Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes

  title={Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes},
  author={Marcus Bantscheff and Carsten Hopf and Mikhail M. Savitski and Antje Dittmann and Paola Grandi and Anne Marie Michon and Judith Schlegl and Yann Abraham and Isabelle Becher and Giovanna Bergamini and Markus Boesche and Manja Delling and Birgit D{\"u}mpelfeld and Dirk Eberhard and Carola Huthmacher and Toby Mathieson and Daniel Poeckel and Val{\'e}rie A. Reader and Katja Strunk and G. M. A. Sweetman and Ulrich Kruse and Gitte Neubauer and Nigel Ramsden and Gerard Drewes},
  journal={Nature Biotechnology},
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. [] Key Result 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…

A novel class of small molecule inhibitors of HDAC6.

Treatment of human acute myeloid leukemia cell line MV4-11 with the selective HDAC6 inhibitors decreases levels of mutant FLT-3 and constitutively active STAT5 and attenuates Erk phosphorylation, all of which are associated with the inhibitor's selective toxicity against leukemia.

Structure-Based Inhibitor Discovery of Class I Histone Deacetylases (HDACs)

An up-to-date overview of the structure-based discovery of Class I HDAC inhibitors, including pan-, isoform-selective and complex-specific inhibitors, aiming to provide an insight into the discovery of additional HDAC inhibitor with greater selectivity, specificity and therapeutic utility.

Chemoproteomics reveals time-dependent binding of histone deacetylase inhibitors to endogenous repressor complexes.

A chemoproteomics strategy for the determination of time-dependent inhibitor binding to endogenous HDACs and HDAC complexes was presented and it was found that unlike hydroxamate type inhibitors, aminobenzamides exhibited slow binding kinetics dependent on association within protein complexes.

A Comparative Study of Target Engagement Assays for HDAC1 Inhibitor Profiling

Two recently developed high-throughput target engagement technologies, NanoBRET and SplitLuc CETSA, are implemented to profile 349 compounds in the Epigenetic-Focused collection for HDAC1 binding and it is found that the twoHDAC1 target engagement assays correlated well with each other and with orthogonal activity-based assays, in particular those carried out in cellular environments rather than with isolated HDAC proteins.

Determination of Slow-Binding HDAC Inhibitor Potency and Subclass Selectivity.

It is found that entinostat, a clinical candidate, inhibits HDACs 1-3 by a two-step slow-binding mechanism with lower potencies than previously reported, and it is shown that RGFP966, commercialized as an HDAC3-selective probe, is a slow- binding inhibitor with inhibitor constants of 57, 31, and 13 nM against HDAC-1-3, respectively.

Determination of Slow-binding HDAC Inhibitor Potency and Subclass Selectivity

It is found that entinostat, a clinical candidate, inhibits HDACs 1–3 by a two-step, slow-binding mechanism with lower potencies than previously reported, and it is shown that RGFP966, commercialized as HDAC3-selective probe, is a slow- binding inhibitor with inhibitor constants of 57 nM, 31 nM and 13 nM againstHDACs1–3, respectively.

Endogenous modulators and pharmacological inhibitors of histone deacetylases in cancer therapy

New evidence showing that HDACs are direct intracellular targets of the potent sphingolipid mediator S1P, the first identified endogenous nuclear regulator of these enzymes, linking sphingoipid metabolism in the nucleus to remodeling of chromatin and epigenetic regulation of gene expression is reviewed.

Selective Inhibition of Histone Deacetylase 10: Hydrogen Bonding to the Gatekeeper Residue is Implicated.

Docking into human HDAC10 homology models indicated that a hydrogen bond between a cap group nitrogen and the gatekeeper residue Glu272 was responsible for potentHDAC10 binding, which provides an optimal platform for the development of HDAC 10-selective inhibitors, as exemplified with the Tubastatin A scaffold.



Determination of the class and isoform selectivity of small-molecule histone deacetylase inhibitors.

Testing a number of clinically relevant HDACis (HDAC inhibitors) against a panel of rhHDAC (recombinant human HDAC) isoforms showed that both pan- HDAC and class-I-specific inhibitor treatment resulted in increased acetylation of histones, but only pan-HDAC inhibitor treatment resulting in increased tubulin acetylations, which is in agreement with their activity towards the HDAC6 isoform.

Activity-based probes for proteomic profiling of histone deacetylase complexes

This work describes an active site-directed chemical probe that contains structural elements of the general HDAC inhibitor suberoylanilide hydroxamic acid (SAHA), as well as benzophenone and alkyne moieties to effect covalent modification and enrichment of HDACs, respectively and indicates that certain HDAC-associated proteins are directly modified by SAHA-BPyne.

Pimelic Diphenylamide 106 Is a Slow, Tight-binding Inhibitor of Class I Histone Deacetylases*

It is shown that a benzamide HDAC inhibitors, a pimelic diphenylamide (106), is a class I HDAC inhibitor, demonstrating no activity against class II HDACs, although inhibition for these enzymes occurs through different mechanisms.

Anticancer activities of histone deacetylase inhibitors

Recent advances in the understanding of the molecular events that underlie the anticancer effects of HDAC inhibitors are summarized and how such information could be used in optimizing the development and application of these agents in the clinic, either as monotherapies or in combination with other anticancer drugs are discussed.

Distinct pharmacological properties of second generation HDAC inhibitors with the benzamide or hydroxamate head group

Comparing the pharmacological properties of selected second generation HDAC inhibitors with the hydroxamate and benzamide head group, namely SAHA, LAQ824/LBH589, CI994, MS275 and MGCD0103 concludes that despite a different HDAC isoenzyme inhibition profile, hydroxamine and Benzamide analogs as studied display similar cellular profiles.

Chemical Phylogenetics of Histone Deacetylases

The synthesis and study of a focused library of cinnamic hydroxamates allowed the identification of a first non-selective HDAC inhibitor, which will guide a more informed use of HDAC inhibitors as chemical probes and therapeutic agents.

Unraveling the hidden catalytic activity of vertebrate class IIa histone deacetylases

Evidence is presented supporting the view that vertebrate class IIa HDACs may have evolved to maintain low basal activities on acetyl-lysines and to efficiently process restricted sets of specific, still undiscovered natural substrates.