1
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McCarthy WJ, Thomas SE, Olaleye T, Boland JA, Floto RA, Williams G, Blundell TL, Coyne AG, Abell C. A Fragment-Based Competitive 19F LB-NMR Platform For Hotspot-Directed Ligand Profiling. Angew Chem Int Ed Engl 2024; 63:e202406846. [PMID: 38896426 DOI: 10.1002/anie.202406846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/19/2024] [Accepted: 06/19/2024] [Indexed: 06/21/2024]
Abstract
Ligand binding hotspots are regions of protein surfaces that form particularly favourable interactions with small molecule pharmacophores. Targeting interactions with these hotspots maximises the efficiency of ligand binding. Existing methods are capable of identifying hotspots but often lack assays to quantify ligand binding and direct elaboration at these sites. Herein, we describe a fragment-based competitive 19F Ligand Based NMR (LB-NMR) screening platform that enables routine, quantitative ligand profiling focused at ligand-binding hotspots. As a proof of concept, the method was applied to 4'-phosphopantetheine adenylyltransferase (PPAT) from Mycobacterium abscessus (Mabs). X-ray crystallographic characterisation of the hits from a 960-member fragment screen identified three ligand-binding hotspots across the PPAT active site. From the fragment hits a collection of 19F reporter candidates were designed and synthesised. By rigorous prioritisation and use of optimisation workflows, a single 19F reporter molecule was generated for each hotspot. Profiling the binding of a set of structurally characterised ligands by competitive 19F LB-NMR with this suite of 19F reporters recapitulated the binding affinity and site ID assignments made by ITC and X-ray crystallography. This quantitative mapping of ligand binding events at hotspot level resolution establishes the utility of the fragment-based competitive 19F LB-NMR screening platform for hotspot-directed ligand profiling.
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Affiliation(s)
- William J McCarthy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
- Present Address: Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, UK, NW1 1AT
| | - Sherine E Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK, CB2 1GA
- Present Address: Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK, CB2 1PD
| | - Tayo Olaleye
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
| | - Jennifer A Boland
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
| | - R Andres Floto
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK, CB2 0QH
- VPD Heart Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, UK, CB2 0BB
| | - Glyn Williams
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK, CB2 1GA
- VPD Heart Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, UK, CB2 0BB
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
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2
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Greenberg HC, Majumdar A, Cheema EK, Kozyryev A, Rokita SE. 19F NMR Reveals the Dynamics of Substrate Binding and Lid Closure for Iodotyrosine Deiodinase as a Complement to Steady-State Kinetics and Crystallography. Biochemistry 2024; 63:2225-2232. [PMID: 39137127 PMCID: PMC11371475 DOI: 10.1021/acs.biochem.4c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Active site lids are common features of enzymes and typically undergo conformational changes upon substrate binding to promote catalysis. Iodotyrosine deiodinase is no exception and contains a lid segment in all of its homologues from human to bacteria. The solution-state dynamics of the lid have now been characterized using 19F NMR spectroscopy with a CF3-labeled enzyme and CF3O-labeled ligands. From two-dimensional 19F-19F NMR exchange spectroscopy, interconversion rates between the free and bound states of a CF3O-substituted tyrosine (45 ± 10 s-1) and the protein label (40 ± 3 s-1) are very similar and suggest a correlation between ligand binding and conformational reorganization of the lid. Both occur at rates that are ∼100-fold faster than turnover, and therefore these steps do not limit catalysis. A simple CF3O-labeled phenol also binds to the active site and induces a conformational change in the lid segment that was not previously detectable by crystallography. Exchange rates of the ligand (130 ± 20 s-1) and protein (98 ± 8 s-1) in this example are faster than those above but remain self-consistent to affirm a correlation between ordering of the lid and binding of the ligand. Both ligands also protect the protein from limited proteolysis, as expected from their ability to stabilize a compact lid structure. However, the minimal turnover of simple phenol substrates indicates that such stabilization may be necessary but is not sufficient for efficient catalysis.
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Affiliation(s)
- Harrison C Greenberg
- Chemistry-Biology Interface Graduate Training Program, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Ekroop Kaur Cheema
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Anton Kozyryev
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Steven E Rokita
- Chemistry-Biology Interface Graduate Training Program, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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3
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Brindani N, Vuong LM, La Serra MA, Salvador N, Menichetti A, Acquistapace IM, Ortega JA, Veronesi M, Bertozzi SM, Summa M, Girotto S, Bertorelli R, Armirotti A, Ganesan AK, De Vivo M. Discovery of CDC42 Inhibitors with a Favorable Pharmacokinetic Profile and Anticancer In Vivo Efficacy. J Med Chem 2024; 67:10401-10424. [PMID: 38866385 PMCID: PMC11215724 DOI: 10.1021/acs.jmedchem.4c00855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024]
Abstract
We previously reported trisubstituted pyrimidine lead compounds, namely, ARN22089 and ARN25062, which block the interaction between CDC42 with its specific downstream effector, a PAK protein. This interaction is crucial for the progression of multiple tumor types. Such inhibitors showed anticancer efficacy in vivo. Here, we describe a second class of CDC42 inhibitors with favorable drug-like properties. Out of the 25 compounds here reported, compound 15 (ARN25499) stands out as the best lead compound with an improved pharmacokinetic profile, increased bioavailability, and efficacy in an in vivo PDX tumor mouse model. Our results indicate that these CDC42 inhibitors represent a promising chemical class toward the discovery of anticancer drugs, with ARN25499 as an additional lead candidate for preclinical development.
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Affiliation(s)
- Nicoletta Brindani
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Linh M. Vuong
- Department
of Dermatology, University of California, Irvine, California 92697, United States
| | - Maria Antonietta La Serra
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Noel Salvador
- Department
of Dermatology, University of California, Irvine, California 92697, United States
| | - Andrea Menichetti
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Isabella Maria Acquistapace
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Jose Antonio Ortega
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Marina Veronesi
- Structural
Biophysics Facility, Istituto Italiano di
Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Sine Mandrup Bertozzi
- Analytical
Chemistry Facility, Istituto Italiano di
Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Maria Summa
- Translational
Pharmacology Facility, Istituto Italiano
di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Stefania Girotto
- Structural
Biophysics Facility, Istituto Italiano di
Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Rosalia Bertorelli
- Translational
Pharmacology Facility, Istituto Italiano
di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Andrea Armirotti
- Analytical
Chemistry Facility, Istituto Italiano di
Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Anand K. Ganesan
- Department
of Dermatology, University of California, Irvine, California 92697, United States
| | - Marco De Vivo
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
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4
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Sinnaeve D, Ben Bouzayene A, Ottoy E, Hofman GJ, Erdmann E, Linclau B, Kuprov I, Martins J, Torbeev V, Kieffer B. Fluorine NMR study of proline-rich sequences using fluoroprolines. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:795-813. [PMID: 37905223 PMCID: PMC10539733 DOI: 10.5194/mr-2-795-2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/28/2021] [Indexed: 11/01/2023]
Abstract
Proline homopolymer motifs are found in many proteins; their peculiar conformational and dynamic properties are often directly involved in those proteins' functions. However, the dynamics of proline homopolymers is hard to study by NMR due to a lack of amide protons and small chemical shift dispersion. Exploiting the spectroscopic properties of fluorinated prolines opens interesting perspectives to address these issues. Fluorinated prolines are already widely used in protein structure engineering - they introduce conformational and dynamical biases - but their use as 19 F NMR reporters of proline conformation has not yet been explored. In this work, we look at model peptides where Cγ -fluorinated prolines with opposite configurations of the chiral Cγ centre have been introduced at two positions in distinct polyproline segments. By looking at the effects of swapping these (4R )-fluoroproline and (4S )-fluoroproline within the polyproline segments, we were able to separate the intrinsic conformational properties of the polyproline sequence from the conformational alterations instilled by fluorination. We assess the fluoroproline 19 F relaxation properties, and we exploit the latter in elucidating binding kinetics to the SH3 (Src homology 3) domain.
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Affiliation(s)
- Davy Sinnaeve
- Univ. Lille, Inserm, Institut Pasteur de Lille, CHU Lille, U1167 – Risk Factors and Molecular Determinants of
Aging-Related Diseases (RID-AGE), 59000 Lille, France
- CNRS, ERL9002 – Integrative Structural Biology, 59000 Lille, France
| | - Abir Ben Bouzayene
- Department of Integrative Structural Biology, IGBMC, University of Strasbourg, Inserm U1258, CNRS UMR 7104, 1 rue Laurent Fries, 67404
Illkirch, France
| | - Emile Ottoy
- Department of Organic and Macromolecular Chemistry, Ghent University,
Campus Sterre, S4, Krijgslaan 281, 9000 Ghent, Belgium
| | - Gert-Jan Hofman
- Department of Organic and Macromolecular Chemistry, Ghent University,
Campus Sterre, S4, Krijgslaan 281, 9000 Ghent, Belgium
- School of Chemistry, University of Southampton, Southampton SO17 1BJ,
United Kingdom
| | - Eva Erdmann
- Department of Integrative Structural Biology, IGBMC, University of Strasbourg, Inserm U1258, CNRS UMR 7104, 1 rue Laurent Fries, 67404
Illkirch, France
| | - Bruno Linclau
- School of Chemistry, University of Southampton, Southampton SO17 1BJ,
United Kingdom
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton SO17 1BJ,
United Kingdom
| | - José C. Martins
- Department of Organic and Macromolecular Chemistry, Ghent University,
Campus Sterre, S4, Krijgslaan 281, 9000 Ghent, Belgium
| | - Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS),
International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg,
CNRS UMR 7006, 67000 Strasbourg, France
| | - Bruno Kieffer
- Department of Integrative Structural Biology, IGBMC, University of Strasbourg, Inserm U1258, CNRS UMR 7104, 1 rue Laurent Fries, 67404
Illkirch, France
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5
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Prosser KE, Kohlbrand AJ, Seo H, Kalaj M, Cohen SM. 19F-Tagged metal binding pharmacophores for NMR screening of metalloenzymes. Chem Commun (Camb) 2021; 57:4934-4937. [PMID: 33870988 PMCID: PMC8137660 DOI: 10.1039/d1cc01231b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study demonstrates the screening of a collection of twelve 19F-tagged metal-binding pharmacophores (MBPs) against the Zn(ii)-dependent metalloenzyme human carbonic anhydrase II (hCAII) by 19F NMR. The isomorphous replacement of Zn(ii) by Co(ii) in hCAII produces enhanced sensitivity and reveals the potential of 19F NMR-based techniques for metalloenzyme ligand discovery.
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Affiliation(s)
- Kathleen E Prosser
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Alysia J Kohlbrand
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Hyeonglim Seo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Mark Kalaj
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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6
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Martínez JD, Manzano AI, Calviño E, Diego AD, Rodriguez de Francisco B, Romanò C, Oscarson S, Millet O, Gabius HJ, Jiménez-Barbero J, Cañada FJ. Fluorinated Carbohydrates as Lectin Ligands: Simultaneous Screening of a Monosaccharide Library and Chemical Mapping by 19F NMR Spectroscopy. J Org Chem 2020; 85:16072-16081. [PMID: 33258593 PMCID: PMC7773211 DOI: 10.1021/acs.joc.0c01830] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Indexed: 02/06/2023]
Abstract
Molecular recognition of carbohydrates is a key step in essential biological processes. Carbohydrate receptors can distinguish monosaccharides even if they only differ in a single aspect of the orientation of the hydroxyl groups or harbor subtle chemical modifications. Hydroxyl-by-fluorine substitution has proven its merits for chemically mapping the importance of hydroxyl groups in carbohydrate-receptor interactions. 19F NMR spectroscopy could thus be adapted to allow contact mapping together with screening in compound mixtures. Using a library of fluorinated glucose (Glc), mannose (Man), and galactose (Gal) derived by systematically exchanging every hydroxyl group by a fluorine atom, we developed a strategy combining chemical mapping and 19F NMR T2 filtering-based screening. By testing this strategy on the proof-of-principle level with a library of 13 fluorinated monosaccharides to a set of three carbohydrate receptors of diverse origin, i.e. the human macrophage galactose-type lectin, a plant lectin, Pisum sativum agglutinin, and the bacterial Gal-/Glc-binding protein from Escherichia coli, it became possible to simultaneously define their monosaccharide selectivity and identify the essential hydroxyls for interaction.
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Affiliation(s)
- J. Daniel Martínez
- CIC
bioGUNE, Basque Research Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Ana I. Manzano
- Centro
de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Eva Calviño
- Centro
de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ana de Diego
- Centro
de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | - Cecilia Romanò
- Centre
for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stefan Oscarson
- Centre
for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Oscar Millet
- CIC
bioGUNE, Basque Research Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Hans-Joachim Gabius
- Institute
of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Basque Research Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48160 Derio, Spain
- Ikerbasque,
Basque Foundation for Science, 48009 Bilbao, Spain
- Department
of Organic Chemistry II, Faculty of Science and Technology, UPV-EHU, 48940 Leioa, Spain
| | - Francisco J. Cañada
- Centro
de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Centro
de Investigación Biomédica en Red-Enfermedades Respiratorias
(CIBERES), Avda Monforte
de Lemos 3-5, 28029 Madrid, Spain
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7
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Lingel A, Vulpetti A, Reinsperger T, Proudfoot A, Denay R, Frommlet A, Henry C, Hommel U, Gossert AD, Luy B, Frank AO. Comprehensive and High-Throughput Exploration of Chemical Space Using Broadband 19 F NMR-Based Screening. Angew Chem Int Ed Engl 2020; 59:14809-14817. [PMID: 32363632 DOI: 10.1002/anie.202002463] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/27/2020] [Indexed: 12/20/2022]
Abstract
Fragment-based lead discovery has become a fundamental approach to identify ligands that efficiently interact with disease-relevant targets. Among the numerous screening techniques, fluorine-detected NMR has gained popularity owing to its high sensitivity, robustness, and ease of use. To effectively explore chemical space, a universal NMR experiment, a rationally designed fragment library, and a sample composition optimized for a maximal number of compounds and minimal measurement time are required. Here, we introduce a comprehensive method that enabled the efficient assembly of a high-quality and diverse library containing nearly 4000 fragments and screening for target-specific binders within days. At the core of the approach is a novel broadband relaxation-edited NMR experiment that covers the entire chemical shift range of drug-like 19 F motifs in a single measurement. Our approach facilitates the identification of diverse binders and the fast ligandability assessment of new targets.
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Affiliation(s)
- Andreas Lingel
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA.,Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Anna Vulpetti
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Tony Reinsperger
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andrew Proudfoot
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Regis Denay
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Alexandra Frommlet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Christelle Henry
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Ulrich Hommel
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Alvar D Gossert
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andreas O Frank
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
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8
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Lingel A, Vulpetti A, Reinsperger T, Proudfoot A, Denay R, Frommlet A, Henry C, Hommel U, Gossert AD, Luy B, Frank AO. Comprehensive and High‐Throughput Exploration of Chemical Space Using Broadband
19
F NMR‐Based Screening. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Andreas Lingel
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Anna Vulpetti
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Tony Reinsperger
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance Karlsruhe Institute of Technology (KIT) 76131 Karlsruhe Germany
| | - Andrew Proudfoot
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
| | - Regis Denay
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Alexandra Frommlet
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
| | - Christelle Henry
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Ulrich Hommel
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Alvar D. Gossert
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance Karlsruhe Institute of Technology (KIT) 76131 Karlsruhe Germany
| | - Andreas O. Frank
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
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9
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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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10
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Coyle J, Walser R. Applied Biophysical Methods in Fragment-Based Drug Discovery. SLAS DISCOVERY 2020; 25:471-490. [PMID: 32345095 DOI: 10.1177/2472555220916168] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Fragment-based drug discovery (FBDD) has come of age in the last decade with the FDA approval of four fragment-derived drugs. Biophysical methods are at the heart of hit discovery and validation in FBDD campaigns. The three most commonly used methods, thermal shift, surface plasmon resonance, and nuclear magnetic resonance, can be daunting for the novice user. We aim here to provide the nonexpert user of these methods with a summary of problems and challenges that might be faced, but also highlight the potential gains that each method can contribute to an FBDD project. While our view on FBDD is slightly biased toward enabling structure-guided drug discovery, most of the points we address in this review are also valid for non-structure-focused FBDD.
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Affiliation(s)
- Joe Coyle
- Astex Pharmaceuticals, Cambridge, UK
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11
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Lu M, Ishima R, Polenova T, Gronenborn AM. 19F NMR relaxation studies of fluorosubstituted tryptophans. JOURNAL OF BIOMOLECULAR NMR 2019; 73:401-409. [PMID: 31435857 PMCID: PMC6878660 DOI: 10.1007/s10858-019-00268-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/05/2019] [Indexed: 05/19/2023]
Abstract
We present 19F longitudinal and transverse relaxation studies for four differently fluorosubstituted L-tryptophans, which carry single F atoms in the indole ring, both in the context of the free amino acid and when located in the cyclophilin A protein. For the free 4F-, 5F-, 6F-, 7F-L-Trp, satisfactory agreement between experimentally measured and calculated relaxation rates was obtained, suggesting that the parameters used for calculating the rates for the indole frame are sufficiently accurate. We also measured and calculated relaxation rates for four differently 19F-tryptophan labeled cyclophilin A proteins, transferring the parameters from the free amino acid to the protein-bound moiety. Our results suggest that 19F relaxation data of the large and rigid indole ring in Trp are only moderately affected by protein motions and provide critical reference points for evaluating fluorine NMR relaxation in the future, especially in fluorotryptophan labeled proteins.
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Affiliation(s)
- Manman Lu
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA
| | - Tatyana Polenova
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.
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12
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Valverde P, Delgado S, Martínez JD, Vendeville JB, Malassis J, Linclau B, Reichardt NC, Cañada FJ, Jiménez-Barbero J, Ardá A. Molecular Insights into DC-SIGN Binding to Self-Antigens: The Interaction with the Blood Group A/B Antigens. ACS Chem Biol 2019; 14:1660-1671. [PMID: 31283166 PMCID: PMC6646960 DOI: 10.1021/acschembio.9b00458] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
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The
dendritic cell-specific intracellular adhesion molecule-3-grabbing
nonintegrin (DC-SIGN) is an important receptor of the immune system.
Besides its role as pathogen recognition receptor (PRR), it also interacts
with endogenous glycoproteins through the specific recognition of
self-glycan epitopes, like LeX. However, this lectin represents
a paradigmatic case of glycan binding promiscuity, and it also has
been shown to recognize antigens with α1−α2 linked
fucose, such as the histo blood group antigens, with similar affinities
to LeX. Herein, we have studied the interaction in solution
between DC-SIGN and the blood group A and B antigens, to get insights
into the atomic details of such interaction. With a combination of
different NMR experiments, we demonstrate that the Fuc coordinates
the primary Ca2+ ion with a single binding mode through
3-OH and 4-OH. The terminal αGal/αGalNAc affords marginal
direct polar contacts with the protein, but provides a hydrophobic
hook in which V351 of the lectin perfectly fits. Moreover, we have
found that αGal, but not αGalNAc, is a weak binder itself
for DC-SIGN, which could endow an additional binding mode for the
blood group B antigen, but not for blood group A.
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Affiliation(s)
- Pablo Valverde
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Sandra Delgado
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - J. Daniel Martínez
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | | | - Julien Malassis
- School of Chemistry, University of Southampton Highfield, Southampton SO17 1BJ, United Kingdom
| | - Bruno Linclau
- School of Chemistry, University of Southampton Highfield, Southampton SO17 1BJ, United Kingdom
| | | | | | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Bizkaia, Spain
- Department of Organic Chemistry II Faculty of Science and Technology, University of the Basque Country, EHU-UPV, Leioa, Spain
| | - Ana Ardá
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
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13
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Martínez JD, Valverde P, Delgado S, Romanò C, Linclau B, Reichardt NC, Oscarson S, Ardá A, Jiménez-Barbero J, Cañada FJ. Unraveling Sugar Binding Modes to DC-SIGN by Employing Fluorinated Carbohydrates. Molecules 2019; 24:molecules24122337. [PMID: 31242623 PMCID: PMC6631030 DOI: 10.3390/molecules24122337] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/12/2019] [Accepted: 06/23/2019] [Indexed: 12/27/2022] Open
Abstract
A fluorine nuclear magnetic resonance (19F-NMR)-based method is employed to assess the binding preferences and interaction details of a library of synthetic fluorinated monosaccharides towards dendritic cell-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN), a lectin of biomedical interest, which is involved in different viral infections, including HIV and Ebola, and is able to recognize a variety of self- and non-self-glycans. The strategy employed allows not only screening of a mixture of compounds, but also obtaining valuable information on the specific sugar–protein interactions. The analysis of the data demonstrates that monosaccharides Fuc, Man, Glc, and Gal are able to bind DC-SIGN, although with decreasing affinity. Moreover, a new binding mode between Man moieties and DC-SIGN, which might have biological implications, is also detected for the first time. The combination of the 19F with standard proton saturation transfer difference (1H-STD-NMR) data, assisted by molecular dynamics (MD) simulations, permits us to successfully define this new binding epitope, where Man coordinates a Ca2+ ion of the lectin carbohydrate recognition domain (CRD) through the axial OH-2 and equatorial OH-3 groups, thus mimicking the Fuc/DC-SIGN binding architecture.
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Affiliation(s)
- J Daniel Martínez
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
| | - Pablo Valverde
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
| | - Sandra Delgado
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
| | - Cecilia Romanò
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
| | - Niels C Reichardt
- CIC biomaGUNE, Paseo Miramon 182, 20009 San Sebastián, Gipuzkoa, Spain.
- CIBER-BBN, Paseo Miramon 182, 20009 San Sebastián, Gipuzkoa, Spain.
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Ana Ardá
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Bizkaia, Spain.
- Department of Organic Chemistry II, Faculty of Science and Technology, EHU-UPV, 48160 Leioa, Spain.
| | - F Javier Cañada
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
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14
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Zawadzka-Kazimierczuk A, Somlyay M, Kaehlig H, Iakobson G, Beier P, Konrat R. 19F multiple-quantum coherence NMR spectroscopy for probing protein-ligand interactions. RSC Adv 2018; 8:40687-40692. [PMID: 35557931 PMCID: PMC9091488 DOI: 10.1039/c8ra09296f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/25/2019] [Accepted: 11/28/2018] [Indexed: 11/23/2022] Open
Abstract
A new 19F NMR method is presented which can be used to detect weak protein binding of small molecules with up to mM affinity. The method capitalizes on the synthetic availability of unique SF5 containing compounds and the generation of five-quantum coherences (5QC). Given the high sensitivity of 5QC relaxation to exchange events (i.e. reversible protein binding) fragments which bind to the target with weak affinity can be identified. The utility of the method in early stage drug discovery programs is demonstrated with applications to two model proteins, the neurotoxic NGAL and the prominent tumor target β-catenin.
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Affiliation(s)
- Anna Zawadzka-Kazimierczuk
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna Vienna Biocenter Campus 5 A-1030 Vienna Austria
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw Żwirki i Wigury 101 02-089 Warsaw Poland
| | - Mate Somlyay
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna Vienna Biocenter Campus 5 A-1030 Vienna Austria
| | - Hanspeter Kaehlig
- Institute of Organic Chemistry, University of Vienna Währinger Strasse 38 A-1090 Vienna Austria
| | - George Iakobson
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nam. 2 160 00 Prague Czech Republic
| | - Petr Beier
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nam. 2 160 00 Prague Czech Republic
| | - Robert Konrat
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna Vienna Biocenter Campus 5 A-1030 Vienna Austria
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15
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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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16
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Dalvit C, Knapp S. 19 F NMR isotropic chemical shift for efficient screening of fluorinated fragments which are racemates and/or display multiple conformers. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:1091-1095. [PMID: 28762528 DOI: 10.1002/mrc.4640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/12/2017] [Accepted: 07/29/2017] [Indexed: 06/07/2023]
Abstract
Fluorine ligand-based NMR spectroscopy is now an established method for performing binding screening against a macromolecular target. Typically, the transverse relaxation rate of the fluorine signals is monitored in the absence and presence of the target. However, useful structural information can sometimes be obtained from the analysis of the fluorine isotropic chemical shift. This is particularly relevant for molecules that are racemates and/or display multiple conformers. The large difference in fluorine isotropic chemical shift between free and bound state deriving mainly from the breaking and/or making of intramolecular and/or intermolecular hydrogen bonds allows the detection of very weak affinity ligands. According to our experimental results, racemates should always be included in the generation of the fluorinated fragment libraries. The selection or the availability of only one of the enantiomers for the fluorinated screening library could result in missing relevant chemical scaffold motifs.
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Affiliation(s)
- Claudio Dalvit
- Faculty of Science, University of Neuchatel, 2000, Neuchatel, Switzerland
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, 60438, Frankfurt, Germany
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford University, Oxford, OX3 7DQ, UK
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17
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Fluorine NMR spectroscopy and computational calculations for assessing intramolecular hydrogen bond involving fluorine and for characterizing the dynamic of a fluorinated molecule. J Fluor Chem 2017. [DOI: 10.1016/j.jfluchem.2017.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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18
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Harner MJ, Mueller L, Robbins KJ, Reily MD. NMR in drug design. Arch Biochem Biophys 2017; 628:132-147. [DOI: 10.1016/j.abb.2017.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 02/09/2023]
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