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Kahler JP, Ji S, Speelman-Rooms F, Vanhoutte R, Verhelst SHL. Phosphinate Esters as Novel Warheads for Quenched Activity-Based Probes Targeting Serine Proteases. ACS Chem Biol 2024; 19:1409-1415. [PMID: 38913607 DOI: 10.1021/acschembio.3c00203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Quenched activity-based probes (qABP) are invaluable tools to visualize aberrant protease activity. Unfortunately, most studies so far have only focused on cysteine proteases, and only a few studies describe the synthesis and use of serine protease qABPs. We recently used phosphinate ester electrophiles as a novel type of reactive group to construct ABPs for serine proteases. Here, we report on the construction of qABPs based on the phosphinate warhead, exemplified by probes for the neutrophil serine proteases. The most successful probes show sub-stoichiometric reaction with human neutrophil elastase, efficient fluorescence quenching, and rapid unquenching of fluorescence upon reaction with target proteases.
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Affiliation(s)
- Jan Pascal Kahler
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49 box 901b, 3000 Leuven, Belgium
| | - Shanping Ji
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49 box 901b, 3000 Leuven, Belgium
| | - Femke Speelman-Rooms
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49 box 901b, 3000 Leuven, Belgium
- Laboratory of Molecular & Cellular Signaling, Department of Cellular and Molecular Medicine, Herestraat 49 box 802, 3000 Leuven, Belgium
| | - Roeland Vanhoutte
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49 box 901b, 3000 Leuven, Belgium
| | - Steven H L Verhelst
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49 box 901b, 3000 Leuven, Belgium
- AG Chemical Proteomics, Leibniz Institute for Analytical Sciences - ISAS, Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
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2
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Goettig P, Koch NG, Budisa N. Non-Canonical Amino Acids in Analyses of Protease Structure and Function. Int J Mol Sci 2023; 24:14035. [PMID: 37762340 PMCID: PMC10531186 DOI: 10.3390/ijms241814035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.
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Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
| | - Nikolaj G. Koch
- Biocatalysis Group, Technische Universität Berlin, 10623 Berlin, Germany;
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Nediljko Budisa
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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3
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Racioppo B, Qiu N, Adibekian A. Serine Hydrolase Activity‐Based Probes for use in Chemical Proteomics. Isr J Chem 2023. [DOI: 10.1002/ijch.202300016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Brittney Racioppo
- Department of Chemistry University of Illinois Chicago Chicago Illinois 60607 United States
- Skaggs Doctoral Program in the Chemical and Biological Sciences, Scripps Research La Jolla California 92037 United States
| | - Nan Qiu
- Department of Chemistry University of Illinois Chicago Chicago Illinois 60607 United States
- Skaggs Doctoral Program in the Chemical and Biological Sciences, Scripps Research La Jolla California 92037 United States
| | - Alexander Adibekian
- Department of Chemistry University of Illinois Chicago Chicago Illinois 60607 United States
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4
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Burster T, Gärtner F, Knippschild U, Zhanapiya A. Activity-Based Probes to Utilize the Proteolytic Activity of Cathepsin G in Biological Samples. Front Chem 2021; 9:628295. [PMID: 33732686 PMCID: PMC7959752 DOI: 10.3389/fchem.2021.628295] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/07/2021] [Indexed: 12/30/2022] Open
Abstract
Neutrophils, migrating to the site of infection, are able to release serine proteases after being activated. These serine proteases comprise cathepsin G (CatG), neutrophil elastase protease 3 (PR3), and neutrophil serine protease 4 (NSP4). A disadvantage of the uncontrolled proteolytic activity of proteases is the outcome of various human diseases, including cardiovascular diseases, thrombosis, and autoimmune diseases. Activity-based probes (ABPs) are used to determine the proteolytic activity of proteases, containing a set of three essential elements: Warhead, recognition sequence, and the reporter tag for detection of the covalent enzyme activity–based probe complex. Here, we summarize the latest findings of ABP-mediated detection of proteases in both locations intracellularly and on the cell surface of cells, thereby focusing on CatG. Particularly, application of ABPs in regular flow cytometry, imaging flow cytometry, and mass cytometry by time-of-flight (CyTOF) approaches is advantageous when distinguishing between immune cell subsets. ABPs can be included in a vast panel of markers to detect proteolytic activity and determine whether proteases are properly regulated during medication. The use of ABPs as a detection tool opens the possibility to interfere with uncontrolled proteolytic activity of proteases by employing protease inhibitors.
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Affiliation(s)
- Timo Burster
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Fabian Gärtner
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Ulm, Germany
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Ulm, Germany
| | - Anuar Zhanapiya
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan
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5
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Walczak M, Chryplewicz A, Olewińska S, Psurski M, Winiarski Ł, Torzyk K, Oleksyszyn J, Sieńczyk M. Phosphonic Analogs of Alanine as Acylpeptide Hydrolase Inhibitors. Chem Biodivers 2021; 18:e2001004. [PMID: 33427376 DOI: 10.1002/cbdv.202001004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/08/2021] [Indexed: 11/12/2022]
Abstract
Acylpeptide hydrolase is a serine protease, which, together with prolyl oligopeptidase, dipeptidyl peptidase IV and oligopeptidase B, belongs to the prolyl oligopeptidase family. Its primary function is associated with the removal of N-acetylated amino acid residues from proteins and peptides. Although the N-acylation occurs in 50-90 % of eukaryotic proteins, the precise functions of this modification remains unclear. Recent findings have indicated that acylpeptide hydrolase participates in various events including oxidized proteins degradation, amyloid β-peptide cleavage, and response to DNA damage. Considering the protein degradation cycle cross-talk between acylpeptide hydrolase and proteasome, inhibition of the first enzyme resulted in down-regulation of the ubiquitin-proteasome system and induction of cancer cell apoptosis. Acylpeptide hydrolase has been proposed as an interesting target for the development of new potential anticancer agents. Here, we present the synthesis of simple derivatives of (1-aminoethyl)phosphonic acid diaryl esters, phosphonic analogs of alanine diversified at the N-terminus and ester rings, as inhibitors of acylpeptide hydrolase and discuss the ability of the title compounds to induce apoptosis of U937 and MV-4-11 tumor cell lines.
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Affiliation(s)
- Maciej Walczak
- Wroclaw University of Science and Technology, Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Agnieszka Chryplewicz
- Wroclaw University of Science and Technology, Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Sandra Olewińska
- Wroclaw University of Science and Technology, Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Mateusz Psurski
- Department of Experimental Oncology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114, Wroclaw, Poland
| | - Łukasz Winiarski
- Wroclaw University of Science and Technology, Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Karolina Torzyk
- Wroclaw University of Science and Technology, Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Józef Oleksyszyn
- Wroclaw University of Science and Technology, Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marcin Sieńczyk
- Wroclaw University of Science and Technology, Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
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6
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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] [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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7
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Kahler JP, Vanhoutte R, Verhelst SHL. Activity-Based Protein Profiling of Serine Proteases in Immune Cells. Arch Immunol Ther Exp (Warsz) 2020; 68:23. [DOI: 10.1007/s00005-020-00586-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 06/11/2020] [Indexed: 12/14/2022]
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9
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Neutrophil Elastase Activity Imaging: Recent Approaches in the Design and Applications of Activity-Based Probes and Substrate-Based Probes. CONTRAST MEDIA & MOLECULAR IMAGING 2019; 2019:7417192. [PMID: 31281234 PMCID: PMC6594253 DOI: 10.1155/2019/7417192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/19/2019] [Indexed: 02/07/2023]
Abstract
The last few decades of protease research has confirmed that a number of important biological processes are strictly dependent on proteolysis. Neutrophil elastase (NE) is a critical protease in immune response and host defense mechanisms in both physiological and disease-associated conditions. Particularly, NE has been identified as a promising biomarker for early diagnosis of lung inflammation. Recent studies have shown an increasing interest in developing methods for NE activity imaging both in vitro and in vivo. Unlike anatomical imaging modalities, functional molecular imaging, including enzymatic activities, enables disease detection at a very early stage and thus constitutes a much more accurate approach. When combined with advanced imaging technologies, opportunities arise for measuring imbalanced proteolytic activities with unprecedented details. Such technologies consist in building the highest resolved and sensitive instruments as well as the most specific probes based either on peptide substrates or on covalent inhibitors. This review outlines strengths and weaknesses of these technologies and discuss their applications to investigate NE activity as biomarker of pulmonary inflammatory diseases by imaging.
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10
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Recent Developments in Peptidyl Diaryl Phoshonates as Inhibitors and Activity-Based Probes for Serine Proteases. Pharmaceuticals (Basel) 2019; 12:ph12020086. [PMID: 31185654 PMCID: PMC6631691 DOI: 10.3390/ph12020086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/06/2019] [Accepted: 06/08/2019] [Indexed: 12/12/2022] Open
Abstract
This review presents current achievements in peptidyl diaryl phosphonates as covalent, specific mechanism-based inhibitors of serine proteases. Along three decades diaryl phosphonates have emerged as invaluable tools in fundamental and applicative studies involving these hydrolases. Such an impact has been promoted by advantageous features that characterize the phosphonate compounds and their use. First, the synthesis is versatile and allows comprehensive structural modification and diversification. Accordingly, reactivity and specificity of these bioactive molecules can be easily controlled by appropriate adjustments of the side chains and the leaving groups. Secondly, the phosphonates target exclusively serine proteases and leave other oxygen and sulfur nucleophiles intact. Synthetic accessibility, lack of toxicity, and promising pharmacokinetic properties make them good drug candidates. In consequence, the utility of peptidyl diaryl phosphonates continuously increases and involves novel enzymatic targets and innovative aspects of application. For example, conjugation of the structures of specific inhibitors with reporter groups has become a convenient approach to construct activity-based molecular probes capable of monitoring location and distribution of serine proteases.
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11
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Romero-Estudillo I, Viveros-Ceballos JL, Cazares-Carreño O, González-Morales A, de Jesús BF, López-Castillo M, Razo-Hernández RS, Castañeda-Corral G, Ordóñez M. 000Synthesis of new α-aminophosphonates: Evaluation as anti-inflammatory agents and QSAR studies. Bioorg Med Chem 2018; 27:2376-2386. [PMID: 30635220 DOI: 10.1016/j.bmc.2018.12.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/21/2018] [Accepted: 12/30/2018] [Indexed: 11/30/2022]
Abstract
In this paper, we report the synthesis of a new series of α-aminophosphonates derivatives based in an efficient three-component reaction. All compounds prepared showed significant anti-inflammatory activity, being the compounds 1a, 1c, 1d, 1f, 2b and 2c the most promising ones, in terms of maximal efficacy (over 95%), potency (ED50 range between 0.7 and 10.1 mg/ear) and relative potency (range from 0.04 to 0.67). Compounds 1a, 1c, 1d and 1f significantly decrease the number of neutrophils (range from 46.7 to 63.0%) and monocytes (18.9-34.1%) in blood samples from the orbital sinus. Additionally, QSAR model revealed that the spherical molecular shape and the location of the HOMO on the phenyl ring improves the anti-inflammatory activity of the compounds. The values of R2, Q2, s and F statistical parameters and the QUIK, asymptotic Q2 and Overfitting rules validate the descriptive and predictive ability of the QSAR model. Altogether these results suggest that these new α-aminophosphonates are potential agents for the treatment of inflammation.
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Affiliation(s)
- Ivan Romero-Estudillo
- CONACYT-Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Mexico
| | - José Luis Viveros-Ceballos
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Mexico
| | - Obed Cazares-Carreño
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Mexico
| | - Angelina González-Morales
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Mexico
| | - Berenice Flores de Jesús
- Facultad de Medicina, Universidad Autónoma del Estado de Morelos, Leñeros esquina Iztaccíhuatl s/n, Cuernavaca 62350, Mexico
| | - Misael López-Castillo
- Facultad de Medicina, Universidad Autónoma del Estado de Morelos, Leñeros esquina Iztaccíhuatl s/n, Cuernavaca 62350, Mexico
| | - Rodrigo Said Razo-Hernández
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Mexico
| | - Gabriela Castañeda-Corral
- Facultad de Medicina, Universidad Autónoma del Estado de Morelos, Leñeros esquina Iztaccíhuatl s/n, Cuernavaca 62350, Mexico.
| | - Mario Ordóñez
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Mexico.
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Joachimiak Ł, Błażewska KM. Phosphorus-Based Probes as Molecular Tools for Proteome Studies: Recent Advances in Probe Development and Applications. J Med Chem 2018; 61:8536-8562. [DOI: 10.1021/acs.jmedchem.8b00249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Łukasz Joachimiak
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
| | - Katarzyna M. Błażewska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
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13
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Schulz-Fincke AC, Blaut M, Braune A, Gütschow M. A BODIPY-Tagged Phosphono Peptide as Activity-Based Probe for Human Leukocyte Elastase. ACS Med Chem Lett 2018; 9:345-350. [PMID: 29670698 DOI: 10.1021/acsmedchemlett.7b00533] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/04/2018] [Indexed: 02/08/2023] Open
Abstract
Human leukocyte elastase plays a crucial role in a variety of inflammatory disorders and represents an important subject of biomedical studies. The chemotype of peptidic phosphonates was employed for the design of a new activity-based probe for human leukocyte elastase. Its structure combines the phosphonate warhead with an adequate peptide portion and a BODIPY fluorophore with a clickable ethinylphenyl moiety at meso position. The probe 6 was assembled by copper-catalyzed alkyne-azide 1,3-dipolar cycloaddition. It was characterized as an active site-directed elastase inhibitor exhibiting a second-order rate constant of inactivation of 88400 M-1s-1. The suitability of 6 as a fluorescent probe for human leukocyte elastase was demonstrated by in-gel fluorescence analysis. Labeling experiments and inhibition data toward a panel of related proteases underlined the selectivity of the probe for the targeted leukocyte elastase.
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Affiliation(s)
- Anna-Christina Schulz-Fincke
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Michael Blaut
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Annett Braune
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
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14
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Guarino C, Gruba N, Grzywa R, Dyguda-Kazimierowicz E, Hamon Y, Łȩgowska M, Skoreński M, Dallet-Choisy S, Marchand-Adam S, Kellenberger C, Jenne DE, Sieńczyk M, Lesner A, Gauthier F, Korkmaz B. Exploiting the S4-S5 Specificity of Human Neutrophil Proteinase 3 to Improve the Potency of Peptidyl Di(chlorophenyl)-phosphonate Ester Inhibitors: A Kinetic and Molecular Modeling Analysis. J Med Chem 2018; 61:1858-1870. [PMID: 29442501 DOI: 10.1021/acs.jmedchem.7b01416] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The neutrophilic serine protease proteinase 3 (PR3) is involved in inflammation and immune response and thus appears as a therapeutic target for a variety of infectious and inflammatory diseases. Here we combined kinetic and molecular docking studies to increase the potency of peptidyl-diphenyl phosphonate PR3 inhibitors. Occupancy of the S1 subsite of PR3 by a nVal residue and of the S4-S5 subsites by a biotinylated Val residue as obtained in biotin-VYDnVP(O-C6H4-4-Cl)2 enhanced the second-order inhibition constant kobs/[I] toward PR3 by more than 10 times ( kobs/[I] = 73000 ± 5000 M-1 s-1) as compared to the best phosphonate PR3 inhibitor previously reported. This inhibitor shows no significant inhibitory activity toward human neutrophil elastase and resists proteolytic degradation in sputa from cystic fibrosis patients. It also inhibits macaque PR3 but not the PR3 from rodents and can thus be used for in vivo assays in a primate model of inflammation.
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Affiliation(s)
- Carla Guarino
- INSERM UMR1100, "Centre d'Etude des Pathologies Respiratoires" , Université de Tours , 37032 Tours , France
| | - Natalia Gruba
- Faculty of Chemistry , University of Gdansk , Wita Stwosza 63 , 80-308 Gdansk , Poland
| | - Renata Grzywa
- Faculty of Chemistry, Division of Medicinal Chemistry and Microbiology , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland
| | - Edyta Dyguda-Kazimierowicz
- Faculty of Chemistry, Advanced Materials Engineering and Modelling Group , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland
| | - Yveline Hamon
- INSERM UMR1100, "Centre d'Etude des Pathologies Respiratoires" , Université de Tours , 37032 Tours , France
| | - Monika Łȩgowska
- Faculty of Chemistry , University of Gdansk , Wita Stwosza 63 , 80-308 Gdansk , Poland
| | - Marcin Skoreński
- Faculty of Chemistry, Division of Medicinal Chemistry and Microbiology , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland
| | - Sandrine Dallet-Choisy
- INSERM UMR1100, "Centre d'Etude des Pathologies Respiratoires" , Université de Tours , 37032 Tours , France
| | - Sylvain Marchand-Adam
- INSERM UMR1100, "Centre d'Etude des Pathologies Respiratoires" , Université de Tours , 37032 Tours , France
| | - Christine Kellenberger
- Architecture et Fonction des Macromolécules Biologiques , CNRS-Unité Mixte de Recherche (UMR) , 13288 Marseille , France
| | - Dieter E Jenne
- Institute of Lung Biology and Disease, German Center for Lung Research (DZL) , Comprehensive Pneumology Center Munich and Max Planck Institute of Neurobiology , 82152 Planegg-Martinsried , Germany
| | - Marcin Sieńczyk
- Faculty of Chemistry, Division of Medicinal Chemistry and Microbiology , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland
| | - Adam Lesner
- Faculty of Chemistry , University of Gdansk , Wita Stwosza 63 , 80-308 Gdansk , Poland
| | - Francis Gauthier
- INSERM UMR1100, "Centre d'Etude des Pathologies Respiratoires" , Université de Tours , 37032 Tours , France
| | - Brice Korkmaz
- INSERM UMR1100, "Centre d'Etude des Pathologies Respiratoires" , Université de Tours , 37032 Tours , France
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15
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Korkmaz B, Lesner A, Guarino C, Wysocka M, Kellenberger C, Watier H, Specks U, Gauthier F, Jenne DE. Inhibitors and Antibody Fragments as Potential Anti-Inflammatory Therapeutics Targeting Neutrophil Proteinase 3 in Human Disease. Pharmacol Rev 2017; 68:603-30. [PMID: 27329045 DOI: 10.1124/pr.115.012104] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Proteinase 3 (PR3) has received great scientific attention after its identification as the essential antigenic target of antineutrophil cytoplasm antibodies in Wegener's granulomatosis (now called granulomatosis with polyangiitis). Despite many structural and functional similarities between neutrophil elastase (NE) and PR3 during biosynthesis, storage, and extracellular release, unique properties and pathobiological functions have emerged from detailed studies in recent years. The development of highly sensitive substrates and inhibitors of human PR3 and the creation of PR3-selective single knockout mice led to the identification of nonredundant roles of PR3 in cell death induction via procaspase-3 activation in cell cultures and in mouse models. According to a study in knockout mice, PR3 shortens the lifespan of infiltrating neutrophils in tissues and accelerates the clearance of aged neutrophils in mice. Membrane exposure of active human PR3 on apoptotic neutrophils reprograms the response of macrophages to phagocytosed neutrophils, triggers secretion of proinflammatory cytokines, and undermines immune silencing and tissue regeneration. PR3-induced disruption of the anti-inflammatory effect of efferocytosis may be relevant for not only granulomatosis with polyangiitis but also for other autoimmune diseases with high neutrophil turnover. Inhibition of membrane-bound PR3 by endogenous inhibitors such as the α-1-protease inhibitor is comparatively weaker than that of NE, suggesting that the adverse effects of unopposed PR3 activity resurface earlier than those of NE in individuals with α-1-protease inhibitor deficiency. Effective coverage of PR3 by anti-inflammatory tools and simultaneous inhibition of both PR3 and NE should be most promising in the future.
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Affiliation(s)
- Brice Korkmaz
- INSERM U-1100, Centre d'Etude des Pathologies Respiratoires and Université François Rabelais, Tours, France (B.K., C.G., F.G.); Faculty of Chemistry, University of Gdansk, Gdansk, Poland (A.L., M.W.); Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 7257, Marseille, France (C.K.); Génétique, Immunothérapie, Chimie et Cancer, Unité Mixte de Recherche 7292, Université François Rabelais, Tours, France (H.W.); Thoracic Diseases Research Unit, Division of Pulmonary and Critical Care Medicine, Mayo Clinic and Foundation, Rochester, Minnesota (U.S.); Comprehensive Pneumology Center, Institute of Lung Biology and Disease, German Center for Lung Research, Munich, Germany (D.E.J.); and Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany (D.E.J.)
| | - Adam Lesner
- INSERM U-1100, Centre d'Etude des Pathologies Respiratoires and Université François Rabelais, Tours, France (B.K., C.G., F.G.); Faculty of Chemistry, University of Gdansk, Gdansk, Poland (A.L., M.W.); Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 7257, Marseille, France (C.K.); Génétique, Immunothérapie, Chimie et Cancer, Unité Mixte de Recherche 7292, Université François Rabelais, Tours, France (H.W.); Thoracic Diseases Research Unit, Division of Pulmonary and Critical Care Medicine, Mayo Clinic and Foundation, Rochester, Minnesota (U.S.); Comprehensive Pneumology Center, Institute of Lung Biology and Disease, German Center for Lung Research, Munich, Germany (D.E.J.); and Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany (D.E.J.)
| | - Carla Guarino
- INSERM U-1100, Centre d'Etude des Pathologies Respiratoires and Université François Rabelais, Tours, France (B.K., C.G., F.G.); Faculty of Chemistry, University of Gdansk, Gdansk, Poland (A.L., M.W.); Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 7257, Marseille, France (C.K.); Génétique, Immunothérapie, Chimie et Cancer, Unité Mixte de Recherche 7292, Université François Rabelais, Tours, France (H.W.); Thoracic Diseases Research Unit, Division of Pulmonary and Critical Care Medicine, Mayo Clinic and Foundation, Rochester, Minnesota (U.S.); Comprehensive Pneumology Center, Institute of Lung Biology and Disease, German Center for Lung Research, Munich, Germany (D.E.J.); and Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany (D.E.J.)
| | - Magdalena Wysocka
- INSERM U-1100, Centre d'Etude des Pathologies Respiratoires and Université François Rabelais, Tours, France (B.K., C.G., F.G.); Faculty of Chemistry, University of Gdansk, Gdansk, Poland (A.L., M.W.); Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 7257, Marseille, France (C.K.); Génétique, Immunothérapie, Chimie et Cancer, Unité Mixte de Recherche 7292, Université François Rabelais, Tours, France (H.W.); Thoracic Diseases Research Unit, Division of Pulmonary and Critical Care Medicine, Mayo Clinic and Foundation, Rochester, Minnesota (U.S.); Comprehensive Pneumology Center, Institute of Lung Biology and Disease, German Center for Lung Research, Munich, Germany (D.E.J.); and Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany (D.E.J.)
| | - Christine Kellenberger
- INSERM U-1100, Centre d'Etude des Pathologies Respiratoires and Université François Rabelais, Tours, France (B.K., C.G., F.G.); Faculty of Chemistry, University of Gdansk, Gdansk, Poland (A.L., M.W.); Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 7257, Marseille, France (C.K.); Génétique, Immunothérapie, Chimie et Cancer, Unité Mixte de Recherche 7292, Université François Rabelais, Tours, France (H.W.); Thoracic Diseases Research Unit, Division of Pulmonary and Critical Care Medicine, Mayo Clinic and Foundation, Rochester, Minnesota (U.S.); Comprehensive Pneumology Center, Institute of Lung Biology and Disease, German Center for Lung Research, Munich, Germany (D.E.J.); and Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany (D.E.J.)
| | - Hervé Watier
- INSERM U-1100, Centre d'Etude des Pathologies Respiratoires and Université François Rabelais, Tours, France (B.K., C.G., F.G.); Faculty of Chemistry, University of Gdansk, Gdansk, Poland (A.L., M.W.); Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 7257, Marseille, France (C.K.); Génétique, Immunothérapie, Chimie et Cancer, Unité Mixte de Recherche 7292, Université François Rabelais, Tours, France (H.W.); Thoracic Diseases Research Unit, Division of Pulmonary and Critical Care Medicine, Mayo Clinic and Foundation, Rochester, Minnesota (U.S.); Comprehensive Pneumology Center, Institute of Lung Biology and Disease, German Center for Lung Research, Munich, Germany (D.E.J.); and Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany (D.E.J.)
| | - Ulrich Specks
- INSERM U-1100, Centre d'Etude des Pathologies Respiratoires and Université François Rabelais, Tours, France (B.K., C.G., F.G.); Faculty of Chemistry, University of Gdansk, Gdansk, Poland (A.L., M.W.); Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 7257, Marseille, France (C.K.); Génétique, Immunothérapie, Chimie et Cancer, Unité Mixte de Recherche 7292, Université François Rabelais, Tours, France (H.W.); Thoracic Diseases Research Unit, Division of Pulmonary and Critical Care Medicine, Mayo Clinic and Foundation, Rochester, Minnesota (U.S.); Comprehensive Pneumology Center, Institute of Lung Biology and Disease, German Center for Lung Research, Munich, Germany (D.E.J.); and Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany (D.E.J.)
| | - Francis Gauthier
- INSERM U-1100, Centre d'Etude des Pathologies Respiratoires and Université François Rabelais, Tours, France (B.K., C.G., F.G.); Faculty of Chemistry, University of Gdansk, Gdansk, Poland (A.L., M.W.); Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 7257, Marseille, France (C.K.); Génétique, Immunothérapie, Chimie et Cancer, Unité Mixte de Recherche 7292, Université François Rabelais, Tours, France (H.W.); Thoracic Diseases Research Unit, Division of Pulmonary and Critical Care Medicine, Mayo Clinic and Foundation, Rochester, Minnesota (U.S.); Comprehensive Pneumology Center, Institute of Lung Biology and Disease, German Center for Lung Research, Munich, Germany (D.E.J.); and Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany (D.E.J.)
| | - Dieter E Jenne
- INSERM U-1100, Centre d'Etude des Pathologies Respiratoires and Université François Rabelais, Tours, France (B.K., C.G., F.G.); Faculty of Chemistry, University of Gdansk, Gdansk, Poland (A.L., M.W.); Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 7257, Marseille, France (C.K.); Génétique, Immunothérapie, Chimie et Cancer, Unité Mixte de Recherche 7292, Université François Rabelais, Tours, France (H.W.); Thoracic Diseases Research Unit, Division of Pulmonary and Critical Care Medicine, Mayo Clinic and Foundation, Rochester, Minnesota (U.S.); Comprehensive Pneumology Center, Institute of Lung Biology and Disease, German Center for Lung Research, Munich, Germany (D.E.J.); and Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany (D.E.J.)
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16
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Ruivo EFP, Gonçalves LM, Carvalho LAR, Guedes RC, Hofbauer S, Brito JA, Archer M, Moreira R, Lucas SD. Clickable 4-Oxo-β-lactam-Based Selective Probing for Human Neutrophil Elastase Related Proteomes. ChemMedChem 2016; 11:2037-42. [DOI: 10.1002/cmdc.201600258] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/28/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Eduardo F. P. Ruivo
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Lídia M. Gonçalves
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Luís A. R. Carvalho
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Stefan Hofbauer
- Instituto de Tecnologia Química e Biológica-António Xavier; Universidade Nova de Lisboa; Avenida da República 2780-157 Oeiras Portugal
- Department for Structural and Computational Biology; Max F. Perutz Laboratories; University of Vienna; 1030 Vienna Austria
| | - José A. Brito
- Instituto de Tecnologia Química e Biológica-António Xavier; Universidade Nova de Lisboa; Avenida da República 2780-157 Oeiras Portugal
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica-António Xavier; Universidade Nova de Lisboa; Avenida da República 2780-157 Oeiras Portugal
| | - Rui Moreira
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Susana D. Lucas
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
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17
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Eipper S, Steiner R, Lesner A, Sienczyk M, Palesch D, Halatsch ME, Zaczynska E, Heim C, Hartmann MD, Zimecki M, Wirtz CR, Burster T. Lactoferrin Is an Allosteric Enhancer of the Proteolytic Activity of Cathepsin G. PLoS One 2016; 11:e0151509. [PMID: 26986619 PMCID: PMC4795699 DOI: 10.1371/journal.pone.0151509] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/29/2016] [Indexed: 11/19/2022] Open
Abstract
Protease-mediated degradation of proteins is critical in a plethora of physiological processes. Neutrophils secrete serine proteases including cathepsin G (CatG), neutrophile elastase (NE), and proteinase 3 (PR3) together with lactoferrin (LF) as a first cellular immune response against pathogens. Here, we demonstrate that LF increases the catalytic activity of CatG at physiological concentration, with its highest enhancing capacity under acidic (pH 5.0) conditions, and broadens the substrate selectivity of CatG. On a functional level, the enzymatic activity of CatG was increased in the presence of LF in granulocyte-derived supernatant. Furthermore, LF enhanced CatG-induced activation of platelets as determined by cell surface expression of CD62P. Consequently, LF-mediated enhancement of CatG activity might promote innate immunity during acute inflammation.
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Affiliation(s)
- Steffen Eipper
- Department of Neurosurgery, Ulm University Medical Centre, Ulm, Germany
| | - Robin Steiner
- Department of Neurosurgery, Ulm University Medical Centre, Ulm, Germany
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Marcin Sienczyk
- Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - David Palesch
- Institute of Molecular Virology, Ulm University Medical Centre, Ulm, Germany
| | | | - Ewa Zaczynska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Christopher Heim
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Marcus D. Hartmann
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Michal Zimecki
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | | | - Timo Burster
- Department of Neurosurgery, Ulm University Medical Centre, Ulm, Germany
- * E-mail:
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18
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Häußler D, Scheidt T, Stirnberg M, Steinmetzer T, Gütschow M. A Bisbenzamidine Phosphonate as a Janus-faced Inhibitor for Trypsin-like Serine Proteases. ChemMedChem 2015; 10:1641-6. [PMID: 26306030 DOI: 10.1002/cmdc.201500319] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Indexed: 12/19/2022]
Abstract
A hybrid approach was applied for the design of an inhibitor of trypsin-like serine proteases. Compound 16 [(R,R)- and (R,S)-diphenyl (4-(1-(4-amidinobenzylamino)-1-oxo-3-phenylpropan-2-ylcarbamoyl)phenylamino)(4-amidinophenyl)methylphosphonate hydrochloride], prepared in a convergent synthetic procedure, possesses a phosphonate warhead prone to react with the active site serine residue in a covalent, irreversible manner. Each of the two benzamidine moieties of 16 can potentially be accommodated in the S1 pocket of the target enzyme, but only the benzamidine close to the phosphonate group would then promote an irreversible interaction. The Janus-faced inhibitor 16 was evaluated against several serine proteases and caused a pronounced inactivation of human thrombin with a second-order rate constant (kinac /Ki) of 59 500 M(-1) s(-1). With human matriptase, 16 showed preference for a reversible mode of inhibition (IC50 =2.6 μM) as indicated by linear progress curves and enzyme reactivation.
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Affiliation(s)
- Daniela Häußler
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany)
| | - Tamara Scheidt
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany)
| | - Marit Stirnberg
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany)
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg (Germany)
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany).
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