Chemical Compounds Targeting DNA Methylation and Hydroxymethylation

Abstract

DNA methylation and its oxidised forms participate in the interpretation and regulation of the human genome. Many questions arise around the enzymes responsible of these chemical modifications of DNA and their roles in regulating these modifications, which are very dynamic but are specific in the location and context (tissues, diseases, etc.). We reviewed here the major enzymes involved in DNA methylation and oxidation, with a focus on the DNA methyltransferases and TET enzymes. The principal compounds that inhibit these enzymes are presented since they will help address these questions.

Focused Screening Identifies Different Sensitivities of Human TET Oxygenases to the Oncometabolite 2-Hydroxyglutarate

“…Thus, an MS assay was developed to directly measure substrate depletion/product formation using dsDNA. Reported MS methods for TET assays, including for kinetic studies, are typically based on LC-MS/MS which employ oligonucleotide hydrolysis to nucleosides for analysis . However, the LC-MS methods require higher amounts of substrate/enzymes and can require downstream processing steps.…”

“…Reported MS methods for TET assays, including for kinetic studies, are typically based on LC-MS/MS which employ oligonucleotide hydrolysis to nucleosides for analysis. 38 However, the LC-MS methods require higher amounts of substrate/enzymes and can require downstream processing steps. To improve sample throughput and assay resolution, we developed a method consisting of solid-phase extraction coupled to MS assay (SPE-MS), as has been applied to other 2OG oxygenases.…”

“…Potent and selective inhibitors will aid in functional studies and evaluation of the TETs as therapeutic targets. Some TET inhibitors are reported, − including metal-chelating 2OG cofactor mimics, such as TCA cycle–related metabolites, including ( S )- and ( R )-2HG, ,− IOX1, 2,4-PDCA, and TETi76; however, knowledge of their selectivity, potency, and cell activities across TET1–3 is limited. The development of TET inhibitors has likely been limited to date by a paucity of assays with sufficient sensitivity and throughput .…”

“…Some TET inhibitors are reported, − including metal-chelating 2OG cofactor mimics, such as TCA cycle–related metabolites, including ( S )- and ( R )-2HG, ,− IOX1, 2,4-PDCA, and TETi76; however, knowledge of their selectivity, potency, and cell activities across TET1–3 is limited. The development of TET inhibitors has likely been limited to date by a paucity of assays with sufficient sensitivity and throughput . Here, we report on the development of robust TET assays, both with isolated enzymes and in cells, which were used to screen a set of 2OG oxygenase–focused inhibitors and related compounds.…”

“…The development of TET inhibitors has likely been limited to date by a paucity of assays with sufficient sensitivity and throughput. 38 Here, we report on the development of robust TET assays, both with isolated enzymes and in cells, which were used to screen a set of 2OG oxygenase–focused inhibitors and related compounds. We observed that several known 2OG oxygenase inhibitors also inhibit TET1–3, including some clinically used PHD inhibitors.…”