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Title: Discorhabdin P, a new enzyme inhibitor from a deep-water Caribbean sponge of the genus Batzella.
Creator: Gunasekera, Sarath P., McCarthy, Peter J., Longley, Ross E., Pomponi, Shirley A., Wright, Amy E., Lobkovsky, E., Clardy, J.
Date Issued: 1999
PURL: http://purl.flvc.org/FCLA/DT/3319100
Subject Headings: Sponges --Research, Marine natural products, discorhabdin P, Enzyme inhibitors
Format: Document (PDF)

Title: In search of MMP specific inhibitors: protein engineering of TIMPs.
Creator: Bahudhanapati, Harinathachari., Charles E. Schmidt College of Science, Department of Biomedical Science
Abstract/Description: The tissue inhibitors of metalloproteinases (TIMPs) are endogenous inhibitors of the matrix metalloproteinases (MMPs). Since unregulated MMP activities are linked to arthritis, cancer, and atherosclerosis, TIMP variants that are selective inhibitors of disease-related MMPs have potential therapeutic value. The structures of TIMP/MMP complexes reveal that most interactions with the MMP involve the N-terminal region of TIMP and the C-D B-strand connector which occupy the primed (right side of...
Show moreThe tissue inhibitors of metalloproteinases (TIMPs) are endogenous inhibitors of the matrix metalloproteinases (MMPs). Since unregulated MMP activities are linked to arthritis, cancer, and atherosclerosis, TIMP variants that are selective inhibitors of disease-related MMPs have potential therapeutic value. The structures of TIMP/MMP complexes reveal that most interactions with the MMP involve the N-terminal region of TIMP and the C-D B-strand connector which occupy the primed (right side of the active site) and unprimed (left side) regions of the active site. Substitutions for Thr2 of N-TIMP- 1 strongly influence MMP selectivity. In this study we found that Arg and Gly, which generally reduce MMP affinity, have less effect on binding to MMP-9. When the Arg mutation is added to the NTIMP-1 mutant with AB loop of TIMP-2, it produced a gelatinase-specific inhibitor with Ki values of 2.8 and 0.4 nM for MMP-2 and MMP-9, respectively. The Gly mutant has a Ki of 2.1 nM for MMP-9 and > 40 uM for MMP-2, indicating that engineered TIMPs can discriminate between MMPs in the same subfamily. In collaboration with Dr. Yingnan Zhang at Genentech, we have developed a protocol for the phage display of full-length human TIMP-2 to identify high-affinity selective inhibitors of human MMP-1, a protease that plays a role in cleaving extracellular matrix (ECM) components, connective tissue remodeling during development, angiogenesis, and apoptosis. We have generated a library containing 2x1010 variants of TIMP-2 randomized at residues 2-6 (L1), at residues 34-40 (L2) and 67-70 (L3)., The L1 library yielded a positive signal for MMP-1 binding. Clones from the L1 library, designated TM1, TM8, TM13, and TM14, were isolated after 5 rounds of selection on immobilized MMP-1 and MMP-3 and found to show a greater selectivity for MMP-1 relative to MMP-3. TM8, which has Ser2 to Asp and Ser4 to Ala substitutions, showed the greatest apparent selectivity of 10-fold toward MMP-1 compared to MMP-3. The various mutations identified by phage display were introduced into recombinant Nterminal TIMP-2 and the variants characterized as inhibitors of an array of MMP catalytic domains. The TM8-based mutant showed pronounced selectivity (> 1000-fold for MMP-1 vs. MMP-3) and may be a step towards the generation of MMP-1-specific inhibitors. Molecular modeling was used to rationalize the structural basis of MMP selectivity in the mutants.
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Date Issued: 2009
PURL: http://purl.flvc.org/FAU/221942
Subject Headings: Metalloproteinases, Inhibitors, Apoptosis, Extracellular matrix proteins, Proteolytic enzymes
Format: Document (PDF)

Title: Thermodynamic Origins of Selectivity in the Interactions of N- TIMP Variants and Metalloproteinases Catalytic Domains.
Creator: Zou, Haiyin, Brew, Keith, Florida Atlantic University, Charles E. Schmidt College of Medicine, Department of Biomedical Science
Abstract/Description: Matrix metalloproteinases (MMPs) constitute the major class of enzymes capable of degrading all protein components of extracellular matrix (ECM) and have important roles in normal physiologic processes of maintaining tissue integrity and remodeling. However, excess MMP activities are associated with many diseases including rheumatoid arthritis and osteoarthritis, cardiomyopathy, and macular degeneration. The activity of MMPs is regulated by their endogenous protein inhibitors, the tissue...
Show moreMatrix metalloproteinases (MMPs) constitute the major class of enzymes capable of degrading all protein components of extracellular matrix (ECM) and have important roles in normal physiologic processes of maintaining tissue integrity and remodeling. However, excess MMP activities are associated with many diseases including rheumatoid arthritis and osteoarthritis, cardiomyopathy, and macular degeneration. The activity of MMPs is regulated by their endogenous protein inhibitors, the tissue inhibitors of metalloproteinases (TIMPs) which are avid broad-spectrum inhibitors of numerous human matrixins (MMPs and ADAMs). Uncontrolled matrix degradation occurs when the balance between TIMPs and MMPs is disrupted, resulting in serious diseases such as cancer, arthritis and chronic tissue ulcers. Thus, the engineering of TIMPs to produce highly selective and efficacious inhibitors of individual MMPs may be utilized for future treatment of diseases. Such engineering requires detailed analysis for the structural and biophysical information of MMP-TIMP interaction. Changes in the dynamics of proteins and solvent that accompany their associations with different binding partners, influence the specificity of binding through entropic effects. From the current studies it appears that the interactions of the inhibitory domains of TIMPs-1 and -2 (N-TIMPs) with MT1-MMP are driven by entropy increases that are partitioned between solvent and conformational entropy (ΔSsolv and ΔSconf), and a large conformational entropy penalty is responsible for the weak inhibition of MT1-MMP by NT1.We investigated how mutations that modify N-TIMP selectivity affect the thermodynamics of interactions with MMP1, MMP3 and MT1-MMP. The weak inhibition of MT1-MMP by N-TIMP-1 is enhanced by mutation of threonine 98, on the edge of the binding ridge, to leucine. This mutation increases the large ΔSconf cost for binding to MT1-MMP but this is offset by a greater increase in ΔSsolv. In contrast, this mutation enhances binding to MMP3 by increasing ΔSconf for the interaction. ΔSsolv and ΔSconf show mutual compensation for all interactions, with characteristic ranges for each MMP. Distinct electrostatic and dynamic features of MMPs are key factors in their selective inhibition.
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Date Issued: 2016
PURL: http://purl.flvc.org/fau/fd/FA00004643
Subject Headings: Metalloproteinases -- Inhibitors., Proteolytic enzymes., Extracellular matrix proteins., Apoptosis.
Format: Document (PDF)

Title: Thermodynamics-structure correlations of interactions between metalloproteinases and tissue inhibitors of metalloproteinase variants.
Creator: Wu, Ying., Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description: The 23 matrix metalloproteinases (MMPs) in humans catalyze the turnover of all protein components of the extracellular matrix (ECM) and have important roles in tissue remodeling, wound healing, embryo implantation, cell migration and shedding of cell surface proteins. Excess MMP activities are associated with many diseases including arthritis, heart disease and cancer. The activities of MMPs are regulated by a family of four protein inhibitors, the tissue inhibitors of metalloproteinases ...
Show moreThe 23 matrix metalloproteinases (MMPs) in humans catalyze the turnover of all protein components of the extracellular matrix (ECM) and have important roles in tissue remodeling, wound healing, embryo implantation, cell migration and shedding of cell surface proteins. Excess MMP activities are associated with many diseases including arthritis, heart disease and cancer. The activities of MMPs are regulated by a family of four protein inhibitors, the tissue inhibitors of metalloproteinases (TIMPs), that are endogenous inhibitors of matrix metalloproteinases (MMPs), ADAMs (A Disintegrin And Metalloproteinase) and ADAMTS (disintegrin-metalloproteinase with thrombospmdin motifs) .... The balance between TIMPs and active metzinicins is very important and imbalances are linked to human diseases such as arthritis, cancer, and atherosclerosis. The engineering of TIMPs to produce specific inhibitors of individual MPs could provide new therapeutic principles for disease treatment, but this requires a detailed understanding of the biophysical and structural basis of the interactions of TIMPs and MMPs and ADAMs.
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Date Issued: 2012
PURL: http://purl.flvc.org/FAU/3356904
Subject Headings: Proteolytic enzymes, Metalloproteinase, Inhibitors, Apoptosis, Extracellular matrix proteins
Format: Document (PDF)

Title: Topological Specificity in Inhibitor Recognition by Matrix Metalloproteinases.
Creator: Lauer-Fields, Janelle, Florida Atlantic University, Brew, Keith, Charles E. Schmidt College of Medicine, Department of Biomedical Science
Abstract/Description: Alterations in activities of one family of proteases, the metzincins have been implicated in an array of physiological and pathological processes. In the present study, metzincin inhibitors were developed by utilizing topologically constrained peptides and pseudopeptides. The endothelin-family framework was used to develop a disulfideconstrained topology. This framework was chosen due to its three-dimensional similarity with a family of endogenous metzincin inhibitors, the tissue inhibitors...
Show moreAlterations in activities of one family of proteases, the metzincins have been implicated in an array of physiological and pathological processes. In the present study, metzincin inhibitors were developed by utilizing topologically constrained peptides and pseudopeptides. The endothelin-family framework was used to develop a disulfideconstrained topology. This framework was chosen due to its three-dimensional similarity with a family of endogenous metzincin inhibitors, the tissue inhibitors of metalloproteases (TIMPs). The collagenous triple-helix was chosen as a second framework, because only a subset of proteolytic enzymes have the capacity to bind and hydrolyze a triple-helix. Both templates were successfully modified to generate an array of inhibitors. These inhibitors displayed subnanomolar to micromolar apparent Ki values, while being moderately selective metzincin inhibitors. In both cases the threedimensional structure was determined to be important for activity. This work encourages the further development of both frameworks as metzincin inhibitors.
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Date Issued: 2007
PURL: http://purl.flvc.org/fau/fd/FA00000867
Subject Headings: Metalloproteinases--Inhibitors, Proteolytic enzymes, Extracellular matrix proteins
Format: Document (PDF)

Title: Proteomic identification of N86-hnRNPU-interacting proteins involved in HIV-1 inhibition.
Creator: Hoxha, Sarah., Harriet L. Wilkes Honors College
Abstract/Description: HIV-1 is the human immunodeficiency virus that can lead to acquired immune deficiency syndrome, or AIDS. Multiple cellular proteins have been identified as playing a critical role in all steps of HIV-1 replication. The heterogeneous nuclear ribonuclear protein U, or hnRNPU is a RNA and DNA binding protein known to influence pre-mRNA processsing, transport to the cytoplasm, intracellular localization, translation and turnover of mRNAs. Recently, the expression of N86-hnRNPU, an N-terminal...
Show moreHIV-1 is the human immunodeficiency virus that can lead to acquired immune deficiency syndrome, or AIDS. Multiple cellular proteins have been identified as playing a critical role in all steps of HIV-1 replication. The heterogeneous nuclear ribonuclear protein U, or hnRNPU is a RNA and DNA binding protein known to influence pre-mRNA processsing, transport to the cytoplasm, intracellular localization, translation and turnover of mRNAs. Recently, the expression of N86-hnRNPU, an N-terminal fragment of hnRNPU, was found to inhibit HIV-1 mRNA export (6). This study primarily aims at identifying proteins that associate with the fragment (N86-hnRNPU) also called H1, and secondarily aims to exclude the possibility that N86-hnRNPU transcripts act as microRNAs.
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Date Issued: 2012
PURL: http://purl.flvc.org/FAU/3359314
Subject Headings: Enzyme inhibitors, Proteinase, Inhibitors, HIV infections, Prevention, HIV infections, Pathogenesis, Antiviral agents
Format: Document (PDF)

Title: A study of Caenorhabditis elegans tissue inhibitor of metalloproteinases.
Creator: Paul, Tamara., Florida Atlantic University, Brew, Keith
Abstract/Description: Tissue Inhibitors of Metalloproteinases (TIMPs) are produced by a wide variety of cell types. Similar to matrixins, the expression of TIMPs in the tissue is also controlled during tissue remodeling and physiological conditions to maintain a balance in the metabolism of extracellular matrix. Disruption of this balance can result in diseases associated with uncontrolled turnover of matrix, such as arthritis, cancer, and cardiovascular disease. Some of the biological processes TIMPs participate...
Show moreTissue Inhibitors of Metalloproteinases (TIMPs) are produced by a wide variety of cell types. Similar to matrixins, the expression of TIMPs in the tissue is also controlled during tissue remodeling and physiological conditions to maintain a balance in the metabolism of extracellular matrix. Disruption of this balance can result in diseases associated with uncontrolled turnover of matrix, such as arthritis, cancer, and cardiovascular disease. Some of the biological processes TIMPs participate in include: regulation of cell morphology and organ morphogenesis, inhibition of angiogenesis, steroidogenesis, and tissue remodeling. One major function of TIMPs is inhibition of Matrix Metaloproteinase (MMPs). This project used bioinformatic techniques to identify two Caenorhabditis elegans TIMP cDNA cloned by BLAST searching of EST database. These TIMP cDNA were amplified, cloned and expressed, proteins were purified. Kinetic studies were carried out to evaluate the inhibitory activities against various MMPs and TACE. This research project will provide some insight on the function of C. elegans TIMPs.
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Date Issued: 2006
PURL: http://purl.flvc.org/fcla/dt/13414
Subject Headings: Endopeptidases--Inhibitors, Proteolytic enzymes, Extracellular matrix proteins, Metalloproteinases--Inhibitors
Format: Document (PDF)

Title: Characterization and optimization of in vitro assay conditions for (1,3)β-glucan synthase activity from Aspergillus fumigatus and Candida albicans for enzyme inhibition screening.
Creator: Wood, R. L., Miller, T. K., Wright, Amy E., McCarthy, Peter J., Taft, C. S., Pomponi, Shirley A., Selitrennikoff, Claude, Harbor Branch Oceanographic Institute
Date Issued: 1998
PURL: http://purl.flvc.org/FCLA/DT/3351974
Subject Headings: Aspergillus fumigatus, Candida albicans, Glucosyltransferases, In vitro, Glucan synthase, Enzyme inhibitors
Format: Document (PDF)

Title: Engineered and natural TIMP mutations.
Creator: Hamze, Asmaa Bilal., Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description: Tissue inhibitors of metalloproteinases (TIMPs) comprise a family of four proteins in humans that modulate the turnover of the extracellular matrix by regulating the activities of endopeptidases that catalyze its degradation, especially the matrix metalloproteinases (MMP). In general, the four TIMPs are broad-spectrum tight binding inhibitors of MMPs with individual differences in specificity. In this study, we attempted to understand the basis of such variation by using membrane type-1 MMP ...
Show moreTissue inhibitors of metalloproteinases (TIMPs) comprise a family of four proteins in humans that modulate the turnover of the extracellular matrix by regulating the activities of endopeptidases that catalyze its degradation, especially the matrix metalloproteinases (MMP). In general, the four TIMPs are broad-spectrum tight binding inhibitors of MMPs with individual differences in specificity. In this study, we attempted to understand the basis of such variation by using membrane type-1 MMP (MT1-MMP) as a model, since it is inefficiently inhibited by TIMP-1 in contrast with the other TIMPs. We designed and engineered mutations in the N-domain of TIMP-1, based on current knowledge of TIMP interactions. By measuring inhibition levels of each mutant against several MMPs, including MT1-MMP, we were able to obtain a triple mutant with an vii improved affinity for MT1-MMP., Our results, along with previous data, confirm that multiple residues in the critical interface segments between TIMPs and MMPs, namely at positions 2, 4, 5, 6, and 98, are key in determining the basic interaction between the two molecules. The second part of this work focused on naturally occurring mutations in TIMP-3 which cause an early form of macular degeneration called Sorsby's Fundus Dystrophy (SFD). The TIMP-3 mutants identified so far share certain features but the mechanism by which they result in macular disease is not yet understood. As an initial step, we expressed recombinant TIMP-3 carrying a truncation mutation, glutamic acid 139 to a stop codon (E139X), and assessed its activity towards representative MMPs and tumor necrosis factor-(Sa (Bconverting enzyme, another metalloproteinase normally inhibited by TIMP-3. Our results indicate that this mutation does not impair the inhibitory activity of TIMP-3., Expression of this mutant in mammalian retinal cells revealed a difference in localization between wild-type and E139X mutant TIMP-3. Therefore, we concluded that the SFD mutations may actually influence the processing and/or binding properties of TIMP-3 in the retina.
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Date Issued: 2008
PURL: http://purl.flvc.org/FAU/186296
Subject Headings: Proteolytic enzymes, Extracellular matrix proteins, Metalloproteinases, Inhibitors, Apoptosis, Retinal degeneration, Research
Format: Document (PDF)

Title: Reciprocal regulation between taurine and glutamate response via Ca2+ - dependent pathways in retinal third-order neurons.
Creator: Bulley, Simon, Shen, Wen
Date Issued: 2010-08-24
PURL: http://purl.flvc.org/fcla/dt/3327274
Subject Headings: Amacrine Cells*/cytology, Amacrine Cells*/drug effects, Amacrine Cells*/metabolism, Ambystoma, Calcium/metabolism, Calcium Channels/metabolism, Cells, Cultured, Enzyme Inhibitors/metabolism, Excitatory Amino Acid Agonists/pharmacology, GABA Antagonists/pharmacology, Glutamic Acid/metabolism, Glycine Agents/pharmacology, Kainic Acid/pharmacology, Membrane Glycoproteins, Membrane Potentials, Neurotransmitter Agents, Retinal Ganglion Cells, Signal Transduction, Synaptic Transmission
Format: Document (PDF)

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