Interrogating the Druggability of the 2‑Oxoglutarate-Dependent Dioxygenase Target Class by Chemical Proteomics

The 2-oxoglutarate-dependent dioxygenase target class comprises around 60 enzymes including several subfamilies with relevance to human disease, such as the prolyl hydroxylases and the Jumonji-type lysine demethylases. Current drug discovery approaches are largely based on small molecule inhibitors targeting the iron/2-oxoglutarate cofactor binding site. We have devised a chemoproteomics approach based on a combination of unselective active-site ligands tethered to beads, enabling affinity capturing of around 40 different dioxygenase enzymes from human cells. Mass-spectrometry-based quantification of bead-bound enzymes using a free-ligand competition-binding format enabled the comprehensive determination of affinities for the cosubstrate 2-oxoglutarate and for oncometabolites such as 2-hydroxyglutarate. We also profiled a set of representative drug-like inhibitor compounds. The results indicate that intracellular competition by endogenous cofactors and high active site similarity present substantial challenges for drug discovery for this target class

Discovery of Tetrahydropyrazolo­pyridine as Sphingosine 1‑Phosphate Receptor 3 (S1P₃)‑Sparing S1P₁ Agonists Active at Low Oral Doses

FTY720 is the first oral small molecule approved for the treatment of people suffering from relapsing–remitting multiple sclerosis. It is a potent agonist of the S1P₁ receptor, but its lack of selectivity against the S1P₃ receptor has been linked to most of the cardiovascular side effects observed in the clinic. These findings have triggered intensive efforts toward the identification of a second generation of S1P₃-sparing S1P₁ agonists. We have recently disclosed a series of orally active tetrahydroisoquinoline (THIQ) compounds matching these criteria. In this paper we describe how we defined and implemented a strategy aiming at the discovery of selective structurally distinct follow-up agonists. This effort culminated with the identification of a series of orally active tetrahydropyrazolo­pyridines

Cell Penetrant Inhibitors of the KDM4 and KDM5 Families of Histone Lysine Demethylases. 2. Pyrido[3,4‑<i>d</i>]pyrimidin-4(3<i>H</i>)‑one Derivatives

Following the discovery of cell penetrant pyridine-4-carboxylate inhibitors of the KDM4 (JMJD2) and KDM5 (JARID1) families of histone lysine demethylases (e.g., <b>1</b>), further optimization led to the identification of non-carboxylate inhibitors derived from pyrido­[3,4-<i>d</i>]­pyrimidin-4­(3<i>H</i>)-one. A number of exemplars such as compound <b>41</b> possess interesting activity profiles in KDM4C and KDM5C biochemical and target-specific, cellular mechanistic assays

Cell Penetrant Inhibitors of the KDM4 and KDM5 Families of Histone Lysine Demethylases. 1. 3‑Amino-4-pyridine Carboxylate Derivatives

Optimization of KDM6B (JMJD3) HTS hit <b>12</b> led to the identification of 3-((furan-2-ylmethyl)­amino)­pyridine-4-carboxylic acid <b>34</b> and 3-(((3-methylthiophen-2-yl)­methyl)­amino)­pyridine-4-carboxylic acid <b>39</b> that are inhibitors of the KDM4 (JMJD2) family of histone lysine demethylases. Compounds <b>34</b> and <b>39</b> possess activity, IC₅₀ ≤ 100 nM, in KDM4 family biochemical (RFMS) assays with ≥50-fold selectivity against KDM6B and activity in a mechanistic KDM4C cell imaging assay (IC₅₀ = 6–8 μM). Compounds <b>34</b> and <b>39</b> are also potent inhibitors of KDM5C (JARID1C) (RFMS IC₅₀ = 100–125 nM)