2. Signaling Pathways
  3. Cell Cycle/DNA Damage
    Epigenetics
  4. HDAC

HDAC

Histone deacetylases

HDAC

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HDAC (Histone deacetylases) are a class of enzymes that remove acetyl groups (O=C-CH3) from an ε-N-acetyl lysine amino acid on ahistone, allowing the histones to wrap the DNA more tightly. This is important because DNA is wrapped around histones, and DNA expression is regulated by acetylation and de-acetylation. Its action is opposite to that of histone acetyltransferase. HDAC proteins are now also called lysine deacetylases (KDAC), to describe their function rather than their target, which also includes non-histone proteins. Together with the acetylpolyamine amidohydrolases and the acetoin utilization proteins, the histone deacetylases form an ancient protein superfamily known as the histone deacetylase superfamily.

HDAC Isoform Specific Products:

HDAC Isoform Comparison
Cat. No. Product Name Effect Purity Chemical Structure
  • HY-161868
    DLC-50
    		Inhibitor
    DLC-50 is a dual inhibitor for PARP-1 and HDAC-1 with IC50 of 1.2 nM and 31 nM. DLC-50 inhibits the proliferation of cancer cells MDA-MB-436, MDA-MB-231, and MCF-7 with IC50 of 0.3, 2.7 and 2.41 μM. DLC-50 induces apoptosis in MDA-MB-231, arrests the cell cycle at G2 phase.
    DLC-50
  • HY-172891
    CDK9/HDAC1/HDAC3-IN-1
    		Inhibitor
    CDK9/HDAC1/HDAC3-IN-1 is dual-functional inhibitor of CDK9 and HDAC. CDK9/HDAC1/HDAC3-IN-1 inhibits the protein activity of CDK9/HDAC/HDAC3 with IC50 s of 0.17  μM, 1.73  μM and 1.11 μM for CDK9, HDAC1, and HDAC3, respectively. CDK9/HDAC1/HDAC3-IN-1 inhibits cancer cells by inducing cell apoptosis and cell cycle arrest in the G2/M phase, as well as tumor growth in a murine TNBC MDA-MB-231 xenograft model. CDK9/HDAC1/HDAC3-IN-1 has a broad-spectrum anti-cancer activity, such as breast cancer, cervical cancer, and liver cancer.
    CDK9/HDAC1/HDAC3-IN-1
  • HY-174409
    HDAC6 ligand-Linker Conjugate 1
    		Degrader
    HDAC6 ligand-linker conjugate 1 is a conjugate of HDAC6 ligand and linker, which can be used to synthesize PROTACs such as PROTAC HDAC6 degrader 5 (HY-174401).
    HDAC6 ligand-Linker Conjugate 1
  • HY-169433
    Naph-Se-TMZ
    		Inhibitor
    Naph-Se-TMZ is a PROTAC-like HDAC1 degrader. Naph-Se-TMZ can reduce the total HDAC activity in glioma cells and enhance the inhibitory effect of Temozolomide (HY-17364). Naph-Se-TMZ consists of the target protein ligand (red part) Temozolomide (HY-17364), the DNA-targeting intercalator (blue part) Nitro-Naphthalimide-C2-acylamide (HY-169437) and the molecular linker (black part). At the same time, the active control of the target protein ligand is: Temozolomide-amino hydrochloride (HY-169439), and the DNA targeting intercalator + linker is: NNISC-2 (HY-169438).
    Naph-Se-TMZ
  • HY-175513
    ZWZH-21
    		Inhibitor
    ZWZH-21 is a selective and orally active HDAC1/2 dual inhibitor with IC50 values of 34 nM for HDAC1 and 41 nM for HDAC2. ZWZH-21 can inhibit HCT116 and SW480 cells growth with IC50 values of 0.524 μM and 1.063 μM, respectively. ZWZH-21 can inhibit proliferation and migration and induces apoptosis in multiple colorectal cancer cells. ZWZH-21 can be used for the research of cancer, such as colorectal cancer.
    ZWZH-21
  • HY-145687
    HDAC-IN-32
    		Inhibitor
    HDAC-IN-32 is a potent HDAC inhibitor with IC50s of 5.2, 11, and 28 nM for HDAC1, HDAC2 and HDAC6, respectively. HDAC-IN-32 possesses potent antiproliferation activities against tumor cells. HDAC-IN-32 shows potent antitumor efficacy in vivo That trigger antitumor immunity.
    HDAC-IN-32
  • HY-162124
    HDAC/NAMPT-IN-1
    		Inhibitor
    HDAC/NAMPT-IN-1 (compound 39h) is a dual inhibitor of HDAC and NAMPT with IC50 values of 0.72-37081 nM and 1618 nM.
    HDAC/NAMPT-IN-1
  • HY-162086
    HDAC-IN-68
    HDAC-IN-68 (Compound 29) is a potent HDAC inhibitor that disrupts microtubule structure and inhibits tumor growth. HDAC-IN-68 significantly inhibits class I HDACs (HDAC1, HDAC2, HDAC3) with IC50 values of 5.1, 11.5 and 8.8 nM, respectively.
    HDAC-IN-68
  • HY-172136
    LSQ-28
    		Inhibitor
    LSQ-28 is an orally active HDAC3 inhibitor with an IC50 of 42 nM, and exhibits potent anticancer, antiproliferative, antimigratory, anti-invasive, and antiwound healing activities. LSQ-28 can be utilized in cancer research.
    LSQ-28
  • HY-169014
    HDAC-IN-77
    		Inhibitor
    HDAC-IN-77 (HL-5s) is an HDAC inhibitor. HDAC-IN-77 can induce ferroptosis and inhibit the Nrf2/HO-1 signaling pathway. HDAC-IN-77 can be used in cancer research.
    HDAC-IN-77
  • HY-170907
    HDAC-IN-85
    		Inhibitor
    HDAC-IN-85 (Compound 1) is a BBB-permeable HDAC inhibitor. HDAC-IN-85 has an inhibitory effect on brain tumor cell lines. HDAC-IN-85 can induce acetylation, leading to DNA double-strand breaks, and induce the ubiquitination of RAD51, disrupting the DNA repair process. HDAC-IN-85 can be used in the research of glioblastoma.
    HDAC-IN-85
  • HY-149497
    HDAC6-IN-19
    		Inhibitor
    HDAC6-IN-19 (Compound 14g) is a HDAC6 inhibitor (IC50: 2.68 nM). HDAC6-IN-19 also inhibits HDAC1, HDAC2 and HDAC3 with IC50s of 61.6 nM, 98.7 nM and 103 nM. HDAC6-IN-19 potently inhibits multiple cancer cell proliferation, including leukemia, colon cancer, melanoma, and breast cancer cell lines.
    HDAC6-IN-19
  • HY-B0809S1
    Theophylline-d3
    		Activator
    Theophylline-d3 is deuterated labeled Theophylline (HY-B0809). Theophylline (1,3-Dimethylxanthine) is a potent phosphodiesterase (PDE) inhibitor, adenosine receptor antagonist, and histone deacetylase (HDAC) activator. Theophylline (1,3-Dimethylxanthine) inhibits PDE3 activity to relax airway smooth muscle. Theophylline (1,3-Dimethylxanthine) has anti-inflammatory activity by increase IL-10 and inhibit NF-κB into the nucleus. Theophylline (1,3-Dimethylxanthine) induces apoptosis. Theophylline (1,3-Dimethylxanthine) can be used for asthma and chronic obstructive pulmonary disease (COPD) research.
    Theophylline-d<sub>3</sub>
  • HY-179654
    ST13
    		Inhibitor
    ST13, an ortho-hydroxyanilide, is a selective, slow- and tight-binding HDAC1 and HDAC2 inhibitor with IC50s of 23 nM and 49 nM, respectively. ST13 shows a weak inhibition of HDAC3 (IC50 = 4.30 μM) and HDAC6 (IC50 > 10 μM). The induced fit mechanism of ST13 proceeds through a two-step process: first, the enzyme and inhibitor rapidly form a collision complex (EI), which then slowly transforms into the stable complex E*I. ST13 induces apoptosis in cancer cells. ST13 can be used for the study of melanoma and triple-negative breast.
    ST13
  • HY-168962
    HDAC-IN-88
    		Inhibitor
    HDAC-IN-88 (Compound HJ-9) is the inhibitor for HDAC that inhibits HDAC6, HDAC1, HDAC2, HDAC8 and HDAC3 with IC50s of 0.226, 1.103, 2.308, 3.255 and 3.864 μM, respectively. HDAC-IN-88 inhibits the proliferation of cancer cell HepG2, HCT116 and MV4-11 with IC50 of 5.47, 9.78 and 0.38 μM, inhibits the migration of HCT116, arrests the cell cycle at G0/G1 phase, and induces apoptosis and autophagy in MV4-11. HDAC-IN-88 reduces ROS level and mitochondrial membrane potential. HDAC-IN-88 exhibits antimalarial activity that inhibits P. falciparum 3D7 with EC50 of 165 nM. HDAC-IN-88 also exhibits anti-angiogenic activity.
    HDAC-IN-88
  • HY-173558
    PD-L1/HDAC3-IN-1
    		Inhibitor
    PD-L1/HDAC3-IN-1 (PH3) is a dual PD-L1/HDAC3 Inhibitor with IC50 values of 89.4 nM and 107 nM for PD-1/PD-L1 and HDAC3, respectively. PD-L1/HDAC3-IN-1 induces cell apoptosis and arrests cell cycle at G0/G1 phase. PD-L1/HDAC3-IN-1 shows anticancer activity both in vivo and in vitro.
    PD-L1/HDAC3-IN-1
  • HY-150595
    HDAC6-IN-10
    		Inhibitor
    HDAC6-IN-10 is a highly selective HDAC6 inhibitor with the IC50 of 0.73 nM. HDAC6-IN-10 has 144~10941-fold selectivity over other HDAC isoforms. HDAC6-IN-10 shows anti-proliferative activities against multiple myeloma cells.
    HDAC6-IN-10
  • HY-107550
    NCT-14b
    		Inhibitor
    NCT-14b is a HDAC6-selective inhibitor. NCT-14b blocks the growth of estrogen receptor α-positive breast cancer MCF-7 cells.
    NCT-14b
  • HY-157490
    PARP/HDAC-IN-1
    		Inhibitor
    PARP/HDAC-IN-1 (compound B102) is a potent dual inhibitor of PARP and HDAC. PARP/HDAC-IN-1 inhibits PARP1, PARP2 and HDAC1 with IC50s of 19.01, 2.13, 1690 nM, respectively.
    PARP/HDAC-IN-1
  • HY-181843
    HDAC-IN-99
    		Inhibitor
    HDAC-IN-99 is a histone deacetylase (HDAC) inhibitor with an IC50 of 37.73 nM, and it exhibits potent inhibitory activity against HDAC1 (IC50 = 48.09 nM), HDAC2 (IC50 = 300.28 nM) and HDAC6 (IC50 = 9.16 nM). HDAC-IN-99 exerts broad-spectrum antiproliferative activity in various cancer cell lines. HDAC-IN-99 induces S-phase cell cycle arrest and apoptosis in colon cancer cells, increases the acetylation levels of histone H3, histone H4 and α-tubulin, and upregulates the expression of p21 as well as the cleavage of caspase-3. HDAC-IN-99 displays antitumor activity in colon cancer xenograft models. HDAC-IN-99 can be used for the research of colon cancer.
    HDAC-IN-99
Cat. No. Product Name / Synonyms Application Reactivity
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Download HDAC Signaling Pathway Map.

TCR, GPCR and HDAC II interaction: Diverse agonists act through G-protein-coupled receptors (GPCRs) to activate the PKC-PKD axis, CaMK, Rho, or MHC binding to antigens stimulates TCR to activate PKD, leading to phosphorylation of class II HDACs. Phospho-HDACs dissociate from MEF2, bind 14-3-3, and are exported to the cytoplasm through a CRM1-dependent mechanism. CRM1 is inhibited by leptomycin B (LMB). Release of MEF2 from class II HDACs allows p300 to dock on MEF2 and stimulate gene expression. Dephosphorylation of class II HDACs in the cytoplasm enables reentry into the nucleus[1].

 

TLR: TLR signaling is initiated by ligand binding to receptors. The recruitment of TLR domain-containing adaptor protein MyD88 is repressed by HDAC6, whereas NF-κB and MTA-1 can be negatively regulated by HDAC1/2/3 and HDAC2, respectively. Acetylation by HATs enhance MKP-1 which inhibits p38-mediated inflammatory responses, while HDAC1/2/3 inhibits MKP-1 activity. HDAC1 and HDAC8 repress, whereas HDAC6 promotes, IRF function in response to viral challenge. HDAC11 inhibits IL-10 expression and HDAC1 and HDAC2 represses IFNγ-dependent activation of the CIITA transcription factor, thus affecting antigen presentation[2][3].

 

IRNAR: IFN-α/β induce activation of the type I IFN receptor and then bring the receptor-associated JAKs into proximity. JAK adds phosphates to the receptor. STATs bind to the phosphates and then phosphorylated by JAKs to form a dimer, leading to nuclear translocation and gene expression. HDACs positively regulate STATs and PZLF to promote antiviral responses and IFN-induced gene expression[2][3].

 

Cell cycle: In G1 phase, HDAC, Retinoblastoma protein (RB), E2F and polypeptide (DP) form a repressor complex. HDAC acts on surrounding chromatin, causing it to adopt a closed chromatin conformation, and transcription is repressed. Prior to the G1-S transition, phosphorylation of RB by CDKs dissociates the repressor complex. Transcription factors (TFs) gain access to their binding sites and, together with the now unmasked E2F activation domain. E2F is then free to activate transcription by contacting basal factors or by contacting histone acetyltransferases, such as CBP, that can alter chromatin structure[4].

 

The function of non-histone proteins is also regulated by HATs/HDACs. p53: HDAC1 impairs the function of p53. p53 is acetylated under conditions of stress or HDAC inhibition by its cofactor CREB binding protein (CBP) and the transcription of genes involved in differentiation is activated. HSP90: HSP90 is a chaperone that complexes with other chaperones, such as p23, to maintain correct conformational folding of its client proteins. HDAC6 deacetylates HSP90. Inhibition of HDAC6 would result in hyperacetylated HSP90, which would be unable to interact with its co-chaperones and properly lead to misfolded client proteins being targeted for degradation via the ubiquitin-proteasome system[5][6].
 

Reference:

[1]. Vega RB, et al. Protein kinases C and D mediate agonist-dependent cardiac hypertrophy through nuclear export of histone deacetylase 5.Mol Cell Biol. 2004 Oct;24(19):8374-85.
[2]. Shakespear MR, et al. Histone deacetylases as regulators of inflammation and immunity. Trends Immunol. 2011 Jul;32(7):335-43.
[3]. Suliman BA, et al. HDACi: molecular mechanisms and therapeutic implications in the innate immune system.Immunol Cell Biol. 2012 Jan;90(1):23-32. 
[4]. Brehm A, et al. Retinoblastoma protein meets chromatin.Trends Biochem Sci. 1999 Apr;24(4):142-5.
[5]. Butler R, et al. Histone deacetylase inhibitors as therapeutics for polyglutamine disorders.Nat Rev Neurosci. 2006 Oct;7(10):784-96
[6]. Minucci S, et al. Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer.Nat Rev Cancer. 2006 Jan;6(1):38-51.

HDAC Isoform Comparison

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