited favorable static binding energy, it showed relatively poor dynamic stability. Overall, DB02187 and T9286 displayed favorable binding features and potential inhibitory activity and may serve as promising candidates for further experimental validation and lead optimization..