Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants

Metal-dependent histone deacetylases
(HDACs) are key epigenetic
regulators that represent promising therapeutic targets for the treatment
of numerous human diseases. Yet the currently FDA-approved HDAC inhibitors
nonspecifically target at least several of the 11 structurally similar
but functionally different HDAC isozymes, which hampers their broad
usage in clinical settings. Selective inhibitors targeting single
HDAC isozymes are being developed, but precise understanding in molecular
terms of their selectivity remains sparse. Here, we show that HDAC8-selective
inhibitors adopt a L-shaped conformation required for their binding
to a HDAC8-specific pocket formed by HDAC8 catalytic tyrosine and
HDAC8 L1 and L6 loops. In other HDAC isozymes, a L1–L6 lock
sterically prevents L-shaped inhibitor binding. Shielding of the HDAC8-specific
pocket by protein engineering decreases potency of HDAC8-selective
inhibitors and affects catalytic activity. Collectively, our results
unravel key HDAC8 active site structural and functional determinants
important for the design of next-generation chemical probes and epigenetic
drugs.