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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.
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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
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Le Roch M, Renault J, Argouarch G, Lenci E, Trabocchi A, Roisnel T, Gouault N, Lalli C. Synthesis and Chemoinformatic Analysis of Fluorinated Piperidines as 3D Fragments for Fragment-Based Drug Discovery. J Org Chem 2024; 89:4932-4946. [PMID: 38451837 DOI: 10.1021/acs.joc.4c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The concise synthesis of a small library of fluorinated piperidines from readily available dihydropyridinone derivatives has been described. The effect of the fluorination on different positions has then been evaluated by chemoinformatic tools. In particular, the compounds' pKa's have been calculated, revealing that the fluorine atoms notably lowered their basicity, which is correlated to the affinity for hERG channels resulting in cardiac toxicity. The "lead-likeness" and three-dimensionality have also been evaluated to assess their ability as useful fragments for drug design. A random screening on a panel of representative proteolytic enzymes was then carried out and revealed that one scaffold is recognized by the catalytic pocket of 3CLPro (main protease of SARS-CoV-2 coronavirus).
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Affiliation(s)
- Myriam Le Roch
- Univ Rennes, CNRS, ISCR-UMR 6226, Rennes F-35000, France
| | | | | | - Elena Lenci
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, Sesto Fiorentino, Florence 50019, Italy
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, Sesto Fiorentino, Florence 50019, Italy
| | - Thierry Roisnel
- Univ Rennes, Centre de Diffractométrie X (CDIFX), ISCR-UMR 6226, Rennes F-35000, France
| | | | - Claudia Lalli
- Univ Rennes, CNRS, ISCR-UMR 6226, Rennes F-35000, France
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3
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Howe PWA. Recent developments in the use of fluorine NMR in synthesis and characterisation. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:1-9. [PMID: 32883447 DOI: 10.1016/j.pnmrs.2020.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 06/11/2023]
Abstract
A review of developments in fluorine NMR of relevance to synthesis, characterisation and industrial applications of small organic molecules. Developments considered include those in spectrometer technology, computational methods and pulse sequences. The review of 80 references outlines applications in areas of identification, quantitation, mixture analysis, reaction monitoring, environmental studies and fragment-based drug design.
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Affiliation(s)
- Peter W A Howe
- Syngenta, Jealott's Hill Research Centre, Bracknell, Berkshire RG42 6EY, UK.
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4
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Substituted 1-methyl-4-phenylpyrrolidin-2-ones – Fragment-based design of N-methylpyrrolidone-derived bromodomain inhibitors. Eur J Med Chem 2020; 191:112120. [DOI: 10.1016/j.ejmech.2020.112120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/16/2020] [Accepted: 02/03/2020] [Indexed: 01/12/2023]
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5
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Troelsen NS, Shanina E, Gonzalez-Romero D, Danková D, Jensen ISA, Śniady KJ, Nami F, Zhang H, Rademacher C, Cuenda A, Gotfredsen CH, Clausen MH. The 3F Library: Fluorinated Fsp 3 -Rich Fragments for Expeditious 19 F NMR Based Screening. Angew Chem Int Ed Engl 2019; 59:2204-2210. [PMID: 31724281 DOI: 10.1002/anie.201913125] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/11/2019] [Indexed: 11/08/2022]
Abstract
Fragment-based drug discovery (FBDD) is a popular method in academia and the pharmaceutical industry for the discovery of early lead candidates. Despite its wide-spread use, the approach still suffers from laborious screening workflows and a limited diversity in the fragments applied. Presented here is the design, synthesis, and biological evaluation of the first fragment library specifically tailored to tackle both these challenges. The 3F library of 115 fluorinated, Fsp3 -rich fragments is shape diverse and natural-product-like with desirable physicochemical properties. The library is perfectly suited for rapid and efficient screening by NMR spectroscopy in a two-stage workflow of 19 F NMR and subsequent 1 H NMR methods. Hits against four diverse protein targets are widely distributed among the fragment scaffolds in the 3F library and a 67 % validation rate was achieved using secondary assays. This collection is the first synthetic fragment library tailor-made for 19 F NMR screening and the results demonstrate that the approach should find broad application in the FBDD community.
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Affiliation(s)
- Nikolaj S Troelsen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Elena Shanina
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424, Potsdam, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Diego Gonzalez-Romero
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus UAM, 28049, Madrid, Spain
| | - Daniela Danková
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Ida S A Jensen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Katarzyna J Śniady
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Faranak Nami
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Hengxi Zhang
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424, Potsdam, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Christoph Rademacher
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424, Potsdam, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Ana Cuenda
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus UAM, 28049, Madrid, Spain
| | - Charlotte H Gotfredsen
- NMR Center⋅DTU, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Mads H Clausen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
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6
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Troelsen NS, Shanina E, Gonzalez‐Romero D, Danková D, Jensen ISA, Śniady KJ, Nami F, Zhang H, Rademacher C, Cuenda A, Gotfredsen CH, Clausen MH. The 3F Library: Fluorinated Fsp
3
‐Rich Fragments for Expeditious
19
F NMR Based Screening. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201913125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nikolaj S. Troelsen
- Center for Nanomedicine and TheranosticsDepartment of ChemistryTechnical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Elena Shanina
- Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14424 Potsdam Germany
- Department of Biology, Chemistry and PharmacyFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | - Diego Gonzalez‐Romero
- Department of Immunology and OncologyCentro Nacional de Biotecnología/CSIC Campus UAM 28049 Madrid Spain
| | - Daniela Danková
- Center for Nanomedicine and TheranosticsDepartment of ChemistryTechnical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Ida S. A. Jensen
- Center for Nanomedicine and TheranosticsDepartment of ChemistryTechnical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Katarzyna J. Śniady
- Center for Nanomedicine and TheranosticsDepartment of ChemistryTechnical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Faranak Nami
- Center for Nanomedicine and TheranosticsDepartment of ChemistryTechnical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Hengxi Zhang
- Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14424 Potsdam Germany
- Department of Biology, Chemistry and PharmacyFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | - Christoph Rademacher
- Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14424 Potsdam Germany
- Department of Biology, Chemistry and PharmacyFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | - Ana Cuenda
- Department of Immunology and OncologyCentro Nacional de Biotecnología/CSIC Campus UAM 28049 Madrid Spain
| | - Charlotte H. Gotfredsen
- NMR Center⋅DTUDepartment of ChemistryTechnical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Mads H. Clausen
- Center for Nanomedicine and TheranosticsDepartment of ChemistryTechnical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
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7
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Dalvit C, Vulpetti A. Ligand-Based Fluorine NMR Screening: Principles and Applications in Drug Discovery Projects. J Med Chem 2018; 62:2218-2244. [DOI: 10.1021/acs.jmedchem.8b01210] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Anna Vulpetti
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
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8
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Novel approaches to probe the binding of recoverin to membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:679-691. [DOI: 10.1007/s00249-018-1304-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/05/2018] [Accepted: 04/13/2018] [Indexed: 02/08/2023]
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