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Mittal R, Patel AP, Debs LH, Nguyen D, Patel K, Grati M, Mittal J, Yan D, Chapagain P, Liu XZ. Intricate Functions of Matrix Metalloproteinases in Physiological and Pathological Conditions. J Cell Physiol 2016; 231:2599-621. [DOI: 10.1002/jcp.25430] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Amit P. Patel
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Luca H. Debs
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Desiree Nguyen
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Kunal Patel
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - M'hamed Grati
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Jeenu Mittal
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Denise Yan
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Prem Chapagain
- Department of Physics; Florida International University; Miami Florida
- Biomolecular Science Institute; Florida International University; Miami Florida
| | - Xue Zhong Liu
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
- Department of Biochemistry; University of Miami Miller School of Medicine; Miami Florida
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Sukker GM, Wazzan N, Ahmed A, Hilal R. Conformation and electronic structure of Carbidopa. A QM/MD study. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633616500024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Carbidopa (CD) is a drug used in combination with L-dopa (LD) in treatment of Parkinson’s disease (PD). CD is an inhibitor for enzyme decarboxylase, yet its mode of action is not entirely known although it is believed to involve enzyme shape recognition. The present work attempts to investigate the conformational preferences of CD. Tight geometry optimization at the density functional theory (DFT)/B3LYP/6-311[Formula: see text]G** level of theory has been carried out. The shallow nature of the potential energy surface (PES) and the presence of several local minima within a small energy range necessitate the launching of DFT-based molecular dynamics (MD) simulations. Two MD experiments were submitted for 35,000 points each. The complete trajectory in time domain of 10.5 ps is analyzed and discussed. The global minimum energy structure of CD is localized and identified by subsequent frequency calculations. The quantum theory of atom in molecules (QTAIMs) is used to extract and compare the quantum chemical topology features of the electron density distribution in CD and LD. Bonding characteristics are analyzed and discussed within the natural bond orbital (NBO) framework.
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Affiliation(s)
- Ghader M. Sukker
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nuha Wazzan
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ashour Ahmed
- Chemistry Department, Faculty of Science, Cairo University, 12613 Giza, Egypt
- University of Rostock, Institute of Physics, D-18051 Rostock, Germany
- University of Rostock, Soil Science, D-18051 Rostock, Germany
- Steinbeis GmbH & Co. KG für Technologietransfer, 70174 Stuttgart, Germany
| | - Rifaat Hilal
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Chemistry Department, Faculty of Science, Cairo University, 12613 Giza, Egypt
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Calò S, Tondi D, Ferrari S, Venturelli A, Ghelli S, Costi MP. Constrained Dansyl Derivatives Reveal Bacterial Specificity of Highly Conserved Thymidylate Synthases. Chembiochem 2008; 9:779-90. [DOI: 10.1002/cbic.200700524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Paul Beckett R. Patent Update Oncologic, Endocrine & Metabolic: Oncologic, Endocrine & Metabolic: Recent advances in the field of matrix metalloproteinase inhibitors. Expert Opin Ther Pat 2008. [DOI: 10.1517/13543776.6.12.1305] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Aschi M, Besker N, Re N, Pochetti G, Coletti C, Gallina C, Mazza F. Stereoselectivity by Enantiomeric Inhibitors of Matrix Metalloproteinase-8: New Insights from Molecular Dynamics Simulations. J Med Chem 2006; 50:211-8. [PMID: 17228863 DOI: 10.1021/jm0608457] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular Dynamics simulations in aqueous solution were performed for the matrix metalloproteinase-8 (MMP-8) free catalytic domain and for its complexes with the (R)- and (S)-[1-(4'-methoxybiphenyl-4-sulfonylamino)-2-methylpropyl] phosphonate. The 144-155 loop of the enzyme undergoes a drastic decrease of mobility once complexed with both enantiomers. The two enantiomers induce a different decrease of conformational entropy upon complexation. The higher affinity of the R-enantiomer can be related to the lower loss of conformational entropy accompanying its binding. The differences in the dynamical behavior of the protein induced by the two enantiomers are discussed at molecular level and the mode of binding of the simulated complexes is compared with that previously determined by X-ray crystallography.
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Affiliation(s)
- Massimiliano Aschi
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L'Aquila, Italia.
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Yannopoulos CG, Xu P, Ni F, Chan L, Pereira OZ, Reddy TJ, Das SK, Poisson C, Nguyen-Ba N, Turcotte N, Proulx M, Halab L, Wang W, Bédard J, Morin N, Hamel M, Nicolas O, Bilimoria D, L'Heureux L, Bethell R, Dionne G. HCV NS5B polymerase-bound conformation of a soluble sulfonamide inhibitor by 2D transferred NOESY. Bioorg Med Chem Lett 2004; 14:5333-7. [PMID: 15454222 DOI: 10.1016/j.bmcl.2004.08.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2004] [Revised: 08/09/2004] [Accepted: 08/09/2004] [Indexed: 10/26/2022]
Abstract
HCV NS5B RNA-dependent RNA polymerase (NS5B) is essential for viral replication and is therefore considered a target for antiviral drug development. From our ongoing screening effort in the search for new anti-HCV agents, a novel inhibitor 1 with low microM activity against the HCV NS5B polymerase was identified. SAR analysis indicated the optimal substitution pattern required for activity, for example, carboxylic acid group at 2-position of thiophene ring. We describe the steps taken to identify and solve the bioactive conformation of derivative 6 through the use of the transferred NOE method (trNOE).
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Ludwig A, Berkhout T, Moores K, Groot P, Chapman G. Fractalkine is expressed by smooth muscle cells in response to IFN-gamma and TNF-alpha and is modulated by metalloproteinase activity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2002; 168:604-12. [PMID: 11777952 DOI: 10.4049/jimmunol.168.2.604] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Fractalkine/CX3C-chemokine ligand 1 is expressed as a membrane-spanning adhesion molecule that can be cleaved from the cell surface to produce a soluble chemoattractant. Within the vasculature, fractalkine is known to be generated by endothelial cells, but to date there are no reports describing its expression by smooth muscle cells (SMC). In this study we demonstrate that IFN-gamma and TNF-alpha, but not IL-1beta, cooperate synergistically to induce fractalkine mRNA and protein expression in cultured aortic SMC. We also report the release of functional, soluble fractalkine from the membranes of stimulated SMC. This release is inhibited by the zinc metalloproteinase inhibitor batimastat, resulting in the accumulation of membrane-associated fractalkine on the SMC surface. Therefore, an SMC-derived metalloproteinase activity is involved in fractalkine shedding. While soluble fractalkine present in SMC-conditioned medium is capable of inducing calcium transients in cells expressing the fractalkine receptor (CX3CR1), blocking experiments using neutralizing Abs reveal that it can be inactivated without affecting the chemotactic activity of SMC-conditioned media on monocytes. However, membrane-bound fractalkine plays a major role in promoting adhesion of monocytic cells to activated SMC. This fractalkine-mediated adhesion is further enhanced in the presence of batimastat, indicating that shedding of fractalkine from the cell surface down-regulates the adhesive properties of SMC. Hence, during vascular inflammation, the synergistic induction of fractalkine by IFN-gamma and TNF-alpha together with its metalloproteinase-mediated cleavage may finely control the recruitment of monocytes to SMC within the blood vessel wall.
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MESH Headings
- Cell Adhesion/immunology
- Cell Membrane/immunology
- Cell Membrane/metabolism
- Cell Membrane/physiology
- Cell Separation
- Cells, Cultured
- Chemokine CX3CL1
- Chemokines, CX3C/biosynthesis
- Chemokines, CX3C/metabolism
- Chemokines, CX3C/physiology
- Culture Media, Conditioned/pharmacology
- Drug Synergism
- Humans
- Interferon-gamma/physiology
- Membrane Proteins/biosynthesis
- Membrane Proteins/metabolism
- Membrane Proteins/physiology
- Metalloendopeptidases/metabolism
- Metalloendopeptidases/physiology
- Monocytes/immunology
- Monocytes/physiology
- Muscle, Smooth/enzymology
- Muscle, Smooth/immunology
- Muscle, Smooth/metabolism
- RNA, Messenger/biosynthesis
- Solubility
- Tumor Cells, Cultured
- Tumor Necrosis Factor-alpha/physiology
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Affiliation(s)
- Andreas Ludwig
- Department of Vascular Biology and Neuroscience, GlaxoSmithKline, Harlow, United Kingdom.
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Dinsmore CJ, Bogusky MJ, Culberson JC, Bergman JM, Homnick CF, Zartman CB, Mosser SD, Schaber MD, Robinson RG, Koblan KS, Huber HE, Graham SL, Hartman GD, Huff JR, Williams TM. Conformational restriction of flexible ligands guided by the transferred noe experiment: potent macrocyclic inhibitors of farnesyltransferase. J Am Chem Soc 2001; 123:2107-8. [PMID: 11456854 DOI: 10.1021/ja003673q] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chen JM, Nelson FC, Levin JI, Mobilio D, Moy FJ, Nilakantan R, Zask A, Powers R. Structure-Based Design of a Novel, Potent, and Selective Inhibitor for MMP-13 Utilizing NMR Spectroscopy and Computer-Aided Molecular Design. J Am Chem Soc 2000. [DOI: 10.1021/ja001547g] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Moy FJ, Chanda PK, Chen JM, Cosmi S, Edris W, Levin JI, Powers R. High-resolution solution structure of the catalytic fragment of human collagenase-3 (MMP-13) complexed with a hydroxamic acid inhibitor. J Mol Biol 2000; 302:671-89. [PMID: 10986126 DOI: 10.1006/jmbi.2000.4082] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The high-resolution solution structure of the catalytic fragment of human collagenase-3 (MMP-13) complexed with a sulfonamide derivative of a hydroxamic acid compound (WAY-151693) has been determined by multidimensional heteronuclear NMR. A total of 30 structures were calculated for residues 7-164 by means of hybrid distance geometry-simulated annealing using a total of 3280 experimental NMR restraints. The atomic rms distribution about the mean coordinate positions for the 30 structures is 0.43(+/-0.05) A for the backbone atoms, 0.80(+/-0.09) A for all atoms, and 0.47(+/-0.04) A for all atoms excluding disordered side-chains. The overall structure of MMP-13 is composed of a beta-sheet consisting of five beta-strands in a mixed parallel and anti-parallel arrangement and three alpha-helices where its overall fold is consistent with previously solved MMP structures. A comparison of the NMR structure of MMP-13 with the published 1.6 A resolution X-ray structure indicates that the major differences between the structures is associated with loop dynamics and crystal-packing interactions. The side-chains of some active-site residues for the NMR and X-ray structures of MMP-13 adopt distinct conformations. This is attributed to the presence of unique inhibitors in the two structures that encounter distinct interactions with MMP-13. The major structural difference observed between the MMP-13 and MMP-1 NMR structures is the relative size and shape of the S1' pocket where this pocket is significantly longer for MMP-13, nearly reaching the surface of the protein. Additionally, MMP-1 and MMP-13 exhibit different dynamic properties for the active-site loop and the structural Zn-binding region. The inhibitor WAY-151693 is well defined in the MMP-13 active-site based on a total of 52 distance restraints. The binding motif of WAY-151693 in the MMP-13 complex is consistent with our previously reported MMP-1:CGS-27023A NMR structure and is similar to the MMP-13: RS-130830 X-ray structure.
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Affiliation(s)
- F J Moy
- Department of Biological Chemistry, Wyeth Research, 85 Bolton St., Cambridge, MA 02140, USA
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Whittaker M, Floyd CD, Brown P, Gearing AJ. Design and therapeutic application of matrix metalloproteinase inhibitors. Chem Rev 1999; 99:2735-76. [PMID: 11749499 DOI: 10.1021/cr9804543] [Citation(s) in RCA: 755] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- M Whittaker
- Departments of Medicinal Chemistry, Biology, and Clinical Research, British Biotech Pharmaceuticals Limited, Oxford, U.K
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Bohacek R, De Lombaert S, McMartin C, Priestle J, Grütter M. Three-Dimensional Models of ACE and NEP Inhibitors and Their Use in the Design of Potent Dual ACE/NEP Inhibitors. J Am Chem Soc 1996. [DOI: 10.1021/ja950818y] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Regine Bohacek
- Research Department, Pharmaceuticals Division, Ciba-Geigy Corporation, Summit, New Jersey 07901, and Department of Core Drug Discovery Technologies, Pharmaceuticals Division, Ciba-Geigy Ltd., Basel, Switzerland
| | - Stéphane De Lombaert
- Research Department, Pharmaceuticals Division, Ciba-Geigy Corporation, Summit, New Jersey 07901, and Department of Core Drug Discovery Technologies, Pharmaceuticals Division, Ciba-Geigy Ltd., Basel, Switzerland
| | - Colin McMartin
- Research Department, Pharmaceuticals Division, Ciba-Geigy Corporation, Summit, New Jersey 07901, and Department of Core Drug Discovery Technologies, Pharmaceuticals Division, Ciba-Geigy Ltd., Basel, Switzerland
| | - John Priestle
- Research Department, Pharmaceuticals Division, Ciba-Geigy Corporation, Summit, New Jersey 07901, and Department of Core Drug Discovery Technologies, Pharmaceuticals Division, Ciba-Geigy Ltd., Basel, Switzerland
| | - Markus Grütter
- Research Department, Pharmaceuticals Division, Ciba-Geigy Corporation, Summit, New Jersey 07901, and Department of Core Drug Discovery Technologies, Pharmaceuticals Division, Ciba-Geigy Ltd., Basel, Switzerland
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