Design, Synthesis, Docking, and Biological Evaluation of Novel Diazide-Containing Isoxazole- and Pyrazole-Based Histone Deacetylase Probes

Abstract

The design, synthesis, docking, and biological evaluation of novel potent HDAC3 and HDAC8 isoxazole- and pyrazole-based diazide probes suitable for Binding Ensemble Profiling with Photoaffinity Labeling (BEProFL) experiments in cells is described. Both the isoxazole- and pyrazole-based probes exhibit low nanomolar inhibitory activity against HDAC3 and HDAC8, respectively. The pyrazole-based probe 3f appears to be one of the most active HDAC8 inhibitors reported in the literature with an IC50 of 17 nM. Our docking studies suggest that unlike the isoxazole-based ligands the pyrazole-based ligands are flexible enough to occupy the second binding site of HDAC8. Probes/inhibitors 2b, 3a, 3c, and 3f exerted the anti-proliferative and neuroprotective activities at micromolar concentrations through inhibition of nuclear HDACs, indicating that they are cell permeable and the presence of an azide or a diazide group does not interfere with the neuroprotection properties, or enhance cellular cytotoxicity, or affect cell permeability.

Synthesis of 1,2-benzisoxazole tethered 1,2,3-triazoles that exhibit anticancer activity in acute myeloid leukemia cell lines by inhibiting histone deacetylases, and inducing p21 and tubulin acetylation

“…Previous studies have reported that the diazide-containing isoxazoles were used to target histone deacetylases. 46 Additionally, 3-substituted-1,2-isoxazole was reported to show potent inhibitory activity against HDAC6. 47 On the other hand, the second deacetylase domain of HDAC6 possesses tubulin deacetylase activity, 48 therefore, we focussed on this domain.…”

Towards Isozyme-Selective HDAC Inhibitors For Interrogating Disease

“…4; Table 1) [80]. For instance, Neelarapu et al used a diazide probe for mapping the surface binding groups of class I HDAC isoforms.…”

“…This compound also inhibited other class I and II HDACs at nM concentrations (Table 1). However, removing the diazide group (9) resulted in reduced selectivity against all HDACs, suggesting the importance of the two azide moieties for HDAC8 selectivity [80]. There are some reported compounds (10)(11)(12)(13) in which modifications to the cap region resulted in class selectivity (Fig.…”

Novel histone deacetylase 8 ligands without a zinc chelating group: Exploring an ‘upside-down’ binding pose

“…28 Synthetic procedures and data for compounds 1a , 1b , 1e and 8 and 2a , 2b , 3a , 3b and 10 were previously reported by us. 19, 29 [4-(Azidomethyl)phenyl]methanol and 2-azidoethanol were synthesized according to the reported methods. 30, 31 …”

“…19, 29 The resulting IC 50 values are given in Table 1. The analysis of the SAR was facilitated by docking of the ligands to HDAC8 (PDB:1T64) 27 using GOLD v.5.1.…”