Application of Machine Learning Models for Predicting pIC50 Values of Plasticizers Against Cytochrome P450 Aromatase

Abstract

This study investigated the application of six machine learning regression algorithms such as Random Forest, CatBoost, K-Nearest Neighbours, XGBoost, LightGBM, and Gradient Boosting, paired with Molecular ACCess System (MACCS) key fingerprints for the quantitative prediction of aromatase (CYP19A1) inhibitory potency, expressed as pIC₅₀. A dataset of 187 compounds was assembled from the ChEMBL database (version 33, Target ID: CHEMBL1978) following by systematic data curation workflow encompassing duplicate removal, pIC₅₀ transformation, and activity-based filtering. Model performance was rigorously evaluated using an 80/20 stratified train/test split, 5-fold cross-validation, and Y-randomisation testing to ensure unbiased assessment of predictive generalisation. Feature selection via CatBoost permutation importance on the held-out test set identified the top 20 predictive MACCS keys from an initial 166-bit space, substantially reducing dimensionality and improving generalisation across all models. Among the algorithms evaluated, CatBoost trained on the top 20 features achieved the strongest test-set performance (R² = 0.693, RMSE = 0.794, MAE = 0.659) with the most stable cross-validation R² (0.062 ± 0.304), outperforming all other algorithms. Y-randomisation testing returned an empirical p-value of <0.01, confirming that model performance reflects genuine structure–activity relationships rather than statistical chance. Permutation importance and SHAP analysis identified nitrogen-containing heterocyclic fragments (MACCS_41, MACCS_145) and halide-bearing substructures (MACCS_109) as the primary structural determinants of aromatase inhibitory potency, consistent with established CYP19A1 pharmacophoric requirements. Application of the model to ten representative plasticizers demonstrated that the refined applicability domain (h^* = 0.423) accommodated eight of the ten compounds, enabling reliable potency predictions across phthalate esters and bisphenol analogues. These findings establish a transparent and reproducible QSAR framework for first-tier endocrine disruption risk screening of plasticizers and highlight the importance of permutation-based feature selection and applicability domain assessment in QSAR model development.