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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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“Genetic or pharmacological targeting of the CoREST complex enhances anti-tumour activity in mice (Bantscheff et al., 2011;Xiong et al., 2020).”
From HDACs and the epigenetic plasticity of cancer cells: target the complexity (2022) · cites this paper as Bantscheff et al., 2011
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Self-citationPvclust: an R package for assessing the uncertainty in hierarchical clustering
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Subramanian, A., Narayan, R., Corsello, S. M., Peck, D. D., Natoli, T. E., Lu, X., Gould, J., Davis, J. F., Tubelli, A. A., Asiedu, J. K., et al. (2017) · Cell · doi:10.1016/j.cell.2017.10.049 · Cited by 3,515
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Metadata
- Authors
- Bantscheff, M., Hopf, C., Savitski, M. M., Dittmann, A., Grandi, P., Michon, A.-M., Schlegl, J., Abraham, Y., Becher, I., Bergamini, G., Boesche, M., Delling, M., Dümpelfeld, B., Eberhard, D., Huthmacher, C., Mathieson, T., Poeckel, D., Reader, V., Strunk, K., Sweetman, G., Kruse, U., Neubauer, G., Ramsden, N. G., & Drewes, G.
- Corresponding author
- Bantscheff, Marcus
- Drewes, Gerard
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2011-01-23
- Volume
- 29
- Issue
- 3
- Pages
- 255-265
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2007139310
- Cited by
- 659
- References
- 50
- Citations by year
- 2026: 15 · 2025: 32 · 2024: 25 · 2023: 33 · 2022: 40 · 2021: 37 · 2020: 33 · 2019: 37 · 2018: 33 · 2017: 46 · 2016: 69 · 2015: 68 · 2014: 54 · 2013: 58 · 2012: 49
- FWCI
- 24.95
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Histone Deacetylase Inhibitors Research
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Keywords
- histone deacetylase inhibitors, chemoproteomics, hydroxamate inhibitors, bufexamac, HDAC6, HDAC10, drug selectivity, affinity capture
- MeSH terms
- Histone Deacetylases, Peptide Mapping, Mass Spectrometry, Protein Interaction Mapping, Proteomics
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