The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“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]
The check wasn’t confident either way, so it gives no verdict — never disputed.
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
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Katoh, K. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf436 · Cited by 17,027
A Rapid Bootstrap Algorithm for the RAxML Web Servers
Stamatakis, A., Hoover, P., & Rougemont, J. (2008) · Systematic Biology · doi:10.1080/10635150802429642 · Cited by 7,028
MAFFT version 5: improvement in accuracy of multiple sequence alignment
Katoh, K., Kuma, K., Toh, H., & Miyata, T. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki198 · Cited by 5,063
Lysine acetylation targets protein complexes and co-regulates major cellular functions
Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L., Rehman, M., Walther, T. C., Olsen, J. V., & Mann, M. (2009) · Science · doi:10.1126/science.1175371 · Cited by 4,040
Recent developments in the MAFFT multiple sequence alignment program
Katoh, K., & Toh, H. (2008) · Briefings in Bioinformatics · doi:10.1093/bib/bbn013 · Cited by 3,629
Anticancer activities of histone deacetylase inhibitors
Bolden, J. E., Peart, M. J., & Johnstone, R. W. (2006) · Nature Reviews Drug Discovery · doi:10.1038/nrd2133 · Cited by 2,919
Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer
Minucci, S., & Pelicci, P. G. (2006) · Nature reviews. Cancer · doi:10.1038/nrc1779 · Cited by 2,234
Sustained hippocampal chromatin regulation in a mouse model of depression and antidepressant action
Tsankova, N. M., Berton, O., Renthal, W., Kumar, A., Neve, R. L., & Nestler, E. J. (2006) · Nature Neuroscience · doi:10.1038/nn1659 · Cited by 1,780
Gregoretti, I., Lee, Y.-M., & Goodson, H. V. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.02.006 · Cited by 1,456
Histone acetyltransferase complexes: one size doesn't fit all
Lee, K. K. W., & Workman, J. L. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2145 · Cited by 1,091
Cited by
Sorted by citations
Items 701–769 of 769
Sahm, B. D. B., Florêncio, K. G. D., Pinto, F. D. C. L., Maia, A. I. V., ROCHA, C. A. M., Jimenez, P. C., Pessoa, O. D. L., Lotufo, T. C. M., Costa-lotufo, L. V., & Wilke, D. V. (2026) · Chemistry & Biodiversity · doi:10.1002/cbdv.202503815
Li, M., Wang, Y., Liang, X., Zhao, C., Tan, W., Gao, R., Hu, Y., Xiang, S., Chen, Z., Hu, L., et al. (2026) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.6c00066
Mishra, A., Yang, W.-B., Liu, T.-S., Thakur, A., Grewal, A. S., Marczyk, J., Stelitano, G., Sharma, R., Rana, M., Singh, G., et al. (2026) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.6c00039
SETDB1 promotes tubulin deacetylation and Golgi fragmentation by HDAC6Preprint
Gunasekaran, G., Gelman, G., Manshirov, O., Listovsky, T., & Gerlitz, G. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.24.734187
Selective histone deacetylase inhibition as a therapeutically relevant strategy in H3K27M-glioma
Groves, A., Kirkland, O. O., Cascio, C. L., Wang, X., Heaslip, C., Marques, J. G., Song, C., Poetschke, R., Wang, T., Chin, D. H., et al. (2026) · Neuro-Oncology · doi:10.1093/neuonc/noag142
Histone deacetylases in neurodegeneration and neuronal plasticity
Mehta, B., Nambiar, S., Shirke, O., Pandita, S., & Markandeya, Y. S. (2026) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2026.06.025
Investigation of the classical histone deacetylases and sirtuins using peptide technologies
Rogers, J. M., & Olsen, C. A. (2026) · Cell chemical biology · doi:10.1016/j.chembiol.2026.08.009
Astapczuk, J., Szewczyk-Roszczenko, O. K., Vassetzky, Y. S., & Czarnomysy, R. (2026) · Pharmacological Research · doi:10.1016/j.phrs.2026.108449
Post-translational modifications of regulatory T cells in autoimmune diseases
Zhang, R., Wei, J., Guo, K., 邹海兰, Xie, L., & Xiao, Y. (2026) · Trends Open · doi:10.1016/j.treopn.2026.09.007
BindingDB Entry 50010822: Environment-sensitive fluorescent inhibitors of histone deacetylase.
BindingDB (2021) · UC San Diego · doi:10.7270/q2tf01wm
BindingDB (2016) · UC San Diego · doi:10.7270/q2qf8rpq
BindingDB (2013) · UC San Diego · doi:10.7270/q24q7wb0
BindingDB Entry 50013364: Thirty Years of HDAC Inhibitors: 2020 Insight and Hindsight.
BindingDB (2022) · UC San Diego · doi:10.7270/q2f76h9k
BindingDB (2023) · UC San Diego · doi:10.7270/q2xg9w57
BindingDB Entry 50010003: Development of a Potent and Selective HDAC8 Inhibitor.
BindingDB (2021) · UC San Diego · doi:10.7270/q2qc0718
BindingDB Entry 50013161: HDAC7 Inhibition by Phenacetyl and Phenylbenzoyl Hydroxamates.
BindingDB (2022) · UC San Diego · doi:10.7270/q2dv1pmp
BindingDB Entry 50007194: Highly fluorescent and HDAC6 selective scriptaid analogues.
BindingDB (2021) · UC San Diego · doi:10.7270/q2jq14bb
BindingDB (2023) · UC San Diego · doi:10.7270/q2cz3c62
BindingDB Entry 50042978: Discovery of the first histone deacetylase 6/8 dual inhibitors.
BindingDB (2014) · UC San Diego · doi:10.7270/q27h1m0s
BindingDB Entry 50017531: Antitumor activity of novel POLA1-HDAC11 dual inhibitors.
BindingDB (2023) · UC San Diego · doi:10.7270/q29z98zb
BindingDB Entry 50033616: A novel HDAC inhibitor with a hydroxy-pyrimidine scaffold.
BindingDB (2012) · UC San Diego · doi:10.7270/q20p10ct
BindingDB (2013) · UC San Diego · doi:10.7270/q29p32r4
BindingDB Entry 50033283: Discovery of histone deacetylase 8 selective inhibitors.
BindingDB (2011) · UC San Diego · doi:10.7270/q2zc835m
BindingDB (2016) · UC San Diego · doi:10.7270/q23f4rck
BindingDB (2014) · UC San Diego · doi:10.7270/q29g5p7j
BindingDB (2022) · UC San Diego · doi:10.7270/q2bk1h5d
BindingDB (2011) · UC San Diego · doi:10.7270/q28g8kzj
Acute kidney injury in zebrafish larvae as a regeneration model for drug discovery
Skvarca, L. B. (2015) · D-Scholarship@Pitt (University of Pittsburgh)
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
