1
|
Pietri GP, Bertuzzi S, Karnicar K, Unione L, Lisnic B, Malic S, Miklic K, Novak M, Calloni I, Santini L, Usenik A, Romano MR, Adamo R, Jonjic S, Turk D, Jiménez-Barbero J, Lenac Rovis T. Antigenic determinants driving serogroup-specific antibody response to Neisseria meningitidis C, W, and Y capsular polysaccharides: Insights for rational vaccine design. Carbohydr Polym 2024; 341:122349. [PMID: 38876728 DOI: 10.1016/j.carbpol.2024.122349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/15/2024] [Accepted: 05/29/2024] [Indexed: 06/16/2024]
Abstract
Meningococcal glycoconjugate vaccines sourced from capsular polysaccharides (CPSs) of pathogenic Neisseria meningitidis strains are well-established measures to prevent meningococcal disease. However, the exact structural factors responsible for antibody recognition are not known. CPSs of Neisseria meningitidis serogroups Y and W differ by a single stereochemical center, yet they evoke specific immune responses. Herein, we developed specific monoclonal antibodies (mAbs) targeting serogroups C, Y, and W and evaluated their ability to kill bacteria. We then used these mAbs to dissect structural elements responsible for carbohydrate-protein interactions. First, Men oligosaccharides were screened against the mAbs using ELISA to select putative lengths representing the minimal antigenic determinant. Next, molecular interaction features between the mAbs and serogroup-specific sugar fragments were elucidated using STD-NMR. Moreover, X-ray diffraction data with the anti-MenW CPS mAb enabled the elucidation of the sugar-antibody binding mode. Our findings revealed common traits in the epitopes of all three sialylated serogroups. The minimal binding epitopes typically comprise five to six repeating units. Moreover, the O-acetylation of the neuraminic acid moieties was fundamental for mAb binding. These insights hold promise for the rational design of optimized meningococcal oligosaccharides, opening new avenues for novel production methods, including chemical or enzymatic approaches.
Collapse
Affiliation(s)
- Gian Pietro Pietri
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Sara Bertuzzi
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Katarina Karnicar
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Luca Unione
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009 Bilbao, Bizkaia, Spain
| | - Berislav Lisnic
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Suzana Malic
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Karmela Miklic
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Matej Novak
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Ilaria Calloni
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | | | - Aleksandra Usenik
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | | | | | - Stipan Jonjic
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Dusan Turk
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009 Bilbao, Bizkaia, Spain; Department of Organic and Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940 Leioa, Bizkaia, Spain; Centro de Investigación Biomédica En Red de Enfermedades Respiratorias, 28029 Madrid, Spain.
| | - Tihana Lenac Rovis
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.
| |
Collapse
|
2
|
Quintana JI, Massaro M, Cagnoni AJ, Nuñez-Franco R, Delgado S, Jiménez-Osés G, Mariño KV, Rabinovich GA, Jiménez-Barbero J, Ardá A. Different roles of the heterodimer architecture of galectin-4 in selective recognition of oligosaccharides and lipopolysaccharides having ABH antigens. J Biol Chem 2024; 300:107577. [PMID: 39019214 PMCID: PMC11362799 DOI: 10.1016/j.jbc.2024.107577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/18/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024] Open
Abstract
The dimeric architecture of tandem-repeat type galectins, such as galectin-4 (Gal-4), modulates their biological activities, although the underlying molecular mechanisms have remained elusive. Emerging evidence show that tandem-repeat galectins play an important role in innate immunity by recognizing carbohydrate antigens present on the surface of certain pathogens, which very often mimic the structures of the human self-glycan antigens. Herein, we have analyzed the binding preferences of the C-domain of Gal-4 (Gal-4C) toward the ABH-carbohydrate histo-blood antigens with different core presentations and their recognition features have been rationalized by using a combined experimental approach including NMR, solid-phase and hemagglutination assays, and molecular modeling. The data show that Gal-4C prefers A over B antigens (two-fold in affinity), contrary to the N-domain (Gal-4N), although both domains share the same preference for the type-6 presentations. The behavior of the full-length Gal-4 (Gal-4FL) tandem-repeat form has been additionally scrutinized. Isothermal titration calorimetry and NMR data demonstrate that both domains within full-length Gal-4 bind to the histo-blood antigens independently of each other, with no communication between them. In this context, the heterodimeric architecture does not play any major role, apart from the complementary A and B antigen binding preferences. However, upon binding to a bacterial lipopolysaccharide containing a multivalent version of an H-antigen mimetic as O-antigen, the significance of the galectin architecture was revealed. Indeed, our data point to the linker peptide domain and the F-face of the C-domain as key elements that provide Gal-4 with the ability to cross-link multivalent ligands, beyond the glycan binding capacity of the dimer.
Collapse
Affiliation(s)
- Jon I Quintana
- CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - Mora Massaro
- Laboratorio de Glicomedicina, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Alejandro J Cagnoni
- Laboratorio de Glicomedicina, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - Sandra Delgado
- CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - Gonzalo Jiménez-Osés
- CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - Karina V Mariño
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gabriel A Rabinovich
- Laboratorio de Glicomedicina, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain; Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, Leioa, Spain; Centro de investigación Biomédica En Red de Enfermedades Respiratorias, Madrid, Spain.
| | - Ana Ardá
- CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain.
| |
Collapse
|
3
|
Atxabal U, Fernández A, Moure MJ, Sobczak K, Nycholat C, Almeida-Marrero V, Oyenarte I, Paulson JC, de la Escosura A, Torres T, Reichardt NC, Jiménez-Barbero J, Ereño-Orbea J. Quantifying Siglec-sialylated ligand interactions: a versatile 19F-T 2 CPMG filtered competitive NMR displacement assay. Chem Sci 2024; 15:10612-10624. [PMID: 38994400 PMCID: PMC11234860 DOI: 10.1039/d4sc01723d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/08/2024] [Indexed: 07/13/2024] Open
Abstract
Sialic-acid-binding immunoglobulin-like lectins (Siglecs) are integral cell surface proteins crucial for the regulation of immune responses and the maintenance of immune tolerance through interactions with sialic acids. Siglecs recognize sialic acid moieties, usually found at the end of N-glycan and O-glycan chains. However, the different Siglecs prefer diverse presentations of the recognized sialic acid, depending on the type of glycosidic linkage used to link to the contiguous Gal/GalNAc or sialic acid moieties. This fact, together with possible O- or N-substitutions at the recognized glycan epitope significantly influences their roles in various immune-related processes. Understanding the molecular details of Siglec-sialoglycan interactions is essential for unraveling their specificities and for the development of new molecules targeting these receptors. While traditional biophysical methods like isothermal titration calorimetry (ITC) have been utilized to measure binding between lectins and glycans, contemporary techniques such as surface plasmon resonance (SPR), microscale thermophoresis (MST), and biolayer interferometry (BLI) offer improved throughput. However, these methodologies require chemical modification and immobilization of at least one binding partner, which can interfere the recognition between the lectin and the ligand. Since Siglecs display a large range of dissociation constants, depending on the (bio)chemical nature of the interacting partner, a general and robust method that could monitor and quantify binding would be highly welcomed. Herein, we propose the application of an NMR-based a competitive displacement assay, grounded on 19F T2-relaxation NMR and on the design, synthesis, and use of a strategic spy molecule, to assess and quantify sialoside ligand binding to Siglecs. We show that the use of this specific approach allows the quantification of Siglec binding for natural and modified sialosides, multivalent sialosides, and sialylated glycoproteins in solution, which differ in binding affinities in more than two orders of magnitude, thus providing invaluable insights into sialoglycan-mediated interactions.
Collapse
Affiliation(s)
- Unai Atxabal
- Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) 48160 Derio Bizkaia Spain
| | - Andrea Fernández
- Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) 48160 Derio Bizkaia Spain
- Glycotechnology Laboratory, CIC biomaGUNE Paseo Miramon 194 San Sebastian 20014 Spain
| | - Maria Jesús Moure
- Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) 48160 Derio Bizkaia Spain
| | - Klaudia Sobczak
- Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) 48160 Derio Bizkaia Spain
| | - Corwin Nycholat
- Departments of Molecular Medicine and Immunology & Microbiology, The Scripps Research Institute 10550 North Torrey Pines Road La Jolla California 92037 USA
| | - Verónica Almeida-Marrero
- Department of Organic Chemistry, Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 28049 Madrid Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 28049 Madrid Spain
| | - Iker Oyenarte
- Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) 48160 Derio Bizkaia Spain
| | - James C Paulson
- Departments of Molecular Medicine and Immunology & Microbiology, The Scripps Research Institute 10550 North Torrey Pines Road La Jolla California 92037 USA
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 28049 Madrid Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 28049 Madrid Spain
| | - Tomás Torres
- Department of Organic Chemistry, Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 28049 Madrid Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 28049 Madrid Spain
- Instituto Madrileño de Estudios Avanzados (IMDEA)-Nanociencia C/Faraday 9 28049 Madrid Spain
| | - Niels C Reichardt
- Glycotechnology Laboratory, CIC biomaGUNE Paseo Miramon 194 San Sebastian 20014 Spain
- CIBER-BBN Paseo Miramon 194 San Sebastian 20014 Spain
| | - Jesús Jiménez-Barbero
- Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) 48160 Derio Bizkaia Spain
- Ikerbasque, Basque Foundation for Science Bilbao Spain
- Department of Organic & Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV 48940 Leioa Bizkaia Spain
- Centro de Investigacion Biomedica en Red de Enfermedades Respiratorias 28029 Madrid Spain
| | - June Ereño-Orbea
- Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) 48160 Derio Bizkaia Spain
- Ikerbasque, Basque Foundation for Science Bilbao Spain
| |
Collapse
|
4
|
Quintana JI, Delgado S, Rábano M, Azkargorta M, Florencio-Zabaleta M, Unione L, Vivanco MDM, Elortza F, Jiménez-Barbero J, Ardá A. The impact of glycosylation on the structure, function, and interactions of CD14. Glycobiology 2024; 34:cwae002. [PMID: 38227775 PMCID: PMC10987292 DOI: 10.1093/glycob/cwae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/21/2023] [Accepted: 12/30/2023] [Indexed: 01/18/2024] Open
Abstract
CD14 is an innate immune receptor that senses pathogen-associated molecular patterns, such as lipopolysaccharide, to activate the innate immune response. Although CD14 is known to be glycosylated, detailed understanding about the structural and functional significance of this modification is still missing. Herein, an NMR and MS-based study, assisted by MD simulations, has provided a 3D-structural model of glycosylated CD14. Our results reveal the existence of a key N-glycosylation site at Asn282 that exclusively contains unprocessed oligomannnose N-glycans that perfectly fit the concave cavity of the bent-solenoid shaped protein. This site is not accessible to glycosidases and is fundamental for protein folding and secretion. A second N-site at Asn151 displays mostly complex N-glycans, with the typical terminal epitopes of the host cell-line expression system (i.e. βGal, α2,3 and α2,6 sialylated βGal, here), but also particularities, such as the lack of core fucosylation. The glycan at this site points outside the protein surface, resulting in N-glycoforms fully exposed and available for interactions with lectins. In fact, NMR experiments show that galectin-4, proposed as a binder of CD14 on monocytes to induce their differentiation into macrophages-like cells, interacts in vitro with CD14 through the recognition of the terminal glycoepitopes on Asn151. This work provides key information about CD14 glycosylation, which helps to better understand its functional roles and significance. Although protein glycosylation is known to be dynamic and influenced by many factors, some of the features found herein (presence of unprocessed N-glycans and lack of core Fuc) are likely to be protein specific.
Collapse
Affiliation(s)
- Jon Imanol Quintana
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Sandra Delgado
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Miriam Rábano
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Mirane Florencio-Zabaleta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Luca Unione
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009, Bilbao, Spain
| | - Maria dM Vivanco
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Félix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Jesús Jiménez-Barbero
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009, Bilbao, Spain
- Department of Organic & Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, Leioa, Bizkaia 48940, Spain
- Centro de Investigacion Biomedica En Red de Enfermedades Respiratorias, Carlos III Health Institute, C. de Melchor Fernández Almagro, 3, Fuencarral-El Pardo, Madrid 28029, Spain
| | - Ana Ardá
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009, Bilbao, Spain
| |
Collapse
|
5
|
Hőgye F, Farkas LB, Balogh ÁK, Szilágyi L, Alnukari S, Bajza I, Borbás A, Fehér K, Illyés TZ, Timári I. Saturation Transfer Difference NMR and Molecular Docking Interaction Study of Aralkyl-Thiodigalactosides as Potential Inhibitors of the Human-Galectin-3 Protein. Int J Mol Sci 2024; 25:1742. [PMID: 38339036 PMCID: PMC10855533 DOI: 10.3390/ijms25031742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Human Galectin-3 (hGal-3) is a protein that selectively binds to β-galactosides and holds diverse roles in both normal and pathological circumstances. Therefore, targeting hGal-3 has become a vibrant area of research in the pharmaceutical chemistry. As a step towards the development of novel hGal-3 inhibitors, we synthesized and investigated derivatives of thiodigalactoside (TDG) modified with different aromatic substituents. Specifically, we describe a high-yielding synthetic route of thiodigalactoside (TDG); an optimized procedure for the synthesis of the novel 3,3'-di-O-(quinoline-2-yl)methyl)-TDG and three other known, symmetric 3,3'-di-O-TDG derivatives ((naphthalene-2yl)methyl, benzyl, (7-methoxy-2H-1-benzopyran-2-on-4-yl)methyl). In the present study, using competition Saturation Transfer Difference (STD) NMR spectroscopy, we determined the dissociation constant (Kd) of the former three TDG derivatives produced to characterize the strength of the interaction with the target protein (hGal-3). Based on the Kd values determined, the (naphthalen-2-yl)methyl, the (quinolin-2-yl)methyl and the benzyl derivatives bind to hGal-3 94, 30 and 24 times more strongly than TDG. Then, we studied the binding modes of the derivatives in silico by molecular docking calculations. Docking poses similar to the canonical binding modes of well-known hGal-3 inhibitors have been found. However, additional binding forces, cation-π interactions between the arginine residues in the binding pocket of the protein and the aromatic groups of the ligands, have been established as significant features. Our results offer a molecular-level understanding of the varying affinities observed among the synthesized thiodigalactoside derivatives, which can be a key aspect in the future development of more effective ligands of hGal-3.
Collapse
Affiliation(s)
- Fanni Hőgye
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
| | - László Bence Farkas
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
| | - Álex Kálmán Balogh
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
| | - László Szilágyi
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
| | - Samar Alnukari
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
| | - István Bajza
- GlycOptim Kft., Egyetem tér 1, H-4032 Debrecen, Hungary;
| | - Anikó Borbás
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Krisztina Fehér
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
| | - Tünde Zita Illyés
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
| | - István Timári
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
| |
Collapse
|
6
|
Kokubu R, Ohno S, Manabe N, Yamaguchi Y. Molecular Dynamics Simulation and Docking of MUC1 O-Glycopeptide. Methods Mol Biol 2024; 2763:373-379. [PMID: 38347427 DOI: 10.1007/978-1-0716-3670-1_32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Advances in computer performance and computational simulations allow increasing sophistication in applications in biological systems. Molecular dynamics (MD) simulations are especially suitable for studying conformation, dynamics, and interaction of flexible biomolecules such as free glycans and glycopeptides. Computer simulations are best performed when the scope and limitations in performance have been thoroughly assessed. Proper outputs are obtained only under suitable parameter settings, and results need to be properly validated. In this chapter, we will introduce an example of molecular dynamics simulations of MUC1 O-glycopeptide and its docking to anti-MUC1 antibody Fv fragment.
Collapse
Affiliation(s)
- Ryoka Kokubu
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Shiho Ohno
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Noriyoshi Manabe
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Yoshiki Yamaguchi
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan.
| |
Collapse
|
7
|
Chen C, Ma B, Wang Y, Cui Q, Yao L, Li Y, Chen B, Feng Y, Tan Z. Structural insight into why S-linked glycosylation cannot adequately mimic the role of natural O-glycosylation. Int J Biol Macromol 2023; 253:126649. [PMID: 37666405 DOI: 10.1016/j.ijbiomac.2023.126649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/21/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
There is an increasing interest in using S-glycosylation as a replacement for the more commonly occurring O-glycosylation, aiming to enhance the resistance of glycans against chemical hydrolysis and enzymatic degradation. However, previous studies have demonstrated that these two types of glycosylation exert distinct effects on protein properties and functions. In order to elucidate the structural basis behind the observed differences, we conducted a systematic and comparative analysis of 6 differently glycosylated forms of a model glycoprotein, CBM, using NMR spectroscopy and molecular dynamic simulations. Our findings revealed that the different stabilizing effects of S- and O-glycosylation could be attributed to altered hydrogen-bonding capability between the glycan and the polypeptide chain, and their diverse impacts on binding affinity could be elucidated by examining the interactions and motion dynamics of glycans in substrate-bound states. Overall, this study underscores the pivotal role of the glycosidic linkage in shaping the function of glycosylation and advises caution when switching glycosylation types in protein glycoengineering.
Collapse
Affiliation(s)
- Chao Chen
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao, Shandong 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yefei Wang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao, Shandong 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao, Shandong 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lishan Yao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao, Shandong 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaohao Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Baoquan Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao, Shandong 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhongping Tan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| |
Collapse
|
8
|
Krylov VB, Gómez-Redondo M, Solovev AS, Yashunsky DV, Brown AJ, Stappers MH, Gow NA, Ardá A, Jiménez-Barbero J, Nifantiev NE. Identification of a new DC-SIGN binding pentamannoside epitope within the complex structure of Candida albicans mannan. Cell Surf 2023; 10:100109. [PMID: 37520856 PMCID: PMC10382935 DOI: 10.1016/j.tcsw.2023.100109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023] Open
Abstract
The dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN) is an innate immune C-type lectin receptor that recognizes carbohydrate-based pathogen associated with molecular patterns of various bacteria, fungi, viruses and protozoa. Although a range of highly mannosylated glycoproteins have been shown to induce signaling via DC-SIGN, precise structure of the recognized oligosaccharide epitope is still unclear. Using the array of oligosaccharides related to selected fragments of main fungal antigenic polysaccharides we revealed a highly specific pentamannoside ligand of DC-SIGN, consisting of α-(1 → 2)-linked mannose chains with one inner α-(1 → 3)-linked unit. This structural motif is present in Candida albicans cell wall mannan and corresponds to its antigenic factors 4 and 13b. This epitope is not ubiquitous in other yeast species and may account for the species-specific nature of fungal recognition via DC-SIGN. The discovered highly specific oligosaccharide ligands of DC-SIGN are tractable tools for interdisciplinary investigations of mechanisms of fungal innate immunity and anti-Candida defense. Ligand- and receptor-based NMR data demonstrated the pentasaccharide-to-DC-SIGN interaction in solution and enabled the deciphering of the interaction topology.
Collapse
Affiliation(s)
- Vadim B. Krylov
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Arsenii S. Solovev
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry V. Yashunsky
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alistair J.P. Brown
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Mark H.T. Stappers
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Neil A.R. Gow
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Ana Ardá
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, 48160 Derio, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science and Technology, Euskadi Plaza 5, 48009 Bilbao, Spain
- Department of Organic & Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, 48940 Leioa, Spain
- Centro de Investigacion Biomedica En Red de Enfermedades Respiratorias, Madrid, Spain
| | - Nikolay E. Nifantiev
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
9
|
Poškaitė G, Wheatley DE, Wells N, Linclau B, Sinnaeve D. Obtaining Pure 1H NMR Spectra of Individual Pyranose and Furanose Anomers of Reducing Deoxyfluorinated Sugars. J Org Chem 2023; 88:13908-13925. [PMID: 37754916 PMCID: PMC10563139 DOI: 10.1021/acs.joc.3c01503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Indexed: 09/28/2023]
Abstract
Due to tautomeric equilibria, NMR spectra of reducing sugars can be complex with many overlapping resonances. This hampers coupling constant determination, which is required for conformational analysis and configurational assignment of substituents. Given that mixtures of interconverting species are physically inseparable, easy-to-use techniques that enable facile full 1H NMR characterization of sugars are of interest. Here, we show that individual spectra of both pyranoside and furanoside forms of reducing fluorosugars can be obtained using 1D FESTA. We discuss the unique opportunities offered by FESTA over standard sel-TOCSY and show how it allows a more complete characterization. We illustrate the power of FESTA by presenting the first full NMR characterization of many fluorosugars, including of the important fluorosugar 2-deoxy-2-fluoroglucose. We discuss in detail all practical considerations for setting up FESTA experiments for fluorosugars, which can be extended to any mixture of fluorine-containing species interconverting slowly on the NMR frequency-time scale.
Collapse
Affiliation(s)
- Gabija Poškaitė
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - David E. Wheatley
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Neil Wells
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Bruno Linclau
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Department
of Organic and Macromolecular Chemistry, Ghent University, Campus
Sterre, Krijgslaan 281-S4, Ghent 9000, Belgium
| | - Davy Sinnaeve
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
- CNRS, EMR9002 Integrative Structural Biology, F-59000 Lille, France
| |
Collapse
|
10
|
Vrablova V, Kosutova N, Blsakova A, Bertokova A, Kasak P, Bertok T, Tkac J. Glycosylation in extracellular vesicles: Isolation, characterization, composition, analysis and clinical applications. Biotechnol Adv 2023; 67:108196. [PMID: 37307942 DOI: 10.1016/j.biotechadv.2023.108196] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/14/2023]
Abstract
This review provides a comprehensive overview of our understanding of the role that glycans play in the formation, loading and release of extracellular vesicles (EVs). The capture of EVs (typically with a size of 100-200 nm) is described, including approaches based on glycan recognition with glycan-based analysis offering highly sensitive detection of EVs. Furthermore, detailed information is provided about the use of EV glycans and glycan processing enzymes as potential biomarkers, therapeutic targets or tools applied for regenerative medicine. The review also provides a short introduction into advanced methods for the characterization of EVs, new insights into the biomolecular corona covering EVs and bioanalytical tools available for glycan analysis.
Collapse
Affiliation(s)
- Veronika Vrablova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovak Republic
| | - Natalia Kosutova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovak Republic
| | - Anna Blsakova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovak Republic
| | - Aniko Bertokova
- Glycanostics sro., Kudlakova 7, Bratislava 841 01, Slovak Republic
| | - Peter Kasak
- Centre for Advanced Materials, Qatar University, P.O. Box 2713, Doha, Qatar.
| | - Tomas Bertok
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovak Republic; Glycanostics sro., Kudlakova 7, Bratislava 841 01, Slovak Republic
| | - Jan Tkac
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 38, Slovak Republic; Glycanostics sro., Kudlakova 7, Bratislava 841 01, Slovak Republic.
| |
Collapse
|
11
|
Wei X, Wang P, Liu F, Ye X, Xiong D. Drug Discovery Based on Fluorine-Containing Glycomimetics. Molecules 2023; 28:6641. [PMID: 37764416 PMCID: PMC10536126 DOI: 10.3390/molecules28186641] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Glycomimetics, which are synthetic molecules designed to mimic the structures and functions of natural carbohydrates, have been developed to overcome the limitations associated with natural carbohydrates. The fluorination of carbohydrates has emerged as a promising solution to dramatically enhance the metabolic stability, bioavailability, and protein-binding affinity of natural carbohydrates. In this review, the fluorination methods used to prepare the fluorinated carbohydrates, the effects of fluorination on the physical, chemical, and biological characteristics of natural sugars, and the biological activities of fluorinated sugars are presented.
Collapse
Affiliation(s)
- Xingxing Wei
- Department of Pharmacy, Changzhi Medical College, No. 161, Jiefang East Street, Changzhi 046012, China
| | - Pengyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Rd. No. 38, Beijing 100191, China (F.L.); (X.Y.)
| | - Fen Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Rd. No. 38, Beijing 100191, China (F.L.); (X.Y.)
| | - Xinshan Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Rd. No. 38, Beijing 100191, China (F.L.); (X.Y.)
| | - Decai Xiong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Rd. No. 38, Beijing 100191, China (F.L.); (X.Y.)
| |
Collapse
|
12
|
Hassan AA, Huang ML. Stereoselective synthesis of photoactivatable Man(β1,4)GlcNAc-based bioorthogonal probes. Tetrahedron Lett 2023; 122:154521. [PMID: 37274137 PMCID: PMC10237449 DOI: 10.1016/j.tetlet.2023.154521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report an operationally facile protocol to prepare photoactivatable probes of the bioactive mammalian disaccharide, Man(β1,4)GlcNAc. Using conformationally restricted mannosyl hemi-acetal donors in a one-pot chlorination, iodination and glycosylation sequence, β-mannosides were generated in excellent diastereoselectivities and yields. Upon accessing the disaccharide, we generated the corresponding photoactivatable probes by appending a diazirine-alkyne equipped linker via a condensation reaction between a diazirine-containing linker and C-1 and C-2 derivatized mannosylamines to furnish the desired C-1 and C-2 modified Man(β1,4)GlcNAc-based probes. This new synthetic protocol greatly simplifies the preparation of this important bioactive disaccharide to enable future work to identify its protein binding partners in cells.
Collapse
Affiliation(s)
- Abdullah A. Hassan
- Department of Molecular Medicine and Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Mia L. Huang
- Department of Molecular Medicine and Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| |
Collapse
|
13
|
Hatvany JB, Gallagher ES. Hydrogen/deuterium exchange for the analysis of carbohydrates. Carbohydr Res 2023; 530:108859. [PMID: 37290371 DOI: 10.1016/j.carres.2023.108859] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/10/2023]
Abstract
Carbohydrates and glycans are integral to many biological processes, including cell-cell recognition and energy storage. However, carbohydrates are often difficult to analyze due to the high degree of isomerism present. One method being developed to distinguish these isomeric species is hydrogen/deuterium exchange-mass spectrometry (HDX-MS). In HDX-MS, carbohydrates are exposed to a deuterated reagent and the functional groups with labile hydrogen atoms, including hydroxyls and amides, exchange with the 1 amu heavier isotope, deuterium. These labels can then be detected by MS, which monitors the mass increase with the addition of D-labels. The observed rate of exchange is dependent on the exchanging functional group, the accessibility of the exchanging functional group, and the presence of hydrogen bonds. Herein, we discuss how HDX has been applied in the solution-phase, gas-phase, and during MS ionization to label carbohydrates and glycans. Additionally, we compare differences in the conformations that are labeled, the labeling timeframes, and applications of each of these methods. Finally, we comment on future opportunities for development and use of HDX-MS to analyze glycans and glycoconjugates.
Collapse
Affiliation(s)
- Jacob B Hatvany
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798, USA
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798, USA.
| |
Collapse
|
14
|
Quintana JI, Atxabal U, Unione L, Ardá A, Jiménez-Barbero J. Exploring multivalent carbohydrate-protein interactions by NMR. Chem Soc Rev 2023; 52:1591-1613. [PMID: 36753338 PMCID: PMC9987413 DOI: 10.1039/d2cs00983h] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Indexed: 02/09/2023]
Abstract
Nuclear Magnetic Resonance (NMR) has been widely employed to assess diverse features of glycan-protein molecular recognition events. Different types of qualitative and quantitative information at different degrees of resolution and complexity can be extracted from the proper application of the available NMR-techniques. In fact, affinity, structural, kinetic, conformational, and dynamic characteristics of the binding process are available. Nevertheless, except in particular cases, the affinity of lectin-sugar interactions is weak, mostly at the low mM range. This feature is overcome in biological processes by using multivalency, thus augmenting the strength of the binding. However, the application of NMR methods to monitor multivalent lectin-glycan interactions is intrinsically challenging. It is well known that when large macromolecular complexes are formed, the NMR signals disappear from the NMR spectrum, due to the existence of fast transverse relaxation, related to the large size and exchange features. Indeed, at the heart of the molecular recognition event, the associated free-bound chemical exchange process for both partners takes place in a particular timescale. Thus, these factors have to be considered and overcome. In this review article, we have distinguished, in a subjective manner, the existence of multivalent presentations in the glycan or in the lectin. From the glycan perspective, we have also considered whether multiple epitopes of a given ligand are presented in the same linear chain of a saccharide (i.e., poly-LacNAc oligosaccharides) or decorating different arms of a multiantennae scaffold, either natural (as in multiantennae N-glycans) or synthetic (of dendrimer or polymer nature). From the lectin perspective, the presence of an individual binding site at every monomer of a multimeric lectin may also have key consequences for the binding event at different levels of complexity.
Collapse
Affiliation(s)
- Jon I Quintana
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
| | - Unai Atxabal
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
| | - Luca Unione
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
| | - Ana Ardá
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
- Department of Organic Chemistry, II Faculty of Science and Technology, EHU-UPV, 48940 Leioa, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Respiratorias, Madrid, Spain
| |
Collapse
|
15
|
Li Y, Wang H, Xu F, Ling L, Ding CF. Linkage-specific identification and quantification of sialylated glycans by TIMS-TOF MS through conjugation with metal complexes. Talanta 2023; 253:123995. [PMID: 36228553 DOI: 10.1016/j.talanta.2022.123995] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
Mass spectrometry is an indispensable technology for the characterization of glycans. However, specific identification of isomeric glycans especially sialylated glycan isomers using mass spectrometry alone is challenging, which is why orthogonal techniques are needed. Aiming to achieve simple, rapid, and specific identification of sialyl-linkage isomers, we reported herein a trapped ion mobility spectrometry time of flight mass spectrometry (TIMS-TOF MS) method for linkage-specific identification of sialylated glycans through conjugation with metal complexes. Two pairs of sialyl-linkage isomers including 3'/6'-sialyllactose (3'/6'-SL) and 3'/6'-sialyl-N-acetyllactosamine (3'/6'-SLN) conjugated with the diethylenetriamine (DETA) or 2,2'; 6',2″-terpyridine (Terpy) ligand and transition metal ion (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, or Zn2+) were studied by TIMS-TOF MS. The two pairs of sialylated isomers were successfully separated with a metal-ligand system, and relative quantification of sialyl-linkage isomers was demonstrated. In addition, the linkage of the sialic acid moiety can also be distinguished with MS/MS in combination with the metal-ligand system.
Collapse
Affiliation(s)
- Yang Li
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Huanhuan Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Fuxing Xu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Ling Ling
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| |
Collapse
|
16
|
Lete MG, Franconetti A, Bertuzzi S, Delgado S, Azkargorta M, Elortza F, Millet O, Jiménez-Osés G, Arda A, Jiménez-Barbero J. NMR Investigation of Protein-Carbohydrate Interactions: The Recognition of Glycans by Galectins Engineered with Fluorotryptophan Residues. Chemistry 2023; 29:e202202208. [PMID: 36343278 PMCID: PMC10107428 DOI: 10.1002/chem.202202208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022]
Abstract
Fluorine (19 F) incorporation into glycan-binding proteins (lectins) has been achieved and exploited to monitor the binding to carbohydrate ligands by nuclear magnetic resonance (NMR) spectroscopy. Galectins are a family of lectins that bind carbohydrates, generally with weak affinities, through a combination of intermolecular interactions including a key CH-π stacking involving a conserved tryptophan residue. Herein, Galectin-3 (Gal3) and Galectin-8 (Gal8) with one and two carbohydrate recognition domains (CRDs), respectively, were selected. Gal3 contains one Trp, whereas Gal8 contains three, one at each binding site and a third one not involved in sugar binding; these were substituted by the corresponding F-Trp analogues. The presence of fluorine did not significantly modify the affinity for glycan binding, which was in slow exchange on the 19 F NMR chemical-shift timescale, even for weak ligands, and allowed binding events taking place at two different binding sites within the same lectin to be individualized.
Collapse
Affiliation(s)
- Marta G Lete
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Antonio Franconetti
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Sara Bertuzzi
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Sandra Delgado
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Félix Elortza
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Oscar Millet
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Gonzalo Jiménez-Osés
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science Plaza Euskadi 5, 48009, Bilbao, Bizkaia, Spain
| | - Ana Arda
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science Plaza Euskadi 5, 48009, Bilbao, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science Plaza Euskadi 5, 48009, Bilbao, Bizkaia, Spain.,Department of Organic Chemistry II Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940, Leioa, Spain.,Centro de Investigación Biomédica En Red de Enfermedades Respiratorias, Madrid, Spain
| |
Collapse
|
17
|
Dal Colle MCS, Fittolani G, Delbianco M. Synthetic Approaches to Break the Chemical Shift Degeneracy of Glycans. Chembiochem 2022; 23:e202200416. [PMID: 36005282 PMCID: PMC10087674 DOI: 10.1002/cbic.202200416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/24/2022] [Indexed: 01/25/2023]
Abstract
NMR spectroscopy is the leading technique for determining glycans' three-dimensional structure and dynamic in solution as well as a fundamental tool to study protein-glycan interactions. To overcome the severe chemical shift degeneracy of these compounds, synthetic probes carrying NMR-active nuclei (e. g., 13 C or 19 F) or lanthanide tags have been proposed. These elegant strategies permitted to simplify the complex NMR analysis of unlabeled analogues, shining light on glycans' conformational aspects and interaction with proteins. Here, we highlight some key achievements in the synthesis of specifically labeled glycan probes and their contribution towards the fundamental understanding of glycans.
Collapse
Affiliation(s)
- Marlene C. S. Dal Colle
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Giulio Fittolani
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Martina Delbianco
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| |
Collapse
|
18
|
Abstract
Fluorinated carbohydrates have found many applications in the glycosciences. Typically, these contain fluorination at a single position. There are not many applications involving polyfluorinated carbohydrates, here defined as monosaccharides in which more than one carbon has at least one fluorine substituent directly attached to it, with the notable exception of their use as mechanism-based inhibitors. The increasing attention to carbohydrate physical properties, especially around lipophilicity, has resulted in a surge of interest for this class of compounds. This review covers the considerable body of work toward the synthesis of polyfluorinated hexoses, pentoses, ketosugars, and aminosugars including sialic acids and nucleosides. An overview of the current state of the art of their glycosidation is also provided.
Collapse
Affiliation(s)
- Kler Huonnic
- School
of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Bruno Linclau
- School
of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
- Department
of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre, Krijgslaan 281-S4, Ghent, 9000, Belgium
| |
Collapse
|
19
|
Effect of ultrasonication on the protein–polysaccharide complexes: a review. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2022. [DOI: 10.1007/s11694-022-01567-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
|
20
|
Mukherjee S, Jana S, Khawas S, Kicuntod J, Marschall M, Ray B, Ray S. Synthesis, molecular features and biological activities of modified plant polysaccharides. Carbohydr Polym 2022; 289:119299. [DOI: 10.1016/j.carbpol.2022.119299] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022]
|
21
|
Coutinho JVP, Macedo-da-Silva J, Mule SN, Kronenberger T, Rosa-Fernandes L, Wrenger C, Palmisano G. Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 131:277-309. [PMID: 35871894 PMCID: PMC9181370 DOI: 10.1016/bs.apcsb.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Molecular Dynamics (MD) is a method used to calculate the movement of atoms and molecules broadly applied to several aspects of science. It involves computational simulation, which makes it, at first glance, not easily accessible. The rise of several automated tools to perform molecular simulations has allowed researchers to navigate through the various steps of MD. This enables to elucidate structural properties of proteins that could not be analyzed otherwise, such as the impact of glycosylation. Glycosylation dictates the physicochemical and biological properties of a protein modulating its solubility, stability, resistance to proteolysis, interaction partners, enzymatic activity, binding and recognition. Given the high conformational and compositional diversity of the glycan chains, assessing their influence on the protein structure is challenging using conventional analytical techniques. In this manuscript, we present a step-by-step workflow to build and perform MD analysis of glycoproteins focusing on the SPIKE glycoprotein of SARS-CoV-2 to appraise the impact of glycans in structure stabilization and antibody occlusion.
Collapse
Affiliation(s)
| | - Janaina Macedo-da-Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Simon Ngao Mule
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Thales Kronenberger
- Department of Internal Medicine VIII, University Hospital Tuebingen, Tuebingen, Germany; Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany; Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), Tuebingen, Germany
| | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Faculty of Science and engineering, Macquarie University, Sydney, NSW, Australia.
| |
Collapse
|
22
|
Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
Collapse
Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| |
Collapse
|
23
|
Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations. J Biomol Struct Dyn 2022; 41:3305-3320. [PMID: 35262462 DOI: 10.1080/07391102.2022.2047109] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In the current study, we have investigated the conformational dynamics of a triantennary (N-glycan1) and tetraantennary (N-glycan2) hybrid N-glycans found on the surface of the HIV glycoprotein using 20 μs long all-atom molecular dynamics (MD) simulations. The main objective of the present study is to elucidate the influence of adding a complex branch on the overall glycan structural dynamics. Our investigation suggests that the average RMSD value increases when a complex branch is added to N-glycan1. However, the RMSD distribution is relatively wider in the case of N-glycan1 compared to N-glycan2, which indicates that multiple complex branches restrict the conformational variability of glycans. A similar observation is obtained from the principal component analysis of both glycans. All the puckering states (4C1 to 1C4) of each monosaccharide except mannose are sampled in our simulations, although the 4C1 chair form is energetically more favorable than 1C4. In N-glycan1, the 1-6 linkage in the mannose branch [Man(9)-α(1-6)-Man(5)] stays in the gauche-gauche cluster, whereas it moves towards trans-gauche in N-glycan2. For both glycans, mannose branches are more flexible than the complex branches, and adding a complex branch does not influence the dynamics of the mannose branches. We have noticed that the end-to-end distance of the complex branch shortens by ∼ 10 Å in the presence of another complex branch. This suggests that in the presence of an additional complex branch, the other complex branch adopts a close folded structure. All these conformational changes involve the selective formation of inter-residue and water-mediated hydrogen-bond networks.
Collapse
|
24
|
Peters T, Creutznacher R, Maass T, Mallagaray A, Ogrissek P, Taube S, Thiede L, Uetrecht C. Norovirus-glycan interactions - how strong are they really? Biochem Soc Trans 2022; 50:347-359. [PMID: 34940787 PMCID: PMC9022987 DOI: 10.1042/bst20210526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 12/25/2022]
Abstract
Infection with human noroviruses requires attachment to histo blood group antigens (HBGAs) via the major capsid protein VP1 as a primary step. Several crystal structures of VP1 protruding domain dimers, so called P-dimers, complexed with different HBGAs have been solved to atomic resolution. Corresponding binding affinities have been determined for HBGAs and other glycans exploiting different biophysical techniques, with mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy being most widely used. However, reported binding affinities are inconsistent. At the extreme, for the same system MS detects binding whereas NMR spectroscopy does not, suggesting a fundamental source of error. In this short essay, we will explain the reason for the observed differences and compile reliable and reproducible binding affinities. We will then highlight how a combination of MS techniques and NMR experiments affords unique insights into the process of HBGA binding by norovirus capsid proteins.
Collapse
Affiliation(s)
- Thomas Peters
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Robert Creutznacher
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Thorben Maass
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Alvaro Mallagaray
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Patrick Ogrissek
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Stefan Taube
- Institute of Virology and Cell Biology, University of Lübeck, 23562 Lübeck, Germany
| | - Lars Thiede
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg & Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany
| | - Charlotte Uetrecht
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg & Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany
- School of Life Sciences, University of Siegen, 57076 Siegen & Deutsches Elektronensynchrotron (DESY), 22607 Hamburg & European XFEL GmbH, 22869 Schenefeld, Germany
| |
Collapse
|
25
|
Timári I, Balla S, Fehér K, Kövér KE, Szilágyi L. 77Se-Enriched Selenoglycoside Enables Significant Enhancement in NMR Spectroscopic Monitoring of Glycan-Protein Interactions. Pharmaceutics 2022; 14:201. [PMID: 35057096 PMCID: PMC8779653 DOI: 10.3390/pharmaceutics14010201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 12/17/2022] Open
Abstract
Detailed investigation of ligand-protein interactions is essential for better understanding of biological processes at the molecular level. Among these binding interactions, the recognition of glycans by lectins is of particular importance in several diseases, such as cancer; therefore, inhibition of glycan-lectin/galectin interactions represents a promising perspective towards developing therapeutics controlling cancer development. The recent introduction of 77Se NMR spectroscopy for monitoring the binding of a selenoglycoside to galectins prompted interest to optimize the sensitivity by increasing the 77Se content from the natural 7.63% abundance to 99%. Here, we report a convenient synthesis of 77Se-enriched selenodigalactoside (SeDG), which is a potent ligand of the medically relevant human galectin-3 protein, and proof of the expected sensitivity gain in 2D 1H, 77Se correlation NMR experiments. Our work opens perspectives for adding isotopically enriched selenoglycans for rapid monitoring of lectin-binding of selenated as well as non-selenated ligands and for ligand screening in competition experiments.
Collapse
Affiliation(s)
- István Timári
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (I.T.); (S.B.)
| | - Sára Balla
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (I.T.); (S.B.)
| | - Krisztina Fehér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary;
- Molecular Recognition and Interaction Research Group, Hungarian Academy of Sciences, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Katalin E. Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary;
- Molecular Recognition and Interaction Research Group, Hungarian Academy of Sciences, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - László Szilágyi
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (I.T.); (S.B.)
| |
Collapse
|
26
|
Fittolani G, Djalali S, Chaube MA, Tyrikos-Ergas T, Dal Colle MCS, Grafmüller A, Seeberger PH, Delbianco M. Deoxyfluorination tunes the aggregation of cellulose and chitin oligosaccharides and highlights the role of specific hydroxyl groups in the crystallization process. Org Biomol Chem 2022; 20:8228-8235. [DOI: 10.1039/d2ob01601j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Using synthetic oligosaccharides, we examined how deoxyfluorination (site and pattern) impact the solubility and aggregation of cellulose and chitin oligomers.
Collapse
Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Surusch Djalali
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Manishkumar A. Chaube
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Marlene C. S. Dal Colle
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Andrea Grafmüller
- Department of Theory and Biosystems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Peter H. Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| |
Collapse
|
27
|
Poveda A, Fittolani G, Seeberger PH, Delbianco M, Jiménez-Barbero J. The Flexibility of Oligosaccharides Unveiled Through Residual Dipolar Coupling Analysis. Front Mol Biosci 2021; 8:784318. [PMID: 34859057 PMCID: PMC8631391 DOI: 10.3389/fmolb.2021.784318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/14/2021] [Indexed: 11/13/2022] Open
Abstract
The intrinsic flexibility of glycans complicates the study of their structures and dynamics, which are often important for their biological function. NMR has provided insights into the conformational, dynamic and recognition features of glycans, but suffers from severe chemical shift degeneracy. We employed labelled glycans to explore the conformational behaviour of a β(1-6)-Glc hexasaccharide model through residual dipolar couplings (RDCs). RDC delivered information on the relative orientation of specific residues along the glycan chain and provided experimental clues for the existence of certain geometries. The use of two different aligning media demonstrated the adaptability of flexible oligosaccharide structures to different environments.
Collapse
Affiliation(s)
- Ana Poveda
- CICbioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Giulio Fittolani
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.,Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, Leioa, Spain.,Centro de Investigacion Biomedica En Red de Enfermedades Respiratorias, Madrid, Spain
| |
Collapse
|
28
|
Černocká H, Římánková L, Ostatná V. Fetuin and asialofetuin at charged surfaces: Influence of sialic acid presence. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
29
|
Berrino E, Michelet B, Martin‐Mingot A, Carta F, Supuran CT, Thibaudeau S. Modulating the Efficacy of Carbonic Anhydrase Inhibitors through Fluorine Substitution. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Emanuela Berrino
- University of Florence NEUROFARBA Dept. Sezione di Scienze Farmaceutiche e Nutraceutiche Via Ugo Schiff 6 50019 Sesto Fiorentino Florence Italy
| | - Bastien Michelet
- Superacid Group in “Organic Synthesis” Team Université de Poitiers CNRS UMR 7285 IC2MP Bât. B28, 4 rue Michel Brunet, TSA 51106 86073 Poitiers Cedex 09 France
| | - Agnès Martin‐Mingot
- Superacid Group in “Organic Synthesis” Team Université de Poitiers CNRS UMR 7285 IC2MP Bât. B28, 4 rue Michel Brunet, TSA 51106 86073 Poitiers Cedex 09 France
| | - Fabrizio Carta
- University of Florence NEUROFARBA Dept. Sezione di Scienze Farmaceutiche e Nutraceutiche Via Ugo Schiff 6 50019 Sesto Fiorentino Florence Italy
| | - Claudiu T. Supuran
- University of Florence NEUROFARBA Dept. Sezione di Scienze Farmaceutiche e Nutraceutiche Via Ugo Schiff 6 50019 Sesto Fiorentino Florence Italy
| | - Sébastien Thibaudeau
- Superacid Group in “Organic Synthesis” Team Université de Poitiers CNRS UMR 7285 IC2MP Bât. B28, 4 rue Michel Brunet, TSA 51106 86073 Poitiers Cedex 09 France
| |
Collapse
|
30
|
Cañada FJ, Canales Á, Valverde P, de Toro BF, Martínez-Orts M, Phillips PO, Pereda A. Conformational and Structural characterization of carbohydrates and their interactions studied by NMR. Curr Med Chem 2021; 29:1147-1172. [PMID: 34225601 DOI: 10.2174/0929867328666210705154046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/30/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022]
Abstract
Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. The versatility of Nuclear Magnetic Resonance spectroscopy (NMR) often makes it the preferred choice to study glycans and carbohydrates in solution media. The most basic NMR parameters, namely chemical shifts, coupling constants and nuclear Overhauser effects, allow defining short or repetitive chain sequences and characterize their structures and local geometries either in the free state or when interacting with other biomolecules, rendering additional information on the molecular recognition processes. The increased accessibility to carbohydrate molecules extensively or selectively labeled with 13C boosts the resolution and detail that analyzed glycan structures can reach. In turn, structural information derived from NMR, complemented with molecular modeling and theoretical calculations can also provide dynamic information on the conformational flexibility of carbohydrate structures. Furthermore, using partially oriented media or paramagnetic perturbations, it has been possible to introduce additional long-range observables rendering structural information on longer and branched glycan chains. In this review, we provide examples of these studies and an overview of the recent and most relevant NMR applications in the glycobiology field.
Collapse
Affiliation(s)
- Francisco Javier Cañada
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Ángeles Canales
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Pablo Valverde
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Beatriz Fernández de Toro
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Mónica Martínez-Orts
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Paola Oquist Phillips
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Amaia Pereda
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| |
Collapse
|
31
|
Fittolani G, Shanina E, Guberman M, Seeberger PH, Rademacher C, Delbianco M. Automatisierte Glykan‐Assemblierung
19
F‐markierter Glykansonden ermöglicht Hochdurchsatz‐NMR‐Untersuchungen von Protein‐Glykan‐Interaktionen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
| | - Elena Shanina
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
| | - Mónica Guberman
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Derzeitige Adresse: Medicinal Chemistry Leibniz-Forschungsinstitut für Molekulare Pharmakologie Robert-Rössle Straße 10 13125 Berlin Deutschland
| | - Peter H. Seeberger
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
| | - Christoph Rademacher
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
- Derzeitige Adresse: Department of Pharmaceutical Chemistry University of Vienna Althanstraße 14 1080 Wien Österreich
- Derzeitige Adresse: Department of Microbiology, Immunobiology and Genetics Max F. Perutz Labs Campus Vienna Biocenter 5 1030 Wien Österreich
| | - Martina Delbianco
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
| |
Collapse
|
32
|
Fittolani G, Shanina E, Guberman M, Seeberger PH, Rademacher C, Delbianco M. Automated Glycan Assembly of 19 F-labeled Glycan Probes Enables High-Throughput NMR Studies of Protein-Glycan Interactions. Angew Chem Int Ed Engl 2021; 60:13302-13309. [PMID: 33784430 PMCID: PMC8252726 DOI: 10.1002/anie.202102690] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/19/2021] [Indexed: 12/23/2022]
Abstract
Protein-glycan interactions mediate important biological processes, including pathogen host invasion and cellular communication. Herein, we showcase an expedite approach that integrates automated glycan assembly (AGA) of 19 F-labeled probes and high-throughput NMR methods, enabling the study of protein-glycan interactions. Synthetic Lewis type 2 antigens were screened against seven glycan binding proteins (GBPs), including DC-SIGN and BambL, respectively involved in HIV-1 and lung infections in immunocompromised patients, confirming the preference for fucosylated glycans (Lex , H type 2, Ley ). Previously unknown glycan-lectin weak interactions were detected, and thermodynamic data were obtained. Enzymatic reactions were monitored in real-time, delivering kinetic parameters. These results demonstrate the utility of AGA combined with 19 F NMR for the discovery and characterization of glycan-protein interactions, opening up new perspectives for 19 F-labeled complex glycans.
Collapse
Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Elena Shanina
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Mónica Guberman
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Current address: Medicinal ChemistryLeibniz-Forschungsinstitut für Molekulare PharmakologieRobert-Rössle Strasse 1013125BerlinGermany
| | - Peter H. Seeberger
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Christoph Rademacher
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Current address: Department of Pharmaceutical ChemistryUniversity of ViennaAlthanstrasse 141080ViennaAustria
- Current address: Department of Microbiology, Immunobiology and GeneticsMax F. Perutz LabsCampus Vienna Biocenter 51030ViennaAustria
| | - Martina Delbianco
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| |
Collapse
|
33
|
Vulpetti A, Dalvit C. Hydrogen Bond Acceptor Propensity of Different Fluorine Atom Types: An Analysis of Experimentally and Computationally Derived Parameters. Chemistry 2021; 27:8764-8773. [PMID: 33949737 DOI: 10.1002/chem.202100301] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 12/29/2022]
Abstract
The propensity of organic fluorine acting as a weak hydrogen bond acceptor (HBA) in intermolecular and intramolecular interactions has been the subject of many experimental and theoretical studies often reaching different conclusions. Over the last few years, new and stronger evidences have emerged for the direct involvement of fluorine in weak hydrogen bond (HB) formation. However, not all the fluorine atom types can act as weak HBA. In this work, the differential HBA propensity of various types of fluorine atoms was analyzed with a particular emphasis for the different types of alkyl fluorides. This was carried out by evaluating ab initio computed parameters, experimental 19 F NMR chemical shifts and small molecule crystallographic structures (extracted from the CSD database). According to this analysis, shielded (with reference to the 19 F NMR chemical shift) alkyl mono-fluorinated motifs display the highest HBA propensity in agreement with solution studies. Although much weaker than other well-characterized HB complexes, the fragile HBs formed by these fluorinated motifs have important implications for the chemical-physical and structural properties of the molecules, chemical reactions, and protein-ligand recognition.
Collapse
Affiliation(s)
- Anna Vulpetti
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4002, Basel, Switzerland
| | | |
Collapse
|
34
|
Berrino E, Michelet B, Martin-Mingot A, Carta F, Supuran CT, Thibaudeau S. Modulating the Efficacy of Carbonic Anhydrase Inhibitors through Fluorine Substitution. Angew Chem Int Ed Engl 2021; 60:23068-23082. [PMID: 34028153 DOI: 10.1002/anie.202103211] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/19/2021] [Indexed: 12/19/2022]
Abstract
The insertion of fluorine atoms and/or fluoroalkyl groups can lead to many beneficial effects in biologically active molecules, such as enhanced metabolic stability, bioavailability, lipophilicity, and membrane permeability, as well as a strengthening of protein-ligand binding interactions. However, this "magic effect" of fluorine atom(s) insertion can often be meaningless. Taking advantage of the wide range of data coming from the quest for carbonic anhydrase (CA) fluorinated inhibitors, this Minireview attempts to give "general guidelines" on how to wisely insert fluorine atom(s) within an inhibitor moiety to precisely enhance or disrupt ligand-protein interactions, depending on the target location of the fluorine substitution in the ligand. Multiple approaches such as ITC, kinetic and inhibition studies, X-ray crystallography, and NMR spectroscopy are useful in dissecting single binding contributions to the overall observed effect. The exploitation of innovative directions made in the field of protein and ligand-based fluorine NMR screening is also discussed to avoid misconduct and finely tune the exploitation of selective fluorine atom insertion in the future.
Collapse
Affiliation(s)
- Emanuela Berrino
- University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Bastien Michelet
- Superacid Group in "Organic Synthesis" Team, Université de Poitiers, CNRS UMR 7285 IC2MP, Bât. B28, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 09, France
| | - Agnès Martin-Mingot
- Superacid Group in "Organic Synthesis" Team, Université de Poitiers, CNRS UMR 7285 IC2MP, Bât. B28, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 09, France
| | - Fabrizio Carta
- University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T Supuran
- University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Sébastien Thibaudeau
- Superacid Group in "Organic Synthesis" Team, Université de Poitiers, CNRS UMR 7285 IC2MP, Bât. B28, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 09, France
| |
Collapse
|
35
|
Hamala V, Červenková Šťastná L, Kurfiřt M, Cuřínová P, Dračínský M, Karban J. Synthesis of multiply fluorinated N-acetyl-D-glucosamine and D-galactosamine analogs via the corresponding deoxyfluorinated glucosazide and galactosazide phenyl thioglycosides. Beilstein J Org Chem 2021; 17:1086-1095. [PMID: 34093878 PMCID: PMC8144920 DOI: 10.3762/bjoc.17.85] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/27/2021] [Indexed: 11/23/2022] Open
Abstract
Multiple fluorination of glycostructures has emerged as an attractive way of modulating their protein affinity, metabolic stability, and lipophilicity. Here we described the synthesis of a series of mono-, di- and trifluorinated N-acetyl-ᴅ-glucosamine and ᴅ-galactosamine analogs. The key intermediates are the corresponding multiply fluorinated glucosazide and galactosazide thioglycosides prepared from deoxyfluorinated 1,6-anhydro-2-azido-β-ᴅ-hexopyranose precursors by ring-opening reaction with phenyl trimethylsilyl sulfide. Nucleophilic deoxyfluorination at C4 and C6 by reaction with DAST, thioglycoside hydrolysis and azide/acetamide transformation completed the synthesis.
Collapse
Affiliation(s)
- Vojtěch Hamala
- Department of Bioorganic Compounds and Nanocomposites, Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic
- University of Chemistry and Technology Prague, Technická 5, 16628 Praha 6, Czech Republic
| | - Lucie Červenková Šťastná
- Department of Bioorganic Compounds and Nanocomposites, Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic
| | - Martin Kurfiřt
- Department of Bioorganic Compounds and Nanocomposites, Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic
- University of Chemistry and Technology Prague, Technická 5, 16628 Praha 6, Czech Republic
| | - Petra Cuřínová
- Department of Bioorganic Compounds and Nanocomposites, Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic
| | - Martin Dračínský
- NMR Spectroscopy group, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 542/2, 16000 Praha, Czech Republic
| | - Jindřich Karban
- Department of Bioorganic Compounds and Nanocomposites, Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic
| |
Collapse
|
36
|
Gómez-Redondo M, Delgado S, Núñez-Franco R, Jiménez-Osés G, Ardá A, Jiménez-Barbero J, Gimeno A. The two domains of human galectin-8 bind sialyl- and fucose-containing oligosaccharides in an independent manner. A 3D view by using NMR. RSC Chem Biol 2021; 2:932-941. [PMID: 34179785 PMCID: PMC8190895 DOI: 10.1039/d1cb00051a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The interaction of human galectin-8 and its two separate N-terminal and C-terminal carbohydrate recognition domains (CRD) to their natural ligands has been analysed using a synergistic combination of experimental NMR and ITC methods, and molecular dynamics simulations. Both domains bind the minimal epitopes N-acetyllactosamine (1) and Galβ1–3GalNAc (2) in a similar manner. However, the N-terminal and C-terminal domains show exquisite and opposing specificity to bind either Neu5Ac- or Fuc-containing ligands, respectively. Moreover, the addition of the high-affinity ligands specific for one of the CRDs does not make any effect on the binding at the alternative one. Thus, the two CRDs behave independently and may simultaneously target different molecular entities to promote clustering through the generation of supramolecular assemblies. NMR, ITC, and MD data show that the two domains of human galectin-8 independently recognize sialyl- and fucosyl-containing glycans.![]()
Collapse
Affiliation(s)
- Marcos Gómez-Redondo
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park Building 800 48160 Derio Spain
| | - Sandra Delgado
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park Building 800 48160 Derio Spain
| | - Reyes Núñez-Franco
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park Building 800 48160 Derio Spain
| | - Gonzalo Jiménez-Osés
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park Building 800 48160 Derio Spain .,lkerbasque, Basque Foundation for Science Plaza Euskadi 5 48009 Bilbao Spain
| | - Ana Ardá
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park Building 800 48160 Derio Spain .,lkerbasque, Basque Foundation for Science Plaza Euskadi 5 48009 Bilbao Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park Building 800 48160 Derio Spain .,lkerbasque, Basque Foundation for Science Plaza Euskadi 5 48009 Bilbao Spain.,Departament of Organic Chemistry ll, Faculty of Science & Technology, University of the Basque Country 48940 Leioa Spain
| | - Ana Gimeno
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park Building 800 48160 Derio Spain
| |
Collapse
|
37
|
Linclau B, Ardá A, Reichardt NC, Sollogoub M, Unione L, Vincent SP, Jiménez-Barbero J. Fluorinated carbohydrates as chemical probes for molecular recognition studies. Current status and perspectives. Chem Soc Rev 2021; 49:3863-3888. [PMID: 32520059 DOI: 10.1039/c9cs00099b] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review provides an extensive summary of the effects of carbohydrate fluorination with regard to changes in physical, chemical and biological properties with respect to regular saccharides. The specific structural, conformational, stability, reactivity and interaction features of fluorinated sugars are described, as well as their applications as probes and in chemical biology.
Collapse
Affiliation(s)
- Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton SO171BJ, UK
| | - Ana Ardá
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain.
| | | | - Matthieu Sollogoub
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Stéphane P Vincent
- Department of Chemistry, Laboratory of Bio-organic Chemistry, University of Namur (UNamur), B-5000 Namur, Belgium
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain. and Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain and Department of Organic Chemistry II, Faculty of Science and Technology, UPV/EHU, 48940 Leioa, Spain
| |
Collapse
|
38
|
Gómez-Redondo M, Ardá A, Gimeno A, Jiménez-Barbero J. Bacterial polysaccharides: conformation, dynamics and molecular recognition by antibodies. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 35-36:1-11. [PMID: 33388123 DOI: 10.1016/j.ddtec.2020.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 02/07/2023]
Abstract
Bacterial infections are the cause of different severe health conditions and new therapies to combat these pathogens have been widely investigated. Carbohydrates, being complex structures covering the surface of bacteria, are considered relevant targets for antibody and vaccine development. The biological activities in pathogenesis of bacterial capsular polysaccharides and lipopolisaccharides and their unique structures have boosted the study of the minimal antigenic binding epitopes and the structural details of antibody-carbohydrate recognition. This review describes the most recent advances on the field, examining the structure, conformation and dynamics of relevant bacterial carbohydrates and their complexes with antibodies. The understanding of key factors governing the recognition process is fundamental for the progress toward the development of specific and efficient bacterial therapeutics.
Collapse
Affiliation(s)
- Marcos Gómez-Redondo
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Ana Ardá
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Ana Gimeno
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48160 Derio, Spain; Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain; Department Organic Chemistry II, Faculty of Science and technology, UPV-EHU, 48940 Leioa, Spain
| |
Collapse
|
39
|
Zhang S, Chen KY, Zou X. Carbohydrate-Protein Interactions: Advances and Challenges. COMMUNICATIONS IN INFORMATION AND SYSTEMS 2021; 21:147-163. [PMID: 34366717 DOI: 10.4310/cis.2021.v21.n1.a7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A carbohydrate, also called saccharide in biochemistry, is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms. For example, sugars are low molecular-weight carbohydrates, and starches are high molecular-weight carbohydrates. Carbohydrates are the most abundant organic substances in nature and essential constituents of all living things. Protein-carbohydrate interactions play important roles in many biological processes, such as cell growth, differentiation, and aggregation. They also have broad applications in pharmaceutical drug design. In this review, we will summarize the characteristic features of protein-carbohydrate interactions and review the computational methods for structure prediction, energy calculations, and kinetic studies of protein-carbohydrate complexes. Finally, we will discuss the challenges in this field.
Collapse
Affiliation(s)
- Shuang Zhang
- Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Kyle Yu Chen
- Rock Bridge High School, 4303 South Providence Rd, Columbia, MO 65203, USA
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| |
Collapse
|
40
|
Bertuzzi S, Gimeno A, Núñez‐Franco R, Bernardo‐Seisdedos G, Delgado S, Jiménez‐Osés G, Millet O, Jiménez‐Barbero J, Ardá A. Unravelling the Time Scale of Conformational Plasticity and Allostery in Glycan Recognition by Human Galectin-1. Chemistry 2020; 26:15643-15653. [PMID: 32780906 PMCID: PMC7756784 DOI: 10.1002/chem.202003212] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 12/12/2022]
Abstract
The interaction of human galectin-1 with a variety of oligosaccharides, from di-(N-acetyllactosamine) to tetra-saccharides (blood B type-II antigen) has been scrutinized by using a combined approach of different NMR experiments, molecular dynamics (MD) simulations, and isothermal titration calorimetry. Ligand- and receptor-based NMR experiments assisted by computational methods allowed proposing three-dimensional structures for the different complexes, which explained the lack of enthalpy gain when increasing the chemical complexity of the glycan. Interestingly, and independently of the glycan ligand, the entropy term does not oppose the binding event, a rather unusual feature for protein-sugar interactions. CLEANEX-PM and relaxation dispersion experiments revealed that sugar binding affected residues far from the binding site and described significant changes in the dynamics of the protein. In particular, motions in the microsecond-millisecond timescale in residues at the protein dimer interface were identified in the presence of high affinity ligands. The dynamic process was further explored by extensive MD simulations, which provided additional support for the existence of allostery in glycan recognition by human galectin-1.
Collapse
Affiliation(s)
- Sara Bertuzzi
- Molecular Recognition and Host-Pathogen InteractionsCIC bioGUNEBasque Research and Technology Alliance, BRTABizkaia Technology Park, Building 80048162DerioBizkaiaSpain
| | - Ana Gimeno
- Molecular Recognition and Host-Pathogen InteractionsCIC bioGUNEBasque Research and Technology Alliance, BRTABizkaia Technology Park, Building 80048162DerioBizkaiaSpain
| | - Reyes Núñez‐Franco
- Molecular Recognition and Host-Pathogen InteractionsCIC bioGUNEBasque Research and Technology Alliance, BRTABizkaia Technology Park, Building 80048162DerioBizkaiaSpain
| | - Ganeko Bernardo‐Seisdedos
- Molecular Recognition and Host-Pathogen InteractionsCIC bioGUNEBasque Research and Technology Alliance, BRTABizkaia Technology Park, Building 80048162DerioBizkaiaSpain
| | - Sandra Delgado
- Molecular Recognition and Host-Pathogen InteractionsCIC bioGUNEBasque Research and Technology Alliance, BRTABizkaia Technology Park, Building 80048162DerioBizkaiaSpain
| | - Gonzalo Jiménez‐Osés
- Molecular Recognition and Host-Pathogen InteractionsCIC bioGUNEBasque Research and Technology Alliance, BRTABizkaia Technology Park, Building 80048162DerioBizkaiaSpain
| | - Oscar Millet
- Molecular Recognition and Host-Pathogen InteractionsCIC bioGUNEBasque Research and Technology Alliance, BRTABizkaia Technology Park, Building 80048162DerioBizkaiaSpain
| | - Jesús Jiménez‐Barbero
- Molecular Recognition and Host-Pathogen InteractionsCIC bioGUNEBasque Research and Technology Alliance, BRTABizkaia Technology Park, Building 80048162DerioBizkaiaSpain
- Ikerbasque—Basque Foundation for Science48013BilbaoBizkaiaSpain
- Department of Organic Chemistry IIUPV/EHUUniversity of the Basque Country48940LeioaBizkaiaSpain
| | - Ana Ardá
- Molecular Recognition and Host-Pathogen InteractionsCIC bioGUNEBasque Research and Technology Alliance, BRTABizkaia Technology Park, Building 80048162DerioBizkaiaSpain
| |
Collapse
|
41
|
Carboni F, Adamo R. Structure-based glycoconjugate vaccine design: The example of Group B Streptococcus type III capsular polysaccharide. DRUG DISCOVERY TODAY. TECHNOLOGIES 2020; 35-36:23-33. [PMID: 33388125 DOI: 10.1016/j.ddtec.2020.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/22/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Microbial surface polysaccharides are important virulence factors and targets for vaccine development. Glycoconjugate vaccines, obtained by covalently linking carbohydrates and proteins, are well established tools for prevention of bacterial infections. Elucidation of the minimal portion involved in the interactions with functional antibodies is of utmost importance for the understanding of their mechanism of induction of protective immune responses and the design of synthetic glycan based vaccines. Typically, this is achieved by combination of different techniques, which include ELISA, glycoarray, Surface Plasmon Resonance in conjunction with approaches for mapping at atomic level the position involved in binding, such as Saturation Transfer NMR and X-ray crystallography. This review provides an overview of the structural studies performed to map glycan epitopes (glycotopes), with focus on the highly complex structure of Group B Streptococcus type III (GBSIII) capsular polysaccharide. Furthermore, it describes the rational process followed to translate the obtained information into the design of a protective glycoconjugate vaccine based on a well-defined synthetic glycan epitope.
Collapse
|
42
|
Structure of a protective epitope reveals the importance of acetylation of Neisseria meningitidis serogroup A capsular polysaccharide. Proc Natl Acad Sci U S A 2020; 117:29795-29802. [PMID: 33158970 PMCID: PMC7703565 DOI: 10.1073/pnas.2011385117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Meningococcal meningitis remains a substantial cause of mortality and morbidity worldwide. Until recently, countries in the African meningitis belt were susceptible to devastating outbreaks, largely attributed to serogroup A Neisseria meningitidis (MenA). Vaccination with glycoconjugates of MenA capsular polysaccharide led to an almost complete elimination of MenA clinical cases. To understand the molecular basis of vaccine-induced protection, we generated a panel of oligosaccharide fragments of different lengths and tested them with polyclonal and monoclonal antibodies by inhibition enzyme-linked immunosorbent assay, surface plasmon resonance, and competitive human serum bactericidal assay, which is a surrogate for protection. The epitope was shown to optimize between three and six repeating units and to be O-acetylated. The molecular interactions between a protective monoclonal antibody and a MenA capsular polysaccharide fragment were further elucidated at the atomic level by saturation transfer difference NMR spectroscopy and X-ray crystallography. The epitope consists of a trisaccharide anchored to the antibody via the O- and N-acetyl moieties through either H-bonding or CH-π interactions. In silico docking showed that 3-O-acetylation of the upstream residue is essential for antibody binding, while O-acetate could be equally accommodated at three and four positions of the other two residues. These results shed light on the mechanism of action of current MenA vaccines and provide a foundation for the rational design of improved therapies.
Collapse
|
43
|
Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
Collapse
Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
| |
Collapse
|
44
|
Affiliation(s)
- Hayden Wilkinson
- NIBRT GlycoScience Group, National Institute for Bioprocessing, Research and Training, Blackrock, Dublin, Ireland
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland, Galway, Ireland
- UCD School of Medicine, College of Health and Agricultural Science, University College Dublin, Dublin, Ireland
| | - Radka Saldova
- NIBRT GlycoScience Group, National Institute for Bioprocessing, Research and Training, Blackrock, Dublin, Ireland
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland, Galway, Ireland
- UCD School of Medicine, College of Health and Agricultural Science, University College Dublin, Dublin, Ireland
| |
Collapse
|
45
|
Täubert S, Zhang YH, Martinez MM, Siepel F, Wöltjen E, Leonov A, Griesinger C. Lanthanide Tagging of Oligonucleotides to Nucleobase for Paramagnetic NMR. Chembiochem 2020; 21:3333-3337. [PMID: 32687667 PMCID: PMC7754328 DOI: 10.1002/cbic.202000417] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/19/2020] [Indexed: 12/03/2022]
Abstract
Although lanthanide tags, which have large anisotropic magnetic susceptibilities, have already been introduced to enrich NMR parameters by long‐range pseudoconact shifts (PCSs) and residual dipolar couplings (RDCs) of proteins, their application to nucleotides has so far been limited to one previous report, due to the high affinities of lanthanides for the phosphodiester backbone of nucleotides and difficult organic synthesis. Herein, we report successful attachment of a lanthanide tag to a chemically synthesized oligonucleotide via a disulfide bond. NMR experiments reveal PCSs of up to 1 ppm and H−H RDCs of up to 8 Hz at 950 MHz. Although weaker magnetic alignment was achieved than with proteins, the paramagnetic data could be fitted to the known structure of the DNA, taking the mobility of the tag into account. While further rigidification of the tag is desirable, this tag could also be used to measure heteronuclear RDCs of 13C,15N‐labeled chemically synthesized DNA and RNA.
Collapse
Affiliation(s)
- Sebastian Täubert
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Yong-Hui Zhang
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Mitcheell Maestre Martinez
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Florian Siepel
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Edith Wöltjen
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Andrei Leonov
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Griesinger
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| |
Collapse
|
46
|
Bertuzzi S, Quintana JI, Ardá A, Gimeno A, Jiménez-Barbero J. Targeting Galectins With Glycomimetics. Front Chem 2020; 8:593. [PMID: 32850631 PMCID: PMC7426508 DOI: 10.3389/fchem.2020.00593] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/08/2020] [Indexed: 01/06/2023] Open
Abstract
Among glycan-binding proteins, galectins, β-galactoside-binding lectins, exhibit relevant biological roles and are implicated in many diseases, such as cancer and inflammation. Their involvement in crucial pathologies makes them interesting targets for drug discovery. In this review, we gather the last approaches toward the specific design of glycomimetics as potential drugs against galectins. Different approaches, either using specific glycomimetic molecules decorated with key functional groups or employing multivalent presentations of lactose and N-acetyl lactosamine analogs, have provided promising results for binding and modulating different galectins. The review highlights the results obtained with these approximations, from the employment of S-glycosyl compounds to peptidomimetics and multivalent glycopolymers, mostly employed to recognize and/or detect hGal-1 and hGal-3.
Collapse
Affiliation(s)
- Sara Bertuzzi
- CIC bioGUNE, Basque Research Technology Alliance, Derio, Spain
| | - Jon I Quintana
- CIC bioGUNE, Basque Research Technology Alliance, Derio, Spain
| | - Ana Ardá
- CIC bioGUNE, Basque Research Technology Alliance, Derio, Spain
| | - Ana Gimeno
- CIC bioGUNE, Basque Research Technology Alliance, Derio, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research Technology Alliance, Derio, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.,Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country - UPV-EHU, Leioa, Spain
| |
Collapse
|
47
|
Abstract
The conformation of a molecule strongly affects its function, as demonstrated for peptides and nucleic acids. This correlation is much less established for carbohydrates, the most abundant organic materials in nature. Recent advances in synthetic and analytical techniques have enabled the study of carbohydrates at the molecular level. Recurrent structural features were identified as responsible for particular biological activities or material properties. In this Minireview, recent achievements in the structural characterization of carbohydrates, enabled by systematic studies of chemically defined oligosaccharides, are discussed. These findings can guide the development of more potent glycomimetics. Synthetic carbohydrate materials by design can be envisioned.
Collapse
Affiliation(s)
- Yang Yu
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Martina Delbianco
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| |
Collapse
|
48
|
Atanasova M, Bagdonas H, Agirre J. Structural glycobiology in the age of electron cryo-microscopy. Curr Opin Struct Biol 2020; 62:70-78. [DOI: 10.1016/j.sbi.2019.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/20/2019] [Accepted: 12/02/2019] [Indexed: 01/05/2023]
|
49
|
Zhang Y, Gómez‐Redondo M, Jiménez‐Osés G, Arda A, Overkleeft HS, Marel GA, Jiménez‐Barbero J, Codée JDC. Synthesis and Structural Analysis of
Aspergillus fumigatus
Galactosaminogalactans Featuring α‐Galactose, α‐Galactosamine and α‐
N
‐Acetyl Galactosamine Linkages. Angew Chem Int Ed Engl 2020; 59:12746-12750. [DOI: 10.1002/anie.202003951] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Yongzhen Zhang
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Marcos Gómez‐Redondo
- CIC bioGUNE Basque Research and Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48160 Derio Bizkaia Spain
| | - Gonzalo Jiménez‐Osés
- CIC bioGUNE Basque Research and Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48160 Derio Bizkaia Spain
| | - Ana Arda
- CIC bioGUNE Basque Research and Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48160 Derio Bizkaia Spain
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A. Marel
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Jesús Jiménez‐Barbero
- CIC bioGUNE Basque Research and Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48160 Derio Bizkaia Spain
- Ikerbasque Basque Foundation for Science Maria Diaz de Haro 3 48013 Bilbao Spain
- Department Organic Chemistry II, Faculty Science & Technology EHU-UPV Leioa Spain
| | - Jeroen D. C. Codée
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| |
Collapse
|
50
|
Zhang Y, Gómez‐Redondo M, Jiménez‐Osés G, Arda A, Overkleeft HS, Marel GA, Jiménez‐Barbero J, Codée JDC. Synthesis and Structural Analysis of
Aspergillus fumigatus
Galactosaminogalactans Featuring α‐Galactose, α‐Galactosamine and α‐
N
‐Acetyl Galactosamine Linkages. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yongzhen Zhang
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Marcos Gómez‐Redondo
- CIC bioGUNE Basque Research and Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48160 Derio Bizkaia Spain
| | - Gonzalo Jiménez‐Osés
- CIC bioGUNE Basque Research and Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48160 Derio Bizkaia Spain
| | - Ana Arda
- CIC bioGUNE Basque Research and Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48160 Derio Bizkaia Spain
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A. Marel
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Jesús Jiménez‐Barbero
- CIC bioGUNE Basque Research and Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48160 Derio Bizkaia Spain
- Ikerbasque Basque Foundation for Science Maria Diaz de Haro 3 48013 Bilbao Spain
- Department Organic Chemistry II, Faculty Science & Technology EHU-UPV Leioa Spain
| | - Jeroen D. C. Codée
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| |
Collapse
|