1
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Geng Y, Cai Q. Role of C9orf72 hexanucleotide repeat expansions in ALS/FTD pathogenesis. Front Mol Neurosci 2024; 17:1322720. [PMID: 38318532 PMCID: PMC10838790 DOI: 10.3389/fnmol.2024.1322720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are progressive neurological disorders that share neurodegenerative pathways and features. The most prevalent genetic causes of ALS/FTD is the GGGGCC hexanucleotide repeat expansions in the first intron region of the chromosome 9 open reading frame 72 (C9orf72) gene. In this review, we comprehensively summarize the accumulating evidences elucidating the pathogenic mechanism associated with hexanucleotide repeat expansions in ALS/FTD. These mechanisms encompass the structural polymorphism of DNA and transcribed RNA, the formation of RNA foci via phase separation, and the cytoplasmic accumulation and toxicities of dipeptide-repeat proteins. Additionally, the formation of G-quadruplex structures significantly impairs the expression and normal function of the C9orf72 protein. We also discuss the sequestration of specific RNA binding proteins by GGGGCC RNA, which further contributes to the toxicity of C9orf72 hexanucleotide repeat expansions. The deeper understanding of the pathogenic mechanism of hexanucleotide repeat expansions in ALS/FTD provides multiple potential drug targets for these devastating diseases.
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Affiliation(s)
- Yanyan Geng
- Clinical Research Institute of the First Affiliated Hospital of Xiamen University, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Qixu Cai
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, China
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2
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Baranowski D, Mieczkowski A, Trzybiński D, Woźniak K, Bednarska-Szczepaniak K, Gdaniec Z, Leśnikowski ZJ. INSIGHTS INTO MOLECULAR STRUCTURE OF ADENOSINE-BORON CLUSTER CONJUGATES AND THEIRS PHENYL ISOSTERS AS ADENOSINE RECEPTOR LIGANDS: NUCLEAR MAGNETIC RESONANCE, CRYSTALLOGRAPHIC AND COMPUTATIONAL STUDIES. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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3
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Zähringer S, Rumpf T, Melesina J, Lang AE, Aktories K, Sippl W, Jung M, Wagner GK. Defined stereoisomers of 2″-amino NAD + and their activity against human sirtuins and a bacterial (ADP-ribosyl) transferase. Bioorg Med Chem 2022; 68:116875. [PMID: 35716588 DOI: 10.1016/j.bmc.2022.116875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 11/02/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an important biomolecule with essential roles at the intersection of energy metabolism, epigenetic regulation and cell signalling. Synthetic analogues of NAD+ are therefore of great interest as chemical tools for medicinal chemistry, chemical biology and drug discovery. Herein, we report the chemical synthesis and full analytical characterisation of three stereoisomers of 2″-amino NAD+, and their biochemical evaluation against two classes of NAD+-consuming enzymes: the human sirtuins 1-3, and the bacterial toxin TccC3. To rationalise the observed activities, molecular docking experiments were carried out with SIRT1 and SIRT2, which identified the correct orientation of the pyrophosphate linkage as a major determinant for activity in this series. These results, together with results from stability tests and a conformational analysis, allow, for the first time, a side-by-side comparison of the chemical and biochemical features, and analytical properties, of different 2″-amino NAD+ stereoisomers. Our findings provide insight into the recognition of co-substrate analogues by sirtuins, and will greatly facilitate the application of these important NAD+ analogues as chemical tool compounds for mechanistic studies with these as well as other NAD+-dependent enyzmes.
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Affiliation(s)
- Sarah Zähringer
- Department of Chemistry, King's College London, Faculty of Natural & Mathematical Sciences, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom; Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Tobias Rumpf
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Jelena Melesina
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany
| | - Alexander E Lang
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Albertstr 25, 79104 Freiburg, Germany
| | - Klaus Aktories
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Albertstr 25, 79104 Freiburg, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Gerd K Wagner
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom.
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4
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Saito Y, Hudson RH. Base-modified fluorescent purine nucleosides and nucleotides for use in oligonucleotide probes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2018. [DOI: 10.1016/j.jphotochemrev.2018.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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5
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Choi YJ, Chang SJ, Gibala KS, Resendiz MJE. 8-Oxo-7,8-dihydroadenine and 8-Oxo-7,8-dihydroadenosine-Chemistry, Structure, and Function in RNA and Their Presence in Natural Products and Potential Drug Derivatives. Chemistry 2017; 23:6706-6716. [PMID: 27960050 DOI: 10.1002/chem.201605163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Indexed: 01/02/2023]
Abstract
A description and history of the role that 8-oxo-7,8-dihydroadenine (8-oxoAde) and 8-oxo-7,8-dihydroadenosine (8-oxoA) have in various fields has been compiled. This Review focusses on 1) the formation of this oxidatively generated modification in RNA, its interactions with other biopolymers, and its potential role in the development/progression of disease; 2) the independent synthesis and incorporation of this modified nucleoside into oligonucleotides of RNA to display the progress that has been made in establishing its behavior in biologically relevant systems; 3) reported synthetic routes, which date back to 1890, along with the progress that has been made in the total synthesis of the nucleobase, nucleoside, and their corresponding derivatives; and 4) the isolation, total synthesis, and biological activity of natural products containing these moieties as the backbone. The current state of research regarding this oxidatively generated lesion as well as its importance in the context of RNA, natural products, and potential as drug derivatives is illustrated using all available examples reported to date.
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Affiliation(s)
- Yu Jung Choi
- Department of Chemistry, University of Colorado Denver, Science Building, 1151 Arapahoe St., Denver, CO, 80204, USA
| | - Stephanie J Chang
- Department of Chemistry, University of Colorado Denver, Science Building, 1151 Arapahoe St., Denver, CO, 80204, USA
| | - Krzysztof S Gibala
- Department of Chemistry, University of Colorado Denver, Science Building, 1151 Arapahoe St., Denver, CO, 80204, USA
| | - Marino J E Resendiz
- Department of Chemistry, University of Colorado Denver, Science Building, 1151 Arapahoe St., Denver, CO, 80204, USA
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6
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Clausen JD, McIntosh DB, Woolley DG, Andersen JP. Determination of the ATP Affinity of the Sarcoplasmic Reticulum Ca(2+)-ATPase by Competitive Inhibition of [γ-(32)P]TNP-8N3-ATP Photolabeling. Methods Mol Biol 2016; 1377:233-59. [PMID: 26695037 DOI: 10.1007/978-1-4939-3179-8_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photoactivation of aryl azides is commonly employed as a means to covalently attach cross-linking and labeling reagents to proteins, facilitated by the high reactivity of the resultant aryl nitrenes with amino groups present in the protein side chains. We have developed a simple and reliable assay for the determination of the ATP binding affinity of native or recombinant sarcoplasmic reticulum Ca(2+)-ATPase, taking advantage of the specific photolabeling of Lys(492) in the Ca(2+)-ATPase by [γ-(32)P]2',3'-O-(2,4,6-trinitrophenyl)-8-azido-adenosine 5'-triphosphate ([γ-(32)P]TNP-8N3-ATP) and the competitive inhibition by ATP of the photolabeling reaction. The method allows determination of the ATP affinity of Ca(2+)-ATPase mutants expressed in mammalian cell culture in amounts too minute for conventional equilibrium binding studies. Here, we describe the synthesis and purification of the [γ-(32)P]TNP-8N3-ATP photolabel, as well as its application in ATP affinity measurements.
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Affiliation(s)
- Johannes D Clausen
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, Building 1160, 8000, Aarhus C, Denmark.
| | - David B McIntosh
- Institute of Infectious Diseases and Molecular Medicine, Division of Chemical Pathology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - David G Woolley
- Institute of Infectious Diseases and Molecular Medicine, Division of Chemical Pathology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Jens Peter Andersen
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, Building 1160, 8000, Aarhus C, Denmark
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7
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Brčić J, Plavec J. G-quadruplex formation of oligonucleotides containing ALS and FTD related GGGGCC repeat. Front Chem Sci Eng 2016. [DOI: 10.1007/s11705-016-1556-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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8
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Huecas S, Marcelo F, Perona A, Ruiz-Ávila LB, Morreale A, Cañada FJ, Jiménez-Barbero J, Andreu JM. Beyond a Fluorescent Probe: Inhibition of Cell Division Protein FtsZ by mant-GTP Elucidated by NMR and Biochemical Approaches. ACS Chem Biol 2015; 10:2382-92. [PMID: 26247422 DOI: 10.1021/acschembio.5b00444] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
FtsZ is the organizer of cell division in most bacteria and a target in the quest for new antibiotics. FtsZ is a tubulin-like GTPase, in which the active site is completed at the interface with the next subunit in an assembled FtsZ filament. Fluorescent mant-GTP has been extensively used for competitive binding studies of nucleotide analogs and synthetic GTP-replacing inhibitors possessing antibacterial activity. However, its mode of binding and whether the mant tag interferes with FtsZ assembly function were unknown. Mant-GTP exists in equilibrium as a mixture of C2'- and C3'-substituted isomers. We have unraveled the molecular recognition process of mant-GTP by FtsZ monomers. Both isomers bind in the anti glycosidic bond conformation: 2'-mant-GTP in two ribose puckering conformations and 3'-mant-GTP in the preferred C2' endo conformation. In each case, the mant tag strongly interacts with FtsZ at an extension of the GTP binding site, which is also supported by molecular dynamics simulations. Importantly, mant-GTP binding induces archaeal FtsZ polymerization into inactive curved filaments that cannot hydrolyze the nucleotide, rather than straight GTP-hydrolyzing assemblies, and also inhibits normal assembly of FtsZ from the Gram-negative bacterium Escherichia coli but is hydrolyzed by FtsZ from Gram-positive Bacillus subtilis. Thus, the specific interactions provided by the fluorescent mant tag indicate a new way to search for synthetic FtsZ inhibitors that selectively suppress the cell division of bacterial pathogens.
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Affiliation(s)
- Sonia Huecas
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Filipa Marcelo
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- UCIBIO, REQUIMTE, Dept. de Química, Faculdade de Ciências
e Tecnologia, UNL, 2829-516 Caparica, Portugal
| | - Almudena Perona
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa, CBMSO−CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Laura B. Ruiz-Ávila
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Antonio Morreale
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa, CBMSO−CSIC, Cantoblanco, 28049 Madrid, Spain
| | - F. Javier Cañada
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jesús Jiménez-Barbero
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - José M. Andreu
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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9
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Pergolizzi G, Cominetti MMD, Butt JN, Field RA, Bowater RP, Wagner GK. Base-modified NAD and AMP derivatives and their activity against bacterial DNA ligases. Org Biomol Chem 2015; 13:6380-98. [PMID: 25974621 DOI: 10.1039/c5ob00294j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We report the chemical synthesis and conformational analysis of a collection of 2-, 6- and 8-substituted derivatives of β-NAD(+) and AMP, and their biochemical evaluation against NAD(+)-dependent DNA ligases from Escherichia coli and Mycobacterium tuberculosis. Bacterial DNA ligases are validated anti-microbial targets, and new strategies for their inhibition are therefore of considerable scientific and practical interest. Our study includes several pairs of β-NAD(+) and AMP derivatives with the same substitution pattern at the adenine base. This has enabled the first direct comparison of co-substrate and inhibitor behaviour against bacterial DNA ligases. Our results suggest that an additional substituent in position 6 or 8 of the adenine base in β-NAD(+) is detrimental for activity as either co-substrate or inhibitor. In contrast, substituents in position 2 are not only tolerated, but appear to give rise to a new mode of inhibition, which targets the conformational changes these DNA ligases undergo during catalysis. Using a molecular modelling approach, we highlight that these findings have important implications for our understanding of ligase mechanism and inhibition, and may provide a promising starting point for the rational design of a new class of inhibitors against NAD(+)-dependent DNA ligases.
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Affiliation(s)
- Giulia Pergolizzi
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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10
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Brčić J, Plavec J. Solution structure of a DNA quadruplex containing ALS and FTD related GGGGCC repeat stabilized by 8-bromodeoxyguanosine substitution. Nucleic Acids Res 2015; 43:8590-600. [PMID: 26253741 PMCID: PMC4787828 DOI: 10.1093/nar/gkv815] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 07/30/2015] [Indexed: 12/13/2022] Open
Abstract
A prolonged expansion of GGGGCC repeat within non-coding region of C9orf72 gene has been identified as the most common cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), which are devastating neurodegenerative disorders. Formation of unusual secondary structures within expanded GGGGCC repeat, including DNA and RNA G-quadruplexes and R-loops was proposed to drive ALS and FTD pathogenesis. Initial NMR investigation on DNA oligonucleotides with four repeat units as the shortest model with the ability to form an unimolecular G-quadruplex indicated their folding into multiple G-quadruplex structures in the presence of K+ ions. Single dG to 8Br-dG substitution at position 21 in oligonucleotide d[(G4C2)3G4] and careful optimization of folding conditions enabled formation of mostly a single G-quadruplex species, which enabled determination of a high-resolution structure with NMR. G-quadruplex structure adopted by d[(G4C2)3GGBrGG] is composed of four G-quartets, which are connected by three edgewise C-C loops. All four strands adopt antiparallel orientation to one another and have alternating syn-anti progression of glycosidic conformation of guanine residues. One of the cytosines in every loop is stacked upon the G-quartet contributing to a very compact and stable structure.
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Affiliation(s)
- Jasna Brčić
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia EN-FIST Center of Excellence, Ljubljana, Slovenia
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11
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Zayas J, Annoual M, Das JK, Felty Q, Gonzalez WG, Miksovska J, Sharifai N, Chiba A, Wnuk SF. Strain Promoted Click Chemistry of 2- or 8-Azidopurine and 5-Azidopyrimidine Nucleosides and 8-Azidoadenosine Triphosphate with Cyclooctynes. Application to Living Cell Fluorescent Imaging. Bioconjug Chem 2015; 26:1519-32. [PMID: 26086070 DOI: 10.1021/acs.bioconjchem.5b00300] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Strain-promoted click chemistry of nucleosides and nucleotides with an azido group directly attached to the purine and pyrimidine rings with various cyclooctynes in aqueous solution at ambient temperature resulted in efficient formation (3 min to 3 h) of fluorescent, light-up, triazole products. The 2- and 8-azidoadenine nucleosides reacted with fused cyclopropyl cyclooctyne, dibenzylcyclooctyne, or monofluorocyclooctyne to produce click products functionalized with hydroxyl, amino, N-hydroxysuccinimide, or biotin moieties. The 5-azidouridine and 5-azido-2'-deoxyuridine were similarly converted to the analogous triazole products in quantitative yields in less than 5 min. The 8-azido-ATP quantitatively afforded the triazole product with fused cyclopropyl cyclooctyne in aqueous acetonitrile (3 h). The novel triazole adducts at the 2- or 8-position of adenine or 5-position of uracil rings induce fluorescence properties which were used for direct imaging in MCF-7 cancer cells without the need for traditional fluorogenic reporters. FLIM of the triazole click adducts demonstrated their potential utility for dynamic measuring and tracking of signaling events inside single living cancer cells.
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Affiliation(s)
| | | | | | | | | | | | - Nima Sharifai
- §Department of Biology, University of Miami, Coral Gables, Florida 33146, United States
| | - Akira Chiba
- §Department of Biology, University of Miami, Coral Gables, Florida 33146, United States
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12
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Dimopoulou A, Manta S, Parmenopoulou V, Kollatos N, Christidou O, Triantakonstanti VV, Schols D, Komiotis D. An easy microwave-assisted synthesis of C8-alkynyl adenine pyranonucleosides as novel cytotoxic antitumor agents. Front Chem 2015; 3:21. [PMID: 25853123 PMCID: PMC4369668 DOI: 10.3389/fchem.2015.00021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/05/2015] [Indexed: 11/13/2022] Open
Abstract
We describe the synthesis of C8-alkynyl adenine pyranonucleosides 4, 5, and 8-phenylethynyl-adenine (II), via Sonogashira cross-coupling reaction under microwave irradiation. Compounds 4e and II were less cytostatic than 5-fluorouracil (almost an order of magnitude) against murine leukemia (L1210) and human cervix carcinoma (HeLa) cells, while the same compounds proved to be more active than 5-fluorouracil against human lymphocyte (CEM) cells.
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Affiliation(s)
- Athina Dimopoulou
- Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly Larissa, Greece
| | - Stella Manta
- Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly Larissa, Greece
| | - Vanessa Parmenopoulou
- Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly Larissa, Greece
| | - Nikolaos Kollatos
- Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly Larissa, Greece
| | - Ourania Christidou
- Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly Larissa, Greece
| | - Virginia V Triantakonstanti
- Laboratory of Organic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki Thessaloniki, Greece
| | - Dominique Schols
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven Leuven, Belgium
| | - Dimitri Komiotis
- Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly Larissa, Greece
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14
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Marcelo F, Huecas S, Ruiz-Ávila LB, Cañada FJ, Perona A, Poveda A, Martín-Santamaría S, Morreale A, Jiménez-Barbero J, Andreu JM. Interactions of bacterial cell division protein FtsZ with C8-substituted guanine nucleotide inhibitors. A combined NMR, biochemical and molecular modeling perspective. J Am Chem Soc 2013; 135:16418-28. [PMID: 24079270 DOI: 10.1021/ja405515r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
FtsZ is the key protein of bacterial cell-division and target for new antibiotics. Selective inhibition of FtsZ polymerization without impairing the assembly of the eukaryotic homologue tubulin was demonstrated with C8-substituted guanine nucleotides. By combining NMR techniques with biochemical and molecular modeling procedures, we have investigated the molecular recognition of C8-substituted-nucleotides by FtsZ from Methanococcus jannaschii (Mj-FtsZ) and Bacillus subtilis (Bs-FtsZ). STD epitope mapping and trNOESY bioactive conformation analysis of each nucleotide were employed to deduce differences in their recognition mode by each FtsZ species. GMP binds in the same anti conformation as GTP, whereas 8-pyrrolidino-GMP binds in the syn conformation. However, the anti conformation of 8-morpholino-GMP is selected by Bs-FtsZ, while Mj-FtsZ binds both anti- and syn-geometries. The inhibitory potencies of the C8-modified-nucleotides on the assembly of Bs-FtsZ, but not of Mj-FtsZ, correlate with their binding affinities. Thus, MorphGTP behaves as a nonhydrolyzable analog whose binding induces formation of Mj-FtsZ curved filaments, resembling polymers formed by the inactive forms of this protein. NMR data, combined with molecular modeling protocols, permit explanation of the mechanism of FtsZ assembly impairment by C8-substituted GTP analogs. The presence of the C8-substituent induces electrostatic remodeling and small structural displacements at the association interface between FtsZ monomers to form filaments, leading to complete assembly inhibition or to formation of abnormal FtsZ polymers. The inhibition of bacterial Bs-FtsZ assembly may be simply explained by steric clashes of the C8-GTP-analogs with the incoming FtsZ monomer. This information may facilitate the design of antibacterial FtsZ inhibitors replacing GTP.
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Affiliation(s)
- Filipa Marcelo
- Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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15
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Faucher F, Doublié S, Jia Z. 8-oxoguanine DNA glycosylases: one lesion, three subfamilies. Int J Mol Sci 2012; 13:6711-6729. [PMID: 22837659 PMCID: PMC3397491 DOI: 10.3390/ijms13066711] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 05/14/2012] [Accepted: 05/24/2012] [Indexed: 11/24/2022] Open
Abstract
Amongst the four bases that form DNA, guanine is the most susceptible to oxidation, and its oxidation product, 7,8-dihydro-8-oxoguanine (8-oxoG) is the most prevalent base lesion found in DNA. Fortunately, throughout evolution cells have developed repair mechanisms, such as the 8-oxoguanine DNA glycosylases (OGG), which recognize and excise 8-oxoG from DNA thereby preventing the accumulation of deleterious mutations. OGG are divided into three subfamilies, OGG1, OGG2 and AGOG, which are all involved in the base excision repair (BER) pathway. The published structures of OGG1 and AGOG, as well as the recent availability of OGG2 structures in both apo- and liganded forms, provide an excellent opportunity to compare the structural and functional properties of the three OGG subfamilies. Among the observed differences, the three-dimensional fold varies considerably between OGG1 and OGG2 members, as the latter lack the A-domain involved in 8-oxoG binding. In addition, all three OGG subfamilies bind 8-oxoG in a different manner even though the crucial interaction between the enzyme and the protonated N7 of 8-oxoG is conserved. Finally, the three OGG subfamilies differ with respect to DNA binding properties, helix-hairpin-helix motifs, and specificity for the opposite base.
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Affiliation(s)
- Frédérick Faucher
- Department of Biomedical and Molecular Sciences, Queen’s University, 18 Stuart Street, Kingston, K7L 3N6, Canada
- Authors to whom correspondence should be addressed; E-Mails: (F.F.); (Z.J.); Tel.: +613-533-6277 (Z.J.); Fax: +613-533-2497 (Z.J.)
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, E314A Given Building, 89 Beaumont Avenue, Burlington, VT 05405, USA; E-Mail:
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen’s University, 18 Stuart Street, Kingston, K7L 3N6, Canada
- Authors to whom correspondence should be addressed; E-Mails: (F.F.); (Z.J.); Tel.: +613-533-6277 (Z.J.); Fax: +613-533-2497 (Z.J.)
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16
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Saftić D, Žinić B, Višnjevac A. DBU induced formation of 8-bromoguanosine dimer with three hydrogen bonds between the GG− base pairs. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.11.086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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17
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Pesnot T, Kempter J, Schemies J, Pergolizzi G, Uciechowska U, Rumpf T, Sippl W, Jung M, Wagner GK. Two-step synthesis of novel, bioactive derivatives of the ubiquitous cofactor nicotinamide adenine dinucleotide (NAD). J Med Chem 2011; 54:3492-9. [PMID: 21528845 DOI: 10.1021/jm1013852] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We report the design and concise synthesis, in two steps from commercially available material, of novel, bioactive derivatives of the enzyme cofactor nicotinamide adenine dinucleotide (NAD). The new synthetic dinucleotides act as sirtuin (SIRT) inhibitors and show isoform selectivity for SIRT2 over SIRT1. An NMR-based conformational analysis suggests that the conformational preferences of individual analogues may contribute to their isoform selectivity.
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Affiliation(s)
- Thomas Pesnot
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
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18
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Dahlmann HA, Sturla SJ. Synthesis of oxygen-linked 8-phenoxyl-deoxyguanosine nucleoside analogues. European J Org Chem 2011; 2011. [PMID: 24273446 DOI: 10.1002/ejoc.201100013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Nucleobase adducts, which form in vivo by the nucleophilic attack of nucleobases on exogenous electrophilic species, can impact conformation and biological influences of the adducted nucleoside. Contemporary studies aim to address the occurrence and relevance of O-linked 8-phenoxy-purine adducts; however, preparative techniques for synthesizing these nucleosides were not previously described. Reported herein is a relatively facile synthesis of O-linked 8-dG phenol adducts with a wide variety of electron-donating, electron-withdrawing, and sterically demanding phenols.
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Affiliation(s)
- Heidi A Dahlmann
- ETH Zürich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 9, Zürich 8006, Switzerland
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19
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Hwu JR, Lin SY, Tsay SC, De Clercq E, Leyssen P, Neyts J. Coumarin−Purine Ribofuranoside Conjugates as New Agents against Hepatitis C Virus. J Med Chem 2011; 54:2114-26. [DOI: 10.1021/jm101337v] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jih Ru Hwu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30013, R.O.C
- Department of Chemistry, National Central University, Jhongli City, Taiwan 32001, R.O.C
| | - Shu-Yu Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30013, R.O.C
| | - Shwu-Chen Tsay
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30013, R.O.C
| | - Erik De Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Pieter Leyssen
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Johan Neyts
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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20
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Dierckx A, Dinér P, El-Sagheer AH, Kumar JD, Brown T, Grøtli M, Wilhelmsson LM. Characterization of photophysical and base-mimicking properties of a novel fluorescent adenine analogue in DNA. Nucleic Acids Res 2011; 39:4513-24. [PMID: 21278417 PMCID: PMC3105426 DOI: 10.1093/nar/gkr010] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To increase the diversity of fluorescent base analogues with improved properties, we here present the straightforward click-chemistry-based synthesis of a novel fluorescent adenine-analogue triazole adenine (AT) and its photophysical characterization inside DNA. AT shows promising properties compared to the widely used adenine analogue 2-aminopurine. Quantum yields reach >20% and >5% in single- and double-stranded DNA, respectively, and show dependence on neighbouring bases. Moreover, AT shows only a minor destabilization of DNA duplexes, comparable to 2-aminopurine, and circular dichroism investigations suggest that AT only causes minimal structural perturbations to normal B-DNA. Furthermore, we find that AT shows favourable base-pairing properties with thymine and more surprisingly also with normal adenine. In conclusion, AT shows strong potential as a new fluorescent adenine analogue for monitoring changes within its microenvironment in DNA.
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Affiliation(s)
- Anke Dierckx
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, University of Gothenburg, S-41296 Gothenburg, Sweden
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21
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Altona C. Conformational analysis of nucleic acids. Determination of backbone geometry of single-helical RNA and DNA in aqueous solution. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19821011201] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Czarnecki JJ, Abbott MS, Selman BR. Photoaffinity labeling with 2-azidoadenosine diphosphate of a tight nucleotide binding site on chloroplast coupling factor 1. Proc Natl Acad Sci U S A 2010; 79:7744-8. [PMID: 16593263 PMCID: PMC347424 DOI: 10.1073/pnas.79.24.7744] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An analog of ADP containing an azido group at the C-2 position of the purine ring has been synthesized and used as an affinity probe of the membrane-bound coupling factor 1 of spinach chloroplast thylakoid membranes. The 2-azido-ADP inhibited light-induced dark binding of ADP at the tight nucleotide binding site on the thylakoid membranes. The 2-azido-ADP itself bound tightly to the thylakoid membranes, with 1 muM as the concentration giving 50% maximum binding. Tight binding of the analog required the thylakoid membranes to be energized, and the nucleotide remained bound after repeated washings of the membranes. The maximum extent of tight binding of the analog (1,2-1.3 nmol/mg of chlorophyll) was stoichiometric with the known coupling factor 1 content of thylakoid membranes but somewhat higher than that observed for ADP (0.5-0.9 nmol per mg of chlorophyll). Tight binding of 2-azido-ADP was decreased by the simultaneous addition of ADP. UV photolysis of washed thylakoid membranes containing tightly-bound 2-azido-[beta-(32)P]ADP resulted in the covalent incorporation of label into the membranes. Isolation of the chloroplast coupling factor 1 from these membranes followed by NaDodSO(4) gel electrophoresis demonstrated that the analog was covalently bound to the beta subunit of the coupling factor complex.
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Affiliation(s)
- J J Czarnecki
- The Institute for Enzyme Research, College of Agricultural and Life Sciences, University of Wisconsin, Madison, Wisconsin 53706
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23
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Millen AL, Manderville RA, Wetmore SD. Conformational Flexibility of C8-Phenoxyl-2′-deoxyguanosine Nucleotide Adducts. J Phys Chem B 2010; 114:4373-82. [DOI: 10.1021/jp911993f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Andrea L. Millen
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Richard A. Manderville
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Stacey D. Wetmore
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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24
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Sannohe Y, Sato K, Matsugami A, Shinohara KI, Mashimo T, Katahira M, Sugiyama H. The orientation of the ends of G-quadruplex structures investigated using end-extended oligonucleotides. Bioorg Med Chem 2009; 17:1870-5. [PMID: 19223183 DOI: 10.1016/j.bmc.2009.01.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Revised: 01/21/2009] [Accepted: 01/22/2009] [Indexed: 01/03/2023]
Abstract
Human telomere DNA is of intense interest because of its role in the biology of both cancer and aging. The single-stranded telomere terminus can adopt the structure of a G-quadruplex, which is of particular important for anticancer drug discovery many researchers have reported various G-quadruplex structures in the human telomere. Although the human telomere consists of a number of tandem repeats, higher-order G-quadruplex structures are less discussed due to the complexity of the structures. Here we examined the orientation of the ends of the G-quadruplex structures with consideration given to higher-order structures. We prepared end-extended and (Br)G-substituted oligonucleotides. Native PAGE analysis, CD measurements and NMR spectroscopy showed that the ends of stable G-quadruplex structures point in opposite directions. Our results indicate that the human telomere DNA is likely to form rod-like higher-order structures. This may provide important information for understanding telomere structure and the development of telomere G-quadruplex-binding molecules as telomerase inhibitors.
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Affiliation(s)
- Yuta Sannohe
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, Japan
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25
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Zhang B, Wagner GK, Weber K, Garnham C, Morgan AJ, Galione A, Guse AH, Potter BVL. 2'-deoxy cyclic adenosine 5'-diphosphate ribose derivatives: importance of the 2'-hydroxyl motif for the antagonistic activity of 8-substituted cADPR derivatives. J Med Chem 2008; 51:1623-36. [PMID: 18303825 DOI: 10.1021/jm7010386] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural features needed for antagonism at the cyclic ADP-ribose (cADPR) receptor are unclear. Chemoenzymatic syntheses of novel 8-substituted 2'-deoxy-cADPR analogues, including 8-bromo-2'-deoxy-cADPR 7, 8-amino-2'-deoxy-cADPR 8, 8- O-methyl-2'-deoxy-cADPR 9, 8-phenyl-2'-deoxy-cADPR 10 and its ribose counterpart 8-phenyl-cADPR 5 are reported, including improved syntheses of established antagonists 8-amino-cADPR 2 and 8-bromo-cADPR 3. Aplysia californica ADP-ribosyl cyclase tolerates even the bulky 8-phenyl-nicotinamide adenine 5'-dinucleotide as a substrate. Structure-activity relationships of 8-substituted cADPR analogues in both Jurkat T-lymphocytes and sea urchin egg homogenate (SUH) were investigated. 2'-OH Deletion decreased antagonistic activity (at least for the 8-amino series), showing it to be an important motif. Some 8-substituted 2'-deoxy analogues showed agonist activity at higher concentrations, among which 8-bromo-2'-deoxy-cADPR 7 was, unexpectedly, a weak but almost full agonist in SUH and was membrane-permeant in whole eggs. Classical antagonists 2 and 3 also showed previously unobserved agonist activity at higher concentrations in both systems. The 2'-OH group, without effect on the Ca (2+)-mobilizing ability of cADPR itself, is an important motif for the antagonistic activities of 8-substituted cADPR analogues.
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Affiliation(s)
- Bo Zhang
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, UK
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26
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Zhang B, Bailey VC, Potter BVL. Chemoenzymatic synthesis of 7-deaza cyclic adenosine 5'-diphosphate ribose analogues, membrane-permeant modulators of intracellular calcium release. J Org Chem 2008; 73:1693-703. [PMID: 18229937 DOI: 10.1021/jo071236p] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An optimized synthetic route to 7-deaza-8-bromo-cyclic adenosine 5'-diphosphate ribose (7-deaza-8-bromo-cADPR 3), an established cell-permeant, hydrolysis-resistant cyclic adenosine 5'-diphosphate ribose (cADPR) antagonist, is presented. Using NMR analysis, we found that 3 adopted a C-2' endo conformation in the N9-linked ribose and a syn conformation about the N9-glycosyl linkage, which are similar to that of cADPR. The synthetic route was also employed to produce 7-deaza-2'-deoxy-cADPR 4, a potential cell-permeant cADPR analogue. 3 and 4 were more stable to chemical hydrolysis, consistent with the observation that 7-deaza-cADPR analogues are more stable than their parent adenosine derivatives. 3 was also found to be stable to enzyme-mediated hydrolysis using CD38 ectoenzyme.
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Affiliation(s)
- Bo Zhang
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
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27
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Schmidt FHG, Hüben M, Gider B, Renault F, Teulade-Fichou MP, Weinhold E. Sequence-specific Methyltransferase-Induced Labelling (SMILing) of plasmid DNA for studying cell transfection. Bioorg Med Chem 2008; 16:40-8. [DOI: 10.1016/j.bmc.2007.04.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2006] [Revised: 11/10/2006] [Accepted: 04/27/2007] [Indexed: 10/23/2022]
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28
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Moreau C, Wagner GK, Weber K, Guse AH, Potter BVL. Structural determinants for N1/N7 cyclization of nicotinamide hypoxanthine 5'-dinucleotide (NHD+) derivatives by ADP-ribosyl cyclase from aplysia californica: Ca2+-mobilizing activity of 8-substituted cyclic inosine 5'-diphosphoribose analogues in T-lymphocytes. J Med Chem 2006; 49:5162-76. [PMID: 16913705 DOI: 10.1021/jm060275a] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of nicotinamide hypoxanthine 5'-dinucleotide (NHD+) analogues modified at C-8 (2-5) and 7-deaza-NHD+ were synthesized, and cyclization in the presence of Aplysia ADP-ribosyl cyclase was studied. All 8-substituted NHD+ analogues were converted into their N1-cyclic forms by the enzyme, while in contrast, 7-deaza-NHD+ 17 was hydrolyzed into 7-deazainosine 5'-diphosphoribose (7-deaza-IDPR) 25. Correlations are made showing that the conformation of the NHD+ substrate is the key to successful cyclization. The pharmacological activities of these novel cIDPR derivatives were evaluated in both permeabilized and intact Jurkat T-lymphocytes. The results show that in permeabilized cells both 8-iodo 1g and 8-N3-N1-cIDPR 1d have an activity comparable to that of cADPR, while 8-iodo 1g and 8-phenyl-N1-cIDPR 1c have a small but significant effect in intact cells and can therefore be regarded as membrane-permeant; thus, cIDPR derivatives are emerging as important novel biological tools to study cADPR-mediated Ca2+ release in T-cells.
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Affiliation(s)
- Christelle Moreau
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
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29
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Zintek LB, Jahnke TS, Nair V. Synthesis and Conformational Studies of New Purine Isodideoxynucleosides. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319608002371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Lawrence B. Zintek
- a Department of Chemistry , The University of Iowa , Iowa City , Iowa , 52242
| | - Tamera S. Jahnke
- a Department of Chemistry , The University of Iowa , Iowa City , Iowa , 52242
| | - Vasu Nair
- a Department of Chemistry , The University of Iowa , Iowa City , Iowa , 52242
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30
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Hamm ML, Cholera R, Hoey CL, Gill TJ. Oligonucleotide incorporation of 8-thio-2'-deoxyguanosine. Org Lett 2006; 6:3817-20. [PMID: 15469357 DOI: 10.1021/ol0484097] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] 8-Thio-2'-deoxyguanosine (SdG) is a useful analogue of the abundant promutagen 8-oxo-2'-deoxyguanosine (OdG). Its synthesis and DNA incorporation using standard phosphoramidite chemistry is reported. To prevent oxidation during DNA synthesis, the sulfur was protected as a 2-(trimethylsilyl)ethyl sulfide. Subsequent treatment with TBAF yielded the desired 8-thiocarbonyl functionality. Melting studies with SdG revealed almost equal stabilities of SdG:dC and SdG:dA base pairs, lending insight into the base-pairing preferences of OdG.
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Affiliation(s)
- Michelle L Hamm
- Department of Chemistry, University of Richmond, Gottwald N-113, Richmond, Virginia 23173, USA.
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31
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Synthesis and properties of purine-type base-discriminating fluorescent (BDF) nucleosides: distinction of thymine by fluorescence-labeled deoxyadenosine derivatives. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.08.157] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Läppchen T, Hartog AF, Pinas VA, Koomen GJ, den Blaauwen T. GTP analogue inhibits polymerization and GTPase activity of the bacterial protein FtsZ without affecting its eukaryotic homologue tubulin. Biochemistry 2005; 44:7879-84. [PMID: 15910002 DOI: 10.1021/bi047297o] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The prokaryotic tubulin homologue FtsZ plays a key role in bacterial cell division. Selective inhibitors of the GTP-dependent polymerization of FtsZ are expected to result in a new class of antibacterial agents. One of the challenges is to identify compounds which do not affect the function of tubulin and various other GTPases in eukaryotic cells. We have designed a novel inhibitor of FtsZ polymerization based on the structure of the natural substrate GTP. The inhibitory activity of 8-bromoguanosine 5'-triphosphate (BrGTP) was characterized by a coupled assay, which allows simultaneous detection of the extent of polymerization (via light scattering) and GTPase activity (via release of inorganic phosphate). We found that BrGTP acts as a competitive inhibitor of both FtsZ polymerization and GTPase activity with a Ki for GTPase activity of 31.8 +/- 4.1 microM. The observation that BrGTP seems not to inhibit tubulin assembly suggests a structural difference of the GTP-binding pockets of FtsZ and tubulin.
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Affiliation(s)
- Tilman Läppchen
- Bioorganic Chemistry, Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, 1018 WS Amsterdam, The Netherlands
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33
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Bookser BC, Matelich MC, Ollis K, Ugarkar BG. Adenosine Kinase Inhibitors. 4. 6,8-Disubstituted Purine Nucleoside Derivatives. Synthesis, Conformation, and Enzyme Inhibition. J Med Chem 2005; 48:3389-99. [PMID: 15857145 DOI: 10.1021/jm048968j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
6,8-Disubstituted purine nucleosides were synthesized and evaluated as adenosine kinase inhibitors (AKIs). A method was developed to selectively substitute arylamines for halogens at C6 and C8 which utilizes alkali salts of arylamino anions. Regioselectivity was found to be counterion dependent. Potassium and sodium salts add selectively to C6 of 6-chloro-8-iodo-9-(2,3,5-tris-O-tert-butyldimethylsilyl-beta-d-ribofuranosyl)purine (7a) while lithium salts add to C6 and C8 positions. Differential 6,8-bisarylamin-N,N'-diylpurine nucleosides such as 8-anilin-N-yl-6-indolin-N-yl-9-(beta-d-ribofuranosyl)purine (10b) can be prepared by employing stepwise reactions of potassium and then lithium salts of different arylamino anions followed by fluoride ion-induced desilylation. Other C8-substituted compounds were prepared by way of either C8 lithiation chemistry or palladium cross-coupling reactions. Several of these compounds were potent AKIs (e.g. 10b, AK IC(50) = 0.019 microM) and are more potent than the previous best purine-based AKI 5'-deoxy-5'-aminoadenosine (AK IC(50) = 0.170 microM). AK inhibitory potency was greatest for those compounds with (1)H NMR evidence of a predominant anti glycosyl bond conformation, whereas most analogues adopt a syn conformation because of steric repulsions between the C8 substituent and the ribose group. The inhibitors are proposed to bind in the anti conformation with the hydrophobic C6 and C8 substituents contributing to AK affinity in a manner similar to the C4 and C5 aryl substituents of the potent diaryltubercidin nucleoside inhibitor series.
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Affiliation(s)
- Brett C Bookser
- Metabasis Therapeutics, Inc., 9390 Towne Centre Drive, San Diego, California 92121, USA. bookser@ mbasis.com
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34
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35
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Proctor DJ, Ma H, Kierzek E, Kierzek R, Gruebele M, Bevilacqua PC. Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate. Biochemistry 2005; 43:14004-14. [PMID: 15518549 DOI: 10.1021/bi048213e] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modified nucleotides allow fundamental energetic and kinetic properties of nucleic acids to be probed. Here, we demonstrate that an RNA hairpin containing the nucleotide analogue 8-bromoguanosine (8BrG or G), gcUUCGgc, has enhanced stability relative to the unmodified hairpin, with DeltaDeltaG(37)(degrees)= -0.69 +/- 0.15 kcal mol(-1) and DeltaT(M) = +6.8 +/- 1.4 degrees C. NMR spectroscopic data suggest that the enhanced stability of gcUUCGgc does not arise from the native state; laser temperature-jump experiments support this notion, as gcUUCGgc and gcUUCGgc have similar unfolding rate constants, but the folding rate constant of gcUUCGgc is 4.1-fold faster at 37.5 degrees C and 2.8-fold faster under isoenergetic conditions. On the basis of these findings, we propose that 8BrG reduces the conformational entropy of the denatured state, resulting in an accelerated conformational search for the native state and enhanced stability.
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Affiliation(s)
- David J Proctor
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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36
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Okamoto A, Ochi Y, Saito I. Fluorometric sensing of the salt-induced B–Z DNA transition by combination of two pyrene-labeled nucleobases. Chem Commun (Camb) 2005:1128-30. [PMID: 15726167 DOI: 10.1039/b416965d] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a new fluorescent DNA sensor containing two pyrene-labeled nucleobases, (Pet)G and (Py)C, and the fluorescence color was altered by the salt-induced B-Z DNA transition.
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Affiliation(s)
- Akimitsu Okamoto
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 615-8510, Japan.
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37
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Wyss PC, Schönholzer P, Arnold W. Synthese von Nucleosiden aus 2-substituierten Imidazolen. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19800630602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Okamoto A, Kanatani K, Ochi Y, Saito Y, Saito I. A novel fluorescent guanine derivative distinguishable of three structures, single strand, duplex, and quadruplex. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.05.136] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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39
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Schäfer HJ, Rathgeber G, Dose K, Kagawa Y. Photoaffinity cross-linking of F1
ATPase from the thermophilic bacterium PS3 by 3′-arylazido-β-alanyl-2-azido ATP. FEBS Lett 2001. [DOI: 10.1016/0014-5793(89)80972-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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40
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Fàbrega C, Macías MJ, Eritja R. Synthesis and properties of oligonucleotides containing 8-bromo-2'-deoxyguanosine. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:251-60. [PMID: 11393401 DOI: 10.1081/ncn-100002085] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The preparation of oligonucleotides containing 8-bromo-2'-deoxyguanosine is described. Substitution of G by 8-bromoguanine on an alternating CG decamer stabilizes the Z-form in such a way that the B-form was not observed. Melting temperatures showed that duplexes in which 8-bromo-2'-deoxyguanosine paired with natural bases were much less stable.
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Affiliation(s)
- C Fàbrega
- European Molecular Biology Laboratory, Heidelberg, Germany
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41
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Costas C, Yuriev E, Meyer KL, Guion TS, Hanna MM. RNA-protein crosslinking to AMP residues at internal positions in RNA with a new photocrosslinking ATP analog. Nucleic Acids Res 2000; 28:1849-58. [PMID: 10756182 PMCID: PMC103291 DOI: 10.1093/nar/28.9.1849] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new photocrosslinking purine analog was synthesized and evaluated as a transcription substrate for Escherichia coli RNA polymerase. This analog, 8-[(4-azidophenacyl)thio]adenosine 5'-triphosphate (8-APAS-ATP) contains an aryl azide photocrosslinking group that is attached to the ATP base via a sulfur-linked arm on the 8 position of the purine ring. This position is not involved in the normal Watson-Crick base pairing needed for specific hybridization. Although 8-APAS-ATP could not replace ATP as a substrate for transcription initiation, once stable elongation complexes were formed, 8-APAS-AMP could be site-specifically incorporated into the RNA, and this transcript could be further elongated, placing the photoreactive analog at internal positions in the RNA. Irradiation of transcription elongation complexes in which the RNA contained the analog exclusively at the 3' end of an RNA 22mer, or a 23mer with the analog 1 nt from the 3' end, produced RNA crosslinks to the RNA polymerase subunits that form the RNA 3' end binding site (beta, beta'). Both 8-APAS-AMP and the related 8-azido-AMP were subjected to conformational modeling as nucleoside monophosphates and in DNA-RNA hybrids. Surprisingly, the lowest energy conformation for 8-APAS-AMP was found to be syn, while that of 8-azido-AMP was anti, suggesting that the conformational properties and transcription substrate properties of 8-azido-ATP should be re-evaluated. Although the azide and linker together are larger in 8-APAS-ATP than in 8-N(3)-ATP, the flexibility of the linker itself allows this analog to adopt several different energetically favorable conformations, making it a good substrate for the RNA polymerase.
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Affiliation(s)
- C Costas
- Designer Genes, Inc., 8281 East Evans Road, Suite 104, Scottsdale, AZ 85260, USA
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Halbfinger E, Major DT, Ritzmann M, Ubl J, Reiser G, Boyer JL, Harden KT, Fischer B. Molecular recognition of modified adenine nucleotides by the P2Y(1)-receptor. 1. A synthetic, biochemical, and NMR approach. J Med Chem 1999; 42:5325-37. [PMID: 10639276 DOI: 10.1021/jm990156d] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The remarkably high potencies of 2-thioether-adenine nucleotides regarding the activation of the P2Y(1)-receptor (P2Y(1)-R) in turkey erythrocyte membranes represent some of the largest substitution-promoted increases in potencies over that of a natural receptor ligand. This paper describes the investigation regarding the origin of the high potency of these P2Y(1)-R ligands over that of ATP. For this study, an integrated approach was employed combining the synthesis of new ATP analogues, their biochemical evaluation, and their SAR analysis involving NMR experiments and theoretical calculations. These experiments and calculations were performed to elucidate the conformation and to evaluate the electronic nature of the investigated P2Y(1)-R ligands. ATP analogues synthesized included derivatives where C2 or C8 positions were substituted with electron-donating groups such as ethers, thioethers, or amines. The compounds were tested for their potency to induce P2Y(1)-R-mediated activation of phospholipase C in turkey erythrocytes and Ca(2+) response in rat astrocytes. 8-Substituted ATP and AMP derivatives had little or no effect on phospholipase C or on calcium levels, whereas the corresponding 2-substituted ATP analogues potently increased the levels of inositol phosphates and ¿Ca(2+)(i). AMP analogues were ineffective except for 2-butylthio-AMP which induced a small Ca(2+) response. P2Y(1)-R activity of these compounds was demonstrated by testing these ligands also on NG108-15 neuroblastoma x glioma hybrid cells. NMR data together with theoretical calculations imply that steric, rather than electronic, effects play a major role in ligand binding to the P2Y(1)-R. Hydrophobic interactions and H-bonds of the C2 substituent appear to be important determinants of a P2Y(1)-R ligand affinity.
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Affiliation(s)
- E Halbfinger
- Department of Chemistry, Gonda-Goldschmied Center, Bar-Ilan University, Ramat-Gan 52900, Israel
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Abstract
Adenosine kinase (AK) is a key enzyme in the regulation of extracellular adenosine and intracellular adenylate levels. Inhibitors of adenosine kinase elevate adenosine to levels that activate nearby adenosine receptors and produce a wide variety of therapeutically beneficial activities. Accordingly, AK is a promising target for new analgesic, neuroprotective, and cardioprotective agents. We determined the structure of human adenosine kinase by X-ray crystallography using MAD phasing techniques and refined the structure to 1.5 A resolution. The enzyme structure consisted of one large alpha/beta domain with nine beta-strands, eight alpha-helices, and one small alpha/beta-domain with five beta-strands and two alpha-helices. The active site is formed along the edge of the beta-sheet in the large domain while the small domain acts as a lid to cover the upper face of the active site. The overall structure is similar to the recently reported structure of ribokinase from Escherichia coli [Sigrell et al. (1998) Structure 6, 183-193]. The structure of ribokinase was determined at 1.8 A resolution and represents the first structure of a new family of carbohydrate kinases. Two molecules of adenosine were present in the AK crystal structure with one adenosine molecule located in a site that matches the ribose site in ribokinase and probably represents the substrate-binding site. The second adenosine site overlaps the ADP site in ribokinase and probably represents the ATP site. A Mg2+ ion binding site is observed in a trough between the two adenosine sites. The structure of the active site is consistent with the observed substrate specificity. The active-site model suggests that Asp300 is an important catalytic residue involved in the deprotonation of the 5'-hydroxyl during the phosphate transfer.
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Affiliation(s)
- I I Mathews
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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Giraldo J, Wodak SJ, van Belle D. Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods. J Mol Biol 1998; 283:863-82. [PMID: 9790845 DOI: 10.1006/jmbi.1998.2139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Barnase, an extracellular endoribonuclease from Bacillus amyloliquefaciens, hydrolyses single-stranded RNA. Its very low catalytic activity toward GpN dinucleotides, where N stands for any nucleoside, is markedly increased when a phosphate is added to the 3'-end, as in GpNp. Here we investigate the conformational properties of GpA and GpAp in solution, in order to determine whether differences in these properties may be related to the changes in enzymatic activity. Two independent 1.3 ns molecular dynamics trajectories are generated for each dinucleotide in the presence of explicit water molecules and counter ions. These trajectories are analysed by monitoring molecular properties, such as the solvent accessible surface area, the distance and orientation between the bases, the behaviour of torsion angles and formation of intramolecular H-bonds. To identify relevant correlations between these parameters, statistical techniques, comprising multiple regression, clustering and discriminant analysis are used. Results show that GpA has a significant propensity to form folded conformations (approximately 50%), fostered by a small number of intramolecular H-bonds, whereas GpAp remains essentially extended. The latter behaviour seems to be due to an H-bond between the terminal phosphate and adenosine ribose group, which restricts rotation about the adenine Agamma angle. We also find that GpA folding is induced by a concerted motion of specific torsion angles, which is closely coupled to the formation of a network of flexible hydrogen bonds. Finally, on the basis of an expression for barnase KM, which incorporates the folded/extended conformational equilibria of the dinucleotide substrates, it is argued that our findings on the differences between these equilibria, can qualitatively rationalize the experimentally measured differences in enzymatic properties.
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Affiliation(s)
- J Giraldo
- Unité de Conformation des Macromolécules Biologiques, Université Libre de Bruxelles CP160/16, Avenue F. D. Roosevelt, 50, Bruxelles, B-1050, Belgium
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Ramsinghani S, Koh DW, Amé JC, Strohm M, Jacobson MK, Slama JT. Syntheses of photoactive analogues of adenosine diphosphate (hydroxymethyl)pyrrolidinediol and photoaffinity labeling of poly(ADP-ribose) glycohydrolase. Biochemistry 1998; 37:7801-12. [PMID: 9601041 DOI: 10.1021/bi9730386] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Two isomeric azidoadenosyl analogues of adenosine diphosphate (hydroxymethyl)pyrrolidinediol [ADP-HPD; Slama, J. T., et al. (1995) J. Med. Chem. 38, 389-393] were synthesized as photoaffinity labels for poly(ADP-ribose) glycohydrolase. 8-Azidoadenosine diphosphate (hydroxymethyl)pyrrolidinediol (8-N3-ADP-HPD) inhibited the enzyme activity by 50% at ca. 1 microM, a concentration 80-fold lower than that where the isomeric 2-azidoadenosine diphosphate (hydroxymethyl)pyrrolidinediol did. [alpha-32P]-8-N3-ADP-HPD was therefore synthesized and used to photoderivatize poly(ADP-ribose) glycohydrolase. Irradiation of recombinant poly(ADP-ribose) glycohydrolase and low concentrations of [alpha-32P]-8-N3-ADP-HPD with short-wave UV light resulted in the covalent incorporation of the photoprobe into the protein, as demonstrated by gel electrophoresis followed by autoradiography or acid precipitation of the protein followed by scintillation counting. No photoincorporation occurred in the absence of UV light. The photoincorporation saturated at low concentrations of the photoprobe and photoprotection was observed in the presence of low concentrations of ADP-HPD, an indication of the specificity of the photoinsertion reaction. These results demonstrate that [alpha-32P]-8-N3-ADP-HPD can be used to specifically covalently photoderivatize the enzyme to characterize the polypetides that constitute the ADP-HPD binding site of poly(ADP-ribose) glycohydrolase. The photoincorporation reaction was further used to determine the ability of ADP-ribose polymers of varying size to compete with [alpha-32P]-8-N3-ADP-HPD for binding to the enzyme. Photoincorporation of [alpha-32P]-8-N3-ADP-HPD was inhibited by 80% in the presence of low concentrations of short, unbranched ADP-ribose oligomers (5-15 ADP-ribose units in length). No similar photoprotection was afforded by the addition of a high-molecular weight highly branched polymer. These results indicate that the photolabel shares a binding site with the short, linear polymer, but not with the long, highly branched polymer.
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Affiliation(s)
- S Ramsinghani
- Department of Medicinal and Biological Chemistry, College of Pharmacy, University of Toledo, Ohio 43606, USA
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Zhou L, Cho BP. Synthesis, characterization, and comparative conformational analysis of N-(deoxyguanosin-8-yl)aminopyrene adducts derived from the isomeric carcinogens 1-, 2-, and 4-nitropyrene. Chem Res Toxicol 1998; 11:35-43. [PMID: 9477224 DOI: 10.1021/tx970115p] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nitrated polycyclic aromatic hydrocarbons are mutagens/carcinogens that undergo in vivo activation by ring-oxidation and nitro-reduction pathways. We report the syntheses and comparative conformational analyses of N-(deoxyguanosin-8-yl)-n-aminopyrene adducts (dG-C8-n-AP, n = 1, 2, 4) derived from the three isomeric mononitropyrenes (1-, 2-, and 4-NP). The C8-amine nitrogens of these adducts have been enriched with 15N to examine the conformation about the pyrenyl-nitrogen and guanyl-nitrogen bonds that link the guanine and the pyrene moiety. These adducts are structurally isomeric, thus providing an interesting opportunity for systematic probing of the isomeric adduct conformations. Spectroscopic data indicated that the three isomeric aminopyrene adducts favor anti-glycosyl conformations, with C2'-endo (S) sugar puckering and a nearly planar conformation at the central amine nitrogen. The data further indicated differences in the extent of pi-electron conjugations about the pyrenyl-nitrogen bond, depending on the location of aminopyrene substitution. Thus while the 1- and 4-isomers both have substitution adjacent to a fused aromatic ring, the 2-isomer is highly symmetric and less sterically hindered. The 2-isomer adopts the most planar conformation, thereby having the most efficient pi-electron delocalization between the guanine and pyrene rings. The isomeric dG-C8-AP adducts and their nitro and amino precursors display physicochemical properties (HPLC retention time, UV pattern, 1H NMR data, mass fragmentation, etc.) distinctly dependent on their structures (1- and 4-isomers versus 2-isomer).
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Affiliation(s)
- L Zhou
- Department of Biomedical Sciences, College of Pharmacy, University of Rhode Island, Kingston 02881, USA
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Hosono K, Gozu H, Hosaka H, Sakamoto K, Yokoyama S, Takai K, Takaku H. Cleavage effect of oligoribonucleotides substituted at the cleavage sites with modified pyrimidine- and purine-nucleosides. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1354:211-8. [PMID: 9427530 DOI: 10.1016/s0167-4781(97)00099-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The precursor of an RNA molecule from T4-infected E. coli cells (p2Spl RNA) has the capacity to cleave itself at specific positions [UpA (139-140) and CpA (170-171)], within a putative loop and stem structure. This sequence-specific cleavage requires at least a monovalent cation and non-ionic detergents. In order to determine the influence of the pyrimidine and purine bases on these sequence-specific cleavage reactions, we studied the cleavage reactions of hairpin loop RNAs substituted at the cleavage sites with modified pyrimidine- and purine-nucleosides. The cleavage was affected by the 2'-hydroxyl groups and the bases of the pyrimidines, and the 6-amino group of the purine.
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Affiliation(s)
- K Hosono
- Department of Industrial Chemistry, Chiba Institute of Technology, Narashino, Japan
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48
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Lesiak KB, Uznanski B, Torrence PF. The solid-phase synthesis of 2'-5'-linked oligoriboadenylates containing 8-bromoadenine. Appl Biochem Biotechnol 1997; 67:33-44. [PMID: 9382489 DOI: 10.1007/bf02787839] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
To increase the accessibility of 8-bromo-2',5'-oligoadenylates, we developed a synthesis of 2'-5'-linked oligoriboadenylates containing varying numbers of 8-bromoadenosine residues based on the use of a CPG-LCA solid support and the phosphoramidite approach. Although N6-benzoyl protection was satisfactory for incorporation of nonmodified adenine residues into 2',5'-oligonucleotides, the effective incorporation of 8-bromoadenine into such 2',5'-linked oligomers required use of a non acyl protecting group. Amidine protection of the purine exocyclic amino function proved compatible with all aspects of the phophoramidite approach and with the hydroxyl protection groups employed.
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Affiliation(s)
- K B Lesiak
- Section on Biomedical Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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49
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Sugiyama H, Kawai K, Matsunaga A, Fujimoto K, Saito I, Robinson H, Wang AH. Synthesis, structure and thermodynamic properties of 8-methylguanine-containing oligonucleotides: Z-DNA under physiological salt conditions. Nucleic Acids Res 1996; 24:1272-8. [PMID: 8614630 PMCID: PMC145791 DOI: 10.1093/nar/24.7.1272] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Various oligonucleotides containing 8-methylguanine (m8G) have been synthesized and their structures and thermodynamic properties investigated. Introduction Of M8G into DNA sequences markedly stabilizes the Z conformation under low salt conditions. The hexamer d(CGC[M8G]CG)2 exhibits a CD spectrum characteristic of the Z conformation under physiological salt conditions. The NOE-restrained refinement unequivocally demonstrated that d(CGC[m8G]CG)2 adopts a Z structure with all guanines in the syn conformation. The refined NMR structure is very similar to the Z form crystal structure of d(CGCGCG)2, with a root mean square deviation of 0.6 between the two structures. The contribution of m8G to the stabilization of Z-DNA has been estimated from the mid-point NaCl concentrations for the B-Z transition of various m8G-containing oligomers. The presence of m8G in d(CGC[m8G]CG)2 stabilizes the Z conformation by at least deltaG = -0.8 kcal/mol relative to the unmodified hexamer. The Z conformation was further stabilized by increasing the number of m8Gs incorporated and destabilized by incorporating syn-A or syn-T, found respectively in the (A,T)-containing alternating and non-alternating pyrimidine-purine sequences. The results suggest that the chemically less reactive m8G base is a useful agent for studying molecular interactions of Z-DNA or other DNA structures that incorporate syn-G conformation.
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Affiliation(s)
- H Sugiyama
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Japan
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50
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Eason RG, Burkhardt DM, Phillips SJ, Smith DP, David SS. Synthesis and characterization of 8-methoxy-2'- deoxyadenosine-containing oligonucleotides to probe the syn glycosidic conformation of 2'-deoxyadenosine within DNA. Nucleic Acids Res 1996; 24:890-7. [PMID: 8600457 PMCID: PMC145706 DOI: 10.1093/nar/24.5.890] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The synthesis of 8-methoxy-2'-deoxyadenosine (moA) protected at N6 as an N,N-dimethylformamidine derivative and incorporation of the modified nucleoside into oligodeoxynucleotides via the phosphoramidite method are described. UV thermal denaturation studies were conducted on duplexes containing moA:G, moA:C and moA:T base pairs to determine the thermodynamic stability of duplexes containing moA relative to their adenosine (A)-containing counterparts. In the case of moA:G base pairs the effect of moA substitution is sequence dependent. In A:G mismatch-containing sequences, which have been shown by structural characterization to have a syn conformational preference at the glycosidic bond of A, moA substitution results in stabilization of the duplex. In contrast, in sequences where the A in the A:G mismatch has been shown to prefer the anti conformation moA substitution is destabilizing to the duplex. Thus moA may be a useful probe for investigating the conformational preferences of the N-glycosidic bond of adenosine within DNA. In addition, moA nucleoside is more resistant to acid-catalyzed depurination than previously described 8-bromo-2'-deoxyadenosine, allowing for facile incorporation into oligonucleotides via automated solid phase DNA synthesis.
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Affiliation(s)
- R G Eason
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
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