Binding of the Microbial Cyclic Tetrapeptide Trapoxin A to the Class I Histone Deacetylase HDAC8

Abstract

Trapoxin A is a microbial cyclic tetrapeptide that is an essentially irreversible inhibitor of class I histone deacetylases (HDACs). The inhibitory warhead is the α,β-epoxyketone side-chain of (2 S,9 S )-2-amino-8-oxo-9,10-epoxydecanoic acid ( l -Aoe), which mimics the side-chain of the HDAC substrate acetyl- l -lysine. We now report the crystal structure of the HDAC8–trapoxin A complex at 1.24 Å resolution, revealing that the ketone moiety of l -Aoe undergoes nucleophilic attack to form a zinc-bound tetrahedral gem-diolate that mimics the tetrahedral intermediate and its flanking transition states in catalysis. Mass spectrometry, activity measurements, and isothermal titration calorimetry confirm that trapoxin A binds tightly ( K d = 3 ± 1 nM) and does not covalently modify the enzyme, so the epoxide moiety of l -Aoe remains intact. Comparison of the HDAC8–trapoxin A complex with the HDAC6-HC toxin complex provides new insight regarding the inhibitory potency of l -Aoe-containing natural products against class I and class II HDACs.