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Werner AD, Krapoth N, Norris MJ, Heine A, Klebe G, Saphire EO, Becker S. Development of a Crystallographic Screening to Identify Sudan Virus VP40 Ligands. ACS OMEGA 2024; 9:33193-33203. [PMID: 39100314 PMCID: PMC11292656 DOI: 10.1021/acsomega.4c04829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/05/2024] [Accepted: 07/05/2024] [Indexed: 08/06/2024]
Abstract
The matrix protein VP40 of the highly pathogenic Sudan virus (genus Orthoebolavirus) is a multifunctional protein responsible for the recruitment of viral nucleocapsids to the plasma membrane and the budding of infectious virions. In addition to its role in assembly, VP40 also downregulates viral genome replication and transcription. VP40's existence in various homo-oligomeric states is presumed to underpin its diverse functional capabilities during the viral life cycle. Given the absence of licensed therapeutics targeting the Sudan virus, our study focused on inhibiting VP40 dimers, the structural precursors to critical higher-order oligomers, as a novel antiviral strategy. We have established a crystallographic screening pipeline for the identification of small-molecule fragments capable of binding to VP40. Dimeric VP40 of the Sudan virus was recombinantly expressed in bacteria, purified, crystallized, and soaked in a solution of 96 different preselected fragments. Salicylic acid was identified as a crystallographic hit with clear electron density in the pocket between the N- and the C-termini of the VP40 dimer. The binding interaction is predominantly coordinated by amino acid residues leucine 158 (L158) and arginine 214 (R214), which are key in stabilizing salicylic acid within the binding pocket. While salicylic acid displayed minimal impact on the functional aspects of VP40, we delved deeper into characterizing the druggability of the identified binding pocket. We analyzed the influence of residues L158 and R214 on the formation of virus-like particles and viral RNA synthesis. Site-directed mutagenesis of these residues to alanine markedly affected both VP40's budding activity and its effect on viral RNA synthesis, underscoring the potential of the salicylic acid binding pocket as a drug target. In summary, our findings lay the foundation for structure-guided drug design to provide lead compounds against Sudan virus VP40.
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Affiliation(s)
| | - Nils Krapoth
- Institute
for Virology, University of Marburg, D-35043 Marburg, Hessen, Germany
- Institut
für Molekulare Biologie gGmbH, D-55128 Mainz, Rheinland-Pfalz, Germany
| | - Michael J. Norris
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Andreas Heine
- Institute
of Pharmaceutical Chemistry, University
of Marburg, D-35032 Marburg, Hessen, Germany
| | - Gerhard Klebe
- Institute
of Pharmaceutical Chemistry, University
of Marburg, D-35032 Marburg, Hessen, Germany
| | | | - Stephan Becker
- Institute
for Virology, University of Marburg, D-35043 Marburg, Hessen, Germany
- Partnersite
Giessen-Marburg-Langen, German Centre for
Infection Research, D-35043 Marburg, Hessen, Germany
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2
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Espeland LO, Georgiou C, Klein R, Bhukya H, Haug BE, Underhaug J, Mainkar PS, Brenk R. An Experimental Toolbox for Structure-Based Hit Discovery for P. aeruginosa FabF, a Promising Target for Antibiotics. ChemMedChem 2021; 16:2715-2726. [PMID: 34189850 PMCID: PMC8518799 DOI: 10.1002/cmdc.202100302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/22/2021] [Indexed: 12/12/2022]
Abstract
FabF (3-oxoacyl-[acyl-carrier-protein] synthase 2), which catalyses the rate limiting condensation reaction in the fatty acid synthesis II pathway, is an attractive target for new antibiotics. Here, we focus on FabF from P. aeruginosa (PaFabF) as antibiotics against this pathogen are urgently needed. To facilitate exploration of this target we have set up an experimental toolbox consisting of binding assays using bio-layer interferometry (BLI) as well as saturation transfer difference (STD) and WaterLOGSY NMR in addition to robust conditions for structure determination. The suitability of the toolbox to support structure-based design of FabF inhibitors was demonstrated through the validation of hits obtained from virtual screening. Screening a library of almost 5 million compounds resulted in 6 compounds for which binding into the malonyl-binding site of FabF was shown. For one of the hits, the crystal structure in complex with PaFabF was determined. Based on the obtained binding mode, analogues were designed and synthesised, but affinity could not be improved. This work has laid the foundation for structure-based exploration of PaFabF.
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Affiliation(s)
- Ludvik Olai Espeland
- Department of BiomedicineUniversity of BergenJonas Lies Vei 915020BergenNorway
- Department of ChemistryUniversity of BergenAllégaten 415007BergenNorway
| | - Charis Georgiou
- Department of BiomedicineUniversity of BergenJonas Lies Vei 915020BergenNorway
| | - Raphael Klein
- Department of BiomedicineUniversity of BergenJonas Lies Vei 915020BergenNorway
- Institute of Pharmacy and BiochemistryJohannes Gutenberg UniversityStaudingerweg 555128MainzGermany
| | - Hemalatha Bhukya
- Department of Organic Synthesis & Process ChemistryCSIR-Indian Institute of Chemical TechnologyTarnakaHyderabad500007India
| | - Bengt Erik Haug
- Department of ChemistryUniversity of BergenAllégaten 415007BergenNorway
| | - Jarl Underhaug
- Department of ChemistryUniversity of BergenAllégaten 415007BergenNorway
| | - Prathama S. Mainkar
- Department of Organic Synthesis & Process ChemistryCSIR-Indian Institute of Chemical TechnologyTarnakaHyderabad500007India
| | - Ruth Brenk
- Department of BiomedicineUniversity of BergenJonas Lies Vei 915020BergenNorway
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Wolter M, Valenti D, Cossar PJ, Levy LM, Hristeva S, Genski T, Hoffmann T, Brunsveld L, Tzalis D, Ottmann C. Fragment-Based Stabilizers of Protein-Protein Interactions through Imine-Based Tethering. Angew Chem Int Ed Engl 2020; 59:21520-21524. [PMID: 32816380 PMCID: PMC7756862 DOI: 10.1002/anie.202008585] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/16/2020] [Indexed: 12/22/2022]
Abstract
Small‐molecule stabilization of protein–protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a “bottom‐up” approach is largely unanswered. We report a novel concept for identifying initial chemical matter for PPI stabilization based on imine‐forming fragments. The imine bond offers a covalent anchor for site‐directed fragment targeting, whereas its transient nature enables efficient analysis of structure–activity relationships. This bond enables fragment identification and optimisation using protein crystallography. We report novel fragments that bind specifically to a lysine at the PPI interface of the p65‐subunit‐derived peptide of NF‐κB with the adapter protein 14‐3‐3. Those fragments that subsequently establish contacts with the p65‐derived peptide, rather than with 14‐3‐3, efficiently stabilize the 14‐3‐3/p65 complex and offer novel starting points for molecular glues.
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Affiliation(s)
- Madita Wolter
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Dario Valenti
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Laura M Levy
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Stanimira Hristeva
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Thorsten Genski
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Torsten Hoffmann
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Dimitrios Tzalis
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
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4
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Wolter M, Valenti D, Cossar PJ, Levy LM, Hristeva S, Genski T, Hoffmann T, Brunsveld L, Tzalis D, Ottmann C. Fragment‐Based Stabilizers of Protein–Protein Interactions through Imine‐Based Tethering. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Madita Wolter
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Dario Valenti
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Peter J. Cossar
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Laura M. Levy
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Stanimira Hristeva
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Thorsten Genski
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Torsten Hoffmann
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Dimitrios Tzalis
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
- Department of Chemistry University of Duisburg-Essen Universitätsstrasse 7 45117 Essen Germany
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Hassaan E, Hohn C, Ehrmann FR, Goetzke FW, Movsisyan L, Hüfner-Wulsdorf T, Sebastiani M, Härtsch A, Reuter K, Diederich F, Klebe G. Fragment Screening Hit Draws Attention to a Novel Transient Pocket Adjacent to the Recognition Site of the tRNA-Modifying Enzyme TGT. J Med Chem 2020; 63:6802-6820. [PMID: 32515955 DOI: 10.1021/acs.jmedchem.0c00115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fragment-based lead discovery was applied to tRNA-guanine transglycosylase, an enzyme modifying post-transcriptionally tRNAs in Shigella, the causative agent of shigellosis. TGT inhibition prevents translation of Shigella's virulence factor VirF, hence reducing pathogenicity. One discovered fragment opens a transient subpocket in the preQ1-recognition site by pushing back an aspartate residue. This step is associated with reorganization of further amino acids structurally transforming a loop adjacent to the recognition site by duplicating the volume of the preQ1-recognition pocket. We synthesized 6-carboxamido-, 6-hydrazido-, and 4-guanidino-benzimidazoles to target the opened pocket, including a dihydro-imidazoquinazoline with a propyn-1-yl exit vector pointing into the transient pocket and displacing a conserved water network. MD simulations and hydration-site analysis suggest water displacement to contribute favorably to ligand binding. A cysteine residue, exclusively present in bacterial TGTs, serves as gatekeeper of the transient subpocket. It becomes accessible upon pocket opening for selective covalent attachment of electrophilic ligands in eubacterial TGTs.
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Affiliation(s)
- Engi Hassaan
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Christoph Hohn
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Frederik R Ehrmann
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - F Wieland Goetzke
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Levon Movsisyan
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Tobias Hüfner-Wulsdorf
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Maurice Sebastiani
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Adrian Härtsch
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Klaus Reuter
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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Glöckner S, Heine A, Klebe G. A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II. Biomolecules 2020; 10:biom10040518. [PMID: 32235320 PMCID: PMC7226012 DOI: 10.3390/biom10040518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 11/16/2022] Open
Abstract
Fragment screening is a powerful tool to identify and characterize binding pockets in proteins. We herein present the results of a proof-of-concept screening campaign of a versatile 96-entry fragment library from our laboratory against the drug target and model protein human carbonic anhydrase II. The screening revealed a novel chemotype for carbonic anhydrase inhibition, as well as less common non-covalent interaction types and unexpected covalent linkages. Lastly, different runs of the PanDDA tool reveal a practical hint for its application.
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7
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Hassaan E, Eriksson P, Geschwindner S, Heine A, Klebe G. Fragments as Novel Starting Points for tRNA-Guanine Transglycosylase Inhibitors Found by Alternative Screening Strategies. ChemMedChem 2020; 15:324-337. [PMID: 31808981 PMCID: PMC7687107 DOI: 10.1002/cmdc.201900604] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/02/2019] [Indexed: 12/02/2022]
Abstract
Crystallography provides structural information crucial for fragment optimization, however several criteria must be met to screen directly on protein crystals as soakable, well-diffracting specimen must be available. We screened a 96-fragment library against the tRNA-modifying enzyme TGT using crystallography. Eight hits, some with surprising binding poses, were detected. However, the amount of data collection, reduction and refinement is assumed substantial. Therefore, having a reliable cascade of fast and cost-efficient methods available for pre-screening before embarking to elaborate crystallographic screening appears beneficial. This allows filtering of compounds to the most promising hits, available to rapidly progress from hit-to-lead. But how to ensure that this workflow is reliable? To answer this question, we also applied SPR and NMR to the same screening sample to study whether identical hits are retrieved. Upon hit-list comparisons, crystallography shows with NMR and SPR, only one overlapping hit and all three methods shared no common hits. This questions a cascade-type screening protocol at least in the current example. Compared to crystallography, SPR and NMR detected higher percentages of non-active-site binders suggesting the importance of running reporter ligand-based competitive screens in SPR and NMR, a requirement not needed in crystallography. Although not specific, NMR proved a more sensitive method relative to SPR and crystallography, as it picked up the highest numbers of binders.
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Affiliation(s)
- Engi Hassaan
- Institute of Pharmaceutical ChemistryPhilipps University MarburgMarbacher Weg 635032MarburgGermany
| | - Per‐Olof Eriksson
- Structure, Biophysics and Fragment-based Lead GenerationDiscovery Sciences, R&D, AstraZeneca431 83GothenburgSweden
| | - Stefan Geschwindner
- Structure, Biophysics and Fragment-based Lead GenerationDiscovery Sciences, R&D, AstraZeneca431 83GothenburgSweden
| | - Andreas Heine
- Institute of Pharmaceutical ChemistryPhilipps University MarburgMarbacher Weg 635032MarburgGermany
| | - Gerhard Klebe
- Institute of Pharmaceutical ChemistryPhilipps University MarburgMarbacher Weg 635032MarburgGermany
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