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Negi G, Sharma A, Chaudhary M, Gupta D, Harshan KH, Parveen N. SARS-CoV-2 Binding to Terminal Sialic Acid of Gangliosides Embedded in Lipid Membranes. ACS Infect Dis 2023; 9:1346-1361. [PMID: 37145972 DOI: 10.1021/acsinfecdis.3c00106] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Multiple recent reports indicate that the S protein of SARS-CoV-2 specifically interacts with membrane receptors and attachment factors other than ACE2. They likely have an active role in cellular attachment and entry of the virus. In this article, we examined the binding of SARS-CoV-2 particles to gangliosides embedded in supported lipid bilayers (SLBs), mimicking the cell membrane-like environment. We show that the virus specifically binds to sialylated (sialic acid (SIA)) gangliosides, i.e., GD1a, GM3, and GM1, as determined from the acquired single-particle fluorescence images using a time-lapse total internal reflection fluorescence (TIRF) microscope. The data of virus binding events, the apparent binding rate constant, and the maximum virus coverage on the ganglioside-rich SLBs show that the virus particles have a higher binding affinity toward the GD1a and GM3 compared to the GM1 ganglioside. Enzymatic hydrolysis of the SIA-Gal bond of the gangliosides confirms that the SIA sugar unit of GD1a and GM3 is essential for virus attachment to the SLBs and even the cell surface sialic acid is critical for the cellular attachment of the virus. The structural difference between GM3/GD1a and GM1 is the presence of SIA at the main or branched chain. We conclude that the number of SIA per ganglioside can weakly influence the initial binding rate of SARS-CoV-2 particles, whereas the terminal or more exposed SIA is critical for the virus binding to the gangliosides in SLBs.
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Affiliation(s)
- Geetanjali Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, 208016 Kanpur, India
| | - Anurag Sharma
- Department of Chemistry, Indian Institute of Technology Kanpur, 208016 Kanpur, India
| | - Monika Chaudhary
- Department of Chemistry, Indian Institute of Technology Kanpur, 208016 Kanpur, India
| | - Divya Gupta
- CSIR-Centre for Cellular and Molecular Biology, 500007 Hyderabad, India
| | - Krishnan H Harshan
- CSIR-Centre for Cellular and Molecular Biology, 500007 Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nagma Parveen
- Department of Chemistry, Indian Institute of Technology Kanpur, 208016 Kanpur, India
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2
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Feng Y, Pogan R, Thiede L, Müller-Guhl J, Uetrecht C, Roos WH. Fucose Binding Cancels out Mechanical Differences between Distinct Human Noroviruses. Viruses 2023; 15:1482. [PMID: 37515170 PMCID: PMC10383637 DOI: 10.3390/v15071482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
The majority of nonbacterial gastroenteritis in humans and livestock is caused by noroviruses. Like most RNA viruses, frequent mutations result in various norovirus variants. The strain-dependent binding profiles of noroviruses to fucose are supposed to facilitate norovirus infection. It remains unclear, however, what the molecular mechanism behind strain-dependent functioning is. In this study, by applying atomic force microscopy (AFM) nanoindentation technology, we studied norovirus-like particles (noroVLPs) of three distinct human norovirus variants. We found differences in viral mechanical properties even between the norovirus variants from the same genogroup. The noroVLPs were then subjected to fucose treatment. Surprisingly, after fucose treatment, the previously found considerable differences in viral mechanical properties among these variants were diminished. We attribute a dynamic switch of the norovirus P domain upon fucose binding to the reduced differences in viral mechanical properties across the tested norovirus variants. These findings shed light on the mechanisms used by norovirus capsids to adapt to environmental changes and, possibly, increase cell infection. Hereby, a new step towards connecting viral mechanical properties to viral prevalence is taken.
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Affiliation(s)
- Yuzhen Feng
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, 9747AG Groningen, The Netherlands
| | - Ronja Pogan
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron (DESY) & Leibniz Institute of Virology (LIV), 22607 Hamburg, Germany
- Faculty V: School of Life Sciences, University of Siegen, 57076 Siegen, Germany
| | - Lars Thiede
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron (DESY) & Leibniz Institute of Virology (LIV), 22607 Hamburg, Germany
- Faculty V: School of Life Sciences, University of Siegen, 57076 Siegen, Germany
| | - Jürgen Müller-Guhl
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron (DESY) & Leibniz Institute of Virology (LIV), 22607 Hamburg, Germany
- Partner Site Hamburg-Lübeck-Borstel-Riems, Bernhard Nocht Institute for Tropical Medicine and German Center for Infection Research (DZIF), 20359 Hamburg, Germany
| | - Charlotte Uetrecht
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron (DESY) & Leibniz Institute of Virology (LIV), 22607 Hamburg, Germany
- Faculty V: School of Life Sciences, University of Siegen, 57076 Siegen, Germany
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, 9747AG Groningen, The Netherlands
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Waerlop G, Janssens Y, Jacobs B, Jarczowski F, Diessner A, Leroux-Roels G, Klimyuk V, Leroux-Roels I, Thieme F. Immune responses in healthy adults elicited by a bivalent norovirus vaccine candidate composed of GI.4 and GII.4 VLPs without adjuvant. Front Immunol 2023; 14:1188431. [PMID: 37435073 PMCID: PMC10331465 DOI: 10.3389/fimmu.2023.1188431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/01/2023] [Indexed: 07/13/2023] Open
Abstract
The development of an efficacious vaccine against norovirus is of paramount importance given its potential to reduce the global burden of norovirus-associated morbidity and mortality. Here, we report a detailed immunological analysis of a phase I, double-blind, placebo-controlled clinical trial performed on 60 healthy adults, ages 18 to 40. Total serum immunoglobulin and serum IgA against vaccine strains and cross-reactive serum IgG against non-vaccine strains were measured by enzyme immunoassays, whereas cell-mediated immune responses were quantified using intracellular cytokine staining by flow cytometry. A significant increase in humoral and cellular responses, e.g., IgA and CD4+ polypositive T cells, was triggered by the GI.4 Chiba 407 (1987) and GII.4 Aomori 2 (2006) VLP-based norovirus vaccine candidate rNV-2v, which is formulated without adjuvant. No booster effect was observed after the second administration in the pre-exposed adult study population. Furthermore, a cross-reactive immune response was elicited, as shown by IgG titers against GI.3 (2002), GII.2 OC08154 (2008), GII.4 (1999), GII.4 Sydney (2012), GII.4 Washington (2018), GII.6 Maryland (2018), and GII.17 Kawasaki 308 (2015). Due to viral infection via mucosal gut tissue and the high variety of potentially relevant norovirus strains, a focus should be on IgA and cross-protective humoral and cell-mediated responses in the development of a broadly protective, multi-valent norovirus vaccine. Clinical trial registration https://clinicaltrials.gov, identifier NCT05508178. EudraCT number: 2019-003226-25.
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Affiliation(s)
- Gwenn Waerlop
- Center for Vaccinology (CEVAC), Ghent University and University Hospital, Ghent, Belgium
| | - Yorick Janssens
- Center for Vaccinology (CEVAC), Ghent University and University Hospital, Ghent, Belgium
| | - Bart Jacobs
- Center for Vaccinology (CEVAC), Ghent University and University Hospital, Ghent, Belgium
| | | | | | - Geert Leroux-Roels
- Center for Vaccinology (CEVAC), Ghent University and University Hospital, Ghent, Belgium
| | | | - Isabel Leroux-Roels
- Center for Vaccinology (CEVAC), Ghent University and University Hospital, Ghent, Belgium
| | - Frank Thieme
- Icon Genetics GmbH, a Denka Company, Halle, Germany
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4
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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: 10] [Impact Index Per Article: 10.0] [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.
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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
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Gerling-Driessen UIM, Hoffmann M, Schmidt S, Snyder NL, Hartmann L. Glycopolymers against pathogen infection. Chem Soc Rev 2023; 52:2617-2642. [PMID: 36820794 DOI: 10.1039/d2cs00912a] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Pathogens including viruses, bacteria, fungi, and parasites continue to shape our lives in profound ways every day. As we have learned to live in parallel with pathogens, we have gained a better understanding of the rules of engagement for how they bind, adhere, and invade host cells. One such mechanism involves the exploitation of host cell surface glycans for attachment/adhesion, one of the first steps of infection. This knowledge has led to the development of glycan-based diagnostics and therapeutics for the treatment and prevention of infection. One class of compounds that has become increasingly important are the glycopolymers. Glycopolymers are macromolecules composed of a synthetic scaffold presenting carbohydrates as side chain motifs. Glycopolymers are particularly attractive because their properties can be tuned by careful choice of the scaffold, carbohydrate/glycan, and overall presentation. In this review, we highlight studies over the past ten years that have examined the role of glycopolymers in pathogen adhesion and host cell infection, biofilm formation and removal, and drug delivery with the aim of examining the direct effects of these macromolecules on pathogen engagement. In addition, we also examine the role of glycopolymers as diagnostics for the detection and monitoring of pathogens.
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Affiliation(s)
- Ulla I M Gerling-Driessen
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
| | - Miriam Hoffmann
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
| | - Stephan Schmidt
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany. .,Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Str. 31, 79104 Freiburg, Germany
| | - Nicole L Snyder
- Department of Chemistry, Davidson College, Davidson, North Carolina 28035, USA
| | - Laura Hartmann
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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Maass T, Ssebyatika G, Brückner M, Breckwoldt L, Krey T, Mallagaray A, Peters T, Frank M, Creutznacher R. Binding of Glycans to the SARS CoV-2 Spike Protein, an Open Question: NMR Data on Binding Site Localization, Affinity, and Selectivity. Chemistry 2022; 28:e202202614. [PMID: 36161798 PMCID: PMC9537997 DOI: 10.1002/chem.202202614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/26/2022] [Accepted: 09/26/2022] [Indexed: 11/25/2022]
Abstract
We have used NMR experiments to explore the binding of selected glycans and glycomimetics to the SARS CoV-2 spike glycoprotein (S-protein) and to its receptor binding domain (RBD). STD NMR experiments confirm the binding of sialoglycans to the S-protein of the prototypic Wuhan strain virus and yield dissociation constants in the millimolar range. The absence of STD effects for sialoglycans in the presence of the Omicron/BA.1 S-protein reflects a loss of binding as a result of S-protein evolution. Likewise, no STD effects are observed for the deletion mutant Δ143-145 of the Wuhan S-protein, thus supporting localization of the binding site in the N-terminal domain (NTD). The glycomimetics Oseltamivir and Zanamivir bind weakly to the S-protein of both virus strains. Binding of blood group antigens to the Wuhan S-protein cannot be confirmed by STD NMR. Using 1 H,15 N TROSY HSQC-based chemical shift perturbation (CSP) experiments, we excluded binding of any of the ligands studied to the RBD of the Wuhan S-protein. Our results put reported data on glycan binding into perspective and shed new light on the potential role of glycan-binding to the S-protein.
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Affiliation(s)
- Thorben Maass
- University of Lübeck: Universitat zu LubeckInstitute of Chemistry and MetabolomicsGERMANY
| | - George Ssebyatika
- University of Lübeck: Universitat zu LubeckInstitute of BiochemistryGERMANY
| | - Marlene Brückner
- University of Lübeck: Universitat zu LubeckInstitute of Chemistry and MetabolomicsGERMANY
| | - Lea Breckwoldt
- University of Lübeck: Universitat zu LubeckInstitute of Chemistry and MetabolomicsGERMANY
| | - Thomas Krey
- University of Lübeck: Universitat zu LubeckInstitute of BiochemistryGERMANY
| | - Alvaro Mallagaray
- University of Lübeck: Universitat zu LubeckInstitute of Chemistry and MetabolomicsGERMANY
| | - Thomas Peters
- Institute for Chemistry and MetabolomicsUniversität zu LübeckRatzeburger Allee 16023562LübeckGERMANY
| | | | - Robert Creutznacher
- University of Lübeck: Universitat zu LubeckInstitute of Chemistry and MetabolomicsGERMANY
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7
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Creutznacher R, Maass T, Veselkova B, Ssebyatika G, Krey T, Empting M, Tautz N, Frank M, Kölbel K, Uetrecht C, Peters T. NMR Experiments Provide Insights into Ligand-Binding to the SARS-CoV-2 Spike Protein Receptor-Binding Domain. J Am Chem Soc 2022; 144:13060-13065. [PMID: 35830336 DOI: 10.1021/jacs.2c05603] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have used chemical shift perturbation (CSP) and saturation transfer difference (STD) NMR experiments to identify and characterize the binding of selected ligands to the receptor-binding domain (RBD) of the spike glycoprotein (S-protein) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We also subjected full-length S-protein to STD NMR experiments, allowing correlations with RBD-based results. CSPs reveal the binding sites for heparin and fondaparinux, and affinities were measured using CSP titrations. We then show that α-2,3-sialyllactose binds to the S-protein but not to the RBD. Finally, combined CSP and STD NMR experiments show that lifitegrast, a compound used for the treatment of dry eye, binds to the linoleic acid (LA) binding pocket with a dissociation constant in the μM range. This is an interesting finding, as lifitegrast lends itself well as a blueprint for medicinal chemistry, eventually furnishing novel entry inhibitors targeting the highly conserved LA binding site.
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Affiliation(s)
- Robert Creutznacher
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Thorben Maass
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Barbora Veselkova
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - George Ssebyatika
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Thomas Krey
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Antiviral & Antivirulence Drugs (AVID), Campus E8.1, 66123 Saarbrücken, Germany
| | - Norbert Tautz
- Center of Structural and Cell Biology in Medicine, Institute of Virology and Cell Biology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Martin Frank
- Biognos AB, Generatorsgatan 1, P.O. Box 8963, SE-402 74 Göteborg, Sweden
| | - Knut Kölbel
- CSSB Center for Structural Systems Biology, Leibniz Institute of Virology (LIV) & Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Charlotte Uetrecht
- CSSB Center for Structural Systems Biology, Leibniz Institute of Virology (LIV) & Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany.,School of Life Sciences, University of Siegen, 57076 Siegen, Germany
| | - Thomas Peters
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
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