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Pappalardo JS, Salmaso S, Levchenko TS, Mastrotto F, Bersani S, Langellotti CA, Vermeulen M, Ghersa F, Quattrocchi V, Zamorano PI, Hartner WC, Toniutti M, Musacchio T, Torchilin VP. Characterization of a Nanovaccine Platform Based on an α1,2-Mannobiose Derivative Shows Species-non-specific Targeting to Human, Bovine, Mouse, and Teleost Fish Dendritic Cells. Mol Pharm 2021; 18:2540-2555. [PMID: 34106726 DOI: 10.1021/acs.molpharmaceut.1c00048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Dendritic cells serve as the main immune cells that trigger the immune response. We developed a simple and cost-effective nanovaccine platform based on the α1',2-mannobiose derivative for dendritic cell targeting. In previous work, we have formulated the α1,2-mannobiose-based nanovaccine platform with plasmid DNA and tested it in cattle against BoHV-1 infection. There, we have shown that the dendritic cell targeting using this nanovaccine platform in vivo can boost the immunogenicity, resulting in a long-lasting immunity. In this work, we aim to characterize the α1',2-mannobiose derivative, which is key in the nanovaccine platform. This DC-targeting strategy takes advantage of the specific receptor known as DC-SIGN and exploits its capacity to bind α1,2-mannobiose that is present at terminal ends of oligosaccharides in certain viruses, bacteria, and other pathogens. The oxidative conjugation of α1',2-mannobiose to NH2-PEG2kDa-DSPE allowed us to preserve the chemical structure of the non-reducing mannose of the disaccharide and the OH groups and the stereochemistry of all carbons of the reducing mannose involved in the binding to DC-SIGN. Here, we show specific targeting to DC-SIGN of decorated micelles incubated with the Raji/DC-SIGN cell line and uptake of targeted liposomes that took place in human, bovine, mouse, and teleost fish DCs in vitro, by flow cytometry. Specific targeting was found in all cultures, demonstrating a species-non-specific avidity for this ligand, which opens up the possibility of using this nanoplatform to develop new vaccines for various species, including humans.
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Affiliation(s)
- Juan Sebastian Pappalardo
- Veterinary Nanomedicine Group, Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB, INTA-CONICET), EEA Bariloche, Instituto Nacional de Tecnología Agropecuaria, Bote Modesta Victoria 4450, San Carlos de Bariloche, Río Negro R8403DVZ, Argentina.,Immunology and Immunomodulators Group, Instituto de Virología e Innovaciones Tecnológicas (IVIT, INTA-CONICET), IV, Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto 2799, William Morris, Buenos Aires B1681FUU, Argentina.,Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Stefano Salmaso
- Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via F. Marzolo, 5, Padova 35121, Padova, Italy
| | - Tatyana S Levchenko
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Francesca Mastrotto
- Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via F. Marzolo, 5, Padova 35121, Padova, Italy
| | - Sara Bersani
- Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via F. Marzolo, 5, Padova 35121, Padova, Italy
| | - Cecilia A Langellotti
- Immunology and Immunomodulators Group, Instituto de Virología e Innovaciones Tecnológicas (IVIT, INTA-CONICET), IV, Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto 2799, William Morris, Buenos Aires B1681FUU, Argentina.,National Council of Scientific and Technical Research (CONICET), Avenida Rivadavia 1917, Ciudad de Buenos Aires C1033AAJ, Argentina
| | - Monica Vermeulen
- National Council of Scientific and Technical Research (CONICET), Avenida Rivadavia 1917, Ciudad de Buenos Aires C1033AAJ, Argentina.,Institute of Experimental Medicine (IMEX, ANM-CONICET), Academia Nacional de Medicina, Pacheco de Melo 3081, Ciudad de Buenos Aires C1425AUM, Argentina
| | - Federica Ghersa
- Veterinary Nanomedicine Group, Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB, INTA-CONICET), EEA Bariloche, Instituto Nacional de Tecnología Agropecuaria, Bote Modesta Victoria 4450, San Carlos de Bariloche, Río Negro R8403DVZ, Argentina.,Parasitology Laboratory, Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA, UNCo-CONICET) Universidad Nacional del Comahue, Quintral 1250, San Carlos de Bariloche, Río Negro R8400FRF, Argentina
| | - Valeria Quattrocchi
- Immunology and Immunomodulators Group, Instituto de Virología e Innovaciones Tecnológicas (IVIT, INTA-CONICET), IV, Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto 2799, William Morris, Buenos Aires B1681FUU, Argentina
| | - Patricia I Zamorano
- Immunology and Immunomodulators Group, Instituto de Virología e Innovaciones Tecnológicas (IVIT, INTA-CONICET), IV, Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto 2799, William Morris, Buenos Aires B1681FUU, Argentina.,National Council of Scientific and Technical Research (CONICET), Avenida Rivadavia 1917, Ciudad de Buenos Aires C1033AAJ, Argentina
| | - William C Hartner
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Micaela Toniutti
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Tiziana Musacchio
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Vladimir P Torchilin
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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2
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Nestor G, Ruda A, Anderson T, Oscarson S, Widmalm G, Gronenborn AM. A detailed picture of a protein-carbohydrate hydrogen-bonding network revealed by NMR and MD simulations. Glycobiology 2020; 31:508-518. [PMID: 32902635 PMCID: PMC8091458 DOI: 10.1093/glycob/cwaa081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 11/12/2022] Open
Abstract
Cyanovirin-N (CV-N) is a cyanobacterial lectin with antiviral activity towards HIV and several other viruses. Here, we identify mannoside hydroxyl protons that are hydrogen bonded to the protein backbone of the CV-N domain B binding site, using NMR spectroscopy. For the two carbohydrate ligands Manα(1→2)ManαOMe and Manα(1→2) Manα(1→6)ManαOMe five hydroxyl protons are involved in hydrogen-bonding networks. Comparison with previous crystallographic results revealed that four of these hydroxyl protons donate hydrogen bonds to protein backbone carbonyl oxygens in solution and in the crystal. Hydrogen bonds were not detected between the side chains of Glu41 and Arg76 with sugar hydroxyls, as previously proposed for CV-N binding of mannosides. Molecular dynamics simulations of the CV-N/Manα(1→2)Manα(1→6)ManαOMe complex confirmed the NMR-determined hydrogen-bonding network. Detailed characterization of CV-N/mannoside complexes provides a better understanding of lectin-carbohydrate interactions and opens up to the use of CV-N and similar lectins as antiviral agents.
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Affiliation(s)
- Gustav Nestor
- Department of Structural Biology, University of Pittsburgh School of Medicine,1051 BST3, 3501 Fifth Ave, Pittsburgh, PA 15261, USA.,Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden
| | - Alessandro Ruda
- Department of Organic Chemistry, Stockholm University, Svante Arrhenius väg 16C, Stockholm, Sweden
| | - Taigh Anderson
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Göran Widmalm
- Department of Organic Chemistry, Stockholm University, Svante Arrhenius väg 16C, Stockholm, Sweden
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine,1051 BST3, 3501 Fifth Ave, Pittsburgh, PA 15261, USA
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3
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Rönnols J, Engström O, Schnupf U, Säwén E, Brady JW, Widmalm G. Inter-residual Hydrogen Bonding in Carbohydrates Unraveled by NMR Spectroscopy and Molecular Dynamics Simulations. Chembiochem 2019; 20:2519-2528. [PMID: 31066963 DOI: 10.1002/cbic.201900301] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Indexed: 12/15/2022]
Abstract
Carbohydrates, also known as glycans in biological systems, are omnipresent in nature where they as glycoconjugates occur as oligo- and polysaccharides linked to lipids and proteins. Their three-dimensional structure is defined by two or three torsion angles at each glycosidic linkage. In addition, transglycosidic hydrogen bonding between sugar residues may be important. Herein we investigate the presence of these inter-residue interactions by NMR spectroscopy in D2 O/[D6 ]DMSO (70:30) or D2 O and by molecular dynamics (MD) simulations with explicit water as solvent for disaccharides with structural elements α-d-Manp-(1→2)-d-Manp, β-d-GlcpNAc-(1→2)-d-Manp, and α-d-Glcp-(1→4)-β-d-Glcp, all of which have been suggested to exhibit inter-residue hydrogen bonding. For the disaccharide β-d-GlcpNAc-(1→2)-β-d-Manp-OMe, the large extent of O5'⋅⋅⋅HO3 hydrogen bonding as seen from the MD simulation is implicitly supported by the 1 H NMR chemical shift and 3 JHO3,H3 value of the hydroxy proton. In the case of α-d-Glcp-(1→4)-β-d-Glcp-OMe, the existence of a transglycosidic hydrogen bond O2'⋅⋅⋅HO3 was proven by the presence of a cross-peak in 1 H,13 C HSQC-TOCSY experiments as a result of direct TOCSY transfer between HO3 of the reducing end residue and H2' (detected at C2') of the terminal residue. The occurrence of inter-residue hydrogen bonding, albeit transient, is judged important for the stabilization of three-dimensional structures, which may be essential in maintaining a conformational state for carbohydrate-protein interactions of glycans to take place in biologically important environments.
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Affiliation(s)
- Jerk Rönnols
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 106 91, Stockholm, Sweden
| | - Olof Engström
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 106 91, Stockholm, Sweden
| | - Udo Schnupf
- Department of Chemistry and Biochemistry, Bradley University, Peoria, IL, 61625, USA
| | - Elin Säwén
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 106 91, Stockholm, Sweden
| | - John W Brady
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 106 91, Stockholm, Sweden
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4
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Brown GD, Bauer J, Osborn HMI, Kuemmerle R. A Solution NMR Approach To Determine the Chemical Structures of Carbohydrates Using the Hydroxyl Groups as Starting Points. ACS OMEGA 2018; 3:17957-17975. [PMID: 31458388 PMCID: PMC6644132 DOI: 10.1021/acsomega.8b02136] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/07/2018] [Indexed: 06/10/2023]
Abstract
An efficient NMR approach is described for determining the chemical structures of the monosaccharide glucose and four disaccharides, namely, nigerose, gentiobiose, leucrose and isomaltulose. This approach uses the 1H resonances of the -OH groups, which are observable in the NMR spectrum of a supercooled aqueous solution, as the starting point for further analysis. The 2D-NMR technique, HSQC-TOCSY, is then applied to fully define the covalent structure (i.e., the topological relationship between C-C, C-H, and O-H bonds) that must be established for a novel carbohydrate before proceeding to further conformational studies. This process also leads to complete assignment of all 1H and 13C resonances. The approach is exemplified by analyzing the monosaccharide glucose, which is treated as if it were an "unknown", and also by fully assigning all the NMR resonances for the four disaccharides that contain glucose. It is proposed that this technique should be equally applicable to the determination of chemical structures for larger carbohydrates of unknown composition, including those that are only available in limited quantities from biological studies. The advantages of commencing the structure elucidation of a carbohydrate at the -OH groups are discussed with reference to the now well-established 2D-/3D-NMR strategy for investigation of peptides/proteins, which employs the -NH resonances as the starting point.
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Affiliation(s)
- Geoffrey D. Brown
- Department of Chemistry and Reading School of Pharmacy, The University of Reading, Whiteknights, Reading RG6 6AP, United Kingdom
| | - Julia Bauer
- Department of Chemistry and Reading School of Pharmacy, The University of Reading, Whiteknights, Reading RG6 6AP, United Kingdom
| | - Helen M. I. Osborn
- Department of Chemistry and Reading School of Pharmacy, The University of Reading, Whiteknights, Reading RG6 6AP, United Kingdom
| | - Rainer Kuemmerle
- Bruker
Biospin AG, NMR Division, Industriestrasse 26, CH-8117 Fallanden, Switzerland
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5
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Nestor G, Anderson T, Oscarson S, Gronenborn AM. Direct Observation of Carbohydrate Hydroxyl Protons in Hydrogen Bonds with a Protein. J Am Chem Soc 2017; 140:339-345. [PMID: 29227646 DOI: 10.1021/jacs.7b10595] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxyl proton resonances of uniformly 13C-labeled Manα(1-2)Manα(1-2)ManαOMe (Man3) bound to cyanovirin-N (CV-N) were detected at ambient temperature in aqueous solution by NMR spectroscopy. The directions of the hydroxyl groups were determined on the basis of NOEs, and a previously unknown hydrogen-bonding network between Man3 and CV-N was discovered. This is the first report on detecting hydroxyl protons of a protein-bound carbohydrate in aqueous solution by NMR. Approaches such as those presented here may open the door for accurately determining intermolecular hydrogen bonds in carbohydrate-protein complexes.
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Affiliation(s)
- Gustav Nestor
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, United States
| | - Taigh Anderson
- Centre for Synthesis and Chemical Biology, University College Dublin , Belfield, Dublin 4, Ireland
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin , Belfield, Dublin 4, Ireland
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, United States
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6
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Battistel MD, Azurmendi HF, Freedberg DI. Glycan OH Exchange Rate Determination in Aqueous Solution: Seeking Evidence for Transient Hydrogen Bonds. J Phys Chem B 2017; 121:683-695. [PMID: 27995788 DOI: 10.1021/acs.jpcb.6b10594] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen bonds (Hbonds) are important stabilizing forces in biomolecules. However, for glycans in aqueous solution, direct NMR detection of Hbonds is elusive because of their transient nature. Here, we present Isotope-based Natural-abundance TOtal correlation eXchange SpectroscopY (INTOXSY), a new 1H-13C heteronuclear single quantum coherence-total correlation spectroscopy based method, to extract OH groups' exchange rate constants (kex) for molecules in natural 13C abundance and show that OH Hbonds can be inferred from "slower" H/D kex. We evaluate kex measured with INTOXSY in light of those extracted with line-shape analysis. Subsequently, we use a set of common glycans to establish a kex reference basis set and to infer the existence of transient Hbonds involving OH donor groups. Then, we report kex values for a series of mono- and disaccharides, as well as for oligosaccharides sialyl Lewis X and β-cyclodextrin, and compare the results with those from the reference set to extract Hbond information. Finally, we utilize NMR experimental data in conjunction with molecular dynamics simulations to establish donor and acceptor Hbond pairs. Our exchange rate measurements indicate that OH/OD exchange rates, kHD, values <10 s-1 are consistent with transient Hbond OH groups and potential acceptor groups can be uncovered through MD simulations.
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Affiliation(s)
- Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration , 10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
| | - Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration , 10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration , 10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
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7
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Blázquez-Sánchez MT, Marcelo F, Fernández-Alonso MC, Poveda A, Jiménez-Barbero J, Vicent C. Cooperative hydrogen bonding in glyco-oligoamides: DNA minor groove binders in aqueous media. Chemistry 2014; 20:17640-52. [PMID: 25359390 DOI: 10.1002/chem.201403911] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Indexed: 12/26/2022]
Abstract
A strategy to create cooperative hydrogen-bonding centers by using strong and directional intramolecular hydrogen-bonding motifs that can survive in aqueous media is presented. In particular, glyco-oligoamides, a family of DNA minor groove binders, with cooperative and non-cooperative hydrogen-bonding donor centers in the carbohydrate residues have been designed, synthesized, and studied by means of NMR spectroscopy and molecular modeling methods. Indeed, two different sugar moieties, namely, β-D-Man-Py-γ-Py-Ind (1; Ind=indole, Man=mannose, Py=pyrrole) and β-D-Tal-Py-γ-Py-Ind (2; Tal=talose), were chosen according to our design. These sugar molecules should present one- or two-directional intramolecular hydrogen bonds. The challenge has been to study the conformation of the glyco-oligoamides at low temperature in physiological media by detecting the exchangeable protons (amide NH and OH resonances) by means of NMR spectroscopic analysis. In addition, two more glyco-oligoamides with non-cooperative hydrogen-bonding centers, that is, β-D-Glc-Py-γ-Py-Ind (3; Glc=glucose), β-D-Gal-Py-γ-Py-Ind (4; Gal=galactose), and the model compounds β-D-Man-Py-NHAc (5) and β-D-Tal-Py-NHAc (6) were synthesized and studied for comparison. We have demonstrated the existence of directional intramolecular hydrogen bonds in 1 and 2 in aqueous media. The unexpected differences in terms of stabilization of the intramolecular hydrogen bonds in 1 and 2 relative to 5 and 6 promoted us to evaluate the influence of CH-π interactions on the establishment of intramolecular hydrogen bonds by using computational methods. Initial binding studies of 1 and 2 with calf-thymus DNA and poly(dA-dT)2 by NMR spectroscopic analysis and molecular dynamics simulations were also carried out. Both new sugar-oligoamides are bound in the minor groove of DNA, thus keeping a stable hairpin structure, as in the free state, in which both intramolecular hydrogen-bonding and CH-π interactions are present.
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8
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Carrero P, Ardá A, Alvarez M, Doyagüez EG, Rivero-Buceta E, Quesada E, Prieto A, Solís D, Camarasa MJ, Peréz-Pérez MJ, Jiménez-Barbero J, San-Félix A. Differential Recognition of Mannose-Based Polysaccharides by Tripodal Receptors Based on a Triethylbenzene Scaffold Substituted with Trihydroxybenzoyl Moieties. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201239] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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9
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Johannessen C, Pendrill R, Widmalm G, Hecht L, Barron LD. Glycan structure of a high-mannose glycoprotein from Raman optical activity. Angew Chem Int Ed Engl 2011; 50:5349-51. [PMID: 21523866 DOI: 10.1002/anie.201008258] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Indexed: 12/11/2022]
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10
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Johannessen C, Pendrill R, Widmalm G, Hecht L, Barron LD. Glycan Structure of a High-Mannose Glycoprotein from Raman Optical Activity. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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11
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Säwén E, Massad T, Landersjö C, Damberg P, Widmalm G. Population distribution of flexible molecules from maximum entropy analysis using different priors as background information: application to the Φ, Ψ-conformational space of the α-(1-->2)-linked mannose disaccharide present in N- and O-linked glycoproteins. Org Biomol Chem 2010; 8:3684-95. [PMID: 20574564 DOI: 10.1039/c003958f] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformational space available to the flexible molecule α-D-Manp-(1-->2)-α-D-Manp-OMe, a model for the α-(1-->2)-linked mannose disaccharide in N- or O-linked glycoproteins, is determined using experimental data and molecular simulation combined with a maximum entropy approach that leads to a converged population distribution utilizing different input information. A database survey of the Protein Data Bank where structures having the constituent disaccharide were retrieved resulted in an ensemble with >200 structures. Subsequent filtering removed erroneous structures and gave the database (DB) ensemble having three classes of mannose-containing compounds, viz., N- and O-linked structures, and ligands to proteins. A molecular dynamics (MD) simulation of the disaccharide revealed a two-state equilibrium with a major and a minor conformational state, i.e., the MD ensemble. These two different conformation ensembles of the disaccharide were compared to measured experimental spectroscopic data for the molecule in water solution. However, neither of the two populations were compatible with experimental data from optical rotation, NMR (1)H,(1)H cross-relaxation rates as well as homo- and heteronuclear (3)J couplings. The conformational distributions were subsequently used as background information to generate priors that were used in a maximum entropy analysis. The resulting posteriors, i.e., the population distributions after the application of the maximum entropy analysis, still showed notable deviations that were not anticipated based on the prior information. Therefore, reparameterization of homo- and heteronuclear Karplus relationships for the glycosidic torsion angles Φ and Ψ were carried out in which the importance of electronegative substituents on the coupling pathway was deemed essential resulting in four derived equations, two (3)J(COCC) and two (3)J(COCH) being different for the Φ and Ψ torsions, respectively. These Karplus relationships are denoted JCX/SU09. Reapplication of the maximum entropy analysis gave excellent agreement between the MD- and DB-posteriors. The information entropies show that the current reparametrization of the Karplus relationships constitutes a significant improvement. The Φ(H) torsion angle of the disaccharide is governed by the exo-anomeric effect and for the dominating conformation Φ(H) = -40 degrees and Ψ(H) = 33 degrees. The minor conformational state has a negative Ψ(H) torsion angle; the relative populations of the major and the minor states are approximately 3 : 1. It is anticipated that application of the methodology will be useful to flexible molecules ranging from small organic molecules to large biomolecules.
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Affiliation(s)
- Elin Säwén
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91, Stockholm, Sweden
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12
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Reina JJ, Díaz I, Nieto PM, Campillo NE, Páez JA, Tabarani G, Fieschi F, Rojo J. Docking, synthesis, and NMR studies of mannosyl trisaccharide ligands for DC-SIGN lectin. Org Biomol Chem 2008; 6:2743-54. [PMID: 18633532 DOI: 10.1039/b802144a] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DC-SIGN, a lectin, which presents at the surface of immature dendritic cells, constitutes nowadays a promising target for the design of new antiviral drugs. This lectin recognizes highly glycosylated proteins present at the surface of several pathogens such as HIV, Ebola virus, Candida albicans, Mycobacterium tuberculosis, etc. Understanding the binding mode of this lectin is a topic of tremendous interest and will permit a rational design of new and more selective ligands. Here, we present computational and experimental tools to study the interaction of di- and trisaccharides with DC-SIGN. Docking analysis of complexes involving mannosyl di- and trisaccharides and the carbohydrate recognition domain (CRD) of DC-SIGN have been performed. Trisaccharides Manalpha1,2[Manalpha1,6]Man 1 and Manalpha1,3[Manalpha1,6]Man 2 were synthesized from an orthogonally protected mannose as a common intermediate. Using these ligands and the soluble extracellular domain (ECD) of DC-SIGN, NMR experiments based on STD and transfer-NOE were performed providing additional information. Conformational analysis of the mannosyl ligands in the free and bound states was done. These studies have demonstrated that terminal mannoses at positions 2 or 3 in the trisaccharides are the most important moiety and present the strongest contact with the binding site of the lectin. Multiple binding modes could be proposed and therefore should be considered in the design of new ligands.
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Affiliation(s)
- José J Reina
- Grupo de Carbohidratos, Instituto de Investigaciones Químicas, CSIC, Universidad de Sevilla, Américo Vespucio 49, Seville, Spain
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