Dehydrogenase Classes
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Systems and Chemical Biology Approaches to Study Cell Function and Response to Toxins
Dissertation submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany for the degree of Doctor of Natural Sciences Presented by MSc. Yingying Jiang born in Shandong, China Oral-examination: Systems and chemical biology approaches to study cell function and response to toxins Referees: Prof. Dr. Rob Russell Prof. Dr. Stefan Wölfl CONTRIBUTIONS The chapter III of this thesis was submitted for publishing under the title “Drug mechanism predominates over toxicity mechanisms in drug induced gene expression” by Yingying Jiang, Tobias C. Fuchs, Kristina Erdeljan, Bojana Lazerevic, Philip Hewitt, Gordana Apic & Robert B. Russell. For chapter III, text phrases, selected tables, figures are based on this submitted manuscript that has been originally written by myself. i ABSTRACT Toxicity is one of the main causes of failure during drug discovery, and of withdrawal once drugs reached the market. Prediction of potential toxicities in the early stage of drug development has thus become of great interest to reduce such costly failures. Since toxicity results from chemical perturbation of biological systems, we combined biological and chemical strategies to help understand and ultimately predict drug toxicities. First, we proposed a systematic strategy to predict and understand the mechanistic interpretation of drug toxicities based on chemical fragments. Fragments frequently found in chemicals with certain toxicities were defined as structural alerts for use in prediction. Some of the predictions were supported with mechanistic interpretation by integrating fragment- chemical, chemical-protein, protein-protein interactions and gene expression data. Next, we systematically deciphered the mechanisms of drug actions and toxicities by analyzing the associations of drugs’ chemical features, biological features and their gene expression profiles from the TG-GATEs database. -
Isocitrate Dehydrogenase Activity Assay Kit (MAK062)
Isocitrate Dehydrogenase Activity Assay Kit Catalog Number MAK062 Storage Temperature –20 C TECHNICAL BULLETIN Product Description Developer 1 vl Isocitrate dehydrogenase (IDH) catalyzes the Catalog Number MAK062E conversion of isocitrate to -ketoglutarate. In eukaryotes, there are three isozymes of IDH, the IDH Positive Control (NADP+) 20 L mitochondrial IDH2 and IDH3, and the cytoplasmic/ Catalog Number MAK062F peroxisomal IDH1. All three IDH family members require the presence of a divalent cation (Mg2+ or Mn2+) NADH Standard, 0.5 mole 1 vl and either the electron-accepting cofactor NADP+ (IDH1 Catalog Number MAK062G and IDH2) or NAD+ (IDH3) for their enzymatic activity. IDH1 and IDH2 mutations resulting in neomorphic Reagents and Equipment Required but Not enzymatic activity are found in certain cancers such as Provided. glioblastoma, acute myeloid leukemia, and colon 96 well flat-bottom plate – It is recommended to use cancer. This neoactivity shows a change in the clear plates for colorimetric assays. substrate specificity resulting in the conversion of Spectrophotometric multiwell plate reader -ketoglutarate to 2-hydroxyglutarate. Mutations in IDH family members are also associated with Ollier disease Precautions and Disclaimer and Maffucci syndrome. This product is for R&D use only, not for drug, household, or other uses. Please consult the Material The Isocitrate Dehydrogenase Activity Assay kit Safety Data Sheet for information regarding hazards provides a simple and direct procedure for measuring and safe handling practices. + + + NADP -dependent, NAD -dependent, or both NADP + and NAD -dependent IDH activity in a variety of Preparation Instructions samples. IDH activity is determined using isocitrate as Briefly centrifuge vials before opening. -
Isocitrate Dehydrogenase 1 (NADP+) (I5036)
Isocitrate Dehydrogenase 1 (NADP+), human recombinant, expressed in Escherichia coli Catalog Number I5036 Storage Temperature –20 °C CAS RN 9028-48-2 IDH1 and IDH2 have frequent genetic alterations in EC 1.1.1.42 acute myeloid leukemia4 and better understanding of Systematic name: Isocitrate:NADP+ oxidoreductase these mutations may lead to an improvement of (decarboxylating) individual cancer risk assessment.6 In addition other studies have shown loss of IDH1 in bladder cancer Synonyms: IDH1, cytosolic NADP(+)-dependent patients during tumor development suggesting this may isocitrate dehydrogenase, isocitrate:NADP+ be involved in tumor progression and metastasis.7 oxidoreductase (decarboxylating), Isocitric Dehydrogenase, ICD1, PICD, IDPC, ICDC, This product is lyophilized from a solution containing oxalosuccinate decarboxylase Tris-HCl, pH 8.0, with trehalose, ammonium sulfate, and DTT. Product Description Isocitrate dehydrogenase (NADP+) [EC 1.1.1.42] is a Purity: ³90% (SDS-PAGE) Krebs cycle enzyme, which converts isocitrate to a-ketoglutarate. The flow of isocitrate through the Specific activity: ³80 units/mg protein glyoxylate bypass is regulated by phosphorylation of isocitrate dehydrogenase, which competes for a Unit definition: 1 unit corresponds to the amount of 1 common substrate (isocitrate) with isocitrate lyase. enzyme, which converts 1 mmole of DL-isocitrate to The activity of the enzyme is dependent on the a-ketoglutarate per minute at pH 7.4 and 37 °C (NADP formation of a magnesium or manganese-isocitrate as cofactor). The activity is measured by observing the 2 complex. reduction of NADP to NADPH at 340 nm in the 7 presence of 4 mM DL-isocitrate and 2 mM MnSO4. -
Preclinical Evaluation of Protein Disulfide Isomerase Inhibitors for the Treatment of Glioblastoma by Andrea Shergalis
Preclinical Evaluation of Protein Disulfide Isomerase Inhibitors for the Treatment of Glioblastoma By Andrea Shergalis A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Medicinal Chemistry) in the University of Michigan 2020 Doctoral Committee: Professor Nouri Neamati, Chair Professor George A. Garcia Professor Peter J. H. Scott Professor Shaomeng Wang Andrea G. Shergalis [email protected] ORCID 0000-0002-1155-1583 © Andrea Shergalis 2020 All Rights Reserved ACKNOWLEDGEMENTS So many people have been involved in bringing this project to life and making this dissertation possible. First, I want to thank my advisor, Prof. Nouri Neamati, for his guidance, encouragement, and patience. Prof. Neamati instilled an enthusiasm in me for science and drug discovery, while allowing me the space to independently explore complex biochemical problems, and I am grateful for his kind and patient mentorship. I also thank my committee members, Profs. George Garcia, Peter Scott, and Shaomeng Wang, for their patience, guidance, and support throughout my graduate career. I am thankful to them for taking time to meet with me and have thoughtful conversations about medicinal chemistry and science in general. From the Neamati lab, I would like to thank so many. First and foremost, I have to thank Shuzo Tamara for being an incredible, kind, and patient teacher and mentor. Shuzo is one of the hardest workers I know. In addition to a strong work ethic, he taught me pretty much everything I know and laid the foundation for the article published as Chapter 3 of this dissertation. The work published in this dissertation really began with the initial identification of PDI as a target by Shili Xu, and I am grateful for his advice and guidance (from afar!). -
(LCHAD) Deficiency / Mitochondrial Trifunctional Protein (MTF) Deficiency
Long chain acyl-CoA dehydrogenase (LCHAD) deficiency / Mitochondrial trifunctional protein (MTF) deficiency Contact details Introduction Regional Genetics Service Long chain acyl-CoA dehydrogenase (LCHAD) deficiency / mitochondrial trifunctional Levels 4-6, Barclay House protein (MTF) deficiency is an autosomal recessive disorder of mitochondrial beta- 37 Queen Square oxidation of fatty acids. The mitochondrial trifunctional protein is composed of 4 alpha London, WC1N 3BH and 4 beta subunits, which are encoded by the HADHA and HADHB genes, respectively. It is characterized by early-onset cardiomyopathy, hypoglycemia, T +44 (0) 20 7762 6888 neuropathy, and pigmentary retinopathy, and sudden death. There is also an infantile F +44 (0) 20 7813 8578 onset form with a hepatic Reye-like syndrome, and a late-adolescent onset form with primarily a skeletal myopathy. Tandem mass spectrometry of organic acids in urine, Samples required and carnitines in blood spots, allows the diagnosis to be unequivocally determined. An 5ml venous blood in plastic EDTA additional clinical complication can occur in the pregnant mothers of affected fetuses; bottles (>1ml from neonates) they may experience maternal acute fatty liver of pregnancy (AFLP) syndrome or Prenatal testing must be arranged hypertension/haemolysis, elevated liver enzymes and low platelets (HELLP) in advance, through a Clinical syndrome. Genetics department if possible. The genes encoding the HADHA and HADHB subunits are located on chromosome Amniotic fluid or CV samples 2p23.3. The pathogenic -
Is Glyceraldehyde-3-Phosphate Dehydrogenase a Central Redox Mediator?
1 Is glyceraldehyde-3-phosphate dehydrogenase a central redox mediator? 2 Grace Russell, David Veal, John T. Hancock* 3 Department of Applied Sciences, University of the West of England, Bristol, 4 UK. 5 *Correspondence: 6 Prof. John T. Hancock 7 Faculty of Health and Applied Sciences, 8 University of the West of England, Bristol, BS16 1QY, UK. 9 [email protected] 10 11 SHORT TITLE | Redox and GAPDH 12 13 ABSTRACT 14 D-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an immensely important 15 enzyme carrying out a vital step in glycolysis and is found in all living organisms. 16 Although there are several isoforms identified in many species, it is now recognized 17 that cytosolic GAPDH has numerous moonlighting roles and is found in a variety of 18 intracellular locations, but also is associated with external membranes and the 19 extracellular environment. The switch of GAPDH function, from what would be 20 considered as its main metabolic role, to its alternate activities, is often under the 21 influence of redox active compounds. Reactive oxygen species (ROS), such as 22 hydrogen peroxide, along with reactive nitrogen species (RNS), such as nitric oxide, 23 are produced by a variety of mechanisms in cells, including from metabolic 24 processes, with their accumulation in cells being dramatically increased under stress 25 conditions. Overall, such reactive compounds contribute to the redox signaling of the 26 cell. Commonly redox signaling leads to post-translational modification of proteins, 27 often on the thiol groups of cysteine residues. In GAPDH the active site cysteine can 28 be modified in a variety of ways, but of pertinence, can be altered by both ROS and 29 RNS, as well as hydrogen sulfide and glutathione. -
Degruyter Chem Chem-2021-0032 347..357 ++
Open Chemistry 2021; 19: 347–357 Research Article Belgin Sever, Mehlika Dilek Altıntop*, Yeliz Demir, Cüneyt Türkeş, Kaan Özbaş, Gülşen Akalın Çiftçi, Şükrü Beydemir*, Ahmet Özdemir A new series of 2,4-thiazolidinediones endowed with potent aldose reductase inhibitory activity https://doi.org/10.1515/chem-2021-0032 received December 2, 2020; accepted February 9, 2021 1 Introduction Abstract: In an effort to identify potent aldose reductase Type 2 diabetes (T2D) is a chronic life-threatening disease (AR) inhibitors, 5-(arylidene)thiazolidine-2,4-diones (1–8), characterized by abnormally high blood glucose levels which were prepared by the solvent-free reaction of 2,4- resulting from impaired response of target tissues to thiazolidinedione with aromatic aldehydes in the presence insulin (insulin resistance) and/or progressively reduced in vitro of urea, were examined for their AR inhibitory function of pancreatic β cells. The global burden of T2D is -( - - - - activities and cytotoxicity. 5 2 Hydroxy 3 methylbenzyli increasing considerably, and therefore there is an urgent ) - - (3) dene thiazolidine 2,4 dione was the most potent AR need to develop safe and potent antidiabetic agents [1–5]. inhibitor in this series, exerting uncompetitive inhibition Polyol pathway is a two-step metabolic pathway K ± with a i value of 0.445 0.013 µM. The IC50 value of in which glucose is reduced to sorbitol, which is then 3 fi - compound for L929 mouse broblast cells was deter converted to fructose. The abnormally activated polyol mined as 8.9 ± 0.66 µM, pointing out its safety as an AR pathway has been reported to participate in the patho- inhibitor. -
And URSPRUNG(1966)
GENETICS OF OCTANOL DEHYDROGENASE IN DROSOPHILA METZIP+ SARAH BEDICHEK PIPKIN Homrd Uniuersity, Washington, D.C.20001 Received October 11, 1967 CTANOL dehydrogenase (ODH) was studied in Drosophila melanogaster first by URSPRUNGand LEONE(1965) and distinguished from alcohol de- hydrogenase by COURTRIGHT,IMBERSKI, and URSPRUNG(1966). The neotropical species Drosophila metzii is polymorphic for complex octanol dehydrogenase patterns which will be shown to depend on two distinct structural genes, ODH,, apparently homologous with the locus studied by COURTRIGHTet al. (1966), and ODH,, responsible for a more slowly migrating isozyme. The ODH loci are un- linked, and variants display unifactorial inheritance. The ODH molecule is con- sidered at least a dimer but probably a tetramer. Isozyme formation can involve combinations of polypeptides produced by either or both of the two structural genes. Genetic evidence will be presented indicating that egg or embryonic and imaginal ODH isozyme patterns depend on the same structural genes. MATERIALS AND METHODS Single flies were assayed in crude homogenates with 1-octanol as substrate, using the agar gel electrophoresis method, with formazan staining according to the method of DR.H. URSPRUNG (1x5). Modifications of the method for the present work included grinding of single flies in a drop of glass distilled water in specially prepared small homogenizers and allowing the electro- phoresis to proceed at 25Ov for forty minutes instead of half an hour. Enzyme assays for the genetic analysis were made on single females aged 4 to 6 days. The smaller males do not provide sufficient enzyme for reliable single fly analysis. Flies for experimental crosses were reared in pair matings on a medium of corn meal-Karo-Brewer’s yeast #2019 (Standard Brands). -
How Is Alcohol Metabolized by the Body?
Overview: How Is Alcohol Metabolized by the Body? Samir Zakhari, Ph.D. Alcohol is eliminated from the body by various metabolic mechanisms. The primary enzymes involved are aldehyde dehydrogenase (ALDH), alcohol dehydrogenase (ADH), cytochrome P450 (CYP2E1), and catalase. Variations in the genes for these enzymes have been found to influence alcohol consumption, alcohol-related tissue damage, and alcohol dependence. The consequences of alcohol metabolism include oxygen deficits (i.e., hypoxia) in the liver; interaction between alcohol metabolism byproducts and other cell components, resulting in the formation of harmful compounds (i.e., adducts); formation of highly reactive oxygen-containing molecules (i.e., reactive oxygen species [ROS]) that can damage other cell components; changes in the ratio of NADH to NAD+ (i.e., the cell’s redox state); tissue damage; fetal damage; impairment of other metabolic processes; cancer; and medication interactions. Several issues related to alcohol metabolism require further research. KEY WORDS: Ethanol-to acetaldehyde metabolism; alcohol dehydrogenase (ADH); aldehyde dehydrogenase (ALDH); acetaldehyde; acetate; cytochrome P450 2E1 (CYP2E1); catalase; reactive oxygen species (ROS); blood alcohol concentration (BAC); liver; stomach; brain; fetal alcohol effects; genetics and heredity; ethnic group; hypoxia The alcohol elimination rate varies state of liver cells. Chronic alcohol con- he effects of alcohol (i.e., ethanol) widely (i.e., three-fold) among individ- sumption and alcohol metabolism are on various tissues depend on its uals and is influenced by factors such as strongly linked to several pathological concentration in the blood T chronic alcohol consumption, diet, age, consequences and tissue damage. (blood alcohol concentration [BAC]) smoking, and time of day (Bennion and Understanding the balance of alcohol’s over time. -
Gene Expression in Buccal Keratinocytes with Emphasis on Carbonyl Metabolism
From the Department of Medical Biochemistry and Biophysics Karolinska Institutet, Stockholm, Sweden GENE EXPRESSION IN BUCCAL KERATINOCYTES WITH EMPHASIS ON CARBONYL METABOLISM Claudia A. Staab Stockholm 2008 All previously published papers were reproduced with permission from the publisher. Published by Karolinska Institutet. Printed by [name of printer] © Claudia A. Staab, 2008 ISBN 978-91-7409-127-4 Printed by 2008 Gårdsvägen 4, 169 70 Solna Une sortie, c'est une entrée que l'on prend dans l'autre sens. Boris Vian ABSTRACT The inner lining of the cheek, the buccal mucosa, is a target for air-borne, dietary and tobacco usage-derived carcinogens, but also interesting from a drug delivery point of view. Cancer arising in the buccal epithelium, buccal squamous cell carcinoma (BSCC), often diagnosed at a late disease stage, is highly aggressive and recurrent, emphasizing the need for novel approaches in diagnosis and therapy. An in vitro model for human buccal carcinogenesis consisting of normal buccal keratinocytes (NBK) and two transformed cell lines of buccal origin was applied to explore mechanisms of buccal carcinogenesis, tumor marker and drug target expression. Two-dimensional gel electrophoresis, DNA microarray analysis, and the application of three bioinformatics programs for data mining allowed for the identification of multiple established and potential novel markers for BSCC, including tumor promoter/suppressor genes. Furthermore, post-confluent culture of NBK in absence and presence of fetal bovine serum was successfully used to induce terminal squamous differentiation (TSD) to various extents and thus enrich for different strata of the epithelium. Here, expression and activity of carbonyl-metabolizing enzymes (CMEs) were assessed in view of their multiple roles in phase I biotransformation. -
Moldx : BCKDHB Gene Test
Local Coverage Article: Billing and Coding: MolDX: BCKDHB Gene Test (A55099) Links in PDF documents are not guaranteed to work. To follow a web link, please use the MCD Website. Contractor Information CONTRACTOR NAME CONTRACT TYPE CONTRACT JURISDICTION STATE(S) NUMBER Noridian Healthcare Solutions, A and B MAC 01111 - MAC A J - E California - Entire State LLC Noridian Healthcare Solutions, A and B MAC 01112 - MAC B J - E California - Northern LLC Noridian Healthcare Solutions, A and B MAC 01182 - MAC B J - E California - Southern LLC Noridian Healthcare Solutions, A and B MAC 01211 - MAC A J - E American Samoa LLC Guam Hawaii Northern Mariana Islands Noridian Healthcare Solutions, A and B MAC 01212 - MAC B J - E American Samoa LLC Guam Hawaii Northern Mariana Islands Noridian Healthcare Solutions, A and B MAC 01311 - MAC A J - E Nevada LLC Noridian Healthcare Solutions, A and B MAC 01312 - MAC B J - E Nevada LLC Noridian Healthcare Solutions, A and B MAC 01911 - MAC A J - E American Samoa LLC California - Entire State Guam Hawaii Nevada Northern Mariana Islands Article Information General Information Article ID Original Effective Date Created on 12/19/2019. Page 1 of 6 A55099 10/17/2016 Article Title Revision Effective Date Billing and Coding: MolDX: BCKDHB Gene Test 12/01/2019 Article Type Revision Ending Date Billing and Coding N/A AMA CPT / ADA CDT / AHA NUBC Copyright Retirement Date Statement N/A CPT codes, descriptions and other data only are copyright 2018 American Medical Association. All Rights Reserved. Applicable FARS/HHSARS apply. Current Dental Terminology © 2018 American Dental Association. -
HADHB Gene Hydroxyacyl-Coa Dehydrogenase Trifunctional Multienzyme Complex Subunit Beta
HADHB gene hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit beta Normal Function The HADHB gene provides instructions for making part of an enzyme complex called mitochondrial trifunctional protein. This enzyme complex functions in mitochondria, the energy-producing centers within cells. Mitochondrial trifunctional protein is made of eight parts (subunits). Four alpha subunits are produced from the HADHA gene, and four beta subunits are produced from the HADHB gene. As the name suggests, mitochondrial trifunctional protein contains three enzymes that each perform a different function. The beta subunits contain one of the enzymes, known as long-chain 3-keto- acyl-CoA thiolase. The alpha subunits contain the other two enzymes. These enzymes are essential for fatty acid oxidation, which is the multistep process that breaks down ( metabolizes) fats and converts them to energy. Mitochondrial trifunctional protein is required to metabolize a group of fats called long- chain fatty acids. Long-chain fatty acids are found in foods such as milk and certain oils. These fatty acids are stored in the body's fat tissues. Fatty acids are a major source of energy for the heart and muscles. During periods of fasting, fatty acids are also an important energy source for the liver and other tissues. Health Conditions Related to Genetic Changes Mitochondrial trifunctional protein deficiency Researchers have identified at least 26 mutations in the HADHB gene that cause mitochondrial trifunctional protein deficiency. These mutations reduce all three enzyme activities of mitochondrial trifunctional protein. Most mutations change one of the protein building blocks (amino acids) used to make the beta subunit. A change in amino acids probably alters the subunit's structure, which disrupts all three activities of the enzyme complex.