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Jana S, Banerjee S, Baidya SK, Ghosh B, Jha T, Adhikari N. A combined ligand-based and structure-based in silico molecular modeling approach to pinpoint the key structural attributes of hydroxamate derivatives as promising meprin β inhibitors. J Biomol Struct Dyn 2024:1-17. [PMID: 38165455 DOI: 10.1080/07391102.2023.2298394] [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: 07/15/2023] [Accepted: 10/16/2023] [Indexed: 01/03/2024]
Abstract
Human meprin β is a Zn2+-containing multidomain metalloprotease enzyme that belongs to the astacin family of the metzincin endopeptidase superfamily. Meprin β, with its diverse tissue expression pattern and wide substrate specificity, plays a significant role in various biological processes, including regulation of IL-6R pathways, lung fibrosis, collagen deposition, cellular migration, neurotoxic amyloid β levels, and inflammation. Again, meprin β is involved in Alzheimer's disease, hyperkeratosis, glomerulonephritis, diabetic kidney injury, inflammatory bowel disease, and cancer. Despite a crucial role in diverse disease processes, no such promising inhibitors of meprin β are marketed to date. Thus, it is an unmet requirement to find novel promising meprin β inhibitors that hold promise as potential therapeutics. In this study, a series of arylsulfonamide and tertiary amine-based hydroxamate derivatives as meprin β inhibitors has been analyzed through ligand-based and structure-based in silico approaches to pinpoint their structural and physiochemical requirements crucial for exerting higher inhibitory potential. This study identified different crucial structural features such as arylcarboxylic acid, sulfonamide, and arylsulfonamide moieties, as well as hydrogen bond donor and hydrophobicity, inevitable for exerting higher meprin β inhibition, providing valuable insight for their further future development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sandeep Jana
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Sandip Kumar Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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Tan K, Jäger C, Geissler S, Schlenzig D, Buchholz M, Ramsbeck D. Synthesis and structure-activity relationships of pyrazole-based inhibitors of meprin α and β. J Enzyme Inhib Med Chem 2023; 38:2165648. [PMID: 36661029 PMCID: PMC9870012 DOI: 10.1080/14756366.2023.2165648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Targeting metalloproteinases has been in the focus of drug design for a long time. However, meprin α and β emerged as potential drug targets just recently and are linked to several diseases with different pathological background. Nevertheless, the validation of meprins as suitable drug targets still requires highly potent and selective inhibitors as chemical probes to elucidate their role in pathophysiology. Albeit highly selective inhibitors of meprin β have already been reported, only inhibitors of meprin α with modest activity or selectivity are known. Starting from recently reported heteroaromatic scaffolds, the aim of this study was the optimisation of meprin α and/or meprin β inhibition while keeping the favourable off-target inhibition profile over other metalloproteases. We report potent pan-meprin inhibitors as well as highly active inhibitors of meprin α with superior selectivity over meprin β. The latter are suitable to serve as chemical probes and enable further target validation.
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Affiliation(s)
- Kathrin Tan
- Department of Drug Design and Target Validation MWT, Fraunhofer Institute for Cell Therapy and Immunology IZI, Biocenter, Halle (Saale), Germany
| | | | - Stefanie Geissler
- Department of Drug Design and Target Validation MWT, Fraunhofer Institute for Cell Therapy and Immunology IZI, Biocenter, Halle (Saale), Germany
| | - Dagmar Schlenzig
- Department of Drug Design and Target Validation MWT, Fraunhofer Institute for Cell Therapy and Immunology IZI, Biocenter, Halle (Saale), Germany
| | - Mirko Buchholz
- Department of Drug Design and Target Validation MWT, Fraunhofer Institute for Cell Therapy and Immunology IZI, Biocenter, Halle (Saale), Germany
| | - Daniel Ramsbeck
- Department of Drug Design and Target Validation MWT, Fraunhofer Institute for Cell Therapy and Immunology IZI, Biocenter, Halle (Saale), Germany,CONTACT Daniel Ramsbeck Department of Drug Design and Target Validation MWT, Fraunhofer Institute for Cell Therapy and Immunology IZI, Biocenter, Weinbergweg 22, Halle (Saale), 06120, Germany
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Bayly-Jones C, Lupton CJ, Fritz C, Venugopal H, Ramsbeck D, Wermann M, Jäger C, de Marco A, Schilling S, Schlenzig D, Whisstock JC. Helical ultrastructure of the metalloprotease meprin α in complex with a small molecule inhibitor. Nat Commun 2022; 13:6178. [PMID: 36261433 PMCID: PMC9581967 DOI: 10.1038/s41467-022-33893-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
The zinc-dependent metalloprotease meprin α is predominantly expressed in the brush border membrane of proximal tubules in the kidney and enterocytes in the small intestine and colon. In normal tissue homeostasis meprin α performs key roles in inflammation, immunity, and extracellular matrix remodelling. Dysregulated meprin α is associated with acute kidney injury, sepsis, urinary tract infection, metastatic colorectal carcinoma, and inflammatory bowel disease. Accordingly, meprin α is the target of drug discovery programs. In contrast to meprin β, meprin α is secreted into the extracellular space, whereupon it oligomerises to form giant assemblies and is the largest extracellular protease identified to date (~6 MDa). Here, using cryo-electron microscopy, we determine the high-resolution structure of the zymogen and mature form of meprin α, as well as the structure of the active form in complex with a prototype small molecule inhibitor and human fetuin-B. Our data reveal that meprin α forms a giant, flexible, left-handed helical assembly of roughly 22 nm in diameter. We find that oligomerisation improves proteolytic and thermal stability but does not impact substrate specificity or enzymatic activity. Furthermore, structural comparison with meprin β reveal unique features of the active site of meprin α, and helical assembly more broadly.
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Affiliation(s)
- Charles Bayly-Jones
- grid.1002.30000 0004 1936 7857Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC Australia
| | - Christopher J. Lupton
- grid.1002.30000 0004 1936 7857Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC Australia
| | - Claudia Fritz
- grid.418008.50000 0004 0494 3022Department for Drug Design and Target Validation (IZI-MWT), Fraunhofer Institute for Cell Therapy and Immunology, Halle, Germany
| | - Hariprasad Venugopal
- grid.1002.30000 0004 1936 7857Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, 3800 VIC Australia
| | - Daniel Ramsbeck
- grid.418008.50000 0004 0494 3022Department for Drug Design and Target Validation (IZI-MWT), Fraunhofer Institute for Cell Therapy and Immunology, Halle, Germany
| | - Michael Wermann
- grid.418008.50000 0004 0494 3022Department for Drug Design and Target Validation (IZI-MWT), Fraunhofer Institute for Cell Therapy and Immunology, Halle, Germany
| | | | - Alex de Marco
- grid.1002.30000 0004 1936 7857Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC Australia
| | - Stephan Schilling
- grid.418008.50000 0004 0494 3022Department for Drug Design and Target Validation (IZI-MWT), Fraunhofer Institute for Cell Therapy and Immunology, Halle, Germany ,grid.427932.90000 0001 0692 3664Hochschule Anhalt, University of Applied Sciences, Köthen, Germany
| | - Dagmar Schlenzig
- grid.418008.50000 0004 0494 3022Department for Drug Design and Target Validation (IZI-MWT), Fraunhofer Institute for Cell Therapy and Immunology, Halle, Germany
| | - James C. Whisstock
- grid.1002.30000 0004 1936 7857Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857EMBL Australia, Monash University, Melbourne, VIC 3800 Australia ,grid.1001.00000 0001 2180 7477ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601 Australia
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Structure and Dynamics of Meprin β in Complex with a Hydroxamate-Based Inhibitor. Int J Mol Sci 2021; 22:ijms22115651. [PMID: 34073350 PMCID: PMC8197800 DOI: 10.3390/ijms22115651] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 11/17/2022] Open
Abstract
The astacin protease Meprin β represents an emerging target for drug development due to its potential involvement in disorders such as acute and chronic kidney injury and fibrosis. Here, we elaborate on the structural basis of inhibition by a specific Meprin β inhibitor. Our analysis of the crystal structure suggests different binding modes of the inhibitor to the active site. This flexibility is caused, at least in part, by movement of the C-terminal region of the protease domain (CTD). The CTD movement narrows the active site cleft upon inhibitor binding. Compared with other astacin proteases, among these the highly homologous isoenzyme Meprin α, differences in the subsites account for the unique selectivity of the inhibitor. Although the inhibitor shows substantial flexibility in orientation within the active site, the structural data as well as binding analyses, including molecular dynamics simulations, support a contribution of electrostatic interactions, presumably by arginine residues, to binding and specificity. Collectively, the results presented here and previously support an induced fit and substantial movement of the CTD upon ligand binding and, possibly, during catalysis. To the best of our knowledge, we here present the first structure of a Meprin β holoenzyme containing a zinc ion and a specific inhibitor bound to the active site. The structural data will guide rational drug design and the discovery of highly potent Meprin inhibitors.
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Tan K, Jäger C, Körschgen H, Geissler S, Schlenzig D, Buchholz M, Stöcker W, Ramsbeck D. Heteroaromatic Inhibitors of the Astacin Proteinases Meprin α, Meprin β and Ovastacin Discovered by a Scaffold-Hopping Approach. ChemMedChem 2021; 16:976-988. [PMID: 33369214 PMCID: PMC8048867 DOI: 10.1002/cmdc.202000822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Indexed: 12/20/2022]
Abstract
Astacin metalloproteinases, in particular meprins α and β, as well as ovastacin, are emerging drug targets. Drug-discovery efforts have led to the development of the first potent and selective inhibitors in the last few years. However, the most recent compounds are based on a highly flexible tertiary amine scaffold that could cause metabolic liabilities or decreased potency due to the entropic penalty upon binding to the target. Thus, the aim of this study was to discover novel conformationally constrained scaffolds as starting points for further inhibitor optimization. Shifting from flexible tertiary amines to rigid heteroaromatic cores resulted in a boost in inhibitory activity. Moreover, some compounds already exhibited higher activity against individual astacin proteinases compared to recently reported inhibitors and also a favorable off-target selectivity profile, thus qualifying them as very suitable chemical probes for target validation.
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Affiliation(s)
- Kathrin Tan
- Department of Drug Design and Target Validation MWTFraunhofer Institute for Cell Therapy and Immunology IZIBiocenter, Weinbergweg 2206120Halle (Saale)Germany
| | - Christian Jäger
- Department of Drug Design and Target Validation MWTFraunhofer Institute for Cell Therapy and Immunology IZIBiocenter, Weinbergweg 2206120Halle (Saale)Germany
- present address: Vivoryon Therapeutics N.V.Weinbergweg 2206120Halle (Saale)Germany
| | - Hagen Körschgen
- Institute of Molecular PhysiologyCell and Matrix BiologyJohannes Gutenberg-University MainzJohann-Joachim-Becher-Weg 755128MainzGermany
| | - Stefanie Geissler
- Department of Drug Design and Target Validation MWTFraunhofer Institute for Cell Therapy and Immunology IZIBiocenter, Weinbergweg 2206120Halle (Saale)Germany
| | - Dagmar Schlenzig
- Department of Drug Design and Target Validation MWTFraunhofer Institute for Cell Therapy and Immunology IZIBiocenter, Weinbergweg 2206120Halle (Saale)Germany
| | - Mirko Buchholz
- Department of Drug Design and Target Validation MWTFraunhofer Institute for Cell Therapy and Immunology IZIBiocenter, Weinbergweg 2206120Halle (Saale)Germany
| | - Walter Stöcker
- Institute of Molecular PhysiologyCell and Matrix BiologyJohannes Gutenberg-University MainzJohann-Joachim-Becher-Weg 755128MainzGermany
| | - Daniel Ramsbeck
- Department of Drug Design and Target Validation MWTFraunhofer Institute for Cell Therapy and Immunology IZIBiocenter, Weinbergweg 2206120Halle (Saale)Germany
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Hou S, Diez J, Wang C, Becker-Pauly C, Fields GB, Bannister T, Spicer TP, Scampavia LD, Minond D. Discovery and Optimization of Selective Inhibitors of Meprin α (Part I). Pharmaceuticals (Basel) 2021; 14:ph14030203. [PMID: 33671080 PMCID: PMC8000592 DOI: 10.3390/ph14030203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
Meprin α and β are zinc-dependent proteinases implicated in multiple diseases including cancers, fibrosis, and Alzheimer’s. However, until recently, only a few inhibitors of either meprin were reported and no inhibitors are in preclinical development. Moreover, inhibitors of other metzincins developed in previous years are not effective in inhibiting meprins suggesting the need for de novo discovery effort. To address the paucity of tractable meprin inhibitors we developed ultrahigh-throughput assays and conducted parallel screening of >650,000 compounds against each meprin. As a result of this effort, we identified five selective meprin α hits belonging to three different chemotypes (triazole-hydroxyacetamides, sulfonamide-hydroxypropanamides, and phenoxy-hydroxyacetamides). These hits demonstrated a nanomolar to micromolar inhibitory activity against meprin α with low cytotoxicity and >30-fold selectivity against meprin β and other related metzincincs. These selective inhibitors of meprin α provide a good starting point for further optimization.
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Affiliation(s)
- Shurong Hou
- Department of Molecular Medicine, The Scripps Research Molecular Screening Center, Scripps Research, Jupiter, FL 33458, USA; (S.H.); (C.W.); (T.B.); (T.P.S.); (L.D.S.)
| | - Juan Diez
- Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, 3321 College Avenue, CCR r.605, Fort Lauderdale, FL 33314, USA;
| | - Chao Wang
- Department of Molecular Medicine, The Scripps Research Molecular Screening Center, Scripps Research, Jupiter, FL 33458, USA; (S.H.); (C.W.); (T.B.); (T.P.S.); (L.D.S.)
| | - Christoph Becker-Pauly
- Unit for Degradomics of the Protease Web, Institute of Biochemistry, University of Kiel, Rudolf-Höber-Str.1, 24118 Kiel, Germany;
| | - Gregg B. Fields
- Department of Chemistry & Biochemistry and I-HEALTH, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA;
| | - Thomas Bannister
- Department of Molecular Medicine, The Scripps Research Molecular Screening Center, Scripps Research, Jupiter, FL 33458, USA; (S.H.); (C.W.); (T.B.); (T.P.S.); (L.D.S.)
| | - Timothy P. Spicer
- Department of Molecular Medicine, The Scripps Research Molecular Screening Center, Scripps Research, Jupiter, FL 33458, USA; (S.H.); (C.W.); (T.B.); (T.P.S.); (L.D.S.)
| | - Louis D. Scampavia
- Department of Molecular Medicine, The Scripps Research Molecular Screening Center, Scripps Research, Jupiter, FL 33458, USA; (S.H.); (C.W.); (T.B.); (T.P.S.); (L.D.S.)
| | - Dmitriy Minond
- Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, 3321 College Avenue, CCR r.605, Fort Lauderdale, FL 33314, USA;
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, 3301 College Avenue, Fort Lauderdale, FL 33314, USA
- Correspondence:
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Discovery and Optimization of Selective Inhibitors of Meprin α (Part II). Pharmaceuticals (Basel) 2021; 14:ph14030197. [PMID: 33673639 PMCID: PMC7997411 DOI: 10.3390/ph14030197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022] Open
Abstract
Meprin α is a zinc metalloproteinase (metzincin) that has been implicated in multiple diseases, including fibrosis and cancers. It has proven difficult to find small molecules that are capable of selectively inhibiting meprin a, or its close relative meprin b, over numerous other metzincins which, if inhibited, would elicit unwanted effects. We recently identified possible molecular starting points for meprin a-specific inhibition through an HTS effort (see part I, preceding paper). Here, in part II, we report further efforts to optimize potency and selectivity. We hope that a hydroxamic acid meprin α inhibitor probe will help define the therapeutic potential for small molecule meprin a inhibition and spur further drug discovery efforts in the area of zinc metalloproteinase inhibition.
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Körschgen H, Jäger C, Tan K, Buchholz M, Stöcker W, Ramsbeck D. A Primary Evaluation of Potential Small-Molecule Inhibitors of the Astacin Metalloproteinase Ovastacin, a Novel Drug Target in Female Infertility Treatment. ChemMedChem 2020; 15:1499-1504. [PMID: 32946206 PMCID: PMC7496240 DOI: 10.1002/cmdc.202000397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Indexed: 01/20/2023]
Abstract
Despite huge progress in hormonal therapy and improved in vitro fertilization methods, the success rates in infertility treatment are still limited. A recently discovered mechanism revealed the interplay between the plasma protein fetuin-B and the cortical granule-based proteinase ovastacin to be a novel key mechanism in the regulation of fertilization. Upon sperm-egg fusion, cleavage of a distinct zona pellucida component by ovastacin destroys the sperm receptor, enhances zona robustness, and eventually provides a definitive block against polyspermy. An untimely onset of this zona hardening prior to fertilization would consequently result in infertility. Physiologically, this process is controlled by fetuin-B, an endogenous ovastacin inhibitor. Here we aimed to discover small-molecule inhibitors of ovastacin that could mimic the effect of fetuin-B. These compounds could be useful lead structures for the development of specific ovastacin inhibitors that can be used in infertility treatment or in vitro fertilization.
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Affiliation(s)
- Hagen Körschgen
- Institute of Molecular PhysiologyCell and Matrix BiologyJohannes Gutenberg University MainzJohann-Joachim-Becher-Weg 755128MainzGermany
| | - Christian Jäger
- Department of Drug Design and Target Validation MWTFraunhofer Institute for Cell Therapy and Immunology IZI BiocenterWeinbergweg 2206120Halle (Saale)Germany
| | - Kathrin Tan
- Department of Drug Design and Target Validation MWTFraunhofer Institute for Cell Therapy and Immunology IZI BiocenterWeinbergweg 2206120Halle (Saale)Germany
| | - Mirko Buchholz
- Department of Drug Design and Target Validation MWTFraunhofer Institute for Cell Therapy and Immunology IZI BiocenterWeinbergweg 2206120Halle (Saale)Germany
| | - Walter Stöcker
- Institute of Molecular PhysiologyCell and Matrix BiologyJohannes Gutenberg University MainzJohann-Joachim-Becher-Weg 755128MainzGermany
| | - Daniel Ramsbeck
- Department of Drug Design and Target Validation MWTFraunhofer Institute for Cell Therapy and Immunology IZI BiocenterWeinbergweg 2206120Halle (Saale)Germany
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Zakiyanov O, Kalousová M, Zima T, Tesař V. Matrix Metalloproteinases in Renal Diseases: A Critical Appraisal. Kidney Blood Press Res 2019; 44:298-330. [PMID: 31185475 DOI: 10.1159/000499876] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 03/10/2019] [Indexed: 11/19/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are endopeptidases within the metzincin protein family that not only cleave extracellular matrix (ECM) components, but also process the non-ECM molecules, including various growth factors and their binding proteins. MMPs participate in cell to ECM interactions, and MMPs are known to be involved in cell proliferation mechanisms and most probably apoptosis. These proteinases are grouped into six classes: collagenases, gelatinases, stromelysins, matrilysins, membrane type MMPs, and other MMPs. Various mechanisms regulate the activity of MMPs, inhibition by tissue inhibitors of metalloproteinases being the most important. In the kidney, intrinsic glomerular cells and tubular epithelial cells synthesize several MMPs. The measurement of circulating MMPs can provide valuable information in patients with kidney diseases. They play an important role in many renal diseases, both acute and chronic. This review attempts to summarize the current knowledge of MMPs in the kidney and discusses recent data from patient and animal studies with reference to specific diseases. A better understanding of the MMPs' role in renal remodeling may open the way to new interventions favoring deleterious renal changes in a number of kidney diseases.
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Affiliation(s)
- Oskar Zakiyanov
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia,
| | - Marta Kalousová
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
| | - Tomáš Zima
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
| | - Vladimír Tesař
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
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Chaudhuri A, Hudait N, Chakraborty SS. Pharmacophore modeling coupled with molecular dynamic simulation approach to identify new leads for meprin-β metalloprotease. Comput Biol Chem 2019; 80:292-306. [PMID: 31054542 DOI: 10.1016/j.compbiolchem.2019.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/23/2019] [Accepted: 04/26/2019] [Indexed: 11/26/2022]
Abstract
Human meprin beta metalloprotease, a small subgroup of the astacin family, is a potent drug target for the treatment of several disorders such as fibrosis, neurodegenerative disease in particular Alzheimer and inflammatory bowel diseases. In this study, a ligand-based pharmacophore approach has been used for the selection of potentially active compounds to understand the inhibitory activities of meprin-β by using the sulfonamide scaffold based inhibitors. Using this dataset, a pharmacophore model (Hypo1) was selected on the basis of a highest correlation coefficient (0.959), lowest total cost (105.89) and lowest root mean square deviation (1.31 Å) values. All the pharmacophore hypotheses generated from the candidate inhibitors comprised four features: two hydrogen-bond acceptor, one hydrogen-bond donor and one zinc binder feature. The best validated pharmacophore model (Hypo1) was used for virtual screening of compounds from several databases. The selective hit compounds were filtered by drug likeness property, acceptable ADMET profile, molecular docking and DFT study. Molecular dynamic simulations with the final 10 hit compounds revealed that a large number of non-covalent interactions were formed with the active site and specificity sub-pockets of the meprin beta metalloprotease. This study assists in the development of the new lead molecules as well as gives a better understanding of their interaction with meprin-β.
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Affiliation(s)
- Ankur Chaudhuri
- Department of Microbiology, West Bengal State University, Barasat, Berunanpukuria, P.O. Malikapur, North 24 Parganas, Kolkata, 700126, West Bengal, India
| | - Nandagopal Hudait
- Department of Microbiology, West Bengal State University, Barasat, Berunanpukuria, P.O. Malikapur, North 24 Parganas, Kolkata, 700126, West Bengal, India; Department of Chemistry, West Bengal State University, Barasat, Berunanpukuria, P.O. Malikapur, North 24 Parganas, Kolkata, 700126, West Bengal, India
| | - Sibani Sen Chakraborty
- Department of Microbiology, West Bengal State University, Barasat, Berunanpukuria, P.O. Malikapur, North 24 Parganas, Kolkata, 700126, West Bengal, India.
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11
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Schulze A, Wermann M, Demuth HU, Yoshimoto T, Ramsbeck D, Schlenzig D, Schilling S. Continuous assays for meprin alpha and beta using prolyl tripeptidyl aminopeptidase (PtP) from Porphyromonas gingivalis. Anal Biochem 2018; 559:11-16. [PMID: 30098994 DOI: 10.1016/j.ab.2018.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 01/17/2023]
Abstract
Common assays for endoprotease activity of meprin α and β are based on cleavage of internally quenched substrates. Although direct and convenient, for meprins these assays bear disadvantages such as, e.g., significant substrate inhibition or potential fluorescence quenching by compounds applied in inhibitor analysis. Here, we present a novel continuous assay by introducing an auxiliary enzyme, prolyl tripeptidyl aminopeptidase (PtP) and the chromogenic substrate KKGYVADAP-p-nitroanilide. We provide a quick strategy for expression and one-step-purification of the auxiliary enzyme. The enzyme kinetic data for meprin α and β suggest hyperbolic v/S-characteristics, the kinetic parameters of substrate conversion by meprin β were Km = 184 ± 32 μM and kcat = 20 ± 4 s-1. We also present conditions for the use of the fluorogenic substrate KKGYVADAP-AMC to assess meprin β activity. The assays were applied for determination of inhibitory parameters of the natural inhibitor actinonin and two recently published hydroxamates. Hence, we present two novel methods, which can be applied to assess inhibitory mechanism and potency with the attractive current drug targets meprin α and β. Furthermore, the assay might also provide implications for analysis of other endoproteases as well as their inhibitors.
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Affiliation(s)
- Anja Schulze
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Drug Design and Target Validation (IZI-MWT), Halle (Saale), Germany
| | - Michael Wermann
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Drug Design and Target Validation (IZI-MWT), Halle (Saale), Germany
| | - Hans-Ulrich Demuth
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Drug Design and Target Validation (IZI-MWT), Halle (Saale), Germany
| | | | - Daniel Ramsbeck
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Drug Design and Target Validation (IZI-MWT), Halle (Saale), Germany
| | - Dagmar Schlenzig
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Drug Design and Target Validation (IZI-MWT), Halle (Saale), Germany
| | - Stephan Schilling
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Drug Design and Target Validation (IZI-MWT), Halle (Saale), Germany.
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12
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Tan K, Jäger C, Schlenzig D, Schilling S, Buchholz M, Ramsbeck D. Tertiary-Amine-Based Inhibitors of the Astacin Protease Meprin α. ChemMedChem 2018; 13:1619-1624. [PMID: 29927060 DOI: 10.1002/cmdc.201800300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/12/2018] [Indexed: 12/24/2022]
Abstract
Metalloproteinases of the astacin family are drawing ever increasing attention as potential drug targets. However, knowledge regarding inhibitors thereof is limited in most cases. Crucial for the development of metalloprotease inhibitors is high selectivity, to avoid side effects brought about by inhibition of off-target proteases and interference with physiological pathways. In this study we aimed at the design of novel selective inhibitors for the astacin proteinase meprin α. Based on a recently identified tertiary amine scaffold, a series of compounds was synthesized and evaluated. The compounds exhibit reasonable inhibitory activity with high selectivity over other metalloproteases. The isoenzyme meprin β is only slightly inhibited. Hence, the present study revealed a novel class of selective meprin α inhibitors with improved selectivity over known compounds.
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Affiliation(s)
- Kathrin Tan
- Department of Drug Design and Target Validation MWT, Fraunhofer Institute for Cell Therapy and Immunology IZI, Biocenter, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Christian Jäger
- Department of Drug Design and Target Validation MWT, Fraunhofer Institute for Cell Therapy and Immunology IZI, Biocenter, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Dagmar Schlenzig
- Department of Drug Design and Target Validation MWT, Fraunhofer Institute for Cell Therapy and Immunology IZI, Biocenter, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Stephan Schilling
- Department of Drug Design and Target Validation MWT, Fraunhofer Institute for Cell Therapy and Immunology IZI, Biocenter, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Mirko Buchholz
- Department of Drug Design and Target Validation MWT, Fraunhofer Institute for Cell Therapy and Immunology IZI, Biocenter, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Daniel Ramsbeck
- Department of Drug Design and Target Validation MWT, Fraunhofer Institute for Cell Therapy and Immunology IZI, Biocenter, Weinbergweg 22, 06120, Halle (Saale), Germany
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13
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Ramsbeck D, Hamann A, Richter G, Schlenzig D, Geissler S, Nykiel V, Cynis H, Schilling S, Buchholz M. Structure-Guided Design, Synthesis, and Characterization of Next-Generation Meprin β Inhibitors. J Med Chem 2018; 61:4578-4592. [PMID: 29694039 DOI: 10.1021/acs.jmedchem.8b00330] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The metalloproteinase meprin β emerged as a current drug target for the treatment of a number of disorders, among those fibrosis, inflammatory bowel disease and Morbus Alzheimer. A major obstacle in the development of metalloprotease inhibitors is target selectivity to avoid side effects by blocking related enzymes with physiological functions. Here, we describe the structure-guided design of a novel series of compounds, based on previously reported highly active meprin β inhibitors. The bioisosteric replacement of the sulfonamide scaffold gave rise to a next generation of meprin inhibitors. Selected compounds based on this novel amine scaffold exhibit high activity against meprin β and also remarkable selectivity over related metalloproteases, i.e., matrix metalloproteases and A disintegrin and metalloproteinases.
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Affiliation(s)
- Daniel Ramsbeck
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Antje Hamann
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Georg Richter
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Dagmar Schlenzig
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Stefanie Geissler
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Vera Nykiel
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Holger Cynis
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Stephan Schilling
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Mirko Buchholz
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
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14
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Adhikari N, Amin SA, Ghosh B, Jha T. Shedding light on designing potential meprin β inhibitors through ligand-based robust validated computational approaches: A proposal to chemists! J Biomol Struct Dyn 2017; 36:3003-3022. [DOI: 10.1080/07391102.2017.1374210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
| | - Sk. Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
| | - Balaram Ghosh
- Department of Pharmacy, BITS-Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
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