1
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Ligorio C, Mata A. Synthetic extracellular matrices with function-encoding peptides. NATURE REVIEWS BIOENGINEERING 2023; 1:1-19. [PMID: 37359773 PMCID: PMC10127181 DOI: 10.1038/s44222-023-00055-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 03/16/2023] [Indexed: 06/28/2023]
Abstract
The communication of cells with their surroundings is mostly encoded in the epitopes of structural and signalling proteins present in the extracellular matrix (ECM). These peptide epitopes can be incorporated in biomaterials to serve as function-encoding molecules to modulate cell-cell and cell-ECM interactions. In this Review, we discuss natural and synthetic peptide epitopes as molecular tools to bioengineer bioactive hydrogel materials. We present a library of functional peptide sequences that selectively communicate with cells and the ECM to coordinate biological processes, including epitopes that directly signal to cells, that bind ECM components that subsequently signal to cells, and that regulate ECM turnover. We highlight how these epitopes can be incorporated in different biomaterials as individual or multiple signals, working synergistically or additively. This molecular toolbox can be applied in the design of biomaterials aimed at regulating or controlling cellular and tissue function, repair and regeneration.
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Affiliation(s)
- Cosimo Ligorio
- Biodiscovery Institute, University of Nottingham, Nottingham, UK
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham, UK
| | - Alvaro Mata
- Biodiscovery Institute, University of Nottingham, Nottingham, UK
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham, UK
- School of Pharmacy, University of Nottingham, Nottingham, UK
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2
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Chang M. Matrix metalloproteinase profiling and their roles in disease. RSC Adv 2023; 13:6304-6316. [PMID: 36825288 PMCID: PMC9942564 DOI: 10.1039/d2ra07005g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/24/2023] [Indexed: 02/25/2023] Open
Abstract
Matrix metalloproteinases (MMPs) play roles in remodelling of the extracellular matrix that occurs during morphogenesis, repair, and angiogenesis. Dysregulation of extracellular matrix remodelling can lead to cell proliferation, invasion, and tissue fibrosis. Identification of a specific MMP(s) in a disease has been challenging due to the presence of 24 closely-related human MMPs, each existing in three forms, of which only one is active and capable of catalysis. This review focuses on methods for MMP profiling, with particular emphasis on the batimastat affinity resin that binds only to the active forms of MMPs and related ADAMs (a disintegrin and metalloproteinases), which are then identified by mass spectrometry. Use of the batimastat affinity resin has identified targets for intervention in several human diseases.
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Affiliation(s)
- Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame Notre Dame IN 46556 USA
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3
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Martin‐Morales L, Manzano S, Rodrigo‐Faus M, Vicente‐Barrueco A, Lorca V, Núñez‐Moreno G, Bragado P, Porras A, Caldes T, Garre P, Gutierrez‐Uzquiza A. Germline gain-of-function MMP11 variant results in an aggressive form of colorectal cancer. Int J Cancer 2023; 152:283-297. [PMID: 36093604 PMCID: PMC9827992 DOI: 10.1002/ijc.34289] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 06/24/2022] [Accepted: 07/06/2022] [Indexed: 01/12/2023]
Abstract
Matrix metalloproteinase-11 (MMP11) is an enzyme with proteolytic activity against matrix and nonmatrix proteins. Although most MMPs are secreted as inactive proenzymes and are later activated extracellularly, MMP11 is activated intracellularly by furin within the constitutive secretory pathway. It is a key factor in physiological tissue remodeling and its alteration may play an important role in the progression of epithelial malignancies and other diseases. TCGA colon and colorectal adenocarcinoma data showed that upregulation of MMP11 expression correlates with tumorigenesis and malignancy. Here, we provide evidence that a germline variant in the MMP11 gene (NM_005940: c.232C>T; p.(Pro78Ser)), identified by whole exome sequencing, can increase the tumorigenic properties of colorectal cancer (CRC) cells. P78S is located in the prodomain region, which is responsible for blocking MMP11's protease activity. This variant was detected in the proband and all the cancer-affected family members analyzed, while it was not detected in healthy relatives. In silico analyses predict that P78S could have an impact on the activation of the enzyme. Furthermore, our in vitro analyses show that the expression of P78S in HCT116 cells increases tumor cell invasion and proliferation. In summary, our results show that this variant could modify the structure of the MMP11 prodomain, producing a premature or uncontrolled activation of the enzyme that may contribute to an early CRC onset in these patients. The study of this gene in other CRC cases will provide further information about its role in CRC development, which might improve patient treatment in the future.
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Affiliation(s)
- Lorena Martin‐Morales
- Molecular Oncology LaboratoryHospital Clínico San CarlosMadridSpain,Health Research Institute of the Hospital Clínico San Carlos (IdISSC)MadridSpain,Laboratory of Cancer Stemness, GIGA‐InstituteUniversity of LiegeLiegeBelgium
| | - Sara Manzano
- Health Research Institute of the Hospital Clínico San Carlos (IdISSC)MadridSpain,Department of Biochemistry and Molecular Biology, Facultad de FarmaciaUniversidad Complutense de MadridMadridSpain,Biodonostia Health Research InstituteSan Sebastian/DonostiaSpain
| | - Maria Rodrigo‐Faus
- Department of Biochemistry and Molecular Biology, Facultad de FarmaciaUniversidad Complutense de MadridMadridSpain
| | - Adrian Vicente‐Barrueco
- Department of Biochemistry and Molecular Biology, Facultad de FarmaciaUniversidad Complutense de MadridMadridSpain,Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Victor Lorca
- Molecular Oncology LaboratoryHospital Clínico San CarlosMadridSpain,Health Research Institute of the Hospital Clínico San Carlos (IdISSC)MadridSpain
| | - Gonzalo Núñez‐Moreno
- Department of Genetics, Health Research Institute‐Fundación Jiménez Díaz University HospitalUniversidad Autónoma de Madrid (IIS‐FJD, UAM)MadridSpain,Bioinformatics Unit, Health Research Institute‐Fundación Jiménez Díaz University HospitalUniversidad Autónoma de Madrid (IIS‐FJD, UAM)MadridSpain
| | - Paloma Bragado
- Health Research Institute of the Hospital Clínico San Carlos (IdISSC)MadridSpain,Department of Biochemistry and Molecular Biology, Facultad de FarmaciaUniversidad Complutense de MadridMadridSpain
| | - Almudena Porras
- Health Research Institute of the Hospital Clínico San Carlos (IdISSC)MadridSpain,Department of Biochemistry and Molecular Biology, Facultad de FarmaciaUniversidad Complutense de MadridMadridSpain
| | - Trinidad Caldes
- Molecular Oncology LaboratoryHospital Clínico San CarlosMadridSpain,Health Research Institute of the Hospital Clínico San Carlos (IdISSC)MadridSpain
| | - Pilar Garre
- Molecular Oncology LaboratoryHospital Clínico San CarlosMadridSpain,Health Research Institute of the Hospital Clínico San Carlos (IdISSC)MadridSpain,Clinical Analysis Service, Molecular Diagnostic UnitIML, Hospital Clínico San CarlosMadridSpain
| | - Alvaro Gutierrez‐Uzquiza
- Health Research Institute of the Hospital Clínico San Carlos (IdISSC)MadridSpain,Department of Biochemistry and Molecular Biology, Facultad de FarmaciaUniversidad Complutense de MadridMadridSpain
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4
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Xu H, Lien T, Bergholtz H, Fleischer T, Djerroudi L, Vincent-Salomon A, Sørlie T, Aittokallio T. Multi-Omics Marker Analysis Enables Early Prediction of Breast Tumor Progression. Front Genet 2021; 12:670749. [PMID: 34149812 PMCID: PMC8209521 DOI: 10.3389/fgene.2021.670749] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/26/2021] [Indexed: 12/13/2022] Open
Abstract
Ductal carcinoma in situ (DCIS) is a preinvasive form of breast cancer with a highly variable potential of becoming invasive and affecting mortality of the patients. Due to the lack of accurate markers of disease progression, many women with detected DCIS are currently overtreated. To distinguish those DCIS cases who are likely to require therapy from those who should be left untreated, there is a need for robust and predictive biomarkers extracted from molecular or genetic profiles. We developed a supervised machine learning approach that implements multi-omics feature selection and model regularization for the identification of biomarker combinations that could be used to distinguish low-risk DCIS lesions from those with a higher likelihood of progression. To investigate the genetic heterogeneity of disease progression, we applied this approach to 40 pure DCIS and 259 invasive breast cancer (IBC) samples profiled with genome-wide transcriptomics, DNA methylation, and DNA copy number variation. Feature selection using the multi-omics Lasso-regularized algorithm identified both known genes involved in breast cancer development, as well as novel markers for early detection. Even though the gene expression-based model features led to the highest classification accuracy alone, methylation data provided a complementary source of features and improved especially the sensitivity of correctly classifying DCIS cases. We also identified a number of repeatedly misclassified DCIS cases when using either the expression or methylation markers. A small panel of 10 gene markers was able to distinguish DCIS and IBC cases with high accuracy in nested cross-validation (AU-ROC = 0.99). The marker panel was not specific to any of the established breast cancer subtypes, suggesting that the 10-gene signature may provide a subtype-agnostic and cost-effective approach for breast cancer detection and patient stratification. We further confirmed high accuracy of the 10-gene signature in an external validation cohort (AU-ROC = 0.95), profiled using distinct transcriptomic assay, hence demonstrating robustness of the risk signature.
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Affiliation(s)
- Haifeng Xu
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo, Oslo, Norway
| | - Tonje Lien
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Helga Bergholtz
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Thomas Fleischer
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Lounes Djerroudi
- Institut Curie, Ensemble Hospitalier, Pôle de Médecine Diagnostique et Théranostique, Département de Pathologie, Paris, France
| | - Anne Vincent-Salomon
- Institut Curie, Ensemble Hospitalier, Pôle de Médecine Diagnostique et Théranostique, Département de Pathologie, Paris, France
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Tero Aittokallio
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo, Oslo, Norway.,Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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5
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Matchett EF, Wang S, Crawford BD. Paralogues of Mmp11 and Timp4 Interact during the Development of the Myotendinous Junction in the Zebrafish Embryo. J Dev Biol 2019; 7:jdb7040022. [PMID: 31816958 PMCID: PMC6955687 DOI: 10.3390/jdb7040022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 02/07/2023] Open
Abstract
The extracellular matrix (ECM) of the myotendinous junction (MTJ) undergoes dramatic physical and biochemical remodeling during the first 48 h of development in zebrafish, transforming from a rectangular fibronectin-dominated somite boundary to a chevron-shaped laminin-dominated MTJ. Matrix metalloproteinase 11 (Mmp11, a.k.a. Stromelysin-3) is both necessary and sufficient for the removal of fibronectin at the MTJ, but whether this protease acts directly on fibronectin and how its activity is regulated remain unknown. Using immunofluorescence, we show that both paralogues of Mmp11 accumulate at the MTJ during this time period, but with Mmp11a present early and later replaced by Mmp11b. Moreover, Mmp11a also accumulates intracellularly, associated with the Z-discs of sarcomeres within skeletal muscle cells. Using the epitope-mediated MMP activation (EMMA) assay, we show that despite having a weaker paired basic amino acid motif in its propeptide than Mmp11b, Mmp11a is activated by furin, but may also be activated by other mechanisms intracellularly. One or both paralogues of tissue inhibitors of metalloproteinase-4 (Timp4) are also present at the MTJ throughout this process, and yeast two-hybrid assays reveal distinct and specific interactions between various domains of these proteins. We propose a model in which Mmp11a activity is modulated (but not inhibited) by Timp4 during early MTJ remodeling, followed by a phase in which Mmp11b activity is both inhibited and spatially constrained by Timp4 in order to maintain the structural integrity of the mature MTJ.
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6
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Tokmina-Roszyk M, Fields GB. Dissecting MMP P 10' and P 11' subsite sequence preferences, utilizing a positional scanning, combinatorial triple-helical peptide library. J Biol Chem 2018; 293:16661-16676. [PMID: 30185620 DOI: 10.1074/jbc.ra118.003266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/01/2018] [Indexed: 11/06/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases that remodel the extracellular matrix environment and mitigate outside-in signaling. Loss of regulation of MMP activity plays a role in numerous pathological states. In particular, aberrant collagenolysis affects tumor invasion and metastasis, osteoarthritis, and cardiovascular and neurodegenerative diseases. To evaluate the collagen sequence preferences of MMPs, a positional scanning synthetic combinatorial library was synthesized herein and was used to investigate the P10' and P11' substrate subsites. The scaffold for the library was a triple-helical peptide mimic of the MMP cleavage site in types I-III collagen. A FRET-based enzyme activity assay was used to evaluate the sequence preferences of eight MMPs. Deconvolution of the library data revealed distinct motifs for several MMPs and discrimination among closely related MMPs. On the basis of the screening results, several individual peptides were designed and evaluated. A triple-helical substrate incorporating Asp-Lys in the P10'-P11' subsites offered selectivity between MMP-14 and MMP-15, whereas Asp-Lys or Trp-Lys in these subsites discriminated between MMP-2 and MMP-9. Future screening of additional subsite positions will enable the design of selective triple-helical MMP probes that could be used for monitoring in vivo enzyme activity and enzyme-facilitated drug delivery. Furthermore, selective substrates could serve as the basis for the design of specific triple-helical peptide inhibitors targeting only those MMPs that play a detrimental role in a disease of interest.
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Affiliation(s)
- Michal Tokmina-Roszyk
- From the Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458 and
| | - Gregg B Fields
- From the Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458 and .,the Department of Chemistry, The Scripps Research Institute/Scripps Florida, Jupiter, Florida 33458
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7
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Bhagwat SR, Hajela K, Kumar A. Proteolysis to Identify Protease Substrates: Cleave to Decipher. Proteomics 2018; 18:e1800011. [DOI: 10.1002/pmic.201800011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 04/03/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Sonali R. Bhagwat
- Discipline of Biosciences and Biomedical Engineering; Indian Institute of Technology; Indore 453552 Simrol India
| | - Krishnan Hajela
- School of Life Sciences; Devi Ahilya Vishwavidyalaya; Indore 452001 India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering; Indian Institute of Technology; Indore 453552 Simrol India
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8
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Determining the Substrate Specificity of Matrix Metalloproteases using Fluorogenic Peptide Substrates. Methods Mol Biol 2018. [PMID: 28299736 DOI: 10.1007/978-1-4939-6863-3_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
A continuous assay method, such as the one that utilizes an increase in fluorescence upon hydrolysis, allows for rapid and convenient kinetic evaluation of proteases. To better understand MMP behaviors toward native substrates, a variety of fluorescence resonance energy transfer (FRET)/intramolecular fluorescence energy transfer (IFET) triple-helical substrates have been constructed to examine the collagenolytic activity of MMP family members. Results of these studies have been valuable for providing insights into (a) the relative triple-helical peptidase activities of the various collagenolytic MMPs, (b) the collagen preferences of these MMPs, and (c) the relative roles of MMP domains and specific residues in efficient collagenolysis. The present chapter provides an overview of MMP FRET triple-helical substrates and describes how to construct and utilize these substrates.
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9
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Xiong J, Gao H. Matrix metalloproteases-responsive nanomaterials for tumor targeting diagnosis and treatment. J Microencapsul 2017; 34:440-453. [PMID: 28617063 DOI: 10.1080/02652048.2017.1343873] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jingyuan Xiong
- Research Center for Public Health and Preventive Medicine, West China School of Public Health, Sichuan University, Chengdu, China
| | - Huile Gao
- Key Laboratory of Drug Targeting and Drug Delivery Systems, West China School of Pharmacy, Sichuan University, Chengdu, China
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10
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Isaacson KJ, Martin Jensen M, Subrahmanyam NB, Ghandehari H. Matrix-metalloproteinases as targets for controlled delivery in cancer: An analysis of upregulation and expression. J Control Release 2017; 259:62-75. [PMID: 28153760 DOI: 10.1016/j.jconrel.2017.01.034] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/18/2017] [Accepted: 01/26/2017] [Indexed: 02/07/2023]
Abstract
While commonly known for degradation of the extracellular matrix, matrix metalloproteinases (MMPs) exhibit broad potential for use in targeting of bioactive and imaging agents in cancer treatment. MMPs are upregulated at all stages of expression in cancers. A comprehensive analysis of published literature on expression of all MMP subtypes at the genetic, protein, and activity levels in normal and diseased tissues indicate targeting applicability in a variety of cancers. This expression significantly increases at advanced cancer stages, providing an improved opportunity for controlled release in higher-stage patients. Since MMPs are integral at every stage of metastasis, MMP roles in cancer are discussed with a focus on MMP distribution and mobility within cells and tumors for cancer targeting applications. Several strategies for MMP utilization in targeting - such as matrix degradation, MMP cleavage, MMP binding, and MMP-induced environmental changes - are addressed.
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Affiliation(s)
- Kyle J Isaacson
- Department of Bioengineering, University of Utah, Salt Lake City, UT, USA; Utah Center for Nanomedicine, Nano Institute of Utah, University of Utah, Salt Lake City, UT, USA
| | - M Martin Jensen
- Department of Bioengineering, University of Utah, Salt Lake City, UT, USA; Utah Center for Nanomedicine, Nano Institute of Utah, University of Utah, Salt Lake City, UT, USA
| | - Nithya B Subrahmanyam
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT, USA; Utah Center for Nanomedicine, Nano Institute of Utah, University of Utah, Salt Lake City, UT, USA
| | - Hamidreza Ghandehari
- Department of Bioengineering, University of Utah, Salt Lake City, UT, USA; Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT, USA; Utah Center for Nanomedicine, Nano Institute of Utah, University of Utah, Salt Lake City, UT, USA.
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11
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Nguyen TTTN, Shynlova O, Lye SJ. Matrix Metalloproteinase Expression in the Rat Myometrium During Pregnancy, Term Labor, and Postpartum. Biol Reprod 2016; 95:24. [PMID: 27251092 PMCID: PMC5029434 DOI: 10.1095/biolreprod.115.138248] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/16/2016] [Indexed: 01/08/2023] Open
Abstract
Pregnancy, spontaneous term labor (TL), and postpartum (PP) involution are associated with changes in the cellular and extracellular matrix composition of the uterus. Both the uterine smooth muscle (myometrium) and the infiltrating peripheral blood leukocytes involved in the activation of labor secrete extracellular matrix-degrading enzymes (matrix metalloproteinases, MMPs) that can modulate cellular behavior and barrier function. MMP expression is induced by mechanical stretch in several tissues. We hypothesized that the expression and activity of myometrial MMPs and their tissue inhibitors (TIMPs) are modulated in preparation for TL and PP involution and are regulated by mechanical stretch of uterine walls imposed by the growing fetus. Myometrial tissues were collected from bilaterally and unilaterally pregnant rats across gestation, TL, and PP. Total RNA and proteins were subjected to real-time PCR and immunoblotting, respectively, and tissue localization and activity was examined by immunohistochemistry and in situ zymography. We found that Mmp7, Mmp11, and Mmp12 mRNA levels were upregulated during TL and PP, while Mmp2, Mmp3, Mmp8, Mmp9, Mmp10, and Mmp13 mRNAs were only upregulated during PP. Timp1–Timp4 were stably expressed throughout gestation with some fluctuations PP. Active MMP2 was induced in the empty uterine horn during gestation and in the gravid PP uterus, suggesting negative regulation by biological mechanical stretch. We conclude that specific subsets of uterine MMPs are differentially regulated in the rat myometrium in preparation for two major events: TL and PP uterine involution.
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Affiliation(s)
- Tina Tu-Thu Ngoc Nguyen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada Department of Physiology, University of Toronto, Canada
| | - Oksana Shynlova
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada Department of Obstetrics and Gynecology, University of Toronto, Canada
| | - Stephen J Lye
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada Department of Physiology, University of Toronto, Canada Department of Obstetrics and Gynecology, University of Toronto, Canada
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12
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WU DEYAO, LI MIN, WANG LINMAO, ZHOU YUNFENG, ZHOU JIAN, PAN HUIXING, QU PING. microRNA-145 inhibits cell proliferation, migration and invasion by targeting matrix metallopeptidase-11 in renal cell carcinoma. Mol Med Rep 2014; 10:393-8. [DOI: 10.3892/mmr.2014.2149] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 03/17/2014] [Indexed: 11/05/2022] Open
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13
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Bracher M, Bezuidenhout D, Lutolf MP, Franz T, Sun M, Zilla P, Davies NH. Cell specific ingrowth hydrogels. Biomaterials 2013; 34:6797-803. [PMID: 23777918 DOI: 10.1016/j.biomaterials.2013.05.057] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 05/24/2013] [Indexed: 01/24/2023]
Abstract
Extracellular mimetic hydrogels formed from peptide crosslinkers and polyethylene glycol monomers permit cell-controlled invasion. The use of matrix metalloproteinase specific peptides might further allow for selective control of different cell-type invasion. In this study, the invasion of fibroblasts and vascular smooth muscle cells (VSMC) into hydrogels polymerised with either a peptide generally permissive for matrix metalloproteinase (MMP) degradation or peptides preferentially cleaved by MMP-14 or MMP-9 enzymes were compared. The two cell-types invaded the MMP permissive hydrogel equally. However, invasion of VSMC into MMP-14 selective peptide crosslinked hydrogels was diametrically opposite in nature to that of fibroblasts whereby VSMC showed a two-fold increase into these hydrogels relative to that observed in permissive hydrogels whilst fibroblasts had a relative two-fold decrease (p < 0.01). These findings are suggestive that invasion and growth of different cell-types in engineered synthetic extracellular matrix mimics may be controlled selectively by the choice of protease specific peptide crosslinker and this could have general utility in tissue regenerative and engineering approaches.
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Affiliation(s)
- Mona Bracher
- Cardiovascular Research Unit, Chris Barnard Division of Cardiothoracic Surgery, University of Cape Town, Department of Health Sciences, Cape Town, South Africa
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14
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Skottrup PD, Sørensen G, Ksiazek M, Potempa J, Riise E. A phage display selected 7-mer peptide inhibitor of the Tannerella forsythia metalloprotease-like enzyme Karilysin can be truncated to Ser-Trp-Phe-Pro. PLoS One 2012; 7:e48537. [PMID: 23119051 PMCID: PMC3485312 DOI: 10.1371/journal.pone.0048537] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 09/26/2012] [Indexed: 01/19/2023] Open
Abstract
Tannerella forsythia is a gram-negative bacteria, which is strongly associated with the development of periodontal disease. Karilysin is a newly identified metalloprotease-like enzyme, that is secreted from T. forsythia. Karilysin modulates the host immune response and is therefore considered a likely drug target. In this study peptides were selected towards the catalytic domain from Karilysin (Kly18) by phage display. The peptides were linear with low micromolar binding affinities. The two best binders (peptide14 and peptide15), shared the consensus sequence XWFPXXXGGG. A peptide15 fusion with Maltose Binding protein (MBP) was produced with peptide15 fused to the N-terminus of MBP. The peptide15-MBP was expressed in E. coli and the purified fusion-protein was used to verify Kly18 specific binding. Chemically synthesised peptide15 (SWFPLRSGGG) could inhibit the enzymatic activity of both Kly18 and intact Karilysin (Kly48). Furthermore, peptide15 could slow down the autoprocessing of intact Kly48 to Kly18. The WFP motif was important for inhibition and a truncation study further demonstrated that the N-terminal serine was also essential for Kly18 inhibition. The SWFP peptide had a Ki value in the low micromolar range, which was similar to the intact peptide15. In conclusion SWFP is the first reported inhibitor of Karilysin and can be used as a valuable tool in structure-function studies of Karilysin.
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Affiliation(s)
- Peter Durand Skottrup
- Biomolecular Interaction Group, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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15
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Knapinska A, Fields GB. Chemical biology for understanding matrix metalloproteinase function. Chembiochem 2012; 13:2002-20. [PMID: 22933318 PMCID: PMC3951272 DOI: 10.1002/cbic.201200298] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Indexed: 12/20/2022]
Abstract
The matrix metalloproteinase (MMP) family has long been associated with normal physiological processes such as embryonic implantation, tissue remodeling, organ development, and wound healing, as well as multiple aspects of cancer initiation and progression, osteoarthritis, inflammatory and vascular diseases, and neurodegenerative diseases. The development of chemically designed MMP probes has advanced our understanding of the roles of MMPs in disease in addition to shedding considerable light on the mechanisms of MMP action. The first generation of protease-activated agents has demonstrated proof of principle as well as providing impetus for in vivo applications. One common problem has been a lack of agent stability at nontargeted tissues and organs due to activation by multiple proteases. The present review considers how chemical biology has impacted the progress made in understanding the roles of MMPs in disease and the basic mechanisms of MMP action.
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Affiliation(s)
| | - Gregg B. Fields
- Departments of Chemistry and Biology Torrey Pines Institute for Molecular Studies 11350 SW Village Parkway, Port St. Lucie, FL 34987 (USA)
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16
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Meyer BS, Rademann J. Extra- and intracellular imaging of human matrix metalloprotease 11 (hMMP-11) with a cell-penetrating FRET substrate. J Biol Chem 2012; 287:37857-67. [PMID: 22927434 DOI: 10.1074/jbc.m112.371500] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Matrix metalloprotease 11 (MMP-11), a protease associated with invasion and aggressiveness of cancerous tissue, was postulated as a prognostic marker for pancreatic, breast, and colon cancer patients. Expression analysis, however, did not reveal localization and regulation of this protease. Thus, cellular tools for the visualization of MMP-11 are highly desirable to monitor presence and activity and to elucidate the functional role of MMP-11. Therefore, fluorescein-Dabcyl-labeled Foerster resonance energy transfer (FRET) substrates were developed. The design focused on enhanced peptide binding to human MMP-11, employing an unusual amino acid for the specificity pocket P1'. The addition of several arginines resulted in a cell-permeable FRET substrate SM-P124 (Ac-GRRRK(Dabcyl)-GGAANC(MeOBn)RMGG-fluorescein). In vitro evaluation of SM-P124 with human MMP-11 showed a 25-fold increase of affinity (k(cat)/K(m) = 9.16 × 10(3) m(-1) s(-1), K(m) = 8 μm) compared with previously published substrates. Incubation of pancreatic adenocarcinoma cell line MIA PaCa-2 and mamma adenocarcinoma cell line MCF-7 with the substrate SM-P124 (5 μm) indicated intra- and extracellular MMP-11 activity. A negative control cell line (Jurkat) showed no fluorescent signal either intra- or extracellularly. Negative control FRET substrate SM-P123 produced only insignificant extracellular fluorescence without any intracellular fluorescence. SM-P124 therefore enabled intra- and extracellular tracking of MMP-11-overexpressing cancers such as pancreatic and breast adenocarcinoma and might contribute to the understanding of the activation pathways leading to MMP-11-mediated invasive processes.
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Affiliation(s)
- B Sina Meyer
- Department of Organic Chemistry, Freie Universität Berlin, Berlin 14195, Germany
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17
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Gallwitz M, Enoksson M, Thorpe M, Hellman L. The extended cleavage specificity of human thrombin. PLoS One 2012; 7:e31756. [PMID: 22384068 PMCID: PMC3288055 DOI: 10.1371/journal.pone.0031756] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 01/18/2012] [Indexed: 12/30/2022] Open
Abstract
Thrombin is one of the most extensively studied of all proteases. Its central role in the coagulation cascade as well as several other areas has been thoroughly documented. Despite this, its consensus cleavage site has never been determined in detail. Here we have determined its extended substrate recognition profile using phage-display technology. The consensus recognition sequence was identified as, P2-Pro, P1-Arg, P1'-Ser/Ala/Gly/Thr, P2'-not acidic and P3'-Arg. Our analysis also identifies an important role for a P3'-arginine in thrombin substrates lacking a P2-proline. In order to study kinetics of this cooperative or additive effect we developed a system for insertion of various pre-selected cleavable sequences in a linker region between two thioredoxin molecules. Using this system we show that mutations of P2-Pro and P3'-Arg lead to an approximate 20-fold and 14-fold reduction, respectively in the rate of cleavage. Mutating both Pro and Arg results in a drop in cleavage of 200-400 times, which highlights the importance of these two positions for maximal substrate cleavage. Interestingly, no natural substrates display the obtained consensus sequence but represent sequences that show only 1-30% of the optimal cleavage rate for thrombin. This clearly indicates that maximal cleavage, excluding the help of exosite interactions, is not always desired, which may instead cause problems with dysregulated coagulation. It is likely exosite cooperativity has a central role in determining the specificity and rate of cleavage of many of these in vivo substrates. Major effects on cleavage efficiency were also observed for residues as far away as 4 amino acids from the cleavage site. Insertion of an aspartic acid in position P4 resulted in a drop in cleavage by a factor of almost 20 times.
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Affiliation(s)
| | | | | | - Lars Hellman
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- * E-mail:
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18
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Selection and Finding of Lead Peptides Dual-targeting MMP14 and Metal Ions by Subtractive Cell Surface Panning and Molecular Docking. Int J Pept Res Ther 2011. [DOI: 10.1007/s10989-011-9276-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Kitahara H, Masumoto J, Parker AL, Maruta F, Kubo N, Shimizu A, Akita N, Miwa S, Kobayashi N, Nakayama J, Miyagawa S. COP35, a Cholangiocarcinoma-Binding Oligopeptide, Interacts with the Clathrin Heavy Chain Accompanied by GRP78. Mol Cancer Res 2011; 9:688-701. [DOI: 10.1158/1541-7786.mcr-10-0470] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Zhu L, Wang H, Wang L, Wang Y, Jiang K, Li C, Ma Q, Gao S, Wang L, Li W, Cai M, Wang H, Niu G, Lee S, Yang W, Fang X, Chen X. High-affinity peptide against MT1-MMP for in vivo tumor imaging. J Control Release 2011; 150:248-55. [PMID: 21295090 PMCID: PMC3085951 DOI: 10.1016/j.jconrel.2011.01.032] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 01/04/2011] [Accepted: 01/25/2011] [Indexed: 12/23/2022]
Abstract
Membrane type-1 matrix metalloproteinase (MT1-MMP) is a key member of the matrix metalloproteinase (MMP) family. It participates in pericellular proteolysis of extracellular matrix (ECM) macromolecules and is essential for many biological and pathological processes, such as tumor development, angiogenesis and metastasis. A ligand that specifically binds to MT1-MMP may facilitate the labeling of this molecule, allow imaging at the cellular and organism levels, and provide a means for targeted drug delivery specific to MT1-MMP. A non-substrate MT1-MMP binding peptide was identified by screening a Ph.D.-12™ phage display peptide library and conjugated with near-infrared fluorescent (NIRF) dye Cy5.5 for tumor imaging. Peptide HWKHLHNTKTFL (denoted as MT1-AF7p) showed high MT1-MMP binding affinity. Computer modeling verified that MT1-AF7p binds to the MT-loop region of MT1-MMP and interacts with MT1-MMP through hydrogen bonding and hydrophobic interactions. MDA-MB-435 xenografts with high MT1-MMP expression had significantly higher tumor accumulation and better tumor contrast than the low MT1-MMP expressing A549 xenografts after intravenous injection of Cy5.5-MT1-AF7p. Using NIRF imaging, we have demonstrated specific targeting of MT1-AF7p to MT1-MMP-expressing tumors. Thus, MT1-AF7p is an important tool for noninvasive monitoring of MT1-MMP expression in tumors, and it shows great potential as an imaging agent for MT1-MMP-positive tumors.
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Affiliation(s)
- Lei Zhu
- Key Laboratory of Molecular Enzymology and Enzyme Engineering of the Ministry of Education, Jilin University, Changchun 130023, P.R. China
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, P.R. China
| | - Huiling Wang
- Key Laboratory of Molecular Enzymology and Enzyme Engineering of the Ministry of Education, Jilin University, Changchun 130023, P.R. China
| | - Lin Wang
- Key Laboratory of Molecular Enzymology and Enzyme Engineering of the Ministry of Education, Jilin University, Changchun 130023, P.R. China
| | - Ye Wang
- Key Laboratory of Molecular Enzymology and Enzyme Engineering of the Ministry of Education, Jilin University, Changchun 130023, P.R. China
| | - Kun Jiang
- Key Laboratory of Molecular Enzymology and Enzyme Engineering of the Ministry of Education, Jilin University, Changchun 130023, P.R. China
| | - Cheng Li
- Key Laboratory of Molecular Enzymology and Enzyme Engineering of the Ministry of Education, Jilin University, Changchun 130023, P.R. China
| | - Qingjie Ma
- China-Japan Union Hospital, Jilin University, Changchun 130033, P.R. China
| | - Shi Gao
- China-Japan Union Hospital, Jilin University, Changchun 130033, P.R. China
| | - Liping Wang
- School of Life Science, Jilin University, Changchun 130021 P.R. China
| | - Wei Li
- School of Life Science, Jilin University, Changchun 130021 P.R. China
| | - Mingjun Cai
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - Gang Niu
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Seulki Lee
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Wei Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - Xuexun Fang
- Key Laboratory of Molecular Enzymology and Enzyme Engineering of the Ministry of Education, Jilin University, Changchun 130023, P.R. China
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
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21
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Mooney JT, Fredericks D, Hearn MTW. Use of phage display methods to identify heptapeptide sequences for use as affinity purification 'tags' with novel chelating ligands in immobilized metal ion affinity chromatography. J Chromatogr A 2010; 1218:92-9. [PMID: 21159343 DOI: 10.1016/j.chroma.2010.10.113] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 10/22/2010] [Accepted: 10/26/2010] [Indexed: 01/30/2023]
Abstract
This study describes the screening of a peptide phage display library for amino acid sequences that bind with different affinities to a novel class of chelating ligands complexed with Ni²+ ions. These chelating ligands are based on the 1,4,7-triazacyclononane (TACN) structure and have been chosen to allow enhanced efficiency in protein capture and decreased propensity for metal ion leakage in the immobilized metal ion affinity chromatographic (IMAC) purification of recombinant proteins. Utilising high stringency screening conditions, various peptide sequences containing multiple histidine, tryptophan, and/or tyrosine residues were identified amongst the different phage peptide sequences isolated. The structures, and particularly the conserved locations of these key amino acid residues within the selected heptapeptides, form a basis to design specific peptide tags for use with these novel TACN ligands as a new mode of IMAC purification of recombinant proteins.
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Affiliation(s)
- Jane T Mooney
- ARC Special Research Centre for Green Chemistry, Building75, Monash University, Clayton, Victoria 3800, Australia
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22
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Enhanced proteolytic degradation of molecularly engineered PEG hydrogels in response to MMP-1 and MMP-2. Biomaterials 2010; 31:7836-45. [PMID: 20667588 DOI: 10.1016/j.biomaterials.2010.06.061] [Citation(s) in RCA: 394] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 06/30/2010] [Indexed: 12/12/2022]
Abstract
Bioactive hydrogels formed by Michael-type addition reactions of end-functionalized poly(ethylene glycol) macromers with cysteine-containing peptides have been described as extracellular matrix mimetics and tissue engineering scaffolds. Although these materials have shown favorable behavior in vivo in tissue repair, we sought to develop materials formulations that would be more rapidly responsive to cell-induced enzymatic remodeling. In this study, protease-sensitive peptides that have increased k(cat) values were characterized and evaluated for their effects on gel degradability. Biochemical properties for soluble peptides and hydrogels were examined for matrix metalloproteinase (MMP)-1 and MMP-2. The most efficient peptide substrates in some cases overlap and in other cases differ between the two enzymes tested, and a range of k(cat) values was obtained. For each enzyme, hydrogels formed using the peptides with higher k(cat) values degraded faster than a reference with lower k(cat). Fibroblasts showed increased cell spreading and proliferation when cultured in 3D hydrogels with faster degrading peptides, and more cell invasion from aortic ring segments embedded in the hydrogels was observed. These faster degrading gels should provide matrices that are easier for cells to remodel and lead to increased cellular infiltration and potentially more robust healing in vivo.
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23
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Affiliation(s)
- Susan L Deutscher
- Biochemistry Department, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri 65211, USA.
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24
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Wyatt RA, Keow JY, Harris ND, Haché CA, Li DH, Crawford BD. The zebrafish embryo: a powerful model system for investigating matrix remodeling. Zebrafish 2010; 6:347-54. [PMID: 19929220 DOI: 10.1089/zeb.2009.0609] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Extracellular matrix (ECM) remodeling is a process that is crucial to the development of embryos, the growth and metastasis of tumors, and wound healing and homeostasis of tissues in adults. As such, it involves dozens of gene products that are regulated by mechanisms operating at transcriptional and multiple posttranslational levels. This complexity of regulation has made the development of a comprehensive understanding of the biology of ECM remodeling in vivo an unusually challenging task, yet such an understanding would be of profound value to our knowledge of and clinical approaches to the treatment of many cancers. The primary effectors of ECM remodeling are the matrix metalloproteinases (MMPs). Homologs of this gene family have been identified in every metazoan examined. We propose that the zebrafish embryo is an ideal system for the study of the regulation of MMP activity, and we present some progress we have made in the development of this organism as a platform for MMP research. We have identified 25 genes encoding MMPs in the zebrafish genome, and 5 genes encoding their endogenous inhibitors, the tissue inhibitors of MMPs. Based on a phylogenetic analysis, we have identified the most probable homologies of these sequences and found that there are two that are of equivocal identity. We have developed 17 antibodies specific to zebrafish MMPs and have begun characterizing the ontogeny of these molecules. Finally, we have developed two novel assays that allow the detection and characterization of active MMPs in vivo (differential in vivo zymography and activity-based protease profiling). In combination with the array of powerful biochemical, genomic, cell, and molecular biological techniques available to zebrafish researchers already, we feel that these new reagents and techniques make the zebrafish the best model system for the study of MMP regulation currently available.
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Affiliation(s)
- Rachael A Wyatt
- Department of Biology, University of New Brunswick, Fredericton, Canada
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25
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Abstract
A continuous assay method, such as the one that utilizes an increase in fluorescence upon hydrolysis, allows for rapid and convenient kinetic evaluation of proteases. To better understand MMP behaviors and to aid in the design of MMP inhibitors, a variety of sequence specificity, phage display, and combinatorial chemistry studies have been performed. Results of these studies have been valuable for defining the differences in MMPs and for creating quenched fluorescent substrates that utilize fluorescence resonance energy transfer (FRET)/intramolecular fluorescence energy transfer (IFET). FRET triple-helical substrates have been constructed to examine the collagenolytic activity of MMP family members. The present chapter provides an overview of MMP and related FRET substrates and describes how to construct and utilize these substrates.
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26
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Fiorentino M, Fu L, Shi YB. Mutational analysis of the cleavage of the cancer-associated laminin receptor by stromelysin-3 reveals the contribution of flanking sequences to site recognition and cleavage efficiency. Int J Mol Med 2009; 23:389-97. [PMID: 19212658 DOI: 10.3892/ijmm_00000143] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The matrix metalloproteinase stromelysin-3 (ST3) has long been implicated to play an important role in cell fate determination during normal and pathological processes. Using the thyroid hormone-dependent Xenopus laevis metamorphosis as a model, we have previously shown that ST3 is required for apoptosis during intestinal remodeling and that laminin receptor (LR) is an in vivo substrate of ST3 during this process. ST3 cleaves LR at two distinct sites that are conserved in mammalian LR. Human ST3 and LR are both associated with tumor development and cancer progression and human LR can also be cleaved by ST3, implicating a role of LR cleavage by ST3 in human cancers. Here, we carried out a series of mutational analyses on the two cleavage sites in LR. Our findings revealed that in addition to primary sequence at the cleavage site (positions P3-P3', with the cleavage occurring between P1-P1'), flanking sequences/conformation also influenced the cleavage of LR by ST3. Furthermore, alanine substitution studies led to a surprising finding that surrounding sequence and/or conformation dictated the site of cleavage in LR by ST3. These results thus have important implications in our understanding of substrate recognition and cleavage by ST3 and argue for the importance of studying ST3 cleavage in the context of full-length substrates. Furthermore, the LR cleavage mutants generated here will also be valuable tools for future studies on the role of LR cleavage by ST3 in vertebrate development and cancer progression.
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Affiliation(s)
- Maria Fiorentino
- Section on Molecular Morphogenesis, Laboratory of Gene Regulation and Development, PCRM, NICHD, NIH, Bethesda, MD 20892, USA
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27
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Nakai R, Salisbury CM, Rosen H, Cravatt BF. Ranking the selectivity of PubChem screening hits by activity-based protein profiling: MMP13 as a case study. Bioorg Med Chem 2009; 17:1101-8. [PMID: 18364257 PMCID: PMC2661618 DOI: 10.1016/j.bmc.2008.03.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Revised: 03/04/2008] [Accepted: 03/04/2008] [Indexed: 12/22/2022]
Abstract
High-throughput screening (HTS) has become an integral part of academic and industrial efforts aimed at developing new chemical probes and drugs. These screens typically generate several 'hits', or lead active compounds, that must be prioritized for follow-up medicinal chemistry studies. Among primary considerations for ranking lead compounds is selectivity for the intended target, especially among mechanistically related proteins. Here, we show how the chemical proteomic technology activity-based protein profiling (ABPP) can serve as a universal assay to rank HTS hits based on their selectivity across many members of an enzyme superfamily. As a case study, four metalloproteinase-13 (MMP13) inhibitors of similar potency originating from a publically supported HTS and reported in PubChem were tested by ABPP for selectivity against a panel of 27 diverse metalloproteases. The inhibitors could be readily separated into two groups: (1) those that were active against several metalloproteases and (2) those that showed high selectivity for MMP13. The latter set of inhibitors was thereby designated as more suitable for future medicinal chemistry optimization. We anticipate that ABPP will find general utility as a platform to rank the selectivity of lead compounds emerging from HTS assays for a wide variety of enzymes.
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Affiliation(s)
- Ryuichiro Nakai
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Cleo M. Salisbury
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hugh Rosen
- The Scripps Research Institute Molecular Screening Center, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Benjamin F. Cravatt
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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28
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Abstract
The interplay between a protease and its substrates is controlled at many different levels, including coexpression, colocalization, binding driven by ancillary contacts, and the presence of natural inhibitors. Here we focus on the most basic parameter that guides substrate recognition by a protease, the recognition specificity at the catalytic cleft. An understanding of this substrate specificity can be used to predict the putative substrates of a protease, to design protease activated imaging agents, and to initiate the design of active site inhibitors. Our group has characterized protease specificities of several matrix metalloproteinases using substrate phage display. Recently, we have adapted this method to a semiautomated platform that includes several high-throughput steps. The semiautomated platform allows one to obtain an order of magnitude more data, thus permitting precise comparisons among related proteases to define their functional distinctions.
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29
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Kubo N, Akita N, Shimizu A, Kitahara H, Parker AL, Miyagawa S. Identification of oligopeptide binding to colon cancer cells separated from patients using laser capture microdissection. J Drug Target 2008; 16:396-404. [PMID: 18569284 DOI: 10.1080/10611860802088796] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The development of intravascular conjugates that efficiently deliver genes or drugs to tumors is limited by the lack of efficacious targeting ligands. Small targeting peptides, such as those iterated by phage display technology, offer enormous potential for these applications. The majority of reports published to date have focused on the identification of peptides isolated for their ability to bind to human cancer cell lines in vitro, and have failed to account for the loss of polarization and de-differentiation of such cells from their in vivo state. Here, we report a novel approach for the identification of peptides capable of binding specifically to cancer cells derived from clinically resected human colon cancer. In this strategy, laser capture microdissection (LCM) is performed on a surgically resected colon cancer specimen to separate only cancer cells from the specimen. Subsequently, biopanning was performed on the LCM-selected colon cancer cells to identify peptide sequences that bound specifically to them. A peptide containing the SPT motif was selected as the most promising consensus sequence binding specifically to the LCM-selected colon cancer cells. Phage clones displaying the SPT motif demonstrated 9-fold higher binding to colon cancer cells derived from a patient than insertless phage (p < 0.05), while, recovery of the SPT phage from the colon cancer cell lines DLD-1 and HCT-15 was 7-fold higher than that of the control insertless phage (p < 0.05). The binding of SPT phage to colon cancer cells from the patient was confirmed by immunofluorescence. Additionally, a synthesized SPT-containing peptide (SPTKSNS) showed binding activity in the absence of mitogenic effects on colon cancer cells in vitro. In summary, we have introduced LCM into a biopanning procedure and identified a small peptide that binds preferentially to colon cancer cells derived from a clinically resected sample. This procedure could be applicable for the design of customized cancer cell targeting methodologies using clinical biopsy samples from human subjects.
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Affiliation(s)
- Naoki Kubo
- Department of Surgery, Shinshu University School of Medicine, Asahi, Matsumoto, Japan.
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30
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Abstract
Molecular imaging is at the forefront in the advancement of in-vivo diagnosis and monitoring of cancer. New peptide-based molecular probes to facilitate cancer detection are rapidly evolving. Peptide-based molecular probes that target apoptosis, angiogenesis, cell signaling and cell adhesion events are in place. Bacteriophage (phage) display technology, a molecular genetic approach to ligand discovery, is commonly employed to identify peptides as tumor-targeting molecules. The peptide itself may perhaps have functional properties that diminish tumor growth or metastasis. More often, a selected peptide is chemically synthesized, coupled to a radiotracer or fluorescent probe, and utilized in the development of new noninvasive molecular imaging probes. A myriad of peptides that bind cancer cells and cancer-associated antigens have been reported from phage library selections. Phage selections have also been performed in live animals to obtain peptides with optimal stability and targeting properties in vivo. To this point, few in-vitro, in-situ, or in-vivo selected peptides have shown success in the molecular imaging of cancer, the notable exception being vascular targeting peptides identified via in-vivo selections. The success of vasculature targeting peptides, such as those with an RGD motif that bind alpha(v)beta(3)integrin, may be due to the abundance and expression patterns of integrins in tumors and supporting vasculature. The discovery of molecular probes that bind tumor-specific antigens has lagged considerably. One promising means to expedite discovery is through the implementation of selected phage themselves as tumor-imaging agents in animals.
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Affiliation(s)
- Jessica Newton
- Department of Biochemistry, University of Missouri, M743 Medical Sciences Bldg., Columbia, MO 65212, USA
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31
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Matziari M, Dive V, Yiotakis A. Matrix metalloproteinase 11 (MMP-11; stromelysin-3) and synthetic inhibitors. Med Res Rev 2007; 27:528-52. [PMID: 16710861 DOI: 10.1002/med.20066] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Matrix metalloproteinase (MMP)-11, or Stromelysin 3, is a particular member of MMP family, a group of zinc-dependent endopeptidases involved in matrix degradation and tissue remodeling. Despite intense efforts since its first characterization 15 years ago, its role and target substrates in different diseases remain largely unknown. While mice with MMP-11 deficiency display no particular phenotype, analysis of different tumorigenesis models with these mice lead to the conclusion that MMP-11 promotes tumor development. In contrast with other MMPs, MMP-11 is unable to degrade any major extracellular matrix component and unlike most of other MMPs that are secreted as inactive proenzymes and activated extracellularly, MMP-11 is secreted under active form. MMP-11 may thus play a unique role in tissue remodeling processes, including those associated with tumor progression. Although MMP-11 and other MMPs have been considered as promising targets to combat cancer, a first series of clinical trials using broad-spectrum MMP inhibitors have not led to significant therapeutic benefits. These disappointing results highlight the need for better understanding of the exact role played by each MMP during the different stages of tumor progression. Among the different strategies to fill this gap, highly specific MMP inhibitors would be of great value. This review provides an update on the selectivity profile of phosphinic MMP-11 synthetic inhibitors developed and discusses the opportunities and limitations to identify inhibitors able to fully discriminate MMP-11 from the other MMPs.
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Affiliation(s)
- Magdalini Matziari
- Department of Chemistry, Laboratory of Organic Chemistry, University of Athens, Panepistimiopolis Zografou 15771, Athens, Greece
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32
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Bachert C, Fimmel C, Linstedt AD. Endosomal trafficking and proprotein convertase cleavage of cis Golgi protein GP73 produces marker for hepatocellular carcinoma. Traffic 2007; 8:1415-23. [PMID: 17662025 DOI: 10.1111/j.1600-0854.2007.00621.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Serum GP73 levels are significantly increased in patients with hepatocellular carcinoma (HCC), potentially providing a marker for early detection. However, GP73 is an integral membrane protein localized to the cis Golgi and is not known to be secreted. Based on its presence in sera, we sought to determine whether GP73 might normally be released from cells and to elucidate the mechanism of this release. Indeed, a soluble form of GP73 was released from cultured cells and compared with the Golgi-localized full-length protein, the molecular weight was slightly reduced, suggesting that cleavage releases the GP73 ectodomain. Sequence analysis revealed a proprotein convertase (PC) consensus site, and, indeed, the ubiquitous PC furin was capable of cleaving purified GP73. Further, alanine substitutions in the PC site blocked both the in vitro and the in vivo cleavage of GP73. Using a cleavage-specific antibody, cleaved GP73 was found in the trans Golgi network and endosomes, suggesting that GP73 cleavage occurs as GP73 cycles distal to the early Golgi. We conclude that the endosomal trafficking of GP73 allows for PC-mediated cleavage, resulting in GP73 secretion, and provides a molecular mechanism for its presence as a serum biomarker for HCC.
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Affiliation(s)
- Collin Bachert
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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33
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Minond D, Lauer-Fields JL, Cudic M, Overall CM, Pei D, Brew K, Moss ML, Fields GB. Differentiation of secreted and membrane-type matrix metalloproteinase activities based on substitutions and interruptions of triple-helical sequences. Biochemistry 2007; 46:3724-33. [PMID: 17338550 PMCID: PMC2569894 DOI: 10.1021/bi062199j] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The turnover of the collagen triple-helical structure (collagenolysis) is a tightly regulated process in normal physiology and has been ascribed to a small number of proteases. Several members of the matrix metalloproteinase (MMPs) family possess collagenolytic activity, and the mechanisms by which these enzymes process triple helices are beginning to be unraveled. The present study has utilized two triple-helical sequences to compare the cleavage-site specificities of 10 MMPs. One substrate featured a continuous Gly-Xxx-Yyy sequence (Pro-Leu-Gly approximately Met-Arg-Gly), while the other incorporated an interruption in the Gly-Xxx-Yyy repeat (Pro-Val-Asn approximately Phe-Arg-Gly). Both sequences were selectively cleaved by MMP-13 while in linear form, but neither proved to be selective within a triple helix. This suggests that the conformational presentation of substrate sequences to a MMP active site is critical for enzyme specificity, in that activities differ when sequences are presented from an unwound triple helix versus an independent single strand. Differences in specificity between secreted and membrane-type (MT) MMPs were also observed for both sequences, where MMP-2 and MT-MMPs showed an ability to hydrolyze a triple helix at an additional site (Gly-Gln bond). Interruption of the triple helix had different effects on secreted MMPs and MT-MMPs, because MT-MMPs could not hydrolyze the Asn-Phe bond but instead cleaved the triple helix closer to the C terminus at a Gly-Gln bond. It is possible that MT-MMPs have a requirement for Gly in the P1 subsite to be able to efficiently process a triple-helical molecule. Analysis of individual kinetic parameters and activation energies indicated different substrate preferences within secreted MMPs, because MMP-13 preferred the interrupted sequence, while MMP-8 showed little discrimination between non-interrupted and interrupted triple helices. On the basis of the present and prior studies, we can assign unique triple-helical peptidase behaviors to the collagenolytic MMPs. Such differences may be significant for understanding MMP mechanisms of action and aid in the development of selective MMP inhibitors.
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Affiliation(s)
- Dmitriy Minond
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991
| | - Janelle L. Lauer-Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991
| | - Mare Cudic
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991
| | - Christopher M. Overall
- University of British Columbia Centre for Blood Research and the Canadian Institutes for Health Research Group in Matrix Dynamics and the Departments of Biochemistry and Molecular Biology, Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Duanqing Pei
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Keith Brew
- College of Biomedical Sciences, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991
| | - Marcia L. Moss
- BioZyme, Inc., 1513 Old White Oak Church Road, Apex, NC 27523-9299
| | - Gregg B. Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991
- Correspondence should be addressed to this author at the Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, Florida 33431-0991. Tel: 561-297-2093; Fax: 561-297-2759; E-mail:
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34
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Hills R, Mazzarella R, Fok K, Liu M, Nemirovskiy O, Leone J, Zack MD, Arner EC, Viswanathan M, Abujoub A, Muruganandam A, Sexton DJ, Bassill GJ, Sato AK, Malfait AM, Tortorella MD. Identification of an ADAMTS-4 cleavage motif using phage display leads to the development of fluorogenic peptide substrates and reveals matrilin-3 as a novel substrate. J Biol Chem 2007; 282:11101-9. [PMID: 17311924 DOI: 10.1074/jbc.m611588200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ADAMTS-4 and ADAMTS-5 are aggrecanases responsible for the breakdown of cartilage aggrecan in osteoarthritis. Multiple ADAMTS-4 cleavage sites have been described in several matrix proteins including aggrecan, versican, and brevican, but no concise predictive cleavage motif has been identified for this protease. By screening a 13-mer peptide library with a diversity of 10(8), we have identified the ADAMTS-4 cleavage motif E-(AFVLMY)-X(0,1)-(RK)-X(2,3)-(ST)-(VYIFWMLA), with Glu representing P1. Several 13-mer peptides containing this motif, including DVQEFRGVTAVIR and HNEFRQRETYMVF, were shown to be substrates for ADAMTS-4. These peptides were found to be specific substrates for ADAMTS-4 as they were not cleaved by ADAMTS-5. Modification of these peptides with donor (6-FAM) and acceptor (QSY-9) molecules resulted in the development of fluorescence-based substrates with a Km of approximately 35 microM. Furthermore, the role of Glu at P1 and Phe at P1' in binding and catalysis was studied by exploring substitution of these amino acids with the D-isomeric forms. Substitution of P1 with dGlu was tolerable for binding, but not catalysis, whereas substitution of P1' with dPhe precluded both binding and catalysis. Similarly, replacement of Glu with Asp at P1 abolished recognition and cleavage of the peptide. Finally, BLAST results of the ADAMTS-4 cleavage motif identified matrilin-3 as a new substrate for ADAMTS-4. When tested, recombinant ADAMTS-4 effectively cleaved intact matrilin-3 at the predicted motif at Glu435/Ala436 generating two species of 45 and 5 kDa.
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Affiliation(s)
- Robert Hills
- Pfizer Global Research and Development, St. Louis, Missouri 63017, USA.
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35
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Lauer-Fields JL, Minond D, Sritharan T, Kashiwagi M, Nagase H, Fields GB. Substrate Conformation Modulates Aggrecanase (ADAMTS-4) Affinity and Sequence Specificity. J Biol Chem 2007; 282:142-50. [PMID: 17095512 DOI: 10.1074/jbc.m605236200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protease-substrate interactions are governed by a variety of structural features. Although the substrate sequence specificities of numerous proteases have been established, "topological specificities," whereby proteases may be classified based on recognition of distinct three-dimensional structural motifs, have not. The aggrecanase members of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) family cleave a variety of proteins but do not seem to possess distinct sequence specificities. In the present study, the topological substrate specificity of ADAMTS-4 (aggrecanase-1) was examined using triple-helical or single-stranded poly(Pro) II helical peptides. Substrate topology modulated the affinity and sequence specificity of ADAMTS-4 with K(m) values indicating a preference for triple-helical structure. In turn, non-catalytic ADAMTS-4 domains were critical for hydrolysis of triple-helical and poly(Pro) II helical substrates. Comparison of ADAMTS-4 with MMP-1 (collagenase 1), MMP-13 (collagenase 3), trypsin, and thermolysin using triple-helical peptide (THP) and single-stranded peptide (SSP) substrates demonstrated that all five proteases possessed efficient "triple-helical peptidase" activity and fell into one of two categories: (k(cat)/K(m))(SSP) > (k(cat)/K(m))(THP) (thermolysin, trypsin, and MMP-13) or (k(cat)/K(m))(THP) > or = (k(cat)/K(m))(SSP) and (K(m))(SSP) > (K(m))(THP) (MMP-1 and ADAMTS-4). Overall these results suggest that topological specificity may be a guiding principle for protease behavior and can be utilized to design specific substrates and inhibitors. The triple-helical and single-stranded poly(Pro) II helical peptides represent the first synthetic substrates successfully designed for aggrecanases.
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Affiliation(s)
- Janelle L Lauer-Fields
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431-0991, USA
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36
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Aggarwal S, Singh P, Topaloglu O, Isaacs JT, Denmeade SR. A Dimeric Peptide That Binds Selectively to Prostate-Specific Membrane Antigen and Inhibits its Enzymatic Activity. Cancer Res 2006; 66:9171-7. [PMID: 16982760 DOI: 10.1158/0008-5472.can-06-1520] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Prostate-specific membrane antigen (PSMA) is highly expressed by both normal and malignant prostate epithelial cells and by the neovasculature of many tumor types; however, it is not expressed by normal endothelial cells or other normal tissues. PSMA, therefore, represents an attractive candidate for selectively targeted therapies for prostate and/or other solid tumors. As an alternative approach to antibody-based anti-PSMA therapies, small peptides that bind selectively to PSMA-producing cells can be used to deliver cytotoxic drugs, protein toxins, and viruses selectively to malignant sites while minimizing systemic toxicity to normal tissues. Small peptides are relatively inexpensive to produce, not immunogenic, and easily coupled to cytotoxic agents. In the present study, a random phage library consisting of linear 12 amino acid peptides was used to identify peptides that bound selectively to PSMA. From a series of monomeric peptides, one with the sequence WQPDTAHHWATL was used to show binding of soluble peptide to PSMA. A dimeric version of this peptide showed markedly enhanced binding to soluble PSMA and an IC50 of 2.2 micromol/L for inhibition of PSMA enzymatic activity. Fluorescently labeled dimeric peptide bound selectively to PSMA-producing prostate cancer cells in vitro with no significant binding to non-PSMA-producing cells. Molecular modeling of the dimeric peptide revealed that histidine residues in close vicinity can efficiently coordinate a divalent ion and hold the peptide in a favorable configuration for binding and subsequent inhibition. These dimeric peptides, therefore, represent putative PSMA-selective targeting agents that are currently being evaluated for selective binding in vivo.
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Affiliation(s)
- Saurabh Aggarwal
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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37
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Scholle MD, Kriplani U, Pabon A, Sishtla K, Glucksman MJ, Kay BK. Mapping protease substrates by using a biotinylated phage substrate library. Chembiochem 2006; 7:834-8. [PMID: 16628754 DOI: 10.1002/cbic.200500427] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe a bacteriophage M13 substrate library encoding the AviTag (BirA substrate) and combinatorial heptamer peptides displayed at the N terminus of the mature form of capsid protein III. Phages are biotinylated efficiently (> or = 50%) when grown in E. coli cells coexpressing BirA, and such viral particles can be immobilized on a streptavidin-coated support and released by protease cleavage within the combinatorial peptide. We have used this library to map the specificity of human Factor Xa and a neuropeptidase, neurolysin (EC3.4.24.16). Validation by analysis of isolated peptide substrates has revealed that neurolysin recognizes the motif hydrophobic-X-Pro-Arg-hydrophobic, where Arg-hydrophobic is the scissile bond.
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Affiliation(s)
- Michael D Scholle
- Combinatorial Biology Unit, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
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38
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Chaparro-Riggers JF, Breves R, Maurer KH, Bornscheuer U. Modulation of Infectivity in Phage Display as a Tool to Determine the Substrate Specificity of Proteases. Chembiochem 2006; 7:965-70. [PMID: 16642518 DOI: 10.1002/cbic.200600051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Proteases play an important role in human and animal diseases. Rapid determination of substrate specificity is possible through the use of substrate phage display; however, current methods possess several drawbacks. They require phage-immobilization and cannot be used for infectivity-destroying or affinity tag-destroying proteases; this can make entire libraries useless. To overcome these limitations, here we introduce infectivity-modulated phage display (IMOP). IMOP uses a protease-resistant and infectivity-reducing tag fused to substrate-displaying polyvalent phages, and the specific cleavage of the substrate increases the infectivity of the phages by releasing the infectivity-reducing tag. The resulting phages were first tested with the infectivity-destroying detergent protease subtilisin; this resulted in a highly specific substrate at a 200-fold enrichment. In a second example, the protease ompT was used and led to an enrichment of the known double-arginine motif. The IMOP system thus substantially improves and simplifies previous systems.
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Affiliation(s)
- Javier F Chaparro-Riggers
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, Greifswald University, Soldmannstrasse 16, 17487 Greifswald, Germany
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39
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Sugimura Y, Hosono M, Wada F, Yoshimura T, Maki M, Hitomi K. Screening for the preferred substrate sequence of transglutaminase using a phage-displayed peptide library: identification of peptide substrates for TGASE 2 and Factor XIIIA. J Biol Chem 2006; 281:17699-706. [PMID: 16636049 DOI: 10.1074/jbc.m513538200] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian transglutaminase (TGase) catalyzes covalent cross-linking of peptide-bound lysine residues or incorporation of primary amines to limited glutamine residues in substrate proteins. Using an unbiased M13 phage display random peptide library, we developed a screening system to elucidate primary structures surrounding reactive glutamine residue(s) that are preferred by TGase. Screening was performed by selecting phage clones expressing peptides that incorporated biotin-labeled primary amine by the catalytic reactions of TGase 2 and activated Factor XIII (Factor XIIIa). We identified several amino acid sequences that were preferred as glutamine donor substrates, most of which have a marked tendency for individual TGases: TGase 2, QxPphiD(P), QxPphi, and QxxphiDP; Factor XIIIa, QxxphixWP (where x and phi represent a non-conserved and a hydrophobic amino acid, respectively). We further confirmed that the sequences were favored for transamidation using modified glutathione S-transferase (GST) for recombinant peptide-GST fusion proteins. Most of the fusion proteins exhibited a considerable increase in incorporation of primary amines over that of modified GST alone. Furthermore, we identified the amino acid sequences that demonstrated higher specificity and inhibitory activity in the cross-linking reactions by TGase 2 and Factor XIIIa.
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Affiliation(s)
- Yoshiaki Sugimura
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
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40
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Affiliation(s)
- John W Kehoe
- Biosciences Division, Argonne National Laboratory, Building 202, Argonne, Illinois 60439, USA
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41
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Amano T, Kwak O, Fu L, Marshak A, Shi YB. The matrix metalloproteinase stromelysin-3 cleaves laminin receptor at two distinct sites between the transmembrane domain and laminin binding sequence within the extracellular domain. Cell Res 2005; 15:150-9. [PMID: 15780176 DOI: 10.1038/sj.cr.7290280] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The matrix metalloproteinase (MMP) stromelysin-3 (ST3) has long been implicated to play an important role in extracellular matrix (ECM) remodeling and cell fate determination during normal and pathological processes. However, like other MMPs, the molecular basis of ST3 function in vivo remains unclear due to the lack of information on its physiological substrates. Furthermore, ST3 has only weak activities toward all tested ECM proteins. Using thyroid hormone-dependent Xenopus laevis metamorphosis as a model, we demonstrated previously that ST3 is important for apoptosis and tissue morphogenesis during intestinal remodeling. Here, we used yeast two-hybrid screen with mRNAs from metamorphosing tadpoles to identify potential substrate of ST3 during development. We thus isolated the 37 kd laminin receptor precursor (LR). We showed that LR binds to ST3 in vitro and can be cleaved by ST3 at two sites, distinct from where other MMPs cleave. Through peptide sequencing, we determined that the two cleavage sites are in the extracellular domain between the transmembrane domain and laminin binding sequence. Furthermore, we demonstrated that these cleavage sites are conserved in human LR. These results together with high levels of human LR and ST3 expression in carcinomas suggest that LR is a likely in vivo substrate of ST3 and that its cleavage by ST3 may alter cell-extracellular matrix interaction, thus, playing a role in mediating the effects of ST3 on cell fate and behavior observed during development and pathogenesis.
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Affiliation(s)
- Tosikazu Amano
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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42
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Uchiyama F, Tanaka Y, Minari Y, Tokui N. Designing scaffolds of peptides for phage display libraries. J Biosci Bioeng 2005; 99:448-56. [PMID: 16233816 DOI: 10.1263/jbb.99.448] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Accepted: 03/02/2005] [Indexed: 11/17/2022]
Abstract
Phage display is a powerful method for the discovery of peptide ligands that are used for analytical tools, drug discovery, and target validations. Phage display technology can produce a huge number of peptides and generate novel peptide ligands. Recently, phage display technology has successfully managed to create peptide ligands that bind to pharmaceutically difficult targets such as the erythropoietin receptor. As a result of the structural analysis of their ligands, we found that the conformational design of peptides in library is important for selecting high-affinity ligands that bind to every target from a phage peptide library. Key issues concern constraints on the conformation of peptides on the phage and the development of chemically synthesized peptides derived from peptides on phage. This review discusses studies related to the conformation of peptides selected from phage display peptide libraries in addition to the conversion from peptides to non-peptides.
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Affiliation(s)
- Fumiaki Uchiyama
- Department of Nutritional Sciences, Graduate School of Nutritional Sciences, Nakamura Gakuen University, 5-7-1 Befu, Jounan-Ku, Fukuoka 814-0198, Japan.
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43
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Abstract
New ligands for a variety of biological targets can be selected from biological or synthetic combinatorial peptide libraries. The use of different libraries to select novel peptides with potential therapeutic applications is reviewed. The possible combination of molecular diversity provided by combinatorial libraries and a rational approach derived from computational modeling is also considered. Advantages and disadvantages of different approaches are compared. Possible strategies to bypass loss of peptide bioactivity in the transition from ligand selection to in vivo use are discussed.
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Affiliation(s)
- Chiara Falciani
- Department of Molecular Biology, University of Siena, I-53100 Siena, Italy
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44
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Albright CF, Graciani N, Han W, Yue E, Stein R, Lai Z, Diamond M, Dowling R, Grimminger L, Zhang SY, Behrens D, Musselman A, Bruckner R, Zhang M, Jiang X, Hu D, Higley A, Dimeo S, Rafalski M, Mandlekar S, Car B, Yeleswaram S, Stern A, Copeland RA, Combs A, Seitz SP, Trainor GL, Taub R, Huang P, Oliff A. Matrix metalloproteinase-activated doxorubicin prodrugs inhibit HT1080 xenograft growth better than doxorubicin with less toxicity. Mol Cancer Ther 2005; 4:751-60. [PMID: 15897239 DOI: 10.1158/1535-7163.mct-05-0006] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Matrix metalloproteinase (MMP)-activated prodrugs were formed by coupling MMP-cleavable peptides to doxorubicin. The resulting conjugates were excellent in vitro substrates for MMP-2, -9, and -14. HT1080, a fibrosarcoma cell line, was used as a model system to test these prodrugs because these cells, like tumor stromal fibroblasts, expressed several MMPs. In cultured HT1080 cells, simple MMP-cleavable peptides were primarily metabolized by neprilysin, a membrane-bound metalloproteinase. MMP-selective metabolism in cultured HT1080 cells was obtained by designing conjugates that were good MMP substrates but poor neprilysin substrates. To determine how conjugates were metabolized in animals, MMP-selective conjugates were given to mice with HT1080 xenografts and the distribution of doxorubicin was determined. These studies showed that MMP-selective conjugates were preferentially metabolized in HT1080 xenografts, relative to heart and plasma, leading to 10-fold increases in the tumor/heart ratio of doxorubicin. The doxorubicin deposited by a MMP-selective prodrug, compound 6, was more effective than doxorubicin at reducing HT1080 xenograft growth. In particular, compound 6 cured 8 of 10 mice with HT1080 xenografts at doses below the maximum tolerated dose, whereas doxorubicin cured 2 of 20 mice at its maximum tolerated dose. Compound 6 was less toxic than doxorubicin at this efficacious dose because mice treated with compound 6 had no detectable changes in body weight or reticulocytes, a marker for marrow toxicity. Hence, MMP-activated doxorubicin prodrugs have a much higher therapeutic index than doxorubicin using HT1080 xenografts as a preclinical model.
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Affiliation(s)
- Charles F Albright
- Bristol-Myers Squibb Pharmaceutical Research Institute, 5 Research Parkway, Wallingford, CT 06492, USA.
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45
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Abstract
To establish efficient and reliable therapeutic delivery into cancer cells, a number of delivery agents and concepts have been investigated in the recent years. Among many improvements in targeted and controlled delivery of therapeutics, cell-targeting peptides have emerged as the most valuable non-immunogenic approach to target cancer cells. Peptides can be incorporated into multicomponent gene-delivery complexes for cell-specific targeting. In contrast to larger molecules such as monoclonal antibodies, peptides have an excellent tumor penetration, which make them ideal carriers of therapeutics to the site of primary tumor and the distant metastatic sites. Here we give an update on the progress made during the last two years on the identification and potential of specific synthetic tumor targeting peptides.
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Affiliation(s)
- Mohsen Shadidi
- Department of Immunology, Molecular Medicine Group, The Norwegian Radium Hospital, Institute for Cancer Research, Montebello, N0310 Oslo, Norway
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46
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Abstract
A continuous assay method, such as one that utilizes an increase in fluorescence upon hydrolysis, allows for rapid and convenient kinetic evaluation of proteases. To better understand MMP behaviors and to aid in the design of MMP inhibitors, a variety of sequence specificity, phage display, and combinatorial chemistry studies have been performed. Results of these studies have been valuable for defining the differences in MMPs and for creating quenched fluorescent substrates that utilize fluorescence resonance energy transfer (FRET)/intramolecular fluorescence energy transfer (IFET). FRET triple-helical substrates have been constructed to examine the collagenolytic activity of MMP family members. The present chapter provides an overview of MMP and related FRET substrates and describes how to construct and utilize these substrates.
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Affiliation(s)
- Gregg B. Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431 U.S.A. Phone 561-297-2093, Fax 561-297-2759
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