Discovery of Highly Selective and Potent HDAC3 Inhibitors Based on a 2-Substituted Benzamide Zinc Binding Group

Abstract

The selectivity of histone deacetylase inhibitors (HDACis) is greatly impacted by the zinc binding groups. In an effort to search for novel zinc binding groups, we applied a parallel medicinal chemistry (PMC) strategy to quickly synthesize substituted benzamide libraries. We discovered a series containing 2-substituted benzamides as the zinc binding group which afforded highly selective and potent HDAC3 inhibitors, exemplified by compound 16 with a 2-methylthiobenzamide. Compound 16 inhibited HDAC3 with an IC 50 of 30 nM and with unprecedented selectivity of >300-fold over all other HDAC isoforms. Interestingly, a subtle change of the 2-methylthio to a 2-hydroxy benzamide in 20 retains HDAC3 potency but loses all selectivity over HDAC 1 and 2. This significant difference in selectivity was rationalized by X-ray crystal structures of HDACis 16 and 20 bound to HDAC2, revealing different binding modes to the catalytic zinc ion. This series of HDAC3 selective inhibitors served as tool compounds for investigating the minimal set of HDAC isoforms that must be inhibited for the HIV latency activation in a Jurkat 2C4 cell model and potentially as leads for selective HDAC3 inhibitors for other indications.

Non-Hydroxamate Zinc-Binding Groups as Warheads for Histone Deacetylases

“…Clinical data on amino benzamide toxicity suggest target- instead of chemical-related side effects, according to observed clinical symptoms shared across different ZBGs [ 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 ]. Until now co-crystallization of amino benzamides has only been successful with HDAC2 (PDB IDs: 4LY1, 3MAX, 5IWG, and 5IX0) [ 76 , 77 , 78 ]. The amino benzamide ZBG generally chelates the zinc ion via the ortho amino group and the amide carbonyl, and it occupies the foot pocket with the phenyl moiety.…”

“…Similarly to classic amino benzamides, compounds with these warheads are predominantly class I-selective with preference for HDAC3 and HDAC8, complementing classic benzamide HDACi. Special emphasis should be placed on the series of Liu et al [ 76 ] with inhibition in the nM range and long residence times of up to 69.4 h for compounds such as 23 . The authors suggested that the much shorter residence time observed for compound 22 is due to a lack of polar interactions, leading to a strongly decreased residence time of 38 min.…”

“…Unfortunately, the compounds of this series suffered from high clearance and off-target effects. Based on crystal structure data from Liu et al [ 76 ], an insight into properties was provided. Noteworthy are the shorter interaction distances between the zinc ion and the chelating groups of 22 and 23 , ranging from 2.0 Å to 2.2 Å for the (OH) and (CO) moieties compared to classic benzamides with distances of 2.1 Å (NH 2 ) to 2.46 Å (CO).…”

“…Figure 9. Schematic SAR of amino benzamide warheads studied by Liu et al[76] with indicated spheres as placeholders for substitution.…”

Medicinal chemistry of histone deacetylase inhibitors

“…Merck & Co employed a parallel medicinal chemistry strategy to synthesize, screen and identify selective HDAC3 inhibitors. They identified compound 3 in which the substitution of 2amino group with 2-methylthio group within ZBG clearly demonstrates selective HDAC3 inhibitory profile (32). It is interesting to mention that the HDAC8 isoform is the most studied isoform from a crystallographic point of view.…”