1,721,135 research outputs found
Small changes for long term impact : optimization of structure kinetic properties : a case of CCR2 antagonists
Full text linkThis thesis focuses on a new approach in drug discovery, the so-called drug-target residence time. Next to more traditional drug discovery efforts, which are based on structure-affinity relationships, this thesis describes the use of an additional parameter __ the structure-kinetic relationships. Knowledge of this additional parameter at the early stages of drug discovery may help the pharmaceutical industry to generate better drug candidates. Additionally, it could save big expenses in the later stages of drug discovery by minimizing the attrition rate of drug candidates due to efficacy problems. In more detail, this thesis focuses on the synthesis of new high affinity and long residence time small molecule antagonists for the chemokine receptor CCR2 - a potential target for the treatment of various inflammatory diseases.UBL - phd migration 201
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
Allosteric modulation and ligand binding kinetics at the Kv11.1 channel
Full text linkKv11.1-induced cardiotoxicity has emerged as an unanticipated adverse effect of many pharmacological agents and has become a major obstacle in drug development over the past decades. In this thesis, allosteric modulation of the Kv11.1 channel has been extensively explored, and negative allosteric modulators were shown to relieve the proarrhythmic effects of structurally and therapeutically diverse Kv11.1 blockers. The most potent modulators may be developed as a new class of antiarrhythmic medications in the future. On the other hand, kinetic binding parameters of a wide range of Kv11.1 blockers at the channel have been thoroughly investigated in this thesis. Association and dissociation rates or residence times are strongly suggested to be integrated with equilibrium affinity values into the future paradigms for a better and more comprehensive evaluation of Kv11.1 liability of drug candidates. The __kon-koff-KD__ kinetic map provides a first and promising classification of Kv11.1 blockers, which could be beneficial and indicative for drug researchers to design compounds with less Kv11.1-mediated cardiac side effects in the early stage of drug development. Hopefully, all findings in this thesis have brought new insights into Kv11.1-induced cardiac arrhythmias, and will offer opportunities for restoring or preventing this kind of arrhythmias in the near future.Chinese Scholarship CouncilUBL - phd migration 201
The ins and outs of ligand binding to CCR2
Full text linkThis thesis provides novel insights in the molecular mechanism of action of antagonists for the chemokine receptor CCR2. CCR2 belongs to the protein family of G protein-coupled receptors (GPCRs). It is involved in several inflammatory diseases and therefore many small molecule antagonists targeting this receptor have been developed over the years. Unfortunately all clinical candidates tested so far appeared to lack efficacy in man, which stresses the need for a better understanding of their mechanism of action. This thesis revealed three separate binding pockets throughout the transmembrane receptor domain via which CCR2 can be pharmacologically modulated. Different routes towards insurmountable antagonism of CCR2 were described, either via noncompetitive or via long residence time antagonists. These results may allow a more rational design of future antagonists, and are equally important to understand the outcomes of studies with existing CCR2 antagonists. In concert with the currently expanding insight in the structure and signalling capacities of GPCRs, the data presented in this thesis allow to better fine-tune the pharmacological modulation of the chemokine receptor CCR2, and GPCRs in generalPeproTechUBL - phd migration 201
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
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
Allosteric Modulation of 'Reproductive' GPCRs : a case for the GnRH and LH receptors
Full text linkG protein-coupled receptors (GPCRs) are currently targeted by more than 30% of the drugs on the market. In the past few years, however, a decline in newly marketed drugs (in general) is observed, stressing the importance of new approaches for drug therapy. One of these new approaches is the development of so-called allosteric modulators. Allosteric ligands bind at a site distinct from the site where the endogenous ligand binds and are capable of changing the receptor conformation. Thereby, a change in the pharmacological responses to the orthosteric ligand will occur. The resulting advantages of allosteric modulation are, for example, increased receptor-subtype selectivity and preservation of the physiological effects (with respect to duration and site of action). Chapter 1 introduces GPCRs and the recent developments in drug research, such as allosteric modulation, involving these proteins. The hypothalamic-pituitary-gonadal (HPG) axis is regulated by a number of G protein-coupled receptors that play an important role in reproduction and sex hormone-dependent diseases. These receptors are therefore referred to as __reproductive__ GPCRs. The main focus of this thesis is on the gonadotropin-releasing hormone (GnRH) (Chapter 3) and luteinizing hormone (LH) receptor (Chapters 4-6). These targets have been classified as class A GPCRs that are usually comprised of a short extracellular N-terminal domain, seven transmembrane (7-TM) __-helices, which are connected by three intra- and extracellular loops, and an intracellular C-terminus. In general, the endogenous ligands of this class of GPCRs bind within the 7-TM domain, referred to as the orthosteric binding site. The LH receptor, however, is an exceptional class A GPCR, because it has two endogenous ligands, LH and hCG, which both bind to the (unusually) large N-terminus. Both the GnRH and LH receptor have high molecular weight (HMW) endogenous ligands that are peptide/protein hormones. One of the advantages of allosteric modulation of these receptors is low molecular weight (LMW) allosteric ligands can be developed that are potentially orally bioavailable, unlike peptidic ligands such as GnRH and LH. Chapter 2 reviews the LMW (orthosteric and allosteric) ligands for GPCRs of the HPG axis that have been reported so far. In Chapter 3, allosteric modulation of the human GnRH receptor by amiloride analogues (e.g. HMA) and a non-peptide antagonistic furan derivative (FD-1) was studied. Firstly, the compounds__ ability to influence the dissociation of a radiolabeled peptide agonist (125I-triptorelin) from human GnRH receptors was investigated. HMA and FD-1 were shown to increase the dissociation rate of 125I-triptorelin, revealing their allosteric inhibitory characteristics. The simultaneous addition of HMA and FD-1 resulted in an additive effect on the dissociation rate. Secondly, in a functional assay it was shown that HMA was a non-competitive antagonist and that FD-1 had both competitive and non-competitive antagonistic properties. Furthermore, the potency of HMA to increase radioligand dissociation was not affected by the presence of FD-1. Simulation of the data obtained in the latter experiment also indicated neutral cooperativity between the binding of HMA and FD-1. Taken together, these results demonstrate that HMA and FD-1 are allosteric inhibitors that bind at two distinct, non-cooperative, allosteric sites. In Chapter 4, the binding of a new low-molecular-weight (LMW) radioligand, [3H]Org 43553, at the LH receptor is characterized. Equilibrium saturation and displacement assays were developed and optimized. Specific binding of [3H]Org 43553 to human LH receptor was saturable with a high affinity (KD = 2.4 _ 0.4 nM). Affinities and potencies of five LMW analogues of Org 43553 were determined, showing a high correlation between these values. A HMW radioligand, such as 125I-hCG, is not suitable for screening for LMW ligands, as they do not compete for the same binding site. This new radioligand, [3H]Org 43553, is therefore a welcome addition in the field of drug research for the LH receptor. In Chapter 5 and Chapter 6, [3H]Org 43553 was used to screen a library of 50 compounds for possible new LMW ligands targeting the LH receptor. Especially, the kinetic radioligand dissociation screen (i.e. to identify allosteric modulators) resulted in the identification of both allosteric inhibitors (Chapter 5) and allosteric enhancers (Chapter 6) of Org 43553. Firstly, a terphenyl derivative was shown to (allosterically) inhibit [3H]Org 43553 binding to the receptor. This led us to synthesize a series of 25 terphenyl derivatives. The most potent compound of this series was LUF5771, which was able to increase the dissociation rate of [3H]Org 43553 by 3.3-fold (at 10 _M). Secondly, several allosteric enhancers of [3H]Org 43553 were identified, each containing a thiazole core. In this case, LUF5419 was chosen to be characterized further as it was one of the most potent compounds, with an ability to decrease the dissociation rate of [3H]Org 43553 by 2.4-fold (at 10 _M). Both LUF5771 and LUF5419 were also tested in a functional assay, where the presence of the first resulted in a 2.4-fold decreased potency of Org 43553, while the latter did not affect the potency. The efficacy of (the partial agonist) Org 43553, however, was unaffected by LUF5771, while LUF5419 caused an enhancement, resulting in full receptor activation when compared to recLH. Interestingly, LUF5771 was also able to allosterically inhibit the potency of recLH (and rec-hCG). LUF5419, however, did not affect the potency or efficacy of recLH. It is noteworthy, that LUF5771 is the first LMW antagonistic/inhibitory ligand reported for the LH receptor to date. Furthermore, the potency to increase radioligand dissociation of LUF5771 was decreased by the presence of LUF5419. These results demonstrate that LUF5771 and LUF5419 are allosteric modulators that bind at the same allosteric site in the LH receptor. In this thesis radioligand dissociation assays were used to identify new allosteric modulators in a more low-throughput fashion. In high-throughput-screening, however, new (allosteric) ligands are often searched for by functional assays (e.g. luciferase reporter-gene assay). In Chapter 7, we report a luciferase inhibitor, which emerged from a luciferase reporter-gene assay screen for LH receptor ligands. Instead of displaying receptor activity this compound was shown to potently inhibit luciferase (i.e. a false positive). Further characterization showed that it was a competitive inhibitor with respect to the substrate luciferin. When a database search yielded another a structurally similar inhibitor, we were triggered to prepare several analogs of the luciferase inhibitors. This yielded a very potent inhibitor with an IC50 value of 0.069 _ 0.01 _M. Further molecular modeling studies suggested that the latter compound can be accommodated in the luciferin binding site. Chapter 7 should serve as an alert to users of luciferase reporter gene assays for possible false positive hits due to direct luciferase inhibition. Finally, in Chapter 8 the general conclusions from the research described in this thesis are presented and future perspectives in this field of research are given. In short, this thesis provides novel insights in the allosteric modulation of __reproductive__ GPCRs. The human GnRH and LH receptor, like several other (class A) GPCRs, can be allosterically modulated. Moreover, both receptors are shown to contain three binding sites of which at least two can be targeted by LMW ligands. The presence of these other allosteric sites may provide other opportunities for the discovery of LMW and orally available ligands for the human GnRH and LH receptor.Schering-Plough Research Institute (Oss, The Netherlands) TI Pharma (Project number D1-105)UBL - phd migration 201
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