240 results on '"Anna Bernardi"'
Search Results
2. Glycomimetic antagonists of BC2L-C lectin: insights from molecular dynamics simulations
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Giulia Antonini, Monica Civera, Kanhaya Lal, Sarah Mazzotta, Annabelle Varrot, Anna Bernardi, and Laura Belvisi
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lectins ,glycomimetics ,molecular dynamics simulations ,C-fucosides ,fucosyl amides ,Biology (General) ,QH301-705.5 - Abstract
Opportunistic infections from multidrug-resistant pathogens such as Burkholderia cenocepacia are a threatening risk for hospital-bound patients suffering from immunocompromised conditions or cystic fibrosis. B. cenocepacia BC2L-C lectin has been linked to bacterial adhesion and biofilm formation, thus hindering its activity is seen as a promising strategy to reduce the severity of the infection. We recently described the first bifunctional ligands of the trimeric N-terminal domain of BC2L-C (BC2L-C–Nt), capable of simultaneously engaging its fucose-specific sugar binding site and a vicinal region at the interface between two monomers. Here, we report a computational workflow for the study of these glycomimetic bifunctional ligands in complex with BC2L-C-Nt, aimed at investigating the molecular basis of ligand binding and the dynamics of glycomimetic/lectin interactions. In particular, we evaluated the use of molecular docking in the protein trimer, followed by refinement using MM-GBSA re-scoring and MD simulations in explicit water. Computational results were compared to experimental data derived from X-ray crystallography and isothermal titration calorimetry. The computational protocol proved suitable to provide a reliable description of the interactions between the ligands and BC2L-C-Nt, highlighting the contribution of MD simulations in explicit solvent for a good fit with the experimental observations. The information achieved in the study and the whole workflow appear promising for the structure-based design of improved BC2L-C-Nt ligands as novel antimicrobials with antiadhesive properties.
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- 2023
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- View/download PDF
3. Identification of New L-Fucosyl and L-Galactosyl Amides as Glycomimetic Ligands of TNF Lectin Domain of BC2L-C from Burkholderia cenocepacia
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Sarah Mazzotta, Giulia Antonini, Francesca Vasile, Emilie Gillon, Jon Lundstrøm, Annabelle Varrot, Laura Belvisi, and Anna Bernardi
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lectins ,fucosides ,N-glycosides ,crystallography ,glycomimetics ,antiadhesive therapy ,Organic chemistry ,QD241-441 - Abstract
The inhibition of carbohydrate-lectin interactions is being explored as an efficient approach to anti adhesion therapy and biofilm destabilization, two alternative antimicrobial strategies that are being explored against resistant pathogens. BC2L-C is a new type of lectin from Burkholderia cenocepacia that binds (mammalian) fucosides at the N-terminal domain and (bacterial) mannosides at the C-terminal domain. This double carbohydrate specificity allows the lectin to crosslink host cells and bacterial cells. We have recently reported the design and generation of the first glycomimetic antagonists of BC2L-C, β-C- or β-N-fucosides that target the fucose-specific N-terminal domain (BC2L-C-Nt). The low water solubility of the designed N-fucosides prevented a full examination of this promising series of ligands. In this work, we describe the synthesis and biophysical evaluation of new L-fucosyl and L-galactosyl amides, designed to be water soluble and to interact with BC2L-C-Nt. The protein–ligand interaction was investigated by Saturation Transfer Difference NMR, Isothermal Titration Calorimetry and crystallographic studies. STD-NMR experiments showed that both fucosyl and galactosyl amides compete with α-methyl fucoside for lectin binding. A new hit compound was identified with good water solubility and an affinity for BC2L-C-Nt of 159 μM (ITC), which represents a one order of magnitude gain over α-methyl fucoside. The x-ray structure of its complex with BC2L-C-Nt was solved at 1.55 Å resolution.
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- 2023
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4. Mannosylated brush copolymers based on poly(ethylene glycol) and poly(ε-caprolactone) as multivalent lectin-binding nanomaterials
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Stefania Ordanini, Wanda Celentano, Anna Bernardi, and Francesco Cellesi
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atom transfer radical polymerization (atrp) ,glycopolymer ,lectin ,poly(ethylene glycol) ,poly(ε-caprolactone) ,ring-opening polymerization (rop) ,Technology ,Chemical technology ,TP1-1185 ,Science ,Physics ,QC1-999 - Abstract
A class of linear and four-arm mannosylated brush copolymers based on poly(ethylene glycol) and poly(ε-caprolactone) is presented here. The synthesis through ring-opening and atom transfer radical polymerizations provided high control over molecular weight and functionality. A post-polymerization azide–alkyne cycloaddition allowed for the formation of glycopolymers with different mannose valencies (1, 2, 4, and 8). In aqueous media, these macromolecules formed nanoparticles that were able to bind lectins, as investigated by concanavalin A binding assay. The results indicate that carbohydrate–lectin interactions can be tuned by the macromolecular architecture and functionality, hence the importance of these macromolecular properties in the design of targeted anti-pathogenic nanomaterials.
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- 2019
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5. DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist.
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Michel Thépaut, Joanna Luczkowiak, Corinne Vivès, Nuria Labiod, Isabelle Bally, Fátima Lasala, Yasmina Grimoire, Daphna Fenel, Sara Sattin, Nicole Thielens, Guy Schoehn, Anna Bernardi, Rafael Delgado, and Franck Fieschi
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Immunologic diseases. Allergy ,RC581-607 ,Biology (General) ,QH301-705.5 - Abstract
The efficient spread of SARS-CoV-2 resulted in a unique pandemic in modern history. Despite early identification of ACE2 as the receptor for viral spike protein, much remains to be understood about the molecular events behind viral dissemination. We evaluated the contribution of C-type lectin receptors (CLRS) of antigen-presenting cells, widely present in respiratory mucosa and lung tissue. DC-SIGN, L-SIGN, Langerin and MGL bind to diverse glycans of the spike using multiple interaction areas. Using pseudovirus and cells derived from monocytes or T-lymphocytes, we demonstrate that while virus capture by the CLRs examined does not allow direct cell infection, DC/L-SIGN, among these receptors, promote virus transfer to permissive ACE2+ Vero E6 cells. A glycomimetic compound designed against DC-SIGN, enable inhibition of this process. These data have been then confirmed using authentic SARS-CoV-2 virus and human respiratory cell lines. Thus, we described a mechanism potentiating viral spreading of infection.
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- 2021
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6. Towards new cholera prophylactics and treatment: Crystal structures of bacterial enterotoxins in complex with GM1 mimics
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Julie Elisabeth Heggelund, Alasdair Mackenzie, Tobias Martinsen, Joel Benjamin Heim, Pavel Cheshev, Anna Bernardi, and Ute Krengel
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Medicine ,Science - Abstract
Abstract Cholera is a life-threatening disease in many countries, and new drugs are clearly needed. C-glycosidic antagonists may serve such a purpose. Here we report atomic-resolution crystal structures of three such compounds in complexes with the cholera toxin. The structures give unprecedented atomic details of the molecular interactions and show how the inhibitors efficiently block the GM1 binding site. These molecules are well suited for development into low-cost prophylactic drugs, due to their relatively easy synthesis and their resistance to glycolytic enzymes. One of the compounds links two toxin B-pentamers in the crystal structure, which may yield improved inhibition through the formation of toxin aggregates. These structures can spark the improved design of GM1 mimics, either alone or as multivalent inhibitors connecting multiple GM1-binding sites. Future developments may further include compounds that link the primary and secondary binding sites. Serving as decoys, receptor mimics may lessen symptoms while avoiding the use of antibiotics.
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- 2017
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7. BC2L-C N-Terminal Lectin Domain Complexed with Histo Blood Group Oligosaccharides Provides New Structural Information
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Rafael Bermeo, Anna Bernardi, and Annabelle Varrot
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tnf-like lectin ,fucosides ,blood group antigen ,crystallography ,Organic chemistry ,QD241-441 - Abstract
Lectins mediate adhesion of pathogens to host tissues, filling in a key role in the first steps of infection. Belonging to the opportunistic pathogen Burkholderia cenocepacia, BC2L-C is a superlectin with dual carbohydrate specificity, believed to mediate cross-linking between bacteria and host cells. Its C-terminal domain binds to bacterial mannosides while its N-terminal domain (BCL2-CN) recognizes fucosylated human epitopes. BC2L-CN presents a tumor necrosis factor alpha (TNF-α) fold previously unseen in lectins with a novel fucose binding mode. We report, here, the production of a novel recombinant form of BC2L-CN (rBC2L-CN2), which allowed better protein stability and unprecedented co-crystallization with oligosaccharides. Isothermal calorimetry measurements showed no detrimental effect on ligand binding and data were obtained on the binding of Globo H hexasaccharide and l-galactose. Crystal structures of rBC2L-CN2 were solved in complex with two blood group antigens: H-type 1 and H-type 3 (Globo H) by X-ray crystallography. They provide new structural information on the binding site, of importance for the structural-based design of glycodrugs as new antimicrobials with antiadhesive properties.
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- 2020
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8. Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase.
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Cinzia Colombo, Črtomir Podlipnik, Leonardo Lo Presti, Masahiro Niikura, Andrew J Bennet, and Anna Bernardi
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Medicine ,Science - Abstract
The rise of drug-resistant influenza A virus strains motivates the development of new antiviral drugs, with different structural motifs and substitution. Recently, we explored the use of a bicyclic (bicyclo[3.1.0]hexane) analogue of sialic acid that was designed to mimic the conformation adopted during enzymatic cleavage within the neuraminidase (NA; sialidase) active site. Given that our first series of compounds were at least four orders of magnitude less active than available drugs, we hypothesized that the new carbon skeleton did not elicit the same interactions as the cyclohexene frameworks used previously. Herein, we tried to address this critical point with the aid of molecular modeling and we proposed new structures with different functionalization, such as the introduction of free ammonium and guanidinium groups and ether side chains other than the 3-pentyl side chain, the characteristic side chain in Oseltamivir. A highly simplified synthetic route was developed, starting from the cyclopropanation of cyclopentenone and followed by an aziridination and further functionalization of the five-member ring. This allowed the efficient preparation of a small library of new bicyclic ligands that were characterized by enzyme inhibition assays against influenza A neuraminidases N1, its H274Y mutant, and N2. The results show that none of the new structural variants synthesized, including those containing guanidinium groups rather than free ammonium ions, displayed activity against influenza A neuraminidases at concentrations less than 2 mM. We conclude that the choice and positioning of functional groups on the bicyclo[3.1.0]hexyl system still need to be properly tuned for producing complementary interactions within the catalytic site.
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- 2018
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9. Pseudo-Mannosylated DC-SIGN Ligands as Potential Adjuvants for HIV Vaccines
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Angela Berzi, Norbert Varga, Sara Sattin, Patrizio Antonazzo, Mara Biasin, Irene Cetin, Daria Trabattoni, Anna Bernardi, and Mario Clerici
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vaccine ,HIV-1 ,adjuvant ,DC-SIGN ,innate immunity ,glycomimetic compounds ,Microbiology ,QR1-502 - Abstract
The development of new and effective adjuvants may play a fundamental role in improving HIV vaccine efficacy. New classes of vaccine adjuvants activate innate immunity receptors, notably toll like receptors (TLRs). Adjuvants targeting the C-Type lectin receptor DC-SIGN may be alternative or complementary to adjuvants based on TRL activation. Herein we evaluate the ability of the glycomimetic DC-SIGN ligand Polyman 19 (PM 19) to modulate innate immune responses. Results showed that PM 19 alone, or in combination with TLR agonists, induces the expression of cytokines, β chemokines and co-stimulatory molecules that may, in turn, modulate adaptive immunity and exert anti-viral effects. These results indicate that the suitability of this compound as a vaccine adjuvant should be further evaluated.
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- 2014
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10. A Facile Synthesis of α-N-Ribosyl-Asparagine and α-N-Ribosyl-Glutamine Building Blocks
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Gaetano Speciale, Filippo Nisic, and Anna Bernardi
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ADP-ribosylation ,glycoconjugates ,ribofuranosyl aminoacids ,Staudinger ligation ,stereoselective synthesis ,Organic chemistry ,QD241-441 - Abstract
Adenosine diphosphate ribosylation (ADP-ribosylation) is a widely occurring post-translational modification of proteins at nucleophilic side chain of amino acid residues. Elucidation of ADP-ribosylation events would benefit greatly from the availability of well-defined ADP-ribosylated peptides and analogues thereof. In this paper we present a novel approach to the chemical synthesis of ribosylated amino acid building blocks using traceless Staudinger ligation. We describe an efficient and stereoselective synthesis of α-N-ribosyl-asparagine (α-N-ribosyl-Asn) and α-N-ribosyl-glutamine (α-N-ribosyl-Gln) building blocks starting from 5-tert-butyldiphenylsilyl-β-d-ribofuranosyl azide. The N-glycosyl aminoacids are produced in good yields as pure α-anomers, suitably protected for peptide synthesis.
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- 2013
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11. Efficient synthesis of phenylene-ethynylene rods and their use as rigid spacers in divalent inhibitors
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Francesca Pertici, Norbert Varga, Arnoud van Duijn, Matias Rey-Carrizo, Anna Bernardi, and Roland J. Pieters
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multivalent carbohydrates ,LecA inhibition ,phenylene ethynylene ,rigid spacers ,Sonogashira reaction ,Science ,Organic chemistry ,QD241-441 - Abstract
The synthesis of phenylene-ethynylene rods and their use as rigid spacers is described. Alternation of a Sonogashira reaction and silyl group cleavage was used to obtain rigid spacers with even and odd numbers of phenylene units. Preliminary applications of these rods in divalent systems are shown. Inhibition studies with Pseudomonas Aeruginosa lectin LecA showed that the rigid spacer proved greatly beneficial for the inhibitory potency.
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- 2013
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12. Targeting a Multidrug-Resistant Pathogen: First Generation Antagonists of Burkholderia cenocepacia’s BC2L-C Lectin
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Rafael Bermeo, Kanhaya Lal, Davide Ruggeri, Daniele Lanaro, Sarah Mazzotta, Francesca Vasile, Anne Imberty, Laura Belvisi, Annabelle Varrot, and Anna Bernardi
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Molecular Medicine ,General Medicine ,Biochemistry - Published
- 2022
13. Glycomimetic ligands block the interaction of SARS-CoV-2 spike protein with C-type lectin co-receptors
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Sara Pollastri, Clara Delaunay, Michel Thépaut, Franck Fieschi, Anna Bernardi, Università degli Studi di Milano = University of Milan (UNIMI), 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), and ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017)
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MESH: Humans ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,SARS-CoV-2 ,viruses ,Metals and Alloys ,COVID-19 ,MESH: Spike Glycoprotein, Coronavirus ,General Chemistry ,Ligands ,Catalysis ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,MESH: RNA, Viral ,Spike Glycoprotein, Coronavirus ,MESH: Ligands ,Materials Chemistry ,Ceramics and Composites ,Humans ,RNA, Viral ,MESH: COVID-19 ,MESH: Protein Binding ,Lectins, C-Type ,MESH: SARS-CoV-2 ,MESH: Lectins, C-Type ,Protein Binding - Abstract
International audience; The C-type lectin receptors DC-SIGN and L-SIGN bind to glycans on the SARS-CoV-2 spike glycoprotein and promote trans-infection of ACE2-expressing cells. We tested C2 triazole-modified mono- and pseudo-di-mannosides as inhibitors of DC/L-SIGN binding to a model mannosylated protein (Man-BSA) and to SARS-CoV2 spike, finding that they inhibit the interaction of both lectins with the spike glycoprotein in a Surface Plasmon Resonance (SPR) assay and are more potent than mannose by up to 36-fold (DC-SIGN) and 10-fold (L-SIGN). The molecules described here are the first known glycomimetic ligands of L-SIGN.
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- 2022
14. Powerful Avidity with a Limited Valency for Virus-Attachment Blockers on DC-SIGN: Combining Chelation and Statistical Rebinding with Structural Plasticity of the Receptor
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Vanessa Porkolab, Martin Lepšík, Stefania Ordanini, Alexander St John, Aline Le Roy, Michel Thépaut, Emanuele Paci, Christine Ebel, Anna Bernardi, Franck Fieschi, 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), Centre de Recherches sur les Macromolécules Végétales (CERMAV), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Università degli Studi di Milano = University of Milan (UNIMI), School of Chemistry [Leeds], and University of Leeds
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General Chemical Engineering ,[SDV]Life Sciences [q-bio] ,General Chemistry ,Settore CHIM/06 - Chimica Organica - Published
- 2023
15. Powerful avidity with a limited valency for virus-attachment blockers on DC SIGN: Combining chelation and statistical rebinding with structural plasticity of the receptor
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Vanessa Porkolab, Martin Lepšík, Stefania Ordanini, Alexander St John, Aline Le Roy, Michel Thépaut, Emanuele Paci, Christine Ebel, Anna Bernardi, and Franck FIESCHI
- Abstract
The C-type lectin receptor DC-SIGN has been highlighted as co-receptor for the spike protein of the SARS-CoV-2 virus. A multivalent glycomimetic ligand, Polyman26, has been found to inhibit DCSIGN- dependent trans-infection of SARS-CoV-2. The molecular details underlying avidity generation in such systems remain poorly characterized. In an effort to dissect the contribution of the known multivalent effects - chelation, clustering and statistical rebinding – we studied a series of dendrimer constructs related to Polyman26 with a rod core rationally designed to engage simultaneously two binding sites of the tetrameric DC-SIGN. Binding properties of these compounds have been studied with a range of biophysical techniques, including recently developed Surface Plasmon Resonance oriented-surface methodology. Using molecular modelling we addressed, for the first time, the impact of the carbohydrate recognition domains’ flexibility of the DC-SIGN tetramer on the compounds’ avidity. We were able to gain deeper insight into the role of different binding modes, which in combination produce a construct with a nM affinity despite a limited valency. This multi-faceted experimental-theoretical approach provides detailed understanding of multivalent ligand/multimeric protein interactions which can lead to future predictions. This work opens the way to the development of new virus attachment blockers adapted to different C-type lectin receptors of viruses.
- Published
- 2022
16. Front Cover: Precision Glycodendrimers for DC‐SIGN Targeting (Eur. J. Org. Chem. 29/2022)
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Giulio Goti, Cinzia Colombo, Silvia Achilli, Corinne Vivès, Michel Thépaut, Joanna Luczkowiak, Nuria Labiod, Rafael Delgado, Franck Fieschi, and Anna Bernardi
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Organic Chemistry ,Physical and Theoretical Chemistry - Published
- 2022
17. Precision Glycodendrimers for DC‐SIGN Targeting**
- Author
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Giulio Goti, Cinzia Colombo, Silvia Achilli, Corinne Vivès, Michel Thépaut, Joanna Luczkowiak, Nuria Labiod, Rafael Delgado, Franck Fieschi, Anna Bernardi, Università degli Studi di Milano = University of Milan (UNIMI), 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), Instituto de Investigación Hospital Universitario 12 de Octubre, and European Project: 642870,H2020,H2020-MSCA-ITN-2014,IMMUNOSHAPE(2015)
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Carbohydrates ,DC-SIGN ,Dendrimers ,Glycomimetics ,Langerin ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,Organic Chemistry ,Settore CHIM/06 - Chimica Organica ,Physical and Theoretical Chemistry - Abstract
International audience; Multivalent ligands of the C‐type lectin receptor DC‐SIGN have emerged as effective antiadhesive agents against various pathogens. Some years ago, we described a hexavalent DC‐SIGN ligand, Polyman‐26, designed to bridge two of the four binding sites displayed by the receptor. In this work, we present our efforts to accomplish simultaneous coordination of all four carbohydrate binding sites of DC‐SIGN through the synthesis of cross‐shaped glycodendrimers. The tailored rigid scaffold allowed multivalent presentation of glycomimetics in a spatially defined fashion, while providing good water solubility to the constructs. Evaluation of the biological activity by SPR assays revealed strong binding avidity towards DC‐SIGN and increased selectivity over langerin. Inhibition of DC‐SIGN binding to SARS‐CoV‐2 spike protein and of DC‐SIGN mediated Ebola virus trans‐infection testifies for the glycodendrimers potential application in infection diseases. The tetravalent platform described here is easily accessible and can be used in modular fashion with different ligands, thus lending itself to multiple applications.Multivalent antagonists able to reach the four carbohydrate recognition domains (CRD) of DC‐SIGN have been prepared. The extended rigid core of these glycodendrimers allows multivalent presentation of glycomimetic molecules in a spatially defined fashion, providing high affinity towards DC‐SIGN and selectivity over other C‐type lectins featuring distinct CRD arrangements. The constructs successfully inhibit DC‐SIGN binding to SARS‐CoV‐2 spike protein and DC‐SIGN mediated trans‐infection by Ebola virus.
- Published
- 2022
18. Interfering with the Sugar Code: Ten Years Later
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Anna Bernardi and Sara Sattin
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Programming language ,Chemistry ,Organic Chemistry ,Code (cryptography) ,Physical and Theoretical Chemistry ,Sugar ,computer.software_genre ,computer - Published
- 2020
19. Rhamnose-based glycomimetic for recruitment of endogenous anti-rhamnose antibodies
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Nives Hribernik, Fabrizio Chiodo, Roland J. Pieters, Anna Bernardi
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- 2022
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20. Glycomimetics as Promising Inhibitors of Ebola Virus, Flavivirus and HIV Infections
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Anna Bernardi, Javier Rojo, and Franck Fieschi
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Flavivirus ,Ebola virus ,biology ,business.industry ,Human immunodeficiency virus (HIV) ,Medicine ,business ,medicine.disease_cause ,biology.organism_classification ,Virology - Abstract
Many pathogens, including emerging ones such as Ebola, Zika, Dengue, SARS-CoV-2, etc. contain relevant envelope glycoproteins. The viruses use these glycoproteins to infect cells that express at their surface specific C-type lectins capable of recognizing the envelope glycans. The carbohydrate–lectin interaction is nowadays considered as a promising target to develop new therapeutic strategies against this type of viral infections. To address this goal, different glycomimetic ligands, as well as multivalent systems, have been developed, mimicking the sugars and their multivalent presentation at the pathogen surface. These systems are designed to interfere efficiently with C-type lectin recognition, inhibiting the entrance of the virus into the target cells. In this chapter, we have prepared a brief overview of the state of the art, including the most relevant multivalent glycomimetics developed for this aim, classified taking into consideration the kind of multivalent scaffold used.
- Published
- 2021
21. Mannosylated brush copolymers based on poly(ethylene glycol) and poly(ε-caprolactone) as multivalent lectin-binding nanomaterials
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Wanda Celentano, Stefania Ordanini, Anna Bernardi, and Francesco Cellesi
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Glycopolymer ,General Physics and Astronomy ,Nanoparticle ,ring-opening polymerization (rop) ,02 engineering and technology ,010402 general chemistry ,lcsh:Chemical technology ,01 natural sciences ,lcsh:Technology ,Full Research Paper ,chemistry.chemical_compound ,glycopolymer ,Copolymer ,Nanotechnology ,General Materials Science ,lcsh:TP1-1185 ,atom transfer radical polymerization (atrp) ,Electrical and Electronic Engineering ,lcsh:Science ,biology ,poly(ethylene glycol) ,lcsh:T ,Ligand binding assay ,021001 nanoscience & nanotechnology ,Combinatorial chemistry ,lcsh:QC1-999 ,0104 chemical sciences ,Nanoscience ,chemistry ,Concanavalin A ,biology.protein ,lectin ,lcsh:Q ,atom transfer radical polymerization (ATRP) ,poly(ε-caprolactone) ,ring-opening polymerization (ROP) ,0210 nano-technology ,Ethylene glycol ,Caprolactone ,lcsh:Physics ,Macromolecule - Abstract
A class of linear and four-arm mannosylated brush copolymers based on poly(ethylene glycol) and poly(ε-caprolactone) is presented here. The synthesis through ring-opening and atom transfer radical polymerizations provided high control over molecular weight and functionality. A post-polymerization azide–alkyne cycloaddition allowed for the formation of glycopolymers with different mannose valencies (1, 2, 4, and 8). In aqueous media, these macromolecules formed nanoparticles that were able to bind lectins, as investigated by concanavalin A binding assay. The results indicate that carbohydrate–lectin interactions can be tuned by the macromolecular architecture and functionality, hence the importance of these macromolecular properties in the design of targeted anti-pathogenic nanomaterials.
- Published
- 2019
22. DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist
- Author
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Daphna Fenel, Fátima Lasala, Anna Bernardi, Guy Schoehn, Michel Thépaut, Joanna Luczkowiak, Rafael L. Delgado, Isabelle Bally, Sara Sattin, Franck Fieschi, Nicole M. Thielens, Corinne Vivès, Yasmina Grimoire, Nuria Labiod, 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), Instituto de Investigación Hospital Universitario 12 de Octubre, Università degli Studi di Milano = University of Milan (UNIMI), and Università degli Studi di Milano [Milano] (UNIMI)
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RNA viruses ,Viral Diseases ,Pulmonology ,Coronaviruses ,viruses ,Cell ,Jurkat cells ,Biochemistry ,Pathogenesis ,Jurkat Cells ,0302 clinical medicine ,Medical Conditions ,Glycomimetic ,Animal Cells ,Lectins ,Chlorocebus aethiops ,Biology (General) ,Receptor ,Immune Response ,Lung ,Pathology and laboratory medicine ,Mannan-binding lectin ,chemistry.chemical_classification ,0303 health sciences ,biology ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,Medical microbiology ,Cell biology ,3. Good health ,medicine.anatomical_structure ,Infectious Diseases ,030220 oncology & carcinogenesis ,Mannosides ,Viruses ,Spike Glycoprotein, Coronavirus ,SARS CoV 2 ,Pathogens ,Cellular Types ,Research Article ,Protein Binding ,Langerin ,SARS coronavirus ,QH301-705.5 ,Immune Cells ,Immunology ,Antigen-Presenting Cells ,Receptors, Cell Surface ,Respiratory Mucosa ,Microbiology ,Virus ,Cell Line ,03 medical and health sciences ,Respiratory Disorders ,Antigens, CD ,Virology ,medicine ,Genetics ,Animals ,Humans ,Lectins, C-Type ,Protein Interactions ,Molecular Biology ,Vero Cells ,030304 developmental biology ,Medicine and health sciences ,Innate immune system ,Biology and life sciences ,SARS-CoV-2 ,Organisms ,Viral pathogens ,Proteins ,COVID-19 ,Covid 19 ,Cell Biology ,Dendritic Cells ,RC581-607 ,Microbial pathogens ,Mannose-Binding Lectins ,chemistry ,Cell culture ,Respiratory Infections ,Vero cell ,biology.protein ,Parasitology ,Immunologic diseases. Allergy ,Glycoprotein ,Cell Adhesion Molecules ,030217 neurology & neurosurgery - Abstract
The efficient spread of SARS-CoV-2 resulted in a unique pandemic in modern history. Despite early identification of ACE2 as the receptor for viral spike protein, much remains to be understood about the molecular events behind viral dissemination. We evaluated the contribution of C-type lectin receptors (CLRS) of antigen-presenting cells, widely present in respiratory mucosa and lung tissue. DC-SIGN, L-SIGN, Langerin and MGL bind to diverse glycans of the spike using multiple interaction areas. Using pseudovirus and cells derived from monocytes or T-lymphocytes, we demonstrate that while virus capture by the CLRs examined does not allow direct cell infection, DC/L-SIGN, among these receptors, promote virus transfer to permissive ACE2+ Vero E6 cells. A glycomimetic compound designed against DC-SIGN, enable inhibition of this process. These data have been then confirmed using authentic SARS-CoV-2 virus and human respiratory cell lines. Thus, we described a mechanism potentiating viral spreading of infection., Author summary For their infectious effectiveness, viruses often use host attachment factors to improve their adhesion to the cell surface. This will mainly increase viruses concentration at cell surfaces, potentiating access and final engagement with their real entry receptors. This mechanism enhances viral infection of target cells or even allow viruses to be captured by non-permissive cells for secondary presentation to permissive cells by a process called trans-infection. While, the entry mechanism of SARS-CoV-2 using the ACE2 entry receptor, is well defined, little is known about additional factors explaining the high transmission rate of this virus. The level of glycosylations on the SARS-CoV-2 Spike protein prompted us to assess whether CLRs of immune cells, regularly diverted by pathogens, could play a role in the spread of SARS-CoV-2. Here, we show that these receptors are able to recognize Spike envelope protein of SARS-CoV-2 and two receptors among the four tested, DC-SIGN and L-SIGN, are able to promote virus trans-infection. This work identifies a new family of alternative SARS-CoV-2 cell receptors involved in uncharacterized dissemination mechanism. Moreover, considering the role of CLRs in immunomodulation, their early involvement opens avenues for understanding the imbalanced innate immune response observed in COVID-19 pathogenesis.
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- 2021
23. One pot synthesis of thio -glycosides via aziridine opening reactions
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Nives Hribernik, Alice Tamburrini, Ermelinda Falletta, Anna Bernardi
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- 2021
- Full Text
- View/download PDF
24. Prediction and Validation of a Druggable Site on Virulence Factor of Drug Resistant Burkholderia cenocepacia
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Annabelle Varrot, Anne Imberty, Anna Bernardi, Francesca Vasile, Rafael Bermeo, Laura Belvisi, Jonathan Cramer, Kanhaya Lal, Beat Ernst, Centre de Recherches sur les Macromolécules Végétales (CERMAV), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Università degli Studi di Milano [Milano] (UNIMI), and University of Basel (Unibas)
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Models, Molecular ,Virtual screening ,Burkholderia cenocepacia ,Virulence Factors ,Protein domain ,Druggability ,Drug resistance ,Fucose binding ,Computational biology ,Antimicrobial resistance ,Catalysis ,Virulence factor ,Ligand design ,Microbiology ,03 medical and health sciences ,Lectins ,Humans ,[CHIM]Chemical Sciences ,Binding site ,030304 developmental biology ,0303 health sciences ,Full Paper ,biology ,030306 microbiology ,Chemistry ,BC2L-C ,Organic Chemistry ,Lectin ,Burkholderia Infections ,General Chemistry ,Full Papers ,biology.organism_classification ,3. Good health ,lectin ,antibacterial ,crystal structure ,Pharmaceutical Preparations ,Glycomimetics ,biology.protein ,Target protein - Abstract
Burkholderia cenocepacia is an opportunistic Gram‐negative bacterium that causes infections in patients suffering from chronic granulomatous diseases and cystic fibrosis. It displays significant morbidity and mortality due to extreme resistance to almost all clinically useful antibiotics. The bacterial lectin BC2L‐C expressed in B. cenocepacia is an interesting drug target involved in bacterial adhesion and subsequent deadly infection to the host. We solved the first high resolution crystal structure of the apo form of the lectin N‐terminal domain (BC2L‐C‐nt) and compared it with the ones complexed with carbohydrate ligands. Virtual screening of a small fragment library identified potential hits predicted to bind in the vicinity of the fucose binding site. A series of biophysical techniques and X‐ray crystallographic screening were employed to validate the interaction of the hits with the protein domain. The X‐ray structure of BC2L‐C‐nt complexed with one of the identified active fragments confirmed the ability of the site computationally identified to host drug‐like fragments. The fragment affinity could be determined by titration microcalorimetry. These structure‐based strategies further provide an opportunity to elaborate the fragments into high affinity anti‐adhesive glycomimetics, as therapeutic agents against B. cenocepacia., A new druggable site for anti‐adhesive therapy. We used fragment‐based virtual screening to explore the druggability of a region in the vicinity of the fucose binding site in a lectin from an opportunistic and highly drug‐resistant pathogen. The crystal structure of the target protein complexed with the lead fragment validated the existence of a secondary binding site, paving the way for the design of potent ligands to be employed in anti‐adhesive therapy.
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- 2021
- Full Text
- View/download PDF
25. One pot synthesis of
- Author
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Nives, Hribernik, Alice, Tamburrini, Ermelinda, Falletta, and Anna, Bernardi
- Abstract
A one-pot aziridine opening reaction by glycosyl thiols generated in situ from the corresponding anomeric thio-acetates affords thio-glycosides with a pseudo-disaccharide structure and an N-linked tether. The scope of the one-pot aziridine opening reaction was explored on a series of mono- and disaccharides, creating a class of pseudo-glycosidic compounds with potential for further functionalization. Unexpected anomerization of glycosyl thiols was observed under the reaction conditions and the influence of temperature, base and solvent on the isomerization was investigated. Single isomers were obtained in good to acceptable yields for mannose, rhamnose and sialic acid derivatives. The class of thio-glycomimetics synthesized can potentially be recognized by various lectins, while presenting hydrolytic and enzymatic stability. The nitrogen functionality incorporated in the glycomimetics can be exploited for further functionalization, including tethering to linkers, scaffolds or peptide residues.
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- 2020
26. Chemo‐Enzymatic Synthesis of S. mansoni O‐Glycans and Their Evaluation as Ligands for C‐Type Lectin Receptors MGL, DC‐SIGN, and DC‐SIGNR
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Anna Cioce, Niels-Christian Reichardt, Corinne Vivès, Anna Bernardi, Alvaro Hernández, Julie Pham, Franck Fieschi, Silvia Achilli, Giulio Goti, Michel Thépaut, CIC BiomaGUNE, CIC BiomaGUNE [Espagne], 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), Università degli Studi di Milano = University of Milan (UNIMI), and Dipartimento di chimica, Universita degli Studi di Milano
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Glycan ,Fucosyltransferase ,Glycoconjugate ,enzymes ,carbohydrates ,Receptors, Cell Surface ,Ligands ,010402 general chemistry ,01 natural sciences ,Catalysis ,Polysaccharides ,C-type lectin ,Humans ,Lectins, C-Type ,Receptor ,microarrays ,chemistry.chemical_classification ,biology ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,glycoconjugates ,lectins ,Lectin ,General Chemistry ,biology.organism_classification ,0104 chemical sciences ,3. Good health ,DC-SIGN ,carbohydrates (lipids) ,Biochemistry ,biology.protein ,Schistosoma mansoni ,Cell Adhesion Molecules - Abstract
International audience; Due to their interactions with C-type lectin receptors (CLRs), glycans from the helminth Schistosoma mansoni represent promising leads for treatment of autoimmune diseases, allergies or cancer. We chemo-enzymatically synthesized nine O-glycans based on the two predominant O-glycan cores observed in the infectious stages of schistosomiasis, the mucin core 2 and the S. mansoni core. The O-glycans were fucosylated next to a selection of N-glycans directly on a microarray slide using a recombinant fucosyltransferase and GDP-fucose or GDP-6-azidofucose as donor. Binding assays with fluorescently labelled human CLRs DC-SIGN, DC-SIGNR and MGL revealed the novel O-glycan O8 as the best ligand for MGL from our panel. Significant binding to DC-SIGN was also found for azido-fucosylated glycans. Contrasting binding specificities were observed between the monovalent carbohydrate recognition domain (CRD) and the tetravalent extracellular domain (ECD) of DC-SIGNR.
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- 2020
27. Structure-Based Design of Glycodendrimer Antagonists for Improved DC-SIGN Targeting
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Michel Thépaut, Franck Fieschi, Anna Bernardi, Giulio Goti, Cinzia Colombo, Corinne Vivès, and Silvia Achilli
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DC-SIGN ,Langerin ,biology ,Chemistry ,biology.protein ,Biophysics ,Structure based ,Avidity ,Biological activity ,Binding site ,Surface plasmon resonance ,Strong binding - Abstract
DC-SIGN multivalent antagonists have emerged as effective antiadhesive agents against various pathogen infections. Recently, our group have shown that high potency can be achieved upon bridging two of the four binding sites displayed by the protein. Here we present our endeavors to accomplish the tetracoordination of DC-SIGN through the synthesis of two cross-shaped glycodendrimers. The choice of a tailored rigid scaffold allowed multivalent presentation of glycomimetics in a spatially defined fashion, while providing good water solubility to the constructs. Evaluation of the biological activity by SPR assay revealed strong binding avidity towards DC-SIGN and increased selectivity over langerin.
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- 2020
28. Development of C-type lectin-oriented surfaces for high avidity glycoconjugates: towards mimicking multivalent interactions on the cell surface
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Corinne Vivès, Vanessa Porkolab, Anna Bernardi, Carlo Pifferi, Ieva Sutkeviciute, Marwa Taouai, Olivier Renaudet, Michel Thépaut, Franck Fieschi, Mohammed Benazza, Stefania Ordanini, 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), Département de Chimie Moléculaire (DCM), Université Grenoble Alpes (UGA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Milano [Milano] (UNIMI), Laboratoire de Glycochimie, des Antimicrobiens et des Agro-ressources - UMR CNRS 7378 (LG2A ), Université de Picardie Jules Verne (UPJV)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), and Università degli Studi di Milano = University of Milan (UNIMI)
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Surface Properties ,Glycoconjugate ,Molecular Conformation ,Receptors, Cell Surface ,010402 general chemistry ,01 natural sciences ,Biochemistry ,03 medical and health sciences ,C-type lectin ,Glycomimetic ,Humans ,Lectins, C-Type ,Avidity ,Physical and Theoretical Chemistry ,Surface plasmon resonance ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,biology ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,Chemistry ,Organic Chemistry ,Lectin ,Surface Plasmon Resonance ,Ligand (biochemistry) ,0104 chemical sciences ,Covalent bond ,Biophysics ,biology.protein ,Cell Adhesion Molecules ,Glycoconjugates - Abstract
International audience; Multivalent interactions between complex carbohydrates and oligomeric C-type lectins govern a wide range of immune responses. Up to date, standard SPR (surface plasmon resonance) competitive assays have largely been to evaluate binding properties from monosaccharide units (low affinity, mM) to multivalent elemental antagonists (moderate affinity, μM). Herein, we report typical case-studies of SPR competitive assays showing that they underestimate the potency of glycoclusters to inhibit the interaction between DC-SIGN and immobilized glycoconjugates. This paper describes the design and implementation of a SPR direct interaction over DC-SIGN oriented surfaces, extendable to other C-type lectin surfaces as such Langerin. This setup provides an overview of intrinsic avidity generation emanating simultaneously from multivalent glycoclusters and from DC-SIGN tetramers organized in nanoclusters at the cell membrane. To do so, covalent biospecific capture of DC-SIGN via StreptagII/StrepTactin interaction preserves tetrameric DC-SIGN, accessibility and topology of its active sites, that would have been dissociated using standard EDC-NHS procedure under acidic conditions. From the tested glycoclusters libraries, we demonstrated that the scaffold architecture, the valency and the glycomimetic-based ligand are crucial to reach nanomolar affinities for DC-SIGN. The glycocluster 3·D illustrates the tightest binding partner in this set for a DC-SIGN surface (KD = 18 nM). Moreover, the selectivity at monovalent scale of glycomimetic D can be easily analyzed at multivalent scale comparing its binding over different C-type lectin immobilized surfaces. This approach may give rise to novel insights into the multivalent binding mechanisms responsible for avidity and make a major contribution to the full characterization of the binding potency of promising specific and multivalent immodulators.
- Published
- 2020
29. BC2L-C N-Terminal Lectin Domain Complexed with Histo Blood Group Oligosaccharides Provides New Structural Information
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Annabelle Varrot, Anna Bernardi, Rafael Bermeo, Centre de Recherches sur les Macromolécules Végétales (CERMAV), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Dipartimento di Chimica [Milano, Italy], Università degli studi di Milano [Milano], Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), and Università degli Studi di Milano [Milano] (UNIMI)
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Models, Molecular ,Burkholderia cenocepacia ,Pharmaceutical Science ,Gene Expression ,Oligosaccharides ,Fucose binding ,Crystallography, X-Ray ,01 natural sciences ,Epitope ,Analytical Chemistry ,law.invention ,Epitopes ,law ,Lectins ,Drug Discovery ,blood group antigen ,0303 health sciences ,biology ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,Chemistry ,Recombinant Proteins ,3. Good health ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM] ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM] ,Biochemistry ,Chemistry (miscellaneous) ,Mannosides ,Recombinant DNA ,Blood Group Antigens ,Molecular Medicine ,Protein Binding ,Article ,lcsh:QD241-441 ,03 medical and health sciences ,lcsh:Organic chemistry ,[CHIM.CRIS]Chemical Sciences/Cristallography ,Humans ,Antigens, Tumor-Associated, Carbohydrate ,Physical and Theoretical Chemistry ,Binding site ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] ,crystallography ,030304 developmental biology ,Fucose ,fucosides ,Binding Sites ,TNF-like lectin ,010405 organic chemistry ,Tumor Necrosis Factor-alpha ,Organic Chemistry ,Lectin ,Isothermal titration calorimetry ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,biology.organism_classification ,Antigens, Differentiation ,0104 chemical sciences ,biology.protein - Abstract
Lectins mediate adhesion of pathogens to host tissues, filling in a key role in the first steps of infection. Belonging to the opportunistic pathogen Burkholderia cenocepacia, BC2L-C is a superlectin with dual carbohydrate specificity, believed to mediate cross-linking between bacteria and host cells. Its C-terminal domain binds to bacterial mannosides while its N-terminal domain (BCL2-CN) recognizes fucosylated human epitopes. BC2L-CN presents a tumor necrosis factor alpha (TNF-α) fold previously unseen in lectins with a novel fucose binding mode. We report, here, the production of a novel recombinant form of BC2L-CN (rBC2L-CN2), which allowed better protein stability and unprecedented co-crystallization with oligosaccharides. Isothermal calorimetry measurements showed no detrimental effect on ligand binding and data were obtained on the binding of Globo H hexasaccharide and l-galactose. Crystal structures of rBC2L-CN2 were solved in complex with two blood group antigens: H-type 1 and H-type 3 (Globo H) by X-ray crystallography. They provide new structural information on the binding site, of importance for the structural-based design of glycodrugs as new antimicrobials with antiadhesive properties.
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- 2020
30. Observation of a Tricyclic[4.1.0.02,4]heptane During a Michael Addition-Ring Closure Reaction and a Computational Study on Its Mechanism of Formation
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Andrew J. Bennet, Marco Farren-Dai, Anna Bernardi, John R. Thompson, and Cinzia Colombo
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chemistry.chemical_classification ,Cyclopentenone ,Heptane ,Bicyclic molecule ,010405 organic chemistry ,Cyclopropanation ,Stereochemistry ,Organic Chemistry ,Ether ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,Ylide ,Michael reaction ,Moiety - Abstract
We describe the formation of a bis-cyclopropane product, a tricyclic[4.1.0.02,4]heptane, that is formed during a Johnson–Corey–Chaykovsky reaction on a cyclopentenone. Two (of four possible) bicyclic products are selectively formed by addition of a COOEt-stabilized sulfur ylide onto the Michael acceptor. The tricyclic product is formed subsequently via a retro Michael elimination of a hindered ether followed by addition of a further cyclopropyl moiety, affecting only one of the two bicyclic products initially formed. The experimental reaction outcome was rationalized using density functional theory (DFT), investigating the different Michael-addition approaches of the sulfur ylide, the transition state (TS) energies for the formation of possible zwitterionic intermediates and subsequent reactions that give rise to cyclopropanation. Selective formation of only two of the four possible products occurs due to the epimerization of unreactive intermediates from the other two pathways, as revealed by energy barr...
- Published
- 2017
31. From optimized monovalent ligands to size-controlled dendrimers: an efficient strategy towards high-activity DC-SIGN antagonists
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Anna Bernardi, Giulio Goti, and Stefania Ordanini
- Subjects
0301 basic medicine ,Stereochemistry ,Human immunodeficiency virus (HIV) ,Mannose ,medicine.disease_cause ,DC-SIGN ,Catalysis ,Mini review ,03 medical and health sciences ,chemistry.chemical_compound ,Dendrimer ,Glycodendrimers ,medicine ,High activity ,biology ,Chemistry ,Ligand ,Organic Chemistry ,Valency ,HIV ,General Chemistry ,Combinatorial chemistry ,Glycomimetics ,Multivalency ,030104 developmental biology ,biology.protein - Abstract
This short review describes our work on the development of dendrimeric antagonists of DC-SIGN, a dendritic cells (DCs) receptor recognizing highly mannosylated structures and primarily involved in the recognition of viruses such as HIV. The structure of pseudo-di-mannoside and pseudo-tri-mannoside compounds was first finely modified to obtain DC-SIGN ligands that were more stable and selective than mannose. Their DC-SIGN affinity differences were amplified once presented on multivalent dendrimer-like scaffolds, including poly-alkyne terminated and phenylene-ethynylene rod-like ones. Libraries of mannosylated dendrimers were synthesized, improving their stability and maximizing their monodispersity. The effect of the dendrimers valency, structure, and size on DC-SIGN affinity and antiviral potency was investigated. Both the valency and the topology of the architectures were revealed as key parameters for activity optimization, together with the intrinsic affinity of the monovalent ligand. The stability, rigidity, and length of the scaffolds were also tuned. The design of geometrically adapted scaffolds afforded one of the most potent inhibitors of DC-SIGN mediated HIV infections to date. This monodispersed, not cytotoxic, and highly active compound was also tested with DCs; its internalization into endolysosomal compartments and its ability to induce the overexpression of signaling molecules makes it a good precursor to produce pathogen-entry inhibitors with immunomodulant properties.
- Published
- 2017
32. Design of Allosteric Stimulators of the Hsp90 ATPase as New Anticancer Leads
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Anna Bernardi, Giorgio Colombo, Nadia Zaffaroni, Elisabetta Moroni, Marzia Pennati, Carlos Sanchez-Martin, Jiahui Tao, Sara Sattin, Ilda D'Annessa, David A. Agard, and Andrea Rasola
- Subjects
0301 basic medicine ,drug design ,ATPase ,Allosteric regulation ,Antineoplastic Agents ,Ligands ,Article ,Catalysis ,03 medical and health sciences ,Rare Diseases ,0302 clinical medicine ,Allosteric Regulation ,modulators ,HSP90 Heat-Shock Proteins ,Cancer ,Adenosine Triphosphatases ,Adenosine triphosphatase ,allostery ,biology ,Chemistry ,Organic Chemistry ,General Chemistry ,hsp90 ,molecular dynamics ,Hsp90 ,In vitro ,Quantitative model ,030104 developmental biology ,Biochemistry ,030220 oncology & carcinogenesis ,Chemical Sciences ,biology.protein ,Protein Binding - Abstract
Allosteric compounds that stimulate Hsp90 adenosine triphosphatase (ATPase) activity were rationally designed, showing anticancer potencies in the low micromolar to nanomolar range. In parallel, the mode of action of these compounds was clarified and a quantitative model that links the dynamic ligand-protein cross-talk to observed cellular and in vitro activities was developed. The results support the potential of using dynamics-based approaches to develop original mechanism-based cancer therapeutics.
- Published
- 2017
33. Development of c-type lectin oriented surfaces for high avidity glycoconjugates: towards mimicking multivalent interactions on the cell surface
- Author
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Corinne Vivès, Vanessa Porkolab, Ieva Sutkeviciute, Marwa Taouai, Franck Fieschi, Olivier Renaudet, Mohammed Benazza, Anna Bernardi, Stefania Ordanini, Carlo Pifferi, and Michel Thépaut
- Subjects
chemistry.chemical_classification ,0303 health sciences ,biology ,Glycoconjugate ,Lectin ,010402 general chemistry ,Ligand (biochemistry) ,01 natural sciences ,0104 chemical sciences ,03 medical and health sciences ,chemistry ,Glycomimetic ,C-type lectin ,Covalent bond ,Biophysics ,biology.protein ,Avidity ,Surface plasmon resonance ,030304 developmental biology - Abstract
Multivalent interactions between complex carbohydrates and oligomeric C-type lectins govern a wide range of immune responses. Up to date, standard SPR (surface plasmon resonance) competitive assays have largely been to evaluate binding properties from monosaccharide units (low affinity, mM) to multivalent elemental antagonists (moderate affinity, µM). Herein, we report typical case-studies of SPR competitive assays showing that they underestimate the potency of glycoclusters to inhibit the interaction between DC-SIGN and immobilized glycoconjugates. This paper describes the design and implementation of a SPR direct interaction over DC-SIGN oriented surfaces, extendable to other C-type lectin surfaces as such Langerin. This setup provides a microscopic overview of intrinsic avidity generation emanating simultaneously from multivalent glycoclusters and from DC-SIGN tetramers that are organized in nanoclusters on the cell membrane. For this purpose, covalent biospecific capture of DC-SIGN via StreptagII /StrepTactin interaction offers the preservation of tetrameric DC-SIGN and the accessibility/functionality of all active sites. From the tested glycoclusters libraries, we demonstrated that the scaffold architecture, the valency and the glycomimetic-based ligand are crucial to reach nanomolar affinities for DC-SIGN. The glycocluster 3.D illustrates the tightest binding partner in this set for a DC-SIGN surface (Kd= 18 nM). Moreover, the selectivity at monovalent scale of glycomimetic D can be easily analyzed at multivalent scale comparing its binding over different C-type lectin immobilized surfaces. This approach may give rise to novel insights into the multivalent binding mechanisms responsible to avidity and make a major contribution to the full characterization of the binding potency of promising specific and multivalent immunomodulators.
- Published
- 2019
- Full Text
- View/download PDF
34. Design and synthesis of glycomimetics: Recent advances
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Anna Bernardi, Alice Tamburrini, and Cinzia Colombo
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Pharmacology ,0303 health sciences ,Glycan ,biology ,Chemistry ,Nanotechnology ,Stereoisomerism ,Metabolic stability ,Oxygen ,03 medical and health sciences ,0302 clinical medicine ,Glycomimetic ,Biomimetics ,Cyclization ,Polysaccharides ,030220 oncology & carcinogenesis ,Drug Discovery ,biology.protein ,Carbohydrate Conformation ,Molecular Medicine ,Animals ,Humans ,Surface plasmon resonance ,030304 developmental biology ,Biological evaluation - Abstract
In the past few decades, our understanding of glycan information-encoding power has notably increased, thus leading to a significant growth also in the design and synthesis of glycomimetic probes. Combining data from multiple analytical sources, such as crystallography, nuclear magnetic resonance spectroscopy, and other biophysical methods (eg, surface plasmon resonance and carbohydrate microarrays) has allowed to shed light on the key interaction events between carbohydrates and their protein-targets. However, the low metabolic stability of carbohydrates and their high hydrophilicity, which translates in low bioavailability, undermine their development as drugs. In this framework, the design of chemically modified analogues (called carbohydrate mimics or glycomimetics) appears as a valid alternative for the development of therapeutic agents. Glycomimetics, as structural and functional mimics of carbohydrates, can replace the native ligands in the interaction with target proteins, but are designed to show enhanced enzymatic stability and bioavailability and, possibly, an improved affinity and selectivity toward the target. In the present account, we specifically focus on the most recent advances in the design and synthesis of glycomimetics. In particular, we highlight the efforts of the scientific community in the development of straightforward synthetic procedures for the preparation of sugar mimics and in their preliminary biological evaluation.
- Published
- 2019
35. A New Surface Plasmon Resonance Assay for In Vitro Screening of Mannose-Binding Lectin Inhibitors
- Author
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Matteo Stravalaci, Marco Gobbi, Alessandro Palmioli, Anna Bernardi, Carlo Perego, Daiana De Blasio, Franca Orsini, Maria Grazia De Simoni, Giulio Goti, Stravalaci, M, De Blasio, D, Orsini, F, Perego, C, Palmioli, A, Goti, G, Bernardi, A, De Simoni, M, and Gobbi, M
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0301 basic medicine ,Dendrimers ,Carbohydrates ,Mannose ,chemical and pharmacologic phenomena ,Mannose-Binding Lectin ,Biochemistry ,Analytical Chemistry ,Mice ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,medicine ,Animals ,Humans ,immunoassay ,Surface plasmon resonance ,Mannan-binding lectin ,mannose binding lectin ,biology ,medicine.diagnostic_test ,glycodendrimer ,Lectin ,inhibitor screening ,Surface Plasmon Resonance ,bacterial infections and mycoses ,Immunity, Innate ,In vitro ,High-Throughput Screening Assays ,Complement system ,030104 developmental biology ,chemistry ,Reperfusion Injury ,Lectin pathway ,Immunoassay ,biology.protein ,Molecular Medicine ,030217 neurology & neurosurgery ,Biotechnology - Abstract
Mannose-binding lectin (MBL) is a circulating protein that acts as a soluble pattern recognition molecule of the innate immunity. It binds to carbohydrate patterns on the surface of pathogens or of altered self-cells, with activation of the lectin pathway of the complement system. Recent evidence indicates that MBL contributes to the pathophysiology of ischemia-reperfusion injury and other conditions. Thus, MBL inhibitors offer promising therapeutic strategies, since they prevent the interaction of MBL with its target sugar arrays. We developed and characterized a novel assay based on surface plasmon resonance for in vitro screening of these compounds, which may be useful before the more expensive and time-consuming in vivo studies. The assay measures the inhibitor's ability to interfere with the binding of murine MBL-A or MBL-C, or of human recombinant MBL, to mannose residues immobilized on the sensor chip surface. We have applied the assay to measure the IC50 of synthetic glycodendrimers, two of them with neuroprotective properties in animal models of MBL-mediated injuries.
- Published
- 2016
36. Pharmacological inhibition of mannose-binding lectin ameliorates neurobehavioral dysfunction following experimental traumatic brain injury
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Luca Longhi, Alessandro Palmioli, Marco Gobbi, Stefano Fumagalli, Gloria Vegliante, Maria Grazia De Simoni, Elisa R. Zanier, Franca Orsini, Matteo Stravalaci, Anna Bernardi, Daiana De Blasio, De Blasio, D, Fumagalli, S, Longhi, L, Orsini, F, Palmioli, A, Stravalaci, M, Vegliante, G, Zanier, E, Bernardi, A, Gobbi, M, and De Simoni, M
- Subjects
Male ,0301 basic medicine ,Mannose ,Pharmacology ,Ligands ,Mice ,chemistry.chemical_compound ,0302 clinical medicine ,Brain Injuries, Traumatic ,Glycosides ,neuroregeneration ,Mannan-binding lectin ,Mice, Knockout ,Dendrimer ,Neurogenesis ,Neurology ,brain trauma ,Sensorimotor Cortex ,medicine.symptom ,Cardiology and Cardiovascular Medicine ,mannose-binding lectin inhibitor ,Protein Binding ,Dendrimers ,Traumatic brain injury ,Ligand ,Inflammation ,Biology ,Mannose-Binding Lectin ,behavior (rodent) ,03 medical and health sciences ,medicine ,Animals ,Sensorimotor cortex ,brain recovery ,Animal ,Lectin ,Original Articles ,Recovery of Function ,medicine.disease ,Neuroregeneration ,Glycoside ,Disease Models, Animal ,030104 developmental biology ,chemistry ,Immunology ,biology.protein ,Neurogenesi ,Neurology (clinical) ,030217 neurology & neurosurgery - Abstract
Mannose-binding lectin is present in the contusion area of traumatic brain-injured patients and in that of traumatic brain-injured mice, where mannose-binding lectin-C exceeds mannose-binding lectin-A. The reduced susceptibility to traumatic brain injury of mannose-binding lectin double knock-out mice (mannose-binding lectin−/−) when compared to wild type mice suggests that mannose-binding lectin may be a therapeutic target following traumatic brain injury. Here, we evaluated the effects of a multivalent glycomimetic mannose-binding lectin ligand, Polyman9, following traumatic brain injury in mice. In vitro surface plasmon resonance assay indicated that Polyman9 dose-dependently inhibits the binding to immobilized mannose residues of plasma mannose-binding lectin-C selectively over that of mannose-binding lectin-A. Male C57Bl/6 mice underwent sham/controlled cortical impact traumatic brain injury and intravenous treatment with Polyman9/saline. Ex-vivo surface plasmon resonance studies confirmed that Polyman9 effectively reduces the binding of plasma mannose-binding lectin-C to immobilized mannose residues. In vivo studies up to four weeks post injury, showed that Polyman9 induces significant improvement in sensorimotor deficits (by neuroscore and beam walk), promotes neurogenesis (73% increase in doublecortin immunoreactivity), and astrogliosis (28% increase in glial fibrillary acid protein). Polyman9 administration in brain-injured mannose-binding lectin−/− mice had no effect on post-traumatic brain-injured functional deficits, suggestive of the specificity of its neuroprotective effects. The neurobehavioral efficacy of Polyman9 implicates mannose-binding lectin-C as a novel therapeutic target for traumatic brain injury.
- Published
- 2016
37. Synthesis of Functionalized 2-(4-Hydroxyphenyl)-3-methylbenzofuran Allosteric Modulators of Hsp90 Activity
- Author
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Giulio Goti, Francesca Berni, David A. Agard, Giorgio Colombo, Sara Sattin, Francesca Vasile, Anna Bernardi, Jiahui Tao, Matteo Panza, and Elisabetta Moroni
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biology ,010405 organic chemistry ,Stereochemistry ,Organic Chemistry ,Allosteric regulation ,Context (language use) ,Nuclear magnetic resonance spectroscopy ,010402 general chemistry ,01 natural sciences ,Hsp90 ,Chemical space ,Epitope ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,biology.protein ,CTD ,Physical and Theoretical Chemistry ,Benzofuran - Abstract
Hsp90 is a molecular chaperone that plays a pivotal role in the cell life cycle. ATP-regulated internal dynamics are critical to Hsp90 function and we recently demonstrated that these dynamics can be modulated in an allosteric fashion; the protein C-terminal domain (CTD) can be effectively targeted with a family of 2-phenyl-benzofuran derivatives. Here we describe the expansion of the initial library, reporting 28 new derivatives that explore the chemical space at opposite ends of the benzofuran scaffold. Interactions of the compounds with a full-length protein homolog were explored by Saturation Transfer Difference (STD) NMR spectroscopy. In this context we also report the interaction epitope of Novobiocin, a known CTD inhibitor.
- Published
- 2016
38. Glycoconjugates and Glycomimetics as Microbial Anti-Adhesives
- Author
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Anna Bernardi and Sara Sattin
- Subjects
0301 basic medicine ,chemistry.chemical_classification ,Dose-Response Relationship, Drug ,Glycoconjugate ,Bioengineering ,Biology ,Metabolic stability ,010402 general chemistry ,01 natural sciences ,Bacterial Adhesion ,Epitope ,Anti-Bacterial Agents ,0104 chemical sciences ,03 medical and health sciences ,030104 developmental biology ,Biochemistry ,chemistry ,Biomimetic Materials ,Microbial adhesion ,Protein target ,Glycoconjugates ,Biotechnology ,Enzymatic degradation - Abstract
Microbial adhesion is an essential step in infection and is mediated primarily by protein-carbohydrate interactions. Antagonists of such interactions have become a promising target for anti-adhesive therapy in several infective diseases. Monovalent protein-sugar interactions are often weak, and most successful anti-adhesive materials consist of multivalent glycoconjugates. Although often very effective in hampering microbial adhesion, natural epitopes often show limited resistance to enzymatic degradation. The use of carbohydrate mimics (glycomimetics) as a replacement for natural sugars potentially allows higher metabolic stability and also higher selectivity towards the desired protein target. In this review we describe the state of the art in the design and synthesis of glycoconjugates and glycomimetics employed for the construction of anti-adhesive biomaterials.
- Published
- 2016
39. Synthesis and evaluation of influenza A viral neuraminidase candidate inhibitors based on a bicyclo[3.1.0]hexane scaffold
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Anna Bernardi, B. Mario Pinto, Andrew J. Bennet, and Cinzia Colombo
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Models, Molecular ,Protein Conformation ,Stereochemistry ,Neuraminidase ,Chemistry Techniques, Synthetic ,010402 general chemistry ,Sialidase ,medicine.disease_cause ,01 natural sciences ,Biochemistry ,Bridged Bicyclo Compounds ,chemistry.chemical_compound ,Protein structure ,Influenza A Virus, H9N2 Subtype ,Viral neuraminidase ,Influenza A virus ,medicine ,Enzyme Inhibitors ,Physical and Theoretical Chemistry ,Influenza A Virus, H5N1 Subtype ,biology ,Bicyclic molecule ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Active site ,3. Good health ,0104 chemical sciences ,Sialic acid ,Drug Design ,biology.protein - Abstract
This manuscript describes a novel class of derivatives based on a bicyclo[3.1.0]hexane scaffold, proposed as mimics of sialic acid in a distorted boat conformation that is on the catalytic pathway of neuraminidases (sialidases). A general synthetic route for these constrained-ring molecules was developed using a photochemical reaction followed by a Johnson-Corey-Chaykovsky cyclopropanation. Functionalization with the goal of occupying the 150-cavity was also exploited. Inhibition assays demonstrated low micromolar inhibition against both group-1 (H5N1) and group-2 (H9N2) influenza neuraminidase subtypes, indicating good affinity for the alpha and beta sialic acid mimics and 150-cavity-targeted derivatives. These results provide a validation of a bicyclo[3.1.0]hexane scaffold as a mimic of a distorted sialic acid bound in the neuraminidase active site during catalysis.
- Published
- 2016
40. Glycodendron-rhenium complexes as luminescent probes for lectin sensing
- Author
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Monica Panigati, Anna Bernardi, Alessandro Palmioli, Palmioli, A, Panigati, M, and Bernardi, A
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chemistry.chemical_classification ,biology ,Aqueous medium ,010405 organic chemistry ,Glycoconjugate ,Organic Chemistry ,Lectin ,chemistry.chemical_element ,Rhenium ,Glycodendron ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Combinatorial chemistry ,Sensing Probe ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,biology.protein ,Luminophore ,Physical and Theoretical Chemistry ,Luminescence ,Luminecence - Abstract
The design, synthesis and characterization of novel glycoconjugate luminescent probes based on dinuclear rhenium(i) complexes are reported. A multivalent platform bearing different carbohydrate moieties (Glc, Gal and Man) was used to target carbohydrate-binding proteins (lectins), exploiting the unique photophysical characteristics of a Re(i) luminophore for protein sensing. Our results show that these glycoconjugates, non-luminescent in aqueous medium, are able to specifically bind different lectins (ConA and PNA) with a consequent enhancement of emission intensity. These findings suggest the use of Re(i)-based glycoconjugates as switch-on luminescent probe tools in biological applications.
- Published
- 2018
41. Rational-Differential Design of Highly Specific Glycomimetic Ligands: Targeting DC-SIGN and Excluding Langerin Recognition
- Author
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Anna Bernardi, Eric Chabrol, Pedro M. Nieto, Vanessa Porkolab, Ieva Sutkeviciute, Stefania Ordanini, Eric Girard, Franck Fieschi, Michel Thépaut, Norbert Varga, María García-Jiménez, 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), Università degli Studi di Milano = University of Milan (UNIMI), Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), Universidad de Sevilla / University of Sevilla-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universidad de Sevilla / University of Sevilla-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), 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), Università degli Studi di Milano [Milano] (UNIMI), and Universidad de Sevilla-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universidad de Sevilla-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)
- Subjects
0301 basic medicine ,Langerin ,HIV Infections ,Receptors, Cell Surface ,medicine.disease_cause ,Ligands ,Biochemistry ,03 medical and health sciences ,Antigen ,Glycomimetic ,Antigens, CD ,medicine ,Humans ,Lectins, C-Type ,Binding site ,Binding Sites ,biology ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,integumentary system ,Chemistry ,Molecular Mimicry ,Rational design ,Lectin ,General Medicine ,Dendritic Cells ,3. Good health ,Cell biology ,DC-SIGN ,Molecular mimicry ,030104 developmental biology ,Mannose-Binding Lectins ,Drug Design ,biology.protein ,Molecular Medicine ,Cell Adhesion Molecules - Abstract
At the surface of dendritic cells, C-type lectin receptors (CLRs) allow the recognition of carbohydrate-based PAMPS or DAMPS (pathogen- or danger-associated molecular patterns, respectively) and promote immune response regulation. However, some CLRs are hijacked by viral and bacterial pathogens. Thus, the design of ligands able to target specifically one CLR, to either modulate an immune response or to inhibit a given infection mechanism, has great potential value in therapeutic design. A case study is the selective blocking of DC-SIGN, involved notably in HIV trans-infection of T lymphocytes, without interfering with langerin-mediated HIV clearance. This is a challenging task due to their overlapping carbohydrate specificity. Toward the rational design of DC-SIGN selective ligands, we performed a comparative affinity study between DC-SIGN and langerin with natural ligands. We found that GlcNAc is recognized by both CLRs; however, selective sulfation are shown to increase the selectivity in favor of langerin. With the combination of site-directed mutagenesis and X-ray structural analysis of the langerin/GlcNS6S complex, we highlighted that 6-sulfation of the carbohydrate ligand induced langerin specificity. Additionally, the K313 residue from langerin was identified as a critical feature of its binding site. Using a rational and a differential approach in the study of CLR binding sites, we designed, synthesized, and characterized a new glycomimetic, which is highly specific for DC-SIGN vs langerin. STD NMR, SPR, and ITC characterizations show that compound 7 conserved the overall binding mode of the natural disaccharide while possessing an improved affinity and a strict specificity for DC-SIGN.
- Published
- 2017
42. Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase
- Author
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Cinzia Colombo, Črtomir Podlipnik, Leonardo Lo Presti, Masahiro Niikura, Andrew J Bennet, and Anna Bernardi
- Subjects
RNA viruses ,lcsh:Medicine ,Chemistry Techniques, Synthetic ,Biochemistry ,Mass Spectrometry ,Analytical Chemistry ,Spectrum Analysis Techniques ,Catalytic Domain ,Influenza A Virus, H9N2 Subtype ,Enzyme Inhibitors ,lcsh:Science ,Pathology and laboratory medicine ,Organic Compounds ,Chromatographic Techniques ,Monosaccharides ,Electrospray Ionization Mass Spectrometry ,Medical microbiology ,Molecular Docking Simulation ,Chemistry ,Influenza A virus ,Physical Sciences ,Viruses ,Pathogens ,Research Article ,Ethers ,Carbohydrates ,Neuraminidase ,Research and Analysis Methods ,Microbiology ,Viral Proteins ,Column Chromatography ,Virology ,Influenza viruses ,Medicine and health sciences ,Influenza A Virus, H5N1 Subtype ,Biology and life sciences ,lcsh:R ,Organic Chemistry ,Organisms ,Viral pathogens ,Chemical Compounds ,Bridged Bicyclo Compounds, Heterocyclic ,Viral Replication ,Microbial pathogens ,Drug Design ,Alcohols ,Sialic Acids ,Enzymology ,lcsh:Q ,Orthomyxoviruses - Abstract
The rise of drug-resistant influenza A virus strains motivates the development of new antiviral drugs, with different structural motifs and substitution. Recently, we explored the use of a bicyclic (bicyclo[3.1.0]hexane) analogue of sialic acid that was designed to mimic the conformation adopted during enzymatic cleavage within the neuraminidase (NA; sialidase) active site. Given that our first series of compounds were at least four orders of magnitude less active than available drugs, we hypothesized that the new carbon skeleton did not elicit the same interactions as the cyclohexene frameworks used previously. Herein, we tried to address this critical point with the aid of molecular modeling and we proposed new structures with different functionalization, such as the introduction of free ammonium and guanidinium groups and ether side chains other than the 3-pentyl side chain, the characteristic side chain in Oseltamivir. A highly simplified synthetic route was developed, starting from the cyclopropanation of cyclopentenone and followed by an aziridination and further functionalization of the five-member ring. This allowed the efficient preparation of a small library of new bicyclic ligands that were characterized by enzyme inhibition assays against influenza A neuraminidases N1, its H274Y mutant, and N2. The results show that none of the new structural variants synthesized, including those containing guanidinium groups rather than free ammonium ions, displayed activity against influenza A neuraminidases at concentrations less than 2 mM. We conclude that the choice and positioning of functional groups on the bicyclo[3.1.0]hexyl system still need to be properly tuned for producing complementary interactions within the catalytic site.
- Published
- 2017
43. New 'clickable' polymeric coating for glycan microarrays
- Author
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Caterina Zilio, Anna Bernardi, Alessandro Palmioli, Matteo Salina, Giovanni Tagliabue, Marco Buscaglia, Roberto Consonni, Marcella Chiari, Zilio, C, Bernardi, A, Palmioli, A, Salina, M, Tagliabue, G, Buscaglia, M, Consonni, R, and Chiari, M
- Subjects
Materials Chemistry2506 Metals and Alloy ,Surface coating ,Microarrays ,Electronic, Optical and Magnetic Material ,Metals and Alloys ,Surfaces, Coatings and Film ,Condensed Matter Physic ,Microarray ,Glycan ,Condensed Matter Physics ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,CHIM/01 - CHIMICA ANALITICA ,Click-chemistry ,CHIM/06 - CHIMICA ORGANICA ,CHIM/05 - SCIENZA E TECNOLOGIA DEI MATERIALI POLIMERICI ,Materials Chemistry ,Electrical and Electronic Engineering ,Instrumentation - Abstract
The interaction of carbohydrates with a variety of biological targets, including antibodies, proteins, viruses and cells are of utmost importance in many aspects of biology. Glycan microarrays are increasingly used to determine the binding specificity of glycan-binding proteins. In this study, a novel slide is reported for the fabrication of glycan arrays that combines the higher sensitivity of a layered Si-SiO2 with a novel approach to form a polymeric coating easily modifiable by subsequent click reaction. The alkyne-containing copolymer, adsorbed from an aqueous solution, produces a coating by a single step procedure and serves as a soft, tridimensional support for the oriented immobilization of carbohydrates via azide/alkyne Cu(I) catalyzed "click" reaction. The equilibrium and kinetics parameters of the interaction of Concanavalin A with eight synthetic glycans were determined using fluorescence microarray and Reflective Phantom Interface (RPI), a recently proposed optical label-free detection approach. The enhancement of fluorescence provided by the Si-SiO2 slides enabled to extend the limit of detection at lower surface densities of lectins, in turn enabling the study of the interaction for a wide range of glycans surface density. Equilibrium dissociation constants of a few nM were extracted for multivalent glycan-lectin binding, mimicking the conditions of biological membranes, whereas hundreds of nM were observed at the lower glycan surface densities. (C) 2015 Elsevier B.V. All rights reserved.
- Published
- 2015
44. Observation of a Tricyclic[4.1.0.0
- Author
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Marco, Farren-Dai, John R, Thompson, Anna, Bernardi, Cinzia, Colombo, and Andrew J, Bennet
- Abstract
We describe the formation of a bis-cyclopropane product, a tricyclic[4.1.0.0
- Published
- 2017
45. Frontispiece: Design of Allosteric Stimulators of the Hsp90 ATPase as New Anticancer Leads
- Author
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David A. Agard, Elisabetta Moroni, Carlos Sanchez-Martin, Giorgio Colombo, Marzia Pennati, Sara Sattin, Jiahui Tao, Andrea Rasola, Anna Bernardi, Nadia Zaffaroni, and Ilda D'Annessa
- Subjects
Biochemistry ,biology ,Chemistry ,Stereochemistry ,ATPase ,Organic Chemistry ,Allosteric regulation ,biology.protein ,General Chemistry ,Hsp90 ,Catalysis - Published
- 2017
46. Facile access to pseudo-thio - 1,2 - dimannoside, a new glycomimetic DC-SIGN antagonist
- Author
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Silvia Achilli, Franck Fieschi, Anna Bernardi, Francesca Vasile, Alice Tamburrini, Cinzia Colombo, Corinne Vivès, Sara Sattin, Dipartimento di Chimica, Università degli Studi di Milano [Milano] (UNIMI), Institut de biologie structurale (IBS - UMR 5075 ), 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)-Centre National de la Recherche Scientifique (CNRS), MP3, SPR, European Project: Immunoshape, Università degli Studi di Milano = University of Milan (UNIMI), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
- Subjects
Models, Molecular ,Stereochemistry ,Clinical Biochemistry ,Disaccharide ,Pharmaceutical Science ,Thio ,Epoxide ,Receptors, Cell Surface ,010402 general chemistry ,01 natural sciences ,Biochemistry ,DC-SIGN ,chemistry.chemical_compound ,Glycomimetic ,Enzymatic hydrolysis ,Drug Discovery ,Humans ,Molecule ,Lectins, C-Type ,Molecular Biology ,biology ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Antagonist ,Surface Plasmon Resonance ,Mannobioside ,0104 chemical sciences ,Thioglycosides ,Drug Design ,Mannosides ,Glycomimetics ,biology.protein ,Molecular Medicine ,Cell Adhesion Molecules ,NOESY - Abstract
International audience; The synthesis and conformational analysis of pseudo-thio-1,2-dimannoside are described. This molecule mimics mannobioside (Manα(1,2)Man) and is an analog of pseudo-1,2-dimannoside, with expected increased stability to enzymatic hydrolysis. A short and efficient synthesis was developed based on an epoxide ring-opening reaction by a mannosyl thiolate, generated in situ from the corresponding thioacetate. NMR-NOESY studies supported by MM3(∗) calculations showed that the pseudo-thio-1,2-dimannoside shares the conformational behavior of the pseudo-1,2-dimannoside and is a structural mimic of the natural disaccharide. Its affinity for DC-SIGN was measured by SPR and found to be comparable to the corresponding O-linked analog, offering good opportunities for further developments.
- Published
- 2017
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47. Glyco-functionalized dinuclear rhenium(i) complexes for cell imaging
- Author
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Luisa De Cola, Alessandro Palmioli, Monica Panigati, Alessandro Aliprandi, Dedy Septiadi, Matteo Mauro, Anna Bernardi, Palmioli, A, Aliprandi, A, Septiadi, D, Mauro, M, Bernardi, A, De Cola, L, and Panigati, M
- Subjects
Glycosylation ,Anomer ,Stereochemistry ,Proton Magnetic Resonance Spectroscopy ,media_common.quotation_subject ,chemistry.chemical_element ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Pyridazine ,HeLa ,chemistry.chemical_compound ,Coordination Complexes ,Humans ,Physical and Theoretical Chemistry ,Internalization ,media_common ,Luminescent Agents ,Microscopy, Confocal ,biology ,010405 organic chemistry ,Optical Imaging ,Organic Chemistry ,Rhenium ,biology.organism_classification ,0104 chemical sciences ,chemistry ,Covalent bond ,Luminescent Measurements ,Selectivity ,HeLa Cells ,Conjugate - Abstract
The design, synthesis and photophysical characterization of four new luminescent glycosylated luminophores based on dinuclear rhenium complexes, namely Glyco-Re, are described. The derivatives have the general formula [Re2(μ-Cl)2(CO)6(μ-pydz-R)] (R-pydz = functionalized 1,2-pyridazine), where a sugar residue (R) is covalently bound to the pyridazine ligand in the β position. Different synthetic pathways have been investigated including the so-called neo-glycorandomization procedure, affording stereoselectively glyco-conjugates containing glucose and maltose in a β anomeric configuration. A multivalent dinuclear rhenium glycodendron bearing three glucose units is also synthesized. All the Glyco-Re conjugates are comprehensively characterized and their photophysical properties and cellular internalization experiments on human cervical adenocarcinoma (HeLa) cells are reported. The results show that such Glyco-Re complexes display interesting bio-imaging properties, i.e. high cell permeability, organelle selectivity, low cytotoxicity and fast internalization. These findings make the presented Glyco-Re derivatives efficient phosphorescent probes suitable for cell imaging application.
- Published
- 2017
48. Glycomimetics and Glycoconjugates as Therapeutics in Infectious Diseases
- Author
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Anna Bernardi and Cinzia Colombo
- Subjects
chemistry.chemical_classification ,medicine.drug_class ,Glycoconjugate ,Antibiotics ,Bacterial enzymes ,Biology ,Small molecule ,Microbiology ,Biochemistry ,chemistry ,Antigen ,Glycomimetic ,Microbial adhesion ,medicine - Abstract
Mimics of natural carbohydrates (glycomimetics) and unnatural glycoconjugates are under intense scrutiny for the development of anti-infective therapies alternative or complementary to classical antibiotics. Three current approaches are reviewed in this article: (1) antiadhesive therapies, that focus on disrupting carbohydrate-protein complexes involved in microbial adhesion to host cells; (2) vaccines that use as antigens either polysaccharide fragments from bacterial and viruses surface or bacterial and viral lectins; (3) small molecule glycomimetic inhibitors of bacterial enzymes and antivirals.
- Published
- 2017
49. Synthesis of potential allosteric modulators of Hsp90 by chemical glycosylation of Eupomatenoid-6
- Author
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Sara Sattin, Anna Bernardi, and Laura Morelli
- Subjects
Glycosylation ,biology ,Stereochemistry ,Organic Chemistry ,Allosteric regulation ,Chemical glycosylation ,General Medicine ,Biochemistry ,Hsp90 ,Analytical Chemistry ,chemistry.chemical_compound ,chemistry ,Mannosylation ,biology.protein ,Molecule ,Glycosyl ,Benzofuran - Abstract
Hsp90 (Heat shock protein-90) is a chaperone protein and an established anti-apoptotic target in cancer therapy. Most of the known small-molecule inhibitors that have shown potent antitumor activity target the Hsp90 N-terminal domain and directly inhibit its ATP-ase activity. Many of these molecules display important secondary effects. A different approach to Hsp90 inhibition consists of targeting the protein C-terminal domain (CTD) and modulating its chaperone activity through allosteric effects. Using an original computational approach, allosteric hot-spots in the CTD have been recently identified that control interdomain communication. A combination of virtual and experimental screening enabled identification of a rhamnosylated benzofuran (Eupomatenoid-2) as a lead for further development. In this paper we describe glycodiversification of Eupomatenoid-2 using chemical glycosylation of the 2-(4'-hydroxyphenyl)benzofuran aglycon (a.k.a. Eupomatenoid-6). Glycosylation of the phenol by glycosyl bromides under basic conditions afforded the desired products in the gluco-, galacto-, and fuco-series. This approach failed in the manno- and rhamno-series. However, mannosylation and rhamnosylation of Eupomatenoid-6 could be obtained under carefully controlled acidic conditions, using O-benzoxazolyl imidate (OBox) donors. The glycosides obtained are currently under investigation as modulators of Hsp90 chaperone activity.
- Published
- 2014
50. A multivalent inhibitor of the DC-SIGN dependent uptake of HIV-1 and Dengue virus
- Author
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Mario Clerici, Javier Rojo, Ieva Sutkeviciute, Rasika Ramdasi, Franck Fieschi, Gerolamo Vettoretti, Anna Daghetti, Ali Amara, Anna Bernardi, Renato Ribeiro-Viana, Norbert Varga, Angela Berzi, Institut de biologie structurale (IBS - UMR 5075 ), 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)-Centre National de la Recherche Scientifique (CNRS), Department of Biomedical and Clinical Sciences, University of Milan, Pathologie cellulaire : aspects moléculaires et viraux / Pathologie et Virologie Moléculaire, Institut Universitaire d'Hématologie (IUH), Université Paris Diderot - Paris 7 (UPD7)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Toronto], University of Toronto, Department of Physiopatology and Transplantation, University of Milan (DEPT), Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universidad de Sevilla-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universidad de Sevilla, inconnu, Inconnu, 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), Università degli Studi di Milano = University of Milan (UNIMI), Universidad de Sevilla / University of Sevilla-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universidad de Sevilla / University of Sevilla-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Université Paris Diderot - Paris 7 (UPD7)-Université Paris Diderot - Paris 7 (UPD7)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)
- Subjects
genetic structures ,Dengue virus ,MESH: Dengue Virus ,medicine.disease_cause ,01 natural sciences ,Dengue fever ,Dengue ,MESH: HIV-1 ,Glycomimetic ,Nanotechnology ,Glycosides ,Receptor ,MESH: Receptors, Cell Surface ,0303 health sciences ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,biology ,MESH: Surface Plasmon Resonance ,3. Good health ,Raji cell ,DC-SIGN ,Mechanics of Materials ,MESH: Cell Adhesion Molecules ,MESH: Antiviral Agents ,Dendrimers ,Biophysics ,Receptors, Cell Surface ,Bioengineering ,010402 general chemistry ,Antiviral Agents ,Cell Line ,Biomaterials ,03 medical and health sciences ,Viral entry ,Glycodendrimers ,medicine ,Humans ,Lectins, C-Type ,Antigen-presenting cell ,030304 developmental biology ,MESH: Humans ,MESH: Dendrimers ,HIV ,Dengue Virus ,Surface Plasmon Resonance ,medicine.disease ,Virology ,MESH: Cell Line ,0104 chemical sciences ,Glycomimetics ,HIV-1 ,Ceramics and Composites ,biology.protein ,Cell Adhesion Molecules ,MESH: Lectins, C-Type - Abstract
International audience; DC-SIGN is a C-type lectin receptor on antigen presenting cells (dendritic cells) which has an important role in some viral infection, notably by HIV and Dengue virus (DV). Multivalent presentation of carbohydrates on dendrimeric scaffolds has been shown to inhibit DC-SIGN binding to HIV envelope glycoprotein gp120, thus blocking viral entry. This approach has interesting potential applications for infection prophylaxis. In an effort to develop high affinity inhibitors of DC-SIGN mediated viral entry, we have synthesized a group of glycodendrimers of different valency that bear different carbohydrates or glycomimetic DC-SIGN ligands and have studied their DC-SIGN binding activity and antiviral properties both in an HIV and a Dengue infection model. Surface Plasmon Resonance (SPR) competition studies have demonstrated that the materials obtained bind efficiently to DC-SIGN with IC50s in the μm range, which depend on the nature of the ligand and on the valency of the scaffold. In particular, a hexavalent presentation of the DC-SIGN selective antagonist 4 displayed high potency, as well as improved accessibility and chemical stability relative to previously reported dendrimers. At low μm concentration the material was shown to block both DC-SIGN mediated uptake of DV by Raji cells and HIV trans-infection of T cells.
- Published
- 2014
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