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Defaix C, Aymes A, Albe Slabi S, Basselin M, Mathé C, Galet O, Kapel R. A new size-exclusion chromatography method for fast rapeseed albumin and globulin quantification. Food Chem 2019; 287:151-159. [DOI: 10.1016/j.foodchem.2019.01.209] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/23/2019] [Accepted: 01/31/2019] [Indexed: 11/29/2022]
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Albe Slabi S, Mathé C, Framboisier X, Defaix C, Mesieres O, Galet O, Kapel R. A new SE-HPLC method for simultaneous quantification of proteins and main phenolic compounds from sunflower meal aqueous extracts. Anal Bioanal Chem 2019; 411:2089-2099. [PMID: 30810794 DOI: 10.1007/s00216-019-01635-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/16/2019] [Accepted: 01/21/2019] [Indexed: 12/22/2022]
Abstract
The aim of this research was to develop a method for simultaneous quantification of proteins and main polyphenolic compounds extracted from oleaginous meal by aqueous media. Size exclusion chromatography with a Biosep column (exclusion range from 1 to 300 kDa) and acetonitrile/water/formic acid (10:89.9:0.1 v/v) eluent at 0.6 mL min-1 yielded the most efficient separation of sunflower proteins and chlorogenic acid monoisomers (3-caffeoylquinic acid, 5-caffeoylquinic acid, and 4-caffeoylquinic acid). After a study of the stability of the extract components, the incorporation of a stabilization buffer (0.5 mol L-1 tris(hydroxymethyl)aminomethane-hydrochloric acid/1.0 mol L-1 sodium chloride at pH 7) was proposed to avoid polyphenol-protein interactions and/or isomeric transformation. The use of 214 nm as the wavelength for protein quantification was also included to minimize the effect of interference from polyphenol-protein interactions on the quantification. Under the used experimental conditions, the protein and chlorogenic acid monoisomer signals remained stable during 300 min at 20 °C (95-125% of the starting value). The developed method was validated and parameters such as specificity, sensitivity, precision, and accuracy were determined. The results from size exclusion chromatography correlated well with the results of protein determination by the reference Kjeldahl method. The proposed method was successfully applied for rapeseed extract analysis making simultaneous quantification of proteins and major rapeseed polyphenols (sinapine and sinapic acid) possible. Graphical abstract.
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Affiliation(s)
- Sara Albe Slabi
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, LRGP, F-54000, Nancy, France
- Avril Group, 75008, Paris, France
| | - Christelle Mathé
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, LRGP, F-54000, Nancy, France
| | - Xavier Framboisier
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, LRGP, F-54000, Nancy, France
| | - Claire Defaix
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, LRGP, F-54000, Nancy, France
- Avril Group, 75008, Paris, France
| | - Odile Mesieres
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, LRGP, F-54000, Nancy, France
| | | | - Romain Kapel
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, LRGP, F-54000, Nancy, France.
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Klein G, Mathé C, Biola-Clier M, Devineau S, Drouineau E, Hatem E, Marichal L, Alonso B, Gaillard JC, Lagniel G, Armengaud J, Carrière M, Chédin S, Boulard Y, Pin S, Renault JP, Aude JC, Labarre J. RNA-binding proteins are a major target of silica nanoparticles in cell extracts. Nanotoxicology 2016; 10:1555-1564. [PMID: 27705051 DOI: 10.1080/17435390.2016.1244299] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Upon contact with biological fluids, nanoparticles (NPs) are readily coated by cellular compounds, particularly proteins, which are determining factors for the localization and toxicity of NPs in the organism. Here, we improved a methodological approach to identify proteins that adsorb on silica NPs with high affinity. Using large-scale proteomics and mixtures of soluble proteins prepared either from yeast cells or from alveolar human cells, we observed that proteins with large unstructured region(s) are more prone to bind on silica NPs. These disordered regions provide flexibility to proteins, a property that promotes their adsorption. The statistical analyses also pointed to a marked overrepresentation of RNA-binding proteins (RBPs) and of translation initiation factors among the adsorbed proteins. We propose that silica surfaces, which are mainly composed of Si-O- and Si-OH groups, mimic ribose-phosphate molecules (rich in -O- and -OH) and trap the proteins able to interact with ribose-phosphate containing molecules. Finally, using an in vitro assay, we showed that the sequestration of translation initiation factors by silica NPs results in an inhibition of the in vitro translational activity. This result demonstrates that characterizing the protein corona of various NPs would be a relevant approach to predict their potential toxicological effects.
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Affiliation(s)
- Géraldine Klein
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France.,b LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay , Gif-sur-Yvette , France
| | - Christelle Mathé
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France.,b LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay , Gif-sur-Yvette , France
| | - Mathilde Biola-Clier
- c Univ. Grenoble Alpes, CEA, INAC-SyMMES, Laboratoire Lésions des Acides Nucléiques , Grenoble , France , and
| | - Stéphanie Devineau
- b LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay , Gif-sur-Yvette , France
| | - Emilie Drouineau
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
| | - Elie Hatem
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
| | - Laurent Marichal
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France.,b LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay , Gif-sur-Yvette , France
| | - Béatrice Alonso
- d CEA-Marcoule, DRF/IBITEC-S/SPI/Li2D, Laboratory 'Innovative technologies for Detection and Diagnostics', BP 17171 , Bagnols-sur-Cèze , France
| | - Jean-Charles Gaillard
- d CEA-Marcoule, DRF/IBITEC-S/SPI/Li2D, Laboratory 'Innovative technologies for Detection and Diagnostics', BP 17171 , Bagnols-sur-Cèze , France
| | - Gilles Lagniel
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
| | - Jean Armengaud
- d CEA-Marcoule, DRF/IBITEC-S/SPI/Li2D, Laboratory 'Innovative technologies for Detection and Diagnostics', BP 17171 , Bagnols-sur-Cèze , France
| | - Marie Carrière
- c Univ. Grenoble Alpes, CEA, INAC-SyMMES, Laboratoire Lésions des Acides Nucléiques , Grenoble , France , and
| | - Stéphane Chédin
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
| | - Yves Boulard
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
| | - Serge Pin
- b LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay , Gif-sur-Yvette , France
| | - Jean-Philippe Renault
- b LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay , Gif-sur-Yvette , France
| | - Jean-Christophe Aude
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
| | - Jean Labarre
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
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Alaoui AE, Faraj A, Pierra C, Boudou V, Johnson R, Mathé C, Gosselin G, Korba B, Imbach JL, Schinazi R, Sommadossi JP. Inhibition of Hepatitis B Virus Replication by Nucleoside Enantiomers of β-2′,3′-Dideoxypurine Analogues. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029600700508] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Various purine β-L-2′,3′-dideoxynucleoside analogues with both sugar and base modifications including β-L-ddG, β-L-ddl, β-L-ddA, 2′-azido-β-L-araddA, 2′-amino-β-L-araddA, 2′,5′-anhydro-β-L-araddA, 2′-azido-β-L-ddA, 2′-amino-β-L-ddA, 2′-fluoro-β-L-ddA, 3′-azido-β-L-ddA, 3′-amino-β-L-ddA, 3′-fluoro-β-L-ddA, 2,6-diamino-β-L-2′,3′-dideoxyfuranosylpurine, 6-cyclopropylamino-β-L-ddA, 2′-azido-6-N-triphenylphosphine-β-L-araddA, 2-amino-6-methylamino-β-L-2′,3′-dideoxyfuranosylpurine, 2-amino-6-cyclopropylamino-β-L-2′,3′-dideoxyfuranosylpurine, 2-amino-6-cyclopentylamino-β-L-2′,3′-dideoxyfuranosylpurine, 2′,3′-didehydro-β-L-ddA and 2′,3′-didehydro-6-N-triphenyl phosphine-β-L-ddA were synthesized and evaluated as potential inhibitors of hepatitis B virus (HBV) replication in HBV DNA-transfected human hepatoblastoma-derived Hep-G2 cells (2.2.15 cells). β-L-ddA, 2′-azido-β-L-ddA, 3′-azido-β-L-ddA, 2″,3′-didehydro-β-L-ddA (β-L-D4A) and a modified base of β-L-D4A, inhibited HBV replication in vitro. β-L-D4A was the more potent and selective antiHBV agent with a 50% effective concentration value of 0.1 μM and a selectivity index of 1800. On the basis of this finding, studies are in progress to synthesize new purine derivatives with the β-L unnatural configuration which hopefully will lead to identifying additional potent and highly selective anti-HBV agents.
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Affiliation(s)
- A.M. El Alaoui
- Department of Pharmacology and Toxicology, The Liver Center, and the Division of Clinical Pharmacology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - A. Faraj
- Department of Pharmacology and Toxicology, The Liver Center, and the Division of Clinical Pharmacology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - C. Pierra
- Laboratoire de Chimie Bioorganique, UMR CNRS 5625, Université de Montpellier II, 34095 Montpellier, France
| | - V. Boudou
- Laboratoire de Chimie Bioorganique, UMR CNRS 5625, Université de Montpellier II, 34095 Montpellier, France
| | - R. Johnson
- Laboratoire de Chimie Bioorganique, UMR CNRS 5625, Université de Montpellier II, 34095 Montpellier, France
| | - C. Mathé
- Laboratoire de Chimie Bioorganique, UMR CNRS 5625, Université de Montpellier II, 34095 Montpellier, France
| | - G. Gosselin
- Laboratoire de Chimie Bioorganique, UMR CNRS 5625, Université de Montpellier II, 34095 Montpellier, France
| | - B.E. Korba
- Division of Molecular Virology and Immunology, Georgetown University, Rockville, MD 20852, USA
| | - J.-L. Imbach
- Laboratoire de Chimie Bioorganique, UMR CNRS 5625, Université de Montpellier II, 34095 Montpellier, France
| | - R.F. Schinazi
- Georgia Research Center for AIDS and HIV Infections, Veterans Affairs Medical Center, Decatur, GA 30033, USA
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - J.-P. Sommadossi
- Department of Pharmacology and Toxicology, The Liver Center, and the Division of Clinical Pharmacology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Mathé C, Devineau S, Aude JC, Lagniel G, Chédin S, Legros V, Mathon MH, Renault JP, Pin S, Boulard Y, Labarre J. Structural determinants for protein adsorption/non-adsorption to silica surface. PLoS One 2013; 8:e81346. [PMID: 24282583 PMCID: PMC3839912 DOI: 10.1371/journal.pone.0081346] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 10/11/2013] [Indexed: 11/18/2022] Open
Abstract
The understanding of the mechanisms involved in the interaction of proteins with inorganic surfaces is of major interest in both fundamental research and applications such as nanotechnology. However, despite intense research, the mechanisms and the structural determinants of protein/surface interactions are still unclear. We developed a strategy consisting in identifying, in a mixture of hundreds of soluble proteins, those proteins that are adsorbed on the surface and those that are not. If the two protein subsets are large enough, their statistical comparative analysis must reveal the physicochemical determinants relevant for adsorption versus non-adsorption. This methodology was tested with silica nanoparticles. We found that the adsorbed proteins contain a higher number of charged amino acids, particularly arginine, which is consistent with involvement of this basic amino acid in electrostatic interactions with silica. The analysis also identified a marked bias toward low aromatic amino acid content (phenylalanine, tryptophan, tyrosine and histidine) in adsorbed proteins. Structural analyses and molecular dynamics simulations of proteins from the two groups indicate that non-adsorbed proteins have twice as many π-π interactions and higher structural rigidity. The data are consistent with the notion that adsorption is correlated with the flexibility of the protein and with its ability to spread on the surface. Our findings led us to propose a refined model of protein adsorption.
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Affiliation(s)
- Christelle Mathé
- Laboratoire de Radiolyse, SIS2M, IRAMIS and UMR3299 CEA-CNRS, Saclay, France
- Service de Biologie Intégrative et Génétique Moléculaire, iBiTec-S, FRE3377 CEA-CNRS-Université Paris-Sud, Saclay, France
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, UMR 8587 CNRS-Université Evry Val d'Essonne, Evry, France
| | - Stéphanie Devineau
- Laboratoire de Radiolyse, SIS2M, IRAMIS and UMR3299 CEA-CNRS, Saclay, France
| | - Jean-Christophe Aude
- Service de Biologie Intégrative et Génétique Moléculaire, iBiTec-S, FRE3377 CEA-CNRS-Université Paris-Sud, Saclay, France
| | - Gilles Lagniel
- Service de Biologie Intégrative et Génétique Moléculaire, iBiTec-S, FRE3377 CEA-CNRS-Université Paris-Sud, Saclay, France
| | - Stéphane Chédin
- Service de Biologie Intégrative et Génétique Moléculaire, iBiTec-S, FRE3377 CEA-CNRS-Université Paris-Sud, Saclay, France
| | - Véronique Legros
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, UMR 8587 CNRS-Université Evry Val d'Essonne, Evry, France
| | | | | | - Serge Pin
- Laboratoire de Radiolyse, SIS2M, IRAMIS and UMR3299 CEA-CNRS, Saclay, France
| | - Yves Boulard
- Service de Biologie Intégrative et Génétique Moléculaire, iBiTec-S, FRE3377 CEA-CNRS-Université Paris-Sud, Saclay, France
- Laboratoire Structure et Dynamique par Résonance Magnétique, SIS2M, IRAMIS and UMR3299 CEA-CNRS, Saclay, France
| | - Jean Labarre
- Service de Biologie Intégrative et Génétique Moléculaire, iBiTec-S, FRE3377 CEA-CNRS-Université Paris-Sud, Saclay, France
- * E-mail:
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Hureau C, Mathé C, Faller P, Mattioli TA, Dorlet P. Folding of the prion peptide GGGTHSQW around the copper(II) ion: identifying the oxygen donor ligand at neutral pH and probing the proximity of the tryptophan residue to the copper ion. J Biol Inorg Chem 2008; 13:1055-64. [DOI: 10.1007/s00775-008-0389-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Accepted: 05/13/2008] [Indexed: 10/22/2022]
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Mathé C, Weill CO, Mattioli TA, Berthomieu C, Houée-Levin C, Tremey E, Nivière V. Assessing the role of the active-site cysteine ligand in the superoxide reductase from Desulfoarculus baarsii. J Biol Chem 2007; 282:22207-16. [PMID: 17545670 DOI: 10.1074/jbc.m700279200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Superoxide reductase is a novel class of non-heme iron proteins that catalyzes the one-electron reduction of O(2)(.) to H(2)O(2), providing an antioxidant defense in some bacteria. Its active site consists of an unusual non-heme Fe(2+) center in a [His(4) Cys(1)] square pyramidal pentacoordination. In this class of enzyme, the cysteine axial ligand has been hypothesized to be an essential feature in the reactivity of the enzyme. Previous Fourier transform infrared spectroscopy studies on the enzyme from Desulfoarculus baarsii revealed that a protonated carboxylate group, proposed to be the side chain of Glu(114), is in interaction with the cysteine ligand. In this work, using pulse radiolysis, Fourier transform infrared, and resonance Raman spectroscopies, we have investigated to what extent the presence of this Glu(114) carboxylic lateral chain affects the strength of the S-Fe bond and the reaction of the iron active site with superoxide. The E114A mutant shows significantly modified pulse radiolysis kinetics for the protonation process of the first reaction intermediate. Resonance Raman spectroscopy demonstrates that the E114A mutation results in both a strengthening of the S-Fe bond and an increase in the extent of freeze-trapping of a Fe-peroxo species after treatment with H(2)O(2) by a specific strengthening of the Fe-O bond. A fine tuning of the strength of the S-Fe bond by the presence of Glu(114) appears to be an essential factor for both the strength of the Fe-O bond and the pK(a) value of the Fe(3+)-peroxo intermediate species to form the reaction product H(2)O(2).
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Affiliation(s)
- Christelle Mathé
- Laboratoire de Chimie et Biologie des Métaux, iRTSV-CEA Grenoble/CNRS/Université Joseph Fourier, 17 Avenue des Martyrs, 38054 Grenoble Cedex 9, France
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Osyczka A, Zhang H, Mathé C, Rich PR, Moser CC, Dutton PL. Role of the PEWY Glutamate in Hydroquinone−Quinone Oxidation−Reduction Catalysis in the Qo Site of Cytochrome bc1. Biochemistry 2006; 45:10492-503. [PMID: 16939201 DOI: 10.1021/bi060013a] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The glutamic acid residue of the conserved PEWY motif of the Q(o) site of cytochrome bc(1) is widely discussed as central to reversible Q(o) site catalysis of two-electron, two-proton hydroquinone-quinone oxidation-reduction. Extensive mutation of this glutamate (E295) to A, V, F, H, K, and Q in purple photosynthetic Rhodobacter capsulatus results in hydroquinone oxidation rates that are between 5 and 50-fold slower than that in the wild type. However, the mutants show little or no detectable effects on hydroquinone or quinone exchange and binding at the Q(o) site nor on subsequent Q(o) site-mediated redox equilibria in the c-chain and b-chain from pH 5-10. Lack of effects of mutations on the E(m)/pH plots rules out involvement of E295 in the strong electron-proton coupling evident in either the FeS center or heme b(L). These detailed equilibrium and kinetic analyses demonstrate that E295 is not irreplaceable in the Q(o) site catalytic mechanism. Rather, E295 and several other Q(o) site residues that can also be widely varied and still support hydroquinone oxidation illustrate the considerable resilience of Q(o) site activity to mutational change in Q(o) site environs. Residues and water molecules appear to cooperate in providing a physical and chemical environment supporting hydroquinone oxidation rates comparable to those seen in nonprotein aqueous environments at electrodes. We suggest that residues at the Q(o) site (and, possibly, other respiratory and photosynthetic quinone and oxygen binding sites) are a product of natural selection primarily acting not to lower catalytic barriers according to the traditional view of enzymatic catalysis but rather to develop specificity by raising barriers in defense of semiquinone loss or energy wasting short-circuit reactions.
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Affiliation(s)
- Artur Osyczka
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Pennsylvania 19104, USA.
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Mathé C, Nivière V, Houée-Levin C, Mattioli TA. Fe3+–η2–peroxo species in superoxide reductase from Treponema pallidum. Comparison with Desulfoarculus baarsii. Biophys Chem 2006; 119:38-48. [PMID: 16084640 DOI: 10.1016/j.bpc.2005.06.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2005] [Revised: 06/29/2005] [Accepted: 06/29/2005] [Indexed: 11/16/2022]
Abstract
Superoxide reductases (SORs) are superoxide (O2-)-detoxifying enzymes that catalyse the reduction of O2- into hydrogen peroxide. Three different classes of SOR have been reported on the basis of the presence or not of an additional N-terminal domain. They all share a similar active site, with an unusual non-heme Fe atom coordinated by four equatorial histidines and one axial cysteine residues. Crucial catalytic reaction intermediates of SOR are purported to be Fe(3+)-(hydro)peroxo species. Using resonance Raman spectroscopy, we compared the vibrational properties of the Fe3+ active site of two different classes of SOR, from Desulfoarculus baarsii and Treponema pallidum, along with their ferrocyanide and their peroxo complexes. In both species, rapid treatment with H2O2 results in the stabilization of a side-on high spin Fe(3+)-(eta(2)-OO) peroxo species. Comparison of these two peroxo species reveals significant differences in vibrational frequencies and bond strengths of the Fe-O2 (weaker) and O-O (stronger) bonds for the T. pallidum enzyme. Thus, the two peroxo adducts in these two SORs have different stabilities which are also seen to be correlated with differences in the Fe-S coordination strengths as gauged by the Fe-S vibrational frequencies. This was interpreted from structural variations in the two active sites, resulting in differences in the electron donating properties of the trans cysteine ligand. Our results suggest that the structural differences observed in the active site of different classes of SORs should be a determining factor for the rate of release of the iron-peroxo intermediate during enzymatic turnover.
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Affiliation(s)
- Christelle Mathé
- Laboratoire de Biophysique du Stress Oxydant, SBE and CNRS URA 2096, Département de Biologie Joliot Curie, CEA Saclay, 91191 Gif-sur-Yvette cedex, France
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Mathé C, Nivière V, Mattioli TA. Fe3+-Hydroxide Ligation in the Superoxide Reductase from Desulfoarculus baarsii Is Associated with pH Dependent Spectral Changes. J Am Chem Soc 2005; 127:16436-41. [PMID: 16305229 DOI: 10.1021/ja053808y] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Superoxide reductase (SOR) catalyzes the reduction of O2*- to H2O2. Its active site consists of a non-heme Fe2+ center in an unusual square-pyramidal [His4 Cys] coordination. Like many SORs, the electronic absorption band corresponding to the oxidized active site of the SOR from Desulfoarculus baarsii exhibits a pH-dependent alkaline transition changing from ca. 644 to 560 nm as the pH increases and with an apparent pKa of 9.0. Variants in which the conserved amino acids glutamate 47 and lysine 48 were replaced by the neutral residues alanine (E47A) and isoleucine (K48I), respectively, exhibited the same alkaline transition but at lower apparent pKa values of 6.7 and 7.6, respectively. Previous work [Nivière, V.; Asso, M.; Weill, C. O.; Lombard, M.; Guigliarelli, B.; Favaudon, V.; Houée-Levin, C. Biochemistry 2004, 43, 808-818] has shown that this alkaline transition is associated with the protonation/deprotonation of an unidentified base, B-, which is neither E47 nor K48. In this work, we show by resonance Raman spectroscopy that at basic pH a high-spin Fe3+-OH species is formed at the active site. The presence of the HO- ligand was directly associated with an absorption band maximum at 560 nm, whereas upon protonation, the band shifts to 644 nm. With respect to our previous work, B- can be identified with this high-spin Fe3+-OH species, which upon protonation results in a water molecule at the active site. Implications for the SOR catalytic cycle are proposed.
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Affiliation(s)
- Christelle Mathé
- Laboratoire de Biophysique du Stress Oxydant, SBE/DBJC and CNRS URA 2096, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France
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Horner O, Mouesca JM, Oddou JL, Jeandey C, Nivière V, Mattioli TA, Mathé C, Fontecave M, Maldivi P, Bonville P, Halfen JA, Latour JM. Mössbauer Characterization of an Unusual High-Spin Side-On Peroxo−Fe3+ Species in the Active Site of Superoxide Reductase from Desulfoarculus baarsii. Density Functional Calculations on Related Models. Biochemistry 2004; 43:8815-25. [PMID: 15236590 DOI: 10.1021/bi0498151] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Superoxide reductase (SOR) is an Fe protein that catalyzes the reduction of superoxide to give H(2)O(2). Recently, the mutation of the Glu47 residue into alanine (E47A) in the active site of SOR from Desulfoarculus baarsii has allowed the stabilization of an iron-peroxo species when quickly reacted with H(2)O(2) [Mathé et al. (2002) J. Am. Chem. Soc. 124, 4966-4967]. To further investigate this non-heme peroxo-iron species, we have carried out a Mössbauer study of the (57)Fe-enriched E47A SOR from D. baarsii reacted quickly with H(2)O(2). Considering the Mössbauer data, we conclude, in conjunction with the other spectroscopic data available and with the results of density functional calculations on related models, that this species corresponds to a high-spin side-on peroxo-Fe(3+) complex. This is one of the first examples of such a species in a biological system for which Mössbauer parameters are now available: delta(/Fe) = 0.54 (1) mm/s, DeltaE(Q) = -0.80 (5) mm/s, and the asymmetry parameter eta = 0.60 (5) mm/s. The Mössbauer and spin Hamiltonian parameters have been evaluated on a model from the side-on peroxo complex (model 2) issued from the oxidized iron center in SOR from Pyrococcus furiosus, for which structural data are available in the literature [Yeh et al. (2000) Biochemistry 39, 2499-2508]. For comparison, similar calculations have been carried out on a model derived from 2 (model 3), where the [CH(3)-S](1)(-) group has been replaced by the neutral [NH(3)](0) group [Neese and Solomon (1998) J. Am. Chem. Soc. 120, 12829-12848]. Both models 2 and 3 contain a formally high-spin Fe(3+) ion (i.e., with empty minority spin orbitals). We found, however, a significant fraction ( approximately 0.6 for 2, approximately 0.8 for 3) of spin (equivalently charge) spread over two occupied (minority spin) orbitals. The quadrupole splitting value for 2 is found to be negative and matches quite well the experimental value. The computed quadrupole tensors are rhombic in the case of 2 and axial in the case of 3. This difference originates directly from the presence of the thiolate ligand in 2. A correlation between experimental isomer shifts for Fe(3+) mononuclear complexes with computed electron densities at the iron nucleus has been built and used to evaluate the isomer shift values for 2 and 3 (0.56 and 0.63 mm/s, respectively). A significant increase of isomer shift value is found upon going from a methylthiolate to a nitrogen ligand for the Fe(3+) ion, consistent with covalency effects due to the presence of the axial thiolate ligand. Considering that the isomer shift value for 3 is likely to be in the 0.61-0.65 mm/s range [Horner et al. (2002) Eur. J. Inorg. Chem., 3278-3283], the isomer shift value for a high-spin eta(2)-O(2) Fe(3+) complex with an axial thiolate group can be estimated to be in the 0.54-0.58 mm/s range. The occurrence of a side-on peroxo intermediate in SOR is discussed in relation to the recent data published for a side-on peroxo-Fe(3+) species in another biological system [Karlsson et al. (2003) Science 299, 1039-1042].
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Affiliation(s)
- Olivier Horner
- Département Réponse et Dynamique Cellulaires, Laboratoire de Physicochimie des Métaux en Biologie, UMR CEA/CNRS/Université Joseph Fourier 5155, France
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12
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Lescot M, Rombauts S, Zhang J, Aubourg S, Mathé C, Jansson S, Rouzé P, Boerjan W. Annotation of a 95-kb Populus deltoides genomic sequence reveals a disease resistance gene cluster and novel class I and class II transposable elements. Theor Appl Genet 2004; 109:10-22. [PMID: 15085260 DOI: 10.1007/s00122-004-1621-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2003] [Accepted: 01/29/2004] [Indexed: 05/24/2023]
Abstract
Poplar has become a model system for functional genomics in woody plants. Here, we report the sequencing and annotation of the first large contiguous stretch of genomic sequence (95 kb) of poplar, corresponding to a bacterial artificial chromosome clone mapped 0.6 centiMorgan from the Melampsora larici-populina resistance locus. The annotation revealed 15 putative genetic objects, of which five were classified as hypothetical genes that were similar only with expressed sequence tags from poplar. Ten putative objects showed similarity with known genes, of which one was similar to a kinase. Three other objects corresponded to the toll/interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat class of plant disease resistance genes, of which two were predicted to encode an amino terminal nuclear localization signal. Four objects were homologous to the Ty1/ copia family of class I transposable elements, one of which was designated Retropop and interrupted one of the disease resistance genes. Two other objects constituted a novel Spm-like class II transposable element, which we designated Magali.
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Affiliation(s)
- M Lescot
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, 9052 Gent, Belgium
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13
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Bertherat J, Bouchard P, Chanson P, Benoît A, Bourgeon M, Brémont C, Kahal Z, Mathé C, Requeda E. [Management of acromegaly in 2003]. Ann Endocrinol (Paris) 2003; 64:I-IV. [PMID: 12773933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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14
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Mathé C, Mattioli TA, Horner O, Lombard M, Latour JM, Fontecave M, Nivière V. Identification of iron(III) peroxo species in the active site of the superoxide reductase SOR from Desulfoarculus baarsii. J Am Chem Soc 2002; 124:4966-7. [PMID: 11982354 DOI: 10.1021/ja025707v] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The active site of superoxide reductase SOR consists of an Fe2+ center in an unusual [His4 Cys1] square-pyramidal geometry. It specifically reduces superoxide to produce H2O2. Here, we have reacted the SOR from Desulfoarculus baarsii directly with H2O2. We have found that its active site can transiently stabilize an Fe3+-peroxo species that we have spectroscopically characterized by resonance Raman. The mutation of the strictly conserved Glu47 into alanine results in a stabilization of this Fe3+-peroxo species, when compared to the wild-type form. These data support the hypothesis that the reaction of SOR proceeds through such a Fe3+-peroxo intermediate. This also suggests that Glu47 might serve to help H2O2 release during the reaction with superoxide.
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Affiliation(s)
- Christelle Mathé
- Laboratoire de Biophysique du Stress Oxydant, SBE/DBJC CEA/SACLAY, 91191 Gif-sur-Yvette Cedex, France
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15
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Salvetti R, Marchand A, Pregnolato M, Verri A, Spadari S, Focher F, Briant M, Sommadossi JP, Mathé C, Gosselin G. 5-(Trifluoromethyl)-beta-l-2'-deoxyuridine, the L-enantiomer of trifluorothymidine: stereospecific synthesis and antiherpetic evaluations. Bioorg Med Chem 2001; 9:1731-8. [PMID: 11425574 DOI: 10.1016/s0968-0896(01)00062-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
As a part of our ongoing work on beta-L-nucleoside analogues as potential antiviral drugs, we have synthesized 5-(trifluoromethyl)-beta-L-2'-deoxyuridine (L-TFT), the hitherto unknown L-enantiomer of trifluorothymidine (CF(3)dUrd, TFT). We have also studied the effect of L-TFT on human and herpes simplex virus (HSV) type 1 and 2 thymidine kinases, and human thymidine phosphorylase, as well as its anti-HSV-1 and anti-HSV-2 activities in cell cultures. L-TFT has been found: (i) to inhibit HSV-1 TK with activity comparable to TFT, with no effect on human TK, (ii) to be phosphorylated by the viral enzyme with similar efficiency to TFT, (iii) to be resistant, in contrast to TFT, to hydrolysis by human thymidine phosphorylase. Unfortunately, when evaluated in cell cultures, L-TFT did not show any anti-HSV-1 and anti-HSV-2 activities.
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Affiliation(s)
- R Salvetti
- Dipartimento di Chimica Farmaceutica, Università degli Studi, I-27100 Pavia, Italy
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Griffon JF, Mathé C, Faraj A, Aubertin AM, De Clercq E, Balzarini J, Sommadossi JP, Gosselin G. Stereospecific synthesis and biological evaluations of beta-L-pentofuranonucleoside derivatives of 5-fluorouracil and 5-fluorocytosine. Eur J Med Chem 2001; 36:447-60. [PMID: 11451533 DOI: 10.1016/s0223-5234(01)01238-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the search for new chemotherapeutic agents, we have focused our work on the synthesis and the study of several unnatural beta-L-nucleoside analogues. In this paper, we report on the synthesis of beta-L-pentofuranonucleosides (and their 2'-deoxy derivatives) of 5-fluorouracil and their inhibitory effects on the proliferation of several murine and human tumor cells. The corresponding 5-fluorocytosine derivatives were also synthesized and their anti-HIV and anti-HBV activities have been evaluated.
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Affiliation(s)
- J F Griffon
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, UMR 5625 CNRS-UM II, Université Montpellier II, case courrier 008, Place Eugène Bataillon, F-34095 Montpellier, France
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Jeannot F, Mathé C, Gosselin G. Synthesis and antiviral evaluation of 3'-C-trifluoromethyl nucleoside derivatives bearing adenine as the base. Nucleosides Nucleotides Nucleic Acids 2001; 20:755-8. [PMID: 11563109 DOI: 10.1081/ncn-100002423] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
3'-deoxy-3'-C-trifluoromethyl- (3), 2',3'-dideoxy-3'-C-trifluoromethyl- (5) and 2',3'-dideoxy-2',3'-didehydro-3'-C-trifluoromethyladenosine (6) derivatives have been synthesized and their antiviral properties examined. All these derivatives were stereospecifically prepared by glycosylation of adenine with a trifluoromethyl sugar precursor (1), followed by appropriate chemical modifications. The prepared compounds were tested for their activity against HIV, but they did not show an antiviral effect.
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Affiliation(s)
- F Jeannot
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, UMR 5625 CNRS-UM II, Université Montpellier II, Place E. Bataillon, 34095 Montpellier, France
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18
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Salvetti R, Pregnolato M, Verri A, Focher F, Spadari S, Marchand A, Mathé C, Gosselin G. Synthesis and in vitro activity of D- and L-enantiomers of 5-(trifluoromethyl)uracil nucleoside derivatives. Nucleosides Nucleotides Nucleic Acids 2001; 20:1123-5. [PMID: 11562969 DOI: 10.1081/ncn-100002502] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Recently, beta-L-nucleoside analogues have emerged as a new class of sugar modified nucleosides with potential antiviral and/or antitumoral activity. As a part of our ongoing research on this topic, we decided to synthesize 5-CF3-beta-L-dUrd (7), the hitherto unknown L-enantiomer of Trifluridine, an antiherpetic drug approved by FDA but only used in topical applications due to concomitant cytotoxicity. 5-CF3-beta-L-dUrd (7) as well as some other related L-nucleoside derivatives were stereospecifically prepared and tested in vitro against viral (HSV-1 and HSV-2) and human thymidine kinases (TK).
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Affiliation(s)
- R Salvetti
- Università di Pavia, V. Taramelli 12, 27100 Pavia, Italy
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19
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Boudou-Vivet V, Mathé C, Gosselin G. Synthesis and antiviral evaluation of C-4-hydrazide derivatives of 2',3'-dideoxycytidine. Nucleosides Nucleotides Nucleic Acids 2001; 20:1029-32. [PMID: 11562952 DOI: 10.1081/ncn-100002484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Syntheses of three hitherto unknown derivatives of 2',3'-dideoxycytidine, namely C-4-(salicylic hydrazide)-ddC, C-4-(N-butyloxycarbonyl-isoleucine hydrazide)-ddC and its N-unprotected chlorhydrate salt have been carried out. These compounds do not induce inhibition of HIV-1 replication in cell culture experiments. Nevertheless, the modifications on the base moiety increased in all cases the lipophilicity of the parent molecule with an acceptable water solubility compared to ddC.
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Affiliation(s)
- V Boudou-Vivet
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, UMR 5625 CNRS-UM II, Université Montpellier II, Place E. Bataillon, 34095 Montpellier, France
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20
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Gaubert G, Mathé C, Imbach J, Eriksson S, Vincenzetti S, Salvatori D, Vita A, Maury G. Unnatural enantiomers of 5-azacytidine analogues: syntheses and enzymatic properties. Eur J Med Chem 2000; 35:1011-9. [PMID: 11137229 DOI: 10.1016/s0223-5234(00)01184-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Although 2'-deoxy-beta-D-5-azacytidine (Decitabine) and beta-D-5-azacytidine display potent antileukemic properties, their therapeutic use is hampered by their sensitivity to nucleophiles and to deamination catalysed by cytidine deaminase. As shown earlier [Shafiee M., Griffon J.-F., Gosselin G., Cambi A., Vincenzetti S., Vita A., Erikson S., Imbach J.-L., Maury G., Biochem. Pharmacol. 56 (1998) 1237-1242], beta-L-enantiomers of cytidine derivatives are resistant to cytidine deaminase. We thus synthesized several 5-azacytosine beta-L-nucleoside analogues to evaluate their enzymatic and biological properties. 2'-Deoxy-beta-L-5-azacytidine (L-Decitabine), beta-L-5-azacytidine, 1-(beta-L-xylo-furanosyl)5-azacytosine, and 1-(2-deoxy-beta-L-threo-pentofuranosyl)5-azacytosine were stereospecifically prepared starting from L-ribose and L-xylose. D- and L-enantiomers of 2'-deoxy-beta-5-azacytidine were weak substrates of human recombinant deoxycytidine kinase (dCK) compared to beta-D-deoxycytidine, whereas both enantiomers of beta-5-azacytidine or the L-xylo-analogues were not substrates of the enzyme. As expected, none of the presently reported derivatives of beta-L-5-azacytidine was a substrate of human recombinant cytidine deaminase (CDA). The prepared compounds were tested for their activity against HIV and HBV and they did not show any significant activity or cytotoxicity. In the case of L-Decitabine, this suggests that the enantioselectivities of concerned enzymes other than dCK and CDA might not be favourable.
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Affiliation(s)
- G Gaubert
- UMR 5625 du CNRS, Département de Chimie, Université Montpellier II, Place Bataillon, 34095 5, Montpellier Cedex, France
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21
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Mathé C, Gosselin G. Synthesis and antiviral evaluation of the beta-L-enantiomers of some thymine 3'-deoxypentofuranonucleoside derivatives. Nucleosides Nucleotides Nucleic Acids 2000; 19:1517-30. [PMID: 11200256 DOI: 10.1080/15257770008045443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
3'-Deoxy-beta-L-erythro- (3), 3'-deoxy-beta-L-threo- (6), 2'-fluoro- (7) and 2'-azido-2',3'-dideoxy-beta-L-erythro- (10) pentofuranonucleoside derivatives of thymine have been synthesized and their antiviral properties examined. All these derivatives were stereospecifically prepared by glycosylation of thymine with a suitable peracylated 3-deoxy-L-erythro-pentofuranose sugar (1), followed by appropriate chemical modifications. The prepared compounds were tested for their activity against HIV, but they did not show an antiviral effect.
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Affiliation(s)
- C Mathé
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, UMR 5625 CNRS-UM-II, Université Montpellier II, Sciences et Techniques du Languedoc, France
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22
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Liu WQ, Vidal M, Mathé C, Périgaud C, Garbay C. Inhibition of the ras-dependent mitogenic pathway by phosphopeptide prodrugs with antiproliferative properties. Bioorg Med Chem Lett 2000; 10:669-72. [PMID: 10762050 DOI: 10.1016/s0960-894x(00)00077-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Phosphopeptide prodrugs bearing two S-acyl-2-thioethyl (SATE) biolabile phosphate protections were developed. They are capable to inhibit the Shc/Grb2 interaction and MAP kinases (ERK1 and ERK2) phosphorylation in cellular assay. The S-acetyl-2-thioethyl (MeSATE) analogue showed an IC50 of 1 microM in the inhibition of the colony formation of tumor cell line NIH3T3/HER2.
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Affiliation(s)
- W Q Liu
- Laboratoire de Pharmacochimie Moléculaire et Structurale, U266 INSERM, UMR 8600 CNRS, Faculté de Pharmacie, Paris, France
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Abstract
Gene prediction methods for eukaryotic genomes still are not fully satisfying. One way to improve gene prediction accuracy, proven to be relevant for prokaryotes, is to consider more than one model of genes. Thus, we used our classification of Arabidopsis thaliana genes in two classes (CU(1) and CU(2)), previously delineated according to statistical features, in the GeneMark gene identification program. For each gene class, as well as for the two classes combined, a Markov model was developed (respectively, GM-CU(1), GM-CU(2) and GM-all) and then used on a test set of 168 genes to compare their respective efficiency. We concluded from this analysis that GM-CU(1) is more sensitive than GM-CU(2) which seems to be more specific to a gene type. Besides, GM-all does not give better results than GM-CU(1) and combining results from GM-CU(1) and GM-CU(2) greatly improve prediction efficiency in comparison with predictions made with GM-all only. Thus, this work confirms the necessity to consider more than one gene model for gene prediction in eukaryotic genomes, and to look for gene classes in order to build these models.
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Affiliation(s)
- C Mathé
- Laboratorium voor Genetica, Department of Genetics, Flanders Interuniversity Institute for Biotechnology (VIB), Universiteit Gent, B-9000, Gent, Belgium
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Abstract
A coding sequence is defined as a DNA sequence coding the primary structure of a protein (a polypeptide). Such a sequence must satisfy a specific constraint, which consists in coding a functional protein. As the genetic code is degenerated, there exists, for a given polypeptide, a set of synonymous sequences which would code the same polypeptide. Translation conditional models are being defined on such sets. The aim of this paper is to give a common formalism. Besides the codon bias model, a few other conditional models will be defined. Statistical estimators and comparison methods will be briefly presented. These models can be used for gene classification, or to find out, in a real sequence, remarkable features. An example will be presented on Escherichia coli genes.
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25
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Mathé C, Imbach JL, Gosselin G. 1,2-di-O-acetyl-5-O-benzoyl-3-deoxy-L-erythro-pentofuran ose, a convenient precursor for the stereospecific synthesis of nucleoside analogues with the unnatural beta-L-configuration. Carbohydr Res 2000; 323:226-9. [PMID: 10782306 DOI: 10.1016/s0008-6215(99)00267-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The title compound 1,2-di-O-acetyl-5-O-benzoyl-3-deoxy-L-erythro-pentofuranose (5), a useful precursor for the stereospecific synthesis of beta-L-nucleoside analogues as potential antiviral agents, has been synthesised by a multi-step reaction sequence from L-xylose with a 38% overall yield. The preparation involved conversion of L-xylose to 1,2-O-isopropylidene-alpha-L-xylofuranose which, upon selective 5-O-benzoylation and subsequent radical deoxygenation, provided the protected 3-deoxy sugar derivative. Finally, cleavage of the acetonide group gave the resulting 5-O-benzoyl-3-deoxy-L-erythro-pentose which was acetylated to afford crystalline alpha,beta-5.
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Affiliation(s)
- C Mathé
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, UMR CNRS-UM II 5625, Université Montpellier II, France.
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Marchand A, Mathé C, Imbach JL, Gosselin G. Synthesis and antiviral evaluation of unnatural beta-L-enantiomers of 3'-fluoro- and 3'-azido-2',3'-dideoxyguanosine derivatives. Nucleosides Nucleotides Nucleic Acids 2000; 19:205-17. [PMID: 10772710 DOI: 10.1080/15257770008033004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
3'-fluoro-2',3'-dideoxy- (3) and 3'-azido-2',3'-dideoxy- (4) beta-L-ribofuranonucleoside derivatives of guanine have been synthesized and their antiviral properties examined. All these derivatives were regioselectively and stereospecifically prepared by glycosylation of 2-N-acetyl-6-O-(diphenylcarbamoyl)guanine 5 with a suitable peracylated L-xylo-furanose sugar 6, followed by appropriate chemical modifications. The prepared compounds were tested for their activity against HIV and HBV viruses, but they did not show significant activity.
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Affiliation(s)
- A Marchand
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, U.M.R. CNRS 5625, Université de Montpellier II, France
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Pavy N, Rombauts S, Déhais P, Mathé C, Ramana DV, Leroy P, Rouzé P. Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences. Bioinformatics 1999; 15:887-99. [PMID: 10743555 DOI: 10.1093/bioinformatics/15.11.887] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The annotation of the Arabidopsis thaliana genome remains a problem in terms of time and quality. To improve the annotation process, we want to choose the most appropriate tools to use inside a computer-assisted annotation platform. We therefore need evaluation of prediction programs with Arabidopsis sequences containing multiple genes. RESULTS We have developed AraSet, a data set of contigs of validated genes, enabling the evaluation of multi-gene models for the Arabidopsis genome. Besides conventional metrics to evaluate gene prediction at the site and the exon levels, new measures were introduced for the prediction at the protein sequence level as well as for the evaluation of gene models. This evaluation method is of general interest and could apply to any new gene prediction software and to any eukaryotic genome. The GeneMark.hmm program appears to be the most accurate software at all three levels for the Arabidopsis genomic sequences. Gene modeling could be further improved by combination of prediction software. AVAILABILITY The AraSet sequence set, the Perl programs and complementary results and notes are available at http://sphinx.rug.ac.be:8080/biocomp/napav/. CONTACT Pierre.Rouze@gengenp.rug.ac.be.
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Affiliation(s)
- N Pavy
- Laboratoire associé de l'INRA, France
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28
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Maga G, Amacker M, Hübscher U, Gosselin G, Imbach JL, Mathé C, Faraj A, Sommadossi JP, Spadari S. Structural determinants of HIV-1 reverse transcriptase stereoselectivity towards (beta)-L-deoxy- and dideoxy-pyrimidine nucleoside triphosphates: molecular basis for the combination of L-dideoxynucleoside analogs with non-nucleoside inhibitors in anti HIV chemotherapy. Nucleosides Nucleotides 1999; 18:795-805. [PMID: 10432681 DOI: 10.1080/15257779908041566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We have compared the HIV-1 RT mutants containing the single substitutions L100I, K103N, V106A, V179D, Y181I and Y188L, known to confer NNI-resistance in treated patients, to HIV-1 RT wt for their sensitivity towards inhibition by D- and L-deoxy- and dideoxy-nucleoside tiphosphates. The results showed a differential effect of the substitutions on the affinity for both D- and L-enantiomers of deoxy- and dideoxy-nucleoside triphosphates and provide a rationale for the utilization of L-dideoxynucleoside analogs with NNI in combination chemotherapy.
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Affiliation(s)
- G Maga
- Istituto di Genetica Biochimica el Evoluzionistica, Consiglio Nazionale delle Ricerche, Pavia, Italy
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Abstract
In the search for inhibitors of HIV integrase, the enzyme involved in the integration of viral DNA into host DNA, we have synthesized and studied a number of analogs of the heterocyclic molecule, chloroquine.
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Affiliation(s)
- C Mathé
- Department of Chemistry, University of Iowa, Iowa City 52242, USA
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30
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Maga G, Amacker M, Hübscher U, Gosselin G, Imbach JL, Mathé C, Faraj A, Sommadossi JP, Spadari S. Molecular basis for the enantioselectivity of HIV-1 reverse transcriptase: role of the 3'-hydroxyl group of the L-(beta)-ribose in chiral discrimination between D- and L-enantiomers of deoxy- and dideoxy-nucleoside triphosphate analogs. Nucleic Acids Res 1999; 27:972-8. [PMID: 9927728 PMCID: PMC148275 DOI: 10.1093/nar/27.4.972] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In order to identify the basis for the relaxed enantio-selectivity of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) and to evaluate possible cross-resistance patterns between L-nucleoside-, D-nucleoside- and non-nucleoside RT inhibitors, to be utilised in anti-HIV-1 combination therapy, we applied an in vitro approach based on the utilisation of six recom-binant HIV-1 RT mutants containing single amino acid substitutions known to confer Nevirapine resistance in treated patients. The mutants were compared on different RNA/DNA and DNA/DNA substrates to the wild type (wt) enzyme for their sensitivity towards inhibition by the D- and L-enantiomers of 2'-deoxy- and 2',3'-dideoxynucleoside triphosphate analogs. The results showed that the 3'-hydroxyl group of the L-(beta)-2'-deoxyribose moiety caused an unfavourable steric hindrance with critic residues in the HIV-1 RT active site and this steric barrier was increased by the Y181I mutation. Elimination of the 3'-hydroxyl group removed this hindrance and significantly improved binding to the HIV-1 RT wt and to the mutants. These results demonstrate the critical role of both the tyrosine 181 of RT and the 3'-position of the sugar ring, in chiral discrimination between D- and L-nucleoside triphosphates. Moreover, they provide an important rationale for the combination of D- and L-(beta)-dideoxynucleoside analogs with non-nucleoside RT inhibitors in anti-HIV chemotherapy, since non-nucleosideinhibitors resistance mutations did not confer cross-resistance to dideoxynucleoside analogs.
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Affiliation(s)
- G Maga
- Institute of Biochemical and Evolutionary Genetics, National Research Council, I-27100, Pavia, Italy.
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31
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Mathé C, Peresetsky A, Déhais P, Van Montagu M, Rouzé P. Classification of Arabidopsis thaliana gene sequences: clustering of coding sequences into two groups according to codon usage improves gene prediction. J Mol Biol 1999; 285:1977-91. [PMID: 9925779 DOI: 10.1006/jmbi.1998.2451] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
While genomic sequences are accumulating, finding the location of the genes remains a major issue that can be solved only for about a half of them by homology searches. Prediction methods are thus required, but unfortunately are not fully satisfying. Most prediction methods implicitly assume a unique model for genes. This is an oversimplification as demonstrated by the possibility to group coding sequences into several classes in Escherichia coli and other genomes. As no classification existed for Arabidopsis thaliana, we classified genes according to the statistical features of their coding sequences. A clustering algorithm using a codon usage model was developed and applied to coding sequences from A. thaliana, E. coli, and a mixture of both. By using it, Arabidopsis sequences were clustered into two classes. The CU1 and CU2 classes differed essentially by the choice of pyrimidine bases at the codon silent sites: CU2 genes often use C whereas CU1 genes prefer T. This classification discriminated the Arabidopsis genes according to their expressiveness, highly expressed genes being clustered in CU2 and genes expected to have a lower expression, such as the regulatory genes, in CU1. The algorithm separated the sequences of the Escherichia-Arabidopsis mixed data set into five classes according to the species, except for one class. This mixed class contained 89 % Arabidopsis genes from CU1 and 11 % E. coli genes, mostly horizontally transferred. Interestingly, most genes encoding organelle-targeted proteins, except the photosynthetic and photoassimilatory ones, were clustered in CU1. By tailoring the GeneMark CDS prediction algorithm to the observed coding sequence classes, its quality of prediction was greatly improved. Similar improvement can be expected with other prediction systems.
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Affiliation(s)
- C Mathé
- Laboratorium voor Genetica Department of Genetics, Flanders Interuniversity Institute for Biotechnology (VIB), Universiteit Gent, Gent, B-9000, Belgium
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Mathé C, Gosselin G, Bergogne MC, Aubertin AM, Obert G, Kirn A, Imbach JL. Synthesis and Antiviral Evaluation of 3'-Deoxy-β-L-erythro-pentofuranosyl Nucleosides of the Five Naturally Occurring Nucleic Acid Bases. Nucleosides, Nucleotides & Nucleic Acids 1995. [DOI: 10.1080/15257779508012424] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Schinazi RF, Gosselin G, Faraj A, Korba BE, Liotta DC, Chu CK, Mathé C, Imbach JL, Sommadossi JP. Pure nucleoside enantiomers of beta-2',3'-dideoxycytidine analogs are selective inhibitors of hepatitis B virus in vitro. Antimicrob Agents Chemother 1994; 38:2172-4. [PMID: 7811039 PMCID: PMC284704 DOI: 10.1128/aac.38.9.2172] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
(-)-beta-L-2',3'-Dideoxycytidine (beta-L-DDC), (+)-beta-D-2',3'-dideoxycytidine (beta-D-DDC), (-)-beta-L-2',3'-dideoxy-5-fluorocytidine (beta-L-FDDC), (-)-beta-L-2',3'-dideoxy-5-fluoro-3'-thiacytidine (beta-L-FTC), and (+)-beta-D-1,3-dioxolane-5-fluorocytidine (beta-D-FDOC) were evaluated for their anti-hepatitis B virus (anti-HBV) activities in HBV-transfected human liver cells (2.2.15). The order of decreasing potency for the compounds at the 90% effect level was beta-D-FDOC > beta-L-FTC > beta-L-FDDC approximately beta-L-DDC >> beta-D-DDC. Inhibition of HBV in transfected liver cells by the cytosine nucleosides was selective. The beta-L-nucleoside-5'-triphosphates were consistently more potent inhibitors of woodchuck hepatitis virus DNA polymerase than the corresponding natural beta-D-enantiomers.
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Affiliation(s)
- R F Schinazi
- Georgia VA Research Center for AIDS and HIV Infections, Veterans Affairs Medical Center, Decatur 30033
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Gosselin G, Schinazi RF, Sommadossi JP, Mathé C, Bergogne MC, Aubertin AM, Kirn A, Imbach JL. Anti-human immunodeficiency virus activities of the beta-L enantiomer of 2',3'-dideoxycytidine and its 5-fluoro derivative in vitro. Antimicrob Agents Chemother 1994; 38:1292-7. [PMID: 8092827 PMCID: PMC188200 DOI: 10.1128/aac.38.6.1292] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The L enantiomer of 2',3'-dideoxycytidine (DDC) was recently shown to inhibit selectively human immunodeficiency virus type 1 (HIV-1) in vitro. In the current study, the potent anti-HIV activity of L-DDC was confirmed and extended to several HIV-1 and HIV-2 strains in various cell culture systems, including primary human lymphocytes and macrophages. Furthermore, its 5-fluoro congener, beta-L-2',3'-dideoxy-5-fluorocytidine (L-FDDC), was found to have more potent anti-HIV activity and a higher therapeutic index in acutely infected human peripheral blood mononuclear cells. These compounds had no marked activity against HIV-1 isolates resistant to the oxathiolane pyrimidine nucleosides (-)-beta-L-2',3'-dideoxy-5-fluoro-3'-thiacytidine [(-)-FTC] and (-)-beta-L-2',3'-dideoxy-3'-thiacytidine, but 3'-azido-3'-deoxythymidine (AZT)-resistant viruses were susceptible to L-DDC and L-FDDC. Cytotoxicity studies with human myeloid progenitor cells indicated that L-DDC and L-FDDC had median inhibitory concentrations comparable to those of AZT, DDC, and FDDC, but L-DDC and L-FDDC were significantly less toxic than AZT, DDC, and FDDC when erythroid progenitor cells were used. L-FDDC had the highest selectivity indices (6,000 and 9,000 for erythroid and myeloid progenitor cells, respectively) of all the compounds evaluated. Further preclinical development of L-FDDC is warranted in order to determine its potential usefulness in the treatment of HIV infections.
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Affiliation(s)
- G Gosselin
- Laboratoire de Chimie Bioorganique, URA Centre National de la Recherche Scientifique 488, Université de Montpellier II, Sciences et Techniques du Languedoc, France
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35
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Gosselin G, Mathé C, Bergogne MC, Aubertin AM, Kirn A, Schinazi RF, Sommadossi JP, Imbach JL. Enantiomeric 2',3'-dideoxycytidine derivatives are potent human immunodeficiency virus inhibitors in cell cultures. C R Acad Sci III 1994; 317:85-9. [PMID: 7987696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
2',3'-dideoxy-beta-L-cytidine (beta-L-DDC) and its 5-fluoro derivative (beta-L-5-F-DDC) have been stereospecifically synthesized by a multi-step reaction sequence from L-xylose and their anti-HIV properties examined. Among these two L-enantiomers, the hitherto unknown beta-L-5-F-DDC emerged as a potent anti-HIV-1 and HIV-2 compound in different cell culture systems, with selectivity indices similar or superior to those of the currently licensed drug DDC which has the natural beta-D configuration.
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Affiliation(s)
- G Gosselin
- Laboratoire de Chimie Bioorganique, URA CNRS 488, Université de Montpellier-II, Sciences et Techniques du Languedoc, Montpellier, France
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36
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Mahé A, Destelle JM, Bruet A, Mathé C, Tuot D, Taveau JF, Quevauvilliers J, Fendler JP. [Deep venous thromboses in erysipelas of the leg. A prospective study of 40 cases]. Presse Med 1992; 21:1022-4. [PMID: 1387215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The treatment of lover limb erysipelas rests on antibiotic therapy directed against streptococci, but the necessity of prescribing a concomitant anticoagulant treatment has not yet been established. The incidence of deep vein thrombosis in patients with erysipelas of the leg in unknown. In a prospective study of 40 patients presenting with this type of skin disease, we looked for deep vein thrombosis, using systematically pulsed Doppler vein exploration combined with ultrasonography and, if necessary, a second Doppler examination and a phlebography. Six cases of deep vein thrombosis were diagnosed. This complication was observed in 5 patients at high risk for deep venous thrombosis; it had never been foreseen at clinical examination.
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Affiliation(s)
- A Mahé
- Service de Médecine interne/Néphrologie, Centre hospitalier intercommunal de Poissy
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Mahé A, Couturier J, Mathé C, Lebras F, Bruet A, Fendler JP. Minimal focal dermal hypoplasia in a man: a case of father-to-daughter transmission. J Am Acad Dermatol 1991; 25:879-81. [PMID: 1761764 DOI: 10.1016/0190-9622(91)70274-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Focal dermal hypoplasia is a rare genetic disorder characterized by diffuse and specific cutaneous lesions. Multiple visceral abnormalities are frequently associated. A minimal form of the disease (only cutaneous and localized to one thigh) is reported in the father of a woman who had typical focal dermal hypoplasia.
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Affiliation(s)
- A Mahé
- Department of Internal Medicine and Dermatology, Centre Hospitalier Intercommunal de Poissy, France
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Mahé A, Bruet A, Mathé C, Hillion Y, Fendler JP. [Systemic scleroderma and primary bronchopulmonary adenocarcinoma. A new case]. Rev Med Interne 1991; 12:375-6. [PMID: 1771318 DOI: 10.1016/s0248-8663(05)80849-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The authors report a case of systemic sclerosis associated with primary lung adenocarcinoma. This association has previously been reported in patients with old scleroderma complicated by extensive fibrosis of the lungs allegedly regarded as a precancerous lesion. The case reported here is of interest owing to the absence of pulmonary fibrosis.
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Affiliation(s)
- A Mahé
- Service de Médecine Interne et Néphrologie, Centre Hospitalier Intercommunal Léon Touhladjian, Poissy
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Duron F, Talbot JN, Piketty ML, Mathé C, Milhaud G, Aubert P. [Circadian rhythm of TSH in cases of extinctive thyroid nodules with normal circulating TSH]. Presse Med 1990; 19:134. [PMID: 2137593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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40
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Bruet A, Sei JF, Mathé C, Teillet L, Fendler JP. [Pyoderma gangrenosum and Vaquez's disease complicated by myelofibrosis. Apropos of a case in a 75-year-old patient]. Rev Med Interne 1989; 10:349-51. [PMID: 2678344 DOI: 10.1016/s0248-8663(89)80034-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- A Bruet
- Service de médecine interne et néphrologie, CHI Poissy
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41
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Cheymol J, Freyss-Béguin M, Bourdais J, Mathé C. [Action of some procaine derivatives on the resistance to hypoxia and on the temperature of the white rat]. Therapie 1965; 20:917-29. [PMID: 5845208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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