Thirty Years of HDAC Inhibitors: 2020 Insight and Hindsight

Multicomponent syntheses enable the discovery of novel quisinostat-derived chemotypes as histone deacetylase inhibitors

In this study, we synthesized and evaluated novel histone deacetylase (HDAC) inhibitors derived from the clinical candidate quisinostat. A library of 16 compounds categorized in three novel chemotypes was rapidly generated using multicomponent reactions (MCRs), enabling efficient structure-activity relationship studies. First, the compounds were evaluated for their activity against the Plasmodium falciparum strains 3D7 and Dd2, the main malaria-causing parasite, identifying compound 18b of the type C series as the most potent. It demonstrated low nanomolar IC50 values (IC50 (3D7) = 0.023 μM; IC50 (Dd2) = 0.047 μM) and high parasite selectivity (SIMRC-5/Pf3D7 > 2174). HDAC inhibition assays confirmed substantial inhibition of the P. falciparum enzyme PfHDAC1 (IC50 = 0.037 μM) as well as of human HDAC1 (IC50 = 0.021 μM) and HDAC6 (IC50 = 0.25 μM). Docking studies suggested distinct binding modes of 18b in P. falciparum and human HDAC1. Additionally, the in vitro anticancer activity was evaluated in Cal27 (head-neck carcinoma), HepG2 (hepatocellular carcinoma), A2780 (ovarian carcinoma), and U87 (glioblastoma) cell lines. Compounds 9b, 9d, and 13f showed potent antiproliferative activity and caspase 3/7 activation, in contrast to 18b. Furthermore, these compounds caused hyperacetylation of histone H3 and α-tubulin, indicating robust cellular target engagement. Overall, in this work we have identified the HDAC inhibitor 18b with selective antiplasmodial and 9b, 9d, and 13f with selective anticancer activities, providing valuable hits for further drug development efforts aimed at creating derivatives with reduced cytotoxicity against non-cancer cells compared to quisinostat.

Discovery of cloxiquine derivatives as potent HDAC inhibitors for the treatment of melanoma via activating PPARγ

The combined treatment with histone deacetylase (HDAC) inhibitors with peroxisome proliferator-activated receptor γ (PPARγ) agonists has displayed significant anticancer efficacy. Based on these results, a series of cloxiquine derivatives were prepared as potent HDAC inhibitors for the treatment of melanoma. Among these compounds, CS4 exhibited excellent inhibitory effects on HDAC1 (IC50 = 38 nM) and HDAC6 (IC50 = 12 nM), and had good antiproliferative effects against A375 and SK-MEL-5 melanoma cells (IC50 values, 1.20 and 0.93 μM, respectively). Mechanism research indicated that CS4 inhibited SK-MEL-5 cell growth by promoting α-tubulin and histone 3 (H3) acetylation. At the metabolic level, treatment with BG11 activated PPARγ and blocked glycolysis in SK-MEL-5 cells, which mediated partial antimelanoma effects of CS4. In addition, CS4 also induced cell cycle arrest at G2, suppressed migration and facilitated apoptosis of SK-MEL-5 cells. More importantly, compound CS4 demonstrated significant in vivo anticancer effect compared with SAHA, and exhibited neglectable toxicity. Consequently, CS4 is the potent HDAC inhibitor, which may be developed as the candidate antimelanoma drug.

Computational insights in repurposing a cardiovascular drug for Alzheimer's disease: the role of aromatic amino acids in stabilizing the drug through π-π stacking interaction

Alzheimer's disease (AD) is a neurological condition that worsens over time and causes linguistic difficulties, cognitive decline, and memory loss. Since AD is a complicated, multifaceted illness, it is critical to identify drugs to combat this degenerative condition. Histone deacetylase 2 (HDAC2) represents a promising epigenetic target for neurodegenerative diseases. So, for this study, we chose HDAC2 as the targeted protein. Repurposing drugs has many advantages, including reduced costs and high profits. There is a lower probability of malfunction because the unique drug candidate has previously completed numerous investigations. In this study, we have taken 58 clinically approved food and drug administration (FDA) drugs utilized in clinical trials for AD. Molecular docking was carried out for the 58 compounds. The telmisartan drug has the highest binding score of -9.4 kcal mol-1. The angiotensin II receptor blocker (ARB) telmisartan has demonstrated some promise in AD research as of the last update in January 2022. However, its exact significance in treating or preventing AD is still being studied. Molecular dynamics (MD) and molecular mechanics with generalized born and surface area solvation (MM-GBSA)/interaction entropy (IE) calculations were carried out to study the structural stability of the complexes. Umbrella sampling (US) techniques are a cutting-edge drug development method to understand more about the interactions between protein and ligand. π-π stacking interactions play a major role in helping the ligand to bind in the zinc bounding domain of the protein. From these analyses, we conclude that telmisartan, which is a cardiovascular drug, is more potent than the other drugs to treat AD. The anti-inflammatory, neuroprotective, and blood-brain barrier-crossing qualities of telmisartan make it a promising therapeutic agent for AD; however, more research, including larger clinical trials, is needed to determine the drug's precise role in treating AD.

Exploring the landscape of post-translational modification in drug discovery

Post-translational modifications (PTMs) play a crucial role in regulating protein function, and their dysregulation is frequently associated with various diseases. The emergence of epigenetic drugs targeting factors such as histone deacetylases (HDACs) and histone methyltransferase enhancers of zeste homolog 2 (EZH2) has led to a significant shift towards precision medicine, offering new possibilities to overcome the limitations of traditional therapeutics. In this review, we aim to systematically explore how small molecules modulate PTMs. We discuss the direct targeting of enzymes involved in PTM pathways, the modulation of substrate proteins, and the disruption of protein-enzyme interactions that govern PTM processes. Additionally, we delve into the emerging strategy of employing multifunctional molecules to precisely regulate the modification levels of proteins of interest (POIs). Furthermore, we examine the specific characteristics of these molecules, evaluating their therapeutic benefits and potential drawbacks. The goal of this review is to provide a comprehensive understanding of PTM-targeting strategies and their potential for personalized medicine, offering a forward-looking perspective on the evolution of precision therapeutics.

A novel histone deacetylase inhibitor protects the blood-brain barrier by regulating NF-κB and Nrf2 signaling pathways in OGD/R injury

Ischemic stroke, a severe cerebrovascular disease, is particularly prevalent among the elderly. Rsearch has indicated that histone deacetylases (HDACs) are pivotal in the pathogenesis of ischemic stroke. We introduce a novel HDACs inhibitor, HDI-1, as a potential therapeutic strategy for this condition. Our study reveals that HDI-1 expedites the restoration of tight junction proteins, Occludin and Claudin-5, in the oxygen-glucose deprivation/reoxygenation (OGD/R) model using human cerebral microvascular endothelial cells (hCMEC/D3). Moreover, HDI-1 mitigates the impairment of cellular monolayer membrane permeability following injury. This effect may stem from HDI-1's ability to selectively suppress the enzymatic activity of HDAC2. By inhibiting the activation of the NF-κB pathway triggered by OGD/R injury, HDI-1 reduces the secretion of pro-inflammatory cytokines IL-1β, IL-6, and TNF-α, thereby diminishing the inflammatory response in hCMEC/D3 cells. Meanwhile, HDI-1 exhibits antioxidant properties by enhancing the Nrf2/HO-1 signaling pathway. Collectively, our findings propose HDI-1 as a promising candidate for ischemic stroke treatment.

Synthesis and Evaluation of 9-epi-Koshidacin B as Selective Inhibitor of Histone Deacetylase 1

A concise synthetic route to an epimer of the recently isolated biologically active cyclic tetrapeptide koshidacin B has been developed, which featured a late-stage functionalization of a macrocyclic scaffold through a cross metathesis reaction. The synthetic 9-epi-koshidacin B showed marginal differences in spectroscopic behavior with that of the natural product but exhibited conformational preferences similar to those reported for analogous substrate chlamydocin. Moreover, it exhibited a useful level of selective inhibition of biologically relevant enzyme histone deacetylase 1 with an IC50 value of 0.145 μM over two other isoforms. Docking studies indicate that the natural product as well as its 9-epimer binds very similarly to the active site of HDAC1 indicating little influence of the configuration of the C9-stereocenter.

c-JUN interacts with HDAC1 as a potential combinatorial therapeutic target in acute myeloid leukemia

Acute myeloid leukemia (AML) is a biologically heterogeneous disease originating from the clonal expansion of hematopoietic stem cells (HSCs). Clonal expansion of hematopoietic stem cell progenitors (HSC-Prog), along with a block in differentiation, are hallmark features of AML. The disease is characterized by poor clinical outcomes, highlighting the urgent need for effective therapeutic strategies and suitable drug targets. We conducted multi-omics analyses, including single-cell RNA sequencing (scRNA-seq), Mendelian randomization (MR), and bulk RNA-seq, to investigate HDAC1's oncogenic role in AML. We identified specific gene signatures at the single-cell level. MR with eQTL data established causal links, and TCGA-LAML RNA-seq provided prognostic insights. Analysis of cellular communication and transcription factors revealed high c-JUN activity in HSC-Prog. We confirmed the association of c-JUN with HDAC1 through Western blotting and Co-immunoprecipitation (Co-IP). Functional validation of c-JUN in AML cells was performed via flow cytometry in vitro. The effectiveness of drugs targeting c-JUN and HDAC1 was assessed in mouse models using live imaging methods like in vivo imaging system (IVIS) and iSMAART. We identified the activity of c-JUN is specifically enhanced in HSC-Prog in AML patients. We suggest a potential regulatory relationship between c-JUN and HDAC1 in AML tumor cells. Inhibition of c-JUN can suppress cell proliferation and CD33 expression in AML, enhancing susceptibility to natural killer (NK) cell-mediated cytotoxicity. The combination of agents targeting c-JUN (Ailanthone) and HDAC1 (Panobinostat) showed robust efficacy in treating AML in xenograft mouse models, outperforming monotherapy. We also observed that the combination of Ailanthone and Panobinostat therapy displayed a safe pharmacological profile without dose-dependent toxicity, suggesting its potential as a therapeutic strategy.

HDAC3_VS_assistant: cheminformatics-driven discovery of histone deacetylase 3 inhibitors

Histone deacetylase 3 (HDAC3) inhibitors keep significant therapeutic promise for treating oncological, neurodegenerative, and inflammatory diseases. In this work, we developed robust QSAR regression models for HDAC3 inhibitory activity and acute toxicity (LD50, intravenous administration in mice). A total of 1751 compounds were curated for HDAC3 activity, and 15,068 for toxicity. The models employed molecular descriptors such as Morgan fingerprints, MACCS-166 keys, and Klekota-Roth, PubChem fingerprints integrated with machine learning algorithms including random forest, gradient boosting regressor, and support vector machine. The HDAC3 QSAR models achieved Q2test values of up to 0.76 and RMSE values as low as 0.58, while toxicity models attained Q2test values of 0.63 and RMSE values down to 0.41, with applicability domain (AD) coverage exceeding 68%. Internal validation by fivefold cross-validation (Q2cv = 0.70 for HDAC3 and 0.60 for toxicity) and y-randomization confirmed model reliability. Shapley additive explanation (SHAP) was also used to explain the influence of modeling features on model prediction results. The most predictive QSAR models are integrated into the developed HDAC3_VS_assistant application, which is freely available at https://hdac3-vs-assistant-v2.streamlit.app/ . Virtual screening conducted using the HDAC3_VS_assistant web application allowed us to reveal a number of potential inhibitors, and the nature of their bonds with the active HDAC3 site was additionally investigated by molecular docking.

Synergizing GA-XGBoost and QSAR modeling: Breaking down activity aliffs in HDAC1 inhibitors

The work being presented now combines severe gradient boosting with Shapley values, a thriving merger within the field of explainable artificial intelligence. We also use a genetic algorithm to analyse the HDAC1 inhibitory activity of a broad pool of 1274 molecules experimentally reported for HDAC1 inhibition. We conduct this analysis to ascertain the HDAC1 inhibitory activity of these molecules. Based on a rigorous investigation of extreme gradient boosting, the proposed method suggests using a genetic algorithm to identify pharmacophoric features. The statistical acceptability of extreme gradient boosting analysis is robust, with parameters such as R2tr = 0.8797, R2L10 % = 0.8831, Q2F1 = 0.9459, Q2F2 = 0.9452, and Q2F3 = 0.9474. This is the driving force behind the invention of nine Py-descriptor-containing genetic algorithms. Shapley additive explanations formed the basis for the interpretation, assigning a significant value to each variable in the model. This is followed by the use of counterfactual cases to analyse the impact of the discovered molecular descriptors on HDAC1 inhibition. An examination of the molecular descriptors, which include acc_N_3B, fsp2NringC8B, fsp3NC7B, and sp2N_sp3C_3B, demonstrates that these descriptors provide insight into the function that the nitrogen atom plays in influencing HDAC1's inhibitory activity. Furthermore, the investigation shed light on the significant role that the hybridized carbon atoms located in sp2 and sp3 play in HDAC1 inhibition. Thus, the QSAR results are in conformity with the reported findings. In addition, activity cliff analysis supports the QSAR findings. Thus, the genetic algorithm-extreme gradient-boosting GA-XGBoost model is easy to understand and makes decent predictions. Based on this, it indicates that "explainable AI" may prove to be beneficial in the future for the purpose of identifying and using structural features in the process of medication development.

Development of a high-throughput platform for quantitation of histone modifications on a new QTOF instrument

Histone post-translational modifications (PTMs) regulate gene expression patterns through epigenetic mechanisms. The 5 histone proteins (H1, H2A, H2B, H3, and H4) are extensively modified, with over 75 distinct modification types spanning more than 200 sites. Despite strong advances in mass spectrometry-based approaches, identification and quantification of modified histone peptides remains challenging due to factors such as isobaric peptides, pseudo-isobaric PTMs, and low stoichiometry of certain marks. Here we describe the development of a new high-throughput method to identify and quantify over 150 modified histone peptides by liquid chromatography-mass spectrometry (LC-MS). Fast gradient microflow liquid chromatography and variable window SWATH data-independent acquisition on a new quadrupole time-of-flight platform is compared to a previous method using nanoflow LC-MS on an Orbitrap hybrid. Histones extracted from cells treated with either a histone deacetylase inhibitor (HDACi) or TGF-beta 1 were analyzed by data-independent acquisition (DIA) on two mass spectrometers: an Orbitrap Exploris 240 with a 55-minute nanoflow LC gradient, and the SCIEX ZenoTOF 7600 with a 10-minute microflow gradient. To demonstrate the reproducibility and speed advantage of the method, 100 consecutive injections of one sample were performed in less than 2 days on the QTOF platform. The result is the comprehensive characterization of histone PTMs achieved in less than 20 minutes of total run time using only 200 ng of sample. Results for drug-treated histone samples are comparable to those produced by the previous method and can be achieved using less than one-third of the instrument time.

HDAC8 as a target in drug discovery: Function, structure and design

Histone deacetylases (HDACs) have emerged as prominent therapeutic targets in drug discovery. Among the members of the HDAC family, HDAC8 exhibits distinct structural and physiological features from other members of the class Ⅰ HDACs. In addition to histones, numerous non-histone substrates such as structural maintenance of chromosomes 3 (SMC3), p53, estrogen-related receptor alpha (ERRα), etc., have been identified for HDAC8, suggesting the involvement of HDAC8 in diverse biological processes. Studies have demonstrated that HDAC8 plays essential roles in certain disease development, e.g., acute myeloid leukemia (AML), neuroblastoma, and X-Linked disorders. Despite several HDAC8 inhibitors have been discovered, only one compound has progressed to clinical studies. Recently, novel strategies targeting HDAC8 have emerged, including identifying innovative zinc-chelating groups (ZBG), developing multi-target drugs, and HDAC8 PROTACs. This review aims to summarize recent progress in developing new HDAC8 inhibitors that incorporate novel strategies and provide an overview of the clinical improvements associated with HDAC8 inhibitors.

PET imaging assist investigation of HDAC6 expression change in MDD and evaluating antidepressant efficacy of a newly developed HDAC6 inhibitor

The histone deacetylase 6 (HDAC6) is closely related to the pathogenesis of depression in epigenetic regulation. However, it remains unclear how HDAC6 expression changes in depression pathophysiology and whether it is a target for antidepressant treatment. Herein, we investigate the expression change of HDAC6 in major depressive disorder (MDD) and evaluate the efficacy of a novel HDAC6 inhibitor, PB200, using positron emission tomography (PET) imaging. PET imaging studies with an HDAC6 PET probe [18F]Bavarostat allied with in vitro experiments demonstrated significantly increased HDAC6 expression in the brains of MDD mice. To investigate if pharmacological inhibition of HDAC6 can exert antidepressant effects, a series of naphthyridine-based HDAC6 inhibitors were designed and synthesized, among which PB200 demonstrated high selectivity and inhibitory activity against HDAC6, favorable metabolic stability, and excellent brain uptake. Moreover, PB200 exhibited significant antidepressant effects by restoring abnormal HDAC6 expression level and alleviating neuroinflammation. These results imply that targeting HDAC6 shows promise as a therapeutic strategy for depression, and PB200 is a potential therapeutic option for treating MDD.

Deciphering the Therapeutic Potential of Novel Pentyloxyamide-Based Class I, IIb HDAC Inhibitors against Therapy-Resistant Leukemia

Histone deacetylase inhibitors (HDACi) are established anticancer drugs, especially in hematological cancers. This study aimed to design, synthesize, and evaluate a set of HDACi featuring a pentyloxyamide connecting unit linker region and substituted phenylthiazole cap groups. A structural optimization program yielded HDACi with nanomolar inhibitory activity against histone deacetylase class I/IIb enzymes. The novel inhibitors (4d and 4m) showed superior antileukemic activity compared to several approved HDACi. Furthermore, 4d and 4m displayed synergistic activity when combined with chemotherapeutics, decitabine, and clofarabine. In vitro pharmacokinetic studies showed the most promising profile for 4d with intermediate microsomal stability, excellent plasma stability, and concentration-independent plasma protein binding. Additionally, 4d demonstrated comparable in vivo pharmacokinetics to vorinostat. When administered in vivo, 4d effectively inhibited the proliferation of leukemia cells without causing toxicity. Furthermore, the binding modes of 4d and 4m to the catalytic domain 2 of HDAC6 from Danio rerio were determined by X-ray crystallography.

Regulation of the Cilia as a Potential Treatment for Senescence and Tumors: A Review

Millions of people worldwide die from malignant tumors every year, and the current clinical treatment is still based on radiotherapy and chemotherapy. Immunotherapy-adjuvant chemotherapy is widely applied, yet resistance to various factors persists in the management of advanced malignancies. Recently researchers have gradually discovered that the integrity of primary cilia is closely related to many diseases. The phenotypic changes in primary cilia are found in some cases of progeria, tumorigenesis, and drug resistance. Primary cilia seem to mediate signaling during these diseases. Hedgehog inhibitors have emerged in recent years to treat tumors by controlling signaling proteins on primary cilia. There is evidence for the use of anti-tumor drugs to treat senescence-related disease. Considering the close relationship between aging and obesity, as well as the obesity is the phenotype of many ciliopathies. Therefore, we speculate that some anti-tumor or anti-aging drugs can treat ciliopathies. Additionally, there is evidence suggesting that anti-aging drugs for tumor treatment, in which the process may be mediated by cilia. This review elucidates for the first time that cilia may be involved in the regulation of senescence, metabolic, tumorigenesis, and tumor resistance and hypothesizes that cilia can be regulated to treat these diseases in the future.

Characterization of molecular interactions between HDAC7 and MEF2A

Interactions of transcriptional corepressors such as histone deacetylase 7 (HDAC7), a class IIa HDAC, with myocyte enhancer factor-2 (MEF2) regulate MEF2 activity. Despite previous investigations exploring interactions between HDAC7 and MEF2, a detailed characterization of the HDAC7-MEF2 functional complex is still lacking. Herein, we first modeled the structure of the HDAC7-MEF2A complex and investigated the inter-protein interactions using all-atom molecular dynamics (MD) simulations. We identified specific amino acids within HDAC7 and MEF2A that participate in interactions such as salt bridges, hydrogen bonds, and hydrophobic interactions. Our results reveal a salt bridge formed between LYS96(HDAC7) and ASP63(MEF2A). Our analysis also predicted formations of reliable hydrogen bonds between SER82(HDAC7) and ASP63(MEF2A) as well as LYS96(HDAC7) and ASP63(MEF2A). In addition, clustering of hydrophobic residues at the interface contributes in stabilizing the HDAC7-MEF2A complex. Results from multiple sequence alignment show that most of the HDAC7 residues that are predicted to associate with MEF2A are conserved in at least three class IIa HDACs and all predicted residues in MEF2A are conserved in MEF2s. We also found that the association of DNA to MEF2A has no significant effect on HDAC7-MEF2A interactions. Our results may also provide useful insights into the interactions between other class IIa HDACs and MEF2s.

Electron Donor-Acceptor Complex-Assisted Photochemical Conversion of O-2-Nitrobenzyl Protected Hydroxamates to Amides

The hydroxamic acid functionality is present in various medicinal agents and has attracted special interest for synthetic transformations in both organic and medicinal chemistry. The N-O bond cleavage of hydroxamic acid derivatives provides an interesting transformation for the generation of various products. We demonstrate, herein, that O-benzyl-type protected hydroxamic acids may undergo photochemical N-O bond cleavage, in the presence or absence of a catalyst, leading to amides. Although some O-benzyl protected aromatic hydroxamates may be photochemically converted to amides in the presence of a base and anthracene as the catalyst, employing O-2-nitrobenzyl group allowed the smooth conversion of both aliphatic and aromatic hydroxamates to primary or secondary amides in good to excellent yields in the presence of an amine, bypassing the need of a catalyst. DFT and UV-Vis studies supported the effective generation of an electron donor-acceptor (EDA) complex between O-2-nitrobenzyl hydroxamates and amines, which enabled the successful product formation under these photochemical conditions. An extensive substrate scope was demonstrated, showcasing that both aliphatic and aromatic hydroxamates are compatible with this protocol, affording a wide variety of primary and secondary amides.

HDAC1-mediated regulation of KDM1A in pemphigus vulgaris: unlocking mechanisms on ERK pathway activation and cohesion loss

Pemphigus vulgaris (PV) is an autoimmune skin disorder characterized by the loss of cell cohesion, with the histone deacetylase 1 (HDAC1) and lysine demethylase 1A (KDM1A) playing critical roles in its pathogenesis. This study aimed to elucidate the molecular mechanisms behind PV, focusing on the function of HDAC1 and KDM1A in disease onset and progression. Based on in vitro and in vivo PV models, we observed a significant increase in HDAC1 mRNA and protein levels in skin tissues of PV patients. Inhibition of HDAC1 ameliorated cell damage and reduced the loss of cell cohesion in human epidermal keratinocytes (HEKs) induced by PV-IgG. Our findings suggest that HDAC1 regulates KDM1A expression through deacetylation, with a notable deficiency in KDM1A expression in PV. Overexpression of KDM1A mitigated cell damage and cohesion loss. The extracellular signal-regulated kinase (ERK) pathway serves as a downstream executor of the HDAC1/KDM1A axis. Inhibiting HDAC1 and increasing KDM1A expression suppressed ERK phosphorylation, reducing PV-related apoptosis. These insights provide a new perspective on treating PV, highlighting the therapeutic potential of targeting HDAC1 expression. The regulatory mechanism of the HDAC1/KDM1A/ERK axis offers crucial clues for understanding PV pathogenesis and developing novel treatments.

Simultaneous inhibition of FLT3 and HDAC by novel 6-ethylpyrazine-2-Carboxamide derivatives provides therapeutic advantages in acute myelocytic leukemia

Synergetic inhibition of FMS-like tyrosine kinase 3 (FLT3) and histone deacetylase (HDAC) by small molecule chimera presents a promising therapeutic approach for acute myeloid leukemia (AML) with FLT3 mutations. In this study, we first observed that the combined use of FLT3 inhibitor gilteritinib and HDAC inhibitor vorinostat increased the survival rate of leukemia xenograft mouse model. Then, we employed a pharmacophore fusion strategy to develop a novel series of FLT3/HDAC dual inhibitors. Among them, compound 25h demonstrated superior inhibitory activity against both FLT3 and HDAC. In particular, compound 25h exhibited enhanced anti-proliferation activity against MOLM-13 cells in comparison to gilteritinib, vorinostat, and their combination, while maintaining reduced cytotoxicity towards normal cells. Mechanistically, the heightened anti-tumor effect of compound 25h was attributed to its more potent regulation of intracellular pathways, notably phosphorylation of ERK, compared to single drug and combination treatments. Furthermore, compound 25h demonstrated superior anti-tumor efficacy in the MOLM-13 xenograft model compared to combination therapy, along with reduced in vivo toxicity. To conclude, we have identified a novel FLT3/HDAC dual inhibitor that could serve as a potential candidate for the treatment of AML.

Rationally designed febuxostat-based hydroxamic acid and its pH-Responsive nanoformulation elicits anti-tumor activity

Attempts to furnish antitumor structural templates that can prevent the occurrence of drug-induced hyperuricemia spurred us to generate xanthine oxidase inhibitor-based hydroxamic acids and anilides. Specifically, the design strategy involved the insertion of febuxostat (xanthine oxidase inhibitor) as a surface recognition part of the HDAC inhibitor pharmacophore model. Investigation outcomes revealed that hydroxamic acid 4 elicited remarkable antileukemic effects mediated via HDAC isoform inhibition. Delightfully, the adduct retained xanthine oxidase inhibitory activity, though xanthine oxidase inhibition was not the underlying mechanism of its cell growth inhibitory effects. Also, compound 4 demonstrated significant in-vivo anti-hyperuricemic (PO-induced hyperuricemia model) and antitumor activity in an HL-60 xenograft mice model. Compound 4 was conjugated with poly (ethylene glycol) poly(aspartic acid) block copolymer to furnish pH-responsive nanoparticles (NPs) in pursuit of circumventing its cytotoxicity towards the normal cell lines. SEM analysis revealed that NPs had uniform size distributions, while TEM analysis ascertained the spherical shape of NPs, indicating their ability to undergo self-assembly. HDAC inhibitor 4 was liberated from the matrix due to the polymeric nanoformulation's pH-responsiveness, and the NPs demonstrated selective cancer cell targeting ability.

Exploring fatty acids from royal jelly as a source of histone deacetylase inhibitors: from the hive to applications in human well-being and health

A differential diet with royal jelly (RJ) during early larval development in honeybees shapes the phenotype, which is probably mediated by epigenetic regulation of gene expression. Evidence indicates that small molecules in RJ can modulate gene expression in mammalian cells, such as the fatty acid 10-hydroxy-2-decenoic acid (10-HDA), previously associated with the inhibition of histone deacetylase enzymes (HDACs). Therefore, we combined computational (molecular docking simulations) and experimental approaches for the screening of potential HDAC inhibitors (HDACi) among 32 RJ-derived fatty acids. Biochemical assays and gene expression analyses (Reverse Transcriptase - quantitative Polymerase Chain Reaction) were performed to evaluate the functional effects of the major RJ fatty acids, 10-HDA and 10-HDAA (10-hydroxy-decanoic acid), in two human cancer cell lines (HCT116 and MDA-MB-231). The molecular docking simulations indicate that these fatty acids might interact with class I HDACs, specifically with the catalytic domain of human HDAC2, likewise well-known HDAC inhibitors (HDACi) such as SAHA (suberoylanilide hydroxamic acid) and TSA (Trichostatin A). In addition, the combined treatment with 10-HDA and 10-HDAA inhibits the activity of human nuclear HDACs and leads to a slight increase in the expression of HDAC-coding genes in cancer cells. Our findings indicate that royal jelly fatty acids collectively contribute to HDAC inhibition and that 10-HDA and 10-HDAA are weak HDACi that facilitate the acetylation of lysine residues of chromatin, triggering an increase in gene expression levels in cancer cells.

Novel dual inhibitor targeting CDC25 and HDAC for treating triple-negative breast cancer

Triple-negative breast cancer (TNBC) presents a significant challenge for treatment due to its aggressive nature and the lack of effective therapies. This study developed dual inhibitors against cell division cycle 25 (CDC25) and histone deacetylases (HDACs) for TNBC treatment. CDC25 phosphatases are crucial for activating cyclin-dependent kinases (CDKs), the master regulators of cell cycle progression. HDACs regulate various biological processes by deacetylating histone and non-histone proteins, affecting gene expression, chromatin structure, cell differentiation, and proliferation. Dysregulations of HDAC and CDC25 are associated with several human malignancies. We generated a group of dual inhibitors for CDC25 and HDAC by combining the molecular structures of CDC25 (quinoline-5,8-dione) and HDAC (hydroxamic acid or benzamide) pharmacophores. The newly developed compounds were evaluated against various solid-tumor, leukemia, and non-malignant breast epithelial cells. Among the synthesized compounds, 18A emerged as a potent inhibitor, demonstrating significant cytotoxicity against TNBC cells, superior to its effects on other cancer types while sparing non-malignant cells. 18A possessed similar HDAC inhibitory activity as MS-275 and potently suppressed CDC25 activity in vitro and the CDK1 dephosphorylation in cells. Additionally, 18A hindered the progression of S and G2/M phases, triggered DNA damage, and induced apoptosis. These findings underscore the potential of 18A as a targeted therapy for TNBC and warrants further preclinical development.

Design, synthesis, and biological evaluation of novel 5,7,4'-trimethoxyflavone sulfonamide-based derivatives as highly potent inhibitors of LRPPRC/STAT3/CDK1

Leucine-rich pentatricopeptide repeat-containing protein (LRPPRC), signal transducer and activator of transcription 3 (STAT3), and cyclin-dependent kinase 1 (CDK1) are promising therapeutic targets for cancer treatment. However, there is a lack of effective inhibitors of LRPPRC, STAT3, and CDK1 in clinic. Our previous study has proved that 5,7,4'-Trimethoxyflavone (TMF) is a novel inhibitor of LRPPRC/STAT3/CDK1. However, the extraction rate of TMF from Tangerine Peel is quite low, and the doses of TMF in cells and mice are rather high. Herein, structural modifications of TMF have led to two series of TMF derivatives including sulfonamide substituted at 3'-position (7a-m) and 3',8-position (11a-m). Among all compounds, 7e, 7k, 11e, and 11g exhibited as effective, broad-spectrum, and potent anticancer agents in vitro. Moreover, 7e, 7k, 11e, and 11g showed better antitumor effects than TMF and clinical used chemotherapy drug capecitabine in vivo with no obvious toxicity. Mechanism studies showed that 11g could bind to LRPPRC, STAT3, and CDK1 to disassociate the LRPPRC-JAK2-STAT3 and JAK2-STAT3-CDK1 complexes, resulting in suppression of JAK2/STAT3 signaling pathway. These findings suggest that 11g may serve as a leading compound for cancer therapy as a triple-target (LRPPRC, STAT3, and CDK1) inhibitor.

Synthesis and biological evaluation of ortho-phenyl phenylhydroxamic acids containing phenothiazine with improved selectivity for class IIa histone deacetylases

Class IIa histone deacetylases (HDACs) have been linked to tumorigenesis in various cancers. Previously, we designed phenylhydroxamic acid LH4f as a potent class IIa HDAC inhibitor. However, it also unselectively inhibited class I and class IIb HDACs. To enhance the compound's selectivity towards class IIa HDACs, the ortho-phenyl group from the selective HDAC7 inhibitor 1 is incorporated into ortho position of the phenylhydroxamic acid in LH4f. Compared to LH4f, most resulting compounds displayed substantially improved selectivity towards the class IIa HDACs. Notably, compound 7 g exhibited the strongest HDAC9 inhibition with an IC50 value of 40 nM. Molecular modelling further identified the key interactions of compound 7 g bound to HDAC9. Compound 7 g significantly inhibited several human cancer cells, induced apoptosis, modulated caspase-related proteins as well as p38, and caused DNA damage. These findings suggest the potential of class IIa HDAC inhibitors as lead compounds for the development of cancer therapeutics.

Recent advances in anticancer mechanisms of molecular glue degraders: focus on RBM39-dgrading synthetic sulfonamide such as indisulam, E7820, tasisulam, and chloroquinoxaline sulfonamide

Synthetic sulfonamide anticancer drugs, including E7820, indisulam, tasisulam, and chloroquinoxaline sulfonamide, exhibit diverse mechanisms of action and therapeutic potential, functioning as molecular glue degraders. E7820 targets RBM39, affecting RNA splicing and angiogenesis by suppressing integrin α2. Phase I studies have demonstrated some stability in advanced solid malignancies; however, further efficacy studies are required. Indisulam causes G1 cell cycle arrest and delays the G1/S transition by modulating splicing through RBM39 degradation via DCAF15. Despite its limited initial efficacy, it shows promise in combination therapies, particularly for hematopoietic malignancies and gliomas. Tasisulam inhibits VEGF signaling, suppresses angiogenesis, and induces apoptosis. Although early trials indicated broad activity, safety concerns have halted its development. Chloroquinoxaline sulfonamide, initially investigated for cell cycle arrest and topoisomerase II inhibition, was discontinued owing to its limited efficacy and toxicity, despite promising initial results. Recent studies revealed the structural interaction of E7820 with DCAF15 and RBM39, although phase II trials on myeloid malignancies have shown limited efficacy. Indisulam is effective against glioblastoma and neuroblastoma, with potential synergy in combination therapies and metabolic disruption. Recent research on tasisulam reveals its potential in cancer therapy by targeting RBM39 degradation through DCAF15-mediated pathways. Understanding these mechanisms could lead to new treatments that affect alternative splicing and improve cancer therapies Overall, although these drugs exhibit promising mechanisms of action, further research is required to optimize their clinical efficacy and safety.

Sirtuins as Potential Targets for Neuroprotection: Mechanisms of Early Brain Injury Induced by Subarachnoid Hemorrhage

Subarachnoid hemorrhage (SAH) is a prevalent cerebrovascular disease with significant global mortality and morbidity rates. Despite advancements in pharmacological and surgical approaches, the quality of life for SAH survivors has not shown substantial improvement. Traditionally, vasospasm has been considered a primary contributor to death and disability following SAH, but anti-vasospastic therapies have not demonstrated significant benefits for SAH patients' prognosis. Emerging studies suggest that early brain injury (EBI) may play a crucial role in influencing SAH prognosis. Sirtuins (SIRTs), a group of NAD + -dependent deacylases comprising seven mammalian family members (SIRT1 to SIRT7), have been found to be involved in neural tissue development, plasticity, and aging. They also exhibit vital functions in various central nervous system (CNS) processes, including cognition, pain perception, mood, behavior, sleep, and circadian rhythms. Extensive research has uncovered the multifaceted roles of SIRTs in CNS disorders, offering insights into potential markers for pathological processes and promising therapeutic targets (such as SIRT1 activators and SIRT2 inhibitors). In this article, we provide an overview of recent research progress on the application of SIRTs in subarachnoid hemorrhage and explore their underlying mechanisms of action.

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.

Discovery of the First-in-Class Dual-Target ROCK/HDAC Inhibitor with Potent Antitumor Efficacy in Vivo That Trigger Antitumor Immunity

Triple-negative breast cancer (TNBC) represents a highly aggressive and heterogeneous malignancy. Currently, multitarget drug approaches present a promising therapeutic approach for TNBC. Utilizing a combinatorial chemistry strategy to construct a virtual screening database, dual ROCK/HDAC-targeting benzothiophene compounds were identified. Notably, compound 10h effectively inhibits ROCK1/2 and HDAC1/2/3/6/8 while demonstrating potent antiproliferative activity against breast cancer cells. In an orthotopic mouse model of breast cancer, 10h significantly suppressed tumor growth without apparent toxicity. Importantly, 10h induced immunogenic cell death (ICD), promoted dendritic cells (DCs) maturation, and activated T cells, thereby initiating antitumor immunity. In conclusion, compound 10h is a novel dual-target ROCK/HDAC inhibitor that represents a promising treatment strategy for TNBC.

Discovery of Novel 5-Cyano-3-phenylindole-Based LSD1/HDAC Dual Inhibitors for Colorectal Cancer Treatment

The dual inhibition of histone lysine-specific demethylase 1 (LSD1) and histone deacetylase (HDAC) has emerged as a promising strategy for cancer therapy. In this study, we report the discovery of novel 5-cyano-3-phenylindole-based LSD1/HDAC dual inhibitors, evaluated through both in vitro and in vivo assays. Among these inhibitors, compound 20c was identified as particularly potent, exhibiting high inhibitory activity against LSD1 (IC50 = 39.0 nM) and HDAC1/2/3/6/8 (IC50 = 1.4, 1.0, 1.3, 2.9, and 16.0 nM, respectively). Compound 20c effectively modulated the expression of biomarkers associated with LSD1 and HDAC inhibition and demonstrated superior antiproliferative activity compared to SAHA and 4SC-202 across multiple colorectal cancer cell lines. Following pharmacokinetic studies, 20c was further assessed in HCT-116 and HT-29 xenograft mouse models. It demonstrated significantly enhanced antitumor efficacy compared to SAHA, without causing observable toxicity. These findings highlight the potential of LSD1/HDAC dual inhibitors for the treatment of malignant cancers.

Molecular Hybrids of Quinoline and Sulfonamide: Design, Synthesis and in Vitro Anticancer Studies

Molecular hybrids of diversely functionalized quinoline and sulfonamide have been designed. Multistep synthetic strategies have been used for the synthesis. The anti-cancer properties have been evaluated against various cancer cell lines including HCT116, A549, U2OS, CCRF-CEM, Jurkat, MOLT-4, RAMOS, and K562. Non-cancer cell lines MRC-5 and BJ were also included for comparison. When examining the effects on A549, HCT116, and U2OS cells, all tested compounds exhibited limited potency with IC50 values exceeding 50 μM, indicating weak activity against these cell lines. Against the ITK high cells Viz. are Jurkat, CCRF-CEM and MOLT-4, 9 e, 9 p and 9 j found to the maximum potent compounds with IC50 values of 7.43±7.40 μM, 13.19±1.25 μM and 5.57±7.56 μM respectively. Similarly, in the BTK high cells screenings, 9 n and 9 e molecules with an IC50 value of 2.76±0.79 μM and 5.47±1.71 μM against RAMOS and K562 respectively are highly potent. Interestingly, all the molecules have exhibited IC50 value >50 μM against the non-cancer cells (MRC-5 and BJ), which indicates the promising non-cytotoxic nature of the molecules.

Epigenetics-targeted drugs: current paradigms and future challenges

Epigenetics governs a chromatin state regulatory system through five key mechanisms: DNA modification, histone modification, RNA modification, chromatin remodeling, and non-coding RNA regulation. These mechanisms and their associated enzymes convey genetic information independently of DNA base sequences, playing essential roles in organismal development and homeostasis. Conversely, disruptions in epigenetic landscapes critically influence the pathogenesis of various human diseases. This understanding has laid a robust theoretical groundwork for developing drugs that target epigenetics-modifying enzymes in pathological conditions. Over the past two decades, a growing array of small molecule drugs targeting epigenetic enzymes such as DNA methyltransferase, histone deacetylase, isocitrate dehydrogenase, and enhancer of zeste homolog 2, have been thoroughly investigated and implemented as therapeutic options, particularly in oncology. Additionally, numerous epigenetics-targeted drugs are undergoing clinical trials, offering promising prospects for clinical benefits. This review delineates the roles of epigenetics in physiological and pathological contexts and underscores pioneering studies on the discovery and clinical implementation of epigenetics-targeted drugs. These include inhibitors, agonists, degraders, and multitarget agents, aiming to identify practical challenges and promising avenues for future research. Ultimately, this review aims to deepen the understanding of epigenetics-oriented therapeutic strategies and their further application in clinical settings.

Pharmacophore modeling, 3D-QSAR, and MD simulation-based overture for the discovery of new potential HDAC1 inhibitors

Histone deacetylases (HDACs) are important epigenetic regulators that modulate the activity of histone and non-histone proteins leading to various cancers. Histone deacetylase 1 (HDAC1) is a member of class 1 HDAC family related to different cancers. However, the nonselective profile of existing HDAC1 inhibitors restricted their clinical utility. Therefore, the identification of new HDAC1 selective inhibitors may be fruitful against cancer therapy. In this present work, a pharmacophore model was built using 60 benzamide-based known HDAC1 selective inhibitors and it was used further to filter the large epigenetic molecular database of small molecules. Further, the 3D-QSAR model was built using the best common pharmacophore hypothesis consisting of higher PLS statistics of R2 of 0.89, Q2 of 0.83, variance ratio (F) of 65.7 and Pearson-r value of 0.94 revealing the model reliability and its high predictive power. The screened hits of the pharmacophore model were then subjected to molecular docking against HDAC1 to identify high-affinity lead molecules. The top 10 hits were ranked from the docking studies using docking scores for lead optimization. The potential hit molecules M1 and M2 identified from the study showed promising interaction during HDAC1 docking and MD simulation studies with acceptable ADME properties. Also, the newly designed lead compounds M11 and M12 may be considered highly potential inhibitors against HDAC1. The 3D-QSAR analysis, conformational requirements, and observations noticed in the MD simulations study will enable the optimization of lead molecules and to design of novel effective, and selective HDAC1 inhibitors in the future.

Slow-Binding and Covalent HDAC Inhibition: A New Paradigm?

The dysregulated post-translational modification of proteins is an established hallmark of human disease. Through Zn2+-dependent hydrolysis of acyl-lysine modifications, histone deacetylases (HDACs) are key regulators of disease-implicated signaling pathways and tractable drug targets in the clinic. Early targeting of this family of 11 enzymes (HDAC1-11) afforded a first generation of broadly acting inhibitors with medicinal applications in oncology, specifically in cutaneous and peripheral T-cell lymphomas and in multiple myeloma. However, first-generation HDAC inhibitors are often associated with weak-to-modest patient benefits, dose-limited efficacies, pharmacokinetic liabilities, and recurring clinical toxicities. Alternative inhibitor design to target single enzymes and avoid toxic Zn2+-binding moieties have not overcome these limitations. Instead, recent literature has seen a shift toward noncanonical mechanistic approaches focused on slow-binding and covalent inhibition. Such compounds hold the potential of improving the pharmacokinetic and pharmacodynamic profiles of HDAC inhibitors through the extension of the drug-target residence time. This perspective aims to capture this emerging paradigm and discuss its potential to improve the preclinical/clinical outlook of HDAC inhibitors in the coming years.

Interplay of Reactive Oxygen Species (ROS) and Epigenetic Remodelling in Cardiovascular Diseases Pathogenesis: A Contemporary Perspective

Cardiovascular diseases (CVDs) continue to be the leading cause of mortality worldwide, necessitating the development of novel therapies. Despite therapeutic advancements, the underlying mechanisms remain elusive. Reactive oxygen species (ROS) show detrimental effects at high concentrations but act as essential signalling molecules at physiological levels, playing a critical role in the pathophysiology of CVD. However, the link between pathologically elevated ROS and CVDs pathogenesis remains poorly understood. Recent research has highlighted the remodelling of the epigenetic landscape as a crucial factor in CVD pathologies. Epigenetic changes encompass alterations in DNA methylation, post-translational histone modifications, adenosine triphosphate (ATP)-dependent chromatin modifications, and noncoding RNA transcripts. Unravelling the intricate link between ROS and epigenetic changes in CVD is challenging due to the complexity of epigenetic signals in gene regulation. This review aims to provide insights into the role of ROS in modulating the epigenetic landscape within the cardiovascular system. Understanding these interactions may offer novel therapeutic strategies for managing CVD by targeting ROS-induced epigenetic changes. It has been widely accepted that epigenetic modifications are established during development and remain fixed once the lineage-specific gene expression pattern is achieved. However, emerging evidence has unveiled its remarkable dynamism. Consequently, it is now increasingly recognized that epigenetic modifications may serve as a crucial link between ROS and the underlying mechanisms implicated in CVD.

Discovery of a Novel and Potent Dual-Targeting Inhibitor of ATM and HDAC2 Through Structure-Based Virtual Screening for the Treatment of Testicular Cancer

Purpose

Dual inhibition of ataxia telangiectasia mutated (ATM) and histone deacetylase 2 (HDAC2) may be a potential strategy to improve antitumor efficacy in testicular cancer.

Methods

A combined virtual screening protocol including pharmacophore modeling and molecular docking was used for screening potent dual-target ATM/HDAC2 inhibitors. In order to obtain the optimal lead compound, the dual ATM/HDAC2 inhibitory activity of the screened compounds was further evaluated using enzyme inhibition methods. The binding stability of the optimal compound to the dual targets was verified by molecular dynamics (MD) simulation. MTT assay and in vivo antitumor experiment were performed to validate antitumor efficacy of the optimal compound in testicular cancer.

Results

Here, we successfully discovered six potent dual-target ATM/HDAC2 inhibitors (AMHs 1-6), which exhibited good inhibitory activity against both ATM and HDAC2. Among them, AMH-4 showed strong inhibitory activity against both ATM (IC50 = 1.12 ± 0.03 nM) and HDAC2 (IC50 = 3.04 ± 0.08 nM). MD simulation indicated that AMH-4 binds to ATM and HDAC2 with satisfactory stability. Importantly, AMH-4 had significant antiproliferative activity on human testicular tumor cells, especially NTERA-2 cL.D1 cells, and no inhibitory effect on normal human testicular cells. In vivo experiments exhibited that AMH-4 was more effective than lartesertib and vorinostat in inhibiting the growth of NTERA-2 cL.D1 xenograft tumors with low toxicity.

Conclusion

Overall, these results suggest that AMH-4 is an effective and low toxicity candidate for the treatment of testicular germ cell tumors.

Global Profiling Lysine Reactivity and Ligandability with Oxidant-Triggered Bioconjugation Chemistry

Due to the high abundance and diverse functions of lysine residues, both in the interior and on the surface of proteins, the development of new methods to characterize their reactivity and ligandability could significantly expand the pool of druggable targets. To date, only a limited number of aminophilic electrophiles have been assessed for interactions with the lysine proteome, resulting in a substantial fraction remaining inaccessible to current probes. Here, to the best of our knowledge, we report the first oxidant-triggered bioconjugation platform for in-depth profiling of lysines. We quantified over 7000 covalently modifiable lysine residues, which significantly expands the coverage of ligandable lysines in the whole proteome. Chemical proteomics enabled the mapping of more than 100 endogenous kinases, thus providing a comprehensive landscape of ligandable catalytic lysines within the kinome. Moreover, we identified a suite of new ligandable lysines such as K60 of ENO1 and K31 of PPIA, offering insights for exploring new functional and targetable residues. These findings could provide valuable clues for the development of targeted covalent inhibitors (TCIs).

Isoalantolactone/hydroxamic acid hybrids as potent dual STAT3/HDAC inhibitors and self-assembled nanoparticles for cancer therapy

Conventional chemotherapy, especially with natural anticancer drugs, usually suffers from poor bioavailability and low tumor accumulation. To address these limitations, we developed a novel approach for modifying natural products in which amphiphilic hydroxamic acid hybrids based on a natural product: isoalantolactone (IAL) were rationally designed. Compound 18 is identified as a highly potent dual signal transducer and activator of transcription 3 (STAT3)/histone deacetylases (HDAC) inhibitor and induces autophagy and apoptosis. 18 exhibits higher antitumor potency than IAL and the hydroxamic acid SAHA in vitro and in vivo. Furthermore, 18 self-assembled in water to form nanoparticles (18 NPs), which facilitated the accumulation of drugs in tumor tissues and promoted their cellular uptake, resulting in superior anticancer efficacy compared to free 18. Compared to drug-drug conjugates, hydroxamic acid hybrids have a smaller molecular weight and can synergize with various anticancer drugs. Overall, these findings indicate that 18 utilizing nanomedicines and dual-target drugs provide an efficient strategy for the rational design of dual-target drugs and the modification of natural products.

Development of peptoid-based heteroaryl-decorated histone deacetylase (HDAC) inhibitors with dual-stage antiplasmodial activity

Dynamics of epigenetic modifications such as acetylation and deacetylation of histone proteins have been shown to be crucial for the life cycle development and survival of Plasmodium falciparum, the deadliest malaria parasite. In this study, we present a novel series of peptoid-based histone deacetylase (HDAC) inhibitors incorporating nitrogen-containing bicyclic heteroaryl residues as a new generation of antiplasmodial peptoid-based HDAC inhibitors. We synthesized the HDAC inhibitors by an efficient multicomponent protocol based on the Ugi four-component reaction. The subsequent screening of 16 compounds from our mini-library identified 6i as the most promising candidate, demonstrating potent activity against asexual blood-stage parasites (IC50Pf3D7 = 30 nM; IC50PfDd2 = 98 nM), low submicromolar activity against liver-stage parasites (IC50PbEEF = 0.25 μM), excellent microsomal stability (t1/2 > 60 min), and low cytotoxicity to HEK293 cells (IC50 = 136 μM).

A Live-Cell Epigenome Manipulation by Photo-Stimuli-Responsive Histone Methyltransferase Inhibitor

Post-translational modifications on the histone H3 tail regulate chromatin structure, impact epigenetics, and hence the gene expressions. Current chemical modulation tools, such as unnatural amino acid incorporation, protein splicing, and sortase-based editing, have allowed for the modification of histones with various PTMs in cellular contexts, but are not applicable for editing native chromatin. The use of small organic molecules to manipulate histone-modifying enzymes alters endogenous histone PTMs but lacks precise temporal and spatial control. To date, there has been no achievement in modulating histone methylation in living cells with spatiotemporal resolution. In this study, a new method is presented for temporally manipulating histone dimethylation H3K9me2 using a photo-responsive inhibitor that specifically targets the methyltransferase G9a on demand. The photo-caged molecule is stable under physiological conditions and cellular environments, but rapidly activated upon exposure to light, releasing the bioactive component that can immediately inhibit the catalytic ability of the G9a in vitro. Besides, this masked compound could also efficiently reactivate the inhibition of methyltransferase activity in living cells, subsequently suppress H3K9me2, a mark that regulates various chromatin functions. Therefore, the chemical system will be a valuable tool for manipulating the epigenome for therapeutic purposes and furthering the understanding of epigenetic mechanisms.

Indolo[3,2-c]isoquinoline Hydroxamic Acid Derivatives as Novel Orally Topoisomerase-Histone Deacetylase Dual Inhibitors for NSCLC Therapy

Based on the synergistic effects of topoisomerase (Top) inhibitors and histone deacetylase (HDAC) inhibitors in cancer therapy, a series of novel Top/HDAC dual inhibitors were designed and synthesized herein. The optimal compound 31 was identified to simultaneously inhibit both Tops and HDACs with potent antiproliferative activity against nonsmall cell lung cancer (NSCLC). Mechanistic studies indicated that compound 31 with increasing reactive oxygen species levels damages DNA, inhibiting cancer cell colony formation and migration and inducing both cancer cell apoptosis and cycle arrest. Noteworthily, compound 31 was orally active in the NSCLC xenograft model, and its antitumor efficacy (TGI = 77.5%, 100 mg/kg) was superior to that of HDAC inhibitor SAHA and SAHA in combination with the Top inhibitor irinotecan. Consequently, this work highlights the therapeutic potential of compound 31 as the Top/HDAC dual inhibitor in NSCLC therapy and provides valuable lead compounds for the further development of antitumor agents in solid tumor therapy.

Metabolic and Epigenetic Mechanisms in Hepatoblastoma: Insights into Tumor Biology and Therapeutic Targets

BACKGROUND

Hepatoblastoma, the most common pediatric liver malignancy, is characterized by significant molecular heterogeneity and poor prognosis in advanced stages. Recent studies highlight the importance of metabolic reprogramming and epigenetic dysregulation in hepatoblastoma pathogenesis. This review aims to explore the metabolic alterations and epigenetic mechanisms involved in hepatoblastoma and how these processes contribute to tumor progression and survival.

METHODS

Relevant literature on metabolic reprogramming, including enhanced glycolysis, mitochondrial dysfunction, and shifts in lipid and amino acid metabolism, as well as epigenetic mechanisms like DNA methylation, histone modifications, and non-coding RNAs, was reviewed. The interplay between these pathways and their potential as therapeutic targets were examined.

RESULTS

Hepatoblastoma exhibits metabolic shifts that support tumor growth and survival, alongside epigenetic changes that regulate gene expression and promote tumor progression. These pathways are interconnected, with metabolic changes influencing the epigenetic landscape and vice versa.

CONCLUSIONS

The dynamic interplay between metabolism and epigenetics in hepatoblastoma offers promising avenues for therapeutic intervention. Future research should focus on integrating metabolic and epigenetic therapies to improve patient outcomes, addressing current gaps in knowledge to develop more effective treatments.

Histone deacetylase 2 and 3 of Sarcoptes scabiei: characterization of a potential drug target

Scabies is a contagious zoonotic parasitic disease that causes a substantial risk to both human and animal health and results in significant financial losses. No vaccine is available for scabies, and drug resistance to the conventional treatment for the disease has increased. Histone deacetylase (HDAC) modifies proteins by removing acetyl moieties from histones, regulates transcription, and is crucial for the immune system and apoptotic processes. This study aimed to clone, express, and determine the immunoreactivity of HDAC-2 and HDAC-3 of scabies mites to investigate their potential as scabies drug targets. The effects of inhibitors on recombinant Sarcoptes scabiei HDAC-2 (rSsHDAC-2) and rSsHDAC-3, as well as on the survival rate and ultrastructure of scabies mites in vitro, were also verified. The findings showed that the inhibitors reduced the acetylase activity of rSsHDAC-2 and rSsHDAC-3. Additionally, these inhibitors could significantly reduce the survival rate of scabies mites, making structural alterations in the mites such as mitochondrial pyknosis and cytoplasmic vacuoles and reaching a fatality rate of 76.7% after 24 h of action. In conclusion, HDAC-2 and HDAC-3 were critical to the survival of scabies mites and might be targeted by medications. Furthermore, the effect of inhibitors on the survival rate and structure of isolated scabies mites provides a new direction for developing therapeutic drugs for scabies.IMPORTANCEIn this study, we successfully cloned and expressed recombinant SsHDAC-2 and SsHDAC-3 in a prokaryotic system and confirmed their acetylation-deacetylase activities. These results provide a solid experimental foundation for subsequent research on SsHDAC-2 and SsHDAC-3. Furthermore, we report for the first time the use of SsHDAC-2 and SsHDAC-3 as drug targets. We demonstrated that the inhibition of these HDACs by pharmacological agents can lead to structural damage in the parasite, thereby impacting the survival activity of the scabies mite. This finding opens up a novel therapeutic avenue for the treatment of scabies.

Interplay between acetylation and ubiquitination controls PSAT1 protein stability in lung adenocarcinoma

Serine is essential to maintain maximal growth and proliferation of cancer cells by providing adequate intermediate metabolites and energy. Phosphoserine aminotransferase 1 (PSAT1) is a key enzyme in de novo serine synthesis. However, little is known about the mechanisms underlying PSAT1 degradation. We found that acetylation was the switch that regulated the degradation of PSAT1 in lung adenocarcinoma (LUAD). Deacetylation of PSAT1 on Lys51 by histone deacetylase 7 (HDAC7) enhanced the interaction between PSAT1 and the deubiquitinase ubiquitin-specific processing protease 14 (USP14), leading to the deubiquitination and stabilization of PSAT1; while acetylation of PSAT1 promoted its interaction with the E3 ligase ubiquitination factor E4B (UBE4B), leading to proteasomal degradation. Acetylation of PSAT1 on Lys51 regulated serine metabolism and tumor proliferation in LUAD. Thus, acetylation and ubiquitination cooperatively regulated the protein homeostasis of PSAT1. In conclusion, our study reveals a key regulatory mechanism for maintaining PSAT1 protein homeostasis in LUAD.

Cancer-Associated Fibroblasts Expressing Sulfatase 1 Facilitate VEGFA-Dependent Microenvironmental Remodeling to Support Colorectal Cancer

Tumor stroma plays a critical role in fostering tumor progression and metastasis. Cancer-associated fibroblasts (CAF) are a major component of the tumor stroma. Identifying the key molecular determinants for the protumor properties of CAFs could enable the development of more effective treatment strategies. In this study, through analyses of single-cell sequencing data, we identified a population of CAFs expressing high levels of sulfatase 1 (SULF1), which was associated with poor prognosis in patients with colorectal cancer. Colorectal cancer models using mice with conditional SULF1 knockout in fibroblasts revealed the tumor-supportive function of SULF1+ CAFs. Mechanistically, SULF1+ CAFs enhanced the release of VEGFA from heparan sulfate proteoglycan. The increased bioavailability of VEGFA initiated the deposition of extracellular matrix and enhanced angiogenesis. In addition, intestinal microbiota-produced butyrate suppressed SULF1 expression in CAFs through its histone deacetylase (HDAC) inhibitory activity. The insufficient butyrate production in patients with colorectal cancer increased the abundance of SULF1+ CAFs, thereby promoting tumor progression. Importantly, tumor growth inhibition by HDAC was dependent on SULF1 expression in CAFs, and patients with colorectal cancer with more SULF1+ CAFs were more responsive to treatment with the HDAC inhibitor chidamide. Collectively, these findings unveil the critical role of SULF1+ CAFs in colorectal cancer and provide a strategy to stratify patients with colorectal cancer for HDAC inhibitor treatment.  Significance: SULF1+ cancer-associated fibroblasts play a tumor-promoting role in colorectal cancer by stimulating extracellular matrix deposition and angiogenesis and can serve as a biomarker for the therapeutic response to HDAC inhibitors in patients.

Rapid Affinity and Microsomal Stability Ranking of Crude Mixture Libraries of Histone Deacetylase Inhibitors

The science of drug discovery involves multiparameter optimization of molecular structures through iterative design-make-test cycles. For medicinal chemistry library synthesis, traditional workflows involve the isolation of each individual compound, gravimetric quantitation, and preparation of a standard concentration solution for biological assays. In this work, we explore ways to expedite this process by testing unpurified library mixtures using a combination of mass spectrometry-based assays for affinity selection and microsomal metabolic stability. Utilizing this approach, microgram quantities of crude library mixtures can be used to identify high affinity, metabolically stable library members for isolation and full characterization. This streamlined approach was demonstrated for the synthesis and evaluation of two libraries of histone deacetylase inhibitors and was shown to generate decision-making data in line with traditional workflows. The advantages of this paradigm include greatly reduced cycle time, reduced material requirements, and concentration of resources on the most promising compounds.

Hydrazide-Based Class I Selective HDAC Inhibitors Completely Reverse Chemoresistance Synergistically in Platinum-Resistant Solid Cancer Cells

In this work, we have synthesized a set of peptoid-based histone deacetylase inhibitors (HDACi) with a substituted hydrazide moiety as zinc-binding group. Subsequently, all compounds were evaluated in biochemical HDAC inhibition assays and for their antiproliferative activity against native and cisplatin-resistant cancer cell lines. The hydrazide derivatives with a propyl or butyl substituent (compounds 5 and 6) emerged as the most potent class I HDAC selective inhibitors (HDAC1-3). Further, compounds 5 and 6 outperformed entinostat in cytotoxicity assays and were able to reverse chemoresistance in cisplatin-resistant A2780 (ovarian) and Cal27 (head-neck) cancer cell lines. Moreover, the hydrazide derivatives 5 and 6 showed strong synergism with cisplatin (combination indices <0.2), again outperforming entinostat, and increased DNA damage, p21, and pro-apoptotic BIM expression, leading to caspase-mediated apoptosis and cell death. Thus, compounds 5 and 6 represent promising lead structures for developing new HDACi capable of reversing chemoresistance in cisplatin resistant cancer cells.

Biological and structural investigation of tetrahydro-β-carboline-based selective HDAC6 inhibitors with improved stability

Our previously reported HDAC6 inhibitor (HDAC6i) Marbostat-100 (4) has provided many arguments for further clinical evaluation. By the substitution of the acidic hydrogen of 4 for different carbon residues, we were able to generate an all-carbon stereocenter, which significantly improves the hydrolytic stability of the inhibitor. Further asymmetric synthesis has shown that the (S)-configured inhibitors preferentially bind to HDAC6. This led to the highly selective and potent methyl-substituted derivative S-29b, which elicited a long-lasting tubulin hyperacetylation in MV4-11 cells. Finally, a crystal structure of the HDAC6/S-29b complex provided mechanistic explanation for the high potency and stereoselectivity of synthesized compound series.

Overview of class I HDAC modulators: Inhibitors and degraders

Class I histone deacetylases (HDACs) are closely associated with the development of a diverse array of diseases, including cancer, neurodegenerative disorders, HIV, and inflammatory diseases. Considering the essential roles in tumorigenesis, class I HDACs have emerged as highly desirable targets for therapeutic strategies, particularly in the field of anticancer drug development. However, the conventional class I HDAC inhibitors faced several challenges such as acquired resistance, inherent toxicities, and limited efficacy in inhibiting non-enzymatic functions of HDAC. To address these problems, novel strategies have emerged, including the development of class I HDAC dual-acting inhibitors, targeted protein degradation (TPD) technologies such as PROTACs, molecular glues, and HyT degraders, as well as covalent inhibitors. This review provides a comprehensive overview of class I HDAC enzymes and inhibitors, by initially introducing their structure and biological roles. Subsequently, we focus on the recent advancements of class I HDAC modulators, including isoform-selective class I inhibitors, dual-target inhibitors, TPDs, and covalent inhibitors, from the perspectives of rational design principles, pharmacodynamics, pharmacokinetics, and clinical progress. Finally, we also provide the challenges and outlines future prospects in the realm of class I HDAC-targeted drug discovery for cancer therapeutics.

Biological function and small molecule inhibitors of histone deacetylase 11

HDAC11, as a rising star in the histone deacetylase (HDAC) family, has attracted widespread interest in the biomedical field in recent years specially owing to its high defatty-acylase activity compared its innate deacetylase activity. Numerous studies have provided evidence indicating the crucial involvement of HDAC11 in cancers, immune responses, and metabolic processes. Several potent and selective HDAC11 inhibitors have been discovered and identified, which is crucial for exploring the function of HDAC11 and its potential therapeutic applications. Herein, we present a critical overview of the current advances in the biological function of HDAC11 and its inhibitors. We initially discuss the physiological functions of HDAC11 and its pathological roles in relevant diseases. Subsequently, our main focus centers on the design strategy and development process of HDAC11 inhibitors. Additionally, we address significant challenges and outline future directions in this field. This perspective may provide guidance for the further development of HDAC11 inhibitors and their prospects in disease treatment.

Novel post-translational modifications of protein by metabolites with immune responses and immune-related molecules in cancer immunotherapy

Tumour immunotherapy is an effective and essential treatment for cancer. However, the heterogeneity of tumours and the complex and changeable tumour immune microenvironment (TME) creates many uncertainties in the clinical application of immunotherapy, such as different responses to tumour immunotherapy and significant differences in individual efficacy. It makes anti-tumour immunotherapy face many challenges. Immunometabolism is a critical determinant of immune cell response to specific immune effector molecules, significantly affecting the effects of tumour immunotherapy. It is attributed mainly to the fact that metabolites can regulate the function of immune cells and immune-related molecules through the protein post-translational modifications (PTMs) pathway. This study systematically summarizes a variety of novel protein PTMs including acetylation, propionylation, butyrylation, succinylation, crotonylation, malonylation, glutarylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation, benzoylation, lactylation and isonicotinylation in the field of tumour immune regulation and immunotherapy. In particular, we elaborate on how different PTMs in the TME can affect the function of immune cells and lead to immune evasion in cancer. Lastly, we highlight the potential treatment with the combined application of target-inhibited protein modification and immune checkpoint inhibitors (ICIs) for improved immunotherapeutic outcomes.

Acetylation of p53 in the Cerebral Cortex after Photothrombotic Stroke

p53 expression and acetylation are crucial for the survival and death of neurons in penumbra. At the same time, the outcome of ischemia for penumbra cells depends largely on the histone acetylation status, but the effect of histone acetyltransferases and deacetylases on non-histone proteins like p53 is largely understudied. With combined in silico and in vitro approach, we have identified enzymes capable of acetylation/deacetylation, distribution, stability, and pro-apoptotic activity of p53 in ischemic penumbra in the course of post-stroke recovery, and also detected involved loci of acetylation in p53. The dynamic regulation of the acetylation of p53 at lysine 320 is controlled by acetyltransferase PCAF and histone deacetylases HDAC1 and HDAC6. The in silico simulation have made it possible to suggest the acetylation of p53 at lysine 320 acetylation may facilitate the shuttling of p53 between the nucleus and cytoplasm in penumbra neurons. Acetylation of p53 at lysine 320 is more preferable than acetylation at lysine 373 and probably promotes survival and repair of penumbra neurons after stroke. Strategies to increase p53 acetylation at lysine 320 via increasing PCAF activity, inhibiting HDAC1 or HDAC6, inhibiting p53, or a combination of these interventions may have therapeutic benefits for stroke recovery and would be promising for neuroprotective therapy of stroke.