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Khalil HH, El-Sheshtawy MM, Khattab SN, Abu-Serie MM, Shehat MG, Teleb M, Haiba NS. Chemosensitization of non-small cell lung cancer to sorafenib via non-hydroxamate s-triazinedione-based MMP-9/10 inhibitors. Bioorg Chem 2024; 144:107155. [PMID: 38306827 DOI: 10.1016/j.bioorg.2024.107155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/03/2024] [Accepted: 01/24/2024] [Indexed: 02/04/2024]
Abstract
Non-small cell lung cancer (NSCLC) continues to be a leading cause of cancer death. Its fatality is associated with angiogenesis and metastasis. While VEGFR inhibitors are expected to be the central pillar for halting lung cancer, several clinical reports declared their subpar activities as monotherapy. These results directed combination studies of VEGFR inhibitors, especially sorafenib (Nexavar®), with various chemotherapeutic agents. Matrix metalloproteinase (MMP) inhibitors are seldom utilized in such combinations despite the expected complementary therapeutic outcome. This could be attributed to the clinical unsuitability of MMP inhibitors from the hydroxamate family. Herein, we report new non-hydroxamate s-triazinedione-based inhibitors of MMP-9 (6b; IC50 = 0.112 μM), and MMP-10 (6e; IC50 = 0.076 μM) surpassing the hydroxamate inhibitor NNGH for chemosensitization of NSCLC to sorafenib. MMPs inhibition profiling of the hits revealed MMP-9 over -2 and MMP-10 over -13 selectivity. 6b and 6e were potent (IC50 = 0.139 and 0.136 µM), safe (SI up to 6.77) and superior to sorafenib (IC50 = 0.506 µM, SI = 6.27) against A549 cells. When combined with sorafenib, the studied MMP inhibitors enhanced its cytotoxic efficacy up to 26 folds as confirmed by CI and DRI values for 6b (CI = 0.160 and DRI = 22.175) and 6e (CI = 0.096 and DRI = 29.060). 6b and 6e exerted anti-invasive activities in A549 cells as single agents (22.66 and 39.67 %) and in sorafenib combinations (29.96 and 91.83 %) compared to untreated control. Both compounds downregulated VEGF in A549 cells by approximately 70 % when combined with sorafenib, highlighting enhanced anti-angiogenic activities. Collectively, combinations of 6b and 6e with sorafenib demonstrated synergistic NSCLC cytotoxicity with pronounced anti-invasive and anti-angiogenic activities introducing a promising start point for preclinical studies.
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Affiliation(s)
- Hosam H Khalil
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria 21321, Egypt
| | - Mohamed M El-Sheshtawy
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria 21321, Egypt
| | - Sherine N Khattab
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria 21321, Egypt.
| | - Marwa M Abu-Serie
- Medical Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Egypt
| | - Michael G Shehat
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt
| | - Mohamed Teleb
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt; Cancer Nanotechnology Research Laboratory (CNRL), Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt
| | - Nesreen S Haiba
- Department of Physics and Chemistry, Faculty of Education, Alexandria University, Egypt
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2
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Morcos CA, Khattab SN, Haiba NS, Bassily RW, Abu-Serie MM, Teleb M. Battling colorectal cancer via s-triazine-based MMP-10/13 inhibitors armed with electrophilic warheads for concomitant ferroptosis induction; the first-in-class dual-acting agents. Bioorg Chem 2023; 141:106839. [PMID: 37703744 DOI: 10.1016/j.bioorg.2023.106839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023]
Abstract
There is an increasing interest in halting CRC by combining ferroptosis with other forms of tumor cell death. However, ferroptosis induction is seldom studied in tandem with inhibiting MMPs. A combination that is expected to enhance the therapeutic outcome based on mechanistic ferroptosis studies highlighting the interplay with MMPs, especially MMP-13 associated with CRC metastasis and poor prognosis. Herein, we report new hybrid triazines capable of simultaneous MMP-10/13 inhibition and ferroptosis induction bridging the gap between their anticancer potentials. The MMP-10/13 inhibitory component of the scaffold was based on the non-hydroxamate model inhibitors. s-Triazine was rationalized as the core inspired by altretamine, an FDA-approved ferroptosis inducer. The ferroptosis pharmacophores were then installed as Michael acceptors via triazole-based spacers. The electrophilic reactivity was tuned by incorporating cyano and/or substituted phenyl groups influencing their electronic and steric properties and enriching the SAR study. Initial screening revealed the outstanding cytotoxicity profiles of the nitrophenyl-tethered chalcone 5e and the cyanoacrylohydrazides bearing p-fluorophenyl 9b and p-bromophenyl 9d appendages. 9b and 9d surpassed NNGH against MMP-10 and -13, especially 9d (IC50 = 0.16 μM). Ferroptosis studies proved that 9d depleted GSH in HCT-116 cells by a relative fold decrement of 0.81 with modest direct GPX4 inhibition, thus inducing lipid peroxidation, the hallmark of ferroptosis, by 1.32 relative fold increment. Docking presumed that 9d could bind to the MMP-10 S1' pocket and active site His221, extend through the MMP-13 hydrophobic pocket, and interact covalently with the GPX4 catalytic selenocysteine. 9d complexed with ferrous oxide nanoparticles was 7.5 folds more cytotoxic than its free precursor against HCT-116 cells. The complex-induced intracellular iron overload, depleted GSH with a relative fold decrement of 0.12, consequently triggering lipid peroxidation and ferroptosis by a 3.94 relative fold increment. Collectively, 9d could be a lead for tuning MMPs selectivity and ferroptosis induction potential to maximize the benefit of such a combination.
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Affiliation(s)
- Christine A Morcos
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria 21321, Egypt
| | - Sherine N Khattab
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria 21321, Egypt.
| | - Nesreen S Haiba
- Department of Physics and Chemistry, Faculty of Education, Alexandria University, Egypt
| | - Rafik W Bassily
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria 21321, Egypt
| | - Marwa M Abu-Serie
- Medical Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Egypt.
| | - Mohamed Teleb
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt; Cancer Nanotechnology Research Laboratory (CNRL), Faculty of Pharmacy, Alexandria University, Alexandria, Egypt.
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3
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Matrix Metalloproteinase-10 in Kidney Injury Repair and Disease. Int J Mol Sci 2022; 23:ijms23042131. [PMID: 35216251 PMCID: PMC8877639 DOI: 10.3390/ijms23042131] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 12/13/2022] Open
Abstract
Matrix metalloproteinase-10 (MMP-10) is a zinc-dependent endopeptidase with the ability to degrade a broad spectrum of extracellular matrices and other protein substrates. The expression of MMP-10 is induced in acute kidney injury (AKI) and chronic kidney disease (CKD), as well as in renal cell carcinoma (RCC). During the different stages of kidney injury, MMP-10 may exert distinct functions by cleaving various bioactive substrates including heparin-binding epidermal growth factor (HB-EGF), zonula occludens-1 (ZO-1), and pro-MMP-1, -7, -8, -9, -10, -13. Functionally, MMP-10 is reno-protective in AKI by promoting HB-EGF-mediated tubular repair and regeneration, whereas it aggravates podocyte dysfunction and proteinuria by disrupting glomerular filtration integrity via degrading ZO-1. MMP-10 is also involved in cancerous invasion and emerges as a promising therapeutic target in patients with RCC. As a secreted protein, MMP-10 could be detected in the circulation and presents an inverse correlation with renal function. Due to the structural similarities between MMP-10 and the other MMPs, development of specific inhibitors targeting MMP-10 is challenging. In this review, we summarize our current understanding of the role of MMP-10 in kidney diseases and discuss the potential mechanisms of its actions.
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Leone G, Pepi S, Consumi M, Lamponi S, Fragai M, Martinucci M, Baldoneschi V, Francesconi O, Nativi C, Magnani A. Sodium hyaluronate-g-2-((N-(6-aminohexyl)-4-methoxyphenyl)sulfonamido)-N-hydroxyacetamide with enhanced affinity towards MMP12 catalytic domain to be used as visco-supplement with increased degradation resistance. Carbohydr Polym 2021; 271:118452. [PMID: 34364546 DOI: 10.1016/j.carbpol.2021.118452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 01/16/2023]
Abstract
The present paper describes the functionalization of sodium hyaluronate (NaHA) with a small molecule (2-((N-(6-aminohexyl)-4-methoxyphenyl)sulfonamido)-N-hydroxyacetamide) (MMPI) having proven inhibitory activity against membrane metalloproteins involved in inflammatory processes (i.e. MMP12). The obtained derivative (HA-MMPI) demonstrated an increased resistance to the in-vitro degradation by hyaluronidase, viscoelastic properties close to those of healthy human synovial fluid, cytocompatibility towards human chondrocytes and nanomolar affinity towards MMP 12. Thus, HA-MMPI can be considered a good candidate as viscosupplement in the treatment of knee osteoarticular disease.
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Affiliation(s)
- Gemma Leone
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy
| | - Simone Pepi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy
| | - Marco Consumi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy
| | - Stefania Lamponi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy
| | - Marco Fragai
- Department of Chemistry, "Ugo Schiff" - University of Florence - Via della Lastruccia 13, 50019 Sesto Fiorentino, FI, Italy; Cerm, University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino, FI, Italy
| | - Marco Martinucci
- Department of Chemistry, "Ugo Schiff" - University of Florence - Via della Lastruccia 13, 50019 Sesto Fiorentino, FI, Italy
| | - Veronica Baldoneschi
- Department of Chemistry, "Ugo Schiff" - University of Florence - Via della Lastruccia 13, 50019 Sesto Fiorentino, FI, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy
| | - Oscar Francesconi
- Department of Chemistry, "Ugo Schiff" - University of Florence - Via della Lastruccia 13, 50019 Sesto Fiorentino, FI, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy
| | - Cristina Nativi
- Department of Chemistry, "Ugo Schiff" - University of Florence - Via della Lastruccia 13, 50019 Sesto Fiorentino, FI, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy
| | - Agnese Magnani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; National Interuniversity Consortium of Materials Science and Technology (INSTM), Via Giusti 9, 50121 Firenze, Italy.
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5
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Cuffaro D, Nuti E, D’Andrea F, Rossello A. Developments in Carbohydrate-Based Metzincin Inhibitors. Pharmaceuticals (Basel) 2020; 13:ph13110376. [PMID: 33182755 PMCID: PMC7696829 DOI: 10.3390/ph13110376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/03/2020] [Accepted: 11/06/2020] [Indexed: 01/03/2023] Open
Abstract
Matrix metalloproteinases (MMPs) and A disintegrin and Metalloproteinase (ADAMs) are zinc-dependent endopeptidases belonging to the metzincin superfamily. Upregulation of metzincin activity is a major feature in many serious pathologies such as cancer, inflammations, and infections. In the last decades, many classes of small molecules have been developed directed to inhibit these enzymes. The principal shortcomings that have hindered clinical development of metzincin inhibitors are low selectivity for the target enzyme, poor water solubility, and long-term toxicity. Over the last 15 years, a novel approach to improve solubility and bioavailability of metzincin inhibitors has been the synthesis of carbohydrate-based compounds. This strategy consists of linking a hydrophilic sugar moiety to an aromatic lipophilic scaffold. This review aims to describe the development of sugar-based and azasugar-based derivatives as metzincin inhibitors and their activity in several pathological models.
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6
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Structure-based design and optimization of pyrimidine- and 1,2,4-triazolo[4,3-a]pyrimidine-based matrix metalloproteinase-10/13 inhibitors via Dimroth rearrangement towards targeted polypharmacology. Bioorg Chem 2020; 96:103616. [DOI: 10.1016/j.bioorg.2020.103616] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 11/15/2022]
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7
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Cerofolini L, Fragai M, Luchinat C. Mechanism and Inhibition of Matrix Metalloproteinases. Curr Med Chem 2019; 26:2609-2633. [PMID: 29589527 DOI: 10.2174/0929867325666180326163523] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 01/02/2023]
Abstract
Matrix metalloproteinases hydrolyze proteins and glycoproteins forming the extracellular matrix, cytokines and growth factors released in the extracellular space, and membrane-bound receptors on the outer cell membrane. The pathological relevance of MMPs has prompted the structural and functional characterization of these enzymes and the development of synthetic inhibitors as possible drug candidates. Recent studies have provided a better understanding of the substrate preference of the different members of the family, and structural data on the mechanism by which these enzymes hydrolyze the substrates. Here, we report the recent advancements in the understanding of the mechanism of collagenolysis and elastolysis, and we discuss the perspectives of new therapeutic strategies for targeting MMPs.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
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8
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Das PK, Biswas R, Anjum N, Das AK, Maiti MK. Rice matrix metalloproteinase OsMMP1 plays pleiotropic roles in plant development and symplastic-apoplastic transport by modulating cellulose and callose depositions. Sci Rep 2018; 8:2783. [PMID: 29426868 PMCID: PMC5807377 DOI: 10.1038/s41598-018-20070-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 01/12/2018] [Indexed: 11/12/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are well-known proteolytic enzymes in animal systems and play roles in tissue differentiation, growth, and defence. Although a few plant MMPs have been reported, their exact functions in development and growth remain elusive. In this study, we characterized the promoter and coding sequence of OsMMP1, one of the putative MMP genes in rice (Oryza sativa). The OsMMP1 catalytic domain is structurally similar to human MMPs with respect to cofactor orientation as predicted by homology modeling. Bacterially expressed recombinant OsMMP1 showed protease activity with bovine serum albumin and gelatin as substrates. Analyses of transcript accumulation and promoter-reporter gene expression revealed that OsMMP1 is spatio-temporally expressed in vegetative and reproductive parts of plants. The plasma membrane-localized OsMMP1 protease affected plant development upon heterologous expression in tobacco and endogenous gene silencing in rice. Transgenic tobacco plants expressing OsMMP1 showed enhanced deposition of cellulose and callose, leading to impairment of symplastic and apoplastic translocations. Moreover, transgenic tobacco tissues exhibited tolerance to oxidative stress-inducing agent by confining the area of tissue death owing to callose lining. Collectively, these findings demonstrate the involvement of a plant MMP in growth, organ differentiation, and development in relation to cell wall modification.
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Affiliation(s)
- Prabir Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Rupam Biswas
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Nazma Anjum
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Mrinal K Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
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9
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Naphade S, Embusch A, Madushani KL, Ring KL, Ellerby LM. Altered Expression of Matrix Metalloproteinases and Their Endogenous Inhibitors in a Human Isogenic Stem Cell Model of Huntington's Disease. Front Neurosci 2018; 11:736. [PMID: 29459817 PMCID: PMC5807396 DOI: 10.3389/fnins.2017.00736] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/18/2017] [Indexed: 11/23/2022] Open
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder characterized by a progressive movement disorder, psychiatric symptoms, and cognitive impairments. HD is caused by a CAG repeat expansion encoding a stretch of polyglutamine residues in the N-terminus of mutant huntingtin (mHTT) protein. Proteolytic processing of mHTT yields toxic fragments, which cause neurotoxicity and massive neuronal cell death predominantly in the striatum and cortex. Inhibition of mHTT cleavage reduces neuronal toxicity suggesting mHTT proteolysis contributes to HD pathogenesis. A previously conducted unbiased siRNA screen in our lab for known human proteases identified matrix metalloproteinases (MMPs) as modifiers of mHTT proteolysis and toxicity. To further study MMP activation in HD, isogenic HD, and control corrected (C116) neural stem cells (NSCs) prepared from HD patient-derived induced pluripotent stem cells were used to examine the role of MMPs and their endogenous inhibitors in this highly relevant model system. We found altered expression of MMP-2 and MMP-9 (gelatinases), MMP-3/10, and MMP-14, activity in HD-NSCs when compared to control C116-NSCs. Dysregulation in MMP activity was accompanied with concomitant changes in levels of endogenous inhibitors of MMPs, called tissue inhibitors of matrix metalloproteinases (TIMPs). Specifically, we observed decreased levels of TIMP-1 and TIMP-2 in HD-NSCs, suggesting part of the altered expression and activity of MMPs is due to lower abundance of these endogenous inhibitors. Immunofluorescence analysis revealed increased MMP/TIMP localization in the nucleus or aggregates of HD-NSCs, suggesting potential interaction with mHTT. TIMP-1 was found to associate with mHTT aggregates in discrete punctate structures in HD-NSCs. These events collectively contribute to increased neurotoxicity in HD. Previous characterization of these NSCs revealed transforming growth factor beta (TGF-β) pathway as the top dysregulated pathway in HD. TGF-β was significantly upregulated in HD-NSCs and addition of TGF-β to HD-NSCs was found to be neuroprotective. To determine if TGF-β regulated MMP and TIMP activity, C116- and HD-NSCs were exogenously treated with recombinant TGF-β. TIMP-1 levels were found to be elevated in response to TGF-β treatment, representing a potential mechanism through which elevated TGF-β levels confer neuroprotection in HD. Studying the mechanism of action of MMPs and TIMPs, and their interactions with mHTT in human isogenic patient-derived NSCs elucidates new mechanisms of HD neurotoxicity and will likely provide novel therapeutics for treatment of HD.
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Affiliation(s)
- Swati Naphade
- The Buck Institute for Research on Aging, Novato, CA, United States
| | | | | | - Karen L Ring
- The Buck Institute for Research on Aging, Novato, CA, United States.,California Institute of Regenerative Medicine, San Francisco, CA, United States
| | - Lisa M Ellerby
- The Buck Institute for Research on Aging, Novato, CA, United States
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10
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Senn N, Ott M, Lanz J, Riedl R. Targeted Polypharmacology: Discovery of a Highly Potent Non-Hydroxamate Dual Matrix Metalloproteinase (MMP)-10/-13 Inhibitor. J Med Chem 2017; 60:9585-9598. [DOI: 10.1021/acs.jmedchem.7b01001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicole Senn
- Institute of Chemistry and
Biotechnology, Center for Organic and Medicinal Chemistry, ZHAW Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Michael Ott
- Institute of Chemistry and
Biotechnology, Center for Organic and Medicinal Chemistry, ZHAW Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Jan Lanz
- Institute of Chemistry and
Biotechnology, Center for Organic and Medicinal Chemistry, ZHAW Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and
Biotechnology, Center for Organic and Medicinal Chemistry, ZHAW Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
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11
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Marino-Puertas L, Goulas T, Gomis-Rüth FX. Matrix metalloproteinases outside vertebrates. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:2026-2035. [PMID: 28392403 DOI: 10.1016/j.bbamcr.2017.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/31/2017] [Accepted: 04/04/2017] [Indexed: 02/07/2023]
Abstract
The matrix metalloproteinase (MMP) family belongs to the metzincin clan of zinc-dependent metallopeptidases. Due to their enormous implications in physiology and disease, MMPs have mainly been studied in vertebrates. They are engaged in extracellular protein processing and degradation, and present extensive paralogy, with 23 forms in humans. One characteristic of MMPs is a ~165-residue catalytic domain (CD), which has been structurally studied for 14 MMPs from human, mouse, rat, pig and the oral-microbiome bacterium Tannerella forsythia. These studies revealed close overall coincidence and characteristic structural features, which distinguish MMPs from other metzincins and give rise to a sequence pattern for their identification. Here, we reviewed the literature available on MMPs outside vertebrates and performed database searches for potential MMP CDs in invertebrates, plants, fungi, viruses, protists, archaea and bacteria. These and previous results revealed that MMPs are widely present in several copies in Eumetazoa and higher plants (Tracheophyta), but have just token presence in eukaryotic algae. A few dozen sequences were found in Ascomycota (within fungi) and in double-stranded DNA viruses infecting invertebrates (within viruses). In contrast, a few hundred sequences were found in archaea and >1000 in bacteria, with several copies for some species. Most of the archaeal and bacterial phyla containing potential MMPs are present in human oral and gut microbiomes. Overall, MMP-like sequences are present across all kingdoms of life, but their asymmetric distribution contradicts the vertical descent model from a eubacterial or archaeal ancestor. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman.
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Affiliation(s)
- Laura Marino-Puertas
- Proteolysis Lab, Structural Biology Unit, "María-de-Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park; c/Baldiri Reixac, 15-21, 08028, Barcelona, Spain
| | - Theodoros Goulas
- Proteolysis Lab, Structural Biology Unit, "María-de-Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park; c/Baldiri Reixac, 15-21, 08028, Barcelona, Spain..
| | - F Xavier Gomis-Rüth
- Proteolysis Lab, Structural Biology Unit, "María-de-Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park; c/Baldiri Reixac, 15-21, 08028, Barcelona, Spain..
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12
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Arylsulfonamides and selectivity of matrix metalloproteinase-2: An overview. Eur J Med Chem 2017; 129:72-109. [DOI: 10.1016/j.ejmech.2017.02.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 12/14/2022]
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13
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Lebida K, Mozrzymas JW. Spike Timing-Dependent Plasticity in the Mouse Barrel Cortex Is Strongly Modulated by Sensory Learning and Depends on Activity of Matrix Metalloproteinase 9. Mol Neurobiol 2016; 54:6723-6736. [PMID: 27744572 PMCID: PMC5622912 DOI: 10.1007/s12035-016-0174-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/28/2016] [Indexed: 12/14/2022]
Abstract
Experience and learning in adult primary somatosensory cortex are known to affect neuronal circuits by modifying both excitatory and inhibitory transmission. Synaptic plasticity phenomena provide a key substrate for cognitive processes, but precise description of the cellular and molecular correlates of learning is hampered by multiplicity of these mechanisms in various projections and in different types of neurons. Herein, we investigated the impact of associative learning on neuronal plasticity in distinct types of postsynaptic neurons by checking the impact of classical conditioning (pairing whisker stroking with tail shock) on the spike timing-dependent plasticity (t-LTP and t-LTD) in the layer IV to II/III vertical pathway of the mouse barrel cortex. Learning in this paradigm practically prevented t-LTP measured in pyramidal neurons but had no effect on t-LTD. Since classical conditioning is known to affect inhibition in the barrel cortex, we examined its effect on tonic GABAergic currents and found a strong downregulation of these currents in the layer II/III interneurons but not in pyramidal cells. Matrix metalloproteinases emerged as crucial players in synaptic plasticity and learning. We report that the blockade of MMP-9 (but not MMP-3) abolished t-LTP having no effect on t-LTD. Moreover, associative learning resulted in an upregulation of gelatinolytic activity within the "trained" barrel. We conclude that LTP induced by spike timing-dependent plasticity (STDP) paradigm is strongly correlated with associative learning and critically depends on the activity of MMP-9.
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Affiliation(s)
- Katarzyna Lebida
- Laboratory of Neuroscience, Department of Biophysics, Wroclaw Medical University, Chalubinskiego 3a, 50-368, Wroclaw, Poland.
| | - Jerzy W Mozrzymas
- Laboratory of Neuroscience, Department of Biophysics, Wroclaw Medical University, Chalubinskiego 3a, 50-368, Wroclaw, Poland.,Department of Animal Molecular Physiology, Institute of Experimental Biology, Wroclaw University, Wroclaw, Poland
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14
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Urbach C, Gordon NC, Strickland I, Lowne D, Joberty-Candotti C, May R, Herath A, Hijnen D, Thijs JL, Bruijnzeel-Koomen CA, Minter RR, Hollfelder F, Jermutus L. Combinatorial Screening Identifies Novel Promiscuous Matrix Metalloproteinase Activities that Lead to Inhibition of the Therapeutic Target IL-13. ACTA ACUST UNITED AC 2015; 22:1442-1452. [PMID: 26548614 DOI: 10.1016/j.chembiol.2015.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/10/2015] [Accepted: 09/28/2015] [Indexed: 12/20/2022]
Abstract
The practical realization of disease modulation by catalytic degradation of a therapeutic target protein suffers from the difficulty to identify candidate proteases, or to engineer their specificity. We identified 23 measurable, specific, and new protease activities using combinatorial screening of 27 human proteases against 24 therapeutic protein targets. We investigate the cleavage of monocyte chemoattractant protein 1, interleukin-6 (IL-6), and IL-13 by matrix metalloproteinases (MMPs) and serine proteases, and demonstrate that cleavage of IL-13 leads to potent inhibition of its biological activity in vitro. MMP-8 degraded human IL-13 most efficiently in vitro and ex vivo in human IL-13 transgenic mouse bronchoalveolar lavage. Hence, MMP-8 is a therapeutic protease lead against IL-13 for inflammatory conditions whereby reported genetic and genomics data suggest an involvement of MMP-8. This work describes the first exploitation of human enzyme promiscuity for therapeutic applications, and reveals both starting points for protease-based therapies and potential new regulatory networks in inflammatory disease.
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Affiliation(s)
- Carole Urbach
- Department of Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK.
| | - Nathaniel C Gordon
- Department of Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK; Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Ian Strickland
- Department of Respiratory, Inflammation and Autoimmunity, MedImmune, Granta Park, Cambridge CB21 6GH, UK
| | - David Lowne
- Department of Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK
| | | | - Richard May
- Department of Respiratory, Inflammation and Autoimmunity, MedImmune, Granta Park, Cambridge CB21 6GH, UK
| | - Athula Herath
- Non Clinical Biostatistics, MedImmune, Granta Park, Cambridge CB21 6GH, UK
| | - DirkJan Hijnen
- Department of Dermatology, University Medical Center, 3508 GA Utrecht, the Netherlands
| | - Judith L Thijs
- Department of Dermatology, University Medical Center, 3508 GA Utrecht, the Netherlands
| | | | - Ralph R Minter
- Department of Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Lutz Jermutus
- Department of Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK
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15
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Schlage P, Kockmann T, Sabino F, Kizhakkedathu JN, Auf dem Keller U. Matrix Metalloproteinase 10 Degradomics in Keratinocytes and Epidermal Tissue Identifies Bioactive Substrates With Pleiotropic Functions. Mol Cell Proteomics 2015; 14:3234-46. [PMID: 26475864 DOI: 10.1074/mcp.m115.053520] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Indexed: 01/29/2023] Open
Abstract
Matrix metalloproteinases (MMPs) are important players in skin homeostasis, wound repair, and in the pathogenesis of skin cancer. It is now well established that most of their functions are related to processing of bioactive proteins rather than components of the extracellular matrix (ECM). MMP10 is highly expressed in keratinocytes at the wound edge and at the invasive front of tumors, but hardly any non-ECM substrates have been identified and its function in tissue repair and carcinogenesis is unclear. To better understand the role of MMP10 in the epidermis, we employed multiplexed iTRAQ-based Terminal Amine Isotopic Labeling of Substrates (TAILS) and monitored MMP10-dependent proteolysis over time in secretomes from keratinocytes. Time-resolved abundance clustering of neo-N termini classified MMP10-dependent cleavage events by efficiency and refined the MMP10 cleavage site specificity by revealing a so far unknown preference for glutamate in the P1 position. Moreover, we identified and validated the integrin alpha 6 subunit, cysteine-rich angiogenic inducer 61 and dermokine as novel direct MMP10 substrates and provide evidence for MMP10-dependent but indirect processing of phosphatidylethanolamine-binding protein 1. Finally, we sampled the epidermal proteome and degradome in unprecedented depth and confirmed MMP10-dependent processing of dermokine in vivo by TAILS analysis of epidermis from transgenic mice that overexpress a constitutively active mutant of MMP10 in basal keratinocytes. The newly identified substrates are involved in cell adhesion, migration, proliferation, and/or differentiation, indicating a contribution of MMP10 to local modulation of these processes during wound healing and cancer development. Data are available via ProteomeXchange with identifier PXD002474.
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Affiliation(s)
- Pascal Schlage
- From the ‡ETH Zurich, Department of Biology,Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Tobias Kockmann
- From the ‡ETH Zurich, Department of Biology,Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Fabio Sabino
- From the ‡ETH Zurich, Department of Biology,Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Jayachandran N Kizhakkedathu
- §University of British Columbia, Department of Pathology and Laboratory Medicine and Department of Chemistry, Centre for Blood Research, 4.401Life Sciences Institute, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - Ulrich Auf dem Keller
- From the ‡ETH Zurich, Department of Biology,Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland;
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16
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Zhang R, Zhang L, Li C, Chen B, Li Q, Fang X, Shen Y. Refolding of Recombinant Histidine-Tagged Catalytic Domain of MMP-13 from Escherichia coli with Ion-Exchange Chromatography for Higher Bioactivity. J LIQ CHROMATOGR R T 2015. [DOI: 10.1080/10826076.2014.917669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Ruiying Zhang
- a Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Shaanxi Alcohol Ether and Biomass Energy Engineering Research Center/Director Key Laboratory of Yulin Desert Plants Resources , Northwest University , Xi'an , P. R. China
| | - Lu Zhang
- a Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Shaanxi Alcohol Ether and Biomass Energy Engineering Research Center/Director Key Laboratory of Yulin Desert Plants Resources , Northwest University , Xi'an , P. R. China
| | - Cong Li
- a Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Shaanxi Alcohol Ether and Biomass Energy Engineering Research Center/Director Key Laboratory of Yulin Desert Plants Resources , Northwest University , Xi'an , P. R. China
| | - Bang Chen
- a Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Shaanxi Alcohol Ether and Biomass Energy Engineering Research Center/Director Key Laboratory of Yulin Desert Plants Resources , Northwest University , Xi'an , P. R. China
| | - Qing Li
- a Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Shaanxi Alcohol Ether and Biomass Energy Engineering Research Center/Director Key Laboratory of Yulin Desert Plants Resources , Northwest University , Xi'an , P. R. China
| | - Xuexun Fang
- b Key Laboratory for Molecular Enzymology & Engineering of Ministry of Education , Jilin University , Chang Chun , P. R. China
| | - Yehua Shen
- a Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Shaanxi Alcohol Ether and Biomass Energy Engineering Research Center/Director Key Laboratory of Yulin Desert Plants Resources , Northwest University , Xi'an , P. R. China
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17
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Orbe J, Sánchez-Arias JA, Rabal O, Rodríguez JA, Salicio A, Ugarte A, Belzunce M, Xu M, Wu W, Tan H, Ma H, Páramo JA, Oyarzabal J. Design, synthesis, and biological evaluation of novel matrix metalloproteinase inhibitors as potent antihemorrhagic agents: from hit identification to an optimized lead. J Med Chem 2015; 58:2465-88. [PMID: 25686153 DOI: 10.1021/jm501940y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Growing evidence suggests that matrix metalloproteinases (MMP) are involved in thrombus dissolution; then, considering that new therapeutic strategies are required for controlling hemorrhage, we hypothesized that MMP inhibition may reduce bleeding by delaying fibrinolysis. Thus, we designed and synthesized a novel series of MMP inhibitors to identify potential candidates for acute treatment of bleeding. Structure-based and knowledge-based strategies were utilized to design this novel chemical series, α-spiropiperidine hydroxamates, of potent and soluble (>75 μg/mL) pan-MMP inhibitors. The initial hit, 12, was progressed to an optimal lead 19d. Racemic 19d showed a remarkable in vitro phenotypic response and outstanding in vivo efficacy; in fact, the mouse bleeding time at 1 mg/kg was 0.85 min compared to 29.28 min using saline. In addition, 19d displayed an optimal ADME and safety profile (e.g., no thrombus formation). Its corresponding enantiomers were separated, leading to the preclinical candidate 5 (described in Drug Annotations series, J. Med. Chem. 2015, ).
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Affiliation(s)
- Josune Orbe
- Atherosclerosis Research Laboratory, ‡Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra , Avenida Pio XII 55, E-31008 Pamplona, Spain
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18
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Lee JY, Choi HY, Ahn HJ, Ju BG, Yune TY. Matrix metalloproteinase-3 promotes early blood-spinal cord barrier disruption and hemorrhage and impairs long-term neurological recovery after spinal cord injury. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:2985-3000. [PMID: 25325922 DOI: 10.1016/j.ajpath.2014.07.016] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 06/21/2014] [Accepted: 07/15/2014] [Indexed: 11/16/2022]
Abstract
After spinal cord injury (SCI), blood-spinal cord barrier (BSCB) disruption by matrix metalloproteinases (MMPs) leads to BSCB permeability and blood cell infiltration, contributing to permanent neurological disability. Herein, we report that MMP-3 plays a critical role in BSCB disruption after SCI in mice. MMP-3 was induced in infiltrated neutrophils and blood vessels after SCI, and NF-κB as a transcription factor was involved in MMP-3 expression. BSCB permeability and blood cell infiltration after injury were more reduced in Mmp3 knockout (KO) mice than in wild-type (WT) mice, which was significantly inhibited by Mmp3 siRNA or a general inhibitor of MMPs, N-isobutyl-N-(4-methoxyphenylsulfonyl)glycyl hydroxamic acid. The level of tight junction proteins, such as occludin and zonula occludens-1, which decreased after SCI, was also higher in Mmp3 KO than in WT mice. Exogenously, MMP-3 injection into the normal spinal cord also induced BSCB permeability. Furthermore, MMP-9 activation after injury was mediated by MMP-3 activation. Finally, improved functional recovery was observed in Mmp3 KO mice compared with WT mice after injury. These results demonstrated the role of MMP-3 in BSCB disruption after SCI for the first time and suggest that the regulation of MMP-3 can be considered a therapeutic target to inhibit BSCB disruption and hemorrhage, and thereby enhance functional recovery after acute SCI.
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Affiliation(s)
- Jee Youn Lee
- Age-Related and Brain Diseases Research Center, School of Medicine, Kyung Hee University, Seoul, Republic of Korea; Neurodegeneration Control Research Center, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Hae Young Choi
- Age-Related and Brain Diseases Research Center, School of Medicine, Kyung Hee University, Seoul, Republic of Korea; Neurodegeneration Control Research Center, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Hyun-Jong Ahn
- Department of Microbiology, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Bong Gun Ju
- Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Tae Young Yune
- Age-Related and Brain Diseases Research Center, School of Medicine, Kyung Hee University, Seoul, Republic of Korea; Neurodegeneration Control Research Center, School of Medicine, Kyung Hee University, Seoul, Republic of Korea; Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Republic of Korea.
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19
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Batra J, Soares AS, Mehner C, Radisky ES. Matrix metalloproteinase-10/TIMP-2 structure and analyses define conserved core interactions and diverse exosite interactions in MMP/TIMP complexes. PLoS One 2013; 8:e75836. [PMID: 24073280 PMCID: PMC3779175 DOI: 10.1371/journal.pone.0075836] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 08/21/2013] [Indexed: 11/18/2022] Open
Abstract
Matrix metalloproteinases (MMPs) play central roles in vertebrate tissue development, remodeling, and repair. The endogenous tissue inhibitors of metalloproteinases (TIMPs) regulate proteolytic activity by binding tightly to the MMP active site. While each of the four TIMPs can inhibit most MMPs, binding data reveal tremendous heterogeneity in affinities of different TIMP/MMP pairs, and the structural features that differentiate stronger from weaker complexes are poorly understood. Here we report the crystal structure of the comparatively weakly bound human MMP-10/TIMP-2 complex at 2.1 Å resolution. Comparison with previously reported structures of MMP-3/TIMP-1, MT1-MMP/TIMP-2, MMP-13/TIMP-2, and MMP-10/TIMP-1 complexes offers insights into the structural basis of binding selectivity. Our analyses identify a group of highly conserved contacts at the heart of MMP/TIMP complexes that define the conserved mechanism of inhibition, as well as a second category of diverse adventitious contacts at the periphery of the interfaces. The AB loop of the TIMP N-terminal domain and the contact loops of the TIMP C-terminal domain form highly variable peripheral contacts that can be considered as separate exosite interactions. In some complexes these exosite contacts are extensive, while in other complexes the AB loop or C-terminal domain contacts are greatly reduced and appear to contribute little to complex stability. Our data suggest that exosite interactions can enhance MMP/TIMP binding, although in the relatively weakly bound MMP-10/TIMP-2 complex they are not well optimized to do so. Formation of highly variable exosite interactions may provide a general mechanism by which TIMPs are fine-tuned for distinct regulatory roles in biology.
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Affiliation(s)
- Jyotica Batra
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, Florida, United States of America
| | - Alexei S. Soares
- Biology Department, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Christine Mehner
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, Florida, United States of America
| | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, Florida, United States of America
- * E-mail:
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20
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Udi Y, Fragai M, Grossman M, Mitternacht S, Arad-Yellin R, Calderone V, Melikian M, Toccafondi M, Berezovsky IN, Luchinat C, Sagi I. Unraveling Hidden Regulatory Sites in Structurally Homologous Metalloproteases. J Mol Biol 2013; 425:2330-46. [DOI: 10.1016/j.jmb.2013.04.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 04/05/2013] [Accepted: 04/05/2013] [Indexed: 01/26/2023]
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21
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Mori M, Massaro A, Calderone V, Fragai M, Luchinat C, Mordini A. Discovery of a New Class of Potent MMP Inhibitors by Structure-Based Optimization of the Arylsulfonamide Scaffold. ACS Med Chem Lett 2013; 4:565-9. [PMID: 24900710 DOI: 10.1021/ml300446a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 03/13/2013] [Indexed: 01/29/2023] Open
Abstract
A new class of potent matrix metalloproteinase (MMP) inhibitors designed by structure-based optimization of the well-known arylsulfonamide scaffold is presented. Molecules show an ethylene linker connecting the sulfonamide group with the P1' aromatic portion and a d-proline residue bearing the zinc-binding group. The affinity improvement provided by these modifications led us to discover a nanomolar MMP inhibitor bearing a carboxylate moiety as zinc-binding group, which might be a promising lead molecule. Notably, a significant selectivity for MMP-8, MMP-12, and MMP-13 was observed with respect to MMP-1 and MMP-7.
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Affiliation(s)
- Mattia Mori
- ProtEra Srl, Scientific Campus, University of Florence, viale delle idee 22, I-50019
Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
| | - Assunta Massaro
- ProtEra Srl, Scientific Campus, University of Florence, viale delle idee 22, I-50019
Sesto Fiorentino, Italy
| | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
- Department
of Chemistry “Ugo
Shiff”, University of Florence,
via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
- Department
of Chemistry “Ugo
Shiff”, University of Florence,
via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Alessandro Mordini
- ICCOM-CNR, Dipartimento
di Chimica “U. Schiff”, via della Lastruccia
13, I-50019 Sesto Fiorentino, Italy
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22
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Bartoloni M, Domínguez BE, Dragoni E, Richichi B, Fragai M, André S, Gabius HJ, Ardá A, Luchinat C, Jiménez-Barbero J, Nativi C. Targeting Matrix Metalloproteinases: Design of a Bifunctional Inhibitor for Presentation by Tumour-Associated Galectins. Chemistry 2012; 19:1896-902. [DOI: 10.1002/chem.201203794] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Indexed: 12/18/2022]
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23
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Batra J, Robinson J, Soares AS, Fields AP, Radisky DC, Radisky ES. Matrix metalloproteinase-10 (MMP-10) interaction with tissue inhibitors of metalloproteinases TIMP-1 and TIMP-2: binding studies and crystal structure. J Biol Chem 2012; 287:15935-46. [PMID: 22427646 DOI: 10.1074/jbc.m112.341156] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Matrix metalloproteinase 10 (MMP-10, stromelysin-2) is a secreted metalloproteinase with functions in skeletal development, wound healing, and vascular remodeling; its overexpression is also implicated in lung tumorigenesis and tumor progression. To understand the regulation of MMP-10 by tissue inhibitors of metalloproteinases (TIMPs), we have assessed equilibrium inhibition constants (K(i)) of putative physiological inhibitors TIMP-1 and TIMP-2 for the active catalytic domain of human MMP-10 (MMP-10cd) using multiple kinetic approaches. We find that TIMP-1 inhibits the MMP-10cd with a K(i) of 1.1 × 10(-9) M; this interaction is 10-fold weaker than the inhibition of the similar MMP-3 (stromelysin-1) catalytic domain (MMP-3cd) by TIMP-1. TIMP-2 inhibits the MMP-10cd with a K(i) of 5.8 × 10(-9) M, which is again 10-fold weaker than the inhibition of MMP-3cd by this inhibitor (K(i) = 5.5 × 10(-10) M). We solved the x-ray crystal structure of TIMP-1 bound to the MMP-10cd at 1.9 Å resolution; the structure was solved by molecular replacement and refined with an R-factor of 0.215 (R(free) = 0.266). Comparing our structure of MMP-10cd·TIMP-1 with the previously solved structure of MMP-3cd·TIMP-1 (Protein Data Bank entry 1UEA), we see substantial differences at the binding interface that provide insight into the differential binding of stromelysin family members to TIMP-1. This structural information may ultimately assist in the design of more selective TIMP-based inhibitors tailored for specificity toward individual members of the stromelysin family, with potential therapeutic applications.
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Affiliation(s)
- Jyotica Batra
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224, USA
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24
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Spinal matrix metalloproteinase 3 mediates inflammatory hyperalgesia via a tumor necrosis factor-dependent mechanism. Neuroscience 2011; 200:199-210. [PMID: 22056600 DOI: 10.1016/j.neuroscience.2011.10.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 10/11/2011] [Accepted: 10/11/2011] [Indexed: 01/30/2023]
Abstract
Matrix metalloproteinases (MMPs) have been implicated in the modulation of synaptic plasticity, glial activation, and long-term potentiation in the CNS. Here we demonstrate for the first time a mechanism for the regulation of nociceptive processing by spinal MMP-3 during peripheral inflammation. We first determined by western blotting that the catalytic (active) form of MMP-3 (cMMP-3) is increased in lumbar spinal cord following peripheral inflammation in rats. The peripheral inflammation-induced thermal hyperalgesia and tactile hypersensitivity was transiently (2-3 h) attenuated by intrathecal (IT) pretreatment with either an MMP-3 inhibitor (NNGH), or a broad spectrum MMP inhibitor (GM6001). In addition, IT delivery of cMMP-3 evoked hypersensitivity, whereas the pro (enzymatically inactive) form of MMP-3 did not. This suggests a pro-algesic effect of spinal MMP-3 mediated by an enzymatic mechanism. This cMMP-3-induced hypersensitivity is concurrent with increased tumor necrosis factor (TNF) in the spinal cord. The hypersensitivity behavior is prevented by intrathecal etanercept (TNF blockade). Treatment with cMMP-3 resulted in an increase in TNF release from spinal primary microglial, but not astrocyte cultures. These findings thus present direct evidence implicating MMP-3 in the coordination of spinal nociceptive processing via a spinal TNF-dependent mechanism.
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25
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Miller JP, Holcomb J, Al-Ramahi I, de Haro M, Gafni J, Zhang N, Kim E, Sanhueza M, Torcassi C, Kwak S, Botas J, Hughes RE, Ellerby LM. Matrix metalloproteinases are modifiers of huntingtin proteolysis and toxicity in Huntington's disease. Neuron 2010; 67:199-212. [PMID: 20670829 DOI: 10.1016/j.neuron.2010.06.021] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2010] [Indexed: 01/27/2023]
Abstract
Proteolytic cleavage of huntingtin (Htt) is known to be a key event in the pathogenesis of Huntington's disease (HD). Our understanding of proteolytic processing of Htt has thus far focused on the protease families-caspases and calpains. Identifying critical proteases involved in Htt proteolysis and toxicity using an unbiased approach has not been reported. To accomplish this, we designed a high-throughput western blot-based screen to examine the generation of the smallest N-terminal polyglutamine-containing Htt fragment. We screened 514 siRNAs targeting the repertoire of human protease genes. This screen identified 11 proteases that, when inhibited, reduced Htt fragment accumulation. Three of these belonged to the matrix metalloproteinase (MMP) family. One family member, MMP-10, directly cleaves Htt and prevents cell death when knocked down in striatal Hdh(111Q/111Q) cells. Correspondingly, MMPs are activated in HD mouse models, and loss of function of Drosophila homologs of MMPs suppresses Htt-induced neuronal dysfunction in vivo.
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Affiliation(s)
- John P Miller
- Buck Institute for Age Research, Novato, CA 94945, USA
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26
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Wilfong EM, Locklear U, Toone EJ. A single step purification for autolytic zinc proteinases. Bioorg Med Chem Lett 2010; 20:280-2. [PMID: 19942433 PMCID: PMC3688063 DOI: 10.1016/j.bmcl.2009.10.114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 10/26/2009] [Accepted: 10/27/2009] [Indexed: 11/24/2022]
Abstract
We describe a novel single-step method for the purification of stromelysin-1 catalytic domain (SCD) via immobilized metal affinity chromatography under denaturing conditions that inhibit proteolytic activity followed by on-column refolding and spontaneous autolysis of the fusion peptide to yield pure, active stromelysin-1 catalytic domain. The methodology provides a general approach for the rapid purification of large quantities of zinc proteinases.
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Affiliation(s)
- Erin M Wilfong
- Department of Chemistry, Duke University, LSRC B120, Durham, NC 27708, United States
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27
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Dragoni E, Calderone V, Fragai M, Jaiswal R, Luchinat C, Nativi C. Biotin-tagged probes for MMP expression and activation: design, synthesis, and binding properties. Bioconjug Chem 2009; 20:719-27. [PMID: 19275207 DOI: 10.1021/bc8003827] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design and synthesis of biotin chain-terminated inhibitors (BTI) showing high affinity for matrix metalloproteinases (MMPs) on one side and high affinity for avidin through the biotinylated tag on the other are reported. The affinity of the designed BTI toward five different MMPs has been evaluated and the simultaneous formation of a highly stable ternary system Avidin-BTI-MMP clearly assessed. This system will permit the development of new approaches to detect, quantify, or collect MMPs in biological samples, with potential applications in vivo.
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Affiliation(s)
- Elisa Dragoni
- Magnetic Resonance Center - University of Florence, Sesto Fiorentino, Italy
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28
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Nikolova V, Koo CY, Ibrahim SA, Wang Z, Spillmann D, Dreier R, Kelsch R, Fischgräbe J, Smollich M, Rossi LH, Sibrowski W, Wülfing P, Kiesel L, Yip GW, Götte M. Differential roles for membrane-bound and soluble syndecan-1 (CD138) in breast cancer progression. Carcinogenesis 2009; 30:397-407. [PMID: 19126645 DOI: 10.1093/carcin/bgp001] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The heparan sulfate proteoglycan syndecan-1 (Sdc1) modulates cell proliferation, adhesion, migration and angiogenesis. Proteinase-mediated shedding converts Sdc1 from a membrane-bound coreceptor into a soluble effector capable of binding the same ligands. In breast carcinomas, Sdc1 overexpression correlates with poor prognosis and an aggressive phenotype. To distinguish between the roles of membrane-bound and shed forms of Sdc1 in breast cancer progression, human MCF-7 breast cancer cells were stably transfected with plasmids overexpressing wild-type (WT), constitutively shed and uncleavable forms of Sdc1. Overexpression of WT Sdc1 increased cell proliferation, whereas overexpression of constitutively shed Sdc1 decreased proliferation. Fibroblast growth factor-2-mediated mitogen-activated protein kinase signaling was reduced following small-interfering RNA (siRNA)-mediated knockdown of Sdc1 expression. Constitutively, membrane-bound Sdc1 inhibited invasiveness, whereas soluble Sdc1 promoted invasion of MCF-7 cells into matrigel matrices. The latter effect was reversed by the matrix metalloproteinase inhibitors N-isobutyl-N-(4-methoxyphenylsufonyl) glycyl hydroxamic acid and tissue inhibitor of metalloproteinase (TIMP)-1. Affymetrix microarray analysis identified TIMP-1, Furin and urokinase-type plasminogen activator receptor as genes differentially regulated in soluble Sdc1-overexpressing cells. Endogenous TIMP-1 expression was reduced in cells overexpressing soluble Sdc1 and increased in those overexpressing the constitutively membrane-bound Sdc1. Moreover, E-cadherin protein expression was downregulated in cells overexpressing soluble Sdc1. Our results suggest that the soluble and membrane-bound forms of Sdc1 play different roles at different stages of breast cancer progression. Proteolytic conversion of Sdc1 from a membrane-bound into a soluble molecule marks a switch from a proliferative to an invasive phenotype, with implications for breast cancer diagnostics and potential glycosaminoglycan-based therapies.
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Affiliation(s)
- Viktoriya Nikolova
- Department of Gynecology and Obstetrics, University Hospital Münster, Münster, Germany
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Pauly T, Ratliff M, Pietrowski E, Neugebauer R, Schlicksupp A, Kirsch J, Kuhse J. Activity-dependent shedding of the NMDA receptor glycine binding site by matrix metalloproteinase 3: a PUTATIVE mechanism of postsynaptic plasticity. PLoS One 2008; 3:e2681. [PMID: 18629001 PMCID: PMC2443283 DOI: 10.1371/journal.pone.0002681] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 06/02/2008] [Indexed: 11/18/2022] Open
Abstract
Functional and structural alterations of clustered postsynaptic ligand gated ion channels in neuronal cells are thought to contribute to synaptic plasticity and memory formation in the human brain. Here, we describe a novel molecular mechanism for structural alterations of NR1 subunits of the NMDA receptor. In cultured rat spinal cord neurons, chronic NMDA receptor stimulation induces disappearance of extracellular epitopes of NMDA receptor NR1 subunits, which was prevented by inhibiting matrix metalloproteinases (MMPs). Immunoblotting revealed the digestion of solubilized NR1 subunits by MMP-3 and identified a fragment of about 60 kDa as MMPs-activity-dependent cleavage product of the NR1 subunit in cultured neurons. The expression of MMP-3 in the spinal cord culture was shown by immunoblotting and immunofluorescence microscopy. Recombinant NR1 glycine binding protein was used to identify MMP-3 cleavage sites within the extracellular S1 and S2-domains. N-terminal sequencing and site-directed mutagenesis revealed S542 and L790 as two putative major MMP-3 cleavage sites of the NR1 subunit. In conclusion, our data indicate that MMPs, and in particular MMP-3, are involved in the activity dependent alteration of NMDA receptor structure at postsynaptic membrane specializations in the CNS.
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Affiliation(s)
- Thorsten Pauly
- Department of Anatomy and Cellular Neurobiology, University of Ulm, Ulm, Germany
| | - Miriam Ratliff
- Department of Anatomy and Cell Biology, University of Heidelberg, Heidelberg, Germany
| | - Eweline Pietrowski
- Department of Anatomy and Cell Biology, University of Heidelberg, Heidelberg, Germany
| | - Rainer Neugebauer
- Department of Anatomy and Cell Biology, University of Heidelberg, Heidelberg, Germany
| | - Andrea Schlicksupp
- Department of Anatomy and Cell Biology, University of Heidelberg, Heidelberg, Germany
| | - Joachim Kirsch
- Department of Anatomy and Cell Biology, University of Heidelberg, Heidelberg, Germany
| | - Jochen Kuhse
- Department of Anatomy and Cell Biology, University of Heidelberg, Heidelberg, Germany
- * E-mail:
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Arendt Y, Banci L, Bertini I, Cantini F, Cozzi R, Del Conte R, Gonnelli L. Catalytic domain of MMP20 (Enamelysin) - the NMR structure of a new matrix metalloproteinase. FEBS Lett 2007; 581:4723-6. [PMID: 17869250 DOI: 10.1016/j.febslet.2007.08.069] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 08/24/2007] [Accepted: 08/27/2007] [Indexed: 11/28/2022]
Abstract
The solution structure of the catalytic domain of MMP-20, a member of the matrix metalloproteinases family not yet structurally characterized, complexed with N-Isobutyl-N-(4-methoxyphenylsulfonyl)glycyl hydroxamic acid (NNGH), is here reported and compared with other MMPs-NNGH adducts. The backbone dynamic has been characterized as well. We have found that, despite the same fold and very high overall similarity, the present structure experiences specific structural and dynamical similarities with some MMPs and differences with others, around the catalytic cavity. The present solution structure, not only contributes to fill the gap of structural knowledge on human MMPs, but also provides further information to design more selective and efficient inhibitors for a specific member of this class of proteins.
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Affiliation(s)
- Yvonne Arendt
- ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino (FI), Italy
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Alcaraz LA, Banci L, Bertini I, Cantini F, Donaire A, Gonnelli L. Matrix metalloproteinase–inhibitor interaction: the solution structure of the catalytic domain of human matrix metalloproteinase-3 with different inhibitors. J Biol Inorg Chem 2007; 12:1197-206. [PMID: 17710450 DOI: 10.1007/s00775-007-0288-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 08/02/2007] [Indexed: 11/30/2022]
Abstract
We structurally characterized the adducts of the catalytic domain of matrix metalloproteinase-3 (MMP3) with three different nonpeptidic inhibitors by solving the solution structure of one adduct [MMP3-N-isobutyl-N-(4-methoxyphenylsulfonyl)glycyl hydroxamic acid] and then by calculating structural models of the other two adducts using a reduced set of experimental NMR data, following a recently proposed procedure (Bertini et al. in J. Med. Chem. 48:7544-7559, 2005). The inhibitors were selected with the criteria of maintaining in all of them the same zinc-coordinating moiety and of selectively changing the substituents and/or the functional groups. The backbone dynamics on various time scales have been characterized as well. The comparison among these structures and with others previously reported allowed us to elucidate fine details of inhibitor-receptor interactions and to develop some criteria, which could guide in optimizing the design of selective inhibitors.
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Affiliation(s)
- Luis A Alcaraz
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino, Italy
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Arnesano F, Banci L, Bertini I, Capozzi F, Ciofi-Baffoni S, Ciurli S, Luchinat C, Mangani S, Rosato A, Turano P, Viezzoli MS. An Italian contribution to structural genomics: Understanding metalloproteins. Coord Chem Rev 2006. [DOI: 10.1016/j.ccr.2006.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Seargent JM, Loadman PM, Martin SW, Naylor B, Bibby MC, Gill JH. Expression of matrix metalloproteinase-10 in human bladder transitional cell carcinoma. Urology 2005; 65:815-20. [PMID: 15833553 DOI: 10.1016/j.urology.2004.11.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2004] [Revised: 10/13/2004] [Accepted: 11/08/2004] [Indexed: 01/26/2023]
Abstract
OBJECTIVES To analyze matrix metalloproteinase-10 (MMP-10) expression in transitional cell carcinoma (TCC) of the bladder, evaluate the correlations between MMP-10 protein expression and clinicopathologic parameters, and address the viability of MMP-10 as a therapeutic target for TCC. MMP-mediated degradation of the extracellular matrix is an important factor in the pathogenesis of tumorigenesis and metastasis. METHODS Using immunohistochemistry, the expression of MMP-10 was assessed using both tissue microarrays and whole sections of archival tissue specimens representative of all grades and stages of human bladder TCC (n = 60). MMP-10 expression was also assessed in histologically normal human bladder tissue (n = 10). The immunostaining results for MMP-10 expression were examined for correlations with tumor grade and stage. RESULTS Unlike most MMPs, MMP-10 was localized primarily in the tumor mass as opposed to the tumor stroma and was detectable in all grades and stages of TCC. Significantly greater levels of MMP-10 protein were observed in superficial (pTa, pT1; n = 38) tumors than in normal bladder tissue (P = 0.01). In contrast to the proposed role of MMPs in tumor invasion, no significant difference was observed between muscle-invasive tumors (pT2 or worse; n = 22) and histologically normal bladder tissue (P = 0.50). MMP-10 expression showed no significant correlation with tumor grade. CONCLUSIONS The data from our study showed that, unlike most MMPs, MMP-10 was not associated with tumor aggression or invasion. Our results suggest that MMP-10 protein levels are significantly greater in the earlier stages of TCC development.
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Affiliation(s)
- Jill M Seargent
- Cancer Research UK Laboratories, Tom Connors Cancer Research Centre, University of Bradford, Bradford, United Kingdom
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Bertini I, Calderone V, Cosenza M, Fragai M, Lee YM, Luchinat C, Mangani S, Terni B, Turano P. Conformational variability of matrix metalloproteinases: beyond a single 3D structure. Proc Natl Acad Sci U S A 2005; 102:5334-9. [PMID: 15809432 PMCID: PMC556229 DOI: 10.1073/pnas.0407106102] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structures of the catalytic domain of matrix metalloproteinase 12 in the presence of acetohydroxamic acid and N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid have been solved by x-ray diffraction in the crystalline state at 1.0 and 1.3-A resolution, respectively, and compared with the previously published x-ray structure at 1.2-A resolution of the adduct with batimastat. The structure of the N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid adduct has been solved by NMR in solution. The three x-ray structures and the solution structure are similar but not identical to one another, the differences being sizably higher in the loops. We propose that many of the loops show a dynamical behavior in solution on a variety of time scales. Different conformations of some flexible regions of the protein can be observed as "frozen" in different crystalline environments. The mobility in solution studied by NMR reveals conformational equilibria in accessible time scales, i.e., from 10(-5) s to ms and more. Averaging of some residual dipolar couplings is consistent with further motions down to 10(-9) s. Finally, local thermal motions of each frozen conformation in the crystalline state at 100 K correlate well with local motions on the picosecond time scale. Flexibility/conformational heterogeneity in crucial parts of the catalytic domain is a rule rather than an exception in matrix metalloproteinases, and its extent may be underestimated by inspection of one x-ray structure. Backbone flexibility may play a role in the difficulties encountered in the design of selective inhibitors, whereas it may be a requisite for substrate binding and broad substrate specificity.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center (Centro di Risonanze Magnetiche), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.
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Engel CK, Pirard B, Schimanski S, Kirsch R, Habermann J, Klingler O, Schlotte V, Weithmann KU, Wendt KU. Structural Basis for the Highly Selective Inhibition of MMP-13. ACTA ACUST UNITED AC 2005; 12:181-9. [PMID: 15734645 DOI: 10.1016/j.chembiol.2004.11.014] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2004] [Revised: 10/28/2004] [Accepted: 11/01/2004] [Indexed: 11/29/2022]
Abstract
Inhibitors for matrix metalloproteinases (MMPs) are under investigation for the treatment of cancer, arthritis, and cardiovascular disease. Here, we report a class of highly selective MMP-13 inhibitors (pyrimidine dicarboxamides) that exhibit no detectable activity against other MMPs. The high-resolution X-ray structures of three molecules of this series bound to MMP-13 reveal a novel binding mode characterized by the absence of interactions between the inhibitors and the catalytic zinc. The inhibitors bind in the S1' pocket and extend into an additional S1' side pocket, which is unique to MMP-13. We analyze the determinants for selectivity and describe the rational design of improved compounds with low nanomolar affinity.
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Affiliation(s)
- Christian K Engel
- Aventis Pharma Deutschland GmbH, A Company of the Sanofi-Aventis Group, Industrial Park Hoechst, D-65926 Frankfurt, Germany
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