La Maladie d’Alzheimer est caractérisée par la formation de dégénérescences neurofibrillaires, constituées de protéine Tau anormalement hyperphosphorylée et agrégée. De nombreuses études traitent de possibles stratégies thérapeutiques basées sur l’inhibition de cette polymérisation, et présentent les effets bénéfiques de certaines molécules dont les polyphénols, mais les résultats obtenus jusque là, manquent de données au niveau moléculaire. Ainsi, après avoir synthétisé, une banque de polyphénols de structures différentes, et 3 peptides représentatifs de la région P de phosphorylation de Tau, c’est en suivant une stratégie combinant la RMN et la modélisation moléculaire, que nous avons évalué les paramètres dynamiques du complexe formé. Ce projet nous a apporté des informations en termes d’affinité, et de relations structure/activité et ainsi, de mieux appréhender les mécanismes d’interactions intervenant dans l’agrégation de Tau par les polyphénols. / Alzheimer's disease is characterized by the formation of neurofibrillary tangles constituted by abnormally hyperphosphorylated and aggregated Tau protein. Many studies deal with potential therapeutic strategies based on the inhibition of this polymerization, and show the beneficial effects of some molecules like polyphenols, but the obtained so far results show a lack of data at the molecular level. Thus, after the synthesis of, a library of polyphenols with different structures, and 3 representative peptides of the P2 phosphorylation Tau region, by following a strategy combining NMR and molecular modeling, we have evaluated dynamic parameters of the formed complex. This project has provided us informations in terms of affinity, and structure / activity relationships, and leading us to a better understanding of the mechanisms led to better understand the mechanisms involved in the aggregation Tau inhibition phenomena by polyphenols.

Les objectifs environnementaux (COP21) visant à réduire les émissions de gaz à effet de serre et l'impact de l'industrie sur la nature, font face au défi de la demande croissante d'énergie et de produits. Les procédés chimiques sont les premiers en cause lorsqu’ils mettent en œuvre des solvants. L'ingénierie des solvants est une solution innovante qui vise à trouver des milieux alternatifs bénins possédant les propriétés de solvant adaptés pour chaque étape du procédé.Dans cette perspective, nous avons étudié les Liquides expansés par un gaz (LEGs), qui sont desliquides dont le volume augmente sous l’effet d’un gaz dissous sous pression. En particulier, le CO2 peut être utilisé comme agent d'expansion pour obtenir des liquides expansés par du CO2(LECs), combinant les avantages du CO2 et du solvant. La phase expansée peut contenir des concentrations élevées de CO2, jusqu'à 80%, selon le solvant, ce qui conduit à une réduction du besoin du solvant organique, mais aussi à des changements des propriétés physicochimiques et de transport de la nouvelle phase expansée. On peut de plus moduler ces propriétés par la pression et la température, d'une manière réversible, et améliorer la séparation des produits. Dans cette étude, différents solvants biosourcés ont été utilisés pour obtenir des systèmes expansés par du CO2, tels que les acétates d'alkyle, les carbonates organiques, les méthoxybenzènes, etc.La connaissance des équilibres de phase, des propriétés de solvatation et de transport est essentielle pour concevoir des processus qui exploitent le comportement particulier de ces systèmes biphasiques. Deux approches principales ont été utilisées pour caractériser ces systèmes. Dans un premier temps, des mesures ont été effectuées dans une cellule à haute pression et à volume variable pour évaluer la polarité au travers du paramètre Kamlet-Taft (KT) *(dipolarité / polarisabilité) dans les solvants expansés par du CO2 sous des pressions allant jusqu'à 30 MPa. La technique utilisée a été la spectroscopie UV-Vis suivant le déplacement hypsochromique du Rouge de Nile, une sonde solvatochromique déjà utilisée pour obtenir les paramètres KT dans des solvants purs. De plus, des mesures d'équilibre vapeur-liquide (ELV) ont été effectuées pour obtenir la composition de la phase expansée à différentes pressions et températures afin de comprendre la solvatation du CO2 dans les solvants organiques et de fournir des informations manquantes dans la littérature. En deuxième lieu, dans une approche plus théorique, les données ELV ont été utilisées pour calculer numériquement d'autres propriétés telles que la densité et la viscosité. Des équations d'état et des simulations par dynamique moléculaire (DM) ont été utilisées ; ces dernières donnant de meilleurs résultats dans un mode prédictif de la masse volumique et permettant de suivre les positions moléculaires au cours du temps, qui peut être liée à de nombreuses propriétés, y compris la viscosité étudiée ici. Ces calculs ont été effectués en utilisant un champ de force de type Amber adapté. Les résultats obtenus dans l’ensemble complètent les données de la littérature existante et apportent de nouvelles informations sur les propriétés des LEGs. Par exemple, le comportement non linéaire de l'expansion volumétrique, vérifié après les déterminations de masse volumique sur les simulations DM à l'équilibre, est une clé dans la compréhension des interactions soluté-solvant ; ainsi que les valeurs KT * obtenues qui confirment la large gamme de polarité couverte par ces systèmes.Enfin, certains systèmes expansés par du CO2 ont été utilisés pour produire des nanoparticules de TiO2 pour panneaux solaires, améliorant leur surface spécifique et donc leur efficacité en tant que semi-conducteurs ; et d’autres ont été appliqués à un processus d'activation enzymatique entraînant une augmentation significative du taux de conversion / Over the last two decades, environmental goals (COP21) aiming to reduce Greenhouse Gasemissions and industry impact on nature, face the challenge of the increasing demand for energyand products. Chemical processes are in the center of the scene because of the use of solvents.Solvent engineering is the strategy to find alternative benign media for different applications, oreven to adapt solvent properties to respond each stage of a process, and represents aninteresting alternative to propose innovative solutions to industrial problems. With this perspective,Gas-expanded Liquids (GXLs), which are liquids whose volume is expanded by a pressurizeddissolved gas, represent a very promising tool yet to be implemented in the industry. CO2 can beused as the expansion agent to obtain CO2-expanded Liquids (CXLs), combining both the CO2and the solvent’s advantages. The expanded phase can contain high concentrations of CO2 (up to80%, depending on the solvent), which can lead not only to an effective reduction of the need foran organic solvent, but also to changes in the physicochemical and transport properties of the newexpanded phase, that can now be tuned by pressure and temperature in a reversible fashion, andimprove product separation. In this study, different bio-sourced solvents have been used to obtainCO2-expanded systems, such as alkyl acetates, organic carbonates, methoxybenzenes, etc.Knowledge of phase equilibria, solvation and transport properties are fundamental to designprocesses that exploit the peculiar behavior of these two-phase systems. Two main approacheshave been used to characterize these systems. At first, physical determinations were carried outin a high pressure, variable volume view cell, to measure polarity through Kamlet-Taft (KT) *parameter (dipolarity/polarizability) in the selected CO2-expanded solvents under pressures up to30 MPa. The technique used was UV-Vis spectroscopy following the hypsochromic shift of NileRed, a solvatochromic probe that has already been used to obtain KT parameters in neat solvents.Also, Vapour-Liquid Equilibria (VLE) measurements were performed to obtain the expanded phasecomposition at different pressures and temperatures as an attempt to understand CO2 solvation inorganic solvents and to provide missing information in literature. In second place, in a moretheoretical approach, VLE data was used to numerically calculate other properties such as densityand viscosity. Both Equations of State (EoS) and Molecular Dynamics (MD) simulations wereused, giving this last technique better results in a pure predictive mode like in the case of densitydeterminations; in addition to the ability to trace molecular positions over time, which can berelated to many properties, including the here studied viscosity. These calculations were carriedout using an Extended AMBER potential, which led to fairly good results compared to specific-usepotentials available in literature, with the advantage of the general-use possibility. From all thesedeterminations, different conclusions were drawn both agreeing with existing and providing newdata to the literature surrounding this promising subject. For instance, the generally non-linearbehavior of volumetric expansion, verified after density determinations on equilibrium MDsimulations, that is key to evaluate solute-solvent interactions; as well as the KT * values obtainedthat confirm the large range of polarity covered by these systems. Finally, some CO2-expandedsystems were used to produce TiO2 nanoparticles for solar panels improving their specific surfaceand therefore their efficiency as semiconductors; and some others applied to an enzyme activationprocess leading to significant enhancement in conversion rate

A fosforilação de proteínas é o tipo de modificação pós-traducional mais recorrente nas vias de sinalização, desempenhando papel central numa vasta gama de eventos celulares. Um completo entendimento das circunstâncias que coordenam o evento de fosforilação permanece como um desafio para a ciência, a despeito do crescente número de abordagens e estudos realizados no assunto. Um mecanismo largamente descrito e aceito como essencial para coordenar a fosforilação de proteínas é a existência de sequências de aminoácidos que facilitam a fosforilação, conhecidos como consensos de fosforilação. Nesse modelo, cada proteína quinase reconhece sítios de fosforilação se os mesmos estiverem inseridos em uma sequência específica de resíduos na estrutura primária do substrato. Porém, com o crescente volume de dados sobre fosforilação, é possível notar a existência de sítios que são validados experimentalmente como fosforilados por uma determinada proteína quinase, que não apresentam o consenso de fosforilação. Neste trabalho, foi testada e comprovada a hipótese de que estes sítios de fosforilação sem consenso sequencial apresentam resíduos localizados em regiões da estrutura terciária adjacentes ao sítio de fosforilação, cuja as características estereoquímicas mimetizam um peptídeo substrato contendo o consenso de fosforilação. Para essa avaliação, utilizando substratos da PKA, foi constatado que mais de 90% dos sítios de fosforilação que não apresentam o consenso na estrutura primária, apresentam essa disposição na estrutura terciária. Resíduos distantes na estrutura primária se apresentam próximos espacialmente na estrutura tridimensional, em uma conformação semelhante a de um sítio com o consenso de fosforilação. Com isso nós propomos a existência de sítios conformacionais de fosforilação. Para confirmar que esses sítios conformacionais poderiam ser cruciais no reconhecimento do substrato, foram construídos modelos da interação da proteína quinase com os substratos, visando demonstrar a viabilidade da interação dos resíduos formadores do consenso conformacional com a proteína quinase de maneira análoga a de um substrato com o consenso de fosforilação. Para a comprovação experimental do fenômeno, foi utilizado o modelo de fosforilação da -Tubulina, no qual foi constatada uma fosforilação no resíduo T253 que depende da atuação dos resíduos K163 e K164 para a interação com a proteína quinase, confirmando a coerência do modelo proposto. Diante da novidade da proposta, dos estudos computacionais feitos e da validação conseguida, torna-se clara a relevância de se estudar a estrutura tridimensional dos substratos de fosforilação, não só como uma forma de aprofundar os conhecimentos gerais na área de fosforilação, mas também como uma alternativa com potencial de ser explorada no desenvolvimento de novas tecnologias / Protein phosphorylation is the most frequent type of post-translational modification in signaling pathway, developing a key role in a wide range of cell events. The full understanding of the circumstances that coordinate the phosphorylation event remains a challenge for science, despite the growing number of approaches and studies on the subject. A broadly described and accepted mechanism as essential for the coordination of protein phosphorylation is the existence of amino acids sequences that contribute to phosphorylation occurrence, known as phosphorylation consensus. In this model, each protein kinase is able to recognize phosphorylation sites inserted in a specific sequence on the primary structure. However, as the data about phosphorylation sites increases, it is possible to notice that there are sites that are validated experimentally as phosphorylated by a particular protein kinase, which do not have the consensus phosphorylation. In this work, it was tested and proved that phosphorylation sites without the sequence consensus presents anchors residues, that are close to the phosphorylation site on the tertiary structure, creating a structural conformation that mimics the stereochemical features of a substrate peptide containing the phosphorylation consensus. For this evaluation, using substrates of PKA, it was found that more than 90% of phosphorylation sites that have no consensus on the primary structure, presented this kind of disposition on the tertiary structure. Distant residues in the primary structure are spatially close on the three-dimensional structure, in a conformation similar to a phosphorylation site containing the consensus. Thus we proposed the existence of conformational phosphorylation sites. To confirm that these conformational sites could be crucial in substrate recognition, it was built kinase-substrate models, aiming to demonstrate the feasibility of residues forming the conformational consensus on the substrate to interact with the kinase analogously to a substrate with consensus phosphorylation. For experimental verification of this phenomenon, we used the phosphorylation model of -Tubulin, in which we observed a phosphorylation at residue T253 that depends of residues K163 and K164 to interact with the protein kinase, confirming the consistency of proposed model. Faced with the novelty of the proposal, the computational data and the experimental validation, it becomes clear the importance of studying the three dimensional structure of phosphorylation sites, not only as a way of achieving deeper knowledge on phosphorylation field, but also as a potential prospect to be explored on the development of new technologies

Nesta pesquisa, calculou-se, por meio da modelagem molecular, parâmetros físico-químicos importantes à capacidade anti-radicalar de compostos fenólicos extraídos de plantas da flora nacional, Chimarrhis turbinata e Arrabidaea samydoides. As propriedades eletrônicas também podem ser analisadas por meio de superfícies representadas por legendas de cores no campo 3D. Mapa de potencial eletrostático, distribuição orbitalar de HOMO e de LUMO e densidade de spin foram superfícies avaliadas neste trabalho. Em adição, estudos de QSAR (Quantitative Structure-Activity Relationships), cálculos de descritores moleculares holísticos por meio dos programas DRAGON e VOLSURF, cálculos estatísticos incluindo algoritmo genético e PLS (Partial Least Squares), demonstraram a influência de determinadas características moleculares como fundamentais à atividade biológica. A pesquisa concluiu que o grupo farmacofórico favorável à atividade antioxidante é estrutura que apresenta predominantemente características hidrofílicas, grupos hidroxila como substituintes, características eletrônicas favoráveis à doação de elétron e à estabilização do radical fenóxi formado, além de reduzido comprometimento estérico. Consideramos que os métodos empregados no trabalho podem ser considerados como abordagem inovadora para a Ciência Cosmética, indicando potencial ação antioxidante, que poderá ser utilizada em formulações antienvelhecimento. / In this research, the calculated physico-chemical parameters, by molecular modelling, have been reported in the literature for supplying important information about the antiradicalar behavior of phenolic compounds, as the studied herein from Chimarrhis turbinata sp. and Arrabidaea samydoides sp. The electronic properties also can be analyzed by means of surfaces represented by legends of colors in the 3D field. Map of electrostatic potential, HOMO and LUMO distribution orbitalar and spin density have been used in this work. In addition, QSAR studies (Quantitative Structure-Activity Relationships), calculations of holistic molecular descriptors by softwares DRAGON and VOLSURF, statistical analysis including genetic algorithm and PLS (Partial Least Squares), demonstrate the influence of the molecular structure in the biological activity. Therefore, pharmacofor favorable to the antioxidant activity structure that presents predominantly characteristic hydrophilic, groups hydroxyl as substituintes, electronic characteristics favorable to the donation of electron and the stabilization of the radical formed, besides reduced inibition esteric. These recent methods can be considered as an innovative approach for Cosmetic Science toward antioxidant action that could be used in antiaging products.

Theoretical studies of the molecular mechanisms responsible for the formation and stability of protein complexes have gained importance due to their practical applications in the understanding of the molecular basis of several diseases, in protein engineering and biotechnology. The objective of this project is to critically analyze and refine a coarse-grained force field for protein-protein interactions based on experimental thermodynamic properties and to apply it to cancer-related S100A4 protein system. Our ultimate goal is to generate knowledge for a better understanding of the physical mechanisms responsible for the association of particular proteins in different environments. We studied the role of short and long-range interactions on the complexation of homo-associations. Furthermore, we analyzed the influence of the pH and its correlation with the charge regulation mechanism. We analyzed and refined the adjustable Lennard-Jones parameter for a mesoscopic model based on experimental second virial data for lysozyme, chymotrypsinogen, and ribonuclease A via Monte Carlo simulations. From of that, the S100A3 protein was used to test the new calibrated parameters. Finally, we evaluated the dimerization process of S100A4 proteins, observing the role of physical-chemistry variables involved in the thermodynamical stability of different oligomers. / Estudos teóricos dos mecanismos moleculares responsáveis pela formação e estabilidade dos complexos de proteínas vêm ganhando importância devido às suas aplicações práticas no entendimento da base molecular de várias doenças, em engenharia de proteínas e biotecnologia. O objetivo deste projeto é analisar criticamente e aperfeiçoar um campo de força de granulidade grossa para interação proteína-proteína com base em propriedades termodinâmicas experimentais e aplicá-lo ao sistema proteico S100A4 relacionado com o câncer. Nosso objetivo final é gerar conhecimento para uma melhor compreensão dos mecanismos físicos responsáveis pelas associações de proteínas particulares em diferentes ambientes. Estudamos o papel das interações de curto e longo alcance na complexação de homo-associações. Além disso, analisamos a influência do pH e sua correlação com o mecanismo de regulação de cargas. Por meio de simulações Monte Carlo, analisamos e refinamos o parametro ajustável de Lennard-Jones para um modelo mesoscópico, usando dados experimentais do segundo virial para a lisozima, o quimotripsinogênio e a ribonuclease A. A partir disso, a proteína S100A3 foi usada para testar os novos parâmetros calibrados. Finalmente, foi avaliado o processo de dimerização das proteínas S100A4, observando o papel de algumas variáveis físico-químicas envolvidas na estabilidade termondinâmica de diferentes oligómeros.

Os Fatores de Crescimento de Fibroblastos (\"Fibroblast Growth Factors\"; FGFs) participam de fenômenos biológicos de grande importância, tais como migração, divisão e diferenciação celulares. O presente trabalho teve como objetivo central a busca de compostos biologicamente ativos através de um desenho racional de peptídeos derivados do FGF-1 e do seu receptor (FGFR-1 ). A partir da análise dos dados disponíveis na literatura, aliada a técnicas de modelagem molecular, foram desenhados, sintetizados e testados dois grupos de peptídeos. O primeiro conjunto (R1 - R3) é constituído por peptídeos lineares derivados do FGFR-1. Os ensaios de atividade mitogênica dos FGFs 1 e 2 em presença dos peptídeos mostram que R1 e R2 foram capazes de inibir a ação mitogênica do FGF-1. Este efeito é seletivo, já que a atividade do FGF-2 não é afetada. A atividade inibitória é dose-dependente para ambos os peptídeos. Os resultados mostram ainda que o efeito é sequência-dependente, já que o peptídeo R3, correspondente à porção e-terminal de R2, é inativo. Por outro lado, o segmento N-terminal de R2 (representado por R1) é suficiente para desencadear o mesmo nível de inibição apresentado pelo peptídeo R2 inteiro. Os peptídeos sintéticos semi-cíclicos F1 - F3, correspondentes a um importante sítio de ligação no FGF-1, foram avaliados quanto à sua capacidade de estimular a síntese de DNA em fibroblastos em cultura. Os dados obtidos mostram que, na faixa de concentração testada (0,1 a 200 µM), o peptídeo F1 é inativo. O peptídeo F2 apresentou atividade mitogênica (ED50 = 60 -70 µM), estimulando a incorporação de timidina tritiada em até 66 % do valor máximo induzido por 10% de soro fetal bovino. Na mesma faixa de concentração, o peptídeo F3 apresentou atividade em níveis inferiores (ED50 > 100 µM) aos apresentados pelo peptídeo F2. Estes resultados indicam que os peptídeos F2 e F3 poderiam mimetizar a superfície correspondente a um sítio de ligação do FGF-1 ao receptor. Além disso, o fato de F2 ser mais ativo que F3 indica que, além dos resíduos hidrofóbicos Y e L (presentes em ambos), o resíduo R presente em F2 exerce um importante papel para a atividade mitogênica do peptídeo. Como já proposto por nós em trabalhos anteriores, os dados apresentados indicam que é possível obter compostos com atividade mitogênica através do desenho racional de estruturas peptídicas derivadas dos FGFs. A análise do conjunto de peptídeos estudados até o momento revela a existência de características químicas comuns a todos aqueles que se mostraram mitogênicos, ou seja, a presença de um núcleo hidrofóbico flanqueado por resíduos polares carregados. / The Fibroblast Growth Factors (FGFs) are involved in very important biological processes like cell migration, division and differentiation. The aim of this work was the search of biologically active compounds through a rational design of peptides derived from FGF-1 and its receptor (FGFR-1). On the basis on several data available in the literature and with the aid of molecular modeling techniques, we designed, synthesized and tested two sets of peptides. The first group (R1-R3) is composed by linear peptides derived from FGFR-1. The mitogenic activity assays of FGF-1 and FGF-2 in the presence of these peptides reveal that R1 and R2 were able to inhibit the mitogenic response elicited by FGF-1. This effect is dose-dependent and selective, since the FGF-2 activity was not affected. Also, the inhibitory activity is sequence-dependent since peptide R3, corresponding to the e-terminal stretch of R2, was inactive. On the other hand, the N-terminal segment of peptide R2, represented by R1, is sufficient to elicit about the same response observed for the longer peptide R2. The semi-cyclic synthetic peptides F1 - F3, corresponding to an important FGF-1 binding site, were tested for their ability to stimulate DNA synthesis on fibroblast cultures. The results show that F1 is inactive in the range tested (0.1 to 200 µM). Peptide F2 was able to elicit a mitogenic activity (ED50 = 60 - 70 µM), stimulating the incorporation of [methyl-3H] thymidine to a level corresponding to 66 % of the maximum response induced by 10 % fetal calf serum. In the same range, peptide F3 was less active (ED50 > 100 µM). These results suggest that peptides F2 and F3 could mimic a surface corresponding to a receptor binding site of FGF-1. Also, the better performance of F2 could be explained by the presence of the residue R (besides Y and L) that could be important to elicit a mitogenic response. These results, together with those presented in former papers, indicate that it is possible to obtain compounds with mitogenic activity through the rational design of peptides derived from the FGFs. The analysis of the assembly of peptides studied allow us to define a chemical pattern shared by all the mitogenic compounds obtained until now, namely the presence of a hydrophobic core flanked by polar charged residues.

The EcoR124INT restriction-modification (R-M) system contains the genes HsdS3, HsdM and HsdR. S3 encodes the N-terminal domain of the wild-type S subunit and has been shown to dimerise in solution (Smith et al., 1998). Following purification of the subunits of the EcoR124INT R-M system, complexes of the methyltransferase S3/M and restriction endonuclease S3/M/R were formed and shown to have activity in vitro, methylating and hydrolysing a symmetrical DNA recognition sequence, respectively. The DNA mimic OCR (overcome classical restriction) protein inhibited the methyltransferase activity in vitro, with maximum inhibition at a 1: 2 molar ratio of (S3/M)2 to an ocr dimer. Dynamic light scattering (DLS), sedimentation equilibrium (SE) and sedimentation velocity (SV) experiments showed S3 to exist as a dimer and S11 (the central conserved domain of S) to exist as a tetramer in solution. M was found to be dimeric in solution, whilst the R protein was monomeric. A complex of S3/M was found to have a stoichiometry (S3/M)2 and a complex of S3/M/R had a stoichiometry of S3/M/R1, even when a 2: 1 molar ratio of R to S3/M, was added. Small angle neutron scattering (SANS) experiments provided values for the radius of gyration (Rg), which for S3 was comparable to that calculated for the recently published crystal structure of the S subunit from Methanococcus jannaschii (Kim et al., 2005). These experiments also showed a decrease in the Dmax in the presence of the 30 bp DNA recognition sequence from 200A to 140A, suggesting a similar conformational change in the positioning of the subunits as has been detected for the wild-type M. EcoR124I and a related type 1 1/2 system AhdI. This change following DNA binding was also observed by SV experiments. Furthermore ab initio modelling from the SANS data has provided a low-resolution structure for the EcoR124INT MTase and its complex with DNA.

Le marquage isotopique par le deutérium et le tritium est largement utilisé en chimie, en biologie ainsi qu’en recherche pharmaceutique.De nombreuses méthodes de marquage par échange isotopique permettent d’atteindre des enrichissements isotopiques élevés, mais elles requièrent généralement l’utilisation de conditions drastiques (température élevée, acidité). Ainsi, une méthode générale de marquage, régiosélective et douce, applicable à une grande variété de substrats, reste encore à développer. Dans le premier volet de cette thèse, nous avons montré que des nanoparticules de ruthénium (RuNP@PVP), synthétisées par l’équipe du Pr. Bruno Chaudret (INSA Toulouse), catalysaient avec une grande efficacité la réaction d’échange H/D sur des amines, des pyridines et des indoles par C‒H activation, sous 2 bars de D2 à 55 °C. L’application à la deutération de huit molécules azotées d'intérêt biologique a montré que la réaction était efficace sans pour autant altérer l’intégrité chimique ou stéréochimique des composés. Cependant, le respect de la stéréochimie originelle d’un centre chiral C‒H activé demeurait un problème majeur. Nous avons donc entrepris l’étude de la réactivité des RuNP@PVP sur différentes classes de substrats azotés chiraux (amines, aminoacides et peptides) dans l’eau ou dans des solvants organiques. Nos résultats ont montré sans ambiguïté que la C-H activation des carbones C(sp3) chiraux s’effectuait efficacement, sélectivement et dans tous les cas avec une rétention totale de configuration. La large gamme d’application de cette procédure a été démontrée par le marquage de 3 amines chirales, 14 aminoacides naturels, 3 aminoesters aromatiques et 4 peptides. D’autre part, notre collaboration avec l’équipe du Pr. Romuald Poteau (INSA Toulouse) a permis d’identifier deux mécanismes réactionnels par simulation ab initio en parfait accord avec nos résultats expérimentaux : le mécanisme par métathèse de liaison σ et le mécanisme d’addition oxydante. Ces deux mécanismes impliquent deux atomes de ruthénium voisins agissant ensemble pour conduire à la formation d’un intermédiaire-clé original dimétallacycle à quatre centres.Le second volet de cette thèse est consacré au développement d’une nouvelle méthode de détermination de la conformation et de l’arrangement relatif de petites molécules auto-assemblées. Elle repose sur la synergie entre chimie de marquage, RMN du tritium à l’état solide et modélisation moléculaire. Nous nous sommes plus particulièrement intéressés au dipeptide diphénylalanine (Phe-Phe) qui, selon le solvant utilisé, peut former des cristaux (structure résolue) ou s’auto-assembler en nanotubes dont la structure atomique reste inconnue. Trois dipeptides Phe-Phe ditritiés sur des positions aromatiques, définies à l’aide de la modélisation moléculaire par le Dr. Yves Boulard (CEA Saclay), ont été synthétisés. La RMN du tritium à l’état solide a permis au Dr. Thibault Charpentier (CEA Saclay) de mesurer, sur des échantillons cristallisés, trois distances inter-tritiums très proches des distances de référence. Cette technique a également mis en évidence un éventuel désordre d’orientation d’un cycle aromatique de Phe-Phe cristallisé. Une modélisation ab initio nous a également incités à entreprendre un double marquage Caryl et Cα de Phe-Phe, ce dernier utilisant les nanoparticules de ruthénium. Les essais de marquage au deutérium avec RuNP@PVP sont très encourageants et des études complémentaires sont en cours dans notre laboratoire pour parvenir au marquage au tritium. Ainsi, nous espérons mettre au point un nouvel outil d’étude structurale permettant d’accéder à la structure atomique de petites molécules intégrées dans des ensembles supramoléculaires complexes (nanotubes, peptides amyloïdes ou membranaires). / Isotopic labeling with deuterium and tritium is extensively used in chemistry, biology and pharmaceutical research.Numerous methods of labeling by isotopic exchange allow high isotopic enrichments but generally require harsh conditions (high temperatures, acidity). As a consequence, a general, regioselective and smooth labeling method that might be applicable to a wide diversity of substrates remains to develop. In the first part of this thesis, we demonstrated that the use of ruthenium nanoparticles, synthesized by Pr. Bruno Chaudret’s team (INSA Toulouse), allowed the mild (2 bar of deuterium gas at 55°C), effective and selective H/D exchange reaction of a large variety of nitrogen-containing compounds, such as pyridines, indoles and primary, secondary and tertiary alkyl amines. The usefulness and the efficiency of this novel methodology was demonstrated by the deuteration of eight nitrogen-containing molecules of biological interest without altering their chemical and stereochemical properties. However, the conservation of the original stereochemistry of an activated chiral C-H center remains a major issue. We studied the reactivity of RuNP@PVP on different categories of nitrogen-containing substrates (amines, aminoacids and peptides) in water or in organic solvents. Our results showed that C-H activation of chiral carbons C(sp3) took place efficiently, selectively and, in all cases, with total retention of configuration. The wide range of applications of this procedure was demonstrated by the labeling of three chiral amines, fourteen aminoacids, three aromatic aminoesters and four peptides. Moreover, our collaboration with Pr. Romuald Poteau’s team (INSA Toulouse) led to the identification of two mechanisms by ab initio simulation in agreement with our experimental results: the σ-bond metathesis mechanism and the oxidative addition mechanism. These two mechanisms imply two vicinal ruthenium atoms leading to the formation an original dimetallacycle key-intermediate with four centers.The second part of this thesis deals with the development of a new method for the determination of the conformation and the relative arrangement of auto-assembled small molecules. It is based on the synergy between labeling chemistry, tritium solid-state NMR and molecular modeling. We focused on the diphenylalanine dipeptide (Phe-Phe) which forms either crystals or self-assembled nanotubes depending on the solvent. If the crystalline atomic structure of Phe-Phe has been solved, the structure of the self-assembled nanotubes of Phe-Phe is still unknown. Three Phe-Phe dipeptides ditritiated on aromatic positions, determined with the help of molecular modeling by Dr. Yves Boulard (CEA Saclay), were synthesized. Tritium solid-state NMR allowed Dr. Thibault Charpentier (CEA Saclay) to measure, on crystallized samples, three inter-tritiums distances very close to the reference distances. This technique also revealed a possible orientational disorder on an aromatic cycle of crystallized Phe-Phe. Ab initio modeling led us to set a double labeling Caryl and Cα on Phe-Phe with ruthenium nanoparticles. Deuteration with RuNP@PVP are very promising and supplementary studies are in progress to perform tritium labeling. We expect to set a new tool of structural study to determine atomic structures of small molecules integrated in supramolecular complexes (nanotubes, amyloid peptides or membranes).

A fosforilação de proteínas é o tipo de modificação pós-traducional mais recorrente nas vias de sinalização, desempenhando papel central numa vasta gama de eventos celulares. Um completo entendimento das circunstâncias que coordenam o evento de fosforilação permanece como um desafio para a ciência, a despeito do crescente número de abordagens e estudos realizados no assunto. Um mecanismo largamente descrito e aceito como essencial para coordenar a fosforilação de proteínas é a existência de sequências de aminoácidos que facilitam a fosforilação, conhecidos como consensos de fosforilação. Nesse modelo, cada proteína quinase reconhece sítios de fosforilação se os mesmos estiverem inseridos em uma sequência específica de resíduos na estrutura primária do substrato. Porém, com o crescente volume de dados sobre fosforilação, é possível notar a existência de sítios que são validados experimentalmente como fosforilados por uma determinada proteína quinase, que não apresentam o consenso de fosforilação. Neste trabalho, foi testada e comprovada a hipótese de que estes sítios de fosforilação sem consenso sequencial apresentam resíduos localizados em regiões da estrutura terciária adjacentes ao sítio de fosforilação, cuja as características estereoquímicas mimetizam um peptídeo substrato contendo o consenso de fosforilação. Para essa avaliação, utilizando substratos da PKA, foi constatado que mais de 90% dos sítios de fosforilação que não apresentam o consenso na estrutura primária, apresentam essa disposição na estrutura terciária. Resíduos distantes na estrutura primária se apresentam próximos espacialmente na estrutura tridimensional, em uma conformação semelhante a de um sítio com o consenso de fosforilação. Com isso nós propomos a existência de sítios conformacionais de fosforilação. Para confirmar que esses sítios conformacionais poderiam ser cruciais no reconhecimento do substrato, foram construídos modelos da interação da proteína quinase com os substratos, visando demonstrar a viabilidade da interação dos resíduos formadores do consenso conformacional com a proteína quinase de maneira análoga a de um substrato com o consenso de fosforilação. Para a comprovação experimental do fenômeno, foi utilizado o modelo de fosforilação da -Tubulina, no qual foi constatada uma fosforilação no resíduo T253 que depende da atuação dos resíduos K163 e K164 para a interação com a proteína quinase, confirmando a coerência do modelo proposto. Diante da novidade da proposta, dos estudos computacionais feitos e da validação conseguida, torna-se clara a relevância de se estudar a estrutura tridimensional dos substratos de fosforilação, não só como uma forma de aprofundar os conhecimentos gerais na área de fosforilação, mas também como uma alternativa com potencial de ser explorada no desenvolvimento de novas tecnologias / Protein phosphorylation is the most frequent type of post-translational modification in signaling pathway, developing a key role in a wide range of cell events. The full understanding of the circumstances that coordinate the phosphorylation event remains a challenge for science, despite the growing number of approaches and studies on the subject. A broadly described and accepted mechanism as essential for the coordination of protein phosphorylation is the existence of amino acids sequences that contribute to phosphorylation occurrence, known as phosphorylation consensus. In this model, each protein kinase is able to recognize phosphorylation sites inserted in a specific sequence on the primary structure. However, as the data about phosphorylation sites increases, it is possible to notice that there are sites that are validated experimentally as phosphorylated by a particular protein kinase, which do not have the consensus phosphorylation. In this work, it was tested and proved that phosphorylation sites without the sequence consensus presents anchors residues, that are close to the phosphorylation site on the tertiary structure, creating a structural conformation that mimics the stereochemical features of a substrate peptide containing the phosphorylation consensus. For this evaluation, using substrates of PKA, it was found that more than 90% of phosphorylation sites that have no consensus on the primary structure, presented this kind of disposition on the tertiary structure. Distant residues in the primary structure are spatially close on the three-dimensional structure, in a conformation similar to a phosphorylation site containing the consensus. Thus we proposed the existence of conformational phosphorylation sites. To confirm that these conformational sites could be crucial in substrate recognition, it was built kinase-substrate models, aiming to demonstrate the feasibility of residues forming the conformational consensus on the substrate to interact with the kinase analogously to a substrate with consensus phosphorylation. For experimental verification of this phenomenon, we used the phosphorylation model of -Tubulin, in which we observed a phosphorylation at residue T253 that depends of residues K163 and K164 to interact with the protein kinase, confirming the consistency of proposed model. Faced with the novelty of the proposal, the computational data and the experimental validation, it becomes clear the importance of studying the three dimensional structure of phosphorylation sites, not only as a way of achieving deeper knowledge on phosphorylation field, but also as a potential prospect to be explored on the development of new technologies

Submitted by Sandra Pereira (srpereira@ufrrj.br) on 2017-03-21T13:39:54Z No. of bitstreams: 1 2015 - Arthur Valbon Rodrigues.pdf: 2339821 bytes, checksum: 867f44f511f5a52dfdcf023619e589a9 (MD5) / Made available in DSpace on 2017-03-21T13:39:54Z (GMT). No. of bitstreams: 1 2015 - Arthur Valbon Rodrigues.pdf: 2339821 bytes, checksum: 867f44f511f5a52dfdcf023619e589a9 (MD5) Previous issue date: 2015-08-04 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / In this work six asymmetric thyourea, derived from benzylamine and phenethylamine, were synthesized by reaction of p-substituted phenyl isothiocyanates in the presence of benzylamine and phenethylamine in toluene as solvent by irradiation in ultrasonic bath, featuring the first report in the literature of the adoption of this method for such molecules. The compounds were obtained in high purity, requiring only one recrystallization from hexane/dichloromethane. Yields were very satisfactory, ranging from 89 to 98%. The compounds were characterized by spectroscopic techniques such as 1H, 13C Nuclear Magnetic Resonance and IR. The synthesized compounds were evaluated by electrochemical potentiodynamic polarization techniques, Electrochemical Impedance Spectroscopy and Linear Polarization Resistance as inhibitors to the corrosion AISI 1020 carbon steel in 1M HCl media. Molecular modeling was used for better visualization of the thiourea structures and to correlate theoretical parameters such as the energy of the symmetrical frontier orbital, Mulliken charge on the sulfur atom and dipole moment with the experimental results for corrosion efficiency. In general, all compounds showed corrosion inhibition efficiency with characteristics of mixed inhibitors with anodic trend, however compounds with nitro substituent showed less efficiency, a fact that may be related to their electrons withdrawing potential, which consequently decreases the electron density at the possible center of chemical adsorption, the sulfur atom. However, compounds which showed no substituent and those that contain electron donating group (OCH3) stood out as inhibitors, highlighting N- (p-methoxyphenyl) -N'-phenetylthiourea, which showed 95% efficiency corrosion inhibition, from Electrochemical Impedance spectroscopy. Thus, the asymmetric thiourea benzyl and phenethyl-substituted, especially methoxy-substituted phenyl, can be considered as promising corrosion inhibitors for carbon steel in acid. / Nesse trabalho de disserta??o foram sintetizadas seis tioureias assim?tricas, derivadas da benzilamina e fenetilamina. A obten??o ocorreu atrav?s da rea??o dos isotiocianatos de fenila p-substituidos na presen?a da benzilamina e fenetilamina em tolueno como solvente atrav?s de irradia??o em banho de ultrassom, sendo o primeiro relato na literatura dessa metodologia para tais mol?culas. Os compostos foram obtidos em alto grau de pureza, sendo necess?ria apenas uma recristaliza??o em hexano/diclorometano. Os rendimentos foram muitos satisfat?rios, variando de 89 ? 98%. Os compostos foram caracterizados por t?cnicas espectrosc?picas como Resson?ncia Magn?tica Nuclear 1H,13C e Infravermelho. Os compostos sintetizados foram avaliados atrav?s das t?cnicas eletroqu?micas de Polariza??o Potenciodin?mica, Espectroscopia de Imped?ncia Eletroqu?mica e Resist?ncia a Polariza??o Linear quanto ? a??o como inibidores de corros?o frente a a?o carbono AISI 1020 em HCl 1 mol.L-1. A Modelagem Molecular foi utilizada para melhor visualiza??o das estruturas das tioureias e correlacionar os par?metros te?ricos como a energia dos orbitais de fronteiras sim?tricos, carga de Mulliken no ?tomo de enxofre e momento dipolar com os resultados experimentais da efici?ncia anticorrosiva. De forma geral, todos apresentaram efici?ncia de inibi??o ? corros?o com caracter?sticas de inibidores mistos com tend?ncia an?dica, por?m os compostos com substituinte nitro apresentaram menor efici?ncia, fato esse que pode estar relacionado ao seu poder retirador de el?trons, que consequentemente, diminui a densidade eletr?nica no poss?vel centro de adsor??o qu?mica, o enxofre. Por?m, os compostos que n?o apresentaram substituintes e os que cont?m grupo doador de el?trons (OCH3) se destacaram como inibidores, dando destaque a N-(p-metoxi-fenil)-N?-fenetiltioureia, que apresentou efici?ncia de 95% de inibi??o da corros?o, pela t?cnica de Espectroscopia de Imped?ncia Eletroqu?mica. Assim, as tioureias assim?tricas benzil e fenetil-substitu?das, especialmente met?xi-fenil substitu?das, podem ser consideradas como promissores agentes inibidores da corros?o para o a?o-carbono em meio ?cido.