Lysine Deacetylase Inhibitors Research Articles

Epigenetic-based differentiation therapy for Acute Myeloid Leukemia

Despite the development of novel therapies for acute myeloid leukemia, outcomes remain poor for most patients, and therapeutic improvements are an urgent unmet need. Although treatment regimens promoting differentiation have succeeded in the treatment of acute promyelocytic leukemia, their role in other acute myeloid leukemia subtypes needs to be explored. Here we identify and characterize two lysine deacetylase inhibitors, CM-444 and CM-1758, exhibiting the capacity to promote myeloid differentiation in all acute myeloid leukemia subtypes at low non-cytotoxic doses, unlike other commercial histone deacetylase inhibitors. Analyzing the acetylome after CM-444 and CM-1758 treatment reveals modulation of non-histone proteins involved in the enhancer–promoter chromatin regulatory complex, including bromodomain proteins. This acetylation is essential for enhancing the expression of key transcription factors directly involved in the differentiation therapy induced by CM-444/CM-1758 in acute myeloid leukemia. In summary, these compounds may represent effective differentiation-based therapeutic agents across acute myeloid leukemia subtypes with a potential mechanism for the treatment of acute myeloid leukemia.

Comparative effects of phosphorylation and acetylation on glycolysis and myofibrillar proteins degradation in postmortem muscle

The study investigated the different effects between protein phosphorylation and acetylation on glycolytic enzyme activity and myofibrillar protein degradation. Lamb longissimus thoracis lumborum muscles were homogenized and then inhibitors were added for incubation at 4 °C. Phosphatase inhibitor was added to produce a high phosphorylation level (PI group) and lysine deacetylase inhibitor was added to produce a high acetylation level (DI group). The lactate and ATP content in the PI group was inhibited compared with that in the DI group (P < 0.05). Phosphofructokinase (PFK) activity was negatively related with the phosphorylation level and was positively related with the acetylation level in the DI group (P < 0.05). The degradation of troponin T and desmin of the DI group were restrained when compared to that in the PI group (P < 0.05). Compared with initial PFK and desmin, the simulation of phosphorylation and acetylation of PFK and desmin showed different electrostatic potential at the surface and a more unstable structure. The phosphorylation level of the DI group was increased, suggesting that the changes of protein acetylation altered protein phosphorylation. In conclusion, compared with protein phosphorylation, protein acetylation had a greater effect on promoting glycolysis and inhibiting protein degradation.

Effects of lysine deacetylase inhibitor treatment on LPS responses of alveolar-like macrophages.

Macrophages are key immune cells that can adapt their metabolic phenotype in response to different stimuli. Lysine deacetylases are important enzymes regulating inflammatory gene expression and lysine deacetylase inhibitors have been shown to exert anti-inflammatory effects in models of chronic obstructive pulmonary disease. We hypothesized that these anti-inflammatory effects may be associated with metabolic changes in macrophages. To validate this hypothesis, we used an unbiased and a targeted proteomic approach to investigate metabolic enzymes, as well as liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry, to quantify metabolites in combination with the measurement of functional parameters in primary murine alveolar-like macrophages after lipopolysaccharide-induced activation in the presence or absence of lysine deacetylase inhibition. We found that lysine deacetylase inhibition resulted in reduced production of inflammatory mediators such as tumor necrosis factor α and interleukin 1β. However, only minor changes in macrophage metabolism were observed, as only one of the lysine deacetylase inhibitors slightly increased mitochondrial respiration while no changes in metabolite levels were seen. However, lysine deacetylase inhibition specifically enhanced expression of proteins involved in ubiquitination, which may be a driver of the anti-inflammatory effects of lysine deacetylase inhibitors. Our data illustrate that a multiomics approach provides novel insights into how macrophages interact with cues from their environment. More detailed studies investigating ubiquitination as a potential driver of lysine deacetylase inhibition will help developing novel anti-inflammatory drugs for difficult-to-treat diseases such as chronic obstructive pulmonary disease.

Potential Role of Lysine Acetylation and Autophagy in Brown Film Formation and Postripening of Lentinula edodes Mycelium.

Lentinula edodes is one of the most widely cultivated edible mushrooms in the world. When cultivated in sawdust, the surface mycelium of L. edodes needs a long postripening stage wherein it forms a brown film (BF) by secreting and accumulating pigments. BF formation is critical for the high quality and yield of fruiting bodies. Protein lysine acetylation (KAC) is an important post-translational modification that regulates growth and development. Previous studies have shown that deacetylase levels are significantly increased during BF formation in the postripening stage of L. edodes. The aim of this study was to assess the role of protein acetylation during BF formation. To this end, we compared the acetylome of L. edodes mycelia before and after BF formation using anti-acetyl antibody-based label-free quantitative proteomics. We identified 5,613 acetylation sites in 1,991 proteins, and quantitative information was available for 4,848 of these sites in 1,815 proteins. Comparative acetylome analysis showed that the modification of 699 sites increased and that of 562 sites decreased during BF formation. Bioinformatics analysis of the differentially acetylated proteins showed significant enrichment in the tricarboxylic acid (TCA) cycle and proteasome pathways. Furthermore, functional assays showed that BF formation is associated with significant changes in the activities of proteasome, citrate synthase, and isocitrate dehydrogenase. Consistent with this hypothesis, the lysine deacetylase inhibitor trichostatin (TSA) delayed autophagy and BF formation in L. edodes. Taken together, KAC and autophagy play important roles in the mycelial BF formation and postripening stage of L. edodes. IMPORTANCE Mycelial BF formation and postripening of L. edodes affects the quality and quantity of its edible fruiting bodies. In this study, we explored the role of protein KAC in this biological process, with the aim of optimizing the cultivation and yield of L. edodes.

Influence of intestinal microbiota on autophagy in colorectal cancer.

e15505 Background: Gut microbiota favors butyrate-forming bacteria and maintains homeostatic balance which is revoked during the development of colorectal cancer (CRC)-associated dysbiosis. Butyrate is a short chain fatty acid that acts as a lysine deacetylase inhibitor and is known to activate the AMPK pathway as well as inhibiting inflammation and ROS production. The role of AMPK activation in diabetes-associated complications including colorectal cancer is poorly understood. This project examines the role of dysbiosis and butyrate on CRC onset and disease progression. Methods: C57BL/6- Apctm1Tyj/J ( APC) mice that spontaneously develop CRC were used and the study included four groups of mice (n = 3 for each): (1) Control C57BL/6, (2) APC, (3) APC treated with probiotics rich in butyrate forming bacteria and (4) APC treated with butyrate. Probiotics and butyrate were administered by oral gavage and intraperitoneally, respectively. Feces were collected at early (when CRC is developed at 8 weeks of age) and late (at 16 weeks of age, day of sacrifice) timepoints, and microbial composition was identified by 16S rRNA sequencing. Mice colons following sacrifice were also harvested for molecular, anatomical, and histological analyses. Results: The butyrate kinase gene was assessed in fecal samples. Butyrate forming bacteria were significantly reduced in APC mice but elevated in APC receiving probiotics when compared to control mice. Anatomically, polyp number was reduced in groups receiving probiotics and butyrate when compared to APC mice without treatment (p &lt; 0.01 for each). Histologically, butyrate and probiotics ameliorated the histological changes observed in in APC mice as assessed by PAS staining. Furthermore, we observed a decrease in goblet cells, and increased number of crypts on distal colon histology. The expression of NADPH Oxidase 4 (NOX4) and TIGAR, a P53 target protein expression were significantly increased in APC mice and restored following the administration of probiotics or butyrate. ROS production assessed by HPLC showed similar pattern across our 4 groups. The expression of the autophagy markers Beclin-1, ATG-12 and LC3-β were restored to control levels after probiotics and butyrate administration. 16S rRNA sequencing of fecal samples revealed significant differences in microbial composition between groups, most significantly at 16 weeks with Lachnospiraceae (ASV 175), Muribaculaceae (ASV 53) and Muribaculaceae (ASV 584) were decreased in APC when compared to control mice ( &lt; -7 Log2 fold change each). Conclusions: Collectively, our data suggests colorectal cancer is associated with dysbiosis characterized by lower abundance of butyrate-forming bacteria. This disruption leads to over-expression of NOX4, and ROS production associated with alteration in autophagy, thus worsening gastrointestinal complications and CRC. Restoring butyrate forming bacteria might serve as an effective adjuvant to therapy in CRC.

Lysine deacetylases (KDACs) regulate PKCõ phosphorylation in response to muscle atrophy

Post‐translational modifications (PTMs) such as acetylation and phosphorylation have been implicated in contractile dysfunction and muscle wasting. Indeed, lysine deacetylase (KDAC) inhibitors attenuate muscle atrophy and delay muscle damage in response to nutrient deprivation, in models of metabolic dysfunction and genetic models of muscle disease (e.g. muscle dystrophy). Historically, lysine acetylation was studied in the regulation of gene transcription, where for instance HDACs remove acetyl groups on lysine residues of histone proteins to suppress gene expression. However, recent evidence demonstrates that non‐histone proteins are acetylated; functioning in protein stability, intracellular signaling, mitochondrial function and muscle contraction. Using C2C12 myotubes stimulated with dexamethasone (Dex) as a model of muscle atrophy, we report that KDAC inhibition using Trichostatin A (TSA) restored myotube size and attenuated Dex‐induced atrophy genes, Murf1 and Atrogin‐1. Despite our current understanding for lysine acetylation in muscle physiology; a role for KDACs in the regulation of muscle signal transduction remains a ‘black box.’ We report that protein kinase C delta (PKCδ) phosphorylation decreased at threonine 505 (T505) and serine 643 (S643), residues important for PKCδ activity, in myotubes in response to muscle atrophy. Interestingly, PKCδ phosphorylation was restored in myotubes treated with a pan‐HDAC inhibitor (TSA) or a class I selective HDAC inhibitor (Apicidin) targeting HDAC1, ‐2, and ‐3 in response to Dex. Moreover, we observed that Dex induced skeletal muscle atrophy rapidly in mice, with weight loss noted by day 3 post Dex and muscle weight loss noted by day 7. Similar to our findings in C2C12 myotubes, Dex attenuated phosphorylation of PKCδ at S643, while KDAC inhibition restored or increased PKCδ phosphorylation at both T505 and S643 in the tibialis anterior. These findings suggest that KDACs act as endogenous regulators of skeletal muscle atrophy through the regulation of PKCδ phosphorylation. Consistent with this hypothesis, we report that KDAC inhibition could not restore myotube size in response to Dex in the presence of a PKCδ inhibitor or when overexpressing a dominant negative PKCδ. Combined, these suggest a non‐canonical role for KDACs in the regulation of muscle physiology outside of its role in chromatin condensation and gene regulation.

Dishevelled-1 DIX and PDZ domain lysine residues regulate oncogenic Wnt signaling.

DVL proteins are central mediators of the Wnt pathway and relay complex input signals into different branches of the Wnt signaling network. However, molecular mechanism(s) that regulate DVL-mediated relay of Wnt signals still remains unclear. Here, for the first time, we elucidate the functional significance of three DVL-1 lysines (K/Lys) which are subject to post-translational acetylation. We demonstrate that K34 Lys residue in the DIX domain regulates subcellular localization of β-catenin, thereby influencing downstream Wnt target gene expression. Additionally, we show that K69 (DIX domain) and K285 (PDZ domain) regulate binding of DVL-1 to Wnt target gene promoters and modulate expression of Wnt target genes including CMYC, OCT4, NANOG, and CCND1, in cell line models and xenograft tumors. Finally, we report that conserved DVL-1 lysines modulate various oncogenic functions such as cell migration, proliferation, cell-cycle progression, 3D-spheroid formation and in-vivo tumor growth in breast cancer models. Collectively, these findings highlight the importance of DVL-1 domain-specific lysines which were recently shown to be acetylated and characterize their influence on Wnt signaling. These site-specific modifications may be subject to regulation by therapeutics already in clinical use (lysine deacetylase inhibitors such as Panobinostat and Vorinostat) or may possibly have prognostic utility in translational efforts that seek to modulate dysfunctional Wnt signaling.

Epigenetic Modifications of the Bone Marrow (BM) Niche in Multiple Myeloma (MM) - a Three-Dimensional (3D) in Vitro Approach

Introduction:Since the discovery of histone modifications by Allfrey et al. in 1964 and their impact on gene transcription, numerous epigenetic mechanisms and potential targets, including writer, eraser and reader proteins, have been identified, which has consequently led to a variety of current clinical “epidrug” applications. In particular hematological neoplasia, e.g. T-cell lymphomas, myelodysplastic syndrome and MM, show good responses to epigenetic modulation. To foster this progress, while fulfilling the crucial role of the BM microenvironment in MM pathogenesis in early preclinical drug development, we are testing novel epigenetic modifying agents provided by the resident Institute of Pharmaceutical Sciences (M.Jung) in MM using an established agarose-based 3D matrix (FAM) platform.Methods: For our purpose semi-adherent MM cell lines as well as primary MM patient (pt) samples are seeded into conical 2mm deep microcavities of the FAM (see Figure 1), whereby the culture period can be extended up to at least 3 weeks in either distance or contact co-culture to HS-5 or pt-derived MSP-1 stromal cell lines. The well-defined conical shape and transparency of the agarose matrices allows straightforward qualitative and quantitative cluster monitoring via non-destructive transmitted light scanner analysis, confocal imaging or histological examinations. In addition, the matrices can be cut and divided precisely to perform viability assays, Western blots and multicolor flow cytometry (CD138, CD38, SlamF7, CXCR4, CXCR7, PD-L1, VLA-4) in parallel and at different time points on days (d) 2 and 4 with (w) or without (w/o) epigenetic treatment or stromal support. To conclusively assess our FAM model in terms of more in-vivo like prolonged proliferation and diminished treatment response, we also performed comparative studies with the widely used 3D liquid overlay technique (LOT).Results: In contrast to LOT, the well-defined, steep microwells of our FAM enabled semi-adherent plasma cells (PCs) to form solid 3D-aggregates and mediated drug resistance to 6nM bortezomib and 3µM auranofin treatment. In this context qualitative confocal analysis of mCherry-transduced RPMI 8226 cells and fluorescent dye staining confirmed uniform drug distribution within the FAM. Moreover, PCs seeded into the microcavities showed prolonged cluster growth in accordance with intratibial MM engraftment in our NOD/SCID mouse model, underlining the more in vivo -like growing conditions within the FAM and its superiority over LOT.To date, our screening approach has comprised 6 lysine deacetylase inhibitors (KDACi) [selective KDAC6i: JS08, JS28 and JS46 as well as entinostat, panobinostat and vorinostat] and three JARID1-selective lysine demethylase inhibitors (KDMi) [SYN22327689, Z425307602 and KDM5-C49]. With regard to cytotoxicity using ATP-dependent assay and flow cytometry, we achieved the most promising results for JS28 and KDM5-C49 in low micromolar concentrations after 2d and 7d, respectively. Additionally, for JS28 we could demonstrate synergism, if combined with bortezomib and a high selectivity for KDAC6 inhibition via Western blot in both 2D and 3D cultures.Whilst 3D stromal co-culture led per se to lower SlamF7 and CXCR4 surface levels, increased PD-L1 expression and the persistence of CD138 and CD38, our data also suggest, that additional treatment with KDACi further modulates expression patterns concerning diminished VLA-4, SlamF7, PD-L1 and CD138 levels.Conclusions: Our FAM platform provides various benefits to MM cells compared to the widely employed LOT, namely 1) solid cluster formation of semi-adherent PCs including more in vivo -like proliferation and drug resistance, 2) examination of contact vs. distance co-culture, 3) simultaneous, non-destructive observation of approx. 880 spheroids per matrix over time, 4) cultivation of proliferating and viable primary MM-pt samples for at least 3 weeks, but most importantly 5) displaying an easy to use high throughput screening platform, which meets the requirement for an in vitro BM model. Our ongoing analysis, including selective KDACi, like Sirtuin-1 or -2-inhibitors and lysine methyltransferase or lysine acetyltransferase inhibitors, will generate more data on rational drug combinations between epidrugs and adhesion-based therapies, including NOX-A12, elotuzumab, daratumumab, indatuximab-ravtansine and durvalumab. [Display omitted] DisclosuresAzab:Cleave Bioscience: Research Funding; Abbvie: Research Funding; Glycomimetics: Research Funding; Targeted Therapeutics LLC: Other: Founder and owner; Tioma: Research Funding; Verastem: Research Funding; Selexys: Research Funding; Cell Works: Research Funding; Cellatrix LLC: Other: Founder and owner; Karyopharm: Research Funding. Engelhardt:German Cancer Aid (#11424): Other: Educational Grant; Janssen Cilag GmbH: Other: Educational Grant; Celgene GmbH: Other: Educational Grant; Amgen GmbH: Other: Educational Grant.

Development and pre-clinical testing of a novel hypoxia-activated KDAC inhibitor

SummaryTumor hypoxia is associated with therapy resistance and poor patient prognosis. Hypoxia-activated prodrugs, designed to selectively target hypoxic cells while sparing normal tissue, represent a promising treatment strategy. We report the pre-clinical efficacy of 1-methyl-2-nitroimidazole panobinostat (NI-Pano, CH-03), a novel bioreductive version of the clinically used lysine deacetylase inhibitor, panobinostat. NI-Pano was stable in normoxic (21% O2) conditions and underwent NADPH-CYP-mediated enzymatic bioreduction to release panobinostat in hypoxia (<0.1% O2). Treatment of cells grown in both 2D and 3D with NI-Pano increased acetylation of histone H3 at lysine 9, induced apoptosis, and decreased clonogenic survival. Importantly, NI-Pano exhibited growth delay effects as a single agent in tumor xenografts. Pharmacokinetic analysis confirmed the presence of sub-micromolar concentrations of panobinostat in hypoxic mouse xenografts, but not in circulating plasma or kidneys. Together, our pre-clinical results provide a strong mechanistic rationale for the clinical development of NI-Pano for selective targeting of hypoxic tumors.

Effects of acetylation on dissociation and phosphorylation of actomyosin in postmortem ovine muscle during incubation at 4 °C in vitro

This study aimed to assess the effects of acetylation levels on actomyosin disassociation and phosphorylation of lamb during incubation at 4 °C. Samples of whole proteins from lamb longissimus thoracis muscles were prepared and assigned into three treatments (high, middle and low acetylation groups). The results showed that deacetylation of myosin heavy chain and actin was inhibited by lysine deacetylase inhibitor trichostatin A and nicotinamide in this study. Phosphorylation levels of myosin heavy chain and actin were inhibited by their acetylation during incubation in vitro. Actomyosin disassociation degree in high acetylation group was significantly lower than that in middle and low acetylation groups (P < 0.05). The ATPase activity in high acetylation group was significantly higher than that in middle and low acetylation groups (P < 0.05). In conclusion, acetylation of myosin heavy chain and actin inhibited actomyosin dissociation by inhibiting their phosphorylation at 4 °C in vitro.

Methylation-directed acetylation of histone H3 regulates developmental sensitivity to histone deacetylase inhibition.

Hydroxamate-based lysine deacetylase inhibitors (KDACis) are approved for clinical use against certain cancers. However, intrinsic and acquired resistance presents a major problem. Treatment of cells with hydroxamates such as trichostatin A (TSA) leads to rapid preferential acetylation of histone H3 already trimethylated on lysine 4 (H3K4me3), although the importance of this H3K4me3-directed acetylation in the biological consequences of KDACi treatment is not known. We address this utilizing Dictyostelium discoideum strains lacking H3K4me3 due to disruption of the gene encoding the Set1 methyltransferase or mutations in endogenous H3 genes. Loss of H3K4me3 confers resistance to TSA-induced developmental inhibition and delays accumulation of H3K9Ac and H3K14Ac. H3K4me3-directed H3Ac is mediated by Sgf29, a subunit of the SAGA acetyltransferase complex that interacts with H3K4me3 via a tandem tudor domain (TTD). We identify an Sgf29 orthologue in Dictyostelium with a TTD that specifically recognizes the H3K4me3 modification. Disruption of the gene encoding Sgf29 delays accumulation of H3K9Ac and abrogates H3K4me3-directed H3Ac. Either loss or overexpression of Sgf29 confers developmental resistance to TSA. Our results demonstrate that rapid acetylation of H3K4me3 histones regulates developmental sensitivity to TSA. Levels of H3K4me3 or Sgf29 will provide useful biomarkers for sensitivity to this class of chemotherapeutic drug.

Identification of Novel MeCP2 Cancer-Associated Target Genes and Post-Translational Modifications.

Abnormal regulation of DNA methylation and its readers has been associated with a wide range of cellular dysfunction. Disruption of the normal function of DNA methylation readers contributes to cancer progression, neurodevelopmental disorders, autoimmune disease and other pathologies. One reader of DNA methylation known to be especially important is MeCP2. It acts a bridge and connects DNA methylation with histone modifications and regulates many gene targets contributing to various diseases; however, much remains unknown about how it contributes to cancer malignancy. We and others previously described novel MeCP2 post-translational regulation. We set out to test the hypothesis that MeCP2 would regulate novel genes linked with tumorigenesis and that MeCP2 is subject to additional post-translational regulation not previously identified. Herein we report novel genes bound and regulated by MeCP2 through MeCP2 ChIP-seq and RNA-seq analyses in two breast cancer cell lines representing different breast cancer subtypes. Through genomics analyses, we localize MeCP2 to novel gene targets and further define the full range of gene targets within breast cancer cell lines. We also further examine the scope of clinical and pre-clinical lysine deacetylase inhibitors (KDACi) that regulate MeCP2 post-translationally. Through proteomics analyses, we identify many additional novel acetylation sites, nine of which are mutated in Rett Syndrome. Our study provides important new insight into downstream targets of MeCP2 and provide the first comprehensive map of novel sites of acetylation associated with both pre-clinical and FDA-approved KDACi used in the clinic. This report examines a critical reader of DNA methylation and has important implications for understanding MeCP2 regulation in cancer models and identifying novel molecular targets associated with epigenetic therapies.

Chromatin Structure and Drug Resistance in Candida spp.

Anti-microbial resistance (AMR) is currently one of the most serious threats to global human health and, appropriately, research to tackle AMR garnishes significant investment and extensive attention from the scientific community. However, most of this effort focuses on antibiotics, and research into anti-fungal resistance (AFR) is vastly under-represented in comparison. Given the growing number of vulnerable, immunocompromised individuals, as well as the positive impact global warming has on fungal growth, there is an immediate urgency to tackle fungal disease, and the disturbing rise in AFR. Chromatin structure and gene expression regulation play pivotal roles in the adaptation of fungal species to anti-fungal stress, suggesting a potential therapeutic avenue to tackle AFR. In this review we discuss both the genetic and epigenetic mechanisms by which chromatin structure can dictate AFR mechanisms and will present evidence of how pathogenic yeast, specifically from the Candida genus, modify chromatin structure to promote survival in the presence of anti-fungal drugs. We also discuss the mechanisms by which anti-chromatin therapy, specifically lysine deacetylase inhibitors, influence the acquisition and phenotypic expression of AFR in Candida spp. and their potential as effective adjuvants to mitigate against AFR.

TGFα Promotes Chemoresistance of Malignant Pleural Mesothelioma.

Background: There is no standard chemotherapy for refractory or relapsing malignant pleural mesothelioma (MPM). Our previous reports nevertheless indicated that a combination of an anthracycline (doxorubicin) and a lysine deacetylase inhibitor (valproic acid, VPA) synergize to induce the apoptosis of MPM cells and reduce tumor growth in mouse models. A Phase I/II clinical trial indicated that this regimen is a promising therapeutic option for a proportion of MPM patients. Methods: The transcriptomes of mesothelioma cells were compared after Illumina HiSeq 4000 sequencing. The expression of differentially expressed genes was inhibited by RNA interference. Apoptosis was determined by cell cycle analysis and Annexin V/7-AAD labeling. Protein expression was assessed by immunoblotting. Preclinical efficacy was evaluated in BALB/c and NOD-SCID mice. Results: To understand the mechanisms involved in chemoresistance, the transcriptomes of two MPM cell lines displaying different responses to VPA-doxorubicin were compared. Among the differentially expressed genes, transforming growth factor alpha (TGFα) was associated with resistance to this regimen. The silencing of TGFα by RNA interference correlated with a significant increase in apoptosis, whereas the overexpression of TGFα desensitized MPM cells to the apoptosis induced by VPA and doxorubicin. The multi-targeted inhibition of histone deacetylase (HDAC), HER2 and TGFα receptor (epidermal growth factor receptor/EGFR) improved treatment efficacy in vitro and reduced tumor growth in two MPM mouse models. Finally, TGFα expression but not EGFR correlated with patient survival. Conclusions: Our data show that TGFα but not its receptor EGFR is a key factor in resistance to MPM chemotherapy. This observation may contribute to casting light on the promising but still controversial role of EGFR signaling in MPM therapy.

Hypoxia-activated pro-drugs of the KDAC inhibitor vorinostat (SAHA)

Hypoxia (lower than normal oxygen) is a characteristic of most solid tumours that results in poor cancer patient prognosis. The difference in cellular environment between normoxia (21% oxygen) or physoxia (4–7.5% oxygen) and hypoxia (<2.0% oxygen) causes increased resistance to radio- and chemotherapy, but also provides the opportunity to selectively release hypoxia-activated pro-drugs. This approach potentially allows targeting of chemotherapies, including lysine deacetylase (KDAC) inhibitors, to the hypoxic fraction of cells. Here, we report initial work on the development of KDAC inhibitors that are selectively released in hypoxic conditions. We have shown that the addition of a 4-nitrobenzyl (NB) or 1-methyl-2-nitroimidazole (NI) bioreductive group onto the hydroxamic acid moiety of SAHA, giving NB-SAHA and NI-SAHA, abolishes KDAC inhibition activity. Both NB-SAHA and NI-SAHA undergo enzyme-mediated bioreduction, in a hypoxia-dependent manner, to release SAHA selectively in <0.1% oxygen. This work provides an important foundation for further investigations into the targeted release of KDAC inhibitors in hypoxic tumours.

Connectivity mapping of a chronic kidney disease progression signature identified lysine deacetylases as novel therapeutic targets

Tubulointerstitial injury is an important determinant of chronic kidney disease progression, yet treatment is limited. Accordingly, we derived a chronic kidney disease progression signature based on aging and disease in Col4a3-/- mice, a model associated with proteinuria and progressive loss of kidney function. Computational drug repurposing with the Connectivity Map identified vorinostat, a lysine deacetylase inhibitor, as a candidate treatment to reverse progression signature gene expression. Vorinostat administration significantly increased the lifespan of Col4a3-/- mice and attenuated tubulointerstitial fibrosis and JNK phosphorylation in the kidneys of Col4a3-/- mice. Invitro, vorinostat reduced albumin- and angiotensin II-induced activation of canonical mitogen-activated protein kinases in kidney tubular epithelial cells. Finally, a subset of murine progression signature genes was differentially expressed across kidney transcriptomic data from patients with focal segmental glomerulosclerosis, IgA nephropathy, and diabetic nephropathy. Thus, our findings suggest that lysine deacetylase inhibition may be a novel treatment to chronic kidney disease associated with proteinuria and progressive tubulointerstitial injury.

Drug Discovery Researches on Modulators of Lysine-Modifying Enzymes Based on Strategic Chemistry Approaches.

Enzymatic and post-translational modifications (PTMs) such as ubiquitination, acetylation, and methylation occur at lysine residues. The PTMs play critical roles in the regulation of the protein functions, and thus, various cellular processes. In addition, aberrations of the PTMs are associated with various diseases, such as cancer and neurodegenerative disorders. Therefore, we hypothesized that modulation of the PTMs and normalization of the PTM abnormalities could be useful as methods to control various cellular mechanisms and as a therapeutic strategy, respectively. To modulate the PTMs, we have focused on lysine-modifying enzymes and have pursued drug discovery researches on ubiquitination inducers, lysine deacetylase (KDAC) inhibitors, and lysine demethylase (KDM) inhibitors. For the identification of the modulators, we have used not only conventional drug design, such as structure-based drug design (SBDD) and ligand-based drug design (LBDD), but also "strategic chemistry approaches," such as drug design based on enzyme catalytic mechanism. As a result, we have identified several modulators which have pharmacological effects in animal models or in cellular studies. In this review, focusing on the drug design based on enzyme catalytic mechanism, our drug discovery researches have been discussed.

Measuring and Interpreting Oxygen Consumption Rates in Whole Fly Head Segments.

Regulated metabolic activity is essential for the normal functioning of living cells. Indeed, altered metabolic activity is causally linked with the progression of cancer, diabetes, neurodegeneration, and aging to name a few. For instance, changes in mitochondrial activity, the cell's metabolic powerhouse, have been characterized in many such diseases. Generally, the oxygen consumption rates of mitochondria were considered a reliable readout of mitochondrial activity and measurements in some of these studies were based on isolated mitochondria or cells. However, such conditions may not represent the complexity of a whole tissue. Recently, we have developed a novel method that enables the dynamic measurement of oxygen consumption rates from whole isolated fly heads. By utilizing this method, we have recorded lower oxygen consumption rates of the whole head segment in young versus aged flies. Secondly, we have discovered that lysine deacetylase inhibitors rapidly alter the oxygen consumption in the whole head. Our novel technique may therefore aid in uncovering new properties of various drugs, which may impact metabolic rates. Furthermore, our method may give a better understanding of metabolic behavior in an experimental setup that more closely resembles physiological states.

Adolescent methylmercury exposure: Behavioral mechanisms and effects of sodium butyrate in mice

Methylmercury (MeHg), an environmental neurotoxicant primarily found in fish, produces neurobehavioral impairment when exposure occurs during gestation. Whether other developmental periods, such as adolescence, display enhanced vulnerability to the behavioral effects of MeHg exposure is only beginning to be explored. Further, little is known about the effects of repeated administration of lysine deacetylase inhibitors, such as sodium butyrate (NaB), on operant behavior. In Experiment 1, male C57BL6/n mice were exposed to 0, 0.3, and 3.0 ppm MeHg (n = 12 each) via drinking water from postnatal days 21 to 60 (murine adolescence). As adults, mice were trained to lever press under an ascending series of fixed-ratio schedules of milk reinforcement selected to enable the analysis of three important parameters of operant behavior using the framework provided by Mathematical Principles of Reinforcement. Adolescent MeHg exposure dose-dependently increased saturation rate, a measure of the retroactive reach of a reinforcer, and decreased minimum response time relative to controls. In Experiment 2, the behavioral effects of repeated NaB administration both alone and following adolescent MeHg exposure were examined. Male C57BL6/n mice were given either 0 or 3.0 ppm MeHg during adolescence and, before behavioral testing, two weeks of once daily i.p. injections of saline or 0.6 g/kg NaB (n = 12 in each cell). Adolescent MeHg exposure again increased saturation rate but did not significantly alter minimum response time. NaB also increased saturation rate in both MeHg exposure groups. These data suggest that the behavioral mechanisms of adolescent MeHg exposure and NaB may be related to the impact of reinforcement on prior responses. Specifically, MeHg and NaB concentrated the effects of reinforcers onto the most recent responses.

Aromatase Acetylation Patterns and Altered Activity in Response to Sirtuin Inhibition.

Aromatase, a cytochrome P450 member, is a key enzyme involved in estrogen biosynthesis and is dysregulated in the majority of breast cancers. Studies have shown that lysine deacetylase inhibitors (KDI) decrease aromatase expression in cancer cells, yet many unknowns remain regarding the mechanism by which this occurs. However, advances have been made to clarify factors involved in the transcriptional regulation of the aromatase gene (CYP19A1). Yet, despite aromatase being a primary target for breast cancer therapy, its posttranslational regulation has been virtually unexplored. Acetylation is a posttranslational modification (PTM) known to alter the activity and stability of many oncoproteins, and given the role of KDIs in regulating aromatase expression, we postulate that aromatase acetylation acts as a novel posttranslational regulatory mechanism that impacts aromatase expression and/or activity in breast cancer. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis revealed that aromatase is basally acetylated on several lysine residues (108, 169, 242, 262, 334, 352, and 354) in MCF-7 cells, and treatment with a SIRT-1 inhibitor induced additional acetylation (376, 390, 440, and 448). These acetylated lysine residues are in regions critical for aromatase activity. Site-directed mutagenesis and overexpression studies demonstrated that K108R/Q or K440R/Q mutations significantly altered aromatase activity in breast cancer cells without altering its subcellular localization.Implications: These findings demonstrate a novel posttranslational regulation of aromatase and uncover novel anticancer effects of deacetylase inhibitors, thus providing new insight for ongoing development of deacetylase inhibitors as cancer therapeutics. Mol Cancer Res; 16(10); 1530-42. ©2018 AACR.