Graph Neural Networks with Multi-Features for Predicting Cocrystals Using APIs and coformers Interactions.

Active pharmaceutical ingredients (APIs) have gained direct pharmaceutical interest, along with their in vitro properties, and thus utilized as auxiliary solid dosage forms upon FDA guidance and approval on pharmaceutical cocrystals when reacting with coformers, as a potential and attractive route for drug substance development. However, screening and selecting suitable and appropriate coformers that may potentially react with APIs to successfully form cocrystals is a time-consuming, inefficient, costly, and labour intensive task. In this study, we implemented graph neural networks to predict the formation of cocrystals using our first created API coformers interactions graph dataset. We further compared our work with previous studies that implemented descriptor-based models (e.g., random forest, support vector machine, extreme gradient boosting, and artificial neural networks). All built graph-based models show compelling performance accuracies (i.e., 91.36, 94.60 and 95. 95% for GCN, GraphSAGE, and R-GCN respectively). Furthermore, R-GCN prevailed among the built graph-based models because of its capability to learn the topological structure of the graph from the additionally provided information (i.e., non-ionic and non-covalent interactions or link information) between APIs and coformers.