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A Systematic Prediction of Multiple Drug-Target Interactions from Chemical, Genomic, and Pharmacological Data

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  • Hua Yu
  • Jianxin Chen
  • Xue Xu
  • Yan Li
  • Huihui Zhao
  • Yupeng Fang
  • Xiuxiu Li
  • Wei Zhou
  • Wei Wang
  • Yonghua Wang

Abstract

In silico prediction of drug-target interactions from heterogeneous biological data can advance our system-level search for drug molecules and therapeutic targets, which efforts have not yet reached full fruition. In this work, we report a systematic approach that efficiently integrates the chemical, genomic, and pharmacological information for drug targeting and discovery on a large scale, based on two powerful methods of Random Forest (RF) and Support Vector Machine (SVM). The performance of the derived models was evaluated and verified with internally five-fold cross-validation and four external independent validations. The optimal models show impressive performance of prediction for drug-target interactions, with a concordance of 82.83%, a sensitivity of 81.33%, and a specificity of 93.62%, respectively. The consistence of the performances of the RF and SVM models demonstrates the reliability and robustness of the obtained models. In addition, the validated models were employed to systematically predict known/unknown drugs and targets involving the enzymes, ion channels, GPCRs, and nuclear receptors, which can be further mapped to functional ontologies such as target-disease associations and target-target interaction networks. This approach is expected to help fill the existing gap between chemical genomics and network pharmacology and thus accelerate the drug discovery processes.

Suggested Citation

  • Hua Yu & Jianxin Chen & Xue Xu & Yan Li & Huihui Zhao & Yupeng Fang & Xiuxiu Li & Wei Zhou & Wei Wang & Yonghua Wang, 2012. "A Systematic Prediction of Multiple Drug-Target Interactions from Chemical, Genomic, and Pharmacological Data," PLOS ONE, Public Library of Science, vol. 7(5), pages 1-14, May.
  • Handle: RePEc:plo:pone00:0037608
    DOI: 10.1371/journal.pone.0037608
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    References listed on IDEAS

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    Cited by:

    1. Chao Huang & Yang Yang & Xuetong Chen & Chao Wang & Yan Li & Chunli Zheng & Yonghua Wang, 2017. "Large-scale cross-species chemogenomic platform proposes a new drug discovery strategy of veterinary drug from herbal medicines," PLOS ONE, Public Library of Science, vol. 12(9), pages 1-20, September.
    2. Qing Ye & Chang-Yu Hsieh & Ziyi Yang & Yu Kang & Jiming Chen & Dongsheng Cao & Shibo He & Tingjun Hou, 2021. "A unified drug–target interaction prediction framework based on knowledge graph and recommendation system," Nature Communications, Nature, vol. 12(1), pages 1-12, December.

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