Research Advances in the Use of Histone Deacetylase Inhibitors for Epigenetic Targeting of Cancer

Discovery of YSR734: A Covalent HDAC Inhibitor with Cellular Activity in Acute Myeloid Leukemia and Duchenne Muscular Dystrophy

Histone deacetylases (HDACs) have emerged as powerful epigenetic modifiers of histone/non-histone proteins via catalyzing the deacetylation of ε-N-acetyl lysines. The dysregulated activity of these Zn2+-dependent hydrolases has been broadly implicated in disease, notably cancer. Clinically, the recurring dose-limiting toxicities of first-generation HDACi sparked a paradigm shift toward safer isoform-specific molecules. With pervasive roles in aggressive diseases, there remains a need for novel approaches to target these enzymes. Herein, we report the discovery of YSR734, a first-in-class covalent HDACi, with a 2-aminobenzanilide Zn2+ chelate and a pentafluorobenzenesulfonamide electrophile. This class I selective proof of concept modified HDAC2Cys274 (catalytic domain), with nM potency against HDAC1-3, sub-μM activity in MV4-11 cells, and limited cytotoxicity in MRC-9 fibroblasts. In C2C12 myoblasts, YSR734 activated muscle-specific biomarkers myogenin/Cav3, causing potent differentiation into myotubes (applications in Duchenne Muscular Dystrophy). Current efforts are focused on improving in vivo ADME toward a preclinical covalent HDACi.

A comprehensive review on pharmacological applications and drug-induced toxicity of valproic acid

Valproic acid, a branching short chain fatty acid, is a popular drug to treat epilepsy and acts as a mood-stabilizing drug. The obstruction of ion channels and Gamma Amino Butyrate transamino butyrate GABA has been linked to antiepileptic effects. Valproic acid has been characterized as a Histone deacetylase inhibitor, functioning directly transcription of gene levels by blocking the deacetylation of histones and increasing the accessibility of transcription sites. Study has been extensively focused on pharmaceutical activity of valproic acid through various pharmacodynamics activity from absorption, distribution and excretion particularly in patients who are resistant to or intolerant of lithium or carbamazepine, as well as those with mixed mania or rapid cycling.

Establishment and Evaluation of Dual HDAC/BET Inhibitors as Therapeutic Options for Germ Cell Tumors and Other Urological Malignancies

Urological malignancies represent major challenges for clinicians, with annually rising incidences. In addition, cisplatin treatment induced long-term toxicities and the development of therapy resistance emphasize the need for novel therapeutics. In this study, we analyzed the effects of novel histone deacetylase (HDAC) and bromodomain and extraterminal domain-containing (BET) inhibitors to combine them into a potent HDAC-BET-fusion molecule and to understand their molecular mode-of-action. Treatment of (cisplatin-resistant) germ cell tumors (GCT), urothelial, renal, and prostate carcinoma cells with the HDAC, BET, and dual inhibitors decreased cell viability, induced apoptosis, and affected the cell cycle. Furthermore, a dual inhibitor considerably decreased tumor burden in GCT xenograft models. On a molecular level, correlating RNA- to ATAC-sequencing data indicated a considerable induction of gene expression, accompanied by site-specific changes of chromatin accessibility after HDAC inhibitor application. Upregulated genes could be linked to intra- and extra-cellular trafficking, cellular organization, and neuronal processes, including neuroendocrine differentiation. Regarding chromatin accessibility on a global level, an equal distribution of active or repressed DNA accessibility has been detected after HDAC inhibitor treatment, questioning the current understanding of HDAC inhibitor function. In summary, our HDAC, BET, and dual inhibitors represent a new treatment alternative for urological malignancies. Furthermore, we shed light on new molecular and epigenetic mechanisms of the tested epi-drugs, allowing for a better understanding of the underlying modes-of-action and risk assessment for the patient.

Arylamine N-Acetyltransferase 1 Activity is Regulated by the Protein Acetylation Status

Arylamine N-acetyltransferase 1 (NAT1) is a drug metabolizing enzyme that influences cancer cell proliferation and survival, especially in breast cancer. Lysine-acetylation is an important Post-Translational Modification (PTM) in the regulation of diverse cellular processes. Histone deacetylases (HDACs) and Sirtuins (SIRT) may have an important role on the NAT1 acetylation status, affecting its catalytic capacity and having an impact on the downstream functions of this protein. The aim of the present work is to investigate the acetylation status of NAT1 in human breast cancer. Breast cancer cell lines MDA-MB-231 (ER-, PR-, HER2-) and ZR-75-1 (estrogen receptor+, PR+, HER2+) were cultured in the presence of HDAC inhibitors (SAHA, TSA) or Sirtuin inhibitors (AGK2, EX527, Sirtinol). Under these conditions, NAT1 protein and gene expression as well as enzymatic activity were quantified. Acetylation of NAT1 protein was evaluated following an immunoprecipitation protocol and acetyl-Lysine quantification. Sirt1 and Sirt2 knockdown were performed and NAT1 protein and NAT1 mRNA expression and catalytic activity were quantified. The treatment of MDA-MB-231 or ZR-75-1 cells with increasing HDAC inhibitors resulted in 2 to 15-fold upregulation in NAT1 message expression. Finally, the catalytic activity of NAT1 in the presence of HDAC inhibition increased 2-fold. Conversely, the inhibition of Sirtuin activity did not cause significant changes in NAT1 message but produced a significant decrease in NAT1 catalytic activity. NAT1 acetylation was higher in the cells treated with HDAC inhibitors, as well as Sirtuin inhibitors. Finally, silencing of Sirt1 and Sirt2 genes by siRNA transient knockdown of each or both genes resulted in reduction of NAT1 protein expression and catalytic activity. The use of HDAC and Sirtuin inhibitors has been demonstrated as a promising powerful therapeutic alternative in various cancers. These inhibitors can significantly attenuate tumor burden by limiting tumor growth and metastasis. These compounds can also induce DNA damage, cell cycle arrest, apoptosis, and autophagy to promote cancer cell death. Several studies have shown that NAT1 is upregulated in cancer cells. The results of the present study show that the acetylation status of NAT1 is an important factor that might have a relevant role in the progression of cancer.

A CTCF-Binding Element and Histone Deacetylation Cooperatively Maintain Chromatin Loops, Linking to Long-Range Gene Regulation in Cancer Genomes

Background

Genes spanning long chromosomal domains are coordinately regulated in human genome, which contribute to global gene dysregulation and carcinogenesis in cancer. It has been noticed that epigenetic modification and chromatin architecture may participate in the regulation process. However, the regulation patterns and functional elements of long-range gene regulation are unclear.

Methods

Based on the clinical transcriptome data from different tumor sets, a novel expressional correlation analysis pipeline was performed to classify the co-regulated regions and subsets of intercorrelated regions. The GLAM2 program was used to predict conserved DNA elements that enriched in regions. Two conserved elements were selected to delete in Ishikawa and HeLa cells by CRISPR-Cas9. SAHA treatment and HDAC knockdown were used to change the histone acetylation status. Using qPCR, MTT, and scratch healing assay, we evaluate the effect on gene expression and cancer cell phenotype. By DNA pull-down and ChIP, the element-binding proteins were testified. 3C and 3D-FISH were performed to depict the alteration in chromatin architecture.

Results

In multiple cancer genomes, we classified subsets of coordinately regulated regions (sub-CRRs) that possibly shared the same regulatory mechanisms and exhibited similar expression patterns. A new conserved DNA element (CRE30) was enriched in sub-CRRs and associated with cancer patient survival. CRE30 could restrict gene regulation in sub-CRRs and affect cancer cell phenotypes. DNA pull-down showed that multiple proteins including CTCF were recruited on the CRE30 locus, and ChIP assay confirmed the CTCF-binding signals. Subsequent results uncovered that as an essential element, CRE30 maintained chromatin loops and mediated a compact chromatin architecture. Moreover, we found that blocking global histone deacetylation induced chromatin loop disruption and CTCF dropping in the region containing CRE30, linked to promoted gene regulation. Additionally, similar effects were observed with CRE30 deletion in another locus of chromosome 8.

Conclusions

Our research clarified a new functional element that recruits CTCF and collaborates with histone deacetylation to maintain high-order chromatin organizations, linking to long-range gene regulation in cancer genomes. The findings highlight a close relationship among conserved DNA element, epigenetic modification, and chromatin architecture in long-range gene regulation process.

Hidden pharmacological activities of valproic acid: A new insight

Valproic acid (VPA) is an approved drug for managing epileptic seizures, bipolar disorders, and migraine. VPA has been shown to elevate the level of gamma-aminobutyric acid (GABA) in the brain through competitive inhibition of GABA transaminase, thus promoting the availability of synaptic GABA and facilitating GABA-mediated responses. VPA, which is a small chain of fatty acids, prevents histone deacetylases (HDACs). HDACs play a crucial role in chromatin remodeling and gene expression through posttranslational changes of chromatin-associated histones. Recent studies reported a possible effect of VPA against particular types of cancers. This effect was partially attributed to its role in regulating epigenetic modifications through the inhibition of HDACs, which affect the expression of genes associated with cell cycle control, cellular differentiation, and apoptosis. In this review, we summarize the current information on the actions of VPA in diseases such as diabetes mellitus, kidney disorders, neurodegenerative diseases, muscular dystrophy, and cardiovascular disorders.

Butyrate: A Review on Beneficial Pharmacological and Therapeutic Effect

Background::

Short-chain fatty acids (SCFAs), generally acetate, propionate along with butyrate, are aliphatic organic acids formed in the gut mucosa through bacterial fermentation of mostly undigested nutritional carbohydrates, again to a minor degree by natural and dietary proteins, such as mucous and shed epithelial cells.

Methods::

Many sources were used to collect information about Butyrate, such as Pub med, Google Scholar, Pubmed, Scopus and other reliable sources.

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Endogenous butyrate formation, absorption, and transportation by colon cells have now been well acknowledged. Butyrate exerts its action features by way of appearing as a histone deacetylase inhibitor, even signaling through a few protein receptors. Lately, butyrate has received special consideration for its favorable result on intestinal equilibrium and also energy metabolism. There is a growing interest in butyrate as its impact on epigenetic mechanisms will result in much more certain and also efficacious healing techniques for the prevention and therapy of various diseases that range from genetic conditions to other body disorders.

Conclusion::

With this assessment, we compile the existing information on the attributes of butyrate, particularly its potential effects and also mechanisms involved in cancer, inflammation, diabetes mellitus, neurological and cardiovascular disorder.

A novel chemical-combination screen in zebrafish identifies epigenetic small molecule candidates for the treatment of Duchenne muscular dystrophy

Background

Duchenne muscular dystrophy (DMD) is a severe neuromuscular disorder and is one of the most common muscular dystrophies. There are currently few effective therapies to treat the disease, although many small-molecule approaches are being pursued. Certain histone deacetylase inhibitors (HDACi) have been shown to ameliorate DMD phenotypes in mouse and zebrafish animal models. The HDACi givinostat has shown promise for DMD in clinical trials. However, beyond a small group of HDACi, other classes of epigenetic small molecules have not been broadly and systematically studied for their benefits for DMD.

Methods

We used an established animal model for DMD, the zebrafish dmd mutant strain sapje. A commercially available library of epigenetic small molecules was used to treat embryonic-larval stages of dmd mutant zebrafish. We used a quantitative muscle birefringence assay in order to assess and compare the effects of small-molecule treatments on dmd mutant zebrafish skeletal muscle structure.

Results

We performed a novel chemical-combination screen of a library of epigenetic compounds using the zebrafish dmd model. We identified candidate pools of epigenetic compounds that improve skeletal muscle structure in dmd mutant zebrafish. We then identified a specific combination of two HDACi compounds, oxamflatin and salermide, that ameliorated dmd mutant zebrafish skeletal muscle degeneration. We validated the effects of oxamflatin and salermide on dmd mutant zebrafish in an independent laboratory. Furthermore, we showed that the combination of oxamflatin and salermide caused increased levels of histone H4 acetylation in zebrafish larvae.

Conclusions

Our results provide novel, effective methods for performing a combination of small-molecule screen in zebrafish. Our results also add to the growing evidence that epigenetic small molecules may be promising candidates for treating DMD.

Ferrocene-containing hybrids as potential anticancer agents: Current developments, mechanisms of action and structure-activity relationships

Cancer is one of the most fatal threatens to human health throughout the world. The major challenges in the control and eradication of cancers are the continuous emergency of drug-resistant cancer and the low specificity of anticancer agents, creating an urgent need to develop novel anticancer agents. Organometallic compounds especially ferrocene derivatives possess remarkable structural and mechanistic diversity, inherent stability towards air, heat and light, low toxicity, low cost, reversible redox, ligand exchange, and catalytic properties, making them promising drug candidates for cancer therapy. Ferrocifen, a ferrocene-phenol hybrid, has demonstrated promising anticancer properties on drug-resistant cancers. Currently, Ferrocifen is in pre-clinical trial against cancers. Obviously, ferrocene moiety is a useful template for the development of novel anticancer agents. This review will provide an overview of ferrocene-containing hybrids with potential application in the treatment of cancers covering articles published between 2010 and 2020. The mechanisms of action, the critical aspects of design and structure-activity relationships are also discussed.

Metabolism and Pharmacokinetic Study of the Boron-Containing Prodrug of Belinostat (ZL277), a Pan HDAC Inhibitor with Enhanced Bioavailability

ZL277 is a prodrug of belinostat with enhanced bioavailability and efficacy as a pan histone deacetylase (HDAC) inhibitor. In this study, we investigated the metabolism and pharmacokinetics of ZL277 in liver S9 fractions, liver microsomes, liver cytosol, and in mice. Metabolic products were identified and quantified by a combination of liquid chromatography and tandem mass spectrometry. The in vitro metabolic profile of ZL277 includes ZL277-B(OH)₂-452, the major oxidative metabolite ZL277-OH-424, the active ingredient belinostat, belinostat amide, belinostat acid, and methylated belinostat in liver S9 fractions. Both ZL277-OH-424 and belinostat underwent further glucuronidation in liver microsome, whereas only ZL277-OH-424, but not belinostat, underwent some level of sulfation in rat liver cytosols. These metabolites were examined in plasma and in a breast tumor model in vivo. They were also examined in urine and feces from mice treated with ZL277. The pharmacokinetic study of ZL277 showed the parameters of active drug belinostat with a half-life (t_1/2) of 10.7 h, an area under curve value (AUC) of 1506.9 ng/mL*h, and a maximum plasma concentration (C_max) of 172 ng/mL, reached 3 h after a single dose of 10 mg/kg. The hydrolysis product of the prodrug, ZL277-B(OH)₂-452 showed an AUC of 8306 ng/mL*h and C_max of 931 ng/mL 3 h after drug administration.

Magnetic Hyperthermia Using Self-Controlled Heating Elements Consisting of Fe-Al Milling Alloy Induces Cancer Cell Apoptosis while Preserving Skeletal Muscle

Necrosis-inducing anticancer drugs enhance high-mobility group box 1 (HMGB1) release during cell necrosis, and HMGB1-induced autophagy in skeletal muscle induces muscle atrophy. We evaluated the efficacy of magnetic hyperthermia therapy (MHT) using a low-energy magnetic field and self-controlled heating elements in tumor treatment. MHT-induced apoptosis by heating mouse subcutaneous tumors at 43°C using a heat-controlling iron-aluminum (Fe-Al) milling alloy. In contrast, MHT using Fe line-induced necrosis by heating to approximately 100°C. Furthermore, MHT with Fe-Al milling alloy reduced stemness. In hyperthermia using age line or Fe-Al milling alloy, both of them provided histological degeneration in skeletal muscle; however, qualitative differences were observed. MHT using Fe-line induced pronounced autophagy, decrease of myosin heavy chain content, and increase in serum HMGB1. In contrast, MHT using Fe-Al milling alloy induced heat shock protein 90 but no autophagy and decreased serum HMGB1. Therefore, MHT using Fe-Al milling alloy might be a good method for local treatment of tumors to reduce skeletal muscle atrophy.

Histone Deacetylases and their Inhibitors in Cancer Epigenetics

Histone deacetylases (HDAC) and histone deacetylase inhibitors (HDACi) have greatly impacted the war on cancer. Their role in epigenetics has significantly altered the development of anticancer drugs used to treat the most rare, persistent forms of cancer. During transcription, HDAC and HDACi are used to regulate the genetic mutations found in cancerous cells by removing and/or preventing the removal of the acetyl group on specific histones. This activity determines the relaxed or condensed conformation of the nucleosome, changing the accessibility zones for transcription factors. These modifications lead to other biological processes for the cell, including cell cycle progression, proliferation, and differentiation. Each HDAC and HDACi class or group has a distinctive mechanism of action that can be utilized to halt the progression of cancerous cell growth. While the use of HDAC- and HDACi-derived compounds are relatively new in treatment of cancers, they have a proven efficacy when the appropriately utilized. This following manuscript highlights the mechanisms of action utilized by HDAC and HDACi in various cancer, their role in epigenetics, current drug manufacturers, and the impact predicative modeling systems have on cancer therapeutic drug discovery.

Silencing Lysine-Specific Histone Demethylase 1 (LSD1) Causes Increased HP1-Positive Chromatin, Stimulation of DNA Repair Processes, and Dysregulation of Proliferation by Chk1 Phosphorylation in Human Endothelial Cells

The methylation of histone lysine residues modifies chromatin conformation and regulates the expression of genes implicated in cell metabolism. Lysine-specific demethylase 1 (LSD1) is a flavin-dependent monoamine oxidase that can demethylate mono- and dimethylated histone lysines 4 and 9 (H3K4 and H3K9). The removal of methyl groups from the lysine residues of histone and non-histone proteins was found to be an important regulatory factor of cell proliferation. However, its role has not been fully elucidated. In this study, we assessed LSD1-mediated cell cycle progression using a human endothelial cell model. The short hairpin RNA knockdown of LSD1 inhibits the G₂/M phase of cell cycle progression by checkpoint kinase 1 (Chk1) phosphorylation (S137). We observed elevated DNA damage, which was consistent with the increased detection of double-strand breaks as well as purines and pyrimidines oxidation, which accompanied the activation of ATR/ATRIP signaling by H2AXS139 phosphorylation. The irreversible pharmacological inhibition of LSD1 by 2-phenylcyclopropylamine (2-PCPA) inactivated its enzymatic activity, causing significant changes in heterochromatin and euchromatin conformation assessed by chromatin assembly factor 1 subunit A (CAF1A) and heterochromatin protein 1 isoform α and γ (HP1α/γ) immunofluorescence analysis. We conclude that the knockdown of LSD1 in endothelial cells leads to increased HP1-positive chromatin, the stimulation of DNA repair processes, and the dysregulation of proliferation machinery.