DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction

Abstract

Computational methods for DDIs and DTIs prediction are essential for accelerating the drug discovery process. We proposed a novel deep learning method DeepDrug, to tackle these two problems within a unified framework. DeepDrug is capable of extracting comprehensive features of both drug and target protein, thus demonstrating a superior prediction performance in a series of experiments. The downstream applications show that DeepDrug is useful in facilitating drug repositioning and discovering the potential drug against specific disease. Background Computational approaches for accurate prediction of drug interactions, such as drug‐drug interactions (DDIs) and drug‐target interactions (DTIs), are highly demanded for biochemical researchers. Despite the fact that many methods have been proposed and developed to predict DDIs and DTIs respectively, their success is still limited due to a lack of systematic evaluation of the intrinsic properties embedded in the corresponding chemical structure. Methods In this paper, we develop DeepDrug, a deep learning framework for overcoming the above limitation by using residual graph convolutional networks (Res‐GCNs) and convolutional networks (CNNs) to learn the comprehensive structure‐ and sequence‐based representations of drugs and proteins. Results DeepDrug outperforms state‐of‐the‐art methods in a series of systematic experiments, including binary‐class DDIs, multi‐class/multi‐label DDIs, binary‐class DTIs classification and DTIs regression tasks. Furthermore, we visualize the structural features learned by DeepDrug Res‐GCN module, which displays compatible and accordant patterns in chemical properties and drug categories, providing additional evidence to support the strong predictive power of DeepDrug. Ultimately, we apply DeepDrug to perform drug repositioning on the whole DrugBank database to discover the potential drug candidates against SARS‐CoV‐2, where 7 out of 10 top‐ranked drugs are reported to be repurposed to potentially treat coronavirus disease 2019 (COVID‐19). Conclusions To sum up, we believe that DeepDrug is an efficient tool in accurate prediction of DDIs and DTIs and provides a promising insight in understanding the underlying mechanism of these biochemical relations.