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Chemical and Biological Data - from Compound Selection to Mode of Action Analysis (and Back Again)

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More and more chemical and biological information is becoming available, both in public databases as well as in company repositories. However, how to make use of this information in chemical biology and drug discovery settings is much less clear. In this work, we will discuss how chemical and biological information from different domains – such as compound bioactivity data, pathway annotations from the bioinformatics domain, and gene expression data – can be used for a variety of purposes, such as the mode-of-action analysis from phenotypic readouts,[1,2] anticipating compound toxicities in early discovery and during lead optimization based on gene expression data3, and for designing and selecting compounds with the desired bioactivities against a range of protein targets4 as well as cell lines5. Another application of much relevance to screening is the design of screening libraries, where we have explored the impact of cytotoxicity in such libraries, iterative screening6 and the utilization of ‘informer sets’.

1. Koutsoukas A, et al. J. Proteomics 2011, 74, 2554 – 2574. 2. Drakakis G, et al. MedChemComm 2014, 5, 386 – 396. 3. Verbist B, et al. Drug Discov. Today 2015, 20, 505 – 513. 4. Van Westen GJP , et al. PLoS Comp. Biol. 2013, 9, e1002899. 5. Cortes-Ciriano I, et al. Bioinformatics 2016, 32, 85 – 95. 6. Paricharak S, et al. ACS Chem. Biol. 2016, 1255–1264.

This talk is part of the Computational and Systems Biology series.

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