Epigenetic assays for chemical biology and drug discovery

Abstract

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.

Investigations on small molecule inhibitors targeting the histone H3K4 tri-methyllysine binding PHD-finger of JmjC histone demethylases

“…It is likely that the increased binding affinity of the longer peptide ligand to the longer reader domain scaffold in our study may contribute to the higher IC 50 values obtained. Indeed, it is well reported that the binding and catalytic activities change with different protein construct length and domain architecture,32 as demonstrated for the KDM5A and the KDM7 subfamilies in this study. Thus, while isolated protein domains and peptide fragments provide useful information, more work with full length proteins and nucleosomes are likely needed for robust evaluation of small-molecule interactions.…”

The timeline of epigenetic drug discovery: from reality to dreams

“…Selection of the most appropriate druggable target with functional impact on the disease is undoubtedly a high relevant consideration. Next to rational chemical medicinal engineering approaches, biological approaches (protein complexes or cells) are essential to identify the functional effects of inhibiting particular enzymes or even isoforms [87, 88]. The EU H2020 COST Action consortium CM1406 (www.EpiChemBio.eu) brought together scientists from the different fields (chemistry, biology, medicine) to address such complex issues.…”

Modern approaches for the screening of epigenetically active xenobiotics

“…В связи с этим интегральную оценку эпигенетической активности ксенобиотиков получают, проводя комплексный анализ влияния ксенобиотиков с использованием методов оценки отдельных механизмов эпигенетической регуляции. Наиболее удобными методами для выявления эпигенетически активных ксенобиотиков являются скрининговые тесты in vitro, способные качественно оценить эпигенетические изменения и обладающие высокой пропускной способностью [71]. С помощью таких тестов можно проанализировать более 30 соединений в одном эксперименте.…”

“…Затем биотиновые метки гибридизуются со стрептавидиновыми (донорными) шариками. При лазерном облучении (680 нм) донорных шариков выделяются короткоживущие молекулы синглетного кислорода, которые взаимодействуют с акцепторными шариками, находящимися в непосредственной близости, при этом испускается усиленный хемилюминесцентный сигнал, детектируемый при 615 нм [71].…”