A computational approach to finding novel targets for existing drugs

PLoS Comput Biol. 2011 Sep;7(9):e1002139. doi: 10.1371/journal.pcbi.1002139. Epub 2011 Sep 1.


Repositioning existing drugs for new therapeutic uses is an efficient approach to drug discovery. We have developed a computational drug repositioning pipeline to perform large-scale molecular docking of small molecule drugs against protein drug targets, in order to map the drug-target interaction space and find novel interactions. Our method emphasizes removing false positive interaction predictions using criteria from known interaction docking, consensus scoring, and specificity. In all, our database contains 252 human protein drug targets that we classify as reliable-for-docking as well as 4621 approved and experimental small molecule drugs from DrugBank. These were cross-docked, then filtered through stringent scoring criteria to select top drug-target interactions. In particular, we used MAPK14 and the kinase inhibitor BIM-8 as examples where our stringent thresholds enriched the predicted drug-target interactions with known interactions up to 20 times compared to standard score thresholds. We validated nilotinib as a potent MAPK14 inhibitor in vitro (IC50 40 nM), suggesting a potential use for this drug in treating inflammatory diseases. The published literature indicated experimental evidence for 31 of the top predicted interactions, highlighting the promising nature of our approach. Novel interactions discovered may lead to the drug being repositioned as a therapeutic treatment for its off-target's associated disease, added insight into the drug's mechanism of action, and added insight into the drug's side effects.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Databases, Protein
  • Drug Discovery / methods*
  • Humans
  • Mitogen-Activated Protein Kinase 14 / antagonists & inhibitors
  • Models, Molecular
  • Molecular Targeted Therapy / methods*
  • Pharmaceutical Preparations / chemistry*
  • Protein Binding
  • Protein Kinase C / antagonists & inhibitors
  • Protein Kinase Inhibitors / chemistry
  • Protein Kinase Inhibitors / pharmacology
  • Proteins / chemistry*
  • Proteins / metabolism
  • Pyrimidines / chemistry
  • Pyrimidines / metabolism
  • Reproducibility of Results
  • Tosyl Compounds / chemistry
  • Tosyl Compounds / metabolism


  • 4-methyl-N-(3-(4-methylimidazol-1-yl)-5-(trifluoromethyl)phenyl)-3-((4-pyridin-3-ylpyrimidin-2-yl)amino)benzamide
  • Pharmaceutical Preparations
  • Protein Kinase Inhibitors
  • Proteins
  • Pyrimidines
  • Tosyl Compounds
  • Protein Kinase C
  • Mitogen-Activated Protein Kinase 14
  • zafirlukast