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Cited by 64Histone Deacetylase Inhibitors ResearchEnzyme function and inhibitionEnzyme Structure and Function

Entropy as a Driver of Selectivity for Inhibitor Binding to Histone Deacetylase 6

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Porter, Nicholas J., Wagner, Florence F., Christianson, David W.·2018·Biochemistry
DOI 10.1021/acs.biochem.8b00367PMC PMC6030506
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Abstract

Among the metal-dependent histone deacetylases, the class IIb isozyme HDAC6 is remarkable because of its role in the regulation of microtubule dynamics in the cytosol. Selective inhibition of HDAC6 results in microtubule hyperacetylation, leading to cell cycle arrest and apoptosis, which is a validated strategy for cancer chemotherapy and the treatment of other disorders. HDAC6 inhibitors generally consist of a Zn 2+ -binding group such as a hydroxamate, a linker, and a capping group; the capping group is a critical determinant of isozyme selectivity. Surprisingly, however, even “capless” inhibitors exhibit appreciable HDAC6 selectivity. To probe the chemical basis for this selectivity, we now report high-resolution crystal structures of HDAC6 complexed with capless cycloalkyl hydroxamate inhibitors 1–4 . Each inhibitor hydroxamate group coordinates to the catalytic Zn 2+ ion with canonical bidentate geometry. Additionally, the olefin moieties of compounds 2 and 4 bind in an aromatic crevice between the side chains of F583 and F643. Reasoning that similar binding could be achieved in the representative class I isozyme HDAC8, we employed isothermal titration calorimetry to study the thermodynamics of inhibitor binding. These measurements indicate that the entropy of inhibitor binding is generally positive for binding to HDAC6 and negative for binding to HDAC8, resulting in ≤313-fold selectivity for binding to HDAC6 relative to HDAC8. Thus, favorable binding entropy contributes to HDAC6 selectivity. Notably, cyclohexenyl hydroxamate 2 represents a promising lead for derivatization with capping groups that may further enhance its impressive 313-fold thermodynamic selectivity for HDAC6 inhibition.

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  • Selective inhibition appears to rely on small structural differences between HDAC1-3 and HDAC6 and on small thermodynamic differences in selective inhibitor binding.

    “Selective inhibition appears to rely on small structural differences between HDAC1-3 and HDAC6 and on small thermodynamic differences in selective inhibitor binding 42-46 .”

    From Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants (2018) · cites this paper as [46]

    The Results and Discussion (ITC) identifies a small structural difference: the aromatic crevice is approximately 1 Å wider in class I HDACs, including HDAC1–3, than in HDAC6. The paper also finds that binding entropy contributes to selectivity, but its thermodynamic measurements compare HDAC6 with HDAC8, not HDAC1–3; extending that mechanism to other class I isozymes is presented as a possibility, not a measured result. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Recent work on HDAC6/inhibitor complexes demonstrates that L1 loop conformational stability is important for interactions of L1 loop residues with inhibitor capping groups to achieve HDAC6 selectivity inhibition.

    “the recent work on HDAC6/inhibitor complexes demonstrate that L1 loop conformational stability is important for the interactions of L1 loop residues with inhibitors capping groups to achieve HDAC6 selectivity inhibition 42-46”

    From Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants (2018) · cites this paper as [46]

    The Introduction (page unavailable) says inhibitor capping groups can interact with residues in the outer active-site cleft, and the ITC discussion links possible active-site rigidity to HDAC6 binding selectivity. Neither passage identifies the L1 loop or demonstrates that its conformational stability enables capping-group interactions. The paper studies largely capless inhibitors, so the specific L1-loop mechanism is not supported by this source. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Porter, N. J., Wagner, F. F., & Christianson, D. W.
Affiliations
  • University of Pennsylvania (US)
  • Broad Institute (US)
Corresponding author
Christianson, David W.
ORCID
Venue
Biochemistry
Publisher
American Chemical Society (ACS)
Published
2018-05-18
Volume
57
Issue
26
Pages
3916-3924
ISSN
  • 0006-2960 (ISSN-L)
  • 1520-4995
DOI
10.1021/acs.biochem.8b00367
PMC
PMC6030506
OpenAlex
W2803420308
Cited by
64
References
13
Citations by year
2026: 5 · 2025: 11 · 2024: 3 · 2023: 4 · 2022: 5 · 2021: 9 · 2020: 14 · 2019: 9 · 2018: 4
FWCI
3.91
Type
journal article
Language
en
Open access
Locations
  • Biochemistry (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
National Institute of General Medical Sciences (GM 49758)
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
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords
HDAC6, HDAC8, histone deacetylase inhibitors, capping groups, isozyme selectivity, binding entropy, zinc coordination, crystal structure
MeSH terms
Histone Deacetylase 6, Histone Deacetylases, Humans, Protein Binding, Repressor Proteins, Crystallography, X-Ray, Entropy, Histone Deacetylase Inhibitors

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