Thermal profiling reveals phenylalanine hydroxylase as an off-target of panobinostat

Becher, Isabelle; Werner, Thilo; Doce, Carola; Zaal, Esther A.; Tögel, Ina; Khan, Crystal A.; Rueger, Anne; Muelbaier, Marcel; Salzer, Elsa; Berkers, Celia R.; Fitzpatrick, Paul F.; Bantscheff, Marcus; Savitski, Mikhail M.

doi:10.1038/nchembio.2185

Cited by 218 publications

(275 citation statements)

References 30 publications

Supporting

Mentioning

247

Contrasting

Unclassified

Order By: Relevance

“…kinase and epigenetic drugs [199, 200]. However, these may be associated with side effects and the possible origins of some of these for epigenetic drugs such as panobinostat have been elucidated using thermal proteome profiling [201]. This approach made use of a cellular thermal shift assay in conjunction with mass spectrometry-based proteomics.…”

Section: Discussionmentioning

confidence: 99%

Epigenetic assays for chemical biology and drug discovery

Gul

2017

Clin Epigenet

View full text Add to dashboard Cite

The implication of epigenetic abnormalities in many diseases and the approval of a number of compounds that modulate specific epigenetic targets in a therapeutically relevant manner in cancer specifically confirms that some of these targets are druggable by small molecules. Furthermore, a number of compounds are currently in clinical trials for other diseases including cardiovascular, neurological and metabolic disorders. Despite these advances, the approved treatments for cancer only extend progression-free survival for a relatively short time and being associated with significant side effects. The current clinical trials involving the next generation of epigenetic drugs may address the disadvantages of the currently approved epigenetic drugs.The identification of chemical starting points of many drugs often makes use of screening in vitro assays against libraries of synthetic or natural products. These assays can be biochemical (using purified protein) or cell-based (using for example, genetically modified, cancer cell lines or primary cells) and performed in microtiter plates, thus enabling a large number of samples to be tested. A considerable number of such assays are available to monitor epigenetic target activity, and this review provides an overview of drug discovery and chemical biology and describes assays that monitor activities of histone deacetylase, lysine-specific demethylase, histone methyltransferase, histone acetyltransferase and bromodomain. It is of critical importance that an appropriate assay is developed and comprehensively validated for a given drug target prior to screening in order to improve the probability of the compound progressing in the drug discovery value chain.

show abstract

Section: Discussionmentioning

confidence: 99%

Epigenetic assays for chemical biology and drug discovery

Gul

2017

Clin Epigenet

View full text Add to dashboard Cite

show abstract

“…2G). Thermal shift assays depend on not only the affinity of the ligand and its concentration at the target but also, the thermodynamics of its binding and protein unfolding (54,55). The latter two were not considered in our prediction and may, therefore, explain the minor offset observed (on average, 0.5 log units).…”

Section: Resultsmentioning

confidence: 79%

Prediction of intracellular exposure bridges the gap between target- and cell-based drug discovery

Mateus

Gordon

Wayne

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Inadequate target exposure is a major cause of high attrition in drug discovery. Here, we show that a label-free method for quantifying the intracellular bioavailability (F ic ) of drug molecules predicts drug access to intracellular targets and hence, pharmacological effect. We determined F ic in multiple cellular assays and cell types representing different targets from a number of therapeutic areas, including cancer, inflammation, and dementia. Both cytosolic targets and targets localized in subcellular compartments were investigated. F ic gives insights on membrane-permeable compounds in terms of cellular potency and intracellular target engagement, compared with biochemical potency measurements alone. Knowledge of the amount of drug that is locally available to bind intracellular targets provides a powerful tool for compound selection in early drug discovery. intracellular drug bioavailability | drug exposure | target engagement | published kinase inhibitor set | MAPK14

show abstract

“…These include, for example, drug affinity responsive target stability (DARTS) [11], stability of proteins from rates of oxidation (SPROX) [12–14], or thermal proteome profiling (TPP) [15–18]. DARTS is based on limited proteolysis (LiP) [19], in which a low concentration of a protease with broad specificity is used to cleave only exposed regions of a protein (generally, loops or unfolded regions).…”

Section: Introductionmentioning

confidence: 99%

Thermal proteome profiling: unbiased assessment of protein state through heat-induced stability changes

2016

View full text Add to dashboard Cite

In recent years, phenotypic-based screens have become increasingly popular in drug discovery. A major challenge of this approach is that it does not provide information about the mechanism of action of the hits. This has led to the development of multiple strategies for target deconvolution. Thermal proteome profiling (TPP) allows for an unbiased search of drug targets and can be applied in living cells without requiring compound labeling. TPP is based on the principle that proteins become more resistant to heat-induced unfolding when complexed with a ligand, e.g., the hit compound from a phenotypic screen. The melting proteome is also sensitive to other intracellular events, such as levels of metabolites, post-translational modifications and protein-protein interactions. In this review, we describe the principles of this approach, review the method and its developments, and discuss its current and future applications. While proteomics has generally focused on measuring relative protein concentrations, TPP provides a novel approach to gather complementary information on protein stability not present in expression datasets. Therefore, this strategy has great potential not only for drug discovery, but also for answering fundamental biological questions.

show abstract

Thermal profiling reveals phenylalanine hydroxylase as an off-target of panobinostat

Cited by 218 publications

References 30 publications

Epigenetic assays for chemical biology and drug discovery

Epigenetic assays for chemical biology and drug discovery

Prediction of intracellular exposure bridges the gap between target- and cell-based drug discovery

Thermal proteome profiling: unbiased assessment of protein state through heat-induced stability changes

Contact Info

Product

Resources

About