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Bioinformatics. 2018 May 1;34(9):1498-1505. doi: 10.1093/bioinformatics/btx800.

gene2drug: a computational tool for pathway-based rational drug repositioning.

Author information

1
Systems and Synthetic Biology Lab, Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (NA) 80078, Italy.
2
Institute for Research in Biomedicine (IRB Barcelona), C/ Baldiri Reixac 10, 08028 Barcelona, Spain.
3
Department of Translational Medicine, Federico II University, 80131 Naples, Italy.
4
Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, 80125 Naples, Italy.

Abstract

Motivation:

Drug repositioning has been proposed as an effective shortcut to drug discovery. The availability of large collections of transcriptional responses to drugs enables computational approaches to drug repositioning directly based on measured molecular effects.

Results:

We introduce a novel computational methodology for rational drug repositioning, which exploits the transcriptional responses following treatment with small molecule. Specifically, given a therapeutic target gene, a prioritization of potential effective drugs is obtained by assessing their impact on the transcription of genes in the pathway(s) including the target. We performed in silico validation and comparison with a state-of-art technique based on similar principles. We next performed experimental validation in two different real-case drug repositioning scenarios: (i) upregulation of the glutamate-pyruvate transaminase (GPT), which has been shown to induce reduction of oxalate levels in a mouse model of primary hyperoxaluria, and (ii) activation of the transcription factor TFEB, a master regulator of lysosomal biogenesis and autophagy, whose modulation may be beneficial in neurodegenerative disorders.

Availability and implementation:

A web tool for Gene2drug is freely available at http://gene2drug.tigem.it. An R package is under development and can be obtained from https://github.com/franapoli/gep2pep.

Contact:

dibernardo@tigem.it.

Supplementary information:

Supplementary data are available at Bioinformatics online.

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