Selective class IIa histone deacetylase inhibition via a nonchelating zinc-binding group

Abstract

In contrast to studies on class I histone deacetylase (HDAC) inhibitors, the elucidation of the molecular mechanisms and therapeutic potential of class IIa HDACs (HDAC4, HDAC5, HDAC7 and HDAC9) is impaired by the lack of potent and selective chemical probes. Here we report the discovery of inhibitors that fill this void with an unprecedented metal-binding group, trifluoromethyloxadiazole (TFMO), which circumvents the selectivity and pharmacologic liabilities of hydroxamates. We confirm direct metal binding of the TFMO through crystallographic approaches and use chemoproteomics to demonstrate the superior selectivity of the TFMO series relative to a hydroxamate-substituted analog. We further apply these tool compounds to reveal gene regulation dependent on the catalytic active site of class IIa HDACs. The discovery of these inhibitors challenges the design process for targeting metalloenzymes through a chelating metal-binding group and suggests therapeutic potential for class IIa HDAC enzyme blockers distinct in mechanism and application compared to current HDAC inhibitors.

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Figure 1: TFMO compounds are cell-active, selective class IIa HDAC inhibitors.
Figure 2: TFMO compounds bind class IIa HDACs with a new zinc-binding mode.
Figure 3: Specific class IIa HDAC binding by a TFMO MBG is lost when replaced with a hydroxamate.
Figure 4: Class IIa HDAC enzyme inhibitors alter gene expression unlike a class I and IIb HDAC inhibitor.
Figure 5: Monocytes harbor transcriptional readouts of class IIa HDAC catalytic activity.
Figure 6: Class IIa HDACs influence monocyte responses to CSFs.

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Acknowledgements

The authors would like to thank A.Y. Rudensky, D. Mathis, C. Benoist and V.K. Kuchroo for their comments during manuscript preparation. We also thank M.S. Sundrud and J.A. Hill for discussions and insight through the execution of this work. We also thank Y. Alekseyev and A. LeClerc of the Boston University Medical Campus Microarray Core facility.

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M.L. and M.A.N. performed experiments, directed the research, and wrote the manuscript. D.S. and S.G. contributed to experimental design. D.R.S., E.B., C. Wells and R.P.T. contributed to chemical synthesis. Q.G.W., M.T., P.K.M. and L.K. contributed to the biological experiments. K.P.M. and D.T.P. performed the crystallographic and computational efforts, and X.H., R.A.R., W.B. and M.S.H. contributed to the crystallographic efforts. G.A.H., M.M.-T., B.S., S.C. and Z.W. contributed to the high-throughput screening efforts. R.P.T. designed and B.J.T., J.X.R., C. Wagner, M.B.M., J.T.M. and J.D.W. contributed to the chemoproteomics efforts.

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Correspondence to Michael A Nolan.

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All authors are present or former employees of Tempero Pharmaceuticals, Inc. or GlaxoSmithKline, as indicated in the affiliations.

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Lobera, M., Madauss, K., Pohlhaus, D. et al. Selective class IIa histone deacetylase inhibition via a nonchelating zinc-binding group. Nat Chem Biol 9, 319–325 (2013). https://doi.org/10.1038/nchembio.1223

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