Orientador: Munir Salomão Skaf / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-22T05:21:38Z (GMT). No. of bitstreams: 1 Souza_PauloCesarTellesde_D.pdf: 16006519 bytes, checksum: 82d3ddc86356ae8c995467ed56947170 (MD5) Previous issue date: 2013 / Resumo: Receptores Nucleares (NRs) são proteínas que regulam a transcrição de genes, sendo alvos importantes para o desenho de fármacos. NRs são formados por quatro domínios, sendo o mais essencial deles, o Domínio de Ligação com o Ligante (LBD), responsável pelo reconhecimento seletivo de ligantes e ativação de sua função. Nesta Tese são utilizadas simulações de Dinâmica Molecular (MD) para o estudo do LBD de dois importantes NRs: Receptor do Hormônio Tireoideano (TR) e Receptor de Estrogênios (ER). Os estudos envolvendo o LBD do TR iniciaram-se pela investigação de um novo segundo sítio de ligação dos hormônios tireoideanos (T3 e T4). Foi mostrado que os hormônios se mantêm ancorados ao segundo sítio, possuindo grande mobilidade e múltiplos modos de ligação. Estimativas do DG de dissociação indicam que este novo sítio deve existir em solução aquosa, sendo T4 o hormônio com maior afinidade e candidato a ligante natural. O segundo objetivo da Tese foi a modelagem molecular da estrutura do LBD do TR sem ligantes (apo-TR) através da combinação de resultados de simulações de MD e experimentos de troca de hidrogênio/deutério. O modelo do apo-TR obtido mostra que a-hélice H12 ancora-se na H3, o que explica as mudanças de hidratação nesta região apontadas pelos experimentos. O terceiro objetivo da Tese foi elucidar os mecanismos moleculares que levam a alterações da atividade em duas mutações dos TRs: M369Ra e P452Lb. As simulações de M369Raindicam que o resíduo mutado interage com T3 no segundo sítio, o que pode explicar o aumento de sua afinidade por este ligante. As simulações de P452Lbsugeriram que esta mutação altera a posição da H12, levando a redução da cavidade de interação com co-ativadores e das interações do T3 com o primeiro sítio. O último estudo da Tese investigou uma conformação alternativa do LBD do ERb , que tem potencial para explicar como este subtipo promove repressão parcial da transcrição de genes regulada pelo ERa. Os cálculos de DG entre as conformaçõs clássica e alternativa indicam que a alternativa é estável, sendo o mínimo global de energia livre. / Abstract: Nuclear receptors (NRs) are proteins that regulate the gene transcription and thus are important targets for drug development. NRs are composed of four structural domains. The most important of them is the Ligand Binding Domain (LBD), responsible for the selective recognition of ligands and activation of NR function. In this Doctoral Thesis, Molecular Dynamics (MD) Simulation are used to study two important NRs LBD: Thyroid Hormone Receptor (TR) and Estrogen Receptor (ER). Studies involving TR began by investigating a new second binding site of thyroid hormones (T3 and T4) in the TR LBD. It has been shown that hormones remain anchored to the second site and have high mobility and multiple binding modes. Estimates of dissociation DG indicate that this new site can exist in aqueous solution. T4 has the higher affinity and may be the natural ligand of this site. The second objetive of the Thesis was the molecular modeling of the TR LBD structure without ligands (apo-TR) by combining results of MD simulations and hydrogen deuterium exchange experiments. The obtained model of apo-TR shows that H12 a-helix is anchored in H3 which explains the hydration changes in this region indicated by the experiments. The third goal was to elucidate the molecular mechanisms that lead to changes in the activity of two TR mutations: M369Ra and P452Lb. Simulations of M369Ra indicate that the mutated residue can interact directly with T3 in the second binding site, explaining the increase of its affinity. Simulations of P452Lbsuggested that this mutation changes the H12 position, leading to loss of ligand interaction with the rst binding site and reduction of coactivator cavity. The last study investigated a new alternative conformation of ERb LBD, which has the potential to explain how this subtype promotes the partial repression of ERagene transcription. Calculation of DG between classic and alternative conformations indicate that the alternative is stable and the global minimum of free energy. / Doutorado / Físico-Química / Doutor em Ciências

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The nuclear receptor superfamily is responsible for regulating the expression of genes involved in development, reproduction and metabolism. These transcription factors control the expression of their target genes through the binding of small molecule regulators to their ligand binding domains. Classical nuclear receptors include the steroid receptors, which bind endocrine hormones and have been important targets of pharmaceutical intervention. However, approximately one half of the human nuclear receptors remain orphans and are without known cognate ligands. Focusing on the Drosophila orthologues of these orphan receptors, this project used mass spectrometry to identify the chemical diversity associated with the receptors following expression in recombinant systems. In a genome-wide screen of Drosophila nuclear receptors, this approach identified co-purifying molecules with a number of receptors. The physiological relevance of these putative ligand/receptor pairs was determined through biochemical analysis, in vivo characterization and structure determination. Ligand(s) or the ligand state was identified for the Drosophila receptors: DHR3, DHR96, E75, Ftz-f1 and USP. Of these, three were validated through the efforts of this project, and independent groups confirmed the remaining two. The most significant findings were the discoveries that the fly nuclear receptor E75 is regulated by heme, gas and redox, and that there is a similar regulatory scheme in the human orthologues, Reverbα and β. Furthermore, crystallization of the heme-bound Rev-erbβ ligand binding domain was also achieved, and this provided key insights into the mechanism of ligand regulation for the Rev-erbs. This project highlighted the role of nuclear receptors in metabolic surveillance. The ligands/signals identified in association with these receptors include: cholesterol, dehydrocholesterol, heme, NO, CO, redox and phospholipids. Unlike the classical steroid hormones, these are not dedicated signaling molecules, but instead are key substrates or products of metabolism. In the context of nuclear receptor signaling, I hypothesize that these metabolites serve as metabolic indicators/signals in the regulation of development and metabolism. Furthermore, four of these Drosophila receptors comprise the ecdysone-response pathway in the developing fly. Taken together, this suggests that both the metabolic state of the organism and steroid hormones drive nuclear receptor regulation of development.

Cytochrome P450 enzymes (P450s) are involved in cancer development and treatment due to their roles in the oxidative metabolism of various endogenous (e.g. oestrogen) and exogenous (e.g. tamoxifen) compounds. It is well-known that intermediate P450 metabolites derived from oestrogen metabolism are associated with breast carcinogenesis. The main aim of this project was to profile the cytochrome P450 and P450-regulatory nuclear receptor mRNAs in a series of breast cancer cell lines (BCCs) and compare this profile with normal breast cells. This study used the qualitative reverse transcriptasepolymerase chain reaction (RT-PCR) to detect mRNA expression of target genes. Results showed CYP1B1, CYP2D6, CYP2J2, CYP2R1, CYP2U1 and CYP4X1 mRNA to be present in all cell lines. CYP2A6, CYP2C8, CYP2C18, CYP2F1 and CYP4Z1 mRNA were expressed in oestrogen receptor (ER)-positiveCaucasian and ER-negative Afro- Caribbean BCCs. Although no differences in P450 mRNA were observed between the different ethnic groups, these preliminary findings suggest potential similarities in the ERpositive Caucasian and ER-negative Afro-Caribbean BCCs which warrant further investigation The CYP4Z1 PCR product was identified as two distinct bands. Specific primer sets were used to demonstrate potential intron retention in CYP4Z1. Using established in vitro models for the study of regulatory mechanisms of CYP4Z1, T47D and ZR-75-1 breast cancer cell lines were used to determine the appropriate nuclear receptors (i.e. progesterone receptor, glucocorticoid receptor or peroxisome proliferator-activated receptor alpha ). These findings suggest that there may be an alternative receptor mechanism involved in CYP4Z1 mRNA induction in these cells. In conjunction, pre-treatment of these two cell lines with the RNA synthesis inhibitor actinomycin D followed by the agonists showed a significant reduction (p < 0.05) of CYP4Z1 mRNA levels and inhibited CYP4Z1 induction by either progesterone, dexamethasone or pirinixic acid, indicating that these agonists have effects on CYP4Z1 mRNA transcription or stability. In contrast, cycloheximide differentially affected the level of CYP4Z1 mRNA induction by these agonists. Taken together, these results suggest that CYP4Z1 mRNA induction in T47D and ZR-75-1 is mediated through differential cell type specific regulatory mechanisms and there is evidence for differential regulation of the splice variants.

CAR (Constitutive Androstane Receptor, NR1I3) et PXR (Pregnane X Receptor, NR1I2) sont deux récepteurs nucléaires dédiés à la reconna issance et à l'élimination de molécules lipophiles potentiellement toxiques pour l'organisme. Ces facteurs de transcription peuvent être activés par des ligands d'origines et de structures diverses (médicaments, polluants environnementaux, produits de l'alimentation et de phytothérapies). L'activation de ces récepteurs entraîne l'expression des gènes majeurs de la fonction de détoxication entéro-hépatique (CYP450, transférases, transporteurs) permettant l'élimination de ces toxiques. Dans ce travail, nous avons dans un premier temps 1) montré que CAR contrôle l'expression de Spot14, une protéine pro-lipogénique, et 2) nous avons identifié une nouvelle isoforme de PXR (PXR-small) codant uniquement pour le domaine de liaison des ligands de PXR. Nous avons pu déterminer les origines de transcription par 5'-RACE PCR et montrer que PXR-small représente environ 10% de l'ensemble des transcrits de PXR dans le tissu hépatique sain par une approche de PCR qua ntitative. Nous avons pu détecter sa présence par western-blot sur des extraits de protéines nucléaires issus de tissus hépatiques et de lignées cellulaires hépatiques. Par des expériences de gel retard, nous avons observé que cette nouvelle isoforme tronquée, qui ne code que pour le LBD de PXR, ne peut pas se lier à l'ADN. Des expériences de gènes rapporteurs suggèrent que cette isoforme se comporte comme un dominant négatif de PXR. Enfin, la présence d'un ilot CpG situé juste en amont de PXR-small suggère que cette nouvelle isoforme pourrait être régulée épigénétiquement par méthylation, notamment dans les cellules tumorales. / CAR (Constitutive Androstane Receptor, NR1I3) and PXR (Pregnane X Receptor, NR1I2) are two nuclear receptors devoted to the recognition and elimination of lipohilic molecules potentially toxic to the body.These transcription factors can be activated by ligands of different origins and structures (drugs, environmental pollutants, food products and herbal medicine...). The activation of these receptors leads to the expression of major genes of the detoxification process (CYP450, transferases, transporters) leading to the elimination of these toxics. In this work, we 1) showed that Spot14, a pro-lipogenic protein, is a target gene of CAR, then 2) we identified a novel isoform of PXR (PXR-small), coding only the ligand binding domain of PXR. By using 5'-RACE PXR, we established the origins of transcription of PXR-small and by quantitative PCR we observed that PXR-small represents about 10% of all PXR transcripts in human liver. By using western blo t, we detect its presence on nuclear protein extracts from liver tissues and hepatic cell lines. In Electromobility shift essays experiments, we observed that PXR-small cannot bind to DNA, while reporter essay experiments suggest that this isoform acts as a dominant negative of PXR. Finally, the presence of a CpG island just upstream of PXR-small suggests that this novel isoform might be regulated epigenetically by methylation, more particularly in tumor cells.

Os receptores ativadores da proliferação de peroxissomos (PPARs) pertencem à superfamília de receptores nucleares que funcionam como fatores transcricionais. Eles exercem um papel fundamental em processos que envolvem, principalmente, o metabolismo lipídico, em resposta à ativação por ligantes naturais e sintéticos como os ácidos graxos e os fibratos, respectivamente. A crescente descoberta de importantes funções fisiológicas, coordenadas pelos PPARs, e a necessidade de se conhecer como os agonistas, atualmente disponíveis, atuam nesses receptores, têm incitado pesquisas que vislumbram sua melhor exploração nos tratamentos de doenças metabólicas e inflamatórias, minimizando os efeitos adversos de ativações suprafisiológicas. Nesse cenário, o presente trabalho buscou compreender melhor as bases estruturais envolvidas nas funções atribuídas aos PPARs e explicar como as interações com seus ligantes ocorrem. Para isso, foram realizadas a subclonagem do domínio de ligação ao ligante do PPAR&alpha;, sua expressão e purificação, seguidas de ensaios cristalográficos e biofísicos, além da abordagem de testes funcionais. Uma vez que a formação de oligômeros está relacionada à funcionalidade desses receptores, foram abordados estudos de oligomerização dos PPARs &alpha; e &gamma;, compreendendo tanto o processo de homo- quanto o de heterodimerização. Os ensaios de cristalização do hPPAR&alpha; LBD complexado a ligantes naturais e sintéticos, resultaram em estruturas cristalográficas que permitiram a identificação dos resíduos envolvidos no reconhecimento dos ligantes e a caracterização de sítios de ligação nunca antes descritos. A presença de ligantes nessas regiões afeta a conformação da proteína e, consequentemente, a modulação de sua função e o recrutamento da maquinaria transcricional. Adicionalmente, as estruturas cristalográficas da proteína complexada a ácidos graxos auxiliaram na compreensão de como essa importante classe de ligantes naturais possui efeitos farmacológicos similares aos de ligantes sintéticos. Esses resultados têm imediato impacto na procura racional de agonistas para esses receptores e se inserem em uma perspectiva de promoção do desenvolvimento científico-tecnológico na área de endocrinologia molecular. / The peroxisome proliferation-activated receptors (PPARs) belong to the nuclear receptors superfamily, acting as transcriptional factors. They play a key role in processes involving essentially lipid metabolism in response to activation by natural and synthetic ligands such as fatty acids and fibrates, respectively. The rising discovery of important physiological functions coordinated by PPARs and the necessity to know how the currently available agonists act on these receptors, have encouraged researches envisioning a better receptor exploration in the treatment of metabolic and inflammatory diseases, minimizing the adverse effects of supraphysiological activations. In this scenario, the present study aimed to better understand the structural basis involved in PPARs functions and elucidates how the interactions with their ligands takes place. For this, the ligand-binding domain of PPAR&alpha; was subjected to subcloning, expression and purification steps, followed by crystallographical and biophysical assays, in addition to functional testing approaches. Since the degree of oligomerization is related to the functionality of these receptors, oligomeric studies of PPARs &alpha; and &gamma; oligomerization were also achieved, comprising both homo- and hetero-dimerization. The co-crystallization assays of hPPAR&alpha; LBD complexed with natural and synthetic ligands resulted in crystallographic structures that allowed the identification of residues involved in ligand recognition and the characterization of novel binding sites. The presence of ligands in these regions affects the conformation of the protein and thereby modulates their function and transcriptional machinery recruitment. Additionally, the crystallographic structures of the protein complexed to fatty acids were valuable for the understanding of how this important class of natural ligands has similar pharmacological effects to those of synthetic ligands. These results have direct impact on rational agonists design to these receptors and are inserted in a perspective of scientifical promotion and technological development in the field of molecular endocrinology.

Les récepteurs nucléaires (RNs) sont des facteurs de transcriptions se liant à des séquences spécifiques d'ADN et activant la transcription de gènes en réponse à la fixation de ligands spécifiques. Parmi tous les RNs impliquées dans l'étiologie des cancers, les récepteurs liés aux œstrogènes ERR jouent un rôle important dans les cancers du sein, de l'ovaire, du colon, de l’endomètre et la prostate. Ce RN est dit orphelin car il ne possède pas de ligand naturel connu à ce jour. Par une approche de biologie structurale intégrative combinant cryo-microscopie électronique, bioinformatique et évolution, mon travail de thèse s'est focalisé sur l'étude structurale de ERR et sur l'origine et l'évolution des RNs. Dans ce contexte, 3 outils informatiques ont été développés. Les résultats obtenus ont permis d'une part la révision des connaissances fondamentales sur l'origine des récepteurs nucléaires et leur évolution. D'autre part, l'étude structurale de ERR a permis d'acquérir de nouvelles données sur la topologie des récepteurs nucléaires stéroidiens fixés sur un élément de réponse ERRE/ERE ainsi que sur le mécanisme allostérique de la liaison du coactivateur PGC-1α sur le dimère de ERR. La résolution du complexe à l'échelle atomique par cryo-microscopie électronique permettra d'ouvrir la voie vers la conception de nouvelles molécules thérapeutiques. / Nuclear receptors (NRs) are transcription factors which bind to specific DNA sequences and activate gene transcription in response to the binding of specific ligands. Among all of the RNs involved in the etiology of cancers, ERR estrogen receptors play an important role in breast, ovarian, colon, endometrial and prostate cancers. This NR is said to be orphan because it does not have a natural ligand known to date. Using an integrative structural biology approach combining cryo-electron microscopy, bioinformatics and evolution, my PhD work focused on the structural study of ERR and the origin and evolution of RNs. In this context, three informatic tools have been developed. The results obtained allowed, on the one hand, the revision of fundamental knowledge on the origin of nuclear receptors and their evolution. On the other hand, structural study of ERR allow us to acquire new data on topology of steroid nuclear receptors fixed on an element of ERRE / ERE response as well as on the allosteric mechanism of the binding of the coactivator PGC-1α on the dimer of ERR. The resolution of the complex at the atomic scale by cryo-electron microscopy will open the way towards the design of new therapeutic molecules.

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 main focus of this project was to optimize a protocol for small molecule ligand co-purification from an in-vivo tissue source. For this purpose, I employed a transgenic zebrafish line called the pLT-gypsy, which expresses a fusion protein containing a tagged-NR LBD (Tiefenbach et al., 2010). The particular line I used to optimize the ligand identification protocol is the pLT-PPARγ zebrafish line, which expresses the tagged-PPARγ receptor's LBD (also called PPARγ-fusion protein). By using rosiglitazone (a known PPARγ ligand) as a positive control, I managed to optimize a protocol to purify the PPARγ-fusion protein and identify the co-purified ligand by mass spectrometry. This protocol can be used to identify the physiological/endogenous ligand for the PPARγ receptor as well as other orphan NRs. Compared to previous methods of ligand identification, this method allows for the identification of the ligand from the tissues where it is functional.

The main focus of this project was to optimize a protocol for small molecule ligand co-purification from an in-vivo tissue source. For this purpose, I employed a transgenic zebrafish line called the pLT-gypsy, which expresses a fusion protein containing a tagged-NR LBD (Tiefenbach et al., 2010). The particular line I used to optimize the ligand identification protocol is the pLT-PPARγ zebrafish line, which expresses the tagged-PPARγ receptor's LBD (also called PPARγ-fusion protein). By using rosiglitazone (a known PPARγ ligand) as a positive control, I managed to optimize a protocol to purify the PPARγ-fusion protein and identify the co-purified ligand by mass spectrometry. This protocol can be used to identify the physiological/endogenous ligand for the PPARγ receptor as well as other orphan NRs. Compared to previous methods of ligand identification, this method allows for the identification of the ligand from the tissues where it is functional.