Matching receptor to odorant with protein language and graph neural networks

Abstract

Odor perception in mammals is triggered by interactions between volatile organic compounds and a subset of hundreds of proteins called olfactory receptors (ORs). Molecules activate these receptors in a complex combinatorial coding allowing mammals to discriminate a vast number of chemical stimuli. Recently, ORs have gained attention as new therapeutic targets following the discovery of their involvement in other physiological processes and diseases. To date, predicting molecule-induced activation for ORs is highly challenging since $43\%$ of ORs have no identified active compound. In this work, we combine [CLS] token from protBERT with a molecular graph and propose a tailored GNN architecture incorporating inductive biases from the protein-molecule binding. We abstract the biological process of protein-molecule activation as the injection of a molecule into a protein-specific environment. On a newly gathered dataset of $46$ $700$ OR-molecule pairs, this model outperforms state-of-the-art models on drug-target interaction prediction as well as standard GNN baselines. Moreover, by incorporating non-bonded interactions the model is able to work with mixtures of compounds. Finally, our predictions reveal a similar activation pattern for molecules within a given odor family, which is in agreement with the theory of combinatorial coding in olfaction.