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Open Access Highly Accessed Research article

Identifying co-targets to fight drug resistance based on a random walk model

Liang-Chun Chen2, Hsiang-Yuan Yeh1*, Cheng-Yu Yeh2, Carlos Roberto Arias2 and Von-Wun Soo12*

Author Affiliations

1 Department of Computer Science, National Tsing Hua University, HsinChu 300, Taiwan

2 Institute of Information Systems and Applications, National Tsing Hua University, HsinChu 300, Taiwan

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BMC Systems Biology 2012, 6:5  doi:10.1186/1752-0509-6-5

Published: 19 January 2012

Abstract

Background

Drug resistance has now posed more severe and emergent threats to human health and infectious disease treatment. However, wet-lab approaches alone to counter drug resistance have so far still achieved limited success due to less knowledge about the underlying mechanisms of drug resistance. Our approach apply a heuristic search algorithm in order to extract active network under drug treatment and use a random walk model to identify potential co-targets for effective antibacterial drugs.

Results

We use interactome network of Mycobacterium tuberculosis and gene expression data which are treated with two kinds of antibiotic, Isoniazid and Ethionamide as our test data. Our analysis shows that the active drug-treated networks are associated with the trigger of fatty acid metabolism and synthesis and nicotinamide adenine dinucleotide (NADH)-related processes and those results are consistent with the recent experimental findings. Efflux pumps processes appear to be the major mechanisms of resistance but SOS response is significantly up-regulation under Isoniazid treatment. We also successfully identify the potential co-targets with literature confirmed evidences which are related to the glycine-rich membrane, adenosine triphosphate energy and cell wall processes.

Conclusions

With gene expression and interactome data supported, our study points out possible pathways leading to the emergence of drug resistance under drug treatment. We develop a computational workflow for giving new insights to bacterial drug resistance which can be gained by a systematic and global analysis of the bacterial regulation network. Our study also discovers the potential co-targets with good properties in biological and graph theory aspects to overcome the problem of drug resistance.