Jenkins, Jeremy, Simms, Benjamin and Bender, Andreas (2011) HTS Fingerprints in target prediction. Journal of Proteomics.

Abstract

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.

Item Type:	Article
Additional Information:	Figure 2 contains chemical structures that are all external structures. Fig 2a contains Pubchem compounds 11810219, 11075845, 9965141 and a compound from Pubmed article 14529481. Fig2b contains the drugs trapoxin and apicidin. They are all publicly known HDAC inhibitors.
Keywords:	High throughput screening fingerprints target prediction similarity compounds
Date Deposited:	26 Apr 2016 23:46
Last Modified:	26 Apr 2016 23:46
URI:	https://oak.novartis.com/id/eprint/4029