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Zhang H, Modenutti C, Nekkanti YPK, Denis M, Bermejo IA, Lefèbre J, Che K, Kim D, Kagelmacher M, Kurzbach D, Nazaré M, Rademacher C. Identification of the Allosteric Binding Site for Thiazolopyrimidine on the C-Type Lectin Langerin. ACS Chem Biol 2022; 17:2728-2733. [PMID: 36153965 PMCID: PMC9594047 DOI: 10.1021/acschembio.2c00626] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Langerin is a mammalian C-type lectin expressed on Langerhans cells in the skin. As an innate immune cell receptor, Langerin is involved in coordinating innate and adaptive immune responses against various incoming threats. We have previously reported a series of thiazolopyrimidines as murine Langerin ligands. Prompted by the observation that its human homologue exhibits different binding specificities for these small molecules, we report here our investigations to define their exact binding site. By using structural comparison and molecular dynamics simulations, we showed that the nonconserved short loops have a high degree of conformational flexibility between the human and murine homologues. Sequence analysis and mutational studies indicated that a pair of residues are essential for the recognition of the thiazolopyrimidines. Taking solvent paramagnetic relaxation enhancement NMR studies together with a series of peptides occupying the same site, we could define the cleft between the short and long loops as the allosteric binding site for these aromatic heterocycles.
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Affiliation(s)
- Hengxi Zhang
- Biomolecular
Systems, 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,Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria,Vienna
Doctoral School of Pharmaceutical, Nutritional and Sport Sciences
(PhaNuSpo), University of Vienna, Universitätsring 1, 1010 Vienna, Austria
| | - Carlos Modenutti
- Biomolecular
Systems, Max Planck Institute of Colloids
and Interfaces, Am Mühlenberg
1 14424 Potsdam, Germany,Departamento
de Química Biológica, Facultad
de Ciencias Exactas y Naturales, C1428EHA Buenos Aires, Argentina,Instituto
de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, C1428EHA Buenos
Aires, Argentina
| | - Yelha Phani Kumar Nekkanti
- Leibniz
Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany,Berlin
Institute of Health (BIH), Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Maxime Denis
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Iris A. Bermejo
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Jonathan Lefèbre
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria,Vienna
Doctoral School of Pharmaceutical, Nutritional and Sport Sciences
(PhaNuSpo), University of Vienna, Universitätsring 1, 1010 Vienna, Austria
| | - Kateryna Che
- Faculty
of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria,Doctoral
School in Chemistry (DoSChem), University
of Vienna, Währingerstr. 42, 1090 Vienna, Austria
| | - Dongyoon Kim
- Biomolecular
Systems, Max Planck Institute of Colloids
and Interfaces, Am Mühlenberg
1 14424 Potsdam, Germany,Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Marten Kagelmacher
- Biomolecular
Systems, 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
| | - Dennis Kurzbach
- Faculty
of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
| | - Marc Nazaré
- Leibniz
Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany,Berlin
Institute of Health (BIH), Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Christoph Rademacher
- Biomolecular
Systems, 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,Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria,
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Hardin NZ, Kocman V, Di Mauro GM, Ravula T, Ramamoorthy A. Metal-Chelated Polymer Nanodiscs for NMR Studies. Angew Chem Int Ed Engl 2019; 58:17246-17250. [PMID: 31529579 PMCID: PMC6861636 DOI: 10.1002/anie.201910118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/11/2019] [Indexed: 01/20/2023]
Abstract
Paramagnetic relaxation enhancement (PRE) is commonly used to speed up spin lattice relaxation time (T1 ) for rapid data acquisition in NMR structural studies. Consequently, there is significant interest in novel paramagnetic labels for enhanced NMR studies on biomolecules. Herein, we report the synthesis and characterization of a modified poly(styrene-co-maleic acid) polymer which forms nanodiscs while showing the ability to chelate metal ions. Cu2+ -chelated nanodiscs are demonstrated to reduce the T1 of protons for both polymer and lipid-nanodisc components. The chelated nanodiscs also decrease the proton T1 values for a water-soluble DNA G-quadruplex. These results suggest that polymer nanodiscs functionalized with paramagnetic tags can be used to speed-up data acquisition from lipid bilayer samples and also to provide structural information from water-soluble biomolecules.
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Affiliation(s)
- Nathaniel Z Hardin
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Vojč Kocman
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Giacomo M Di Mauro
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Thirupathi Ravula
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
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Nepravishta R, Walpole S, Tailford L, Juge N, Angulo J. Deriving Ligand Orientation in Weak Protein-Ligand Complexes by DEEP-STD NMR Spectroscopy in the Absence of Protein Chemical-Shift Assignment. Chembiochem 2018; 20:340-344. [PMID: 30379391 PMCID: PMC6468252 DOI: 10.1002/cbic.201800568] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Indexed: 01/07/2023]
Abstract
Differential epitope mapping saturation transfer difference (DEEP‐STD) NMR spectroscopy is a recently developed powerful approach for elucidating the structure and pharmacophore of weak protein–ligand interactions, as it reports key information on the orientation of the ligand and the architecture of the binding pocket.1 The method relies on selective saturation of protein residues in the binding site and the generation of a differential epitope map by observing the ligand, which depicts the nature of the protein residues making contact with the ligand in the bound state. Selective saturation requires knowledge of the chemical‐shift assignment of the protein residues, which can be obtained either experimentally by NMR spectroscopy or predicted from 3D structures. Herein, we propose a simple experimental procedure to expand the DEEP‐STD NMR methodology to protein–ligand cases in which the spectral assignment of the protein is not available. This is achieved by experimentally identifying the chemical shifts of the residues present in binding hot‐spots on the surface of the receptor protein by using 2D NMR experiments combined with a paramagnetic probe.
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Affiliation(s)
- Ridvan Nepravishta
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Samuel Walpole
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Louise Tailford
- The Gut Microbes and Health Institute Strategic Program, Quadram Institute of Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - Nathalie Juge
- The Gut Microbes and Health Institute Strategic Program, Quadram Institute of Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
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