51
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Kwak H, Lee SH, Kim SH, Lee YM, Park BK, Lee YJ, Jun JY, Kim C, Kim SJ, Kim Y. Controlling self-assembly of zinc(II)-benzoate coordination complexes with 1,4-bis(4-pyridyl)ethane by varying solvent and ligand-to-metal ratio: Their catalytic activities. Polyhedron 2009. [DOI: 10.1016/j.poly.2008.11.048] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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52
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Rouffet M, Denhez C, Bourguet E, Bohr F, Guillaume D. In silico study of MMP inhibition. Org Biomol Chem 2009; 7:3817-25. [DOI: 10.1039/b910543c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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53
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Kwak H, Lee SH, Kim SH, Lee YM, Park BK, Lee EY, Lee YJ, Kim C, Kim SJ, Kim Y. Substituent effects of pyrazine on construction of crystal structures of Zn(II)-benzoate complexes and their catalytic activities (dinuclear, trinuclear, and pentanuclear to 1-D and 2-D). Polyhedron 2008. [DOI: 10.1016/j.poly.2008.08.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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54
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Specific targeting of metzincin family members with small-molecule inhibitors: Progress toward a multifarious challenge. Bioorg Med Chem 2008; 16:8781-94. [DOI: 10.1016/j.bmc.2008.08.058] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 08/22/2008] [Accepted: 08/26/2008] [Indexed: 12/20/2022]
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55
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Jacobsen FE, Buczynski MW, Dennis EA, Cohen SM. A macrophage cell model for selective metalloproteinase inhibitor design. Chembiochem 2008; 9:2087-95. [PMID: 18666306 PMCID: PMC2826882 DOI: 10.1002/cbic.200800148] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Indexed: 11/06/2022]
Abstract
The desire to inhibit zinc-dependent matrix metalloproteinases (MMPs) has, over the course of the last 30 years, led to the development of a plethora of MMP inhibitors that bind directly to the active-site metal. With one exception, all of these drugs have failed in clinical trials, due to many factors, including an apparent lack of specificity for MMPs. To address the question of whether these inhibitors are selective for MMPs in a biological setting, a cell-based screening method is presented to compare the relative activities of zinc, heme iron, and non-heme iron enzymes in the presence of these compounds using the RAW264.7 macrophage cell line. We screened nine different zinc-binding groups (ZBGs), four established MMP inhibitors (MMPis), and two novel MMP inhibitors developed in our laboratory to determine their selectivities against five different metalloenzymes. Using this model, we identified two nitrogen donor compounds--2,2'-dipyridylamine (DPA) and triazacyclononane (TACN)--as the most selective ZBGs for zinc metalloenzyme inhibitor development. We also demonstrated that the model could predict known nonspecific interactions of some of the most commonly used MMPis, and could also give cross-reactivity information for newly developed MMPis. This work demonstrates the utility of cell-based assays in both the design and the screening of novel metalloenzyme inhibitors.
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Affiliation(s)
- Faith E. Jacobsen
- Department of Chemistry and Biochemistry, University of California in San Diego, La Jolla, CA 92093-0358
| | - Matthew W. Buczynski
- Department of Chemistry and Biochemistry, University of California in San Diego, La Jolla, CA 92093-0358
- Department of Pharmacology, University of California in San Diego, La Jolla, CA 92093-0601
| | - Edward A. Dennis
- Department of Chemistry and Biochemistry, University of California in San Diego, La Jolla, CA 92093-0358
- Department of Pharmacology, University of California in San Diego, La Jolla, CA 92093-0601
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of California in San Diego, La Jolla, CA 92093-0358
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56
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Verma RP, Hansch C. Combating the Threat of Anthrax: A Quantitative Structure−Activity Relationship Approach. Mol Pharm 2008; 5:745-59. [DOI: 10.1021/mp8000149] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rajeshwar P. Verma
- Department of Chemistry, Pomona College, 645 North College Avenue, Claremont, California 91711
| | - Corwin Hansch
- Department of Chemistry, Pomona College, 645 North College Avenue, Claremont, California 91711
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57
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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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58
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Agrawal A, Romero-Perez D, Jacobsen JA, Villarreal FJ, Cohen SM. Zinc-binding groups modulate selective inhibition of MMPs. ChemMedChem 2008; 3:812-20. [PMID: 18181119 PMCID: PMC2836234 DOI: 10.1002/cmdc.200700290] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Indexed: 12/29/2022]
Abstract
The need for selective matrix metalloproteinase (MMP) inhibition is of interest because of the range of pathologies mediated by different MMP isoforms. The development of more selective MMP inhibitors (MMPi) may help to overcome some of the undesired side effects that have hindered the clinical success of these compounds. In an effort to devise new approaches to selective inhibitors, herein we describe several novel MMPi and show that their selectivity is dependent on the nature of the zinc-binding group (ZBG). This is in contrast to most current MMPi, which obtain isoform selectivity solely from the peptidomimetic backbone portion of the compound. In the present study, six different hydroxypyrone and hydroxypyridinone ZBGs were appended to a common biphenyl backbone and the inhibition efficiency of each inhibitor was determined in vitro (IC(50) values) against MMP-1, -2, -3, -7, -8, -9, -12, and -13. The results show that the selectivity profile of each inhibitor is different as a result of the various ZBGs. Computational modeling studies were used to explain some trends in the observed selectivity profiles. To assess the importance of the ZBG in a biological model, two of the semiselective, potent MMPi (and one control) were evaluated using an isolated perfused rat heart system. Hearts were subjected to ischemia reperfusion injury, and recovery of contractile function was examined. In this model, only one of the two MMPi showed significant and sustained heart recovery, demonstrating that the choice of ZBG can have a significant effect in a relevant pathophysiological endpoint.
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Affiliation(s)
- Arpita Agrawal
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Diego Romero-Perez
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Jennifer A. Jacobsen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Francisco J. Villarreal
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
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59
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Efficient synthesis and metal cations complexation of some novel dinaphthosulfide-substituted macrocyclic diamides. J INCL PHENOM MACRO 2008. [DOI: 10.1007/s10847-008-9408-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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60
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Wang SH, Wang SF, Xuan W, Zeng ZH, Jin JY, Ma J, Tian GR. Nitro as a novel zinc-binding group in the inhibition of carboxypeptidase A. Bioorg Med Chem 2008; 16:3596-601. [DOI: 10.1016/j.bmc.2008.02.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2008] [Revised: 02/01/2008] [Accepted: 02/05/2008] [Indexed: 11/28/2022]
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61
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JIN JY, WANG SF, XUAN W, SHENG JW, WANG SH, TIAN GR. Synthesis and Evaluation of Optical 2-Benzyl-5-bromo-4-oxopentanoic Acids as Transition-state Analog Inhibitors against Carboxypeptidase A. CHINESE J CHEM 2008. [DOI: 10.1002/cjoc.200890013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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62
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Hayashi R, Jin X, Cook GR. Synthesis and evaluation of novel heterocyclic MMP inhibitors. Bioorg Med Chem Lett 2007; 17:6864-70. [PMID: 18029173 PMCID: PMC2574968 DOI: 10.1016/j.bmcl.2007.10.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 10/02/2007] [Accepted: 10/05/2007] [Indexed: 11/23/2022]
Abstract
A variety of novel heterocyclic compounds were synthesized and evaluated for MMP inhibition. Broad spectrum inhibition of MMPs 1, 2, 9, and 12 was found with pyridinone-based compounds while N-heterocyclic triazoles and tetrazoles were largely ineffective. A highly selective tetrazole inhibitor for MMP-2 was discovered.
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Affiliation(s)
- Ryuji Hayashi
- Center for Protease Research, Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, ND 58105, USA
| | - Xiaomin Jin
- Center for Protease Research, Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, ND 58105, USA
| | - Gregory R. Cook
- Center for Protease Research, Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, ND 58105, USA
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63
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Seebeck B, Reulecke I, Kämper A, Rarey M. Modeling of metal interaction geometries for protein-ligand docking. Proteins 2007; 71:1237-54. [DOI: 10.1002/prot.21818] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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64
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Dinuclear Zinc (II) Complexes of Macrocyclic Polyamine Ligands Containing an Imidazolium Bridge: Synthesis, Characterization, and Their Interaction with Plasmid DNA. Int J Mol Sci 2007. [DOI: 10.3390/i8070606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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65
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Zhao YC, Zhang J, Huang Y, Wang GQ, Yu XQ. DNA cleavage promoted by 2,9-dimethyl-4,7-diazadecane-2,9-dithiol (DDD) derivatives. Bioorg Med Chem Lett 2007; 17:2745-8. [PMID: 17369043 DOI: 10.1016/j.bmcl.2007.02.072] [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: 11/09/2006] [Revised: 02/03/2007] [Accepted: 02/27/2007] [Indexed: 11/29/2022]
Abstract
Three piperidine derivatives of 2,9-dimethyl-4,7-diazadecane-2,9-dithiol (DDD), NEPDDD, NEMPDDD, and NEMMPDDD, were synthesized and used as catalysts in DNA cleavage. Under physiological conditions, a series of experiments have been done. The effects of DNA cleavage with three ligands were studied under different concentrations, cleavage time, and pH values. The results strongly suggested that the plasmid DNA (pUC 19) can be cleaved efficiently by these ligands. For the cleavage reaction catalyzed by NEMPDDD, Form I DNA could convert to Form II completely, and the DNA-cleavage mechanism involved an oxidative pathway.
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Affiliation(s)
- Yuan-Cong Zhao
- Department of Chemistry, Key Laboratory of Green Chemistry and Technology (Ministry of Education), Sichuan University, Chengdu 610064, PR China
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66
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Johnson SL, Chen LH, Pellecchia M. A high-throughput screening approach to anthrax lethal factor inhibition. Bioorg Chem 2007; 35:306-12. [PMID: 17320146 PMCID: PMC2020844 DOI: 10.1016/j.bioorg.2006.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 12/27/2006] [Accepted: 12/29/2006] [Indexed: 11/22/2022]
Abstract
A high-throughput screening approach was used to identify new inhibitors of the metallo-protease lethal factor from Bacillus anthracis. A library of approximately 14,000 compounds was screened using a fluorescence-based in vitro assay and hits were further characterized enzymatically via measurements of IC50 and Ki values against a small panel of metallo-proteases. This study led to the identification of new scaffolds that inhibit LF and the Botulinum Neurotoxin Type A in the low micromolar range, while sparing the human metallo-proteases MMP-2 and MMP-9. Therefore, these scaffolds could be further exploited for the development of potent and selective anti-toxin agents.
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Affiliation(s)
| | | | - Maurizio Pellecchia
- * To whom correspondence should be addressed: Tel. 858.646.3159 Fax. 858.795.5225
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67
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Rella MR, Williard PG. Oxidation of peptides by methyl(trifluoromethyl)dioxirane: the protecting group matters. J Org Chem 2007; 72:525-31. [PMID: 17221970 PMCID: PMC3220948 DOI: 10.1021/jo061910n] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Representative Boc-protected and acetyl-protected peptide methyl esters bearing alkyl side chains undergo effective oxidation using methyl(trifluoromethyl)dioxirane (1b) under mild conditions. We observe a protecting group dependency in the chemoselectivity displayed by the dioxirane 1b. N-Hydroxylation occurs in the case of the Boc-protected peptides, and side chain hydroxylation takes place in the case of acetyl-protected peptides. Both are attractive transformations since they yield derivatized peptides that serve as valuable synthons.
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Affiliation(s)
| | - Paul G. Williard
- Department of Chemistry, Brown University, Providence, Rhode Island 02912
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68
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Jacobsen FE, Lewis JA, Heroux KJ, Cohen SM. Characterization and evaluation of pyrone and tropolone chelators for use in metalloprotein inhibitors. Inorganica Chim Acta 2007. [DOI: 10.1016/j.ica.2006.07.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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69
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Karmakar A, Sarma RJ, Baruah JB. Self-assembly of neutral dinuclear and trinuclear zinc-benzoate complexes. INORG CHEM COMMUN 2006. [DOI: 10.1016/j.inoche.2006.07.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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70
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Tekeste T, Vahrenkamp H. “Inhibition” of the Enzyme Model TpPh,MeZn–OH by Diketo Compounds. Eur J Inorg Chem 2006. [DOI: 10.1002/ejic.200600813] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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71
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Lewis JA, Mongan J, McCammon JA, Cohen SM. Evaluation and Binding-Mode Prediction of Thiopyrone-Based Inhibitors of Anthrax Lethal Factor. ChemMedChem 2006; 1:694-7. [PMID: 16902919 DOI: 10.1002/cmdc.200600102] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jana A Lewis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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