Related Experiment Video
Updated: May 11, 2026
Fluorescence-Based Detection of FEN1 Nuclease Activity and Screening of Small-Molecule Inhibitors
Published on: June 27, 2025
Structure-based virtual screening identifies novel small-molecule inhibitors targeting the endonuclease active site
Tianzhu Shen1, Hongfei Shen1, Yun Kong1
1The Second Affiliated Hospital of Jiaxing University, Jiaxing, 314000, China.
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 candidate compounds with predicted affinity toward APE1 was identified. Representative hit compounds from different databases were further subjected to binding mode analysis and 100 ns molecular dynamics simulations. Computational analyses suggested that these candidate compounds were able to maintain hydrogen-bonding and hydrophobic interactions with key residues in the APE1 active site. Among them, DB02187 and T9286 exhibited more favorable computational performance than 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 predicted binding features and may represent candidate scaffolds for future experimental validation and lead optimization.
Insights
Apurinic/apyrimidinic endonuclease 1 (APE1) is a cancer target. Virtual screening identified potential drug candidates, DB02187 and T9286, showing promising binding and stability for APE1 inhibition.
Area of Science:
- Biochemistry
- Computational Chemistry
- Drug Discovery
Background:
- Apurinic/apyrimidinic endonuclease 1 (APE1) is crucial in DNA repair and linked to cancer progression and treatment resistance.
- APE1's role makes it a significant target for developing novel anticancer therapies.
Purpose of the Study:
- To identify novel small molecules with inhibitory potential against APE1 using structure-based virtual screening.
- To evaluate the binding affinity and stability of candidate compounds computationally.
Main Methods:
- A structure-based virtual screening workflow was employed, screening over 1.5 million compounds against the APE1 active site (PDB ID: 7TC2).
- Multi-step filtering included drug-likeness, molecular docking, interaction fingerprint analysis, conformational strain energy assessment, and MM/GBSA calculations.
- Selected compounds underwent binding mode analysis and 100 ns molecular dynamics simulations to assess dynamic stability and interactions.
Main Results:
- The screening identified several candidate compounds with predicted affinity for the APE1 active site.
- Compounds DB02187 and T9286 demonstrated superior computational performance, including complex stability and favorable binding interactions, compared to a reference ligand.
- While HIT107168463 showed good static binding energy, its dynamic stability was less favorable.
Conclusions:
- DB02187 and T9286 exhibit promising computational features for APE1 inhibition.
- These compounds represent potential scaffolds for further experimental validation and lead optimization in anticancer drug development.
