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1. 2-Nitrobenzyl Esters of Penam and Cephem Derivatives as Inhibitors of Penicillin-Binding Proteins

Author: UCL - SST/IMCN/MOST - Molecules, Solids and Reactivity, ULg - Centre d’Ingénierie des Protéines (CIP), Brulé, Cédric, Grugier, Jérôme, Brans, Alain, Joris, Bernard, Sauvage, Eric, Dive, Georges, Marchand-Brynaert, Jacqueline, UCL - SST/IMCN/MOST - Molecules, Solids and Reactivity, ULg - Centre d’Ingénierie des Protéines (CIP), Brulé, Cédric, Grugier, Jérôme, Brans, Alain, Joris, Bernard, Sauvage, Eric, Dive, Georges, and Marchand-Brynaert, Jacqueline
Abstract: Nitroveratrole esters (i.e. 4,5-dimethoxy-2-nitrobenzyl (NV) esters) of penicillin and cephalosporin derivatives have been prepared in the course of a program dedicated to photosensitive protein microarrays. Surprisingly, some molecules revealed to be acylating inhibitors of R39 and BlaR-CTD proteins (two representative Penicillin Binding Proteins (PBPs)), while being bad substrates of beta-lactamases (bacterial defense enzymes). Electrostatic potential maps and docking experiments showed that the 2-nitro group of NV esters could play the role of a carboxylate in the penam series.
Published: 2013

2. Discovery and preliminary SARs of keto-indoles as novel indoleamine 2,3-dioxygenase (IDO) inhibitors

Author: FUNDP - Autre, Euroscreen SA - Gosselies, Belgique, ULg - Centre d’Ingénierie des Protéines, UCL - SSS/DDUV - Institut de Duve, UCL - SSS/LDRI - Louvain Drug Research Institute, Dolusic, Eduard, Larrieu, Pierre, Blanc, Sébastien, Sapunaric, Frédéric, Pouyez, Jenny, Moineaux, Laurence, Colette, Delphine, Stroobant, Vincent, Pilotte, Luc, Colau, Didier, Ferain, Thierry, Fraser, Graeme, Galleni, Moreno, Frère, Jean-Marie, Masereel, Bernard, Van den Eynde, Benoît, Wouters, Johan, Frédérick, Raphaël, FUNDP - Autre, Euroscreen SA - Gosselies, Belgique, ULg - Centre d’Ingénierie des Protéines, UCL - SSS/DDUV - Institut de Duve, UCL - SSS/LDRI - Louvain Drug Research Institute, Dolusic, Eduard, Larrieu, Pierre, Blanc, Sébastien, Sapunaric, Frédéric, Pouyez, Jenny, Moineaux, Laurence, Colette, Delphine, Stroobant, Vincent, Pilotte, Luc, Colau, Didier, Ferain, Thierry, Fraser, Graeme, Galleni, Moreno, Frère, Jean-Marie, Masereel, Bernard, Van den Eynde, Benoît, Wouters, Johan, and Frédérick, Raphaël
Abstract: Indoleamine 2,3-dioxygenase (IDO) is an important new therapeutic target for the treatment of cancer. With the aim of discovering novel IDO inhibitors, a virtual screen was undertaken and led to the discovery of the keto-indole derivative 1a endowed with an inhibitory potency in the micromolar range. Detailed kinetics were performed and revealed an uncompetitive inhibition profile. Preliminary SARs were drawn in this series and corroborated the putative binding orientation as suggested by docking.
Published: 2011

3. Indol-2-yl ethanones as novel indoleamine 2,3-dioxygenase (IDO) inhibitors

Author: FUNDP - Autre, UCL - SSS/DDUV - Institut de Duve, Euroscreen SA - Gosselies, Belgique, ULg - Centre d’Ingénierie des Protéines, UCL - SSS/LDRI - Louvain Drug Research Institute, Dolusic, Eduard, Larrieu, Pierre, Blanc, Sébastien, Sapunaric, Frédéric, Norberg, Bernadette, Moineaux, Laurence, Colette, Delphine, Stroobant, Vincent, Pilotte, Luc, Colau, Didier, Ferain, Thierry, Fraser, Graeme, Galleni, Moreno, Frère, Jean-Marie, Masereel, Bernard, Van den Eynde, Benoît, Wouters, Johan, Frédérick, Raphaël, FUNDP - Autre, UCL - SSS/DDUV - Institut de Duve, Euroscreen SA - Gosselies, Belgique, ULg - Centre d’Ingénierie des Protéines, UCL - SSS/LDRI - Louvain Drug Research Institute, Dolusic, Eduard, Larrieu, Pierre, Blanc, Sébastien, Sapunaric, Frédéric, Norberg, Bernadette, Moineaux, Laurence, Colette, Delphine, Stroobant, Vincent, Pilotte, Luc, Colau, Didier, Ferain, Thierry, Fraser, Graeme, Galleni, Moreno, Frère, Jean-Marie, Masereel, Bernard, Van den Eynde, Benoît, Wouters, Johan, and Frédérick, Raphaël
Abstract: Indoleamine 2,3-dioxygenase (IDO) is a heme dioxygenase which has been shown to be involved in the pathological immune escape of diseases such as cancer. The synthesis and structure-activity relationships (SAR) of a novel series of IDO inhibitors based on the indol-2-yl ethanone scaffold is described. In vitro and in vivo biological activities have been evaluated, leading to compounds with IC(50) values in the micromolar range in both tests. Introduction of small substituents in the 5- and 6-positions of the indole ring, indole N-methylation and variations of the aromatic side chain are all well tolerated. An iron coordinating group on the linker is a prerequisite for biological activity, thus corroborating the virtual screening results.
Published: 2011

4. New acylnitroso compounds for the asymmetric oxyamination of dienes

Author: UCL - SC/CHIM - Département de chimie, Université de Liège - Centre d'Ingénierie des Protéines, Gouverneur, Veronique, McCarthy, SJ, Mineur, C., Belotti, D, Dive, G., Ghosez, Léon, UCL - SC/CHIM - Département de chimie, Université de Liège - Centre d'Ingénierie des Protéines, Gouverneur, Veronique, McCarthy, SJ, Mineur, C., Belotti, D, Dive, G., and Ghosez, Léon
Abstract: A series of new enantiomerically pure acylnitroso compounds have been prepared and tested as dienophiles for the asymmetric oxyamination of dienes. Very high selectivities were obtained with acylnitroso compounds derived from diphenylmethoxymethyl pyrrolidine 2c, the C-2-symmetric pyrrolidines 2d-e and camphorsultam 2f. (C) 1998 Elsevier Science Ltd. All rights reserved.
Published: 1998

5. New Gamma-lactam Homologs of Penems

Author: UCL - SC/CHIM - Département de chimie, Université de Liège - Centre d'Ingénierie des Protéines, Marchand-Brynaert, Jacqueline, Couplet, Blandine, Dive, Georges, Ghosez, Léon, UCL - SC/CHIM - Département de chimie, Université de Liège - Centre d'Ingénierie des Protéines, Marchand-Brynaert, Jacqueline, Couplet, Blandine, Dive, Georges, and Ghosez, Léon
Abstract: 3-Ethylthiohomopenems 5a and 5b were prepared from alpha-amino-gamma-butyrolactone. Compound 5a showed weak antibacterial properties.
Published: 1993

6. Squalamine and Aminosterol Mimics Inhibit the Peptidoglycan Glycosyltransferase Activity of PBP1b

Author: Boes, Adrien, Brunel, Jean Michel, Derouaux, Adeline, Kerff, Frédéric, Bouhss, Ahmed, Touze, Thierry, Breukink, Eefjan, Terrak, Mohammed, Sub Membrane Biochemistry & Biophysics, Membrane Biochemistry and Biophysics, Brunel, Jean Michel, Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, Université de Liège, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Membranes et cibles thérapeutiques (MCT), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Biomédicale des Armées (IRBA), Centre d’Ingénierie des Protéines [Université de Liège] = Centre for Protein Engineering [University of Liège] (CIP), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Structure et activité des biomolécules normales et pathologiques (SABNP), Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Department of Chemical Biology and Organic Chemistry, Utrecht University [Utrecht], Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Aix Marseille Université (AMU), Centre d'Ingénierie des Protéines, Université de Liège-Institut de Chimie B6, Sub Membrane Biochemistry & Biophysics, Membrane Biochemistry and Biophysics, Enveloppes Bactériennes et Antibiotiques (ENVBAC), Département Microbiologie (Dpt Microbio), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Department Biochemistry of Membranes
Subjects: 0301 basic medicine, Microbiology (medical), Glycan, [SDV]Life Sciences [q-bio], Peptidoglycan, cationic aminosterols, 010402 general chemistry, 01 natural sciences, Microbiology, Biochemistry, Bacterial cell structure, Article, 03 medical and health sciences, chemistry.chemical_compound, Pharmacology, Toxicology and Pharmaceutics(all), squalamine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Glycosyltransferase, Pharmacology (medical), General Pharmacology, Toxicology and Pharmaceutics, chemistry.chemical_classification, Pharmacology, Squalamine, biology, Lipid II, lcsh:RM1-950, Peptidoglycan glycosyltransferase activity, 0104 chemical sciences, 030104 developmental biology, Enzyme, Toxicology and Pharmaceutics(all), lcsh:Therapeutics. Pharmacology, Infectious Diseases, PBP1b, chemistry, Cationic aminosterols, biology.protein, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases
Abstract: International audience; Peptidoglycan (PG) is an essential polymer of the bacterial cell wall and a major antibacterial target. Its synthesis requires glycosyltransferase (GTase) and transpeptidase enzymes that, respectively, catalyze glycan chain elongation and their cross-linking to form the protective sacculus of the bacterial cell. The GTase domain of bifunctional penicillin-binding proteins (PBPs) of class A, such as Escherichia coli PBP1b, belong to the GTase 51 family. These enzymes play an essential role in PG synthesis, and their specific inhibition by moenomycin was shown to lead to bacterial cell death. In this work, we report that the aminosterol squalamine and mimic compounds present an unexpected mode of action consisting in the inhibition of the GTase activity of the model enzyme PBP1b. In addition, selected compounds were able to specifically displace the lipid II from the active site in a fluorescence anisotropy assay, suggesting that they act as competitive inhibitors.
Published: 2020
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7. Crystal structure of undecaprenyl-pyrophosphate phosphatase and its role in peptidoglycan biosynthesis

Author: Martin Caffrey, Frédéric Kerff, Chia-Ying Huang, R. Warshamanage, Vincent Olieric, Nicole Howe, Meitian Wang, Meriem El Ghachi, Phillip J. Stansfeld, Dietmar Weichert, Thierry Touzé, Centre d'Ingénierie des Protéines, Université de Liège, Trinity College Dublin, The Swiss Light Source (SLS) (SLS-PSI), Paul Scherrer Institute (PSI), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Biochemistry [Oxford], University of Oxford [Oxford], ANR-11-BSV3-0002,BACTOPRENYL,Elucidation du métabolisme de l'undécaprényl phosphate, un lipide essentiel pour la biosynthèse des polymères de la paroi bactérienne(2011), Centre d’Ingénierie des Protéines [Université de Liège] = Centre for Protein Engineering [University of Liège] (CIP), and University of Oxford
Subjects: 0301 basic medicine, Science, Molecular Sequence Data, General Physics and Astronomy, Peptidoglycan, Crystallography, X-Ray, Models, Biological, 01 natural sciences, Article, Protein Structure, Secondary, General Biochemistry, Genetics and Molecular Biology, Bacterial cell structure, 03 medical and health sciences, chemistry.chemical_compound, Polyisoprenyl Phosphates, 0103 physical sciences, QD, Amino Acid Sequence, Pyrophosphatases, lcsh:Science, Multidisciplinary, 010304 chemical physics, Escherichia coli Proteins, General Chemistry, Flippase, Periplasmic space, QP, Phosphoric Monoester Hydrolases, Cell biology, QR, A-site, 030104 developmental biology, chemistry, Membrane protein, Structural biology, Cytoplasm, [SDV.IB]Life Sciences [q-bio]/Bioengineering, lcsh:Q
Abstract: As a protective envelope surrounding the bacterial cell, the peptidoglycan sacculus is a site of vulnerability and an antibiotic target. Peptidoglycan components, assembled in the cytoplasm, are shuttled across the membrane in a cycle that uses undecaprenyl-phosphate. A product of peptidoglycan synthesis, undecaprenyl-pyrophosphate, is converted to undecaprenyl-phosphate for reuse in the cycle by the membrane integral pyrophosphatase, BacA. To understand how BacA functions, we determine its crystal structure at 2.6 Å resolution. The enzyme is open to the periplasm and to the periplasmic leaflet via a pocket that extends into the membrane. Conserved residues map to the pocket where pyrophosphorolysis occurs. BacA incorporates an interdigitated inverted topology repeat, a topology type thus far only reported in transporters and channels. This unique topology raises issues regarding the ancestry of BacA, the possibility that BacA has alternate active sites on either side of the membrane and its possible function as a flippase., Bacterial cell wall components are assembled in a transmembrane cycle that involves the membrane integral pyrophosphorylase, BacA. Here the authors solve the crystal structure of BacA which shows an interdigitated inverted topology repeat that hints towards a flippase function for BacA.
Published: 2018
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8. Crystal structure and biochemical characterization of the transmembrane PAP2 type phosphatidylglycerol phosphate phosphatase from Bacillus subtilis

Author: Alexandre Lambion, L. Vogeley, Dominique Mengin-Lecreulx, Sophie Roure, Juan-Carlos Rengifo-Gonzalez, Eric Sauvage, Sabine Peslier, Thierry Touzé, Paulette Charlier, Meriem El Ghachi, Frédéric Kerff, Maryline Foglino, Nicole Howe, Annick Guiseppi, Martin Caffrey, Guillaume Manat, François Delbrassine, Rodolphe Auger, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Trinity College Dublin, Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Schneider Electric (Grenoble), Schneider Electric, Transporteurs membranaires, chimioresistance et drug-design (TMCD2), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Club Rhumatismes et Inflammation, Centre d'Ingénierie des Protéines, Université de Liège-Institut de Chimie B6, Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Laboratoire de chimie bactérienne ( LCB ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Transporteurs membranaires, chimioresistance et drug-design ( TMCD2 ), Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Schneider Electric ( SE), Centre d’Ingénierie des Protéines [Université de Liège] = Centre for Protein Engineering [University of Liège] (CIP), and Université de Liège
Subjects: Models, Molecular, 0301 basic medicine, 030106 microbiology, Phosphatase, Phosphatidate Phosphatase, Bacillus subtilis, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Glycerophospholipids, Crystallography, X-Ray, Substrate Specificity, [ SDE ] Environmental Sciences, 03 medical and health sciences, Cellular and Molecular Neuroscience, chemistry.chemical_compound, Catalytic Domain, Hydrolase, Escherichia coli, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Pharmacology, chemistry.chemical_classification, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, [ SDV.BC ] Life Sciences [q-bio]/Cellular Biology, Cell Membrane, Genetic Complementation Test, Active site, Phosphatidylglycerols, Cell Biology, Phosphatidic acid, biology.organism_classification, Transmembrane protein, Enzyme, Solubility, Biochemistry, chemistry, Genes, Bacterial, [SDE]Environmental Sciences, Mutagenesis, Site-Directed, biology.protein, Molecular Medicine, [ SDV.GEN ] Life Sciences [q-bio]/Genetics
Abstract: International audience; Type 2 phosphatidic acid phosphatases (PAP2s) can be either soluble or integral membrane enzymes. In bacteria, integral membrane PAP2s play major roles in the metabolisms of glycerophospholipids, undecaprenyl-phosphate (C-55-P) lipid carrier and lipopolysaccharides. By in vivo functional experiments and biochemical characterization we show that the membrane PAP2 coded by the Bacillus subtilis yodM gene is the principal phosphatidylglycerol phosphate (PGP) phosphatase of B. subtilis. We also confirm that this enzyme, renamed bsPgpB, has a weaker activity on C-55-PP. Moreover, we solved the crystal structure of bsPgpB at 2.25 resolution, with tungstate (a phosphate analog) in the active site. The structure reveals two lipid chains in the active site vicinity, allowing for PGP substrate modeling and molecular dynamic simulation. Site-directed mutagenesis confirmed the residues important for substrate specificity, providing a basis for predicting the lipids preferentially dephosphorylated by membrane PAP2s.
Published: 2017
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9. The Role of Active Site Flexible Loops in Catalysis and of Zinc in Conformational Stability of Bacillus cereus 569/H/9 β-Lactamase*

Author: Andreas Ioannis Karsisiotis, Andr eacute Matagne, Micha eumll Nigen, Christina Redfield, Gordon C. K. Roberts, Nicolas Willet, Caroline Montagner, Christian Damblon, Mireille Dumoulin, Olivier Jacquin, Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, Université de Liège, Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), School of Biological Sciences, University of Essex, Henry Wellcome Laboratories of Structural Biology, Department of Molecular and Cell Biology [Leicester], University of Leicester-University of Leicester, Département de Chimie, Department of Biochemistry, University of Oxford [Oxford], Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, Liege, Belgique, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), University of Oxford, and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Stereochemistry, [SDV]Life Sciences [q-bio], chemistry.chemical_element, Zinc, 010402 general chemistry, 01 natural sciences, Biochemistry, Protein Structure, Secondary, beta-Lactamases, Catalysis, Enzyme catalysis, 03 medical and health sciences, symbols.namesake, Bacillus cereus, Catalytic Domain, Molecular Biology, Protein Unfolding, chemistry.chemical_classification, biology, Chemistry, Active site, Cell Biology, Nuclear magnetic resonance spectroscopy, 0104 chemical sciences, Gibbs free energy, Crystallography, 030104 developmental biology, Enzyme, Protein Structure and Folding, biology.protein, symbols, Protein folding, Hydrophobic and Hydrophilic Interactions
Abstract: Metallo-β-lactamases catalyse the hydrolysis of most β-lactam antibiotics and hence represent a major clinical concern. The development of inhibitors for these enzymes is complicated by the diversity and flexibility of their substrate binding sites, motivating research into their structure and function. In this study, we examined the conformational properties of the Bacillus cereus β-lactamase II in the presence of chemical denaturants using a variety of biochemical and biophysical techniques. The apoenzyme was found to unfold cooperatively, with a Gibbs free energy of stabilization (∆G°) of 32 ± 2 kJ·mol^−1 . For holoBcII, a first noncooperative transition leads to multiple interconverting native-like states, in which both zinc atoms remain bound in an apparently unaltered active site and the protein displays a well-organized compact hydrophobic core with structural changes confined to the enzyme surface, but with no catalytic activity. 2D NMR data revealed that the loss of activity occurs concomitantly with perturbations in two loops that border the enzyme active site. A second cooperative transition, corresponding to global unfolding, is observed at higher denaturant concentrations, with ∆G° value of 65 ± 1.4 kJ·mol^−1 . These combined data highlight the importance of the two zinc ions in maintaining structure as well as a relatively well-defined conformation for both active site loops in order to maintain enzymatic activity.
Published: 2016
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10. Membrane Topology and Biochemical Characterization of the Escherichia coli BacA Undecaprenyl-Pyrophosphate Phosphatase

Author: Manat , Guillaume, El Ghachi , Meriem, Auger , Rodolphe, Baouche , Karima, Olatunji , Samir, Kerff , Frédéric, Touzé , Thierry, Mengin-Lecreulx , Dominique, Bouhss , Ahmed, Cascales , Eric, Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Centre d'Ingénierie des Protéines, Université de Liège-Institut de Chimie B6, ANR-11-BSV3-0002,BACTOPRENYL,Elucidation du métabolisme de l'undécaprényl phosphate, un lipide essentiel pour la biosynthèse des polymères de la paroi bactérienne ( 2011 ), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-11-BSV3-0002,BACTOPRENYL,Elucidation du métabolisme de l'undécaprényl phosphate, un lipide essentiel pour la biosynthèse des polymères de la paroi bactérienne(2011), Centre d’Ingénierie des Protéines [Université de Liège] = Centre for Protein Engineering [University of Liège] (CIP), and Université de Liège
Subjects: Protein family, Glutamine, [SDV]Life Sciences [q-bio], Amino Acid Motifs, Molecular Sequence Data, Phosphatase, Phosphatidate Phosphatase, lcsh:Medicine, Biology, Arginine, Catalysis, Substrate Specificity, Cell membrane, 03 medical and health sciences, Escherichia coli, Serine, medicine, Amino Acid Sequence, Phosphorylation, lcsh:Science, Integral membrane protein, 030304 developmental biology, 0303 health sciences, Phosphotransferases (Phosphate Group Acceptor), Multidisciplinary, Sequence Homology, Amino Acid, [ SDV ] Life Sciences [q-bio], 030306 microbiology, Escherichia coli Proteins, Cell Membrane, Genetic Complementation Test, lcsh:R, Membrane Proteins, Periplasmic space, Lipids, Phosphoric Monoester Hydrolases, Transmembrane protein, Protein Structure, Tertiary, medicine.anatomical_structure, Biochemistry, Membrane protein, Membrane topology, Mutagenesis, Site-Directed, lcsh:Q, Research Article
Abstract: International audience; Several integral membrane proteins exhibiting undecaprenyl-pyrophosphate (C55-PP) phosphatase activity were previously identified in Escherichia coli that belonged to two distinct protein families: the BacA protein, which accounts for 75% of the C55-PP phosphatase activity detected in E. coli cell membranes, and three members of the PAP2 phosphatidic acid phosphatase family, namely PgpB, YbjG and LpxT. This dephosphorylation step is required to provide the C55-P carrier lipid which plays a central role in the biosynthesis of various cell wall polymers. We here report detailed investigations of the biochemical properties and membrane topology of the BacA protein. Optimal activity conditions were determined and a narrow-range substrate specificity with a clear preference for C55-PP was observed for this enzyme. Alignments of BacA protein sequences revealed two particularly well-conserved regions and several invariant residues whose role in enzyme activity was questioned by using a site-directed mutagenesis approach and complementary in vitro and in vivo activity assays. Three essential residues Glu21, Ser27, and Arg174 were identified, allowing us to propose a catalytic mechanism for this enzyme. The membrane topology of the BacA protein determined here experimentally did not validate previous program-based predicted models. It comprises seven transmembrane segments and contains in particular two large periplasmic loops carrying the highly-conserved active site residues. Our data thus provide evidence that all the different E. coli C55-PP phosphatases identified to date (BacA and PAP2) catalyze the dephosphorylation of C55-PP molecules on the same (outer) side of the plasma membrane.
Published: 2015
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11. New MraYAA Inhibitors with an Aminoribosyl Uridine Structure and an Oxadiazole

Author: Hongwei Wan, Raja Ben Othman, Laurent Le Corre, Mélanie Poinsot, Martin Oliver, Ana Amoroso, Bernard Joris, Thierry Touzé, Rodolphe Auger, Sandrine Calvet-Vitale, Michaël Bosco, Christine Gravier-Pelletier, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Ecole Supérieure des Sciences et de Technologie de Hammam Sousse (ESSTHS), Unité de Physiologie et Génétique Bactériennes, Centre d'Ingénierie des Protéines, Département des Sciences de la Vie, Université de Liège, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Université Paris Cité (UPCité)
Subjects: Microbiology (medical), Infectious Diseases, MraY transferase, inhibitors synthesis, muraymycin analogs, molecular modeling, inhibition tests, [CHIM]Chemical Sciences, Pharmacology (medical), General Pharmacology, Toxicology and Pharmaceutics, Biochemistry, Microbiology
Abstract: International audience; New inhibitors of the bacterial transferase MraY from Aquifex aeolicus (MraYAA), based on the aminoribosyl uridine central core of known natural MraY inhibitors, have been designed to generate interaction of their oxadiazole linker with the key amino acids (H324 or H325) of the enzyme active site, as observed for the highly potent inhibitors carbacaprazamycin, muraymycin D2 and tunicamycin. A panel of ten compounds was synthetized notably thanks to a robust microwave-activated one-step sequence for the synthesis of the oxadiazole ring that involved the O-acylation of an amidoxime and subsequent cyclization. The synthetized compounds, with various hydrophobic substituents on the oxadiazole ring, were tested against the MraYAA transferase activity. Although with poor antibacterial activity, nine out of the ten compounds revealed the inhibition of the MraYAA activity in the range of 0.8 µM to 27.5 µM.
Published: 2022
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12. Disorder is a critical component of lipoprotein sorting in Gram-negative bacteria

Author: Seung-Hyun Cho, Joanna Szewczyk, Jessica El Rayes, Michaël Deghelt, Bogdan I. Iorga, Naemi Csoma, Jean-François Collet, André Matagne, Université Catholique de Louvain = Catholic University of Louvain (UCL), Centre d'Ingénierie des Protéines, Université de Liège, Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), J.S. was a research fellow of FRIA and J.-F.C. is an Investigator of FRFS-WELBIO. This work was funded by WELBIO (grant no. WELBIO-CR-20190-03), by grants from F.R.S.-FNRS, from Fédération Wallonie-Bruxelles (ARC 17/22-087), from the European Commission via the International Training Network Train2Target (721484) and from the EOS Excellence in Research Program of FWO and F.R.S.-FNRS (G0G0818N)., and UCL - SSS/DDUV/BCHM - Biochimie-Recherche métabolique
Subjects: Models, Molecular, Gram-negative bacteria, Protein Conformation, Lipoproteins, 03 medical and health sciences, Escherichia coli, Inner membrane, Molecular Biology, 030304 developmental biology, 0303 health sciences, biology, Chemistry, Escherichia coli Proteins, 030302 biochemistry & molecular biology, Gene Expression Regulation, Bacterial, Cell Biology, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Cell biology, Intrinsically Disordered Proteins, Protein Transport, Protein folding, Cell envelope, Bacterial outer membrane, Linker, Biogenesis, Bacterial Outer Membrane Proteins, Lipoprotein
Abstract: Gram-negative bacteria express structurally diverse lipoproteins in their cell envelope. Here, we find that approximately half of lipoproteins destined to the Escherichia coli outer membrane display an intrinsically disordered linker at their N terminus. Intrinsically disordered regions are common in proteins, but establishing their importance in vivo has remained challenging. As we sought to unravel how lipoproteins mature, we discovered that unstructured linkers are required for optimal trafficking by the Lol lipoprotein sorting system, whereby linker deletion re-routes three unrelated lipoproteins to the inner membrane. Focusing on the stress sensor RcsF, we found that replacing the linker with an artificial peptide restored normal outer-membrane targeting only when the peptide was of similar length and disordered. Overall, this study reveals the role played by intrinsic disorder in lipoprotein sorting, providing mechanistic insight into the biogenesis of these proteins and suggesting that evolution can select for intrinsic disorder that supports protein function. Approximately half of lipoproteins destined to the Escherichia coli outer membrane display intrinsically disordered linker peptides at their N termini, which are required for optimal trafficking by the Lol lipoprotein sorting system.
Published: 2021
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13. Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family

Author: Eric Girard, Vanessa Delfosse, Claudine Mayer, Marc Delarue, Olivier Poch, Catherine Birck, Patrick Schultz, Michaël Delmarcelle, Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ingénierie des Protéines [Université de Liège] = Centre for Protein Engineering [University of Liège] (CIP), Université de Liège, Biochimie Structurale, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche des Cordeliers ( CRC (UMR_S 872) ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de biologie structurale ( IBS - UMR 5075 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Institut de génétique et biologie moléculaire et cellulaire ( IGBMC ), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre d'Ingénierie des Protéines, Université de Liège-Institut de Chimie B6, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Université Paris Descartes - Paris 5 (UPD5)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], and Peney, Maité
Subjects: Pyrococcus abyssi, Proteases, Protein Conformation, medicine.medical_treatment, Computational Biology/Macromolecular Structure Analysis, lcsh:Medicine, Sequence alignment, Crystallography, X-Ray, Substrate Specificity, 03 medical and health sciences, Pyrococcus, Protein structure, Biophysics/Macromolecular Assemblies and Machines, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, medicine, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Histone octamer, lcsh:Science, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Biochemistry/Experimental Biophysical Methods, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Protease, biology, lcsh:R, 030302 biochemistry & molecular biology, Biochemistry/Chemical Biology of the Cell, biology.organism_classification, Archaea, Biochemistry/Macromolecular Assemblies and Machines, Biochemistry, Peptide transport, Biophysics/Experimental Biophysical Methods, lcsh:Q, Peptides, Peptide Hydrolases, Research Article
Abstract: International audience; Self-compartmentalizing proteases orchestrate protein turnover through an original architecture characterized by a central catalytic chamber. Here we report the first structure of an archaeal member of a new self-compartmentalizing protease family forming a cubic-shaped octamer with D(4) symmetry and referred to as CubicO. We solved the structure of the Pyrococcus abyssi Pab87 protein at 2.2 A resolution using the anomalous signal of the high-phasing-power lanthanide derivative Lu-HPDO3A. A 20 A wide channel runs through this supramolecular assembly of 0.4 MDa, giving access to a 60 A wide central chamber holding the eight active sites. Surprisingly, activity assays revealed that Pab87 degrades specifically d-amino acid containing peptides, which have never been observed in archaea. Genomic context of the Pab87 gene showed that it is surrounded by genes involved in the amino acid/peptide transport or metabolism. We propose that CubicO proteases are involved in the processing of d-peptides from environmental origins.
Published: 2009
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14. The linker region plays a key role in the adaptation to cold of the cellulase from an Antarctic bacterium

Author: Mirjam Czjzek, Charles Gerday, Colette Duez, Guillaume Sonan, Véronique Receveur-Bréchot, Nushin Aghajari, Richard Haser, Interactions et Modulateurs de Réponses (IMR), Centre National de la Recherche Scientifique (CNRS), Centre d’Ingénierie des Protéines [Université de Liège] = Centre for Protein Engineering [University of Liège] (CIP), Université de Liège, Résonance Magnétique Nucléaire des Biomolécules, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre d'Ingénierie des Protéines, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Biochemistry
Subjects: MESH: Enzyme Stability, MESH: Mutation, Protein Conformation, MESH: Cold Temperature, Acclimatization, MESH: Acclimatization, Cellulase, Biochemistry, Catalysis, Pseudoalteromonas haloplanktis, 03 medical and health sciences, MESH: Protein Conformation, Enzyme Stability, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Psychrophile, Molecular Biology, 030304 developmental biology, Thermostability, chemistry.chemical_classification, 0303 health sciences, biology, 030306 microbiology, Chemistry, MESH: Pseudoalteromonas, Life Sciences, MESH: Cellulase, Cell Biology, Protein engineering, biology.organism_classification, MESH: Catalysis, Cold Temperature, Pseudoalteromonas, Enzyme, Mutation, biology.protein, Biophysics, Linker, Cysteine, Research Article
Abstract: International audience; The psychrophilic cellulase, Cel5G, from the Antarctic bacterium Pseudoalteromonas haloplanktis is composed of a catalytic module (CM) joined to a carbohydrate-binding module (CBM) by an unusually long, extended and flexible linker region (LR) containing three loops closed by three disulfide bridges. To evaluate the possible role of this region in cold adaptation, the LR was sequentially shortened by protein engineering, successively deleting one and two loops of this module, whereas the last disulfide bridge was also suppressed by replacing the last two cysteine residue by two alanine residues. The kinetic and thermodynamic properties of the mutants were compared with those of the full-length enzyme, and also with those of the cold-adapted CM alone and with those of the homologous mesophilic enzyme, Cel5A, from Erwinia chrysanthemi. The thermostability of the mutated enzymes as well as their relative flexibility were evaluated by differential scanning calorimetry and fluorescence quenching respectively. The topology of the structure of the shortest mutant was determined by SAXS (small-angle X-ray scattering). The data indicate that the sequential shortening of the LR induces a regular decrease of the specific activity towards macromolecular substrates, reduces the relative flexibility and concomitantly increases the thermostability of the shortened enzymes. This demonstrates that the long LR of the full-length enzyme favours the catalytic efficiency at low and moderate temperatures by rendering the structure not only less compact, but also less stable, and plays a crucial role in the adaptation to cold of this cellulolytic enzyme.
Published: 2007
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15. Prenatal and childhood exposure to chlordecone and adiposity of seven-year-old children in the Timoun mother–child cohort study in Guadeloupe (French West Indies)

Author: Nathalie Costet, Antoine Lafontaine, Florence Rouget, Léah Michineau, Christine Monfort, Jean-Pierre Thomé, Philippe Kadhel, Luc Multigner, Sylvaine Cordier, Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), École des Hautes Études en Santé Publique [EHESP] (EHESP), CHU Pointe-à-Pitre/Abymes [Guadeloupe], Centre d’Ingénierie des Protéines [Université de Liège] = Centre for Protein Engineering [University of Liège] (CIP), Université de Liège, General Health Directorate [DGS RMC11129NNA, R17142NN], Fondation de France [69263], and Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )
Subjects: Male, Dichlorodiphenyl Dichloroethylene, West Indies, Health, Toxicology and Mutagenesis, Cohort Studies, Pregnancy, Prenatal exposure, Childhood exposure, Humans, Obesity, Child, Guadeloupe, Adiposity, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, [SDV.MHEP.PED]Life Sciences [q-bio]/Human health and pathology/Pediatrics, Infant, Newborn, Public Health, Environmental and Occupational Health, [SDV.MHEP.EM]Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, Mother-Child Relations, Chlordecone, Prenatal Exposure Delayed Effects, Biomonitoring, Premature Birth, Organochlorine pesticides, Female, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract: Background Exposure to persistent environmental organic pollutants may contribute to the development of obesity among children. Chlordecone is a persistent organochlorine insecticide with estrogenic properties that was used in the French West Indies (1973–1993) and is still present in the soil and the water and food consumed by the local population. We studied the association between prenatal and childhood exposure to chlordecone and the adiposity of prepubertal children. Methods Within the Timoun Mother–Child Cohort Study in Guadeloupe (French West Indies), 575 children had a medical examination at seven years of age, including adiposity measurements. A Structural Equation Modeling approach was used to create a global adiposity score from four adiposity indicators: the BMI z-score, percentage of fat mass, sum of the tricipital and subscapular skinfold thickness, and waist-to-height ratio. Chlordecone concentrations were measured in cord blood at birth and in the children’s blood at seven years of age. Models were adjusted for prenatal and postnatal covariates. Sensitivity analyses accounted for co-exposure to PCB-153 and pp’-DDE. Mediation analyses, including intermediate birth outcomes, were conducted. Results Prenatal chlordecone exposure tended to be associated with increased adiposity at seven years of age, particularly in boys. However, statistical significance was only reached in the third quartile of exposure and neither linear nor non-linear trends could be formally identified. Consideration of preterm birth or birth weight in mediation analyses did not modify the results, as adjustment for PCB-153 and pp’-DDE co-exposures. Conclusion Globally, we found little evidence of an association between chlordecone exposure during the critical in utero or childhood periods of development and altered body-weight homeostasis in childhood. Nevertheless, some associations we observed at seven years of age, although non-significant, were consistent with those observed at earlier ages and would be worth investing during further follow-ups of children of the Timoun Mother–Child Cohort Study when they reach puberty.
Published: 2022
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16. Intervalence Transitions in Mixed Valence Bis(tetrathiafulvalene) Compounds

Author: Khalid Lahlil, F. Menou, Alec Moradpour, Christopher Bowlas, Dominique Dehareng, Georges Dive, Jean-Pierre Launay, Jacques Bonvoisin, Patrick Cassoux, Laboratoire de Physique des Solides (LPS), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11), Laboratoire de chimie de coordination (LCC), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Groupe NanoSciences (CEMES-GNS), Centre d'élaboration de matériaux et d'études structurales (CEMES), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Centre d'Ingénierie des Protéines, Université de Liège, Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut de Chimie de Toulouse (ICT), Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), and Centre d’Ingénierie des Protéines [Université de Liège] = Centre for Protein Engineering [University of Liège] (CIP)
Subjects: Mixed-valence organic compounds, Stereochemistry, Radical, TTF DERIVATIVES, Electron Transfer, 010402 general chemistry, 01 natural sciences, Biochemistry, Catalysis, Electron transfer, chemistry.chemical_compound, Colloid and Surface Chemistry, Ab initio quantum chemistry methods, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Spectroelectrochemistry, Valence (chemistry), 010405 organic chemistry, Chemistry, Synthon, General Chemistry, 0104 chemical sciences, Crystallography, Excited state, Cyclic voltammetry, Tetrathiafulvalene, Semiempirical AM1
Abstract: International audience; The series of new bis(tetrathiafulva1ene) [bis(TTF)] compounds 10-12a,b have been synthetized with the TTF-like synthon 8a,b, previously used to prepare the pyrazine-fused bis("F) 7a,b. These compounds exhibit four reversible sequential one-electron oxidation steps, on the basis of cyclic voltammetry. For the cation radicals 7b.+,10 .+,and 12.+, generated electrochemically, rather intense and broad bands in the near-IR region, specific of class 11 mixed valence compounds, were found. Theoretical calculations at the semiempirical AM1 level as well as at the ab-initio level indicated that these cation radicals are charge-distributions localized as related to mixed valence species. These calculations also allowed the low-energy absorption bands to be assigned to intervalence transitions; these transitions imply the existence of multiple low-lying excited states that are non-adiabatically coupled to the ground-state of these open-shell species.
Published: 1995
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17. Disorder is a critical component of lipoprotein sorting in Gram-negative bacteria

Author: André Matagne, Joanna Szewczyk, Jean-François Collet, Jessica El Rayes, Bogdan I. Iorga, Seung-Hyun Cho, Michaël Deghelt, De Duve Institute, Université Catholique de Louvain = Catholic University of Louvain (UCL), Centre d'Ingénierie des Protéines, Université de Liège, Institut de Chimie des Substances Naturelles (ICSN), and Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: chemistry.chemical_classification, 0303 health sciences, Gram-negative bacteria, biology, 030306 microbiology, Chemistry, [SDV]Life Sciences [q-bio], Peptide, biology.organism_classification, medicine.disease_cause, Cell biology, 03 medical and health sciences, medicine, Inner membrane, Bacterial outer membrane, Linker, Escherichia coli, Biogenesis, 030304 developmental biology, Lipoprotein
Abstract: We thank Asma Boujtat for technical help. We are indebted to the members of the Collet laboratory and to Nassos Typas (EMBL, Heidelberg) for helpful suggestions and discussions and to Tom Silhavy (Princeton) for providing bacterial strains. J.S. was a research fellow of the FRIA and J.F.C. is an Investigator of the FRFS-WELBIO. This work was funded by the WELBIO, by grants from the F.R.S.-FNRS, from the Fédération Wallonie-Bruxelles (ARC 17/22-087), from the European Commission via the International Training Network Train2Target (721484), and from the EOS Excellence in Research Program of the FWO and FRS-FNRS (G0G0818N).; Gram-negative bacteria express structurally diverse lipoproteins in their envelope. Here we found that approximately half of lipoproteins destined to the Escherichia coli outer membrane display an intrinsically disordered linker at their N-terminus. Intrinsically disordered regions are common in proteins, but establishing their importance in vivo has remained challenging. Here, as we sought to unravel how lipoproteins mature, we discovered that unstructured linkers are required for optimal trafficking by the Lol lipoprotein sorting system: linker deletion re-routes three unrelated lipoproteins to the inner membrane. Focusing on the stress sensor RcsF, we found that replacing the linker with an artificial peptide restored normal outer membrane targeting only when the peptide was of similar length and disordered. Overall, this study reveals the role played by intrinsic disorder in lipoprotein sorting, providing mechanistic insight into the biogenesis of these proteins and suggesting that evolution can select for intrinsic disorder that supports protein function.
Published: 2021

18. SPOR Proteins Are Required for Functionality of Class A Penicillin-Binding Proteins in Escherichia coli

Author: Pazos, Manuel, Peters, Katharina, Boes, Adrien, Safaei, Yalda, Kenward, Calem, Caveney, Nathanael A., Laguri, Cedric, Breukink, Eefjan, Strynadka, Natalie C.J., Simorre, Jean Pierre, Terrak, Mohammed, Vollmer, Waldemar, Sub Membrane Biochemistry & Biophysics, Membrane Biochemistry and Biophysics, The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, Université de Liège, Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of Northern British Columbia [Prince George] (UNBC), Department of Molecular and Cellular Physiology, Stanford University, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Membrane Biochemistry and Biophysics, Utrecht University [Utrecht], Sub Membrane Biochemistry & Biophysics, and ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017)
Subjects: cell division, Models, Molecular, Molecular Biology and Physiology, Penicillin binding proteins, Cell division, Protein Conformation, DEDD, Peptidoglycan, medicine.disease_cause, Cefsulodin, Microbiology, Peptidoglycan synthases, Bacterial cell structure, 03 medical and health sciences, chemistry.chemical_compound, Virology, medicine, Escherichia coli, Penicillin-Binding Proteins, peptidoglycan synthases, Escherichia coli Infections, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 030306 microbiology, Chemistry, Escherichia coli Proteins, Periplasmic space, QR1-502, 3. Good health, Cell biology, Anti-Bacterial Agents, Enzyme, SPOR domain, Peptidoglycan Glycosyltransferase, Research Article, Protein Binding
Abstract: Escherichia coli has four SPOR proteins that bind peptidoglycan, of which FtsN is essential for cell division. DamX and DedD are suggested to have semiredundant functions in cell division based on genetic evidence. Here, we solved the structure of the SPOR domain of DedD, and we show that both DamX and DedD interact with and stimulate the synthetic activity of the peptidoglycan synthases PBP1A and PBP1B, suggesting that these class A PBP enzymes act in concert with peptidoglycan-binding proteins during cell division., Sporulation-related repeat (SPOR) domains are present in many bacterial cell envelope proteins and are known to bind peptidoglycan. Escherichia coli contains four SPOR proteins, DamX, DedD, FtsN, and RlpA, of which FtsN is essential for septal peptidoglycan synthesis. DamX and DedD may also play a role in cell division, based on mild cell division defects observed in strains lacking these SPOR domain proteins. Here, we show by nuclear magnetic resonance (NMR) spectroscopy that the periplasmic part of DedD consists of a disordered region followed by a canonical SPOR domain with a structure similar to that of the SPOR domains of FtsN, DamX, and RlpA. The absence of DamX or DedD decreases the functionality of the bifunctional transglycosylase-transpeptidase penicillin-binding protein 1B (PBP1B). DamX and DedD interact with PBP1B and stimulate its glycosyltransferase activity, and DamX also stimulates the transpeptidase activity. DedD also binds to PBP1A and stimulates its glycosyltransferase activity. Our data support a direct role of DamX and DedD in enhancing the activity of PBP1B and PBP1A, presumably during the synthesis of the cell division septum.
Published: 2020
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19. Mass and charge distributions of amyloid fibers involved in neurodegenerative diseases: mapping heterogeneity and polymorphism

Author: François Legrand, M. Sallanon, C. Marquette, Jonathan Pansieri, Mohammad A. Halim, Vincent Forge, Sabine Chierici, Simona Denti, Philippe Dugourd, Rodolphe Antoine, Mireille Dumoulin, Charlotte Vendrely, Xavier Dagany, Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut Lumière Matière [Villeurbanne] (ILM), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Equipe de recherche sur les relations matrice extracellulaire-cellules (ERRMECe), Fédération INSTITUT DES MATÉRIAUX DE CERGY-PONTOISE (I-MAT), Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine, Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, Université de Liège, Centre de Recherches des Instituts Groupés, Haute Ecole Libre Mosane (CRIG), Radiopharmaceutiques biocliniques (LRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Département de Chimie Moléculaire (DCM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Amyloid Fibres : From Foldopathies to NanoDesign [?-2019] (AFFOND [?-2019]), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), InBios-Centre for Protein Engineering, Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and GON, Nathalie
Subjects: 0301 basic medicine, chemistry.chemical_classification, education.field_of_study, biology, Tau protein, Population, Peptide, General Chemistry, Mass spectrometry, Charge detection, 03 medical and health sciences, 030104 developmental biology, chemistry, Polymorphism (materials science), mental disorders, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, biology.protein, Biophysics, [CHIM]Chemical Sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], education, Amyloid fibers
Abstract: International audience; Heterogeneity and polymorphism are generic features of amyloid fibers with some important effects on the related disease development. We report here the characterization, by charge detection mass spectrometry, of amyloid fibers made of three polypeptides involved in neurodegenerative diseases: Aβ1–42 peptide, tau and α-synuclein. Beside the mass of individual fibers, this technique enables to characterize the heterogeneity and the polymorphism of the population. In the case of Aβ1–42 peptide and tau protein, several coexisting species could be distinguished and characterized. In the case of α-synuclein, we show how the polymorphism affects the mass and charge distributions.
Published: 2018
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20. Insight into the dual function of lipid phosphate phosphatase PgpB involved in two essential cell-envelope metabolic pathways in Escherichia coli

Author: Dominique Mengin-Lecreulx, Rodolphe Auger, Xudong Tian, Guillaume Manat, Frédéric Kerff, Thierry Touzé, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Enveloppes Bactériennes et Antibiotiques (ENVBAC), Département Microbiologie (Dpt Microbio), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, Université de Liège, Belgium Program InterUniversity Attraction Poles (IAP n° 7/44), and ANR-11-BSV3-0002,BACTOPRENYL,Elucidation du métabolisme de l'undécaprényl phosphate, un lipide essentiel pour la biosynthèse des polymères de la paroi bactérienne(2011)
Subjects: Models, Molecular, Thermotolerance, 0301 basic medicine, [SDV]Life Sciences [q-bio], Amino Acid Motifs, Phosphatase, Phosphatidate Phosphatase, lcsh:Medicine, Biochemistry, Microbiology, Article, Substrate Specificity, Gene Knockout Techniques, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Polyisoprenyl Phosphates, Biosynthesis, Catalytic triad, Escherichia coli, Penicillin-Binding Proteins, lcsh:Science, Multidisciplinary, Chemistry, Escherichia coli Proteins, Hydrolysis, Cell Membrane, Genetic Complementation Test, lcsh:R, Membrane Proteins, Phosphatidylglycerols, Lipid-phosphate phosphatase, Metabolic pathway, 030104 developmental biology, Membrane protein, lcsh:Q, Peptidoglycan Glycosyltransferase, Peptidoglycan, Cell envelope, Metabolic Networks and Pathways, 030217 neurology & neurosurgery
Abstract: Ubiquitous PAP2 lipid phosphatases are involved in a wide array of central physiological functions. PgpB from Escherichia coli constitutes the archetype of this subfamily of membrane proteins. It displays a dual function by catalyzing the biosynthesis of two essential lipids, the phosphatidylglycerol (PG) and the undecaprenyl phosphate (C55-P). C55-P constitutes a lipid carrier allowing the translocation of peptidoglycan subunits across the plasma membrane. PG and C55-P are synthesized in a redundant manner by PgpB and other PAP2 and/or unrelated membrane phosphatases. Here, we show that PgpB is the sole, among these multiple phosphatases, displaying this dual activity. The inactivation of PgpB does not confer any apparent growth defect, but its inactivation together with another PAP2 alters the cell envelope integrity increasing the susceptibility to small hydrophobic compounds. Evidence is also provided of an interplay between PAP2s and the peptidoglycan polymerase PBP1A. In contrast to PGP hydrolysis, which relies on a His/Asp/His catalytic triad of PgpB, the mechanism of C55-PP hydrolysis appeared as only requiring the His/Asp diad, which led us to hypothesize distinct processes. Moreover, thermal stability analyses highlighted a substantial structural change upon phosphate binding by PgpB, supporting an induced-fit model of action.
Published: 2020
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21. Different Vancomycin-IntermediateStaphylococcus aureusPhenotypes Selected from the Same ST100-hVISA Parental Strain

Author: Marta Mollerach, Arabela Cuirolo, Dominique Mengin-Lecreulx, Ana Maria Amoroso, Sabrina Di Gregorio, Olivier Verlaine, Bernard Joris, Silvina Fernández, Angela Famiglietti, Departamento de Microbiología, Inmunología y Biotecnología, Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Unité de Physiologie et Génétique Bactériennes, Centre d'Ingénierie des Protéines, Département des Sciences de la Vie, Université de Liège, Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Laboratorio de Bacteriología Clínica, Hospital de Clínicas José de San Martín, Universidad de Buenos Aires [Buenos Aires], Departamento de Microbiología, Inmunología y Biotecnología [Buenos Aires], Facultad de Farmacia y Bioquímica [Buenos Aires] (FFYB), Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Laboratorio de Bacteriología Clínica [Buenos Aires]
Subjects: 0301 basic medicine, Autolysis (biology), MRSA ST100, [SDV]Life Sciences [q-bio], vancomycin, Mutant, Gene Expression, MRSA, medicine.disease_cause, purl.org/becyt/ford/1 [https], chemistry.chemical_compound, Cell Wall, Gene expression, Mechanisms, ST100, Staphylococcal Infections, Phenotype, Anti-Bacterial Agents, 3. Good health, VISA, Staphylococcus aureus, Vancomycin, CIENCIAS NATURALES Y EXACTAS, medicine.drug, Microbiology (medical), Otras Ciencias Biológicas, 030106 microbiology, Immunology, Microbial Sensitivity Tests, Peptidoglycan, Biology, Microbiology, hVISA, Ciencias Biológicas, 03 medical and health sciences, Bacterial Proteins, medicine, Humans, Penicillin-Binding Proteins, Selection, Genetic, purl.org/becyt/ford/1.6 [https], STAPHYLOCOCCUS AUREUS, Pharmacology, [ SDV ] Life Sciences [q-bio], Vancomycin Resistance, VANCOMYCIN, VIS, chemistry, Mutation, DNA Transposable Elements, Parental strain
Abstract: The aim of this study is to characterize the factors related to peptidoglycan metabolism in isogenic hVISA/VISA ST100 strains. Recently, we reported the increase in IS256 transposition in invasive hVISA ST100 clinical strains isolated from the same patient (D1 and D2) before and after vancomycin treatment and two laboratory VISA mutants (D23C9 and D2P11) selected from D2 in independent experiments. High performance liquid chromatography-mass spectrometry (HPLC-MS) analysis of peptidoglycan muropeptides showed increased proportion of monomeric muropeptides and a concomitant decrease in the proportion of tetrameric muropeptide in D2 and derived mutants when compared to the original strain D1. In addition, strain D2 and its derived mutants showed an increase in cell wall thickness with increased pbp2 gene expression. The VISA phenotype was not stable in D2P11 and showed a reduced autolysis profile. On the other hand, the mutant D23C9 differentiates from D2 and D2P11 in the autolysis profile, and pbp4 transcription profile. D2-derived mutants exhibited differences in the susceptibility to other antimicrobials. Our results highlight the possibility of selection of different VISA phenotypes from a single hVISA-ST100 genetic background. Fil: Di Gregorio, Sabrina Noelia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Fernandez, Silvina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología; Argentina Fil: Cuirolo, Arabela Ximena. Université de Liège; Bélgica. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Verlaine, Olivier. Université de Liège; Bélgica Fil: Amoroso, Ana. Université de Liège; Bélgica Fil: Mengin Lecreulx, Dominique. Université Paris Sud; Francia Fil: Famiglietti, Angela María Rosa. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; Argentina Fil: Joris, Bernard. Université de Liège; Bélgica Fil: Mollerach, Marta Eugenia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Published: 2017
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22. Bacterial Transferase MraY, a Source of Inspiration towards New Antibiotics

Author: Nicolas Pietrancosta, Sandrine Calvet-Vitale, Nathalie Evrard-Todeschi, Christine Gravier-Pelletier, Laurent Le Corre, Ahmed Bouhss, Mickaël J Fer, Samir Olatunji, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Modélisation et Immunologie pour la Thérapie (CBMIT), Université Paris Descartes - Paris 5 (UPD5), Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Trinity College Dublin, Structure et activité des biomolécules normales et pathologiques (SABNP), Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Évry-Val-d'Essonne (UEVE), Centre d'Ingénierie des Protéines, Université de Liège-Institut de Chimie B6, Enveloppes Bactériennes et Antibiotiques (ENVBAC), Département Microbiologie (Dpt Microbio), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Systèmes glutamatergiques normaux et pathologiques = Normal and Pathologic Glutamatergic Neurons (NPS), Neuroscience Paris Seine (NPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Analyse, Interactions Moléculaires et Cellulaires (LBM-E2), Laboratoire des biomolécules (LBM UMR 7203), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Chimie Moléculaire de Paris Centre (FR 2769), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: nucleoside antibiotics, Research groups, medicine.drug_class, [SDV]Life Sciences [q-bio], Antibiotics, Transferases (Other Substituted Phosphate Groups), Computational biology, Peptidoglycan, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Biology, 01 natural sciences, Biochemistry, MraY, Structure-Activity Relationship, Antibiotic resistance, Bacterial Proteins, biological evaluations, Transferases, Drug Discovery, medicine, Transferase, Peptidoglycan biosynthesis, Enzyme Inhibitors, triazoles, ComputingMilieux_MISCELLANEOUS, Pharmacology, Binding Sites, Bacteria, 010405 organic chemistry, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Organic Chemistry, 3. Good health, 0104 chemical sciences, Anti-Bacterial Agents, molecular modelling, Molecular Docking Simulation, 010404 medicinal & biomolecular chemistry, Docking (molecular), Drug Design, docking, Molecular Medicine, mutagenesis
Abstract: The bacterial resistance to antibiotics constitutes more than ever a severe public health problem. The enzymes involved in bacterial peptidoglycan biosynthesis are pertinent targets for developing new antibiotics, notably the MraY transferase that is not targeted by any marketed drug. Many research groups are currently working on the study or the inhibition of this enzyme. After a concise overview of the role, mechanism and inhibition of MraY, the structure–activity relationships of 5’-triazole-containing aminoribosyluridine inhibitors, we previously synthetized, will be presented. The recently published MraY X-ray structures allowed us to achieve a molecular virtual high-throughput screening of commercial databases and our in-house library resulting in the identification of promising compounds for the further development of new antibiotics.
Published: 2018
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23. 5′-Methylene-triazole-substituted-aminoribosyl uridines as MraY inhibitors: synthesis, biological evaluation and molecular modeling

Author: Ahmed Bouhss, Nicolas Pietrancosta, Christine Gravier-Pelletier, Dominique Mengin-Lecreulx, Ana Maria Amoroso, Sandrine Calvet-Vitale, Laurent Le Corre, Bernard Joris, Mariana Patrão, Michael Fer, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Enveloppes Bactériennes et Antibiotiques (ENVBAC), Département Microbiologie (Dpt Microbio), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Unité de Physiologie et Génétique Bactériennes, Centre d'Ingénierie des Protéines, Département des Sciences de la Vie, Université de Liège, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques ( LCBPT - UMR 8601 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Centre National de la Recherche Scientifique ( CNRS ), Enveloppes Bactériennes et Antibiotiques ( ENVBAC ), Département Microbiologie ( Dpt Microbio ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, and Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay
Subjects: Models, Molecular, Molecular model, Stereochemistry, [SDV]Life Sciences [q-bio], Triazole, Transferases (Other Substituted Phosphate Groups), Alkyne, Chemistry Techniques, Synthetic, Microbial Sensitivity Tests, 010402 general chemistry, 01 natural sciences, Biochemistry, chemistry.chemical_compound, Bacterial Proteins, Transferases, Catalytic Domain, Enzyme Inhibitors, Physical and Theoretical Chemistry, Methylene, Uridine, chemistry.chemical_classification, [ SDV ] Life Sciences [q-bio], 010405 organic chemistry, Organic Chemistry, Biological activity, Triazoles, Cycloaddition, Anti-Bacterial Agents, 0104 chemical sciences, chemistry, Azide, Antibacterial activity, Bacillus subtilis
Abstract: International audience; The straightforward synthesis of 5'-methylene-[1,4]-triazole-substituted aminoribosyl uridines is described. Two families of compounds were synthesized from a unique epoxide which was regioselectively opened by acetylide ions (for compounds II) or azide ions (for compounds III). Sequential diastereoselective glycosylation with a ribosyl fluoride derivative, Cu(i)-catalyzed azide-alkyne cycloaddition (CuAAC) with various complementary azide and alkyne partners afforded the targeted compounds after final deprotection. The biological activity of the 16 resulting compounds together with that of 14 previously reported compounds I, lacking the 5' methylene group, was evaluated on the MraY transferase activity. Out of the 30 tested compounds, 18 compounds revealed MraY inhibition with IC50 ranging from 15 to 150 μM. A molecular modeling study was performed to rationalize the observed structure-activity relationships (SAR), which allowed us to correlate the activity of the most potent compounds with an interaction involving Leu191 of MraYAA. The antibacterial activity was also evaluated and seven compounds exhibited a good activity against Gram-positive bacterial pathogens with MIC ranging from 8 to 32 μg mL(-1), including the methicillin resistant Staphylococcus aureus (MRSA).
Published: 2015
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24. Protein–polysaccharide complexes for enhanced protein delivery in hyaluronic acid templated calcium carbonate microparticles

Author: Bathabile Ramalapa, Emmanuel Garcion, Marylène Vandevenne, Thomas Cordonnier, Oscar Crasson, Moreno Galleni, Frank Boury, Alain Gibaud, Design and Application of Innovative Local Treatments in Glioblastoma (CRCINA-ÉQUIPE 17), Centre de Recherche en Cancérologie et Immunologie Nantes-Angers (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), Laboratory for Biological Macromolecules [Liège, Belgium], Université de Liège-Center for Protein Engineering-Institut de Chimie B6 [Liège, Belgium], Institut des Molécules et Matériaux du Mans (IMMM), Le Mans Université (UM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), The authors are thankful for the European financial support in the frame of the NanoFar program, an Erasmus Mundus Joint Doctorate (EMJD) program in nanomedicine and pharmaceutical innovation. We also thank the National Funds for Scientific Research, Belgium (FNRS) for financial support., Bernardo, Elizabeth, Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes), Centre d’Ingénierie des Protéines [Université de Liège] = Centre for Protein Engineering [University of Liège] (CIP), and Université de Liège
Subjects: Materials science, medicine.medical_treatment, Two-hybrid screening, Biomedical Engineering, [SDV.CAN]Life Sciences [q-bio]/Cancer, 02 engineering and technology, 010402 general chemistry, Polysaccharide, 01 natural sciences, chemistry.chemical_compound, Thrombin, [SDV.CAN] Life Sciences [q-bio]/Cancer, Chitin binding, Vaterite, Hyaluronic acid, medicine, General Materials Science, chemistry.chemical_classification, Protease, General Chemistry, General Medicine, 021001 nanoscience & nanotechnology, Fusion protein, 3. Good health, 0104 chemical sciences, Biochemistry, chemistry, 0210 nano-technology, medicine.drug
Abstract: International audience; The controlled delivery of proteins within calcium carbonate (CaCO 3) particles is currently widely investigated. The success of these carriers is driven by ionic interactions between the encapsulated proteins and the particles. This poses a great limitation on the successful loading of proteins that have no ionic affinity to CaCO 3. In this study, we explored the use of polysaccharide–protein interactions to strongly enhance the encapsulation of proteins in CaCO 3 microparticles. Previously, Vandevenne and colleagues inserted a human chitin binding domain (ChBD) that has intrinsic affinity for hyaluronic acid (HA) into a b-lactamase (BlaP). This generated chimeric protein, named BlaPChBD, was shown to be fully bifunctional. In this study we showed that this hybrid protein can associate with HA and be successfully loaded into vaterite CaCO 3 microparticles using supercritical CO 2 (ScCO 2) technology aided by the templating effect of HA on CaCO 3. The presence of ChBD inserted into BlaP increased the encapsulation of the protein by 6-fold when complexed with HA. Furthermore, thrombin cleavage sites were engineered on both sides of the inserted ChBD in the chimeric BlaP to achieve release of the protein from the micro-particles by protease cleavage. Our results showed that thrombin cleavage increased the release of the protein from the microparticles within 36 hours from o20% to 87%. In conclusion, the presence of ChBD successfully improved the encapsulation yield of the protein while retaining up to 82% of its activity and efficient release of the protein from the microparticles was achieved by protease cleavage.
Published: 2017
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25. Multimodal imaging Gd-nanoparticles functionalized with Pittsburgh compound B or a nanobody for amyloid plaques targeting

Author: C. Marquette, François Lux, Eric Allémann, Éva Tóth, Mireille Dumoulin, Laurence Heinrich-Balard, Olivier Tillement, Pascaline Rivory, Maria João Saraiva, Jean-François Morfin, Jonathan Pansieri, Nathalie Martine Stransky-Heilkron, Marie Plissonneau, Vincent Forge, Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Nano-H S.A.S, Nano-H S.A.S, 38070 Saint Quentin Fallavier, France, Institut Lumière Matière [Villeurbanne] (ILM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), School of Pharmaceutical Sciences, Université de Genève = University of Geneva (UNIGE), Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, Université de Liège, Matériaux, ingénierie et science [Villeurbanne] (MATEIS), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Instituto de Inovação e Investigação em Saúde (I3S), University of Porto, Portugal, Molecular Neurobiology Group, IBMC - Institute for Molecular & Cell Biology, University of Porto, 4150-180 Porto, Portugal., GON, Nathalie, Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), University of Geneva [Switzerland], Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), and Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)
Subjects: 0301 basic medicine, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, Medicine (miscellaneous), Nanoparticle, Amylin, Peptide, Gadolinium, Plaque, Amyloid, Multimodal Imaging, chemistry.chemical_compound, Amyloid disease, Mice, General Materials Science, chemistry.chemical_classification, ddc:615, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Aniline Compounds, biology, Brain, Immunohistochemistry, Islet Amyloid Polypeptide, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], amyloid imaging, Materials science, Amyloid, Biomedical Engineering, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Bioengineering, Development, 03 medical and health sciences, Alzheimer Disease, Animals, Humans, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Amyloid beta-Peptides, PIB, amyloidoses, gadolinium-based nanoparticles, Single-Domain Antibodies, Combinatorial chemistry, In vitro, nanobody, Transthyretin, Thiazoles, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, 030104 developmental biology, chemistry, Diabetes Mellitus, Type 2, biology.protein, Biophysics, Nanoparticles, Pittsburgh compound B, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: Aim: Gadolinium-based nanoparticles were functionalized with either the Pittsburgh compound B or a nanobody (B10AP) in order to create multimodal tools for an early diagnosis of amyloidoses. Materials & methods: The ability of the functionalized nanoparticles to target amyloid fibrils made of β-amyloid peptide, amylin or Val30Met-mutated transthyretin formed in vitro or from pathological tissues was investigated by a range of spectroscopic and biophysics techniques including fluorescence microscopy. Results: Nanoparticles functionalized by both probes efficiently interacted with the three types of amyloid fibrils, with KD values in 10 micromolar and 10 nanomolar range for, respectively, Pittsburgh compound B and B10AP nanoparticles. Moreover, they allowed the detection of amyloid deposits on pathological tissues. Conclusion: Such functionalized nanoparticles could represent promising flexible and multimodal imaging tools for the early diagnostic of amyloid diseases, in other words, Alzheimer's disease, Type 2 diabetes mellitus and the familial amyloidotic polyneuropathy.
Published: 2017
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26. Gd-nanoparticles functionalization with specific peptides for ß-amyloid plaques targeting

Author: Éva Tόth, François Lux, Cédric Louis, Pierre Mowat, Eric Allémann, Laurence Heinrich-Balard, Mireille Dumoulin, Jonathan Pansieri, Richard Cohen, Nathalie Martine Stransky-Heilkron, Marie Plissonneau, C. Marquette, Olivier Tillement, Pascaline Rivory, Maria João Saraiva, Vincent Forge, Jean-François Morfin, Nano-H SAS, 38070, Saint Quentin Fallavier, France., Nano-H SAS, 38070, Saint Quentin Fallavier, France, Institut Lumière Matière [Villeurbanne] (ILM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Matériaux, ingénierie et science [Villeurbanne] (MATEIS), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), School of Pharmaceutical Sciences, University of Geneva [Switzerland], Centre for Protein Engineering (CIP), Institut de Chimie (B6) - Sart Tilman, Laboratoire d’Enzymologie et Repliement des Protéines, Université de Liège, Laboratoire de biochimie et biologie moléculaire, Hospices Civils de Lyon (HCL)-Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL), Department of Molecular Neurobiology, Institute for Molecular and Cell Biology, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), Centre d’Ingénierie des Protéines [Université de Liège] = Centre for Protein Engineering [University of Liège] (CIP), and Universidade do Porto = University of Porto
Subjects: 0301 basic medicine, Pathology, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Gene Expression, Metal Nanoparticles, Pharmaceutical Science, Medicine (miscellaneous), Gadolinium, Plaque, Amyloid, Peptide, Beta-amyloid, Hippocampus, Applied Microbiology and Biotechnology, Mice, chemistry.chemical_compound, 0302 clinical medicine, Peptide-targeting, Prealbumin, MRI contrast agent, Beta-amyloid fibrils, chemistry.chemical_classification, ddc:615, biology, medicine.diagnostic_test, Alzheimer's disease, Magnetic Resonance Imaging, Contrast agent, Positron emission tomography, Molecular Medicine, Female, Alzheimer’s disease, FibrilsMRI, Protein Binding, medicine.medical_specialty, Gadolinium based nanoparticles, Amyloid, Biomedical Engineering, Mice, Transgenic, Bioengineering, macromolecular substances, Fibril, Amyloid imaging, 03 medical and health sciences, Alzheimer Disease, medicine, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Peptidetargeting, Amyloid beta-Peptides, Research, Surface Plasmon Resonance, medicine.disease, Peptide Fragments, Disease Models, Animal, Kinetics, Transthyretin, 030104 developmental biology, chemistry, Mutation, Biophysics, biology.protein, Peptides, Pittsburgh compound B, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, 030217 neurology & neurosurgery
Abstract: Background Amyloidoses are characterized by the extracellular deposition of insoluble fibrillar proteinaceous aggregates highly organized into cross-β structure and referred to as amyloid fibrils. Nowadays, the diagnosis of these diseases remains tedious and involves multiple examinations while an early and accurate protein typing is crucial for the patients’ treatment. Routinely used neuroimaging techniques such as magnetic resonance imaging (MRI) and positron emission tomography (PET) using Pittsburgh compound B, [11C]PIB, provide structural information and allow to assess the amyloid burden, respectively, but cannot discriminate between different amyloid deposits. Therefore, the availability of efficient multimodal imaging nanoparticles targeting specific amyloid fibrils would provide a minimally-invasive imaging tool useful for amyloidoses typing and early diagnosis. In the present study, we have functionalized gadolinium-based MRI nanoparticles (AGuIX) with peptides highly specific for Aβ amyloid fibrils, LPFFD and KLVFF. The capacity of such nanoparticles grafted with peptide to discriminate among different amyloid proteins, was tested with Aβ(1–42) fibrils and with mutated-(V30M) transthyretin (TTR) fibrils. Results The results of surface plasmon resonance studies showed that both functionalized nanoparticles interact with Aβ(1–42) fibrils with equilibrium dissociation constant (Kd) values of 403 and 350 µM respectively, whilst they did not interact with V30M-TTR fibrils. Similar experiments, performed with PIB, displayed an interaction both with Aβ(1–42) fibrils and V30M-TTR fibrils, with Kd values of 6 and 10 µM respectively, confirming this agent as a general amyloid fibril marker. Thereafter, the ability of functionalized nanoparticle to target and bind selectively Aβ aggregates was further investigated by immunohistochemistry on AD like-neuropathology brain tissue. Pictures clearly indicated that KLVFF-grafted or LPFFD-grafted to AGuIX nanoparticle recognized and bound the Aβ amyloid plaque localized in the mouse hippocampus. Conclusion These results constitute a first step for considering these functionalized nanoparticles as a valuable multimodal imaging tool to selectively discriminate and diagnose amyloidoses. Electronic supplementary material The online version of this article (doi:10.1186/s12951-016-0212-y) contains supplementary material, which is available to authorized users.
Published: 2016
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27. Synthesis and characterization of multimodal Gd-Nanoparticles vectorized for Amyloidosis diagnosis, and their affinity evaluation using Biacore

Author: Plissonneau, Marie, Mowat, Pierre, Heinrich-Balard, Laurence, Rivory, Pascaline, Stransky-Heilkron, N., Marquette, C., Lux, François, Allémann, Eric, Louis, C., Forge, V., Montet, X., Dumoulin, M., Tillement, Olivier, Institut Lumière Matière [Villeurbanne] (ILM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Nano-H SAS, Nano-H, Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Matériaux, ingénierie et science [Villeurbanne] (MATEIS), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), School of Pharmaceutical Sciences, Université de Genève = University of Geneva (UNIGE), Centre d’Ingénierie des Protéines, Université de Liège, and University of Geneva [Switzerland]
Subjects: [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging
Abstract: International audience; Amyloidosis is a systemic disorder in which proteins form insoluble aggregates (or fibrils) in extracellular tissues. Depending of the protein nature and its deposition area, this accumulation could lead to different pathologies. In this project, we focus on three kind of amyloidosis forms: i) Amyloid Aβ, ii) Islet Amyloid PolyPeptide IAPP, iii) Transthyretin TTR, which are respectively responsible of Alzheimer Disease, type II diabetes and finely cardiomyopathy and polyneuropathy. We are investigating two different strategies to target the fibrils: i) Camelid heavy chain antibody fragment (or Nanobody)[1], ii) Peptides derived from the protein responsible of the aggregate.
Published: 2014

28. Structure-Based Design of Benzoxazoles as new inhibitors for D-Alanyl-D-Alanine Ligase

Author: Stéphane Vandevuer, Isabelle Ortmans, Colette Duez, Isabelle Tytgat, Martine Prévost, Finton Sirockin, Annick Dejaegere, Evelina Colacino, Paul M. Tulkens, Jacques H. Poupaert, Françoise Van Bambeke, Unité de Pharmacologie cellulaire et moléculaire, Université Catholique de Louvain = Catholic University of Louvain (UCL), Structure et Fonction des Membranes Biologiques et Bioinformatique génomique et structurale, Université Libre de Buxelles, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), Unité de Chimie Pharmaceutique et Radiopharmacie (UCL-CMFA 7340), Centre d'Ingénierie des Protéines, and Université de Liège
Subjects: animal structures, Binding free energy, Stereochemistry, 010402 general chemistry, 01 natural sciences, Bacterial cell structure, Drug design, Docking, 03 medical and health sciences, chemistry.chemical_compound, Biosynthesis, Antibiotics, Drug Discovery, IC50, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, DNA ligase, D-Ala-D-Ala ligase, biology, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Organic Chemistry, Active site, AutoDock, 0104 chemical sciences, Computer Science Applications, carbohydrates (lipids), Enzyme, chemistry, Docking (molecular), biology.protein
Abstract: International audience; D-Alanyl – D-alanine ligase is an enzyme which catalyzes the dimerization of D-alanine, and, as such, has an essential role in bacterial cell wall biosynthesis. It has been shown that inhibition of D-alanyl – D-alanine ligase prevents bacterial growth. D-Alanyl – D-alanine ligase represents therefore a viable antimicrobial target. The 3D structure of this enzyme complexed with a phosphinophosphate inhibitor has been reported, which allows for structure-based design studies. Four softwares (LUDI, MCSS, Autodock, and Glide) developed either for fragment or full-molecule docking were compared and scored for their ability to position in the active site four prototypic ligands: two inhibitors, i.e. a phosphinophosphate derivative and D-cycloserine, D-alanine and D-alanyl – D-alanine. Best performances were obtained with Glide and MCSS. A short series of novel derivatives based on a 2-phenylbenzoxazole scaffold was designed de novo on the basis of computational data. The best compound was found to fully inhibit the D-alanyl – D-alanine ligase of E. faecalis with an IC50 of 400 mM.
Published: 2009
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29. Electronic and Molecular Properties of an Adsorbed Protein Monolayer Probed by Two-Color Sum-Frequency Generation Spectroscopy

Author: Jean-Marie Frère, Sophie Hanique, André Peremans, Cédric Volcke, Laurent Dreesen, Yves Caudano, Alaa Addin Mani, Yannick Sartenaer, Christophe Humbert, Paul Thiry, LASMOS Laboratory, Facultés Universitaires Notre Dame de la Paix (FUNDP), Centre d'Ingénierie des Protéines, and Université de Liège
Subjects: Protein Conformation, Surface Properties, Green Fluorescent Proteins, Substrate (electronics), Microscopy, Atomic Force, Molecular physics, Vibration, Protein Structure, Secondary, symbols.namesake, Species Specificity, Monolayer, Electrochemistry, Molecule, Animals, General Materials Science, Spectroscopy, ComputingMilieux_MISCELLANEOUS, Platinum, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], Chemistry, Spectrum Analysis, Membranes, Artificial, Surfaces and Interfaces, Condensed Matter Physics, Crystallography, Atomic electron transition, Mutation, symbols, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Adsorption, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Absorption (chemistry), Raman spectroscopy, Sum frequency generation spectroscopy
Abstract: Two-color sum-frequency generation spectroscopy (2C-SFG) is used to probe the molecular and electronic properties of an adsorbed layer of the green fluorescent protein mutant 2 (GFPmut2) on a platinum (111) substrate. First, the spectroscopic measurements, performed under different polarization combinations, and atomic force microscopy (AFM) show that the GFPmut2 proteins form a fairly ordered monolayer on the platinum surface. Next, the nonlinear spectroscopic data provide evidence of particular coupling phenomena between the GFPmut2 vibrational and electronic properties. This is revealed by the occurrence of two doubly resonant sum-frequency generation processes for molecules having both their Raman and infrared transition moments in a direction perpendicular to the sample plane. Finally, our 2C-SFG analysis reveals two electronic transitions corresponding to the absorption and fluorescence energy levels which are related to two different GFPmut2 conformations: the B (anionic) and I forms, respectively. Their observation and wavelength positions attest the keeping of the GFPmut2 electronic properties upon adsorption on the metallic surface.
Published: 2004
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30. Design and synthesis of imidazoline derivatives active on glucose homeostasis in a rat model of type II diabetes. 1. Synthesis and biological activities of N-benzyl-N'-(arylalkyl)-2-(4',5'-dihydro-1'H-imidazol-2'-yl)piperazines

Author: Jean Jacques Godfroid, P. Renard, E. Touboul, Bruno Pfeiffer, G. Le Bihan, B. Guardiola-Lemaitre, Luc Pénicaud, T. Bellahsene, Xuan Wang, Georges Dive, D. Manechez, Alain Ktorza, A. Lamouri, Frédéric Rondu, CAN-FOR, National Institute of Advanced Science and Technology, Centre d'Ingénierie des Protéines, Université de Liège, Institut de recherches Servier (INSTITUT DE RECHERCHES SERVIER), INSTITUT SERVIER, Métabolisme Plasticité et Mitochondrie [lié à l'ex IFR 31] (LMPM), IFR 31 Louis Bugnard (IFR 31), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physiopathologie de la nutrition (LPN), and Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Blood Glucose, Male, Models, Molecular, medicine.medical_specialty, Adrenergic receptor, Imidazoline receptor, 010402 general chemistry, 01 natural sciences, Chemical synthesis, Piperazines, Receptors, Adrenergic, alpha-2, In vivo, Internal medicine, Diabetes mellitus, Drug Discovery, medicine, Animals, Homeostasis, Glucose homeostasis, Rats, Wistar, B cell, ComputingMilieux_MISCELLANEOUS, 010405 organic chemistry, Chemistry, Imidazoles, Glucose Tolerance Test, Streptozotocin, medicine.disease, Rats, 0104 chemical sciences, 3. Good health, Disease Models, Animal, medicine.anatomical_structure, Endocrinology, Diabetes Mellitus, Type 2, Drug Design, Molecular Medicine, Cattle, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, medicine.drug
Abstract: The physiopathology of non-insulin-dependent diabetes mellitus is associated with a dysfunction in the regulation of insulin secretion. The alpha 2-adrenoceptors have been reported to be involved in this alteration, although alpha 2-antagonists containing an imidazoline ring may stimulate insulin secretion independently of alpha 2-adrenoceptor blockage. Recently, a new "imidazoline-binding site" involved in the control of K(+)-ATP channels in the B cell has been proposed. In the course of searching for new antidiabetic agents, 1-alkyl-2-(4',5'-dihydro-1'H-imidazol-2'-yl)-4-benzylpiperazines, 1-benzyl-2-(4',5'-dihydro-1'H-imidazol-2'-yl)-4-alkylpiperazines, and 1-benzyl-2-(4',5'-dihydro-1'H-imidazol-2'-yl)-4-benzylpiperazines have been designed and evaluated as potential adrenoceptor antagonists. Pharmacological evaluation was performed in vivo using glucose tolerance tests performed on a rat model of type II diabetes obtained by injection of a low dose (35 mg/kg) of streptozotocin (STZ). For some compounds, binding experiments were performed on alpha 2 adrenoceptors and I1 and I2 imidazoline-binding sites. The biological and physicochemical data have been combined with molecular modeling studies to establish structure-activity relationships. The most active compound was 1-(2',4'-dichlorobenzyl)-2-(4',5'-dihydro-1'H-imidazol-2'-yl)- 4-methylpiperazine (7f); intraperitoneal administration (100 mumol/kg) of 7f strongly improved glucose tolerance in STZ diabetic rats. This effect seemed at least partly mediated by a significant increase of insulin secretion. Other compounds of the same family (7b, 16f, 23b) have also shown potent activity. We found no correlation between in vivo antihyperglycemic properties and in vitro affinities for alpha 2-adrenoceptors or I1, and I2 binding sites. These compounds can be considered as antihyperglycemic agents potentially useful for treatment of type II diabetes and are currently under complementary investigation.
Published: 1997

31. Wave packets in a bifurcating region of an energy landscape: Diels-Alder dimerization of cyclopentadiene

Author: Benjamin Lasorne, Michèle Desouter-Lecomte, Georges Dive, Laboratoire de Chimie Physique D'Orsay (LCPO), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre d'Ingénierie des Protéines, Université de Liège, and Département de Chimie
Subjects: 010304 chemical physics, Chemistry, Wave packet, Quantum dynamics, General Physics and Astronomy, Semiclassical physics, Energy landscape, Dissipation, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, Bond length, symbols.namesake, Quantum mechanics, 0103 physical sciences, symbols, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Physical and Theoretical Chemistry, Hamiltonian (quantum mechanics), ComputingMilieux_MISCELLANEOUS, Bifurcation
Abstract: Quantum dynamics in a valley ridge inflection (VRI) point region is analyzed in the case of the Diels-Alder endo-dimerization of cyclopentadiene pointed out recently by [Caramella et al., J. Am. Chem. Soc. 124, 1130 (2002)]. The VRI point is located along the reaction path connecting the bispericyclic symmetrical transition structure put in evidence by Caramella et al. and the transition state of the Cope rearrangement. Dynamics is carried out by using constrained Hamiltonian methodology. The active coordinates are the first formed C–C bond length and the difference between the two other C–C bond lengths which achieve the dimerization as 4+2 or 2+4 adducts. A two-dimensional (2D) minimum-energy surface have been computed at the Becke 3 Lee–Yong–Parr∕6‐31G* level. The energy landscape can be classified as an uphill ridge-pitchfork VRI bifurcation according to a recent classification of bifurcation events [W. Quapp, J. Mol. Struct. 695–696, 95 (2004)]. Dynamics does not describe the thermal reaction but concerns wave packets which could be prepared by pulse reagents, i.e., by coherent control. We analyze how the shape and initial location on the ground potential-energy surface are linked to the synchronous or asynchronous mechanism of the final step after the first transition state. We use a one-dimensional model of optimum control theory to check the feasibility of such a coherent preparation. The wave-packet evolution in the VRI domain is well explained by semiclassical predictions even with the negative curvature of the unstable ridge. Finally, a crude model of dissipation has been introduced to test the stability of the 2D predictions.
Published: 2005
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32. Synthesis of β-lactam-zidovudine pronucleosides as potential selective narrow-spectrum antibacterial agents.

Author: Rosales-Hurtado M, Faure F, Sannio F, Verdirosa F, Feller G, Carretero E, Vo-Hoang Y, Licznar-Fajardo P, Peyrottes S, Docquier JD, and Gavara L
Subjects: Gram-Negative Bacteria drug effects, Nucleosides chemistry, Nucleosides pharmacology, Nucleosides chemical synthesis, Molecular Structure, beta-Lactamases metabolism, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents chemical synthesis, Anti-Bacterial Agents chemistry, beta-Lactams pharmacology, beta-Lactams chemical synthesis, beta-Lactams chemistry, Microbial Sensitivity Tests, Zidovudine pharmacology, Zidovudine chemical synthesis, Zidovudine chemistry
Abstract: Since the discovery of penicillin, the forerunner of the most widely used class of antibiotics ( i.e. β-lactams), natural compounds and their derivatives represented a major source of antibacterial therapeutic products whose availability enabled modern medical practices (invasive surgery, organ transplant, etc .). However, the relentless emergence of resistant bacteria is challenging the long-term efficacy of antibiotics, also decreasing their economic attractiveness for big pharma, leading to a significant decay in antibacterial development in the 21 st century and an increased use of last-resort drugs such as carbapenems or colistin. Indeed, bacteria evolved an arsenal of resistance mechanisms, leading to the emergence of totally-drug resistant isolates, already sporadically isolated among Gram-negative bacterial species. To face this deadly peril, it is fundamental to explore new ground-breaking approaches. In view of the significance of both β-lactam antibiotics and the production of one or more β-lactamases as the major resistance mechanism (especially in Gram-negative bacteria), we implemented an original approach to selectively deliver antibacterial zidovudine (AZT) exploiting the β-lactamase-mediated hydrolysis of a β-lactam-conjugate prodrug. The synthesis of the targeted pronucleosides was performed in 5-7 steps and based on an original Pd-catalyzed cross-coupling reaction. Enzymatic and microbiological evaluations were performed to evaluate the synthesized pronucleosides, yielding new insights into molecular recognition of β-lactamase enzymes. This approach would potentially allow a targeted and selective eradication of antibiotic-resistant β-lactamase-producing (opportunistic) pathogens, as the inactive prodrug is unable to harm the commensal microbial flora.
Published: 2025
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33. Ticagrelor alters the membrane of Staphylococcus aureus and enhances the activity of vancomycin and daptomycin without eliciting cross-resistance.

Author: Leeten K, Jacques N, Esquembre LA, Schneider DC, Straetener J, Henriksen C, Musumeci L, Putters F, Melo S, Sánchez-López E, Giera M, Penoy N, Piel G, Verlaine O, Amoroso A, Joris B, Slavetinsky CJ, Goffin E, Pirotte B, Frees D, Brötz-Oesterhelt H, Lancellotti P, and Oury C
Subjects: Bacillus subtilis drug effects, Bacillus subtilis genetics, Methicillin-Resistant Staphylococcus aureus drug effects, Methicillin-Resistant Staphylococcus aureus genetics, Drug Synergism, Drug Resistance, Multiple, Bacterial, Humans, Daptomycin pharmacology, Vancomycin pharmacology, Anti-Bacterial Agents pharmacology, Ticagrelor pharmacology, Microbial Sensitivity Tests, Cell Membrane drug effects, Staphylococcus aureus drug effects, Staphylococcus aureus genetics
Abstract: Infections with multidrug-resistant bacteria pose a major healthcare problem which urges the need for novel treatment options. Besides its potent antiplatelet properties, ticagrelor has antibacterial activity against Gram-positive bacteria, including methicillin- and vancomycin-resistant Staphylococcus aureus (MRSA and VRSA). Several retrospective studies in cardiovascular patients support an antibacterial effect of this drug which is not related to its antiplatelet activity. We investigated the mechanism of action of ticagrelor in Staphylococcus aureus and model Bacillus subtilis, and assessed cross-resistance with two conventional anti-MRSA antibiotics, vancomycin and daptomycin. Bacillus subtilis bioreporter strains revealed ticagrelor-induced cell envelope-related stress responses. Sub-inhibitory drug concentrations caused membrane depolarization, impaired positioning of both the peripheral membrane protein MinD and the peptidoglycan precursor lipid II, and it affected cell shape. At the MIC, ticagrelor destroyed membrane integrity, indicated by the influx of membrane impermeable dyes, and lipid aggregate formation. Whole-genome sequencing of in vitro -generated ticagrelor-resistant MRSA clones revealed mutations in genes encoding ClpP, ClpX, and YjbH. Lipidomic analysis of resistant clones displayed changes in levels of the most abundant lipids of the Staphylococcus aureus membrane, for example, cardiolipins, phosphatidylglycerols, and diacylglycerols. Exogeneous cardiolipin, phosphatidylglycerol, or diacylglycerol antagonized the antibacterial properties of ticagrelor. Ticagrelor enhanced MRSA growth inhibition and killing by vancomycin and daptomycin in both exponential and stationary phases. Finally, no cross-resistance was observed between ticagrelor and daptomycin, or vancomycin. Our study demonstrates that ticagrelor targets multiple lipids in the cytoplasmic membrane of Gram-positive bacteria, thereby retaining activity against multidrug-resistant staphylococci including daptomycin- and vancomycin-resistant strains.IMPORTANCEInfections with multidrug-resistant bacteria pose a major healthcare problem with an urgent need for novel treatment options. The antiplatelet drug ticagrelor possesses antibacterial activity against Gram-positive bacteria including methicillin-resistant and vancomycin-resistant Staphylococcus aureus strains. We report a unique, dose-dependent, antibacterial mechanism of action of ticagrelor, which alters the properties and integrity of the bacterial cytoplasmic membrane. Ticagrelor retains activity against multidrug-resistant staphylococci, including isolates carrying the most common in vivo selected daptomycin resistance mutations and vancomycin-intermediate Staphylococcus aureus . Our data support the use of ticagrelor as adjunct therapy against multidrug-resistant strains. Because of the presence of multiple non-protein targets of this drug within the bacterial membrane, resistance development is expected to be slow. All these findings corroborate the accumulating observational clinical evidence for a beneficial anti-bacterial effect of ticagrelor in cardiovascular patients in need of such treatment., Competing Interests: The authors declare no conflict of interest.
Published: 2024
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34. Reversing the relative time courses of the peptide bond reaction with oligopeptides of different lengths and charged amino acid distributions in the ribosome exit tunnel.

Author: Joiret M, Kerff F, Rapino F, Close P, and Geris L
Abstract: The kinetics of the protein elongation cycle by the ribosome depends on intertwined factors. One of these factors is the electrostatic interaction of the nascent protein with the ribosome exit tunnel. In this computational biology theoretical study, we focus on the rate of the peptide bond formation and its dependence on the ribosome exit tunnel electrostatic potential profile. We quantitatively predict how oligopeptides of variable lengths can affect the peptide bond formation rate. We applied the Michaelis-Menten model as previously extended to incorporate the mechano-biochemical effects of forces on the rate of reaction at the catalytic site of the ribosome. For a given pair of carboxy-terminal amino acid substrate at the P- and an aminoacyl-tRNA at the A-sites, the relative time courses of the peptide bond formation reaction can be reversed depending on the oligopeptide sequence embedded in the tunnel and their variable lengths from the P-site. The reversal is predicted to occur from a shift in positions of charged amino acids upstream in the oligopeptidyl-tRNA at the P-site. The position shift must be adjusted by clever design of the oligopeptide probes using the electrostatic potential profile along the exit tunnel axial path. These predicted quantitative results bring strong evidence of the importance and relative contribution of the electrostatic interaction of the ribosome exit tunnel with the nascent peptide chain during elongation., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© 2024 The Author(s).)
Published: 2024
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35. Structure-Based Optimization of 1,2,4-Triazole-3-Thione Derivatives: Improving Inhibition of NDM-/VIM-Type Metallo-β-Lactamases and Synergistic Activity on Resistant Bacteria.

Author: Bersani M, Failla M, Vascon F, Gianquinto E, Bertarini L, Baroni M, Cruciani G, Verdirosa F, Sannio F, Docquier JD, Cendron L, Spyrakis F, Lazzarato L, and Tondi D
Abstract: The worldwide emergence and dissemination of Gram-negative bacteria expressing metallo-β-lactamases (MBLs) menace the efficacy of all β-lactam antibiotics, including carbapenems, a last-line treatment usually restricted to severe pneumonia and urinary tract infections. Nonetheless, no MBL inhibitor is yet available in therapy. We previously identified a series of 1,2,4-triazole-3-thione derivatives acting as micromolar inhibitors of MBLs in vitro, but devoid of synergistic activity in microbiological assays. Here, via a multidisciplinary approach, including molecular modelling, synthesis, enzymology, microbiology, and X-ray crystallography, we optimized this series of compounds and identified low micromolar inhibitors active against clinically relevant MBLs (NDM-1- and VIM-type). The best inhibitors increased, to a certain extent, the susceptibility of NDM-1- and VIM-4-producing clinical isolates to meropenem. X-ray structures of three selected inhibitors in complex with NDM-1 elucidated molecular recognition at the base of potency improvement, confirmed in silico predicted orientation, and will guide further development steps.
Published: 2023
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36. Nucleoside Derivatives of 2,6-Diaminopurine Antivirals: Base-Modified Nucleosides with Broad-Spectrum Antimicrobial Properties.

Author: Grazia Martina M, Giammarino F, Vicenti I, Groaz E, Rozenski J, Incerti M, Sannio F, Docquier JD, Zazzi M, and Radi M
Subjects: Humans, Nucleosides chemistry, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Gram-Negative Bacteria, Gram-Positive Bacteria, Antiviral Agents chemistry, Viruses
Abstract: The plethora of viral outbreaks experienced in the last decade, together with the widespread distribution of many re-emerging and newly emerging viruses, emphasize the urgent need for novel broad-spectrum antivirals as tools for early intervention in case of future epidemics. Non-natural nucleosides have been at the forefront for the treatment of infectious diseases for many years and still represent one of the most successful classes of antiviral molecules on the market. In the attempt to explore the biologically relevant chemical space of this class of antimicrobials, we describe herein the development of novel base-modified nucleosides by converting previously identified 2,6-diaminopurine antivirals into the corresponding D/L ribonucleosides, acyclic nucleosides and prodrug derivatives. A phenotypic screening against viruses belonging to different families (Flaviviridae, Coronaviridae, Retroviridae) and against a panel of Gram-positive and Gram-negative bacteria, allowed to identify a few interesting molecules with broad-spectrum antimicrobial activities., (© 2023 Wiley-VCH Verlag GmbH.)
Published: 2023
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37. Zidovudine-β-Lactam Pronucleoside Strategy for Selective Delivery into Gram-Negative Bacteria Triggered by β-Lactamases.

Author: Rosales-Hurtado M, Sannio F, Lari L, Verdirosa F, Feller G, Carretero E, Vo-Hoang Y, Licznar-Fajardo P, Docquier JD, and Gavara L
Subjects: beta-Lactamases, Zidovudine pharmacology, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Gram-Negative Bacteria, beta-Lactams pharmacology, Prodrugs chemistry
Abstract: Addressing antibacterial resistance is a major concern of the modern world. The development of new approaches to meet this deadly threat is a critical priority. In this article, we investigate a new approach to negate bacterial resistance: exploit the β-lactam bond cleavage by β-lactamases to selectively trigger antibacterial prodrugs into the bacterial periplasm. Indeed, multidrug-resistant Gram-negative pathogens commonly produce several β-lactamases that are able to inactivate β-lactam antibiotics, our most reliable and widely used therapeutic option. The chemical structure of these prodrugs is based on a monobactam promoiety, covalently attached to the active antibacterial substance, zidovudine (AZT). We describe the synthesis of 10 prodrug analogues ( 5a-h ) in four to nine steps and their biological activity. Selective enzymatic activation by a panel of β-lactamases is demonstrated, and subsequent structure-activity relationships are discussed. The best compounds are further evaluated for their activity on both laboratory strains and clinical isolates, preliminary stability, and toxicity.
Published: 2023
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38. A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome and its significance for the elongation cycle kinetics.

Author: Joiret M, Kerff F, Rapino F, Close P, and Geris L
Abstract: The central function of the large subunit of the ribosome is to catalyze peptide bond formation. This biochemical reaction is conducted at the peptidyl transferase center (PTC). Experimental evidence shows that the catalytic activity is affected by the electrostatic environment around the peptidyl transferase center. Here, we set up a minimal geometrical model fitting the available x-ray solved structures of the ribonucleic cavity around the catalytic center of the large subunit of the ribosome. The purpose of this phenomenological model is to estimate quantitatively the electrostatic potential and electric field that are experienced during the peptidyl transfer reaction. At least two reasons motivate the need for developing this quantification. First, we inquire whether the electric field in this particular catalytic environment, made only of nucleic acids, is of the same order of magnitude as the one prevailing in catalytic centers of the proteic enzymes counterparts. Second, the protein synthesis rate is dependent on the nature of the amino acid sequentially incorporated in the nascent chain. The activation energy of the catalytic reaction and its detailed kinetics are shown to be dependent on the mechanical work exerted on the amino acids by the electric field, especially when one of the four charged amino acid residues (R, K, E, D) has previously been incorporated at the carboxy-terminal end of the peptidyl-tRNA. Physical values of the electric field provide quantitative knowledge of mechanical work, activation energy and rate of the peptide bond formation catalyzed by the ribosome. We show that our theoretical calculations are consistent with two independent sets of previously published experimental results. Experimental results for E.coli in the minimal case of the dipeptide bond formation when puromycin is used as the final amino acid acceptor strongly support our theoretically derived reaction time courses. Experimental Ribo-Seq results on E. coli and S. cerevisiae comparing the residence time distribution of ribosomes upon specific codons are also well accounted for by our theoretical calculations. The statistical queueing time theory was used to model the ribosome residence time per codon during nascent protein elongation and applied for the interpretation of the Ribo-Seq data. The hypo-exponential distribution fits the residence time observed distribution of the ribosome on a codon. An educated deconvolution of this distribution is used to estimate the rates of each elongation step in a codon specific manner. Our interpretation of all these results sheds light on the functional role of the electrostatic profile around the PTC and its impact on the ribosome elongation cycle., Competing Interests: All authors declare the absence of any conflict of interest., (© 2023 The Author(s).)
Published: 2023
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39. The impact of counterions in biological activity: case study of antibacterial alkylguanidino ureas.

Author: Ardino C, Sannio F, Pasero C, Botta L, Dreassi E, Docquier JD, and D'Agostino I
Subjects: Reproducibility of Results, Amines, Anti-Bacterial Agents pharmacology
Abstract: Trifluoroacetic acid (TFA), due to its strong acidity and low boiling point, is extensively used in protecting groups-based synthetic strategies. Indeed, synthetic compounds bearing basic functions, such as amines or guanidines (commonly found in peptido or peptidomimetic derivatives), developed in the frame of drug discovery programmes, are often isolated as trifluoroacetate (TF-Acetate) salts and their biological activity is assessed as such in in vitro, ex vivo, or in vivo experiments. However, the presence of residual amounts of TFA was reported to potentially affect the accuracy and reproducibility of a broad range of cellular assays (e. g. antimicrobial susceptibility testing, and cytotoxicity assays) limiting the further development of these derivatives. Furthermore, the impact of the counterion on biological activity, including TF-Acetate, is still controversial. Herein, we present a focused case study aiming to evaluate the activity of an antibacterial AlkylGuanidino Urea (AGU) compound obtained as TF-Acetate (1a) and hydrochloride (1b) salt forms to highlight the role of counterions in affecting the biological activity. We also prepared and tested the corresponding free base (1c). The exchange of the counterions applied to polyguanidino compounds represents an unexplored and challenging field, which required significant efforts for the successful optimization of reliable methods of preparation, also reported in this work. In the end, the biological evaluation revealed a quite similar biological profile for the salt derivatives 1a and 1b and a lower potency was found for the free base 1c., (© 2022. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)
Published: 2023
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40. Peptaibol Analogs Show Potent Antibacterial Activity against Multidrug Resistant Opportunistic Pathogens.

Author: Dalla Torre C, Sannio F, Battistella M, Docquier JD, and De Zotti M
Subjects: Antimicrobial Cationic Peptides pharmacology, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Bacteria, Staphylococcus aureus, Microbial Sensitivity Tests, Pseudomonas aeruginosa, Drug Resistance, Multiple, Bacterial, Peptaibols, Acinetobacter baumannii
Abstract: New classes of antibacterial drugs are urgently needed to address the global issue of antibiotic resistance. In this context, peptaibols are promising membrane-active peptides since they are not involved in innate immunity and their antimicrobial activity does not involve specific cellular targets, therefore reducing the chance of bacterial resistance development. Trichogin GA IV is a nonhemolytic, natural, short-length peptaibol active against Gram-positive bacteria and resistant to proteolysis. In this work, we report on the antibacterial activity of cationic trichogin analogs. Several peptides appear non-hemolytic and strongly active against many clinically relevant bacterial species, including antibiotic-resistant clinical isolates, such as Staphylococcus aureus , Acinetobacter baumannii , and extensively drug-resistant Pseudomonas aeruginosa , against which there are only a limited number of antibiotics under development. Our results further highlight how the modification of natural peptides is a valuable strategy for obtaining improved antibacterial agents with potential therapeutic applications.
Published: 2023
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41. Discovery and Optimization of a Novel Macrocyclic Amidinourea Series Active as Acidic Mammalian Chitinase Inhibitors.

Author: Balestri LJI, Trivisani CI, Orofino F, Fiorucci D, Truglio GI, D'Agostino I, Poggialini F, Botta L, Docquier JD, and Dreassi E
Abstract: Our research group has been involved for a long time in the development of macrocyclic amidinoureas (MCAs) as antifungal agents. The mechanistic investigation drove us to perform an in silico target fishing study, which allowed the identification of chitinases as one of their putative targets, with 1a showing a submicromolar inhibition of Trichoderma viride chitinase. In this work, we investigated the possibility to further inhibit the corresponding human enzymes, acidic mammalian chitinase (AMCase) and chitotriosidase (CHIT1), involved in several chronic inflammatory lung diseases. Thus, we first validated the inhibitory activity of 1a against AMCase and CHIT1 and then designed and synthesized new derivatives aimed at improving the potency and selectivity against AMCase. Among them, compound 3f emerged for its activity profile along with its promising in vitro ADME properties. We also gained a good understanding of the key interactions with the target enzyme through in silico studies., Competing Interests: The authors declare no competing financial interest., (© 2023 American Chemical Society.)
Published: 2023
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42. Chemical Optimization of Selective Pseudomonas aeruginosa LasB Elastase Inhibitors and Their Impact on LasB-Mediated Activation of IL-1β in Cellular and Animal Infection Models.

Author: Everett MJ, Davies DT, Leiris S, Sprynski N, Llanos A, Castandet JM, Lozano C, LaRock CN, LaRock DL, Corsica G, Docquier JD, Pallin TD, Cridland A, Blench T, Zalacain M, and Lemonnier M
Subjects: Animals, Mice, Kinetics, Models, Animal, Pancreatic Elastase, Pseudomonas aeruginosa, Virulence Factors
Abstract: LasB elastase is a broad-spectrum exoprotease and a key virulence factor of Pseudomonas aeruginosa , a major pathogen causing lung damage and inflammation in acute and chronic respiratory infections. Here, we describe the chemical optimization of specific LasB inhibitors with druglike properties and investigate their impact in cellular and animal models of P. aeruginosa infection. Competitive inhibition of LasB was demonstrated through structural and kinetic studies. In vitro LasB inhibition was confirmed with respect to several host target proteins, namely, elastin, IgG, and pro-IL-1β. Furthermore, inhibition of LasB-mediated IL-1β activation was demonstrated in macrophage and mouse lung infection models. In mice, intravenous administration of inhibitors also resulted in reduced bacterial numbers at 24 h. These highly potent, selective, and soluble LasB inhibitors constitute valuable tools to study the proinflammatory impact of LasB in P. aeruginosa infections and, most importantly, show clear potential for the clinical development of a novel therapy for life-threatening respiratory infections caused by this opportunistic pathogen.
Published: 2023
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43. Optimization of 1,2,4-Triazole-3-thiones toward Broad-Spectrum Metallo-β-lactamase Inhibitors Showing Potent Synergistic Activity on VIM- and NDM-1-Producing Clinical Isolates.

Author: Legru A, Verdirosa F, Vo-Hoang Y, Tassone G, Vascon F, Thomas CA, Sannio F, Corsica G, Benvenuti M, Feller G, Coulon R, Marcoccia F, Devente SR, Bouajila E, Piveteau C, Leroux F, Deprez-Poulain R, Deprez B, Licznar-Fajardo P, Crowder MW, Cendron L, Pozzi C, Mangani S, Docquier JD, Hernandez JF, and Gavara L
Subjects: Humans, HeLa Cells, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents chemistry, beta-Lactamases metabolism, Microbial Sensitivity Tests, beta-Lactamase Inhibitors pharmacology, beta-Lactamase Inhibitors chemistry, Thiones pharmacology
Abstract: Metallo-β-lactamases (MBLs) contribute to the resistance of Gram-negative bacteria to carbapenems, last-resort antibiotics at hospital, and MBL inhibitors are urgently needed to preserve these important antibacterial drugs. Here, we describe a series of 1,2,4-triazole-3-thione-based inhibitors displaying an α-amino acid substituent, which amine was mono- or disubstituted by (hetero)aryl groups. Compounds disubstituted by certain nitrogen-containing heterocycles showed submicromolar activities against VIM-type enzymes and strong NDM-1 inhibition ( K i = 10-30 nM). Equilibrium dialysis, native mass spectrometry, isothermal calorimetry (ITC), and X-ray crystallography showed that the compounds inhibited both VIM-2 and NDM-1 at least partially by stripping the catalytic zinc ions. These inhibitors also displayed a very potent synergistic activity with meropenem (16- to 1000-fold minimum inhibitory concentration (MIC) reduction) against VIM-type- and NDM-1-producing ultraresistant clinical isolates, including Enterobacterales and Pseudomonas aeruginosa . Furthermore, selected compounds exhibited no or moderate toxicity toward HeLa cells, favorable absorption, distribution, metabolism, excretion (ADME) properties, and no or modest inhibition of several mammalian metalloenzymes.
Published: 2022
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44. Optimization of Pyrazole Compounds as Antibiotic Adjuvants Active against Colistin- and Carbapenem-Resistant Acinetobacter baumannii .

Author: Sannio F, Brizzi A, Del Prete R, Avigliano M, Simone T, Pagli C, Ferraro T, De Luca F, Paolino M, Corelli F, Mugnaini C, and Docquier JD
Abstract: The diffusion of antibiotic-resistant, Gram-negative, opportunistic pathogens, an increasingly important global public health issue, causes a significant socioeconomic burden. Acinetobacter baumannii isolates, despite causing a lower number of infections than Enterobacterales, often show multidrug-resistant phenotypes. Carbapenem resistance is also rather common, prompting the WHO to include carbapenem-resistant A. baumannii as a "critical priority" for the discovery and development of new antibacterial agents. In a previous work, we identified several series of compounds showing either direct-acting or synergistic activity against relevant Gram-negative species, including A. baumannii. Among these, two pyrazole compounds, despite being devoid of any direct-acting activity, showed remarkable synergistic activity in the presence of a subinhibitory concentration of colistin on K. pneumoniae and A. baumannii and served as a starting point for the synthesis of new analogues. In this work, a new series of 47 pyrazole compounds was synthesized. Some compounds showed significant direct-acting antibacterial activity on Gram-positive organisms. Furthermore, an evaluation of their activity as potential antibiotic adjuvants allowed for the identification of two highly active compounds on MDR Acinetobacter baumannii , including colistin-resistant isolates. This work confirms the interest in pyrazole amides as a starting point for the optimization of synergistic antibacterial compounds active on antibiotic-resistant, Gram-negative pathogens.
Published: 2022
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45. 1,2,4-Triazole-3-thione analogues with an arylakyl group at position 4 as metallo-β-lactamase inhibitors.

Author: Gavara L, Verdirosa F, Sevaille L, Legru A, Corsica G, Nauton L, Sandra Mercuri P, Sannio F, De Luca F, Hadjadj M, Cerboni G, Vo Hoang Y, Licznar-Fajardo P, Galleni M, Docquier JD, and Hernandez JF
Subjects: Humans, Anti-Bacterial Agents pharmacology, beta-Lactamases metabolism, Carbapenems pharmacology, Ceftazidime, Ceftriaxone, Ethylenes, HeLa Cells, Ligands, Meropenem, Microbial Sensitivity Tests, Triazoles chemistry, Triazoles pharmacology, Zinc, beta-Lactamase Inhibitors chemistry, beta-Lactamase Inhibitors pharmacology, Thiones
Abstract: Metallo-β-lactamases (MBLs) represent an increasingly serious threat to public health because of their increased prevalence worldwide in relevant opportunistic Gram-negative pathogens. MBLs efficiently inactivate widely used and most valuable β-lactam antibiotics, such as oxyiminocephalosporins (ceftriaxone, ceftazidime) and the last-resort carbapenems. To date, no MBL inhibitor has been approved for therapeutic applications. We are developing inhibitors characterized by a 1,2,4-triazole-3-thione scaffold as an original zinc ligand and few promising series were already reported. Here, we present the synthesis and evaluation of a new series of compounds characterized by the presence of an arylalkyl substituent at position 4 of the triazole ring. The alkyl link was mainly an ethylene, but a few compounds without alkyl or with an alkyl group of various lengths up to a butyl chain were also synthesized. Some compounds in both sub-series were micromolar to submicromolar inhibitors of tested VIM-type MBLs. A few of them were broad-spectrum inhibitors, as they showed significant inhibitory activity on NDM-1 and, to a lesser extent, IMP-1. Among these, several inhibitors were able to significantly reduce the meropenem MIC on VIM-1- and VIM-4- producing clinical isolates by up to 16-fold. In addition, ACE inhibition was absent or moderate and one promising compound did not show toxicity toward HeLa cells at concentrations up to 250 μM. This series represents a promising basis for further exploration. Finally, molecular modelling of representative compounds in complex with VIM-2 was performed to study their binding mode., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)
Published: 2022
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46. Towards Innovative Antibacterial Correctors for Cystic Fibrosis Targeting the Lung Microbiome with a Multifunctional Effect.

Author: Martina MG, Sannio F, Crespan E, Pavone M, Simoncini A, Barbieri F, Perini C, Pesce E, Maga G, Pedemonte N, Docquier JD, and Radi M
Subjects: Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Cystic Fibrosis Transmembrane Conductance Regulator genetics, Humans, Lung, Mutation, Cystic Fibrosis drug therapy, Cystic Fibrosis genetics, Microbiota
Abstract: Cystic fibrosis (CF) is a genetic disease caused by loss-of-function mutations in the CFTR gene, which codes for a defective ion channel. This causes an electrolyte imbalance and results in a spiral of negative effects on multiple organs, most notably the accumulation of thick mucus in the lungs, chronic respiratory tract infections and inflammation leading to pulmonary exacerbation and premature death. Progressive decline of lung function is mainly linked to persistent or recurring infections, mostly caused by bacteria, which require treatments with antibiotics and represent one of the major life-limiting factors in subjects with CF. Treatment of such a complex disease require multiple drugs with a consequent therapeutic burden and complications caused by drug-drug interactions and rapid emergence of bacterial drug resistance. We report herein our recent efforts in developing innovative multifunctional antibiotics specifically tailored to CF by a direct action on bacterial topoisomerases and a potential indirect effect on the pulmonary mucociliary clearance mediated by ΔF508-CFTR correction. The obtained results may pave the way for the development of a simplified therapeutic approach with a single agent acting as multifunctional Antibacterial-Corrector., (© 2022 Wiley-VCH GmbH.)
Published: 2022
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47. 1,2,4-Triazole-3-Thione Analogues with a 2-Ethylbenzoic Acid at Position 4 as VIM-type Metallo-β-Lactamase Inhibitors.

Author: Verdirosa F, Gavara L, Sevaille L, Tassone G, Corsica G, Legru A, Feller G, Chelini G, Mercuri PS, Tanfoni S, Sannio F, Benvenuti M, Cerboni G, De Luca F, Bouajila E, Vo Hoang Y, Licznar-Fajardo P, Galleni M, Pozzi C, Mangani S, Docquier JD, and Hernandez JF
Subjects: Anti-Bacterial Agents chemistry, Anti-Bacterial Agents pharmacology, Escherichia coli, Humans, Microbial Sensitivity Tests, Triazoles chemistry, beta-Lactamases metabolism, Thiones pharmacology, beta-Lactamase Inhibitors chemistry
Abstract: Metallo-β-lactamases (MBLs) are increasingly involved as a major mechanism of resistance to carbapenems in relevant opportunistic Gram-negative pathogens. Unfortunately, clinically efficient MBL inhibitors still represent an unmet medical need. We previously reported several series of compounds based on the 1,2,4-triazole-3-thione scaffold. In particular, Schiff bases formed between diversely 5-substituted-4-amino compounds and 2-carboxybenzaldehyde were broad-spectrum inhibitors of VIM-type, NDM-1 and IMP-1 MBLs. Unfortunately, these compounds were unable to restore antibiotic susceptibility of MBL-producing bacteria, probably because of poor penetration and/or susceptibility to hydrolysis. To improve their microbiological activity, we synthesized and characterized compounds where the hydrazone-like bond of the Schiff base analogues was replaced by a stable ethyl link. This small change resulted in a narrower inhibition spectrum, as all compounds were poorly or not inhibiting NDM-1 and IMP-1, but showed a significantly better activity on VIM-type enzymes, with K i values in the μM to sub-μM range. The resolution of the crystallographic structure of VIM-2 in complex with one of the best inhibitors yielded valuable information about their binding mode. Interestingly, several compounds were shown to restore the β-lactam susceptibility of VIM-type-producing E. coli laboratory strains and also of K. pneumoniae clinical isolates. In addition, selected compounds were found to be devoid of toxicity toward human cancer cells at high concentration, thus showing promising safety., (© 2022 Wiley-VCH GmbH.)
Published: 2022
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48. A Sub-Micromolar MraY AA Inhibitor with an Aminoribosyl Uridine Structure and a ( S , S )-Tartaric Diamide: Synthesis, Biological Evaluation and Molecular Modeling.

Author: Oliver M, Le Corre L, Poinsot M, Bosco M, Wan H, Amoroso A, Joris B, Bouhss A, Calvet-Vitale S, and Gravier-Pelletier C
Subjects: Bacterial Proteins chemistry, Molecular Dynamics Simulation, Transferases (Other Substituted Phosphate Groups), Uridine chemistry, Uridine pharmacology, Diamide, Transferases chemistry
Abstract: New inhibitors of the bacterial tranferase MraY are described. Their structure is based on an aminoribosyl uridine scaffold, which is known to be important for the biological activity of natural MraY inhibitors. A decyl alkyl chain was introduced onto this scaffold through various linkers. The synthesized compounds were tested against the MraY AA transferase activity, and the most active compound with an original ( S , S )-tartaric diamide linker inhibits MraY activity with an IC 50 equal to 0.37 µM. Their antibacterial activity was also evaluated on a panel of Gram-positive and Gram-negative strains; however, the compounds showed no antibacterial activity. Docking and molecular dynamics studies revealed that this new linker established two stabilizing key interactions with N190 and H325, as observed for the highly potent inhibitors carbacaprazamycin, muraymycin D2 and tunicamycin.
Published: 2022
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49. Was the Last Bacterial Common Ancestor a Monoderm after All?

Author: Léonard RR, Sauvage E, Lupo V, Perrin A, Sirjacobs D, Charlier P, Kerff F, and Baurain D
Subjects: Bayes Theorem, Gram-Negative Bacteria genetics, Phylogeny, Bacteria genetics, Gram-Positive Bacteria genetics
Abstract: The very nature of the last bacterial common ancestor (LBCA), in particular the characteristics of its cell wall, is a critical issue to understand the evolution of life on earth. Although knowledge of the relationships between bacterial phyla has made progress with the advent of phylogenomics, many questions remain, including on the appearance or disappearance of the outer membrane of diderm bacteria (also called Gram-negative bacteria). The phylogenetic transition between monoderm (Gram-positive bacteria) and diderm bacteria, and the associated peptidoglycan expansion or reduction, requires clarification. Herein, using a phylogenomic tree of cultivated and characterized bacteria as an evolutionary framework and a literature review of their cell-wall characteristics, we used Bayesian ancestral state reconstruction to infer the cell-wall architecture of the LBCA. With the same phylogenomic tree, we further revisited the evolution of the division and cell-wall synthesis ( dcw ) gene cluster using homology- and model-based methods. Finally, extensive similarity searches were carried out to determine the phylogenetic distribution of the genes involved with the biosynthesis of the outer membrane in diderm bacteria. Quite unexpectedly, our analyses suggest that all cultivated and characterized bacteria might have evolved from a common ancestor with a monoderm cell-wall architecture. If true, this would indicate that the appearance of the outer membrane was not a unique event and that selective forces have led to the repeated adoption of such an architecture. Due to the lack of phenotypic information, our methodology cannot be applied to all extant bacteria. Consequently, our conclusion might change once enough information is made available to allow the use of an even more diverse organism selection.
Published: 2022
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50. Purification and Characterization of Trehalase From Acyrthosiphon pisum, a Target for Pest Control.

Author: Neyman V, Francis F, Matagne A, Dieu M, Michaux C, and Perpète EA
Subjects: Animals, Insect Proteins genetics, Insect Proteins metabolism, Phylogeny, Aphids enzymology, Insect Control, Trehalase genetics, Trehalase metabolism
Abstract: Insect trehalases are glycoside hydrolases essential for trehalose metabolism and stress resistance. We here report the extraction and purification of Acyrthosiphon pisum soluble trehalase (ApTreh-1), its biochemical and structural characterization, as well as the determination of its kinetic properties. The protein has been purified by ammonium sulphate precipitation, first followed by an anion-exchange and then by an affinity chromatography. The SDS-PAGE shows a main band at 70 kDa containing two isoforms of ApTreh-1 (X1 and X2), identified by mass spectrometry and slightly contrasting in the C-terminal region. A phylogenetic tree, a multiple sequence alignment, as well as a modelled 3D-structure were constructed and they all reveal the ApTreh-1 similarity to other insect trehalases, i.e. the two signature motifs 179 PGGRFRELYYWDTY 192 and 479 QWDFPNAWPP 489 , a glycine-rich region 549 GGGGEY 554 , and the catalytic residues Asp336 and Glu538. The optimum enzyme activity occurs at 45 °C and pH 5.0, with K m and V max values of ~ 71 mM and ~ 126 µmol/min/mg, respectively. The present structural and functional characterization of soluble A. pisum trehalase enters the development of new strategies to control the aphids pest without significant risk for non-target organisms and human health., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
Published: 2022
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