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Chemical phylogenetics of histone deacetylases
Open accessAbstract
The broad study of histone deacetylases in chemistry, biology and medicine relies on tool compounds to derive mechanistic insights. A phylogenetic analysis of Class I and II HDACs as targets of a comprehensive, structurally diverse panel of inhibitors revealed unexpected isoform selectivity even among compounds widely perceived as non-selective. The synthesis and study of a focused library of cinnamic hydroxamates allowed the identification of a first non-selective HDAC inhibitor. These data will guide a more informed use of HDAC inhibitors as chemical probes and therapeutic agents.
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“They have also been demonstrated to possess greater isoform selectivity profiles, targeting specifically only the class I subgroup of HDACs (6-10, 26, 38, 39).”
From Histone Deacetylase (HDAC) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation but Not Transcription and Cell Viability (2013) · cites this paper as [26]
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“but their selectivity profiles extended well beyond these isoforms as reported previously (12, 13, 26, 29, 30, 38).”
From Histone Deacetylase (HDAC) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation but Not Transcription and Cell Viability (2013) · cites this paper as [26]
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In the citing paper
“This is consistent with previous reports postulating that an intramolecular hydrogen bond between the amine and carbonyl must be broken to permit successful zinc chelation, and a desolvation penalty is paid for this rearrangement to occur (1, 25-28, 34).”
From Histone Deacetylase (HDAC) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation but Not Transcription and Cell Viability (2013) · cites this paper as [26]
Experimental — accuracy not yet measuredIn the citing paper
“Class IIa enzymes (Lahm et al., 2007) as well as HDAC3 (Madsen and Olsen, 2012a), HDAC8 (Bradner et al., 2010), and HDAC11 (Inks et al., 2012) removed the physiologically non-relevant trifluoroacetamide (Ktfa).”
From Histone deacetylase 11 is an ε-N-Myristoyllysine hydrolase (2018) · cites this paper as Bradner et al., 2010
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Self-citation
Metadata
- Authors
- Bradner, J. E., West, N., Grachan, M. L., Greenberg, E. F., Haggarty, S. J., Warnow, T., & Mazitschek, R.
- Affiliations
- Broad Institute (US)
- Harvard University (US)
- The University of Texas at Austin (US)
- Corresponding author
- Bradner, James E
- Mazitschek, Ralph
- Venue
- Nature Chemical Biology
- Published
- 2010-02-07
- Volume
- 6
- Issue
- 3
- Pages
- 238-243
- ISSN
- 1552-4450 (ISSN-L)
- 1552-4469
- PMC
- PMC2822059
- OpenAlex
- W2083784041
- Semantic Scholar
- 68c4985bcae290a761e64065e7e4cfe062700c7f
- Cited by
- 720
- References
- 31
- Citations by year
- 2026: 18 · 2025: 25 · 2024: 27 · 2023: 28 · 2022: 37 · 2021: 50 · 2020: 41 · 2019: 34 · 2018: 39 · 2017: 42 · 2016: 61 · 2015: 64 · 2014: 53 · 2013: 67 · 2012: 62
- FWCI
- 27.21
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Chemical Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Wellcome Trust
- National Institutes of Health (n01co12400-79-0-22)
- Centers for Disease Control and Prevention (N01-C0-012400)
- National Institute on Drug Abuse (R01DA028301)
- National Cancer Institute (N01-CO-012400, K08CA128972, P01CA078048, T32CA079443)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Histone Deacetylase Inhibitors Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Enzyme function and inhibition
- Health Sciences › Medicine › Pharmacology (medical) › Cholinesterase and Neurodegenerative Diseases
- Keywords
- histone deacetylase, histone deacetylase inhibitors, isoform selectivity, class I HDACs, class II HDACs, class IIa HDACs, focused libraries, chemical probes, enzyme inhibition mechanism
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