Journal
MOLECULAR SYSTEMS BIOLOGY
Volume 7, Issue -, Pages -Publisher
WILEY
DOI: 10.1038/msb.2011.5
Keywords
chemical genomics; data mining; drug discovery; ligand screening; systems chemical biology
Categories
Funding
- Ministry of Education, Culture, Sports, Science and Technology, Japan
- Japan Society for the Promotion of Science (JSPS)
- Targeted Proteins Research Program
- New Energy and Industrial Technology Development Organization (NEDO)
- National Institute of Information and Communications Technology (NICT) of Japan
- Ono Pharmaceutical Co Ltd
- National Institute of Biomedical Innovation
- Suntory Institute for Bioorganic Research
- Takeda Science Foundation
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [0923679] Funding Source: National Science Foundation
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The discovery of novel bioactive molecules advances our systems-level understanding of biological processes and is crucial for innovation in drug development. For this purpose, the emerging field of chemical genomics is currently focused on accumulating large assay data sets describing compound-protein interactions (CPIs). Although new target proteins for known drugs have recently been identified through mining of CPI databases, using these resources to identify novel ligands remains unexplored. Herein, we demonstrate that machine learning of multiple CPIs can not only assess drug polypharmacology but can also efficiently identify novel bioactive scaffold-hopping compounds. Through a machine-learning technique that uses multiple CPIs, we have successfully identified novel lead compounds for two pharmaceutically important protein families, G-protein-coupled receptors and protein kinases. These novel compounds were not identified by existing computational ligand-screening methods in comparative studies. The results of this study indicate that data derived from chemical genomics can be highly useful for exploring chemical space, and this systems biology perspective could accelerate drug discovery processes. Molecular Systems Biology 7: 472; published online 1 March 2011; doi:10.1038/msb.2011.5
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