S-COPHY: A deep learning model for predicting the chemical class of compounds as cosmetics or pharmaceuticals based on single 3D molecular images

Non-animal-based in vitro and in silico approaches for the safety assessment of cosmetic ingredients, recently referred to as Next Generation Risk Assessment (NGRA)/New Approach Methodologies (NAMs), are evolving rapidly as approaches to provide a basis for the regulatory acceptance of new materials. However, predictive models should be applied only to chemicals within the chemical space defined by the dataset used in generating the model. Thus, only predictions for new molecules that are relatively similar to the modeling set can considered reliable with strong confidence. In this study, we developed the S-COPHY model, which employs deep learning to classify new compounds based on their structural similarity to a large collection of pharmaceutical and cosmetic compounds. S-COPHY shows high predictive accuracy both internally and externally, and in particular, there were only a few instances where pharmaceuticals were incorrectly predicted as cosmetics. The use of deep learning enabled the automatic generation of input data from SMILES (Simplified Molecular Input Line Entry System) information, resulting in more consistent model outcomes. Furthermore, GRAD-CAM (Gradient-weighted Class Activation Map) analysis provided insights into the specific structures that contribute to the model's predictions. The potentiality of S-COPHY to identify characteristic structures associated with pharmaceutical-like activity indicates its potential value in supporting safety assessments of cosmetic ingredients. Our results indicate that the S-COPHY model is a promising approach to support decision-making in large chemical spaces, thereby contributing to the safety evaluation of cosmetic ingredients. Expansion of the model to other categories, such as pesticides, could further extend its applicability.