Deep Graph Networks for Drug Repurposing With Multi-Protein Targets
Davide Bacciu, Federico Errica, Alessio Gravina, Lorenzo Madeddu, Marco Podda, Giovanni Stilo
Abstract
In the early phases of the COVID-19 pandemic, repurposing of drugs approved for use in other diseases helped counteract the aggressiveness of the virus. Therefore, the availability of effective and flexible methodologies to speed up and prioritize the repurposing process is fundamental to tackle present and future challenges to worldwide health. This work addresses the problem of drug repurposing through the lens of deep learning for graphs, by designing an architecture that exploits both structural and biological information to propose a reduced set of drugs that may be effective against an unknown disease. Our main contribution is a method to repurpose a drug against multiple proteins, rather than the most common single-drug/single-protein setting. The method leverages graph embeddings to encode the relevant proteins’ and drugs’ information based on gene ontology data and structural similarities. Finally, we publicly release a comprehensive and unified data repository for graph-based analysis to foster further studies on COVID-19 and drug repurposing. We empirically validate the proposed approach in a general drug repurposing setting, showing that it generalizes better than single protein repurposing schemes. We conclude the manuscript with an exemplified application of our method to the COVID-19 use case. All source code is publicly available.