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Lookup NU author(s): Professor Malcolm Young
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Given the tremendous growth of bioactivity databases, the use of computational tools to predict protein targets of small molecules has been gaining importance in recent years. Applications span a wide range, from the 'designed polypharmacology' of compounds to mode-of-action analysis. In this review, we firstly survey databases that can be used for ligand-based target prediction and which have grown tremendously in size in the past. We furthermore outline methods for target prediction that exist, both based on the knowledge of bioactivities from the ligand side and methods that can be applied in situations when a protein structure is known. Applications of successful in silico target identification attempts are discussed in detail, which were based partly or in whole on computational target predictions in the first instance. This includes the authors' own experience using target prediction tools, in this case considering phenotypic antibacterial screens and the analysis of high-throughput screening data. Finally, we will conclude with the prospective application of databases to not only predict, retrospectively, the protein targets of a small molecule, but also how to design ligands with desired polypharmacology in a prospective manner. (C) 2011 Elsevier B.V. All rights reserved.
Author(s): Koutsoukas A, Simms B, Kirchmair J, Bond PJ, Whitmore AV, Zimmer S, Young MP, Jenkins JL, Glick M, Glen RC, Bender A
Publication type: Review
Publication status: Published
Journal: Journal of Proteomics
Year: 2011
Volume: 74
Issue: 12
Pages: 2554-2574
Print publication date: 18/06/2011
ISSN (print): 1874-3919
ISSN (electronic): 1876-7737
Publisher: ELSEVIER SCIENCE BV
URL: http://dx.doi.org/10.1016/j.jprot.2011.05.011
DOI: 10.1016/j.jprot.2011.05.011
