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From in silico target prediction to multi-target drug design: Current databases, methods and applications

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.

Publication metadata

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



DOI: 10.1016/j.jprot.2011.05.011