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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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Protein Secondary Structure Affects Glycan Clustering in Native Mass Spectrometry. Life (Basel) 2021; 11:life11060554. [PMID: 34208397 PMCID: PMC8231113 DOI: 10.3390/life11060554] [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: 05/02/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 01/01/2023] Open
Abstract
Infection by the humannoroviruses (hNoV), for the vast majority of strains, requires attachment of the viral capsid to histo blood group antigens (HBGAs). The HBGA-binding pocket is formed by dimers of the protruding domain (P dimers) of the capsid protein VP1. Several studies have focused on HBGA binding to P dimers, reporting binding affinities and stoichiometries. However, nuclear magnetic resonance spectroscopy (NMR) and native mass spectrometry (MS) analyses yielded incongruent dissociation constants (KD) for the binding of HBGAs to P dimers and, in some cases, disagreed on whether glycans bind at all. We hypothesized that glycan clustering during electrospray ionization in native MS critically depends on the physicochemical properties of the protein studied. It follows that the choice of a reference protein is crucial. We analysed carbohydrate clustering using various P dimers and eight non-glycan binding proteins serving as possible references. Data from native and ion mobility MS indicate that the mass fraction of β-sheets has a strong influence on the degree of glycan clustering. Therefore, the determination of specific glycan binding affinities from native MS must be interpreted cautiously.
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Creutznacher R, Schulze E, Wallmann G, Peters T, Stein M, Mallagaray A. Chemical-Shift Perturbations Reflect Bile Acid Binding to Norovirus Coat Protein: Recognition Comes in Different Flavors. Chembiochem 2020; 21:1007-1021. [PMID: 31644826 PMCID: PMC7186840 DOI: 10.1002/cbic.201900572] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Indexed: 12/31/2022]
Abstract
Bile acids have been reported as important cofactors promoting human and murine norovirus (NoV) infections in cell culture. The underlying mechanisms are not resolved. Through the use of chemical shift perturbation (CSP) NMR experiments, we identified a low-affinity bile acid binding site of a human GII.4 NoV strain. Long-timescale MD simulations reveal the formation of a ligand-accessible binding pocket of flexible shape, allowing the formation of stable viral coat protein-bile acid complexes in agreement with experimental CSP data. CSP NMR experiments also show that this mode of bile acid binding has a minor influence on the binding of histo-blood group antigens and vice versa. STD NMR experiments probing the binding of bile acids to virus-like particles of seven different strains suggest that low-affinity bile acid binding is a common feature of human NoV and should therefore be important for understanding the role of bile acids as cofactors in NoV infection.
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Affiliation(s)
- Robert Creutznacher
- University of Lübeck, Center of Structural and Cell Biology in Medicine (CSCM)Institute of Chemistry and MetabolomicsRatzeburger Allee 16023562LübeckGermany
| | - Eric Schulze
- Max Planck Institute for Dynamics of Complex Technical SystemsMolecular Simulations and Design GroupSandtorstrasse 139106MagdeburgGermany
| | - Georg Wallmann
- University of Lübeck, Center of Structural and Cell Biology in Medicine (CSCM)Institute of Chemistry and MetabolomicsRatzeburger Allee 16023562LübeckGermany
| | - Thomas Peters
- University of Lübeck, Center of Structural and Cell Biology in Medicine (CSCM)Institute of Chemistry and MetabolomicsRatzeburger Allee 16023562LübeckGermany
| | - Matthias Stein
- Max Planck Institute for Dynamics of Complex Technical SystemsMolecular Simulations and Design GroupSandtorstrasse 139106MagdeburgGermany
| | - Alvaro Mallagaray
- University of Lübeck, Center of Structural and Cell Biology in Medicine (CSCM)Institute of Chemistry and MetabolomicsRatzeburger Allee 16023562LübeckGermany
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Bücher KS, Konietzny PB, Snyder NL, Hartmann L. Heteromultivalent Glycooligomers as Mimetics of Blood Group Antigens. Chemistry 2019; 25:3301-3309. [PMID: 30431195 DOI: 10.1002/chem.201804505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/26/2018] [Indexed: 12/19/2022]
Abstract
Precision glycomacromolecules have proven to be important tools for the investigation of multivalent carbohydrate-lectin interactions by presenting multiple glycan epitopes on a highly-defined synthetic scaffold. Herein, we present a new strategy for the versatile assembly of heteromultivalent glycomacromolecules that contain different carbohydrate motifs in proximity within the side chains. A new building block suitable for the solid-phase polymer synthesis of precision glycomacromolecules was developed with a branching point in the side chain that bears a free alkyne and a TIPS-protected alkyne moiety, which enables the subsequent attachment of different carbohydrate motifs by on-resin copper-mediated azide-alkyne cycloaddition reactions. Applying this synthetic strategy, heteromultivalent glycooligomers presenting fragments of histo-blood group antigens and human milk oligosaccharides were synthesized and tested for their binding behavior towards bacterial lectin LecB.
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Affiliation(s)
- Katharina S Bücher
- Institute of Organic and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Patrick B Konietzny
- Institute of Organic and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nicole L Snyder
- Department of Chemistry, Davidson College, Davidson, NC, USA
| | - Laura Hartmann
- Institute of Organic and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Hamark C, Pendrill R, Landström J, Dotson Fagerström A, Sandgren M, Ståhlberg J, Widmalm G. Enantioselective Binding of Propranolol and Analogues Thereof to Cellobiohydrolase Cel7A. Chemistry 2018; 24:17975-17985. [PMID: 30255965 DOI: 10.1002/chem.201803104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Indexed: 12/28/2022]
Abstract
At the catalytic site for the hydrolysis of cellulose the enzyme cellobiohydrolase Cel7A binds the enantiomers of the adrenergic beta-blocker propranolol with different selectivity. Methyl-to-hydroxymethyl group modifications of propranolol, which result in higher affinity and improved selectivity, were herein studied by 1 H,1 H and 1 H,13 C scalar spin-spin coupling constants as well as utilizing the nuclear Overhauser effect (NOE) in conjunction with molecular dynamics simulations of the ligands per se, which showed the presence of all-antiperiplanar conformations, except for the one containing a vicinal oxygen-oxygen arrangement governed by the gauche effect. For the ligand-protein complexes investigated by NMR spectroscopy using, inter alia, transferred NOESY and saturation-transfer difference (STD) NMR experiments the S-isomers were shown to bind with a higher affinity and a conformation similar to that preferred in solution, in contrast to the R-isomer. The fact that the S-form of the propranolol enantiomer is pre-arranged for binding to the protein is also observed for a crystal structure of dihydroxy-(S)-propranolol and Cel7A presented herein. Whereas the binding of propranolol is entropy driven, the complexation with the dihydroxy analogue is anticipated to be favored also by an enthalpic term, such as for its enantiomer, that is, dihydroxy-(R)-propranolol, because hydrogen-bond donation replaces the corresponding bonding from hydroxyl groups in glucosyl residues of the natural substrate. In addition to a favorable entropy component, albeit lesser in magnitude, this represents an effect of enthalpy-to-entropy compensation in ligand-protein interactions.
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Affiliation(s)
- Christoffer Hamark
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Robert Pendrill
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Jens Landström
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | | | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 75007, Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 75007, Uppsala, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691, Stockholm, Sweden
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Monaco S, Tailford LE, Juge N, Angulo J. Differential Epitope Mapping by STD NMR Spectroscopy To Reveal the Nature of Protein-Ligand Contacts. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707682] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Serena Monaco
- School of Pharmacy; University of East Anglia; Norwich Research Park Norwich UK
| | - Louise E. Tailford
- The Gut Health And Food Safety Institute Strategic Program; Quadram Institute of Bioscience; NR47UA Norwich Research Park Norwich UK
| | - Nathalie Juge
- The Gut Health And Food Safety Institute Strategic Program; Quadram Institute of Bioscience; NR47UA Norwich Research Park Norwich UK
| | - Jesus Angulo
- School of Pharmacy; University of East Anglia; Norwich Research Park Norwich UK
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Monaco S, Tailford LE, Juge N, Angulo J. Differential Epitope Mapping by STD NMR Spectroscopy To Reveal the Nature of Protein-Ligand Contacts. Angew Chem Int Ed Engl 2017; 56:15289-15293. [PMID: 28977722 PMCID: PMC5725711 DOI: 10.1002/anie.201707682] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/08/2017] [Indexed: 11/21/2022]
Abstract
Saturation transfer difference (STD) NMR spectroscopy is extensively used to obtain epitope maps of ligands binding to protein receptors, thereby revealing structural details of the interaction, which is key to direct lead optimization efforts in drug discovery. However, it does not give information about the nature of the amino acids surrounding the ligand in the binding pocket. Herein, we report the development of the novel method differential epitope mapping by STD NMR (DEEP‐STD NMR) for identifying the type of protein residues contacting the ligand. The method produces differential epitope maps through 1) differential frequency STD NMR and/or 2) differential solvent (D2O/H2O) STD NMR experiments. The two approaches provide different complementary information on the binding pocket. We demonstrate that DEEP‐STD NMR can be used to readily obtain pharmacophore information on the protein. Furthermore, if the 3D structure of the protein is known, this information also helps in orienting the ligand in the binding pocket.
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Affiliation(s)
- Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Louise E Tailford
- The Gut Health And Food Safety Institute Strategic Program, Quadram Institute of Bioscience, NR47UA, Norwich Research Park, Norwich, UK
| | - Nathalie Juge
- The Gut Health And Food Safety Institute Strategic Program, Quadram Institute of Bioscience, NR47UA, Norwich Research Park, Norwich, UK
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
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Marchetti R, Perez S, Arda A, Imberty A, Jimenez‐Barbero J, Silipo A, Molinaro A. "Rules of Engagement" of Protein-Glycoconjugate Interactions: A Molecular View Achievable by using NMR Spectroscopy and Molecular Modeling. ChemistryOpen 2016; 5:274-96. [PMID: 27547635 PMCID: PMC4981046 DOI: 10.1002/open.201600024] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 12/20/2022] Open
Abstract
Understanding the dynamics of protein-ligand interactions, which lie at the heart of host-pathogen recognition, represents a crucial step to clarify the molecular determinants implicated in binding events, as well as to optimize the design of new molecules with therapeutic aims. Over the last decade, advances in complementary biophysical and spectroscopic methods permitted us to deeply dissect the fine structural details of biologically relevant molecular recognition processes with high resolution. This Review focuses on the development and use of modern nuclear magnetic resonance (NMR) techniques to dissect binding events. These spectroscopic methods, complementing X-ray crystallography and molecular modeling methodologies, will be taken into account as indispensable tools to provide a complete picture of protein-glycoconjugate binding mechanisms related to biomedicine applications against infectious diseases.
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Affiliation(s)
- Roberta Marchetti
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Serge Perez
- Department Molecular Pharmacochemistry UMR 5063CNRS and University of GrenobleAlpes, BP 5338041 Grenoble cedex 9France
| | - Ana Arda
- Bizkaia Technological ParkCIC bioGUNEBuilding 801A-148160Derio-BizkaiaSpain
| | - Anne Imberty
- Centre de Recherche sur les CNRSand University of Grenoble Macromolécules Végétales, UPR 5301Alpes, BP 5338041Grenoble cedex 9France
| | | | - Alba Silipo
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Antonio Molinaro
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
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9
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Marcelo F, Garcia-Martin F, Matsushita T, Sardinha J, Coelho H, Oude-Vrielink A, Koller C, André S, Cabrita EJ, Gabius HJ, Nishimura SI, Jiménez-Barbero J, Cañada FJ. Delineating Binding Modes of Gal/GalNAc and Structural Elements of the Molecular Recognition of Tumor-Associated Mucin Glycopeptides by the Human Macrophage Galactose-Type Lectin. Chemistry 2014; 20:16147-55. [DOI: 10.1002/chem.201404566] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Indexed: 01/05/2023]
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10
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Zhang W, Li R, Shin R, Wang Y, Padmalayam I, Zhai L, Krishna NR. Identification of the binding site of an allosteric ligand using STD-NMR, docking, and CORCEMA-ST calculations. ChemMedChem 2013; 8:1629-33. [PMID: 23894090 DOI: 10.1002/cmdc.201300267] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Indexed: 01/20/2023]
Abstract
Singling out the truth: A combined application of STD-NMR, molecular docking, and CORCEMA-ST calculations is described as an attractive, easily applicable tool for the identification and validation of the binding site for allosteric ligands, with potential application as an aid in drug discovery research.
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Affiliation(s)
- Wei Zhang
- Drug Discovery Division, Southern Research Institute, 2000 9th Avenue South, Birmingham, AL 35205 (USA).
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11
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Mandal PK, Branson TR, Hayes ED, Ross JF, Gavín JA, Daranas AH, Turnbull WB. Towards a Structural Basis for the Relationship Between Blood Group and the Severity of El Tor Cholera. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201109068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Mandal PK, Branson TR, Hayes ED, Ross JF, Gavín JA, Daranas AH, Turnbull WB. Towards a structural basis for the relationship between blood group and the severity of El Tor cholera. Angew Chem Int Ed Engl 2012; 51:5143-6. [PMID: 22488789 PMCID: PMC3505909 DOI: 10.1002/anie.201109068] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 03/06/2012] [Indexed: 01/31/2023]
Affiliation(s)
- Pintu K Mandal
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT UK
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