1
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Hochban PMM, Heyder L, Heine A, Diederich WE. What doesn't fit is made to fit: Pim-1 kinase adapts to the configuration of stilbene-based inhibitors. Arch Pharm (Weinheim) 2024:e2400094. [PMID: 38631036 DOI: 10.1002/ardp.202400094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024]
Abstract
Recently, we have developed novel Pim-1 kinase inhibitors starting from a dihydrobenzofuran core structure using a computational approach. Here, we report the design and synthesis of stilbene-based Pim-1 kinase inhibitors obtained by formal elimination of the dihydrofuran ring. These inhibitors of the first design cycle, which were obtained as inseparable cis/trans mixtures, showed affinities in the low single-digit micromolar range. To be able to further optimize these compounds in a structure-based fashion, we determined the X-ray structures of the protein-ligand-complexes. Surprisingly, only the cis-isomer binds upon crystallization of the cis/trans-mixture of the ligands with Pim-1 kinase and the substrate PIMTIDE, the binding mode being largely consistent with that predicted by docking. After crystallization of the exclusively trans-configured derivatives, a markedly different binding mode for the inhibitor and a concomitant rearrangement of the glycine-rich loop is observed, resulting in the ligand being deeply buried in the binding pocket.
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Affiliation(s)
- Phil M M Hochban
- Institut für Pharmazeutische Chemie, Zentrum für Tumor und Immunbiologie, Philipps-Universität Marburg, Marburg, Germany
| | - Lukas Heyder
- Institut für Pharmazeutische Chemie, Zentrum für Tumor und Immunbiologie, Philipps-Universität Marburg, Marburg, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Wibke E Diederich
- Institut für Pharmazeutische Chemie, Zentrum für Tumor und Immunbiologie, Philipps-Universität Marburg, Marburg, Germany
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2
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Werner AD, Schauflinger M, Norris MJ, Klüver M, Trodler A, Herwig A, Brandstädter C, Dillenberger M, Klebe G, Heine A, Saphire EO, Becker K, Becker S. The C-terminus of Sudan ebolavirus VP40 contains a functionally important CX nC motif, a target for redox modifications. Structure 2023; 31:1038-1051.e7. [PMID: 37392738 DOI: 10.1016/j.str.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/10/2023] [Accepted: 06/06/2023] [Indexed: 07/03/2023]
Abstract
The Ebola virus matrix protein VP40 mediates viral budding and negatively regulates viral RNA synthesis. The mechanisms by which these two functions are exerted and regulated are unknown. Using a high-resolution crystal structure of Sudan ebolavirus (SUDV) VP40, we show here that two cysteines in the flexible C-terminal arm of VP40 form a stabilizing disulfide bridge. Notably, the two cysteines are targets of posttranslational redox modifications and interact directly with the host`s thioredoxin system. Mutation of the cysteines impaired the budding function of VP40 and relaxed its inhibitory role for viral RNA synthesis. In line with these results, the growth of recombinant Ebola viruses carrying cysteine mutations was impaired and the released viral particles were elongated. Our results revealed the exact positions of the cysteines in the C-terminal arm of SUDV VP40. The cysteines and/or their redox status are critically involved in the differential regulation of viral budding and viral RNA synthesis.
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Affiliation(s)
| | | | - Michael J Norris
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Michael Klüver
- Institute for Virology, Philipps-University of Marburg, Marburg, Germany
| | - Anna Trodler
- Institute for Virology, Philipps-University of Marburg, Marburg, Germany
| | - Astrid Herwig
- Institute for Virology, Philipps-University of Marburg, Marburg, Germany
| | - Christina Brandstädter
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Melissa Dillenberger
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Gerhard Klebe
- Institute for Pharmaceutical Chemistry, Philipps-University of Marburg, Marburg, Germany
| | - Andreas Heine
- Institute for Pharmaceutical Chemistry, Philipps-University of Marburg, Marburg, Germany
| | | | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Stephan Becker
- Institute for Virology, Philipps-University of Marburg, Marburg, Germany.
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3
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Klee LS, Gárdonyi M, Hüfner T, Heine A, Klebe G. Mutational Studies of Aldose Reductase to Trace a Transient Pocket Opening and to Explain Ligand Affinity Cliffs. ChemMedChem 2023; 18:e202300222. [PMID: 37278327 DOI: 10.1002/cmdc.202300222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/07/2023]
Abstract
Human aldose reductase, a target for the development of inhibitors for preventing diabetic complications, displays a transient specificity pocket which opens upon binding with specific, potent inhibitors. We investigated the opening mechanism of this pocket by mutating leucine residues involved in the gate keeping mechanism to alanine. Two isostructural inhibitors distinguished only by a single nitro to carboxy group replacement, have a 1000-fold difference in their binding affinity to the wild type. This difference is reduced to 10-fold in the mutated variants as the nitro derivative loses in affinity but conserves binding to the open transient pocket. The affinity of the carboxylate analog is minimally altered but the analog binding preference changes from the closed to open state of the transient pocket. Differences in the solvation properties of ligands and the transient pocket as well as changes from induced fit to conformational selections provide an explanation for the altered behavior of the ligands with respect to their binding to the different variants.
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Affiliation(s)
- Lea-Sophie Klee
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Marina Gárdonyi
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Tobias Hüfner
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
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4
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Obermann W, Azri MFD, Konopka L, Schmidt N, Magari F, Sherman J, Silva LMR, Hermosilla C, Ludewig AH, Houhou H, Haeberlein S, Luo MY, Häcker I, Schetelig MF, Grevelding CG, Schroeder FC, Lau GSK, Taubert A, Rodriguez A, Heine A, Yeo TC, Grünweller A, Taroncher-Oldenburg G. Broad anti-pathogen potential of DEAD box RNA helicase eIF4A-targeting rocaglates. Sci Rep 2023; 13:9297. [PMID: 37291191 PMCID: PMC10250355 DOI: 10.1038/s41598-023-35765-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
Inhibition of eukaryotic initiation factor 4A has been proposed as a strategy to fight pathogens. Rocaglates exhibit the highest specificities among eIF4A inhibitors, but their anti-pathogenic potential has not been comprehensively assessed across eukaryotes. In silico analysis of the substitution patterns of six eIF4A1 aa residues critical to rocaglate binding, uncovered 35 variants. Molecular docking of eIF4A:RNA:rocaglate complexes, and in vitro thermal shift assays with select recombinantly expressed eIF4A variants, revealed that sensitivity correlated with low inferred binding energies and high melting temperature shifts. In vitro testing with silvestrol validated predicted resistance in Caenorhabditis elegans and Leishmania amazonensis and predicted sensitivity in Aedes sp., Schistosoma mansoni, Trypanosoma brucei, Plasmodium falciparum, and Toxoplasma gondii. Our analysis further revealed the possibility of targeting important insect, plant, animal, and human pathogens with rocaglates. Finally, our findings might help design novel synthetic rocaglate derivatives or alternative eIF4A inhibitors to fight pathogens.
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Affiliation(s)
- Wiebke Obermann
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marburg, Germany
| | | | - Leonie Konopka
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marburg, Germany
| | - Nina Schmidt
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marburg, Germany
| | - Francesca Magari
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marburg, Germany
| | - Julian Sherman
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Liliana M R Silva
- Institute of Parasitology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Carlos Hermosilla
- Institute of Parasitology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Andreas H Ludewig
- Boyce Thompson Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Hicham Houhou
- Institute of Parasitology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Simone Haeberlein
- Institute of Parasitology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Mona Yiting Luo
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Irina Häcker
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Marc F Schetelig
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Christoph G Grevelding
- Institute of Parasitology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Frank C Schroeder
- Boyce Thompson Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | | | - Anja Taubert
- Institute of Parasitology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Ana Rodriguez
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marburg, Germany
| | - Tiong Chia Yeo
- Sarawak Biodiversity Centre, Kuching, Sarawak, Malaysia.
| | - Arnold Grünweller
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marburg, Germany.
| | - Gaspar Taroncher-Oldenburg
- Sarawak Biodiversity Centre, Kuching, Sarawak, Malaysia.
- Gaspar Taroncher Consulting, Philadelphia, PA, USA.
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5
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Rüger F, Heine A, Vornicescu D, Keusgen M. Tetrathiaporphyrine: A Novel Natural Product from
Allium
Subgenus
Melanocrommyum. European J Org Chem 2023. [DOI: 10.1002/ejoc.202201481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Fabian Rüger
- Philipps University of Marburg Institute of Pharmaceutical Chemistry Marbacher Weg 6 35032 Marburg Germany
| | - Andreas Heine
- Philipps University of Marburg Institute of Pharmaceutical Chemistry Marbacher Weg 6 35032 Marburg Germany
| | - Doru Vornicescu
- Philipps University of Marburg Institute of Pharmaceutical Chemistry Marbacher Weg 6 35032 Marburg Germany
| | - Michael Keusgen
- Philipps University of Marburg Institute of Pharmaceutical Chemistry Marbacher Weg 6 35032 Marburg Germany
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6
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Braun NJ, Huber S, Schmacke LC, Heine A, Steinmetzer T. Boroleucine-Derived Covalent Inhibitors of the ZIKV Protease. ChemMedChem 2023; 18:e202200336. [PMID: 36325810 PMCID: PMC10100045 DOI: 10.1002/cmdc.202200336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 11/02/2022] [Indexed: 11/06/2022]
Abstract
The Zika virus (ZIKV) remains a potential threat to the public health due to the lack of both an approved vaccination or a specific treatment. In this work, a series of peptidic inhibitors of the ZIKV protease with boroleucine as P1 residue was synthesized. The highest affinities with Ki values down to 8 nM were observed for compounds with basic residues in both P2 and P3 position and at the N-terminus. The low potency of reference compounds containing leucine, leucine-amide or isopentylamide as P1 residue suggested a covalent binding mode of the boroleucine-derived inhibitors. This was finally proven by crystal structure determination of the most potent inhibitor from this series in complex with the ZIKV protease.
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Affiliation(s)
- Niklas J Braun
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Simon Huber
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Luna C Schmacke
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
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7
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Weiss MS, Wollenhaupt J, Correy GJ, Fraser JS, Heine A, Klebe G, Krojer T, Thunissen M, Pearce NM. Of problems and opportunities-How to treat and how to not treat crystallographic fragment screening data. Protein Sci 2022; 31:e4391. [PMID: 36040268 PMCID: PMC9424839 DOI: 10.1002/pro.4391] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/17/2022] [Accepted: 07/11/2022] [Indexed: 11/23/2022]
Abstract
In their recent commentary in Protein Science, Jaskolski et al. analyzed three randomly picked diffraction data sets from fragment-screening group depositions from the PDB and, based on that, they claimed that such data are principally problematic. We demonstrate here that if such data are treated properly, none of the proclaimed criticisms persist.
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Affiliation(s)
- Manfred S. Weiss
- Macromolecular CrystallographyHelmholtz‐Zentrum BerlinBerlinGermany
| | - Jan Wollenhaupt
- Macromolecular CrystallographyHelmholtz‐Zentrum BerlinBerlinGermany
| | - Galen J. Correy
- Department of Bioengineering and Therapeutic SciencesUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic SciencesUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Andreas Heine
- Institute of Pharmaceutical ChemistryPhilipps University MarburgMarburgGermany
| | - Gerhard Klebe
- Institute of Pharmaceutical ChemistryPhilipps University MarburgMarburgGermany
| | | | | | - Nicholas M. Pearce
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamAmsterdamThe Netherlands
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8
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Sebastiani M, Behrens C, Dörr S, Gerber HD, Benazza R, Hernandez-Alba O, Cianférani S, Klebe G, Heine A, Reuter K. Structural and Biochemical Investigation of the Heterodimeric Murine tRNA-Guanine Transglycosylase. ACS Chem Biol 2022; 17:2229-2247. [PMID: 35815944 DOI: 10.1021/acschembio.2c00368] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In tRNAAsp, tRNAAsn, tRNATyr, and tRNAHis of most bacteria and eukaryotes, the anticodon wobble position may be occupied by the modified nucleoside queuosine, which affects the speed and the accuracy of translation. Since eukaryotes are not able to synthesize queuosine de novo, they have to salvage queuine (the queuosine base) as a micronutrient from food and/or the gut microbiome. The heterodimeric Zn2+ containing enzyme tRNA-guanine transglycosylase (TGT) catalyzes the insertion of queuine into the above-named tRNAs in exchange for the genetically encoded guanine. This enzyme has attracted medical interest since it was shown to be potentially useful for the treatment of multiple sclerosis. In addition, TGT inactivation via gene knockout leads to the suppressed cell proliferation and migration of certain breast cancer cells, which may render this enzyme a potential target for the design of compounds supporting breast cancer therapy. As a prerequisite to fully exploit the medical potential of eukaryotic TGT, we have determined and analyzed a number of crystal structures of the functional murine TGT with and without bound queuine. In addition, we have investigated the importance of two residues of its non-catalytic subunit on dimer stability and determined the Michaelis-Menten parameters of murine TGT with respect to tRNA and several natural and artificial nucleobase substrates. Ultimately, on the basis of available TGT crystal structures, we provide an entirely conclusive reaction mechanism for this enzyme, which in detail explains why the TGT-catalyzed insertion of some nucleobases into tRNA occurs reversibly while that of others is irreversible.
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Affiliation(s)
- Maurice Sebastiani
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Christina Behrens
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Stefanie Dörr
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Hans-Dieter Gerber
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Rania Benazza
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI─FR2048, 67087 Strasbourg, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI─FR2048, 67087 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI─FR2048, 67087 Strasbourg, France
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
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9
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Nguyen A, Gemmecker G, Softley CA, Movsisyan LD, Pfaffeneder T, Heine A, Reuter K, Diederich F, Sattler M, Klebe G. 19F-NMR Unveils the Ligand-Induced Conformation of a Catalytically Inactive Twisted Homodimer of tRNA-Guanine Transglycosylase. ACS Chem Biol 2022; 17:1745-1755. [PMID: 35763700 DOI: 10.1021/acschembio.2c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the structural arrangements of protein oligomers can support the design of ligands that interfere with their function in order to develop new therapeutic concepts for disease treatment. Recent crystallographic studies have elucidated a novel twisted and functionally inactive form of the homodimeric enzyme tRNA-guanine transglycosylase (TGT), a putative target in the fight against shigellosis. Active-site ligands have been identified that stimulate the rearrangement of one monomeric subunit by 130° against the other one to form an inactive twisted homodimer state. To assess whether the crystallographic observations also reflect the conformation in solution and rule out effects from crystal packing, we performed 19F-NMR spectroscopy with the introduction of 5-fluorotryptophans at four sites in TGT. The inhibitor-induced conformation of TGT in solution was assessed based on 19F-NMR chemical shift perturbations. We investigated the effect of C(4) substituted lin-benzoguanine ligands and identified a correlation between dynamic protein rearrangements and ligand-binding features in the corresponding crystal structures. These involve the destabilization of a helix next to the active site and the integrity of a flexible loop-helix motif. Ligands that either completely lack an attached C(4) substituent or use it to stabilize the geometry of the functionally competent dimer state do not indicate the presence of the twisted dimer form in the NMR spectra. The perturbation of crucial structural motifs in the inhibitors correlates with an increasing formation of the inactive twisted dimer state, suggesting these ligands are able to shift a conformational equilibrium from active C2-symmetric to inactive twisted dimer conformations. These findings suggest a novel concept for the design of drug candidates for further development.
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Affiliation(s)
- Andreas Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, Marburg D-35032, Germany
| | - Gerd Gemmecker
- Biomolecular NMR, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, Garching D-85747, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Charlotte A Softley
- Biomolecular NMR, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, Garching D-85747, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Levon D Movsisyan
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, HCI, Zürich CH-8093, Switzerland
| | - Toni Pfaffeneder
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, HCI, Zürich CH-8093, Switzerland
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, Marburg D-35032, Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, Marburg D-35032, Germany
| | - François Diederich
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, HCI, Zürich CH-8093, Switzerland
| | - Michael Sattler
- Biomolecular NMR, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, Garching D-85747, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, Marburg D-35032, Germany
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10
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Huber S, Braun NJ, Schmacke LC, Quek JP, Murra R, Bender D, Hildt E, Luo D, Heine A, Steinmetzer T. Structure-Based Optimization and Characterization of Macrocyclic Zika Virus NS2B-NS3 Protease Inhibitors. J Med Chem 2022; 65:6555-6572. [PMID: 35475620 DOI: 10.1021/acs.jmedchem.1c01860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Zika virus (ZIKV) is a human pathogenic arbovirus. So far, neither a specific treatment nor a vaccination against ZIKV infections has been approved. Starting from our previously described lead structure, a series of 29 new macrocyclic inhibitors of the Zika virus protease containing different linker motifs have been synthesized. By selecting hydrophobic d-amino acids as part of the linker, numerous inhibitors with Ki values < 5 nM were obtained. For 12 inhibitors, crystal structures in complex with the ZIKV protease up to 1.30 Å resolution were determined, which contribute to the understanding of the observed structure-activity relationship (SAR). In immunofluorescence assays, an antiviral effect was observed for compound 26 containing a d-homocyclohexylalanine residue in its linker segment. Due to its excellent selectivity profile and low cytotoxicity, this inhibitor scaffold could be a suitable starting point for the development of peptidic drugs against the Zika virus and related flaviviruses.
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Affiliation(s)
- Simon Huber
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Niklas J Braun
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Luna C Schmacke
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Jun Ping Quek
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921
| | - Robin Murra
- Federal Institute for Vaccines and Biomedicines, Department of Virology, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
| | - Daniela Bender
- Federal Institute for Vaccines and Biomedicines, Department of Virology, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
| | - Eberhard Hildt
- Federal Institute for Vaccines and Biomedicines, Department of Virology, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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11
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Sandner A, Ngo K, Sager CP, Scheer F, Daude M, Diederich WE, Heine A, Klebe G. Which Properties Allow Ligands to Open and Bind to the Transient Binding Pocket of Human Aldose Reductase? Biomolecules 2021; 11:biom11121837. [PMID: 34944481 PMCID: PMC8699021 DOI: 10.3390/biom11121837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
The transient specificity pocket of aldose reductase only opens in response to specific ligands. This pocket may offer an advantage for the development of novel, more selective ligands for proteins with similar topology that lack such an adaptive pocket. Our aim was to elucidate which properties allow an inhibitor to bind in the specificity pocket. A series of inhibitors that share the same parent scaffold but differ in their attached aromatic substituents were screened using ITC and X-ray crystallography for their ability to occupy the pocket. Additionally, we investigated the electrostatic potentials and charge distribution across the attached terminal aromatic groups with respect to their potential to bind to the transient pocket of the enzyme using ESP calculations. These methods allowed us to confirm the previously established hypothesis that an electron-deficient aromatic group is an important prerequisite for opening and occupying the specificity pocket. We also demonstrated from our crystal structures that a pH shift between 5 and 8 does not affect the binding position of the ligand in the specificity pocket. This allows for a comparison between thermodynamic and crystallographic data collected at different pH values.
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Affiliation(s)
- Anna Sandner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (A.S.); (K.N.); (A.H.)
| | - Khang Ngo
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (A.S.); (K.N.); (A.H.)
| | - Christoph P. Sager
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (A.S.); (K.N.); (A.H.)
| | - Frithjof Scheer
- Institut für Pharmazeutische Chemie, Zentrum für Tumor und Immunbiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße 3, 35032 Marburg, Germany; (F.S.); (W.E.D.)
| | - Michael Daude
- Zentrum für Tumor und Immunbiologie, Core Facility Medicinal Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 3, 35043 Marburg, Germany;
| | - Wibke E. Diederich
- Institut für Pharmazeutische Chemie, Zentrum für Tumor und Immunbiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße 3, 35032 Marburg, Germany; (F.S.); (W.E.D.)
- Zentrum für Tumor und Immunbiologie, Core Facility Medicinal Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 3, 35043 Marburg, Germany;
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (A.S.); (K.N.); (A.H.)
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (A.S.); (K.N.); (A.H.)
- Correspondence: ; Tel.: +49-6421-28-21313
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12
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Nguyen D, Abdullin D, Heubach CA, Pfaffeneder T, Nguyen A, Heine A, Reuter K, Diederich F, Schiemann O, Klebe G. Entschlüsselung der ligandeninduzierten Verdrehung eines homodimeren Enzyms mit Hilfe der gepulsten Elektron‐Elektron‐Doppelresonanz‐Spektroskopie. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Dzung Nguyen
- Institut für Pharmazeutische Chemie Philipps-Universität Marburg Marbacher Weg 8 35032 Marburg Deutschland
| | - Dinar Abdullin
- Institut für Physikalische und Theoretische Chemie Rheinische Friedrich-Wilhelms-Universität Bonn Wegelerstr. 12 53115 Bonn Deutschland
| | - Caspar A. Heubach
- Institut für Physikalische und Theoretische Chemie Rheinische Friedrich-Wilhelms-Universität Bonn Wegelerstr. 12 53115 Bonn Deutschland
| | - Toni Pfaffeneder
- Laboratorium für Organische Chemie ETH Zürich Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Andreas Nguyen
- Institut für Pharmazeutische Chemie Philipps-Universität Marburg Marbacher Weg 8 35032 Marburg Deutschland
| | - Andreas Heine
- Institut für Pharmazeutische Chemie Philipps-Universität Marburg Marbacher Weg 8 35032 Marburg Deutschland
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie Philipps-Universität Marburg Marbacher Weg 8 35032 Marburg Deutschland
| | - François Diederich
- Laboratorium für Organische Chemie ETH Zürich Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Olav Schiemann
- Institut für Physikalische und Theoretische Chemie Rheinische Friedrich-Wilhelms-Universität Bonn Wegelerstr. 12 53115 Bonn Deutschland
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie Philipps-Universität Marburg Marbacher Weg 8 35032 Marburg Deutschland
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13
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Metz A, Wollenhaupt J, Glöckner S, Messini N, Huber S, Barthel T, Merabet A, Gerber HD, Heine A, Klebe G, Weiss MS. Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking. Acta Crystallogr D Struct Biol 2021; 77:1168-1182. [PMID: 34473087 PMCID: PMC8411975 DOI: 10.1107/s2059798321008196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/09/2021] [Indexed: 11/10/2022] Open
Abstract
In recent years, crystallographic fragment screening has matured into an almost routine experiment at several modern synchrotron sites. The hits of the screening experiment, i.e. small molecules or fragments binding to the target protein, are revealed along with their 3D structural information. Therefore, they can serve as useful starting points for further structure-based hit-to-lead development. However, the progression of fragment hits to tool compounds or even leads is often hampered by a lack of chemical feasibility. As an attractive alternative, compound analogs that embed the fragment hit structurally may be obtained from commercial catalogs. Here, a workflow is reported based on filtering and assessing such potential follow-up compounds by template docking. This means that the crystallographic binding pose was integrated into the docking calculations as a central starting parameter. Subsequently, the candidates are scored on their interactions within the binding pocket. In an initial proof-of-concept study using five starting fragments known to bind to the aspartic protease endothiapepsin, 28 follow-up compounds were selected using the designed workflow and their binding was assessed by crystallography. Ten of these compounds bound to the active site and five of them showed significantly increased affinity in isothermal titration calorimetry of up to single-digit micromolar affinity. Taken together, this strategy is capable of efficiently evolving the initial fragment hits without major synthesis efforts and with full control by X-ray crystallography.
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Affiliation(s)
- Alexander Metz
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Steffen Glöckner
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Niki Messini
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Simon Huber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Tatjana Barthel
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Ahmed Merabet
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Hans-Dieter Gerber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Andreas Heine
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
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14
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Wollenhaupt J, Barthel T, Metz A, Lima GMA, Wallacher D, Jagudin E, Krojer T, Feiler CG, Heine A, Mueller U, Klebe G, Weiss MS. Efficiently from library to hit – crystallographic fragment screening in Berlin via structurally diverse compound libraries. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321091261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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15
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Klebe G, Nguyen D, Abdullin D, Heubach CA, Pfaffeneder T, Nguyen A, Heine A, Reuter K, Diederich F, Schiemann O. Unraveling a ligand-induced twist of a homodimeric enzyme by pulsed electron-electron double resonance. Angew Chem Int Ed Engl 2021; 60:23419-23426. [PMID: 34387025 PMCID: PMC8597004 DOI: 10.1002/anie.202108179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Indexed: 11/30/2022]
Abstract
Mechanistic insights into protein–ligand interactions can yield chemical tools for modulating protein function and enable their use for therapeutic purposes. For the homodimeric enzyme tRNA‐guanine transglycosylase (TGT), a putative virulence target of shigellosis, ligand binding has been shown by crystallography to transform the functional dimer geometry into an incompetent twisted one. However, crystallographic observation of both end states does neither verify the ligand‐induced transformation of one dimer into the other in solution nor does it shed light on the underlying transformation mechanism. We addressed these questions in an approach that combines site‐directed spin labeling (SDSL) with distance measurements based on pulsed electron–electron double resonance (PELDOR or DEER) spectroscopy. We observed an equilibrium between the functional and twisted dimer that depends on the type of ligand, with a pyranose‐substituted ligand being the most potent one in shifting the equilibrium toward the twisted dimer. Our experiments suggest a dissociation–association mechanism for the formation of the twisted dimer upon ligand binding.
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Affiliation(s)
- Gerhard Klebe
- Univ. of Marburg, Inst. Pharmaceut. Chem., Marbacher Weg 6, D35032, Marburg, GERMANY
| | - Dzung Nguyen
- Philipps-Universität Marburg: Philipps-Universitat Marburg, Pharmaceutical Chemistry, GERMANY
| | - Dinar Abdullin
- Universität Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn, Physical and Theoretical Chemistry, GERMANY
| | - Caspar A Heubach
- Universität Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn, Physical and Theoretical Chemistry, GERMANY
| | - Toni Pfaffeneder
- ETH-Zürich LOC: Eidgenossische Technische Hochschule Zurich Laboratorium fur Organische Chemie, Organic Chemistry, SWITZERLAND
| | - Andreas Nguyen
- Philipps-Universität Marburg: Philipps-Universitat Marburg, Pharmaceutical Chemistry, GERMANY
| | - Andreas Heine
- Philipps-Universität Marburg: Philipps-Universitat Marburg, Pharmaceutical Chemistry, GERMANY
| | - Klaus Reuter
- Philipps-Universität Marburg: Philipps-Universitat Marburg, Pharmaceutical Chemistry, GERMANY
| | - Francois Diederich
- ETH Zurich Department of Chemistry and Applied Biosciences: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Organic Chemistry, SWITZERLAND
| | - Olav Schiemann
- Universität Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn, Physical and Theoretical Chemistry, GERMANY
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16
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Nguyen D, Xie X, Jakobi S, Terwesten F, Metz A, Nguyen TXP, Palchykov VA, Heine A, Reuter K, Klebe G. Targeting a Cryptic Pocket in a Protein-Protein Contact by Disulfide-Induced Rupture of a Homodimeric Interface. ACS Chem Biol 2021; 16:1090-1098. [PMID: 34081441 DOI: 10.1021/acschembio.1c00296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interference with protein-protein interfaces represents an attractive as well as challenging option for therapeutic intervention and drug design. The enzyme tRNA-guanine transglycosylase, a target to fight Shigellosis, is only functional as a homodimer. Although we previously produced monomeric variants by site-directed mutagenesis, we only crystallized the functional dimer, simply because upon crystallization the local protein concentration increases and favors formation of the dimer interface, which represents an optimal and highly stable packing of the protein in the solid state. Unfortunately, this prevents access to structural information about the interface geometry in its monomeric state and complicates the development of modulators that can interfere with and prevent dimer formation. Here, we report on a cysteine-containing protein variant in which, under oxidizing conditions, a disulfide linkage is formed. This reinforces a novel packing geometry of the enzyme. In this captured quasi-monomeric state, the monomer units arrange in a completely different way and, thus, expose a loop-helix motif, originally embedded into the old interface, now to the surface. The motif adopts a geometry incompatible with the original dimer formation. Via the soaking of fragments into the crystals, we identified several hits accommodating a cryptic binding site next to the loop-helix motif and modulated its structural features. Our study demonstrates the druggability of the interface by breaking up the homodimeric protein using an introduced disulfide cross-link. By rational concepts, we increased the potency of these fragments to a level where we confirmed their binding by NMR to a nondisulfide-linked TGT variant. The idea of intermediately introducing a disulfide linkage may serve as a general concept of how to transform a homodimer interface into a quasi-monomeric state and give access to essential structural and design information.
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Affiliation(s)
- Dzung Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Xiulan Xie
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Stephan Jakobi
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Felix Terwesten
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Alexander Metz
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - T. X. Phong Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Vitalii A. Palchykov
- Research Institute of Chemistry and Geology, Oles Honchar Dnipro National University, 72 Gagarina Avenue, Dnipro 49010, Ukraine
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
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17
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Heine A, Hustig-Kittler V, Schröder M, Desole S, Boesche M, Obst A, Stubbe B, Ewert R. [Evaluation of Weaning Success in Long-Term Invasively Ventilated Patients at a Weaning Center]. Pneumologie 2021; 75:447-452. [PMID: 33853134 DOI: 10.1055/a-1346-6208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Despite the use of enormous personnel and other resources in German weaning centers, approximately 20 % of patients currently fail to get weaned from mechanical ventilation (MV) and need out-of-hospital ventilation.Between 03/2015 and 11/2019, we carried out a pilot project with 33 patients (48 % female, mean age 68 ± 11 years at hospital admission) in order to re-evaluate their options of a possible weaning from MV. At this stage the patients had been invasively ventilated for 475 ± 775 days. The mean stay in our weaning center was 26 ± 19 days. 24/33 (73.53 %) patients were successfully weaned from MV. Of those, 11/24 (44 %) were discharged with non-invasive out-of-hospital ventilation. The completely weaned patients had a survival period of 3 or 12 months (92 % and 77 %), respectively. In those discharged with non-invasive ventilation, the survival period of 3 or months was 91 % and 81 %, respectively. In those discharged with invasive ventilation, this was 86 % and 71 %, respectively.The current results demonstrate that even those undergoing long-term out-of-hospital invasive ventilation can be successfully weaned from MV. Therefore, we suggest regular re-evaluations of weaning opportunities in invasively ventilated ambulatory patients.
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Affiliation(s)
- A Heine
- Universitätsmedizin Greifswald, Klinik für Innere Medizin B, Bereich Pneumologie und Weaningzentrum, Greifswald
| | - V Hustig-Kittler
- Universitätsmedizin Greifswald, Klinik für Innere Medizin B, Bereich Pneumologie und Weaningzentrum, Greifswald
| | - M Schröder
- Universitätsmedizin Greifswald, Zentrale physikalische Medizin, Rehabilitation und Sportmedizin, Greifswald
| | - S Desole
- Universitätsmedizin Greifswald, Klinik für Innere Medizin B, Bereich Pneumologie und Weaningzentrum, Greifswald
| | - M Boesche
- Universitätsmedizin Greifswald, Klinik für Innere Medizin B, Bereich Pneumologie und Weaningzentrum, Greifswald
| | - A Obst
- Universitätsmedizin Greifswald, Klinik für Innere Medizin B, Bereich Pneumologie und Weaningzentrum, Greifswald
| | - B Stubbe
- Universitätsmedizin Greifswald, Klinik für Innere Medizin B, Bereich Pneumologie und Weaningzentrum, Greifswald
| | - R Ewert
- Universitätsmedizin Greifswald, Klinik für Innere Medizin B, Bereich Pneumologie und Weaningzentrum, Greifswald
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18
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Wollenhaupt J, Barthel T, Lima GMA, Metz A, Wallacher D, Jagudin E, Huschmann FU, Hauß T, Feiler CG, Gerlach M, Hellmig M, Förster R, Steffien M, Heine A, Klebe G, Mueller U, Weiss MS. Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin. J Vis Exp 2021. [PMID: 33749678 DOI: 10.3791/62208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Fragment screening is a technique that helps to identify promising starting points for ligand design. Given that crystals of the target protein are available and display reproducibly high-resolution X-ray diffraction properties, crystallography is among the most preferred methods for fragment screening because of its sensitivity. Additionally, it is the only method providing detailed 3D information of the binding mode of the fragment, which is vital for subsequent rational compound evolution. The routine use of the method depends on the availability of suitable fragment libraries, dedicated means to handle large numbers of samples, state-of-the-art synchrotron beamlines for fast diffraction measurements and largely automated solutions for the analysis of the results. Here, the complete practical workflow and the included tools on how to conduct crystallographic fragment screening (CFS) at the Helmholtz-Zentrum Berlin (HZB) are presented. Preceding this workflow, crystal soaking conditions as well as data collection strategies are optimized for reproducible crystallographic experiments. Then, typically in a one to two-day procedure, a 96-membered CFS-focused library provided as dried ready-to-use plates is employed to soak 192 crystals, which are then flash-cooled individually. The final diffraction experiments can be performed within one day at the robot-mounting supported beamlines BL14.1 and BL14.2 at the BESSY II electron storage ring operated by the HZB in Berlin-Adlershof (Germany). Processing of the crystallographic data, refinement of the protein structures, and hit identification is fast and largely automated using specialized software pipelines on dedicated servers, requiring little user input. Using the CFS workflow at the HZB enables routine screening experiments. It increases the chances for successful identification of fragment hits as starting points to develop more potent binders, useful for pharmacological or biochemical applications.
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Affiliation(s)
| | - Tatjana Barthel
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin; Structural Biochemistry Group, Institute for Chemistry and Biochemistry, Freie Universität Berlin
| | | | - Alexander Metz
- Drug Design Group, Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg
| | | | | | - Franziska U Huschmann
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin; Drug Design Group, Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg
| | - Thomas Hauß
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin
| | | | - Martin Gerlach
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin
| | | | - Ronald Förster
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin
| | | | - Andreas Heine
- Drug Design Group, Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg
| | - Gerhard Klebe
- Drug Design Group, Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg
| | - Uwe Mueller
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin
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19
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Sandner A, Ngo K, Schiebel J, Pizarroso AIM, Schmidt L, Wenzel B, Steinmetzer T, Ostermann A, Heine A, Klebe G. How a Fragment Draws Attention to Selectivity Discriminating Features between the Related Proteases Trypsin and Thrombin. J Med Chem 2021; 64:1611-1625. [PMID: 33471524 DOI: 10.1021/acs.jmedchem.0c01809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the S1 pocket, the serine proteases thrombin and trypsin commonly feature Asp189 and a Ala190Ser and Glu192Gln exchange. Nevertheless, thrombin cleaves peptide chains solely after Arg, and trypsin after Lys and Arg. Thrombin exhibits a Na+-binding site next to Asp189, which is missing in trypsin. The fragment benzylamine shows direct H-bonding to Asp189 in trypsin, while in thrombin, it forms an H-bond to Glu192. A series of fragments and expanded ligands were studied against both enzymes and mutated variants by crystallography and ITC. The selectivity-determining features of both S1 pockets are difficult to assign to one dominating factor. The Ala190Ser and Glu192Gln replacements may be regarded as highly conserved as no structural and affinity changes are observed between both proteases. With respect to charge distribution, Glu192, together with the thrombin-specific sodium ion, helps in creating an electrostatic gradient across the S1 pocket. This feature is definitely absent in trypsin but important for selectivity along with solvation-pattern differences in the S1 pocket.
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Affiliation(s)
- Anna Sandner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Khang Ngo
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Johannes Schiebel
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | | | - Linda Schmidt
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Benjamin Wenzel
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Torsten Steinmetzer
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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20
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Oebbeke M, Siefker C, Wagner B, Heine A, Klebe G. Fragment‐Bindung an die Kinase‐Scharnier‐Region: Wenn Ladungsverteilung und lokale p
K
a
‐Verschiebungen etablierte Bioisosterie‐Konzepte fehlleiten. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Matthias Oebbeke
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
| | - Christof Siefker
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
| | - Björn Wagner
- Roche Innovation Center Grenzacherstr. 124 4070 Basel Schweiz
| | - Andreas Heine
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
| | - Gerhard Klebe
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
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21
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Oebbeke M, Siefker C, Wagner B, Heine A, Klebe G. Fragment Binding to Kinase Hinge: If Charge Distribution and Local pK a Shifts Mislead Popular Bioisosterism Concepts. Angew Chem Int Ed Engl 2021; 60:252-258. [PMID: 33021032 PMCID: PMC7821265 DOI: 10.1002/anie.202011295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Indexed: 12/25/2022]
Abstract
Medicinal‐chemistry optimization follows strategies replacing functional groups and attaching larger substituents at a promising lead scaffold. Well‐established bioisosterism rules are considered, however, it is difficult to estimate whether the introduced modifications really match the required properties at a binding site. The electron density distribution and pKa values are modulated influencing protonation states and bioavailability. Considering the adjacent H‐bond donor/acceptor pattern of the hinge binding motif in a kinase, we studied by crystallography a set of fragments to map the required interaction pattern. Unexpectedly, benzoic acid and benzamidine, decorated with the correct substituents, are totally bioisosteric just as carboxamide and phenolic OH. A mono‐dentate pyridine nitrogen out‐performs bi‐dentate functionalities. The importance of correctly designing pKa values of attached functional groups by additional substituents at the parent scaffold is rendered prominent.
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Affiliation(s)
- Matthias Oebbeke
- Philipps Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, 35032, Marburg, Germany
| | - Christof Siefker
- Philipps Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, 35032, Marburg, Germany
| | - Björn Wagner
- Roche Innovation Center, Grenzacherstr. 124, 4070, Basel, Switzerland
| | - Andreas Heine
- Philipps Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Philipps Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, 35032, Marburg, Germany
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22
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Nguyen A, Nguyen D, Phong Nguyen TX, Sebastiani M, Dörr S, Hernandez-Alba O, Debaene F, Cianférani S, Heine A, Klebe G, Reuter K. The Importance of Charge in Perturbing the Aromatic Glue Stabilizing the Protein-Protein Interface of Homodimeric tRNA-Guanine Transglycosylase. ACS Chem Biol 2020; 15:3021-3029. [PMID: 33166460 DOI: 10.1021/acschembio.0c00700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Bacterial tRNA-guanine transglycosylase (Tgt) is involved in the biosynthesis of the modified tRNA nucleoside queuosine present in the anticodon wobble position of tRNAs specific for aspartate, asparagine, histidine, and tyrosine. Inactivation of the tgt gene leads to decreased pathogenicity of Shigella bacteria. Therefore, Tgt constitutes a putative target for Shigellosis drug therapy. Since it is only active as homodimer, interference with dimer-interface formation may, in addition to active-site inhibition, provide further means to disable this protein. A cluster of four aromatic residues seems important to stabilize the homodimer. We mutated residues of this aromatic cluster and analyzed each mutated variant with respect to the dimer and thermal stability or enzyme activity by applying native mass spectrometry, a thermal shift assay, enzyme kinetics, and X-ray crystallography. Our structural studies indicate a strong influence of pH on the homodimer stability. Apparently, protonation of a histidine within the aromatic cluster supports the collapse of an essential structural motif within the dimer interface at slightly acidic pH.
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Affiliation(s)
- Andreas Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Dzung Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Tran Xuan Phong Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Maurice Sebastiani
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Stefanie Dörr
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France
| | - François Debaene
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
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23
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Duerr GD, Heine A, Hamiko M, Zimmer S, Luetkens JA, Nattermann J, Rieke G, Isaak A, Jehle J, Held SAE, Wasmuth JC, Wittmann M, Strassburg CP, Brossart P, Coburn M, Treede H, Nickenig G, Kurts C, Velten M. Parameters predicting COVID-19-induced myocardial injury and mortality. Life Sci 2020. [PMID: 32918975 DOI: 10.1016/j.lfs.2020.11840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
UNLABELLED Clinical manifestations of COVID-19 affect many organs, including the heart. Cardiovascular disease is a dominant comorbidity and prognostic factors predicting risk for critical courses are highly needed. Moreover, immunomechanisms underlying COVID-induced myocardial damage are poorly understood. OBJECTIVE To elucidate prognostic markers to identify patients at risk. RESULTS Only patients with pericardial effusion (PE) developed a severe disease course, and those who died could be identified by a high CD8/Treg/monocyte ratio. Ten out of 19 COVID-19 patients presented with PE, 7 (78%) of these had elevated APACHE-II mortality risk-score, requiring mechanical ventilation. At admission, PE patients showed signs of systemic and cardiac inflammation in NMR and impaired cardiac function as detected by transthoracic echocardiography (TTE), whereas parameters of myocardial injury e.g. high sensitive troponin-t (hs-TnT) were not yet increased. During the course of disease, hs-TnT rose in 8 of the PE-patients above 16 ng/l, 7 had to undergo ventilatory therapy and 4 of them died. FACS at admission showed in PE patients elevated frequencies of CD3+CD8+ T cells among all CD3+ T-cells, and lower frequencies of Tregs and CD14+HLA-DR+-monocytes. A high CD8/Treg/monocyte ratio predicted a severe disease course in PE patients, and was associated with high serum levels of antiviral cytokines. By contrast, patients without PE and PE patients with a low CD8/Treg/monocyte ratio neither had to be intubated, nor died. CONCLUSIONS PE predicts cardiac injury in COVID-19 patients. Therefore, TTE should be performed at admission. Immunological parameters for dysfunctional antiviral immunity, such as the CD8/Treg/monocyte ratio used here, supports risk assessment by predicting poor prognosis.
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Affiliation(s)
- G D Duerr
- Department of Cardiovascular Surgery, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - A Heine
- Department of Internal Medicine III for Hematology, Oncology, Rheumatology and Immune-Oncology, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - M Hamiko
- Department of Cardiovascular Surgery, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - S Zimmer
- Department of Internal Medicine II - Cardiology, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - J A Luetkens
- Department of Radiology, Quantitative Imaging Lab Bonn (QILaB), University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - J Nattermann
- Department of Internal Medicine I, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - G Rieke
- Department of Internal Medicine I, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - A Isaak
- Department of Radiology, Quantitative Imaging Lab Bonn (QILaB), University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - J Jehle
- Department of Internal Medicine II - Cardiology, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - S A E Held
- Department of Internal Medicine III for Hematology, Oncology, Rheumatology and Immune-Oncology, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - J C Wasmuth
- Department of Internal Medicine I, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - M Wittmann
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - C P Strassburg
- Department of Internal Medicine I, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - P Brossart
- Department of Internal Medicine III for Hematology, Oncology, Rheumatology and Immune-Oncology, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - M Coburn
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - H Treede
- Department of Cardiovascular Surgery, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - G Nickenig
- Department of Internal Medicine II - Cardiology, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - C Kurts
- Institute for Experimental Immunology, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany.
| | - M Velten
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany.
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24
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Wienen-Schmidt B, Oebbeke M, Ngo K, Heine A, Klebe G. Two Methods, One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses. ChemMedChem 2020; 16:292-300. [PMID: 33029876 PMCID: PMC7821316 DOI: 10.1002/cmdc.202000565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/02/2020] [Indexed: 11/10/2022]
Abstract
In lead optimization, protein crystallography is an indispensable tool to analyze drug binding. Binding modes and non-covalent interaction inventories are essential to design follow-up synthesis candidates. Two protocols are commonly applied to produce protein-ligand complexes: cocrystallization and soaking. Because of its time and cost effectiveness, soaking is the more popular method. Taking eight ligand hinge binders of protein kinase A, we demonstrate that cocrystallization is superior. Particularly for flexible proteins, such as kinases, and larger ligands cocrystallization captures more reliable the correct binding pose and induced protein adaptations. The geometrical discrepancies between soaking and cocrystallization appear smaller for fragment-sized ligands. For larger flexible ligands that trigger conformational changes of the protein, soaking can be misleading and underestimates the number of possible polar interactions due to inadequate, highly impaired positions of protein amino-acid side and main chain atoms. Thus, if applicable cocrystallization should be the gold standard to study protein-ligand complexes.
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Affiliation(s)
- Barbara Wienen-Schmidt
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Matthias Oebbeke
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Khang Ngo
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
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25
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Verspohl SH, Schulze-Koops H, Heine A, Schäfer VS. [Prevalence and treatment of rheumatological adverse events due to immune checkpoint inhibitor therapy]. Z Rheumatol 2020; 79:797-808. [PMID: 32926217 DOI: 10.1007/s00393-020-00873-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Immune checkpoint inhibitors (ICI) have essentially improved the treatment options for various malignant diseases. They lead to an activation of the immune system and subsequent attack of tumor cells by affecting the immune system and preventing tumor cells from avoiding detection. In addition to this desired effect, immune-related adverse events (irAE) can occur in nearly all organ systems and therefore also rheumatological irAE (rh-irAE). OBJECTIVE The occurrence of rh-irAE has been described in various publications and is specifically investigated in this review. The aim is to provide an overview on the prevalence, severity, treatment options and altered tumor response in patients with rh-irAE. MATERIAL AND METHODS We conducted a literature search for studies and case reports on rh-irAE under ICI therapy in PubMed up to January 2020 using the PICO model. RESULTS A total of 18 publications were included, most of which were clinical studies (n = 13) and the rest case reports (n = 5). Several rh-irAE can occur with a wide variety of manifestations of which arthralgia, arthritis and myositis were the most common. Other rheumatic diseases, such as vasculitis, connective tissue diseases and sarcoidosis were less frequently described. The published prevalence of rh-irAE varied with a prevalence between 2.3% and 6.6%. Treatment of rh-irAE depends on the severity and most patients receive nonsteroidal anti-inflammatory drugs and glucocorticosteroids. In some cases, conventional DMARDs, such as methotrexate and biological DMARDs, were administered. Patients with rh-irAE in general had a higher tumor response rate compared to patients without side effects. CONCLUSION A close observation of patients and early detection of rh-irAE are important in order to treat these side effects in time. Further prospective studies are necessary to systematically investigate rh-irAE.
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Affiliation(s)
- S H Verspohl
- Medizinische Klinik und Poliklinik III, Klinik für Hämatologie, Onkologie, Rheumatologie und klinische Immunologie, Universitätsklinikum Bonn, Venusberg Campus 1, 53127, Bonn, Deutschland
| | - H Schulze-Koops
- Sektion Rheumatologie und Klinische Immunologie, Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-Universität München, München, Deutschland
| | - A Heine
- Medizinische Klinik und Poliklinik III, Klinik für Hämatologie, Onkologie, Rheumatologie und klinische Immunologie, Universitätsklinikum Bonn, Venusberg Campus 1, 53127, Bonn, Deutschland
| | - V S Schäfer
- Medizinische Klinik und Poliklinik III, Klinik für Hämatologie, Onkologie, Rheumatologie und klinische Immunologie, Universitätsklinikum Bonn, Venusberg Campus 1, 53127, Bonn, Deutschland.
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26
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Duerr GD, Heine A, Hamiko M, Zimmer S, Luetkens JA, Nattermann J, Rieke G, Isaak A, Jehle J, Held SAE, Wasmuth JC, Wittmann M, Strassburg CP, Brossart P, Coburn M, Treede H, Nickenig G, Kurts C, Velten M. Parameters predicting COVID-19-induced myocardial injury and mortality. Life Sci 2020; 260:118400. [PMID: 32918975 PMCID: PMC7480277 DOI: 10.1016/j.lfs.2020.118400] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 11/02/2022]
Abstract
Clinical manifestations of COVID-19 affect many organs, including the heart. Cardiovascular disease is a dominant comorbidity and prognostic factors predicting risk for critical courses are highly needed. Moreover, immunomechanisms underlying COVID-induced myocardial damage are poorly understood. OBJECTIVE To elucidate prognostic markers to identify patients at risk. RESULTS Only patients with pericardial effusion (PE) developed a severe disease course, and those who died could be identified by a high CD8/Treg/monocyte ratio. Ten out of 19 COVID-19 patients presented with PE, 7 (78%) of these had elevated APACHE-II mortality risk-score, requiring mechanical ventilation. At admission, PE patients showed signs of systemic and cardiac inflammation in NMR and impaired cardiac function as detected by transthoracic echocardiography (TTE), whereas parameters of myocardial injury e.g. high sensitive troponin-t (hs-TnT) were not yet increased. During the course of disease, hs-TnT rose in 8 of the PE-patients above 16 ng/l, 7 had to undergo ventilatory therapy and 4 of them died. FACS at admission showed in PE patients elevated frequencies of CD3+CD8+ T cells among all CD3+ T-cells, and lower frequencies of Tregs and CD14+HLA-DR+-monocytes. A high CD8/Treg/monocyte ratio predicted a severe disease course in PE patients, and was associated with high serum levels of antiviral cytokines. By contrast, patients without PE and PE patients with a low CD8/Treg/monocyte ratio neither had to be intubated, nor died. CONCLUSIONS PE predicts cardiac injury in COVID-19 patients. Therefore, TTE should be performed at admission. Immunological parameters for dysfunctional antiviral immunity, such as the CD8/Treg/monocyte ratio used here, supports risk assessment by predicting poor prognosis.
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Affiliation(s)
- G D Duerr
- Department of Cardiovascular Surgery, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - A Heine
- Department of Internal Medicine III for Hematology, Oncology, Rheumatology and Immune-Oncology, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - M Hamiko
- Department of Cardiovascular Surgery, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - S Zimmer
- Department of Internal Medicine II - Cardiology, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - J A Luetkens
- Department of Radiology, Quantitative Imaging Lab Bonn (QILaB), University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - J Nattermann
- Department of Internal Medicine I, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - G Rieke
- Department of Internal Medicine I, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - A Isaak
- Department of Radiology, Quantitative Imaging Lab Bonn (QILaB), University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - J Jehle
- Department of Internal Medicine II - Cardiology, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - S A E Held
- Department of Internal Medicine III for Hematology, Oncology, Rheumatology and Immune-Oncology, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - J C Wasmuth
- Department of Internal Medicine I, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - M Wittmann
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - C P Strassburg
- Department of Internal Medicine I, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - P Brossart
- Department of Internal Medicine III for Hematology, Oncology, Rheumatology and Immune-Oncology, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - M Coburn
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - H Treede
- Department of Cardiovascular Surgery, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - G Nickenig
- Department of Internal Medicine II - Cardiology, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - C Kurts
- Institute for Experimental Immunology, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany.
| | - M Velten
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany.
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27
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Braun NJ, Quek JP, Huber S, Kouretova J, Rogge D, Lang‐Henkel H, Cheong EZK, Chew BLA, Heine A, Luo D, Steinmetzer T. Structure-Based Macrocyclization of Substrate Analogue NS2B-NS3 Protease Inhibitors of Zika, West Nile and Dengue viruses. ChemMedChem 2020; 15:1439-1452. [PMID: 32501637 PMCID: PMC7497253 DOI: 10.1002/cmdc.202000237] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Indexed: 11/06/2022]
Abstract
A series of cyclic active-site-directed inhibitors of the NS2B-NS3 proteases from Zika (ZIKV), West Nile (WNV), and dengue-4 (DENV4) viruses has been designed. The most potent compounds contain a reversely incorporated d-lysine residue in the P1 position. Its side chain is connected to the P2 backbone, its α-amino group is converted into a guanidine to interact with the conserved Asp129 side chain in the S1 pocket, and its C terminus is connected to the P3 residue via different linker segments. The most potent compounds inhibit the ZIKV protease with Ki values <5 nM. Crystal structures of seven ZIKV protease inhibitor complexes were determined to support the inhibitor design. All the cyclic compounds possess high selectivity against trypsin-like serine proteases and furin-like proprotein convertases. Both WNV and DENV4 proteases are inhibited less efficiently. Nonetheless, similar structure-activity relationships were observed for these enzymes, thus suggesting their potential application as pan-flaviviral protease inhibitors.
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Affiliation(s)
- Niklas J. Braun
- Institute of Pharmaceutical ChemistryPhilipps UniversityMarbacher Weg 635032MarburgGermany
| | - Jun P. Quek
- Lee Kong Chian School of MedicineNanyang Technological University, EMB 03–0759 Nanyang DriveSingapore636921Singapore
- Institute of Structural BiologyNanyang Technological University EMB 06–0159 Nanyang DriveSingapore636921Singapore
| | - Simon Huber
- Institute of Pharmaceutical ChemistryPhilipps UniversityMarbacher Weg 635032MarburgGermany
| | - Jenny Kouretova
- Institute of Pharmaceutical ChemistryPhilipps UniversityMarbacher Weg 635032MarburgGermany
| | - Dorothee Rogge
- Institute of Pharmaceutical ChemistryPhilipps UniversityMarbacher Weg 635032MarburgGermany
| | - Heike Lang‐Henkel
- Institute of Pharmaceutical ChemistryPhilipps UniversityMarbacher Weg 635032MarburgGermany
| | - Ezekiel Z. K. Cheong
- School of Biological SciencesNanyang Technological University60 Nanyang Dr.Singapore637551Singapore
| | - Bing L. A. Chew
- Lee Kong Chian School of MedicineNanyang Technological University, EMB 03–0759 Nanyang DriveSingapore636921Singapore
- Institute of Structural BiologyNanyang Technological University EMB 06–0159 Nanyang DriveSingapore636921Singapore
- Institute of Health TechnologiesInterdisciplinary Graduate ProgrammeNanyang Technological University61 Nanyang Dr.Singapore637335Singapore
| | - Andreas Heine
- Institute of Pharmaceutical ChemistryPhilipps UniversityMarbacher Weg 635032MarburgGermany
| | - Dahai Luo
- Lee Kong Chian School of MedicineNanyang Technological University, EMB 03–0759 Nanyang DriveSingapore636921Singapore
- Institute of Structural BiologyNanyang Technological University EMB 06–0159 Nanyang DriveSingapore636921Singapore
- School of Biological SciencesNanyang Technological University60 Nanyang Dr.Singapore637551Singapore
| | - Torsten Steinmetzer
- Institute of Pharmaceutical ChemistryPhilipps UniversityMarbacher Weg 635032MarburgGermany
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28
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Stieler M, Büchold C, Schmitt M, Heine A, Hils M, Pasternack R, Klebe G. Structure-Based Design of FXIIIa-Blockers: Addressing a Transient Hydrophobic Pocket in the Active Site of FXIIIa. ChemMedChem 2020; 15:900-905. [PMID: 32181986 PMCID: PMC7317430 DOI: 10.1002/cmdc.202000056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/16/2020] [Indexed: 01/23/2023]
Abstract
Blood coagulation factor XIII (FXIII, F13) is considered to be a promising target for anticoagulants with reduced bleeding risk because of its unique position in the coagulation cascade downstream of thrombin. However, until now, no potent drug addressing FXIII has been available, indeed no compound has even entered clinical trials yet. In 2013, we published the co-crystal structure of FXIII in the active state (FXIIIa°), thereby providing a detailed map of the active site for the rational design of potent FXIIIa blockers. Here we report, for the first time, a structure-based approach to improving the affinity of FXIIIa inhibitors. FXIII was crystallized in complex with a methyl thiazole moiety to address a novel transient hydrophobic pocket close to the catalytic center. By subsequent structure-based design to rationalize the introduction of an ethyl ester, the potency of the inhibitor was improved significantly compared to that of the parent lead compound. The occupancy of the hydrophobic pocket described here might turn out to be a key step in the development of a potent reversible and orally available FXIIIa blocker.
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Affiliation(s)
- Martin Stieler
- Department of Pharmaceutical ChemistryPhilipps-UniversitätMarbacher Weg 635032MarburgGermany
| | | | | | - Andreas Heine
- Department of Pharmaceutical ChemistryPhilipps-UniversitätMarbacher Weg 635032MarburgGermany
| | - Martin Hils
- Zedira GmbH Roesslerstrasse 8364293DarmstadtGermany
| | | | - Gerhard Klebe
- Department of Pharmaceutical ChemistryPhilipps-UniversitätMarbacher Weg 635032MarburgGermany
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29
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Wollenhaupt J, Metz A, Barthel T, Lima GMA, Heine A, Mueller U, Klebe G, Weiss MS. F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening. Structure 2020; 28:694-706.e5. [PMID: 32413289 DOI: 10.1016/j.str.2020.04.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/02/2020] [Accepted: 04/23/2020] [Indexed: 11/15/2022]
Abstract
Crystallographic fragment screening (CFS) provides excellent starting points for projects concerned with drug discovery or biochemical tool compound development. One of the fundamental prerequisites for effective CFS is the availability of a versatile fragment library. Here, we report on the assembly of the 1,103-compound F2X-Universal Library and its 96-compound sub-selection, the F2X-Entry Screen. Both represent the available fragment chemistry and are highly diverse in terms of their 3D-pharmacophore variations. Validation of the F2X-Entry Screen in CFS campaigns using endothiapepsin and the Aar2/RNaseH complex yielded hit rates of 30% and 21%, respectively, and revealed versatile binding sites. Dry presentation of the libraries allows CFS campaigns to be carried out with or without the co-solvent DMSO present. Most of the hits in our validation campaigns could be reproduced also in the absence of DMSO. Consequently, CFS can be carried out more efficiently and for a wider range of conditions and targets.
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Affiliation(s)
- Jan Wollenhaupt
- Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany; Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Alexander Metz
- Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany
| | - Tatjana Barthel
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany; Freie Universität Berlin, Institute for Chemistry and Biochemistry, Structural Biochemistry Group, Takustr. 5, 14195 Berlin, Germany
| | - Gustavo M A Lima
- MAX IV Laboratory, Macromolecular Crystallography Group, Lund University, 22100 Lund, Sweden
| | - Andreas Heine
- Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany
| | - Uwe Mueller
- MAX IV Laboratory, Macromolecular Crystallography Group, Lund University, 22100 Lund, Sweden
| | - Gerhard Klebe
- Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
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Konstantinidou M, Magari F, Sutanto F, Haupenthal J, Jumde VR, Ünver MY, Heine A, Camacho CJ, Hirsch AKH, Klebe G, Dömling A. Rapid Discovery of Aspartyl Protease Inhibitors Using an Anchoring Approach. ChemMedChem 2020; 15:680-684. [PMID: 32187447 PMCID: PMC7317454 DOI: 10.1002/cmdc.202000024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/20/2020] [Indexed: 11/11/2022]
Abstract
Pharmacophore searches that include anchors, fragments contributing above average to receptor binding, combined with one‐step syntheses are a powerful approach for the fast discovery of novel bioactive molecules. Here, we are presenting a pipeline for the rapid and efficient discovery of aspartyl protease inhibitors. First, we hypothesized that hydrazine could be a multi‐valent warhead to interact with the active site Asp carboxylic acids. We incorporated the hydrazine anchor in a multicomponent reaction and created a large virtual library of hydrazine derivatives synthetically accessible in one‐step. Next, we performed anchor‐based pharmacophore screening of the libraries and resynthesized top‐ranked compounds. The inhibitory potency of the molecules was finally assessed by an enzyme activity assay and the binding mode confirmed by several soaked crystal structures supporting the validity of the hypothesis and approach. The herein reported pipeline of tools will be of general value for the rapid generation of receptor binders beyond Asp proteases.
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Affiliation(s)
- Markella Konstantinidou
- Department of Pharmacy Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Francesca Magari
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Fandi Sutanto
- Department of Pharmacy Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Jörg Haupenthal
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Varsha R Jumde
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - M Yagiz Ünver
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Carlos Jamie Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Anna K H Hirsch
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Alexander Dömling
- Department of Pharmacy Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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32
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Glöckner S, Ngo K, Wagner B, Heine A, Klebe G. The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II. Biomolecules 2020; 10:E509. [PMID: 32230853 PMCID: PMC7226267 DOI: 10.3390/biom10040509] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/12/2022] Open
Abstract
The fluorination of lead-like compounds is a common tool in medicinal chemistry to alter molecular properties in various ways and with different goals. We herein present a detailed study of the binding of fluorinated benzenesulfonamides to human Carbonic Anhydrase II by complementing macromolecular X-ray crystallographic observations with thermodynamic and kinetic data collected with the novel method of kinITC. Our findings comprise so far unknown alternative binding modes in the crystalline state for some of the investigated compounds as well as complex thermodynamic and kinetic structure-activity relationships. They suggest that fluorination of the benzenesulfonamide core is especially advantageous in one position with respect to the kinetic signatures of binding and that a higher degree of fluorination does not necessarily provide for a higher affinity or more favorable kinetic binding profiles. Lastly, we propose a relationship between the kinetics of binding and ligand acidity based on a small set of compounds with similar substitution patterns.
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Affiliation(s)
- Steffen Glöckner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (S.G.); (K.N.); (A.H.)
| | - Khang Ngo
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (S.G.); (K.N.); (A.H.)
| | - Björn Wagner
- F. Hoffmann-La Roche AG, Pharmaceutical Research & Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland;
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (S.G.); (K.N.); (A.H.)
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (S.G.); (K.N.); (A.H.)
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33
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Glöckner S, Ngo K, Sager CP, Hüfner-Wulsdorf T, Heine A, Klebe G. Conformational Changes in Alkyl Chains Determine the Thermodynamic and Kinetic Binding Profiles of Carbonic Anhydrase Inhibitors. ACS Chem Biol 2020; 15:675-685. [PMID: 32027480 DOI: 10.1021/acschembio.9b00895] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Thermodynamics and kinetics of protein-ligand binding are both important aspects for the design of novel drug molecules. Presently, thermodynamic data are collected with isothermal titration calorimetry, while kinetic data are mostly derived from surface plasmon resonance. The new method of kinITC provides both thermodynamic and kinetic data from calorimetric titration measurements. The present study demonstrates the convenient collection of calorimetric data suitable for both thermodynamic and kinetic analysis for two series of congeneric ligands of human carbonic anhydrase II and correlates these findings with structural data obtained by macromolecular crystallography to shed light on the importance of shape complementarity for thermodynamics and kinetics governing a protein-ligand binding event. The study shows how minute chemical alterations change preferred ligand conformation and can be used to manipulate thermodynamic and kinetic signatures of binding. They give rise to the observation that analogous n-alkyl and n-alkyloxy derivatives of identical chain length swap their binding kinetic properties at unchanged binding affinity.
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Affiliation(s)
- Steffen Glöckner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Khang Ngo
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Christoph P Sager
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Tobias Hüfner-Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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34
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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35
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Ngo K, Collins-Kautz C, Gerstenecker S, Wagner B, Heine A, Klebe G. Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins? J Med Chem 2020; 63:3274-3289. [DOI: 10.1021/acs.jmedchem.9b02061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Khang Ngo
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Chelsey Collins-Kautz
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Stefan Gerstenecker
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Björn Wagner
- Pharma Research Non-Clinical Safety, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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36
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Wienen-Schmidt B, Schmidt D, Gerber HD, Heine A, Gohlke H, Klebe G. Surprising Non-Additivity of Methyl Groups in Drug-Kinase Interaction. ACS Chem Biol 2019; 14:2585-2594. [PMID: 31638770 DOI: 10.1021/acschembio.9b00476] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Drug optimization is guided by biophysical methods with increasing popularity. In the context of lead structure modifications, the introduction of methyl groups is a simple but potentially powerful approach. Hence, it is crucial to systematically investigate the influence of ligand methylation on biophysical characteristics such as thermodynamics. Here, we investigate the influence of ligand methylation in different positions and combinations on the drug-kinase interaction. Binding modes and complex structures were analyzed using protein crystallography. Thermodynamic signatures were measured via isothermal titration calorimetry (ITC). An extensive computational analysis supported the understanding of the underlying mechanisms. We found that not only position but also stereochemistry of the methyl group has an influence on binding potency as well as the thermodynamic signature of ligand binding to the protein. Strikingly, the combination of single methyl groups does not lead to additive effects. In our case, the merger of two methyl groups in one ligand leads to an entirely new alternative ligand binding mode in the protein ligand complex. Moreover, the combination of the two methyl groups also resulted in a nonadditive thermodynamic profile of ligand binding. Molecular dynamics (MD) simulations revealed distinguished characteristic motions of the ligands in solution explaining the pronounced thermodynamic changes. The unexpected drastic change in protein ligand interaction highlights the importance of crystallographic control even for minor modifications such as the introduction of a methyl group. For an in-depth understanding of ligand binding behavior, MD simulations have shown to be a powerful tool.
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Affiliation(s)
- Barbara Wienen-Schmidt
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Denis Schmidt
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Hans-Dieter Gerber
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute for Complex Systems - Structural Biochemistry (ICS 6), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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37
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Sandner A, Hüfner-Wulsdorf T, Heine A, Steinmetzer T, Klebe G. Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding. J Med Chem 2019; 62:9753-9771. [PMID: 31633354 DOI: 10.1021/acs.jmedchem.9b01196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Structural fixation of a ligand in its bioactive conformation may, due to entropic reasons, improve affinity. We present a congeneric series of thrombin ligands with a variety of functional groups triggering preorganization prior to binding. Fixation in solution and complex formation have been characterized by crystallography, isothermal titration calorimetry (ITC), and molecular dynamics (MD) simulations. First, we show why these preorganizing modifications do not affect the overall binding mode and how key interactions are preserved. Next, we demonstrate how preorganization thermodynamics can be largely dominated by enthalpy rather than entropy because of the significant population of low-energy conformations. Furthermore, a salt bridge is shielded by actively reducing its surface exposure, thus leading to an enhanced enthalpic binding profile. Our results suggest that the consideration of the ligand solution ensemble by MD simulation is necessary to predict preorganizing modifications that enhance the binding behavior of already promising binders.
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Affiliation(s)
- Anna Sandner
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Tobias Hüfner-Wulsdorf
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Torsten Steinmetzer
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
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38
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Heine A, Siefker C, Klebe G. A case study of fragment screening: protein kinase A and PIM1-kinase. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319095123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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39
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Kanitz M, Blanck S, Heine A, Gulyaeva AA, Gorbalenya AE, Ziebuhr J, Diederich WE. Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus. Virology 2019; 533:21-33. [PMID: 31078932 PMCID: PMC7111312 DOI: 10.1016/j.virol.2019.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 01/05/2023]
Abstract
Cavally virus (CavV) is a mosquito-borne plus-strand RNA virus in the family Mesoniviridae (order Nidovirales). We present X-ray structures for the CavV 3C-like protease (3CLpro), as a free enzyme and in complex with a peptide aldehyde inhibitor mimicking the P4-to-P1 residues of a natural substrate. The 3CLpro structure (refined to 1.94 Å) shows that the protein forms dimers. The monomers are comprised of N-terminal domains I and II, which adopt a chymotrypsin-like fold, and a C-terminal α-helical domain III. The catalytic Cys-His dyad is assisted by a complex network of interactions involving a water molecule that mediates polar contacts between the catalytic His and a conserved Asp located in the domain II-III junction and is suitably positioned to stabilize the developing positive charge of the catalytic His in the transition state during catalysis. The study also reveals the structural basis for the distinct P2 Asn-specific substrate-binding pocket of mesonivirus 3CLpros. First structure of a 3CLpro of an invertebrate RNA virus. Structural basis of the unique substrate specificity defined by Asn at the P2 position of mesonivirus 3CLpro substrates. Emerging role of a conserved Asp residue that assists the Cys-His catalytic dyad in vertebrate and invertebrate 3CLpros.
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Affiliation(s)
- Manuel Kanitz
- Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany; Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Sandra Blanck
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Anastasia A Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany.
| | - Wibke E Diederich
- Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany; Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany.
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40
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Badran MJ, Bertoletti N, Keils A, Heine A, Klebe G, Marchais-Oberwinkler S. Mutational and structural studies uncover crucial amino acids determining activity and stability of 17β-HSD14. J Steroid Biochem Mol Biol 2019; 189:135-144. [PMID: 30836176 DOI: 10.1016/j.jsbmb.2019.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/20/2019] [Accepted: 02/22/2019] [Indexed: 01/31/2023]
Abstract
17β-Hydroxysteroid dehydrogenase type 14 (17β-HSD14) catalyzes the conversion of highly active estrogens and androgens into their less active oxidized forms in presence of NAD+ as cofactor. The crystal structure of 17β-HSD14 has been determined, however, the role of individual amino acids likely involved in the enzymatic function remains poorly understood. Objective of this study was to further characterize the enzyme by site-directed mutagenesis considering five amino acids next to the catalytic center. The tools used for the characterization of the enzyme variants are X-ray crystallography and enzyme kinetics. Lys158 was confirmed to belong to the catalytic triad. Tyr253', located on the C-terminal loop of the adjacent monomer, enters into the active site of the neighboring monomer and interacts with the catalytic Tyr154. Therefore, Tyr253' helps to tie the two monomers together. Cys255, located at the interface between both monomers, can form a disulfide bridge with the Cys255' from the adjacent monomer. In contrast to the contact provided by Tyr253, the latter interaction is not crucial for dimer formation. His93 and Gln148 are located at the rim of the substrate binding pocket. His93 does not interact directly with the ligand in the active site. However, it influences the turnover of the enzyme. The Gln148 restricts in size the access tunnel of the substrate to the binding pocket.
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Affiliation(s)
- Mohammed J Badran
- Institute for Pharmaceutical Chemistry, Philipps University Marburg, 35032 Marburg, Germany
| | - Nicole Bertoletti
- Institute for Pharmaceutical Chemistry, Philipps University Marburg, 35032 Marburg, Germany
| | - Aline Keils
- Institute for Pharmaceutical Chemistry, Philipps University Marburg, 35032 Marburg, Germany
| | - Andreas Heine
- Institute for Pharmaceutical Chemistry, Philipps University Marburg, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institute for Pharmaceutical Chemistry, Philipps University Marburg, 35032 Marburg, Germany
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41
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Jumde VR, Mondal M, Gierse RM, Unver MY, Magari F, van Lier RCW, Heine A, Klebe G, Hirsch AKH. Design and Synthesis of Bioisosteres of Acylhydrazones as Stable Inhibitors of the Aspartic Protease Endothiapepsin. ChemMedChem 2018; 13:2266-2270. [PMID: 30178575 PMCID: PMC6282583 DOI: 10.1002/cmdc.201800446] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Indexed: 12/11/2022]
Abstract
Acylhydrazone‐based dynamic combinatorial chemistry (DCC) is a powerful strategy for the rapid identification of novel hits. Even though acylhydrazones are important structural motifs in medicinal chemistry, their further progression in development may be hampered by major instability and potential toxicity under physiological conditions. It is therefore of paramount importance to identify stable replacements for acylhydrazone linkers. Herein, we present the first report on the design and synthesis of stable bioisosteres of acylhydrazone‐based inhibitors of the aspartic protease endothiapepsin as a follow‐up to a DCC study. The most successful bioisostere is equipotent, bears an amide linker, and we confirmed its binding mode by X‐ray crystallography. Having some validated bioisosteres of acylhydrazones readily available might accelerate hit‐to‐lead optimization in future acylhydrazone‐based DCC projects.
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Affiliation(s)
- Varsha R Jumde
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands.,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Milon Mondal
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Robin M Gierse
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands.,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus Building E8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Saarbrücken, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - M Yagiz Unver
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Francesca Magari
- Drug Design Group AG Klebe, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35032, Marburg, Germany
| | - Roos C W van Lier
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Andreas Heine
- Drug Design Group AG Klebe, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Drug Design Group AG Klebe, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35032, Marburg, Germany
| | - Anna K H Hirsch
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands.,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus Building E8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Saarbrücken, Campus Building E8.1, 66123, Saarbrücken, Germany
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42
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Schiebel J, Gaspari R, Wulsdorf T, Ngo K, Sohn C, Schrader TE, Cavalli A, Ostermann A, Heine A, Klebe G. Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes. Nat Commun 2018; 9:3559. [PMID: 30177695 PMCID: PMC6120877 DOI: 10.1038/s41467-018-05769-2] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 07/26/2018] [Indexed: 11/09/2022] Open
Abstract
Hydrogen bonds are key interactions determining protein-ligand binding affinity and therefore fundamental to any biological process. Unfortunately, explicit structural information about hydrogen positions and thus H-bonds in protein-ligand complexes is extremely rare and similarly the important role of water during binding remains poorly understood. Here, we report on neutron structures of trypsin determined at very high resolutions ≤1.5 Å in uncomplexed and inhibited state complemented by X-ray and thermodynamic data and computer simulations. Our structures show the precise geometry of H-bonds between protein and the inhibitors N-amidinopiperidine and benzamidine along with the dynamics of the residual solvation pattern. Prior to binding, the ligand-free binding pocket is occupied by water molecules characterized by a paucity of H-bonds and high mobility resulting in an imperfect hydration of the critical residue Asp189. This phenomenon likely constitutes a key factor fueling ligand binding via water displacement and helps improving our current view on water influencing protein-ligand recognition.
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Affiliation(s)
- Johannes Schiebel
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.,Computational Sciences, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Roberto Gaspari
- Computational Sciences, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Tobias Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Khang Ngo
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Christian Sohn
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Tobias E Schrader
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich, Lichtenbergstraße 1, 85748, Garching, Germany
| | - Andrea Cavalli
- Computational Sciences, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstraße 1, 85748, Garching, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.
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43
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Wienen-Schmidt B, Wulsdorf T, Jonker HRA, Saxena K, Kudlinzki D, Linhard V, Sreeramulu S, Heine A, Schwalbe H, Klebe G. On the Implication of Water on Fragment-to-Ligand Growth in Kinase Binding Thermodynamics. ChemMedChem 2018; 13:1988-1996. [DOI: 10.1002/cmdc.201800438] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Barbara Wienen-Schmidt
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Tobias Wulsdorf
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Hendrik R. A. Jonker
- Institut für Organische Chemie und Chemische Biologie, Deutsches Zentrum für Translationale Krebsforschung (DKTK); Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Straße 7, N160-3.14 60438 Frankfurt am Main Germany
| | - Krishna Saxena
- Institut für Organische Chemie und Chemische Biologie, Deutsches Zentrum für Translationale Krebsforschung (DKTK); Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Straße 7, N160-3.14 60438 Frankfurt am Main Germany
| | - Denis Kudlinzki
- Institut für Organische Chemie und Chemische Biologie, Deutsches Zentrum für Translationale Krebsforschung (DKTK); Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Straße 7, N160-3.14 60438 Frankfurt am Main Germany
| | - Verena Linhard
- Institut für Organische Chemie und Chemische Biologie, Deutsches Zentrum für Translationale Krebsforschung (DKTK); Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Straße 7, N160-3.14 60438 Frankfurt am Main Germany
| | - Sridhar Sreeramulu
- Institut für Organische Chemie und Chemische Biologie, Deutsches Zentrum für Translationale Krebsforschung (DKTK); Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Straße 7, N160-3.14 60438 Frankfurt am Main Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Harald Schwalbe
- Institut für Organische Chemie und Chemische Biologie, Deutsches Zentrum für Translationale Krebsforschung (DKTK); Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Straße 7, N160-3.14 60438 Frankfurt am Main Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
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44
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Heine A, Siefker C, Klebe G. Fragment screening on protein kinase A and PIM1-kinase. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318092264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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45
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Metz A, Huschmann F, Schiebel J, Müller U, Weiss M, Heine A, Klebe G. High-throughput crystallographic fragment screening for drug discovery. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318094858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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46
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Ehrmann FR, Kalim J, Pfaffeneder T, Bernet B, Hohn C, Schäfer E, Botzanowski T, Cianférani S, Heine A, Reuter K, Diederich F, Klebe G. Austausch der Proteinkontaktflächen in der homodimeren tRNA-Guanin-Transglycosylase: ein Weg der funktionellen Regulation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Frederik Rainer Ehrmann
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Jorna Kalim
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Toni Pfaffeneder
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Bruno Bernet
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Christoph Hohn
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Elisabeth Schäfer
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse Bio-Organique; Université de Strasbourg; CNRS, IPHC UMR 7178; 67000 Strasbourg Frankreich
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique; Université de Strasbourg; CNRS, IPHC UMR 7178; 67000 Strasbourg Frankreich
| | - Andreas Heine
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
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47
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Espinel D, Jordan R, Pinoni V, Martinez J, Verbanaz S, giorgio P, Eusebio M, Navarro K, Bustos A, Becker V, Giovanakis M, Heine A, Efron E. A prospective study on active surveillance of bacterial colonization in oncohaematological patients and its association with bacteraemias. Int J Infect Dis 2018. [DOI: 10.1016/j.ijid.2018.04.3484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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48
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Ehrmann FR, Kalim J, Pfaffeneder T, Bernet B, Hohn C, Schäfer E, Botzanowski T, Cianférani S, Heine A, Reuter K, Diederich F, Klebe G. Swapping Interface Contacts in the Homodimeric tRNA-Guanine Transglycosylase: An Option for Functional Regulation. Angew Chem Int Ed Engl 2018; 57:10085-10090. [DOI: 10.1002/anie.201804627] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/04/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Frederik Rainer Ehrmann
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Jorna Kalim
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Switzerland
| | - Toni Pfaffeneder
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Switzerland
| | - Bruno Bernet
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Switzerland
| | - Christoph Hohn
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Switzerland
| | - Elisabeth Schäfer
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Switzerland
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse Bio-Organique; Université de Strasbourg; CNRS, IPHC UMR 7178; 67000 Strasbourg France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique; Université de Strasbourg; CNRS, IPHC UMR 7178; 67000 Strasbourg France
| | - Andreas Heine
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Switzerland
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
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49
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Movsisyan LD, Schäfer E, Nguyen A, Ehrmann FR, Schwab A, Rossolini T, Zimmerli D, Wagner B, Daff H, Heine A, Klebe G, Diederich F. Sugar Acetonides are a Superior Motif for Addressing the Large, Solvent-Exposed Ribose-33 Pocket of tRNA-Guanine Transglycosylase. Chemistry 2018; 24:9957-9967. [PMID: 29939431 DOI: 10.1002/chem.201801756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/10/2018] [Indexed: 11/09/2022]
Abstract
The intestinal disease shigellosis caused by Shigella bacteria affects over 120 million people annually. There is an urgent demand for new drugs as resistance against common antibiotics emerges. Bacterial tRNA-guanine transglycosylase (TGT) is a druggable target and controls the pathogenicity of Shigella flexneri. We report the synthesis of sugar-functionalized lin-benzoguanines addressing the ribose-33 pocket of TGT from Zymomonas mobilis. Ligand binding was analyzed by isothermal titration calorimetry and X-ray crystallography. Pocket occupancy was optimized by variation of size and protective groups of the sugars. The participation of a polycyclic water-cluster in the recognition of the sugar moiety was revealed. Acetonide-protected ribo- and psicofuranosyl derivatives are highly potent, benefiting from structural rigidity, good solubility, and metabolic stability. We conclude that sugar acetonides have a significant but not yet broadly recognized value in drug development.
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Affiliation(s)
- Levon D Movsisyan
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Elisabeth Schäfer
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Andreas Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Frederik R Ehrmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Anatol Schwab
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Thomas Rossolini
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Daniel Zimmerli
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Björn Wagner
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Hamina Daff
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
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50
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Wienen-Schmidt B, Jonker HRA, Wulsdorf T, Gerber HD, Saxena K, Kudlinzki D, Sreeramulu S, Parigi G, Luchinat C, Heine A, Schwalbe H, Klebe G. Paradoxically, Most Flexible Ligand Binds Most Entropy-Favored: Intriguing Impact of Ligand Flexibility and Solvation on Drug–Kinase Binding. J Med Chem 2018; 61:5922-5933. [DOI: 10.1021/acs.jmedchem.8b00105] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Barbara Wienen-Schmidt
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Hendrik R. A. Jonker
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Tobias Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Hans-Dieter Gerber
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Krishna Saxena
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Denis Kudlinzki
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Sridhar Sreeramulu
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM/CIRMMP) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM/CIRMMP) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Harald Schwalbe
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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