ACY-738

Reagent Authentication Certificate:

Chemical Probes Portal ACY-738.pdf

Protein target name:

HDAC6

Recommended Concentration for use in cells:

10 nM - 1 uM

Probe Availability

MedChem Express (1375465-91-0)

Probe Information

Target and Probe Information

Target Details

Target class:

Epigenetics

Subclass:

HDAC

HUGO symbol:

HDAC6

Entrez gene ID:

10013

Target alias:

Histone deacetylase 6, CPBHM, HD6, JM21, PPP1R90

Probe Details

Chemical Probes Portal ID:

CPP1485

PubChem CID:

57381425

ChEMBL ID:

CHEMBL3655950

SMILES string:

C1CC1(C2=CC=CC=C2)NC3=NC=C(C=N3)C(=O)NO

InChi Key:

LIIWIMDSZVNYHY-UHFFFAOYSA-N

Validation in Cells and Model Organisms

In vitro validation

On target activity

Potency:

IC50

1.7 nM

Potency assay:

Enzyme assay with recombinant enzyme

Off target activity

Potency (off target):

IC50

Off target protein and potency:

HDAC1: 94 nM, HDAC2: 128 nM, HDAC3: 218 nM

Potency assay (off target):

Enzyme assay, recombinant protein

In cell validation

On target activity in cells

Potency assay (cells):

In RN46A-B12 cells, ACY-738 (2.5 uM) increased acetylation of alpha-tubulin at K40 as detected by western blot.

Target engagement assay (cells):

Indirect, substrate acetylation assay

Off target activity in cells

Potency assay, off target (cells):

In RN46A-B12 cells, ACY-738 (2.5 uM) did not affect histone H3K9 acetylation.

In vivo validation

Organism:

male NIH Swiss mice

Dose:

5 mg/kg

Route of delivery:

Intraperitoneal

Plasma half life:

0.2 h

Cmax:

494 ng/mL

Organ of Interest

Organ (O):

Brain

Target engagement assay:

In whole-brain lysate after treatment, alpha-tubulin acetylation increased in multiple brain regions (cortex, hippocampus, DRN, and cerebellum). An increase in alpha-tubulin acetlyation was not observed in the brains of flHDAC6^nestin-cre mice (neural-crest specific HDAC6 knock out in C57BL6 mice) beyond the already elevated levels. No changes in the acetylation of H3K9 were detected.

Ratio of probe in organ to plasma (O:P):

AUC brain:plasma=1.22

Primary Reference

Reference (doi):

10.1038/npp.2013.207

Reference (PMID):

23954848

SAB Rating

Rating for use in Cells

3 review(s)

Rating for use in Model Organisms

3 review(s)

SAB Members

SAB Comments

ACY-738 is a very potent HDAC6 inhibitor (IC50 of 1.7 nM) with >50-100X selectivity against other HDAC isoforms. It has poor PK, and thus has to be administered by either IV or IP routes. Calculated physicochemical properties: MW 270.3, PSA 87.1, AlogP 1.32, clogD pH 7 1.28, HBDon 3 (in water 2 since the hydroxamic acid is highly ionized), HBAcc 5, Nrot 4, Ligand Efficiency (LE) 0.588, Lipophilicity Ligand Efficiency (LipE) 7.49. Although quite a few HDAC inhibitors have been approved as drugs and more are in clinical trials (Vorinostat, Panobinostat, Entinostat, Mocetinostat, Belinistat, Quisinostat, Chidamide, Abexinostat, ACY-1215), ACY-738 seems to be the only >50-100X selective HDAC6 inhibitor (against other 10 HDACs). Despite the fact that it has poor PK and it as to be administered either IV or IP (plasma half-life of 0.2 h), it showed good brain-to-plasma ratio of 1.22. Thus it can be used to tease out the role of HDAC6 in brain for the prevention (and hopefully for the treatment) of Alzheimer’s and development of novel first-in-class antidepressants. The lower level for cell potency is not clear: only 2.5 uM was reported. The probe needs to be profiled over a large panel of cell lines to have a better understanding of the cellular doses as well as applicability. Several crystal structures of HDAC6 catalytic domain 2 are available in RCSB with approved drugs and other similar compounds. Thus, this chemical probe can be improved in terms of in vivo exposure, half-life, and route of administration, while capitalizing on HDAC selectivity and brain exposure.

While this probe is highly potent for the intended target in vitro, the cellular potency is not discerned as these experiments were only carried out at a single dose (2.5 microM). I would like to see cellular experiments performed at lower doses in order to assess the cellular potency of this compound. In addition, because of the chemical nature of this compound, off-target selectivity on other epigenetic targets in addition to GPCRs and kinases would enhance its value. For the animal studies in wild-type and knockout backgrounds, it would be useful to know the absolute levels of tubulin acetylation (as opposed to relative to vehicle). This will enable a comparison of the wild-type-treated response relative to the knockout baseline.

ACY-738

Probe Availability

Probe Information

Target Details

Histone deacetylase 6, CPBHM, HD6, JM21, PPP1R90

Probe Details

In vitro validation

In cell validation

In vivo validation

Primary Reference

Supporting Organizations

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ACY-738

Probe Availability

Probe Information

Target Details

Histone deacetylase 6, CPBHM, HD6, JM21, PPP1R90

Probe Details

In vitro validation

In cell validation

In vivo validation

Primary Reference

Supporting Organizations

Interested in supporting the portal?