1
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Hammerschmidt SJ, Maus H, Weldert AC, Gütschow M, Kersten C. Improving binding entropy by higher ligand symmetry? - A case study with human matriptase. RSC Med Chem 2023; 14:969-982. [PMID: 37252099 PMCID: PMC10211324 DOI: 10.1039/d3md00125c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023] Open
Abstract
Understanding different contributions to the binding entropy of ligands is of utmost interest to better predict affinity and the thermodynamic binding profiles of protein-ligand interactions and to develop new strategies for ligand optimization. To these means, the largely neglected effects of introducing higher ligand symmetry, thereby reducing the number of energetically distinguishable binding modes on binding entropy using the human matriptase as a model system, were investigated. A set of new trivalent phloroglucinol-based inhibitors that address the roughly symmetric binding site of the enzyme was designed, synthesized, and subjected to isothermal titration calorimetry. These highly symmetric ligands that can adopt multiple indistinguishable binding modes exhibited high entropy-driven affinity in line with affinity-change predictions.
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Affiliation(s)
- Stefan J Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Staudingerweg 5 55128 Mainz Germany
| | - Hannah Maus
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Staudingerweg 5 55128 Mainz Germany
| | - Annabelle C Weldert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Staudingerweg 5 55128 Mainz Germany
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn An der Immenburg 4 53121 Bonn Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Staudingerweg 5 55128 Mainz Germany
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2
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de Almeida Barros R, Meriño-Cabrera Y, Severiche Castro JG, Rodrigues da Silva Júnior N, Schultz H, de Andrade RJ, Aguilar de Oliveira JV, de Oliveira Ramos HJ, de Almeida Oliveira MG. Inhibition constant and stability of tripeptide inhibitors of gut trypsin-like enzyme of the soybean pest Anticarsia gemmatalis. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 110:e21887. [PMID: 35315942 DOI: 10.1002/arch.21887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/08/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Insects overcome the action of natural protease inhibitors (PIs) due to evolutionary adaptations through endogenous proteolysis and reprogramming proteases. Insect adaptations complicate the formulation of IP-based crop protection products. However, small peptides designed based on the active site of enzymes have shown promising results that could change this scenario. GORE1 and GORE2 are designed tripeptides that reduce the survival of Anticarsia gemmatalis when ingested orally. In this article, the stability and ability of the peptides to bind trypsin-like enzymes of A. gemmatalis were evaluated by molecular dynamics (MD) simulations. The ability of the peptides to inhibit trypsin-like enzymes in vivo was compared with the SKTI protein by feeding A. gemmatalis larvae at different concentrations, followed by an inhibition persistence assay. During the MD simulation of enzyme-ligand complexes, both peptides showed a small variation of root-mean-square deviation and root-mean-square fluctuation, suggesting that these molecules reach equilibrium when forming a complex with the trypsin-like enzyme. Furthermore, both peptides form hydrogen bonds with substrate recognition sites of A. gemmatalis trypsin-like enzyme, with GORE2 having more interactions than GORE1. Larvae of A. gemmatalis exposed to the peptides and SKTI showed a similar reduction in proteolytic activity, but the persistence of inhibition of trypsin-like enzyme was longer in peptide-fed insects. Despite their size, the peptides exhibit important active and substrate binding site interactions, stability during complex formation, and steadiness effects in vivo. The results provide fundamental information for the development of mimetic molecules and help in decision-making for the selection of delivery methods for larger-scale experiments regarding similar molecules.
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Affiliation(s)
- Rafael de Almeida Barros
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - Yaremis Meriño-Cabrera
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - José G Severiche Castro
- Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
- Departamento de Física, Universidad de Sucre, Sincelejo, Sucre, Colombia
| | - Neilier Rodrigues da Silva Júnior
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - Halina Schultz
- Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Rafael J de Andrade
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - João V Aguilar de Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - Humberto J de Oliveira Ramos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - Maria G de Almeida Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
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3
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Ahmed Al-Hadhrami N, Ladwig A, Rahman A, Rozas I, Paul G Malthouse J, Evans P. Synthesis of 2-guanidinyl pyridines and their trypsin inhibition and docking. Bioorg Med Chem 2020; 28:115612. [PMID: 32690267 DOI: 10.1016/j.bmc.2020.115612] [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: 05/11/2020] [Revised: 06/18/2020] [Accepted: 06/23/2020] [Indexed: 10/24/2022]
Abstract
A range of guanidine-based pyridines, and related compounds, have been prepared (19 examples). These compounds were evaluated in relation to their competitive inhibition of bovine pancreatic trypsin. Results demonstrate that compounds in which the guanidinyl substituent can form an intramolecular hydrogen bond (IMHB) with the pyridinyl nitrogen atom (6a-p) are better trypsin inhibitors than their counterparts (10-13) that are unable to form an IMHB. Among the compounds 6a-p, examples containing a 5-halo substituent were, generally, found to be better trypsin inhibitors. This trend was inversely related to electronegativity, thus, 1-(5-iodopyridin-2-yl)guanidinium ion 6e (Ki = 0.0151 mM) was the optimum inhibitor in the 5-halo series. Amongst the isomeric methyl substituted compounds, 1-(3-methylpyridin-2-yl)guanidinium ion 6h demonstrated optimum levels of trypsin inhibition (Ki = 0.0140 mM). In order to rationalise the measured enzyme inhibition, selected compounds were docked with bovine and human trypsin with a view to understanding active site occupancy and taken together with the Ki values the order of inhibitory ability suggests that the 5-halo 2-guanidinyl pyridine inhibitors form a halogen bond with the catalytically active serine hydroxy group.
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Affiliation(s)
- Nahlah Ahmed Al-Hadhrami
- School of Chemistry, Centre for Synthesis and Chemical Biology, University College Dublin, Dublin D04 N2E2, Ireland
| | - Angelique Ladwig
- School of Chemistry, Centre for Synthesis and Chemical Biology, University College Dublin, Dublin D04 N2E2, Ireland
| | - Adeyemi Rahman
- School of Chemistry, TBSI, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Isabel Rozas
- School of Chemistry, TBSI, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - J Paul G Malthouse
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, Conway Institute, University College Dublin, Dublin D04 N2E2, Ireland
| | - Paul Evans
- School of Chemistry, Centre for Synthesis and Chemical Biology, University College Dublin, Dublin D04 N2E2, Ireland.
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4
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Béliveau F, Tarkar A, Dion SP, Désilets A, Ghinet MG, Boudreault PL, St-Georges C, Marsault É, Paone D, Collins J, Macphee CH, Campobasso N, Groy A, Cottom J, Ouellette M, Pope AJ, Leduc R. Discovery and Development of TMPRSS6 Inhibitors Modulating Hepcidin Levels in Human Hepatocytes. Cell Chem Biol 2019; 26:1559-1572.e9. [DOI: 10.1016/j.chembiol.2019.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/06/2019] [Accepted: 09/03/2019] [Indexed: 02/06/2023]
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5
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Islam MR, Ihenacho K, Park JW, Islam IS. Plasmid DNA nicking- a Novel Activity of Soybean Trypsin Inhibitor and Bovine Aprotinin. Sci Rep 2019; 9:11596. [PMID: 31406183 PMCID: PMC6690959 DOI: 10.1038/s41598-019-48068-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 07/16/2019] [Indexed: 11/09/2022] Open
Abstract
Protease inhibitors, such as trypsin inhibitor, serum alpha-1 antitrypsin, or liver aprotinin, are a class of proteins that competitively bind and block the catalytic activity of proteolytic enzymes with wide ranging biological functions. A significant number of protease inhibitors have also been shown to possess antimicrobial activity, presumed to contribute in defense against pathogenic microorganisms as plants with higher levels of protease inhibitors tend to exhibit increased resistance towards pathogens. Two proposed mechanisms for the antimicrobial activity are combating microbial proteases that play roles in disease development and disruption of microbial cell wall & membrane necessary for survival. Here we show for the first time a novel activity of soybean trypsin inhibitor and bovine aprotinin that they nick supercoiled, circular plasmid DNA. A number of experiments conducted to demonstrate the observed DNA nicking activity is inherent, rather than a co-purified, contaminating nuclease. The nicking of the plasmid results in markedly reduced efficiencies in transformation of E. coli and transfection of HEK293T cells. Thus, this work reveals yet a new mechanism for the antimicrobial activity by protease inhibitors.
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Affiliation(s)
- M Rafiq Islam
- Laboratory of Biochemistry, Northwest Missouri State University, 7314 N. Tullis Ave, Kansas City, Missouri, 64158, United States of America.
| | - Kelvin Ihenacho
- Laboratory of Biochemistry, Northwest Missouri State University, 7314 N. Tullis Ave, Kansas City, Missouri, 64158, United States of America
| | - Jae Whan Park
- Laboratory of Biochemistry, Northwest Missouri State University, 7314 N. Tullis Ave, Kansas City, Missouri, 64158, United States of America
| | - I Sakif Islam
- Laboratory of Biochemistry, Northwest Missouri State University, 7314 N. Tullis Ave, Kansas City, Missouri, 64158, United States of America
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6
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Abstract
Matriptase-2 (MT2) is a membrane-anchored proteolytic enzyme. It acts as the proteolytic key regulator in human iron homeostasis. A high expression level can lead to iron overload diseases, whereas mutations in the gene encoding MT2, TMPRSS6, may result in various forms of iron deficiency anemia. Recently, MT2 has been reported as a positive prognostic factor in breast and prostate cancers. However, the exact functions of MT2 in various pathophysiological conditions are still not fully understood. In this review, we describe the synthetic tools designed and synthesized to regulate or monitor MT2 proteolytic activity and present the latest knowledge about the role of MT2 in iron homeostasis and cancer.
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7
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Mangold M, Gütschow M, Stirnberg M. A Short Peptide Inhibitor as an Activity-Based Probe for Matriptase-2. Pharmaceuticals (Basel) 2018; 11:ph11020049. [PMID: 29883401 PMCID: PMC6027297 DOI: 10.3390/ph11020049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 12/19/2022] Open
Abstract
Matriptase-2 is a type II transmembrane serine protease and a key regulator of systemic iron homeostasis. Since the activation mechanism and several features of the physiological role of matriptase-2 are not fully understood, there is strong need for analytical tools to perform tasks such as distinguishing active and inactive matriptase-2. For this purpose we present a short biotinylated peptide derivative with a chloromethyl ketone group, biotin-RQRR-CMK, as an activity-based probe for matriptase-2. Biotin-RQRR-CMK was kinetically characterized and exhibited a second-order rate constant of inactivation (kinac/Ki) of 10,800 M−1 s−1 towards the matriptase-2 activity in the supernatant of transfected human embryonic kidney (HEK) cells. Biotin-RQRR-CMK was able to label active matriptase-2, as visualized in western blot experiments. Pretreatment with aprotinin, an active-site directed inhibitor of serine proteases, protected matriptase-2 from the reaction with biotin-RQRR-CMK.
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Affiliation(s)
- Martin Mangold
- Pharmaceutical Chemistry I, Pharmaceutical Institute, University of Bonn, Bonn 53113, Germany.
| | - Michael Gütschow
- Pharmaceutical Chemistry I, Pharmaceutical Institute, University of Bonn, Bonn 53113, Germany.
| | - Marit Stirnberg
- Pharmaceutical Chemistry I, Pharmaceutical Institute, University of Bonn, Bonn 53113, Germany.
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8
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Schulz-Fincke AC, Tikhomirov AS, Braune A, Girbl T, Gilberg E, Bajorath J, Blaut M, Nourshargh S, Gütschow M. Design of an Activity-Based Probe for Human Neutrophil Elastase: Implementation of the Lossen Rearrangement To Induce Förster Resonance Energy Transfers. Biochemistry 2018; 57:742-752. [PMID: 29286643 DOI: 10.1021/acs.biochem.7b00906] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human neutrophil elastase is an important regulator of the immune response and plays a role in host defense mechanisms and further physiological processes. The uncontrolled activity of this serine protease may cause severe tissue alterations and impair inflammatory states. The design of an activity-based probe for human neutrophil elastase reported herein relies on a sulfonyloxyphthalimide moiety as a new type of warhead that is linker-connected to a coumarin fluorophore. The inhibitory potency of the activity-based probe was assessed against several serine and cysteine proteases, and the selectivity for human neutrophil elastase (Ki = 6.85 nM) was determined. The adequate fluorescent tag of the probe allowed for the in-gel fluorescence detection of human neutrophil elastase in the low nanomolar range. The coumarin moiety and the anthranilic acid function of the probe, produced in the course of a Lossen rearrangement, were part of two different Förster resonance energy transfers.
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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
| | - Alexander S Tikhomirov
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn , An der Immenburg 4, 53121 Bonn, Germany.,Gause Institute of New Antibiotics , 11 Bolshaya Pirogovskaya Street, Moscow 119021, Russia
| | - Annett Braune
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke , Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Tamara Girbl
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London , Charterhouse Square, London EC1M 6BQ, U.K
| | - Erik Gilberg
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn , An der Immenburg 4, 53121 Bonn, Germany.,Department of Life Science Informatics, B-IT, LIMES Program Unit of Chemical Biology and Medicinal Chemistry, University of Bonn , Dahlmannstrasse 2, 53113 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit of Chemical Biology and Medicinal Chemistry, University of Bonn , Dahlmannstrasse 2, 53113 Bonn, Germany
| | - Michael Blaut
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke , Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Sussan Nourshargh
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London , Charterhouse Square, London EC1M 6BQ, U.K
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn , An der Immenburg 4, 53121 Bonn, Germany
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9
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Beckmann AM, Glebov K, Walter J, Merkel O, Mangold M, Schmidt F, Becker-Pauly C, Gütschow M, Stirnberg M. The intact Kunitz domain protects the amyloid precursor protein from being processed by matriptase-2. Biol Chem 2017; 397:777-90. [PMID: 27078672 DOI: 10.1515/hsz-2015-0263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 04/11/2016] [Indexed: 11/15/2022]
Abstract
Proteolytic processing of the amyloid precursor protein (APP) leads to amyloid-β (Aβ) peptides. So far, the mechanism of APP processing is insufficiently characterized at the molecular level. Whereas the knowledge of Aβ generation by several proteases has been expanded, the contribution of the Kunitz-type protease inhibitor domain (KPI) present in two major APP isoforms to the complex proteolytic processing of APP is poorly understood. In this study, we have identified KPI-containing APP as a very potent, slow-binding inhibitor for the membrane-bound proteolytic regulator of iron homeostasis matriptase-2 by forming stable complexes with its target protease in HEK cells. Inhibition and complex formation depend on the intact KPI domain. By inhibiting matriptase-2, KPI-containing APP is protected from matriptase-2-mediated proteolysis within the Aβ region, thus preventing the generation of N-terminally truncated Aβ.
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10
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Modulating the selectivity of matriptase-2 inhibitors with unnatural amino acids. Eur J Med Chem 2017; 129:110-123. [DOI: 10.1016/j.ejmech.2017.02.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/19/2017] [Accepted: 02/05/2017] [Indexed: 12/12/2022]
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11
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Beckmann AM, Gilberg E, Gattner S, Huang TL, Vanden Eynde JJ, Mayence A, Bajorath J, Stirnberg M, Gütschow M. Evaluation of bisbenzamidines as inhibitors for matriptase-2. Bioorg Med Chem Lett 2016; 26:3741-5. [DOI: 10.1016/j.bmcl.2016.05.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 10/21/2022]
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12
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Häußler D, Mangold M, Furtmann N, Braune A, Blaut M, Bajorath J, Stirnberg M, Gütschow M. Phosphono Bisbenzguanidines as Irreversible Dipeptidomimetic Inhibitors and Activity-Based Probes of Matriptase-2. Chemistry 2016; 22:8525-35. [DOI: 10.1002/chem.201600206] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Daniela Häußler
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Martin Mangold
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Norbert Furtmann
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
- Department of Life Science Informatics, B-IT; LIMES Program Unit Chemical Biology and Medicinal Chemistry; University of Bonn; Dahlmannstrasse 2 53113 Bonn Germany
| | - Annett Braune
- Department of Gastrointestinal Microbiology; German Institute of Human Nutrition Potsdam-Rehbruecke; Arthur-Scheunert-Allee 114-116 14558 Nuthetal Germany
| | - Michael Blaut
- Department of Gastrointestinal Microbiology; German Institute of Human Nutrition Potsdam-Rehbruecke; Arthur-Scheunert-Allee 114-116 14558 Nuthetal Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT; LIMES Program Unit Chemical Biology and Medicinal Chemistry; University of Bonn; Dahlmannstrasse 2 53113 Bonn Germany
| | - Marit Stirnberg
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Michael Gütschow
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
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13
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Lee J, Kim B, Kim TH, Lee SH, Park HD, Chung K, Lee SH, Paek S, Kim EE, Yoon S, Kim A. A Food Effect Study of an Oral Thrombin Inhibitor and Prodrug Approach To Mitigate It. Mol Pharm 2016; 13:1197-205. [PMID: 26886576 DOI: 10.1021/acs.molpharmaceut.5b00637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
LB30870, a new direct thrombin inhibitor, showed 80% reduction in oral bioavailability in fed state. The present study aims to propose trypsin binding as a mechanism for such negative food effect and demonstrate a prodrug approach to mitigate food effect. Effect of food composition on fed state oral bioavailability of LB30870 was studied in dogs. Various prodrugs were synthesized, and their solubility, permeability, and trypsin binding affinity were measured. LB30870 and prodrugs were subject to cocrystallization with trypsin, and the X-ray structures of cocrystals were determined. Food effect was studied in dogs for selected prodrugs. Protein or lipid meal appeared to affect oral bioavailability of LB30870 in dogs more than carbohydrate meal. Blocking both carboxyl and amidine groups of LB30870 resulted in trypsin Ki values orders of magnitude higher than that of LB30870. Prodrugs belonged to either Biopharmaceutical Classification System I, II, or III. X-ray crystallography revealed that prodrugs did not bind to trypsin, but instead their hydrolysis product at the amidine blocking group formed cocrystal with trypsin. A prodrug with significantly less food effect than LB30870 was identified. Binding of prodrugs to food components such as dietary fiber appeared to counteract the positive effect brought with the prodrug approach. Further formulation research is warranted to enhance the oral bioavailability of prodrugs. In conclusion, this study is the first to demonstrate that the negative food effect of LB30870 can be attributed to trypsin binding. Trypsin binding study is proposed as a screening tool during lead optimization to minimize food effect.
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Affiliation(s)
- Jihye Lee
- College of Pharmacy, CHA University , 521 CHA Bio Complex, 335 Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Korea
| | - Bongchan Kim
- LG Life Sciences, R&D Center ,188, Munji-ro, Yuseong-gu, Daejeon 34122, Korea
| | - Tae Hun Kim
- LG Life Sciences, R&D Center ,188, Munji-ro, Yuseong-gu, Daejeon 34122, Korea
| | - Sun Hwa Lee
- LG Life Sciences, R&D Center ,188, Munji-ro, Yuseong-gu, Daejeon 34122, Korea
| | - Hee Dong Park
- LG Life Sciences, R&D Center ,188, Munji-ro, Yuseong-gu, Daejeon 34122, Korea
| | - Kyungha Chung
- LG Life Sciences, R&D Center ,188, Munji-ro, Yuseong-gu, Daejeon 34122, Korea
| | - Sung-Hack Lee
- LG Life Sciences, R&D Center ,188, Munji-ro, Yuseong-gu, Daejeon 34122, Korea
| | - Seungyup Paek
- LG Life Sciences, R&D Center ,188, Munji-ro, Yuseong-gu, Daejeon 34122, Korea
| | - Eunice EunKyeong Kim
- Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea
| | - SukKyoon Yoon
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation , 41061 Daegu, Korea
| | - Aeri Kim
- College of Pharmacy, CHA University , 521 CHA Bio Complex, 335 Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Korea
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14
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Beckmann AM, Maurer E, Lülsdorff V, Wilms A, Furtmann N, Bajorath J, Gütschow M, Stirnberg M. En Route to New Therapeutic Options for Iron Overload Diseases: Matriptase-2 as a Target for Kunitz-Type Inhibitors. Chembiochem 2016; 17:595-604. [PMID: 26762582 DOI: 10.1002/cbic.201500651] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Indexed: 02/04/2023]
Abstract
The cell-surface serine protease matriptase-2 is a critical stimulator of iron absorption by negatively regulating hepcidin, the key hormone of iron homeostasis. Thus, it has attracted much attention as a target in primary and secondary iron overload diseases. Here, we have characterised Kunitz-type inhibitors hepatocyte growth factor activator inhibitor 1 (HAI-1) and HAI-2 as powerful, slow-binding matriptase-2 inhibitors. The binding modes of the matriptase-2-HAI complexes were suggested by molecular modelling. Different assays, including cell-free and cell-based measurements of matriptase-2 activity, determination of inhibition constants and evaluation of matriptase-2 inhibition by analysis of downstream effects in human liver cells, demonstrated that matriptase-2 is an excellent target for Kunitz inhibitors. In particular, HAI-2 is considered a promising scaffold for the design of potent and selective matriptase-2 inhibitors.
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Affiliation(s)
| | - Eva Maurer
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Verena Lülsdorff
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Annika Wilms
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Norbert Furtmann
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.,Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Dahlmannstrasse 2, 53113, Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Dahlmannstrasse 2, 53113, Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Marit Stirnberg
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
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15
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3,1-Benzothiazines, 1,4-Benzodioxines and 1,4-Benzoxazines as Inhibitors of Matriptase-2: Outcome of a Focused Screening Approach. Pharmaceuticals (Basel) 2016; 9:ph9010002. [PMID: 26771619 PMCID: PMC4812366 DOI: 10.3390/ph9010002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 01/05/2016] [Accepted: 01/07/2016] [Indexed: 12/30/2022] Open
Abstract
The liver enzyme matriptase-2 is a multi-domain, transmembrane serine protease with an extracellular, C-terminal catalytic domain. Synthetic low-molecular weight inhibitors of matriptase-2 have potential as therapeutics to treat iron overload syndromes, in particular in patients with β-thalassemia. A sub-library of 64 compounds was screened for matriptase-2 inhibition and several active compounds were identified. (S)-Ethyl 2-(benzyl(3-((4-carbamidoylphenoxy)methyl)-2,3-dihydrobenzo[b][1,4]dioxin-6-yl)amino)-2-oxoacetate ((S)-12) showed an IC50 value of less than 10 µM. Structure-activity relationships were discussed and proposals to design new matriptase-2 inhibitors were made.
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16
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Furtmann N, Häußler D, Scheidt T, Stirnberg M, Steinmetzer T, Bajorath J, Gütschow M. Limiting the Number of Potential Binding Modes by Introducing Symmetry into Ligands: Structure-Based Design of Inhibitors for Trypsin-Like Serine Proteases. Chemistry 2015; 22:610-25. [DOI: 10.1002/chem.201503534] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Indexed: 12/18/2022]
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17
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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: 0.6] [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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18
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Gitlin A, Dębowski D, Karna N, Łęgowska A, Stirnberg M, Gütschow M, Rolka K. Inhibitors of Matriptase-2 Based on the Trypsin Inhibitor SFTI-1. Chembiochem 2015; 16:1601-7. [DOI: 10.1002/cbic.201500200] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Indexed: 12/12/2022]
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19
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He LW, Dai WC, Li NG. Development of Orally Active Thrombin Inhibitors for the Treatment of Thrombotic Disorder Diseases. Molecules 2015; 20:11046-62. [PMID: 26083038 PMCID: PMC6272601 DOI: 10.3390/molecules200611046] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 06/10/2015] [Indexed: 12/16/2022] Open
Abstract
Thrombotic disorders represent the major share of the various cardiovascular diseases, and significant progress has been made in the development of synthetic thrombin inhibitors as new anticoagulants. In addition to the development of highly potent and selective inhibitors with improved safety and suitable half-life, several allosteric inhibitors have been designed and synthesized, that did not fully nullify the procoagulant signal and thus could result in reduced bleeding complications. Furthermore, natural products with thrombin inhibitory activity have been isolated, and some natural products have been modified in order to improve their inhibitory activity and metabolic stability. This review summarizes the development of orally active thrombin inhibitors for the treatment of thrombotic disorder diseases, which could serve as a reference for the interested researchers.
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Affiliation(s)
- Li-Wei He
- Department of Medicinal Chemistry, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Wei-Chen Dai
- Department of Medicinal Chemistry, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Nian-Guang Li
- Department of Medicinal Chemistry, Nanjing University of Chinese Medicine, Nanjing 210023, China.
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20
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Häußler D, Gütschow M. Synthesis of a Fluorescent-Labeled Bisbenzamidine Containing the Central (6,7-Dimethoxy-4-coumaryl)Alanine Building Block. HETEROATOM CHEMISTRY 2015. [DOI: 10.1002/hc.21269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Daniela Häußler
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; D-53121 Bonn Germany
| | - Michael Gütschow
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; D-53121 Bonn Germany
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21
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van Soom J, Cuzzucoli Crucitti G, Gladysz R, van der Veken P, Di Santo R, Stuyver I, Buck V, Lambeir AM, Magdolen V, Joossens J, Augustyns K. The first potent diphenyl phosphonate KLK4 inhibitors with unexpected binding kinetics. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00288e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We report the first highly potent and selective small-molecule KLK4 inhibitors, showing surprising reversible binding kinetics.
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22
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Wysocka M, Gruba N, Miecznikowska A, Popow-Stellmaszyk J, Gütschow M, Stirnberg M, Furtmann N, Bajorath J, Lesner A, Rolka K. Substrate specificity of human matriptase-2. Biochimie 2014; 97:121-7. [DOI: 10.1016/j.biochi.2013.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/01/2013] [Indexed: 01/22/2023]
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