HDAC1 Protein Research Articles

Development of Novel Hydroxy Amide‐Based HDAC1 Inhibitors: Integrated Pharmacophore Modelling, 3D‐QSAR, and Virtual Screening Studies

AbstractHistone deacetylases (HDAC) are well‐established epigenetic targets for cancer therapy, with several HDAC inhibitors already approved for clinical use. Despite their potential, the clinical application of HDAC inhibitors, particularly HDAC1‐selective compounds, faces significant challenges. These include poor pharmacokinetics, limited bioavailability, and a lack of selectivity, which often necessitates to combine these inhibitors with other drugs for improved efficacy. Their limitations as standalone therapies emphasize the urgent need for further research and development. In this study, the dataset of 71 compounds were used to generate various pharmacophore models, among them DDRRR_1 was generated as the best pharmacophore model with a survival score of 6.148. The 3D‐QSAR data of theses compound showed a significant result with the values of R2 = 0.95 and Q2 = 0.87 in the atom‐based model and R2 = 0.901 and Q2 = 0.77 in the field‐based model. R‐group enumeration study generated novel 6426 compounds which was further screened through virtual screening study. The top‐scoring compound was M1 with the highest docking score (−8.804 kcal/mol) where hydroxy amide is important for interaction with HDAC1 protein. The ADME analysis demonstrated the compound's drug‐like characteristics. Overall, all hit compounds showed pharmacokinetic characteristics found within the range that is considered safe for human usage. This study findings have the potential to be applied further in the development of HDAC1 inhibitors for the treatment of gastric cancer.

Protective effect of Shenqi Wenfei Formula against lipopolysaccharide/cigarette smoke-induced COPD in Rat based on gut microbiota and network pharmacology analysis.

The incidence of chronic obstructive pulmonary disease (COPD) appears to be increasing and evidence suggests that the intestinal flora may play a causative role in its development. Previous studies found that the Shenqi Wenfei Formula (SQWF) can regulate pyroptosis via the NLRP3/GSDMD pathway, thereby reducing the inflammatory response in the lungs of COPD model rats. However, there is no information on whether the drug's effects are associated with intestinal flora. Therefore, this study investigates whether the effects of SQWF are mediated through the regulation of intestinal flora, aiming to elucidate the underlying mechanisms of its therapeutic impact on COPD. COPD was induced in rats using lipopolysaccharide and cigarette smoke, followed by intragastric administration of SQWF or physiological saline The targets of SQWF, associated signaling pathways, and key bacterial groups were investigated using 16S rRNA sequencing, network pharmacology, and bioinformatics techniques. The prediction results were validated using quantitative reverse transcription PCR, western blotting, and immunofluorescence, among other methods. SQWF treatment was found to alleviate COPD in model rats. Treatment was also observed to restore the balance of the intestinal flora in the rats, especially by reducing the abundance of g_Parabacteroides. Bioinformatics predictions identified g_Parabacteroides metabolites, RelA, HDAC1, and enriched neutrophil extracellular trap formation pathways as core targets of SQWF in COPD. qRT-PCR and Western blotting results showed that SQWF treatment reduced ReLA and HDAC1 mRNA and protein expression, along with decreased myeloperoxidase and neutrophil elastase levels in the nucleus. Treatment with SQWF was found to restore the imbalance of intestinal g_Parabacteroides in COPD and also regulate the expression of the ReLA and HDAC1 genes, thereby reducing pulmonary neutrophil extracellular traps and alleviating lung inflammation.

Repurposing of DrugBank molecules as dual non-hydroxamate HDAC8 and HDAC2 inhibitors by pharmacophore modeling, molecular docking, and molecular dynamics studies

HDAC8 and HDAC2 are recently reported to be overexpressed in cervical cancer. To date, studies related to the use of dual targeted HDAC inhibitor to treat cervical cancer are not well explored. Again, majority of the selective HDAC inhibitors discovered so far are hydroxamic acids, which have multiple adverse side-effects due to their strong zinc chelating ability. In this study, we repurposed DrugBank molecules to identify novel non hydroxamate compounds as potential HDAC8/2 dual inhibitors that can be effective for cervical cancer management. Therefore, a comprehensive integrated in silico approach, involving two-tier virtual screening, has been adopted. An initial e-pharmacophore model generation based on the co-ligands associated with HDAC8 and HDAC2 and subsequent PBVS of 12223 drug molecules were performed which eventually yielded 658 hits having fitness scores ≥ 1.0 for both the proteins. Then, SBVS for these hits was done using Glide XP method into the HDAC8 and HDAC2 crystal structures which resulted in 52 hits having XPGS ≤ −9.0 kcal/mol against both the proteins. Following this, they were re-docked into other HDAC isoforms to confirm isoform selectivity. DB11747, DB03973, DB03812, DB07890, and DB03448 were identified as top hits and were finally subjected to molecular dynamics simulation for stability of the complexes and MM-GBSA studies to calculate binding free energies. These hits have stable interactions with both HDAC8 and HDAC2 protein binding sites. In silico ADMET studies brought to limelight the promising pharmacokinetics and safety profiles of the hits. In silico cytotoxicity prediction studies also revealed potent anticancer activity.

Abstract 4129974: Increased Expression of Histone Deacetylases-2 and -6 in Left Ventricular Myocardium of Dogs with Chronic Heart Failure

Background: Histone deacetylases (HDACs) -2 and -6 are localized in the nucleus and cytoplasm of cells and have been implicated in the development of left ventricular (LV) hypertrophy, cardiac interstitial fibrosis, inflammation and worsening of LV systolic and diastolic function thus contributing to progressive worsening of heart failure (HF) with reduced ejection fraction (HFrEF) as well as HF with preserved ejection fraction (HFpEF). There is considerable interest in the application of small molecules that inhibit the activity of HDAC proteins in HF in the hope of fostering clinical benefit. Purpose: In the present study we examined the expression of HDAC-2 and -6 in LV tissue from normal (NL) dogs and dogs with chronic HF (LVEF <35%) produced by multiple sequential intracoronary microembolizations. Methods: Studies were performed in LV tissue from 7 NL dogs and 7 HF dogs. HDAC-2 and -6 protein levels were determined by Western blotting in the lysate of homogenate and 9000g supernatant (cytosolic) fractions prepared from powder of approximately 200 mg frozen LV tissue. After determining the protein by Lowry method, approximately 30 μg homogenate and 15 μg supernatant for HDAC-2 and 8 μg protein for both homogenate and supernatant for HDAC-6 were separated on 4%-20% SDS-PAGE and transferred on PVDF membrane. Band intensities were quantified in densitometric units (du). All data were normalized to glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Results: HDAC-2 proteins levels normalized to GAPDH were higher in the cytosol (0.59 ± 0.10 vs. 0.17 ± 0.04, p<0.05 vs. NL) and homogenate (0.75 ± 0.12 vs. 0.55 ± 0.10, not statistically significant) of LV tissue of dogs with HF compared to NL dogs. HDAC-6 protein levels were higher in the homogenate (2.54 ± 0.36 vs. 0.57 ± 0.19, p<0.05 vs. NL) and the cytosol (0.96 ± 0.15 vs. 0.78 ± 0.13, not statistically significant) of LV tissue of dogs with HF compared to NL dogs. Conclusions: These findings indicate upregulation of protein levels of HDAC-2 and -6 isoforms in LV myocardium of dogs with chronic HF. These abnormalities are likely to contribute to worsening HF. Selective inhibition of HDAC-2 and -6 represents a potential therapeutic approach for the treatment of both HFrEF and HFpEF.

Inhibition of cytokine-like protein 1 transcription hinders wound-healing process in diabetic rats.

This study explored the function and mechanism of cytokine-like protein 1 (CYTL1) in regulating the wound-healing process of rats with diabetes mellitus (DM). A wound was made in diabetic rats, in which CYTL1 overexpression or HDAC1 expression-interfering adenovirus was injected. The wound area on day 0, 7, 14 and 21 was observed and photographed to calculate the wound-healing rate. The wound tissues were collected for H&E, Masson staining and CD31 immunohistochemistry. The HDAC1 and CYTL1 mRNA and protein expressions in wound tissues were detected by RT-qPCR and western blot. The regulation of HDAC1 on CYTL1 was predicted by hTFtarget and AnimalTFDB database. The H3K27Ac level in the CYTL1 promoter was detected by chromatin immunoprecipitation (ChIP). Diabetic rats with CYTL1 overexpression or interfered HDAC1 expression had accelerated the wound-healing rate, in which massive fibroblasts, attenuated inflammatory infiltration and increased collagen and microvessel density were observed. Further experiments found that HDAC1 can inhibit CYTL1 transcription and expression by inhibiting H3K27Ac expression in CYTL1 promoter. Collected evidence showed HDAC1 can inhibit CYTL1 transcription by down-regulating the H3K27Ac level in CYTL1 promoter to slow down the wound-healing process in diabetic ulcer rats.

Design and synthesis of triazolopyridine derivatives as potent JAK/HDAC dual inhibitors with broad-spectrum antiproliferative activity

A series of triazolopyridine-based dual JAK/HDAC inhibitors were rationally designed and synthesised by merging different pharmacophores into one molecule. All triazolopyridine derivatives exhibited potent inhibitory activities against both targets and the best compound 4-(((5-(benzo[d][1, 3]dioxol-5-yl)-[1, 2, 4]triazolo[1, 5-a]pyridin-2-yl)amino)methyl)-N-hydroxybenzamide (19) was dug out. 19 was proved to be a pan-HDAC and JAK1/2 dual inhibitor and displayed high cytotoxicity against two cancer cell lines MDA-MB-231 and RPMI-8226 with IC50 values in submicromolar range. Docking simulation revealed that 19 fitted well into the active sites of HDAC and JAK proteins. Moreover, 19 exhibited better metabolic stability in vitro than SAHA. Our study demonstrated that compound 19 was a promising candidate for further preclinical studies.

Histone deacetylase expression following cisplatin-induced acute kidney injury in male and female mice.

The chemotherapeutic agent cisplatin accumulates in the kidneys, leading to acute kidney injury (AKI). Preclinical and clinical studies have demonstrated sex-dependent outcomes of cisplatin-AKI. Deranged histone deacetylase (HDAC) activity is hypothesized to promote the pathogenesis of male murine cisplatin-AKI; however, it is unknown whether there are sex differences in the kidney HDACs. We hypothesized that there would be sex-specific Hdac expression, localization, or enzymatic activity, which may explain sexual dimorphic responses to cisplatin-AKI. In normal human kidney RNA samples, HDAC10 was significantly greater in the kidneys of women compared with men, whereas HDAC1, HDAC6, HDAC10, and HDAC11 were differentially expressed between the kidney cortex and medulla, regardless of sex. In a murine model of cisplatin-AKI (3 days after a 15 mg/kg injection), we found few sex- or cisplatin-related differences in Hdac kidney transcripts among the mice. Although Hdac9 was significantly greater in female mice compared with male mice, HDAC9 protein localization did not differ. Hdac7 transcripts were greater in the inner medulla of cisplatin-AKI mice, regardless of sex, and this agreed with a greater HDAC7 abundance. HDAC activity within the cortex, outer medulla, and inner medulla was significantly lower in cisplatin-AKI mice but did not differ between the sexes. In agreement with these findings, a class I HDAC inhibitor did not improve kidney injury or function. In conclusion, even though cisplatin-AKI was evident and there were transcript level differences among the different kidney regions in this model, there were few sex- or cisplatin-dependent effects on kidney HDAC localization or activity.NEW & NOTEWORTHY Kidney histone deacetylases (HDACs) are abundant in male and female mice, and the inner medulla has the greatest HDAC activity. A low dose of cisplatin caused acute kidney injury (AKI) in these mice, but there were few changes in kidney HDACs at the RNA/protein/activity level. A class I HDAC inhibitor failed to improve AKI outcomes. Defining the HDAC isoform, cellular source, and interventional timing is necessary to determine whether HDAC inhibition is a therapeutic strategy to prevent cisplatin-AKI in both sexes.

Effect of allyl isothiocyanate on 4-HNE induced glucocorticoid resistance in COPD and the underlying mechanism

Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory condition, and its clinical management primarily targets bronchodilation and anti-inflammatory therapy. However, these treatments often fail to directly address the progression of COPD, particularly its associated glucocorticoid (GC) resistance. This study elucidates the mechanisms underlying GC resistance in COPD and explores the therapeutic potential of allyl isothiocyanate (AITC) in modulating MRP1 transport. We assessed the levels of the oxidative stress product 4-HNE, HDAC2 protein, inflammatory markers, and pulmonary function indices using animal and cell models of GC-resistant COPD. The cascade effects of these factors were investigated through interventions involving AITC, protein inhibitors, and dexamethasone (DEX). Cigarette smoke-induced oxidative stress in COPD leads to the accumulation of the lipid peroxidation product 4-HNE, which impairs HDAC2 protein activity and diminishes GC-mediated anti-inflammatory sensitivity due to disrupted histone deacetylation. AITC regulates MRP1, facilitating the effective efflux of 4-HNE from cells, thereby reducing HDAC2 protein degradation and restoring dexamethasone sensitivity in COPD. These findings elucidate the mechanism of smoking-induced GC resistance in COPD and highlight MRP1 as a potential therapeutic target, as well as the enormous potential of AITC for combined GC therapy in COPD, promoting their clinical applications.

HDAC1 and FOXK1 mediate EGFR-TKI resistance of non-small cell lung cancer through miR-33a silencing

BackgroundThe development of acquired EGFR-TKI treatment resistance is still a major clinical challenge in the treatment of non-small cell lung cancer (NSCLC). This study aimed to investigate the role of HDAC1/FOXK1/miR-33a signaling in EGFR-TKI resistance.MethodsThe expression levels of miR‐33a, HDAC1, and FOXK1 were examined using quantitative polymerase chain reaction (PCR) and bioinformatics analysis. Cell proliferation, migration, and apoptosis were explored by cell number assay, Transwell, and flow cytometry assays, respectively. After overexpression or knockdown of HDAC1, miR-33a expression in the cells, cell functions were tested. Immunoprecipitation and correlation analyses were used to evaluate the interaction between HDAC1 and FOXK1 protein. The tumor-suppressive role of miR-33a was investigated by animal experiments.ResultsThe suppression of miR-33a increased TKI resistance by affecting cell proliferation, migration, and apoptosis in gefitinib-resistant cells. HDAC1 is the key upstream molecule that inhibits miR-33 expression. HDAC1 upregulation increased gefitinib resistance by its binding to FOXK1 in cells to silence miR-33a expression. MiR-33a overexpression exerts tumor-suppressive effects by negatively regulating ABCB7 and p70S6K1 expression. Moreover, overexpression of miR-33a inhibited tumor growth in a xenograft nude mouse model.ConclusionsHDAC1/FOXK1 upregulation and miR-33a silencing are new mechanisms of EGFR-TKI resistance in NSCLC.

The effect of intra spinal administration of cerium oxide nanoparticles on central pain mechanism: An experimental study.

This study investigated Cerium oxide nanoparticles (CeONPs) effect on central neuropathic pain (CNP). The compressive method of spinal cord injury (SCI) model was used for pain induction. Three groups were formed by a random allocation of 24 rats. In the treatment group, CeONPs were injected above and below the lesion site immediately after inducing SCI. pain symptoms were evaluated using acetone, Radian Heat, and Von Frey tests weekly for six weeks. Finally, we counted fibroblasts using H&E staining. We evaluated the expression of Cx43, GAD65 and HDAC2 proteins using the western blot method. The analysis of results was done by PRISM software. At the end of the study, we found that CeONPs reduced pain symptoms to levels similar to those observed in normal animals. CeONPs also increased the expression of GAD65 and Cx43 proteins but did not affect HDAC2 inhibition. CeONPs probably have a pain-relieving effect on chronic pain by potentially preserving GAD65 and Cx43 protein expression and hindering fibroblast infiltration.

LINC00847 drives pancreatic cancer progression by targeting the miR-455-3p/HDAC4 axis.

Pancreatic cancer (PC) is a common malignant tumor of the digestive system, posing a serious threat to the life of patients. This study aims to investigate the role of LINC00847 and the LINC00847/miR-455-3p/HDAC4 mechanism in PC progression. The RNA levels of LINC00847, miR-455-3p and HDAC4 were determined by RT-qPCR. HDAC4 protein level was assessed by western blotting. Colony formation and CCK-8 assays were employed to test the proliferation of PC cells. Transwell and scratch assays were conducted to evaluate the cell invasive and migratory abilities, respectively. The effect of LINC00847 silencing on PC cells in vivo was verified using a mouse xenograft model. The correlation among LINC00847, miR-455-3p and HDAC4 was ascertained by dual-luciferase reporter (DLR) assay and Pearson's correlation analysis. The result showed that LINC00847 mainly localized in the cytoplasm was upregulated in PC cells and tissues. Downregulating LINC00847 hindered migration, proliferation, and invasion of PC cells in vitro. Moreover, it also suppressed tumor growth in an in vivo xenograft model. LINC00847 was found to directly target miR-455-3p. miR-455-3p overexpression inhibited cell proliferation and invasion. In addition, HDAC4 was confirmed to be a target gene of miR-455-3p, and HDAC4 overexpression overturned the impact of LINC00847 knockdown on PC cell progression. Our findings reveal that LINC00847 potentially plays a key role in the carcinogenesis of PC progression. This effect may be mediated via regulating the miR-455-3p/HDAC4 axis. This study provides insights into the intricate molecular mechanisms underlying PC and opens avenues for potential therapeutic interventions.

MIIP downregulates PD-L1 expression through HDAC6 in cutaneous melanoma

PurposeImmune checkpoint inhibitors have improved the objective response rate and survival of melanoma patients. However, there are still many melanoma patients suffering from disease progression due to primary or secondary immune checkpoint inhibitor resistance, as is observed in the failure of anti-PD1/PD-L1 therapy. While the expression of valuable markers, such as TMB, MSI, and PD-L1, could serve as effective predictors of anti-checkpoint inhibitor therapies, tumor cell PD-L1 expression and its regulating mechanism would significantly affect the anti-PD-1 immunotherapy response and efficacy. Therefore, it is urgent to determine the function of PD-1/PD-L1 expression in melanoma and its associated pathways to enhance the efficacy of anti-PD-1 therapies.MethodsA cohort of 133 patients with histologically confirmed melanoma from Tianjin Medical University Cancer Institute & Hospital were included in this study. We performed immunohistochemical staining to detect the expression of Migration and invasion inhibitory protein (MIIP), HDAC6 and PD-L1. Kaplan–Meier and log-rank test were used for survival analysis. As for vitro, Western blot was used in melanoma cell lines to verify the signaling pathway that MIIP regulates PD-L1 expression.ResultsMIIP expression was decreased in melanoma and that the negative expression of MIIP was correlated with worse overall survival. The positive expression of HDAC6, a molecule that is downstream of MIIP, had a positive trend with decreased overall survival. At the same time, the positive expression of PD-L1, a crucial costimulatory molecule, was associated with decreased overall survival. Furthermore, there was a positive association between HDAC6 and PD-L1 protein expression (p < 0.01), and this correlation is more prominent in cutaneous melanoma than acral melanoma. In cutaneous melanoma cell lines, we found that increasing MIIP led to decreased HDAC6, pSTAT3, and PD-L1 expression. Knocking down MIIP led to increased HDAC6, pSTAT3, and PD-L1 expression. Combining the published results, showing that HDAC6 can regulate PD-L1 expression through STAT3, our present data suggest that MIIP inhibits the expression of PD-L1 by downregulating HDAC6 in melanoma. Most importantly, methods for targeting MIIP-HDAC6-PD-L1 pathways, such as treatment with HDAC6 inhibitors, might indicate a new therapeutic approach for enhancing immune checkpoint inhibitor therapies in melanoma.ConclusionsOur findings highlight the immunomodulatory effects of MIIP in the inhibition of PD-L1 expression by downregulating HDAC6 in melanoma. Methods for targeting MIIP-HDAC6-PD-L1 pathways might be new therapeutic approaches for enhancing immune checkpoint inhibitor therapies in melanoma.

TM4SF1 is a molecular facilitator that distributes cargo proteins intracellularly in endothelial cells in support of blood vessel formation.

Transmembrane-4 L-six family member-1 (TM4SF1) is an atypical tetraspanin that is highly and selectively expressed in proliferating endothelial cells and plays an essential role in blood vessel development. TM4SF1 forms clusters on the cell surface called TMED (TM4SF1-enriched microdomains) and recruits other proteins that internalize along with TM4SF1 via microtubules to intracellular locations including the nucleus. We report here that tumor growth and wound healing are inhibited in Tm4sf1-heterozygous mice. Investigating the mechanisms of TM4SF1 activity, we show that 12 out of 18 signaling molecules examined are recruited to TMED on the surface of cultured human umbilical vein endothelial cells (HUVEC) and internalize along with TMED; notable among them are PLCγ and HDAC6. When TM4SF1 is knocked down in HUVEC, microtubules are heavily acetylated despite normal levels of HDAC6 protein, and, despite normal levels of VEGFR2, are unable to proliferate. Together, our studies indicate that pathological angiogenesis is inhibited when levels of TM4SF1 are reduced as in Tm4sf1-heterozygous mice; a likely mechanism is that TM4SF1 regulates the intracellular distribution of signaling molecules necessary for endothelial cell proliferation and migration.

Early life stress-induced aortic endothelial dysfunction is mediated by endothelium-specific HDAC9

Early life stress (ELS) is highly prevalent worldwide and has been associated with an elevated risk of developing cardiovascular disease (CVD) in adulthood. We previously showed that maternal separation with early weaning (MSEW), an established ELS model of neglect in mice, leads to blunted endothelium-dependent relaxation as well as increased histone deacetylase (HDAC) activity. We hypothesized that specific HDAC isoform(s) mediate the ELS-induced endothelial dysfunction. In a screen of all HDAC isoforms, HDAC1, 6, and 9 gene expression were significantly elevated in aortas from male adult MSEW and normally reared (NR) C57BL6/J mice (N=3/group, p&lt;0.05). Western blot analysis found that only HDAC9 protein abundance was significantly elevated in aortas from male MSEW as compared to NR mice (N=6/group, p=0.01). Detection of HDAC9 via immunohistochemistry was greater in the aortic endothelium of MSEW mice compared to NR (N=5/group). Subsequently, vascular reactivity was measured with wire myography on tamoxifen inducible endothelium-specific HDAC9KO (Cdh5CreERT2-HDAC9) MSEW and NR adult mice to determine the role of HDAC9 in MSEW-induced endothelial dysfunction. Male mice exposed to MSEW displayed blunted aortic endothelial-dependent relaxation to acetylcholine compared to NR, whereas endothelial-specific knockout of HDAC9 (HDAC9KO) restored endothelial-dependent relaxation (NR: Emax=89.27%±4.15, N=5; MSEW: Emax=48.12%±22.12, N=2; NR HDAC9 KO: Emax=68.98%±4.73, N=5, MSEW HDAC9KO: Emax=70.50%±1.85, N=3). Females demonstrated no difference between MSEW and NR endothelial dependent relaxation, however, HDAC9KO MSEW displayed blunted relaxation compared to all other groups (NR: Emax= 77.14%±4.86, N=5; MSEW: Emax=84.30%±8.71, N=2; NR HDAC9 KO: Emax=70.80%±5.87, N=5, MSEW HDAC9KO: Emax=69.76%±9.10, N=4). Endothelial-independent relaxation to sodium nitroprusside (SNP) was similar in all groups in both sexes (Male: NR: Emax=96.92%±1.26, N=5; MSEW: Emax=100%±0, N=2; NR HDAC9 KO: Emax=96.52%±3.484, N=5; MSEW HDAC9KO: Emax=100%±0, N=3; Female: NR: Emax=98.58%±0.42, N=5; MSEW: Emax=100%±0, N=2; NR HDAC9 KO: Emax=98.48%±1.08, N=5; MSEW HDAC9KO: Emax=99.15%±0.85, N=4). These findings suggest that HDAC9 mediates ELS-induced endothelial dysfunction in males, however, HDAC9 may play a protective role in females. Future studies aim to further investigate sex-dependent differences in the specific role of HDAC9 in ELS related CVD. NIH P01 HL158500, F31HL165863-01, T32GM135028. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

KN-93 promotes HDAC4 nucleus translocation to promote fatty acid oxidation in myocardial infarction

Myocardial infarction (MI) is a potentially fatal disease that causes a significant number of deaths worldwide. The strategy of increasing fatty acid oxidation in myocytes is considered a therapeutic avenue to accelerate metabolism to meet energy demands. We conducted the study aiming to investigate the effect of KN-93, which induces histone deacetylase (HDAC)4 shuttling to the nucleus, on fatty acid oxidation and the expression of related genes.A mouse model of myocardial infarction was induced by isoprenaline administration. Heart damage was assessed by the detection of cardiac injury markers. The level of fatty acid oxidation level was evaluated by testing the expression of related genes. Both immunofluorescence and immunoblotting in the cytosol or nucleus were utilized to observe the distribution of HDAC4. The interaction between HDAC4 and specificity protein (SP)1 was confirmed by co-immunoprecipitation. The acetylation level of SP1 was tested after KN-93 treatment and HDAC4 inhibitor. Oxygen consumption rate and immunoblotting experiments were used to determine whether the effect of KN-93 on increasing fatty acid oxidation is through HDAC4 and SP1.Administration of KN-93 significantly reduced cardiac injury in myocardial infarction and promoted fatty acid oxidation both in vitro and in vivo. KN-93 was shown to mediate nuclear translocation of HDAC4. HDAC4 was found to interact with SP1 and reduce SP1 acetylation. HDAC4 or SP1 inhibitors attenuated the effect of KN-93 on fatty acid oxidation.In conclusion, KN-93 promotes HDAC4 translocation to the nucleus, thereby potentially enhancing fatty acid oxidation by SP1.

An in silico drug repurposing approach to identify HDAC1 inhibitors against glioblastoma

Despite considerable improvement in therapy and diagnosis, brain tumors remain a global public health concern. Among all brain tumors, 80% are due to Glioblastoma. The average survival rate of a patient once diagnosed with glioblastoma is 15 months. Lately, the role of peptidase enzymes, especially Neprilysin, a neutral endopeptidase, is gaining attention for its role in tumor growth regulation. Neprilysin expressions are positively correlated with several tumors including GBM and reduced expression of NEP protein is associated with the pathogenesis of multiple tumors. One of the main reasons for NEP protein downregulation is the action of Histone deacetylase (HDAC) enzymes, especially HDAC1. Additionally, studies have reported that increased levels of HDAC1 are responsible for downregulating NEP gene expression. Hence, HDAC1 inhibition can be a good target to elevate NEP levels, which can be a good therapeutic approach to GBM. This study utilizes the computational drug repurposing tool, Schrodinger Maestro to identify HDAC1 inhibitors from the ZINC15 database.1379 FDA-approved drugs from the ZINC15 database were screened through molecular docking. Based on docking score and ligand-protein interaction, the top ten molecules were selected which were then subjected to binding energy calculation and molecular dynamics (MD) simulations. The three most active drugs from the MD simulations- ZINC22010649 (Panobinostat), ZINC4392649 (Tasimelteon) and ZINC1673 (Melphalan), were tested on C6 and U87 MG glioblastoma cells for cytotoxicity and HDAC1 protein levels using western blot analysis. Among the three drugs, Panobinostat exhibited potent cytotoxic action and showed a significant reduction in the HDAC1 protein levels. Communicated by Ramaswamy H. Sarma

AtHD2D is involved in regulating lateral root development and participates in abiotic stress response in Arabidopsis

Roots are essential to terrestrial plants, as their growth and morphology are crucial for plant development. The growth of the roots is affected and regulated by several internal and external environmental signals and metabolic pathways. Among them, chromatin modification plays an important regulatory role. In this study, we explore the potential roles of the histone deacetylase AtHD2D in root development and lay the foundation for further research on the biological processes and molecular mechanisms of AtHD2D in the future. Our study indicates that AtHD2D affects the root tip microenvironment homeostasis by affecting the gene transcription levels required to maintain the root tip microenvironment. In addition, we confirmed that AtHD2D is involved in regulating Arabidopsis lateral root development and further explained the possible role of AtHD2D in auxin-mediated lateral root development. AtHD2D can effectively enhance the resistance of Arabidopsis thaliana to abiotic stress. We believe that AtHD2D is involved in coping with abiotic stress by promoting the development of lateral roots. Overexpression of AtHD2D promotes the accumulation of reactive oxygen species (ROS) in roots, indicating that AtHD2D is also involved in developing lateral roots mediated by ROS. Previous studies have shown that the overexpression of AtHD2D can effectively enhance the resistance of Arabidopsis thaliana to abiotic stress. Based on our data, we believe that AtHD2D participates in the response to abiotic stress by promoting the development of lateral roots. AtHD2D-mediated lateral root development provides new ideas for studying the mechanism of HDAC protein in regulating root development.

Clinicopathological Significance of Nucleosome Remodeling and Deacetylase Complex Expression in Endometrial Carcinoma.

Only a few studies have examined the expression of nucleosome remodeling and deacetylase complex in endometrial carcinoma (EC). The aim of this study was to analyze the expressions of histone deacetylase (HDAC1), HDAC2, and chromodomain helicase DNA-binding protein 4 (CHD4) in EC. Sixty cases of EC were categorized into two clusters based on the expression levels of the three proteins. Cluster 1 (C1) exhibited elevated expressions of HDAC2 and CHD4 compared with cluster 2 (C2). Notably, 75% of cases in C2 represented non-aggressive histological types, whereas 37.5% of cases in C1 manifested aggressive types. C2 exclusively comprised pathological tumor stage 1 (pT1) tumors, whereas C1 included pT2 and pT3 tumors. In C1, 25% of cases displayed aberrant p53 expression, contrasting with the absence of such expression in C2. Furthermore, only one patient in C2 experienced disease recurrence, whereas 20.8% of patients in C1 developed recurrent tumors. High HDAC2 and CHD4 expression may be associated with adverse clinicopathological characteristics in EC. Further studies are needed to validate these results.

Abstract 6055: COOTO-Me (10e) acts as a molecular glue to target NCOR/HDAC3 degradation

Abstract Histone deacetylase 3 (HDAC3) is overexpressed in cancer cells and functions as transcription repression complex with nuclear receptor corepressor (NCOR) to inhibit gene transcription. The pan-HDAC inhibitors have been approved for T-cell lymphoma with evident side effects. The selective HDAC3 inhibitors needs to be developed. Proteolysis-targeting chimera (PROTAC) approach is taken to design HDAC3 degraders with unsolved bioavailability obstacle. We screened small molecules with HDAC3 degradation ability and found two small molecules derived from glycyrrhetinic acid, methyl 2-cyano-3-oxo-18β-olean-1,9(11), 12-trien-30-oate (COOTO, 10e) and methyl 2-cyano-3,12-dioxo-18β-olean-1,9(11)-dien-30-oate (CDODO-Me, 10d), selectively decreased HDAC3 protein with increased acetylation of Histone 3. We explored the mechanism of HDAC3 degradation and found that 10e interrupted the interaction of HDAC3 with NCOR and induced degradation of both HDAC3 and NCOR protein. Biotin labeled 10e shows binding to both HDAC3 and NCOR directly as well as to E3 ligases SIAH2 and ITCH. Mass spectrometry analysis profiling reveals covalent interactions of 10e with multiple cysteine sites of SIAH2 in the binding regions for NCOR and HDAC3. Silencing SIAH2 blocks degradation of HDAC3. N-Acetylcysteine and GSH block the binding of 10e to HDAC3, NCOR and SIAH2. In addition, 10e decreased the levels of c-FLIP protein and increased the levels of NOXA protein leading to apoptosis induction. These data suggest that 10e functions as a molecular glue to attract SIAH2 to HDAC3 and NCOR to cause degradation through covalent binding. Citation Format: Ping Gong, Min Huang, Xin Li, Haoling Wang, Samuel Waxman, Linxiang Zhao, Yongkui Jing. COOTO-Me (10e) acts as a molecular glue to target NCOR/HDAC3 degradation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6055.

CircAKT3 alleviates postoperative cognitive dysfunction by stabilizing the feedback cycle of miR-106a-5p/HDAC4/MEF2C axis in hippocampi of aged mice

Circular RNAs (circRNAs) have garnered significant attention in the field of neurodegenerative diseases including Alzheimer’s diseases due to their covalently closed loop structure. However, the involvement of circRNAs in postoperative cognitive dysfunction (POCD) is still largely unexplored. To identify the genes differentially expressed between non-POCD (NPOCD) and POCD mice, we conducted the whole transcriptome sequencing initially in this study. According to the expression profiles, we observed that circAKT3 was associated with hippocampal neuronal apoptosis in POCD mice. Moreover, we found that circAKT3 overexpression reduced apoptosis of hippocampal neurons and alleviated POCD. Subsequently, through bioinformatics analysis, our data showed that circAKT3 overexpression in vitro and in vivo elevated the abundance of miR-106a-5p significantly, resulting in a decrease of HDAC4 protein and an increase of MEF2C protein. Additionally, this effect of circAKT3 was blocked by miR-106a-5p inhibitor. Interestingly, MEF2C could activate the transcription of miR-106a-5p promoter and form a positive feedback loop. Therefore, our findings revealed more potential modulation ways between circRNA-miRNA and miRNA-mRNA, providing different directions and targets for preclinical studies of POCD.