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66 results for “HDAC6”
Data From: Harnessing Deep Belief Networks for Selective HDAC6 Inhibitors Identification
<p>This dataset contains the results from virtual screening of SPECS library after predicting the selectivity of molecules against HDAC6 over using a Deep Belief Network model that was trained and tested by the authors.</p> <p>The docking poses of 10 molecules with best docking scores were given along with their MMGBSA scores. </p> <p>The MD trajectory files along with the analysis were also provided for the selected three molecules as well as the reference molecule (co-crystalized ligand).</p>
HDAC6 screening dataset using tau-based substrate in an enzymatic assay yields selective inhibitors and activators
<p><strong>Structure and information of the data file</strong></p> <p>DATA SET; Contains the information to which data set this information belongs. There are four possibilities denoted 1 to 4. Data set1: Enzymatic assay of human HDAC6 with commercial peptide substrate. Data set2: Enzymatic assay of human HDAC6 with custom peptide substrate. Data set3: Hit confirmation of the active molecules of the enzymatic assay of human HDAC6 with custom peptide substrate. Data set4: Determination of IC50 values for inhibition of enzymatic assay of human HDAC6 with custom peptide substrate.</p> <p>INTERNAL NAME; An internal name which enables identification of the compound within data sets from Fraunhofer ITMP ScreeningPort.</p> <p>TYPE; Type of data. Either 'inhibition' for normalized inhibition values or 'IC50' for enzymatic IC50.</p> <p>RELATION; Relation between TYPE and VALUE, always '='.</p> <p>VALUE; Value of the normalized inhibition or the enzymatic IC50.</p> <p>UNITS; Unit of the value. Either '%' for the normalized inhibition or 'uM' for the enzymatic IC50.</p> <p>NAME; Trade name of the chemical compound.</p> <p>SMILES; The canonical Smile of the chemical compound.</p> <p> </p> <p><strong>A</strong><strong>bstract</strong></p> <p>Histone deacetylase 6 (HDAC6) and HDAC10 are unique among the other HDACs as they consist of two domains instead of one. Only in the case of HDAC6 both domains are active resulting in a number of unique deacetylase reactions. Interestingly, HDAC6 can regulate the microtubule network and plays a role in the degradation of misfolded and aggregated proteins. We therefore developed a substrate (Boc-Ile-Asp-(Dimethyl)Lys-(Ac)Lys-aminoluciferin) based on a critical acetylation site of misfolded human Tau, a hallmark of Alzheimer’s Disease. This substrate was used to screen a 5632 compound encompassing repurposing library at 10 µM in a coupled, luminescence based assay. The assay was miniaturised to 10 µL per enzymatic reaction. For comparison, a generic HDAC substrate (BOC-Gly-(Ac)Lys-aminoluciferin) was also used to screen the same library. Both substrates rely on a cascade of enzymatic reactions. First, HDAC6 deacetylates the substrate followed by cleavage of aminluciferin from the peptide by porcine Trypsin and conversion of the aminoluciferin using firefly Luciferase. Compounds with an activity of at least 75% inhibition against the custom human Tau based substrate were confirmed in triplicates at the screening concentration of 10 µM. Confirmed hits, activity of at least 75%, where analysed in 8 point or 15 point dose response curves, depending on their activity. The data presented here encompass both primary data sets including 5632 compounds as well as 249 values from hit confirmation screening against the hTau based substrate and 151 IC<sub>50</sub> values from confirmed hits.</p> <p> </p> <p><strong>Methods of data generation</strong></p> <p><strong>Enzymatic assay of human HDAC6 with commercial peptide substrate. </strong></p> <p>The assay using the commercial peptide substrate (BOC-Gly-(Ac)Lys-aminoluciferin) was obtained from Promega Inc.. In the beginning the assay buffer is thawed and the lyophilized substrate is dissolved according to the technical manual (Promega Inc.) to create the substrate reagent. HDAC6 (obtained from BPS Biosciences) is dissolved in assay buffer at 0.2 nM, which is twice the final assay concentration. Compounds and controls are added to the plates using acoustic dispensing to reach a final concentration of 10 µM in the assay followed by 5 µl enzyme solution per well. Plates are centrifuged shortly and incubated for 10 min at RT. Afterwards, 5 µL/well substrate solution are added to the wells, centrifuged shortly and incubated for 10 min prior detection of the luminescence signal on a multimode reader. Primary screening was done at one concentration (10 µM) in singlicates.</p> <p> </p> <p><strong>Enzymatic assay of human HDAC6 with custom peptide substrate. </strong></p> <p>The assay was designed based on a commercial HDAC6 assay available from Promega Inc. This luminescence assay works by an aminoluciferin coupled HDAC6 peptide substrate. Upon deacetylation of the peptidic substrate by HDAC6 (obtained from BPS Biosciences) Trypsin (obtained from Sigma-Aldrich) can cleave the aminoluciferine from the peptide which can be converted by Luciferase (obtained from AAT Bioquest) to the detected signal. First, a twofold concentrated enzyme solution was generated, consisting of 4 nM HDAC6 and 0.1% BSA in HEPES buffer (25 mM HEPES, 137 mM NaCl, 2.7 mM KCl and 1 mM MgCl2, pH 7.0). Second, a twofold peptide solution was generated containing 100 µM custom made peptide (Boc-Ile-Asp-(Dimethyl)Lys-(Ac)Lys-aminoluciferin) in HEPES buffer. Compounds and controls are added to the plates using acoustic dispensing to reach a final concentration of 10 µM in the assay followed by 5 µl enzyme solution per well. Plates are centrifuged shortly and 5 µL/well peptide solution are added to the wells, centrifuged shortly and incubated for 30 min at RT. Afterwards, 5 µL detection reagent (0.067 mg/mL Luciferase, 133.3 µM ATP, 0.133 mg/mL Trypsin in HEPES buffer) were added to each well. Plates were centrifuged shortly and measured on a multimode reader after 30 min incubation at RT in the dark. Primary screening was done at one concentration (10 µM) in singlicates.</p> <p> </p> <p><strong>Hit confirmation of the active molecules of the enzymatic assay of human HDAC6 with custom peptide substrate</strong></p> <p>The assay was designed based on a commercial HDAC6 assay available from Promega Inc. This luminescence assay works by an aminoluciferin coupled HDAC6 peptide substrate. Upon deacetylation of the peptidic substrate by HDAC6 (obtained from BPS Biosciences) Trypsin (obtained from Sigma-Aldrich) can cleave the aminoluciferine from the peptide which can be converted by Luciferase (obtained from AAT Bioquest) to the detected signal. First, a twofold concentrated enzyme solution was generated, consisting of 4 nM HDAC6 and 0.1% BSA in HEPES buffer (25 mM HEPES, 137 mM NaCl, 2.7 mM KCl and 1 mM MgCl2, pH 7.0). Second, a twofold peptide solution was generated containing 100 µM custom made peptide (Boc-Ile-Asp-(Dimethyl)Lys-(Ac)Lys-aminoluciferin) in HEPES buffer. Compounds and controls are added to the plates using acoustic dispensing to reach a final concentration of 10 µM in the assay followed by 5 µl enzyme solution per well. Plates are centrifuged shortly and 5 µL/well peptide solution are added to the wells, centrifuged shortly and incubated for 30 min at RT. Afterwards, 5 µL detection reagent (0.067 mg/mL Luciferase, 133.3 µM ATP, 0.133 mg/mL Trypsin in HEPES buffer) were added to each well. Plates were centrifuged shortly and measured on a multimode reader after 30 min incubation at RT in the dark. Hit confirmation was done at one concentration (10 µM) in triplicates.</p> <p> </p> <p><strong>Determination of IC50 values for inhibition of enzymatic assay of human HDAC6 with custom peptide substrate</strong></p> <p>The assay was designed based on a commercial HDAC6 assay available from Promega Inc. This luminescence assay works by an aminoluciferin coupled HDAC6 peptide substrate. Upon deacetylation of the peptidic substrate by HDAC6 (obtained from BPS Biosciences) Trypsin (obtained from Sigma-Aldrich) can cleave the aminoluciferine from the peptide which can be converted by Luciferase (obtained from AAT Bioquest) to the detected signal. First, a twofold concentrated enzyme solution was generated, consisting of 4 nM HDAC6 and 0.1% BSA in HEPES buffer (25 mM HEPES, 137 mM NaCl, 2.7 mM KCl and 1 mM MgCl2, pH 7.0). Second, a twofold peptide solution was generated containing 100 µM custom made peptide (Boc-Ile-Asp-(Dimethyl)Lys-(Ac)Lys-aminoluciferin) in HEPES buffer. Compounds and controls are added to the plates using acoustic dispensing to reach a final concentration of 10 µM in the assay followed by 5 µl enzyme solution per well. Plates are centrifuged shortly and 5 µL/well peptide solution are added to the wells, centrifuged shortly and incubated for 30 min at RT. Afterwards, 5 µL detection reagent (0.067 mg/mL Luciferase, 133.3 µM ATP, 0.133 mg/mL Trypsin in HEPES buffer) were added to each well. Plates were centrifuged shortly and measured on a multimode reader after 30 min incubation at RT in the dark. IC50 values were determined using 7 point dose response curves (DRCs) between 20 µM and 312 nM. In case inhibition values were not below 50% additional 7 point DRCs were measured, starting at 312 nm with a dilution factor of 2. All DRCs were recorded in triplicates.</p>
Human Histone Deacetylase 6 (HDAC6); A Target Enabling Package
<p>HDAC6 is a cytosolic deacetylase with diverse roles in cellular trafficking, autophagy and cell signalling. Specifically targeting the unique zinc-finger ubiquitin-binding domain (ZnF-UBD) of HDAC6 may be an attractive strategy in myeloma and lymphoma but no inhibitor has been reported to date. Presented here are 4 co-crystal structures of HDAC6 ZnF-UBD in complex with different compounds, and associated SPR, ITC and FP assays.</p>
HDAC6 protein-protein interaction network in CNS
<p>HDAC6 stands out as a distinctive member within the histone deacetylase family due to its predominant presence in the cytosol, facilitating its interaction with a wide array of non-histone proteins. Its dysregulation has been linked to various outcomes, encompassing diverse cancer types, immune-related disorders, and neurological conditions, including Alzheimer's, Parkinson's, ALS, Huntington's, Charcot-Marie-Tooth disease, and Rett syndrome.</p><p>The current network represents the known HDAC6 interactions in the central nervous system (CNS).</p><p>The latest version of the current network is available in WikiPathways under accession number WP5426.</p>
Selective HDAC6 Inhibitor ACY 241 in Combination With Nivolumab in Patients With Unresectable Non Small Cell Lung Cancer
ClinicalTrials.gov study NCT02635061. IPD Sharing: NO. Countries: 1. Publications: 1.
Safety,Tolerability and MTD KA2507 (HDAC6 Inhibitor) in Patients With Solid Tumours
ClinicalTrials.gov study NCT03008018. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Network-based assessment of HDAC6 activity is highly predictive of pre-clinical and clinical responses to the HDAC6 inhibitor ricolinostat [array]
GEO Series GSE180606. Homo sapiens; Mus musculus. 30 samples. Type: Expression profiling by array.
Ramalin ameliorates Alzheimer's disease pathology by targeting BACE1, HDAC6, and MAPK pathways
GEO Series GSE304876. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Targeting HDAC6 to treat heart failure with preserved ejection fraction (HFpEF)
GEO Series GSE249414. Mus musculus. 68 samples. Type: Expression profiling by high throughput sequencing.
Hdac6 regulates Tip60-p400 function in stem cells (gene expression)
GEO Series GSE42208. Mus musculus. 8 samples. Type: Expression profiling by array.
Modeling Spastic Paraplegia 4 using Human Corticospinal Motor Neuron enriched Cortical Organoids Uncovers Genotype–Phenotype Distinctions and HDAC6-Targetable Pathology
GEO Series GSE316534. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
ARID1A loss in pancreas leads to islet developmental defect and metabolic disturbance ,Islet cell ChIP-Seq HDAC6 arid1a
GEO Series GSE220638. Mus musculus. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Endogenous expression of inactive lysine deacetylases KDAC6 (HDAC6) and KDAC8 (HDAC8)
GEO Series GSE228549. Homo sapiens. 22 samples. Type: Expression profiling by high throughput sequencing.
Gene expression profile changes in HDAC6 knockdown HT1080 cells cells after TLR3 stimulation
GEO Series GSE43218. Homo sapiens. 4 samples. Type: Expression profiling by array.
HDAC6-LINC00461 pathway as a potential target for glioblastoma therapy
GEO Series GSE182220. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
HDAC6 inhibitor ACY241 evokes transcriptional changes in tumor-associated T cells and macrophages
GEO Series GSE197278. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Hdac6 regulates Tip60-p400 function in stem cells
GEO Series GSE42329. Mus musculus. 15 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array.
Phenotypic Screening with Deep Learning Identifies HDAC6 Inhibitors as Cardioprotective Agents in Mouse Models of Dilated Cardiomyopathy
GEO Series GSE179656. Mus musculus. 25 samples. Type: Expression profiling by high throughput sequencing.
Evaluation of genetic inactivation of lysine deacetylases KDAC6 (HDAC6) and KDAC8 (HDAC8) versus treatment with KDAC-selective inhibitors
GEO Series GSE251743. Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
Gene expression following treatment with HDAC6 inhibitor C1A
GEO Series GSE64662. Homo sapiens. 12 samples. Type: Expression profiling by array.
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