Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public Concentration–Response Data

High-throughput screening (HTS) programs have generated abundant data on numerous chemicals, supporting the discovery of toxicity mechanisms and advancing understanding of adverse outcome pathways (AOPs) in chemical toxicity. However, organizing and interpreting these data for predictive modeling remain challenging due to inconsistent repository formats, varied program objectives, heterogeneous assay targets, and differences in experimental protocols, including concentration ranges. To address these limitations, we developed a hierarchical mechanistic modeling framework that systematically structures and interprets concentration response HTS data. The model integrated curated data sets by mapping metadata from 455 PubChem assays to 216 protein targets and 103 biological pathways in WikiPathways. Assay-level concentration-response data were organized within a biologically layered hierarchy to construct AOP-based models. The resulting models generated pathway-level toxicity scores that quantified compound potency by integrating inferred protein activity and downstream pathway perturbations. In total, 103 pathways were statistically associated with five <i>in vivo</i> toxicity endpoints: acute systemic, maternal, developmental, human hepatotoxicity, and preclinical hepatotoxicity. This hierarchical framework leverages HTS metadata to predict diverse <i>in vivo</i> toxicity outcomes and enhance mechanistic interpretability of pathway-level effects. It links chemical bioactivity to adverse outcomes, providing a quantitative basis for compound ranking, potency assessment, and hazard prediction. Overall, this framework offers a structured, scalable method for integrating large bioactivity data sets into computational toxicology, supporting chemical risk assessment and early-stage drug discovery.