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
antiproliferative 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.