MTGGF: A Metabolism Type-Aware Graph Generative Model for Molecular Metabolite Prediction

Metabolism in vivo turns small molecules (e.g., drugs) into metabolites (new molecules), which brings unexpected safety issues in drug development. However, it is costly to determine metabolites by biological assays. Recent computational methods provide new promising approaches by predicting possible metabolites. Rule-based methods utilize predefined reaction-derived rules to infer metabolites. However, they are powerless to new metabolic reaction patterns. In contrast, rule-free methods leverage sequence-to-sequence machine translation to generate metabolites. Nevertheless, they are insufficient to characterize molecule structures, and bear weak interpretability. To address these issues in rule-free methods, this manuscript proposes a novel metabolism type-aware graph generative framework (MTGGF) for molecular metabolite prediction. It contains a two-stage learning process, including a pre-training on a large general chemical reaction dataset, and a fine-tuning on three smaller type-specific metabolic reaction datasets. Its core, an elaborate graph-to-graph generative model, treats both atoms and bonds as bipartite vertices, and molecules as bipartite graphs, such that it can embed rich information of molecule structures and ensure the integrity of generated metabolite structures. The comparison with state-of-the-art methods demonstrates its superiority. Furthermore, the ablation study validates the contributions of its two graph encoding components and its reaction-type-specific fine-tuning models. More importantly, based on interactive attention between a molecule and its metabolites, the case studies on five approved drugs reveal that there exist crucial substructures specific to metabolism types. It is anticipated that this framework can boost the risk evaluation of drug metabolites. The codes are available at https://github.com/zpczaizheli/Metabolite .