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Wang M, Alabi A, Gu HM, Gill G, Zhang Z, Jarad S, Xia XD, Shen Y, Wang GQ, Zhang DW. Identification of amino acid residues in the MT-loop of MT1-MMP critical for its ability to cleave low-density lipoprotein receptor. Front Cardiovasc Med 2022; 9:917238. [PMID: 36093157 PMCID: PMC9452735 DOI: 10.3389/fcvm.2022.917238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Low-density lipoprotein receptor (LDLR) mediates clearance of plasma LDL cholesterol, preventing the development of atherosclerosis. We previously demonstrated that membrane type 1-matrix metalloproteinase (MT1-MMP) cleaves LDLR and exacerbates the development of atherosclerosis. Here, we investigated determinants in LDLR and MT1-MMP that were critical for MT1-MMP-induced LDLR cleavage. We observed that deletion of various functional domains in LDLR or removal of each of the five predicted cleavage sites of MT1-MMP on LDLR did not affect MT1-MMP-induced cleavage of the receptor. Removal of the hemopexin domain or the C-terminal cytoplasmic tail of MT1-MMP also did not impair its ability to cleave LDLR. On the other hand, mutant MT1-MMP, in which the catalytic domain or the MT-loop was deleted, could not cleave LDLR. Further Ala-scanning analysis revealed an important role for Ile at position 167 of the MT-loop in MT1-MMP’s action on LDLR. Replacement of Ile167 with Ala, Thr, Glu, or Lys resulted in a marked loss of the ability to cleave LDLR, whereas mutation of Ile167 to a non-polar amino acid residue, including Leu, Val, Met, and Phe, had no effect. Therefore, our studies indicate that MT1-MMP does not require a specific cleavage site on LDLR. In contrast, an amino acid residue with a hydrophobic side chain at position 167 in the MT-loop is critical for MT1-MMP-induced LDLR cleavage.
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Affiliation(s)
- Maggie Wang
- The Department of Pediatrics and Group on the Molecular Cell Biology of Lipids, Faculty of Medicine Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
| | - Adekunle Alabi
- The Department of Pediatrics and Group on the Molecular Cell Biology of Lipids, Faculty of Medicine Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
| | - Hong-mei Gu
- The Department of Pediatrics and Group on the Molecular Cell Biology of Lipids, Faculty of Medicine Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
| | - Govind Gill
- The Department of Pediatrics and Group on the Molecular Cell Biology of Lipids, Faculty of Medicine Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
| | - Ziyang Zhang
- The Department of Pediatrics and Group on the Molecular Cell Biology of Lipids, Faculty of Medicine Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
| | - Suha Jarad
- The Department of Pediatrics and Group on the Molecular Cell Biology of Lipids, Faculty of Medicine Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
| | - Xiao-dan Xia
- The Department of Pediatrics and Group on the Molecular Cell Biology of Lipids, Faculty of Medicine Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Orthopedics, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, China
| | - Yishi Shen
- The Department of Pediatrics and Group on the Molecular Cell Biology of Lipids, Faculty of Medicine Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
| | - Gui-qing Wang
- Department of Orthopedics, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, China
| | - Da-wei Zhang
- The Department of Pediatrics and Group on the Molecular Cell Biology of Lipids, Faculty of Medicine Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Da-wei Zhang,
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Peeney D, Liu Y, Lazaroff C, Gurung S, Stetler-Stevenson WG. OUP accepted manuscript. Carcinogenesis 2022; 43:405-418. [PMID: 35436325 PMCID: PMC9167030 DOI: 10.1093/carcin/bgac037] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/23/2022] [Accepted: 04/15/2022] [Indexed: 11/12/2022] Open
Abstract
Tissue inhibitors of metalloproteinases (TIMPs) are a conserved family of proteins that were originally identified as endogenous inhibitors of matrixin and adamalysin endopeptidase activity. The matrixins and adamalysins are the major mediators of extracellular matrix (ECM) turnover, thus making TIMPs important regulators of ECM structure and composition. Despite their high sequence identity and relative redundancy in inhibitory profiles, each TIMP possesses unique biological characteristics that are independent of their regulation of metalloproteinase activity. As our understanding of TIMP biology has evolved, distinct roles have been assigned to individual TIMPs in cancer progression. In this respect, data regarding TIMP2's role in cancer have borne conflicting reports of both tumor suppressor and, to a lesser extent, tumor promoter functions. TIMP2 is the most abundant TIMP family member, prevalent in normal and diseased mammalian tissues as a constitutively expressed protein. Despite its apparent stable expression, recent work highlights how TIMP2 is a cell stress-induced gene product and that its biological activity can be dictated by extracellular posttranslational modifications. Hence an understanding of TIMP2 molecular targets, and how its biological functions evolve in the progressing tumor microenvironment may reveal new therapeutic opportunities. In this review, we discuss the continually evolving functions of TIMP proteins, future perspectives in TIMP research, and the therapeutic utility of this family, with a particular focus on TIMP2.
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Affiliation(s)
- David Peeney
- To whom correspondence should be addressed. Tel: 240-858-3233;
| | - Yueqin Liu
- Laboratory of Pathology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Carolyn Lazaroff
- Laboratory of Pathology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Sadeechya Gurung
- Laboratory of Pathology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
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Dauvé J, Belloy N, Rivet R, Etique N, Nizet P, Pietraszek-Gremplewicz K, Karamanou K, Dauchez M, Ramont L, Brézillon S, Baud S. Differential MMP-14 Targeting by Lumican-Derived Peptides Unraveled by In Silico Approach. Cancers (Basel) 2021; 13:cancers13194930. [PMID: 34638415 PMCID: PMC8507859 DOI: 10.3390/cancers13194930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022] Open
Abstract
Lumican, a small leucine-rich proteoglycan (SLRP) of the extracellular matrix (ECM), displays anti-tumor properties through its direct interaction with MMP-14. Lumican-derived peptides, such as lumcorin (17 amino acids) or L9M (10 amino acids), are able to inhibit the proteolytic activity of MMP-14 and melanoma progression. This work aimed to visualize the interactions of lumican-derived peptides and MMP-14. Molecular modeling was used to characterize the interactions between lumican-derived peptides, such as lumcorin, L9M, and cyclic L9M (L9Mc, 12 amino acids), and MMP-14. The interaction of L9Mc with MMP-14 was preferential with the MT-Loop domain while lumcorin interacted more with the catalytic site. Key residues in the MMP-14 amino acid sequence were highlighted for the interaction between the inhibitory SLRP-derived peptides and MMP-14. In order to validate the in silico data, MMP-14 activity and migration assays were performed using murine B16F1 and human HT-144 melanoma cells. In contrast to the HT-144 melanoma cell line, L9Mc significantly inhibited the migration of B16F1 cells and the activity of MMP-14 but with less efficacy than lumican and lumcorin. L9Mc significantly inhibited the proliferation of B16F1 but not of HT-144 cells in vitro and primary melanoma tumor growth in vivo. Thus, the site of interaction between the domains of MMP-14 and lumcorin or L9Mc were different, which might explain the differences in the inhibitory effect of MMP-14 activity. Altogether, the biological assays validated the prediction of the in silico study. Possible and feasible improvements include molecular dynamics results.
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Affiliation(s)
- Jonathan Dauvé
- P3M, Multi-Scale Molecular Modeling Platform, Université de Reims Champagne Ardenne, 51097 Reims, France; (J.D.); (N.B.); (M.D.)
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, 51095 Reims, France; (R.R.); (N.E.); (P.N.); (K.K.); (L.R.); (S.B.)
| | - Nicolas Belloy
- P3M, Multi-Scale Molecular Modeling Platform, Université de Reims Champagne Ardenne, 51097 Reims, France; (J.D.); (N.B.); (M.D.)
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, 51095 Reims, France; (R.R.); (N.E.); (P.N.); (K.K.); (L.R.); (S.B.)
| | - Romain Rivet
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, 51095 Reims, France; (R.R.); (N.E.); (P.N.); (K.K.); (L.R.); (S.B.)
| | - Nicolas Etique
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, 51095 Reims, France; (R.R.); (N.E.); (P.N.); (K.K.); (L.R.); (S.B.)
| | - Pierre Nizet
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, 51095 Reims, France; (R.R.); (N.E.); (P.N.); (K.K.); (L.R.); (S.B.)
| | | | - Konstantina Karamanou
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, 51095 Reims, France; (R.R.); (N.E.); (P.N.); (K.K.); (L.R.); (S.B.)
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, 26110 Patras, Greece
| | - Manuel Dauchez
- P3M, Multi-Scale Molecular Modeling Platform, Université de Reims Champagne Ardenne, 51097 Reims, France; (J.D.); (N.B.); (M.D.)
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, 51095 Reims, France; (R.R.); (N.E.); (P.N.); (K.K.); (L.R.); (S.B.)
| | - Laurent Ramont
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, 51095 Reims, France; (R.R.); (N.E.); (P.N.); (K.K.); (L.R.); (S.B.)
- CHU Reims, Service Biochimie Pharmacologie-Toxicologie, 51092 Reims, France
| | - Stéphane Brézillon
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, 51095 Reims, France; (R.R.); (N.E.); (P.N.); (K.K.); (L.R.); (S.B.)
| | - Stéphanie Baud
- P3M, Multi-Scale Molecular Modeling Platform, Université de Reims Champagne Ardenne, 51097 Reims, France; (J.D.); (N.B.); (M.D.)
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, 51095 Reims, France; (R.R.); (N.E.); (P.N.); (K.K.); (L.R.); (S.B.)
- Correspondence:
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Xia XD, Alabi A, Wang M, Gu HM, Yang RZ, Wang G, Zhang DW. Membrane-type I matrix metalloproteinase (MT1-MMP), lipid metabolism and therapeutic implications. J Mol Cell Biol 2021; 13:513-526. [PMID: 34297054 PMCID: PMC8530520 DOI: 10.1093/jmcb/mjab048] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Lipids exert many essential physiological functions, such as serving as a structural component of biological membranes, storing energy, and regulating cell signal transduction. Dysregulation of lipid metabolism can lead to dyslipidemia related to various human diseases, such as obesity, diabetes, and cardiovascular disease. Therefore, lipid metabolism is strictly regulated through multiple mechanisms at different levels, including the extracellular matrix. Membrane-type I matrix metalloproteinase (MT1-MMP), a zinc-dependent endopeptidase, proteolytically cleaves extracellular matrix components, and non-matrix proteins, thereby regulating many physiological and pathophysiological processes. Emerging evidence supports the vital role of MT1-MMP in lipid metabolism. For example, MT1-MMP mediates ectodomain shedding of low-density lipoprotein receptor and increases plasma low-density lipoprotein cholesterol levels and the development of atherosclerosis. It also increases the vulnerability of atherosclerotic plaque by promoting collagen cleavage. Furthermore, it can cleave the extracellular matrix of adipocytes, affecting adipogenesis and the development of obesity. Therefore, the activity of MT1-MMP is strictly regulated by multiple mechanisms, such as autocatalytic cleavage, endocytosis and exocytosis, and post-translational modifications. Here, we summarize the latest advances in MT1-MMP, mainly focusing on its role in lipid metabolism, the molecular mechanisms regulating the function and expression of MT1-MMP, and their pharmacotherapeutic implications.
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Affiliation(s)
- Xiao-Dan Xia
- Department of Orthopedics, The Sixth Affiliated Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan 511500, China.,Department of Pediatrics and Group on the Molecular and Cell Biology of Lipids, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6R 2G3, Canada
| | - Adekunle Alabi
- Department of Pediatrics and Group on the Molecular and Cell Biology of Lipids, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6R 2G3, Canada
| | - Maggie Wang
- Department of Pediatrics and Group on the Molecular and Cell Biology of Lipids, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6R 2G3, Canada
| | - Hong-Mei Gu
- Department of Pediatrics and Group on the Molecular and Cell Biology of Lipids, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6R 2G3, Canada
| | - Rui Zhe Yang
- Department of Pediatrics and Group on the Molecular and Cell Biology of Lipids, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6R 2G3, Canada
| | - Guiqing Wang
- Department of Orthopedics, The Sixth Affiliated Hospital (Qingyuan People's Hospital), Guangzhou Medical University, Qingyuan 511500, China
| | - Da-Wei Zhang
- Department of Pediatrics and Group on the Molecular and Cell Biology of Lipids, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6R 2G3, Canada
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Rahman F, Nguyen TM, Adekoya OA, Campestre C, Tortorella P, Sylte I, Winberg JO. Inhibition of bacterial and human zinc-metalloproteases by bisphosphonate- and catechol-containing compounds. J Enzyme Inhib Med Chem 2021; 36:819-830. [PMID: 33757387 PMCID: PMC7993378 DOI: 10.1080/14756366.2021.1901088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Compounds containg catechol or bisphosphonate were tested as inhibitors of the zinc metalloproteases, thermolysin (TLN), pseudolysin (PLN) and aureolysin (ALN) which are bacterial virulence factors, and the human matrix metalloproteases MMP-9 and -14. Inhibition of virulence is a putative strategy in the development of antibacterial drugs, but the inhibitors should not interfere with human enzymes. Docking indicated that the inhibitors bound MMP-9 and MMP-14 with the phenyl, biphenyl, chlorophenyl, nitrophenyl or methoxyphenyl ringsystem in the S1'-subpocket, while these ringsystems entered the S2'- or S1 -subpockets or a region involving amino acids in the S1'- and S2'-subpockets of the bacterial enzymes. An arginine conserved among the bacterial enzymes seemed to hinder entrance deeply into the S1'-subpocket. Only the bisphosphonate containing compound RC2 bound stronger to PLN and TLN than to MMP-9 and MMP-14. Docking indicated that the reason was that the conserved arginine (R203 in TLN and R198 in PLN) interacts with phosphate groups of RC2.
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Affiliation(s)
- Fatema Rahman
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Tra-Mi Nguyen
- Department of Pharmacy, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Olayiwola A Adekoya
- Department of Pharmacy, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Cristina Campestre
- Department of Pharmacy, University of "G. d'Annunzio" Chieti, Chieti, Italy
| | - Paolo Tortorella
- Department of Pharmacy, Science of Pharmacy, University "A. Moro" Bari, Bari, Italy
| | - Ingebrigt Sylte
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Jan-Olof Winberg
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
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Zoghi S, Khamirani HJ, Dastgheib SA, Dianatpour M, Ghaffarieh A. An analysis of inhibition of the severe acute respiratory syndrome coronavirus 2 RNA-dependent RNA polymerase by zinc ion: an in silico approach. Future Virol 2021. [PMCID: PMC8074572 DOI: 10.2217/fvl-2020-0369] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Background: Coronavirus disease 2019 is caused by exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It was reported that Zn2+ is an inhibitor of severe acute respiratory syndrome coronavirus (SARS-CoV). We hypothesize that the same applies to the newly discovered SARS-CoV-2. Material & methods: We compared the structure of RNA-dependent RNA polymerase between SARS-CoV and SARS-CoV-2. The RdRp’s binding to Zn2+ was studied by metal ion-binding site prediction and docking server. Results: Several regions containing key residues were detected. The functional aspartic acid residues RdRp, 618D, 760D and 761D were among the predicted Zn2+-binding residues. Conclusion: The most probable mechanism of inhibition of RdRp by Zn2+ is binding to the active aspartic acid triad while other binding sites can further destabilize the enzyme or interfere with the fidelity-check mechanism. The most probable mechanism of inhibition of RNA polymerase by Zn2+ is binding to the active aspartic acid triad while other binding sites can further destabilize the enzyme or interfere with the fidelity-check mechanism. #Zinc #SARS_CoV_2 #COVID_19.
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Affiliation(s)
- Sina Zoghi
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hossein Jafari Khamirani
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Mehdi Dianatpour
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Alireza Ghaffarieh
- Massachusetts Eye & Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
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Raeeszadeh-Sarmazdeh M, Do LD, Hritz BG. Metalloproteinases and Their Inhibitors: Potential for the Development of New Therapeutics. Cells 2020; 9:E1313. [PMID: 32466129 PMCID: PMC7290391 DOI: 10.3390/cells9051313] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 02/06/2023] Open
Abstract
The metalloproteinase (MP) family of zinc-dependent proteases, including matrix metalloproteinases (MMPs), a disintegrin and metalloproteases (ADAMs), and a disintegrin and metalloproteinase with thrombospondin motifs (ADAMTSs) plays a crucial role in the extracellular matrix (ECM) remodeling and degradation activities. A wide range of substrates of the MP family includes ECM components, chemokines, cell receptors, and growth factors. Metalloproteinases activities are tightly regulated by proteolytic activation and inhibition via their natural inhibitors, tissue inhibitors of metalloproteinases (TIMPs), and the imbalance of the activation and inhibition is responsible in progression or inhibition of several diseases, e.g., cancer, neurological disorders, and cardiovascular diseases. We provide an overview of the structure, function, and the multifaceted role of MMPs, ADAMs, and TIMPs in several diseases via their cellular functions such as proteolysis of other cell signaling factors, degradation and remodeling of the ECM, and other essential protease-independent interactions in the ECM. The significance of MP inhibitors targeting specific MMP or ADAMs with high selectivity is also discussed. Recent advances and techniques used in developing novel MP inhibitors and MP responsive drug delivery tools are also reviewed.
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Affiliation(s)
- Maryam Raeeszadeh-Sarmazdeh
- Chemical and Materials Engineering Department, University of Nevada, Reno, NV 89557, USA; (L.D.D.); (B.G.H.)
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Aharon L, Aharoni SL, Radisky ES, Papo N. Quantitative mapping of binding specificity landscapes for homologous targets by using a high-throughput method. Biochem J 2020; 477:1701-1719. [PMID: 32296833 PMCID: PMC7376575 DOI: 10.1042/bcj20200188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/11/2020] [Accepted: 04/14/2020] [Indexed: 01/08/2023]
Abstract
To facilitate investigations of protein-protein interactions (PPIs), we developed a novel platform for quantitative mapping of protein binding specificity landscapes, which combines the multi-target screening of a mutagenesis library into high- and low-affinity populations with sophisticated next-generation sequencing analysis. Importantly, this method generates accurate models to predict affinity and specificity values for any mutation within a protein complex, and requires only a few experimental binding affinity measurements using purified proteins for calibration. We demonstrated the utility of the approach by mapping quantitative landscapes for interactions between the N-terminal domain of the tissue inhibitor of metalloproteinase 2 (N-TIMP2) and three matrix metalloproteinases (MMPs) having homologous structures but different affinities (MMP-1, MMP-3, and MMP-14). The binding landscapes for N-TIMP2/MMP-1 and N-TIMP2/MMP-3 showed the PPIs to be almost fully optimized, with most single mutations giving a loss of affinity. In contrast, the non-optimized PPI for N-TIMP2/MMP-14 was reflected in a wide range of binding affinities, where single mutations exhibited a far more attenuated effect on the PPI. Our new platform reliably and comprehensively identified not only hot- and cold-spot residues, but also specificity-switch mutations that shape target affinity and specificity. Thus, our approach provides a methodology giving an unprecedentedly rich quantitative analysis of the binding specificity landscape, which will broaden the understanding of the mechanisms and evolutionary origins of specific PPIs and facilitate the rational design of specific inhibitors for structurally similar target proteins.
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Affiliation(s)
- Lidan Aharon
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Shay-Lee Aharoni
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville 32224, Florida, USA
| | - Niv Papo
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Levi N, Papismadov N, Solomonov I, Sagi I, Krizhanovsky V. The ECM path of senescence in aging: components and modifiers. FEBS J 2020; 287:2636-2646. [PMID: 32145148 DOI: 10.1111/febs.15282] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/25/2019] [Accepted: 03/04/2020] [Indexed: 11/29/2022]
Abstract
The extracellular matrix (ECM) is a key noncellular component in all organs and tissues. It is composed of a large number of proteins including collagens, glycoproteins (GP), and ECM-associated proteins, which show diversity of biochemical and biophysical functions. The ECM is dynamic both in normal physiology of tissues and under pathological conditions. One cellular phenomenon associated with changes in both ECM components expression and in ECM remodeling enzymes secretion is cellular senescence. It represents a stable state form of cell cycle arrest induced in proliferating cells by various forms of stress. Short-term induction of senescence is essential for tumor suppression and tissue repair. However, long-term presence of senescent cells in tissues may have a detrimental role in promoting tissue damage and aging. Up to date, there is insufficient knowledge about the interplay between the ECM and senescence cells. Since changes in the ECM occur in many physiological and pathological conditions in which senescent cells are present, a better understanding of ECM-senescence interactions is necessary. Here, we will review the functions of the different ECM components and will discuss the current knowledge about their regulation in senescent cells and their influence on the senescence state.
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Affiliation(s)
- Naama Levi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nurit Papismadov
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Inna Solomonov
- Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Irit Sagi
- Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Valery Krizhanovsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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10
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The past, present and future perspectives of matrix metalloproteinase inhibitors. Pharmacol Ther 2020; 207:107465. [DOI: 10.1016/j.pharmthera.2019.107465] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022]
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Fischer T, Riedl R. Inhibitory Antibodies Designed for Matrix Metalloproteinase Modulation. Molecules 2019; 24:molecules24122265. [PMID: 31216704 PMCID: PMC6631688 DOI: 10.3390/molecules24122265] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 01/20/2023] Open
Abstract
The family of matrix metalloproteinases (MMPs) consists of a set of biological targets that are involved in a multitude of severe pathogenic events such as different forms of cancers or arthritis. Modulation of the target class with small molecule drugs has not led to the anticipated success until present, as all clinical trials failed due to unacceptable side effects or a lack of therapeutic outcome. Monoclonal antibodies offer a tremendous therapeutic potential given their high target selectivity and good pharmacokinetic profiles. For the treatment of a variety of diseases there are already antibody therapies available and the number is increasing. Recently, several antibodies were developed for the selective inhibition of single MMPs that showed high potency and were therefore investigated in in vivo studies with promising results. In this review, we highlight the progress that has been achieved toward the design of inhibitory antibodies that successfully modulate MMP-9 and MMP-14.
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Affiliation(s)
- Thomas Fischer
- Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland.
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland.
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12
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Arkadash V, Radisky ES, Papo N. Combinatorial engineering of N-TIMP2 variants that selectively inhibit MMP9 and MMP14 function in the cell. Oncotarget 2018; 9:32036-32053. [PMID: 30174795 PMCID: PMC6112833 DOI: 10.18632/oncotarget.25885] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/21/2018] [Indexed: 12/21/2022] Open
Abstract
Developing selective inhibitors for proteolytic enzymes that share high sequence homology and structural similarity is important for achieving high target affinity and functional specificity. Here, we used a combination of yeast surface display and dual-color selective library screening to obtain selective inhibitors for each of the matrix metalloproteinases (MMPs) MMP14 and MMP9 by modifying the non-specific N-terminal domain of the tissue inhibitor of metalloproteinase-2 (N-TIMP2). We generated inhibitor variants with 30- to 1175-fold improved specificity to each of the proteases, respectively, relative to wild type N-TIMP2. These biochemical results accurately predicted the selectivity and specificity obtained in cell-based assays. In U87MG cells, the activation of MMP2 by MMP14 was inhibited by MMP14-selective blockers but not MMP9-specific inhibitors. Target specificity was also demonstrated in MCF-7 cells stably expressing either MMP14 or MMP9, with only the MMP14-specific inhibitors preventing the mobility of MMP14-expressing cells. Similarly, the mobility of MMP9-expressing cells was inhibited by the MMP9-specific inhibitors, yet was not altered by the MMP14-specific inhibitors. The strategy developed in this study for improving the specificity of an otherwise broad-spectrum inhibitor will likely enhance our understanding of the basis for target specificity of inhibitors to proteolytic enzymes, in general, and to MMPs, in particular. We, moreover, envision that this study could serve as a platform for the development of next-generation, target-specific therapeutic agents. Finally, our methodology can be extended to other classes of proteolytic enzymes and other important target proteins.
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Affiliation(s)
- Valeria Arkadash
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA
| | - Niv Papo
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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13
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Sylte I, Dawadi R, Malla N, von Hofsten S, Nguyen TM, Solli AI, Berg E, Adekoya OA, Svineng G, Winberg JO. The selectivity of galardin and an azasugar-based hydroxamate compound for human matrix metalloproteases and bacterial metalloproteases. PLoS One 2018; 13:e0200237. [PMID: 30075004 PMCID: PMC6075749 DOI: 10.1371/journal.pone.0200237] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/22/2018] [Indexed: 02/07/2023] Open
Abstract
Inhibitors targeting bacterial enzymes should not interfere with enzymes of the host, and knowledge about structural determinants for selectivity is important for designing inhibitors with a therapeutic potential. We have determined the binding strengths of two hydroxamate compounds, galardin and compound 1b for the bacterial zinc metalloproteases, thermolysin, pseudolysin and auerolysin, known to be bacterial virulence factors, and the two human zinc metalloproteases MMP-9 and MMP-14. The active sites of the bacterial and human enzymes have huge similarities. In addition, we also studied the enzyme-inhibitor interactions by molecular modelling. The obtained Ki values of galardin for MMP-9 and MMP-14 and compound 1b for MMP-9 are approximately ten times lower than previously reported. Compound 1b binds stronger than galardin to both MMP-9 and MMP-14, and docking studies indicated that the diphenyl ether moiety of compound 1b obtains more favourable interactions within the S´1-subpocket than the 4-methylpentanoyl moiety of galardin. Both compounds bind stronger to MMP-9 than to MMP-14, which appears to be due to a larger S´1-subpocket in the former enzyme. Galardin, but not 1b, inhibits the bacterial enzymes, but the galardin Ki values were much larger than for the MMPs. The docking indicates that the S´1-subpockets of the bacterial proteases are too small to accommodate the diphenyl ether moiety of 1b, while the 4-methylpentanoyl moiety of galardin enters the pocket. The present study indicates that the size and shape of the ligand structural moiety entering the S´1-subpocket is an important determinant for selectivity between the studied MMPs and bacterial MPs.
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Affiliation(s)
- Ingebrigt Sylte
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Rangita Dawadi
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Nabin Malla
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Susannah von Hofsten
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Tra-Mi Nguyen
- Department of Pharmacy, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Ann Iren Solli
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Eli Berg
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Olayiwola A. Adekoya
- Department of Pharmacy, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Gunbjørg Svineng
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Jan-Olof Winberg
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
- * E-mail:
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14
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Shirian J, Arkadash V, Cohen I, Sapir T, Radisky ES, Papo N, Shifman JM. Converting a broad matrix metalloproteinase family inhibitor into a specific inhibitor of MMP-9 and MMP-14. FEBS Lett 2018; 592:1122-1134. [PMID: 29473954 DOI: 10.1002/1873-3468.13016] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/11/2018] [Accepted: 02/19/2018] [Indexed: 12/22/2022]
Abstract
MMP-14 and MMP-9 are two well-established cancer targets for which no specific clinically relevant inhibitor is available. Using a powerful combination of computational design and yeast surface display technology, we engineered such an inhibitor starting from a nonspecific MMP inhibitor, N-TIMP2. The engineered purified N-TIMP2 variants showed enhanced specificity toward MMP-14 and MMP-9 relative to a panel of off-target MMPs. MMP-specific N-TIMP2 sequence signatures were obtained that could be understood from the structural perspective of MMP/N-TIMP2 interactions. Our MMP-9 inhibitor exhibited 1000-fold preference for MMP-9 vs. MMP-14, which is likely to translate into significant differences under physiological conditions. Our results provide new insights regarding evolution of promiscuous proteins and optimization strategies for design of inhibitors with single-target specificities.
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Affiliation(s)
- Jason Shirian
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Valeria Arkadash
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Itay Cohen
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tamila Sapir
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL, USA
| | - Niv Papo
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
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15
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Decaneto E, Vasilevskaya T, Kutin Y, Ogata H, Grossman M, Sagi I, Havenith M, Lubitz W, Thiel W, Cox N. Solvent water interactions within the active site of the membrane type I matrix metalloproteinase. Phys Chem Chem Phys 2018; 19:30316-30331. [PMID: 28951896 DOI: 10.1039/c7cp05572b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Matrix metalloproteinases (MMP) are an important family of proteases which catalyze the degradation of extracellular matrix components. While the mechanism of peptide cleavage is well established, the process of enzyme regeneration, which represents the rate limiting step of the catalytic cycle, remains unresolved. This step involves the loss of the newly formed N-terminus (amine) and C-terminus (carboxylate) protein fragments from the site of catalysis coupled with the inclusion of one or more solvent waters. Here we report a novel crystal structure of membrane type I MMP (MT1-MMP or MMP-14), which includes a small peptide bound at the catalytic Zn site via its C-terminus. This structure models the initial product state formed immediately after peptide cleavage but before the final proton transfer to the bound amine; the amine is not present in our system and as such proton transfer cannot occur. Modeling of the protein, including earlier structural data of Bertini and coworkers [I. Bertini, et al., Angew. Chem., Int. Ed., 2006, 45, 7952-7955], suggests that the C-terminus of the peptide is positioned to form an H-bond network to the amine site, which is mediated by a single oxygen of the functionally important Glu240 residue, facilitating efficient proton transfer. Additional quantum chemical calculations complemented with magneto-optical and magnetic resonance spectroscopies clarify the role of two additional, non-catalytic first coordination sphere waters identified in the crystal structure. One of these auxiliary waters acts to stabilize key intermediates of the reaction, while the second is proposed to facilitate C-fragment release, triggered by protonation of the amine. Together these results complete the enzymatic cycle of MMPs and provide new design criteria for inhibitors with improved efficacy.
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Affiliation(s)
- Elena Decaneto
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße. 34-36, D-45470, Mülheim an der Ruhr, Germany.
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16
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Zhong Y, Lu YT, Sun Y, Shi ZH, Li NG, Tang YP, Duan JA. Recent opportunities in matrix metalloproteinase inhibitor drug design for cancer. Expert Opin Drug Discov 2017; 13:75-87. [PMID: 29088927 DOI: 10.1080/17460441.2018.1398732] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION The overexpression of matrix metalloproteinase (MMP) plays an important role in the context of tumor invasion and metastasis, and MMP-2 has been characterized as the most validated target for cancer. Therefore, it is necessary to design matrix metalloproteinase inhibitors (MMPIs) that would be active and selective against MMP-2 but non-selective toward other MMPs. Areas covered: This article clearly describes the structural character of MMP-2 followed by a review of the recent development of selective MMP-2 inhibitors based on their basic structures. Expert opinion: Over the past 30 years, MMPs have been considered to be attractive cancer targets, and several different types of synthetic inhibitors have been identified as anticancer agents, but only a small number of small MMPIs have been examined in clinical trials, and none of these molecules has been established as anticancer drugs due to their adverse effects. One major possibility is that the MMPIs used in clinical trials were broad-spectrum drugs that also inhibited the anti-tumor effects and influenced the mediation of the normal physiological processes of MMPs. MMP-2 has recently been characterized as the most validated target for cancer. Therefore, the design and synthesis of selective MMP-2 inhibitors would be helpful for the treatment of cancer.
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Affiliation(s)
- Yue Zhong
- a Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae , Nanjing University of Chinese Medicine , Nanjing , China
| | - Yu-Ting Lu
- a Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae , Nanjing University of Chinese Medicine , Nanjing , China
| | - Ying Sun
- a Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae , Nanjing University of Chinese Medicine , Nanjing , China
| | - Zhi-Hao Shi
- a Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae , Nanjing University of Chinese Medicine , Nanjing , China.,b Department of Organic Chemistry , China Pharmaceutical University , Nanjing , China
| | - Nian-Guang Li
- a Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae , Nanjing University of Chinese Medicine , Nanjing , China
| | - Yu-Ping Tang
- a Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae , Nanjing University of Chinese Medicine , Nanjing , China.,c Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization and College of Pharmacy , Shaanxi University of Chinese Medicine , Xianyang , China
| | - Jin-Ao Duan
- a Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae , Nanjing University of Chinese Medicine , Nanjing , China
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17
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Singh M, Tyagi SC. Metalloproteinases as mediators of inflammation and the eyes: molecular genetic underpinnings governing ocular pathophysiology. Int J Ophthalmol 2017; 10:1308-1318. [PMID: 28861360 DOI: 10.18240/ijo.2017.08.20] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/01/2017] [Indexed: 12/18/2022] Open
Abstract
There are many vision threatening diseases of the eye affecting millions of people worldwide. In this article, we are summarizing potential role of various matrix metalloproteinases (MMPs); the Zn (2+)-dependent endoproteases in eye health along with pathogenesis of prominent ocular diseases such as macular degeneration, diabetic retinopathy, and glaucoma via understanding MMPs regulation in affected patients, interactions of MMPs with their substrate molecules, and key regulatory functions of tissue inhibitor of metalloproteinases (TIMPs) towards maintaining overall homeostasis.
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Affiliation(s)
- Mahavir Singh
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Suresh C Tyagi
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
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18
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Radisky ES, Raeeszadeh-Sarmazdeh M, Radisky DC. Therapeutic Potential of Matrix Metalloproteinase Inhibition in Breast Cancer. J Cell Biochem 2017; 118:3531-3548. [PMID: 28585723 PMCID: PMC5621753 DOI: 10.1002/jcb.26185] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 06/05/2017] [Indexed: 12/14/2022]
Abstract
Matrix metalloproteinases (MMPs) are a family of zinc endopeptidases that cleave nearly all components of the extracellular matrix as well as many other soluble and cell-associated proteins. MMPs have been implicated in normal physiological processes, including development, and in the acquisition and progression of the malignant phenotype. Disappointing results from a series of clinical trials testing small molecule, broad spectrum MMP inhibitors as cancer therapeutics led to a re-evaluation of how MMPs function in the tumor microenvironment, and ongoing research continues to reveal that these proteins play complex roles in cancer development and progression. It is now clear that effective targeting of MMPs for therapeutic benefit will require selective inhibition of specific MMPs. Here, we provide an overview of the MMP family and its biological regulators, the tissue inhibitors of metalloproteinases (TIMPs). We then summarize recent research from model systems that elucidate how specific MMPs drive the malignant phenotype of breast cancer cells, including acquisition of cancer stem cell features and induction of the epithelial-mesenchymal transition, and we also outline clinical studies that implicate specific MMPs in breast cancer outcomes. We conclude by discussing ongoing strategies for development of inhibitors with therapeutic potential that are capable of selectively targeting the MMPs most responsible for tumor promotion, with special consideration of the potential of biologics including antibodies and engineered proteins based on the TIMP scaffold. J. Cell. Biochem. 118: 3531-3548, 2017. © 2017 The Authors. Journal of Cellular Biochemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville 32224, Florida
| | | | - Derek C Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville 32224, Florida
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19
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Intrinsic dynamics study identifies two amino acids of TIMP-1 critical for its LRP-1-mediated endocytosis in neurons. Sci Rep 2017; 7:5375. [PMID: 28710453 PMCID: PMC5511134 DOI: 10.1038/s41598-017-05039-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 05/24/2017] [Indexed: 01/28/2023] Open
Abstract
The tissue inhibitor of metalloproteinases-1 (TIMP-1) exerts inhibitory activity against matrix metalloproteinases and cytokine-like effects. We previously showed that TIMP-1 reduces neurite outgrowth in mouse cortical neurons and that this cytokine-like effect depends on TIMP-1 endocytosis mediated by the low-density lipoprotein receptor-related protein-1 (LRP-1). To gain insight into the interaction between TIMP-1 and LRP-1, we considered conformational changes that occur when a ligand binds to its receptor. TIMP-1 conformational changes have been studied using biomolecular simulations, and our results provide evidence for a hinge region that is critical for the protein movement between the N- and C-terminal TIMP-1 domains. In silico mutants have been proposed on residues F12 and K47, which are located in the hinge region. Biological analyses of these mutants show that F12A or K47A mutation does not alter MMP inhibitory activity but impairs the effect of TIMP-1 on neurite outgrowth. Interestingly, these mutants bind to LRP-1 but are not endocytosed. We conclude that the intrinsic dynamics of TIMP-1 are not involved in its binding to LRP-1 but rather in the initiation of endocytosis and associated biological effects.
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20
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Levin M, Udi Y, Solomonov I, Sagi I. Next generation matrix metalloproteinase inhibitors - Novel strategies bring new prospects. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017. [PMID: 28636874 DOI: 10.1016/j.bbamcr.2017.06.009] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymatic proteolysis of cell surface proteins and extracellular matrix (ECM) is critical for tissue homeostasis and cell signaling. These proteolytic activities are mediated predominantly by a family of proteases termed matrix metalloproteinases (MMPs). The growing evidence in recent years that ECM and non-ECM bioactive molecules (e.g., growth factors, cytokines, chemokines, on top of matrikines and matricryptins) have versatile functions redefines our view on the roles matrix remodeling enzymes play in many physiological and pathological processes, and underscores the notion that ECM proteolytic reaction mechanisms represent master switches in the regulation of critical biological processes and govern cell behavior. Accordingly, MMPs are not only responsible for direct degradation of ECM molecules but are also key modulators of cardinal bioactive factors. Many attempts were made to manipulate ECM degradation by targeting MMPs using small peptidic and organic inhibitors. However, due to the high structural homology shared by these enzymes, the majority of the developed compounds are broad-spectrum inhibitors affecting the proteolytic activity of various MMPs and other zinc-related proteases. These inhibitors, in many cases, failed as therapeutic agents, mainly due to the bilateral role of MMPs in pathological conditions such as cancer, in which MMPs have both pro- and anti-tumorigenic effects. Despite the important role of MMPs in many human diseases, none of the broad-range synthetic MMP inhibitors that were designed have successfully passed clinical trials. It appears that, designing highly selective MMP inhibitors that are also effective in vivo, is not trivial. The challenges related to designing selective and effective metalloprotease inhibitors, are associated in part with the aforesaid high structural homology and the dynamic nature of their protein scaffolds. Great progress was achieved in the last decade in understanding the biochemistry and biology of MMPs activity. This knowledge, combined with lessons from the past has drawn new "boundaries" for the development of the next-generation MMP inhibitors. These novel agents are currently designed to be highly specific, capable to discriminate between the homologous MMPs and ideally administered as a short-term topical treatment. In this review we discuss the latest progress in the fields of MMP inhibitors in terms of structure, function and their specific activity. The development of novel highly specific inhibitors targeting MMPs paves the path to study complex biological processes associated with ECM proteolysis in health and disease. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman.
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Affiliation(s)
- Maxim Levin
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yael Udi
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Inna Solomonov
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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21
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Arkadash V, Yosef G, Shirian J, Cohen I, Horev Y, Grossman M, Sagi I, Radisky ES, Shifman JM, Papo N. Development of High Affinity and High Specificity Inhibitors of Matrix Metalloproteinase 14 through Computational Design and Directed Evolution. J Biol Chem 2017; 292:3481-3495. [PMID: 28087697 DOI: 10.1074/jbc.m116.756718] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 01/12/2017] [Indexed: 12/13/2022] Open
Abstract
Degradation of the extracellular matrices in the human body is controlled by matrix metalloproteinases (MMPs), a family of more than 20 homologous enzymes. Imbalance in MMP activity can result in many diseases, such as arthritis, cardiovascular diseases, neurological disorders, fibrosis, and cancers. Thus, MMPs present attractive targets for drug design and have been a focus for inhibitor design for as long as 3 decades. Yet, to date, all MMP inhibitors have failed in clinical trials because of their broad activity against numerous MMP family members and the serious side effects of the proposed treatment. In this study, we integrated a computational method and a yeast surface display technique to obtain highly specific inhibitors of MMP-14 by modifying the natural non-specific broad MMP inhibitor protein N-TIMP2 to interact optimally with MMP-14. We identified an N-TIMP2 mutant, with five mutations in its interface, that has an MMP-14 inhibition constant (Ki ) of 0.9 pm, the strongest MMP-14 inhibitor reported so far. Compared with wild-type N-TIMP2, this variant displays ∼900-fold improved affinity toward MMP-14 and up to 16,000-fold greater specificity toward MMP-14 relative to other MMPs. In an in vitro and cell-based model of MMP-dependent breast cancer cellular invasiveness, this N-TIMP2 mutant acted as a functional inhibitor. Thus, our study demonstrates the enormous potential of a combined computational/directed evolution approach to protein engineering. Furthermore, it offers fundamental clues into the molecular basis of MMP regulation by N-TIMP2 and identifies a promising MMP-14 inhibitor as a starting point for the development of protein-based anticancer therapeutics.
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Affiliation(s)
- Valeria Arkadash
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel
| | - Gal Yosef
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel
| | - Jason Shirian
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Itay Cohen
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel
| | - Yuval Horev
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel
| | - Moran Grossman
- Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel.
| | - Niv Papo
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel.
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22
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Decaneto E, Lubitz W, Ogata H. Structural Studies of Matrix Metalloproteinase by X-Ray Diffraction. Methods Mol Biol 2017; 1579:49-60. [PMID: 28299732 DOI: 10.1007/978-1-4939-6863-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Matrix Metalloproteinases (MMPs) are a family of proteolytic enzymes whose endopeptidase activity is dependent on the presence of specific metal ions. MT1-MMP (or MMP-14), which has been implicated in tumor progression and cellular invasion, contains a membrane-spanning region located C-terminal to a hemopexin-like domain and an N-terminal catalytic domain. We recombinantly expressed the catalytic domain of human MT1-MMP in E. coli and purified it from inclusion bodies using a refolding protocol that yielded significant quantities of active protein. Crystals of MT1-MMP were obtained using the vapour diffusion method. Here, we describe the protocols used for crystallization and the data analysis together with the resulting diffraction pattern.
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Affiliation(s)
- Elena Decaneto
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany.
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23
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Cerofolini L, Amar S, Lauer JL, Martelli T, Fragai M, Luchinat C, Fields GB. Bilayer Membrane Modulation of Membrane Type 1 Matrix Metalloproteinase (MT1-MMP) Structure and Proteolytic Activity. Sci Rep 2016; 6:29511. [PMID: 27405411 PMCID: PMC4942797 DOI: 10.1038/srep29511] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 06/20/2016] [Indexed: 11/23/2022] Open
Abstract
Cell surface proteolysis is an integral yet poorly understood physiological process. The present study has examined how the pericellular collagenase membrane-type 1 matrix metalloproteinase (MT1-MMP) and membrane-mimicking environments interplay in substrate binding and processing. NMR derived structural models indicate that MT1-MMP transiently associates with bicelles and cells through distinct residues in blades III and IV of its hemopexin-like domain, while binding of collagen-like triple-helices occurs within blades I and II of this domain. Examination of simultaneous membrane interaction and triple-helix binding revealed a possible regulation of proteolysis due to steric effects of the membrane. At bicelle concentrations of 1%, enzymatic activity towards triple-helices was increased 1.5-fold. A single mutation in the putative membrane interaction region of MT1-MMP (Ser466Pro) resulted in lower enzyme activation by bicelles. An initial structural framework has thus been developed to define the role(s) of cell membranes in modulating proteolysis.
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Affiliation(s)
- Linda Cerofolini
- Giotto Biotech S.R.L., Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Sabrina Amar
- Department of Chemistry &Biochemistry, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
| | - Janelle L Lauer
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Tommaso Martelli
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino (FI), Italy.,Department of Chemistry "U. Schiff", University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy
| | - Marco Fragai
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino (FI), Italy.,Department of Chemistry "U. Schiff", University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy
| | - Claudio Luchinat
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino (FI), Italy.,Department of Chemistry "U. Schiff", University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy
| | - Gregg B Fields
- Department of Chemistry &Biochemistry, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA.,Department of Chemistry, The Scripps Research Institute/Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.,Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, 33458, Port St. Lucie, FL 34987, USA
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24
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Zou H, Wu Y, Brew K. Thermodynamic Basis of Selectivity in the Interactions of Tissue Inhibitors of Metalloproteinases N-domains with Matrix Metalloproteinases-1, -3, and -14. J Biol Chem 2016; 291:11348-58. [PMID: 27033700 DOI: 10.1074/jbc.m116.720250] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Indexed: 01/18/2023] Open
Abstract
The four tissue inhibitors of metalloproteinases (TIMPs) are potent inhibitors of the many matrixins (MMPs), except that TIMP1 weakly inhibits some MMPs, including MMP14. The broad-spectrum inhibition of MMPs by TIMPs and their N-domains (NTIMPs) is consistent with the previous isothermal titration calorimetric finding that their interactions are entropy-driven but differ in contributions from solvent and conformational entropy (ΔSsolv, ΔSconf), estimated using heat capacity changes (ΔCp). Selective engineered NTIMPs have potential applications for treating MMP-related diseases, including cancer and cardiomyopathy. Here we report isothermal titration calorimetric studies of the effects of selectivity-modifying mutations in NTIMP1 and NTIMP2 on the thermodynamics of their interactions with MMP1, MMP3, and MMP14. The weak inhibition of MMP14 by NTIMP1 reflects a large conformational entropy penalty for binding. The T98L mutation, peripheral to the NTIMP1 reactive site, enhances binding by increasing ΔSsolv but also reduces ΔSconf However, the same mutation increases NTIMP1 binding to MMP3 in an interaction that has an unusual positive ΔCp This indicates a decrease in solvent entropy compensated by increased conformational entropy, possibly reflecting interactions involving alternative conformers. The NTIMP2 mutant, S2D/S4A is a selective MMP1 inhibitor through electrostatic effects of a unique MMP-1 arginine. Asp-2 increases reactive site polarity, reducing ΔCp, but increases conformational entropy to maintain strong binding to MMP1. There is a strong negative correlation between ΔSsolv and ΔSconf for all characterized interactions, but the data for each MMP have characteristic ranges, reflecting intrinsic differences in the structures and dynamics of their free and inhibitor-bound forms.
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Affiliation(s)
- Haiyin Zou
- From the Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida 33431
| | - Ying Wu
- From the Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida 33431
| | - Keith Brew
- From the Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida 33431
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25
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Mendes DE, Wong-On-Wing A, Berkman CE. Phosphoramidate-based peptidomimetic inhibitors of membrane type-1 matrix metalloproteinase. J Enzyme Inhib Med Chem 2015; 31:167-71. [PMID: 25815671 DOI: 10.3109/14756366.2015.1010528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Membrane-type I matrix metalloproteinases (MT1-MMP) is an enzyme critical to the remodeling and homeostasis of extracellular matrix, and when over expressed it contributes to metastasis and cancer cell progression. Because of its role and implication as a biomarker that is upregulated in various cancers, MT1-MMP has become an attractive target for drug discovery. A small pilot library of peptidomimetics containing a phosphoramidate core as a zinc-binding group was synthesized and tested for inhibitory potency against MT1-MMP. From this library, a novel two residue peptidomimetic scaffold was identified that confers potency against MT1-MMP at submicromolar concentrations. The results of this study confirm that for this scaffold, valine is favored as a P1 residue and leucine in the P1' position. Furthermore, steric tolerance was observed for the N-terminus, thus implicating that a second-generation library could be constructed to extend the scaffold to P2 without concomitant loss of affinity within the MT1-MMP catalytic domain.
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Affiliation(s)
- Desiree E Mendes
- a Department of Chemistry , Washington State University , Pullman , Washington , DC , USA
| | - Annie Wong-On-Wing
- a Department of Chemistry , Washington State University , Pullman , Washington , DC , USA
| | - Clifford E Berkman
- a Department of Chemistry , Washington State University , Pullman , Washington , DC , USA
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26
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Radisky ES, Radisky DC. Matrix metalloproteinases as breast cancer drivers and therapeutic targets. Front Biosci (Landmark Ed) 2015; 20:1144-63. [PMID: 25961550 DOI: 10.2741/4364] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Members of the matrix metalloproteinase (MMP) family have been identified as poor prognosis markers for breast cancer patients and as drivers of many facets of the tumor phenotype in experimental models. Early enthusiasm for MMPs as therapeutic targets was tempered following disappointing clinical trials that utilized broad spectrum, small molecule catalytic site inhibitors. However, subsequent research has continued to define key roles for MMPs as breast cancer promoters, to elucidate the complex roles that that these proteins play in breast cancer development and progression, and to identify how these roles are linked to specific and unique biochemical features of individual members of the MMP family. Here, we provide an overview of the structural features of the MMPs, then discuss clinical studies identifying which MMP family members are linked with breast cancer development and new experimental studies that reveal how these specific MMPs may play unique roles in the breast cancer microenvironment. We conclude with a discussion of the most promising avenues for development of therapeutic agents capable of targeting the tumor-promoting properties of MMPs.
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Affiliation(s)
- Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224,
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27
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Gaffney J, Solomonov I, Zehorai E, Sagi I. Multilevel regulation of matrix metalloproteinases in tissue homeostasis indicates their molecular specificity in vivo. Matrix Biol 2015; 44-46:191-9. [PMID: 25622911 DOI: 10.1016/j.matbio.2015.01.012] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/18/2015] [Accepted: 01/18/2015] [Indexed: 11/16/2022]
Abstract
The matrix metalloproteinases (MMPs) play a crucial role in irreversible remodeling of the extracellular matrix (ECM) in normal homeostasis and pathological states. Accumulating data from various studies strongly suggest that MMPs are tightly regulated, starting from the level of gene expression all the way to zymogen activation and endogenous inhibition, with each level controlled by multiple factors. Recent in vivo findings indicate that cell-ECM and cell-cell interactions, as well as ECM bio-active products, contribute an additional layer of regulation at all levels, indicating that individual MMP expression and activity in vivo are highly coordinated and tissue specific processes.
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Affiliation(s)
- Jean Gaffney
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel; Department of Natural Sciences, Baruch College, New York, NY, USA
| | - Inna Solomonov
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Eldar Zehorai
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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28
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Udi Y, Grossman M, Solomonov I, Dym O, Rozenberg H, Moreno V, Cuniasse P, Dive V, Arroyo A, Sagi I. Inhibition Mechanism of Membrane Metalloprotease by an Exosite-Swiveling Conformational Antibody. Structure 2015; 23:104-115. [DOI: 10.1016/j.str.2014.10.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 10/07/2014] [Accepted: 10/13/2014] [Indexed: 11/25/2022]
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29
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Enzymatic turnover of macromolecules generates long-lasting protein-water-coupled motions beyond reaction steady state. Proc Natl Acad Sci U S A 2014; 111:17857-62. [PMID: 25425663 DOI: 10.1073/pnas.1410144111] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The main focus of enzymology is on the enzyme rates, substrate structures, and reactivity, whereas the role of solvent dynamics in mediating the biological reaction is often left aside owing to its complex molecular behavior. We used integrated X-ray- and terahertz- based time-resolved spectroscopic tools to study protein-water dynamics during proteolysis of collagen-like substrates by a matrix metalloproteinase. We show equilibration of structural kinetic transitions in the millisecond timescale during degradation of the two model substrates collagen and gelatin, which have different supersecondary structure and flexibility. Unexpectedly, the detected changes in collective enzyme-substrate-water-coupled motions persisted well beyond steady state for both substrates while displaying substrate-specific behaviors. Molecular dynamics simulations further showed that a hydration funnel (i.e., a gradient in retardation of hydrogen bond (HB) dynamics toward the active site) is substrate-dependent, exhibiting a steeper gradient for the more complex enzyme-collagen system. The long-lasting changes in protein-water dynamics reflect a collection of local energetic equilibrium states specifically formed during substrate conversion. Thus, the observed long-lasting water dynamics contribute to the net enzyme reactivity, impacting substrate binding, positional catalysis, and product release.
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30
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Pietraszek K, Chatron-Colliet A, Brézillon S, Perreau C, Jakubiak-Augustyn A, Krotkiewski H, Maquart FX, Wegrowski Y. Lumican: A new inhibitor of matrix metalloproteinase-14 activity. FEBS Lett 2014; 588:4319-24. [DOI: 10.1016/j.febslet.2014.09.040] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/24/2014] [Accepted: 09/24/2014] [Indexed: 11/27/2022]
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31
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Chemical specificity and conformational flexibility in proteinase-inhibitor interaction: scaffolds for promiscuous binding. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:151-7. [PMID: 25151636 DOI: 10.1016/j.pbiomolbio.2014.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/26/2014] [Accepted: 08/02/2014] [Indexed: 11/24/2022]
Abstract
One of the most important roles of proteins in cellular milieu is recognition of other biomolecules including other proteins. Protein-protein complexes are involved in many essential cellular processes. Interfaces of protein-protein complexes are traditionally known to be conserved in evolution and less flexible than other solvent interacting tertiary structural surface. But many examples are emerging where these features do not hold good. An understanding of inter-play between flexibility and sequence conservation is emerging, providing a fresh dimension to the paradigm of sequence-structure-function relationship. The functional manifestation of the inter-relation between sequence conservation and flexibility of interface is exemplified in this review using proteinase-inhibitor protein complexes.
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32
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Sharabi O, Shirian J, Grossman M, Lebendiker M, Sagi I, Shifman J. Affinity- and specificity-enhancing mutations are frequent in multispecific interactions between TIMP2 and MMPs. PLoS One 2014; 9:e93712. [PMID: 24710006 PMCID: PMC3977929 DOI: 10.1371/journal.pone.0093712] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 03/05/2014] [Indexed: 12/04/2022] Open
Abstract
Multispecific proteins play a major role in controlling various functions such as signaling, regulation of transcription/translation, and immune response. Hence, a thorough understanding of the atomic-level principles governing multispecific interactions is important not only for the advancement of basic science but also for applied research such as drug design. Here, we study evolution of an exemplary multispecific protein, a Tissue Inhibitor of Matrix Metalloproteinases 2 (TIMP2) that binds with comparable affinities to more than twenty-six members of the Matrix Metalloproteinase (MMP) and the related ADAMs families. We postulate that due to its multispecific nature, TIMP2 is not optimized to bind to any individual MMP type, but rather embodies a compromise required for interactions with all MMPs. To explore this hypothesis, we perform computational saturation mutagenesis of the TIMP2 binding interface and predict changes in free energy of binding to eight MMP targets. Computational results reveal the non-optimality of the TIMP2 binding interface for all studied proteins, identifying many affinity-enhancing mutations at multiple positions. Several TIMP2 point mutants predicted to enhance binding affinity and/or binding specificity towards MMP14 were selected for experimental verification. Experimental results show high abundance of affinity-enhancing mutations in TIMP2, with some point mutations producing more than ten-fold improvement in affinity to MMP14. Our computational and experimental results collaboratively demonstrate that the TIMP2 sequence lies far from the fitness maximum when interacting with its target enzymes. This non-optimality of the binding interface and high potential for improvement might characterize all proteins evolved for binding to multiple targets.
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Affiliation(s)
- Oz Sharabi
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jason Shirian
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Moran Grossman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Mario Lebendiker
- Wolfson Center for Structural Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Julia Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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33
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Pahwa S, Stawikowski MJ, Fields GB. Monitoring and Inhibiting MT1-MMP during Cancer Initiation and Progression. Cancers (Basel) 2014; 6:416-35. [PMID: 24549119 PMCID: PMC3980612 DOI: 10.3390/cancers6010416] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 02/07/2014] [Accepted: 02/08/2014] [Indexed: 12/14/2022] Open
Abstract
Membrane-type 1 matrix metalloproteinase (MT1-MMP) is a zinc-dependent type-I transmembrane metalloproteinase involved in pericellular proteolysis, migration and invasion. Numerous substrates and binding partners have been identified for MT1-MMP, and its role in collagenolysis appears crucial for tumor invasion. However, development of MT1-MMP inhibitors must consider the substantial functions of MT1-MMP in normal physiology and disease prevention. The present review examines the plethora of MT1-MMP activities, how these activities relate to cancer initiation and progression, and how they can be monitored in real time. Examination of MT1-MMP activities and cell surface behaviors can set the stage for the development of unique, selective MT1-MMP inhibitors.
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Affiliation(s)
- Sonia Pahwa
- Department of Pharmaceutical Sciences, College of Pharmacy, The University of Oklahoma, 1110 North Stonewall Avenue, Oklahoma City, OK 73117, USA.
| | - Maciej J Stawikowski
- Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL 34987, USA.
| | - Gregg B Fields
- Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL 34987, USA.
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34
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Ogata H, Decaneto E, Grossman M, Havenith M, Sagi I, Lubitz W, Knipp M. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of membrane type 1 matrix metalloproteinase. Acta Crystallogr F Struct Biol Commun 2014; 70:232-5. [PMID: 24637763 PMCID: PMC3936455 DOI: 10.1107/s2053230x13034857] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 12/30/2013] [Indexed: 12/13/2022] Open
Abstract
Membrane type 1 matrix metalloproteinase (MT1-MMP) belongs to the large family of zinc-dependent endopeptidases termed MMPs that are located in the extracellular matrix. MT1-MMP was crystallized at 277 K using the vapour-diffusion method with PEG as a precipitating agent. Data sets for MT1-MMP were collected to 2.24 Å resolution at 100 K. The crystals belonged to space group P4(3)2(1)2, with unit-cell parameters a = 62.99, c = 122.60 Å. The crystal contained one molecule per asymmetric unit, with a Matthews coefficient (VM) of 2.90 Å(3) Da(-1); the solvent content is estimated to be 57.6%.
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Affiliation(s)
- Hideaki Ogata
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Elena Decaneto
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
- Physikalische Chemie II, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Moran Grossman
- Physikalische Chemie II, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Martina Havenith
- Physikalische Chemie II, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Irit Sagi
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Markus Knipp
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
- Physikalische Chemie II, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
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35
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Nuti E, Casalini F, Santamaria S, Fabbi M, Carbotti G, Ferrini S, Marinelli L, La Pietra V, Novellino E, Camodeca C, Orlandini E, Nencetti S, Rossello A. Selective Arylsulfonamide Inhibitors of ADAM-17: Hit Optimization and Activity in Ovarian Cancer Cell Models. J Med Chem 2013; 56:8089-103. [DOI: 10.1021/jm4011753] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elisa Nuti
- Dipartimento
di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Francesca Casalini
- Dipartimento
di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | | | - Marina Fabbi
- Dipartimento
di Terapie Oncologiche Integrate, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Largo R. Benzi 10, 16132 Genova, Italy
| | - Grazia Carbotti
- Dipartimento
di Terapie Oncologiche Integrate, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Largo R. Benzi 10, 16132 Genova, Italy
| | - Silvano Ferrini
- Dipartimento
di Terapie Oncologiche Integrate, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Largo R. Benzi 10, 16132 Genova, Italy
| | - Luciana Marinelli
- Dipartimento
di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Valeria La Pietra
- Dipartimento
di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Ettore Novellino
- Dipartimento
di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Caterina Camodeca
- Dipartimento
di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | | | - Susanna Nencetti
- Dipartimento
di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Armando Rossello
- Dipartimento
di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
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36
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Batra J, Soares AS, Mehner C, Radisky ES. Matrix metalloproteinase-10/TIMP-2 structure and analyses define conserved core interactions and diverse exosite interactions in MMP/TIMP complexes. PLoS One 2013; 8:e75836. [PMID: 24073280 PMCID: PMC3779175 DOI: 10.1371/journal.pone.0075836] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 08/21/2013] [Indexed: 11/18/2022] Open
Abstract
Matrix metalloproteinases (MMPs) play central roles in vertebrate tissue development, remodeling, and repair. The endogenous tissue inhibitors of metalloproteinases (TIMPs) regulate proteolytic activity by binding tightly to the MMP active site. While each of the four TIMPs can inhibit most MMPs, binding data reveal tremendous heterogeneity in affinities of different TIMP/MMP pairs, and the structural features that differentiate stronger from weaker complexes are poorly understood. Here we report the crystal structure of the comparatively weakly bound human MMP-10/TIMP-2 complex at 2.1 Å resolution. Comparison with previously reported structures of MMP-3/TIMP-1, MT1-MMP/TIMP-2, MMP-13/TIMP-2, and MMP-10/TIMP-1 complexes offers insights into the structural basis of binding selectivity. Our analyses identify a group of highly conserved contacts at the heart of MMP/TIMP complexes that define the conserved mechanism of inhibition, as well as a second category of diverse adventitious contacts at the periphery of the interfaces. The AB loop of the TIMP N-terminal domain and the contact loops of the TIMP C-terminal domain form highly variable peripheral contacts that can be considered as separate exosite interactions. In some complexes these exosite contacts are extensive, while in other complexes the AB loop or C-terminal domain contacts are greatly reduced and appear to contribute little to complex stability. Our data suggest that exosite interactions can enhance MMP/TIMP binding, although in the relatively weakly bound MMP-10/TIMP-2 complex they are not well optimized to do so. Formation of highly variable exosite interactions may provide a general mechanism by which TIMPs are fine-tuned for distinct regulatory roles in biology.
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Affiliation(s)
- Jyotica Batra
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, Florida, United States of America
| | - Alexei S. Soares
- Biology Department, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Christine Mehner
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, Florida, United States of America
| | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, Florida, United States of America
- * E-mail:
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37
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Fischer T, Riedl R. Strategic targeting of multiple water-mediated interactions: a concise and rational structure-based design approach to potent and selective MMP-13 inhibitors. ChemMedChem 2013; 8:1457-61, 1572. [PMID: 23894097 PMCID: PMC4281860 DOI: 10.1002/cmdc.201300278] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Fischer
- Institute for Chemistry and Biological Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820 Wädenswil (Switzerland) www.icbc.zhaw.ch/organic‐chemistry
| | - Rainer Riedl
- Institute for Chemistry and Biological Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820 Wädenswil (Switzerland) www.icbc.zhaw.ch/organic‐chemistry
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38
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Burrows GG, Van't Hof W, Newell LF, Reddy A, Wilmarth PA, David LL, Raber A, Bogaerts A, Pinxteren J, Deans RJ, Maziarz RT. Dissection of the human multipotent adult progenitor cell secretome by proteomic analysis. Stem Cells Transl Med 2013; 2:745-57. [PMID: 23981727 DOI: 10.5966/sctm.2013-0031] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Multipotent adult progenitor cells (MAPCs) are adult adherent stromal stem cells currently being assessed in acute graft versus host disease clinical trials with demonstrated immunomodulatory capabilities and the potential to ameliorate detrimental autoimmune and inflammation-related processes. Our previous studies documented that MAPCs secrete factors that play a role in regulating T-cell activity. Here we expand our studies using a proteomics approach to characterize and quantify MAPC secretome components secreted over 72 hours in vitro under steady-state conditions and in the presence of the inflammatory triggers interferon-γ and lipopolysaccharide, or a tolerogenic CD74 ligand, RTL1000. MAPCs differentially responded to each of the tested stimuli, secreting molecules that regulate the biological activity of the extracellular matrix (ECM), including proteins that make up the ECM itself, proteins that regulate its construction/deconstruction, and proteins that serve to attach and detach growth factors from ECM components for redistribution upon appropriate stimulation. MAPCs secreted a wide array of proteases, some detectable in their zymogen forms. MAPCs also secreted protease inhibitors that would regulate protease activity. MAPCs secreted chemokines and cytokines that could provide molecular guidance cues to various cell types, including neutrophils, macrophages, and T cells. In addition, MAPCs secreted factors involved in maintenance of a homeostatic environment, regulating such diverse programs as innate immunity, angiogenesis/angiostasis, targeted delivery of growth factors, and the matrix-metalloprotease cascade.
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39
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Udi Y, Fragai M, Grossman M, Mitternacht S, Arad-Yellin R, Calderone V, Melikian M, Toccafondi M, Berezovsky IN, Luchinat C, Sagi I. Unraveling Hidden Regulatory Sites in Structurally Homologous Metalloproteases. J Mol Biol 2013; 425:2330-46. [DOI: 10.1016/j.jmb.2013.04.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 04/05/2013] [Accepted: 04/05/2013] [Indexed: 01/26/2023]
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40
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Abstract
The matrix metalloproteinases (MMPs) exhibit a broad array of activities, some catalytic and some non-catalytic in nature. An overall lack of selectivity has rendered small molecule, active site targeted MMP inhibitors problematic in execution. Inhibitors that favor few or individual members of the MMP family often take advantage of interactions outside the enzyme active site. We presently focus on peptide-based MMP inhibitors and probes that do not incorporate conventional Zn2+ binding groups. In some cases, these inhibitors and probes function by binding only secondary binding sites (exosites), while others bind both exosites and the active site. A myriad of MMP mediated-activities beyond selective catalysis can be inhibited by peptides, particularly cell adhesion, proliferation, motility, and invasion. Selective MMP binding peptides comprise highly customizable, unique imaging agents. Areas of needed improvement for MMP targeting peptides include binding affinity and stability.
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Jung YS, Liu XW, Chirco R, Warner RB, Fridman R, Kim HRC. TIMP-1 induces an EMT-like phenotypic conversion in MDCK cells independent of its MMP-inhibitory domain. PLoS One 2012; 7:e38773. [PMID: 22701711 PMCID: PMC3372473 DOI: 10.1371/journal.pone.0038773] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 05/12/2012] [Indexed: 12/16/2022] Open
Abstract
Matrix metalloproteinases (MMPs) and their endogenous inhibitors (TIMPs) regulate epithelial-mesenchymal transition (EMT) critical for the development of epithelial organs as well as cancer cell invasion. TIMP-1 is frequently overexpressed in several types of human cancers and serves as a prognostic marker. The present study investigates the roles of TIMP-1 on the EMT process and formation of the lumen-like structure in a 3D Matrigel culture of MDCK cells. We show that TIMP-1 overexpression effectively prevents cell polarization and acinar-like structure formation. TIMP-1 induces expression of the developmental EMT transcription factors such as SLUG, TWIST, ZEB1 and ZEB2, leading to downregulation of epithelial marker and upregulation of mesenchymal markers. Importantly, TIMP-1's ability to induce the EMT-like process is independent of its MMP-inhibitory domain. To our surprise, TIMP-1 induces migratory and invasive properties in MDCK cells. Here, we present a novel finding that TIMP-1 signaling upregulates MT1-MMP and MMP-2 expression, and potentiates MT1-MMP activation of pro-MMP-2, contributing to tumor cell invasion. In spite of the fact that TIMP-1, as opposed to TIMP-2, does not interact with and inhibit MT1-MMP, TIMP-1 may act as a key regulator of MT1-MMP/MMP-2 axis. Collectively, our findings suggest a model in which TIMP-1 functions as a signaling molecule and also as an endogenous inhibitor of MMPs. This concept represents a paradigm shift in the current view of TIMP-1/MT1-MMP interactions and functions during cancer development/progression.
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Affiliation(s)
- Young Suk Jung
- Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Xu-Wen Liu
- Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Rosemarie Chirco
- Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Richard B. Warner
- Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Rafael Fridman
- Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Hyeong-Reh Choi Kim
- Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- * E-mail:
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Batra J, Robinson J, Soares AS, Fields AP, Radisky DC, Radisky ES. Matrix metalloproteinase-10 (MMP-10) interaction with tissue inhibitors of metalloproteinases TIMP-1 and TIMP-2: binding studies and crystal structure. J Biol Chem 2012; 287:15935-46. [PMID: 22427646 DOI: 10.1074/jbc.m112.341156] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Matrix metalloproteinase 10 (MMP-10, stromelysin-2) is a secreted metalloproteinase with functions in skeletal development, wound healing, and vascular remodeling; its overexpression is also implicated in lung tumorigenesis and tumor progression. To understand the regulation of MMP-10 by tissue inhibitors of metalloproteinases (TIMPs), we have assessed equilibrium inhibition constants (K(i)) of putative physiological inhibitors TIMP-1 and TIMP-2 for the active catalytic domain of human MMP-10 (MMP-10cd) using multiple kinetic approaches. We find that TIMP-1 inhibits the MMP-10cd with a K(i) of 1.1 × 10(-9) M; this interaction is 10-fold weaker than the inhibition of the similar MMP-3 (stromelysin-1) catalytic domain (MMP-3cd) by TIMP-1. TIMP-2 inhibits the MMP-10cd with a K(i) of 5.8 × 10(-9) M, which is again 10-fold weaker than the inhibition of MMP-3cd by this inhibitor (K(i) = 5.5 × 10(-10) M). We solved the x-ray crystal structure of TIMP-1 bound to the MMP-10cd at 1.9 Å resolution; the structure was solved by molecular replacement and refined with an R-factor of 0.215 (R(free) = 0.266). Comparing our structure of MMP-10cd·TIMP-1 with the previously solved structure of MMP-3cd·TIMP-1 (Protein Data Bank entry 1UEA), we see substantial differences at the binding interface that provide insight into the differential binding of stromelysin family members to TIMP-1. This structural information may ultimately assist in the design of more selective TIMP-based inhibitors tailored for specificity toward individual members of the stromelysin family, with potential therapeutic applications.
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Affiliation(s)
- Jyotica Batra
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224, USA
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Sela-Passwell N, Kikkeri R, Dym O, Rozenberg H, Margalit R, Arad-Yellin R, Eisenstein M, Brenner O, Shoham T, Danon T, Shanzer A, Sagi I. Antibodies targeting the catalytic zinc complex of activated matrix metalloproteinases show therapeutic potential. Nat Med 2011; 18:143-7. [PMID: 22198278 DOI: 10.1038/nm.2582] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 10/25/2011] [Indexed: 12/12/2022]
Abstract
Endogenous tissue inhibitors of metalloproteinases (TIMPs) have key roles in regulating physiological and pathological cellular processes. Imitating the inhibitory molecular mechanisms of TIMPs while increasing selectivity has been a challenging but desired approach for antibody-based therapy. TIMPs use hybrid protein-protein interactions to form an energetic bond with the catalytic metal ion, as well as with enzyme surface residues. We used an innovative immunization strategy that exploits aspects of molecular mimicry to produce inhibitory antibodies that show TIMP-like binding mechanisms toward the activated forms of gelatinases (matrix metalloproteinases 2 and 9). Specifically, we immunized mice with a synthetic molecule that mimics the conserved structure of the metalloenzyme catalytic zinc-histidine complex residing within the enzyme active site. This immunization procedure yielded selective function-blocking monoclonal antibodies directed against the catalytic zinc-protein complex and enzyme surface conformational epitopes of endogenous gelatinases. The therapeutic potential of these antibodies has been demonstrated with relevant mouse models of inflammatory bowel disease. Here we propose a general experimental strategy for generating inhibitory antibodies that effectively target the in vivo activity of dysregulated metalloproteinases by mimicking the mechanism employed by TIMPs.
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Affiliation(s)
- Netta Sela-Passwell
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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Grossman M, Born B, Heyden M, Tworowski D, Fields GB, Sagi I, Havenith M. Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site. Nat Struct Mol Biol 2011; 18:1102-8. [PMID: 21926991 DOI: 10.1038/nsmb.2120] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 07/07/2011] [Indexed: 01/16/2023]
Abstract
Solvent dynamics can play a major role in enzyme activity, but obtaining an accurate, quantitative picture of solvent activity during catalysis is quite challenging. Here, we combine terahertz spectroscopy and X-ray absorption analyses to measure changes in the coupled water-protein motions during peptide hydrolysis by a zinc-dependent human metalloprotease. These changes were tightly correlated with rearrangements at the active site during the formation of productive enzyme-substrate intermediates and were different from those in an enzyme-inhibitor complex. Molecular dynamics simulations showed a steep gradient of fast-to-slow coupled protein-water motions around the protein, active site and substrate. Our results show that water retardation occurs before formation of the functional Michaelis complex. We propose that the observed gradient of coupled protein-water motions may assist enzyme-substrate interactions through water-polarizing mechanisms that are remotely mediated by the catalytic metal ion and the enzyme active site.
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Affiliation(s)
- Moran Grossman
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
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Bahudhanapati H, Zhang Y, Sidhu SS, Brew K. Phage display of tissue inhibitor of metalloproteinases-2 (TIMP-2): identification of selective inhibitors of collagenase-1 (metalloproteinase 1 (MMP-1)). J Biol Chem 2011; 286:31761-70. [PMID: 21715326 DOI: 10.1074/jbc.m111.253328] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tissue inhibitor of metalloproteinases-2 (TIMP-2) is a broad spectrum inhibitor of the matrix metalloproteinases (MMPs), which function in extracellular matrix catabolism. Here, phage display was used to identify variants of human TIMP-2 that are selective inhibitors of human MMP-1, a collagenase whose unregulated action is linked to cancer, arthritis, and fibrosis. Using hard randomization of residues 2, 4, 5, and 6 (L1) and soft randomization of residues 34-40 (L2) and 67-70 (L3), a library was generated containing 2 × 10(10) variants of TIMP-2. Five clones were isolated after five rounds of selection with MMP-1, using MMP-3 as a competitor. The enriched phages selectively bound MMP-1 relative to MMP-3 and contained mutations only in L1. The most selective variant (TM8) was used to generate a second library in which residues Cys(1)-Gln(9) were soft-randomized. Four additional clones, selected from this library, showed a similar affinity for MMP-1 as wild-type TIMP-2 but reduced affinity for MMP-3. Variants of the N-terminal domain of TIMP-2 (N-TIMP-2) with the sequences of the most selective clones were expressed and characterized for inhibitory activity against eight MMPs. All were effective inhibitors of MMP-1 with nanomolar K(i) values, but TM8, containing Ser(2) to Asp and Ser(4) to Ala substitutions, was the most selective having a nanomolar K(i) value for MMP-1 but no detectable inhibitory activity toward MMP-3 and MMP-14 up to 10 μM. This study suggests that phage display and selection with other MMPs may be an effective method for discovering tissue inhibitor of metalloproteinase variants that discriminate between specified MMPs as targets.
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Affiliation(s)
- Harinath Bahudhanapati
- Department of Basic Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida 33431, USA
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Remacle AG, Shiryaev SA, Radichev IA, Rozanov DV, Stec B, Strongin AY. Dynamic interdomain interactions contribute to the inhibition of matrix metalloproteinases by tissue inhibitors of metalloproteinases. J Biol Chem 2011; 286:21002-12. [PMID: 21518756 DOI: 10.1074/jbc.m110.200139] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Because of their important function, matrix metalloproteinases (MMPs) are promising drug targets in multiple diseases, including malignancies. The structure of MMPs includes a catalytic domain, a hinge, and a hemopexin domain (PEX), which are followed by a transmembrane and cytoplasmic tail domains or by a glycosylphosphatidylinositol linker in membrane-type MMPs (MT-MMPs). TIMPs-1, -2, -3, and -4 are potent natural regulators of the MMP activity. These are the inhibitory N-terminal and the non-inhibitory C-terminal structural domains in TIMPs. Based on our structural modeling, we hypothesized that steric clashes exist between the non-inhibitory C-terminal domain of TIMPs and the PEX of MMPs. Conversely, a certain mobility of the PEX relative to the catalytic domain is required to avoid these obstacles. Because of its exceedingly poor association constant and, in contrast with TIMP-2, TIMP-1 is inefficient against MT1-MMP. We specifically selected an MT1-MMP·TIMP-1 pair to test our hypothesis, because any improvement of the inhibitory potency would be readily recorded. We characterized the domain-swapped MT1-MMP chimeras in which the PEX of MMP-2 (that forms a complex with TIMP-2) and of MMP-9 (that forms a complex with TIMP-1) replaced the original PEX in the MT1-MMP structure. In contrast with the wild-type MT1-MMP, the diverse proteolytic activities of the swapped-PEX chimeras were then inhibited by both TIMP-1 and TIMP-2. Overall, our studies suggest that the structural parameters of both domains of TIMPs have to be taken into account for their re-engineering to harness the therapeutic in vivo potential of the novel TIMP-based MMP antagonists with constrained selectivity.
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Affiliation(s)
- Albert G Remacle
- Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA
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Sela-Passwell N, Trahtenherts A, Krüger A, Sagi I. New opportunities in drug design of metalloproteinase inhibitors: combination between structure-function experimental approaches and systems biology. Expert Opin Drug Discov 2011; 6:527-42. [PMID: 22646077 DOI: 10.1517/17460441.2011.560936] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION MMPs (matrix metalloproteinases) and ADAMs (a disintegrin and metalloproteinases) are endopeptidases central to the degradation and remodeling of the extracellular matrix. These proteases also exhibit regulatory activity in cell signaling pathways and thus tissue homeostasis under normal conditions and in many diseases. Consequently, individual members of the MMP and ADAM protein families were identified as important therapeutic targets. However, designing effective inhibitors in vivo for this class of enzymes appears to be extremely challenging. This is attributed to the broad structural similarity of their active sites and to the dynamic functional interconnectivity of MMPs with other proteases, their inhibitors, and substrates (the so-called degradome) in healthy and disease tissues. AREAS COVERED The article covers the progress in designing metalloproteinase inhibitors, based on recent advancements in our understanding of enzyme structures and their function as master regulators. It also discusses the potential of utilizing structure-based drug design strategies in conjunction with systems biology experimental approaches for designing potent and therapeutically effective metalloproteinase inhibitors. EXPERT OPINION We highlight the use of protein-based drug design strategies, for example, antibodies and protein scaffolds, targeting extracatalytic domains, which are central to proteolytic and non-proteolytic enzyme functions. Such rationally designed function-blocking inhibitors may create new opportunities in disease management and in emerging therapies that require control of dysregulated MMP activity without causing severe side effects. Importantly, the lessons learned from studying these protein-based inhibitors can be implemented to design new and effective small or medium sized synthetic antagonists.
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Affiliation(s)
- Netta Sela-Passwell
- The Weizmann Institute of Science, Department of Biological Regulation , Rehovot 76100 , Israel
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Kucera K, Harrison LM, Cappello M, Modis Y. Ancylostoma ceylanicum excretory-secretory protein 2 adopts a netrin-like fold and defines a novel family of nematode proteins. J Mol Biol 2011; 408:9-17. [PMID: 21352830 DOI: 10.1016/j.jmb.2011.02.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 02/12/2011] [Accepted: 02/15/2011] [Indexed: 10/18/2022]
Abstract
Hookworms are human parasites that have devastating effects on global health, particularly in underdeveloped countries. Ancylostoma ceylanicum infects humans and animals, making it a useful model organism to study disease pathogenesis. A. ceylanicum excretory-secretory protein 2 (AceES-2), a highly immunoreactive molecule secreted by adult worms at the site of intestinal attachment, is partially protective when administered as a mucosal vaccine against hookworm anemia. The crystal structure of AceES-2 determined at 1.75 Å resolution shows that it adopts a netrin-like fold similar to that found in tissue inhibitors of matrix metalloproteases (TIMPs) and in complement factors C3 and C5. However, recombinant AceES-2 does not significantly inhibit the 10 most abundant human matrix metalloproteases or complement-mediated cell lysis. The presence of a highly acidic surface on AceES-2 suggests that it may function as a cytokine decoy receptor. Several small nematode proteins that have been annotated as TIMPs or netrin-domain-containing proteins display sequence homology in structurally important regions of AceES-2's netrin-like fold. Together, our results suggest that AceES-2 defines a novel family of nematode netrin-like proteins, which may function to modulate the host immune response to hookworm and other parasites.
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Affiliation(s)
- Kaury Kucera
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
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