A Cell‐Permeable Ester Derivative of the JmjC Histone Demethylase Inhibitor IOX1

Abstract

The 2-oxoglutarate (2OG)-dependent Jumonji C domain (JmjC) family is the largest family of histone lysine demethylases. There is interest in developing small-molecule probes that modulate JmjC activity to investigate their biological roles. 5-Carboxy-8-hydroxyquinoline (IOX1) is the most potent broad-spectrum inhibitor of 2OG oxygenases, including the JmjC demethylases, reported to date; however, it suffers from low cell permeability. Here, we describe structure–activity relationship studies leading to the discovery of an n-octyl ester form of IOX1 with improved cellular potency (EC50 value of 100 to 4 μm). These findings are supported by in vitro inhibition and selectivity studies, docking studies, activity versus toxicity analysis in cell cultures, and intracellular uptake measurements. The n-octyl ester was found to have improved cell permeability; it was found to inhibit some JmjC demethylases in its intact ester form and to be more selective than IOX1. The n-octyl ester of IOX1 should find utility as a starting point for the development of JmjC inhibitors and as a use as a cell-permeable tool compound for studies investigating the roles of 2OG oxygenases in epigenetic regulation.

Epigenetic targets and drug discovery Part 2: Histone demethylation and DNA methylation

“…Due to the poor cell permeability of IOX1, a series of 8-hydroxyquinoline derivatives has been designed. An n-octyl ester derivative of IOX1 was reported by Schiller et al, which showed not only high cell permeability but also high selectivity and even less toxicity with preserving cell viability (Schiller et al, 2014) (Table 2). Comparing the complex structures of KDM4A with IOX1 and the n-octyl ester derivative of IOX1 by docking, it was discovered that the KDM4A active site can accommodate IOX1 ester derivatives, but the length of the alkyl chain is likely to affect the binding affinity.…”

Histone Lysine Demethylase Inhibitors

“…5-carboxy-8-hydroxyquinoline (later named IOX1) ( Fig. 4) was initially identified in a large screen as a potent and somewhat specific inhibitor of the KDM4 family (King et al 2010;Hopkinson et al 2013), and was later derivatized to improve cell permeability (compound 5 [Schiller et al 2014]) ( Fig. 4) and specificity (Feng et al 2015), with a 2-1H-benzo[d ]imidazole substituted compound (6p) (Fig.…”

Jumonji C Demethylases in Cellular Senescence

“…Further work on these compounds will be necessary to determine on-target toxicity and specificity for certain JmjC demethylases. More recently, 5-carboxy-8-hydroxyquinoline (IOX1) has been shown to inhibit a broad spectrum of JmjC demethylases by binding at the αKG binding pocket (87). Although IOX1 directly binds the αKG binding pocket to affect JmjC demethylase activity, it also chelates iron (II), which may produce negative effects on iron-dependent proteins (87).…”