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Related Concept Videos

Heterochromatin02:38

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...
Anaphase Promoting Complex00:50

Anaphase Promoting Complex

The stepwise destruction of specific proteins is necessary for the progression and completion of the cell cycle. Such proteins are ubiquitinated by ubiquitin ligases and then subsequently destroyed by the proteasome. The SCF (Skp1/Cullin/F-box) and the anaphase-promoting complex (APC) are two important ubiquitin ligases involved in cell cycle progression. While SCF is active throughout the cell cycle, APC gets activated during metaphase to anaphase transition. Cdc20 or Cdh1 binds to APC and...
Histone Modification02:32

Histone Modification

The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
Histone Modification02:32

Histone Modification

The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
Inhibition of Cdk Activity02:34

Inhibition of Cdk Activity

The orderly progression of the cell cycle depends on the activation of Cdk protein by binding to its cyclin partner. However, the cell cycle must be restricted when undergoing abnormal changes. Most cancers correlate to the deregulated cell cycle, and since Cdks are a central component of the cell cycle, Cdk inhibitors are extensively studied to develop anticancer agents. For instance, cyclin D associates with several Cdks, such as Cdk 4/6, to form an active complex. The cyclin D-Cdk4/6 complex...
Inhibition of CDK Activity02:34

Inhibition of CDK Activity

The orderly progression of the cell cycle depends on the activation of Cdk protein by binding to its cyclin partner. However, the cell cycle must be restricted when undergoing abnormal changes. Most cancers correlate to the deregulated cell cycle, and since Cdks are a central component of the cell cycle, Cdk inhibitors are extensively studied to develop anticancer agents. For instance, cyclin D associates with several Cdks, such as Cdk 4/6, to form an active complex. The cyclin D-Cdk4/6 complex...

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Related Experiment Video

Updated: May 12, 2026

Assays for Validating Histone Acetyltransferase Inhibitors
09:11

Assays for Validating Histone Acetyltransferase Inhibitors

Published on: August 6, 2020

A cyclodextrin-capped histone deacetylase inhibitor.

Jahangir Amin1, Antonino Puglisi, James Clarke

  • 1Dept. of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, East Sussex, UK. j.amin@sussex.ac.uk

Bioorganic & Medicinal Chemistry Letters
|April 18, 2013
PubMed
Summary
This summary is machine-generated.

A novel beta-cyclodextrin (βCD)-capped histone deacetylase (HDAC) inhibitor showed HDAC inhibition but lacked cellular activity, differing from its aryl-capped counterpart SAHA.

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Simultaneous Measurement of HDAC1 and HDAC6 Activity in HeLa Cells Using UHPLC-MS
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Last Updated: May 12, 2026

Assays for Validating Histone Acetyltransferase Inhibitors
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Simultaneous Measurement of HDAC1 and HDAC6 Activity in HeLa Cells Using UHPLC-MS
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Single-Step Enrichment of a TAP-Tagged Histone Deacetylase of the Filamentous Fungus Aspergillus nidulans for Enzymatic Activity Assay
09:07

Single-Step Enrichment of a TAP-Tagged Histone Deacetylase of the Filamentous Fungus Aspergillus nidulans for Enzymatic Activity Assay

Published on: May 1, 2019

Area of Science:

  • Medicinal Chemistry
  • Biochemistry
  • Molecular Biology

Background:

  • Histone deacetylase (HDAC) inhibitors are crucial in cancer therapy.
  • SAHA (vorinostat) is an established HDAC inhibitor with an aryl cap.
  • Exploring alternative capping strategies for HDAC inhibitors is of therapeutic interest.

Purpose of the Study:

  • To synthesize and evaluate a novel HDAC inhibitor featuring a beta-cyclodextrin (βCD) cap.
  • To investigate the impact of replacing an aryl cap with a large saccharidic scaffold on HDAC inhibition.
  • To assess the cellular activity of the synthesized βCD-capped HDAC inhibitor.

Main Methods:

  • Synthesis of a βCD-capped HDAC inhibitor (compound 3) with an alkyl linker and hydroxamic acid.
  • In vitro HDAC inhibition assays to compare compound 3 with SAHA.
  • Molecular docking studies to rationalize binding to the HDAC8 active site.
  • Cellular activity assays to determine biological efficacy.

Main Results:

  • Compound 3 was successfully synthesized, incorporating a βCD cap, alkyl linker, and zinc-binding hydroxamic acid.
  • In vitro studies demonstrated that compound 3 inhibits HDAC, albeit to a lesser extent than SAHA.
  • Molecular docking provided insights into the binding of compound 3 within the HDAC8 active site.
  • Compound 3 exhibited no cellular activity in the tested assays.

Conclusions:

  • Replacing the aryl cap of SAHA with a βCD scaffold results in a molecule with reduced HDAC inhibitory potency.
  • The lack of cellular activity suggests that the βCD cap may hinder cellular uptake or target engagement in a cellular context.
  • Further structural modifications are needed to enhance the cellular efficacy of βCD-capped HDAC inhibitors.