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Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes

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 quanti... Full description

Journal Title: Nature biotechnology 2011-03, Vol.29 (3), p.255-265
Main Author: Bantscheff, Marcus
Other Authors: Drewes, Gerard , 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
Format: Electronic Article Electronic Article
Language: English
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Publisher: New York, NY: Nature Publishing Group
ID: ISSN: 1087-0156
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title: Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes
format: Article
creator:
  • Bantscheff, Marcus
  • Drewes, Gerard
  • 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
subjects:
  • Antimitotic agents
  • Antineoplastic agents
  • Biological and medical sciences
  • Biotechnology
  • Enzyme inhibitors
  • Enzymes
  • Fundamental and applied biological sciences. Psychology
  • Health aspects
  • Health. Pharmaceutical industry
  • Histone Deacetylases - chemistry
  • Histone Deacetylases - metabolism
  • Hydrolases
  • Industrial applications and implications. Economical aspects
  • Mass Spectrometry - methods
  • Miscellaneous
  • Peptide Mapping - methods
  • Phylogenetics
  • Physiological aspects
  • Protein folding
  • Protein Interaction Mapping - methods
  • Proteomics
  • Proteomics - methods
ispartof: Nature biotechnology, 2011-03, Vol.29 (3), p.255-265
description: 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.
language: eng
source:
identifier: ISSN: 1087-0156
fulltext: no_fulltext
issn:
  • 1087-0156
  • 1546-1696
url: Link


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titleChemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes
creatorBantscheff, Marcus ; Drewes, Gerard ; 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
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descriptionThe 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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subjectAntimitotic agents ; Antineoplastic agents ; Biological and medical sciences ; Biotechnology ; Enzyme inhibitors ; Enzymes ; Fundamental and applied biological sciences. Psychology ; Health aspects ; Health. Pharmaceutical industry ; Histone Deacetylases - chemistry ; Histone Deacetylases - metabolism ; Hydrolases ; Industrial applications and implications. Economical aspects ; Mass Spectrometry - methods ; Miscellaneous ; Peptide Mapping - methods ; Phylogenetics ; Physiological aspects ; Protein folding ; Protein Interaction Mapping - methods ; Proteomics ; Proteomics - methods
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descriptionThe 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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abstractThe 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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pmid21258344
doi10.1038/nbt.1759
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