Les acides gras polyinsaturés à longue chaîne (AGPI-LC) de la série n-3 jouent un rôle essentiel dans le fonctionnement cérébral, notamment dans le maintien des processus de plasticité synaptique et de mémoire au cours du vieillissement. Il est maintenant bien admis que ces acides gras peuvent moduler la transcription de gènes impliqués dans les processus de plasticité synaptique sous-tendant les performances mnésiques via leur liaison à des récepteurs nucléaires tels que les PPAR (peroxisome proliferator-activated receptor) et les RXR (retinoid X receptor). Les RXR sont les partenaires communs d’hétérodimérisation de nombreux autres récepteurs, dont le récepteur nucléaire de l’acide rétinoïque (AR), RAR (retinoic acid receptor), métabolite actif de la vitamine A. Ainsi, les RXR jouent un rôle majeur dans la régulation des voies de signalisation des AGPI n-3 et des rétinoïdes.Dans ce contexte, l’objectif de notre travail était de mieux comprendre les mécanismes mis en jeu dans l’action des AGPI-LC n-3 sur les processus neurobiologiques qui sous-tendent les performances mnésiques au cours du vieillissement, notamment en abordant de manière spécifique les mécanismes mis en jeu dans les interactions entre les voies de signalisation des AGPI-LC n-3 et des rétinoïdes. Les approches expérimentales mises en place ont consisté notamment à évaluer chez le rat âgé les effets de supplémentations nutritionnelles en AGPI-LC n-3 et/ou vitamine A sur les performances de mémoire, ainsi que l’action du DHA administré seul sur différents types de mémoire dépendants de l’hippocampe.Nos principaux résultats montrent une altération du métabolisme des acides gras et de la vitamine A au cours du vieillissement. Ces changements métaboliques sont associés à une hypoexpression des voies de signalisation des AGPI n-3 et des rétinoïdes, accompagnée de déficits mnésiques. Nous montrons par ailleurs un effet synergique d’une supplémentation nutritionnelle en AGPI-LC n-3 et en vitamine A sur le maintien des performances de mémoire chez l’animal âgé. De plus, cette supplémentation permet de prévenir, dans l’hippocampe, les changements de composition en AGPI n-3 ainsi que l’hypoexpression des ARNm de RXRγ et de kinases régulées par l’AR et les AGPI n-3.Ces résultats plaident en faveur d’une action synergique des AGPI-LC n-3 et de la vitamine A sur le maintien des performances mnésiques au cours du vieillissement, via une action combinée sur leurs voies de signalisation, lesquelles participeraient ainsi au maintien de certains processus de plasticité synaptique sous-tendant la mémoire et qui se trouvent être altérés avec l’âge. / N-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFAs) play a critical role in brain functioning, notably in the maintenance of synaptic plasticity and memory processes during aging. It is now well accepted that n-3 PUFAs can modulate transcription of genes involved in synaptic plasticity processes underlying the memory performances through binding and activating nuclear receptors such as PPARs (peroxisome proliferator-activated receptors), and RXRs (retinoid X receptors). RXRs are the common heterodimerization partner of numerous nuclear receptors, among them the retinoic acid receptor (RAR), which binds retinoic acid (RA), the active metabolite of vitamin A. Thus, RXRs play a key role in the regulation of n-3 PUFA and retinoid signaling pathways.In this context, the aim of this work was to study the mechanisms involved in the action of n-3 PUFAs on neurobiological processes underlying the memory performances during aging, and more particularly by assessing specifically the molecular mechanisms involved in interactions between n-3 PUFA and retinoid signaling pathways. For this purpose, we studied the effects of dietary supplementations in n-3 PUFAs and/or vitamin A on memory performances in aged rats. We also studied the specific effect of unesterified DHA pharmacological treatments on different hippocampal-dependent memory tasks.Our main results showed impairments in fatty acid and vitamin A metabolism during aging. These modifications were associated with an hypoexpression of n-3 PUFA and retinoid signaling pathways, and memory deficits. Furthermore, we demonstrated a synergetic effect of the joint n-3 LC-PUFA and vitamin A dietary supplementation on the maintenance of memory performances in aged rats. Moreover, in the hippocampus, this supplementation prevented the n-3 PUFA compositional changes, and also the mRNA hypoexpression of RXRγ and of several kinases regulated by RA and n-3 PUFAs which were observed during aging.These results suggest a beneficial synergetic effect of n-3 LC-PUFAs and vitamin A on the maintenance of memory performances during aging, through a combined action on their signaling pathways, which could be involved in the maintenance of synaptic plasticity processes underlying memory performances impaired during aging.

Os projetos genoma têm fornecido uma grande quantidade de informação sobre a arquitetura gênica e sobre a configuração física de suas respectivas regiões flanqueadoras (RF). Estas RF contêm informações com o potencial de auxiliar na elucidação de vários processos biológicos, como os mecanismos de expressão gênica e de sua regulação. Estes mecanismos são de extrema importância para a compreensão do correto funcionamento dos organismos e das patologias que os afetam. Uma parte significativa dos mecanismos de controle de expressão gênica atuam na fase transcricional. Na base destes mecanismos está o recrutamento de proteínas que se ligam às regiões promotoras da transcrição, as quais são segmentos específicos de DNA que podem estar localizados tanto próximos à região de início da transcrição (TSS) quanto a centenas ou até a milhares de pares de bases dela. Essas proteínas compõem a maquinaria transcricional e podem ativar ou inibir o processo de transcrição. Experimentalmente, os segmentos regulatórios podem ser identificadas utilizando métodos complexos de biologia molecular, tais como SELEX, ChiP-ChiP, ChIP-Seq, dentre outros. Uma estratégia alternativa aos métodos experimentais é a utilização de metodologias computacionais. Análises computacionais tendem a ser mais rápidas, baratas e flexíveis do que protocolos experimentais, além de poderem ser utilizadas em larga escala. Atualmente, os métodos computacionais disponíveis necessitam de informações experimentais para a definição de padrões globais de preferências de sequências de DNA para a ligação de fatores de transcrição (TFBS, em inglês transcription factor binding sites). Entretanto, esses métodos apresentam uma elevada taxa de falso positivos e, por vezes, apresentam também taxas significativas de falso negativos, além de serem limitados ao estudo de fatores de transcrição de espécies bem conhecidas, o que diminui a área de aplicação dos mesmos. Diante deste cenário, o uso de métodos computacionais que não necessitem da informação referente aos sítios de ligação, bem como os que utilizem parâmetros mais robustos de detecção dos resultados, em detrimento dos escores de pontuação provindos de alinhamentos, podem acrescentar uma sensível melhoria ao processos de predição de regiões regulatórias. Neste projeto, foi desenvolvido um novo modelo computacional (TFBSAnalyzer) para análise e identificação de TFBS em elementos regulatórios, que utiliza técnicas de modelagem molecular para a construção de complexos entre um fator de transcrição ancorado a estruturas de DNA com sequências variáveis de bases e, através de cálculos termodinâmicos de entalpia de ligação, determina uma função de pontuação baseada na energia de ligação e realiza a predição de sítios de ligação ao DNA para o fator de transcrição em análise. Esta abordagem foi testada com três fatores de transcrição como sistemas-modelo, pertencentes à família dos receptores nucleares, a saber: o receptor de estrógeno ER-alfa (Estrogen Receptor Alpha), o receptor de ácido retinoico RAR-beta (Retinoid Acid Receptor Beta) e o receptor X retinóico RXR (Retinoid X Receptor). Os modelos previstos computacionalmente foram comparados aos dados experimentais disponíveis para estes receptores nucleares, os quais apresentaram as seguintes taxas de FP/FN: 10%/0 para RAR-beta e RXR, 21%/6% para ER-alfa. Também simulamos um experimento de ChIP-seq do ER-alfa no genoma humano, cujos genes selecionados foram submetidos a uma análise de enriquecimento de fatores de transcrição curados experimentalmente, que fazem sua regulação, revelando que o receptor de estrógeno está realmente envolvido no processo. Para mostrar a aplicabilidade geral de nosso método, nós modelamos a distribuição de energia de ligação para o receptor NHR-28 isoforma a de Caenorhabditis elegans com DNA . Obtivemos distribuições de energia semelhantes àquelas encontradas para os NRs modelos, portanto seria possível aplicar o método para buscar possíveis TFBSs para este receptor no genoma de C. elegans. Os dados gerados e as metodologias desenvolvidas neste projeto devem acrescentar uma sensível melhoria aos processos de predição de regiões regulatórias e consequentemente auxiliar no entendimento dos mecanismos envolvidos no processo de expressão gênica e de sua regulação. / The genome projects have provided a lot of information about the genetic architecture, as well as on the physical configuration of their flanking regions (FR). These FR have the potential to aid in the elucidation of many biological processes, such as the mechanisms involved in gene expression and its regulation. These mechanisms are extremely important for undeerstanfind the correct functioning of organisms as well as the pathologies that affect them. A significant part of the control mechanisms of gene expression act during transcription. On the basis of this mechanisms is the recruitment of proteins that bind to promoter regions of transcription, which are specific segments of DNA that can be located either near the transcription start site or at hundreds or even thousands of base pairs away. These proteins form the transcription machinery, which can activate or inhibit the transcription process. The regulatory segments can be identified experimentally using complex methods of molecular biology, such as SELEX, ChIP-chip, ChIP-seq, among others. An alternative strategy to these experimental methods is the use of computational methodologies for predicting regulatory regions. Computational analysis tend to be faster, cheaper and more flexible than the experimental protocols, and can be used on a larger scale. Currently, the available computational methods require information previously obtained from experiments in order to define global standards of preference of DNA-Binding sequences for transcription factors (TFBS - Transcription Factor Binding Sites). However, these methods have a high rate of false positives and sometimes also have significant rates of false negatives, besides being limited to the study of transcription factors of well-known species, which decreases their application area. In this scenario, the use of computational methods that do not require previous information concerning the binding sites and use more robust parameters of results detection, instead of alignment scores, may add significant improvement to the processes of predicting regulatory regions. In this project, we developed a new computational model TFBSAnalyzer) for analysis and identification of regulatory elements using molecular modeling techniques for the construction of complexes between a transcription factor bound to specific DNA structures with variable sequences of bases and, by means of thermodynamic calculations of bond enthalpy, provides a scoring function based on the binding energy and predicts the DNA binding sites for the transcription factor in analysis. This approach was tested initially with three transcription factors as models, belonging to the nuclear receptor family, namely estrogen receptor ER-alpha (Estrogen Receptor Alpha), the retinoic acid receptor RAR-beta (Retinoid Acid Receptor Beta) and the retinoic X receptor RXR (Retinoid X Receptor). The computationally predicted models were compared to experimental data available for these nuclear receptors, and presented the following rates of FP/FN: 10%/0 for RAR-beta and RXR, 21%/6% for ER-alpha. We also simulated an experiment of ChIP-seq with ER-alpha with the human genome, where the selected genes were subjected to a transcription factor enrichment analysis, with curated information, revealing that the estrogen receptor is indeed involved in their regulation. To show that our method has a general applicability, we modeled the binding energy distribution for the NHR-28 receptor, isoform a, from Caenorhabditis elegans. The energy distributions obtained were similar to the ones obtained for the model NR, so it would be possible to use the method and search for possible TFBS in the C. elegans genome. The data generated and the methodologies developed in this project should add a significant improvement to the prediction processes of regulatory regions and, consequently, help to understand the mechanisms involved in the gene expression process and its regulation.

In marine teleosts that spawn pelagic eggs (pelagophils), the process of oocyte hydration that occurs during meiosis resumption is a key physiological process for the survival of the eggs in the ocean. Previous studies have discovered the role of a teleost-specific aquaporin water channel (Aqp1b) during fish oocyte hydration, but direct experimental evidence for the function of Aqp1b in oocytes is still lacking. In addition, the molecular regulation of the Aqp1b-mediated mechanism remains poorly understood. In this context, the main objectives of the present thesis were to investigate the evolutionary origin of aqp1ab in teleosts, to provide functional evidence of the role of Aqp1b during oocyte hydration, and to begin to dissect the molecular mechanisms involved in the transcriptional regulation of aqp1b in the oocyte of marine teleosts. By integrating the molecular phylogeny with synteny and structural analyses we show that the teleost aqp1aa and -1ab paralogs (previously annotated as aqp1a and -1b, respectively) arose by tandem duplication, and that the Aqp1ab C-terminus is the most rapidly evolving subdomain within the vertebrate aquaporin superfamily. The functional role of Aqp1ab was investigated in Atlantic halibut (Hippoglossus hippoglossus), a marine acanthomorph teleost that spawns one of the largest pelagic eggs known. Using immunological inhibition of Aqp1ab in halibut oocytes and artificial expression of the halibut paralog Aqp1aa, we demonstrate that Aqp1ab is required for full hydration of oocytes undergoing meiotic maturation. To investigate the aqp1ab transcriptional regulation in oocytes, we isolated the 5’-flanking region of the gilthead seabream (Sparus aurata) aqp1ab gene which contains regulatory cis-elements for the nuclear progestin receptor (Pgr) and SOX transcription factors. The Pgr, as well as sox3 and -8b transcripts, are co-expressed in seabream oo-gonia, whereas in primary growth oocytes, when aqp1ab mRNA and protein are synthesized, the Pgr is translocated into the nucleus. In contrast, sox9b is highly expressed in more advanced oocytes showing the depletion of aqp1ab transcripts. In the seabream, four different pgr transcript variants are expressed in primary growth ovaries which are generated by alternative pre-mRNA splicing. Seabream wild-type Pgr shows the highest transactivation response to progestins such as 17α,20β-dihydroxy-4-pregnen-3-one (17,20β-P) and 17α,20β,21-trihydroxy-4-pregnen-3-one (17,20β,21-P), whereas two of the N-terminally truncated Pgr isoforms regulate novel nuclear and cytosolic mechanisms of dominant-negative repression of Pgr-mediated transcription. Transactivation assays on the aqp1ab promoter demonstrated that aqp1ab transcription is dependent on wild-type Pgr, with Sox3 and -8b acting synergistically, while Sox9b acts as a repressor. Incubation of primary ovarian explants in vitro with 17,20β-P, followed by chromatin immunoprecipitation, confirmed that 17,20β-P-activated Pgr enhanced aqp1ab promoter activation. The production of 17,20β-P in seabream primary growth ovaries in vivo was consistent with the expression of P450c17-II (Cyp17a2) and 20β-hydroxysteroid dehydrogenase (Cbr1), enzymes needed for progestins synthesis, in granulosa cells associated with primary growth oocytes, and with a high concentration of 17,20β-P. Incubation of primary ovarian explants with recombinant piscine follicle-stimulating hormone (rFsh) in vitro stimulated 17,20β-P synthesis, which was reduced in the presence of Cbr1 inhibitors. The rFsh-mediated production of 17,20β-P correlated with the up-regulation of cyp17a2 and cbr1 transcription, as well as of wild-type pgr mRNA and protein levels. Altogether, these data suggest that aqp1ab transcription in seabream primary growth oocytes is under Fsh regulation through the synthesis of progestins. The results of this thesis show that the Aqp1ab mediated mechanism for oocyte hy-dration is likely conserved in marine teleosts. In addition, the tight transcriptional reg-ulation of Aqp1ab during oogenesis highlights the essential physiological role of this water channel and opens new research avenues for understanding the molecular basis of egg formation in marine fish. / La hidratación de los oocitos de teleósteos marinos que producen huevos pelágicos es clave para la supervivencia de los embriones en el océano. Estudios previos han descu-bierto el papel de una acuaporina específica de teleósteos (Aqp1b) durante este proceso, pero se carece todavía de evidencias experimentales directas, así como información sobre la regulación molecular de la Aqp1ab. En la presente tesis, estudios iniciales con el fletan Atlántico (Hippoglossus hippoglossus) confirman que los parálogos aqp1aa y -1ab de teleósteos han surgido probablemente por duplicación génica en tándem, y han demostrado el papel esencial de la Aqp1ab durante la hidratación del oocito. Para investigar el control transcripcional del gen aqp1ab en los oocitos de la dorada (Sparus aurata) se ha aislado su región promotora, la cual contiene elementos cis-reguladores de unión al receptor nuclear de progestinas (Pgr), como la 17α,20β-dihidroxi-4-pregnen-3-ona (17,20β-P), y factores de transcripción Sox. Estudios de localización subcelular indican que el Pgr aparece en el citoplasma de las oogonias, así como en el núcleo de oocitos en crecimiento primario (pre-vitelogénicos) coincidiendo con la activación de la expresión de aqp1ab. En este estadio también se expresan cuatro isoformas diferentes del Pgr, dos de las cuales pueden inhibir la transcripción mediada por el Pgr de forma dominante negativa. Las oogonias también expresan sox3 y -8b, mientras que el sox9b aparece en el estadio de alveolo cortical, cuando se reduce la expresión de aqp1ab. Ex-perimentos de transactivación indican que el Pgr activa la transcripción de aqp1ab, con Sox3 y -8b actuando de forma sinérgica, mientras que el Sox9b reprime este mecanismo. El papel del Pgr se ha investigado sobre explantes ováricos pre-vitelogénicos incubados in vitro, lo cual ha demostrado que la 17,20β-P, producida en las células de la granulosa en respuesta a la hormona folículo estimulante, activa el promotor de aqp1ab en el oocito induciendo la síntesis de Aqp1ab. Los resultados de esta tesis revelan por primera vez una estricta regulación transcripcional del gen aqp1ab durante la oogénesis de teleósteos marinos, lo cual remarca la función fisiológica esencial de este canal de agua durante la formación de los huevos pelágicos.

Creating receptors for control of transcription with arbitrary small molecules has widespread applications including gene therapy, biosensors, and enzyme engineering. Using the combination of high throughput docking, codon randomization, and chemical complementation, we have created new receptors to control transcription with small molecules. Chemical complementation, a new method of protein engineering, was used to discover retinoid X receptors (RXR) variants that are activated by compounds that do not activate wild-type RXR. A first library of 32,768 RXR variants was designed for the synthetic retinoid-like compound LG335. The library produced ligand-receptor pairs with LG335 that have a variety of EC50s and efficacies. One engineered variant has essentially the reverse ligand specificity of wild-type RXR and is transcriptionally active at 10 and #64979;fold lower LG335 concentration than wild-type RXR with 9cRA in yeast. The activity of this variant in mammalian cells correlates with its activity in yeast. A second library of 262,144 RXR variants was designed for two purposes: (i) to develop a high-throughput chemical complementation method to select variants that have high efficacies and low EC50s; and (ii) to find variants which are activated by small molecules not known to bind RXR variants. Selection conditions were manipulated to find only variants with high efficacies and low EC50s. This library was also selected for variants that activate transcription specifically in response to gamma-oxo-1-pyrenebutyric acid (OPBA), which is different from any known RXR ligand. OPBA was chosen as a potential ligand using high-throughput docking with the software program FlexX. Two variants are activated by OPBA with an EC50 of 5 mM. This is only ten-fold greater than the EC50 of wild type RXR with its ligand 9cRA (500 nM) in yeast. An improved method synthesizing LG335 and a method for quantifying intracellular ligand concentrations were developed. Although the LG335 synthetic method has an additional step, the overall yield was improved to 8% from 4% in the original publication. Liquid chromatography and mass spectrometry was used to quantify the intracellular concentration of LG335, which was found to be within four fold of the LG335 concentration in the media.

The human vitamin D receptor (hVDR) is a member of the nuclear receptor superfamily, involved in calcium and phosphate homeostasis; hence implicated in a number of diseases, such as Rickets and Osteoporosis. This receptor binds 1α,25-dihydroxyvitamin D3 (also referred to as 1,25(OH)2D3) and other known ligands, such as lithocholic acid. Specific interactions between the receptor and ligand are crucial for the function and activation of this receptor, as implied by the single point mutation, H305Q, causing symptoms of Type II Rickets. In this work, further understanding of the significant and essential interactions between the ligand and the receptor were deciphered, through a combination of rational and random mutagenesis. A hVDR mutant, H305F, was engineered with increased sensitivity towards lithocholic acid, with an EC50 value of 10 µM and 40 + 14 fold activation in mammalian cell assays, while maintaining wild-type activity with 1,25(OH)2D3. Furthermore, via random mutagenesis, a hVDR mutant, H305F/H397Y, was discovered to bind a novel small molecule, cholecalciferol, a precursor in the 1α,25-dihydroxyvitamin D3 biosynthetic pathway, which does not activate wild-type hVDR. This variant, H305F/H397Y, binds and activates in response to cholecalciferol concentrations as low as 100 nM, with an EC50 value of 300 nM and 70 + 11 fold activation in mammalian cell assays.

Nuclear receptors (NRs) are important transcription factors involved in the regulation of a variety of physiological processes such as embryonic development, cell differentiation and homeostasis (for review, see Mangelsdorf et al., 1995 TenBaum and Baniahrned, 1997). In contrast to membrane bound receptors, they bind small lipophilic ligands and function in the nucleus as ligand-modulated transcription factors. The ligands for nuclear receptors include steroids (glucocorticoids, progestins, mineralocorticoids, androgens and estrogens), vitamin D3, retinoids, thyroid hormone, prostaglandins, farnesoids etc. Several other nuclear receptors are classified as orphan receptors for which no ligand has yet been identified. More than 300 nuclear receptors have now been identified and together these proteins comprise the single largest family of metazoan transcription factors, the nuclear receptor superfamily. Recently, a unified nomenclature has been evolved (nuclear receptor nomenclature committee, 1999), a summary of which is presented in Table 1.

Le récepteur X des farnésoïdes (FXR) fait partie de la superfamille des récepteurs nucléaires et agit comme un facteur de transcription suite à la liaison d’un ligand spécifique. Le récepteur FXR, activé par les acides biliaires, joue un rôle essentiel dans le métabolisme des lipides et du glucose en plus de réguler l’homéostasie des acides biliaires. Notre laboratoire a récemment mis en évidence une nouvelle voie de régulation du récepteur PPARγ en réponse au récepteur de la ghréline. En effet, la ghréline induit l’activation transcriptionnelle de PPARγ via une cascade de signalisation impliquant les kinases Erk1/2 et Akt, supportant un rôle périphérique de la ghréline dans les pathologies associées au syndrome métabolique. Il est de plus en plus reconnu que la cascade métabolique impliquant PPARγ fait également intervenir un autre récepteur nucléaire, FXR. Dans ce travail, nous montrons que la ghréline induit l’activation transcriptionnelle de FXR de manière dose-dépendante et induit également la phosphorylation du récepteur sur ses résidus sérine. En utilisant des constructions tronquées ABC et CDEF de FXR, nous avons démontré que la ghréline régule l’activité de FXR via les domaines d’activation AF-1 et AF-2. L’effet de la ghréline et du ligand sélectif GW4064 sur l’induction de FXR est additif. De plus, nous avons démontré que FXR est la cible d’une autre modification post-traductionnelle, soit la sumoylation. En effet, FXR est un substrat cellulaire des protéines SUMO-1 et SUMO-3 et la sumoylation du récepteur est ligand-indépendante. SUMO-1 et SUMO-3 induisent l’activation transcriptionnelle de FXR de façon dose-dépendante. Nos résultats indiquent que la lysine 122 est le site prédominant de sumoylation par SUMO-1, quoiqu’un mécanisme de coopération semble exister entre les différents sites de sumoylation de FXR. Avec son rôle émergeant dans plusieurs voies du métabolisme lipidique, l’identification de modulateurs de FXR s’avère être une approche fort prometteuse pour faire face à plusieurs pathologies associées au syndrome métabolique et au diabète de type 2. / The farnesoid X receptor (FXR) is a ligand-activated transcription factor within the nuclear receptor superfamily. FXR is activated by bile acids and plays a crucial role in the regulation of glucose and lipid metabolism and in bile acid homeostasis. Our group has recently identified the contribution of the ghrelin receptor in the regulation of the nuclear receptor PPARγ. Indeed, ghrelin triggers transcriptional activation of PPARγ through a concerted signaling cascade involving Erk1/2 and Akt kinases. These results support the peripheral actions of ghrelin in diseases associated with the metabolic syndrome. It is recognized that there is interplay between PPARγ metabolic cascade and FXR. Here, we demonstrate that ghrelin promotes FXR transcriptional activity in a dose-dependent manner and also promotes its phosphorylation on serine residues. By using truncated ABC and CDEF constructs of FXR, we found that ghrelin induces FXR activity through the AF-1 and AF-2 activation domains. The ghrelin-induced FXR activity is additive to the induction by the selective agonist GW4064. Also, we demonstrate that FXR is the target of sumoylation, another post-translational modification. In particular, FXR is modified by SUMO-1 and SUMO-3 in a ligand-independent manner. SUMO-1 and SUMO-3 promote dose-dependent transcriptional activity of FXR. Our results show that lysine 122 is the prevalent site of sumoylation by SUMO-1, though a compensation mechanism seems to exist between the various sumoylation sites of FXR. With its emerging role in several metabolic cascades, identification of FXR modulators represents a promising approach for the treatment of the metabolic syndrome and type 2 diabetes.

Le criblage virtuel est largement employé pour la recherche de nouveaux médicaments.La sélection de structures pour les méthodes de criblage virtuel basées sur la structure reste problématique. Nous avons montré que les propriétés physico-chimiques du site de liaison, critères simples et peu coûteux en temps de calcul, pouvaient être utilisées pour guider celle-ci.L’évaluation des méthodes de criblage virtuel, critique pour vérifier leur fiabilité, repose sur la qualité de banques d’évaluation. Nous avons construit la NRLiSt BDB, n’incluant que des données vérifiées manuellement et prenant en compte le profil pharmacologique des ligands. Une étude à l’aide du logiciel Surflex-Dock montre qu’elle devrait devenir la base de données de référence, pour l’évaluation des méthodes de criblage virtuel et pour rechercher de nouveaux ligands des récepteurs nucléaires. L’application d’un protocole hiérarchique de criblage in silico/in vitro, a permis d’identifier de nouveaux composés inhibiteurs de l’IL-6, potentiellement utilisables dans le traitement de la polyarthrite rhumatoïde. Les résultats in vitro devront être confirmés par des tests in vivo. / Virtual screening is widely used in drug discovery processes.Structure selection in structure-based virtual screening methods is still problematic. We showed that simple and “low cost” binding site physico-chemical properties could be used to guide structure selection.The evaluation of virtual screening methods, necessary to ensure their reliability, relies on benchmarking databases quality. We created the NRLiSt BDB, gathering only manually curated data and taking into account ligands pharmacological profiles. A study using Surflex-Dock showed that the NRLiSt BDB should become the reference, both for the evaluation of virtual screening methods and for the identification of new ligands of the nuclear receptors.The use of a in silico/invitro hierarchical approach screening allowed to identify new IL-6 inhibitors, that could be used in rheumatoid arthritis treatment. In vitro results should be confirmed in vivo.

[Truncated abstract] Breast cancer is the cause of significant suffering and death in our community. It is now estimated that the risk of developing breast cancer for an Australian woman before the age of 85 is 1 in 8, with this risk rising for unknown reasons. While mortality rates from breast cancer are falling due to increased awareness and early detection, few new treatments have been developed from an advanced understanding of the molecular basis of the disease. From decades of scientific research it is clear that estrogen (E2) has a large role to play in breast cancer. However, the basic mechanism behind E2 action in breast cancer remains unclear. E2 plays a fundamental role in breast cancer cell proliferation and is highly expressed in breast cancers, thus, it is important to understand both E2 and its receptor, the estrogen receptor (ER). The ER is a member of the nuclear receptor (NR) superfamily. The NR superfamily consists of a large group of proteins which regulate a large number of homeostatic proteins together with regulator proteins termed coregulators and corepressors. SRA (steroid receptor RNA activator) is the only known RNA coactivator and augments transactivation by NRs. SRA has been demonstrated to play an important role in mediating E2 action (Lanz et al., 1999; Lanz et al., 2003) and its expression is aberrant in many human breast tumors, suggesting a potential role in breast tumorigenesis (Murphy et al., 2000). Despite evidence that an alternative splice variant of SRA exists as a protein (Chooniedass-Kothari et al., 2004), it has been conclusively shown that SRA can function as an RNA transcript to coactivate NR transcription (Lanz et al., 1999; Lanz et al., 2002; Lanz et al., 2003). The precise mechanism by which SRA augments ER activity remains unknown. However, it is currently hypothesized that SRA acts as an RNA scaffold for other coregulators at the transcription initiation site. Several SRA stem loops have been identified as important for SRA function, including structure (STR) 1, 5 and 7 (Lanz et al., 2002; Zhao et al., 2007). Previously, I sought to identify SRA-binding proteins using a specific stem-loop structure of SRA (STR7) that was identified as both important for its coactivator function (Lanz et al., 2002) and also as a target for proteins from breast cancer cell extracts (Hatchell, 2002). From a yeast E. Hatchell Abstract iii III hybrid screen using STR7 as bait, I identified a novel protein which was named SLIRP (Patent Number: WO/2007/009194): SRA stem-Loop Interacting RNA-binding Protein (Hatchell, 2002; Hatchell et al., 2006). '...' This thesis demonstrates that SLIRP modulates NR transactivation, provides mechanistic insight into interactions between SRA, SRC-1, HSP-60 and NCoR and suggests that SLIRP may regulate mitochondrial function. These studies contribute significantly to the growing field of NR biology, and contribute more specifically to the elucidation of estrogen action in breast cancer. Furthermore, it lays a strong and exciting foundation for further studies to evaluate SLIRP as a biomarker and potential therapeutic target in hormone dependent cancers.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.