In silico drug repositioning based on the integration of chemical, genomic and pharmacological spaces

BACKGROUND: Drug repositioning refers to the identification of new indications for existing drugs. Drug-based inference methods for drug repositioning apply some unique features of drugs for new indication prediction. Complementary information is provided by these different features. It is therefore necessary to integrate these features for more accurate in silico drug repositioning. RESULTS: In this study, we collect 3 different types of drug features (i.e., chemical, genomic and pharmacological spaces) from public databases. Similarities between drugs are separately calculated based on each of the features. We further develop a fusion method to combine the 3 similarity measurements. We test the inference abilities of the 4 similarity datasets in drug repositioning under the guilt-by-association principle. Leave-one-out cross-validations show the integrated similarity measurement IntegratedSim receives the best prediction performance, with the highest AUC value of 0.8451 and the highest AUPR value of 0.2201. Case studies demonstrate IntegratedSim produces the largest numbers of confirmed predictions in most cases. Moreover, we compare our integration method with 3 other similarity-fusion methods using the datasets in our study. Cross-validation results suggest our method improves the prediction accuracy in terms of AUC and AUPR values. CONCLUSIONS: Our study suggests that the 3 drug features used in our manuscript are valuable information for drug repositioning. The comparative results indicate that integration of the 3 drug features would improve drug-disease association prediction. Our study provides a strategy for the fusion of different drug features for in silico drug repositioning.