1,721,095 research outputs found
Identification of a More Potent Analogue of the Naturally Occurring Alkaloid Huperzine A. Predictive Molecular Modeling of Its Interaction with AChE
No full textHuperzine A (HA), a potent reversible inhibitor of acetylcholinesterase (AChE), is an important psychotherapeutic agent for improving cognitive function in Alzheimer's patients through the enhancement of central cholinergic tone. This molecule takes on added value in that it has recently been shown to exhibit neuroprotective properties (glutamate toxicity blocking activity) in vitro. Based upon our cumulative SAR information and to some extent the predicted binding site of HA within Torpedo AChE, we chose to investigate the synthesis and biology of certain C-10 substituted analogues. The important finding was made that introduction of an axial methyl group into the C-10 position of huperzine A increased the potency for AChE inhibition 8-fold; the corresponding equatorial isomer was about 1.5-fold less active than huperzine A. The introduction of substituents larger than methyl resulted in a drop in activity. For example, the ethyl analogue was found to be about 100-fold less active than huperzine A, indicating that while it is still capable of binding to Torpedo AChE, some steric interaction with the 'walls' of the active site gorge must result. Through the use of molecular modeling methods involving the docking of these analogues to the reported X-ray crystal structure of Torpedo AChE, it is clearly evident that the C-10 axial methyl group points into a hydrophobic region of the enzyme, while the equatorial methyl group is directed to a less favorable hydrophilic region. Substituents larger than methyl were found to result in a conformational energy penalty. The ready explanation of this structure-activity relationship data provides further evidence in support of our modeling studies aimed at establishing huperzine A's binding site in AChE. This knowledge should facilitate the identification of other structural analogues of huperzine A likely to exhibit an improved therapeutic profile
Synthesis and in vitro Characterization of Triazole-Stapled Bim Alpha-Helical Peptides
No full textvii, 22 p.The Bcl-2 protein family has been shown to play a vital role in the cell apoptosis process. Within this family is Bim, a pro-apoptotic protein, which forms a heterodimer with Bcl-2 allowing for the eventual release of caspases from the mitochondria leading to cell death, a necessity for normal cell functioning. Optimizing this interaction between the two proteins may allow for the development of tracers for in vitro and in vivo assays and possibly a means to combat the rapid proliferation of cells, a hallmark of cancer. The goal of the research presented in this paper is to stabilize the region of the Bim peptide, residues 85-106, which interacts with Bcl-2. Successful synthesis will induce α-helicity allowing for increased binding affinity and cell permeability as well as inhibition of proteolytic degradation. Stabilization was attempted by means of “click chemistry” and the formation of a triazole staple in an i and i+4 amino acid position. Analysis of the stapled peptides through a fluorescence polarization competitive binding assay showed minimal difference in IC50 values between linear and stapled α-helical peptides.University of Michigan Cancer Center. University of Michigan. Ann Arbor, Michigan
Structure-based design and discovery of small molecule inhibitors of protein -protein interactions.
No full textProtein-protein interactions represent a large and important class of targets for human therapeutics. The design of small molecule inhibitors of protein-protein interactions, however, is a challenging area in medicinal chemistry. This dissertation focuses on applying computational methods to design and discover small molecule inhibitors to target two protein-protein interactions, namely the MDM2 - p53 interaction and the XIAP - caspase-9 interaction, respectively. Using a structure-based de novo design strategy, a class of spiro-oxindole compounds was designed as a new class of small molecule inhibitors of the MDM2-p53 interactions. This study led to one of the most potent, non-peptidic, small molecule inhibitors of the MDM2-p53 interaction discovered to date. Molecular dynamics simulations and free energy calculations have been employed to explore the dynamic behavior of MDM2 in complex with the spiro-oxindole inhibitors and to investigate the contributions of specific chemical groups in the spiro-oxindole inhibitor to binding affinities. In addition to de novo design, virtual screening was used to discover new small molecule inhibitors of the MDM2-p53 interaction. Novel inhibitors with binding affinity in the nanomolar range were identified. Additional cellular studies demonstrate that one of the most potent hits identified has a mechanism of action consistent with targeting the MDM2-p53 interaction and represents a promising new class of non-peptide inhibitors of the MDM2-p53 interaction. A virtual screening strategy was also employed to discover novel small molecule inhibitors of the XIAP-caspase 9 interaction. The most potent identified compound binds to XIAP BIR3 with an affinity similar to that of the natural Smac peptide. It was showed that this lead compound inhibits cell growth and induces apoptosis in cancer cells with high levels of XIAP. Water molecules play an important role in protein-ligand interactions. However their precise contribution to the free-energy of binding is not known. A computational study was carried out to determine the binding free energy of interfacial water molecules in protein-ligand complexes using the double-decoupling free energy simulation method on two HIV-1 protease-inhibitor complexes. This study led to a deeper understanding of several important factors that influence the free energy contributions of interfacial water molecules to protein-ligand binding.PhDBioinformaticsBiological SciencesPharmacy sciencesPure SciencesUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/126345/2/3245744.pd
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Structure based design of peptide-mimetic STAT3 inhibitors.
No full textSTAT3 belongs to the Signal Transducers and Activators of Transcription (STATs) family of proteins which functions as an intracellular effectors for cytokines and growth factors. A growing body of evidence has established a link between abnormal STAT3 signaling observed in many cancers and the dynamic genetic reprogramming that characterizes malignant transformation. Persistent STAT3 activity is documented in a wide variety of blood and solid tumors. While normal STAT3 signaling promotes growth and survival; persistent STAT3 signaling translates into a marked increase in its downstream gene products which alter the cell's apoptotic and proliferation programs. As a therapeutic strategy, inhibiting STAT3 can kill tumor cells by inducing apoptosis and sensitizing chemo-resistant cancer cells to cytotoxic agents. To inhibit persistent STAT3 signaling we designed, synthesized and evaluated peptide mimetics based on a peptide sequence from the STAT3 docking site on the gp130 receptor, pYLPQTV. Our inhibitors target STAT3's SH2 domain and in doing so our goal is to reduce STAT3's interactions with (1) cytokine receptors and/or JAKs; (2) other proteins; and (3) DNA. Our computational modeling of the gp130 peptide in complex with the STAT3 protein predicts that it adopts a beta-turn. As a tactic to constrain the peptide in its predicted binding conformation, we incorporated known monocyclic beta-turn mimetic scaffolds such as Freidinger lactams and 7- and 8-5 aza-bicyclic scaffolds in doing so we obtained a significant improvement in binding affinity (35 fold compared to our lead). Moreover, pull down analysis in various cell lines demonstrate our inhibitors containing the 8-5 aza-bicyclic scaffold are selective for STAT3 over other STAT family members and significantly reduced levels of c-Myc and phospho-STAT3 levels in DU 145 prostate cancer cells.PhDPharmacy sciencesPure SciencesUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/127107/2/3354158.pd
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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