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Arimondo PB, Essig S, Schopfer U, Rufer A. Advances in Chemical Probing Concepts for Chemical Biology Applications. Chembiochem 2023; 24:e202300319. [PMID: 37501334 DOI: 10.1002/cbic.202300319] [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: 04/20/2023] [Revised: 05/10/2023] [Indexed: 07/29/2023]
Abstract
Chemical probes allow us to identify, validate and confirm novel targets for therapeutic applications, enable the development of drug candidates, and open the way to new therapeutic strategies, vaccines and diagnostic tools.
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Affiliation(s)
- Paola B Arimondo
- Institut Pasteur, Université Paris Cité, CNRS UMR n° 3523 Chem4Life, Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, 75015, Paris, France
| | - Sebastian Essig
- Bayer AG, Research & Development, Pharmaceuticals, Drug Discovery Sciences, Life Science Technologies, Aprather Weg 18a, Gebäude 460, Raum 345, 42113, Wuppertal, Germany
| | - Ulrich Schopfer
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Arne Rufer
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 065/208 A, 4070, Basel, Switzerland
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Gehrlein A, Udayar V, Anastasi N, Morella ML, Ruf I, Brugger D, von der Mark S, Thoma R, Rufer A, Heer D, Pfahler N, Jochner A, Niewoehner J, Wolf L, Fueth M, Ebeling M, Villaseñor R, Zhu Y, Deen MC, Shan X, Ehsaei Z, Taylor V, Sidransky E, Vocadlo DJ, Freskgård PO, Jagasia R. Targeting neuronal lysosomal dysfunction caused by β-glucocerebrosidase deficiency with an enzyme-based brain shuttle construct. Nat Commun 2023; 14:2057. [PMID: 37045813 PMCID: PMC10097658 DOI: 10.1038/s41467-023-37632-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 03/24/2023] [Indexed: 04/14/2023] Open
Abstract
Mutations in glucocerebrosidase cause the lysosomal storage disorder Gaucher's disease and are the most common risk factor for Parkinson's disease. Therapies to restore the enzyme's function in the brain hold great promise for treating the neurological implications. Thus, we developed blood-brain barrier penetrant therapeutic molecules by fusing transferrin receptor-binding moieties to β-glucocerebrosidase (referred to as GCase-BS). We demonstrate that these fusion proteins show significantly increased uptake and lysosomal efficiency compared to the enzyme alone. In a cellular disease model, GCase-BS rapidly rescues the lysosomal proteome and lipid accumulations beyond known substrates. In a mouse disease model, intravenous injection of GCase-BS leads to a sustained reduction of glucosylsphingosine and can lower neurofilament-light chain plasma levels. Collectively, these findings demonstrate the potential of GCase-BS for treating GBA1-associated lysosomal dysfunction, provide insight into candidate biomarkers, and may ultimately open a promising treatment paradigm for lysosomal storage diseases extending beyond the central nervous system.
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Affiliation(s)
- Alexandra Gehrlein
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland.
| | - Vinod Udayar
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Nadia Anastasi
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Martino L Morella
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
- Department of Anatomy and Neurosciences, Amsterdam University Medical Center | VUmc, Amsterdam, Netherlands
| | - Iris Ruf
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Doris Brugger
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Sophia von der Mark
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Ralf Thoma
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Arne Rufer
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Dominik Heer
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Nina Pfahler
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
- Interfaculty Institute of Biochemistry & Structural Biology Biochemistry (IFIB), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Anton Jochner
- Roche Pharma Research and Early Development, Therapeutic Modalities Large Molecule Research, Roche Innovation Center Munich, Roche Diagnostics GmbH, Penzberg, Germany
| | - Jens Niewoehner
- Roche Pharma Research and Early Development, Therapeutic Modalities Large Molecule Research, Roche Innovation Center Munich, Roche Diagnostics GmbH, Penzberg, Germany
| | - Luise Wolf
- Roche Pharma Research and Early Development, Data & Analytics, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Matthias Fueth
- Roche Pharma Research and Early Development, Pharmaceutical Science, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Martin Ebeling
- Roche Pharma Research and Early Development, Pharmaceutical Science, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Roberto Villaseñor
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Yanping Zhu
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Matthew C Deen
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Xiaoyang Shan
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Zahra Ehsaei
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Verdon Taylor
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Ellen Sidransky
- Molecular Neurogenetics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Per-Ola Freskgård
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
- BioArctic AB, Stockholm, Sweden
| | - Ravi Jagasia
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland.
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Rufer A, Hartnack S, Ringer SK. [The importance of a veterinary anaesthetist and pain treatment according to dog and cat owners]. SCHWEIZ ARCH TIERH 2023; 165:115-0. [PMID: 36718713 DOI: 10.17236/sat00385] [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] [Indexed: 02/01/2023]
Abstract
INTRODUCTION In Switzerland, compared to the United Kingdom or the United States of America, fewer veterinary anaesthetists are employed in private practice, which raises the question about the reason. The present survey aimed at investigating the awareness of pet owners concerning the specialization of veterinary anaesthesia and the value they attribute to such a specialist. Also, estimation of pain in dogs and cats and the importance of its treatment from the point of view of the pet owners was analysed. Furthermore, the necessity of veterinary anaesthetists in private practice and the influencing factors were investigated. The survey was created on LimeSurvey, an online tool for questionnaires and sent to dog and cat owners of the small animal clinic of the University Hospital of Zurich. 317 fully completed questionnaires were evaluated. In general, pet owners appreciated the specialization of veterinary anaesthesiology. Great importance was attributed to the supervision of anaesthesia and analgesic therapy by a specialist. A preliminary talk with an anaesthetist would be appreciated. Owners would be willing to cover additional costs for a specialized anaesthetist, if recommended by the private veterinarian, and to bring their animal to the University Hospital, in case of an increased anaesthetic risk.
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Affiliation(s)
- A Rufer
- Abteilung für Anästhesiologie, Departement für klinische Diagnostik und Services, Vetsuisse-Fakultät, Universität Zürich
| | - S Hartnack
- Abteilung für Epidemiologie, Vetsuisse-Fakultät, Universität Zürich
| | - S K Ringer
- Abteilung für Anästhesiologie, Departement für klinische Diagnostik und Services, Vetsuisse-Fakultät, Universität Zürich
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Ruf A, Banner DW, Benz J, Bertschinger J, Burger D, Crisci M, Cuppuleri S, Debulpaep M, Grabulovski D, Gsell B, Huber W, Kusznir E, Laeremans T, Matile H, Pecoraro V, Rufer A, Schlatter D, Steyeart J, Stihle M, Thoma R, Weber M, Wiget A. Fyn, Fab, Xap: evaluation of different protein binders as crystallization aids. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312097267] [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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Schlatter D, Brack S, Banner DW, Batey S, Benz J, Bertschinger J, Huber W, Joseph C, Rufer A, van der Klooster A, Weber M, Grabulovski D, Hennig M. Generation, characterization and structural data of chymase binding proteins based on the human Fyn kinase SH3 domain. MAbs 2012; 4:497-508. [PMID: 22653218 PMCID: PMC3499344 DOI: 10.4161/mabs.20452] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [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] [Indexed: 12/15/2022] Open
Abstract
The serine protease chymase (EC = 3.4.21.39) is expressed in the secretory granules of mast cells, which are important in allergic reactions. Fynomers, which are binding proteins derived from the Fyn SH3 domain, were generated against human chymase to produce binding partners to facilitate crystallization, structure determination and structure-based drug discovery, and to provide inhibitors of chymase for therapeutic applications. The best Fynomer was found to bind chymase with a KD of 0.9 nM and koff of 6.6x10 (-4) s (-1) , and to selectively inhibit chymase activity with an IC 50 value of 2 nM. Three different Fynomers were co-crystallized with chymase in 6 different crystal forms overall, with diffraction quality in the range of 2.25 to 1.4 Å resolution, which is suitable for drug design efforts. The X-ray structures show that all Fynomers bind to the active site of chymase. The conserved residues Arg15-Trp16-Thr17 in the RT-loop of the chymase binding Fynomers provide a tight interaction, with Trp16 pointing deep into the S1 pocket of chymase. These results confirm the suitability of Fynomers as research tools to facilitate protein crystallization, as well as for the development of assays to investigate the biological mechanism of targets. Finally, their highly specific inhibitory activity and favorable molecular properties support the use of Fynomers as potential therapeutic agents.
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Affiliation(s)
- Daniel Schlatter
- F. Hoffmann-La Roche Ltd, Pharma Research & Early Development, Discovery Technologies, Basel, Switzerland
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Riek U, Scholz R, Konarev P, Rufer A, Suter M, Nazabal A, Ringler P, Chami M, Müller SA, Neumann D, Forstner M, Hennig M, Zenobi R, Engel A, Svergun D, Schlattner U, Wallimann T. Structural properties of AMP-activated protein kinase: dimerization, molecular shape, and changes upon ligand binding. J Biol Chem 2008; 283:18331-43. [PMID: 18372250 DOI: 10.1074/jbc.m708379200] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Heterotrimeric AMP-activated protein kinase (AMPK) is crucial for energy homeostasis of eukaryotic cells and organisms. Here we report on (i) bacterial expression of untagged mammalian AMPK isoform combinations, all containing gamma(1), (ii) an automated four-dimensional purification protocol, and (iii) biophysical characterization of AMPK heterotrimers by small angle x-ray scattering in solution (SAXS), transmission and scanning transmission electron microscopy (TEM, STEM), and mass spectrometry (MS). AMPK in solution at low concentrations (~1 mg/ml) largely consisted of individual heterotrimers in TEM analysis, revealed a precise 1:1:1 stoichiometry of the three subunits in MS, and behaved as an ideal solution in SAXS. At higher AMPK concentrations, SAXS revealed concentration-dependent, reversible dimerization of AMPK heterotrimers and formation of higher oligomers, also confirmed by STEM mass measurements. Single particle reconstruction and averaging by SAXS and TEM, respectively, revealed similar elongated, flat AMPK particles with protrusions and an indentation. In the lower AMPK concentration range, addition of AMP resulted in a significant decrease of the radius of gyration by approximately 5% in SAXS, which indicates a conformational switch in AMPK induced by ligand binding. We propose a structural model involving a ligand-induced relative movement of the kinase domain resulting in a more compact heterotrimer and a conformational change in the kinase domain that protects AMPK from dephosphorylation of Thr(172), thus positively affecting AMPK activity.
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Affiliation(s)
- Uwe Riek
- Institute of Cell Biology, Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
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Burgermeister E, Schnoebelen A, Flament A, Benz J, Stihle M, Gsell B, Rufer A, Ruf A, Kuhn B, Märki HP, Mizrahi J, Sebokova E, Niesor E, Meyer M. A novel partial agonist of peroxisome proliferator-activated receptor-gamma (PPARgamma) recruits PPARgamma-coactivator-1alpha, prevents triglyceride accumulation, and potentiates insulin signaling in vitro. Mol Endocrinol 2005; 20:809-30. [PMID: 16373399 DOI: 10.1210/me.2005-0171] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [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: 11/19/2022] Open
Abstract
Partial agonists of peroxisome proliferator-activated receptor-gamma (PPARgamma), also termed selective PPARgamma modulators, are expected to uncouple insulin sensitization from triglyceride (TG) storage in patients with type 2 diabetes mellitus. These agents shall thus avoid adverse effects, such as body weight gain, exerted by full agonists such as thiazolidinediones. In this context, we describe the identification and characterization of the isoquinoline derivative PA-082, a prototype of a novel class of non-thiazolidinedione partial PPARgamma ligands. In a cocrystal with PPARgamma it was bound within the ligand-binding pocket without direct contact to helix 12. The compound displayed partial agonism in biochemical and cell-based transactivation assays and caused preferential recruitment of PPARgamma-coactivator-1alpha (PGC1alpha) to the receptor, a feature shared with other selective PPARgamma modulators. It antagonized rosiglitazone-driven transactivation and TG accumulation during de novo adipogenic differentiation of murine C3H10T1/2 mesenchymal stem cells. The latter effect was mimicked by overexpression of wild-type PGC1alpha but not its LXXLL-deficient mutant. Despite failing to promote TG loading, PA-082 induced mRNAs of genes encoding components of insulin signaling and adipogenic differentiation pathways. It potentiated glucose uptake and inhibited the negative cross-talk of TNFalpha on protein kinase B (AKT) phosphorylation in mature adipocytes and HepG2 human hepatoma cells. PGC1alpha is a key regulator of energy expenditure and down-regulated in diabetics. We thus propose that selective recruitment of PGC1alpha to favorable PPARgamma-target genes provides a possible molecular mechanism whereby partial PPARgamma agonists dissociate TG accumulation from insulin signaling.
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Affiliation(s)
- Elke Burgermeister
- Pharmaceuticals Division, Department of Vascular and Metabolic Diseases, Fa. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
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Baer K, Al-Hasani H, Parvaresch S, Corona T, Rufer A, Nölle V, Bergschneider E, Klein HW. Dimerization-induced activation of soluble insulin/IGF-1 receptor kinases: an alternative mechanism of activation. Biochemistry 2001; 40:14268-78. [PMID: 11714281 DOI: 10.1021/bi015588g] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [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: 11/28/2022]
Abstract
To study the role of kinase dimerization in the activation of the insulin receptor (IR) and the insulin-like growth factor receptor-1 (IGF-1R), we have cloned, expressed, and purified monomeric and dimeric forms of the corresponding soluble kinase domains via the baculovirus expression system. Dimerization of the kinases was achieved by fusion of the kinase domains to the homodimeric glutathione S-transferase (GST). Kinetic analyses revealed that kinase dimerization results in substantial increases (10-100-fold) in the phosphotransferase activity in both the auto- and substrate phosphorylation reactions. Furthermore, kinase dimerization rendered the autophosphorylation reaction concentration-independent. However, whereas dimerization was required for the rapid autophosphorylation of the kinases, it was not essential for the enhanced kinase activity in substrate phosphorylation reactions. Comparison of HPLC-phosphopeptide maps of the monomeric and dimeric kinases revealed that dimerization leads to an increased phosphorylation of the regulatory activation loop of the kinases, strongly suggesting that bis- and trisphosphorylation of the activation loop are mediated by transphosphorylation within the kinase dimers. Most strikingly, limited proteolysis revealed that GST-mediated dimerization by itself had a major impact on the conformation of the activation loop by stabilizing a conformation that corresponds to the active, phosphorylated form of the kinase. Thus, in analogy to the insulin/IGF-1-ligated holoreceptors, the dimeric GST-kinases are primed to rapid autophosphorylation by an increase in the local concentration of both phosphoryl donor and phosphoryl acceptor sites and by a dimerization-induced conformational change of the activation loop that leads to an efficient transphosphorylation of the regulatory tyrosine residues.
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Affiliation(s)
- K Baer
- Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, 50674 Cologne, Germany
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