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Othman H, Wieninger SA, ElAyeb M, Nilges M, Srairi-Abid N. In Silico prediction of the molecular basis of ClTx and AaCTx interaction with matrix metalloproteinase-2 (MMP-2) to inhibit glioma cell invasion. J Biomol Struct Dyn 2016; 35:2815-2829. [DOI: 10.1080/07391102.2016.1231633] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Houcemeddine Othman
- Laboratory of venoms and therapeutic biomolecules (LR11IPT08), Institut Pasteur de Tunis, Tunis, Tunisia
- Faculté des Sciences de Bizerte, Université de Carthage, Bizerte, Tunisia
| | - Silke Andrea Wieninger
- Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, Paris, France
| | - Mohamed ElAyeb
- Laboratory of venoms and therapeutic biomolecules (LR11IPT08), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Michael Nilges
- Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, Paris, France
| | - Najet Srairi-Abid
- Laboratory of venoms and therapeutic biomolecules (LR11IPT08), Institut Pasteur de Tunis, Tunis, Tunisia
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Nara H, Sato K, Kaieda A, Oki H, Kuno H, Santou T, Kanzaki N, Terauchi J, Uchikawa O, Kori M. Design, synthesis, and biological activity of novel, potent, and highly selective fused pyrimidine-2-carboxamide-4-one-based matrix metalloproteinase (MMP)-13 zinc-binding inhibitors. Bioorg Med Chem 2016; 24:6149-6165. [PMID: 27825552 DOI: 10.1016/j.bmc.2016.09.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 09/03/2016] [Accepted: 09/06/2016] [Indexed: 02/07/2023]
Abstract
Matrix metalloproteinase-13 (MMP-13), a member of the collagenase family of enzymes, has been implicated to play a key role in the pathology of osteoarthritis. Recently, we have reported the discovery of a series of quinazoline-2-carboxamide based non-zinc-binding MMP-13 selective inhibitors, as exemplified by compound 1. We then continued our research of a novel class of zinc-binding inhibitors to obtain follow-up compounds with different physicochemical, pharmacokinetic, and biological activity profiles. In order to design selective MMP-13 inhibitors, we adopted a strategy of connecting a zinc-binding group with the quinazoline-2-carboxamide system, a unique S1' binder, by an appropriate linker. Among synthesized compounds, a triazolone inhibitor 35 exhibited excellent potency (IC50=0.071nM) and selectivity (greater than 170-fold) over other MMPs (MMP-1, 2, 3, 7, 8, 9, 10, 12, and 14) and tumor necrosis factor-α converting enzyme (TACE). In this article, the design, synthesis, and biological activity of novel zinc-binding MMP-13 inhibitors are described.
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Affiliation(s)
- Hiroshi Nara
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kenjiro Sato
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Akira Kaieda
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hideyuki Oki
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Haruhiko Kuno
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Takashi Santou
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Naoyuki Kanzaki
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Jun Terauchi
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Osamu Uchikawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masakuni Kori
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
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53
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Thakur V, Bedogni B. The membrane tethered matrix metalloproteinase MT1-MMP at the forefront of melanoma cell invasion and metastasis. Pharmacol Res 2016; 111:17-22. [DOI: 10.1016/j.phrs.2016.05.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 05/13/2016] [Accepted: 05/17/2016] [Indexed: 01/18/2023]
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54
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Agamennone M, Belov DS, Laghezza A, Ivanov VN, Novoselov AM, Andreev IA, Ratmanova NK, Altieri A, Tortorella P, Kurkin AV. Fragment-Based Discovery of 5-Arylisatin-Based Inhibitors of Matrix Metalloproteinases 2 and 13. ChemMedChem 2016; 11:1892-8. [DOI: 10.1002/cmdc.201600266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/21/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Mariangela Agamennone
- Dipartimento di Farmacia; Università “G. d'Annunzio”; Chieti Via dei Vestini 31 66013 Chieti Italy
| | - Dmitry S. Belov
- EDASA Scientific srls; Via Stingi 37 66050 San Salvo Italy
- Chemistry Department; Lomonosov Moscow State University; 119991, GSP-2 Leninskie gory, 1/3 Moscow Russia
| | - Antonio Laghezza
- Dipartimento di Farmacia-Scienze del Farmaco; Università degli Studi “Aldo Moro” di Bari; Via Orabona 4 70126 Bari Italy
| | - Vladimir N. Ivanov
- Chemistry Department; Lomonosov Moscow State University; 119991, GSP-2 Leninskie gory, 1/3 Moscow Russia
| | - Anton M. Novoselov
- Chemistry Department; Lomonosov Moscow State University; 119991, GSP-2 Leninskie gory, 1/3 Moscow Russia
| | - Ivan A. Andreev
- EDASA Scientific srls; Via Stingi 37 66050 San Salvo Italy
- Chemistry Department; Lomonosov Moscow State University; 119991, GSP-2 Leninskie gory, 1/3 Moscow Russia
| | - Nina K. Ratmanova
- Chemistry Department; Lomonosov Moscow State University; 119991, GSP-2 Leninskie gory, 1/3 Moscow Russia
| | - Andrea Altieri
- EDASA Scientific srls; Via Stingi 37 66050 San Salvo Italy
| | - Paolo Tortorella
- Dipartimento di Farmacia-Scienze del Farmaco; Università degli Studi “Aldo Moro” di Bari; Via Orabona 4 70126 Bari Italy
| | - Alexander V. Kurkin
- Chemistry Department; Lomonosov Moscow State University; 119991, GSP-2 Leninskie gory, 1/3 Moscow Russia
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Ruddy JM, Ikonomidis JS, Jones JA. Multidimensional Contribution of Matrix Metalloproteinases to Atherosclerotic Plaque Vulnerability: Multiple Mechanisms of Inhibition to Promote Stability. J Vasc Res 2016; 53:1-16. [PMID: 27327039 PMCID: PMC7196926 DOI: 10.1159/000446703] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/07/2016] [Indexed: 12/17/2022] Open
Abstract
The prevalence of atherosclerotic disease continues to increase, and despite significant reductions in major cardiovascular events with current medical interventions, an additional therapeutic window exists. Atherosclerotic plaque growth is a complex integration of cholesterol penetration, inflammatory cell infiltration, vascular smooth muscle cell (VSMC) migration, and neovascular invasion. A family of matrix-degrading proteases, the matrix metalloproteinases (MMPs), contributes to all phases of vascular remodeling. The contribution of specific MMPs to endothelial cell integrity and VSMC migration in atherosclerotic lesion initiation and progression has been confirmed by the increased expression of these proteases in plasma and plaque specimens. Endogenous blockade of MMPs by the tissue inhibitors of metalloproteinases (TIMPs) may attenuate proteolysis in some regions, but the progression of matrix degeneration suggests that MMPs predominate in atherosclerotic plaque, precipitating vulnerability. Plaque neovascularization also contributes to instability and, coupling the known role of MMPs in angiogenesis to that of atherosclerotic plaque growth, interest in targeting MMPs to facilitate plaque stabilization continues to accumulate. This article aims to review the contributions of MMPs and TIMPs to atherosclerotic plaque expansion, neovascularization, and rupture vulnerability with an interest in promoting targeted therapies to improve plaque stabilization and decrease the risk of major cardiovascular events.
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Affiliation(s)
- Jean Marie Ruddy
- Division of Vascular Surgery, Department of Surgery, Medical University of South Carolina, Charleston, S.C., USA
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56
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Fu J, Li S, Feng R, Ma H, Sabeh F, Roodman GD, Wang J, Robinson S, Guo XE, Lund T, Normolle D, Mapara MY, Weiss SJ, Lentzsch S. Multiple myeloma-derived MMP-13 mediates osteoclast fusogenesis and osteolytic disease. J Clin Invest 2016; 126:1759-72. [PMID: 27043283 DOI: 10.1172/jci80276] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/18/2016] [Indexed: 12/27/2022] Open
Abstract
Multiple myeloma (MM) cells secrete osteoclastogenic factors that promote osteolytic lesions; however, the identity of these factors is largely unknown. Here, we performed a screen of human myeloma cells to identify pro-osteoclastogenic agents that could potentially serve as therapeutic targets for ameliorating MM-associated bone disease. We found that myeloma cells express high levels of the matrix metalloproteinase MMP-13 and determined that MMP-13 directly enhances osteoclast multinucleation and bone-resorptive activity by triggering upregulation of the cell fusogen DC-STAMP. Moreover, this effect was independent of the proteolytic activity of the enzyme. Further, in mouse xenograft models, silencing MMP-13 expression in myeloma cells inhibited the development of osteolytic lesions. In patient cohorts, MMP-13 expression was localized to BM-associated myeloma cells, while elevated MMP-13 serum levels were able to correctly predict the presence of active bone disease. Together, these data demonstrate that MMP-13 is critical for the development of osteolytic lesions in MM and that targeting the MMP-13 protein - rather than its catalytic activity - constitutes a potential approach to mitigating bone disease in affected patients.
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McCracken JM, Jiang L, Deshpande KT, O'Neil MF, Pritchard MT. Differential effects of hyaluronan synthase 3 deficiency after acute vs chronic liver injury in mice. FIBROGENESIS & TISSUE REPAIR 2016; 9:4. [PMID: 27042213 PMCID: PMC4818527 DOI: 10.1186/s13069-016-0041-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/16/2016] [Indexed: 01/16/2023]
Abstract
Background Hyaluronan (HA) is a ubiquitous extracellular matrix (ECM) glycosaminoglycan synthesized by three different enzymes, hyaluronan synthase (HAS)1, 2, and 3. HA synthesis mediated by HAS3 promotes inflammation and is pathogenic in animal models of human lung and intestinal disease. Liver fibrosis is a common endpoint to chronic liver injury and inflammation for which there is no cure. Although plasma HA is a commonly used biomarker for liver disease, if and how HA contributes to disease pathogenesis remains unclear. Here, we tested the hypothesis that HA synthesized by HAS3 enhances inflammation and fibrosis. To test this hypothesis, we exposed wild-type or Has3−/− mice to carbon tetrachloride (CCl4) once (acute) or ten (chronic) times. Results HAS3-deficient mice exhibited increased hepatic injury and inflammatory chemokine production 48 h after acute CCl4; this was associated with a threefold reduction in plasma HA levels and alterations in the proportions of specific molecular weight HA polymer pools. Hepatic accumulation of fibrosis-associated transcripts was also greater in livers from HAS3-deficient mice compared to controls after acute CCl4 exposure. Surprisingly, fibrosis was not different between genotypes. Hepatic matrix metalloproteinase (MMP)13 mRNA and MMP13 activity was greater in livers from Has3-null mice after chronic CCl4; this was prevented by a MMP13-specific inhibitor. Collectively, these data suggest that Has3, or more likely HA produced by HAS3, limits hepatic inflammation after acute injury and attenuates MMP13-mediated matrix metabolism after chronic injury. Conclusions These data suggest that HA should be investigated further as a novel therapeutic target for acute and chronic liver disease. Electronic supplementary material The online version of this article (doi:10.1186/s13069-016-0041-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer M McCracken
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160 USA
| | - Lu Jiang
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160 USA
| | - Krutika T Deshpande
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160 USA
| | - Maura F O'Neil
- Department of Pathology, University of Kansas Medical Center, Kansas City, KS 66160 USA
| | - Michele T Pritchard
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160 USA
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58
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Paclitaxel-induced epithelial damage and ectopic MMP-13 expression promotes neurotoxicity in zebrafish. Proc Natl Acad Sci U S A 2016; 113:E2189-98. [PMID: 27035978 PMCID: PMC4839466 DOI: 10.1073/pnas.1525096113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Paclitaxel is a microtubule-stabilizing chemotherapeutic agent that is widely used in cancer treatment and in a number of curative and palliative regimens. Despite its beneficial effects on cancer, paclitaxel also damages healthy tissues, most prominently the peripheral sensory nervous system. The mechanisms leading to paclitaxel-induced peripheral neuropathy remain elusive, and therapies that prevent or alleviate this condition are not available. We established a zebrafish in vivo model to study the underlying mechanisms and to identify pharmacological agents that may be developed into therapeutics. Both adult and larval zebrafish displayed signs of paclitaxel neurotoxicity, including sensory axon degeneration and the loss of touch response in the distal caudal fin. Intriguingly, studies in zebrafish larvae showed that paclitaxel rapidly promotes epithelial damage and decreased mechanical stress resistance of the skin before induction of axon degeneration. Moreover, injured paclitaxel-treated zebrafish skin and scratch-wounded human keratinocytes (HEK001) display reduced healing capacity. Epithelial damage correlated with rapid accumulation of fluorescein-conjugated paclitaxel in epidermal basal keratinocytes, but not axons, and up-regulation of matrix-metalloproteinase 13 (MMP-13, collagenase 3) in the skin. Pharmacological inhibition of MMP-13, in contrast, largely rescued paclitaxel-induced epithelial damage and neurotoxicity, whereas MMP-13 overexpression in zebrafish embryos rendered the skin vulnerable to injury under mechanical stress conditions. Thus, our studies provide evidence that the epidermis plays a critical role in this condition, and we provide a previously unidentified candidate for therapeutic interventions.
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Fischer T, Riedl R. Molecular Recognition of the Catalytic Zinc(II) Ion in MMP-13: Structure-Based Evolution of an Allosteric Inhibitor to Dual Binding Mode Inhibitors with Improved Lipophilic Ligand Efficiencies. Int J Mol Sci 2016; 17:314. [PMID: 26938528 PMCID: PMC4813177 DOI: 10.3390/ijms17030314] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/02/2016] [Accepted: 02/14/2016] [Indexed: 11/21/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are a class of zinc dependent endopeptidases which play a crucial role in a multitude of severe diseases such as cancer and osteoarthritis. We employed MMP-13 as the target enzyme for the structure-based design and synthesis of inhibitors able to recognize the catalytic zinc ion in addition to an allosteric binding site in order to increase the affinity of the ligand. Guided by molecular modeling, we optimized an initial allosteric inhibitor by addition of linker fragments and weak zinc binders for recognition of the catalytic center. Furthermore we improved the lipophilic ligand efficiency (LLE) of the initial inhibitor by adding appropriate zinc binding fragments to lower the clogP values of the inhibitors, while maintaining their potency. All synthesized inhibitors showed elevated affinity compared to the initial hit, also most of the novel inhibitors displayed better LLE. Derivatives with carboxylic acids as the zinc binding fragments turned out to be the most potent inhibitors (compound 3 (ZHAWOC5077): IC50 = 134 nM) whereas acyl sulfonamides showed the best lipophilic ligand efficiencies (compound 18 (ZHAWOC5135): LLE = 2.91).
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Affiliation(s)
- Thomas Fischer
- Center for Organic and Medicinal Chemistry, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences ZHAW, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland.
| | - Rainer Riedl
- Center for Organic and Medicinal Chemistry, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences ZHAW, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland.
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60
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Pavan M, Galesso D, Secchieri C, Guarise C. Hyaluronic acid alkyl derivative: A novel inhibitor of metalloproteases and hyaluronidases. Int J Biol Macromol 2016; 84:221-6. [DOI: 10.1016/j.ijbiomac.2015.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/01/2015] [Indexed: 12/18/2022]
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Ruminski PG, Massa M, Strohbach J, Hanau CE, Schmidt M, Scholten JA, Fletcher TR, Hamper BC, Carroll JN, Shieh HS, Caspers N, Collins B, Grapperhaus M, Palmquist KE, Collins J, Baldus JE, Hitchcock J, Kleine HP, Rogers MD, McDonald J, Munie GE, Messing DM, Portolan S, Whiteley LO, Sunyer T, Schnute ME. Discovery of N-(4-Fluoro-3-methoxybenzyl)-6-(2-(((2S,5R)-5-(hydroxymethyl)-1,4-dioxan-2-yl)methyl)-2H-tetrazol-5-yl)-2-methylpyrimidine-4-carboxamide. A Highly Selective and Orally Bioavailable Matrix Metalloproteinase-13 Inhibitor for the Potential Treatment of Osteoarthritis. J Med Chem 2015; 59:313-27. [PMID: 26653735 DOI: 10.1021/acs.jmedchem.5b01434] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Matrix metalloproteinase-13 (MMP-13) is a zinc-dependent protease responsible for the cleavage of type II collagen, the major structural protein of articular cartilage. Degradation of this cartilage matrix leads to the development of osteoarthritis. We previously have described highly potent and selective carboxylic acid containing MMP-13 inhibitors; however, nephrotoxicity in preclinical toxicology species precluded development. The accumulation of compound in the kidneys mediated by human organic anion transporter 3 (hOAT3) was hypothesized as a contributing factor for the finding. Herein we report our efforts to optimize the MMP-13 potency and pharmacokinetic properties of non-carboxylic acid leads resulting in the identification of compound 43a lacking the previously observed preclinical toxicology at comparable exposures.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dean M Messing
- Pharmacokinetics, Dynamics, and Metabolism, Pfizer , 700 North Main Street, Cambridge, Massachusetts 02139, United States
| | - Silvia Portolan
- Pharmacokinetics, Dynamics, and Metabolism, Pfizer , 700 North Main Street, Cambridge, Massachusetts 02139, United States
| | - Laurence O Whiteley
- Drug Safety, Pfizer , 1 Burtt Road, Andover, Massachusetts 01810, United States
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62
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Maize KM, Kurbanov EK, Johnson RL, Amin EA, Finzel BC. Ligand-induced expansion of the S1' site in the anthrax toxin lethal factor. FEBS Lett 2015; 589:3836-41. [PMID: 26578066 DOI: 10.1016/j.febslet.2015.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 10/27/2015] [Accepted: 11/02/2015] [Indexed: 12/31/2022]
Abstract
The Bacillus anthracis lethal factor (LF) is one component of a tripartite exotoxin partly responsible for persistent anthrax cytotoxicity after initial bacterial infection. Inhibitors of the zinc metalloproteinase have been investigated as potential therapeutic agents, but LF is a challenging target because inhibitors lack sufficient selectivity or possess poor pharmaceutical properties. These structural studies reveal an alternate conformation of the enzyme, induced upon binding of specific inhibitors, that opens a previously unobserved deep pocket termed S1'(∗) which might afford new opportunities to design selective inhibitors that target this subsite.
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Affiliation(s)
- Kimberly M Maize
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, 8-101 Weaver-Densford Hall, Minneapolis, MN 55455, United States
| | - Elbek K Kurbanov
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, 8-101 Weaver-Densford Hall, Minneapolis, MN 55455, United States
| | - Rodney L Johnson
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, 8-101 Weaver-Densford Hall, Minneapolis, MN 55455, United States
| | - Elizabeth Ambrose Amin
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, 8-101 Weaver-Densford Hall, Minneapolis, MN 55455, United States
| | - Barry C Finzel
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, 8-101 Weaver-Densford Hall, Minneapolis, MN 55455, United States.
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63
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Abdul-Muneer PM, Pfister BJ, Haorah J, Chandra N. Role of Matrix Metalloproteinases in the Pathogenesis of Traumatic Brain Injury. Mol Neurobiol 2015; 53:6106-6123. [PMID: 26541883 DOI: 10.1007/s12035-015-9520-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 10/28/2015] [Indexed: 12/17/2022]
Abstract
Traumatic brain injury (TBI) is a major cause of mortality and morbidity worldwide. Studies revealed that the pathogenesis of TBI involves upregulation of MMPs. MMPs form a large family of closely related zinc-dependent endopeptidases, which are primarily responsible for the dynamic remodulation of the extracellular matrix (ECM). Thus, they are involved in several normal physiological processes like growth, development, and wound healing. During pathophysiological conditions, MMPs proteolytically degrade various components of ECM and tight junction (TJ) proteins of BBB and cause BBB disruption. Impairment of BBB causes leakiness of the blood from circulation to brain parenchyma that leads to microhemorrhage and edema. Further, MMPs dysregulate various normal physiological processes like angiogenesis and neurogenesis, and also they participate in the inflammatory and apoptotic cascades by inducing or regulating the specific mediators and their receptors. In this review, we explore the roles of MMPs in various physiological/pathophysiological processes associated with neurological complications, with special emphasis on TBI.
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Affiliation(s)
- P M Abdul-Muneer
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
| | - Bryan J Pfister
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - James Haorah
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Namas Chandra
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
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64
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Knapinska AM, Dreymuller D, Ludwig A, Smith L, Golubkov V, Sohail A, Fridman R, Giulianotti M, LaVoi TM, Houghten RA, Fields GB, Minond D. SAR Studies of Exosite-Binding Substrate-Selective Inhibitors of A Disintegrin And Metalloprotease 17 (ADAM17) and Application as Selective in Vitro Probes. J Med Chem 2015; 58:5808-24. [PMID: 26192023 DOI: 10.1021/acs.jmedchem.5b00354] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
ADAM17 is implicated in several debilitating diseases. However, drug discovery efforts targeting ADAM17 have failed due to the utilization of zinc-binding inhibitors. We previously reported discovery of highly selective nonzinc-binding exosite-targeting inhibitors of ADAM17 that exhibited not only enzyme isoform selectivity but synthetic substrate selectivity as well ( J. Biol. Chem. 2013, 288, 22871). As a result of SAR studies presented herein, we obtained several highly selective ADAM17 inhibitors, six of which were further characterized in biochemical and cell-based assays. Lead compounds exhibited low cellular toxicity and high potency and selectivity for ADAM17. In addition, several of the leads inhibited ADAM17 in a substrate-selective manner, which has not been previously documented for inhibitors of the ADAM family. These findings suggest that targeting exosites of ADAM17 can be used to obtain highly desirable substrate-selective inhibitors. Additionally, current inhibitors can be used as probes of biological activity of ADAM17 in various in vitro and, potentially, in vivo systems.
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Affiliation(s)
- Anna M Knapinska
- ∥Florida Atlantic University, 5353 Parkside Drive, Jupiter, Florida 33458, United States
| | - Daniela Dreymuller
- ⊥Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Andreas Ludwig
- ⊥Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Lyndsay Smith
- ∥Florida Atlantic University, 5353 Parkside Drive, Jupiter, Florida 33458, United States
| | - Vladislav Golubkov
- ‡Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Anjum Sohail
- §Wayne State University, 8200 Scott Hall, 540 East Canfield Avenue, Detroit, Michigan 48201, United States
| | - Rafael Fridman
- §Wayne State University, 8200 Scott Hall, 540 East Canfield Avenue, Detroit, Michigan 48201, United States
| | - Marc Giulianotti
- †Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States.,∇Department of Chemistry, Center for Drug Discovery and Innovation, University of South Florida, Tampa, Florida 33612, United States
| | - Travis M LaVoi
- †Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Richard A Houghten
- †Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Gregg B Fields
- ∥Florida Atlantic University, 5353 Parkside Drive, Jupiter, Florida 33458, United States.,#The Scripps Research Institute/Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Dmitriy Minond
- †Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
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65
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Santamaria S, Nuti E, Cercignani G, La Regina G, Silvestri R, Supuran CT, Rossello A. Kinetic characterization of 4,4′-biphenylsulfonamides as selective non-zinc binding MMP inhibitors. J Enzyme Inhib Med Chem 2015; 30:947-54. [DOI: 10.3109/14756366.2014.1000889] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Elisa Nuti
- Dipartimento di Farmacia, Università di Pisa, Pisa, Italy,
| | - Giovanni Cercignani
- Dipartimento di Biologia, Unità di Biochimica, Università di Pisa, Pisa, Italy,
- Istituto di Biofisica del CNR, Area della Ricerca di Pisa, Pisa, Italy,
| | - Giuseppe La Regina
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Roma, Italy, and
| | - Romano Silvestri
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Roma, Italy, and
| | - Claudiu T. Supuran
- Laboratorio di Chimica Bioinorganica, Polo Scientifico, Università degli Studi di Firenze, Florence, Italy
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66
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Fields GB. New strategies for targeting matrix metalloproteinases. Matrix Biol 2015; 44-46:239-46. [PMID: 25595836 PMCID: PMC4466128 DOI: 10.1016/j.matbio.2015.01.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 01/27/2023]
Abstract
The development of matrix metalloproteinase (MMP) inhibitors has often been frustrated by a lack of specificity and subsequent off-target effects. More recently, inhibitor design has considered secondary binding sites (exosites) to improve specificity. Small molecules and peptides have been developed that bind exosites in the catalytic (CAT) domain of MMP-13, the CAT or hemopexin-like (HPX) domain of MT1-MMP, and the collagen binding domain (CBD) of MMP-2 and MMP-9. Antibody-based approaches have resulted in selective inhibitors for MMP-9 and MT1-MMP that target CAT domain exosites. Triple-helical “mini-proteins” have taken advantage of collagen binding exosites, producing a family of novel probes. A variety of non-traditional approaches that incorporate exosite binding into the design process has yielded inhibitors with desirable selectivities within the MMP family.
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Affiliation(s)
- Gregg B Fields
- Florida Atlantic University, Department of Chemistry & Biochemistry, 5353 Parkside Drive, Building MC17, Jupiter, FL 33458, United States; The Scripps Research Institute/Scripps Florida, Department of Chemistry, 130 Scripps Way, Jupiter, FL 33458, United States; Torrey Pines Institute for Molecular Studies, Department of Chemistry, 11350 SW Village Parkway, Port St. Lucie, FL 34987, United States; Torrey Pines Institute for Molecular Studies, Department of Biology, 11350 SW Village Parkway, Port St. Lucie, FL 34987, United States.
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67
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3D virtual screening of large combinatorial spaces. Methods 2015; 71:14-20. [DOI: 10.1016/j.ymeth.2014.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 06/18/2014] [Accepted: 06/19/2014] [Indexed: 12/16/2022] Open
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68
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Lanz J, Riedl R. Merging allosteric and active site binding motifs: de novo generation of target selectivity and potency via natural-product-derived fragments. ChemMedChem 2014; 10:451-4. [PMID: 25487909 PMCID: PMC4506557 DOI: 10.1002/cmdc.201402478] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Indexed: 12/26/2022]
Abstract
The de novo design of molecules from scratch with tailored biological activity is still the major intellectual challenge in chemical biology and drug discovery. Herein we validate natural-product-derived fragments (NPDFs) as excellent molecular seeds for the targeted de novo discovery of lead structures for the modulation of therapeutically relevant proteins. The application of this de novo approach delivered, in synergy with the combination of allosteric and active site binding motifs, highly selective and ligand-efficient non-zinc-binding (3: 4-{[5-(2-{[(3-methoxyphenyl)methyl]carbamoyl}eth-1-yn-1-yl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl]methyl}benzoic acid) as well as zinc-binding (4: 4-({5-[2-({[3-(3-carboxypropoxy)phenyl]methyl}carbamoyl)eth-1-yn-1-yl]-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl}methyl)benzoic acid) uracil-based MMP-13 inhibitors presenting IC50 values of 11 nm (3: LE=0.35) and 6 nm (4: LE=0.31).
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Affiliation(s)
- Jan Lanz
- Institute for Chemistry and Biological Chemistry, Zurich University of Applied SciencesEinsiedlerstrasse 31, 8820 Wädenswil (Switzerland) E-mail: Homepage:http://www.icbc.zhaw.ch/organic-chemistry
| | - Rainer Riedl
- Institute for Chemistry and Biological Chemistry, Zurich University of Applied SciencesEinsiedlerstrasse 31, 8820 Wädenswil (Switzerland) E-mail: Homepage:http://www.icbc.zhaw.ch/organic-chemistry
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69
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Spicer TP, Jiang J, Taylor AB, Choi JY, Hart PJ, Roush WR, Fields GB, Hodder PS, Minond D. Characterization of selective exosite-binding inhibitors of matrix metalloproteinase 13 that prevent articular cartilage degradation in vitro. J Med Chem 2014; 57:9598-611. [PMID: 25330343 PMCID: PMC4255739 DOI: 10.1021/jm501284e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Matrix metalloproteinase 13 (MMP-13) has been shown to be the main collagenase responsible for degradation of articular cartilage during osteoarthritis and therefore represents a target for drug development. As a result of high-throughput screening and structure-activity relationship studies, we identified a novel, highly selective class of MMP-13 inhibitors (compounds 1 (Q), 2 (Q1), and 3 (Q2)). Mechanistic characterization revealed a noncompetitive nature of these inhibitors with binding constants in the low micromolar range. Crystallographic analyses revealed two binding modes for compound 2 in the MMP-13 S1' subsite and in an S1/S2* subsite. Type II collagen- and cartilage-protective effects exhibited by compounds 1, 2, and 3 suggested that these compounds might be efficacious in future in vivo studies. Finally, these compounds were also highly selective when tested against a panel of 30 proteases, which, in combination with a good CYP inhibition profile, suggested low off-target toxicity and drug-drug interactions in humans.
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Affiliation(s)
- Timothy P Spicer
- Lead Identification Division, Translational Research Institute, ‡Department of Molecular Therapeutics, and §Department of Chemistry, Scripps Florida, The Scripps Research Institute , Jupiter, Florida 33458, United States
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70
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Zhang H, Wang Y, Xu F. Impact of the subtle differences in MMP-12 structure on Glide-based molecular docking for pose prediction of inhibitors. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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71
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Nara H, Sato K, Naito T, Mototani H, Oki H, Yamamoto Y, Kuno H, Santou T, Kanzaki N, Terauchi J, Uchikawa O, Kori M. Discovery of Novel, Highly Potent, and Selective Quinazoline-2-carboxamide-Based Matrix Metalloproteinase (MMP)-13 Inhibitors without a Zinc Binding Group Using a Structure-Based Design Approach. J Med Chem 2014; 57:8886-902. [DOI: 10.1021/jm500981k] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroshi Nara
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kenjiro Sato
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Takako Naito
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hideyuki Mototani
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hideyuki Oki
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yoshio Yamamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Haruhiko Kuno
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Takashi Santou
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Naoyuki Kanzaki
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Jun Terauchi
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Osamu Uchikawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masakuni Kori
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
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72
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Fabre B, Ramos A, de Pascual-Teresa B. Targeting Matrix Metalloproteinases: Exploring the Dynamics of the S1′ Pocket in the Design of Selective, Small Molecule Inhibitors. J Med Chem 2014; 57:10205-19. [DOI: 10.1021/jm500505f] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Benjamin Fabre
- Departamento de Química
y Bioquímica, Facultad de Farmacia, Universidad CEU San Pablo, Urbanización Monteprincipe, 28668 Madrid, Spain
| | - Ana Ramos
- Departamento de Química
y Bioquímica, Facultad de Farmacia, Universidad CEU San Pablo, Urbanización Monteprincipe, 28668 Madrid, Spain
| | - Beatriz de Pascual-Teresa
- Departamento de Química
y Bioquímica, Facultad de Farmacia, Universidad CEU San Pablo, Urbanización Monteprincipe, 28668 Madrid, Spain
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73
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Golizeh M, Abusarah J, Benderdour M, Sleno L. Covalent Binding of 4-Hydroxynonenal to Matrix Metalloproteinase 13 Studied by Liquid Chromatography–Mass Spectrometry. Chem Res Toxicol 2014; 27:1556-65. [DOI: 10.1021/tx5002095] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Makan Golizeh
- Chemistry
Department/Pharmaqam, Université du Québec à Montréal, Montreal, Quebec H3C 3P8, Canada
| | - Jamilah Abusarah
- Orthopaedic
Research Laboratory, Hôpital du Sacré-Coeur, University of Montreal, Montreal, Quebec H4J 1C5, Canada
| | - Mohamed Benderdour
- Orthopaedic
Research Laboratory, Hôpital du Sacré-Coeur, University of Montreal, Montreal, Quebec H4J 1C5, Canada
| | - Lekha Sleno
- Chemistry
Department/Pharmaqam, Université du Québec à Montréal, Montreal, Quebec H3C 3P8, Canada
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74
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Meides A, Gutschalk CM, Devel L, Beau F, Czarny B, Hensler S, Neugebauer J, Dive V, Angel P, Mueller MM. Effects of selective MMP-13 inhibition in squamous cell carcinoma depend on estrogen. Int J Cancer 2014; 135:2749-59. [PMID: 24676718 DOI: 10.1002/ijc.28866] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 11/11/2013] [Accepted: 12/06/2013] [Indexed: 12/15/2022]
Abstract
Matrix metalloproteinases like MMP-13 cleave and remodel the extracellular matrix and thereby play a crucial role in tumor progression in vivo. Using a highly selective inhibitor to block MMP-13 protein activity, we demonstrate a striking inhibitory effect on invasive tumor growth and vascularization in murine skin squamous cell carcinoma (SCC). Therapy outcome critically depends on animal age in C57Bl/6 mice and was successful in old female but not in young female mice. Treatment success was recovered by ovariectomy in young and abolished by 17ß-estradiol supplementation in old mice, suggesting a hormone dependent inhibitor effect. Responsiveness of the tumorigenic keratinocytes BDVII and fibroblasts to 17ß-estradiol was confirmed in vitro, where MMP-13 inhibitor treatment led to a reduction of cell invasion and vascular endothelial growth factor (VEGF) release. This correlated well with a less invasive and vascularized tumor in treated mice in vivo. 17ß-estradiol supplementation also reduced invasion and VEGF release in vitro with no additional reduction on MMP-13 inhibitor treatment. This suggests that low 17ß-estradiol levels in old mice in vivo lead to enhanced MMP-13 levels and VEGF release, allowing a more effective inhibitor treatment compared to young mice. In our study, we present a strong link between lower estrogen levels in old female mice, an elevated MMP-13 level, which results in a more effective MMP-13 inhibitor treatment in fibroblasts and SCC cells in vitro and in vivo.
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Affiliation(s)
- Alice Meides
- Group Tumor and Microenvironment, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
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75
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Interactions of Oxidative Stress and Neurovascular Inflammation in the Pathogenesis of Traumatic Brain Injury. Mol Neurobiol 2014; 51:966-79. [DOI: 10.1007/s12035-014-8752-3] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 05/13/2014] [Indexed: 12/12/2022]
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76
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Abstract
The extracellular matrix (ECM) is an essential component of the human body that is responsible for the proper function of various organs. Changes in the ECM have been implicated in the pathogenesis of several cardiovascular conditions including atherosclerosis, restenosis, and heart failure. Matrix components, such as collagens and noncollagenous proteins, influence the function and activity of vascular cells, particularly vascular smooth muscle cells and macrophages. Matrix proteins have been shown to be implicated in the development of atherosclerotic complications, such as plaque rupture, aneurysm formation, and calcification. ECM proteins control ECM remodeling through feedback signaling to matrix metalloproteinases (MMPs), which are the key players of ECM remodeling in both normal and pathological conditions. The production of MMPs is closely related to the development of an inflammatory response and is subjected to significant changes at different stages of atherosclerosis. Indeed, blood levels of circulating MMPs may be useful for the assessment of the inflammatory activity in atherosclerosis and the prediction of cardiovascular risk. The availability of a wide variety of low-molecular MMP inhibitors that can be conjugated with various labels provides a good perspective for specific targeting of MMPs and implementation of imaging techniques to visualize MMP activity in atherosclerotic plaques and, most interestingly, to monitor responses to antiatheroslerosis therapies. Finally, because of the crucial role of ECM in cardiovascular repair, the regenerative potential of ECM could be successfully used in constructing engineered scaffolds and vessels that mimic properties of the natural ECM and consist of the native ECM components or composite biomaterials. These scaffolds possess a great promise in vascular tissue engineering.
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77
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Kang SG, Araya-Secchi R, Wang D, Wang B, Huynh T, Zhou R. Dual inhibitory pathways of metallofullerenol Gd@C₈₂(OH)₂₂ on matrix metalloproteinase-2: molecular insight into drug-like nanomedicine. Sci Rep 2014; 4:4775. [PMID: 24758941 PMCID: PMC3998016 DOI: 10.1038/srep04775] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/04/2014] [Indexed: 12/14/2022] Open
Abstract
Cancer metastasis is an important criterion to evaluate tumor malignancy. Matrix metalloproteinases (MMPs) play a crucial role in cancer proliferation and migration by virtue of their proteolytic functions in angiogenesis and extracelluar matrix (ECM) degradation, making them potential targets of anti-metastaic therapeutics. Recently we showed with both in vivo and in vitro experiments that metallofullerenol Gd@C82(OH)22 can effectively inhibit MMP-2 and MMP-9 with high antitumoral efficacy. Furthermore, our in silico study revealed that Gd@C82(OH)22 could indirectly inhibit the proteolysis of MMP-9 via allosteric modulation exclusively at the ligand specificity S1′ loop. Here, we expand our study toward another gelatinase, MMP-2, using molecular dynamics simulations. Despite the high structural similarity with 64.3% sequence identity, their responses to Gd@C82(OH)22 were quite different. Toward MMP-2, Gd@C82(OH)22 could block either the Zn2+-catalylitic site directly or the S1′ loop indirectly. Surface electrostatics uniquely determines the initial adsorption of Gd@C82(OH)22 on MMP-2, and then its further location of the most favorable binding site(s). These findings not only illustrated how the inhibitory mechanism of Gd@C82(OH)22 is distinguished between the two gelatinase MMPs with atomic details, but also shed light on the de novo design of anti-metastatic nanotherapeutics with enhanced target specificity.
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Affiliation(s)
- Seung-gu Kang
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Raul Araya-Secchi
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Deqiang Wang
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Bo Wang
- Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
| | - Tien Huynh
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Ruhong Zhou
- 1] Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA [2] Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China [3] Department of Chemistry, Columbia University, New York, NY 10027, USA
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78
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Krimmer SG, Betz M, Heine A, Klebe G. Methyl, Ethyl, Propyl, Butyl: Futile But Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors. ChemMedChem 2014; 9:833-46. [DOI: 10.1002/cmdc.201400013] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Indexed: 11/11/2022]
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79
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Fabre B, Filipiak K, Díaz N, Zapico JM, Suárez D, Ramos A, de Pascual-Teresa B. An Integrated Computational and Experimental Approach to Gaining Selectivity for MMP-2 within the Gelatinase Subfamily. Chembiochem 2014; 15:399-412. [DOI: 10.1002/cbic.201300698] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Indexed: 12/27/2022]
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80
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Romanchikova N, Trapencieris P, Zemītis J, Turks M. A novel matrix metalloproteinase-2 inhibitor triazolylmethyl aziridine reduces melanoma cell invasion, angiogenesis and targets ERK1/2 phosphorylation. J Enzyme Inhib Med Chem 2013; 29:765-72. [DOI: 10.3109/14756366.2013.855207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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81
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Yang CC, Lin CY, Wang HS, Lyu SR. Matrix metalloproteases and tissue inhibitors of metalloproteinases in medial plica and pannus-like tissue contribute to knee osteoarthritis progression. PLoS One 2013; 8:e79662. [PMID: 24223987 PMCID: PMC3817135 DOI: 10.1371/journal.pone.0079662] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 09/24/2013] [Indexed: 01/23/2023] Open
Abstract
Osteoarthritis (OA) is characterized by degradation of the cartilage matrix, leading to pathologic changes in the joints. However, the pathogenic effects of synovial tissue inflammation on OA knees are not clear. To investigate whether the inflammation caused by the medial plica is involved in the pathogenesis of osteoarthritis, we examined the expression of matrix metalloproteinases (MMPs), tissue inhibitors of metalloproteinases (TIMPs), interleukin (IL)-1β, and tumor necrosis factor (TNF)-α in the medial plica and pannus-like tissue in the knees of patients with medial compartment OA who underwent either arthroscopic medial release (stage II; 15 knee joints from 15 patients) or total knee replacement (stage IV; 18 knee joints from 18 patients). MMP-2, MMP-3, MMP-9, IL-1β, and TNF-α mRNA and protein levels measured, respectively, by quantitative real-time PCR and Quantibody human MMP arrays, were highly expressed in extracts of medial plica and pannus-like tissue from stage IV knee joints. Immunohistochemical staining also demonstrated high expression of MMP-2, MMP-3, and MMP-9 in plica and pannus-like tissue of stage IV OA knees and not in normal cartilage. Some TIMP/MMP ratios decreased significantly in both medial plica and pannus-like tissue as disease progressed from stage II to stage IV. Furthermore, the migration of cells from the pannus-like tissue was enhanced by IL-1β, while plica cell migration was enhanced by TNF-α. The results suggest that medial plica and pannus-like tissue may be involved in the process of cartilage degradation in medial compartment OA of the knee.
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Affiliation(s)
- Chih-Chang Yang
- Department of Anatomy, National Yang-Ming University, Taipei, Taiwan, R.O.C.
| | - Cheng-Yu Lin
- Department of Anatomy, National Yang-Ming University, Taipei, Taiwan, R.O.C.
| | - Hwai-Shi Wang
- Department of Anatomy, National Yang-Ming University, Taipei, Taiwan, R.O.C.
- * E-mail: (HSW); (SRL)
| | - Shaw-Ruey Lyu
- Joint Center, Tzu-Chi Dalin General Hospital, Chiayi, Taiwan, R.O.C.
- Tzu-Chi University, Hualien, Taiwan, R.O.C.
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82
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Kreituss I, Rozenberga E, Zemītis J, Trapencieris P, Romanchikova N, Turks M. Discovery of aziridine-triazole conjugates as selective MMP-2 inhibitors. Chem Heterocycl Compd (N Y) 2013. [DOI: 10.1007/s10593-013-1351-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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83
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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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84
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Di Pizio A, Laghezza A, Tortorella P, Agamennone M. Probing the S1' site for the identification of non-zinc-binding MMP-2 inhibitors. ChemMedChem 2013; 8:1475-82, 1421. [PMID: 23873724 DOI: 10.1002/cmdc.201300186] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/01/2013] [Indexed: 11/05/2022]
Abstract
Matrix metalloproteinases (MMPs) are zinc-dependent enzymes involved in several pathological states. Among them, MMP-2 is a relevant therapeutic target because of its role in cancer development and progression. Many MMP inhibitors (MMPIs) have been discovered over the last 30 years, and the majority of them contain a functional group that binds the zinc ion (zinc-binding group; ZBG). Unfortunately, no MMPIs have reached the market yet, owing to toxic effects due to unselective interactions of the ZBG. The new generation of MMPIs that do not bind the zinc ion could overcome problems of selectivity and toxicity, but have so far been developed only for MMP-8, -12, and -13. In this work, a virtual screening protocol was established by combining ligand- and structure-based methods to identify non-zinc-binding MMP-2 inhibitors using a new-generation MMP-8 inhibitor as a probe to find unexplored interactions in the MMP-2 S1' site. The screening allowed the identification of micromolar MMP-2 inhibitors that putatively avoid binding the zinc ion, as demonstrated by docking calculations. The LIA model, built to correlate predicted and experimental binding energies of the identified non-zinc-binding MMP-2 hits, underpins the reliability of the predicted docking poses.
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Affiliation(s)
- Antonella Di Pizio
- Dipartimento di Farmacia, Università "G. d'Annunzio" Chieti, Via dei Vestini 31, 66013 Chieti, Italy
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85
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Kalva S, Saranyah K, Suganya PR, Nisha M, Saleena LM. Potent inhibitors precise to S1' loop of MMP-13, a crucial target for osteoarthritis. J Mol Graph Model 2013; 44:297-310. [PMID: 23938376 DOI: 10.1016/j.jmgm.2013.06.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/21/2013] [Accepted: 06/23/2013] [Indexed: 11/30/2022]
Abstract
Matrix metalloproteinase-13 (MMP-13) is the primary MMP involved in cartilage degradation through its particular ability to cleave type-II collagen. This protein is expressed by chondrocytes and synovial cells in human osteoarthritis and rheumatoid arthritis; hence, it is an attractive target for the treatment of arthritic diseases. Currently available inhibitors lack specificity for metalloproteinase because of a common Zn binding site in MMPs; thus, there is a need to identify selective MMP-13 inhibitors for osteoarthritis therapy. Because selectivity is the major concern, both ligand-based and protein-based pharmacophore methodologies were used to identity potent and selective MMP-13 inhibitors. Different hypotheses were validated, and the best hypothesis was used to screen Zinc (natural and chemical) databases to seek novel scaffolds as MMP-13 inhibitors. The identified hits were validated using different strategies, such as Glide Standard precision, extra precision, E-model energies and receiver operating curve (ROC). In addition, potent inhibitors were selected based on two criteria: a similar binding mode as that of the active site PB3 crystal ligand and crucial amino acid interactions that are catalytically important for the function of MMP-13. The candidate potent inhibitors ZINC 02535232, ZINC 08399795, ZINC 12419118 and ZINC 00624580 nearly reproduced the H-bond interactions formed in the crystal structure of 1XUC with reasonable RMSD values exhibiting a novel interaction pattern that was not previously observed in MMP-13 inhibitors. The identified potent hits with diverse chemical scaffolds may be useful in designing new MMP-13 inhibitors.
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Affiliation(s)
- Sukesh Kalva
- Department of Bioinformatics, SRM University, SRM Nagar, Kattankulathur, Kancheepuram District, Chennai 603203, India
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86
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Stawikowska R, Cudic M, Giulianotti M, Houghten RA, Fields GB, Minond D. Activity of ADAM17 (a disintegrin and metalloprotease 17) is regulated by its noncatalytic domains and secondary structure of its substrates. J Biol Chem 2013; 288:22871-9. [PMID: 23779109 DOI: 10.1074/jbc.m113.462267] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
ADAM proteases are implicated in multiple diseases, but no drugs based on ADAM inhibition exist. Most of the ADAM inhibitors developed to date feature zinc-binding moieties that target the active site zinc, which leads to a lack of selectivity and off target toxicity. Targeting secondary substrate binding sites (exosites) can potentially work as an alternative strategy for drug discovery; however, there are only a few reports of potential exosites in ADAM protease structures. In the study presented here, we utilized a series of TNFα-based substrates to probe ADAM10 and 17 interactions with its canonical substrate to identify the structural features that determine ADAM protease substrate specificity. We found that noncatalytic domains of ADAM17 did not directly bind the substrates used in the study but affected the binding nevertheless, most likely because of steric hindrance. Additionally, noncatalytic domains of ADAM17 affected the size/shape of the carbohydrate-binding pocket contained within the catalytic domain of ADAM17. This suggests that noncatalytic domains of ADAM17 play a role in substrate specificity and might help explain differences in substrate repertoires of ADAM17 and its closest homologue, ADAM10. We also addressed the question of which substrate features can affect ADAM protease specificity. We found that all ADAM proteases tested (i.e., ADAM10, 12, and 17) significantly decreased activity when the TNFα-derived sequence was induced into α-helical conformation, suggesting that conformation plays a role in determining ADAM protease substrate specificity. These findings can help in the discovery of ADAM isoform- and substrate-specific inhibitors.
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Affiliation(s)
- Roma Stawikowska
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, USA
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87
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Mori M, Massaro A, Calderone V, Fragai M, Luchinat C, Mordini A. Discovery of a New Class of Potent MMP Inhibitors by Structure-Based Optimization of the Arylsulfonamide Scaffold. ACS Med Chem Lett 2013; 4:565-9. [PMID: 24900710 DOI: 10.1021/ml300446a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 03/13/2013] [Indexed: 01/29/2023] Open
Abstract
A new class of potent matrix metalloproteinase (MMP) inhibitors designed by structure-based optimization of the well-known arylsulfonamide scaffold is presented. Molecules show an ethylene linker connecting the sulfonamide group with the P1' aromatic portion and a d-proline residue bearing the zinc-binding group. The affinity improvement provided by these modifications led us to discover a nanomolar MMP inhibitor bearing a carboxylate moiety as zinc-binding group, which might be a promising lead molecule. Notably, a significant selectivity for MMP-8, MMP-12, and MMP-13 was observed with respect to MMP-1 and MMP-7.
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Affiliation(s)
- Mattia Mori
- ProtEra Srl, Scientific Campus, University of Florence, viale delle idee 22, I-50019
Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
| | - Assunta Massaro
- ProtEra Srl, Scientific Campus, University of Florence, viale delle idee 22, I-50019
Sesto Fiorentino, Italy
| | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
- Department
of Chemistry “Ugo
Shiff”, University of Florence,
via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
- Department
of Chemistry “Ugo
Shiff”, University of Florence,
via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Alessandro Mordini
- ICCOM-CNR, Dipartimento
di Chimica “U. Schiff”, via della Lastruccia
13, I-50019 Sesto Fiorentino, Italy
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88
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Lei H, Leong D, Smith LR, Barton ER. Matrix metalloproteinase 13 is a new contributor to skeletal muscle regeneration and critical for myoblast migration. Am J Physiol Cell Physiol 2013; 305:C529-38. [PMID: 23761625 DOI: 10.1152/ajpcell.00051.2013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Efficient skeletal muscle repair and regeneration require coordinated remodeling of the extracellular matrix (ECM). Previous reports have indicated that matrix metalloproteinases (MMPs) play the pivotal role in ECM remodeling during muscle regeneration. The goal of the current study was to determine if the interstitial collagenase MMP-13 was involved in the muscle repair process. Using intramuscular cardiotoxin injections to induce acute muscle injury, we found that MMP-13 expression and activity transiently increased during the regeneration process. In addition, in muscles from mdx mice, which exhibit chronic injury, MMP-13 expression and protein levels were elevated. In differentiating C2C12 cells, a murine myoblast cell line, Mmp13 expression was most pronounced after myoblast fusion and during myotube formation. Using pharmacological inhibition of MMP-13 to test whether MMP-13 activity is necessary for the proliferation, differentiation, migration, and fusion of C2C12 cells, we found a dramatic blockade of myoblast migration, as well as a delay in differentiation. In contrast, C2C12 cells with stable overexpression of MMP-13 showed enhanced migration, without affecting myoblast maturation. Taken together, these results support a primary role for MMP-13 in myoblast migration that leads to secondary effects on differentiation.
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Affiliation(s)
- Hanqin Lei
- Department of Anatomy and Cell Biology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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89
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Papp A, Szommer T, Barna L, Gyimesi G, Ferdinandy P, Spadoni C, Darvas F, Fujita T, Urge L, Dormán G. Enhanced hit-to-lead process using bioanalogous lead evolution and chemogenomics: application in designing selective matrix metalloprotease inhibitors. Expert Opin Drug Discov 2013; 2:707-23. [PMID: 23488960 DOI: 10.1517/17460441.2.5.707] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The authors describe an innovative approach for designing novel inhibitors. This approach effectively integrates the emerging chemogenomics concept of target-family-based drug discovery with bioanalogous design strategies, including privileged structures, molecular frameworks as well as bioisosteric and bioanalogous/isofunctional modifications. The authors applied this method in the design of selective inhibitors of matrix metalloproteases (MMPs), also referred to as matrixins, on the basis of a unique analysis of the ligand-target knowledge base, the 'matrixinome'. For this analysis, the authors created an annotated MMP database containing ∼ 300 inhibitors with their published activity profile. The ligand space was then arranged into a lead evolution tree, where the substructural transformations in each virtual step led to marked changes in the activity pattern. This allowed subtype-specific privileged fragments to be extracted as well as modifications, which improve activity and/or selectivity. Furthermore, the compounds with the preferred activity profile were correlated with sequence homology as well as binding site similarity within the target family, thereby leading to the identification of substructural modifications that turn non-selective, biohomologous structures into selective inhibitors. The matrixinomic application of the authors' approach, therefore, provides an example of how the combination of ligand space knowledge with sequence-related data can radically improve the outcome of the lead optimisation process to achieve higher selectivity within a given target family.
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Affiliation(s)
- Akos Papp
- AMRI Hungary, Inc., Záhony utca 7, 1031 Budapest, Hungary +361 6666 129 ; +361 6666 110 ;
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90
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Higashi S, Hirose T, Takeuchi T, Miyazaki K. Molecular design of a highly selective and strong protein inhibitor against matrix metalloproteinase-2 (MMP-2). J Biol Chem 2013; 288:9066-76. [PMID: 23395821 DOI: 10.1074/jbc.m112.441758] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Synthetic inhibitors of matrix metalloproteinases (MMPs), designed previously, as well as tissue inhibitors of metalloproteinases (TIMPs) lack enzyme selectivity, which has been a major obstacle for developing inhibitors into safe and effective MMP-targeted drugs. Here we designed a fusion protein named APP-IP-TIMP-2, in which the ten amino acid residue sequence of APP-derived MMP-2 selective inhibitory peptide (APP-IP) is added to the N terminus of TIMP-2. The APP-IP and TIMP-2 regions of the fusion protein are designed to interact with the active site and the hemopexin-like domain of MMP-2, respectively. The reactive site of the TIMP-2 region, which has broad specificity against MMPs, is blocked by the APP-IP adduct. The recombinant APP-IP-TIMP-2 showed strong inhibitory activity toward MMP-2 (Ki(app) = 0.68 pm), whereas its inhibitory activity toward MMP-1, MMP-3, MMP-7, MMP-8, MMP-9, or MT1-MMP was six orders of magnitude or more weaker (IC50 > 1 μm). The fusion protein inhibited the activation of pro-MMP-2 in the concanavalin A-stimulated HT1080 cells, degradation of type IV collagen by the cells, and the migration of stimulated cells. Compared with the decapeptide APP-IP (t½ = 30 min), APP-IP-TIMP-2 (t½ ≫ 96 h) showed a much longer half-life in cultured tumor cells. Therefore, the fusion protein may be a useful tool to evaluate contributions of proteolytic activity of MMP-2 in various pathophysiological processes. It may also be developed as an effective anti-tumor drug with restricted side effects.
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Affiliation(s)
- Shouichi Higashi
- Department of Genome System Science, Graduate School of Nanobioscience, Yokohama City University, 641-12, Maioka-cho, Totsuka-ku, Yokohama 244-0813, Japan.
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91
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Czarny B, Stura EA, Devel L, Vera L, Cassar-Lajeunesse E, Beau F, Calderone V, Fragai M, Luchinat C, Dive V. Molecular Determinants of a Selective Matrix Metalloprotease-12 Inhibitor: Insights from Crystallography and Thermodynamic Studies. J Med Chem 2013; 56:1149-59. [DOI: 10.1021/jm301574d] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bertrand Czarny
- CEA, Service
d’Ingénierie
Moléculaire des Protéines (SIMOPRO), Gif/Yvette 91191
Cedex, France
| | - Enrico A. Stura
- CEA, Service
d’Ingénierie
Moléculaire des Protéines (SIMOPRO), Gif/Yvette 91191
Cedex, France
| | - Laurent Devel
- CEA, Service
d’Ingénierie
Moléculaire des Protéines (SIMOPRO), Gif/Yvette 91191
Cedex, France
| | - Laura Vera
- CEA, Service
d’Ingénierie
Moléculaire des Protéines (SIMOPRO), Gif/Yvette 91191
Cedex, France
| | | | - Fabrice Beau
- CEA, Service
d’Ingénierie
Moléculaire des Protéines (SIMOPRO), Gif/Yvette 91191
Cedex, France
| | - Vito Calderone
- Magnetic
Resonance Center (CERM),
University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino,
Italy
| | - Marco Fragai
- Magnetic
Resonance Center (CERM),
University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino,
Italy
| | - Claudio Luchinat
- Magnetic
Resonance Center (CERM),
University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino,
Italy
| | - Vincent Dive
- CEA, Service
d’Ingénierie
Moléculaire des Protéines (SIMOPRO), Gif/Yvette 91191
Cedex, France
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92
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Design, synthesis and evaluation of 6-oxo-1, 6-dihydropyrimidine-2,5-dicarboxamide derivatives as MMP 13 inhibitors. Chem Res Chin Univ 2012. [DOI: 10.1007/s40242-012-2131-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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93
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An integrated computational approach to rationalize the activity of non-zinc-binding MMP-2 inhibitors. PLoS One 2012; 7:e47774. [PMID: 23144829 PMCID: PMC3493580 DOI: 10.1371/journal.pone.0047774] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 09/17/2012] [Indexed: 11/29/2022] Open
Abstract
Matrix metalloproteinases are a family of Zn-proteases involved in tissue remodeling and in many pathological conditions. Among them MMP-2 is one of the most relevant target in anticancer therapy. Commonly, MMP inhibitors contain a functional group able to bind the zinc ion and responsible for undesired side effects. The discovery of potent and selective MMP inhibitors not bearing a zinc-binding group is arising for some MMP family members and represents a new opportunity to find selective and non toxic inhibitors. In this work we attempted to get more insight on the inhibition process of MMP-2 by two non-zinc-binding inhibitors, applying a general protocol that combines several computational tools (docking, Molecular Dynamics and Quantum Chemical calculations), that all together contribute to rationalize experimental inhibition data. Molecular Dynamics studies showed both structural and mechanical-dynamical effects produced by the ligands not disclosed by docking analysis. Thermodynamic Integration provided relative binding free energies consistent with experimentally observed activity data. Quantum Chemical calculations of the tautomeric equilibrium involving the most active ligand completed the picture of the binding process. Our study highlights the crucial role of the specificity loop and suggests that enthalpic effect predominates over the entropic one.
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94
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Molecular mechanism of pancreatic tumor metastasis inhibition by Gd@C82(OH)22 and its implication for de novo design of nanomedicine. Proc Natl Acad Sci U S A 2012; 109:15431-6. [PMID: 22949663 DOI: 10.1073/pnas.1204600109] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Pancreatic adenocarcinoma is the most lethal of the solid tumors and the fourth-leading cause of cancer-related death in North America. Matrix metalloproteinases (MMPs) have long been targeted as a potential anticancer therapy because of their seminal role in angiogenesis and extracellular matrix (ECM) degradation of tumor survival and invasion. However, the inhibition specificity to MMPs and the molecular-level understanding of the inhibition mechanism remain largely unresolved. Here, we found that endohedral metallofullerenol Gd@C(82)(OH)(22) can successfully inhibit the neoplastic activity with experiments at animal, tissue, and cellular levels. Gd@C(82)(OH)(22) effectively blocks tumor growth in human pancreatic cancer xenografts in a nude mouse model. Enzyme activity assays also show Gd@C(82)(OH)(22) not only suppresses the expression of MMPs but also significantly reduces their activities. We then applied large-scale molecular-dynamics simulations to illustrate the molecular mechanism by studying the Gd@C(82)(OH)(22)-MMP-9 interactions in atomic detail. Our data demonstrated that Gd@C(82)(OH)(22) inhibits MMP-9 mainly via an exocite interaction, whereas the well-known zinc catalytic site only plays a minimal role. Steered by nonspecific electrostatic, hydrophobic, and specific hydrogen-bonding interactions, Gd@C(82)(OH)(22) exhibits specific binding modes near the ligand-specificity loop S1', thereby inhibiting MMP-9 activity. Both the suppression of MMP expression and specific binding mode make Gd@C(82)(OH)(22) a potentially more effective nanomedicine for pancreatic cancer than traditional medicines, which usually target the proteolytic sites directly but fail in selective inhibition. Our findings provide insights for de novo design of nanomedicines for fatal diseases such as pancreatic cancer.
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95
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Reich R, Hoffman A, Veerendhar A, Maresca A, Innocenti A, Supuran CT, Breuer E. Carbamoylphosphonates Control Tumor Cell Proliferation and Dissemination by Simultaneously Inhibiting Carbonic Anhydrase IX and Matrix Metalloproteinase-2. Toward Nontoxic Chemotherapy Targeting Tumor Microenvironment. J Med Chem 2012; 55:7875-82. [DOI: 10.1021/jm300981b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Reuven Reich
- Institute for Drug Research, The Hebrew University of Jerusalem, School of Pharmacy,
P.O. Box 12065, Jerusalem IL 91120, Israel
| | - Amnon Hoffman
- Institute for Drug Research, The Hebrew University of Jerusalem, School of Pharmacy,
P.O. Box 12065, Jerusalem IL 91120, Israel
| | - Ainelly Veerendhar
- Institute for Drug Research, The Hebrew University of Jerusalem, School of Pharmacy,
P.O. Box 12065, Jerusalem IL 91120, Israel
| | - Alfonso Maresca
- Universita degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica
Bioinorganica, Rm. 188, Via della Lastruccia 3, I-50019 Sesto Fiorentino
(Florence), Italy
| | - Alessio Innocenti
- Universita degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica
Bioinorganica, Rm. 188, Via della Lastruccia 3, I-50019 Sesto Fiorentino
(Florence), Italy
| | - Claudiu T. Supuran
- Universita degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica
Bioinorganica, Rm. 188, Via della Lastruccia 3, I-50019 Sesto Fiorentino
(Florence), Italy
| | - Eli Breuer
- Institute for Drug Research, The Hebrew University of Jerusalem, School of Pharmacy,
P.O. Box 12065, Jerusalem IL 91120, Israel
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96
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Minond D, Cudic M, Bionda N, Giulianotti M, Maida L, Houghten RA, Fields GB. Discovery of novel inhibitors of a disintegrin and metalloprotease 17 (ADAM17) using glycosylated and non-glycosylated substrates. J Biol Chem 2012; 287:36473-87. [PMID: 22927435 DOI: 10.1074/jbc.m112.389114] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A disintegrin and metalloprotease (ADAM) proteases are implicated in multiple diseases, but no drugs based on ADAM inhibition exist. Most of the ADAM inhibitors developed to date feature zinc-binding moieties that target the active site zinc, which leads to a lack of selectivity and off-target toxicity. We hypothesized that secondary binding site (exosite) inhibitors should provide a viable alternative to active site inhibitors. Potential exosites in ADAM structures have been reported, but no studies describing substrate features necessary for exosite interactions exist. Analysis of ADAM cognate substrates revealed that glycosylation is often present in the vicinity of the scissile bond. To study whether glycosylation plays a role in modulating ADAM activity, a tumor necrosis factor α (TNFα) substrate with and without a glycan moiety attached was synthesized and characterized. Glycosylation enhanced ADAM8 and -17 activities and decreased ADAM10 activity. Metalloprotease (MMP) activity was unaffected by TNFα substrate glycosylation. High throughput screening assays were developed using glycosylated and non-glycosylated substrate, and positional scanning was conducted. A novel chemotype of ADAM17-selective probes was discovered from the TPIMS library (Houghten, R. A., Pinilla, C., Giulianotti, M. A., Appel, J. R., Dooley, C. T., Nefzi, A., Ostresh, J. M., Yu, Y., Maggiora, G. M., Medina-Franco, J. L., Brunner, D., and Schneider, J. (2008) Strategies for the use of mixture-based synthetic combinatorial libraries. Scaffold ranking, direct testing in vivo, and enhanced deconvolution by computational methods. J. Comb. Chem. 10, 3-19; Pinilla, C., Appel, J. R., Borràs, E., and Houghten, R. A. (2003) Advances in the use of synthetic combinatorial chemistry. Mixture-based libraries. Nat. Med. 9, 118-122) that preferentially inhibited glycosylated substrate hydrolysis and spared ADAM10, MMP-8, and MMP-14. Kinetic studies revealed that ADAM17 inhibition occurred via a non-zinc-binding mechanism. Thus, modulation of proteolysis via glycosylation may be used for identifying novel, potentially exosite binding compounds. The newly described ADAM17 inhibitors represent research tools to investigate the role of ADAM17 in the progression of various diseases.
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Affiliation(s)
- Dmitriy Minond
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, USA.
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97
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Iyer RP, Patterson NL, Fields GB, Lindsey ML. The history of matrix metalloproteinases: milestones, myths, and misperceptions. Am J Physiol Heart Circ Physiol 2012; 303:H919-30. [PMID: 22904159 DOI: 10.1152/ajpheart.00577.2012] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since the discovery of tadpole collagenase in 1962, the matrix metalloproteinase (MMP) family has emerged as a significant proteinase group with recognized effects on the cardiovascular system. Over the last 40 years, many milestones have been achieved, from the identification of the first MMP, to the generation of the first MMP cDNA clone and null mouse, to the clinical approval of the first MMP inhibitor. Over the years, a few myths and misunderstandings have interwoven into the truths. In this review, we will discuss the major milestones of MMP research, as well as review the misinterpretations and misperceptions that have evolved. Clarifying the confusions and dispelling the myths will both provide a better understanding of MMP properties and functions and focus the cardiovascular field on the outstanding research questions that need to be addressed.
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Affiliation(s)
- Rugmani Padmanabhan Iyer
- San Antonio Cardiovascular Proteomics Center, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78245, USA
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98
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Devel L, Beau F, Amoura M, Vera L, Cassar-Lajeunesse E, Garcia S, Czarny B, Stura EA, Dive V. Simple pseudo-dipeptides with a P2' glutamate: a novel inhibitor family of matrix metalloproteases and other metzincins. J Biol Chem 2012; 287:26647-56. [PMID: 22689580 DOI: 10.1074/jbc.m112.380782] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A series of pseudo-peptides with general formula X-l-Glu-NH(2) (with X corresponding to an acyl moiety with a long aryl-alkyl side chain) have been synthesized, evaluated as inhibitors of matrix metalloproteases (MMPs), and found to display remarkable nanomolar affinity. The loss in potency associated with a substitution of the P(2)' l-glutamate by a l-glutamine corroborates the importance of a carboxylate at this position. The binding mode of some of these inhibitors was characterized in solution and by x-ray crystallography in complex with various MMPs. The x-ray crystal structures reveal an unusual binding mode with the glutamate side chain chelating the active site zinc ion. Competition experiments between these inhibitors and acetohydroxamic acid, a small zinc-binding molecule, are in accord with the crystallographic results. One of these pseudo-dipeptides displays potency and selectivity toward MMP-12 similar to the best MMP-12 inhibitors reported to date. This novel family of pseudo peptides opens new opportunities to develop potent and selective inhibitors for several metzincins.
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Affiliation(s)
- Laurent Devel
- CEA (Commissariat à l'Energie Atomique), iBiTec-S, Service d'Ingénierie Moléculaire de Protéines (SIMOPRO), CE Saclay, 91191 Gif/Yvette, Cedex, France.
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99
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Kalva S, Vadivelan S, Sanam R, Jagarlapudi SARP, Saleena LM. Lead identification and optimization of novel collagenase inhibitors; pharmacophore and structure based studies. Bioinformation 2012; 8:301-8. [PMID: 22553386 PMCID: PMC3338973 DOI: 10.6026/97320630008301] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 04/03/2012] [Indexed: 11/23/2022] Open
Abstract
In this study, chemical feature based pharmacophore models of MMP-1, MMP-8 and MMP-13 inhibitors have been developed with the aid of HypoGen module within Catalyst program package. In MMP-1 and MMP-13, all the compounds in the training set mapped HBA and RA, while in MMP-8, the training set mapped HBA and HY. These features revealed responsibility for the high molecular bioactivity, and this is further used as a three dimensional query to screen the knowledge based designed molecules. These pharmacophore models for collagenases picked up some potent and novel inhibitors. Subsequently, docking studies were performed for the potent molecules and novel hits were suggested for further studies based on the docking score and active site interactions in MMP-1, MMP-8 and MMP-13.
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Affiliation(s)
- Sukesh Kalva
- Department of Bioinformatics, SRM University, SRM Nagar, Kattankulathur - 603 203, Kancheepuram District, Chennai, India
| | - S Vadivelan
- Informatics, GVK Biosciences Private Limited, 443, Guna Complex, 9th Floor Annexe I Building, Anna Salai, Teynampet
- E.G.S.Pillay College of Pharmacy, Old Nagore Road, Nagapattinam 611 002, Tamilnadu, India
| | - Ramadevi Sanam
- Informatics, GVK Biosciences Private Limited, 443, Guna Complex, 9th Floor Annexe I Building, Anna Salai, Teynampet
| | - Sarma ARP Jagarlapudi
- Informatics, GVK Biosciences Private Limited, 443, Guna Complex, 9th Floor Annexe I Building, Anna Salai, Teynampet
| | - Lilly M Saleena
- Department of Bioinformatics, SRM University, SRM Nagar, Kattankulathur - 603 203, Kancheepuram District, Chennai, India
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Zhang J, Yang W, Piquemal JP, Ren P. Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential. J Chem Theory Comput 2012; 8:1314-1324. [PMID: 22754403 PMCID: PMC3383645 DOI: 10.1021/ct200812y] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
As the second most abundant cation in human body, zinc is vital for the structures and functions of many proteins. Zinc-containing matrix metalloproteinases (MMPs) have been widely investigated as potential drug targets in a range of diseases ranging from cardiovascular disorders to cancers. However, it remains a challenge in theoretical studies to treat zinc in proteins with classical mechanics. In this study, we examined Zn(2+) coordination with organic compounds and protein side chains using a polarizable atomic multipole based electrostatic model. We find that polarization effect plays a determining role in Zn(2+) coordination geometry in both matrix metalloproteinase (MMP) complexes and in zinc-finger proteins. In addition, the relative binding free energies of selected inhibitors binding with MMP13 have been estimated and compared with experimental results. While not directly interacting with the small molecule inhibitors, the permanent and polarizing field of Zn(2+) exerts a strong influence on the relative affinities of the ligands. The simulation results also reveal the polarization effect on binding is ligand dependent and thus difficult to be incorporated into fixed-charge models implicitly.
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Affiliation(s)
- Jiajing Zhang
- Department of Biomedical Engineering, The University of Texas at Austin, TX 78712
| | - Wei Yang
- The Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
| | - Jean-Philip Piquemal
- UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, TX 78712
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