A new computational drug repurposing method using established disease-drug pair knowledge

MOTIVATION Drug repurposing is a potential alternative to the classical drug discovery pipeline. Repurposing involves finding novel indications for already approved drugs. In this work, we present a novel machine learning-based method for drug repurposing. This method explores the anti-similarity between drugs and a disease to uncover new uses for the drugs. More specifically, our proposed method takes into account three sources of information: i) large scale gene expression profiles corresponding to human cell lines treated with small molecules, ii) gene expression profile of a human disease and iii) the known relationship between FDA-approved drugs and diseases. Using these data, our proposed method learns a similarity metric through a supervised machine learning-based algorithm such that a disease and its associated FDA-approved drugs have smaller distance than the other disease-drug pairs. RESULTS We validated our framework by showing that the proposed method incorporating distance metric learning technique can retrieve FDA-approved drugs for their approved indications. Once validated, we used our approach to identify a few strong candidates for repurposing. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.