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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Jordan C, Hayashi T, Löbbert A, Fan J, Teschers CS, Siebold K, Aufiero M, Pape F, Campbell E, Axer A, Bussmann K, Bergander K, Köhnke J, Gossert AD, Gilmour R. Probing the Origin of Affinity in the GM1-Cholera Toxin Complex through Site-Selective Editing with Fluorine. ACS CENTRAL SCIENCE 2024; 10:1481-1489. [PMID: 39220706 PMCID: PMC11363330 DOI: 10.1021/acscentsci.4c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 09/04/2024]
Abstract
Carbohydrates regulate an inimitable spectrum of biological functions, yet successfully leveraging this therapeutic avenue continues to be frustrated by low affinities with glycan-specific proteins. A conspicuous exception is the interaction of monosialotetrahexosylganglioside (GM1) with the carbohydrate-recognition domain of cholera toxin from Vibrio cholerae: this is one of the strongest protein-carbohydrate interactions known. To establish the importance of a long-discussed key hydrogen bond between C2 of the terminal galactose of GM1 and the B subunit pentamer of cholera toxin (CTB5), the total synthesis of a selectively fluorinated GM1 epitope was conducted in 19 steps. This process of molecular editing (Oδ-H → Fδ-) strategically deletes the hydrogen bond donor while retaining the localized partial charge of the substituent. Comparison of the binding affinity of F-GM1/CTB5 with native GM1, the GM1 carbohydrate epitope, and meta-mononitrophenyl-α-galactoside (MNPG) revealed a trend that fully supports the importance of this key interaction. These NMR data suggest that F-GM1 binds in a closely similar conformation as native GM1. Crystallographic analyses of the complex also confirm that the OH → F bioisosteric exchange at C2 of the terminal galactose induces a ring conformation that eliminates key hydrogen bonds: these interactions are compensated for by inter- and intramolecular fluorine-specific interactions.
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Affiliation(s)
- Christina Jordan
- Institute
for Organic Chemistry, University of Münster, 48149 Münster, Germany
| | - Taiki Hayashi
- Institute
for Organic Chemistry, University of Münster, 48149 Münster, Germany
| | | | - Jingran Fan
- Institut
für Lebensmittelchemie, Leibniz Universität
Hannover, 30167 Hannover, Germany
| | | | - Kathrin Siebold
- Institute
for Organic Chemistry, University of Münster, 48149 Münster, Germany
| | - Marialuisa Aufiero
- Institute
for Organic Chemistry, University of Münster, 48149 Münster, Germany
| | - Felix Pape
- Institute
for Organic Chemistry, University of Münster, 48149 Münster, Germany
| | - Emma Campbell
- Institute
for Organic Chemistry, University of Münster, 48149 Münster, Germany
| | - Alexander Axer
- Institute
for Organic Chemistry, University of Münster, 48149 Münster, Germany
| | - Kathrin Bussmann
- Institute
for Organic Chemistry, University of Münster, 48149 Münster, Germany
| | - Klaus Bergander
- Institute
for Organic Chemistry, University of Münster, 48149 Münster, Germany
| | - Jesko Köhnke
- Institut
für Lebensmittelchemie, Leibniz Universität
Hannover, 30167 Hannover, Germany
| | | | - Ryan Gilmour
- Institute
for Organic Chemistry, University of Münster, 48149 Münster, Germany
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3
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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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4
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Lang S, Fletcher DA, Petit AP, Luise N, Fyfe P, Zuccotto F, Porter D, Hope A, Bellany F, Kerr C, Mackenzie CJ, Wyatt PG, Gray DW. Application of an NMR/Crystallography Fragment Screening Platform for the Assessment and Rapid Discovery of New HIV-CA Binding Fragments. ChemMedChem 2024; 19:e202400025. [PMID: 38581280 DOI: 10.1002/cmdc.202400025] [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: 01/26/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/08/2024]
Abstract
Identification and assessment of novel targets is essential to combat drug resistance in the treatment of HIV/AIDS. HIV Capsid (HIV-CA), the protein playing a major role in both the early and late stages of the viral life cycle, has emerged as an important target. We have applied an NMR fragment screening platform and identified molecules that bind to the N-terminal domain (NTD) of HIV-CA at a site close to the interface with the C-terminal domain (CTD). Using X-ray crystallography, we have been able to obtain crystal structures to identify the binding mode of these compounds. This allowed for rapid progression of the initial, weak binding, fragment starting points to compounds 37 and 38, which have 19F-pKi values of 5.3 and 5.4 respectively.
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Affiliation(s)
- Stuart Lang
- Cresset Discovery, New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG80SSS
| | - Daniel A Fletcher
- BioAscent Discovery Ltd, Bo'Ness Road, Newhouse, Lanarkshire, ML1 5UH
| | | | - Nicola Luise
- Alira Health, Av. De Josep Tarradellas, 123, 7th Floor, 08029, Barcelona, Spain
| | - Paul Fyfe
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | - Fabio Zuccotto
- Vertex Pharmaceuticals (Europe) Ltd, 86-88, Jubilee Avenue, Milton Park, Abingdon, Oxfordshire, OX14 4RW
| | - David Porter
- Evotec (UK) Ltd, Dorothy Crowfoot Hodgkin Campus, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ
| | - Anthony Hope
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | - Fiona Bellany
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | - Catrina Kerr
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | | | - Paul G Wyatt
- Sitala Bio Ltd, Unit D6, Grain House Mill Court, Great Shelford, Cambridge, CB22 5LD
| | - David W Gray
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
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5
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Faderl D, Chenakkara A, Jouda M, MacKinnon N, Gossert AD, Korvink JG. Accelerated Screening of Protein-Ligand Interactions via Parallel T2-Weighted 19F-MRI. Anal Chem 2024; 96:9859-9865. [PMID: 38830623 PMCID: PMC11190876 DOI: 10.1021/acs.analchem.4c00333] [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: 01/17/2024] [Revised: 04/22/2024] [Accepted: 04/29/2024] [Indexed: 06/05/2024]
Abstract
In drug discovery, ligands are sought that modulate the (mal-)function of medicinally relevant target proteins. In order to develop new drugs, typically a multitude of potential ligands are initially screened for binding and subsequently characterized for their affinity. Nuclear magnetic resonance (NMR) is a well-established and highly sensitive technology for characterizing such interactions. However, it has limited throughput, because only one sample can be measured at a time. In contrast, magnetic resonance imaging (MRI) is inherently parallel and MR parameters can conveniently be encoded in its images, potentially offering increased sample throughput. We explore this application using a custom-built 9-fold sample holder and a 19F-MRI coil. With this setup, we show that ligand binding can be detected by T2-weighted 19F-MRI using 4-(trifluoromethyl)benzamidine (TFBA) and trypsin as the reporter ligand and target protein, respectively. Furthermore, we demonstrate that the affinity of nonfluorinated ligands can be determined in a competition format by monitoring the dose-dependent displacement of TFBA. By comparing 19F-T2-weighted MR images of TFBA in the presence of different benzamidine (BA) concentrations-all recorded in parallel-the affinity of BA could be derived. Therefore, this approach promises parallel characterization of protein-ligand interactions and increased throughput of biochemical assays, with potential for increased sensitivity when combined with hyperpolarization techniques.
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Affiliation(s)
- Dilara Faderl
- Institute
of Microstructure Technology, Karlsruhe
Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Ajmal Chenakkara
- Institute
of Microstructure Technology, Karlsruhe
Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Mazin Jouda
- Institute
of Microstructure Technology, Karlsruhe
Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Neil MacKinnon
- Institute
of Microstructure Technology, Karlsruhe
Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | | | - Jan G. Korvink
- Institute
of Microstructure Technology, Karlsruhe
Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
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6
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Myers SH, Poppi L, Rinaldi F, Veronesi M, Ciamarone A, Previtali V, Bagnolini G, Schipani F, Ortega Martínez JA, Girotto S, Di Stefano G, Farabegoli F, Walsh N, De Franco F, Roberti M, Cavalli A. An 19F NMR fragment-based approach for the discovery and development of BRCA2-RAD51 inhibitors to pursuit synthetic lethality in combination with PARP inhibition in pancreatic cancer. Eur J Med Chem 2024; 265:116114. [PMID: 38194775 DOI: 10.1016/j.ejmech.2023.116114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/11/2024]
Abstract
The BRCA2-RAD51 interaction remains an intriguing target for cancer drug discovery due to its vital role in DNA damage repair mechanisms, which cancer cells become particularly reliant on. Moreover, RAD51 has many synthetically lethal partners, including PARP1-2, which can be exploited to induce synthetic lethality in cancer. In this study, we established a 19F-NMR-fragment based approach to identify RAD51 binders, leading to two initial hits. A subsequent SAR program identified 46 as a low micromolar inhibitor of the BRCA2-RAD51 interaction. 46 was tested in different pancreatic cancer cell lines, to evaluate its ability to inhibit the homologous recombination DNA repair pathway, mediated by BRCA2-RAD51 and trigger synthetic lethality in combination with the PARP inhibitor talazoparib, through the induction of apoptosis. Moreover, we further analyzed the 46/talazoparib combination in 3D pancreatic cancer models. Overall, 46 showed its potential as a tool to evaluate the RAD51/PARP1-2 synthetic lethality mechanism, along with providing a prospect for further inhibitors development.
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Affiliation(s)
- Samuel H Myers
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genoa, Italy
| | - Laura Poppi
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Francesco Rinaldi
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genoa, Italy; Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Marina Veronesi
- Structural Biophysics Facility, Istituto Italiano di Tecnologia, 16163, Genoa, Italy; D3 PharmaChemistry, Istituto Italiano di Tecnologia, 16163, Genoa, Italy
| | - Andrea Ciamarone
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genoa, Italy
| | - Viola Previtali
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genoa, Italy
| | - Greta Bagnolini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Fabrizio Schipani
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genoa, Italy
| | | | - Stefania Girotto
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genoa, Italy; Structural Biophysics Facility, Istituto Italiano di Tecnologia, 16163, Genoa, Italy
| | - Giuseppina Di Stefano
- Department of Surgical and Medical Sciences, University of Bologna, 40126, Bologna, Italy
| | - Fulvia Farabegoli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Naomi Walsh
- School of Biotechnology, Dublin City University, D09 NR58, Dublin, Ireland
| | | | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.
| | - Andrea Cavalli
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genoa, Italy; Swiss Federal Institute of Technology Lausanne (EPFL), Switzerland
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7
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Hymon D, Martins J, Richter C, Sreeramulu S, Wacker A, Ferner J, Patwardhan NN, Hargrove AE, Schwalbe H. NMR 1H, 19F-based screening of the four stem-looped structure 5_SL1-SL4 located in the 5'-untranslated region of SARS-CoV 2 RNA. RSC Med Chem 2024; 15:165-177. [PMID: 38283228 PMCID: PMC10809358 DOI: 10.1039/d3md00322a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/16/2023] [Indexed: 01/30/2024] Open
Abstract
Development of new antiviral medication against the beta-coronavirus SARS-CoV-2 (SCoV2) is actively being pursued. Both NMR spectroscopy and crystallography as structural screening technologies have been utilised to screen the viral proteome for binding to fragment libraries. Here, we report on NMR screening of elements of the viral RNA genome with two different ligand libraries using 1H-NMR-screening experiments and 1H and 19F NMR-screening experiments for fluorinated compounds. We screened against the 5'-terminal 119 nucleotides located in the 5'-untranslated region of the RNA genome of SCoV2 and further dissected the four stem-loops into its constituent RNA elements to test specificity of binding of ligands to shorter and longer viral RNA stretches. The first library (DRTL-F library) is enriched in ligands binding to RNA motifs, while the second library (DSI-poised library) represents a fragment library originally designed for protein screening. Conducting screens with two different libraries allows us to compare different NMR screening methodologies, describe NMR screening workflows, validate the two different fragment libraries, and derive initial leads for further downstream medicinal chemistry optimisation.
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Affiliation(s)
- Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | - Jason Martins
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | | | - Amanda E Hargrove
- Department of Chemistry, Duke University Durham North Carolina 27708 USA
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
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8
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Jiang Y, Wu Y, Wang J, Ma Y, Yu H, Wang Z. Fragment-based Drug Discovery Strategy and its Application to the Design of SARS-CoV-2 Main Protease Inhibitor. Curr Med Chem 2024; 31:6204-6226. [PMID: 38529602 DOI: 10.2174/0109298673294251240229070740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/10/2024] [Accepted: 02/14/2024] [Indexed: 03/27/2024]
Abstract
Severe Acute Respiratory Syndrome Coronavirus Type 2 (SARS-CoV-2) emerged at the end of 2019, causing a highly infectious and pathogenic disease known as 2019 coronavirus disease. This disease poses a serious threat to human health and public safety. The SARS-CoV-2 main protease (Mpro) is a highly sought-after target for developing drugs against COVID-19 due to its exceptional specificity. Its crystal structure has been extensively documented. Numerous strategies have been employed in the investigation of Mpro inhibitors. This paper is primarily concerned with Fragment-based Drug Discovery (FBDD), which has emerged as an effective approach to drug design in recent times. Here, we summarize the research on the approach of FBDD and its application in developing inhibitors for SARS-CoV-2 Mpro.
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Affiliation(s)
- Yu Jiang
- Inner Mongolia Key Laboratory of Disease-Related Biomarkers, The Second Affiliated Hospital, Baotou Medical College, Baotou, China
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Yingnan Wu
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Jing Wang
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Yuheng Ma
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Hui Yu
- School of Basic Medicine, Baotou Medical College, Baotou, China
| | - Zhanli Wang
- Inner Mongolia Key Laboratory of Disease-Related Biomarkers, The Second Affiliated Hospital, Baotou Medical College, Baotou, China
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9
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Furihata K, Tashiro M. NMR screening method based on 19F spin-spin relaxation time for analyses of fluorinated compound bound to proteins. ANAL SCI 2024; 40:219-223. [PMID: 37838626 DOI: 10.1007/s44211-023-00435-0] [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: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023]
Abstract
NMR screening methods based on 19F spin-spin relaxation time (19F-T2) were applied to fluorinated compounds bound to human serum albumin. Diflunisal and fleroxacin (the fluorinated compounds) contain two and three fluorine atoms per molecule, respectively, and are suitable as the model system for 19F NMR analysis. It was shown that 19F-T2 was more sensitive in monitoring the binding affinity to the target protein than 19F spin-lattice relaxation time (19F-T1). The comparisons of 19F signal intensities acquired at different echo times using 19F-T2 pulse sequence were also shown to be an effective means of assessing complex formation for fluorinated compounds.
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Affiliation(s)
- Kazuo Furihata
- Division of Agriculture and Agricultural Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Mitsuru Tashiro
- Department of Chemistry, College of Science and Technology, Meisei University, Hino, Tokyo, 191-8506, Japan.
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10
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Babagond V, Katagi K, Pandith A, Akki M, Jaggal A. Unique development of a new dual application probe for selective detection of antiparallel G-quadruplex sequences. Analyst 2023; 148:5507-5513. [PMID: 37789760 DOI: 10.1039/d3an01109g] [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: 10/05/2023]
Abstract
G-Quadruplex (G4) structures play vital roles in many biological processes; consequently, they have been implicated in various human diseases like cancer, Alzheimer's disease etc. The selective detection of G4 DNA structures is of great interest for understanding their roles and biological functions. Hence, development of multifunctional fluorescent probes is indeed essential. In this investigation, we have synthesized a quinolinium based dual application probe (QnMF) that presents molecular rotor properties. This dual application molecular rotor is able to detect selectively antiparallel G4 sequences (22AG in 100 mM NaCl) through a turn-on response over other G4 topologies. The QnMF also contains a distinct fluorine-19 that undergoes a significant chemical shift in response to microenvironmental changes around the molecule when bound to G4 structures. The probe QnMF exhibits significantly brighter fluorescence emissions in glycerol (ε × ϕ = 2800 cm-1 M-1) and relatively less brighter fluorescence emissions in methanol (ε × ϕ = 40.5 cm-1 M-1). The restricted rotation inherent property of the QnMF molecular rotor is responsible for brighter fluorescence and leads to enhancement in the fluorescence upon binding to the G4 structure. Overall, the probe's dual detection method makes it useful for monitoring the G4 structures that are abundant and plays a vital role in living organisms.
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Affiliation(s)
- Vardhaman Babagond
- Research Centre, Department of Chemistry, Karnatak University's Karnatak Science College Dharwad, Karnataka, India.
| | - Kariyappa Katagi
- Research Centre, Department of Chemistry, Karnatak University's Karnatak Science College Dharwad, Karnataka, India.
| | - Anup Pandith
- International Ph.D. Program in Biomedical Engineering (IPBME), College of Biomedical Engineering, Taipei Medical University, Taipei City 11031, Taiwan, Republic of China
| | - Mahesh Akki
- Research Centre, Department of Chemistry, Karnatak University's Karnatak Science College Dharwad, Karnataka, India.
| | - Ashwini Jaggal
- Research Centre, Department of Chemistry, Karnatak University's Karnatak Science College Dharwad, Karnataka, India.
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11
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Woodman TJ, Lloyd MD. Analysis of enzyme reactions using NMR techniques: A case study with α-methylacyl-CoA racemase (AMACR). Methods Enzymol 2023; 690:159-209. [PMID: 37858529 DOI: 10.1016/bs.mie.2023.07.005] [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] [Indexed: 10/21/2023]
Abstract
α-Methylacyl-CoA racemase (AMACR; P504S) catalyzes the conversion of R-2-methylacyl-CoA esters into their corresponding S-2-methylacyl-CoA epimers enabling their degradation by β-oxidation. The enzyme also catalyzes the key epimerization reaction in the pharmacological activation pathway of ibuprofen and related drugs. AMACR protein levels and enzymatic activity are increased in prostate cancer, and the enzyme is a recognized drug target. Key to the development of novel treatments based on AMACR inhibition is the development of functional assays. Synthesis of substrates and purification of recombinant human AMACR are described. Incubation of R- or S-2-methylacyl-CoA esters with AMACR in vitro resulted in formation of epimers (at a near 1-1 ratio at equilibrium) via removal of their α-protons to form an enolate intermediate followed by reprotonation. Conversion can be conveniently followed by incubation in buffer containing 2H2O followed by 1H NMR analysis to monitor conversion of the α-methyl doublet to a single peak upon deuterium incorporation. Incubation of 2-methylacyl-CoA esters containing leaving groups results in an elimination reaction, which was also characterized by 1H NMR. The synthesis of substrates, including a double labeled substrate for mechanistic studies, and subsequent analysis is also described.
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Affiliation(s)
- Timothy J Woodman
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom.
| | - Matthew D Lloyd
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom.
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12
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Abstract
Although fragment-based drug discovery (FBDD) has been successfully implemented and well-explored for protein targets, its feasibility for RNA targets is emerging. Despite the challenges associated with the selective targeting of RNA, efforts to integrate known methods of RNA binder discovery with fragment-based approaches have been fruitful, as a few bioactive ligands have been identified. Here, we review various fragment-based approaches implemented for RNA targets and provide insights into experimental design and outcomes to guide future work in the area. Indeed, investigations surrounding the molecular recognition of RNA by fragments address rather important questions such as the limits of molecular weight that confer selective binding and the physicochemical properties favorable for RNA binding and bioactivity.
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Affiliation(s)
- Blessy M. Suresh
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Amirhossein Taghavi
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L. Childs-Disney
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
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13
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Janeena A, Jayaraman N, Shanmugam G, Easwaramoorthi S, Ayyadurai N. Electrochemical Response of Redox Amino Acid Encoded Fluorescence Protein for Hydroxychloroquine Sensing. Appl Biochem Biotechnol 2023; 195:992-1013. [PMID: 36260248 PMCID: PMC9581447 DOI: 10.1007/s12010-022-04142-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2022] [Indexed: 01/24/2023]
Abstract
The sudden rise in the demand has led to large-scale production of hydroxychloroquine (HCQ) in the global market for various diseases such as malaria, rheumatic arthritis, and systemic lupus erythematous and prophylactic treatment of early SARS-CoV-2 outbreak. Thorough monitoring of HCQ intake patients is in high demand; hence, we have developed a redox amino acid encoded fluorescent protein-based electrochemical biosensor for sensitive and selective detection of HCQ. This electrochemical biosensor is generated based on the two-electron transfer process between redox amino acid (3,4-dihydroxy-L-phenylalanine, DOPA) encoded bio-redox protein and the HCQ forms the conjugate. The DOPA residue in the bio-redox protein specifically binds with HCQ, thereby producing a remarkable electrochemical response on the glassy carbon electrode. Experimental results show that the developed biosensor selectively and sensitively detects the HCQ in spiked urine samples. The reagent-free bio-redox capacitor detects HCQ in the range of 90 nM to 4.4 µM in a solution with a detection limit of 58 nM, signal to noise ratio of 3:1, and strong anti-interference ability. Real-time screening, quantification, and relative mean recoveries of HCQ on spiked urine samples were monitored through electron shuttling using bio-redox protein and were found to be 97 to 101%. Overall, the developed bio-redox protein-based sensor has specificity, selectivity, reproducibility, and sensitivity making it potentially attractive for the sensing of HCQ and also applicable to clinical research.
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Affiliation(s)
- Asuma Janeena
- Biotechnology and Biochemistry, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute, Chennai, India
- Academy of Scientific and Industrial Research (AcSIR), 201002, Ghaziabad, India
| | - Narayanan Jayaraman
- Inorganic and Physical Chemistry, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute, Chennai, India
| | - Ganesh Shanmugam
- Academy of Scientific and Industrial Research (AcSIR), 201002, Ghaziabad, India
- Organic and Bio-Organic Chemistry, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute, Chennai, India
| | - Shanmugam Easwaramoorthi
- Academy of Scientific and Industrial Research (AcSIR), 201002, Ghaziabad, India.
- Inorganic and Physical Chemistry, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute, Chennai, India.
| | - Niraikulam Ayyadurai
- Biotechnology and Biochemistry, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute, Chennai, India.
- Academy of Scientific and Industrial Research (AcSIR), 201002, Ghaziabad, India.
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14
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Stahlecker J, Klett T, Schwer M, Jaag S, Dammann M, Ernst LN, Braun MB, Zimmermann MO, Kramer M, Lämmerhofer M, Stehle T, Coles M, Boeckler FM. Revisiting a challenging p53 binding site: a diversity-optimized HEFLib reveals diverse binding modes in T-p53C-Y220C. RSC Med Chem 2022; 13:1575-1586. [PMID: 36561072 PMCID: PMC9749929 DOI: 10.1039/d2md00246a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/05/2022] [Indexed: 11/30/2022] Open
Abstract
The cellular tumor antigen p53 is a key component in cell cycle control. The mutation Y220C heavily destabilizes the protein thermally but yields a druggable crevice. We have screened the diversity-optimized halogen-enriched fragment library against T-p53C-Y220C with STD-NMR and DSF to identify hits, which we validated by 1H,15N-HSQC NMR. We could identify four hits binding in the Y220C cleft, one hit binding covalently and four hits binding to an uncharacterized binding site. Compound 1151 could be crystallized showing a flip of C220 and thus opening subsite 3. Additionally, 4482 was identified to alkylate cysteines. Data shows that the diversity-optimized HEFLib leads to multiple diverse hits. The identified scaffolds can be used to further optimize interactions with T-p53C-Y220C and increase thermal stability.
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Affiliation(s)
- Jason Stahlecker
- Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Theresa Klett
- Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Martin Schwer
- Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Simon Jaag
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Marcel Dammann
- Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Larissa N Ernst
- Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Michael B Braun
- Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 34 72076 Tübingen Germany
| | - Markus O Zimmermann
- Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Markus Kramer
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 18 72076 Tübingen Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 34 72076 Tübingen Germany
| | - Murray Coles
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen Max-Planck-Ring 5 72076 Tübingen Germany
| | - Frank M Boeckler
- Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen Sand 14 72076 Tübingen Germany
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15
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Rajbanshi B, Das K, Roy D, Saha S, Nath Roy M. Exploring 2:1 Inclusion Complexes of cyclodextrins and Antispasmodics, Alverine citrate for Enhancing bioavailability and Sustained Dischargement. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Peacock DM, Kelly MJS, Shokat KM. Probing the KRas Switch II Groove by Fluorine NMR Spectroscopy. ACS Chem Biol 2022; 17:2710-2715. [PMID: 36166818 PMCID: PMC9594042 DOI: 10.1021/acschembio.2c00566] [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] [Indexed: 01/19/2023]
Abstract
While there has been recent success in the development of KRasG12C inhibitors, unmet needs for selective inhibitors of KRasG12D and the remaining oncogenic KRas proteins remain. Here, we applied trifluoromethyl-containing ligands of KRas proteins as competitive probe ligands to assay the occupancy of the switch II pocket by 19F NMR spectroscopy. Structure-activity-relationship studies of probe ligands increased the sensitivity of the assay and identified structures that differentially detected each nucleotide state of KRasG12D. These differences in selectivity, combined with the high resolution of 19F NMR spectroscopy, enabled this method to be expanded to assay both nucleotide states of the protein simultaneously.
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Affiliation(s)
- D. Matthew Peacock
- Department
of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Mark J. S. Kelly
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San
Francisco, California 94158, United States
| | - Kevan M. Shokat
- Department
of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States,Howard
Hughes Medical Institute, San Francisco, California 94158, United States,E-mail:
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17
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Ayotte Y, Woo S, LaPlante SR. Practical Considerations and Guidelines for Spectral Referencing for Fluorine NMR Ligand Screening. ACS OMEGA 2022; 7:13155-13163. [PMID: 35474811 PMCID: PMC9026065 DOI: 10.1021/acsomega.2c00613] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Fluorine (19F) NMR strategies are increasingly being employed for evaluating ligand binding to macromolecules, among many other uses. 19F NMR offers many advantages as a result of its sensitive spin 1/2 nucleus, 100% natural abundance, and wide chemical shift range. Moreover, because of its absence from biological samples, one can directly monitor ligand binding without background interference from the macromolecule. Therefore, all these aforementioned features make it an attractive approach for screening compounds. However, the detection of ligand binding, especially those with weak affinities, can require interpretations of minor changes in chemical shifts. Thus, chemical shift referencing is critical for accurate measurements and interpretations. Unfortunately, one cannot rely on spectrometer indirect referencing alone, and internal chemical references have sample-dependent issues. Here, we evaluated 10 potential candidate compounds that could serve as 19F NMR chemical references. Multiple factors were systematically evaluated for each candidate to monitor the suitability for 19F NMR screening purposes. These factors include aqueous solubility, buffer compatibility, salt compatibility, aqueous stability, tolerability to pH changes, temperature changes, and compound pooling. It was concluded that there was no ideal candidate, but five compounds had properties that met the screening requirements.
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Affiliation(s)
- Yann Ayotte
- Centre
Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
- NMX
Research and Solutions Inc., 500 boulevard Cartier Ouest, Suite 6000, Laval, Québec H7V 5B7, Canada
| | - Simon Woo
- Centre
Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
- NMX
Research and Solutions Inc., 500 boulevard Cartier Ouest, Suite 6000, Laval, Québec H7V 5B7, Canada
| | - Steven R. LaPlante
- Centre
Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
- NMX
Research and Solutions Inc., 500 boulevard Cartier Ouest, Suite 6000, Laval, Québec H7V 5B7, Canada
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18
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Balboni B, Tripathi SK, Veronesi M, Russo D, Penna I, Giabbai B, Bandiera T, Storici P, Girotto S, Cavalli A. Identification of Novel GSK-3β Hits Using Competitive Biophysical Assays. Int J Mol Sci 2022; 23:ijms23073856. [PMID: 35409221 PMCID: PMC8998611 DOI: 10.3390/ijms23073856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/05/2023] Open
Abstract
Glycogen synthase kinase 3 beta (GSK-3β) is an evolutionarily conserved serine-threonine kinase dysregulated in numerous pathologies, such as Alzheimer’s disease and cancer. Even though GSK-3β is a validated pharmacological target most of its inhibitors have two main limitations: the lack of selectivity due to the high homology that characterizes the ATP binding site of most kinases, and the toxicity that emerges from GSK-3β complete inhibition which translates into the impairment of the plethora of pathways GSK-3β is involved in. Starting from a 1D 19F NMR fragment screening, we set up several biophysical assays for the identification of GSK-3β inhibitors capable of binding protein hotspots other than the ATP binding pocket or to the ATP binding pocket, but with an affinity able of competing with a reference binder. A phosphorylation activity assay on a panel of several kinases provided selectivity data that were further rationalized and corroborated by structural information on GSK-3β in complex with the hit compounds. In this study, we identified promising fragments, inhibitors of GSK-3β, while proposing an alternative screening workflow that allows facing the flaws that characterize the most common GSK-3β inhibitors through the identification of selective inhibitors and/or inhibitors able to modulate GSK-3β activity without leading to its complete inhibition.
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Affiliation(s)
- Beatrice Balboni
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; (B.B.); (S.K.T.)
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Shailesh Kumar Tripathi
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; (B.B.); (S.K.T.)
| | - Marina Veronesi
- D3 Pharmachemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; (M.V.); (D.R.); (I.P.); (T.B.)
| | - Debora Russo
- D3 Pharmachemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; (M.V.); (D.R.); (I.P.); (T.B.)
| | - Ilaria Penna
- D3 Pharmachemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; (M.V.); (D.R.); (I.P.); (T.B.)
| | - Barbara Giabbai
- Structural Biology Laboratory, Elettra Sincrotrone Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy; (B.G.); (P.S.)
| | - Tiziano Bandiera
- D3 Pharmachemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; (M.V.); (D.R.); (I.P.); (T.B.)
| | - Paola Storici
- Structural Biology Laboratory, Elettra Sincrotrone Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy; (B.G.); (P.S.)
| | - Stefania Girotto
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; (B.B.); (S.K.T.)
- Correspondence: (S.G.); (A.C.); Tel.: +39-010-2896-983 (S.G.); +39-010-2897-403 (A.C.)
| | - Andrea Cavalli
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; (B.B.); (S.K.T.)
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Correspondence: (S.G.); (A.C.); Tel.: +39-010-2896-983 (S.G.); +39-010-2897-403 (A.C.)
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19
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Development of 1H{ 19F} saturation transfer difference experiments for detection of a fluorinated compound bound to proteins. ANAL SCI 2022; 38:825-829. [PMID: 35318618 DOI: 10.1007/s44211-022-00098-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/09/2022] [Indexed: 11/27/2022]
Abstract
The 1H{19F} saturation transfer difference (STD) experiment presented here incorporates the WATERGATE W5 sequence to observe protein-ligand interactions in a human serum albumin (HSA)-fleroxacin complex. In conventional STD experiments, 1H of proteins are first saturated, and the ligands bound to these proteins are then observed. The method proposed here reverses this process: fluorine atoms in fleroxacin are selectively saturated, and saturation transfer then occurs to protons of fleroxacin as well as to those of HSA. The combined use of the present 1H{19F} STD and conventional STD methods is expected to provide better insight in the analysis of the role of fluorine atoms in a fluorinated compound.
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20
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Yin G, Lv G, Zhang J, Jiang H, Lai T, Yang Y, Ren Y, Wang J, Yi C, Chen H, Huang Y, Xiao C. Early-stage structure-based drug discovery for small GTPases by NMR spectroscopy. Pharmacol Ther 2022; 236:108110. [PMID: 35007659 DOI: 10.1016/j.pharmthera.2022.108110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/13/2022]
Abstract
Small GTPase or Ras superfamily, including Ras, Rho, Rab, Ran and Arf, are fundamental in regulating a wide range of cellular processes such as growth, differentiation, migration and apoptosis. They share structural and functional similarities for binding guanine nucleotides and hydrolyzing GTP. Dysregulations of Ras proteins are involved in the pathophysiology of multiple human diseases, however there is still a stringent need for effective treatments targeting these proteins. For decades, small GTPases were recognized as 'undruggable' targets due to their complex regulatory mechanisms and lack of deep pockets for ligand binding. NMR has been critical in deciphering the structural and dynamic properties of the switch regions that are underpinning molecular switch functions of small GTPases, which pave the way for developing new effective inhibitors. The recent progress of drug or lead molecule development made for small GTPases profoundly delineated how modern NMR techniques reshape the field of drug discovery. In this review, we will summarize the progress of structural and dynamic studies of small GTPases, the NMR techniques developed for structure-based drug screening and their applications in early-stage drug discovery for small GTPases.
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Affiliation(s)
- Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China.
| | - Guohua Lv
- Division of Histology & Embryology, Medical College, Jinan University, Guangzhou 511486, Guangdong, China
| | - Jerry Zhang
- University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA
| | - Hongmei Jiang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Tianqi Lai
- Division of Histology & Embryology, Medical College, Jinan University, Guangzhou 511486, Guangdong, China
| | - Yushan Yang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Yong Ren
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Jing Wang
- College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Chenju Yi
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China; Research Institute of Xi'an Jiaotong University, Zhejiang, Hangzhou, Zhejiang Province 311215, PR China
| | - Yun Huang
- Howard Hughes Medical Institute, Chevy Chase 20815, MD, USA; Department of Physiology & Biophysics, Weill Cornell Medicine, New York 10065, NY, USA.
| | - Chaoni Xiao
- College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
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21
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de Castro GV, Ciulli A. Estimating the cooperativity of PROTAC-induced ternary complexes using 19F NMR displacement assay. RSC Med Chem 2021; 12:1765-1770. [PMID: 34778777 DOI: 10.1039/d1md00215e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/17/2021] [Indexed: 01/11/2023] Open
Abstract
Cooperativity is an important parameter to understand the ternary complexes formed by protein degraders. We developed fluorine NMR competition binding experiments to determine cooperativity of PROTACs. We show applicability to estimate both positive and negative cooperativity, also with homo-dimerizers, and highlight key features and considerations for optimal assay development.
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Affiliation(s)
- Guilherme Vieira de Castro
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee Dow Street Dundee DD1 5EH UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee Dow Street Dundee DD1 5EH UK
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22
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Buchholz CR, Pomerantz WCK. 19F NMR viewed through two different lenses: ligand-observed and protein-observed 19F NMR applications for fragment-based drug discovery. RSC Chem Biol 2021; 2:1312-1330. [PMID: 34704040 PMCID: PMC8496043 DOI: 10.1039/d1cb00085c] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022] Open
Abstract
19F NMR has emerged as a powerful tool in drug discovery, particularly in fragment-based screens. The favorable magnetic resonance properties of the fluorine-19 nucleus, the general absence of fluorine in biological settings, and its ready incorporation into both small molecules and biopolymers, has enabled multiple applications of 19F NMR using labeled small molecules and proteins in biophysical, biochemical, and cellular experiments. This review will cover developments in ligand-observed and protein-observed 19F NMR experiments tailored towards drug discovery with a focus on fragment screening. We also cover the key advances that have furthered the field in recent years, including quantitative, structural, and in-cell methodologies. Several case studies are described for each application to highlight areas for innovation and to further catalyze new NMR developments for using this versatile nucleus.
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Affiliation(s)
- Caroline R Buchholz
- Department of Medicinal Chemistry, University of Minnesota 308 Harvard Street SE Minneapolis Minnesota 55455 USA
| | - William C K Pomerantz
- Department of Medicinal Chemistry, University of Minnesota 308 Harvard Street SE Minneapolis Minnesota 55455 USA
- Department of Chemistry, University of Minnesota 207 Pleasant St. SE Minneapolis Minnesota 55455 USA
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23
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Sharaf NG, Shahgholi M, Kim E, Lai JY, VanderVelde DG, Lee AT, Rees DC. Characterization of the ABC methionine transporter from Neisseria meningitidis reveals that lipidated MetQ is required for interaction. eLife 2021; 10:69742. [PMID: 34409939 PMCID: PMC8416018 DOI: 10.7554/elife.69742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/18/2021] [Indexed: 01/05/2023] Open
Abstract
NmMetQ is a substrate-binding protein (SBP) from Neisseria meningitidis that has been identified as a surface-exposed candidate antigen for meningococcal vaccines. However, this location for NmMetQ challenges the prevailing view that SBPs in Gram-negative bacteria are localized to the periplasmic space to promote interaction with their cognate ABC transporter embedded in the bacterial inner membrane. To elucidate the roles of NmMetQ, we characterized NmMetQ with and without its cognate ABC transporter (NmMetNI). Here, we show that NmMetQ is a lipoprotein (lipo-NmMetQ) that binds multiple methionine analogs and stimulates the ATPase activity of NmMetNI. Using single-particle electron cryo-microscopy, we determined the structures of NmMetNI in the presence and absence of lipo-NmMetQ. Based on our data, we propose that NmMetQ tethers to membranes via a lipid anchor and has dual function and localization, playing a role in NmMetNI-mediated transport at the inner membrane and moonlighting on the bacterial surface.
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Affiliation(s)
- Naima G Sharaf
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
| | - Mona Shahgholi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Esther Kim
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Jeffrey Y Lai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
| | - David G VanderVelde
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Allen T Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
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24
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Fujisaku T, So FTK, Igarashi R, Shirakawa M. Machine-Learning Optimization of Multiple Measurement Parameters Nonlinearly Affecting the Signal Quality. ACS MEASUREMENT SCIENCE AU 2021; 1:20-26. [PMID: 36785732 PMCID: PMC9836064 DOI: 10.1021/acsmeasuresciau.1c00009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Determination of optimal measurement parameters is essential for measurement experiments. They can be manually optimized if the linear correlation between them and the corresponding signal quality is known or easily determinable. However, in practice, this correlation is often nonlinear and not known a priori; hence, complicated trial and error procedures are employed for finding optimal parameters while avoiding local optima. In this work, we propose a novel approach based on machine learning for optimizing multiple measurement parameters, which nonlinearly influence the signal quality. Optically detected magnetic resonance measurements of nitrogen-vacancy centers in fluorescent nanodiamonds were used as a proof-of-concept system. We constructed a suitable dataset of optically detected magnetic resonance spectra for predicting the optimal laser and microwave powers that deliver the highest contrast and signal-to-noise ratio values by means of linear regression, neural networks, and random forests. The model developed by the considered neural network turned out to have a coefficient of determination significantly higher than that of the other methods. The proposed method thus provided a novel approach for the rapid setting of measurement parameters that influence the signal quality in a nonlinear way, opening a gate for fields like nuclear magnetic resonance, electron paramagnetic resonance, and fluorescence microscopy to benefit from it.
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Affiliation(s)
- Takahiro Fujisaku
- Institute
for Quantum Life Science, National Institutes
for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto 615-8510, Japan
| | - Frederick Tze Kit So
- Institute
for Quantum Life Science, National Institutes
for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
- Institute
for Chemical Research, Kyoto University,
Gokasho, Uji, Kyoto 611-0011, Japan
| | - Ryuji Igarashi
- Institute
for Quantum Life Science, National Institutes
for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
- National
Institute for Radiological Sciences, National Institute for Quantum
and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
- JST,
PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Masahiro Shirakawa
- Institute
for Quantum Life Science, National Institutes
for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto 615-8510, Japan
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25
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Cañada FJ, Canales Á, Valverde P, de Toro BF, Martínez-Orts M, Phillips PO, Pereda A. Conformational and Structural characterization of carbohydrates and their interactions studied by NMR. Curr Med Chem 2021; 29:1147-1172. [PMID: 34225601 DOI: 10.2174/0929867328666210705154046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/30/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022]
Abstract
Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. The versatility of Nuclear Magnetic Resonance spectroscopy (NMR) often makes it the preferred choice to study glycans and carbohydrates in solution media. The most basic NMR parameters, namely chemical shifts, coupling constants and nuclear Overhauser effects, allow defining short or repetitive chain sequences and characterize their structures and local geometries either in the free state or when interacting with other biomolecules, rendering additional information on the molecular recognition processes. The increased accessibility to carbohydrate molecules extensively or selectively labeled with 13C boosts the resolution and detail that analyzed glycan structures can reach. In turn, structural information derived from NMR, complemented with molecular modeling and theoretical calculations can also provide dynamic information on the conformational flexibility of carbohydrate structures. Furthermore, using partially oriented media or paramagnetic perturbations, it has been possible to introduce additional long-range observables rendering structural information on longer and branched glycan chains. In this review, we provide examples of these studies and an overview of the recent and most relevant NMR applications in the glycobiology field.
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Affiliation(s)
- Francisco Javier Cañada
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Ángeles Canales
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Pablo Valverde
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Beatriz Fernández de Toro
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Mónica Martínez-Orts
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Paola Oquist Phillips
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Amaia Pereda
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
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26
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Phạm TTT, Rainey JK. On-cell nuclear magnetic resonance spectroscopy to probe cell surface interactions. Biochem Cell Biol 2021; 99:683-692. [PMID: 33945753 DOI: 10.1139/bcb-2021-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy allows determination of atomic-level information about intermolecular interactions, molecular structure, and molecular dynamics in the cellular environment. This may be broadly divided into studies focused on obtaining detailed molecular information in the intracellular context ("in-cell") or those focused on characterizing molecules or events at the cell surface ("on-cell"). In this review, we outline some key NMR techniques applied for on-cell NMR studies through both solution-state and solid-state NMR and survey studies that have used these techniques to uncover key information. We particularly focus on application of on-cell NMR spectroscopy to characterize ligand interactions with cell surface membrane proteins such as G-protein coupled receptors (GPCRs), receptor tyrosine kinases, etc. These techniques allow for quantification of binding affinities, competitive binding assays, delineation of portions of ligands involved in binding, ligand bound-state conformational determination, evaluation of receptor structuring and dynamics, and inference of distance constraints characteristic of the ligand-receptor bound state. Excitingly, it is possible to avoid the barriers of production and purification of membrane proteins while obtaining directly physiologically-relevant information through on-cell NMR. We also provide a briefer survey of the applicability of on-cell NMR approaches to other classes of cell surface molecule.
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Affiliation(s)
- Trần Thanh Tâm Phạm
- Dalhousie University, 3688, Department of Biochemistry & Molecular Biology, Halifax, Nova Scotia, Canada;
| | - Jan K Rainey
- Dalhousie University, 3688, Department of Biochemistry & Molecular Biology, Halifax, Canada;
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27
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Grayson JD, Baumgartner MP, Santos Souza CD, Dawes SJ, El Idrissi IG, Louth JC, Stimpson S, Mead E, Dunbar C, Wolak J, Sharman G, Evans D, Zhuravleva A, Roldan MS, Colabufo NA, Ning K, Garwood C, Thomas JA, Partridge BM, de la Vega de Leon A, Gillet VJ, Rauter AP, Chen B. Amyloid binding and beyond: a new approach for Alzheimer's disease drug discovery targeting Aβo-PrP C binding and downstream pathways. Chem Sci 2021; 12:3768-3785. [PMID: 34163650 PMCID: PMC8179515 DOI: 10.1039/d0sc04769d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/08/2021] [Indexed: 01/18/2023] Open
Abstract
Amyloid β oligomers (Aβo) are the main toxic species in Alzheimer's disease, which have been targeted for single drug treatment with very little success. In this work we report a new approach for identifying functional Aβo binding compounds. A tailored library of 971 fluorine containing compounds was selected by a computational method, developed to generate molecular diversity. These compounds were screened for Aβo binding by a combined 19F and STD NMR technique. Six hits were evaluated in three parallel biochemical and functional assays. Two compounds disrupted Aβo binding to its receptor PrPC in HEK293 cells. They reduced the pFyn levels triggered by Aβo treatment in neuroprogenitor cells derived from human induced pluripotent stem cells (hiPSC). Inhibitory effects on pTau production in cortical neurons derived from hiPSC were also observed. These drug-like compounds connect three of the pillars in Alzheimer's disease pathology, i.e. prion, Aβ and Tau, affecting three different pathways through specific binding to Aβo and are, indeed, promising candidates for further development.
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Affiliation(s)
- James D Grayson
- Department of Chemistry, University of Sheffield Brookhill Sheffield S3 7HF UK
| | - Matthew P Baumgartner
- Computational Chemistry and Cheminformatics, Eli Lilly and Company, Lilly Biotechnology Center San Diego CA 92121 USA
| | | | - Samuel J Dawes
- Department of Chemistry, University of Sheffield Brookhill Sheffield S3 7HF UK
- Faculty of Biological Sciences, University of Leeds Leeds LS2 9JT UK
| | | | - Jennifer C Louth
- Department of Chemistry, University of Sheffield Brookhill Sheffield S3 7HF UK
| | - Sasha Stimpson
- Department of Chemistry, University of Sheffield Brookhill Sheffield S3 7HF UK
| | - Emma Mead
- Computational Chemistry and Chemoinformatics, Eli Lilly and Company Erl Wood Windlesham GU20 6PH UK
| | - Charlotte Dunbar
- Computational Chemistry and Chemoinformatics, Eli Lilly and Company Erl Wood Windlesham GU20 6PH UK
| | - Joanna Wolak
- Computational Chemistry and Chemoinformatics, Eli Lilly and Company Erl Wood Windlesham GU20 6PH UK
| | - Gary Sharman
- Computational Chemistry and Chemoinformatics, Eli Lilly and Company Erl Wood Windlesham GU20 6PH UK
| | - David Evans
- Computational Chemistry and Chemoinformatics, Eli Lilly and Company Erl Wood Windlesham GU20 6PH UK
| | | | | | - Nicola Antonio Colabufo
- Univ Bari, Biofordrug Via Edoardo Orabona 4 I-70125 Bari Italy
- Univ Bari, Dipartimento Farm Sci Farmaco Via Edoardo Orabona 4 I-70125 Bari Italy
| | - Ke Ning
- Sheffield Institute of Translational Neuroscience, University of Sheffield Sheffield S10 2HQ UK
| | - Claire Garwood
- Sheffield Institute of Translational Neuroscience, University of Sheffield Sheffield S10 2HQ UK
| | - James A Thomas
- Department of Chemistry, University of Sheffield Brookhill Sheffield S3 7HF UK
| | | | | | | | - Amélia P Rauter
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa ED C8, 5 piso 1749-016 Lisboa Portugal
| | - Beining Chen
- Department of Chemistry, University of Sheffield Brookhill Sheffield S3 7HF UK
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28
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Gimenez D, Phelan A, Murphy CD, Cobb SL. 19F NMR as a tool in chemical biology. Beilstein J Org Chem 2021; 17:293-318. [PMID: 33564338 PMCID: PMC7849273 DOI: 10.3762/bjoc.17.28] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022] Open
Abstract
We previously reviewed the use of 19F NMR in the broad field of chemical biology [Cobb, S. L.; Murphy, C. D. J. Fluorine Chem. 2009, 130, 132-140] and present here a summary of the literature from the last decade that has the technique as the central method of analysis. The topics covered include the synthesis of new fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein-protein interactions, protein-ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate biosynthesis and biodegradation of fluorinated organic compounds is also described.
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Affiliation(s)
- Diana Gimenez
- Department of Chemistry, Durham University, South Road, Durham, DH13LE, UK
| | - Aoife Phelan
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cormac D Murphy
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Steven L Cobb
- Department of Chemistry, Durham University, South Road, Durham, DH13LE, UK
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29
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Applications of Solution NMR in Drug Discovery. Molecules 2021; 26:molecules26030576. [PMID: 33499337 PMCID: PMC7865596 DOI: 10.3390/molecules26030576] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
During the past decades, solution nuclear magnetic resonance (NMR) spectroscopy has demonstrated itself as a promising tool in drug discovery. Especially, fragment-based drug discovery (FBDD) has benefited a lot from the NMR development. Multiple candidate compounds and FDA-approved drugs derived from FBDD have been developed with the assistance of NMR techniques. NMR has broad applications in different stages of the FBDD process, which includes fragment library construction, hit generation and validation, hit-to-lead optimization and working mechanism elucidation, etc. In this manuscript, we reviewed the current progresses of NMR applications in fragment-based drug discovery, which were illustrated by multiple reported cases. Moreover, the NMR applications in protein-protein interaction (PPI) modulators development and the progress of in-cell NMR for drug discovery were also briefly summarized.
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30
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Binas O, de Jesus V, Landgraf T, Völklein AE, Martins J, Hymon D, Kaur Bains J, Berg H, Biedenbänder T, Fürtig B, Lakshmi Gande S, Niesteruk A, Oxenfarth A, Shahin Qureshi N, Schamber T, Schnieders R, Tröster A, Wacker A, Wirmer‐Bartoschek J, Wirtz Martin MA, Stirnal E, Azzaoui K, Richter C, Sreeramulu S, José Blommers MJ, Schwalbe H. 19 F NMR-Based Fragment Screening for 14 Different Biologically Active RNAs and 10 DNA and Protein Counter-Screens. Chembiochem 2021; 22:423-433. [PMID: 32794266 PMCID: PMC7436455 DOI: 10.1002/cbic.202000476] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/11/2020] [Indexed: 11/17/2022]
Abstract
We report here the nuclear magnetic resonance 19 F screening of 14 RNA targets with different secondary and tertiary structure to systematically assess the druggability of RNAs. Our RNA targets include representative bacterial riboswitches that naturally bind with nanomolar affinity and high specificity to cellular metabolites of low molecular weight. Based on counter-screens against five DNAs and five proteins, we can show that RNA can be specifically targeted. To demonstrate the quality of the initial fragment library that has been designed for easy follow-up chemistry, we further show how to increase binding affinity from an initial fragment hit by chemistry that links the identified fragment to the intercalator acridine. Thus, we achieve low-micromolar binding affinity without losing binding specificity between two different terminator structures.
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Affiliation(s)
- Oliver Binas
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Tom Landgraf
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Albrecht Eduard Völklein
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Jason Martins
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Hannes Berg
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Thomas Biedenbänder
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Santosh Lakshmi Gande
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Anna Niesteruk
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Tatjana Schamber
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Alix Tröster
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Julia Wirmer‐Bartoschek
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Maria Alexandra Wirtz Martin
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Kamal Azzaoui
- Saverna TherapeuticsGewerbestrasse 244123AllschwilSwitzerland
| | - Christian Richter
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | | | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
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31
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Diethelm-Varela B. Using NMR Spectroscopy in the Fragment-Based Drug Discovery of Small-Molecule Anticancer Targeted Therapies. ChemMedChem 2020; 16:725-742. [PMID: 33236493 DOI: 10.1002/cmdc.202000756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/21/2020] [Indexed: 12/19/2022]
Abstract
Against the challenge of providing personalized cancer care, the development of targeted therapies stands as a promising approach. The discovery of these agents can benefit from fragment-based drug discovery (FBDD) methods that help guide ligand design and provide key structural information on the targets of interest. In particular, nuclear magnetic resonance spectroscopy is a promising biophysical tool in fragment discovery due to its detection capabilities and versatility. This review provides an overview of FBDD, describes the basis of NMR-based fragment screening, summarizes some exciting technical advances reported over the past decades, and closes with a discussion of selected case studies where this technique has been used as part of drug discovery campaigns to produce lead compounds towards the design of anti-cancer targeted therapies.
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Affiliation(s)
- Benjamin Diethelm-Varela
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD 21201, USA
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32
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Rüdisser SH, Goldberg N, Ebert MO, Kovacs H, Gossert AD. Efficient affinity ranking of fluorinated ligands by 19F NMR: CSAR and FastCSAR. JOURNAL OF BIOMOLECULAR NMR 2020; 74:579-594. [PMID: 32556806 DOI: 10.1007/s10858-020-00325-x] [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: 04/01/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Fluorine NMR has recently gained high popularity in drug discovery as it allows efficient and sensitive screening of large numbers of ligands. However, the positive hits found in screening must subsequently be ranked according to their affinity in order to prioritize them for follow-up chemistry. Unfortunately, the primary read-out from the screening experiments, namely the increased relaxation rate upon binding, is not proportional to the affinity of the ligand, as it is polluted by effects such as exchange broadening. Here we present the method CSAR (Chemical Shift-anisotropy-based Affinity Ranking) for reliable ranking of fluorinated ligands by NMR, without the need of isotope labeled protein, titrations or setting up a reporter format. Our strategy is to produce relaxation data that is directly proportional to the binding affinity. This is achieved by removing all other contributions to relaxation as follows: (i) exchange effects are efficiently suppressed by using high power spin lock pulses, (ii) dipolar relaxation effects are approximately subtracted by measuring at two different magnetic fields and (iii) differences in chemical shift anisotropy are normalized using calculated values. A similar ranking can be obtained with the simplified approach FastCSAR that relies on a measurement of a single relaxation experiment at high field (preferably > 600 MHz). An affinity ranking obtained in this simple way will enable prioritizing ligands and thus improve the efficiency of fragment-based drug design.
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Affiliation(s)
- Simon H Rüdisser
- Institute for Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland
- Biomolecular NMR Spectroscopy Platform, ETH Zürich, 8093, Zürich, Switzerland
| | - Nils Goldberg
- Institute for Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland
- Biomolecular NMR Spectroscopy Platform, ETH Zürich, 8093, Zürich, Switzerland
| | - Marc-Olivier Ebert
- Laboratorium für Organische Chemie, ETH Zürich, 8093, Zürich, Switzerland
| | | | - Alvar D Gossert
- Institute for Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland.
- Biomolecular NMR Spectroscopy Platform, ETH Zürich, 8093, Zürich, Switzerland.
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33
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Baranowski MR, Warminski M, Jemielity J, Kowalska J. 5'-fluoro(di)phosphate-labeled oligonucleotides are versatile molecular probes for studying nucleic acid secondary structure and interactions by 19F NMR. Nucleic Acids Res 2020; 48:8209-8224. [PMID: 32514551 PMCID: PMC7470941 DOI: 10.1093/nar/gkaa470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/19/2020] [Accepted: 05/22/2020] [Indexed: 01/03/2023] Open
Abstract
The high sensitivity of 19F nucleus to changes in the chemical environment has promoted the use of fluorine-labeled molecular probes to study structure and interactions of nucleic acids by 19F NMR. So far, most efforts have focused on incorporating the fluorine atom into nucleobase and ribose moieties using either monomer building blocks for solid-phase synthesis, or nucleoside triphosphates for enzymatic synthesis. Here, we report a simple and efficient synthesis of 5'-fluoromonophosphorylated and 5'-fluorodiphosphorylated oligodeoxyribonucleotides, which combines solid-phase and in-solution synthesis methods and requires only commercially available nucleoside phosphoramidites, followed by their evaluation as 19F NMR probes. We confirmed that the fluorine atom at the oligonucleotide 5' end did not alter the secondary structure of DNA fragments. Moreover, at the same time, it enabled real-time 19F NMR monitoring of various DNA-related biophysical processes, such as oligonucleotide hybridization (including mismatch identification), G-quadruplex folding/unfolding and its interactions with thrombin, as well as formation of an i-motif structure and its interaction with small-molecule ligands.
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Affiliation(s)
- Marek R Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Stefana Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
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Paladino A, Woodford MR, Backe SJ, Sager RA, Kancherla P, Daneshvar MA, Chen VZ, Bourboulia D, Ahanin EF, Prodromou C, Bergamaschi G, Strada A, Cretich M, Gori A, Veronesi M, Bandiera T, Vanna R, Bratslavsky G, Serapian SA, Mollapour M, Colombo G. Chemical Perturbation of Oncogenic Protein Folding: from the Prediction of Locally Unstable Structures to the Design of Disruptors of Hsp90-Client Interactions. Chemistry 2020; 26:9459-9465. [PMID: 32167602 PMCID: PMC7415569 DOI: 10.1002/chem.202000615] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Indexed: 12/20/2022]
Abstract
Protein folding quality control in cells requires the activity of a class of proteins known as molecular chaperones. Heat shock protein-90 (Hsp90), a multidomain ATP driven molecular machine, is a prime representative of this family of proteins. Interactions between Hsp90, its co-chaperones, and client proteins have been shown to be important in facilitating the correct folding and activation of clients. Hsp90 levels and functions are elevated in tumor cells. Here, we computationally predict the regions on the native structures of clients c-Abl, c-Src, Cdk4, B-Raf and Glucocorticoid Receptor, that have the highest probability of undergoing local unfolding, despite being ordered in their native structures. Such regions represent potential ideal interaction points with the Hsp90-system. We synthesize mimics spanning these regions and confirm their interaction with partners of the Hsp90 complex (Hsp90, Cdc37 and Aha1) by Nuclear Magnetic Resonance (NMR). Designed mimics selectively disrupt the association of their respective clients with the Hsp90 machinery, leaving unrelated clients unperturbed and causing apoptosis in cancer cells. Overall, selective targeting of Hsp90 protein-protein interactions is achieved without causing indiscriminate degradation of all clients, setting the stage for the development of therapeutics based on specific chaperone:client perturbation.
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Affiliation(s)
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Rebecca A Sager
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- College of Medicine, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Priyanka Kancherla
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Michael A Daneshvar
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Victor Z Chen
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Elham F Ahanin
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | | | | | | | | | | | - Marina Veronesi
- D3-PharmaChemistry, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Tiziano Bandiera
- D3-PharmaChemistry, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Renzo Vanna
- Institute for Photonics and Nanotechnologies, IFN-CNR, c/o Dept. of Physics, Politecnico di Milano, Piazza L. Da Vinci 32, 20133, Milano, Italy
| | - Gennady Bratslavsky
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Stefano A Serapian
- University of Pavia, Department of Chemistry, Viale Taramelli 10, 27100, Pavia, Italy
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Giorgio Colombo
- SCITEC-CNR, via Mario Bianco 9, 20131, Milano, Italy
- University of Pavia, Department of Chemistry, Viale Taramelli 10, 27100, Pavia, Italy
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35
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Furihata K, Tashiro M. Identification of Binding Epitopes of a Fluorinated Compound Bound to Proteins Using 1H and 19F NMR Spectroscopy. ANAL SCI 2020; 36:881-883. [PMID: 32037346 DOI: 10.2116/analsci.19n033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
1H/19F NMR-based screening methods were applied to a human serum albumin-fleroxacin complex. Fleroxacin contains three fluorine atoms in a molecule, which is suitable as a model fluorinated compound for NMR analysis with 1H and 19F detection. The 19F{1H} and 1H{1H} saturation transfer difference spectra were acquired and the 1H/19F spin-lattice relaxation rates were measured with and without any selective irradiation of protein resonance to identify the binding epitopes of fleroxacin. Because several 1H signals of fleroxacin resonated close to water, its precise signal intensities were unavailable. The 19F NMR-based screening methods successfully provide complementary information, indicating its importance in the analysis of fluorinated compounds.
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Affiliation(s)
- Kazuo Furihata
- Division of Agriculture and Agricultural Life Sciences, The University of Tokyo
| | - Mitsuru Tashiro
- Department of Chemistry, College of Science and Technology, Meisei University
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36
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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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37
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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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38
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Stadmiller SS, Aguilar JS, Waudby CA, Pielak GJ. Rapid Quantification of Protein-Ligand Binding via 19F NMR Lineshape Analysis. Biophys J 2020; 118:2537-2548. [PMID: 32348722 PMCID: PMC7231920 DOI: 10.1016/j.bpj.2020.03.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/19/2020] [Indexed: 12/14/2022] Open
Abstract
Fluorine incorporation is ideally suited to many NMR techniques, and incorporation of fluorine into proteins and fragment libraries for drug discovery has become increasingly common. Here, we use one-dimensional 19F NMR lineshape analysis to quantify the kinetics and equilibrium thermodynamics for the binding of a fluorine-labeled Src homology 3 (SH3) protein domain to four proline-rich peptides. SH3 domains are one of the largest and most well-characterized families of protein recognition domains and have a multitude of functions in eukaryotic cell signaling. First, we showe that fluorine incorporation into SH3 causes only minor structural changes to both the free and bound states using amide proton temperature coefficients. We then compare the results from lineshape analysis of one-dimensional 19F spectra to those from two-dimensional 1H-15N heteronuclear single quantum coherence spectra. Their agreement demonstrates that one-dimensional 19F lineshape analysis is a robust, low-cost, and fast alternative to traditional heteronuclear single quantum coherence-based experiments. The data show that binding is diffusion limited and indicate that the transition state is highly similar to the free state. We also measured binding as a function of temperature. At equilibrium, binding is enthalpically driven and arises from a highly positive activation enthalpy for association with small entropic contributions. Our results agree with those from studies using different techniques, providing additional evidence for the utility of 19F NMR lineshape analysis, and we anticipate that this analysis will be an effective tool for rapidly characterizing the energetics of protein interactions.
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Affiliation(s)
| | - Jhoan S Aguilar
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Christopher A Waudby
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina; Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina.
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39
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Noh H, Lim T, Park BY, Han MS. A Fluorescence-Based High-Throughput Screening Method for Olefin Metathesis Using a Ratiometric Fluorescent Probe. Org Lett 2020; 22:1703-1708. [PMID: 31855442 DOI: 10.1021/acs.orglett.9b04462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
(Z)-1,8-Di(pyren-1-yl)oct-4-ene (1) was prepared as a probe for olefin metathesis. The conversions of substrate by olefin metathesis under various conditions were calculated using the ratiometric fluorescence intensity change of 1. The conversions calculated by 1 and gas chromatography were consistent. These results show that conversions of olefin metathesis can be simply obtained from the fluorescence change of 1 and this method can be applied to the high-throughput screening (HTS) method for various olefin metathesis.
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Affiliation(s)
- Hyeongju Noh
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Taeho Lim
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Byoung Yong Park
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Min Su Han
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
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40
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Chrominski M, Baranowski MR, Chmielinski S, Kowalska J, Jemielity J. Synthesis of Trifluoromethylated Purine Ribonucleotides and Their Evaluation as 19F NMR Probes. J Org Chem 2020; 85:3440-3453. [PMID: 31994393 PMCID: PMC7497640 DOI: 10.1021/acs.joc.9b03198] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protected guanosine and adenosine ribonucleosides and guanine nucleotides are readily functionalized with CF3 substituents within the nucleobase. Protected guanosine is trifluoromethylated at the C8 position under radical-generating conditions in up to 95% yield and guanosine 5'-oligophosphates in up to 35% yield. In the case of adenosine, the selectivity of trifluoromethylation depends heavily on the functional group protection strategy and leads to a set of CF3-modified nucleosides with different substitution patterns (C8, C2, or both) in up to 37% yield. Further transformations based on phosphorimidazolide chemistry afford various CF3-substituted mono- and dinucleoside oligophosphates in good yields. The utility of the trifluoromethylated nucleotides as probes for 19F NMR-based real-time enzymatic reaction monitoring is demonstrated with three different human nucleotide hydrolases (Fhit, DcpS, and cNIIIB). Substrate and product(s) resonances were sufficiently separated to enable effective tracking of each enzymatic activity of interest.
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Affiliation(s)
- Mikolaj Chrominski
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Marek R Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Sebastian Chmielinski
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
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41
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Nasr JJ, Shalan S. Validated 1H and 19F nuclear magnetic resonance for the quantitative determination of the hepatitis C antiviral drugs sofosbuvir, ledipasvir, and daclatasvir in tablet dosage forms. Microchem J 2020. [DOI: 10.1016/j.microc.2019.104437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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42
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Kang C. 19F-NMR in Target-based Drug Discovery. Curr Med Chem 2019; 26:4964-4983. [PMID: 31187703 DOI: 10.2174/0929867326666190610160534] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/14/2018] [Accepted: 03/13/2019] [Indexed: 02/06/2023]
Abstract
Solution NMR spectroscopy plays important roles in understanding protein structures, dynamics and protein-protein/ligand interactions. In a target-based drug discovery project, NMR can serve an important function in hit identification and lead optimization. Fluorine is a valuable probe for evaluating protein conformational changes and protein-ligand interactions. Accumulated studies demonstrate that 19F-NMR can play important roles in fragment- based drug discovery (FBDD) and probing protein-ligand interactions. This review summarizes the application of 19F-NMR in understanding protein-ligand interactions and drug discovery. Several examples are included to show the roles of 19F-NMR in confirming identified hits/leads in the drug discovery process. In addition to identifying hits from fluorinecontaining compound libraries, 19F-NMR will play an important role in drug discovery by providing a fast and robust way in novel hit identification. This technique can be used for ranking compounds with different binding affinities and is particularly useful for screening competitive compounds when a reference ligand is available.
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Affiliation(s)
- CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
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43
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Nikolaev Y, Ripin N, Soste M, Picotti P, Iber D, Allain FHT. Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis. Nat Methods 2019; 16:743-749. [PMID: 31363225 PMCID: PMC6837886 DOI: 10.1038/s41592-019-0495-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
Abstract
Cellular behavior is controlled by the interplay of diverse biomolecules. Most experimental methods, however, can only monitor a single molecule class or reaction type at a time. We developed an in vitro nuclear magnetic resonance spectroscopy (NMR) approach, which permitted dynamic quantification of an entire 'heterotypic' network-simultaneously monitoring three distinct molecule classes (metabolites, proteins and RNA) and all elementary reaction types (bimolecular interactions, catalysis, unimolecular changes). Focusing on an eight-reaction co-transcriptional RNA folding network, in a single sample we recorded over 35 time points with over 170 observables each, and accurately determined five core reaction constants in multiplex. This reconstruction revealed unexpected cross-talk between the different reactions. We further observed dynamic phase-separation in a system of five distinct RNA-binding domains in the course of the RNA transcription reaction. Our Systems NMR approach provides a deeper understanding of biological network dynamics by combining the dynamic resolution of biochemical assays and the multiplexing ability of 'omics'.
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Affiliation(s)
- Yaroslav Nikolaev
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland.
| | - Nina Ripin
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Martin Soste
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Paola Picotti
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Dagmar Iber
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Frédéric H-T Allain
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland.
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44
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Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase. Nat Commun 2019; 10:2534. [PMID: 31182716 PMCID: PMC6557900 DOI: 10.1038/s41467-019-10190-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/26/2019] [Indexed: 01/10/2023] Open
Abstract
The suppressor of cytokine signaling 2 (SOCS2) acts as substrate recognition subunit of a Cullin5 E3 ubiquitin ligase complex. SOCS2 binds to phosphotyrosine-modified epitopes as degrons for ubiquitination and proteasomal degradation, yet the molecular basis of substrate recognition has remained elusive. Here, we report co-crystal structures of SOCS2-ElonginB-ElonginC in complex with phosphorylated peptides from substrates growth hormone receptor (GHR-pY595) and erythropoietin receptor (EpoR-pY426) at 1.98 Å and 2.69 Å, respectively. Both peptides bind in an extended conformation recapitulating the canonical SH2 domain-pY pose, but capture different conformations of the EF loop via specific hydrophobic interactions. The flexible BG loop is fully defined in the electron density, and does not contact the substrate degron directly. Cancer-associated SNPs located around the pY pocket weaken substrate-binding affinity in biophysical assays. Our findings reveal insights into substrate recognition and specificity by SOCS2, and provide a blueprint for small molecule ligand design. The suppressor of cytokine signaling 2 (SOCS2) is a component of the Cullin5 E3 ubiquitin ligase complex. Here the authors provide insights into substrate recognition and specificity of SOCS2 by determining the crystal structures of the SOCS2-ElonginB-ElonginC in complex with phosphorylated peptides from two of its substrates the growth hormone receptor and erythropoietin receptor.
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45
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Dalvit C, Parent A, Vallée F, Mathieu M, Rak A. Fast NMR Methods for Measuring in the Direct and/or Competition Mode the Dissociation Constants of Chemical Fragments Interacting with a Receptor. ChemMedChem 2019; 14:1115-1127. [DOI: 10.1002/cmdc.201900152] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Indexed: 12/16/2022]
Affiliation(s)
| | - Annick Parent
- Bio Structure and BiophysicsIntegrated Drug DiscoverySanofi R&D 13, Quai Jules Guesde—BP 14 94403 Vitry sur Seine Cedex France
| | - Francois Vallée
- Bio Structure and BiophysicsIntegrated Drug DiscoverySanofi R&D 13, Quai Jules Guesde—BP 14 94403 Vitry sur Seine Cedex France
| | - Magali Mathieu
- Bio Structure and BiophysicsIntegrated Drug DiscoverySanofi R&D 13, Quai Jules Guesde—BP 14 94403 Vitry sur Seine Cedex France
| | - Alexey Rak
- Bio Structure and BiophysicsIntegrated Drug DiscoverySanofi R&D 13, Quai Jules Guesde—BP 14 94403 Vitry sur Seine Cedex France
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46
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Sensitive Water Ligand Observed via Gradient Spectroscopy with 19F Detection for Analysis of Fluorinated Compounds Bound to Proteins. MAGNETOCHEMISTRY 2019. [DOI: 10.3390/magnetochemistry5020029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The water ligand observed via a gradient spectroscopy type experiment with 19F detection was applied to selectively detect fluorinated compounds with affinity to the target proteins. The 19F signals of bound and unbound compounds were observed as opposite phases, which was advantageous to distinguish the binding state. The proposed NMR method was optimized based on the 19F{1H} saturation transfer difference pulse sequence, and various inversion pulses for the water resonance were evaluated with the aim of high sensitivity.
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de Castro GV, Ciulli A. Spy vs. spy: selecting the best reporter for 19F NMR competition experiments. Chem Commun (Camb) 2019; 55:1482-1485. [PMID: 30644956 PMCID: PMC6369734 DOI: 10.1039/c8cc09790a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 12/27/2018] [Indexed: 12/15/2022]
Abstract
Systematic characterization of a series of fluorinated VHL ligands, varying binding affinity and position of the trifluoromethyl group, qualifies a spy molecule for competitive 19F NMR screening and reveals guiding principles to develop highly sensitive assays with low material consumption.
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Affiliation(s)
- Guilherme Vieira de Castro
- Division of Biological Chemistry and Drug Discovery
, School of Life Sciences
, University of Dundee
,
Dow Street
, Dundee
, DD1 5EH
, UK
.
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery
, School of Life Sciences
, University of Dundee
,
Dow Street
, Dundee
, DD1 5EH
, UK
.
| |
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Polshakov VI, Batuev EA, Mantsyzov AB. NMR screening and studies of target–ligand interactions. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
Drug discovery is an extremely difficult and challenging endeavor with a very high failure rate. The task of identifying a drug that is safe, selective, and effective is a daunting proposition because disease biology is complex and highly variable across patients. Metabolomics enables the discovery of disease biomarkers, which provides insights into the molecular and metabolic basis of disease and may be used to assess treatment prognosis and outcome. In this regard, metabolomics has evolved to become an important component of the drug discovery process to resolve efficacy and toxicity issues and as a tool for precision medicine. A detailed description of an experimental protocol is presented that outlines the application of NMR metabolomics to the drug discovery pipeline. This includes (1) target identification by understanding the metabolic dysregulation in diseases, (2) predicting the mechanism of action of newly discovered or existing drug therapies, (3) and using metabolomics to screen a chemical lead to assess biological activity. Unlike other OMICS approaches, the metabolome is "fragile" and may be negatively impacted by improper sample collection, storage, and extraction procedures. Similarly, biologically irrelevant conclusions may result from incorrect data collection, preprocessing or processing procedures, or the erroneous use of univariate and multivariate statistical methods. These critical concerns are also addressed in the protocol.
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