1,721,032 research outputs found
Synthesis and biological evaluation of Santacruzamate-A based analogues
No full textSeveral derivatives of Santacruzamate-A, a natural product that is structurally related to SAHA, were synthesized to explore the potential of carbamates and oxalylamides as novel biasing element for targeting the catalytic site of zinc-dependent histone deacetylases (HDACs). An additional class of Santacruzamate-A derivatives was synthesized to investigate the influence of the cap group and the linker element on HDAC inhibitory activity. All compounds were evaluated in dose response for their in vitro cytotoxic activity in MTT assay in HCT116 cells. HDAC inhibitory activity was evaluated in vitro by western blot analysis for histone hyperacetylation assay and biochemically for representative human HDACs isoforms. Two novel compounds were identified to exhibit potent time dependent anti proliferative activity. However, unlike hydroxamic acid analogues, the tested Santacruzamate-A derivatives showed no noticeable HDAC inhibitory activity. The ethylcarbamate moiety as unusual zinc-binding group displayed no ability to coordinate the zinc ion and thus, presumably, was not able to reproduce known inhibitor-substrate zinc-binding group interactions with the HDAC catalytic site. This study confirmed that the accommodation of the zinc-binding group is deeply critical of the positioning of the linker and the projection of the cap group toward the different surface pockets of the enzyme
Fluorescence anisotropy imaging in drug discovery
No full textNon-invasive measurement of drug-target engagement can provide critical insights in the molecular pharmacology of small molecule drugs. Fluorescence polarization/fluorescence anisotropy measurements are commonly employed in protein/cell screening assays. However, the expansion of such measurements to the in vivo setting have proven difficult until recently. With the advent of high-resolution fluorescence anisotropy microscopy it is now possible to perform kinetic measurements of intracellular drug distribution and target engagement in commonly used mouse models. In this review we discuss the background, current advances and future perspectives in intravital fluorescence anisotropy measurements to derive pharmacokinetic and pharmacodynamic measurements in single cells and whole organs
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Variations on the Author
Full text link“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
Full text linkWe 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
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Development of CoraFluors: A Versatile, Target-agnostic Assay Technology Platform Optimized for Chemical Biology Research
No full textBiology uses strategic, coordinated proximity events to orchestrate complex cellular pathways essential to homeostasis, survival, and propagation. The interrogation of biological systems with chemogenomic approaches has led to a prolific era of research in the life sciences. Critical to these strategies are the availability of sensitive, quantitative, and flexible assay technologies that allow scientists to accurately measure binding events between biomolecules (or with their small molecule ligands), as well as their abundance – ideally in both biochemical and cellular contexts. Experimental designs based on time-resolved Förster resonance energy transfer (TR-FRET) are uniquely suited to study proximity at the biomolecular level, offering both high sensitivity and specificity. However, the paucity of synthetically accessible and biocompatible luminescent lanthanide complexes, which are essential reagents for TR-FRET-based approaches, and their poor cellular permeability have limited broader adaptation of TR-FRET beyond homogeneous and extracellular assay applications.
In this Dissertation, I discuss the development of CoraFluors, a new class of synthetically tractable luminescent macrotricyclic terbium complexes optimized for TR-FRET-based chemogenomic applications. I apply CoraFluor technology in the development of novel, domain-selective assays for Keap1 (Kelch-like ECH-associated protein 1). Using cell-permeable CoraFluor derivatives, I also describe the adaptation of these reagents to enable isoform-selective, cell-free and live-cell ligand displacement assays for HDAC1 (histone deacetylase 1). In addition, I discuss a universal nanobody-based strategy that expands the toolbox of TR-FRET donor labeling approaches for a wide range of biochemical assays.
Utilizing the novel CoraFluors, I develop a TR-FRET-based strategy for the quantification of target engagement and protein abundance of endogenous proteins of interest (POIs) in whole cell extracts. This methodology overcomes many inherent limitations of existing assay technologies such as Western blot, ELISA (enzyme-linked immunosorbent assay), and luminescence-based platforms. Importantly, this strategy is compatible with unmodified cell lines expressing native POIs. My approach enabled the quantitative characterization of the natural product celastrol, a p-quinone methide-containing pentacyclic triterpenoid, as a broad cysteine-targeting E3 ubiquitin ligase warhead for targeted protein degradation applications.
Lastly, I develop a TR-FRET-based approach to resolve the often-deceptive isoform and complex selectivity of HDAC inhibitors. My findings show that widely used probes can display misleading activity in static biochemical assays, and I provide evidence that dynamic processes govern the isoform and complex selectivity of these ligands in cellular contexts. These data reconcile the previous apparent disconnect between biochemical inhibitory profiles and corresponding cellular activities of HDAC inhibitors and urge a comprehensive reinterpretation of studies that have used these chemical probes to interrogate epigenetic and other cellular processes.
Overall, my research establishes CoraFluor TR-FRET technology as a target-agnostic, flexible, sensitive, and quantitative assay platform for a wide array of chemical biology approaches and has advanced our mechanistic understanding of epigenetic gene regulatory complexes
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe 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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