In Silico Discovery of ABZI Nitrogen Heterocycle STING Agonists via 3D-QSAR, Molecular Dynamics, and AI-Based...

Background/Objectives: The stimulator of interferon genes (STING) pathway plays a central role in innate immune signaling and represents an attractive therapeutic target for cancer immunotherapy. Amidobenzimidazole (ABZI) derivatives have emerged as promising non-nucleotide STING agonists with improved drug-like properties compared to cyclic dinucleotides. However, current ABZI compounds still exhibit limited oral bioavailability and cross-species potency discrepancies. In addition, potential systemic toxicity remains a concern, indicating the need for further structural optimization. Methods: In this study, a comprehensive computer-aided drug design strategy was employed to systematically investigate ABZI derivatives and identify novel STING agonists with enhanced activity and favorable pharmacokinetic profiles. A 3D quantitative structure-activity relationship (3D-QSAR) model was constructed using the Topomer CoMFA approach based on a dataset of 109 reported ABZI compounds. Guided by the contour map analysis, new chemical groups were introduced through a fragment growth method, generating a large virtual library. The library was subsequently filtered via molecular docking, molecular dynamics simulations, and MM-PBSA binding free energy calculations. Results: Among the newly designed ABZI compounds, five compounds displayed lower binding free energies than D59, with M13 and M44 showing reductions exceeding 6.7 kcal/mol. This work demonstrates the effectiveness of an integrated in silico design strategy for the discovery of novel STING agonists. Conclusions: The identified compounds represent promising candidates for subsequent experimental validation and may support the development of nitrogen heterocycle-based STING agonists for antitumor applications.