The Zinc-Binding Group Effect: Lessons from Non-Hydroxamic Acid Vorinostat Analogs

Geurs, Silke; Clarisse, Dorien; De Bosscher, Karolien; D’hooghe, Matthias

doi:10.1021/acs.jmedchem.3c00226

Cited by 58Histone Deacetylase Inhibitors ResearchEnzyme function and inhibitionCholinesterase and Neurodegenerative Diseases

The Zinc-Binding Group Effect: Lessons from Non-Hydroxamic Acid Vorinostat Analogs

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Geurs, Silke, Clarisse, Dorien, De Bosscher, Karolien, D’hooghe, Matthias·2023·Journal of Medicinal Chemistry

DOI 10.1021/acs.jmedchem.3c00226

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Abstract

Histone deacetylases (HDACs) are enzymes pursued as drug targets in various cancers and several non-oncological conditions, such as inflammation and neurodegenerative disorders. In the past decade, HDAC inhibitors (HDACi) have emerged as relevant pharmaceuticals, with many efforts devoted to the development of new representatives. However, the growing safety concerns regarding the established hydroxamic acid-based HDAC inhibitors tend to drive current research more toward the design of inhibitors bearing alternative zinc-binding groups (ZBGs). This Perspective presents an overview of all non-hydroxamic acid ZBGs that have been incorporated into the clinically approved prototypical HDACi, suberoylanilide hydroxamic acid (vorinostat). This provides the unique opportunity to compare the inhibition potential and biological effects of different ZBGs in a direct way, as the compounds selected for this Perspective differ only in their ZBG. To that end, different strategies used to select a ZBG, its properties, activity, and liabilities are discussed.

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Most HDACi employ hydroxamic acid as a ZBG, but class I HDACs (particularly HDACs 1-3) tend to be the only class of HDACs inhibited by 2-amino anilides as a ZBG.
“While most HDACi tend to employ a hydroxamic acid as a ZBG, class I HDACs (particularly HDACs 1–3) tend to be the only class of HDACs inhibited by 2-amino anilides as a ZBG (Figure 4A) [9–13].”
From Medicinal chemistry advances in targeting class I histone deacetylases (2023) · cites this paper as [13]
RGFP966 has emerged as the most frequently employed tool for HDAC3 pharmacologic inhibition in biological studies.
“For this reason, RGFP966 (Figure 11) has emerged as the most frequently employed tool for HDAC3 pharmacologic inhibition in biological studies [9, 13, 67, 69–71].”
From Medicinal chemistry advances in targeting class I histone deacetylases (2023) · cites this paper as [13]
The Introduction and Conclusions discuss HDAC inhibitors generally, but neither identifies RGFP966 or compares how often HDAC3 inhibitors are used in biological studies. Searches for “RGFP966,” “RGFP 966,” and HDAC3 tool compounds found no passage addressing the claim. (LLM, conf=0.76)
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Authors: Geurs, S., Clarisse, D., De Bosscher, K., & D’hooghe, M.
Affiliations: Ghent University (BE)
Translational Nuclear Receptor Research, VIB-UGent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B-9052 Ghent, Belgium
Corresponding author: D’hooghe, Matthias
ORCID: Geurs, Silke
Clarisse, Dorien
D’hooghe, Matthias
Venue: Journal of Medicinal Chemistry
Publisher: American Chemical Society (ACS)
Published: 2023-06-05
Volume: 66
Issue: 12
Pages: 7698-7729
ISSN: 0022-2623 (ISSN-L)
1520-4804
DOI: 10.1021/acs.jmedchem.3c00226
OpenAlex: W4379468009
Cited by: 58
References: 206
Citations by year: 2026: 20 · 2025: 19 · 2024: 14 · 2023: 5
FWCI: 1.53
Type: journal article
Language: en
Open access: green
biblio.ugent.be
Licence: other-oa
doi.org/10.15223/policy-029 (stm-asf)
doi.org/10.15223/policy-037 (stm-asf)
doi.org/10.15223/policy-045 (stm-asf)
Locations: Journal of Medicinal Chemistry (publishedVersion)
PubMed (publishedVersion)
Ghent University Academic Bibliography (Ghent University) (submittedVersion, other-oa)
Funders: Fonds Wetenschappelijk Onderzoek
Bijzonder Onderzoeksfonds UGent
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 › Cholinesterase and Neurodegenerative Diseases
Keywords: histone deacetylase inhibitors, vorinostat, zinc-binding groups, drug safety
MeSH terms: Vorinostat, Histone Deacetylases, Hydroxamic Acids, Zinc, Histone Deacetylase Inhibitors

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The Zinc-Binding Group Effect: Lessons from Non-Hydroxamic Acid Vorinostat Analogs

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