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Espadinha M, De Loose J, Corthaut S, Thys S, Van Rymenant Y, Verhulst E, Benramdane S, Filippi N, Augustyns K, Van Wielendaele P, Pintelon I, De Meester I, Van der Veken P. Active site-directed probes targeting dipeptidyl peptidases 8 and 9. Eur J Med Chem 2024; 270:116389. [PMID: 38593588 DOI: 10.1016/j.ejmech.2024.116389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/13/2024] [Accepted: 04/02/2024] [Indexed: 04/11/2024]
Abstract
Dipeptidyl peptidases (DPP) 8 and 9 are intracellular serine proteases that play key roles in various biological processes and recent findings highlight DPP8 and DPP9 as potential therapeutic targets for hematological and inflammasome-related diseases. Despite the substantial progress, the precise biological functions of these proteases remain elusive, and the lack of selective chemical tools hampers ongoing research. In this paper, we describe the synthesis and biochemical evaluation of the first active site-directed DPP8/9 probes which are derived from DPP8/9 inhibitors developed in-house. Specifically, we synthesized fluorescent inhibitors containing nitrobenzoxadiazole (NBD), dansyl (DNS) and cyanine-3 (Cy3) reporters to visualize intracellular DPP8/9. We demonstrate that the fluorescent inhibitors have high affinity and selectivity towards DPP8/9 over related S9 family members. The NBD-labeled DPP8/9 inhibitors were nominated as the best in class compounds to visualize DPP8/9 in human cells. Furthermore, a method has been developed for selective labeling and visualization of active DPP8/9 in vitro by fluorescence microscopy. A collection of potent and selective biotinylated DPP8/9-targeting probes was also prepared by replacing the fluorescent reporter with a biotin group. The present work provides the first DPP8/9-targeting fluorescent compounds as useful chemical tools for the study of DPP8 and DPP9's biological functions.
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Affiliation(s)
| | - Joni De Loose
- Laboratory of Medical Biochemistry, University of Antwerp, Belgium
| | - Sam Corthaut
- Laboratory of Medical Biochemistry, University of Antwerp, Belgium
| | - Sofie Thys
- Laboratory of Cell Biology and Histology, University of Antwerp, Belgium
| | | | - Emile Verhulst
- Laboratory of Medical Biochemistry, University of Antwerp, Belgium
| | - Siham Benramdane
- Laboratory of Medicinal Chemistry, University of Antwerp, Belgium
| | - Nicolò Filippi
- Laboratory of Medicinal Chemistry, University of Antwerp, Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, University of Antwerp, Belgium
| | | | - Isabel Pintelon
- Laboratory of Cell Biology and Histology, University of Antwerp, Belgium
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2
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Leo F, Lood R, Thomsson KA, Nilsson J, Svensäter G, Wickström C. Characterization of MdpS: an in-depth analysis of a MUC5B-degrading protease from Streptococcus oralis. Front Microbiol 2024; 15:1340109. [PMID: 38304711 PMCID: PMC10830703 DOI: 10.3389/fmicb.2024.1340109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Oral biofilms, comprising hundreds of bacteria and other microorganisms on oral mucosal and dental surfaces, play a central role in oral health and disease dynamics. Streptococcus oralis, a key constituent of these biofilms, contributes significantly to the formation of which, serving as an early colonizer and microcolony scaffold. The interaction between S. oralis and the orally predominant mucin, MUC5B, is pivotal in biofilm development, yet the mechanism underlying MUC5B degradation remains poorly understood. This study introduces MdpS (Mucin Degrading Protease from Streptococcus oralis), a protease that extensively hydrolyses MUC5B and offers an insight into its evolutionary conservation, physicochemical properties, and substrate- and amino acid specificity. MdpS exhibits high sequence conservation within the species and also explicitly among early biofilm colonizing streptococci. It is a calcium or magnesium dependent serine protease with strict physicochemical preferences, including narrow pH and temperature tolerance, and high sensitivity to increasing concentrations of sodium chloride and reducing agents. Furthermore, MdpS primarily hydrolyzes proteins with O-glycans, but also shows activity toward immunoglobulins IgA1/2 and IgM, suggesting potential immunomodulatory effects. Significantly, MdpS extensively degrades MUC5B in the N- and C-terminal domains, emphasizing its role in mucin degradation, with implications for carbon and nitrogen sequestration for S. oralis or oral biofilm cross-feeding. Moreover, depending on substrate glycosylation, the amino acids serine, threonine or cysteine triggers the enzymatic action. Understanding the interplay between S. oralis and MUC5B, facilitated by MdpS, has significant implications for the management of a healthy eubiotic oral microenvironment, offering potential targets for interventions aimed at modulating oral biofilm composition and succession. Additionally, since MdpS does not rely on O-glycan removal prior to extensive peptide backbone hydrolysis, the MdpS data challenges the current model of MUC5B degradation. These findings emphasize the necessity for further research in this field.
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Affiliation(s)
- Fredrik Leo
- Department of Oral Biology and Pathology, Faculty of Odontology, Malmö University, Malmö, Sweden
- Genovis AB, Kävlinge, Sweden
| | - Rolf Lood
- Genovis AB, Kävlinge, Sweden
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Kristina A. Thomsson
- Proteomics Core Facility, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Jonas Nilsson
- Proteomics Core Facility, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Gunnel Svensäter
- Department of Oral Biology and Pathology, Faculty of Odontology, Malmö University, Malmö, Sweden
| | - Claes Wickström
- Department of Oral Biology and Pathology, Faculty of Odontology, Malmö University, Malmö, Sweden
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Chalmers JD, Kettritz R, Korkmaz B. Dipeptidyl peptidase 1 inhibition as a potential therapeutic approach in neutrophil-mediated inflammatory disease. Front Immunol 2023; 14:1239151. [PMID: 38162644 PMCID: PMC10755895 DOI: 10.3389/fimmu.2023.1239151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/14/2023] [Indexed: 01/03/2024] Open
Abstract
Neutrophils have a critical role in the innate immune response to infection and the control of inflammation. A key component of this process is the release of neutrophil serine proteases (NSPs), primarily neutrophil elastase, proteinase 3, cathepsin G, and NSP4, which have essential functions in immune modulation and tissue repair following injury. Normally, NSP activity is controlled and modulated by endogenous antiproteases. However, disruption of this homeostatic relationship can cause diseases in which neutrophilic inflammation is central to the pathology, such as chronic obstructive pulmonary disease (COPD), alpha-1 antitrypsin deficiency, bronchiectasis, and cystic fibrosis, as well as many non-pulmonary pathologies. Although the pathobiology of these diseases varies, evidence indicates that excessive NSP activity is common and a principal mediator of tissue damage and clinical decline. NSPs are synthesized as inactive zymogens and activated primarily by the ubiquitous enzyme dipeptidyl peptidase 1, also known as cathepsin C. Preclinical data confirm that inactivation of this protease reduces activation of NSPs. Thus, pharmacological inhibition of dipeptidyl peptidase 1 potentially reduces the contribution of aberrant NSP activity to the severity and/or progression of multiple inflammatory diseases. Initial clinical data support this view. Ongoing research continues to explore the role of NSP activation by dipeptidyl peptidase 1 in different disease states and the potential clinical benefits of dipeptidyl peptidase 1 inhibition.
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Affiliation(s)
- James D. Chalmers
- Department of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Ralph Kettritz
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin, Berlin, Germany
| | - Brice Korkmaz
- INSERM UMR-1100, Research Center for Respiratory Diseases, University of Tours, Tours, France
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Lee I, Tantisirivat P, Edgington-Mitchell LE. Chemical Tools to Image the Activity of PAR-Cleaving Proteases. ACS BIO & MED CHEM AU 2023; 3:295-304. [PMID: 37599791 PMCID: PMC10436261 DOI: 10.1021/acsbiomedchemau.3c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 08/22/2023]
Abstract
Protease-activated receptors (PARs) comprise a family of four G protein-coupled receptors (GPCRs) that have broad functions in health and disease. Unlike most GPCRs, PARs are uniquely activated by proteolytic cleavage of their extracellular N termini. To fully understand PAR activation and function in vivo, it is critical to also study the proteases that activate them. As proteases are heavily regulated at the post-translational level, measures of total protease abundance have limited utility. Measures of protease activity are instead required to inform their function. This review will introduce several classes of chemical probes that have been developed to measure the activation of PAR-cleaving proteases. Their strengths, weaknesses, and applications will be discussed, especially as applied to image protease activity at the whole organism, tissue, and cellular level.
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Affiliation(s)
- Irene
Y. Lee
- Department
of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology
Institute, The University of Melbourne, Parkville, Victoria 3052 Australia
| | - Piyapa Tantisirivat
- Department
of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology
Institute, The University of Melbourne, Parkville, Victoria 3052 Australia
| | - Laura E. Edgington-Mitchell
- Department
of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology
Institute, The University of Melbourne, Parkville, Victoria 3052 Australia
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Ćwilichowska N, Świderska KW, Dobrzyń A, Drąg M, Poręba M. Diagnostic and therapeutic potential of protease inhibition. Mol Aspects Med 2022; 88:101144. [PMID: 36174281 DOI: 10.1016/j.mam.2022.101144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/20/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022]
Abstract
Proteases are enzymes that hydrolyze peptide bonds in proteins and peptides; thus, they control virtually all biological processes. Our understanding of protease function has advanced considerably from nonselective digestive enzymes to highly specialized molecular scissors that orchestrate complex signaling networks through a limited proteolysis. The catalytic activity of proteases is tightly regulated at several levels, ranging from gene expression through trafficking and maturation to posttranslational modifications. However, when this delicate balance is disturbed, many diseases develop, including cancer, inflammatory disorders, diabetes, and neurodegenerative diseases. This new understanding of the role of proteases in pathologic physiology indicates that these enzymes represent excellent molecular targets for the development of therapeutic inhibitors, as well as for the design of chemical probes to visualize their redundant activity. Recently, numerous platform technologies have been developed to identify and optimize protease substrates and inhibitors, which were further used as lead structures for the development of chemical probes and therapeutic drugs. Due to this considerable success, the clinical potential of proteases in therapeutics and diagnostics is rapidly growing and is still not completely explored. Therefore, small molecules that can selectively target aberrant protease activity are emerging in diseases cells. In this review, we describe modern trends in the design of protease drugs as well as small molecule activity-based probes to visualize selected proteases in clinical settings.
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Affiliation(s)
- Natalia Ćwilichowska
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Karolina W Świderska
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Agnieszka Dobrzyń
- Nencki Institute of Experimental Biology, Ludwika Pasteura 3, 02-093, Warsaw, Poland
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Marcin Poręba
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland.
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Mongkolpathumrat P, Kijtawornrat A, Suwan E, Unajak S, Panya A, Pusadee T, Kumphune S. Anti-Protease Activity Deficient Secretory Leukocyte Protease Inhibitor (SLPI) Exerts Cardioprotective Effect against Myocardial Ischaemia/Reperfusion. Biomedicines 2022; 10:biomedicines10050988. [PMID: 35625725 PMCID: PMC9138276 DOI: 10.3390/biomedicines10050988] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 12/02/2022] Open
Abstract
Inhibition of proteases shows therapeutic potential. Our previous studies demonstrated the cardioprotection by the Secretory Leukocyte Protease Inhibitor (SLPI) against myocardial ischaemia/reperfusion (I/R) injury. However, it is unclear whether the cardioprotective effect of SLPI seen in our previous works is due to the inhibition of protease enzymes. Several studies demonstrate that the anti-protease independent activity of SLPI could provide therapeutic benefits. Here, we show for the first time that recombinant protein of anti-protease deficient mutant SLPI (L72K, M73G, L74G) (mt-SLPI) could significantly reduce cell death and intracellular reactive oxygen species (ROS) production against an in vitro simulated I/R injury. Furthermore, post-ischaemic treatment of mt-SLPI is found to significantly reduce infarct size and cardiac biomarkers lactate dehydrogenase (LDH) and creatine kinase-MB (CK-MB) activity, improve cardiac functions, attenuate I/R induced-p38 MAPK phosphorylation, and reduce apoptotic regulatory protein levels, including Bax, cleaved-Caspase-3 and total Capase-8, in rats subjected to an in vivo I/R injury. Additionally, the beneficial effect of mt-SLPI was not significantly different from the wildtype (wt-SLPI). In summary, SLPI could provide cardioprotection without anti-protease activity, which could be more clinically beneficial in terms of providing cardioprotection without interfering with basal serine protease activity.
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Affiliation(s)
- Podsawee Mongkolpathumrat
- Graduate Programs in Biomedical Sciences, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok 65000, Thailand;
- Integrative Biomedical Research Unit (IBRU), Faculty of Allied Health Sciences, Naresuan University, Phitsanulok 65000, Thailand
- Biomedical Engineering Institute (BMEI), Chiang Mai University, Chiang Mai 50200, Thailand
| | - Anusak Kijtawornrat
- Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Eukote Suwan
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok 10900, Thailand;
| | - Sasimanas Unajak
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Aussara Panya
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Tonapha Pusadee
- Department of Plant and Soil Science, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Sarawut Kumphune
- Integrative Biomedical Research Unit (IBRU), Faculty of Allied Health Sciences, Naresuan University, Phitsanulok 65000, Thailand
- Biomedical Engineering Institute (BMEI), Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: ; Tel.: +66-624-693-987
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Saidi A, Wartenberg M, Madinier JB, Ilango G, Seren S, Korkmaz B, Lecaille F, Aucagne V, Lalmanach G. Monitoring Human Neutrophil Activation by a Proteinase 3 Near-Infrared Fluorescence Substrate-Based Probe. Bioconjug Chem 2021; 32:1782-1790. [PMID: 34269060 DOI: 10.1021/acs.bioconjchem.1c00267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A near-infrared fluorescent (NIRF) substrate-based probe (SBP) was conceived to monitor secreted human proteinase 3 (hPR3) activity. This probe, called pro3-SBP, is shaped by a fused peptide hairpin loop structure, which associates a hPR3 recognition domain (Val-Ala-Asp-Nva-Ala-Asp-Tyr-Gln, where Nva is norvaline) and an electrostatic zipper (consisting of complementary polyanionic (d-Glu)5 and polycationic (d-Arg)5 sequences) in close vicinity of the N- and C-terminal FRET couple (fluorescent donor, sulfoCy5.5; dark quencher, QSY21). Besides its subsequent stability, no intermolecular fluorescence quenching was detected following its complete hydrolysis by hPR3, advocating that pro3-SBP could further afford unbiased imaging. Pro3-SBP was specifically hydrolyzed by hPR3 (kcat/Km= 440 000 ± 5500 M-1·s-1) and displayed a sensitive detection threshold for hPR3 (subnanomolar concentration range), while neutrophil elastase showed a weaker potency. Conversely, pro3-SBP was not cleaved by cathepsin G. Pro3-SBP was successfully hydrolyzed by conditioned media of activated human neutrophils but not by quiescent neutrophils. Moreover, unlike unstimulated neutrophils, a strong NIRF signal was specifically detected by confocal microscopy following neutrophil ionomycin-induced degranulation. Fluorescence release was abolished in the presence of a selective hPR3 inhibitor, indicating that pro3-SBP is selectively cleaved by extracellular hPR3. Taken together, the present data support that pro3-SBP could be a convenient tool, allowing straightforward monitoring of human neutrophil activation.
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Affiliation(s)
- Ahlame Saidi
- Université de Tours, Tours 37032, France.,UMR 1100, Research Center for Respiratory Diseases (CEPR), Team: "Proteolytic Mechanisms in Inflammation", INSERM, Tours 37032, France
| | - Mylène Wartenberg
- Université de Tours, Tours 37032, France.,UMR 1100, Research Center for Respiratory Diseases (CEPR), Team: "Proteolytic Mechanisms in Inflammation", INSERM, Tours 37032, France
| | - Jean-Baptiste Madinier
- Center for Molecular Biophysics (CBM), Team: "Molecular, Structural and Chemical Biology″, CNRS UPR 4301, Orléans 45071, France
| | - Guy Ilango
- IBiSA Electron Microscopy Platform, Université de Tours, Tours 37032, France
| | - Seda Seren
- Université de Tours, Tours 37032, France.,UMR 1100, Research Center for Respiratory Diseases (CEPR), Team: "Proteolytic Mechanisms in Inflammation", INSERM, Tours 37032, France
| | - Brice Korkmaz
- Université de Tours, Tours 37032, France.,UMR 1100, Research Center for Respiratory Diseases (CEPR), Team: "Proteolytic Mechanisms in Inflammation", INSERM, Tours 37032, France
| | - Fabien Lecaille
- Université de Tours, Tours 37032, France.,UMR 1100, Research Center for Respiratory Diseases (CEPR), Team: "Proteolytic Mechanisms in Inflammation", INSERM, Tours 37032, France
| | - Vincent Aucagne
- Center for Molecular Biophysics (CBM), Team: "Molecular, Structural and Chemical Biology″, CNRS UPR 4301, Orléans 45071, France
| | - Gilles Lalmanach
- Université de Tours, Tours 37032, France.,UMR 1100, Research Center for Respiratory Diseases (CEPR), Team: "Proteolytic Mechanisms in Inflammation", INSERM, Tours 37032, France
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