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Liu C, Tang J, Chen Y, Zhang Q, Lin J, Wu S, Han J, Liu Z, Wu C, Zhuo Y, Li Y. Intracellular Zn 2+ promotes extracellular matrix remodeling in dexamethasone-treated trabecular meshwork. Am J Physiol Cell Physiol 2024; 326:C1293-C1307. [PMID: 38525543 DOI: 10.1152/ajpcell.00725.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/26/2024] [Accepted: 03/09/2024] [Indexed: 03/26/2024]
Abstract
Given the widespread application of glucocorticoids in ophthalmology, the associated elevation of intraocular pressure (IOP) has long been a vexing concern for clinicians, yet the underlying mechanisms remain inconclusive. Much of the discussion focuses on the extracellular matrix (ECM) of trabecular meshwork (TM). It is widely agreed that glucocorticoids impact the expression of matrix metalloproteinases (MMPs), leading to ECM deposition. Since Zn2+ is vital for MMPs, we explored its role in ECM alterations induced by dexamethasone (DEX). Our study revealed that in human TM cells treated with DEX, the level of intracellular Zn2+ significantly decreased, accompanied by impaired extracellular Zn2+ uptake. This correlated with changes in several Zrt-, Irt-related proteins (ZIPs) and metallothionein. ZIP8 knockdown impaired extracellular Zn2+ uptake, but Zn2+ chelation did not affect ZIP8 expression. Resembling DEX's effects, chelation of Zn2+ decreased MMP2 expression, increased the deposition of ECM proteins, and induced structural disarray of ECM. Conversely, supplementation of exogenous Zn2+ in DEX-treated cells ameliorated these outcomes. Notably, dietary zinc supplementation in mice significantly reduced DEX-induced IOP elevation and collagen content in TM, thereby rescuing the visual function of the mice. These findings underscore zinc's pivotal role in ECM regulation, providing a novel perspective on the pathogenesis of glaucoma.NEW & NOTEWORTHY Our study explores zinc's pivotal role in mitigating extracellular matrix dysregulation in the trabecular meshwork and glucocorticoid-induced ocular hypertension. We found that in human trabecular meshwork cells treated with dexamethasone, intracellular Zn2+ significantly decreased, accompanied by impaired extracellular Zn2+ uptake. Zinc supplementation rescues visual function by modulating extracellular matrix proteins and lowering intraocular pressure, offering a direction for further exploration in glaucoma management.
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Affiliation(s)
- Canying Liu
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
| | - Jiahui Tang
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
| | - Yuze Chen
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
| | - Qi Zhang
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
| | - Jicheng Lin
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
| | - Siting Wu
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
| | - Jiaxu Han
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
| | - Zhe Liu
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
| | - Caiqing Wu
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
| | - Yehong Zhuo
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
| | - Yiqing Li
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
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Hayun H, Coban M, Bhagat AK, Ozer E, Alfonta L, Caulfield TR, Radisky ES, Papo N. Utilizing genetic code expansion to modify N-TIMP2 specificity towards MMP-2, MMP-9, and MMP-14. Sci Rep 2023; 13:5186. [PMID: 36997589 PMCID: PMC10063552 DOI: 10.1038/s41598-023-32019-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/21/2023] [Indexed: 04/01/2023] Open
Abstract
Matrix metalloproteinases (MMPs) regulate the degradation of extracellular matrix (ECM) components in biological processes. MMP activity is controlled by natural tissue inhibitors of metalloproteinases (TIMPs) that non-selectively inhibit the function of multiple MMPs via interaction with the MMPs' Zn2+-containing catalytic pocket. Recent studies suggest that TIMPs engineered to confer MMP specificity could be exploited for therapeutic purposes, but obtaining specific TIMP-2 inhibitors has proved to be challenging. Here, in an effort to improve MMP specificity, we incorporated the metal-binding non-canonical amino acids (NCAAs), 3,4-dihydroxyphenylalanine (L-DOPA) and (8-hydroxyquinolin-3-yl)alanine (HqAla), into the MMP-inhibitory N-terminal domain of TIMP2 (N-TIMP2) at selected positions that interact with the catalytic Zn2+ ion (S2, S69, A70, L100) or with a structural Ca2+ ion (Y36). Evaluation of the inhibitory potency of the NCAA-containing variants towards MMP-2, MMP-9 and MMP-14 in vitro revealed that most showed a significant loss of inhibitory activity towards MMP-14, but not towards MMP-2 and MMP-9, resulting in increased specificity towards the latter proteases. Substitutions at S69 conferred the best improvement in selectivity for both L-DOPA and HqAla variants. Molecular modeling provided an indication of how MMP-2 and MMP-9 are better able to accommodate the bulky NCAA substituents at the intermolecular interface with N-TIMP2. The models also showed that, rather than coordinating to Zn2+, the NCAA side chains formed stabilizing polar interactions at the intermolecular interface with MMP-2 and MMP-9. Our findings illustrate how incorporation of NCAAs can be used to probe-and possibly exploit-differential tolerance for substitution within closely related protein-protein complexes as a means to improve specificity.
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Affiliation(s)
- Hezi Hayun
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, 84105, Beer-Sheva, Israel
| | - Matt Coban
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, 310 Griffin Building, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Ashok Kumar Bhagat
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Eden Ozer
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Lital Alfonta
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Thomas R Caulfield
- Departments of Neuroscience, Artificial Intelligence and Informatics, Computational Biology and Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Jacksonville, FL, 32224, USA.
| | - Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, 310 Griffin Building, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.
| | - Niv Papo
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, 84105, Beer-Sheva, Israel.
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3
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Hayun H, Coban M, Bhagat AK, Ozer E, Alfonta L, Caulfield TR, Radisky ES, Papo N. Utilizing genetic code expansion to modify N-TIMP2 specificity towards MMP-2, MMP-9, and MMP-14. RESEARCH SQUARE 2023:rs.3.rs-2446107. [PMID: 36712032 PMCID: PMC9882641 DOI: 10.21203/rs.3.rs-2446107/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Matrix metalloproteinases (MMPs) regulate the degradation of extracellular matrix (ECM) components in biological processes. MMP activity is controlled by natural tissue inhibitors of metalloproteinases (TIMPs) that non-selectively inhibit the function of multiple MMPs via interaction with the MMPs' Zn 2+ -containing catalytic pocket. Recent studies suggest that TIMPs engineered to confer MMP specificity could be exploited for therapeutic purposes, but obtaining specific TIMP-2 inhibitors has proved to be challenging. Here, in an effort to improve MMP specificity, we incorporated the metal-binding non-canonical amino acids (NCAAs), 3,4-dihydroxyphenylalanine (L-DOPA) and (8-hydroxyquinolin-3-yl)alanine (HqAla), into the MMP-inhibitory N-terminal domain of TIMP2 (N-TIMP2) at selected positions that interact with the catalytic Zn 2+ ion (S2, S69, A70, L100) or with a structural Ca 2+ ion (Y36). Evaluation of the inhibitory potency of the NCAA-containing variants towards MMP-2, MMP-9 and MMP-14 in vitro revealed that most showed a significant loss of inhibitory activity towards MMP-14, but not towards MMP-2 and MMP-9, resulting in increased specificity towards the latter proteases. Substitutions at S69 conferred the best improvement in selectivity for both L-DOPA and HqAla variants. Molecular modeling revealed how MMP-2 and MMP-9 are better able to accommodate the bulky NCAA substituents at the intermolecular interface with N-TIMP2. The models also showed that, rather than coordinating to Zn 2+ , the NCAA side chains formed stabilizing polar interactions at the intermolecular interface with MMP-2 and MMP-9. The findings illustrate how incorporation of NCAAs can be used to probe and exploit differential tolerance for substitution within closely related protein-protein complexes to achieve improved specificity.
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Affiliation(s)
| | | | | | | | | | | | | | - Niv Papo
- Ben-Gurion University of the Negev
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Varghese A, Chaturvedi SS, Fields GB, Karabencheva-Christova TG. A synergy between the catalytic and structural Zn(II) ions and the enzyme and substrate dynamics underlies the structure-function relationships of matrix metalloproteinase collagenolysis. J Biol Inorg Chem 2021; 26:583-597. [PMID: 34228191 DOI: 10.1007/s00775-021-01876-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/28/2021] [Indexed: 10/20/2022]
Abstract
Matrix metalloproteinases (MMPs) are Zn(II) dependent endopeptidases involved in the degradation of collagen. Unbalanced collagen breakdown results in numerous pathological conditions, including cardiovascular and neurodegenerative diseases and tumor growth and invasion. Matrix metalloproteinase-1 (MMP-1) is a member of the MMPs family. The enzyme contains catalytic and structural Zn(II) ions. Despite many studies on the enzyme, there is little known about the synergy between the two Zn(II) metal ions and the enzyme and substrate dynamics in MMP-1 structure-function relationships. We performed a computational study of the MMP-1•triple-helical peptide (THP) enzyme•substrate complex to provide this missing insight. Our results revealed Zn(II) ions' importance in modulating the long-range correlated motions in the MMP-1•THP complex. Overall, our results reveal the importance of the catalytic Zn(II) and the role of the structural Zn(II) ion in preserving the integrity of the enzyme active site and the overall enzyme-substrate complex synergy with the dynamics of the enzyme and the substrate. Notably, both Zn(II) sites participate in diverse networks of long-range correlated motions that involve the CAT and HPX domains and the THP substrate, thus exercising a complex role in the stability and functionality of the MMP-1•THP complex. Both the Zn(II) ions have a distinct impact on the structural stability and dynamics of the MMP-1•THP complex. The study shifts the paradigm from the "local role" of the Zn(II) ions with knowledge about their essential role in the long-range dynamics and stability of the overall enzyme•substrate (ES) complex.
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Affiliation(s)
- Ann Varghese
- Department of Chemistry, Michigan Technological University, Houghton, MI, 49931, USA
| | - Shobhit S Chaturvedi
- Department of Chemistry, Michigan Technological University, Houghton, MI, 49931, USA
| | - Gregg B Fields
- Department of Chemistry and Biochemistry and I-HEALTH, Florida Atlantic University, Jupiter, FL, 33458, USA
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5
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Polymerizable Matrix Metalloproteinases' Inhibitors with Potential Application for Dental Restorations. Biomedicines 2021; 9:biomedicines9040366. [PMID: 33807479 PMCID: PMC8065691 DOI: 10.3390/biomedicines9040366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/19/2021] [Accepted: 03/26/2021] [Indexed: 12/21/2022] Open
Abstract
Collagen cleavage by matrix metalloproteinase (MMP) is considered a major cause of dental resins long term failure. Most MMP inhibitors display significant toxicity and are unsuitable for dental resins’ applications. Here we report a study of a new class of inhibitors that display the unique property of being co-polymerizable with other vinyl compounds present in commercial dental resins, limiting their release and potential toxicity. Computational affinity towards the active site of different MMP-1; -2; -8; -9 and -13 of several compounds showed interesting properties and were synthesized. These free compounds were tested concerning their toxicity upon contact with two different cell types, with no substantial decrease in cell viability at high concentrations. Even so, compound’s safety can be further improved upon copolymerization with commercial dental resins, limiting their release.
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6
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Patra S, Saravanan P, Das B, Subramanian V, Patra S. Scaffold-based Screening and Molecular Dynamics Simulation Study to Identify Two Structurally Related Phenolic Compounds as Potent MMP1 Inhibitors. Comb Chem High Throughput Screen 2020; 23:757-774. [PMID: 32342802 DOI: 10.2174/1386207323666200428114216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/19/2019] [Accepted: 01/14/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Matrix metalloproteinase 1 are zinc-dependent endopeptidases responsible for the controlled breakdown of the extracellular matrix resulting in the maintenance of homeostasis. Dysregulation of MMP1 leads to the progression of various pathological conditions like cancer, rheumatoid arthritis, cardiovascular disease, skin damage and fibrotic disorder. Thus, MMP1 inhibition is the potential drug target of many synthetic MMP1 inhibitors but lack of substrate specificity hinders their clinical applicability. Hence, inhibitors from natural products have gained widespread attention. OBJECTIVE The present study attempts screening of novel MMP1 inhibitors from the ZINC database based on experimentally reported natural inhibitors of MMP1 as a scaffold. METHODS Molecular docking study was performed with 19 experimentally reported natural inhibitors spanning across nine different classes followed by virtual screening using the selected compounds. The selected compounds were subjected to molecular dynamics simulation. RESULTS Twenty compounds were screened with a cut-off of -9.0 kcal/mol of predicted free energy of binding, which further converged to 6 hits after docking studies. After comparing the docking result of 6 screened hits, two best compounds were selected. ZINC02436922 had the best interaction with six hydrogen bond formation to a relatively confined region in the S1'site of MMP1 and -10.01 kcal/mol of predicted free energy of binding. ZINC03075557 was the secondbest compound with -9.57 kcal/mol predicted binding free energy. Molecular dynamics simulation of ZINC02436922 and ZINC03075557 corroborates docking study. CONCLUSION This study indicated phenolic compounds ZINC02436922 and ZINC03075557 as potential MMP1 inhibitors.
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Affiliation(s)
- Swagata Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Parameswaran Saravanan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Bhaskar Das
- Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | | | - Sanjukta Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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7
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The past, present and future perspectives of matrix metalloproteinase inhibitors. Pharmacol Ther 2020; 207:107465. [DOI: 10.1016/j.pharmthera.2019.107465] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022]
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8
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Virtual screening identification and chemical optimization of substituted 2-arylbenzimidazoles as new non-zinc-binding MMP-2 inhibitors. Bioorg Med Chem 2020; 28:115257. [DOI: 10.1016/j.bmc.2019.115257] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 01/02/2023]
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9
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Mendoza-Wilson AM, Balandrán-Quintana RR. Computational and Experimental Progress on the Structure and Chemical Reactivity of Procyanidins: Their Potential as Metalloproteinases Inhibitors. CURR ORG CHEM 2019. [DOI: 10.2174/1385272822666180828114021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Matrix metalloproteinases (MMPs) are enzymes involved in various physiological
processes essential for living beings, but the loss of the regulatory control by endogenous
inhibitors of MMPs, leads to the development of serious diseases such as cardiovascular
system affections, cancer, and metastasis. For these reasons, exogenous inhibitors
are required for these enzymes, which are able to control the proteolytic activity
and are selective towards the different MMPs, besides properties which, from the
pharmacological point of view, are necessary to be effective under physiological
conditions. Based on these expectations, some bioactive compounds that are abundant in
the human diet, like procyanidins (PCs) have emerged as potential exogenous inhibitors
of MMPs. This review presents the advances of experimental and computational investigations
carried out to date on the structure and chemical reactivity of PCs, to support the basis of their potential
use as MMP inhibitors. For such purpose, specific sites among MMPs identified for a selective inhibition, the
role of PCs in the regulation of MMPs by posttranscriptional mechanisms at the level of microRNAs, modulation
of reactive oxygen species (ROS), effects on tissue inhibitors of MMPs (TIMPs), the crosslinking of PCs
with the extracellular matrix proteins, as well as direct interaction between PCs and MMPs, are discussed.
Methods for isolation and synthesis of PCs, as well as hydrophilicity properties, bioavailability, and susceptibility
to be metabolized in oral intake, are also addressed. The information gathered in this review could additionally
help to visualize future research related to this topic.
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Affiliation(s)
- Ana María Mendoza-Wilson
- Centro de Investigacion en Alimentacion y Desarrollo, A.C., Coordinacion de Tecnologia de Alimentos de Origen Vegetal, Carretera a La Victoria km 0.6, 83304, Hermosillo, Son, Mexico
| | - René Renato Balandrán-Quintana
- Centro de Investigacion en Alimentacion y Desarrollo, A.C., Coordinacion de Tecnologia de Alimentos de Origen Vegetal, Carretera a La Victoria km 0.6, 83304, Hermosillo, Son, Mexico
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Sun L, Xie S, Ji X, Zhang J, Wang D, Lee SJ, Lee H, He H, Yang VC. MMP-2-responsive fluorescent nanoprobes for enhanced selectivity of tumor cell uptake and imaging. Biomater Sci 2018; 6:2619-2626. [PMID: 30109310 DOI: 10.1039/c8bm00593a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is difficult to develop highly selective substrate-based fluorescent nanoprobes for specific matrix metalloproteinases (MMPs) due to overlapping substrate specificities among the family of MMP enzymes. To resolve this issue, we have developed novel fluorescent nanoprobes that are highly selective for soluble MMP-2. Herein, MMP-2-responsive nanoprobes were prepared by immobilizing fluorescent fusion proteins on nickel ferrite nanoparticles via the His-tag nickel chelation mechanism. The fusion protein consisted of a fluorescent mCherry protein with a cell penetrating peptide (CPP) moiety. An MMP-2 cleavage site was also introduced within the fusion protein, which was directly linked to the nickel ferrite nanoparticles. The selectivity of nanoprobes was modulated by hiding the cleavage site of MMP-2 substrates deeply inside the system, which could result in strong steric hindrance between the nanoprobes and MMPs, especially for membrane-tethered MMPs such as MMP-14. A cell-based assay demonstrated that the nanoprobes could only be activated by tumor cells secreting soluble MMP-2, but not membrane-tethered MMP-14. To further evaluate the contribution of the steric hindrance effect on the nanoprobes, a truncated recombinant MMP-14 was employed to confer their cleavage activity as compared to native membrane-tethered MMP-14. Furthermore, a designed probe with a diminished steric hindrance effect was proved to be activated by membrane-tethered type MMP-14. The results indicated that the design of fluorescent nanoprobes employing the steric hindrance effect can greatly enhance the selectivity of MMP-responsive nanoprobes realizing the specific detection of soluble MMP-2 in a tumor microenvironment. We believe that highly selective MMP-2-responsive fluorescent nanoprobes have broad impacts on biomedical applications including molecular imaging and labeling for tumor detection.
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Affiliation(s)
- Lu Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
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Nuti E, Cuffaro D, Bernardini E, Camodeca C, Panelli L, Chaves S, Ciccone L, Tepshi L, Vera L, Orlandini E, Nencetti S, Stura EA, Santos MA, Dive V, Rossello A. Development of Thioaryl-Based Matrix Metalloproteinase-12 Inhibitors with Alternative Zinc-Binding Groups: Synthesis, Potentiometric, NMR, and Crystallographic Studies. J Med Chem 2018; 61:4421-4435. [DOI: 10.1021/acs.jmedchem.8b00096] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Elisa Nuti
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Doretta Cuffaro
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Elisa Bernardini
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Caterina Camodeca
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Laura Panelli
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Sílvia Chaves
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Lidia Ciccone
- CEA, Institut des Sciences du Vivant Frédéric Joliot, Service d’Ingénierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, Gif-sur-Yvette 91190, France
- Synchrotron SOLEIL, L’Orme des Merisiers,
Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Livia Tepshi
- CEA, Institut des Sciences du Vivant Frédéric Joliot, Service d’Ingénierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Laura Vera
- CEA, Institut des Sciences du Vivant Frédéric Joliot, Service d’Ingénierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, Gif-sur-Yvette 91190, France
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Elisabetta Orlandini
- Dipartimento di Scienze della Terra, Università di Pisa, via Santa Maria 53, 56126 Pisa, Italy
| | - Susanna Nencetti
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Enrico A. Stura
- CEA, Institut des Sciences du Vivant Frédéric Joliot, Service d’Ingénierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - M. Amélia Santos
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Vincent Dive
- CEA, Institut des Sciences du Vivant Frédéric Joliot, Service d’Ingénierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Armando Rossello
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
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Abstract
Matrix metalloproteinases (MMPs) are structurally related endopeptidases. They are also known as metzincins due to their interaction with zinc ion of the conserved methionine (Met) at the active site. MMPs play an important role in physiological and signaling processes of wound healing, bone resorption and angiogenesis. The structure of MMPs consists of signal peptide, propeptide, catalytic domain, hinge region and hemopexin-like domain. MMP-9 shares high structural and functional similarities with MMP-2, therefore designing selective MMP-9 inhibitors (MMPIs) is challenging. The selectivity can be achieved by targeting S2 subsite of MMP-9 that is having difference with MMP-2. Further, targeting its exosite and protein disulfide isomerase may also provide selective MMPIs. The review highlights the molecular features and basis of MMP-9 enzyme action. The MMPIs reported in the recent years have also been included.
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13
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Jana S, Singh SK. Identification of selective MMP-9 inhibitors through multiple e-pharmacophore, ligand-based pharmacophore, molecular docking, and density functional theory approaches. J Biomol Struct Dyn 2018; 37:944-965. [DOI: 10.1080/07391102.2018.1444510] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Srabanti Jana
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Sushil K. Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
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14
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Sun L, Xie S, Qi J, Liu E, Liu D, Liu Q, Chen S, He H, Yang VC. Cell-Permeable, MMP-2 Activatable, Nickel Ferrite and His-Tagged Fusion Protein Self-Assembled Fluorescent Nanoprobe for Tumor Magnetic-Targeting and Imaging. ACS APPLIED MATERIALS & INTERFACES 2017; 9:39209-39222. [PMID: 29058417 DOI: 10.1021/acsami.7b12918] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Matrix metalloproteinases (MMPs) activatable imaging probe has been explored for tumor detection. However, activation of the probe is mainly done in the extracellular space without intracellular uptake of the probe for more sensitivity. Although cell-penetrating peptides (CPPs) have been demonstrated to enable intracellular delivery of the imaging probe, they nevertheless encounter off-target delivery of the cargos to normal tissues. Herein, we have developed a dual MMP-2-activatable and tumor cell-permeable magnetic nanoprobe to simultaneously achieve selective and intracellular tumor imaging. This novel imaging probe was constructed by self-assembling a hexahistidine-tagged (His-tagged) fluorescent fusion protein chimera and nickel ferrite nanoparticles via a chelation mechanism. The His-tagged fluorescent protein chimera consisted of a red fluorescent protein mCherry that acted as the fluorophore, the low-molecular-weight protamine peptide as the CPP, and the MMP-2 cleavage sequence fused with the hexahistidine tag, whereas the nickel ferrite nanoparticles functioned as the His-tagged protein binder and also the fluorescent quencher. Both in vitro and in vivo results revealed that this imaging probe would not only remain nonpermeable to normal tissues, thereby offsetting the nonselective cellular uptake, but was also suppressed of fluorescent signals during magnetic tumor-targeting in the circulation, primarily because of the masking of the CPP activity and quenching of the fluorophore by the associated NiFe2O4 nanoparticles. However, these properties were recovered or "turned on" by the action of tumor-associated MMP-2 stimuli, leading to cell penetration of the nanoprobes as well as fluorescence restoration and visualization within the tumor cells. In this regard, the presented tumor-activatable and cell-permeable system deems to be an appealing platform to achieve selective tumor imaging and intracellular protein delivery. Its impact is therefore significant, far-reaching, and wide-spread.
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Affiliation(s)
- Lu Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin 300070, PR China
| | - Shuping Xie
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin 300070, PR China
| | - Jing Qi
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin 300070, PR China
| | - Ergang Liu
- Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, PR China
| | - Di Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin 300070, PR China
| | - Quan Liu
- Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, PR China
| | - Sunhui Chen
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin 300070, PR China
| | - Huining He
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin 300070, PR China
| | - Victor C Yang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin 300070, PR China
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan , Ann Arbor Michigan 48109-1065, United States
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15
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Meng F, Yang H, Jack C, Zhang H, Moller A, Spivey D, Page RC, Tierney DL, Crowder MW. Biochemical characterization and zinc binding group (ZBGs) inhibition studies on the catalytic domain of MMP7 (cdMMP7). J Inorg Biochem 2016; 165:7-17. [DOI: 10.1016/j.jinorgbio.2016.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/05/2016] [Accepted: 10/13/2016] [Indexed: 02/08/2023]
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16
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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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Bourguet E, Brazhnik K, Sukhanova A, Moroy G, Brassart-Pasco S, Martin AP, Villena I, Bellon G, Sapi J, Nabiev I. Design, Synthesis, and Use of MMP-2 Inhibitor-Conjugated Quantum Dots in Functional Biochemical Assays. Bioconjug Chem 2016; 27:1067-81. [DOI: 10.1021/acs.bioconjchem.6b00065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Erika Bourguet
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, SFR Cap-Santé, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
| | - Kristina Brazhnik
- Laboratoire de Recherche en Nanosciences, LRN - EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe shosse, 115409 Moscow, Russian Federation
| | - Alyona Sukhanova
- Laboratoire de Recherche en Nanosciences, LRN - EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe shosse, 115409 Moscow, Russian Federation
| | - Gautier Moroy
- Molécules Thérapeutiques In Silico, INSERM UMR-S 973, Université Paris Diderot, Sorbonne Paris Cité, 35 rue Hélène Brion, 75013 Paris, France
| | - Sylvie Brassart-Pasco
- Laboratoire de Biochimie et de Biologie moléculaire, MEDyC, UMR CNRS/URCA 7369, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
| | - Anne-Pascaline Martin
- Laboratoire de Biochimie et de Biologie moléculaire, MEDyC, UMR CNRS/URCA 7369, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
- Laboratoire de Parasitologie-Mycologie, EA3800, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51100 Reims, France
| | - Isabelle Villena
- Laboratoire de Parasitologie-Mycologie, EA3800, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51100 Reims, France
| | - Georges Bellon
- Laboratoire de Biochimie et de Biologie moléculaire, MEDyC, UMR CNRS/URCA 7369, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
| | - Janos Sapi
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, SFR Cap-Santé, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
| | - Igor Nabiev
- Laboratoire de Recherche en Nanosciences, LRN - EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe shosse, 115409 Moscow, Russian Federation
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18
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Lee SE, Chen Q, Bhat R, Petkiewicz S, Smith JM, Ferry VE, Correia AL, Alivisatos AP, Bissell MJ. Reversible Aptamer-Au Plasmon Rulers for Secreted Single Molecules. NANO LETTERS 2015; 15:4564-70. [PMID: 26039492 PMCID: PMC4545488 DOI: 10.1021/acs.nanolett.5b01161] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plasmon rulers, consisting of pairs of gold nanoparticles, allow single-molecule analysis without photobleaching or blinking; however, current plasmon rulers are irreversible, restricting detection to only single events. Here, we present a reversible plasmon ruler, comprised of coupled gold nanoparticles linked by a single aptamer, capable of binding individual secreted molecules with high specificity. We show that the binding of target secreted molecules to the reversible plasmon ruler is characterized by single-molecule sensitivity, high specificity, and reversibility. Such reversible plasmon rulers should enable dynamic and adaptive live-cell measurement of secreted single molecules in their local microenvironment.
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Affiliation(s)
- Somin Eunice Lee
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Electrical & Computer Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Corresponding Authors: . Phone: (510) 486-4999. . Phone: (510) 486-4365. . Phone: (734) 764-7054
| | - Qian Chen
- Material Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry and Materials Science & Engineering, University of California, Berkeley, California 94720, United States
| | - Ramray Bhat
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Molecular Reproduction Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Shayne Petkiewicz
- Material Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry and Materials Science & Engineering, University of California, Berkeley, California 94720, United States
| | - Jessica M. Smith
- Material Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry and Materials Science & Engineering, University of California, Berkeley, California 94720, United States
| | - Vivian E. Ferry
- Material Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry and Materials Science & Engineering, University of California, Berkeley, California 94720, United States
| | - Ana Luisa Correia
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - A. Paul Alivisatos
- Material Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli Energy NanoScience Institute, University of California, Berkeley, California 94720, United States
- Corresponding Authors: . Phone: (510) 486-4999. . Phone: (510) 486-4365. . Phone: (734) 764-7054
| | - Mina J. Bissell
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Corresponding Authors: . Phone: (510) 486-4999. . Phone: (510) 486-4365. . Phone: (734) 764-7054
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19
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Gupta SP. QSAR Studies on Hydroxamic Acids: A Fascinating Family of Chemicals with a Wide Spectrum of Activities. Chem Rev 2015; 115:6427-90. [DOI: 10.1021/cr500483r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Satya P. Gupta
- Department of Applied Sciences, National Institute of Technical Teachers’ Training and Research, Shamla
Hills, Bhopal-462002, India
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20
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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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21
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Chung IC, Chen LC, Chung AK, Chao M, Huang HY, Hsueh C, Tsang NM, Chang KP, Liang Y, Li HP, Chang YS. Matrix metalloproteinase 12 is induced by heterogeneous nuclear ribonucleoprotein K and promotes migration and invasion in nasopharyngeal carcinoma. BMC Cancer 2014; 14:348. [PMID: 24885469 PMCID: PMC4033617 DOI: 10.1186/1471-2407-14-348] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 05/06/2014] [Indexed: 01/10/2023] Open
Abstract
Background Overexpression of heterogeneous nuclear ribonucleoprotein K (hnRNP K), a DNA/RNA binding protein, is associated with metastasis in nasopharyngeal carcinoma (NPC). However, the mechanisms underlying hnRNP K-mediated metastasis is unclear. The aim of the present study was to determine the role of matrix metalloproteinase (MMP) in hnRNP K-mediated metastasis in NPC. Methods We studied hnRNP K-regulated MMPs by analyzing the expression profiles of MMP family genes in NPC tissues and hnRNP K-knockdown NPC cells using Affymetrix microarray analysis and quantitative RT-PCR. The association of hnRNP K and MMP12 expression in 82 clinically proven NPC cases was determined by immunohistochemical analysis. The hnRNP K-mediated MMP12 regulation was determined by zymography and Western blot, as well as by promoter, DNA pull-down and chromatin immunoprecipitation (ChIP) assays. The functional role of MMP12 in cell migration and invasion was demonstrated by MMP12-knockdown and the treatment of MMP12-specific inhibitor, PF-356231. Results MMP12 was overexpressed in NPC tissues, and this high level of expression was significantly correlated with high-level expression of hnRNP K (P = 0.026). The levels of mRNA, protein and enzyme activity of MMP12 were reduced in hnRNP K-knockdown NPC cells. HnRNP K interacting with the region spanning −42 to −33 bp of the transcription start site triggered transcriptional activation of the MMP12 promoter. Furthermore, inhibiting MMP12 by MMP12 knockdown and MMP12-specific inhibitor, PF-356231, significantly reduced the migration and invasion of NPC cells. Conclusions Overexpression of MMP12 was significantly correlated with hnRNP K in NPC tissues. HnRNP K can induce MMP12 expression and enzyme activity through activating MMP12 promoter, which promotes cell migration and invasion in NPC cells. In vitro experiments suggest that NPC metastasis with high MMP12 expression may be treated with PF-356231. HnRNP K and MMP12 may be potential therapeutic markers for NPC, but additional validation studies are warranted.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Hsin-Pai Li
- Molecular Medicine Research Center, Chang Gung University, 259 Wen-Hwa Ist Road, Taoyuan, Kwei-shan 333, Taiwan.
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22
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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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23
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Matrix metalloproteinases in cancer: their value as diagnostic and prognostic markers and therapeutic targets. Tumour Biol 2013; 34:2041-51. [PMID: 23681802 DOI: 10.1007/s13277-013-0842-8] [Citation(s) in RCA: 273] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 05/03/2013] [Indexed: 02/07/2023] Open
Abstract
Biomarkers are used as tools in cancer diagnostics and in treatment stratification. In most cancers, there are increased levels of one or several members of the matrix metalloproteinases (MMPs). This is a family of proteolytic enzymes that are involved in many phases of cancer progression, including angiogenesis, invasiveness, and metastasis. It has therefore been expected that MMPs could serve as both diagnostic and prognostic markers in cancer patients, but despite a huge number of studies, it has been difficult to establish MMPs as cancer biomarkers. In the present paper, we assess some of the challenges associated with MMP research as well as putative reasons for the conflicting data on the value of these enzymes as diagnostic and prognostic markers in cancer patients. We also review the prognostic value of a number of MMPs in patients with lung, colorectal, breast, and prostate cancers. The review also discusses MMPs as potential target molecules for therapeutic agents and new strategies for development of such drugs.
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24
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Jin Y, Roycik MD, Bosco DB, Cao Q, Constantino MH, Schwartz MA, Sang QXA. Matrix metalloproteinase inhibitors based on the 3-mercaptopyrrolidine core. J Med Chem 2013; 56:4357-73. [PMID: 23631440 DOI: 10.1021/jm400529f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
New series of pyrrolidine mercaptosulfide, 2-mercaptocyclopentane arylsulfonamide, and 3-mercapto-4-arylsulfonamidopyrrolidine matrix metalloproteinase inhibitors (MMPIs) were designed, synthesized, and evaluated. Exhibiting unique properties over other MMPIs (e.g., hydroxamates), these newly reported compounds are capable of modulating activities of several MMPs in the low nanomolar range, including MMP-2 (~2 to 50 nM), MMP-13 (~2 to 50 nM), and MMP-14 (~4 to 60 nM). Additionally these compounds are selective to intermediate- and deep-pocket MMPs but not shallow-pocketed MMPs (e.g., MMP-1, ~850 to >50,000 nM; MMP-7, ~4000 to >25,000 nM). Our previous work with the mercaptosulfide functionality attached to both cyclopentane and pyrrolidine frameworks demonstrated that the cis-(3S,4R)-stereochemistry was optimal for all of the MMPs tested. However, in our newest compounds an interesting shift of preference to the trans form of the mercaptosulfonamides was observed with increased oxidative stability and biological compatibility. We also report several kinetic and biological characteristics showing that these compounds may be used to probe the mechanistic activities of MMPs in disease.
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Affiliation(s)
- Yonghao Jin
- Department of Chemistry and Biochemistry and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
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25
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Natural products as a gold mine for selective matrix metalloproteinases inhibitors. Bioorg Med Chem 2012; 20:4164-71. [DOI: 10.1016/j.bmc.2012.04.063] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 04/17/2012] [Accepted: 04/18/2012] [Indexed: 11/20/2022]
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26
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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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Ryu JH, Lee A, Huh MS, Chu J, Kim K, Kim BS, Choi K, Kwon IC, Park JW, Youn I. Measurement of MMP Activity in Synovial Fluid in Cases of Osteoarthritis and Acute Inflammatory Conditions of the Knee Joints Using a Fluorogenic Peptide Probe-Immobilized Diagnostic Kit. Am J Cancer Res 2012; 2:198-206. [PMID: 22375158 PMCID: PMC3287423 DOI: 10.7150/thno.3477] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 10/22/2011] [Indexed: 01/30/2023] Open
Abstract
PURPOSE A fluorogenic peptide probe-immobilized diagnostic kit was used to analyze MMP activity in the synovial fluids (SFs) from patients with osteoarthritis (OA) and acute inflammatory conditions of the knee joint. METHODS The MMP diagnostic kit containing a polymer-conjugated MMP probe immobilized on a 96-well plate was utilized for high-throughput screening of MMP activity in SFs from OA patients (n = 33) and patients with acute inflammatory conditions of the knee joint (n = 5). RESULTS Compared to SF from OA patients, SF from patients with acute inflammatory conditions of the knee joint presented stronger NIR fluorescent signals. In gelatin zymography, most samples from patients with acute inflammatory conditions of the knee joint also displayed 92 kDa (pro-form) MMP-9 and faint 84 kDa (active form) MMP-9, while SF from OA patients did not display detectable MMP-9 activity . CONCLUSION The presence of a strong fluorescence signal from the MMP diagnostic kit corresponded well with patients with acute inflammatory conditions of the knee joint. The results suggest that our MMP diagnostic kit can be useful in differentiation between early stages of OA and acute inflammatory conditions of the knee joint.
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Gupta SP, Patil VM. Specificity of binding with matrix metalloproteinases. EXPERIENTIA SUPPLEMENTUM (2012) 2012; 103:35-56. [PMID: 22642189 DOI: 10.1007/978-3-0348-0364-9_2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Matrix metalloproteinases (MMPs) regulate a wide range of biological functions; hence, they have invited great attention for the studies on their structures and functions, and since their overactivation leads to several diseases, the design and discovery of their potent inhibitors have become the need of the day. Since there have been so far discovered 28 different types of human MMPs, the specificity of binding of inhibitors with each different MMP needs special attention. The chapter presents the X-ray crystallographic and NMR studies on three-dimensional structures of a number of MMPs to reveal their catalytic site, subsites, specificity of binding with substrate and inhibitors, and catalytic mechanism. In addition to catalytic site, MMPs possess some subsites designated by unprimed and primed S, e.g., S1, S2, S3 and S1', S2', S3'. Among these, the S1' pocket varies the most among the different MMPs varying in both the amino acid makeup and depth of the pocket (shallow, intermediate, and deep pocket MMPs). This, along with the flexibility in the structures of MMPs, could be of great help in the design and the development of selective MMP inhibitors (MMPIs). The determination of affinity of inhibitors and the cleavage position of peptide substrates is mainly based on P1'-S1' interaction (P1', the group in inhibitor or substrate binding to S1' pocket of the enzyme), and it is the main determinant for the affinity of inhibitors and the cleavage position of peptide substrates.
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Affiliation(s)
- Satya P Gupta
- Department of Pharmaceutical Technology, Meerut Institute of Engineering and Technology, Meerut 250 005, Uttar Pradesh, India.
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29
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Domingo R, Chibale K, Sturrock ED. The significance of the C(α) substituent in the selective inhibition of matrix metalloproteinases 1 and 9. Biol Chem 2011. [PMID: 21972974 DOI: 10.1515/bc-2011-165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Matrix metalloproteinases (MMPs) cleave and degrade most components of the extracellular matrix, and unregulated MMP activity has been correlated to cancer and metastasis. Hence there is a burgeoning need to develop inhibitors that bind selectively to structurally similar MMPs. The inhibition profiles of peptidomimetics containing C(α) substituents at the α,β unsaturated carbon were evaluated against the recombinant forms of ADAM17, MMP1, and MMP9. The dicarboxylic acid D2 and hydroxamate C2 inhibited MMP9 but not MMP1. The unsaturated compound E2 displayed selective inhibition for MMP1, compared with the saturated precursor C2, with an IC(50) value of 3.91 μm. The molecular basis for this selectivity was further investigated by the molecular docking of E2 and D2 into the active sites of MMP1 and MMP9. These data demonstrate hydrogen-bonding interactions between the carbonyl group of the C(α) substituent of E2 and the side chain of Asn180 present in the active site of MMP1. Conversely, the docked MMP9-D2 structure shows hydrophobic and hydrogen bonding between the ligand's morpholine substituent and second carboxylic acid group with Leu187 and an amide, respectively. This study suggests that substituents other than P(1)' and P(2)' may confer selectivity among MMPs and may aid in the search for novel lead compounds.
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Affiliation(s)
- Riyad Domingo
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, Cape Town, South Africa
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Domingo R, Chibale K, Sturrock ED. The significance of the C(α) substituent in the selective inhibition of matrix metalloproteinases 1 and 9. Biol Chem 2011; 392:1003-10. [PMID: 21972974 DOI: 10.1515/bc.2011.165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Matrix metalloproteinases (MMPs) cleave and degrade most components of the extracellular matrix, and unregulated MMP activity has been correlated to cancer and metastasis. Hence there is a burgeoning need to develop inhibitors that bind selectively to structurally similar MMPs. The inhibition profiles of peptidomimetics containing C(α) substituents at the α,β unsaturated carbon were evaluated against the recombinant forms of ADAM17, MMP1, and MMP9. The dicarboxylic acid D2 and hydroxamate C2 inhibited MMP9 but not MMP1. The unsaturated compound E2 displayed selective inhibition for MMP1, compared with the saturated precursor C2, with an IC(50) value of 3.91 μm. The molecular basis for this selectivity was further investigated by the molecular docking of E2 and D2 into the active sites of MMP1 and MMP9. These data demonstrate hydrogen-bonding interactions between the carbonyl group of the C(α) substituent of E2 and the side chain of Asn180 present in the active site of MMP1. Conversely, the docked MMP9-D2 structure shows hydrophobic and hydrogen bonding between the ligand's morpholine substituent and second carboxylic acid group with Leu187 and an amide, respectively. This study suggests that substituents other than P(1)' and P(2)' may confer selectivity among MMPs and may aid in the search for novel lead compounds.
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Affiliation(s)
- Riyad Domingo
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, Cape Town, South Africa
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Nuti E, Casalini F, Santamaria S, Gabelloni P, Bendinelli S, Da Pozzo E, Costa B, Marinelli L, La Pietra V, Novellino E, Margarida Bernardo M, Fridman R, Da Settimo F, Martini C, Rossello A. Synthesis and biological evaluation in U87MG glioma cells of (ethynylthiophene)sulfonamido-based hydroxamates as matrix metalloproteinase inhibitors. Eur J Med Chem 2011; 46:2617-29. [PMID: 21514700 DOI: 10.1016/j.ejmech.2011.03.033] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 03/02/2011] [Accepted: 03/15/2011] [Indexed: 12/31/2022]
Abstract
Matrix metalloproteinases (MMPs) are important factors in gliomas since these enzymes facilitate invasion into the surrounding brain and participate in neovascularization. In particular, the gelatinases (MMP-2 and MMP-9), and more recently MMP-25, have been shown to be highly expressed in gliomas and have been associated with disease progression. Thus, inhibition of these MMPs may represent a promising non-cytotoxic approach to glioma treatment. We report herein the synthesis and biological evaluation of a series of 4-butylphenyl(ethynylthiophene)sulfonamido-based hydroxamates. Among the new compounds tested, a promising derivative, 5a, was identified, which exhibits nanomolar inhibition of MMP-2, MMP-9, and MMP-25, but weak inhibitory activity toward other members of the MMP family. This compound also exhibited anti-invasive activity of U87MG glioblastoma cells at nanomolar concentrations, without affecting cell viability.
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Affiliation(s)
- Elisa Nuti
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy
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Optimization of matrix metalloproteinase fluorogenic probes for osteoarthritis imaging. Amino Acids 2010; 41:1113-22. [DOI: 10.1007/s00726-010-0769-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2009] [Accepted: 09/02/2010] [Indexed: 10/18/2022]
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Giangreco I, Nicolotti O, Carotti A, De Carlo F, Gargano G, Bellotti R. Analysis of X-ray structures of matrix metalloproteinases via chaotic map clustering. BMC Bioinformatics 2010; 11:500. [PMID: 20932281 PMCID: PMC3098083 DOI: 10.1186/1471-2105-11-500] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 10/08/2010] [Indexed: 01/13/2023] Open
Abstract
Background Matrix metalloproteinases (MMPs) are well-known biological targets implicated in tumour progression, homeostatic regulation, innate immunity, impaired delivery of pro-apoptotic ligands, and the release and cleavage of cell-surface receptors. With this in mind, the perception of the intimate relationships among diverse MMPs could be a solid basis for accelerated learning in designing new selective MMP inhibitors. In this regard, decrypting the latent molecular reasons in order to elucidate similarity among MMPs is a key challenge. Results We describe a pairwise variant of the non-parametric chaotic map clustering (CMC) algorithm and its application to 104 X-ray MMP structures. In this analysis electrostatic potentials are computed and used as input for the CMC algorithm. It was shown that differences between proteins reflect genuine variation of their electrostatic potentials. In addition, the analysis has been also extended to analyze the protein primary structures and the molecular shapes of the MMP co-crystallised ligands. Conclusions The CMC algorithm was shown to be a valuable tool in knowledge acquisition and transfer from MMP structures. Based on the variation of electrostatic potentials, CMC was successful in analysing the MMP target family landscape and different subsites. The first investigation resulted in rational figure interpretation of both domain organization as well as of substrate specificity classifications. The second made it possible to distinguish the MMP classes, demonstrating the high specificity of the S1' pocket, to detect both the occurrence of punctual mutations of ionisable residues and different side-chain conformations that likely account for induced-fit phenomena. In addition, CMC demonstrated a potential comparable to the most popular UPGMA (Unweighted Pair Group Method with Arithmetic mean) method that, at present, represents a standard clustering bioinformatics approach. Interestingly, CMC and UPGMA resulted in closely comparable outcomes, but often CMC produced more informative and more easy interpretable dendrograms. Finally, CMC was successful for standard pairwise analysis (i.e., Smith-Waterman algorithm) of protein sequences and was used to convincingly explain the complementarity existing between the molecular shapes of the co-crystallised ligand molecules and the accessible MMP void volumes.
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Affiliation(s)
- Ilenia Giangreco
- Dipartimento Farmaco-Chimico, University of Bari, via Orabona 4, Bari, Italy
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Rocha JR, Freitas RF, Montanari CA. The GRID/CPCA approach in drug discovery. Expert Opin Drug Discov 2010; 5:333-46. [DOI: 10.1517/17460441003652959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Heinz A, Jung MC, Duca L, Sippl W, Taddese S, Ihling C, Rusciani A, Jahreis G, Weiss AS, Neubert RHH, Schmelzer CEH. Degradation of tropoelastin by matrix metalloproteinases--cleavage site specificities and release of matrikines. FEBS J 2010; 277:1939-56. [PMID: 20345904 DOI: 10.1111/j.1742-4658.2010.07616.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To provide a basis for the development of approaches to treat elastin-degrading diseases, the aim of this study was to investigate the degradation of the natural substrate tropoelastin by the elastinolytic matrix metalloproteinases MMP-7, MMP-9, and MMP-12 and to compare the cleavage site specificities of the enzymes using complementary MS techniques and molecular modeling. Furthermore, the ability of the three proteases to release bioactive peptides was studied. Tropoelastin was readily degraded by all three MMPs. Eighty-nine cleavage sites in tropoelastin were identified for MMP-12, whereas MMP-7 and MMP-9 were found to cleave at only 58 and 63 sites, respectively. Cleavages occurred predominantly in the N-terminal and C-terminal regions of tropoelastin. With respect to the cleavage site specificities, the study revealed that all three MMPs similarly tolerate hydrophobic and/or aliphatic amino acids, including Pro, Gly, Ile, and Val, at P(1)'. MMP-7 shows a strong preference for Leu at P(1)', which is also well accepted by MMP-9 and MMP-12. Of all three MMPs, MMP-12 best tolerates bulky charged and aromatic amino acids at P(1)'. All three MMPs showed a clear preference for Pro at P(3) that could be structurally explained by molecular modeling. Analysis of the generated peptides revealed that all three MMPs show a similar ability to release bioactive sequences, with MMP-12 producing the highest number of these peptides. Furthermore, the generated peptides YTTGKLPYGYGPGG, YGARPGVGVGGIP, and PGFGAVPGA, containing GxxPG motifs that have not yet been proven to be bioactive, were identified as new matrikines upon biological activity testing.
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Affiliation(s)
- Andrea Heinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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To bind zinc or not to bind zinc: an examination of innovative approaches to improved metalloproteinase inhibition. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2009; 1803:72-94. [PMID: 19712708 DOI: 10.1016/j.bbamcr.2009.08.006] [Citation(s) in RCA: 219] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 08/12/2009] [Accepted: 08/12/2009] [Indexed: 12/14/2022]
Abstract
This short review highlights some recent advances in matrix metalloproteinase inhibitor (MMPi) design and development. Three distinct approaches to improved MMP inhibition are discussed: (1) the identification and investigation of novel zinc-binding groups (ZBGs), (2) the study of non-zinc-binding MMPi, and (3) mechanism-based MMPi that form covalent adducts with the protein. Each of these strategies is discussed and their respective advantages and remaining challenges are highlighted. The studies discussed here bode well for the development of ever more selective, potent, and well-tolerated MMPi for treating several important disease pathologies.
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Holmes IP, Gaines S, Watson SP, Lorthioir O, Walker A, Baddeley SJ, Herbert S, Egan D, Convery MA, Singh OMP, Gross JW, Strelow JM, Smith RH, Amour AJ, Brown D, Martin SL. The identification of beta-hydroxy carboxylic acids as selective MMP-12 inhibitors. Bioorg Med Chem Lett 2009; 19:5760-3. [PMID: 19703773 DOI: 10.1016/j.bmcl.2009.07.155] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 07/30/2009] [Accepted: 07/31/2009] [Indexed: 11/18/2022]
Abstract
A new class of selective MMP-12 inhibitors have been identified via high throughput screening. Crystallization with MMP-12 confirmed the mode of binding and allowed initial optimization to be carried out using classical structure based design.
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Affiliation(s)
- Ian P Holmes
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
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Salum LB, Polikarpov I, Andricopulo AD. Structure-based approach for the study of estrogen receptor binding affinity and subtype selectivity. J Chem Inf Model 2009; 48:2243-53. [PMID: 18937440 DOI: 10.1021/ci8002182] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Estrogens exert important physiological effects through the modulation of two human estrogen receptor (hER) subtypes, alpha (hERalpha) and beta (hERbeta). Because the levels and relative proportion of hERalpha and hERbeta differ significantly in different target cells, selective hER ligands could target specific tissues or pathways regulated by one receptor subtype without affecting the other. To understand the structural and chemical basis by which small molecule modulators are able to discriminate between the two subtypes, we have applied three-dimensional target-based approaches employing a series of potent hER-ligands. Comparative molecular field analysis (CoMFA) studies were applied to a data set of 81 hER modulators, for which binding affinity values were collected for both hERalpha and hERbeta. Significant statistical coefficients were obtained (hERalpha, q(2) = 0.76; hERbeta, q(2) = 0.70), indicating the internal consistency of the models. The generated models were validated using external test sets, and the predicted values were in good agreement with the experimental results. Five hER crystal structures were used in GRID/PCA investigations to generate molecular interaction fields (MIF) maps. hERalpha and hERbeta were separated using one factor. The resulting 3D information was integrated with the aim of revealing the most relevant structural features involved in hER subtype selectivity. The final QSAR and GRID/PCA models and the information gathered from 3D contour maps should be useful for the design of novel hER modulators with improved selectivity.
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Affiliation(s)
- Lívia B Salum
- Laboratorio de Quimica Medicinal e Computacional, Centro de Biotecnologia Molecular Estrutural, Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo, Av Trabalhador Sao-Carlense 400, 13560-970 Sao Carlos-SP, Brazil
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Abstract
Analysis of the three-dimensional structures of protein ligand complexes provides valuable insight into both the common interaction patterns within a target family and the discriminating features between the different members of a target family. Knowledge of the common interaction patterns helps to design target family focused chemical libraries for hit finding, while the discriminating features can be exploited to optimize the selectivity profile of a lead compound against particular member of a target family. Herein, we review the computational tools which have been developed to analyze crystal structures of members of a target family.
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Affiliation(s)
- Bernard Pirard
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institute for Biomedical Research, Basel, Switzerland
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Marques SM, Nuti E, Rossello A, Supuran CT, Tuccinardi T, Martinelli A, Santos MA. Dual inhibitors of matrix metalloproteinases and carbonic anhydrases: iminodiacetyl-based hydroxamate-benzenesulfonamide conjugates. J Med Chem 2008; 51:7968-79. [PMID: 19053764 DOI: 10.1021/jm800964f] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Matrix metalloproteinases (MMPs) and carbonic anhydrases (CAs) are two classes of zinc enzymes with different roles and catalytic targets, such as the degradation of most of the extracellular matrix (ECM) proteins and the regulation of the CO(2)/HCO(3)(-) equilibrium in the cells, respectively. Both families have isoforms which were proved to be involved in several stages of carcinogenic processes, and so the selective inhibition of these enzymes might be of interest in cancer therapy. We report herein the design, synthesis, and in vitro evaluation of a series of compounds possessing the iminodiacetic acid as the main backbone and two functional groups attached, namely, the hydroxamic acid and the arylsulfonamide (ArSO(2)NH(2)) moieties, to enable the inhibition of MMPs and CAs, respectively. These compounds were demonstrated to strongly inhibit both MMPs and CAs, some of them from the nanomolar to subnanomolar range. Furthermore, a docking study for MMPs was reported for the most promising compound in order to investigate its binding interactions with the different MMPs.
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Affiliation(s)
- Sérgio M Marques
- Centro de Química Estrutural, Instituto Superior Técnico, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
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Jacobsen FE, Lewis JA, Cohen SM. The design of inhibitors for medicinally relevant metalloproteins. ChemMedChem 2008; 2:152-71. [PMID: 17163561 DOI: 10.1002/cmdc.200600204] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A number of metalloproteins are important medicinal targets for conditions ranging from pathogenic infections to cancer. Many but not all of these metalloproteins contain a zinc(II) ion in the protein active site. Small-molecule inhibitors of these metalloproteins are designed to bind directly to the active site metal ions. In this review several metalloproteins of interest are discussed, including matrix metalloproteinases (MMPs), histone deacetylases (HDACs), anthrax lethal factor (LF), and others. Different strategies that have been employed to design effective inhibitors against these proteins are described, with an effort to highlight the strengths and drawbacks of each approach. An emphasis is placed on examining the bioinorganic chemistry of these metal active sites and how a better understanding of the coordination chemistry in these systems may lead to improved inhibitors. It is hoped that this review will help inspire medicinal, biological, and inorganic chemists to tackle this important problem by considering all aspects of metalloprotein inhibitor design.
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Affiliation(s)
- Faith E Jacobsen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
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Abstract
Biological experiments often produce enormous amount of data, which are usually analyzed by data clustering. Cluster analysis refers to statistical methods that are used to assign data with similar properties into several smaller, more meaningful groups. Two commonly used clustering techniques are introduced in the following section: principal component analysis (PCA) and hierarchical clustering. PCA calculates the variance between variables and groups them into a few uncorrelated groups or principal components (PCs) that are orthogonal to each other. Hierarchical clustering is carried out by separating data into many clusters and merging similar clusters together. Here, we use an example of human leukocyte antigen (HLA) supertype classification to demonstrate the usage of the two methods. Two programs, Generating Optimal Linear Partial Least Square Estimations (GOLPE) and Sybyl, are used for PCA and hierarchical clustering, respectively. However, the reader should bear in mind that the methods have been incorporated into other software as well, such as SIMCA, statistiXL, and R.
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Taddese S, Weiss AS, Neubert RHH, Schmelzer CEH. Mapping of macrophage elastase cleavage sites in insoluble human skin elastin. Matrix Biol 2008; 27:420-8. [PMID: 18334288 DOI: 10.1016/j.matbio.2008.02.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2007] [Revised: 02/03/2008] [Accepted: 02/04/2008] [Indexed: 10/22/2022]
Abstract
Macrophage elastase (MMP-12) is a member of the family of matrix metalloproteinases (MMPs) and is active against multiple extracellular protein substrates such as elastin. Its effect on elastin is central to emphysema in the lung and photoaging of skin. Its expression in the skin increases on photodamaged skin and upon aging. Detecting and characterizing peptides cleaved in elastin, therefore, helps to understand such degradative disease processes in the skin and is also needed to assist in the rational design of agents that specifically inhibit the degradation. In this study, cleavage sites of MMP-12 in human skin elastin were extensively investigated. The peptides formed as a result of cleavages by this enzyme in the human skin elastin were characterized using mass spectrometry. A total of 41 peptides ranging from 4 to 41 amino acids were identified and 36 cleavage sites were determined. Amino acids encoded by exons 5, 6, 26, 28-31 were particularly susceptible to cleavages by MMP-12 and none or very few cleavages were detected from domains encoded by the remaining exons. The amino acid preferences of the different subsites on the catalytic domain of MMP-12 were analyzed.
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Affiliation(s)
- Samuel Taddese
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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Moroy G, Denhez C, El Mourabit H, Toribio A, Dassonville A, Decarme M, Renault JH, Mirand C, Bellon G, Sapi J, Alix AJP, Hornebeck W, Bourguet E. Simultaneous presence of unsaturation and long alkyl chain at P1′ of Ilomastat confers selectivity for gelatinase A (MMP-2) over gelatinase B (MMP-9) inhibition as shown by molecular modelling studies. Bioorg Med Chem 2007; 15:4753-66. [PMID: 17512742 DOI: 10.1016/j.bmc.2007.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 04/26/2007] [Accepted: 05/02/2007] [Indexed: 10/23/2022]
Abstract
Structural analogues of Ilomastat (Galardin), containing unsaturation(s) and chain extension carrying bulky phenyl group or alkyl moieties at P'1 were synthesized and purified by centrifugal partition chromatography. They were analyzed for their inhibitory capacity towards MMP-1, MMP-2, MMP-3, MMP-9 and MMP-14, main endopeptidases involved in tumour progression. Presence of unsaturation(s) decreased the inhibitory potency of compounds but, in turn increased their selectivity for gelatinases. 2b and 2d derivatives with a phenyl group inhibited preferentially MMP-9 with IC50 equal to 45 and 38 nM, respectively, but also display activity against MMP-2 (IC50 equal to 280 and 120 nM, respectively). Molecular docking computations confirmed affinity of these substances for both gelatinases. With aims to obtain a specific gelatinase A (MMP-2) inhibitor, P'1 of Ilomastat was modified to carry one unsaturation coupled to an alkyl chain with pentylidene group. Docking studies indicated that MMP-2, but not MMP-9, could accommodate such substitution; indeed 2a proved to inhibit MMP-2 (IC50=123 nM), while displaying no inhibitory capacity towards MMP-9.
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Affiliation(s)
- Gautier Moroy
- Laboratoire de Spectroscopies et Structures Biomoléculaires (LSSBM), Faculté des Sciences, IFR53 Biomolécules, Université de Reims-Champagne-Ardenne, BP 1039, 51687 Reims Cedex 2, France
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Minond D, Lauer-Fields JL, Cudic M, Overall CM, Pei D, Brew K, Moss ML, Fields GB. Differentiation of secreted and membrane-type matrix metalloproteinase activities based on substitutions and interruptions of triple-helical sequences. Biochemistry 2007; 46:3724-33. [PMID: 17338550 PMCID: PMC2569894 DOI: 10.1021/bi062199j] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The turnover of the collagen triple-helical structure (collagenolysis) is a tightly regulated process in normal physiology and has been ascribed to a small number of proteases. Several members of the matrix metalloproteinase (MMPs) family possess collagenolytic activity, and the mechanisms by which these enzymes process triple helices are beginning to be unraveled. The present study has utilized two triple-helical sequences to compare the cleavage-site specificities of 10 MMPs. One substrate featured a continuous Gly-Xxx-Yyy sequence (Pro-Leu-Gly approximately Met-Arg-Gly), while the other incorporated an interruption in the Gly-Xxx-Yyy repeat (Pro-Val-Asn approximately Phe-Arg-Gly). Both sequences were selectively cleaved by MMP-13 while in linear form, but neither proved to be selective within a triple helix. This suggests that the conformational presentation of substrate sequences to a MMP active site is critical for enzyme specificity, in that activities differ when sequences are presented from an unwound triple helix versus an independent single strand. Differences in specificity between secreted and membrane-type (MT) MMPs were also observed for both sequences, where MMP-2 and MT-MMPs showed an ability to hydrolyze a triple helix at an additional site (Gly-Gln bond). Interruption of the triple helix had different effects on secreted MMPs and MT-MMPs, because MT-MMPs could not hydrolyze the Asn-Phe bond but instead cleaved the triple helix closer to the C terminus at a Gly-Gln bond. It is possible that MT-MMPs have a requirement for Gly in the P1 subsite to be able to efficiently process a triple-helical molecule. Analysis of individual kinetic parameters and activation energies indicated different substrate preferences within secreted MMPs, because MMP-13 preferred the interrupted sequence, while MMP-8 showed little discrimination between non-interrupted and interrupted triple helices. On the basis of the present and prior studies, we can assign unique triple-helical peptidase behaviors to the collagenolytic MMPs. Such differences may be significant for understanding MMP mechanisms of action and aid in the development of selective MMP inhibitors.
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Affiliation(s)
- Dmitriy Minond
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991
| | - Janelle L. Lauer-Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991
| | - Mare Cudic
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991
| | - Christopher M. Overall
- University of British Columbia Centre for Blood Research and the Canadian Institutes for Health Research Group in Matrix Dynamics and the Departments of Biochemistry and Molecular Biology, Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Duanqing Pei
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Keith Brew
- College of Biomedical Sciences, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991
| | - Marcia L. Moss
- BioZyme, Inc., 1513 Old White Oak Church Road, Apex, NC 27523-9299
| | - Gregg B. Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991
- Correspondence should be addressed to this author at the Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, Florida 33431-0991. Tel: 561-297-2093; Fax: 561-297-2759; E-mail:
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Baronas-Lowell D, Lauer-Fields JL, Al-Ghoul M, Fields GB. Proteolytic profiling of the extracellular matrix degradome. Methods Mol Biol 2007; 386:167-202. [PMID: 18604946 DOI: 10.1007/978-1-59745-430-8_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The profiling of protein function is one of the most challenging scientific tasks in the postgenomic age. Traditional protein expression methodologies have focused only on the quantification of proteins under varying conditions or pathologies. Determining the functional differences between protein populations allows for a more accurate view of the outcomes in normal vs diseased proteomes. Because the presence or absence of a protein's function can affect its complex surroundings (consisting of multiple other proteins and substrates), the study of proteome functionality yields information on protein-protein interactions, amplification cascades, signaling pathways, and posttranslational modifications. Of significant interest are proteinases, as proteolysis is responsible for tight regulation of various cellular and tissue processes. Proteinase activities, or lack there of, alter the proteome makeup by regulating other proteins or by generating cleavage products. This chapter describes current proteolytic profiling technologies using activity or target-based formats. In particular, the analysis of collagenolytic matrix metalloproteinase activity using fluorogenic triple-helical substrates is discussed.
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Affiliation(s)
- Diane Baronas-Lowell
- Department of Chemistry & Biochemistry, Florida Atlantic University, Boca Raton, USA
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Minond D, Lauer-Fields JL, Cudic M, Overall CM, Pei D, Brew K, Visse R, Nagase H, Fields GB. The Roles of Substrate Thermal Stability and P2 and P1′ Subsite Identity on Matrix Metalloproteinase Triple-helical Peptidase Activity and Collagen Specificity. J Biol Chem 2006; 281:38302-13. [PMID: 17065155 DOI: 10.1074/jbc.m606004200] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hydrolysis of collagen (collagenolysis) is one of the committed steps in extracellular matrix turnover. Within the matrix metalloproteinase (MMP) family distinct preferences for collagen types are seen. The substrate determinants that may guide these specificities are unknown. In this study, we have utilized 12 triple-helical substrates in combination with 10 MMPs to better define the contributions of substrate sequence and thermal stability toward triple helicase activity and collagen specificity. In general, MMP-13 was found to be distinct from MMP-8 and MT1-MMP(Delta279-523), in that enhanced substrate thermal stability has only a modest effect on activity, regardless of sequence. This result correlates to the unique collagen specificity of MMP-13 compared with MMP-8 and MT1-MMP, in that MMP-13 hydrolyzes type II collagen efficiently, whereas MMP-8 and MT1-MMP are similar in their preference for type I collagen. In turn, MMP-1 was the least efficient of the collagenolytic MMPs at processing increasingly thermal stable triple helices and thus favors type III collagen, which has a relatively flexible cleavage site. Gelatinases (MMP-2 and MMP-9(Delta444-707)) appear incapable of processing more stable helices and are thus mechanistically distinct from collagenolytic MMPs. The collagen specificity of MMPs appears to be based on a combination of substrate sequence and thermal stability. Analysis of the hydrolysis of triple-helical peptides by an MMP mutant indicated that Tyr(210) functions in triple helix binding and hydrolysis, but not in processing triple helices of increasing thermal stabilities. Further exploration of MMP active sites and exosites, in combination with substrate conformation, may prove valuable for additional dissection of collagenolysis and yield information useful in the design of more selective MMP inhibitors.
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Affiliation(s)
- Dmitriy Minond
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991, USA
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48
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Mestres J. Representativity of target families in the Protein Data Bank: impact for family-directed structure-based drug discovery. Drug Discov Today 2006; 10:1629-37. [PMID: 16376823 DOI: 10.1016/s1359-6446(05)03593-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Analysis of the population of enzyme structures in the Protein Data Bank across all levels of the functional classification based on enzyme commission (EC) numbers reveals that, in spite of the almost exponential growth in the number of structures deposited, progress in achieving complete occupancy at all EC levels is relatively slow. Moreover, inspection of the distribution of the population among the members of the different enzyme families uncovers a strong bias towards enzymes widely recognized as therapeutically relevant targets. The low representativity levels identified in some target families warn on the current scope and applicability of structure-based approaches to family-directed strategies in drug discovery.
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Affiliation(s)
- Jordi Mestres
- Chemogenomics Laboratory, Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica and Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.
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Vulpetti A, Crivori P, Cameron A, Bertrand J, Brasca MG, D'Alessio R, Pevarello P. Structure-based approaches to improve selectivity: CDK2-GSK3beta binding site analysis. J Chem Inf Model 2005; 45:1282-90. [PMID: 16180905 DOI: 10.1021/ci0500280] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An evaluation and comparison of two different approaches, GRID/CPCA and GRIND/CPCA (CPCA = consensus principal component analysis; GRIND = GRid-INdependent Descriptors), suitable for visualizing the structural differences between related proteins is presented. Ten crystal structures of CDK2/cyclin A and GSK3beta solved in-house with different inhibitors were compared with the aim of highlighting regions that could be potential sites for gaining selectivity for CDK2 versus GSK3beta. The analyses pointed out remarkable differences in the backs of the CDK2-GSK3beta ATP binding pockets that guided the optimization toward a selective benzodipyrazole CDK2 inhibitor. The gain in selectivity can be associated with the two main differences in the ATP pocket between the enzymes. Phe80 of CDK2, the so-called gatekeeper residue often exploited for the design of kinase selective ligands, is replaced by a leucine in GSK3beta, and Ala144 is replaced by a cysteine. As a consequence of these mutations, CDK2 has a less elongated and less flat buried region at the back of the ATP pocket.
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Affiliation(s)
- Anna Vulpetti
- Nerviano Medical Sciences, Viale Pasteur 10, 20014 Nerviano (MI), Italy.
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50
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Dublanchet AC, Ducrot P, Andrianjara C, O'Gara M, Morales R, Compère D, Denis A, Blais S, Cluzeau P, Courté K, Hamon J, Moreau F, Prunet ML, Tertre A. Structure-based design and synthesis of novel non-zinc chelating MMP-12 inhibitors. Bioorg Med Chem Lett 2005; 15:3787-90. [PMID: 16002291 DOI: 10.1016/j.bmcl.2005.05.079] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2004] [Revised: 11/17/2004] [Accepted: 05/12/2005] [Indexed: 10/25/2022]
Abstract
A new class of MMP-12 inhibitors was discovered and optimized using structure-based drug design methods. Modeling studies using a known MMP-12 crystal structure identified a new interaction mode for these new MMP-12 inhibitors. Further optimization resulted in the discovery of a compound displaying nanomolar activity against MMP-12 and which was co-crystallized with MMP-12.
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Affiliation(s)
- Anne-Claude Dublanchet
- Department of Chemistry, Pfizer Global Research and Development, Fresnes Laboratories, 3-9 rue de la Loge, BP 100, F-94265 Fresnes Cedex, France.
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