1
|
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
|
2
|
Corredor M, Carbajo D, Domingo C, Pérez Y, Bujons J, Messeguer A, Alfonso I. Dynamic Covalent Identification of an Efficient Heparin Ligand. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Miriam Corredor
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Daniel Carbajo
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Cecilia Domingo
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Yolanda Pérez
- NMR Facility, Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Jordi Bujons
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Angel Messeguer
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| |
Collapse
|
3
|
Corredor M, Carbajo D, Domingo C, Pérez Y, Bujons J, Messeguer A, Alfonso I. Dynamic Covalent Identification of an Efficient Heparin Ligand. Angew Chem Int Ed Engl 2018; 57:11973-11977. [DOI: 10.1002/anie.201806770] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Miriam Corredor
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Daniel Carbajo
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Cecilia Domingo
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Yolanda Pérez
- NMR Facility, Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Jordi Bujons
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Angel Messeguer
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| |
Collapse
|
4
|
Franconetti A, Nuñez-Franco R, de Gonzalo G, Iglesias-Sigüenza J, Álvarez E, Cabrera-Escribano F. Fingerprinting the Nature of Anions in Pyrylium Complexes: Dual Binding Mode for Anion-π Interactions. Chemphyschem 2018; 19:327-334. [PMID: 29215788 DOI: 10.1002/cphc.201700981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/06/2017] [Indexed: 12/13/2022]
Abstract
The interplay between noncovalent interactions that involve oxygenated heteroaromatic rings have been studied for the first time in this work. In particular, we report an advance in knowledge-based anion-π interactions together with (C-H)+ ⋅⋅⋅anion contacts. To understand how the anion modulates these interactions, the synthesis of pyrylium salts with a variety of anions was performed by using an anionic metathesis methodology. The synthesized pyrylium complexes were classified in series, for example, anions derived from halogens, from oxoacids, from p-block elements, and from transition metals. Crystallographic data, DFT calculations, and NMR spectroscopy methods provided access to an overall insight into the noncovalent behavior of the anion in this kind of system. Based on the DFT calculations and 1 H NMR spectroscopy, pyrylium protons can be used as chemical tags to detect noncovalent interactions in this type of compound.
Collapse
Affiliation(s)
- Antonio Franconetti
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Reyes Nuñez-Franco
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, C/ Profesor García González 1, 41012, Sevilla, Spain
| | - Gonzalo de Gonzalo
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, C/ Profesor García González 1, 41012, Sevilla, Spain
| | - Javier Iglesias-Sigüenza
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, C/ Profesor García González 1, 41012, Sevilla, Spain
| | - Eleuterio Álvarez
- Instituto de Investigaciones Químicas, C.S.I.C., Universidad de Sevilla, Av. Américo Vespucio 49, Isla de la Cartuja, 41092, Sevilla, Spain
| | - Francisca Cabrera-Escribano
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, C/ Profesor García González 1, 41012, Sevilla, Spain
| |
Collapse
|
5
|
Franconetti A, Jiménez-Barbero J, Cabrera-Escribano F. The Stabilization of Glycosyl Cations Through Cooperative Noncovalent Interactions: A Theoretical Perspective. Chemphyschem 2018; 19:659-665. [DOI: 10.1002/cphc.201700988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/25/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Antonio Franconetti
- Department of Organic Chemistry; Faculty of Chemistry; University of Seville; C/ Profesor García González 1 41012 Sevilla Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition and Host-Pathogen Interactions; CIC bioGUNE; Bizkaia Technology Park, Building 801 A 48170 Derio Spain
- Basque Foundation for Science; Maria Diaz de Haro 13 48009 Bilbao Spain
- Department of Organic Chemistry II; Faculty of Science and Technology; University of the BasqueCountry; 48940 Leioa Bizkaia Spain
| | - Francisca Cabrera-Escribano
- Department of Organic Chemistry; Faculty of Chemistry; University of Seville; C/ Profesor García González 1 41012 Sevilla Spain
| |
Collapse
|
6
|
Unione L, Alcalá M, Echeverria B, Serna S, Ardá A, Franconetti A, Cañada FJ, Diercks T, Reichardt N, Jiménez-Barbero J. Fluoroacetamide Moieties as NMR Spectroscopy Probes for the Molecular Recognition of GlcNAc-Containing Sugars: Modulation of the CH-π Stacking Interactions by Different Fluorination Patterns. Chemistry 2017; 23:3957-3965. [PMID: 28124793 PMCID: PMC5484281 DOI: 10.1002/chem.201605573] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Indexed: 12/13/2022]
Abstract
We herein propose the use of fluoroacetamide and difluoroacetamide moieties as sensitive tags for the detection of sugar–protein interactions by simple 1H and/or 19F NMR spectroscopy methods. In this process, we have chosen the binding of N,N′‐diacetyl chitobiose, a ubiquitous disaccharide fragment in glycoproteins, by wheat‐germ agglutinin (WGA), a model lectin. By using saturation‐transfer difference (STD)‐NMR spectroscopy, we experimentally demonstrate that, under solution conditions, the molecule that contained the CHF2CONH‐ moiety is the stronger aromatic binder, followed by the analogue with the CH2FCONH‐ group and the natural molecule (with the CH3CONH‐ fragment). In contrast, the molecule with the CF3CONH‐ isoster displayed the weakest intermolecular interaction (one order of magnitude weaker). Because sugar–aromatic CH–π interactions are at the origin of these observations, these results further contribute to the characterization and exploration of these forces and offer an opportunity to use them to unravel complex recognition processes.
Collapse
Affiliation(s)
- Luca Unione
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 801 A, 48170, Derio, Spain
| | - Maria Alcalá
- Glycotechnology Laboratory, CICbiomaGUNE, Paseo Miramón, 20014, Donostia-San Sebastian, Spain
| | - Begoña Echeverria
- Glycotechnology Laboratory, CICbiomaGUNE, Paseo Miramón, 20014, Donostia-San Sebastian, Spain
| | - Sonia Serna
- Glycotechnology Laboratory, CICbiomaGUNE, Paseo Miramón, 20014, Donostia-San Sebastian, Spain
| | - Ana Ardá
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 801 A, 48170, Derio, Spain
| | - Antonio Franconetti
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, Profesor García González 1, 41012, Sevilla, Spain
| | - F Javier Cañada
- Department of Chemical and Physical Biology, CIB-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Tammo Diercks
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 801 A, 48170, Derio, Spain
| | - Niels Reichardt
- Glycotechnology Laboratory, CICbiomaGUNE, Paseo Miramón, 20014, Donostia-San Sebastian, Spain.,CIBER-BBN, Paseo Miramón, 20009, Donostia-San Sebastián, Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 801 A, 48170, Derio, Spain.,Basque Foundation for Science, Maria Diaz de Haro 13, 48009, Bilbao, Spain.,Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, 48940, Leioa, Bizkaia, Spain
| |
Collapse
|
7
|
Ye H, Hai Y, Ren Y, You L. Versatile Dynamic Covalent Assemblies for Probing π-Stacking and Chirality Induction from Homotopic Faces. Chemistry 2017; 23:3804-3809. [DOI: 10.1002/chem.201606040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Hebo Ye
- State Key Laboratory of Structural Chemistry; Fujian Institute of Research on the Structure of Matter; Chinese Academy of Sciences; Fuzhou 350002 P.R. China
| | - Yu Hai
- State Key Laboratory of Structural Chemistry; Fujian Institute of Research on the Structure of Matter; Chinese Academy of Sciences; Fuzhou 350002 P.R. China
- College of Material Science and Engineering; Fujian Normal University; Fuzhou 350007 P.R. China
| | - Yulong Ren
- State Key Laboratory of Structural Chemistry; Fujian Institute of Research on the Structure of Matter; Chinese Academy of Sciences; Fuzhou 350002 P.R. China
| | - Lei You
- State Key Laboratory of Structural Chemistry; Fujian Institute of Research on the Structure of Matter; Chinese Academy of Sciences; Fuzhou 350002 P.R. China
| |
Collapse
|
8
|
Kennedy CR, Lin S, Jacobsen EN. The Cation-π Interaction in Small-Molecule Catalysis. Angew Chem Int Ed Engl 2016; 55:12596-624. [PMID: 27329991 PMCID: PMC5096794 DOI: 10.1002/anie.201600547] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Indexed: 11/11/2022]
Abstract
Catalysis by small molecules (≤1000 Da, 10(-9) m) that are capable of binding and activating substrates through attractive, noncovalent interactions has emerged as an important approach in organic and organometallic chemistry. While the canonical noncovalent interactions, including hydrogen bonding, ion pairing, and π stacking, have become mainstays of catalyst design, the cation-π interaction has been comparatively underutilized in this context since its discovery in the 1980s. However, like a hydrogen bond, the cation-π interaction exhibits a typical binding affinity of several kcal mol(-1) with substantial directionality. These properties render it attractive as a design element for the development of small-molecule catalysts, and in recent years, the catalysis community has begun to take advantage of these features, drawing inspiration from pioneering research in molecular recognition and structural biology. This Review surveys the burgeoning application of the cation-π interaction in catalysis.
Collapse
Affiliation(s)
- C Rose Kennedy
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA, 02138, USA
| | - Song Lin
- Department of Chemistry, University of California, Berkeley, 535 Latimer Hall, Berkeley, CA, 94720, USA
| | - Eric N Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA, 02138, USA.
| |
Collapse
|
9
|
Kennedy CR, Lin S, Jacobsen EN. Die Kation-π-Wechselwirkung in der Katalyse mit niedermolekularen Verbindungen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600547] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- C. Rose Kennedy
- Department of Chemistry and Chemical Biology; Harvard University; 12 Oxford St Cambridge MA 02138 USA
| | - Song Lin
- Department of Chemistry; University of California, Berkeley; 535 Latimer Hall Berkeley CA 94720 USA
| | - Eric N. Jacobsen
- Department of Chemistry and Chemical Biology; Harvard University; 12 Oxford St Cambridge MA 02138 USA
| |
Collapse
|