A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information

Yunan Luo, Xinbin Zhao, Jingtian Zhou, Jinglin Yang, Yanqing Zhang, Wenhua Kuang, Jian Peng (), Ligong Chen () and Jianyang Zeng ()
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Yunan Luo: Tsinghua University
Xinbin Zhao: Tsinghua University
Jingtian Zhou: Tsinghua University
Jinglin Yang: Tsinghua University
Yanqing Zhang: Tsinghua University
Wenhua Kuang: Tsinghua University
Jian Peng: University of Illinois at Urbana-Champaign
Ligong Chen: Tsinghua University
Jianyang Zeng: Tsinghua University

Nature Communications, 2017, vol. 8, issue 1, 1-13

Abstract: Abstract The emergence of large-scale genomic, chemical and pharmacological data provides new opportunities for drug discovery and repositioning. In this work, we develop a computational pipeline, called DTINet, to predict novel drug–target interactions from a constructed heterogeneous network, which integrates diverse drug-related information. DTINet focuses on learning a low-dimensional vector representation of features, which accurately explains the topological properties of individual nodes in the heterogeneous network, and then makes prediction based on these representations via a vector space projection scheme. DTINet achieves substantial performance improvement over other state-of-the-art methods for drug–target interaction prediction. Moreover, we experimentally validate the novel interactions between three drugs and the cyclooxygenase proteins predicted by DTINet, and demonstrate the new potential applications of these identified cyclooxygenase inhibitors in preventing inflammatory diseases. These results indicate that DTINet can provide a practically useful tool for integrating heterogeneous information to predict new drug–target interactions and repurpose existing drugs.

Date: 2017
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DOI: 10.1038/s41467-017-00680-8

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