Nous nous intéressons à l'utilisation de la technologie manycore des cartes graphiques dans le cadre de la Chimie théorique. Nous soutenons la nécessité pour ce domaine d'être capable de tirer profit de cette technologie. Nous montrons la faisabilité et les limites de l'utilisation de cartes graphiques en Chimie théorique par le portage sur GPU de deux méthodes de calcul en modélisation moléculaire. Ces deux méthodes n’intégrerons ultérieurement au programme de docking moléculaire AlgoGen. L'accélération et la performance énergétique ont été examinées au cours de ce travail.Le premier programme NCIplot implémente la méthodologie NCI qui permet de détecter et de caractériser les interactions non-covalentes dans un système chimique. L'approche NCI se révèle être idéale pour l'utilisation de cartes graphiques comme notre analyse et nos résultats le montrent. Le meilleur portage que nous avons obtenu, a permis de constater des facteurs d'accélération allant jusqu'à 100 fois plus vite par rapport au programme NCIplot. Nous diffusons actuellement librement notre portage GPU : cuNCI.Le second travail de portage sur GPU se base sur GAMESS qui est un logiciel complexe de portée internationale implémentant de nombreuses méthodes quantiques. Nous nous sommes intéressés à la méthode combinée DFTB/FMO/PCM pour le calcul quantique de l'énergie potentielle d'un complexe. Nous sommes intervenus dans la partie du programme calculant l'effet du solvant. Ce cas s'avère moins favorable à l'utilisation de cartes graphiques, cependant nous avons su obtenir une accélération. / In this research work we are interested in the use of the manycore technology of graphics cards in the framework of approaches coming from the field of Theoretical Chemistry. We support the need for Theoretical Chemistry to be able to take advantage of the use of graphics cards. We show the feasibility as well as the limits of the use of graphics cards in the framework of the theoretical chemistry through two usage of GPU on different approaches.We first base our research work on the GPU implementation of the NCIplot program. The NCIplot program has been distributed since 2011 by Julia CONTRERAS-GARCIA implementing the NCI methodology published in 2010. The NCI approach is proving to be an ideal candidate for the use of graphics cards as demonstrated by our analysis of the NCIplot program, as well as the performance achieved by our GPU implementations. Our best implementation (VHY) shows an acceleration factors up to 100 times faster than the NCIplot program. We are currently freely distributing this implementation in the cuNCI program.The second GPU accelerated work is based on the software GAMESS-US, a free competitor of GAUSSIAN. GAMESS is an international software that implements many quantum methods. We were interested in the simultaneous use of DTFB, FMO and PCM methods. The frame is less favorable to the use of graphics cards however we have been able to accelerate the part carried by two K20X graphics cards.

A monoaminoxidase (MAO) é uma enzima importante, que pode atuar como alvo terapêutico. Inibidores da MAO-A apresentam atividade no tratamento de distúrbios de humor, enquanto os inibidores seletivos da MAO-B tem uso, especialmente, no tratamento da Doença de Parkinson. O conhecimento das interações ENZIMA-INIBIDOR é importante no planejamento de fármacos. Nesse contexto, foram realizados estudos das enzimas MAO-A e MAO-B com diferentes ligantes, através da combinação das metodologias de docking, Dinâmica Molecular e Ensemble Docking. Foram escolhidos os ligantes derivados da 1,4-naftoquinona (1,4-NQ), lapachol, menadiona, norlapachol, A2, B2 e C2, os inibidores comerciais clorgilina (MAO-A) e selegilina (MAO-B) e os substratos naturais serotonina (MAO-A) e dopamina (MAO-B). Os resultados do docking mostraram interação de todos os ligantes com algum dos resíduos da "gaiola aromática" (FAD, Tyr407/Tyr444 para MAO-A, Tyr398/Tyr435 para MAO-B), uma importante região catalítica da MAO. Além disso, a seletividade observada experimentalmente da menadiona com a MAO-B também foi observada no docking. Através da DM, foi possível observar algumas diferenças conformacionais entre as estruturas da MAO-A e MAO-B, que podem explicar a seletividade entre as duas isoformas, como por exemplo, distâncias entre resíduos do sítio ativo e ligações de hidrogênio. A partir do Ensemble Docking, foi verificado que a conformação do receptor influencia significativamente o escore das interações ENZIMA+LIGANTE para ligantes volumosos. / Monoamine oxidase (MAO) is an important enzyme that acts as therapeutic target. MAO-A inhibitors show pharmacological activity in the treatment of mood disorders, whereas MAO-B inhibitors are used especially in treatment of Parkinson's Disease. Knowledge of enzyme-inhibitor interactions is important in drug design. Therefore, studies of MAO-A and MAO-B enzymes with different ligands were performed by combining docking, Molecular Dynamics and Ensemble Docking methodologies. Ligands derived from 1,4-naphthoquinone, lapachol, menadione, nor-lapachol, A2, B2, C2, commercial inhibitors clorgyline (MAO-A) and selegiline (MAO-B) and the natural substrates serotonin (MAO-A) and dopamine (MAO-B) were chosen. The docking results shows interactions of all ligands with some residue of the "aromatic cage” (FAD cofactor, Tyr407/Tyr444 for MAO-A and Tyr398/Tyr435 for MAO-B), an important catalytic region of MAO. Furthermore, the experimentally observed selectivity of menadione with MAO-B was also observed by Docking. In Molecular Dynamics results, conformational differences were observed between MAO-A and MAO-B structures, which could explain the selectivity observed between isoforms, e.g. distances between residues of the active site and hydrogen bonds. Ensemble Docking results shows that the conformation of the receptor significantly influence the score of ENZYME+LIGAND interactions for bulky ligands.

[pt] As constantes mudanças no mercado levaram a um redirecionamento do foco empresarial para o consumidor final. Assim, as formas tradicionais de distribuição que empurravam a produção para o mercado, passaram a ser substituídas por novas formas onde o abastecimento é puxado pela necessidade de mercado. Entre estas novas formas de distribuição apresenta-se o sistema Cross Docking. Nesta dissertação, esse sistema será apresentado, buscando compreender sua estrutura e seus objetivos. O Cross Docking opera transferindo a mercadoria diretamente da área de recebimento para a área de embarque, sem armazená-la, buscando com isso oferecer melhores serviços e manter a oferta constante de produtos. Além disso, a pesquisa tem como objetivo identificar as vantagens e desvantagens do seu uso e os obstáculos de implementação. Será realizada também uma pesquisa de campo, onde uma observação simples da realidade terá como base a Empresa Brasileira de Correios e Telégrafos - ECT. Esta análise se deve ao fato da ECT operar de acordo com a filosofia do sistema Cross Docking, ou seja, as encomendas urgentes fluem pelo centro de distribuição, sendo imediatamente transferidas para as docas de expedição, sem paradas. Dessa forma, a pesquisa busca realizar um diagnóstico da distribuição utilizando-se como referência a ECT. Para essa empresa são avaliados tanto o seu desempenho operacional como a execução dos seus serviços de encomendas expressas, com base nos dois índices de performance utilizados pela própria empresa: produtividade e qualidade (nível de serviço). / [en] The frequent changes in the market turned any company`s focus to the final consumer. So, the ordinary distribution techniques, which usually pushed the production to the market, has being replaced by new techniques, where the product supplies are pulled by the market needs. One of these new ways of distribution is the Cross Docking system. This master`s thesis will present this system, in order to understand its structure and its aims. The Cross Docking concept immediately transfers the merchandise received at the point of reception, to the point of delivery, with the minimum time in between. So, this system can offer better service levels and keep a constant supply of products. In addition, this research has the purpose of identifying the main advantages and disadvantages derived from the use of this system and the main obstacles for its implementation. It will also make a field research, which will have the Empresa Brasileira de Correios e Telégrafos - ECT - as a basis for a simple observation of the reality. That is because the ECT operates with the same philosophy of the Cross Docking system, in which orders do not stay inside the Distribution Center but are immediately transferred to the outbound docks. So, this research has the purpose of diagnosing the distribution system, using the express services of ECT as the field research case study and the performance indexes such as, productivity and service level.

La chémoinformatique et la bioinformatique sont des disciplines devenues indispensables à la découverte de médicaments. De nos jours, les industries pharmaceutiques consacrent près de 10% de leur budget de recherche et développement, à la recherche de médicaments assisté par ordinateur (Kapetanovic 2008). Cette émergence peut s’expliquer à la fois par le développement des architectures de calculs mais aussi par le faible coup qu’engendrent des analyses in silico par rapport à des tests in-vitro.Les essais biologiques qui ont été menés depuis des décennies afin d’identifier des médicaments potentiels, commencent à former une source très importante de données et plusieurs bases de données commencent à les répertorier. La disponibilité de ce type de données a favorisé le développement d’un nouvel axe de recherche appelé la "chémogénomique" et qui s’intéresse à l’étude et à l’identification des associations possibles entre plusieurs molécules et plusieurs cibles. Ainsi, la chémogénomique permet de déterminer le profil biologique d’une molécule et nous renseigne sur sa capacité à devenir une touche intéressante mais aussi à identifier ses possibles effets indésirables. Des méthodes de chémoinformatique permettent d’utiliser ces sources de données à des fins d’apprentissage et établir des modèles prédictifs qui permettront par la suite de faire des prédictions pour connaitre l’activité d’une molécule.Cette thèse a porté sur le développement et l'utilisation de méthodes de prédictions d’association protéine-ligand. La prédiction d’une association est importante en vue d’un criblage virtuel et peut s’effectuer à l’aide de plusieurs méthodes. Au sein du laboratoire, on s’intéresse plus particulièrement au profilage de bases de données de molécules (chimiothèques) contre une série de cibles afin d’établir leur profil biologique. J’ai donc essayé au cours de ma thèse de mettre au point des modèles prédictifs d’association protéine-ligand pour un grand nombre de cibles, valider des méthodes de criblage virtuel récentes à des fins de profilage mais aussi établir un protocole de profilage automatisé, qui décide du choix de la méthode de criblage la plus adaptée en s’appuyant sur les propriétés physico-chimiques du ligand à profiler et de l’éventuelle cible. / Chemoinformatics and bioinformatics methods are now necessary in every drug discovery program. Pharmaceutical industries dedicate more than 10% of their research and development investment in computer aided drug design (Kapetanovic 2008). The emergence of these tools can be explained by the increasing availability of high performance calculating machines and also by the low cost of in silico analysis compared to in vitro tests.Biological tests that were performed over last decades are now a valuable source of information and a lot of databases are trying to list them. This huge amount of information led to the birth of a new research field called “chemogenomics”. The latter is focusing on the identification of all possible associations between all possible molecules and all possible targets. Thus, using chemogenomics approaches, one can obtain a biological profile of a molecule and even anticipate possible side effects.This thesis was focused on the development of approaches that aim to predict the binding of molecules to targets. In our lab, we focus on profiling molecular databases in order to get their full biological profile. Thus, my main work was related to this context and I tried to develop predictive models to assess the binding of ligands to proteins, to validate some virtual screening methods for profiling purpose, and finally, I developed an automatic hybrid profiling workflow that selects the best fitted virtual screening approach to use according the ligand/target context.

abstract: There is a growing need for interplanetary travel technology development. There are hence plans to build deep space human habitats, communication relays, and fuel depots. These can be classified as large space structures. To build large structures, it is essential that these are modular in nature. With modularization of structures, it becomes essential that interconnection of modules is developed. Docking systems enable interconnection of modules. The state-of-the-art technology in docking systems is the Power Data Grapple Fixture (PDGF), used on the International Space Station by the Canadarm2 robotic arm to grapple, latch onto and provide power to the object it has grappled. The PDGF is operated by highly skilled astronauts on the ISS and are prone to human errors. Therefore, there is a need for autonomous docking. Another issue with the PDGF is that it costs around 1 to 2 million US dollars to build the 26-inch diameter docking mechanism. Hence, there is a growing need to build a lower cost and scalable, smaller docking systems. Building scalable smaller docking systems will hence enable testing them on small satellites. With the increasing need for small, low cost, autonomous docking systems, this thesis has been proposed. This thesis focuses on modeling and autonomous control of an electromagnetic probe and cone docking mechanism. The electromagnetic docking system is known to be a highly nonlinear system. Hence, this work discusses various control strategies for this docking system using a levitation strategy. / Dissertation/Thesis / Masters Thesis Electrical Engineering 2018

Le transporteur NTT1 est responsable pour l'import d'ATP dans les chloroplastes afin de maintenir le métabolisme en période d'activité réduite ou nulle de la photosynthèse. Cependant, le mécanisme moléculaire de ce transporteur est encore méconnu, essentiellement du à la difficulté de manipulation des protéines membranaires. Nous avons réussi à développer un protocole pour la production de ce transporteur, permettant une bon rendement de solubilisation et obtention de protéines purifiées pour des études structurales. Combinant des caractérisations biochimiques et biophysiques, nous avons pu identifier des conditions de préparation d'échantillons qui ont mené aux premiers cristaux. Afin d'étendre notre connaissance sur les transporteurs de nucléotides, nous avons également entrepris des études structurales et fonctionnelles sur AAC, le transporteur ADP/ATP des mitochondries. AAC et NTT1 appartiennent à des familles de protéines différentes mais ont des fonctions voisines. À partir de la première structure d'AAC déjà connue, nous avons recherché par des criblages in silico de nouvelles molécules se liant au transporteur de façon compétitive avec le nucléotide et pouvant ainsi inhiber le transport. Les outils de docking ont été mis en place et ont permis à partir d'une librairie de 75000 composés d'identifier 17 molécules. Ensuite, nous avons testés ces molécules expérimentalement et montré qu'une d'entre elles inhibent le transport. De plus, trois nouveaux analogues d'ADP ont également été identifiés comme inhibiteurs. / Chloroplast NTT1 mediates external supply of ATP in the plastids, which is pre- requisite for the maintenance of plastid metabolism during limited or missing photosynthetic activity. However, their molecular mechanism remains poorly understood, primarily due to the difficulty of producing and purifying functional recombinant forms of these transporters. We have successfully developed a protocol for the production of this transporter, that is compatible for efficient solubilization and good yield of purified protein. Combining biochemical and biophysical analyses, we could characterize the protein solution and identify conditions from which first crystals could be obtained. To further extend our work with nucleotide transporter, structural and functional studies on mitochondrial ADP/ATP carrier (AAC) have been performed. AAC and NTT1 belong to different families but exhibit similar functional features. To discover small-molecule inhibitors of AAC's transport for structural studies, virtual docking of compounds was performed into the AAC active site, using the already known structure of AAC. Docking tools were installed and screening a large library of 75,000 compounds allowed the identification of 17 molecules. The experimental binding assay for AAC, revealed that one of the compounds has inhibitory activity in the micromolar regime. In addition, 3 novel ADP analogues showing inhibitory effect against ATP transport of AAC have also been identified.

Made available in DSpace on 2016-08-17T18:39:51Z (GMT). No. of bitstreams: 1 6444.pdf: 3522778 bytes, checksum: e657a2294785a690eced6ba83c6225fa (MD5) Previous issue date: 2014-08-28 / In this work the crystal structures of two 3 (phenoxymethyl)-4-phenylbut-3-en-ones were determined and the resulting 3D strutures were used as input for docking studies in the lethal factor (LF) of bacillus anthracis. The results were then compared with those of a known inhibitor.(3E)-3-(4-nitrophenoxymethyl)-4- phenylbut-3-en-2-one (1): the conformation about the C═C double bond [1.348 (2) Å] is E with the ketone group almost co-planar [C C C C torsion angle = 7.2 (2)°] but the phenyl group twisted away [C C C C =160.93 (17)°]. The terminal aromatic rings are almost perpendicular to each other [dihedral angle = 81.61 (9)°] giving themolecule an overall U-shape. The crystal packing feature benzene-C H O (aldehyde) contacts that lead to supramolecular helical chains along the b axis. These are connected by π π interactions between benzene and phenyl rings [inter-centroid distance = 3.6648 (14) Å] resulting in the formation of a supramolecular layer in the bc plane.(3E)-3-(2,4-dinitrophenoxymethyl)-4-phenylbut- 3-en-2-one (2): the conformation about the C=C double bond [1.345 (2) Å] is E, with the ketonemoiety almost coplanar [C C C C torsion angle = 9.5(2) °] along with the phenyl ring [C C C C = 5.9 (2) °]. The aromatic rings are almost perpendicular to each other [dihedral angle = 86.66 (7) °]. The 4-nitro moiety is approximately coplanar with the benzene ring to which it is attached [O N C C = 4.2 (2) °], whereas the one in the ortho position is twisted [O N C C = 138.28 (13) °]. The molecules associate via C H O interactions, involving both O atoms from the 2-nitro group, to form a helical supramolecular chain along [010]. Nitro nitro N O interactions [2.8461 (19) Å] connect the chains into layers that stack along[001]. The docking results, using as a target the lethal factor (LF) of bacillus anthracis, show that both Compound 1 and 2 located themselves in the same cavity where the known inhibitor is located, and making most of the interactions this last one does with the amino acid residues that are important for the enzyme activity, so that it can be postulated that they can be also inhibitors. Moreover, Compound 1adopts a pose closer to that of the inhibitor whereas Compound 2 is rotated so that an important interaction is missed, this may indicate that this last one can be a less effective inhibitor than Compound 1. / Neste trabalho, as estruturas cristalinas dos dois 3(fenoximetil)-4-fenilbut-3-en-onas foram determinadas e as estruturas 3D resultantes foram utilizadas como entrada para estudos de docking no fator letal (LF) do bacillus anthracis. Os resultados foram comparados com os de um inibidor conhecido (3E)-3-(4-nitrofenoximetil)-4- fenilbut-3-en-2-ona(1): a conformação ao redor da ligação dupla C═C[1,348 (2) Â] é E, com o grupo cetona quase co-planar [ângulo de torção C-C-C-C =7,2(2) °], mas o grupo fenila está torcido [C-C-C-C =160,93(17)°]. Os anéis aromáticos terminais estão quase perpendiculares entre eles [ângulo diedro =81,61(9)°], o que dá a molécula a forma de U. O empacotamento cristalino apresenta contatos benzeno- C-H O (cetona) que levam a cadeias supramoleculares helicoidais ao longo do eixo b. Estas por sua vez estão ligadas através de interações π-π entre o benzeno e o anel fenila, [distância inter-centróide = 3,6648(14)Å], resultando na formação de uma camada supramolecular no plano bc (3E)-3-(2,4-dinitrofenoximetil)-4-fenilbut- 3-en-2-ona (2): a conformação em torno da ligação dupla C=C[1,345 (2) Å] é E, com a cetona quase coplanar [ângulo de torção C-C-C-C =9,5(2)°], juntamente com o anel de fenila [C-C-C-C =5,9(2)°]. Os anéis aromáticos estão quase perpendiculares entre si [ângulo diedro =86,66(7)°]. O grupo 4-nitro é aproximadamente coplanar ao anel benzeno ao qual está ligado [S-N-C-C =4,2(2) °], enquanto que o grupo na posição orto está torcido [S-N-C-C =138,28(13)°]. As moléculas se associam através de interações C-H...O, envolvendo ambos os átomos de O do grupo 2-nitro, de modo a formar uma cadeia supramolecular helicoidal ao longo da direção [010]. Interações nitro-nitro N...O [2,8461 (19)Å] unem as cadeias em camadas que se empilham ao longo da direção [001]. Os resultados do docking molecular, utilizando como alvo o fator letal (LF) de bacillus anthracis, mostram que tanto o Composto 1 como o 2, colocaram-se na mesma cavidade que o inibidor conhecido está localizado, e fazem a maior parte das interações que este último faz com os resíduos de aminoácidos, que são importantes para a atividade da enzima, de modo que também podem ser inibidores. Além disso, o Composto 1 adota uma pose mais próxima da do inibidor, ao passo que o Composto 2 está rodado de modo que uma interação importante é perdida, isso pode indicar, que este último, pode ser um inibidor menos eficaz do que o Composto 1.

Submitted by Alison Vanceto (alison-vanceto@hotmail.com) on 2016-09-27T12:14:06Z No. of bitstreams: 1 TeseNB.pdf: 25264059 bytes, checksum: f823e6e565d3555a5d49056afd7c39fe (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-27T20:08:42Z (GMT) No. of bitstreams: 1 TeseNB.pdf: 25264059 bytes, checksum: f823e6e565d3555a5d49056afd7c39fe (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-27T20:08:48Z (GMT) No. of bitstreams: 1 TeseNB.pdf: 25264059 bytes, checksum: f823e6e565d3555a5d49056afd7c39fe (MD5) / Made available in DSpace on 2016-09-27T20:08:56Z (GMT). No. of bitstreams: 1 TeseNB.pdf: 25264059 bytes, checksum: f823e6e565d3555a5d49056afd7c39fe (MD5) Previous issue date: 2015-06-30 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / In this work are presented the in silico study of the formation of complexes between organochalcogens compounds with enzymes COX-1 and COX-2 that were carried out in order to study their potential to act as selective inhibitors of COX-2 and thus as anti-inflammatories, as well as the results of in vitro and in vivo experiments of this activity. There were modeled and studied 15 organochalcogens compounds and their enantiomers, with a structure similar to that of the selective drug celecoxib. Compounds 2-(phenylseleno)-2-(2-ethyl-X)acetophenones-4’Y-substituted , with Y = H, Br, CH3, OCH3, NO2 and X = SO2, SO, S, were modeled using as starting point the crystallographic structure of the compound with Y = Br and X = SO. The three dimensional structures of the COX-1 and COX-2 enzymes were obtained from the PDB. The results of the molecular docking calculations were evaluated considering the patterns of orientations/conformations, intermolecular interactions, π interactions and scores. The results of these experiments allowed to propose a mechanism of action as well as a preferred bonding mode that would explain the activity of these compounds as possible inhibitors of COX-2, which is a condition necessary to act as anti-inflammatory. In particular, the compound where Y = OCH3 and X = SO2 (5-OCH3) being selective to COX-2 is the one with the best chances to act as an anti-inflammatory. This is because the OCH3 substituent occupied the S1 subsite of the enzyme, maintaining the interaction with His90 and the SO2 moiety interacts with the Tyr355, an important amino acid for the metabolism of the COX-2 substrate, the arachidonic acid. The other interactions made by the compound, such as π interactions, are important for fixing the ligand in the active site, although they are not directly related to its selectivity. The experiments in vitro and in vivo confirm the in silico results, as the enzyme immunoassay showed that this compound exhibits greater inhibition of COX-2 relative to COX-1. Furthermore, the activity of the 5-OCH3 compound was evaluated with the classical models of edema formation, that is the carrageenan and zymosan induced inflammation in the rat paw, resulting in a significant reduction in paw thickness after two hours and decreasing of the temperature after one hour of the application of the anti-inflammatory agent. As the best results were obtained for the model of paw edema elicited by carrageenan this suggests that the compound acts better in the case of acute inflammation. / Neste trabalho são apresentados o estudo in silico da formação de complexos entre compostos organocalcogênios e as enzimas COX-1 e COX-2 realizado com o objetivo de estudar seu potencial para atuar como inibidores seletivos da COX-2, e portanto como anti-inflamatórios, bem como os resultados dos experimentos in vitro e in vivo desta atividade. Na presente pesquisa, foram modelados e estudados 15 compostos organocalcogênios e seus enantiômeros, com estrutura similar à do fármaco seletivo celecoxibe. Os compostos da família 2-(fenilseleno)-2-(etil-X)acetofenonas-4’Y-substituídas, com Y = H, Br, CH3, OCH3, NO2 e X = SO2, SO, S, foram modelados tendo como ponto de partida a estrutura cristalográfica do composto da mesma família com Y = Br e X= SO. As estruturas tridimensionais das enzimas COX-1 e COX-2 foram obtidas no PDB. Os resultados dos cálculos de docking molecular foram avaliados considerando-se o padrão de orientações/conformações, as interações intermoleculares, as interações π e os escores. OS resultados desses experimentos permitiram propor um mecanismo de ação, bem como um modo de ligação preferencial para explicar a atuação desses compostos como possíveis inibidores da COX-2, condição necessária para atuar como anti-inflamatório. Em particular, o composto com Y = OCH3 e X = SO2 (5-OCH3) é o que apresentou o melhor potencial para atuar como anti-inflamatório, sendo seletivo à COX-2. Isto porque o substituinte OCH3 ocupou o subsítio S1 dessa enzima, mantendo a interação com a His90 e o grupo SO2, apresentou interação com a Tyr355, aminoácido importante para o metabolismo do substrato da COX-2, o ácido araquidônico. As outras interações feitas pelo composto, como as interações π, são importantes para fixação do ligante ao sítio ativo, embora não estejam diretamente ligadas com a sua seletividade. Os experimentos in vitro e in vivo permitiram confirmar os resultados dos experimentos in silico, uma vez que o ensaio imunoenzimático mostrou que este composto apresenta maior inibição da COX-2 em relação à COX-1. Ainda, a atividade do composto 5-OCH3 foi avaliada em modelo de edema de pata induzido por carragenina e zymosan, como agentes irritantes, resultando em uma diminuição significativa da espessura das patas após duas horas e diminuição da temperatura após uma hora da aplicação do agente anti-inflamatório. Uma vez que os melhores resultados foram obtidos para o modelo do edema de pata com a carragenina isto sugere o composto atua melhor no caso da inflamação aguda.

A monoaminoxidase (MAO) é uma enzima importante, que pode atuar como alvo terapêutico. Inibidores da MAO-A apresentam atividade no tratamento de distúrbios de humor, enquanto os inibidores seletivos da MAO-B tem uso, especialmente, no tratamento da Doença de Parkinson. O conhecimento das interações ENZIMA-INIBIDOR é importante no planejamento de fármacos. Nesse contexto, foram realizados estudos das enzimas MAO-A e MAO-B com diferentes ligantes, através da combinação das metodologias de docking, Dinâmica Molecular e Ensemble Docking. Foram escolhidos os ligantes derivados da 1,4-naftoquinona (1,4-NQ), lapachol, menadiona, norlapachol, A2, B2 e C2, os inibidores comerciais clorgilina (MAO-A) e selegilina (MAO-B) e os substratos naturais serotonina (MAO-A) e dopamina (MAO-B). Os resultados do docking mostraram interação de todos os ligantes com algum dos resíduos da "gaiola aromática" (FAD, Tyr407/Tyr444 para MAO-A, Tyr398/Tyr435 para MAO-B), uma importante região catalítica da MAO. Além disso, a seletividade observada experimentalmente da menadiona com a MAO-B também foi observada no docking. Através da DM, foi possível observar algumas diferenças conformacionais entre as estruturas da MAO-A e MAO-B, que podem explicar a seletividade entre as duas isoformas, como por exemplo, distâncias entre resíduos do sítio ativo e ligações de hidrogênio. A partir do Ensemble Docking, foi verificado que a conformação do receptor influencia significativamente o escore das interações ENZIMA+LIGANTE para ligantes volumosos. / Monoamine oxidase (MAO) is an important enzyme that acts as therapeutic target. MAO-A inhibitors show pharmacological activity in the treatment of mood disorders, whereas MAO-B inhibitors are used especially in treatment of Parkinson's Disease. Knowledge of enzyme-inhibitor interactions is important in drug design. Therefore, studies of MAO-A and MAO-B enzymes with different ligands were performed by combining docking, Molecular Dynamics and Ensemble Docking methodologies. Ligands derived from 1,4-naphthoquinone, lapachol, menadione, nor-lapachol, A2, B2, C2, commercial inhibitors clorgyline (MAO-A) and selegiline (MAO-B) and the natural substrates serotonin (MAO-A) and dopamine (MAO-B) were chosen. The docking results shows interactions of all ligands with some residue of the "aromatic cage” (FAD cofactor, Tyr407/Tyr444 for MAO-A and Tyr398/Tyr435 for MAO-B), an important catalytic region of MAO. Furthermore, the experimentally observed selectivity of menadione with MAO-B was also observed by Docking. In Molecular Dynamics results, conformational differences were observed between MAO-A and MAO-B structures, which could explain the selectivity observed between isoforms, e.g. distances between residues of the active site and hydrogen bonds. Ensemble Docking results shows that the conformation of the receptor significantly influence the score of ENZYME+LIGAND interactions for bulky ligands.

Submitted by Jean Medeiros (jeanletras@uepb.edu.br) on 2018-04-03T17:12:16Z No. of bitstreams: 1 PDF - Jamire Muriel da Silva.pdf: 79224513 bytes, checksum: ff26bbe18b441c71eeb70cb1f6f88b39 (MD5) / Approved for entry into archive by Secta BC (secta.csu.bc@uepb.edu.br) on 2018-04-10T15:03:47Z (GMT) No. of bitstreams: 1 PDF - Jamire Muriel da Silva.pdf: 79224513 bytes, checksum: ff26bbe18b441c71eeb70cb1f6f88b39 (MD5) / Made available in DSpace on 2018-04-10T15:04:05Z (GMT). No. of bitstreams: 1 PDF - Jamire Muriel da Silva.pdf: 79224513 bytes, checksum: ff26bbe18b441c71eeb70cb1f6f88b39 (MD5) Previous issue date: 2018-02-28 / A highly efficient drug that does not cause collateral damage in the treatment of varied types of cancer has been the desire of many study groups. Over the years, this has been arousing the academic interest worldwide in the search for healing or less harmful and more effective treatments. In this perspective, this work sought the development of a series of new acrylate derivatives coupled to nitrogenous nuclei with potential antitumor action, in the perspective of obtaining compounds with high potentiality and specificity. Therefore, 11 new acrylate derivatives coupled to acridine, quinolinic, indolic and pyridine nuclei have been planned and developed, 10 of which are inedited in the literature. The compounds were obtained from the condensation of different aromatic aldehydes with different reactive methylene groups through a Knovenagel type reaction in ethanolic and basic medium. Fifteen compounds were obtained, four of them intermediates (JM-01, AC-01, ACN-01 and AC-02) and 11 final compounds that presented yields of 51-86% and melting range ranging from 1 to 4 ºC, which gives a certain guarantee of the purity of the products. The structures of the obtained derivatives were elucidated by infrared-IR techniques, mass spectrometry and by 1H NMR and 13C NMR spectroscopy, showing absorption bands characteristic of the functional groupsproposed in the structures, especially the bands and signals of the common vinyl hydrogen in all compounds ranging from 5.73 to 9.30 ppm, thus proving the success of the proposed synthesis. The mass spectra corroborated with the success of the syntheses, presenting masses with expected values. The derivatives were submitted to a docking study, with scores varying from -58.8549 to -16.1303, with the best results being attributed to ICIP, ACMD, PAIP and CAIC derivatives. Interaction tests with DNA were performed by means of an evaluation of absorbance spectroscopy, observing the interaction of the compounds with the targets. In the analysis of interaction with DNA, four of them (ICIP, CAQA, CAAC and ACIP) showed interaction with DNA shifting the wavelength. Among of all derivatives, the ICIP stood out for the good results, both in the docking study, with value close to the reference drug, and with interaction with DNA, by presenting hyperchromic effect, allowing an interaction on both sides of the molecule, and also for being a inedited compound. This molecule presents itself as promising compound for the continuity of the evaluations as a drug candidate. / Um fármaco altamente eficiente e que não provoque danos colaterais no tratamento dos mais diversos tipos de câncer tem sido o desejo de muitos grupos de estudos. E isso, vem a cada ano despertando o interesse acadêmico mundial em busca da cura ou de tratamentos menos nocivos e mais eficazes. Nessa perspectiva, este trabalho buscou o desenvolvimento de uma série de novos derivados acrilatos acoplados a núcleos nitrogenados com potencial ação antitumoral, na perspectiva de obtenção de compostos com elevada potencialidade e especificidades. Para tanto, planejou-se e desenvolveu-se 11 novos derivados acrilatos acoplados a núcleos acridínicos, quinolínicos, indólicos e piridínicos dos quais 10 são inéditos na literatura. Os compostos foram obtidos a partir da condensação de diferentes aldeídos aromáticos com diferentes grupos metilenos reativos através de uma reação do tipo Knovenagel em meio etanólico e básico. Foram obtidos 15 compostos sendo quatro deles intermediários (JM-01, AC-01, ACN-01 E AC-02) e 11 compostos finais que apresentaram rendimentos de 51 a 86 %, e faixa de fusão variando de 1 a 4 ºC que dão certa garantia de pureza dos produtos. As estruturas dos derivados obtidos foram elucidadas por técnicas infravermelho-IV, espectrometria de massas e por espectroscopia de RMN de 1^H e 13^C apresentando bandas de absorção características dos grupos funcionais propostos nas estruturas, principalmente as bandas e sinais do hidrogênio vinílico comum em todos os compostos variando entre 5,73 e 9,30 ppm comprovando assim o sucesso da síntese proposta. Os espectros de massas vieram mais ainda corroborar com o sucesso das sínteses, apresentando massas com valores esperados. Os derivados foram submetidos a estudo de docking apresentando scores variando de -58,8549 a -16,1303 destacando-se com melhores resultados os derivados ICIP, ACMD, PAIP e CAIC. Os testes de interação com, DNA foram realizados através de avaliação de espectroscopia de absorbância observando a interação dos compostos com os alvos. Nas análises de interação com DNA, verificou-se que quatro delas o ICIP, CAQA, CAAC e ACIP apresentaram interação com DNA deslocando o comprimento de onda. De todos os derivados, o ICIP se destacou pelos bons resultados, tanto no estudo de docking com valor próximo ao fármaco de referência, como com interação com DNA apresentando efeito hipercrômico, possibilitando uma interação pelos dois lados da molécula, e também por ser um composto inédito. Esse composto se apresenta com promissor para a continuidade das avaliações como candidatos a fármacos.