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1
Ruiz, Carmona Sergio. "Virtual screening for novel mechanisms of action: applications and methodological developments." Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/400297.
Full textAbstract:
The main motivation of this thesis has been to validate, improve and develop new methods with respect to the ones available nowadays in the area of drug discovery, in order to be able to study more challenging targets in the near future that currently are out of our reach.
As the productivity of the pharmaceutical industry is decreasing year after year over the last decades, the improvement of such methods would be a step forward. As we are mostly a computational lab, this thesis has focused on different computational approaches such as docking, molecular dynamics or chemoinformatics.
On the first part of the thesis (first author on the publication in PLoS Computational Biology in 2014), I worked on Docking-based Virtual Screening (VS). Particularly, in validating rDock, a little-known but very powerful program that was published and released during this thesis as open source software. In order to validate it, we performed several benchmarking experiments with DUD and ASTEX sets to compare the performance of rDock against Glide and AutoDock Vina, two commonly used docking programs. The capabilities of rDock with respect to binding mode prediction (predict how a ligand structure will be upon binding to its receptor) and virtual screening (selecting the most likely active ligands amongst thousands or millions of drug-like molecules) were compared with Glide and Vina, and we demonstrated that rDock performed as well as them.
On the second project of the thesis (first author on the publication in Nature Chemistry in 2016), we wanted to develop a novel computational tool for drug discovery not only that was complementary to the existing ones, but also that improved them by adding new ways of interpreting the data.
Taking advantage of the already known technique of Steered Molecular Dynamics (SMD), we proposed an approach consisting in reducing the size of the system, focusing around a key interaction point and running SMD to discriminate between active and inactive ligands.
This approach, or as we call it: "Dynamic Undocking", is intended to foster drug design efforts in the lead optimization stage by improving the efficiency of the in silico assessment of protein-ligand binding affinity.
After a positive retrospective assessment of the method using different systems of the DUD set, a prospective validation was required to evaluate its feasibility in a real drug discovery project. Hsp90 was selected as the test system: A fragment library was created and a subset of fragments was selected for a first stage of docking-based VS. About 300.000 ligands were docked with rDock and the top-scoring ones were subjected to Dynamic Undocking. In a collaboration with Vernalis, a pharmaceutical company in the UK, we tested tens of compounds selected with Dynamic Undocking and we were able not only to find positive and novel hits but also to improve hit-rate with respect to standard fragment screening by almost 10 fold.
Finally, we had the opportunity to participate in the D3R Grand Challenge 2015 where we could apply all the methods from this thesis (first author on the publication in Journal of Computer-Aided Molecular Design in 2016). This challenge was designed as a blind public test where different groups around the world tried to predict the binding mode and the affinity of a set of ligands for their respective protein target. Our approach consisted in a combination of docking and Dynamic Undocking and our results were placed amongst the best for the two systems of the challenge. We also discussed how the level of available data and previous knowledge on each of the systems impacted on the final results.<br>La motivación principal de esta tesis ha sido validar, mejorar y desarrollar nuevos métodos con relación a los disponibles hoy en día en el área del desarrollo de fármacos, para en un futuro poder estudiar dianas que actualmente están fuera de nuestro alcance.
Debido a que la productividad de la industria farmacéutica está disminuyendo durante los últimos años, una mejora en los métodos disponibles sería un gran paso adelante. Esta tesis se ha centrado en diferentes métodos computacionales, como el docking o la dinámica molecular.
En la primera de las partes, trabajé en el cribado virtual (Virtual Screening) basado en docking. Concretamente, participé en la validación del programa de docking rDock mediante la comparación con dos programas muy usados hoy en día de su capacidad de predecir correctamente el modo de unión de un ligando con su proteína diana y de sus resultados en el cribado virtual de posibles fármacos.
En la segunda parte de la tesis, participé en el desarrollo de un método computacional novedoso en el diseño de fármacos que complementase y mejorase los métodos actualmente disponibles. Éste método, bautizado en inglés como “Dynamic Undocking”, consiste en una implementación específica de dinámica molecular mediante la cual somos capaces de detectar si un ligando puede ser activo o inactivo de manera rápida y eficiente. Se validó el método de manera retrospectiva y posteriormente se aplicó en otro proyecto con el objetivo de encontrar nuevos posibles fármacos para una proteína relacionada con cáncer. Gracias a una colaboración con una empresa del Reino Unido, encontramos nuevos ligandos de manera que aumentamos la tasa de éxito con relación a un método estándar en casi 10 veces.
Por último, participé en el “D3R Grand Challenge 2015”, un experimento a escala mundial donde los participantes aplicaron diferentes métodos y compararon sus resultados respecto a dos métricas distintas: la predicción del modo de unión y la capacidad de ordenar los ligandos proporcionados por la organización por su afinidad respecto a la proteína diana. En nuestro caso, aplicamos una combinación de docking y “Dynamic Undocking” con unos resultados excelentes.
2
Jaworek, Karolina. "Screening for novel brain tumour initiation mechanisms at single cell resolution." Thesis, Bangor University, 2016. https://research.bangor.ac.uk/portal/en/theses/screening-for-novel-brain-tumour-initiation-mechanisms-at-single-cell-resolution(3bb44859-bc78-4fce-a7df-0f47d2dd6b4e).html.
Full textAbstract:
Despite progress in our understanding of origin and development of brain tumours, more efficient therapeutic approaches addressing the high recurrence rate and poor prognosis of brain tumours remain urgently needed, in particular for the most aggressive glioblastomas (GBMs). In this work, I used the Drosophila brain tumour (brat) mutant as an in vivo model to identify potential mechanisms of brain tumour initiation. The human brat orthologue, Trim3, has a conserved tumour suppressor function in GBMs. I applied a single cell transcriptome microarray technique to compare intermediate neural progenitor cells harvested from live brat versus control larval brains, at a developmental stage when the first signs of molecular transformation into tumour initiation cells are observed in the mutants but no over-proliferation can yet be detected. I identified 1132 transcripts differentially expressed (threshold: -0.5Log2FC0.5). My gene ontology-based analysis revealed that metabolic pathways, RNA processing and protein synthesis are among the most represented functional categories. I validated the screen data via qPCRs, and translated gene expression findings into human GBM tissues and cell lines. I found 21 out of 24 human orthologue transcripts tested to be also differentially expressed in GBMs compared to control human brain tissues, suggesting the possibility of conserved roles. Finally, I examined in more detail selected individual transcripts. Of note, I showed that loss of two candidates found upregulated in brain tumour initiation cells and in GBMs, mob3 and l(2)k09022, causes severe impairment of normal postembryonic neural stem cell proliferation. I also demonstrated that another candidate, YME1L1, which contributes to mitochondrial proteostasis and respiration, is up regulated in tumour initiation cells and in GBMs at both mRNA and protein levels, suggesting it may promote tumour initiation by altering mitochondria function. In summary, the work I developed lays an original foundation for future studies of brain tumour initiation mechanisms.
3
Wang, An Qi. "Screening of hepatoprotective constituents from herbal medicines and investigation on the underlying mechanisms." Thesis, University of Macau, 2017. http://umaclib3.umac.mo/record=b3690819.
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4
Ibaraki, Alicia. "Mechanisms that perpetuate health disparities: physician stereotypes & bias." Thesis, University of Oregon, 2018. http://hdl.handle.net/1794/23088.
Full textAbstract:
Purpose: Although Asian Americans are the only racial group for whom cancer is the leading cause of death, colorectal cancer screening is consistently lower than that of White Americans. Physicians also recommend colorectal cancer screening to Asian Americans at nearly half the rate as White Americans. This study tests a mechanism that may underlie low recommendation rates. I based my hypothesis on a conceptual model that integrates the literature on information processing and decision making with Asian American stereotypes.
Methods: I conducted an online study of primary care physicians and measured their cancer screening referral behavior in response to clinical vignettes. I used the existing Asian Attitude Implicit Association Test (IAT) and developed a new Health Attitude IAT to measure implicit attitudes about Asian American foreignness and health advantages, respectively. Explicit attitudes about these constructs were also assessed through self-report. I used binary logistic regression models to evaluate the association of attitudes about Asian Americans foreignness and health advantage with screening recommendation.
Results: My sample included 167 physicians (23% response rate). I found strong implicit bias that Asians are foreign (Cohen’s d = 1.09) and strong implicit bias favoring a white health advantage (Cohen’s d = -0.86). There were weaker explicit biases that Asians are foreign (Cohen’s d = 0.62). Explicit beliefs about health advantage favored Asians (Cohen’s d = 0.73). Physician race, age and gender were significant moderators of bias score. .I found no evidence of a race based screening disparity and no association between implicit or explicit bias scores and making a cancer screening recommendation.
Conclusions: Foreign and health advantage biases exist among a sample of physicians, but may not influence cancer screening recommendation behavior. Physicians demonstrated both implicitly and explicitly held attitudes that Asian Americans are perpetual foreigners. Physicians also reported explicit beliefs that Asian Americans have health advantages relative to other races. Implicitly, their attitudes indicated that White Americans are a healthier group. Further research should address whether race-based cancer screening disparities persist in real world settings, both in terms of screening completion, and physician recommendation. If disparities still exist, alternate explanatory mechanisms should be identified.
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Thistlethwaite, Rebecca Janette. "Identification of genetic variation in heat stress, genotype screening for and mechanisms of tolerance in wheat." Thesis, The University of Sydney, 2017. http://hdl.handle.net/2123/17339.
Full textAbstract:
Increasing global climatic variability will most likely increase temperatures and reduce annual rainfall in many cropping regions in the coming years. Changes in seasonal conditions are likely to have a significant impact on all food crops including wheat. This thesis aims to (1) identify genetic diversity for high temperature tolerance in bread wheat by evaluating a large number of genotypes across years and sowing dates, (2) evaluate a subset of germplasm was using different screening methods for heat tolerance (in-field controlled environment chambers and glasshouses) and (3) compare different screening methods, Field experiments were conducted between 2012 and 2015 to identify superior genotypes with tolerance to high temperature from Australian and international wheat germplasm. Yield and yield components and phenological and physiological traits were assessed each season. Mean maximum temperature between heading and maturity demonstrated that for every 1 °C rise in mean maximum temperature, grain yield decreased by approximately 230kg/ha. A subset of twenty genotypes was maintained across all years and times of sowing to assess trait stability under heat stress. A significant genotype x environment interaction was observed for yield and yield components and the size of the interaction differed by trait. In-field controlled environment chambers were designed to implement a heat shock at anthesis on normally sown materials to assess the validity of late sowing as a method for heat tolerance screening. The heat shock applied at anthesis using chambers consistently reduced grain number more than TKW, largely due to negative impacts on pollen viability. A glasshouse experiment was conducted to impose a heat shock to the same subset of twenty genotypes. Plants were heated for three days at pollen formation (meiosis) and anthesis. Heat shock at meiosis had a greater impact on yield components than heat shock at anthesis. An ideotype for the warmer conditions in northwestern NSW was developed from the trait responses and relationships with productivity traits such as yield, kernel weight and screenings. Such an ideotype would be short-statured, maintain and prolong greenness at booting and anthesis, maintain and produce larger grain, extend the vegetative period and produce a 1:1 ratio of grain to biomass.
6
Niegowski, Damian. "Structural biology of integral membrane proteins from methods to molecular mechanisms /." Doctoral thesis, Stockholm : Department of Biochemistry and Biophysics, Stockholm Univeristy, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-30069.
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Tsipa, Anastasia Isavella. "Understanding the factors and mechanisms that influence colorectal cancer screening uptake among socially deprived and non-deprived populations." Thesis, University of Leeds, 2018. http://etheses.whiterose.ac.uk/22226/.
Full textAbstract:
Colorectal cancer (CRC) is the second most common cause of cancer death in the UK. Since the introduction of the NHS Bowel Cancer Screening Programme CRC incidence and mortality rates have reduced, however, screening uptake in the overall population remains suboptimal and is disproportionately low among populations with low socioeconomic status (SES) and Black and Minority Ethnic populations. This thesis aimed to critically assess the available evidence of public health interventions to improve CRC screening and to examine the possible mechanisms of socioeconomic inequalities in CRC screening uptake within a UK setting. A systematic review and meta-analysis (Study 1) of randomised controlled trials (RCTs) to increase CRC screening uptake was conducted. Data from 102 RCTs including 1.94 million participants were analysed and intervention effectiveness was examined by level of SES. Interventions significantly improved screening uptake, especially among low SES populations, and helped reduce - but not eliminate - SES disparities. Specific intervention strategies were highlighted as effective among low SES groups. Study 2 used qualitative interviews (N = 27) to explore the views of different socioeconomic and sociodemographic population subgroups and identify the barriers and facilitators to CRC screening. Results highlighted both practical and emotional factors that influenced screening decisions and revealed both similarities and differences in the views of different subgroups. Study 3 used cross-sectional, observational, survey data (N = 206) to explore key sociodemographic and psychosocial variables as potential moderators and mediators of screening intention. Results indicated that psychosocial variables mediated the effects of past behaviour on screening intention and identified some differences by educational attainment and area-level deprivation. This thesis argues the importance of considering both sociodemographic and psychosocial factors in relation to improving CRC screening uptake and reducing inequalities. Results highlighted key determinants of CRC screening participation and identified specific pathways via which sociodemographic and psychosocial variables interact to affect screening intention. This thesis provides an evidentiary basis that can be used to inform future public health initiatives and/or interventions that aim to reduce the CRC inequality gap.
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Piotrowska, Barbara. "Investigating the performance and underlying mechanisms of a novel screening measure for developmental dyslexia : implications for early identification." Thesis, Edinburgh Napier University, 2018. http://researchrepository.napier.ac.uk/Output/1253563.
Full textAbstract:
Developmental dyslexia is a common disorder affecting around 10% of the British population characterized by difficulties with reading despite adequate intelligence and education (IDA, 2007). Although most researchers and practitioners would agree that early identification is key in limiting negative consequences of reading problems, this is still difficult to achieve due to theoretical and practical inconsistencies in the field. This thesis focuses on investigating a novel, computer and tablet-based “dot-to-dot” (DtD) task that may aid the process of identification particularly in pre-reading children and English as additional language (EAL) individuals who, by definition, are more susceptible to misidentification. Performance on this task was tested in primary school children (N = 457) and in adults (N = 111) together with a set of dyslexia-sensitive, vision and reasoning tests. Performance on DtD (especially the first sector error) demonstrated significant differences between children at high and low risk of dyslexia (as assessed by Lucid Rapid), as well as between children prospectively identified as poor and typical readers. DtD measures added small but statistically significant unique contributions to the models predicting reading scores and reading level group membership, and DtD measures could distinguish between poor and typical readers as well as between adults with and without diagnosed dyslexia. The findings provide evidence for the DtD test to be a useful addition to existing tests as it presumably relates to a number of mechanisms in line with automaticity and cerebellar deficits theories of dyslexia. It also has a potential to identify a distinct type of dyslexia that is not related to phonological processing which has important theoretical and practical implications.
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Theodorou, Andria Soteri. "Screening and delineation of molecular mechanisms of action of HbF inducing agents for the treatment of β-thalassaemia". Thesis, King's College London (University of London), 2015. http://kclpure.kcl.ac.uk/portal/en/theses/screening-and-delineation-of-molecular-mechanisms-of-action-of-hbf-inducing-agents-for-the-treatment-of-thalassaemia(fbad43de-f2b2-49a1-980b-b6dfcc1a25c5).html.
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Current agents used for pharmacological reactivation of foetal haemoglobin (HbF) have limited application due to moderate therapeutic properties, variable patient response and potential cytotoxic effects. Therefore, identification of novel HbF inducing agents is still a major research goal to this day. Identification of new potential HbF inducers has been mainly based on screening of drug libraries. However, this approach has not been very successful in generating new promising agents. In the current project, I employed two approaches for identifying potential HbF inducers: 1) screening of agents that are structurally similar to compounds with known HbF inducing activity; 2) investigating molecular pathways of a known HbF inducer with the aim of identifying suitable targets for therapeutic manipulation and target-based drug design. The first approach involved screening of eleven xanthines including caffeine and nine hydroxystilbenic derivatives of resveratrol as potential HbF inducers. However, none of the agents had a potent enough HbF inducing activity in order to be considered as promising therapeutic agents. In the second approach, decitabine was chosen based on its high HbF inducing activity and moderate cytotoxicity in K562 cells and primary human erythroid cultures. Chromatin immunoprecipitation was used to characterise epigenetic changes in the β-globin gene locus, and quantitative real-time PCR for investigation of changes in gene expression levels of ten erythroid-related genes, in the presence of the agent. A quantitative iTRAQ proteomic approach coupled with mass spectrometry was used for identification of changes in the proteome of decitabine-treated and un-treated primary human erythroid cultures. The findings suggest that decitabine induces HbF production through activation of signal transduction pathways rather than through hypomethylation of gene promoters. One such possible pathway is the NF-κB pathway. Among the differentially expressed proteins, twenty-seven proteins were associated with the action of decitabine. Two of those proteins, ARHGAP4 and EGLN2, were previously implicated in hydroxyurea-mediated induction of γ-globin gene expression and hypoxia-mediated erythropoiesis, respectively. In addition, the de-ubiquitinating enzyme USP11 was substantially modulated in the presence of decitabine. The exact role of these proteins in γ-globin expression remains to be established.
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White, Rose. "Cyclin dependent kinase like 5 (CDKL5) mutation screening in Rett Syndrome and related clinical disorders." Thesis, The University of Sydney, 2007. https://hdl.handle.net/2123/28108.
Full textAbstract:
Rett Syndrome (RTT) is a severe neurodevelopmental disorder affecting
almost exclusively females, with an incidence of 1 in 8,000 by 15 yrs of age.
The disorder encompasses a wide spectrum of clinical phenotypes. Up to
95% of classical RTT and a lesser proportion (20%-60%) of those with
atypical forms of RTT patients carry mutations in the X-linked MECP2 gene
(Methyl-CpG binding protein 2), the first gene discovered to be associated
with this disorder. Mutations in the X-Iinked CDKL5 gene (cyclin-dependent
kinase-like 5) have also been found to cause atypical RTT (in particular, the
early onset seizure variant), autism, X-Iinked infantile spasm syndrome
(ISSX), intellectual disability and other severe neurological disorders.
This study investigates the speculation that CDKL5 deficiency may underlie
a significant proportion of RTT cases that were not linked to MECP2
mutations. It is also investigates the possibility that CDKL5 mutations may
lead to other non-RTT syndrome neurological disorders.
The clinical cohort consisted of MECP2 mutation-negative RTT patients
(91), males with X-Iinked mental retardation (8), patients with ISSX (52),
patients with autism (59) and other patients with intellectual disability with or
without seizures (39). The 21 coding exons of CDKL5 were screened by
Denaturing High Performance Liquid Chromatography and direct
sequencing.
In all, six polymorphic variations and one probably pathogenic mutation
were identified, accounting for 46 of the 249 patients in this cohort (17%).
Each individual identified with a variation had the clinical feature of seizures.
Based on other studies, it appears that the key feature that points to a
CDKL5 mutation will be the presence of severe early onset seizures,
particularly infantile spasms. The results of mutation screening in this cohort
lead us to conclude that pathogenic CDKL5 mutations are unlikely to be
identified in neurological disorders unless a RTT-like phenotype with severe
early-onset seizures are present.
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Meier, Dieter [Verfasser], Rainer [Akademischer Betreuer] Kalscheuer, and Peter [Gutachter] Proksch. "Screening for novel antimicrobial agents and elucidation of the corresponding mechanisms / Dieter Meier ; Gutachter: Peter Proksch ; Betreuer: Rainer Kalscheuer." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2020. http://d-nb.info/1216330239/34.
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Lévy, Hugo. "Towards well-posed and versatile numerical solutions of scalar-tensor theories of gravity with screening mechanisms : applications at sub-Solar system scales." Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASP119.
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Les théories tenseur-scalaires de la gravité font partie des alternatives à la Relativité Générale les plus convaincantes, résilientes, et riches en termes de phénoménologie. Les modèles encore viables aujourd'hui reposent sur des mécanismes d'écrantage afin d'être compatibles avec les tests locaux de la gravité, tout en conservant une certaine pertinence physique. La recherche de ces champs scalaires hypothétiques dépend alors de notre capacité à concevoir des expériences adaptées à leur phénoménologie. Hélas, cette tâche est grandement entravée par la difficulté de modéliser suffisamment précisément les effets de cinquième force dans des configurations réalistes. En effet, cela nécessite de résoudre des équations aux dérivées partielles semi-linéaires en présence de distributions de masse non-triviales, ce pour quoi les méthodes purement analytiques ne sont que d'un usage limité. Dans cette perspective, le présent travail de thèse traite ce problème via le développement d'un outil numérique polyvalent visant à obtenir des solutions bien posées aux équations de Klein-Gordon non-linéaires qui apparaissent dans de tels modèles de gravité modifiée. L'outil en question, nommé femtoscope, s'appuie sur la méthode des éléments finis. Celle-ci permet de représenter des géométries arbitrairement complexes et des problèmes multi-échelles par le biais de raffinement locaux du maillage. Les non-linéarités sont quant à elles traitées par la méthode de Newton. La nouveauté majeure apportée par femtoscope est sa gestion des conditions aux limites asymptotiques — i.e. lorsque le comportement du champ n'est connu qu'infiniment loin des sources — dont la prise en compte de manière appropriée est souvent essentielle en vue d'obtenir des solutions numériques pourvues de sens physique. Pour ce faire, nous utilisons la méthode des éléments finis inversés. Nous nous appuyons ensuite sur femtoscope pour étudier la gravité tenseur-scalaire aux échelles sub-système Solaire. En utilisant un modèle réaliste de la Terre, nous traitons la question relative à la détectabilité d'une cinquième force de type caméléon, au moyen de missions de géodésie spatiale telles que GRACE-FO. L'influence de l'atmosphère terrestre ainsi que la rétroaction d'un satellite sur le champ scalaire sont toutes deux prises en compte. Nous constatons que la cinquième force a un effet supposément mesurable sur la dynamique orbitale d'un point matériel, mais que la connaissance imparfaite de la distribution de masse à l'intérieur de la Terre donne lieu à des dégénérescences qui réduisent considérablement le pouvoir contraignant de ce type de mission. Ces dégénérescences peuvent en principe être levées en réalisant l'expérience à deux altitudes différentes. Enfin, nous ouvrons de nouvelles perspectives en explorant la possibilité de tester les théories tenseur-scalaires avec écrantage en se servant d'horloges atomiques. L'idée des expériences que nous décrivons est d'exploiter la contribution du champ scalaire sur le décalage vers le rouge gravitationnel, cette dernière étant absente en Relativité Générale. On souligne le fait que de telles expériences sont de nature profondément différente des recherches de cinquième force<br>Scalar-tensor theories of gravity are among the most compelling, resilient and phenomenologically-rich alternatives to General Relativity. Viable models make use of screening mechanisms in order to be consistent with local tests of gravity whilst still retaining physical relevance. The hunt for such hypothetical scalar fields therefore hinges on the design of sophisticated model-dependent experiments. Alas, this task is greatly hampered by the difficulty of accurately modeling fifth force effects in realistic setups. Indeed, the latter requires solving semi-linear partial differential equations in the presence of complex matter distributions, for which analytical approaches are clearly insufficient. In this perspective, the present PhD work tackles this issue by developing a versatile numerical tool devoted to obtaining well-posed solutions to the nonlinear Klein-Gordon equations arising in such modified gravity models. The tool, called femtoscope, builds on the finite element method which allows one to deal with arbitrarily complex geometries and multi-scale problems through local mesh refinement. Nonlinearities, on the other hand, are handled via Newton's method. The novelty and most important feature of femtoscope is its careful treatment of asymptotic boundary conditions — i.e. when the field's behavior is only known infinitely far away from the sources — which is often essential to obtain physically meaningful numerical solutions. This is achieved by employing the inverted finite element method. We then make use of femtoscope to investigate screened scalar-tensor gravity at sub-Solar system scales. Using a realistic model of the Earth, we address the question of the detectability of a putative chameleon fifth force in orbit by means of GRACE-FO-like space geodesy missions. The influence of the atmosphere as well as the backreaction of spacecraft on the scalar field are both considered. We find that, although the fifth force has a supposedly measurable effect on the dynamics of a point-like spacecraft, the imperfect knowledge of the mass distribution inside the Earth gives rise to degeneracies, which in turn severely limit the constraining power of such space missions. These degeneracies can in principle be lifted by performing the experiment at two different altitudes. Finally, we open up new perspectives by exploring the possibility of testing screened scalar-tensor theories with atomic clocks, exploiting the distinctive imprint of the scalar field on the gravitational redshift with respect to General Relativity. It is emphasized that such experiments are profoundly different in nature from fifth force searches
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Veeranki, Sreenivas P., and Shimin Zheng. "Trends and Determinants of Up-to-date Status with Colorectal Cancer Screening in Tennessee, 2002-2008." Digital Commons @ East Tennessee State University, 2014. https://dc.etsu.edu/etsu-works/49.
Full textAbstract:
BACKGROUND:
Screening rates for colorectal cancer (CRC) are increasing nationwide including Tennessee (TN); however, their up-to-date status is unknown. The objective of this study is to determine the trends and characteristics of TN adults who are up-to-date status with CRC screening during 2002-2008.
METHODS:
We examined data from the TN Behavioral Risk Factor Surveillance System for 2002, 2004, 2006 and 2008 to estimate the proportion of respondents aged 50 years and above who were up-to-date status with CRC screening, defined as an annual home fecal occult blood test and/or sigmoidoscopy or colonoscopy in the past 5 years. We identified trends in up-to-status in all eligible respondents. Using multivariable logistic regression models, we delineated key characteristics of respondents who were up-to-date status.
RESULTS:
During 2002-2008, the proportion of respondents with up-to-date status for CRC screening increased from 49% in 2002- 55% in 2006 and then decreased to 46% in 2008. The screening rates were higher among adults aged 65-74 years, those with some college education, those with annual household income ≥$35,000 and those with health-care access. In 2008, the respondents who were not up-to-date status with CRC screening included those with no health-care coverage (adjusted odds ratio [OR] 0.46, 95% confidence interval [CI] 0.33-0.63), those aged 50-54 years (OR 0.62, 95% CI 0.46-0.82) and those with annual household income
CONCLUSIONS:
TN adults who are up-to-date status with CRC screening are increasing, but not across all socio-demographic subgroups. The results identified specific subgroups to be targeted by screening programs, along with continued efforts to educate public and providers about the importance of CRC screening.
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L'hôte, Valentin. "Senolytic drug discovery and mechanisms of action in BRAF-V600E oncogene-induced senescence." Thesis, université Paris-Saclay, 2022. http://www.theses.fr/2022UPASL042.
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En réponse à l'expression d'oncogène (tel que BRAF-V600E), à des traitements génotoxiques ou à d'autres stress, les cellules eucaryotes peuvent éviter l'apoptose et déclencher la sénescence. La sénescence est un destin cellulaire caractérisé par un arrêt prolifératif quasi-irréversible et une reprogrammation transcriptionnelle profonde, conduisant notamment à une sécrétion importante de facteurs inflammatoires collectivement appelés phénotype sécrétoire associé à la sénescence (SASP). En raison de l'augmentation de la demande sécrétoire et de stress chroniques, la protéostase peut être perturbée en sénescence. Comme elle limite la prolifération de cellules susceptibles de présenter un potentiel pré-néoplastique, la sénescence est un processus essentiel de suppression tumorale ; cependant, l'accumulation de cellules sénescentes au cours du vieillissement, dans des contextes pathologiques, ou après chimiothérapie ou radiothérapie, est préjudiciable et entraîne un dysfonctionnement tissulaire. Les sénolytiques sont des composés qui induisent sélectivement l'apoptose dans les cellules sénescentes tout en épargnant les cellules normales, et leur application thérapeutique s'est avérée une stratégie pharmacologique efficace dans différents contextes pathologiques où la sénescence joue un rôle moteur. Le but de ce projet était d'identifier de nouveaux composés sénolytiques, notamment dans la sénescence induite par BRAF-V600E, et de caractériser leurs mécanismes d'action, ajoutant ainsi à la compréhension de la régulation des voies de survie cellulaire en sénescence. Les cardioglycosides constituent une classe de composés qui ont été identifiés comme de puissants sénolytiques dans le criblage d'une chimiothèque de repositionnement. Nous avons montré que les cellules sénescentes BRAF-V600E étaient remarquablement sensibles à la sénolyse induite par les cardioglycosides. Nous avons démontré que les cellules sénescentes BRAF-V600E ont un flux autophagique accru, essentiel à leur survie, et que les cardioglycosides agissent comme sénolytiques en inhibant l'autophagie via la transduction du signal par la Na,K-ATPase. En conséquence, le blocage de l'autophagie par d'autres voies, comme avec la chloroquine, était également sénolytique. Pour mieux comprendre la régulation de l'autophagie et de la protéostase en sénescence et identifier de nouvelles cibles sénolytiques, nous avons ensuite évalué le stress du réticulum endoplasmique et la réponse aux protéines mal repliées (UPR) dans différents modèles de sénescence. En parallèle, nous avons criblé diverses chimiothèques, dans lesquelles nous avons identifié des sénolytiques potentiels ciblant différentes facettes de la protéostase. Notamment, nous avons découvert que le senseur de l'UPR Ire1 était régulé à la hausse en sénescence induite par l'expression d'oncogènes. Ire1 régule le destin cellulaire par plusieurs voies, et de nombreux composés qui modulent de manière différentielle son activité sont disponibles. Nous avons donc utilisé un panel de modulateurs d'Ire1 pour commencer à caractériser son rôle en sénescence, et établir de nouvelles stratégies sénolytiques. En résumé, nos résultats soulignent le potentiel sénolytique du ciblage de l'autophagie et de la protéostase dans la sénescence induite par l'expression d'oncogènes, et l'importance de caractériser en détails les mécanismes d'action des sénolytiques pour identifier de nouvelles cibles et voies de régulation<br>In response to oncogene expression (such as BRAF-V600E), genotoxic insults, or other stresses, eukaryotic cells can suppress apoptosis and enter senescence. Senescence is a cell fate characterized by a quasi-irreversible proliferative arrest and deep transcriptional reprogramming, notably leading to an important secretion of inflammatory factors collectively termed the senescence-associated secretory phenotype (SASP). Due to increased secretory demands and chronic stress, proteostasis may be challenged in senescence. As it limits the proliferation of cells possibly bearing pre-neoplastic potential, senescence is an essential tumor suppressing process; however, the accumulation of senescent cells during aging, in pathological contexts, or following chemotherapy or radiotherapy, is detrimental and leads to tissue dysfunction. Senolytics are drugs that selectively induce apoptosis in senescent cells while sparing normal cells, and their therapeutical application has proved a valuable pharmacological strategy in pathological contexts in which senescence plays a driving role. The aim of this project was to identify novel senolytic compounds, notably in BRAF-V600E-induced senescence, and to characterize their mechanisms of action, thereby adding to the understanding of cell survival pathways regulation in senescence. Cardioglycosides constitute a class of drugs that were identified as potent senolytics in the screen of a repurposing library. We showed that BRAF-V600E senescent cells were remarkably sensitive to senolysis induced by cardioglycosides. We demonstrated that BRAF-V600E senescent cells have a heightened autophagy flux that is essential to their survival, and that cardioglycosides acted as senolytics by inhibiting autophagy through Na,K-ATPase signal transduction. Accordingly, blocking autophagy through other routes such as with chloroquine was also senolytic. To gain insight into the regulation of autophagy and proteostasis in senescence and identify new senolytic targets, we then assessed endoplasmic reticulum stress and the unfolded protein response (UPR) in different senescence models. In parallel, we screened various chemical libraries, in which we identified potential senolytics targeting different facets of proteostasis. Interestingly, we found that UPR sensor Ire1 was upregulated in oncogene-induced senescence. Ire1 regulates cell fate through several pathways, and many small compounds that differentially modulate its activity are available. We thus employed a panel of Ire1 modulators to begin characterizing its role in senescence, and establish novel senolytic strategies. Collectively, our results highlight the senolytic potential of targeting autophagy and proteostasis in oncogene-induced senescence, and the importance of deciphering the mechanisms of action of senolytics to identify new targets and regulatory pathways
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AMADORI, LETIZIA. "IDENTIFICATION OF MOLECULAR MECHANISMS RESPONSIBLE FOR DEGRADATION OF THE TUMOR SUPPRESSOR PROTEIN NUMB IN CANCER." Doctoral thesis, Università degli Studi di Milano, 2014. http://hdl.handle.net/2434/234136.
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ABSTRACT
NUMB was initially described as a cell fate determinant involved in neurogenesis. More recently, NUMB has been implicated in different types of human cancers, in which it has a tumor suppressor role. In particular, data from our laboratory revealed that loss of NUMB protein occurred in approximately 50% of breast cancers and 30% of non-small cell lung cancers, and leads to increased oncogenic NOTCH activity and decreased p53 tumor suppressor function.
Mechanistically, loss of NUMB in human breast cancers is due to its deregulated ubiquitination and ensuing proteasomal degradation, as witnessed by the restoration of physiological NUMB levels in NUMB-deficient primary breast tumor cells upon proteasome inhibition with MG-132. Therefore, the molecular mechanism underlying NUMB degradation in cancer most likely involves deregulation of components of the cellular machinery normally regulating the ubiquitination/phosphorylation status of the NUMB protein, such as E3-ubiquitin ligases/kinases.
In this thesis, we devised a high-throughput phenotypic screening to identify the molecular determinants responsible for NUMB loss among E3 ligase family. The screening assay measures restoration of NUMB expression upon siRNA-mediated silencing of candidate enzymes, in a NUMB-deficient model-system. We identified the breast cancer epithelial cell line MDA-MB-361, as a suitable cell model system for the screening assay as it recapitulates the phenotype of NUMB-deficient primary tumor cells. Indeed, NUMB protein levels in these cells are restored to physiological levels by MG-132 treatment. For the high-throughput phenotypic assay, we developed and optimized for a miniaturized format, a NUMB capture ELISA assay.
Using the high-throughput screening platform, we assessed the involvement of over 600 E3 ligases in NUMB downregulation, and identified 21 candidate E3 ligases. We then went through the validation of these 21 candidate hits, which is the topic of this thesis. Upon validation of the top six candidates of E3 ligases list, we confirmed that the E3 ligase, RBX1 (RING-Box 1), mediates the downregulation of NUMB in both MDA-MB-361 cells and human primary NUMB-deficient breast and lung tumor cells. Indeed, we demonstrated that silencing RBX1 in these cells restores NUMB protein levels, while no effect was observed in NUMB-proficient cell lines or primary tumor cells. Moreover, we also established a physical interaction between NUMB and RBX1 in MDA-MB-361 cells indicating that RBX1 directly mediates NUMB degradation.
RBX1 belongs to the tetrameric E3 ligase complex, Skp1/Cullin1/F-box (SCF), in which the specificity for substrates is mediated by the F-box protein. Intriguingly, among the 21 candidates from the high-throughput screening, we identified the F-box protein, FBXW8 (F-box and WD repeat domain containing 8), which has been described to form a complex with RBX1. We, therefore, assessed the role of FBXW8 in NUMB donwregulation in high-resolution studies in MDA-MB-361 cells and confirmed its involvement. We are currently validating FBXW8 also in primary tumors cells from human breast and lung cancers.
In conclusion, our data indicate that an SCF E3 ligase complex involving RBX1 and FBXW8, likely mediates NUMB hyperdegradation in human cancers. This result has potential translational ramifications as RBX1 and FBXW8 could represent novel molecular targets for therapeutic intervention in NUMB-deficient cancers.
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Jayol, Aurélie. "Résistance à la colistine chez les bacilles Gram négatif." Thesis, Bordeaux, 2018. http://www.theses.fr/2018BORD0179/document.
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Les entérobactéries productrices de carbapénèmases peuvent être responsables d’impasses thérapeutiques puisque ces souches sont multirésistantes aux antibiotiques. La colistine, un antibiotique de la famille des polymyxines, fait partie des molécules de derniers recours potentiellement utilisables pour le traitement des patients infectés par ces souches. Son utilisation est ainsi en augmentation constante mais des résistances émergent.Ce travail a contribué à l’amélioration du diagnostic de la résistance à la colistine par le développement de deux nouveaux outils diagnostiques : un test rapide, le Rapid Polymyxin NP test et un milieu de culture sélectif, la gélose SuperPolymyxin. Il a permis d’identifier de nouvelles mutations chromosomiques au sein des gènes pmrA, pmrB, phoP, phoQ, mgrB et crrB responsables de l’acquisition de résistances et d’hétérorésistance à la colistine chez K. pneumoniae et K. oxytoca. Il a révélé que les mutations chromosomiques et les résistances plasmidiques étaient additionnelles et pouvaient entraîner l’acquisition d’un haut niveau de résistance à la colistine chez E. coli. Il a permis d’identifier une épidémie de souches de K. pneumoniae productrices de la carbapénèmase OXA-48 et résistantes à la colistine en France en 2014. Il a démontré que Hafnia était un genre d’entérobactéries présentant une résistance naturelle de bas niveau à la colistine. Enfin, il a permis de proposer une option thérapeutique, le ceftazidime/avibactam en association ou non avec l’aztréonam, pour traiter les patients infectés par les souches de K. pneumoniae productrices de carbapénèmases et résistantes à la colistine.Ce travail a ainsi contribué à améliorer les connaissances sur la résistance à la colistine chez les BGN au niveau du diagnostic, des mécanismes de résistance acquis, des résistances naturelles, et de l’épidémiologie et a permis de proposer des combinaisons d’antibiotiques actives in vitro sur les souches de K. pneumoniae productrices de carbapénèmases et résistantes à la colistine<br>Carbapenemase-producing Enterobacteriaceae may be responsible for therapeutic impasses since these strains are multidrug-resistant. Colistin, an antibiotic of the polymyxin family, is one of the last-resort molecules potentially usable for the treatment of patients infected with these strains. Its use is thus constantly increasing but resistances emerge.This work contributed to improve the diagnosis of colistin resistance by developing two new diagnostic tools: a rapid test, the Rapid Polymyxin NP test and a selective culture medium, the SuperPolymyxin agar. It identified new chromosomal mutations within the pmrA, pmrB, phoP, phoQ, mgrB and crrB genes responsible for the acquisition of colistin resistance and heteroresistance in K. pneumoniae and K. oxytoca. It revealed that chromosomal mutations and plasmid resistance were additional and could lead to the acquisition of a high level of colistin resistance in E. coli. It identified an outbreak caused by colistin-resistant OXA-48-producing K. pneumoniae strains in France in 2014. It demonstrated that Hafnia was a genus of enterobacteria with low-level intrinsic resistance to colistin. Finally, it suggested a therapeutic option, the ceftazidime / avibactam in combination or not with aztreonam, to treat patients infected with colistin-resistant and carbapenemase-producing K. pneumoniae.This work has significantly contributed to improve the knowledge of colistin resistance in Gram negatives in diagnostic, in characterization of acquired or intrinsic resistance mechanisms, and in epidemiology
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Kramm, Anneke. "Identification and characterisation of epigenetic mechanisms in osteoblast differentiation of human mesenchymal stem cells." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:b6f7a356-b20f-4988-8770-8bebc233bf4b.
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A major therapeutic challenge in musculoskeletal regenerative medicine is how to effectively replenish bone tissue lost due to pathological conditions such as fracture, osteoporosis, or rheumatoid arthritis. Mesenchymal stem cells are currently investigated for applications in bone-tissue engineering and human bone marrow-derived mesenchymal stem cells (hMSCs) could be a promising source for generation of tissue-engineered bone. However, the therapeutic potential of MSCs has not been fully exploited due to a lack of knowledge regarding the identity, nature, and differentiation of hMSCs. Epigenetic mechanisms regulating the chromatin structure as well as specific gene transcription are crucial in determination of stem cell differentiation. With the aim to systematically identify epigenetic factors that modulate MSC differentiation, the work in this thesis encompasses an approach to identify epigenetic mechanisms underlying, initiating, and promoting osteoblast differentiation, and the investigation of individual epigenetic modulators. Various osteogenic inducers were validated for differentiation of MSCs and an assay allowing assessment of differentiation outcome was developed. This assay was subsequently employed in knockdown experiments with lentiviral short hairpin RNAs and inhibitor screens with small molecules targeting putative druggable epigenetic modulator classes. This approach identified around 100 epigenetic modulator candidates involved in osteoblast differentiation, of these candidates approximately 2/3 downregulated and 1/3 upregulated alkaline phosphatase (ALP) activity. Serving as a proof-of-concept, orthogonal validation experiments employing locked nucleic acid (LNA) knockdown were performed to validate a subset of candidates. Two identified target genes were selected for further investigation. Bromodomain-containing protein 4 (BRD4) was identified as one component of epigenetic regulation; its inhibition led to a decrease in ALP expression, downregulation of key osteoblast transcription factors Runx2 and Osterix, as well as impaired bone matrix formation. Knockdown of lysine (K)-specific demethylase 1A (KDM1A/LSD1) upregulated ALP activity and treatment with a small molecule inhibitor targeting KDM1A led to an increase in ALP, RUNX2, and bone sialoprotein expression. Intriguingly, in a transgenic mouse model overexpressing Kdm1a a decrease in bone volume and bone mineral density was observed, thus supporting the hypothesis that KDM1A is a central regulator of osteoblast differentiation.
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Sleigh, James Nicholas. "Model systems for exploring new therapeutic interventions and disease mechanisms in spinal muscular atrophies (SMAs)." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:378416c5-a586-4a2a-980c-81dfff6803df.
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Spinal muscular atrophy (SMA) and Charcot-Marie-Tooth disease type 2D (CMT2D)/distal SMA type V (dSMAV) are two incurable neuromuscular disorders that predominantly manifest during childhood and adolescence. Both conditions are caused by mutations in widely and constitutively expressed genes that encode proteins with essential housekeeping functions, yet display specific lower motor neuron pathology. SMA results from recessive inactivating mutations in the survival motor neuron 1 (SMN1) gene, while CMT2D/dSMAV manifests due to dominant point mutations in the glycyl-tRNA synthetase (GlyRS) gene, GARS. Using a number of different model systems, ranging from Caenorhabditis elegans to the mouse, this thesis aimed to identify potential novel therapeutic compounds for SMA, and to increase our understanding of the mechanisms underlying both diseases. I characterised a novel C. elegans allele, which possesses a point mutation in the worm SMN1 orthologue, smn-1, and showed its potential for large-scale screening by highlighting 4-aminopyridine in a screen for compounds able to improve the mutant motility defect. Previously, the gene encoding three isoforms of chondrolectin (Chodl) was shown to be alternatively spliced in the spinal cord of SMA mice before disease onset. I performed functional analyses of the three isoforms in neuronal cells with experimentally reduced Smn levels, and determined that the dysregulation of Chodl likely reflects a combination of compensatory mechanism and contributor to pathology, rather than mis-splicing. Finally, working with two Gars mutant mice and a new Drosophila model, I have implicated semaphorin-plexin pathways and axonal guidance in the GlyRS toxic gain-of-function disease mechanism of CMT2D/dSMAV.
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Lundkvist, Jonas. "The role of economic evaluations in health care decision making /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-423-6/.
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Sardari, Lodriche Soroush. "Natural antifungals, screening, isolation, synthesis, and mechanism of action." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape17/PQDD_0006/NQ29103.pdf.
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Ishii, Takafumi. "Novel antitumor microbial metabolites obtained through the mechanism-oriented screening." Kyoto University, 2000. http://hdl.handle.net/2433/151634.
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Soroush, Fariborz. "A Novel Microfluidic System for Screening Anti-inflammatory Therapeutics." Diss., Temple University Libraries, 2018. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/500666.
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Mechanical Engineering<br>Ph.D.<br>Inflammation is a crucial physiological protective response of body to infection or injury. However, in pathological conditions such as sepsis or radiation damage, the body may exhibit a strong inflammatory response and cause organ damage. Loss of barrier function and leukocyte dysfunction plays an important role during inflammation (e.g. sepsis, radiation exposure, etc.) and induces tissue injury through release of proteases and oxygen radicals. Currently, pharmacological therapies for inflammatory conditions are supportive and there is an urgent need for specific treatments to effectively target key points in neutrophil-endothelial interaction. Our research team has developed a novel microfluidic system to study the mechanisms by which Protein Kinase C isotype delta (PKCδ) impacts neutrophil-endothelial interactions and its inhibition can protect vascular endothelial integrity and attenuate sepsis-induced tissue damage. This novel system will allow for rational design of next generation therapeutics for treating inflammation. We will utilize our novel biomimetic microfluidic assay (bMFA) to systematically delineate the mechanism by which PKCδ regulates individual steps in neutrophil recruitment to the inflamed/activated endothelium. In Specific Aim 1, we will investigate the impact of PKCδ inhibition on neutrophil interaction with endothelial cells as well as adhesion molecules expression. In Specific Aim 2, we will test the specificity of the PKCδ inhibitor in microcirculation and among different species. In Specific Aim 3, we will investigate the role of PKCδ in crosstalk between neutrophils and endothelial cells and endothelium integrity after high dose X-ray irradiation. Our findings indicate that PKCδ inhibition significantly reduces neutrophil interactions with the endothelium during acute inflammation. Our novel biomimetic microfluidic assay (bMFA) provides a rapid screening system for testing the specific response of novel therapeutics. Moreover, results indicate that in many cases the response of murine cells to inflammatory signals may be a poor predictor of response in human cells. Furthermore, our discoveries indicate a key role for PKCδ regulation of radiation-induced changes in endothelial cell barrier structure and function, expression of several key cell adhesion molecules, neutrophil-endothelial cell interaction and leukocyte migration through the endothelium. Our findings indicate that PKCδ-TAT peptide inhibitor may offer an important approach for treating inflammatory disease and we propose that PKCδ inhibition may serve as a novel medical countermeasure for treating radiation-induced vascular damage. Findings from this study will not only elucidate the mechanisms of action for this novel therapeutic but also provide a roadmap for the rational design of future therapeutics for acute inflammatory diseases. The long-term goal of this work is to establish microfluidic devices as a novel prescreening tool for screening therapeutics to allow for fast and precise prediction of response in human. This allows for efficient design of therapeutics using human cells and tissues, designing proper drug carrier, and planning possible future clinical studies.<br>Temple University--Theses
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Hearn, Jessica M. "Integrating cell screening and mechanism of action data for organometallic anticancer agents." Thesis, University of Warwick, 2015. http://wrap.warwick.ac.uk/68071/.
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Both acquired and intrinsic drug resistance are established clinical problems in many areas of medicine. This is particularly evident with the growing resistance to platinum chemotherapy agents in cancer treatment programmes. New, alternative treatments for platinum-resistance patients are needed, with comparable potency, no platinum cross- resistance, better safety profiles and which target non-repairable areas of the cell, reducing acquired resistance. This thesis focuses on osmium- and iridium-based organometallic anticancer agents to fill this clinical need. Previous work has validated their potency, safety and activity in platinum-resistant cancers, however, their mechanism of action (MOA) was yet to be identified. Knowing the MOA of new compounds is essential for personalising and stratifying cancer treatment, allowing for better patient selection and prediction of treatment outcomes. Often identifying the biological target of a new therapeutic is not essential. Instead, quantifying the cellular response to that treatment, and identifying cell types which hold beneficial biological properties to optimise compound effects, is more effective. This thesis has applied the principles of systems biology to study the whole cell effect of osmium and iridium compounds in epithelial ovarian cancer. Cells were studied at the transcriptional, translational and structural level to investigate compound response, integrating a selection of these findings using novel statistical modelling. Results propose that these compounds induce oxidative stress in cancer cells, and subsequently damage DNA to exert antiproliferative effects at submicromolar concentrations. This is the first example of studying organometallic compounds using this combination of techniques, and is a promising work flow for future efforts in this area.
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Rickardson, Linda. "New Methods to Screen for Cancer Drugs and to Evaluate their Mechanism of Action." Doctoral thesis, Uppsala University, Clinical Pharmacology, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8440.
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<p>Cancer is a common disease and due to problems with resistance against cancer drugs and the limited benefit from chemotherapy in many diagnoses, there is a need to develop new cancer drugs. In this thesis new methods to screen for cancer drugs and to evaluate their mechanism of action are discussed. </p><p>In Paper I, it was found that by studying the gene expression of a cell line panel and combining the data with sensitivity data of a number of cytotoxic drugs, it was possible to cluster compounds according to mechanism of action as well as identifying genes associated with chemosensitivity.</p><p>In Paper II, studies of compounds with selective activity in drug-resistant cell lines revealed the glucocorticoids as a group of interesting compounds. The glucocorticoid receptor was overexpressed in 8226/Dox40 and the difference in sensitivity was abolished when the cells were treated with a glucocorticoid receptor antagonist.</p><p>In Paper III, an image-based screening method for new proteasome inhibitors was successfully developed and the compounds disulfiram, PDTC and NSC 95397 were identified as inhibitors of the proteasome.</p><p>In Paper IV, disulfiram and PDTC were shown to induce cytotoxic activity, to inhibit the activation of the transcription factor NFkappaB and to inhibit the degradation of proteins normally degraded by the proteasome.</p><p>In Paper V, NSC 95397 was shown to be cytotoxic to all cells in the resistance-based cell line panel as well as to patient samples from a variety of cancer diagnoses. Connectivity Map was successfully used as a tool to propose a new mechanism of action of NSC 95397. The gene expression induced by NSC 95397-treatment was similar to that induced by several proteasome inhibitors not present in the Connectivity Map.</p>
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Khihon, Rokhas Maria. "Development of an assay for screening drug candidates for mechanism-based inhibition of human CYP3A4." Thesis, Södertörn University College, School of Life Sciences, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:sh:diva-1770.
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<p>Cytochrome P450 (CYP) constitutes a superfamily of heme- containing enzymes that catalyze the oxidative biotransformation of structurally diverse xenobiotics including pharmaceuticals and drugs. Cytochrome P450 3A4 is not only the most abundant isoform in human liver but is also responsible for metabolizing approximately 60% of therapeutic drugs. This feature makes CYP3A4 highly susceptible to both reversible and irreversible, such as mechanism-based, inhibition. Mechanism-based inhibition is characterized by being time dependent as well as NADPH and concentration dependent, when some drugs are converted by CYPs to reactive metabolites. The inactivation of CYP3A4 can be due to chemical modification of the heme, the protein, or both by covalent binding of modified heme to the protein. Compared to reversible inhibition, mechanism-based inhibition of CYP3A4 more frequently causes unfavourable drug- drug interactions (DDI), as the inactivated CYP3A4 has to be replaced by newly synthesized CYP3A4 protein. DDI can lead to higher exposure of co-administered drugs, sometimes leading to toxicity. For these reasons, drug metabolism groups within pharmaceutical companies need a well established screening assay to assess mechanism-based inactivation of major human P450 enzymes by new chemical substances that are being developed by the company. Historically, adverse drug interactions were found in clinical trials or after the drugs were commercially released. That caused pharmaceutical companies large economical losses, since a large portion of development cost was in vain.Medivir AB is a small pharmaceutical company that would like to set up a screening method to be used to test candidate drugs for CYP3A4 mechanism-based inhibition. The central aim of this master degree project was to set up a screening assay to test irreversible inhibition of CYP3A4 and validate it with known inhibitors. Using the validated assay, a number of in-house project compounds will be measured for inhibition potential and the results analyzed for structure-activity correlations. Relationships between some functional groups and mechanism-based inhibition can provide insight for improvement of drug candidates and inhibition liability. The assay was based on microsomes containing recombinant human CYP3A4 and activity measured by conversion of the substrate dibenzylfluorescein into a fluorescent product. The product was quantified by measurement of fluorescence in a 96-well plate reader. Optimization was achieved by determining the reaction linearity with time and enzyme concentration. When possible the Km for the probe substrate was also determined. The effect of different backgrounds was studied to settle on a compensation for the enzyme activity. The effect of DMSO on CYP3A4 mediated metabolism of the substrate was studied to determine the acceptable solvent concentration. The concentration responsible for 50% inhibition (IC50) was also determined for several known inhibitors and compared with literature data.</p><br>The master thesis was performed at Medivir AB, a small pharmaceutical company in Stockholm.
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Méar, Loren. "Recherche de biomarqueurs de l’endométriose par des approches de protéomique et de génomique intégrative Endometriosis screening in patients attending an IVF clinic: a proof-of-concept retrospective cohort study. Polymorphisms and endometriosis: a systematic review and meta-analyses The eutopic endometrium proteome in endometriosis reveals candidate markers and molecular mechanisms of physiopathology Biomarqueurs de l’endométriose : où en sommes-nous ?" Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLV099.
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L'endométriose est une pathologie gynécologique oestrogèno-dépendante et inflammatoire caractérisée par le développement d’endomètre fonctionnel hors de la cavité utérine. Cette maladie est fréquente puisqu’il est estimé que 10% des femmes en activité génitale en seraient atteintes.Bien qu’il existe des formes asymptomatiques de l’endométriose, cette pathologie peut également entrainer des symptômes douloureux ainsi qu’une infertilité ; impactant fortement la qualité de vie des femmes atteintes d’endométriose.À ce jour, l’absence de test de dépistage non invasif fiable explique en partie que plusieurs années sont nécessaires pour diagnostiquer une endométriose. L’identification de potentiels biomarqueurs de l’endométriose représente donc un enjeu majeur pour améliorer la prise en charge.L’objectif de cette thèse est d’identifier de potentiels biomarqueurs de l’endométriose en utilisant différentes approches, parmi lesquelles la protéomique et la génomique intégrative. Les technologies « Omiques » ayant démontré leur pertinence pour la recherche et la caractérisation de marqueurs biologiques en santé humaine.Ainsi, quatre axes de recherche distincts ont été menés au cours de ce projet. Le premier correspond à une étude preuve de concept pour un test biologique afin d’identifier les femmes à risques parmi les patientes en protocole de fécondation in vitro (FIV). Le second, basé sur des méta-analyses, a permis l’identification de marqueurs génétiques (polymorphismes) prédisposant potentiellement à l’endométriose. Pour les deux derniers, nous avons essayé d’identifier des biomarqueurs de l’endométriose au niveau de l’endomètre eutopique par intégration rétrospective de données transcriptomiques et par une approche de protéomique différentielle.Ce travail collaboratif interdisciplinaire, nous a permis d’identifier des signatures moléculaires de l’endométriose aux niveaux génétique et protéique.Bien que nécessitant des analyses complémentaires, nos résultats sont prometteurs et pourraient à l’avenir permettre d’améliorer la prise en charge des patientes<br>Endometriosis is a common gynecological estrogen dependent disorder, affecting 10% of women in reproductive age. The disease is characterized by the presence of functional endometrial tissue outside of uterine cavity. Although asymptomatic forms of endometriosis, this disease results in chronic pelvic pain and infertility. This strongly and negatively impacts the quality of life of women with endometriosis.To date, the diagnosis of endometriosis takes many years because of the lack of non-invasive diagnostic tools. The identification of biomarkers seems to be a priority in the field of endometriosis research.Interestingly, “Omics” technologies demonstrated their relevance for the search, identification and characterization of potential disease biomarkers with significant achievements in many areas of human health.The present project aims at discovering potential biomarkers of endometriosis using a panel of approaches, among which proteomics and integrative genomics.Four axes of research have been followed for this project: i) development of a biological test to identify high risk population for women undergoing IVF procedure; ii) multiple meta-analyses to identify potential genetic markers associated with endometriosis risk; and finally identify potential biomarkers of endometriosis using iii) integrative genomics for a retrospective transcriptomics-based study and iv) differential proteomics of eutopic endometrium.These combined approaches, based on strong interdisciplinarity, allowed us to improve our knowledge of endometriosis and to identify potential biomarkers especially polymorphisms predisposing to endometriosis and a molecular signature of the disease at protein level.Upon confirmation, our results could lead to the development of a non-invasive and early diagnosis of this debilitating disease. In the future, our research should thus contribute to improve the care of patients
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Hunte, Cyril Kenrick. "Loan default and the efficacy of the screening mechanism : the case of the development bank in Guyana /." The Ohio State University, 1993. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487843688957261.
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Zhu, Seng. "Study of the mechanism of Tunneling nanotubes formation and their role in aggregate proteins transfer between cells." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLS377.
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Les Tunneling nanotubes (TNT) sont des protrusions cellulaires à base d'actine qui médient la communication cellulaire en transférant des cargos cellulaires. Les différents types de communication intercellulaires sont de plus en plus considérés comme des cibles potentielles pour le traitement de différentes maladies, telles que les maladies infectieuses liées aux virus et bactéries, les cancers ou les maladies neurodégénératives. Des études récentes ont mis en évidence un mécanisme de propagation d'agrégats protéiques ressemblant à la propagation du prion dans diverses maladies neurodégénératives non infectieuses telles que la maladie d'Alzheimer (AD), la démence frontotemporelle (FTD), la maladie de Parkinson (PD) et la maladie de Huntington. Ces maladies se caractérisent par l'accumulation de protéines mal repliées dans le cerveau des patients. Ainsi, on peut envisager de nouvelles stratégies thérapeutiques pour bloquer la propagation des protéines anormales dans tout le cerveau. Il a été démontré que les TNT pourraient jouer un rôle essentiel dans la propagation des agrégats de prions au sein du système nerveux central (SNC) et périphérique. Par conséquent, l'étude du mécanisme de la formation de TNT pourrait fournir de nouvelles idées sur le mécanisme de propagation de la maladie et de nouvelles cibles thérapeutiques. L'objectif de ma thèse était d'étudier le rôle du transfert des agrégats de protéines par les TNT entre les cellules et d'étudier le mécanisme de formation des TNT. Dans notre laboratoire, nous avons déjà montré que les TNT permettent le transfert de prions entre les cellules. Dans la première partie de mon doctorat, j'ai confirmé que les transferts d'agrégats de prions entre les cellules de CAD neuronales se faisaient par les TNT à l'intérieur de vésicules endocytiques (Zhu et al., 2015). De plus, en collaboration avec un collègue, nous avons fourni des preuves que les agrégats de prions pourraient être transférés entre des astrocytes primaires et des neurones et que ce transfert était médié par un contact cellulaire (Victoria et al., 2016). J'ai également collaboré à une autre étude où nous avons montré que les agrégats d'α-synucléine (caractéristiques de la maladie de Parkinson) peuvent être transférés entre les cellules à l'intérieur des lysosomes, et que ce transfert intercellulaire est médié par les TNT (Abounit et al., 2016). Dans mon deuxième projet, afin d'étudier le mécanisme de la formation de TNT, j'ai effectué un crible à haut débit pour les Rab GTPase. J'ai trouvé que Rab8 et Rab11 peuvent favoriser la formation des TNT, et que les cascades Rab8-VAMP3, Rab11-ERM et Rab8-Rab11 sont impliquées dans la formation des TNT. Mes données suggèrent que la polymérisation de l'actine et le trafic de membranes sont impliqués dans la formation des TNT. Ces résultats permettent d'éclairer le mécanisme de la formation des TNT et de fournir des preuves moléculaires que les Rab GTPases régulent ce processus<br>Tunneling nanotubes are actin-based cell protrusions that mediate cell-to-cell communication by transferring cellular cargos. The different types of intercellular communication are increasing by being considered as potential targets for the treatment of various diseases, such as infectious diseases linked to viruses and bacteria, cancers or neurodegenerative diseases. Recent studies have highlighted a prion-like mechanism of propagation of protein misfolding in a variety of common, non-infectious, neurodegenerative diseases such as Alzheimer’s disease (AD), Frontotemporal dementia (FTD), Parkinson’s disease (PD), and Polyglutamine (PolyQ) diseases, which are characterized by the accumulation of misfolded proteins in the brain of patients. Thus, new therapeutic strategies to block propagation of protein misfolding throughout the brain can be envisaged. It has been shown that TNTs might play a critical role in spreading of prion aggregates within the CNS and from the periphery. Therefore, the study of mechanism of TNT formation could provide new insights on the mechanism of disease propagation and novel therapeutic targets. The aim of my thesis was to study the role of TNT-mediate protein aggregates transfer between cells and to investigate the mechanism of TNT formation. In our lab, we already reported TNT mediate prion transfer between cells. In the first part of my PhD, I further confirmed that prion aggregates transfer between neuronal CAD cells through TNT inside endocytic vesicles (Zhu et al., 2015). Furthermore in collaboration with a colleague, we provided evidences that prion aggregates could transfer between primary astrocytes and neurons and the transfer was mediated by cell-to-cell contact (Victoria et al., 2016). I also collaborated to another study where we showed that α-synuclein aggregates (Parkinson’s disease) can transfer between cells inside lysosomes, and the intercellular transfer is mediated by TNTs (Abounit et al., 2016).In my second project, in order to investigate the mechanism of TNT formation, I performed a High-content screening of Rab GTPase. I found that Rab8 and Rab11 can promote TNT formation, that Rab8-VAMP3, Rab11-ERM and Rab8-Rab11 cascades are involved in TNT formation. My data suggests that both actin polymerization and membrane trafficking are involved in TNT formation. These results help to shed light on the mechanism of TNT formation, and provide molecular evidences that Rab GTPases regulate this process
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Kitahara, Nao. "Study on screening of novel pathogenic factors of Candida albicans by proteome analysis and its putative virulent mechanism." Kyoto University, 2016. http://hdl.handle.net/2433/215600.
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Kyoto University (京都大学)<br>0048<br>新制・課程博士<br>博士(農学)<br>甲第19774号<br>農博第2170号<br>新制||農||1040(附属図書館)<br>学位論文||H28||N4990(農学部図書室)<br>32810<br>京都大学大学院農学研究科応用生命科学専攻<br>(主査)教授 植田 充美, 教授 栗原 達夫, 教授 矢﨑 一史<br>学位規則第4条第1項該当
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Zeng, Chunxi. "Riboswitch-targeted Drug Discovery: Investigation of Factors that Affect the T Box Transcription Antitermination Mechanism." Ohio University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1451943674.
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Malvezzi, Alberto. "Modelos de virtual Screening de inibidores da cruzaína: desenvolvimento e validação experimental." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/46/46135/tde-10082016-115529/.
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Com o objetivo de buscar e identificar novo(s) inibidor(es) da cruzaína uma cisteíno-protease do Trypanosoma cruzi, o agente etiológico da doença de Chagas foram propostos, validados e, a seguir, aplicados sobre a biblioteca de compostos ZINC (3.294.714 compostos), dois modelos de virtual screening (Modelos I e II). Os modelos de virtual screening propostos, contendo seqüências de filtros físicoquímicos, farmacofóricos, de docking e de seleção por inspeção visual, foram construídos a partir de informações de 13 complexos da cruzaína e de 20 complexos de outras cisteínoprotease, cujas estruturas estão disponíveis no PDB. Numa primeira etapa, o reconhecimento detalhado das características estruturais da cruzaína foi realizado por inspeção visual; pelos campos de interação molecular, gerados pelo programa GRID; pela identificação das propriedades de interação molecular na superfície da cavidade, geradas pelo programa CA VBASE e; por simulações de dinâmica molecular. O Modelo I de virtual screeníng - obtido a partir do reconhecimento das estruturas dos 13 complexos da cruzaína depositadas no PDB - foi aplicado sobre o ZINC, selecionando 10 compostos, dos quais 6 compostos foram adquiridos e submetidos ao teste de inibição enzimática da cruzaína, para a validação experimental do modelo. Observou-se que 3 destes compostos (ZINC02470662, ZINC02682879 e ZINC03192044, respectivamente) não mostraram inibição significativa da cruzaína, nas condições experimentais utilizadas, até a concentração de 7 mM, enquanto que os 3 restantes (ZINC02663001, ZINC01936854 e ZINC03326243, respectivamente) apresentaram inibição enzimática inespecífica, sugerindo que estes últimos agem pelo mecanismo promíscuo. O mecanismo promíscuo de inibição enzimática, foi verificado pela adição de 0,1% Triton X-100 no ensaio enzimático, observando-se a correspondente perda de inibição da cruzaína. Para estes compostos, a confirmação do mecanismo promíscuo foi feita observando-se a perda de inibição da enzima, após o aumento em dez vezes da concentração da cruzaína no ensaio enzimático. O Modelo II - obtido a partir do reconhecimento das estruturas dos 13 complexos da cruzaína e dos 20 complexos de outras cisteíno-proteases, identificadas na busca por cavidades similares à cruzaína - foi aplicado sobre o banco de dados ZINC,selecionando 55 compostos dos quais 19 foram adquiridos e submetidos ao teste de inibição enzimática da cruzaína, para validação experimental do modelo. Observou-se que o composto ZINC01794422 apresentou inibição específica da enzima com constante de inibição no valor de Ki = 21 µM, enquanto que os demais 18 compostos não mostraram inibição significativa, nas condições experimentais utilizadas, até a concentração de 592 µM. O mecanismo promíscuo de inibição enzimática não foi observado, uma vez que todos os testes foram realizados com 0,1% de Triton X-100. O Modelo II identificou, ainda, mais dois inibidores da cruzaína (ZINC04899534 e ZINC01547017) que, por serem estruturalmente semelhantes aos utilizados na construção do modelo e já terem sido descritos na literatura, não foram adquiridos ou testados nos ensaios enzimáticos. Considerando apenas o novo inibidor identificado, o Modelo II apresentou uma taxa de acerto de 5,3%. Este valor esta de acordo com as taxas de acerto encontradas na literatura que variam entre 1 a 50% .<br>In order to search and identify new cruzain inhibitor(s) - a cysteine-protease of Trypanosoma cruzi, the etiologic agent of Chagas disease - two virtual screening schemes(Models I and II) were proposed, validated- and applied to the ZINC database (3.294.714 compounds). The proposed virtual screening models, bearing a sequence of different physicalchemical, pharmacophore and docking filters, as well as a visual inspection filter, were built from information taken from 13 cruzain complexes and from 20 complexes of other cysteine proteases, having their structures available in PDB. In a first step, a detailed recognition of the cruzain structural features and characteristics was performed through visual inspection of the enzyme environment; followed by the analysis of GRID generated molecular interaction fields; through the identification of molecular interaction properties exposed at the enzyme cavity surface, generated by the CAVBASE program; and by molecular dynamics simulations. The virtual screening Model I, - generated from the structural characteristics recognized from 13 PDB cruzain complexes - when applied to the ZINC database selected 10 compounds. For the experimental validation ofthe model, six ofthese compounds have been acquired and were tested as cruzain inhibitors. It was observed that three of the tested compounds (ZINC02470662, ZINC02682879 and ZINC03192044, respectively) did not show any significant cruzain inhibition, up to 7 mM. Meanwhile the other three tested compounds (ZINC02663001, ZINC01936854 and ZINC03326243, respectively) showed an unspecific cruzain inhibition, suggesting that an enzyme inhibition by promiscuous mechanism occurred. This mechanism was verified by the addition of 0.1% Triton X-100 on the enzymatic assay with a concomitant loss of cruzain inhibition activity. For these compounds, the confirmation of the promiscuous mechanism was also done, observing the loss of enzyme inhibition, after a ten times increase in the cruzain concentration on the enzymatic assay. The virtual screenmg Model II - generated from the structural characteristics recognized from 13 cruzain complexes and 20 complexes of other cysteine proteases, that have been identified on a search for cavities similar to cruzain - selected 55 compounds, when applied to the ZINC database. In order to experimentally validate the model, nineteen compounds have been acquired and were tested as cruzain inhibitors. It has been observed that one compound, ZINC01794422, showed a specific cruzain inhibition (Ki = 21 µM), while the other eighteen showed no significant inhibition, up to 592 µM concentration. The promiscuous mechanism of enzymatic inhibition was not observed, since 0.1% of Triton X-100 was added in ali assays. Additionally, Model II identified two other cruzain inhibitors (ZINC04899534 and ZINC01547017). However, these compounds have not been acquired or tested, since they are known cruzain inhibitors - already described in the literature and are structurally similar to the inhibitors used in the construction of the mode!. Referring to new inhibitors found, Model II showed a hit rate of 5,3%. This value is in agreement with those found in the literature, which ranges from 1 to 50%.
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Lôme, Vincent. "Des agents chimiosensibilisants pour lutter contre la résistance aux antibiotiques chez les bactéries Gram-négatif : criblage et caractérisation." Thesis, Aix-Marseille, 2017. http://www.theses.fr/2017AIXM0063.
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Les bactéries Gram-négatif possèdent une structure d'enveloppe, ainsi que des pompes d'efflux (i.e., systèmes de transport actif permettant de détoxifier la cellule bactérienne) qui les rendent naturellement résistantes aux antibiotiques. Ces deux caractéristiques constituent de véritables barrières qui s'opposent à l'accumulation d'une grande variété d'antibiotiques près de leur cible, à l'intérieur de la bactérie. La perturbation des mécanismes s’opposant à l’accumulation d’antibiotiques par des agents chimiosensibilisants représente une stratégie prometteuse.L’objectif de cette thèse était de mieux comprendre les mécanismes d'inhibition de la résistance qui s’oppose à l’accumulation d’antibiotiques chez les bactéries Gram- négatif.Dans un premier temps l'activité de divers agents chimiosensibilisants synthétiques a été caractérisée. Trois dérivés ont été identifiés pour augmenter significativement l'activité synergique avec les antibiotiques, préalablement observée avec le géraniol. Ces dérivés ont montré une activité inhibitrice des pompes d'efflux ou perméabilisatrice de la membrane externe, pouvant être à l'origine des synergies observées.Dans un second temps, une méthode de criblage a été mise au point, en permettant la détection spécifique des agents chimiosensibilisants tout en décrivant leur mécanisme d'action.Ces travaux de thèse ont participé à proposer une solution thérapeutique brevetée au stade pré-clinique. Ils ont en outre permis de mettre en place des outils originaux pour identifier de nouveaux chimiosensibilisants, mais aussi pour mieux comprendre comment perturber les barrières s'opposant à l'accumulation d'antibiotiques<br>Gram-negative bacteria are naturally resistant to many classes of antibiotics thanks to their ability to control the accumulation of drugs. Decreasing membrane barrier permeability and producing efflux pumps that expel drugs outside bacteria, represent the prevalent mechanisms of this resistance. One of the most promising solutions consists in restoring antibiotic activity by targeting such barriers to accumulation, with chemosensitizers.The purpose of my PhD was to better understand the inhibition of resistance that opposes the accumulation of antibiotics in Gram-negative bacteria.In the first stage of the study, the activity of various synthetic chemosensitizers has been characterized. Three compounds were identified to significantly increase the synergistic activity with antibiotics, that was previously observed with geraniol. These derivatives showed an efflux pump inhibition or an outer membrane permeabilization effect, that could be related to the observed synergy.In the second stage of the study, a screening method has been developed for the specific detection of chemosensitizers, while describing their mechanism of action.This work participated in proposing a patented therapeutic solution in the preclinical stage. This study has led to new tools to identify novel chemosensitizers, but also to better understand how to impair the barriers opposing the accumulation of antibiotics
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Pérez, María del Carmen Marín. "Benchmarking and applications of a computational photobiology tool for design of novel and highly fluorescent rhodopsin proteins." Doctoral thesis, Università di Siena, 2019. http://hdl.handle.net/11365/1070289.
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In recent years, world economy and technological advancement have been transformed by Genomics, which allows us to study, design and build biologically relevant molecules. Genomics is already deeply embedded in industries as diverse as pharmaceutical, food and agricultural, environmental and bio-tech in general. Fast and cheap tools for gene sequencing,
protein expression and analysis are commonly used for high-throughput genomic-related studies. However, due to experimental difficulties and long time scales (e.g., protein crystallization), protein structure determination, and thus the fundamental structure function rationalization, cannot presently be performed at the same fast pace: a fact that is slowing down the discovery of proteins with new features, as well as ex novo design. These difficulties are particularly felt in the field of photobiology, where the crystal structure of Bovine rhodopsin (Rh, retina dim-light visual photo-receptor), still remains the
only structure of a vertebrate photo-receptor sensor available for photobiological studies since the year 2000. Rhodopsins constitute a class of light-triggered proteins that can be found throughout the whole spectrum of living organisms, and represent the perfect blue-print for building light-activated bio-molecular machines. In principle, the problem of not having a sufficient number of rhodopsins molecular structures could be circumvented and overcome with the construction of accurate atomistic computer models of the set of studied photoreceptors, which would allow: (i) in silico fundamental structure-function characterization, (ii) thorough and detailed screening of mutant series, and even (iii) ex novo design. Nevertheless, such models should also be constructed using a fast, relatively cheap, reliable and standardized protocol, of known accuracy. In this thesis, we refine and test the Automatic Rhodopsin Modeling (ARM) computational protocol, which we demonstrate as being capable of helping to address the above issues. Such protocol has the primary target of generating congruous quantum mechanical/molecular mechanical (QM/MM) models of rhodopsins, with the aim of facilitating systematic rhodopsin-mutants studies. The cornerstone of this thesis is the validation of the ARM protocol as a successful attempt to provide a basis for the standardization and reproducibility of rhodopsin QM/MM models, aimed to study the behaviour of photoactive molecules. First, we validate the ARM protocol, which employs a CASPT2//CASSCF/AMBER scheme, for a benchmark set of rhodopsins from different biological kingdoms. We show that ARM is able to reproduce and predict absorption trends in rhodopsin protein sets, with blue-shifted values not much displaced (a few kcal/mol) from the observed data. Secondly, we present how to use this protocol towards a better design of novel mutations as applications for Optogenetics, an innovative biological tool aimed to visualize and control neuron signals through light. Two different microbial rhodopsins are studied:
Krokinobacter eikastus rhodopsin 2 (KR2), a light-driven outward sodium pump, and Anabaena sensory rhodopsin (ASR), a light sensor. In both cases, the qualitative and quantitative information acquired from the ARM-obtained QM/MM models reveal nature (electrostatic or steric) and extent of the mutation-induced changes on the retinal configuration, which, in turn, are the cause of the shift in the absorption wavelength of the relative mutants. Finally, we explore the fluorescence of ASR mutants, particularly useful for the visualization of neuronal activity. The target of this work is to use QM/MM simulations to understand the opposite behaviour observed in two blue-shifted ASR mutants, where one presents a negligible fluorescence, while the other displays one order of magnitude enhanced fluorescence, with respect to the wild type protein. Our QM/MM models show that specific electrostatic and steric interactions control the character mixing of different electronic states, opening a path to the rational engineering of highly fluorescent rhodopsins. In conclusion, within the limits of its automation, the ARM protocol allows the study of ground and excited states of specific photoactive proteins: rhodopsins. This opens the way to an improved molecular-level understanding of rhodopsin photochemistry and photobiology. The results obtained highlight the importance of having a standardized, effective and automatic protocol, which renders this kind of studies more efficient and accessible, by drastically shortening the time required to produce accurate and congruous QM/MM models. For the above reasons the author of the present thesis believes that ARM stands as an important cogwheel in the virtuous cycle between experimental and theoretical work, aimed to prepare the photobiological tools for tomorrow’s needs.
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Mucs, Daniel. "Computational methods for prediction of protein-ligand interactions." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/computational-methods-for-prediction-of-proteinligand-interactions(33ad0b24-ef7b-4dff-8e28-597a2f34e079).html.
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This thesis contains three main sections. In the first section, we examine methodologies to discriminate Type II protein kinase inhibitors from the Type I inhibitors. We have studied the structure of 55 Type II kinase inhibitors and have notice specific descriptive geometric features. Using this information we have developed a pharmacophore and a shape based screening approach. We have found that these methods did not effectively discriminate between the two inhibitor types used independently, but when combined in a consecutive way – pharmacophore search first, then shape based screening, we have found a method that successfully filtered out all Type I molecules. The effect of protonation states and using different conformer generators were studied as well. This method was then tested on a freely available database of decoy molecules and again shown to be discriminative. In the second section of the thesis, we implement and assess swarm-based docking methods. We implement a repulsive particle swarm optimization (RPSO) based conformational search approach into Autodock 3.05. The performance of this approach with different parameters was then tested on a set of 51 protein ligand complexes. The effect of using different factoring for the cognitive, social and repulsive terms and the importance of the inertia weight were explored. We found that the RPSO method gives similar performance to the particle swarm optimization method. Compared to the genetic algorithm approach used in Autodock 3.05, our RPSO method gives better results in terms of finding lower energy conformations. In the final, third section we have implemented a Monte Carlo (MC) based conformer searching approach into Gaussian03. This enables high level quantum mechanics/molecular mechanics (QM/MM) potentials to be used in docking molecules in a protein active site. This program was tested on two Zn2+ ion-containing complexes, carbonic anhydrase II and cytidine deaminase. The effects of different QM region definitions were explored in both systems. A consecutive and a parallel docking approach were used to study the volume of the active site explored by the MC search algorithm. In case of the carbonic anhydrase II complex, we have used 1,2-difluorobenzene as a ligand to explore the favourable interactions within the binding site. With the cytidine deaminase complex, we have evaluated the ability of the approach to discriminate the native pose from other higher energy conformations during the exploration of the active site of the protein. We find from our initial calculations, that our program is able to perform a conformational search in both cases, and the effect of QM region definition is noticeable, especially in the description of the hydrophobic interactions within the carbonic anhydrase II system. Our approach is also able to find poses of the cytidine deaminase ligand within 1 Å of the native pose.
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Hao, Yanwei. "Auxin-mediated fruit development and ripening : new insight on the role of ARFs and their action mechanism in tomato (S. lycopersicum)." Thesis, Toulouse, INPT, 2014. http://www.theses.fr/2014INPT0094/document.
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L'auxine est une hormone végétale qui coordonne plusieurs processus de développement des plantes à travers la régulation d'un ensemble spécifique de gènes. Les Auxin Response Factors (ARF) sont des régulateurs transcriptionnels qui modulent l'expression de gènes de réponse à l’auxine. Des données récentes montrent que les membres de la famille des ARF sont impliqués dans la régulation du développement des fruits de la nouaison à la maturation. L'objectif principal de la thèse est d’étudier la part qui revient aux ARF dans le contrôle du développement et de la maturation des fruits et d’en comprendre les mécanismes d’action. L’analyse des données d’expression disponibles dans les bases de données a révélé que, parmi tous les ARF de tomates, SlARF2 affiche le plu haut niveau d'expression dans le fruit avec un profil distinctif d’expression associé à la maturation. Nous avons alors entrepris la caractérisation fonctionnelle de SlARF2 afin d’explorer son rôle dans le développement et la maturation des fruits. Deux paralogues, SlARF2A et SlARF2B, ont été identifiés dans le génome de la tomate. Nous avons montré que l’expression de SlARF2A dans le fruit est régulée par l'éthylène tandis que celle de SlARF2B est induite par l'auxine. La sous-expression de SlARF2A, comme celle de SlARF2B, entraine un retard de maturation alors que l’inhibition simultanée des deux paralogues conduit à une inhibition plus sévère de la maturation suggérant une redondance fonctionnelle entre les deux paralogues lors de la maturation des fruits. Les fruits présentant une sous-expression des gènes SlARF2 produisent de faibles quantités d'éthylène, montrent une faible accumulation de pigments et une plus grande fermeté. Le traitement avec de l'éthylène exogène ne peut pas inverser les phénotypes de défaut de maturation suggérant que SlARF2 pourrait agir en aval de la voie de signalisation de l'éthylène. L'expression des gènes clés de biosynthèse et de signalisation de l'éthylène est fortement perturbée dans les lignées sous-exprimant SlARF2 et les gènes majeurs qui contrôlent le processus de maturation (RIN, CNR, NOR, TAGL1) sont sensiblement sous-régulés. Les données suggèrent que SlARF2 est essentiel pour la maturation des fruits et qu’il pourrait agir au croisement des voies de signalisation de l'auxine et de l'éthylène. Dans le but de mieux comprendre les mécanismes moléculaires par lesquels les ARF régulent l'expression des gènes de réponse à l'auxine, nous avons étudié l'interaction des SlARFs avec des partenaires protéiques ciblés, principalement les co-répresseurs de type Aux/IAA et Topless (TPL) décrits comme les acteurs clés dans la répression des gènes dépendant de la signalisation auxinique. Une fois les gènes codant pour les membres de la famille TPL de tomate isolés, une approche double hybride dans la levure a permis d’établir des cartes exhaustives d'interactions protéine-protéine entre les membres des ARFs et des Aux/IAA d’une part et les ARFs et les TPL d’autre part. L'étude a révélé que les Aux/IAA interagissent préférentiellement avec les SlARF activateurs et qu’à l’inverse les Sl-TPL interagissent uniquement avec les SlARF répresseurs. Les données favorisent l'hypothèse que les ARF activateurs recrutent les Sl-TPL via leur interaction avec les Aux/IAA, tandis que les ARF répresseurs peuvent interagir directement avec les Sl-TPL. Les études d’interactions ont permis également d’identifier de nouveaux partenaires comme les protéines VRN5 et LHP1, composantes des complexes Polycomb PRC impliqués dans la repression par voie épigénétique de la transcription par modification de l'état de méthylation des histones. Au total, le travail de thèse apporte un nouvel éclairage sur le rôle et les mécanismes d'action des ARF et identifie SlARF2 comme un nouvel élément du réseau de régulation contrôlant le processus de maturation des fruits chez la tomate<br>The plant hormone auxin coordinates plant development through the regulation of a specific set of auxin-regulated genes and Auxin Response Factors (ARFs) are transcriptional regulators modulating the expression of auxin-response genes. Recent data demonstrated that members of this gene family are able to regulate fruit set and fruit ripening. ARFs are known to act in concert with Aux/IAA to control auxin-dependent transcriptional activity of target genes. However, little is known about other partners of ARFs. The main objective of the thesis research project was to gain more insight on the involvement of ARFs in fruit development and ripening and to uncover their interaction with other protein partners beside Aux/IAAs. Mining the tomato expression databases publicly available revealed that among all tomato ARFs, SlARF2 displays the highest expression levels in fruit with a marked ripening-associated pattern of expression. This prompted us to uncover the physiological significance of SlARF2 and in particular to investigate its role in fruit development and ripening. Two paralogs, SlARF2A and SlARF2B, were identified in the tomato genome and transactivation assay in a single cell system revealed that the two SlARF2 proteins are nuclear localized and act as repressors of auxin-responsive genes. In fruit tissues, SlARF2A is ethylene-regulated while SlARF2B is auxin-induced. Knock-down of SlARF2A or SlARF2B results in altered ripening with spiky fruit phenotype, whereas simultaneous down-regulation of SlARF2A and SlARF2B leads to more severe ripening inhibition suggesting a functional redundancy among the two SlARF2 paralogs during fruit ripening. Double knock-down fruits produce less climacteric ethylene and show delayed pigment accumulation and higher firmness. Exogenous ethylene treatment cannot reverse the ripening defect phenotypes suggesting that SlARF2 may act downstream of ethylene signaling. The expression of key ethylene biosynthesis and signaling genes is dramatically disturbed in SlARF2 down-regulated fruit and major regulators of the ripening process, like RIN, CNR, NOR, TAGL1, are under-expressed. The data support the notion that SlARF2 is instrumental to fruit ripening and may act at the crossroads of auxin and ethylene signaling. Altogether, while ethylene is known as a key hormone of climacteric fruit ripening, the ripening phenotypes associated with SlARF2 down-regulation bring unprecedented evidence supporting the role of auxin in the control of this developmental process. To further extend our knowledge of the molecular mechanism by which ARFs regulate the expression of auxin-responsive genes we sought to investigate interactions SlARF and putative partners, mainly Aux/IAAs and Topless co-reppressors (TPLs) reported to be key players in gene repression dependent on auxin signaling. To this end, genes encoding all members of the tomato TPL family were isolated and using a yeast-two-hybrid approach comprehensive protein-protein interaction maps were constructed. The study revealed that Aux/IAA interact preferentially with activator SlARFs while Sl-TPLs interact only with repressor SlARFs. The data support the hypothesis that activator ARFs recruit Sl-TPLs co-repressors via Aux/IAAs as intermediates, while repressor ARFs can physically interact with Sl-TPLs. Further investigation indicated that SlARFs and Sl-TPLs can interact with polycomb complex PRC1 PRC2 components, VRN5 and LHP1, known to be essential players of epigenetic repression of gene transcription through the modification of histones methylation status. These data establish a potential link between ARFs and epigenetic regulation and thereby open new and original perspectives in understanding the mode of action of ARFs. Altogether, the thesis work provides new insight on the role of ARFs and their underlying action mechanisms, and defines SlARF2 as a new component of the regulatory network controlling the ripening process in tomato
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De, Veer Simon J. "Development of novel protease inhibitors for epidermal kallikrein proteases." Thesis, Queensland University of Technology, 2014. https://eprints.qut.edu.au/114508/1/Simon_de%20Veer_Thesis.pdf.
Full textAbstract:
Preserving the integrity of the skin's outermost layer (the epidermis) is vital for humans to thrive in hostile surroundings. Covering the entire body, the epidermis forms a thin but impenetrable cellular cordon that repels external assaults and blocks the escape of water and electrolytes from within. This structure exists in a perpetual state of repair and regeneration where the production of new cellular subunits (keratinocytes) at the base of the epidermis is offset by the gradual release of terminally differentiated corneocytes from the surface. It is increasingly clear that proteinases (hereafter termed proteases) are essential for assembling and maintaining the epidermal barrier. More than thirty proteases are expressed by keratinocytes or immune cells that infiltrate the skin, and the activity of each must be maintained within narrow limits and confined to the correct time and place. Accordingly, dysregulated proteolytic activity is a common factor in a multitude of skin disorders that range in severity from relatively mild to life-threatening.
Serine proteases from the kallikrein-related peptidase (KLK) family are widely recognised as key modulators of epidermal barrier function. For several decades, KLK proteases have been regarded as major contributors to the natural shedding of corneocytes from the skin's surface by degrading (corneo)desmosomes in the stratum corneum. Additionally, controlled KLK proteolytic activity influences the step-wise processing of key molecules involved in hydration and acidification (pro-filaggrin), and anti-microbial defence (cathelicidins).
Further, KLK proteases have prominent roles in the response to barrier disruption that involve stimulating inflammation and alerting the immune system. Thus, failure to properly control KLK proteolytic activity represents a significant threat to epidermal barrier function, as seen in a spectrum of skin disorders, including Netherton syndrome and atopic dermatitis.
The focus of this study was to develop novel inhibitors for three KLK proteases with the strongest links to epidermal (patho)physiology (KLK5, KLK7 and KLK14) by engineering the naturally occurring cyclic peptide, sunflower trypsin inhibitor-1 (SFTI-1). Initially, each target protease was screened against a dedicated library of individually synthesised peptide substrates (sparse matrix library) to identify sequence combinations that bound to the active site with high affinity. This approach yielded a series of efficient tetrapeptide substrates for each protease that outperformed existing substrates from conventional screening methods, such as positional scanning and phage display. Strikingly, the optimal substrates for KLK5, KLK7 and KLK14 each displayed a unique physicochemical signature, indicating that the active site of each protease was configured to recognise distinct cleavage motifs. This phenomenon was explored in more detail by analysing structures of diverse serine proteases from the S1A (chymo)trypsin fold, which identified several points of high sequence variation in the active site cleft that likely contribute to divergent cleavage site specificities.
Subsequently, favoured cleavage sequences for KLK5, KLK7 and KLK14 were substituted into the contact β-strand of SFTI-1 to generate inhibitor variants with improved affinity and selectivity. Whereas most inhibitor design strategies based on Laskowski inhibitors (including SFTI-1) focus mainly on optimising the interaction between protease and inhibitor, this study paired binding loop modifications with a second step that aimed to refine the intramolecular hydrogen bond network, as shown recently for engineered SFTI variants targeting KLK4. Like the previous study, improving the tendency for an inhibitor to form intramolecular hydrogen bonds generally led to improvements in inhibitory activity.
However, it was also evident that certain hydrogen bonds were detrimental, revealing that the quantity of hydrogen bonds should not be the only criteria during this screening process.
Additionally, the iterative optimisation of inhibitors for KLK5 highlighted the need to consider both sides of the reactive site when engineering Laskowski inhibitors as generating a selective KLK5 variant was dependent on substituting the P2′ residue. Using this design process, it was possible to successfully re-direct the inhibitory activity of SFTI-1 to three separate protease targets that showed varying affinity for the wild-type inhibitor.
To delve further into the Laskowski mechanism, SFTI-1 was used as a model system to explore the molecular basis for Laskowski inhibitor potency and specificity. Here, inhibitor association and dissociation kinetics were characterised for a series of variants with different binding sequences and hydrogen bond tendencies. These analyses revealed that the primary determinant for rapid association was the pre-organised conformation of the inhibitor binding loop rather than its sequence, whereas coordinated inter- and intramolecular interactions promoted efficient religation and slow dissociation. As the conformation of the binding loop is conserved, inhibitor selectivity dictated by the binding sequence was found to arise from modulating the off-rate. Performing additional analyses on eight fold-divergent inhibitor families revealed that these concepts were generally applicable to Laskowski inhibitors, providing broad new insights on protease inhibitor function and design. These findings were subsequently applied to engineer an additional series of potent inhibitors with broad-range activity.
Finally, the substrates and inhibitors developed for KLK5, KLK7 and KLK14 were used in biological assays to investigate the activity and significance of each target protease in healthy and diseased skin. KLK peptide substrates were applied to profile KLK hyperactivity in skin extracts from transgenic KLK5 mice and Spink5-/- mice. Additionally, KLK inhibitors were used to sequentially block different KLKs in gel-based and in situ zymography experiments. Selective and broad-range inhibitors were also evaluated in ex vivo desquamation assays to examine the relative importance of KLK5, KLK7 and KLK14 during corneocyte shedding, which revealed a major role for KLK7. Collectively, these findings shed light on the individual contributions of KLK proteases to maintaining the epidermal barrier and identify a series of therapeutic leads for further development as novel treatments for skin disorders associated with dysregulated KLK proteolytic activity.
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Smith, Bryan Ronain. "Nanoparticulate platforms for molecular imaging of atherosclerosis and breast cancer." Columbus, Ohio : Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1150309580.
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Ceng, Jia-Shao, and 曾嘉卲. "THE DEVELOPMENT OF NOVEL RICE SCREENING MECHANISMS." Thesis, 2010. http://ndltd.ncl.edu.tw/handle/96584468748412361739.
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碩士<br>大同大學<br>機械工程學系(所)<br>98<br>The purpose of this thesis is to develop new modes use other than vibration screen, and its main function is testing for a small amount of rice. It also has the same function and performance with existing vibrating screen machine. Finally in order to combine automated inspection machine, developed a special rice elevator, aimed at connecting the test procedure and selection process in this thesis.
In order to reach the function the new screen machine should be have, this thesis will try to experiment and discuss three aspects, namely, photoelectric, wind-type and roller type. Photoelectric: when CDS is covered, its resistance will be change, to make the voltage amplitude and pulse width change, and so as a basis for CDS classification; wind-type: using the same wind blowing over the rice which one is fall down, and rice falling distance with the force will vary depending on size and weight; roller type: the production of a specific mesh into a cylinder shape, use scroll all the way to reach to the classification of rice.
This thesis is successfully found out new method to select the rice and it has the same function and performance of the vibration screen. Finally develop a special rice elevator.
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PutraSetyawan, Rendy, and 希主望. "Comparison of Procurement Auction Alternative Mechanisms: Bidder Screening and Contract Incentive." Thesis, 2016. http://ndltd.ncl.edu.tw/handle/234844.
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Hsu, Shuo-Chen, and 許碩辰. "Cytotoxic screening of 2,6-Disubstituted Amidoanthraquinones and Anticancer Molecular Mechanisms Studies." Thesis, 2006. http://ndltd.ncl.edu.tw/handle/78181669452794934138.
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碩士<br>高雄醫學大學<br>藥理學研究所碩士班<br>94<br>In recent years, anthraquinones derivatives have been proved to possess various of biological activities including anticancer: antibacterial, anti-multiple sclerosis, vasodilatation and supperes intestine creeps effects.
Our research team has reported that hundreds synthesized small-molecule disubstituted anthraquinones have cytotoxic effects on various cancer cell lines. We found the different of anthraquinone derivatives (1,4 1,5 1,8 and 2,6 disubstituted derivatives) have demonstrated different cytotoxic potency (Huang et al.2001-2006).
For investigation the anticancer molecular mechanisms of the new 2,6 diamidoanthraquinone derivers, we focus on two compound, B7(CHH20060607) and B9(CHH20060609), study their molecular mechanisms of cytotoxic effects.
After cytotoxicity test, we found B7 & B9 possessed different inhibitory effect on various of tumor cell lines: human hepatoma cell(HepG2. 2.2.15), rat glioma cell(C6) and lung carcinoma cell(A549). Our results have indicated the IC50 of B7 on HepG2, 2.2.15, C6 and A549 cell are 0.27, 0.41, 0.28, 0.47 ?嵱, and the IC50 of B9 are 10.57, 10.28, 20.10, 12.30 ?嵱, respectively.
At low concentrations of B7 (0.05 ?嵱) or B9 (1 ?嵱) both caused cell cycle arrest at G0/G1 phase at 24hr or 72hr, this effect similar to the natural anthraquinone emodin. In contrast, the clinical anticancer drugs mitoxantrone and adriamycin both induced cell cycle arrest on G2/M phase which demonstrated different action mechanism.
The results of TUNEL assay have demonstrated that B7 and B9 both caused significant apoptosis change in HepG2 cells. B7(0.5-20 μM) and B9(1-30 μM) both shown a dose- response phenomenon.
Nitric oxide (NO) is a muti-regulated molecule in hepatocyte. B7 and B9 induced the increase of the intracellular “NO” release which might result in the formation of toxic reaction products, such as peroxynitrite that induced cell apoptosis. In our Western blot analysis, the “iNOS” expression and upstream “NFκB” activity both were found significent promotion.
With the Western bloting assessment, we detect other apoptosis signals: Fas, Fas Ligand, FADD, Caspase-3 and antiapoptosis signal:Bcl-2. Simutaneouly, Our results pointed out that B7 and B9 both can increase the activation of apoptoatic signal(Fas, Fas Ligand, FADD, Caspase-3, p53) and decreased the antiapoptosis Bcl-2 level. It were also indicated that B7 and B9 both could decrease the Cyclin D1 expression and change pERK and pAKT proliferative signal.
In conclusion, our data have shown the CHH20060607(B7) is a potential new anticancer drugs. Both B7 and B9 increase the release of NO synthesis, activating the apoptosis signal (Fas, Fas L, FADD, Caspase-3, p53, p27),and decreased both the antiapoptotic signal Bcl-2 protein expression and proliferative signal(pERK, pAKT).
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Su, Chun-Ting, and 蘇峻霆. "Screening of Anti-HSV Agents and Study of Their Antiviral Mechanisms." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/60553137907608451482.
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碩士<br>國立臺灣大學<br>醫事技術學研究所<br>92<br>Herpes Simplex Virus (HSV) types 1 and 2 infections are the cause of cold sores and genital herpes as well as life-threatening or sight-impairing disease mainly in immunocompromized patients, pregnant women and newborns. After primary infections, HSV can establish persistent infection in nervous system and may reactivate intermittently upon appropriate stimuli. Because of the wide popularity, high ability to transmit and the difficulty to develop prophylactic vaccines, development of chemotherapy is comparatively important. To date, the most widely used and successful chemotherapy are nucleoside analogue agents such as acyclovir (ACV), which inhibits viral DNA polymerase after being phosphorylated by HSV thymidine kinase (TK). However, development of nucleoside analogue-resistant HSV strains has been reported in immunocompromised individuals. Thus, there is a need to develop novel anti-HSV agents to substitute for or to complement conventional anti-HSV chemotherapy. In this study we first screened a total of 960 candidate chemicals for their antiviral activity. Seventy-three of these candidate chemicals were further confirmed to have definite antiviral activity by plaque reduction assay. Among these 73 chemicals, 14 have a 50% effective concentration (EC50) lower than 1 μM. The cytotoxicity concentration (CC50) of these chemicals was subsequently determined by MTT assay and the selective index (SI) for each chemical was thus calculated. One potential drug, 12-2 8G, with SI=17 was further analyzed. By in vitro assay, HSV-1 replication was not significantly inhibited when 12-2 8G was added at viral entry, virus pretreatment or cell pretreatment. In the time-of-addition assay, 12-2 8G was shown to inhibit HSV-1 replication between 6 and 12 hours after infection. It is likely that 12-2 8G block HSV-1 infection at early or late stage. However, there was no interaction between 12-2 8G and ACV based on isobologram analysis. 12-2 8G did not significantly inhibit HSV DNA replication. We will perform time-of-addition assay and RT-PCR to further clarify the target(s) of 12-2 8G. Such information will be helpful in the development and designing of antiviral agents in the future.
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Lee, Kao Yuan, and 李高源. "Screening of potential herbal medicines for life extension and investigation of their molecular mechanisms." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/97amgn.
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Lin, Shih-Chao, and 林士超. "Establish a Model for Screening Antiviral Compounds against High Contagious Viruses and Investigating the Underlying Mechanisms." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/kj88an.
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博士<br>國立中興大學<br>醫學生物科技博士學位學程<br>106<br>High contagious viruses can lead to rapid and robust outbreaks, causing heavy casualties worldwide. However, it usually lacks of available vaccine or antiviral drug against these high contagious infections, such as Middle East Respiratory Syndrome coronavirus (MERS-CoV), chikungunya virus, Zika virus, and Venezuelan equine encephalitis virus (VEEV). In contrast to the time-consuming process of discovering and developing new drugs, we attempted to adapt the current natural products, polyphenols, from plants for screening potential antiviral agents. Here, we evaluated the survival rates of infected cells, the viral genomic RNA and titers with or without compound treatments, and observed the decrease viral proteins to identify antiviral natural compounds. The results show that resveratrol can not only suppress the MERS-CoV infection through reducing the apoptotic proteins expression but dampen the VEEV infection by down-regulating GSK-AKT pathway. Also, nobiletin but not 5’-demethylnobiletin can suppress chikungunya virus replication while phloretin but not phlorizin inhibited two Zika virus strains, MR766 and PRVABC59, via limiting the glycolysis pathway. Overall, we established a platform for screening and investigating potent natural compounds against high contagious viruses as well as demonstrates that natural compounds merit further investigations in developing animal studies and clinical trials.
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Lai, Yi-Hua, and 賴怡樺. "Establishment of anti-cancer drug screening platforms for lung cancer: The identification of effective drugs and functional mechanisms." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/86hvd5.
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博士<br>國立中興大學<br>分子生物學研究所<br>101<br>High mortality lung cancer is the most frequent cause of cancer deaths worldwide,including Taiwan. Because of cancer cell metastasis, cancer patients have poor prognosis. The process of cancer metastasis, cancer cells via peripheral vascular or lymphatic move to other parts of the division and growth. The process not only regulate tumor suppressor gene or oncogene expression, cancer cells also secrete angiogenic factors to promote angiogenesis and accelerate cancer metastasis. A lot of pharmacologists try to find the answers from the traditional Chinese herb medicines. However, there is no specific and high-throughput way to screen thousands of these “health-care” herbs to unknown anti-cancer pathway. According to our previous studies, we have identified a novel suppressor gene (HLJ1) which might relate to patients’ survival rate in NSCLC and can be used as a potential drug target. The vascular endothelial angiogenic factors (VEGF) plays essential roles in the activation of many downstream signalling pathways, promotion of angiogenesis and cancer metastasis and is expected to be a potent target for cancer therapy. In this study, we establish three platforms of drug screening. The first and second platforms were the HLJ1 and VEGF-targeting drug-screening platforms which analyze the HLJ1 and VEGF promoter activities by reporter gene assay. Utilizing these platforms, we can screen herbal medicines with lung cancer cell growth inhibition and angiogenesis regulation and investigate their mechanisms. Third platform was computer-aided drug design (CADD) method, we used CADD to develope novel c-Src inhibitors. By CADD, it is easy to identify candidate compounds for biological validation, and increase the successful rate of new drug development. Utilizing drug screening platforms of reporter gene, we identified several herbal compounds from a Chinese herbal library with the capacity to enhance HLJ1 promoter activity or inhibit VEGF transcription and thereby inhibited cancer cell migration and invasion. Among the herbal drugs identified the andrographolide most significantly induced HLJ1 expression and suppressed tumorigenesis both in vitro and in vivo. The andrographolide upregulated HLJ1 via JunB activation, which modulates AP-2α binding at the MMP-2 promoter and represses the expression of MMP-2. Microarray transcriptomic analysis was performed to comprehensively depict the andrographolide-regulated signalling pathways. We showed that andrographolide can affect genes that are dominantly involved in the cell cycle, apoptosis and adhesion-related biological signalling, including mitogen-activated protein kinase, focal adhesion and tight junction pathways, indicating the diverse effects of andrographolide on anticancer invasion and proliferation. In addition, we also found that strophanthin could decrease VEGF mRNA expression and inhibit cancer cell invasion, migration, anchorage-independent and -dependent growth and tumor growth. The tube formation assay was revealed that strophanthin can suppress angiogenesis. Furthermore, the expression of VEGF121, VEGF165 and VEGF189 of VEGF isoforms were repressed by strophanthin. The third platform, computational virtual screening of Src inhibitor by docking on Y418 site, is performed to find the candidate drugs which could bind on Src Y418 site. The results showed that several compounds can suppress Src phosphorylation, especially antihelminthic niclosamide. We demonstrated that niclosamide could reduce src phorsphorylation and lung cancer cell viability, and induce apoptosis, suggesting that niclosamide may have the potential for the clinical treatment or prevention of lung cancer progression in humans. Moreover, we also analyzed the effect of structural changes in the niclosamide molecule on its ability. The result showed that one of the niclosamide derivatives (W3312) was more effective than niclosamide in cell viability. In summary, niclosamide can suppress Src activity and related signaling pathway and make great potential for the clinical treatment. In conclusion, the HLJ1-targeting, VEGF-targeting drug-screening platforms and CADD are useful for screening of novel anticancer compounds. Using these platforms, we identified andrographolide, strophanthin and niclosamide potentially as promising new anticancer agents that could suppress tumor growth and invasion in NSCLC.
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Chen, Ju-Ling, and 陳儒伶. "In vitro Constitutive Androstane Receptor (CAR) Activation Screening System Establishment and CAR-activation Mechanisms Study of Coumarin Derivatives." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/56n868.
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Jurke, Clinton J. "Evaluation of components of sclerotinia stem rot (Sclerotinia sclerotiorum) management in canola : seeding rates, avoidance mechanisms, and physiological resistance screening methodologies." 2003. http://hdl.handle.net/1993/19941.
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Chi, Chih-Wen, and 紀智文. "The screening of neuroprotective components against A-beta or glutamate-induced toxicity from Chinese medicine and elucidating the mechanisms of neuroprotection." Thesis, 2000. http://ndltd.ncl.edu.tw/handle/54747542249812614207.
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碩士<br>國立陽明大學<br>生物藥學研究所<br>88<br>英文摘要：
For searching the neuroprotective agents against glutamate-induced neurotoxicity, ninety-one fractions of crude extracts from twenty-seven kinds of Chinese herbal medicine were screened by using cortical neurons as model system. The cell viability was determined by MTT reduction assay. The preliminary results showed that the water extraction of Panax ginseng C.A. Meyer and five fractions of water extraction of Origanum vulgare L. were the most effective to reduce the neurotoxicity induced by glutamate. The mechanisms of neuroprotective effect of these fractions against glutamate-induced neurotoxicity were therefore investigated. The glutamate-induced production of reactive oxygen species (ROS) in cortical neurons was determined by 2’,7’-dichlorofluorescein diacetate assay. Treatment of cortical neurons with 5 M of glutamate for 30 min increased the ROS level to be 2.1 fold of that in control cells. Pretreatment of fractions 28-30 or 28-39 of Origanum vulgare L. significantly decreased the glutamate-induced increase of ROS level in cortical neurons. Water extraction of Panax ginseng C.A. Meyer, however, did not affect the ROS level induced by glutamate. Treatment of cortical neurons with 5 M of glutamate elevated the intracellular concentration of calcium to be 2.1 fold of that in control cells. Fractions 28-30 or 28-39 of Origanum vulgare L. or water extraction of Panax ginseng C.A. Meyer blocked the glutamate-induced increase of intracellular concentration of calcium. The increase of calcium concentration activates the activity of nNOS and leads to the production of NO, thereby elevating the intracellular level of cGMP. Water extraction of Panax ginseng C.A. Meyer and fraction 28-30 of Origanum vulgare L. significantly decreased the glutamate-induced increase of intracellular concentration of cGMP in cortical neurons. Fractions 28-39 of Origanum vulgare L., however, did not show any effect on the intracellular concentration of cGMP induced by glutamate.
In search of the neuroprotective reagents against A-induced neurotoxicity, the same crude extracts were screened on Neuro 2A cells. A was toxic to Neuro 2A cells as determined by MTT reduction assay. The cell viability, however, was not affected by the treatment of Aas determined by LDH release and trypan blue exclusion. The proliferation of Neuro 2 A cells was found to be blocked by A as determined by cell number counting and the incorporation of BrdU. Inhibitor studies suggested that the signaling pathway of ERK, PI3K and tyrosine phosphorylation may be involved in the proliferation of Neuro 2A cells. Therefore, tyrosine phosphorylation of proteins, activation of ERK, JNK, and the association of PI3K with tyrosine phosphorylated proteins were elucidated. Results showed that : (1) A decreased the association of PI3K with tyrosine phosphorylated proteins, (2) A did not affect ERK activation, (3) A increased or decreased the tyrosine phosphorylation of proteins, (4) A25-35 increased transitorily the JNK activation.
Among the ninety-one fractions, thirteen fractions of water extraction of Origanum vulgare L. were potential to decrease the neurotoxicity induced by A as determined by MTT reduction. The mechanism of neuroprotective effect of these fractions against A-induced neurotoxicity was investigated. CD spectra showed that fraction OV 9-21C and 16-20-16 of Origanum vulgare L interfered the A25-35 aggregation, and fraction 16-1-2 of Origanum vulgare L. did not change A25-35 aggregation. Thus, the neuroprotective effect of Origanum vulgare L. may be mediated by altering the A25-35 aggregation.
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Wang, Shaoyu. "Structure-activity screening of platinum intercalators and molecular mechanisms for the cytotoxicity of 56MESS - [Pt(5,6-Dimethyl-Phen)(1S,2S-DACH)]²⁺." Thesis, 2011. http://handle.uws.edu.au:8081/1959.7/506756.
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Efficacy of existing clinical anticancer drugs including cisplatin and its analogues is greatly limited by drug resistance and side effects. Anticancer compounds with novel structures and different mechanisms of action have been sought to expand anticancer activity and to minimise these limitations. First part of this project evaluated the structure-activity relationships for a class of novel platinum metallointercalators using cytotoxicity screening against cancer cell lines, and subsequently identified lead compounds. Second part elucidated the biological mechanisms underlying the cytotoxic action of a lead compound with a genome-wide gene expression profiling technology (or transcriptomics) using a eukaryotic model organism yeast Saccharomyces cerevisiae. These analyses identified the disruption of iron and copper metabolism as the major molecular mechanism of cytotoxic action of the lead compound. The novel platinum(II) metallointercalators studied are of the type of [Pt(IL)(AL)]2+, where IL is the intercalating ligand, such as 1,10-phenanthroline (phen), and AL is the ancillary ligand, either chiral 1,2-diaminocyclohexane (S,S-DACH, R,R-DACH), or achiral 1,2-diaminoethylene (EN). Nineteen (19) platinum metallointercalators, eleven (11) cucurbit[n]ural encapsulated forms of these complexes and three (3) non-platinum metal helicates were screened against cisplatin-sensitive (L1210) and resistant (L1210cisR) murine leukaemia cell lines using a standard methylthiazolyldiphenyl-tetrazolium bromide (MTT) assay. These metal complexes are water-soluble. They exhibited a wide range of cytotoxicities. The complex - [Pt(5,6-dimethyl-1,10-phen)(1S,2S-DACH)]2+ (56MESS) was found to be 163-fold more active than cisplatin against the L1210cisR cell line whereas complexes such as [Pt(4-methyl-phen)(EN)]2+ (4MEEN) are inactive. Correlation analysis of the cytotoxicity data with structures revealed three major structure-activity relationships. Chirality of the DACH ligand, the position and electronegativity of functional groups substituted in the intercalating ligand and type of ancillary ligands (i.e DACH or EN) profoundly influenced the cytotoxicity of these complexes. Encapsulation of metal complexes by different sized curcurbit[n]urals led to varied cytotoxicities. Analysis of these data resulted in the identification of three lead complexes including 56MESS, which has excellent activity in L1210 as well as in L1210cisR cell lines. To understand the biological mechanisms underlying the cytotoxicity of the lead complex 56MESS, genes and pathways in response to 56MESS treatment, in parallel to cisplatin treatment, were investigated using transcriptomics in yeast Saccharomyces cerevisiae. Ninety-three (93) genes were revealed to be important for the cytotoxicity of 56MESS as these genes altered their expressions in response to 56MESS challenge. Bioinformatics analysis of these genes showed that defective iron and copper metabolisms are implicated for the cytotoxic action of this compound. The suppression of biosynthesis of sulphur-containing amino acids and arginine and function of mitochondria could also play a role in the cytotoxicity of 56MESS. In comparison, one hundred and sixty-five (165) genes altered their expressions in response to cisplatin treatment. The genes involved in sulphur uptake and its assimilation and response to DNA damage were up-regulated while the genes involved in de novo purine biosynthesis and one carbon metabolism were suppressed by cisplatin. The differences in the major pathways in response to 56MESS and cisplatin suggest that these two platinum agents have different molecular mechanisms for their cytotoxicity. Cellular assays and gene deletion mutant screenings validated these transcriptomic findings. The results from inductively coupled plasma optical emission spectrometry (ICP-OES) revealed that 56MESS treatment reduced concentrations of the intracellular iron and copper, and increased that of manganese. Analysis of viability phenotypes of deletion mutants of the key genes including FTR1 in the iron and copper metabolisms further supported their involvement in the cytotoxicity of 56MESS. The data therefore suggested that iron and copper transporters were the molecular targets of 56MESS. Further biochemical and mutant analyses showed that glutathione, oxidative stress and mitochondria were important in 56MESS' cytotoxicity. 56MESS treatment arrested cells in G1 phase of the cell cycle. The cytotoxicity data, the structure-activity relationships and the elucidated molecular mechanisms of the most active platinum metallointercalator 56MESS suggested that the platinum metallointercalators of the type [Pt(IL)(AL)]2+ have potential as anticancer agents. The findings reported in this thesis can be used for further development of these complexes.
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Li, Liao. "Chemical Forays of Fungal Metabolites." Phd thesis, 2018. http://hdl.handle.net/1885/148782.
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This thesis contains six chapters and the research presented within focuses on three parts. The first part (chapter one to three) was the isolation of antibacterial and antioxidant mushroom metabolites, and the synthesis towards analogues of discovered natural products. The following part (chapter four) was to assess antioxidant activities of synthetic compounds and investigate their SAR (structure-activity relationship), by use of a developed DPPH assay. The last part (chapter five to six) was the discovery of an abiotic halogenation reaction among a class of fungal metabolites, azaphilones. A series of their synthetic analogues were applied as model compounds to understand the mechanism of the discovered unusual and facile non-enzymatic nucleophilic halogenation reaction.
Chapter one is a review of antioxidants in mushrooms. The components with antioxidant activities discovered from mushrooms were summarised by their chemical structures and representative samples were listed. In addition, the potential mechanisms of those antioxidants were described in this chapter.
In chapter two, extracts of 20 mushrooms from PNG (Papua New Guinea) were screened against both Gram-positive and Gram-negative bacteria, six of them were chosen as chemical survey candidates for their strong antibacterial activities. Extracts of 37 PNG mushrooms were screened for their antioxidant using a modified DPPH assay, 14 of them were chosen as chemical survey candidates based on their antioxidant capacities. In chemical examination guided by bioactivity, five natural products including two novel furan fatty acids (2.1-2.2) and three known compounds, i.e. grifolin (2.3), grifolic acid (2.4) and grifolic acid methyl ether (2.5), were isolated from four selected mushroom samples.
Chapter three described the synthetic efforts towards analogues of three isolated antioxidant fungal metabolites (2.3-2.5). Inspired by 15 synthetic targets, a short and versatile general synthetic route was established to deliver 40 compounds possessing structures related to the natural products. Based on these structures, a compound library was established for antioxidant assessment in the following SAR research. The synthetic work resulted in the preparation of 33 novel structures.
In chapter four, various antioxidant assays and their working mechanisms were reviewed, as well as their corresponding advantages and drawbacks. A developed DPPH assay was optimised to offer an accurate and reproducible antioxidant evaluation for SAR research in the achieved compound library. The results indicated that a structure with an aromatic ring to be allylated with a carbon chain in addition to the presence of phenols, is required to show an antioxidant activity, and the increased length of a carbon chain (more prenyl units) enhances the antioxidant activity.
Chapter five focused on naturally occurring organohalogen compounds with biotic origins. The representative halogenated natural products with a variety of bioactivities were categorised following a chemical structural classification as well as a bioactive classification, to showcase both their structural diversity and bioactive variety. The biosynthetic mechanisms of halogenated natural products were reviewed in this chapter.
Chapter six detailed the investigation of a novel halogenation reaction that was discovered to be occurring with some azaphilone fungal metabolites, for example the conversion of (+)-deschlorosclerotiorin (6.2) into (+)-sclerotiorin (6.1). Various non-halogenated model compounds with an azaphilone core structure were created to shed light on the authenticity of numerous halogenated azaphilones reported as natural products. The ensuing synthetic work resulted in an efficient general procedure producing the required targets. The following investigation of the halogenation revealed a novel, facile, non-enzymatic nucleophilic reaction and its proposed mechanism is discussed. The synthetic efforts resulted in the creation of 22 novel structures.
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Yuan-ShuoHsueh and 薛元碩. "Establishment of a Drug Screening Platform to Study the Effects and Mechanisms of Tyrosine kinase Inhibitors and a Novel HSPAA1 Inhibitor (NVP-AUY922) on Mutant KIT-expression GIST." Thesis, 2012. http://ndltd.ncl.edu.tw/handle/39080318730110331378.
Full textAbstract:
博士<br>國立成功大學<br>臨床藥學與藥物科技研究所<br>101<br>Background
Advanced gastrointestinal stromal tumors (GIST), a KIT oncogene-driven tumor, on imatinib mesylate (IM) treatment may develop secondary KIT mutations to confer IM-resistant phenotype. Second-line sunitinib malate (SU) therapy is largely ineffective for IM-resistant GISTs with secondary exon 17 (activation-loop domain) mutations. Nowadays, several KIT tyrosine kinase inhibitors (TKIs) and heat shock protein 90 (HSP90AA1) inhibitors are under investigation for IM and/or SU-resistant GIST patients. However, there is no notable improvement. In this study, we used commercial available TKIs and a new class of HSP90AA1 inhibitor, NVP-AUY922 (AUY922), to evaluate their potencies for treatment on IM and/or SU-resistant GISTs and to clarify the detailed mechanisms.
Methods and Results
First, we established an in vitro cell-based platform consisting of a series of COS-1 cells expressing KIT cDNA constructs encoding common primary±secondary mutations observed in GISTs, to compare the activity of several commercially available TKIs on inhibiting the phosphorylation of mutant KIT proteins at their clinically achievable plasma steady-state concentration (Css). The inhibitory efficacies on KIT exon 11/17 mutants were further validated by growth inhibition assay on GIST48 cells, and underlying molecular-structure mechanisms were investigated by molecular modeling. Our results showed that SU more effectively inhibited mutant KIT with secondary exon 13 or 14 mutations than those with secondary exon 17 mutations, as clinically indicated. On contrary, at individual Css, nilotinib and sorafenib more profoundly inhibited the phosphorylation of KIT with secondary exon 17 mutations and the growth of GIST48 cells than IM, SU, and dasatinib. Molecular modeling analysis showed fragment deletion of exon 11 and point mutation on exon 17 would lead to a shift of KIT conformational equilibrium toward active form, for which nilotinib and sorafenib bound more stably than IM and SU.
In the other hand, we demonstrated that AUY922 is effective in inhibiting the growth of GIST cells expressing mutant KIT protein, the IM-sensitive GIST882 and IM-resistant GIST48 cells. The growth inhibition was accompanied with a sustained reduction of both total and phospho-KIT proteins and the induction of apoptosis in both cell lines. Surprisingly, AUY922-induced KIT reduction could be partially reversed by pharmacological inhibition of either autophagy or proteasome degradation pathway. The blockade of autophagy alone led to the accumulation of the KIT protein, highlighting the role of autophagy in endogenous KIT turnover. The involvement of autophagy in endogenous and AUY922-induced KIT protein turnover was further confirmed by the colocalization of KIT with MAP1LC3B-, acridine orange-, or SQSTM1-labeled autophagosome, and by the accumulation of KIT in GIST cells by silencing either BECN1 or ATG5 to disrupt autophagosome activity. In addition, AUY922 could reduce KIT mRNA at transcription level without affecting its mRNA stability. Further studies showed that AUY922 treatment would reduce the nuclear activities and protein levels of several transcription factors, such as CEBP, TP53, RELA, and HIF1A in GIST cells. Experiments using DNA affinity precipitation and chromatin immune-precipitation assays showed that TP53 could bind on KIT promoter region (from -365 to -30 nucleotides upstream of the transcriptional start site), and its binding activity was significantly reduced after AUY922 treatment.
Conclusions
Taken together, we show that nilotinib and sorafenib are more active in IM-resistant GISTs with secondary exon 17 mutation than SU that deserve further clinical investigation. Moreover, the results of AUY922 not only highlight its potential application for the treatment of KIT-expressing GISTs, but also provide the first evidence for the involvement of autophagy in endogenous and HSP90AA1 inhibitor-induced KIT degradation in GIST882 and GIST48 cells.