Cited by 683Histone Deacetylase Inhibitors ResearchAdvanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

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Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes

Bantscheff, Marcus, Hopf, Carsten, Savitski, Mikhail M, Dittmann, Antje, Grandi, Paola, Michon, Anne-Marie, Schlegl, Judith, Abraham, Yann, Becher, Isabelle, Bergamini, Giovanna, Boesche, Markus, Delling, Manja, Dümpelfeld, Birgit, Eberhard, Dirk, Huthmacher, Carola, Mathieson, Toby, Poeckel, Daniel, Reader, Valérie, Strunk, Katja, Sweetman, Gavain, Kruse, Ulrich, Neubauer, Gitte, Ramsden, Nigel G, Drewes, Gerard·2011·Nature Biotechnology

DOI 10.1038/nbt.1759

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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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Self-citation
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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: Bantscheff, Marcus
Hopf, Carsten
Savitski, Mikhail M
Dittmann, Antje
Grandi, Paola
Schlegl, Judith
Abraham, Yann
Becher, Isabelle
Bergamini, Giovanna
Eberhard, Dirk
Mathieson, Toby
Reader, Valérie
Sweetman, Gavain
Neubauer, Gitte
Ramsden, Nigel G
Drewes, Gerard
Venue: Nature Biotechnology
Publisher: Springer Science and Business Media LLC
Published: 2011-01-23
Volume: 29
Issue: 3
Pages: 255-265
ISSN: 0733-222X (ISSN-L)
1087-0156
1546-1696
DOI: 10.1038/nbt.1759
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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Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes

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