Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes

Abstract

The development of selective histone deacetylase (HDAC) inhibitors with anti-cancer and anti-inflammatory properties remains challenging in large part owing to the difficulty of probing the interaction of small molecules with megadalton protein complexes. A combination of affinity capture and quantitative mass spectrometry revealed the selectivity with which 16 HDAC inhibitors target multiple HDAC complexes scaffolded by ELM-SANT domain subunits, including a novel mitotic deacetylase complex (MiDAC). Inhibitors clustered according to their target profiles with stronger binding of aminobenzamides to the HDAC NCoR complex than to the HDAC Sin3 complex. We identified several non-HDAC targets for hydroxamate inhibitors. HDAC inhibitors with distinct profiles have correspondingly different effects on downstream targets. We also identified the anti-inflammatory drug bufexamac as a class IIb (HDAC6, HDAC10) HDAC inhibitor. Our approach enables the discovery of novel targets and inhibitors and suggests that the selectivity of HDAC inhibitors should be evaluated in the context of HDAC complexes and not purified catalytic subunits.

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Figure 1: Mapping of HDAC drug target complexes in chemical space and in proteome space.
Figure 2: HDAC inhibitor drug targets and target complexes are defined by chemoproteomics profiling of drugs and compounds used as research tools.
Figure 3: Deconvolution of protein complexes by co-IP analysis confirms the identification of novel HDAC complexes.
Figure 4: Class I HDACs and DNTTIP1 form a mitotic deacetylase complex (MiDAC).
Figure 5: Differential effects of HDAC inhibitors on histone and tubulin acetylation.
Figure 6: The nonsteroidal anti-inflammatory drug bufexamac is a novel class IIb HDAC inhibitor.

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Acknowledgements

This work was supported by a grant from the German Bundesministerium für Bildung und Forschung (Spitzencluster BioRN, Verbundprojekt Inkubator/Teilprojekt INE-TP01) to Cellzome AG. We are grateful to N. Garcia-Altrieth, M. Jundt, M. Löttgers, J.-I. Huber, M. Klös-Hudak, J. Krause, B. Kröh, A. Podszuweit, T. Rudi and K. Weis for expert technical assistance, to C. Gemünd and V. Wolowski for the development of software and database tools, and to F. Weisbrodt for help with the figures. We would like to thank T. Edwards, O. Rausch and D. Simmons for suggestions and support.

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A.D., D.E., A.-M.M., and K.S. performed biochemical and cell biological experiments; V.R. synthesized and sourced compounds; D.P. performed the interferon assay; I.B. analyzed histone modifications; B.D., M.D. and M. Boesche prepared peptide samples and operated mass spectrometers; M. Bantscheff, M.M.S., T.M. and G.S. established and conducted mass spectrometry data handling processes; M.M.S., Y.A., C. Huthmacher and J.S. contributed data analysis and visualization; M. Bantscheff, C. Hopf, P.G. and G.D. analyzed data, planned and supervised experiments, and conceptualized the project; G.B., U.K., G.N. and N.G.R. contributed ideas and supported the work; and M. Bantscheff and G.D. wrote the paper.

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Correspondence to Marcus Bantscheff or Gerard Drewes.

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The authors are employees of Cellzome AG or Cellzome UK Ltd. These companies funded the work.

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Supplementary Tables 1–5, Supplementary Synthetic Procedures and Supplementary Figs. 1–10 (PDF 4173 kb)

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Bantscheff, M., Hopf, C., Savitski, M. et al. Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes. Nat Biotechnol 29, 255–265 (2011). https://doi.org/10.1038/nbt.1759

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