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

doi:10.15302/J-QB-022-0320

Quant. Biol.

2023, Vol. 11

Issue (3) : 260-274 https://doi.org/10.15302/J-QB-022-0320

RESEARCH ARTICLE

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

Qijin Yin¹, Rui Fan², Xusheng Cao², Qiao Liu³(

), Rui Jiang¹(

), Wanwen Zeng³(

)

¹. Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China
². College of Software, Nankai University, Tianjin 300350, China
³. Department of Statistics, Stanford University, Stanford, CA 94305, USA

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Abstract

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.

Keywords drug-drug interaction drug-target interaction graph neural network deep learning

Corresponding Author(s): Qiao Liu,Rui Jiang,Wanwen Zeng

Just Accepted Date: 16 March 2023 Online First Date: 21 April 2023 Issue Date: 08 October 2023

Cite this article:

Qijin Yin,Rui Fan,Xusheng Cao, et al. DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction[J]. Quant. Biol., 2023, 11(3): 260-274.

URL:

https://academic.hep.com.cn/qb/EN/10.15302/J-QB-022-0320
https://academic.hep.com.cn/qb/EN/Y2023/V11/I3/260

Fig.1 Model diagram of DeepDrug.

Fig.2 Benchmark results for DeepDrug on the binary DDI tasks.

Fig.3 Benchmark results for DeepDrug on the DTIs classification and regression tasks.

Fig.4 Drug embeddings for DeepDrug.

Fig.5 Drug repositioning for SARS-CoV-2.

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