Enzymes In Health Research Articles

RNA modifying enzymes in health and disease.

Dihydrouridine is a universally conserved tRNA modification installed by enzymes that are important for human health. High expression of dihydrouridine synthase 2 predicts poor patient outcomes in non small cell lung cancer for reasons as yet unclear. Here, we show that DUS2 suppresses ferroptosis, a metal-dependent non-apoptotic form of cell death that is emerging as a therapeutic target in lung cancer. Elevated DUS2 correlates with resistance to ferroptosis inducers and loss of DUS2 causes increased sensitivity with concomitant accumulation of toxic lipid peroxides. Mechanistically, DUS2 is required to maintain tRNA CysGCA levels and support translation of cysteine-rich proteins including metallothioneins that serve as key regulators of both metal and redox homeostasis. DUS2 knockout cells are more susceptible to zinc intoxication and have lower levels of reduced glutathione, which partially explains their sensitivity to ferroptosis.

Generation and Validation of an Anti-Human PANK3 Mouse Monoclonal Antibody.

Coenzyme A (CoA) is an essential co-factor at the intersection of diverse metabolic pathways. Cellular CoA biosynthesis is regulated at the first committed step—phosphorylation of pantothenic acid—catalyzed by pantothenate kinases (PANK1,2,3 in humans, PANK3 being the most highly expressed). Despite the critical importance of CoA in metabolism, the differential roles of PANK isoforms remain poorly understood. Our investigations of PANK proteins as potential precision oncology collateral lethality targets (PANK1 is co-deleted as part of the PTEN locus in some highly aggressive cancers) were severely hindered by a dearth of commercial antibodies that can reliably detect endogenous PANK3 protein. While we successfully validated commercial antibodies for PANK1 and PANK2 using CRISPR knockout cell lines, we found no commercial antibody that could detect endogenous PANK3. We therefore set out to generate a mouse monoclonal antibody against human PANK3 protein. We demonstrate that a clone (Clone MDA-299-62A) can reliably detect endogenous PANK3 protein in cancer cell lines, with band-specificity confirmed by CRISPR PANK3 knockout and knockdown cell lines. Sub-cellular fractionation shows that PANK3 is overwhelmingly cytosolic and expressed broadly across cancer cell lines. PANK3 monoclonal antibody MDA-299-62A should prove a valuable tool for researchers investigating this understudied family of metabolic enzymes in health and disease.

Activity-Based Probes for Proteases Pave the Way to Theranostic Applications.

Proteases are important enzymes in health and disease. Their activities are regulated at multiple levels. In fact, proteases are synthesized as inactive proenzymes (zymogens) that are activated by proteolytic removal of their pro-peptide sequence and can remain active or their activity can be attenuated by complex formation with specific endogenous inhibitors or by limited proteolysis or degradation. Consequently, quite often, only a fraction of the protease molecules is in the active/functional form, thus, the abundance of a protease is not always linearly proportional to the (patho)physiological function(s). Therefore, assays to determine the active forms of proteases are needed, not only in research but also in molecular diagnosis and therapy. Activity-based probes (ABPs) are chemical entities that bind covalently to the active enzyme/protease. ABPs carry a detection tag to enable localization and quantification of specific enzymatic/proteolytic activities with applications in molecular imaging and diagnosis. Moreover, ABPs act as suicide inhibitors of proteases, which can be exploited for delineation of the functional role(s) of a given protease in (patho) biological context and as potential therapeutics. In this sense, ABPs represent new theranostic agents. We outline recent developments pertaining to ABPs for proteases with potential therapeutic applications, with the aim to highlight their importance in theranostics.

Associations between Intra-Pancreatic Fat Deposition, Pancreas Size, and Pancreatic Enzymes in Health and after an Attack of Acute Pancreatitis

Introduction: Ectopic fat deposition in the pancreas is involved in the pathogenesis of metabolic sequelae following an attack of pancreatitis. However, its relationship with the exocrine pancreas has never been explored in this setting. The aim was to investigate the associations between intra-pancreatic fat deposition (IPFD), pancreas size, and pancreatic enzymes. Methods: This cross-sectional study recruited individuals with a history of acute pancreatitis and healthy controls. All participants underwent 3T magnetic resonance imaging, from which IPFD, total pancreas volume (TPV), and pancreas diameters (across the head, body, and tail) were measured independently by 2 raters in a blinded fashion. Circulating levels of pancreatic amylase, pancreatic lipase, and chymotrypsin were measured in a fasted state. A series of linear regression analyses was conducted, accounting for possible confounders. Results: A total of 108 individuals with pancreatitis and 60 healthy controls were studied. There was a statistically significant difference in IPFD (p < 0.001), but not in TPV (p = 0.389), between the groups. In the post-pancreatitis group, IPFD was significantly inversely associated with pancreas tail diameter (β = −0.736, p = 0.036 in the most adjusted model). In the control group, IPFD was significantly inversely associated with TPV (β = −3.557, p = 0.026 in the most adjusted model). Levels of pancreatic amylase were significantly directly associated with pancreas tail diameter in the post-pancreatitis group (β = 3.891, p = 0.042 in the most adjusted model), whereas levels of pancreatic lipase were significantly inversely associated with TPV in the control group (β = −10.533, p = 0.024 in the most adjusted model). Conclusion: Increased IPFD in individuals after an attack of pancreatitis is associated with reduced pancreas tail diameter, which is in turn associated with reduced circulating levels of pancreatic amylase. The relationship between IPFD and the exocrine pancreas warrants further investigations.

Physiological and Pathological Roles of Aldose Reductase.

Aldose reductase (AR) is an aldo-keto reductase that catalyzes the first step in the polyol pathway which converts glucose to sorbitol. Under normal glucose homeostasis the pathway represents a minor route of glucose metabolism that operates in parallel with glycolysis. However, during hyperglycemia the flux of glucose via the polyol pathway increases significantly, leading to excessive formation of sorbitol. The polyol pathway-driven accumulation of osmotically active sorbitol has been implicated in the development of secondary diabetic complications such as retinopathy, nephropathy, and neuropathy. Based on the notion that inhibition of AR could prevent these complications a range of AR inhibitors have been developed and tested; however, their clinical efficacy has been found to be marginal at best. Moreover, recent work has shown that AR participates in the detoxification of aldehydes that are derived from lipid peroxidation and their glutathione conjugates. Although in some contexts this antioxidant function of AR helps protect against tissue injury and dysfunction, the metabolic transformation of the glutathione conjugates of lipid peroxidation-derived aldehydes could also lead to the generation of reactive metabolites that can stimulate mitogenic or inflammatory signaling events. Thus, inhibition of AR could have both salutary and injurious outcomes. Nevertheless, accumulating evidence suggests that inhibition of AR could modify the effects of cardiovascular disease, asthma, neuropathy, sepsis, and cancer; therefore, additional work is required to selectively target AR inhibitors to specific disease states. Despite past challenges, we opine that a more gainful consideration of therapeutic modulation of AR activity awaits clearer identification of the specific role(s) of the AR enzyme in health and disease.

Cystathionine-β-Synthase: Molecular Regulation and Pharmacological Inhibition.

Cystathionine-β-synthase (CBS), the first (and rate-limiting) enzyme in the transsulfuration pathway, is an important mammalian enzyme in health and disease. Its biochemical functions under physiological conditions include the metabolism of homocysteine (a cytotoxic molecule and cardiovascular risk factor) and the generation of hydrogen sulfide (H2S), a gaseous biological mediator with multiple regulatory roles in the vascular, nervous, and immune system. CBS is up-regulated in several diseases, including Down syndrome and many forms of cancer; in these conditions, the preclinical data indicate that inhibition or inactivation of CBS exerts beneficial effects. This article overviews the current information on the expression, tissue distribution, physiological roles, and biochemistry of CBS, followed by a comprehensive overview of direct and indirect approaches to inhibit the enzyme. Among the small-molecule CBS inhibitors, the review highlights the specificity and selectivity problems related to many of the commonly used “CBS inhibitors” (e.g., aminooxyacetic acid) and provides a comprehensive review of their pharmacological actions under physiological conditions and in various disease models.

Xenobiotic Metabolising Enzymes: Impact on Pathologic Conditions, Drug Interactions and Drug Design.

The biotransformation of xenobiotics is a homeostatic defensive response of the body against bioactive invaders. Xenobiotic metabolizing enzymes, important for the metabolism, elimination and detoxification of exogenous agents, are found in most tissues and organs and are distinguished into phase I and phase II enzymes, as well as phase III transporters. The cytochrome P450 superfamily of enzymes plays a major role in the biotransformation of most xenobiotics as well as in the metabolism of important endogenous substrates such as steroids and fatty acids. The activity and the potential toxicity of numerous drugs are strongly influenced by their biotransformation, mainly accomplished by the cytochrome P450 enzymes, one of the most versatile enzyme systems. In this review, considering the importance of drug metabolising enzymes in health and disease, some of our previous research results are presented, which, combined with newer findings, may assist in the elucidation of xenobiotic metabolism and in the development of more efficient drugs. Study of drug metabolism is of major importance for the development of drugs and provides insight into the control of human health. This review is an effort towards this direction and may find useful applications in related medical interventions or help in the development of more efficient drugs.

Circadian periodicity and effect of gender, age, diet and smoking on circulating plasma lipid peroxides and antioxidant enzymes in healthy Indians of different age groups

ABSTRACT This study aims at assessing circadian rhythm characteristics of oxidants and antioxidants, testing for any effect of gender, age, diet and smoking status. Blood samples from clinically healthy Indians (103 males and 59 females, 7–75 years of age) were collected at 6-hour intervals for 24 hours for determination of MDA, SOD, CAT, GPx and GR. Data were analyzed by the single and population-mean cosinor to estimate circadian rhythm characteristics. The latter were further analyzed by multi-factor analysis of variance. A marked circadian rhythm was documented for all variables. Its parameters were found to undergo marked changes as a function of age. Males differed from females in terms of the rhythm-adjusted mean (MESOR) of CAT and GPx and of the 24-hour amplitude of GR. The MESOR of GPx differed between vegetarians and omnivores. Smoking status affected the MESOR of MDA and CAT and the 24-hour amplitude of CAT. As oxidative stress is being reported for most diseases, the mapping of circadian rhythms in oxidant and antioxidant enzymes in health may help refine reference values, thereby allowing the early detection of pathophysiological conditions, prompting the early institution of treatment. Abbreviations CAT: Catalase; FRAP: Ferric Reducing Antioxidant Power; GPx: Glutathione Peroxidase; GR: Glutathione Reductase; GSH: Glutathione; MDA: Malondialdehyde; MESOR: Midline Estimating Statistic Of Rhythm; ROS: Reactive Oxygen Species; SCN: Suprachiasmatic Nuclei; SOD: Superoxide Dismutase; TBARs: Thiobarbituric acid reactive substances; XPA: Xeroderma Pigmentosum, Complementation Group A (DNA Damage Recognition And Repair Factor)

Genetic Alterations in Oxidant and Anti-Oxidant Enzymes in the Vascular System.

Cardiovascular diseases (CVD) are one of the prime causes of mortality worldwide. Experimental animal models have become a valuable tool to investigate and further advance our knowledge on etiology, pathophysiology and intervention. They also provide a great opportunity to understand the contribution of different genes and effector molecules in the pathogenesis and development of diseases at the sub-cellular levels. High levels of reactive oxygen species (ROS) have been associated with the progression of CVD such as ischemic heart disease (IHD), myocardial infarction, hypertension, atherosclerosis, aortic aneurysm, aortic dissection and others. On the contrary, low levels of antioxidants were associated with exacerbated cardiovascular event. Major focus of this review is on vascular pathogenesis that leads to CVD, with special emphasis on the roles of oxidant/antioxidant enzymes in health and disease progression in vascular cells including vascular endothelium. The major oxidant enzymes that have been implicated with the progression of CVD include NADPH Oxidase, nitric oxide synthase, monoamine oxidase, and xanthine oxidoreductase. The major antioxidant enzymes that have been attributed to normalizing the levels of oxidative stress include superoxide dismutases, catalase and glutathione peroxidases (GPx), and thioredoxin. Cardiovascular phenotypes of major oxidants and antioxidants knockout and transgenic animal models are discussed here.

Biochemical and functional characterization of the human tissue kallikrein 9.

Human tissue kallikrein 9 (KLK9) is a member of the kallikrein-related family of proteases. Despite its known expression profile, much less is known about the functional roles of this protease and its implications in normal physiology and disease. We present here the first data on the biochemical characterization of KLK9, investigate parameters that affect its enzymatic activity (such as inhibitors) and provide preliminary insights into its putative substrates. We show that mature KLK9 is a glycosylated chymotrypsin-like enzyme with strong preference for tyrosine over phenylalanine at the P1 cleavage position. The enzyme activity is enhanced by Mg2+ and Ca2+, but is reversibly attenuated by Zn2+ KLK9 is inhibited in vitro by many naturally occurring or synthetic protease inhibitors. Using a combination of degradomic and substrate specificity assays, we identified candidate KLK9 substrates in two different epithelial cell lines [the non-tumorigenic human keratinocyte cells (HaCaT) and the tumorigenic tongue squamous carcinoma cells (SCC9)]. Two potential KLK9 substrates [KLK10 and midkine (MDK)] were subjected to further validation. Taken together, our data delineate some functional and biochemical properties of KLK9 for future elucidation of the role of this enzyme in health and disease.

Detection of Active Mammalian GH31 α-Glucosidases in Health and Disease Using In-Class, Broad-Spectrum Activity-Based Probes.

The development of small molecule activity-based probes (ABPs) is an evolving and powerful area of chemistry. There is a major need for synthetically accessible and specific ABPs to advance our understanding of enzymes in health and disease. α-Glucosidases are involved in diverse physiological processes including carbohydrate assimilation in the gastrointestinal tract, glycoprotein processing in the endoplasmic reticulum (ER), and intralysosomal glycogen catabolism. Inherited deficiency of the lysosomal acid α-glucosidase (GAA) causes the lysosomal glycogen storage disorder, Pompe disease. Here, we design a synthetic route for fluorescent and biotin-modified ABPs for in vitro and in situ monitoring of α-glucosidases. We show, through mass spectrometry, gel electrophoresis, and X-ray crystallography, that α-glucopyranose configured cyclophellitol aziridines label distinct retaining α-glucosidases including GAA and ER α-glucosidase II, and that this labeling can be tuned by pH. We illustrate a direct diagnostic application in Pompe disease patient cells, and discuss how the probes may be further exploited for diverse applications.

Azide–alkyne cycloaddition-mediated cyclization of phosphonopeptides and their evaluation as PTP1B binders and enrichment tools

Protein tyrosine phosphatases (PTPs) are important enzymes in health and disease, and chemical tools are crucial to understand and modulate their biological roles. PTP1B is involved in diabetes, obesity and cancer. One of the main challenges for the design of chemical tools for PTP1B is the homology to TCPTP, making tool selectivity a highly challenging task. Here, we aimed to study if azide–alkyne cycloaddition-mediated cyclization of a peptide inhibitor could increase its selectivity toward PTP1B over TCPTP, and if cyclic and linear peptide binders can be applied as enrichment tools of endogenous PTP1B. While the cyclization of the peptide binders did not improve the selectivity toward PTP1B over TCPTP, it enhanced strongly the efficiency to co-precipitate endogenous PTP1B out of cell lysates. Our results show that fine-tuning the molecular structure of peptidic pull-down baits can greatly enhance their efficiency compared to the parental peptide sequences.

The PRMT5 arginine methyltransferase: many roles in development, cancer and beyond.

Post-translational arginine methylation is responsible for regulation of many biological processes. The protein arginine methyltransferase 5 (PRMT5, also known as Hsl7, Jbp1, Skb1, Capsuleen, or Dart5) is the major enzyme responsible for mono- and symmetric dimethylation of arginine. An expanding literature demonstrates its critical biological function in a wide range of cellular processes. Histone and other protein methylation by PRMT5 regulate genome organization, transcription, stem cells, primordial germ cells, differentiation, the cell cycle, and spliceosome assembly. Metazoan PRMT5 is found in complex with the WD-repeat protein MEP50 (also known as Wdr77, androgen receptor coactivator p44, or Valois). PRMT5 also directly associates with a range of other protein factors, including pICln, Menin, CoPR5 and RioK1 that may alter its subcellular localization and protein substrate selection. Protein substrate and PRMT5-MEP50 post-translation modifications induce crosstalk to regulate PRMT5 activity. Crystal structures of C. elegans PRMT5 and human and frog PRMT5-MEP50 complexes provide substantial insight into the mechanisms of substrate recognition and procession to dimethylation. Enzymological studies of PRMT5 have uncovered compelling insights essential for future development of specific PRMT5 inhibitors. In addition, newly accumulating evidence implicates PRMT5 and MEP50 expression levels and their methyltransferase activity in cancer tumorigenesis, and, significantly, as markers of poor clinical outcome, marking them as potential oncogenes. Here, we review the substantial new literature on PRMT5 and its partners to highlight the significance of understanding this essential enzyme in health and disease.

Bacterial bile metabolising gene abundance in Crohn's, ulcerative colitis and type 2 diabetes metagenomes.

We performed an analysis to determine the importance of bile acid modification genes in the gut microbiome of inflammatory bowel disease and type 2 diabetic patients. We used publicly available metagenomic datasets from the Human Microbiome Project and the MetaHIT consortium, and determined the abundance of bile salt hydrolase gene (bsh), 7 alpha-dehydroxylase gene (adh) and 7-alpha hydroxysteroid dehydrogenase gene (hsdh) in fecal bacteria in diseased populations of Crohn's disease (CD), Ulcerative Colitis (UC) and Type 2 diabetes mellitus (T2DM). Phylum level abundance analysis showed a significant reduction in Firmicute-derived bsh in UC and T2DM patients but not in CD patients, relative to healthy controls. Reduction of adh and hsdh genes was also seen in UC and T2DM patients, while an increase was observed in the CD population as compared to healthy controls. A further analysis of the bsh genes showed significant differences in the correlations of certain Firmicutes families with disease or healthy populations. From this observation we proceeded to analyse BSH protein sequences and identified BSH proteins clusters representing the most abundant strains in our analysis of Firmicute bsh genes. The abundance of the bsh genes corresponding to one of these protein clusters was significantly reduced in all disease states relative to healthy controls. This cluster includes bsh genes derived from Lachospiraceae, Clostridiaceae, Erysipelotrichaceae and Ruminococcaceae families. This metagenomic analysis provides evidence of the importance of bile acid modifying enzymes in health and disease. It further highlights the importance of identifying gene and protein clusters, as the same gene may be associated with health or disease, depending on the strains expressing the enzyme, and differences in the enzymes themselves.

The human DEPhOsphorylation database DEPOD: a 2015 update.

Phosphatases are crucial enzymes in health and disease, but the knowledge of their biological roles is still limited. Identifying substrates continues to be a great challenge. To support the research on phosphatase–kinase–substrate networks we present here an update on the human DEPhOsphorylation Database: DEPOD (http://www.depod.org or http://www.koehn.embl.de/depod). DEPOD is a manually curated open access database providing human phosphatases, their protein and non-protein substrates, dephosphorylation sites, pathway involvements and external links to kinases and small molecule modulators. All internal data are fully searchable including a BLAST application. Since the first release, more human phosphatases and substrates, their associated signaling pathways (also from new sources), and interacting proteins for all phosphatases and protein substrates have been added into DEPOD. The user interface has been further optimized; for example, the interactive human phosphatase–substrate network contains now a ‘highlight node’ function for phosphatases, which includes the visualization of neighbors in the network.

Genetics of the First Seven Proprotein Convertase Enzymes in Health and Disease

Members of the substilisin/kexin like proprotein convertase (PCSK) protease family cleave and convert immature pro-proteins into their biologically active forms. By cleaving for example prohormones, cytokines and cell membrane proteins, PCSKs participate in maintaining the homeostasis in a healthy human body. Conversely, erratic enzymatic function is thought to contribute to the pathogenesis of a wide variety of diseases, including obesity and hypercholestrolemia. The first characterized seven PCSK enzymes (PCSK1-2, FURIN, PCSK4-7) process their substrates at a motif made up of paired basic amino acid residues. This feature results in a variable degree of biochemical redundancy in vitro, and consequently, shared substrate molecules between the different PCSK enzymes. This redundancy has confounded our understanding of the specific biological functions of PCSKs. The physiological roles of these enzymes have been best illustrated by the phenotypes of genetically engineered mice and patients that carry mutations in the PCSK genes. Recent developments in genome-wide methodology have generated a large amount of novel information on the genetics of the first seven proprotein convertases. In this review we summarize the reported genetic alterations and their associated phenotypes.

Selective activation of heme oxygenase-2 by menadione.

While substantial progress has been made in elucidating the roles of heme oxygenases-1 (HO-1) and-2 (HO-2) in mammals, our understanding of the functions of these enzymes in health and disease is still incomplete. A significant amount of our knowledge has been garnered through the use of nonselective inhibitors of HOs, and our laboratory has recently described more selective inhibitors for HO-1. In addition, our appreciation of HO-1 has benefitted from the availability of tools for increasing its activity through enzyme induction. By comparison, there is a paucity of information about HO-2 activation, with only a few reports appearing in the literature. This communication describes our observations of the up to 30-fold increase in the in-vitro activation of HO-2 by menadione. This activation was due to an increase in Vmax and was selective, in that menadione did not increase HO-1 activity.

NADPH Oxidases: Molecular Understanding Finally Reaching the Clinical Level?

NADPH oxidases (Nox) have been the subject of very intensive research over the past several years, which has led to in-depth understanding of the function of these enzymes in health and disease. Discovery of novel Nox enzymes and identification of a very wide range of tissue expression has increased our understanding of how NADPH oxidases may regulate so many distinct cellular functions and how the dysfunction of these enzymes may lead to disease. The present Forum issue summarizes the most novel aspects of NADPH oxidase biology, focusing on linking the molecular basis of NADPH oxidase function, compartmentalization, and differential expression patterns to diseases such as those of the pulmonary system, inflammation, central nervous system disorders, endothelial and vascular dysfunction, as well as disorders involving angiogenesis and stem cell and endothelial progenitor cell functions. Establishing these links may be the first step for future therapeutic use of NADPH oxidase inhibitors, which are discussed at length within this Forum issue.

Functional Proteomics on Zinc‐Dependent Metalloproteinases using Inhibitor Probes

Metzincins are a family of zinc(II)-dependent metalloproteinases with well known members such as the matrix metalloproteinases (MMPs) and A disintegrin and metalloproteinases (ADAMs). Metzincins are largely responsible for the modulation and regulation of the extracellular matrix by proteolytic degradation of extracellular matrix (ECM) proteins, and by liberation or production of biologically active proteins from their pro-forms. Since metzincin activity is strictly regulated in vivo, novel analysis methods are necessary to elucidate the role of the active enzymes in health and disease. This concept gives an overview of available methods, and describes an approach to use synthetic metzincin inhibitors as affinity probes for selective determination of active metzincins in biological and clinical samples.

Prostaglandin catabolizing enzymes

The primary catabolic pathway of prostaglandins and related eicosanoids is initiated by the oxidation of 15(S)-hydroxyl group catalyzed by NAD +-dependent 15-hydroxyprostaglandin dehydrogenase (15-PGDH) followed by the reduction of Δ 13 double bond catalyzed by NADPH/NADH dependent Δ 13-15-ketoprostaglandin reductase (13-PGR). 13-PGR was also found to exhibit NADP +-dependent leukotriene B 4 12-hydroxydehydrogenase (12-LTB 4DH) activity. These enzymes are considered to be the key enzymes responsible for biological inactivation of prostaglandins and related eicosanoids. A separate catabolic pathway of thromboxane involves the oxidation of thromboxane B 2 (TXB 2) at C-11 catalyzed by NAD +-dependent 11-hydroxythromboxane B 2 dehydrogenase (11-TXB 2DH). The product of this reaction, 11-dehydro-TXB 2, has been considered to be a more reliable quantitative index of thromboxane formation in the circulation. Recent biochemical and molecular biological studies have revealed interesting catalytic properties, structure, and activity relationship, and regulation of gene expression of these three enzymes. Future investigation may shed more light on the roles of these enzymes in health and diseases.