Irit Sagi is Incumbent of the Maurizio Pontecorvo Professorial Chair in the Department of Biological Regulation at the Weizmann Institute of Science, Rehovot, Israel. Jean P. Gaffney completed her postdoctoral work in Dr. Sagi’s laboratory at the Weizmann Institute of Science, Rehovot, Israel. She is an Assistant Professor of Chemistry at Baruch College, City University of New York, New York, NY, USA.

• List of Contributors ix1 Matrix Metalloproteinases: From Structure to Function 1Maciej J. Stawikowski and Gregg B. Fields1.1 Introduction 11.2 Structures of MMPs 11.2.1 General MMP structure and domain organization 11.2.2 Catalytic domain 21.2.3 Catalytic mechanism 31.2.4 Fibronectin type II-like inserts 31.2.5 Linker region 41.2.6 Hemopexin-like domain 61.2.7 Transmembrane domain and cytoplasmic tail 71.3 Overview of MMP substrate specificity 81.3.1 ECM substrates 91.3.2 Cell surface substrates 101.3.3 Intracellular MMP targets 111.4 Selective mechanisms of action 131.4.1 Collagenolysis 131.4.2 Gelatinolysis 15Acknowledgments 16References 162 Dynamics and Mechanism of Substrate Recognition by Matrix Metalloproteases 23Ivan E. Collier and Gregory I. Goldberg2.1 Introduction 232.2 Conformational flexibility of MMPs is inexorably linked to collagen proteolysis 242.3 Dynamics of MMP-2 and MMP-9 interaction with gelatin 262.4 Surface diffusion: a common mechanism for substrate interaction adapted by MMP-2 and MMP-9 262.5 Dynamics of MMP interaction with collagen fibrils 282.6 Mechanism of interaction of MMP-1, MMP-2, MMP-9, and MMP-14 with collagen substrate involves surface diffusion 282.7 Mechanism of MMP-1 diffusion on native collagen fibrils 302.8 Triple helical collagen cleavage – diffusion coupling 312.9 Conclusions 34References 363 Matrix Metalloproteinases: From Structure to Function 41Marco Fragai and Claudio Luchinat3.1 Introduction 413.2 Classification and structural features 423.3 Catalytic mechanism 453.4 Intra- and inter-domain flexibility 473.5 Elastin and collagen degradation 47References 544 Metzincin Modulators 61Dmitry Minond4.1 Inhibitors 614.1.1 Antibodies: targeting beyond the active site 614.1.2 Peptide-based inhibitors 654.1.3 Small molecules: non-zinc binding exosite inhibitors 684.1.4 Protein-based inhibitors 78Summary and future directions 80References 815 Therapeutics Targeting Matrix Metalloproteinases 85Jillian Cathcart, Ashleigh Pulkoski-Gross, Stanley Zucker, and Jian Cao5.1 Introduction 855.2 Peptidomimetic MMP inhibitors 865.3 Structure-based MMPI drug design 875.4 Mechanism-based MMPI design 895.5 Allosteric MMPI design 905.6 Macromolecular MMP inhibitors 915.7 Chemically-modified tetracyclines 935.8 Alternative approaches 945.9 MMPs as anti-targets 955.10 Conclusions 97References 986 Matrix Metalloproteinase Modification of Extracellular Matrix-Mediated Signaling 103Howard C. Crawford and Sharon M. Stack6.1 Introduction 1036.2 The extracellular matrix as a source for signaling ligands 1046.3 ECM and mechanosensory signal transduction 1066.4 Matrix remodeling and modification of mechano-sensory signaling 1086.5 Conclusions and future directions 109References 1097 Meprin and ADAM Metalloproteases: Two Sides of the Same Coin? 115Christoph Becker-Pauly and Stefan Rose-John7.1 Introduction 1157.2 Meprin metalloproteases 1167.3 Structure of meprin α and meprin β 1167.4 Proteomics for the identification of meprin substrates 1187.5 Meprins in health and disease 1187.6 Proteolytic back-and-forth of meprins and ADAMs 1197.7 Collagen fibril formation 1197.8 Angiogenesis and cancer 1207.9 Inflammation 1217.10 ADAM Proteases 1217.11 The ADAM family of proteases 1237.12 Orchestration of different pathways by ADAM17 1237.13 Regulation of ADAM17 activity 1237.14 Role of ADAM17 in vivo 1257.15 Role of ADAM17 in humans 125References 1268 Subtracting Matrix Out of the Equation: New Key Roles of Matrix Metalloproteinases in Innate Immunity and Disease 131Antoine Dufour and Christopher M. Overall8.1 The tale of a frog’s tail 1318.2 The MMP family 1328.3 Making the cut as immune regulators 1338.4 Enter the “omics” era: genomics, proteomics and degradomics 1378.5 ECM versus non-ECM MMP substrates 1388.6 Moonlighting protein substrates: intracellular proteins cleaved outside the cell 1428.7 Intracellular protein substrates cleaved inside the cell by MMPs 1438.8 Non-proteolytic roles of MMPs: missed in the myth? 1458.9 The fairy tail of a frog has an unexpected ending 149Acknowledgements 149References 1499 MMPs: From Genomics to Degradomics 153Barbara Grünwald, Pascal Schlage, Achim Krüger, and Ulrich auf dem Keller9.1 Introduction 1539.1.1 Genomics: general aspects 1549.1.2 The genomics approach to MMP function in cancer 1559.1.3 Taking first steps towards MMP inhibition in cancer therapy 1569.1.4 Lessons from the failure of unselective MMP inhibition 1579.1.5 Limitations of the genomic approach to MMP function 1609.1.6 Approaching proteolysis as a system 1619.2 Degradomics – An Overview 1649.2.1 Global assessment of MMP expression and activity 1669.2.2 Defining MMP active site specificity 1689.2.3 MMP substrate degradomics 1699.2.4 Targeted degradomics 1719.2.5 Data integration and repositories 1739.3 Conclusions 174Acknowledgments 174References 17410 MMPs in Biology and Medicine 183Di Jia, Roopali Roy, and Marsha A. Moses10.1 Introduction 18310.2 Functional roles of MMPs and ADAMs 18410.2.1 ECM remodeling 18410.2.2 Processing of growth factors and receptors 18510.2.3 Modulation of cell migration, invasion, proliferation, and epithelial to mesenchymal transition (EMT) 18610.2.4 Regulation of angiogenesis 18710.3 MMPs as diagnostic and prognostic biomarkers of cancer 18710.3.1 Breast cancer 18810.3.2 Prostate cancer 18910.3.3 Lung cancer 19010.3.4 Pancreatic cancer 19110.3.5 Ovarian cancer 19210.4 MMPs/ADAMs as diagnostic and prognostic biomarkers for non-neoplastic diseases 19210.4.1 Cardiovascular diseases 19310.4.2 Endometriosis 19310.4.3 Preeclampsia 19510.4.4 Arthritis 19610.5 MMPs as biomarkers of therapeutic efficacy 19710.6 MMP-specific molecular imaging for noninvasive disease detection 20110.7 Conclusions 202Acknowledgments 203References 203Index 215

Irit Sagi is Incumbent of the Maurizio Pontecorvo Professorial Chair in the Department of Biological Regulation at the Weizmann Institute of Science, Rehovot, Israel. Jean P. Gaffney completed her postdoctoral work in Dr. Sagi’s laboratory at the Weizmann Institute of Science, Rehovot, Israel. She is an Assistant Professor of Chemistry at Baruch College, City University of New York, New York, NY, USA.

• List of Contributors ix1 Matrix Metalloproteinases: From Structure to Function 1Maciej J. Stawikowski and Gregg B. Fields1.1 Introduction 11.2 Structures of MMPs 11.2.1 General MMP structure and domain organization 11.2.2 Catalytic domain 21.2.3 Catalytic mechanism 31.2.4 Fibronectin type II-like inserts 31.2.5 Linker region 41.2.6 Hemopexin-like domain 61.2.7 Transmembrane domain and cytoplasmic tail 71.3 Overview of MMP substrate specificity 81.3.1 ECM substrates 91.3.2 Cell surface substrates 101.3.3 Intracellular MMP targets 111.4 Selective mechanisms of action 131.4.1 Collagenolysis 131.4.2 Gelatinolysis 15Acknowledgments 16References 162 Dynamics and Mechanism of Substrate Recognition by Matrix Metalloproteases 23Ivan E. Collier and Gregory I. Goldberg2.1 Introduction 232.2 Conformational flexibility of MMPs is inexorably linked to collagen proteolysis 242.3 Dynamics of MMP-2 and MMP-9 interaction with gelatin 262.4 Surface diffusion: a common mechanism for substrate interaction adapted by MMP-2 and MMP-9 262.5 Dynamics of MMP interaction with collagen fibrils 282.6 Mechanism of interaction of MMP-1, MMP-2, MMP-9, and MMP-14 with collagen substrate involves surface diffusion 282.7 Mechanism of MMP-1 diffusion on native collagen fibrils 302.8 Triple helical collagen cleavage – diffusion coupling 312.9 Conclusions 34References 363 Matrix Metalloproteinases: From Structure to Function 41Marco Fragai and Claudio Luchinat3.1 Introduction 413.2 Classification and structural features 423.3 Catalytic mechanism 453.4 Intra- and inter-domain flexibility 473.5 Elastin and collagen degradation 47References 544 Metzincin Modulators 61Dmitry Minond4.1 Inhibitors 614.1.1 Antibodies: targeting beyond the active site 614.1.2 Peptide-based inhibitors 654.1.3 Small molecules: non-zinc binding exosite inhibitors 684.1.4 Protein-based inhibitors 78Summary and future directions 80References 815 Therapeutics Targeting Matrix Metalloproteinases 85Jillian Cathcart, Ashleigh Pulkoski-Gross, Stanley Zucker, and Jian Cao5.1 Introduction 855.2 Peptidomimetic MMP inhibitors 865.3 Structure-based MMPI drug design 875.4 Mechanism-based MMPI design 895.5 Allosteric MMPI design 905.6 Macromolecular MMP inhibitors 915.7 Chemically-modified tetracyclines 935.8 Alternative approaches 945.9 MMPs as anti-targets 955.10 Conclusions 97References 986 Matrix Metalloproteinase Modification of Extracellular Matrix-Mediated Signaling 103Howard C. Crawford and Sharon M. Stack6.1 Introduction 1036.2 The extracellular matrix as a source for signaling ligands 1046.3 ECM and mechanosensory signal transduction 1066.4 Matrix remodeling and modification of mechano-sensory signaling 1086.5 Conclusions and future directions 109References 1097 Meprin and ADAM Metalloproteases: Two Sides of the Same Coin? 115Christoph Becker-Pauly and Stefan Rose-John7.1 Introduction 1157.2 Meprin metalloproteases 1167.3 Structure of meprin α and meprin β 1167.4 Proteomics for the identification of meprin substrates 1187.5 Meprins in health and disease 1187.6 Proteolytic back-and-forth of meprins and ADAMs 1197.7 Collagen fibril formation 1197.8 Angiogenesis and cancer 1207.9 Inflammation 1217.10 ADAM Proteases 1217.11 The ADAM family of proteases 1237.12 Orchestration of different pathways by ADAM17 1237.13 Regulation of ADAM17 activity 1237.14 Role of ADAM17 in vivo 1257.15 Role of ADAM17 in humans 125References 1268 Subtracting Matrix Out of the Equation: New Key Roles of Matrix Metalloproteinases in Innate Immunity and Disease 131Antoine Dufour and Christopher M. Overall8.1 The tale of a frog’s tail 1318.2 The MMP family 1328.3 Making the cut as immune regulators 1338.4 Enter the “omics” era: genomics, proteomics and degradomics 1378.5 ECM versus non-ECM MMP substrates 1388.6 Moonlighting protein substrates: intracellular proteins cleaved outside the cell 1428.7 Intracellular protein substrates cleaved inside the cell by MMPs 1438.8 Non-proteolytic roles of MMPs: missed in the myth? 1458.9 The fairy tail of a frog has an unexpected ending 149Acknowledgements 149References 1499 MMPs: From Genomics to Degradomics 153Barbara Grünwald, Pascal Schlage, Achim Krüger, and Ulrich auf dem Keller9.1 Introduction 1539.1.1 Genomics: general aspects 1549.1.2 The genomics approach to MMP function in cancer 1559.1.3 Taking first steps towards MMP inhibition in cancer therapy 1569.1.4 Lessons from the failure of unselective MMP inhibition 1579.1.5 Limitations of the genomic approach to MMP function 1609.1.6 Approaching proteolysis as a system 1619.2 Degradomics – An Overview 1649.2.1 Global assessment of MMP expression and activity 1669.2.2 Defining MMP active site specificity 1689.2.3 MMP substrate degradomics 1699.2.4 Targeted degradomics 1719.2.5 Data integration and repositories 1739.3 Conclusions 174Acknowledgments 174References 17410 MMPs in Biology and Medicine 183Di Jia, Roopali Roy, and Marsha A. Moses10.1 Introduction 18310.2 Functional roles of MMPs and ADAMs 18410.2.1 ECM remodeling 18410.2.2 Processing of growth factors and receptors 18510.2.3 Modulation of cell migration, invasion, proliferation, and epithelial to mesenchymal transition (EMT) 18610.2.4 Regulation of angiogenesis 18710.3 MMPs as diagnostic and prognostic biomarkers of cancer 18710.3.1 Breast cancer 18810.3.2 Prostate cancer 18910.3.3 Lung cancer 19010.3.4 Pancreatic cancer 19110.3.5 Ovarian cancer 19210.4 MMPs/ADAMs as diagnostic and prognostic biomarkers for non-neoplastic diseases 19210.4.1 Cardiovascular diseases 19310.4.2 Endometriosis 19310.4.3 Preeclampsia 19510.4.4 Arthritis 19610.5 MMPs as biomarkers of therapeutic efficacy 19710.6 MMP-specific molecular imaging for noninvasive disease detection 20110.7 Conclusions 202Acknowledgments 203References 203Index 215

Irit Sagi is Incumbent of the Maurizio Pontecorvo Professorial Chair in the Department of Biological Regulation at the Weizmann Institute of Science, Rehovot, Israel. Jean P. Gaffney completed her postdoctoral work in Dr. Sagi’s laboratory at the Weizmann Institute of Science, Rehovot, Israel. She is an Assistant Professor of Chemistry at Baruch College, City University of New York, New York, NY, USA.

• List of Contributors ix1 Matrix Metalloproteinases: From Structure to Function 1Maciej J. Stawikowski and Gregg B. Fields1.1 Introduction 11.2 Structures of MMPs 11.2.1 General MMP structure and domain organization 11.2.2 Catalytic domain 21.2.3 Catalytic mechanism 31.2.4 Fibronectin type II-like inserts 31.2.5 Linker region 41.2.6 Hemopexin-like domain 61.2.7 Transmembrane domain and cytoplasmic tail 71.3 Overview of MMP substrate specificity 81.3.1 ECM substrates 91.3.2 Cell surface substrates 101.3.3 Intracellular MMP targets 111.4 Selective mechanisms of action 131.4.1 Collagenolysis 131.4.2 Gelatinolysis 15Acknowledgments 16References 162 Dynamics and Mechanism of Substrate Recognition by Matrix Metalloproteases 23Ivan E. Collier and Gregory I. Goldberg2.1 Introduction 232.2 Conformational flexibility of MMPs is inexorably linked to collagen proteolysis 242.3 Dynamics of MMP-2 and MMP-9 interaction with gelatin 262.4 Surface diffusion: a common mechanism for substrate interaction adapted by MMP-2 and MMP-9 262.5 Dynamics of MMP interaction with collagen fibrils 282.6 Mechanism of interaction of MMP-1, MMP-2, MMP-9, and MMP-14 with collagen substrate involves surface diffusion 282.7 Mechanism of MMP-1 diffusion on native collagen fibrils 302.8 Triple helical collagen cleavage – diffusion coupling 312.9 Conclusions 34References 363 Matrix Metalloproteinases: From Structure to Function 41Marco Fragai and Claudio Luchinat3.1 Introduction 413.2 Classification and structural features 423.3 Catalytic mechanism 453.4 Intra- and inter-domain flexibility 473.5 Elastin and collagen degradation 47References 544 Metzincin Modulators 61Dmitry Minond4.1 Inhibitors 614.1.1 Antibodies: targeting beyond the active site 614.1.2 Peptide-based inhibitors 654.1.3 Small molecules: non-zinc binding exosite inhibitors 684.1.4 Protein-based inhibitors 78Summary and future directions 80References 815 Therapeutics Targeting Matrix Metalloproteinases 85Jillian Cathcart, Ashleigh Pulkoski-Gross, Stanley Zucker, and Jian Cao5.1 Introduction 855.2 Peptidomimetic MMP inhibitors 865.3 Structure-based MMPI drug design 875.4 Mechanism-based MMPI design 895.5 Allosteric MMPI design 905.6 Macromolecular MMP inhibitors 915.7 Chemically-modified tetracyclines 935.8 Alternative approaches 945.9 MMPs as anti-targets 955.10 Conclusions 97References 986 Matrix Metalloproteinase Modification of Extracellular Matrix-Mediated Signaling 103Howard C. Crawford and Sharon M. Stack6.1 Introduction 1036.2 The extracellular matrix as a source for signaling ligands 1046.3 ECM and mechanosensory signal transduction 1066.4 Matrix remodeling and modification of mechano-sensory signaling 1086.5 Conclusions and future directions 109References 1097 Meprin and ADAM Metalloproteases: Two Sides of the Same Coin? 115Christoph Becker-Pauly and Stefan Rose-John7.1 Introduction 1157.2 Meprin metalloproteases 1167.3 Structure of meprin α and meprin β 1167.4 Proteomics for the identification of meprin substrates 1187.5 Meprins in health and disease 1187.6 Proteolytic back-and-forth of meprins and ADAMs 1197.7 Collagen fibril formation 1197.8 Angiogenesis and cancer 1207.9 Inflammation 1217.10 ADAM Proteases 1217.11 The ADAM family of proteases 1237.12 Orchestration of different pathways by ADAM17 1237.13 Regulation of ADAM17 activity 1237.14 Role of ADAM17 in vivo 1257.15 Role of ADAM17 in humans 125References 1268 Subtracting Matrix Out of the Equation: New Key Roles of Matrix Metalloproteinases in Innate Immunity and Disease 131Antoine Dufour and Christopher M. Overall8.1 The tale of a frog’s tail 1318.2 The MMP family 1328.3 Making the cut as immune regulators 1338.4 Enter the “omics” era: genomics, proteomics and degradomics 1378.5 ECM versus non-ECM MMP substrates 1388.6 Moonlighting protein substrates: intracellular proteins cleaved outside the cell 1428.7 Intracellular protein substrates cleaved inside the cell by MMPs 1438.8 Non-proteolytic roles of MMPs: missed in the myth? 1458.9 The fairy tail of a frog has an unexpected ending 149Acknowledgements 149References 1499 MMPs: From Genomics to Degradomics 153Barbara Grünwald, Pascal Schlage, Achim Krüger, and Ulrich auf dem Keller9.1 Introduction 1539.1.1 Genomics: general aspects 1549.1.2 The genomics approach to MMP function in cancer 1559.1.3 Taking first steps towards MMP inhibition in cancer therapy 1569.1.4 Lessons from the failure of unselective MMP inhibition 1579.1.5 Limitations of the genomic approach to MMP function 1609.1.6 Approaching proteolysis as a system 1619.2 Degradomics – An Overview 1649.2.1 Global assessment of MMP expression and activity 1669.2.2 Defining MMP active site specificity 1689.2.3 MMP substrate degradomics 1699.2.4 Targeted degradomics 1719.2.5 Data integration and repositories 1739.3 Conclusions 174Acknowledgments 174References 17410 MMPs in Biology and Medicine 183Di Jia, Roopali Roy, and Marsha A. Moses10.1 Introduction 18310.2 Functional roles of MMPs and ADAMs 18410.2.1 ECM remodeling 18410.2.2 Processing of growth factors and receptors 18510.2.3 Modulation of cell migration, invasion, proliferation, and epithelial to mesenchymal transition (EMT) 18610.2.4 Regulation of angiogenesis 18710.3 MMPs as diagnostic and prognostic biomarkers of cancer 18710.3.1 Breast cancer 18810.3.2 Prostate cancer 18910.3.3 Lung cancer 19010.3.4 Pancreatic cancer 19110.3.5 Ovarian cancer 19210.4 MMPs/ADAMs as diagnostic and prognostic biomarkers for non-neoplastic diseases 19210.4.1 Cardiovascular diseases 19310.4.2 Endometriosis 19310.4.3 Preeclampsia 19510.4.4 Arthritis 19610.5 MMPs as biomarkers of therapeutic efficacy 19710.6 MMP-specific molecular imaging for noninvasive disease detection 20110.7 Conclusions 202Acknowledgments 203References 203Index 215