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Jo J, Upadhyay T, Woods EC, Park KW, Pedowitz NJ, Jaworek-Korjakowska J, Wang S, Valdez TA, Fellner M, Bogyo M. Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of S. aureus Infections. bioRxiv 2023:2023.12.11.571116. [PMID: 38168396 PMCID: PMC10760020 DOI: 10.1101/2023.12.11.571116] [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] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Staphylococcus aureus is a major human pathogen responsible for a wide range of systemic infections. Since its propensity to form biofilms in vivo poses formidable challenges for both detection and treatment, tools that can be used to specifically image S. aureus biofilms are highly valuable for clinical management. Here we describe the development of oxadiazolonebased activity-based probes to target the S. aureus-specific serine hydrolase FphE. Because this enzyme lacks homologs in other bacteria, it is an ideal target for selective imaging of S. aureus infections. Using X-ray crystallography, direct cell labeling and mouse models of infection we demonstrate that oxadiazolone-based probes enable specific labeling of S. aureus bacteria through the direct covalent modification of the FphE active site serine. These results demonstrate the utility of the oxadizolone electrophile for activity-based probes (ABPs) and validate FphE as a target for development of imaging contrast agents for the rapid detection of S. aureus infections.
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Affiliation(s)
- Jeyun Jo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tulsi Upadhyay
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emily C. Woods
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ki Wan Park
- Department of Otolaryngology–Head & Neck Surgery Divisions, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nichole J. Pedowitz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Sijie Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tulio A. Valdez
- Department of Otolaryngology–Head & Neck Surgery Divisions, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthias Fellner
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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2
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Gan J, Pinto-Fernández A, Flierman D, Akkermans JJLL, O’Brien DP, Greenwood H, Scott HC, Fritz G, Knobeloch KP, Neefjes J, van Dam H, Ovaa H, Ploegh HL, Kessler BM, Geurink PP, Sapmaz A. USP16 is an ISG15 cross-reactive deubiquitinase that targets pro-ISG15 and ISGylated proteins involved in metabolism. Proc Natl Acad Sci U S A 2023; 120:e2315163120. [PMID: 38055744 PMCID: PMC10722975 DOI: 10.1073/pnas.2315163120] [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: 09/12/2023] [Accepted: 11/02/2023] [Indexed: 12/08/2023] Open
Abstract
Interferon-induced ubiquitin (Ub)-like modifier ISG15 covalently modifies host and viral proteins to restrict viral infections. Its function is counteracted by the canonical deISGylase USP18 or Ub-specific protease 18. Notwithstanding indications for the existence of other ISG15 cross-reactive proteases, these remain to be identified. Here, we identify deubiquitinase USP16 as an ISG15 cross-reactive protease by means of ISG15 activity-based profiling. Recombinant USP16 cleaved pro-ISG15 and ISG15 isopeptide-linked model substrates in vitro, as well as ISGylated substrates from cell lysates. Moreover, interferon-induced stimulation of ISGylation was increased by depletion of USP16. The USP16-dependent ISG15 interactome indicated that the deISGylating function of USP16 may regulate metabolic pathways. Targeted enzymes include malate dehydrogenase, cytoplasmic superoxide dismutase 1, fructose-bisphosphate aldolase A, and cytoplasmic glutamic-oxaloacetic transaminase 1. USP16 may thus contribute to the regulation of a subset of metabolism-related proteins during type-I interferon responses.
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Affiliation(s)
- Jin Gan
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA02115
| | - Adán Pinto-Fernández
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, OxfordOX3 7FZ, United Kingdom
| | - Dennis Flierman
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Jimmy J. L. L. Akkermans
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center LUMC, Leiden2333 ZC, The Netherlands
| | - Darragh P. O’Brien
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, OxfordOX3 7FZ, United Kingdom
| | - Helene Greenwood
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, OxfordOX3 7FZ, United Kingdom
| | - Hannah Claire Scott
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
| | - Günter Fritz
- Department of Cellular Microbiology, University of Hohenheim, Stuttgart70599, Germany
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Faculty of Medicine, Department of Molecular Genetics, University of Freiburg, Freiburg79106, Germany
- Centre for Integrative Biological Signalling Studies, Department of Molecular Genetics, University of Freiburg, Freiburg79104, Germany
| | - Jacques Neefjes
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center LUMC, Leiden2333 ZC, The Netherlands
| | - Hans van Dam
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Hidde L. Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA02115
| | - Benedikt M. Kessler
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, OxfordOX3 7FZ, United Kingdom
| | - Paul P. Geurink
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Aysegul Sapmaz
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
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3
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Zhou L, He F, Xiang X, Dong C, Xiang T, Li X, Li H, Bu L, Wang Y, Ma X. Radioactive and Fluorescent Dual Modality Cysteine Cathepsin B Activity-Based Probe for Cancer Theranostics. Mol Pharm 2023. [PMID: 37289648 DOI: 10.1021/acs.molpharmaceut.3c00148] [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: 06/10/2023]
Abstract
Cysteine cathepsin B (CTS-B) is a crucial enzyme that is overexpressed in numerous malignancies and contributes to the invasion and metastasis of cancer. Therefore, this study sets out to develop and evaluate an activity-based multimodality theranostic agent targeting CTS-B for cancer imaging and therapy. A CTS-B activity-based probe, BMX2, was synthesized and labeled efficiently with 68Ga and 90Y to produce 68Ga-BMX2 for multimodality imaging and 90Y-BMX2 for radiation therapy. The affinity and specificity of BMX2 binding with the CTS-B enzyme were determined by fluorescent western blots using recombined active human CTS-B enzyme (rh-CTS-B) and four cancer cell lines including HeLa, HepG2, MCF7, and U87MG, with CA074 as the CTS-B inhibitor for control. Confocal laser scanning microscope imaging and cell uptake measurement were also performed. Then, in vivo PET imaging and fluorescence imaging were acquired on HeLa xenografts. Finally, the therapeutic effect of 90Y-BMX2 was tested. BMX2 could be specifically activated by rh-CTS-B and stably bound to the enzyme. The binding of BMX2 with CTS-B is time-dependent and enzyme concentration-dependent. Although CTS-B expression varied between cell lines, all showed significant uptake of BMX2 and 68Ga-BMX2. In vivo optical and PET imaging showed a high tumor uptake of BMX2 and 68Ga-BMX2 and accumulation for more than 24 h. 90Y-BMX2 could significantly inhibit HeLa tumor growth. The development of 68Ga/90Y-BMX2, a radioactive and fluorescent dual modality theranostic agent, demonstrated an effective theranostic approach for PET diagnostic imaging, fluorescence imaging, and radionuclide therapy of cancers, which may have a potential for clinical translation for cancer theranostics in the future.
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Affiliation(s)
- Lianbo Zhou
- Department of Nuclear Medicine, The 2nd Xiangya Hospital of Central South University, 139 Middle Renmin Road, Changsha 410011, PR China
| | - Feng He
- Department of Nuclear Medicine, The 2nd Xiangya Hospital of Central South University, 139 Middle Renmin Road, Changsha 410011, PR China
| | - Xin Xiang
- Department of Nuclear Medicine, The 2nd Xiangya Hospital of Central South University, 139 Middle Renmin Road, Changsha 410011, PR China
| | - Chuning Dong
- Department of Nuclear Medicine, The 2nd Xiangya Hospital of Central South University, 139 Middle Renmin Road, Changsha 410011, PR China
| | - Tian Xiang
- Department of Nuclear Medicine, The 2nd Xiangya Hospital of Central South University, 139 Middle Renmin Road, Changsha 410011, PR China
| | - Xian Li
- Department of Nuclear Medicine, The 2nd Xiangya Hospital of Central South University, 139 Middle Renmin Road, Changsha 410011, PR China
| | - Hong Li
- Department of Nuclear Medicine, The 2nd Xiangya Hospital of Central South University, 139 Middle Renmin Road, Changsha 410011, PR China
| | - Lihong Bu
- Molecular Imaging Centre, Renmin Hospital of Wuhan University, 99 Zhang Zhi Dong Road, Wuhan 430060, PR China
| | - Yunhua Wang
- Department of Nuclear Medicine, The 2nd Xiangya Hospital of Central South University, 139 Middle Renmin Road, Changsha 410011, PR China
| | - Xiaowei Ma
- Department of Nuclear Medicine, The 2nd Xiangya Hospital of Central South University, 139 Middle Renmin Road, Changsha 410011, PR China
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Janiszewski T, Kołt S, Ciastoń I, Vizovisek M, Poręba M, Turk B, Drąg M, Kozieł J, Kasperkiewicz P. Investigation of osteoclast cathepsin K activity in osteoclastogenesis and bone loss using a set of chemical reagents. Cell Chem Biol 2023; 30:159-174.e8. [PMID: 36696904 DOI: 10.1016/j.chembiol.2023.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 05/17/2021] [Revised: 08/28/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023]
Abstract
Cathepsin K (CatK) is a lysosomal cysteine protease whose highest expression is found in osteoclasts, which are the cells responsible for bone resorption. Investigations of the functions and physiological relevance of CatK have often relied on antibody-related techniques, which makes studying its activity patterns a challenging task. Hence, we developed a set of chemical tools for the investigation of CatK activity. We show that our probe is a valuable tool for monitoring the proteolytic activation of CatK during osteoclast formation. Moreover, we demonstrate that our inhibitor of CatK impedes osteoclastogenesis and bone resorption and that CatK is stored in its active form in osteoclasts within their lysosomal compartment and mainly in the ruffled borders of osteoclasts. Given that our probe recognizes active CatK within living cells without exhibiting any observed cytotoxicity in the several models tested, we expect that it would be well suited to theranostic applications in CatK-related diseases.
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Affiliation(s)
- Tomasz Janiszewski
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Sonia Kołt
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Izabela Ciastoń
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Matej Vizovisek
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Marcin Poręba
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, 1000 Ljubljana, Slovenia
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Kozieł
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Paulina Kasperkiewicz
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
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5
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Su Q, Schröder SP, Lelieveld LT, Ferraz MJ, Verhoek M, Boot RG, Overkleeft HS, Aerts JMFG, Artola M, Kuo CL. Corrigendum: Xylose-Configured Cyclophellitols as Selective Inhibitors for Glucocerebrosidase. Chembiochem 2023; 24:e202300728. [PMID: 36725348 PMCID: PMC11062055 DOI: 10.1002/cbic.202300728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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6
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Ramos-Llorca A, Decraecker L, Cacheux VMY, Zeiburlina I, De bruyn M, Battut L, Moreno-Cinos C, Ceradini D, Espinosa E, Dietrich G, Berg M, De Meester I, Van Der Veken P, Boeckxstaens G, Lambeir AM, Denadai-Souza A, Augustyns K. Chemically diverse activity-based probes with unexpected inhibitory mechanisms targeting trypsin-like serine proteases. Front Chem 2023; 10:1089959. [PMID: 36688031 PMCID: PMC9849758 DOI: 10.3389/fchem.2022.1089959] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Activity-based probes (ABP) are molecules that bind covalently to the active form of an enzyme family, making them an attractive tool for target and biomarker identification and drug discovery. The present study describes the synthesis and biochemical characterization of novel activity-based probes targeting trypsin-like serine proteases. We developed an extensive library of activity-based probes with "clickable" affinity tags and a diaryl phosphonate warhead. A wide diversity was achieved by including natural amino acid analogs as well as basic polar residues as side chains. A detailed enzymatic characterization was performed in a panel of trypsin-like serine proteases. Their inhibitory potencies and kinetic profile were examined, and their IC50 values, mechanism of inhibition, and kinetic constants were determined. The activity-based probes with a benzyl guanidine side chain showed the highest inhibitory effects in the panel. Surprisingly, some of the high-affinity probes presented a reversible inhibitory mechanism. On the other hand, probes with different side chains exhibited the expected irreversible mechanism. For the first time, we demonstrate that not only irreversible probes but also reversible probes can tightly label recombinant proteases and proteases released from human mast cells. Even under denaturing SDS-PAGE conditions, reversible slow-tight-binding probes can label proteases due to the formation of high-affinity complexes and slow dissociation rates. This unexpected finding will transform the view on the required irreversible nature of activity-based probes. The diversity of this library of activity-based probes combined with a detailed enzyme kinetic characterization will advance their applications in proteomic studies and drug discovery.
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Affiliation(s)
- Alba Ramos-Llorca
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Lisse Decraecker
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Valérie M. Y. Cacheux
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Irena Zeiburlina
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Michelle De bruyn
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Louise Battut
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Carlos Moreno-Cinos
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Eric Espinosa
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Gilles Dietrich
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Maya Berg
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Ingrid De Meester
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Pieter Van Der Veken
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Guy Boeckxstaens
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Anne-Marie Lambeir
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Alexandre Denadai-Souza
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium,*Correspondence: Koen Augustyns,
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Su Q, Schröder SP, Lelieveld LT, Ferraz MJ, Verhoek M, Boot RG, Overkleeft HS, Aerts JMFG, Artola M, Kuo CL. Corrigendum: Xylose-Configured Cyclophellitols as Selective Inhibitors for Glucocerebrosidase. Chembiochem 2022:e202200728. [PMID: 36581583 DOI: 10.1002/cbic.202200728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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8
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Mehner C, Hockla A, Coban M, Madden B, Estrada R, Radisky DC, Radisky ES. Activity-based protein profiling reveals active serine proteases that drive malignancy of human ovarian clear cell carcinoma. J Biol Chem 2022; 298:102146. [PMID: 35716777 PMCID: PMC9304776 DOI: 10.1016/j.jbc.2022.102146] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/14/2022] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is an understudied poor prognosis subtype of ovarian cancer lacking in effective targeted therapies. Efforts to define molecular drivers of OCCC malignancy may lead to new therapeutic targets and approaches. Among potential targets are secreted proteases, enzymes which in many cancers serve as key drivers of malignant progression. Here, we found that inhibitors of trypsin-like serine proteases suppressed malignant phenotypes of OCCC cell lines. To identify the proteases responsible for malignancy in OCCC, we employed activity-based protein profiling to directly analyze enzyme activity. We developed an activity-based probe featuring an arginine diphenylphosphonate warhead to detect active serine proteases of trypsin-like specificity and a biotin handle to facilitate affinity purification of labeled proteases. Using this probe, we identified active trypsin-like serine proteases within the complex proteomes secreted by OCCC cell lines, including two proteases in common, tissue plasminogen activator and urokinase-type plasminogen activator. Further interrogation of these proteases showed that both were involved in cancer cell invasion and proliferation of OCCC cells and were also detected in in vivo models of OCCC. We conclude the detection of tissue plasminogen activator and urokinase-type plasminogen activator as catalytically active proteases and significant drivers of the malignant phenotype may point to these enzymes as targets for new therapeutic strategies in OCCC. Our activity-based probe and profiling methodology will also serve as a valuable tool for detection of active trypsin-like serine proteases in models of other cancers and other diseases.
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Affiliation(s)
- Christine Mehner
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA,Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Alexandra Hockla
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Mathew Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Benjamin Madden
- Medical Genome Facility Proteomics Core, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Derek C. Radisky
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA,For correspondence: Evette S. Radisky
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9
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Li M, Patel HV, Cognetta AB, Smith TC, Mallick I, Cavalier JF, Previti ML, Canaan S, Aldridge BB, Cravatt BF, Seeliger JC. Identification of cell wall synthesis inhibitors active against Mycobacterium tuberculosis by competitive activity-based protein profiling. Cell Chem Biol 2022; 29:883-896.e5. [PMID: 34599873 PMCID: PMC8964833 DOI: 10.1016/j.chembiol.2021.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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: 04/16/2021] [Revised: 07/08/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022]
Abstract
The identification and validation of a small molecule's targets is a major bottleneck in the discovery process for tuberculosis antibiotics. Activity-based protein profiling (ABPP) is an efficient tool for determining a small molecule's targets within complex proteomes. However, how target inhibition relates to biological activity is often left unexplored. Here, we study the effects of 1,2,3-triazole ureas on Mycobacterium tuberculosis (Mtb). After screening ∼200 compounds, we focus on 4 compounds that form a structure-activity series. The compound with negligible activity reveals targets, the inhibition of which is functionally less relevant for Mtb growth and viability, an aspect not addressed in other ABPP studies. Biochemistry, computational docking, and morphological analysis confirms that active compounds preferentially inhibit serine hydrolases with cell wall and lipid metabolism functions and that disruption of the cell wall underlies biological activity. Our findings show that ABPP identifies the targets most likely relevant to a compound's antibacterial activity.
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Affiliation(s)
- Michael Li
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Hiren V Patel
- Department of Microbiology and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Armand B Cognetta
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Trever C Smith
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
| | - Ivy Mallick
- Aix-Marseille Université, CNRS, LISM, IMM FR3479, 13402 Marseille, France
| | | | - Mary L Previti
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Stéphane Canaan
- Aix-Marseille Université, CNRS, LISM, IMM FR3479, 13402 Marseille, France
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
| | - Benjamin F Cravatt
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jessica C Seeliger
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA.
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10
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Su Q, Schröder SP, Lelieveld LT, Ferraz MJ, Verhoek M, Boot RG, Overkleeft HS, Aerts JMFG, Artola M, Kuo C. Xylose-Configured Cyclophellitols as Selective Inhibitors for Glucocerebrosidase. Chembiochem 2021; 22:3090-3098. [PMID: 34459538 PMCID: PMC8596838 DOI: 10.1002/cbic.202100396] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/29/2021] [Indexed: 02/03/2023]
Abstract
Glucocerebrosidase (GBA), a lysosomal retaining β-d-glucosidase, has recently been shown to hydrolyze β-d-xylosides and to transxylosylate cholesterol. Genetic defects in GBA cause the lysosomal storage disorder Gaucher disease (GD), and also constitute a risk factor for developing Parkinson's disease. GBA and other retaining glycosidases can be selectively visualized by activity-based protein profiling (ABPP) using fluorescent probes composed of a cyclophellitol scaffold having a configuration tailored to the targeted glycosidase family. GBA processes β-d-xylosides in addition to β-d-glucosides, this in contrast to the other two mammalian cellular retaining β-d-glucosidases, GBA2 and GBA3. Here we show that the xylopyranose preference also holds up for covalent inhibitors: xylose-configured cyclophellitol and cyclophellitol aziridines selectively react with GBA over GBA2 and GBA3 in vitro and in vivo, and that the xylose-configured cyclophellitol is more potent and more selective for GBA than the classical GBA inhibitor, conduritol B-epoxide (CBE). Both xylose-configured cyclophellitol and cyclophellitol aziridine cause accumulation of glucosylsphingosine in zebrafish embryo, a characteristic hallmark of GD, and we conclude that these compounds are well suited for creating such chemically induced GD models.
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Affiliation(s)
- Qin Su
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Sybrin P. Schröder
- Department of Bio-organic SynthesisLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Lindsey T. Lelieveld
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Maria J. Ferraz
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Marri Verhoek
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Rolf G. Boot
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Herman S. Overkleeft
- Department of Bio-organic SynthesisLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Marta Artola
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Chi‐Lin Kuo
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
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11
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Blum G, Verhelst SHL, Ma X. Editorial: Development and Applications of New Activity-Based Probes. Front Chem 2021; 9:754294. [PMID: 34568289 PMCID: PMC8458641 DOI: 10.3389/fchem.2021.754294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/19/2021] [Indexed: 11/23/2022] Open
Affiliation(s)
- Galia Blum
- The Faculty of Medicine, The School of Pharmacy, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel.,The Wohl Institute for Translational Medicine, The Goldyne Savad Institute for Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Steven H L Verhelst
- KU Leuven, Department of Cellular and Molecular Medicine, Leuven, Belgium.,Leibniz Institute for Analytical Sciences ISAS, Dortmund, Germany
| | - Xiaowei Ma
- Department of Nuclear Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
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12
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Henneberg LT, Schulman BA. Decoding the messaging of the ubiquitin system using chemical and protein probes. Cell Chem Biol 2021; 28:889-902. [PMID: 33831368 PMCID: PMC7611516 DOI: 10.1016/j.chembiol.2021.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 01/15/2021] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 12/29/2022]
Abstract
Post-translational modification of proteins by ubiquitin is required for nearly all aspects of eukaryotic cell function. The numerous targets of ubiquitylation, and variety of ubiquitin modifications, are often likened to a code, where the ultimate messages are diverse responses to target ubiquitylation. E1, E2, and E3 multiprotein enzymatic assemblies modify specific targets and thus function as messengers. Recent advances in chemical and protein tools have revolutionized our ability to explore the ubiquitin system, through enabling new high-throughput screening methods, matching ubiquitylation enzymes with their cellular targets, revealing intricate allosteric mechanisms regulating ubiquitylating enzymes, facilitating structural revelation of transient assemblies determined by multivalent interactions, and providing new paradigms for inhibiting and redirecting ubiquitylation in vivo as new therapeutics. Here we discuss the development of methods that control, disrupt, and extract the flow of information across the ubiquitin system and have enabled elucidation of the underlying molecular and cellular biology.
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Affiliation(s)
- Lukas T Henneberg
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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13
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Yim JJ, Harmsen S, Flisikowski K, Flisikowska T, Namkoong H, Garland M, van den Berg NS, Vilches-Moure JG, Schnieke A, Saur D, Glasl S, Gorpas D, Habtezion A, Ntziachristos V, Contag CH, Gambhir SS, Bogyo M, Rogalla S. A protease-activated, near-infrared fluorescent probe for early endoscopic detection of premalignant gastrointestinal lesions. Proc Natl Acad Sci U S A 2021; 118:e2008072118. [PMID: 33443161 DOI: 10.1073/pnas.2008072118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Fluorescence imaging is currently being actively developed for surgical guidance; however, it remains underutilized for diagnostic and endoscopic surveillance of incipient colorectal cancer in high-risk patients. Here we demonstrate the utility and potential for clinical translation of a fluorescently labeled cathepsin-activated chemical probe to highlight gastrointestinal lesions. This probe stays optically dark until it is activated by proteases produced by tumor-associated macrophages and accumulates within the lesions, enabling their detection using an endoscope outfitted with a fluorescence detector. We evaluated the probe in multiple murine models and a human-scale porcine model of gastrointestinal carcinogenesis. The probe provides fluorescence-guided surveillance of gastrointestinal lesions and augments histopathological analysis by highlighting areas of dysplasia as small as 400 µm, which were visibly discernible with significant tumor-to-background ratios, even in tissues with a background of severe inflammation and ulceration. Given these results, we anticipate that this probe will enable sensitive fluorescence-guided biopsies, even in the presence of highly inflamed colorectal tissue, which will improve early diagnosis to prevent gastrointestinal cancers.
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14
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Abstract
Combinatorial and modular methods to synthesize small molecule modulators of protein activity have proven to be powerful tools in the development of new drug-like molecules. Over the past decade, these methodologies have been adapted toward utilization in the development of activity- and affinity-based chemical probes, as well as in chemoproteomic profiling. In this review, we will discuss how methods like multicomponent reactions, DNA-encoded libraries, phage displays, and others provide new ways to rapidly screen novel chemical probes against proteins of interest.
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Affiliation(s)
- Antonie J van der Zouwen
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
| | - Martin D Witte
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
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15
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Van Rymenant Y, Tanc M, Van Elzen R, Bracke A, De Wever O, Augustyns K, Lambeir AM, Kockx M, De Meester I, Van Der Veken P. In Vitro and In Situ Activity-Based Labeling of Fibroblast Activation Protein with UAMC1110-Derived Probes. Front Chem 2021; 9:640566. [PMID: 33996747 PMCID: PMC8114891 DOI: 10.3389/fchem.2021.640566] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/08/2021] [Indexed: 12/29/2022] Open
Abstract
Fibroblast activation protein (FAP) is a proline-selective protease that belongs to the S9 family of serine proteases. It is typically highly expressed in the tumor microenvironment (TME) and especially in cancer-associated fibroblasts, the main cell components of the tumor stroma. The exact role of its enzymatic activity in the TME remains largely unknown. Hence, tools that enable selective, activity-based visualization of FAP within the TME can help to unravel FAP’s function. We describe the synthesis, biochemical characterization, and application of three different activity-based probes (biotin-, Cy3-, and Cy5-labeled) based on the FAP-inhibitor UAMC1110, an in-house developed molecule considered to be the most potent and selective FAP inhibitor available. We demonstrate that the three probes have subnanomolar FAP affinity and pronounced selectivity with respect to the related S9 family members. Furthermore, we report that the fluorescent Cy3- and Cy5-labeled probes are capable of selectively detecting FAP in a cellular context, making these chemical probes highly suitable for further biological studies. Moreover, proof of concept is provided for in situ FAP activity staining in patient-derived cryosections of urothelial tumors.
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Affiliation(s)
- Yentl Van Rymenant
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Muhammet Tanc
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - An Bracke
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Olivier De Wever
- Laboratory of Experimental Cancer Research, Faculty of Medicine and Health Sciences, University of Ghent, Ghent, Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Anne-Marie Lambeir
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Ingrid De Meester
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Pieter Van Der Veken
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
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16
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Beroske L, Van den Wyngaert T, Stroobants S, Van der Veken P, Elvas F. Molecular Imaging of Apoptosis: The Case of Caspase-3 Radiotracers. Int J Mol Sci 2021; 22:ijms22083948. [PMID: 33920463 PMCID: PMC8069194 DOI: 10.3390/ijms22083948] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 12/19/2022] Open
Abstract
The molecular imaging of apoptosis remains an important method for the diagnosis and monitoring of the progression of certain diseases and the evaluation of the efficacy of anticancer apoptosis-inducing therapies. Among the multiple biomarkers involved in apoptosis, activated caspase-3 is an attractive target, as it is the most abundant of the executioner caspases. Nuclear imaging is a good candidate, as it combines a high depth of tissue penetration and high sensitivity, features necessary to detect small changes in levels of apoptosis. However, designing a caspase-3 radiotracer comes with challenges, such as selectivity, cell permeability and transient caspase-3 activation. In this review, we discuss the different caspase-3 radiotracers for the imaging of apoptosis together with the challenges of the translation of various apoptosis-imaging strategies in clinical trials.
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Affiliation(s)
- Lucas Beroske
- Molecular Imaging Center Antwerp, University of Antwerp, 2610 Wilrijk, Belgium; (L.B.); (T.V.d.W.); (S.S.)
- Department of Nuclear Medicine, Antwerp University Hospital, 2650 Edegem, Belgium
- Laboratory of Medicinal Chemistry, University of Antwerp, 2610 Wilrijk, Belgium;
| | - Tim Van den Wyngaert
- Molecular Imaging Center Antwerp, University of Antwerp, 2610 Wilrijk, Belgium; (L.B.); (T.V.d.W.); (S.S.)
- Department of Nuclear Medicine, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Sigrid Stroobants
- Molecular Imaging Center Antwerp, University of Antwerp, 2610 Wilrijk, Belgium; (L.B.); (T.V.d.W.); (S.S.)
- Department of Nuclear Medicine, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Pieter Van der Veken
- Laboratory of Medicinal Chemistry, University of Antwerp, 2610 Wilrijk, Belgium;
| | - Filipe Elvas
- Molecular Imaging Center Antwerp, University of Antwerp, 2610 Wilrijk, Belgium; (L.B.); (T.V.d.W.); (S.S.)
- Department of Nuclear Medicine, Antwerp University Hospital, 2650 Edegem, Belgium
- Correspondence:
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17
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Abstract
Tuberculosis (TB), caused by the bacterial pathogen Mycobacterium tuberculosis (Mtb), infects 10 million people a year. An estimated 25% of humans harbor latent TB infections, an asymptomatic form of the disease. In both active and latent infections, Mtb relies on cell wall peptidoglycan for viability. In the current work, we synthesized fluorescent analogues of β-lactam antibiotics to study two classes of enzymes that maintain Mtb's peptidoglycan: penicillin-binding proteins (PBPs) and l,d-transpeptidases (LDTs). This set of activity-based probes included analogues of three classes of β-lactams: a monobactam (aztreonam-Cy5), a cephalosporin (cephalexin-Cy5), and a carbapenem (meropenem-Cy5). We used these probes to profile enzyme activity in protein gel-resolved lysates of Mtb. All three out-performed the commercial reagent Bocillin-FL, a penam. Meropenem-Cy5 was used to identify β-lactam targets by mass spectrometry, including PBPs, LDTs, and the β-lactamase BlaC. New probes were also used to compare PBP and LDT activity in two metabolic states: dormancy and active replication. We provide the first direct evidence that Mtb dynamically regulates the enzymes responsible for maintaining peptidoglycan in dormancy. Lastly, we profiled drug susceptibility in lysates and found that meropenem inhibits PBPs, LDTs, and BlaC.
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Affiliation(s)
- Samantha R. Levine
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92617, United States
| | - Kimberly E. Beatty
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92617, United States
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18
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Liu S, Ten Dijke P. Uncovering the deubiquitinase activity landscape of breast cancer. Oncoscience 2021; 7:85-87. [PMID: 33457450 PMCID: PMC7781487 DOI: 10.18632/oncoscience.518] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/26/2020] [Indexed: 12/02/2022] Open
Abstract
Breast cancer is a highly heterogeneous disease with dynamic changes in the tumor microenvironment. Precision medicine will in the future provide the possibility to treat each individual cancer patient with the right (combination) therapy specifically tailored to personal needs. However, in order to accomplish this, more accurate biomarkers for precise diagnosis, prognosis, therapy response, and target-specific drugs are required. Although an increasing number of (epi)genetic driving alterations have been reported in breast cancer, the major stumbling block for clinical application of many of them is that they are difficult to therapeutically target. Deubiquitinases (DUBs) are emerging drug targets that play important roles in cancer progression. Hence, we devoted our efforts to uncover the global DUB activity landscape of breast cancer in order to discover potential novel biomarkers or therapeutic targets. We developed a specific DUB activity-based inhibitor and probe and applied it to obtain new insights into breast cancer.
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Affiliation(s)
- Sijia Liu
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands.,Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Peter Ten Dijke
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands.,Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
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19
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Hira J, Uddin MJ, Haugland MM, Lentz CS. From Differential Stains to Next Generation Physiology: Chemical Probes to Visualize Bacterial Cell Structure and Physiology. Molecules 2020; 25:E4949. [PMID: 33114655 PMCID: PMC7663024 DOI: 10.3390/molecules25214949] [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: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022] Open
Abstract
Chemical probes have been instrumental in microbiology since its birth as a discipline in the 19th century when chemical dyes were used to visualize structural features of bacterial cells for the first time. In this review article we will illustrate the evolving design of chemical probes in modern chemical biology and their diverse applications in bacterial imaging and phenotypic analysis. We will introduce and discuss a variety of different probe types including fluorogenic substrates and activity-based probes that visualize metabolic and specific enzyme activities, metabolic labeling strategies to visualize structural features of bacterial cells, antibiotic-based probes as well as fluorescent conjugates to probe biomolecular uptake pathways.
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Affiliation(s)
- Jonathan Hira
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Md. Jalal Uddin
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Marius M. Haugland
- Department of Chemistry and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway;
| | - Christian S. Lentz
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
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20
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Fellner M, Lentz CS, Jamieson SA, Brewster JL, Chen L, Bogyo M, Mace PD. Structural Basis for the Inhibitor and Substrate Specificity of the Unique Fph Serine Hydrolases of Staphylococcus aureus. ACS Infect Dis 2020; 6:2771-2782. [PMID: 32865965 DOI: 10.1021/acsinfecdis.0c00503] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 12/23/2022]
Abstract
Staphylococcus aureus is a prevalent bacterial pathogen in both community and hospital settings, and its treatment is made particularly difficult by resilience within biofilms. Within this niche, serine hydrolase enzymes play a key role in generating and maintaining the biofilm matrix. Activity-based profiling has previously identified a family of serine hydrolases, designated fluorophosphonate-binding hydrolases (Fph's), some of which contribute to the virulence of S. aureus in vivo. These 10 Fph proteins have limited annotation and have few, if any, characterized bacterial or mammalian homologues. This suggests unique hydrolase functions even within bacterial species. Here we report structures of one of the most abundant Fph family members, FphF. Our structures capture FphF alone, covalently bound to a substrate analogue and bound to small molecule inhibitors that occupy the hydrophobic substrate-binding pocket. In line with these findings, we show that FphF has promiscuous esterase activity toward hydrophobic lipid substrates. We present docking studies that characterize interactions of inhibitors and substrates within the active site environment, which can be extended to other Fph family members. Comparison of FphF to other esterases and the wider Fph protein family suggest that FphF forms a new esterase subfamily. Our data suggest that other Fph enzymes, including the virulence factor FphB, are likely to have more restricted substrate profiles than FphF. This work demonstrates a clear molecular rationale for the specificity of fluorophosphonate probes that target FphF and provides a structural template for the design of enhanced probes and inhibitors of the Fph family of serine hydrolases.
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Affiliation(s)
- Matthias Fellner
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Christian S. Lentz
- Pathology, Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, United States
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT − The Arctic University of Norway, Tromsø N-9037, Norway
| | - Sam A. Jamieson
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Jodi L. Brewster
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Linhai Chen
- Pathology, Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, United States
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Matthew Bogyo
- Pathology, Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Peter D. Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
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21
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Sperinde G, Bremer M, Maun HR, Baruch A, Lazarus RA, Koerber JT, Vij R, Yi T, Fischer SK, Staton T. Development of a specific immunoassay to selectively measure active tryptase in airway samples. Bioanalysis 2020; 12:1377-88. [PMID: 32975431 DOI: 10.4155/bio-2020-0182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aim: Tryptase is a tetrameric trypsin-like serine protease contained within the secretory granules of mast cells and is an important mediator of allergic inflammatory responses in respiratory diseases. Detection of active tryptase in the airway may provide important information about asthma and other respiratory diseases. Materials & Methods: An activity based probe has been incorported within an immunoassay to allow for measurement of active tryptase in human tissues. Results: A specific Simoa immunoassay to measure active tryptase in nasosorption samples was developed and qualified using an activity-based probe label and a specific antitryptase capture antibody. Conclusion: The assay was capable of measuring active tryptase in human samples, which will enable evaluation of the role of tryptase proteolytic activity in human disease.
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22
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Chen S, Yim JJ, Bogyo M. Synthetic and biological approaches to map substrate specificities of proteases. Biol Chem 2020; 401:165-182. [PMID: 31639098 DOI: 10.1515/hsz-2019-0332] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023]
Abstract
Proteases are regulators of diverse biological pathways including protein catabolism, antigen processing and inflammation, as well as various disease conditions, such as malignant metastasis, viral infection and parasite invasion. The identification of substrates of a given protease is essential to understand its function and this information can also aid in the design of specific inhibitors and active site probes. However, the diversity of putative protein and peptide substrates makes connecting a protease to its downstream substrates technically difficult and time-consuming. To address this challenge in protease research, a range of methods have been developed to identify natural protein substrates as well as map the overall substrate specificity patterns of proteases. In this review, we highlight recent examples of both synthetic and biological methods that are being used to define the substrate specificity of protease so that new protease-specific tools and therapeutic agents can be developed.
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Affiliation(s)
- Shiyu Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joshua J Yim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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23
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Faucher F, Bennett JM, Bogyo M, Lovell S. Strategies for Tuning the Selectivity of Chemical Probes that Target Serine Hydrolases. Cell Chem Biol 2020; 27:937-952. [PMID: 32726586 PMCID: PMC7484133 DOI: 10.1016/j.chembiol.2020.07.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 05/23/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 02/08/2023]
Abstract
Serine hydrolases comprise a large family of enzymes that have diverse roles in key cellular processes, such as lipid metabolism, cell signaling, and regulation of post-translation modifications of proteins. They are also therapeutic targets for multiple human pathologies, including viral infection, diabetes, hypertension, and Alzheimer disease; however, few have well-defined substrates and biological functions. Activity-based probes (ABPs) have been used as effective tools to both profile activity and screen for selective inhibitors of serine hydrolases. One broad-spectrum ABP containing a fluorophosphonate electrophile has been used extensively to advance our understanding of diverse serine hydrolases. Due to the success of this single reagent, several robust chemistries have been developed to further diversify and tune the selectivity of ABPs used to target serine hydrolases. In this review, we highlight approaches to identify selective serine hydrolase ABPs and suggest new synthetic methodologies that could be applied to further advance probe development.
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Affiliation(s)
- Franco Faucher
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - John M Bennett
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Scott Lovell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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24
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Janiszewski T, Kołt S, Kaiserman D, Snipas SJ, Li S, Kulbacka J, Saczko J, Bovenschen N, Salvesen G, Drąg M, Bird PI, Kasperkiewicz P. Noninvasive optical detection of granzyme B from natural killer cells with enzyme-activated fluorogenic probes. J Biol Chem 2020; 295:9567-9582. [PMID: 32439802 DOI: 10.1074/jbc.ra120.013204] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/11/2020] [Indexed: 12/31/2022] Open
Abstract
Natural killer (NK) cells are key innate immunity effectors that combat viral infections and control several cancer types. For their immune function, human NK cells rely largely on five different cytotoxic proteases, called granzymes (A/B/H/K/M). Granzyme B (GrB) initiates at least three distinct cell death pathways, but key aspects of its function remain unexplored because selective probes that detect its activity are currently lacking. In this study, we used a set of unnatural amino acids to fully map the substrate preferences of GrB, demonstrating previously unknown GrB substrate preferences. We then used these preferences to design substrate-based inhibitors and a GrB-activatable activity-based fluorogenic probe. We show that our GrB probes do not significantly react with caspases, making them ideal for in-depth analyses of GrB localization and function in cells. Using our quenched fluorescence substrate, we observed GrB within the cytotoxic granules of human YT cells. When used as cytotoxic effectors, YT cells loaded with GrB attacked MDA-MB-231 target cells, and active GrB influenced its target cell-killing efficiency. In summary, we have developed a set of molecular tools for investigating GrB function in NK cells and demonstrate noninvasive visual detection of GrB with an enzyme-activated fluorescent substrate.
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Affiliation(s)
- Tomasz Janiszewski
- Wroclaw University of Science and Technology, Department of Chemical Biology and Bioimaging, Wroclaw, Poland
| | - Sonia Kołt
- Wroclaw University of Science and Technology, Department of Chemical Biology and Bioimaging, Wroclaw, Poland
| | - Dion Kaiserman
- Monash University, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Clayton, VIC, Australia
| | - Scott J Snipas
- Sanford-Burnham Prebys Medical Discovery Institute, NCI-designated Cancer Center, La Jolla, California, USA
| | - Shuang Li
- University Medical Center Utrecht, Department of Pathology, Utrecht, The Netherlands
| | - Julita Kulbacka
- Wroclaw Medical University, Department of Molecular and Cellular Biology, Wroclaw, Poland
| | - Jolanta Saczko
- Wroclaw Medical University, Department of Molecular and Cellular Biology, Wroclaw, Poland
| | - Niels Bovenschen
- University Medical Center Utrecht, Department of Pathology, Utrecht, The Netherlands
| | - Guy Salvesen
- Sanford-Burnham Prebys Medical Discovery Institute, NCI-designated Cancer Center, La Jolla, California, USA
| | - Marcin Drąg
- Wroclaw University of Science and Technology, Department of Chemical Biology and Bioimaging, Wroclaw, Poland.,Sanford-Burnham Prebys Medical Discovery Institute, NCI-designated Cancer Center, La Jolla, California, USA
| | - Phillip I Bird
- Monash University, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Clayton, VIC, Australia
| | - Paulina Kasperkiewicz
- Wroclaw University of Science and Technology, Department of Chemical Biology and Bioimaging, Wroclaw, Poland
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25
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Gruba N, Bielecka E, Wysocka M, Wojtysiak A, Brzezińska-Bodal M, Sychowska K, Kalińska M, Magoch M, Pęcak A, Falkowski K, Wiśniewska M, Sąsiadek L, Płaza K, Kroll E, Pejkovska A, Rehders M, Brix K, Dubin G, Kantyka T, Potempa J, Lesner A. Development of Chemical Tools to Monitor Human Kallikrein 13 (KLK13) Activity. Int J Mol Sci 2019; 20:E1557. [PMID: 30925705 DOI: 10.3390/ijms20071557] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/14/2019] [Accepted: 03/25/2019] [Indexed: 12/17/2022] Open
Abstract
Kallikrein 13 (KLK13) was first identified as an enzyme that is downregulated in a subset of breast tumors. This serine protease has since been implicated in a number of pathological processes including ovarian, lung and gastric cancers. Here we report the design, synthesis and deconvolution of libraries of internally quenched fluorogenic peptide substrates to determine the specificity of substrate binding subsites of KLK13 in prime and non-prime regions (according to the Schechter and Berger convention). The substrate with the consensus sequential motive ABZ-Val-Arg-Phe-Arg-ANB-NH2 demonstrated selectivity towards KLK13 and was successfully converted into an activity-based probe by the incorporation of a chloromethylketone warhead and biotin bait. The compounds described may serve as suitable tools to detect KLK13 activity in diverse biological samples, as exemplified by overexpression experiments and targeted labeling of KLK13 in cell lysates and saliva. In addition, we describe the development of selective activity-based probes targeting KLK13, to our knowledge the first tool to analyze the presence of the active enzyme in biological samples.
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26
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Weber A, Elliott PR, Pinto-Fernandez A, Bonham S, Kessler BM, Komander D, El Oualid F, Krappmann D. A Linear Diubiquitin-Based Probe for Efficient and Selective Detection of the Deubiquitinating Enzyme OTULIN. Cell Chem Biol 2017; 24:1299-1313.e7. [PMID: 28919039 PMCID: PMC5658516 DOI: 10.1016/j.chembiol.2017.08.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 07/10/2017] [Accepted: 08/01/2017] [Indexed: 11/19/2022]
Abstract
The methionine 1 (M1)-specific deubiquitinase (DUB) OTULIN acts as a negative regulator of nuclear factor κB signaling and immune homeostasis. By replacing Gly76 in distal ubiquitin (Ub) by dehydroalanine we designed the diubiquitin (diUb) activity-based probe UbG76Dha-Ub (OTULIN activity-based probe [ABP]) that couples to the catalytic site of OTULIN and thereby captures OTULIN in its active conformation. The OTULIN ABP displays high selectivity for OTULIN and does not label other M1-cleaving DUBs, including CYLD. The only detectable cross-reactivities were the labeling of USP5 (Isopeptidase T) and an ATP-dependent assembly of polyOTULIN ABP chains via Ub-activating E1 enzymes. Both cross-reactivities were abolished by the removal of the C-terminal Gly in the ABP's proximal Ub, yielding the specific OTULIN probe UbG76Dha-UbΔG76 (OTULIN ABPΔG76). Pull-downs demonstrate that substrate-bound OTULIN associates with the linear ubiquitin chain assembly complex (LUBAC). Thus, we present a highly selective ABP for OTULIN that will facilitate studying the cellular function of this essential DUB.
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Affiliation(s)
- Aurelia Weber
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Paul R Elliott
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Sarah Bonham
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Farid El Oualid
- UbiQ Bio BV, Science Park 408, 1098 XH Amsterdam, the Netherlands.
| | - Daniel Krappmann
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.
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27
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Hewings DS, Flygare JA, Bogyo M, Wertz IE. Activity-based probes for the ubiquitin conjugation-deconjugation machinery: new chemistries, new tools, and new insights. FEBS J 2017; 284:1555-1576. [PMID: 28196299 PMCID: PMC7163952 DOI: 10.1111/febs.14039] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [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: 11/09/2016] [Revised: 01/21/2017] [Accepted: 02/10/2017] [Indexed: 12/17/2022]
Abstract
The reversible post‐translational modification of proteins by ubiquitin and ubiquitin‐like proteins regulates almost all cellular processes, by affecting protein degradation, localization, and complex formation. Deubiquitinases (DUBs) are proteases that remove ubiquitin modifications or cleave ubiquitin chains. Most DUBs are cysteine proteases, which makes them well suited for study by activity‐based probes. These DUB probes report on deubiquitinase activity by reacting covalently with the active site in an enzyme‐catalyzed manner. They have proven to be important tools to study DUB selectivity and proteolytic activity in different settings, to identify novel DUBs, and to characterize deubiquitinase inhibitors. Inspired by the efficacy of activity‐based probes for DUBs, several groups have recently reported probes for the ubiquitin conjugation machinery (E1, E2, and E3 enzymes). Many of these enzymes, while not proteases, also posses active site cysteine residues and can be targeted by covalent probes. In this review, we will discuss how features of the probe (cysteine‐reactive group, recognition element, and reporter tag) affect reactivity and suitability for certain experimental applications. We will also review the diverse applications of the current probes, and discuss the need for new probe types to study emerging aspects of ubiquitin biology.
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Affiliation(s)
- David S Hewings
- Discovery Chemistry, Genentech, South San Francisco, CA, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.,Discovery Oncology, Genentech, South San Francisco, CA, USA.,Department of Pathology, Stanford University School of Medicine, CA, USA
| | - John A Flygare
- Discovery Chemistry, Genentech, South San Francisco, CA, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, CA, USA
| | - Ingrid E Wertz
- Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.,Discovery Oncology, Genentech, South San Francisco, CA, USA
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28
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Hewings DS, Flygare JA, Wertz IE, Bogyo M. Activity-based probes for the multicatalytic proteasome. FEBS J 2017; 284:1540-1554. [PMID: 28107776 DOI: 10.1111/febs.14016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 11/09/2016] [Revised: 12/22/2016] [Accepted: 01/16/2017] [Indexed: 12/17/2022]
Abstract
Proteasomes are multisubunit protease complexes responsible for degrading most intracellular proteins. In addition to removing damaged proteins, they regulate many important cellular processes through the controlled degradation of transcription factors, cell cycle regulators, and enzymes. Eukaryotic proteasomes have three catalytic subunits, β1, β2, and β5, that each has different substrate specificities. Additionally, although we know that diverse cell types express proteasome variants with distinct activity and specificity profiles, the functions of these different pools of proteasomes are not fully understood. Covalent inhibitors of the protease activity of the proteasome have been developed as drugs for hematological malignancies and are currently under investigation for other diseases. Therefore, there is a need for tools that allow direct monitoring of proteasome activity in live cells and tissues. Activity-based probes have proven valuable for biochemical and cell biological studies of the role of individual proteasome subunits, and for evaluating the efficacy and selectivity of proteasome inhibitors. These probes react covalently with the protease active sites, and contain a reporter tag to identify the probe-labeled proteasome subunits. This review will describe the development of broad-spectrum and subunit-specific proteasome activity-based probes, and discuss how these probes have contributed to our understanding of proteasome biology, and to the development of proteasome inhibitors.
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Affiliation(s)
- David S Hewings
- Discovery Chemistry, Genentech, South San Francisco, CA, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.,Discovery Oncology, Genentech, South San Francisco, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - John A Flygare
- Discovery Chemistry, Genentech, South San Francisco, CA, USA
| | - Ingrid E Wertz
- Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.,Discovery Oncology, Genentech, South San Francisco, CA, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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29
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Kasperkiewicz P, Poreba M, Groborz K, Drag M. Emerging challenges in the design of selective substrates, inhibitors and activity-based probes for indistinguishable proteases. FEBS J 2017; 284:1518-1539. [PMID: 28052575 PMCID: PMC7164106 DOI: 10.1111/febs.14001] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [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: 09/24/2016] [Revised: 12/02/2016] [Accepted: 01/03/2017] [Indexed: 12/31/2022]
Abstract
Proteases are enzymes that hydrolyze the peptide bond of peptide substrates and proteins. Despite significant progress in recent years, one of the greatest challenges in the design and testing of substrates, inhibitors and activity‐based probes for proteolytic enzymes is achieving specificity toward only one enzyme. This specificity is particularly important if the enzyme is present with other enzymes with a similar catalytic mechanism and substrate specificity but completely different functionality. The cross‐reactivity of substrates, inhibitors and activity‐based probes with other enzymes can significantly impair or even prevent investigations of a target protease. In this review, we describe important concepts and the latest challenges, focusing mainly on peptide‐based substrate specificity techniques used to distinguish individual enzymes within major protease families.
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Affiliation(s)
- Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Poland
| | - Marcin Poreba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Poland
| | - Katarzyna Groborz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Poland
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Poland
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30
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Lentz CS, Ordonez AA, Kasperkiewicz P, La Greca F, O’Donoghue AJ, Schulze CJ, Powers JC, Craik CS, Drag M, Jain SK, Bogyo M. Design of Selective Substrates and Activity-Based Probes for Hydrolase Important for Pathogenesis 1 (HIP1) from Mycobacterium tuberculosis. ACS Infect Dis 2016; 2:807-815. [PMID: 27739665 PMCID: PMC5109297 DOI: 10.1021/acsinfecdis.6b00092] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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] [Indexed: 01/02/2023]
Abstract
Although serine proteases are important mediators of Mycobacterium tuberculosis (Mtb) virulence, there are currently no tools to selectively block or visualize members of this family of enzymes. Selective reporter substrates or activity-based probes (ABPs) could provide a means to monitor infection and response to therapy using imaging methods. Here, we use a combination of substrate selectivity profiling and focused screening to identify optimized reporter substrates and ABPs for the Mtb "Hydrolase important for pathogenesis 1" (Hip1) serine protease. Hip1 is a cell-envelope-associated enzyme with minimal homology to host proteases, making it an ideal target for probe development. We identified substituted 7-amino-4-chloro-3-(2-bromoethoxy)isocoumarins as irreversible inhibitor scaffolds. Furthermore, we used specificity data to generate selective reporter substrates and to further optimize a selective chloroisocoumarin inhibitor. These new reagents are potentially useful in delineating the roles of Hip1 during pathogenesis or as diagnostic imaging tools for specifically monitoring Mtb infections.
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Affiliation(s)
| | | | - Paulina Kasperkiewicz
- Division
of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego
27, 50-370 Wroclaw, Poland
| | - Florencia La Greca
- Department of Pharmaceutical Chemistry, University of California—San Francisco, San Francisco, United States
| | - Anthony J. O’Donoghue
- Department of Pharmaceutical Chemistry, University of California—San Francisco, San Francisco, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California—San Diego, La Jolla, California 92093 United States
| | | | - James C. Powers
- Department of
Chemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California—San Francisco, San Francisco, United States
| | - Marcin Drag
- Division
of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego
27, 50-370 Wroclaw, Poland
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31
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Edgington-Mitchell LE, Wartmann T, Fleming AK, Gocheva V, van der Linden WA, Withana NP, Verdoes M, Aurelio L, Edgington-Mitchell D, Lieu T, Parker BS, Graham B, Reinheckel T, Furness JB, Joyce JA, Storz P, Halangk W, Bogyo M, Bunnett NW. Legumain is activated in macrophages during pancreatitis. Am J Physiol Gastrointest Liver Physiol 2016; 311:G548-60. [PMID: 27514475 PMCID: PMC5075999 DOI: 10.1152/ajpgi.00047.2016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 07/18/2016] [Indexed: 01/31/2023]
Abstract
Pancreatitis is an inflammatory disease of the pancreas characterized by dysregulated activity of digestive enzymes, necrosis, immune infiltration, and pain. Repeated incidence of pancreatitis is an important risk factor for pancreatic cancer. Legumain, a lysosomal cysteine protease, has been linked to inflammatory diseases such as atherosclerosis, stroke, and cancer. Until now, legumain activation has not been studied during pancreatitis. We used a fluorescently quenched activity-based probe to assess legumain activation during caerulein-induced pancreatitis in mice. We detected activated legumain by ex vivo imaging, confocal microscopy, and gel electrophoresis. Compared with healthy controls, legumain activity in the pancreas of caerulein-treated mice was increased in a time-dependent manner. Legumain was localized to CD68(+) macrophages and was not active in pancreatic acinar cells. Using a small-molecule inhibitor of legumain, we found that this protease is not essential for the initiation of pancreatitis. However, it may serve as a biomarker of disease, since patients with chronic pancreatitis show strongly increased legumain expression in macrophages. Moreover, the occurrence of legumain-expressing macrophages in regions of acinar-to-ductal metaplasia suggests that this protease may influence reprogramming events that lead to inflammation-induced pancreatic cancer.
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Affiliation(s)
| | - Thomas Wartmann
- Department of Surgery, Division of Experimental Surgery, Otto-von-Guericke University, Magdeburg, Germany
| | - Alicia K Fleming
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Jacksonville, Florida
| | - Vasilena Gocheva
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Nimali P Withana
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Martijn Verdoes
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud UMC, Nijmegen, The Netherlands
| | - Luigi Aurelio
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Daniel Edgington-Mitchell
- Laboratory for Turbulence Research in Aerospace and Combustion, Department of Mechanical and Aerospace Engineering, Monash University, Melbourne, Victoria, Australia
| | - TinaMarie Lieu
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Belinda S Parker
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Thomas Reinheckel
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - John B Furness
- Department of Anatomy and Neuroscience, University of Melbourne and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria Australia
| | - Johanna A Joyce
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Peter Storz
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Jacksonville, Florida
| | - Walter Halangk
- Department of Surgery, Division of Experimental Surgery, Otto-von-Guericke University, Magdeburg, Germany
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Nigel W Bunnett
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia; Department of Pharmacology, University of Melbourne, Parkville, Victoria, Australia; and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash University, Parkville, Victoria, Australia
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32
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Wang J, Lin Q. Chemical proteomics approach reveals the direct targets and the heme-dependent activation mechanism of artemisinin in Plasmodium falciparum using an artemisinin-based activity probe. Microb Cell 2016; 3:230-231. [PMID: 28357359 PMCID: PMC5349152 DOI: 10.15698/mic2016.05.503] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Artemisinin and its analogues are currently the most effective anti-malarial drugs. The activation of artemisinin requires the cleavage of the endoperoxide bridge in the presence of iron sources. Once activated, artemisinins attack macromolecules through alkylation and propagate a series of damages, leading to parasite death. Even though several parasite proteins have been reported as artemisinin targets, the exact mechanism of action (MOA) of artemisinin is still controversial and its high potency and specificity against the malaria parasite could not be fully accounted for. Recently, we have developed an unbiased chemical proteomics approach to directly probe the MOA of artemisinin in P. falciparum. We synthesized an artemisinin analogue with an alkyne tag, which can be coupled with biotin through click chemistry. This enabled selective purification and identification of 124 protein targets of artemisinin. Many of these targets are critical for the parasite survival. In vitro assays confirmed the specific artemisinin binding and inhibition of selected targets. We thus postulated that artemisinin kills the parasite through disrupting its biochemical landscape. In addition, we showed that artemisinin activation requires heme, rather than free ferrous iron, by monitoring the extent of protein binding using a fluorescent dye coupled with the alkyne-tagged artemisinin. The extremely high level of heme released from the hemoglobin digestion by the parasite makes artemisinin exceptionally potent against late-stage parasites (trophozoite and schizont stages) compared to parasites at early ring stage, which have low level of heme, mainly derived from endogenous synthesis. Such a unique activation mechanism also confers artemisinin with extremely high specificity against the parasites, while the healthy red blood cells are unaffected. Our results provide a sound explanation of the MOA of artemisinin and its specificity against malaria parasites, which may benefit the optimization of treatment strategies and the battle against the emerging drug resistance.
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Affiliation(s)
- Jigang Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing 210023, China. ; Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
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33
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Schipper-Krom S, Juenemann K, Jansen AH, Wiemhoefer A, van den Nieuwendijk R, Smith DL, Hink MA, Bates GP, Overkleeft H, Ovaa H, Reits E. Dynamic recruitment of active proteasomes into polyglutamine initiated inclusion bodies. FEBS Lett 2013; 588:151-9. [PMID: 24291262 DOI: 10.1016/j.febslet.2013.11.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [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: 08/08/2013] [Revised: 11/15/2013] [Accepted: 11/18/2013] [Indexed: 11/20/2022]
Abstract
Neurodegenerative disorders such as Huntington's disease are hallmarked by neuronal intracellular inclusion body formation. Whether proteasomes are irreversibly recruited into inclusion bodies in these protein misfolding disorders is a controversial subject. In addition, it has been proposed that the proteasomes may become clogged by the aggregated protein fragments, leading to impairment of the ubiquitin-proteasome system. Here, we show by fluorescence pulse-chase experiments in living cells that proteasomes are dynamically and reversibly recruited into inclusion bodies. As these recruited proteasomes remain catalytically active and accessible to substrates, our results challenge the concept of proteasome sequestration and impairment in Huntington's disease, and support the reported absence of proteasome impairment in mouse models of Huntington's disease.
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Affiliation(s)
- Sabine Schipper-Krom
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, The Netherlands
| | - Katrin Juenemann
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, The Netherlands
| | - Anne H Jansen
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, The Netherlands
| | - Anne Wiemhoefer
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, The Netherlands
| | - Rianne van den Nieuwendijk
- Department of Bio-Organic Synthesis, Institute of Chemistry, University of Leiden, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Donna L Smith
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, Great Maze Pond, SE1 9RT London, United Kingdom
| | - Mark A Hink
- Section Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, 1090 GE Amsterdam, The Netherlands
| | - Gillian P Bates
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, Great Maze Pond, SE1 9RT London, United Kingdom
| | - Hermen Overkleeft
- Department of Bio-Organic Synthesis, Institute of Chemistry, University of Leiden, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Huib Ovaa
- Department of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Eric Reits
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, The Netherlands.
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34
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Baggelaar MP, Janssen FJ, van Esbroeck ACM, den Dulk H, Allarà M, Hoogendoorn S, McGuire R, Florea BI, Meeuwenoord N, van den Elst H, van der Marel GA, Brouwer J, Di Marzo V, Overkleeft HS, van der Stelt M. Development of an activity-based probe and in silico design reveal highly selective inhibitors for diacylglycerol lipase-α in brain. Angew Chem Int Ed Engl 2013; 52:12081-5. [PMID: 24173880 DOI: 10.1002/anie.201306295] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/11/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Marc P Baggelaar
- Dept. of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC Leiden (The Netherlands)
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35
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Yang J, Chaurand P, Norris JL, Porter NA, Caprioli RM. Activity-based probes linked with laser-cleavable mass tags for signal amplification in imaging mass spectrometry: analysis of serine hydrolase enzymes in mammalian tissue. Anal Chem 2012; 84:3689-95. [PMID: 22424244 PMCID: PMC3328658 DOI: 10.1021/ac300203v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [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] [Indexed: 01/24/2023]
Abstract
A novel functional imaging mass spectrometry technology is described that utilizes activity-based probes for imaging enzyme active sites in tissue sections. We demonstrate this technology using an activity-based probe (fluorophosphate) that is specific for serine hydrolases. A dendrimer containing multiple mass tags that is attached to the activity-based probe is used to analyze the binding sites of the probe through release and measurement of the mass tags on laser irradiation. A generation 8 poly(amido amine) dendrimer with 1024 amino groups was labeled with an azide group, and then, more than 900 mass tags were attached in order to achieve signal amplification of nearly 3 orders of magnitude. The experimental protocol first involves binding of the activity-based probe containing an alkyne group to serine hydrolases in the tissue section followed by attachment of the dendrimer labeled with mass tags to the bound probe by Click chemistry. On irradiation of the labeled tissue by the laser beam in a raster pattern, the mass tags are liberated and recorded by the mass analyzer; consequently, the ion image of the mass tag reveals the distribution of serine hydrolases in the tissue. This process was shown using rat brain and mouse embryo sections. Targeted imaging has the advantage of providing high spatial resolution and high sensitivity through the use of signal amplification chemistry with high target specificity through the use of an enzyme activity probe.
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Affiliation(s)
- Junhai Yang
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Pierre Chaurand
- Department of Chemistry, Université de Montréal, Montréal, Canada
| | - Jeremy L. Norris
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Ned A. Porter
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
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