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Basaran R, Ning X, Budhadev D, Hondow N, Guo Y, Zhou D. Probing the pH-dependency of DC-SIGN/R multivalent lectin-glycan interactions using polyvalent glycan-gold nanoparticles. NANOSCALE ADVANCES 2024; 6:2198-2208. [PMID: 38633047 PMCID: PMC11019501 DOI: 10.1039/d3na01013a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/04/2024] [Indexed: 04/19/2024]
Abstract
The dendritic cell tetrameric lectin, DC-SIGN, and its closely related endothelial cell lectin, DC-SIGNR (collectively abbreviated as DC-SIGN/R) play a key role in the binding and transmission of deadly viruses, including Ebola, HIV, HCV, and SARS-CoV-2. Their virus binding/release processes involve a gradually acidifying environment following the natural intracellular trafficking pathways. Therefore, understanding DC-SIGN/R's pH-dependent binding properties with glycan ligands is of great importance. We have recently developed densely glycosylated gold nanoparticles (glycan-GNPs) as a powerful new tool for probing DC-SIGN/R multivalent lectin-glycan interaction (MLGI) mechanisms. They can provide not only quantitative MLGI affinities but also important structural information, such as binding site orientation and binding modes. Herein, we further employ the glycan-GNP probes to investigate the pH dependency of DC-SIGN/R MLGI properties. We find that DC-SIGN/R MLGIs exhibit distinct pH dependence over the normal physiological (7.4) to lysosomal (∼4.6) pH range. DC-SIGN binds glycan-GNPs strongly and stably from pH 7.4 to ∼5.8, but the binding is weakened significantly as pH decreases to ≤5.4 and may be fully dissociated at pH 4.6. This behaviour is fully consistent with DC-SIGN's role as an endocytic recycling receptor. In contrast, DC-SIGNR's affinity with glycan-GNPs is enhanced with the decreasing pH from 7.4 to 5.4, peaking at pH 5.4, and then reduced as pH is further lowered. Interestingly, both DC-SIGN/R binding with glycan-GNPs are found to be partially reversible in a pH-dependent manner.
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Affiliation(s)
- Rahman Basaran
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds Leeds LS2 9JT UK
| | - Xinyu Ning
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds Leeds LS2 9JT UK
| | - Darshita Budhadev
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds Leeds LS2 9JT UK
| | - Nicole Hondow
- School of Chemical and Process Engineering, University of Leeds Leeds LS2 9JT UK
| | - Yuan Guo
- School of Food Science and Nutrition, Astbury Centre for Structural Molecular Biology, University of Leeds Leeds LS2 9JT UK
| | - Dejian Zhou
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds Leeds LS2 9JT UK
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Thrasher CJ, Jia F, Yee DW, Kubiak JM, Wang Y, Lee MS, Onoda M, Hart AJ, Macfarlane RJ. Rationally Designing the Supramolecular Interfaces of Nanoparticle Superlattices with Multivalent Polymers. J Am Chem Soc 2024. [PMID: 38622048 DOI: 10.1021/jacs.4c02617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
In supramolecular materials, multiple weak binding groups can act as a single collective unit when confined to a localized volume, thereby producing strong but dynamic bonds between material building blocks. This principle of multivalency provides a versatile means of controlling material assembly, as both the number and the type of supramolecular moieties become design handles to modulate the strength of intermolecular interactions. However, in materials with building blocks significantly larger than individual supramolecular moieties (e.g., polymer or nanoparticle scaffolds), the degree of multivalency is difficult to predict or control, as sufficiently large scaffolds inherently preclude separated supramolecular moieties from interacting. Because molecular models commonly used to examine supramolecular interactions are intrinsically unable to examine any trends or emergent behaviors that arise due to nanoscale scaffold geometry, our understanding of the thermodynamics of these massively multivalent systems remains limited. Here we address this challenge via the coassembly of polymer-grafted nanoparticles and multivalent polymers, systematically examining how multivalent scaffold size, shape, and spacing affect their collective thermodynamics. Investigating the interplay of polymer structure and supramolecular group stoichiometry reveals complicated but rationally describable trends that demonstrate how the supramolecular scaffold design can modulate the strength of multivalent interactions. This approach to self-assembled supramolecular materials thus allows for the manipulation of polymer-nanoparticle composites with controlled thermal stability, nanoparticle organization, and tailored meso- to microscopic structures. The sophisticated control of multivalent thermodynamics through precise modulation of the nanoscale scaffold geometry represents a significant advance in the ability to rationally design complex hierarchically structured materials via self-assembly.
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Affiliation(s)
- Carl J Thrasher
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Fei Jia
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Daryl W Yee
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Joshua M Kubiak
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yuping Wang
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Margaret S Lee
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Michika Onoda
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - A John Hart
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Robert J Macfarlane
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Budhadev D, Hooper J, Rocha C, Nehlmeier I, Kempf AM, Hoffmann M, Krüger N, Zhou D, Pöhlmann S, Guo Y. Polyvalent Nano-Lectin Potently Neutralizes SARS-CoV-2 by Targeting Glycans on the Viral Spike Protein. JACS AU 2023; 3:1755-1766. [PMID: 37388683 PMCID: PMC10302749 DOI: 10.1021/jacsau.3c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023]
Abstract
Mutations in spike (S) protein epitopes allow SARS-CoV-2 variants to evade antibody responses induced by infection and/or vaccination. In contrast, mutations in glycosylation sites across SARS-CoV-2 variants are very rare, making glycans a potential robust target for developing antivirals. However, this target has not been adequately exploited for SARS-CoV-2, mostly due to intrinsically weak monovalent protein-glycan interactions. We hypothesize that polyvalent nano-lectins with flexibly linked carbohydrate recognition domains (CRDs) can adjust their relative positions and bind multivalently to S protein glycans, potentially exerting potent antiviral activity. Herein, we displayed the CRDs of DC-SIGN, a dendritic cell lectin known to bind to diverse viruses, polyvalently onto 13 nm gold nanoparticles (named G13-CRD). G13-CRD bound strongly and specifically to target glycan-coated quantum dots with sub-nM Kd. Moreover, G13-CRD neutralized particles pseudotyped with the S proteins of Wuhan Hu-1, B.1, Delta variant and Omicron subvariant BA.1 with low nM EC50. In contrast, natural tetrameric DC-SIGN and its G13 conjugate were ineffective. Further, G13-CRD potently inhibited authentic SARS-CoV-2 B.1 and BA.1, with <10 pM and <10 nM EC50, respectively. These results identify G13-CRD as the 1st polyvalent nano-lectin with broad activity against SARS-CoV-2 variants that merits further exploration as a novel approach to antiviral therapy.
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Affiliation(s)
- Darshita Budhadev
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - James Hooper
- School
of Food Science & Nutrition and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Cheila Rocha
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Faculty
of Biology and Psychology, Georg-August-University
Göttingen, 37073 Göttingen, Germany
| | - Inga Nehlmeier
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Amy Madeleine Kempf
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Faculty
of Biology and Psychology, Georg-August-University
Göttingen, 37073 Göttingen, Germany
| | - Markus Hoffmann
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Faculty
of Biology and Psychology, Georg-August-University
Göttingen, 37073 Göttingen, Germany
| | - Nadine Krüger
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Dejian Zhou
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Stefan Pöhlmann
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Faculty
of Biology and Psychology, Georg-August-University
Göttingen, 37073 Göttingen, Germany
| | - Yuan Guo
- School
of Food Science & Nutrition and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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Hooper J, Budhadev D, Fernandez Ainaga DL, Hondow N, Zhou D, Guo Y. Polyvalent Glycan Functionalized Quantum Nanorods as Mechanistic Probes for Shape-Selective Multivalent Lectin-Glycan Recognition. ACS APPLIED NANO MATERIALS 2023; 6:4201-4213. [PMID: 37006911 PMCID: PMC10043877 DOI: 10.1021/acsanm.2c05247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/24/2023] [Indexed: 06/19/2023]
Abstract
Multivalent lectin-glycan interactions (MLGIs) are widespread in biology and hold the key to many therapeutic applications. However, the underlying structural and biophysical mechanisms for many MLGIs remain poorly understood, limiting our ability to design glycoconjugates to potently target specific MLGIs for therapeutic intervention. Glycosylated nanoparticles have emerged as a powerful biophysical probe for MLGIs, although how nanoparticle shape affects the MLGI molecular mechanisms remains largely unexplored. Herein, we have prepared fluorescent quantum nanorods (QRs), densely coated with α-1,2-manno-biose ligands (QR-DiMan), as multifunctional probes to investigate how scaffold geometry affects the MLGIs of a pair of closely related, tetrameric viral receptors, DC-SIGN and DC-SIGNR. We have previously shown that a DiMan-capped spherical quantum dot (QD-DiMan) gives weak cross-linking interactions with DC-SIGNR but strong simultaneous binding with DC-SIGN. Against the elongated QR-DiMan, DC-SIGN retains similarly strong simultaneous binding of all four binding sites with a single QR-DiMan (apparent K d ≈ 0.5 nM, ∼1.8 million-fold stronger than the corresponding monovalent binding), while DC-SIGNR gives both weak cross-linking and strong individual binding interactions, resulting in a larger binding affinity enhancement than that with QD-DiMan. S/TEM analysis of QR-DiMan-lectin assemblies reveals that DC-SIGNR's different binding modes arise from the different nanosurface curvatures of the QR scaffold. The glycan display at the spherical ends presents too high a steric barrier for DC-SIGNR to bind with all four binding sites; thus, it cross-links between two QR-DiMan to maximize binding multivalency, whereas the more planar character of the cylindrical center allows the glycans to bridge all binding sites in DC-SIGNR. This work thus establishes glycosylated QRs as a powerful biophysical probe for MLGIs not only to provide quantitative binding affinities and binding modes but also to demonstrate the specificity of multivalent lectins in discriminating different glycan displays in solution, dictated by the scaffold curvature.
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Affiliation(s)
- James Hooper
- School
of Food Science and Nutrition and Astbury Centre for Structural Molecular
Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Darshita Budhadev
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | | | - Nicole Hondow
- School
of Chemical and Process Engineering, University
of Leeds, Leeds LS2 9JT, United
Kingdom
| | - Dejian Zhou
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yuan Guo
- School
of Food Science and Nutrition and Astbury Centre for Structural Molecular
Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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Martínez-Bailén M, Rojo J, Ramos-Soriano J. Multivalent glycosystems for human lectins. Chem Soc Rev 2023; 52:536-572. [PMID: 36545903 DOI: 10.1039/d2cs00736c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human lectins are involved in a wide variety of biological processes, both physiological and pathological, which have attracted the interest of the scientific community working in the glycoscience field. Multivalent glycosystems have been employed as useful tools to understand carbohydrate-lectin binding processes as well as for biomedical applications. The review shows the different scaffolds designed for a multivalent presentation of sugars and their corresponding binding studies to lectins and in some cases, their biological activities. We summarise this research by organizing based on lectin types to highlight the progression in this active field. The paper provides an overall picture of how these contributions have furnished relevant information on this topic to help in understanding and participate in these carbohydrate-lectin interactions.
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Affiliation(s)
- Macarena Martínez-Bailén
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), CSIC - Universidad de Sevilla, Av. Américo Vespucio 49, Seville 41092, Spain.
| | - Javier Rojo
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), CSIC - Universidad de Sevilla, Av. Américo Vespucio 49, Seville 41092, Spain.
| | - Javier Ramos-Soriano
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), CSIC - Universidad de Sevilla, Av. Américo Vespucio 49, Seville 41092, Spain.
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