Wassermoleküle spielen oft eine entscheidende Rolle bei der Bindung von Liganden an Proteine. Zum einen ist dies in ihrer Eigenschaft als Wasserstoffbrückendonor und -akzeptor begründet, die es ermöglicht Wechselwirkung zwischen Ligand und Rezeptor zu vermitteln. Zum anderen stellen die Desolvatisierungsenthalpie und -entropie einer Bindetasche während der Ligandbindung einen entscheidenden Anteil der Bindungsaffinität dar. Obwohl man sich dieser Einflüsse seit langem bewusst ist, sind aktuelle Methoden des computerbasierten Wirkstoffdesigns nur in sehr begrenztem Umfang in der Lage, die entsprechenden Effekte zu erfassen und vorherzusagen. Da experimentelle Daten über die Effekte von Wassermolekülen in Protein-Ligand Komplexen von Natur aus schwierig zu erhalten sind, untersucht die vorliegende Arbeit eine Modellbindetasche einer Cytochrom c Peroxidase Mutante (CCP W191G) mit Hilfe von Molecular Modeling Techniken. Diese polare und solvatisierte Kavität ist strukturell sehr gut charakterisiert und bindet kleine, kationische Heterozyklen zusammen mit unterschiedlichen Mengen an Wassermolekülen. Für die Untersuchungen wurden strukturell ähnliche Liganden mit einem unterschiedlichen Wechselwirkungsmuster ausgewählt. Davon ausgehend wurde die Möglichkeit zweier Docking-Programme, den Grad der Wasserverdrängung durch den Liganden zusammen mit dem Bindungsmodus vorherzusagen, untersucht. Die dynamischen Eigenschaften der Bindetaschenwassermoleküle wurden mittels Molekulardynamiksimulationen studiert. Schließlich wurden diese rein strukturellen Betrachtungen durch eine energetische/thermodynamische Analyse komplettiert. Die Anwendung dieser unterschiedlichen Verfahren liefert einige neue Erkenntnisse über die untersuchte Modellbindetasche. Trotz der relativen Einfachheit der kleinen Kavität der CCP W191G Mutante war die vollständige Charakterisierung und eine korrekte (retrospektive) Vorhersage des Wasser-Wechselwirkungsmuster der Ligand-Komplexe nicht trivial. Zusammenfassend kann man festhalten, dass insgesamt eine gute Übereinstimmung zwischen den durch Computersimulationen erhaltenen Ergebnissen und den kristallographischen Daten erzielt wurde. Unerwartete Befunde, die auf den ersten Blick mit den kristallographischen Beobachtungen nicht übereinstimmen, können ebenso durch Limitationen in den Kristallstrukturen bedingt sein. Darüber hinaus gaben die Ergebnisse auch eine Hilfestellung, welches Verfahren zur Beantwortung einer Fragestellung im Rahmen von Wassermolekülen im Wirkstoffdesign geeignet sind. Schließlich wurden ebenso die Begrenzungen der jeweiligen Methoden aufgezeigt. / Water molecules play an important role for the binding of small molecule ligands to proteins. One of the reasons for this is their ability to act as a hydrogen bond donor and acceptor at the same time. Additionally, the enthalpy and entropy of desolvation of the pocket is one large contribution to the overall binding affinity. Although this is long known, prediction of these effects by current methods of computer-aided drug design is rather limited. Since experimental information about water effects in protein-ligand complexes are inherently difficult to obtain, in the present work a well-suited model binding site of a mutant of the cytochrome c peroxidase (CCP W191G) is studied using molecular modeling techniques. This polar and solvated cavity is structurally very well characterized and several small, cationic heterocycles bind together with a different amount of water molecules. For this study structurally similar ligands which have a different interaction pattern where chosen. First, the ability of two docking programs to predict cavity desolvation upon ligand binding was investigated. The dynamic properties of the binding site water molecules where studied by means of molecular dynamic simulations. Ultimately, the pure structural considerations addressed in this work were complemented by an energetic/thermodynamic analysis. The application of the different methods offered some new insights into the studied model binding site. Despite the relative simplicity of the small cavity of the CCP W191G mutant, a complete characterization and a correct (retrospective) prediction of the water interaction network in ligand complexes of this model binding site is not trivial. In summary, an overall good agreement between computational results and crystallographic data is obtained. Unexpected findings, which at first sight disagree with crystallographic observations, may also be due to limitations of the crystal structures. In addition, the results help to decide which method is appropriate to address a certain question in the context of water molecules in drug design. Also, the limitations of the respective methods are exposed.

L’adénosine est un neuromodulateur ubiquitaire impliqué dans différents processus physiologiques et neuroprotecteurs du système nerveux central. Elle agit via quatre sous-types de récepteurs couplés à protéine G (A1, A2a, A2b et A3). Le récepteur A2a (A2aR) est fortement exprimé dans des régions riches en dopamine, avec de fortes concentrations dans la zone du caudate-putamen du cerveau, où elle a un rôle important dans la transmission neuronale et dans le processus dégénératif d’origine extrapyramidale. Ainsi, le blocage du récepteur A2a s’est révélé être une cible prometteuse pour le traitement des maladies neurodégénératives tels la Maladie de Parkinson (MP) et la Maladie d’Alzheimer (MA). A ce jour, seulement trois composés sont en phase clinique dans le cadre du traitement de la MP. Toutefois, bien que très affins, ils ne possèdent pas des propriétés ADME ou une sélectivité optimales.Au début de ce projet, la sous-structure Tic-hydantoïne a été identifiée comme présentant une bonne affinité pour A2aR. Après étude des fonctions manquantes de cette molécule et en respectant les éléments pharmacophoriques nécessaires pour une bonne activité, nous avons imaginé et évalué dans la structure co-cristallisé du A2aR et du ligand antagoniste de référence ZM241385 différentes modulations autour de l’hétérocycle. Ceci a permis de proposer la famille des Tic-guanidines, qui présente une fonction donneur de liaison hydrogène avec le résidu Asn253 du site et qui a été synthétisé après optimisation d’un chemin synthétique original. De plus, 1700 molécules ont été conçues de novo et évaluées in silico. Parmi les familles potentiellement intéressantes, deux d’entre elles, les quinolizidinones et les amino-imidazopyridines ont été synthétisées et évaluées in vitro afin de déterminer leur affinité vis-à-vis le récepteur A2a ainsi que leur cytotoxicité vis-à-vis les cellules neuronales. / Adenosine is a ubiquitous neuromodulator able to regulate many physiological processes and plays an important neuroprotective role in the central nervous system. Its effects are transmitted by four distinct G protein receptor subtypes designated A1, A2a, A2b, and A3. A2a receptors (A2aR) show a restricted distribution, being characteristic of the dopamine enriched areas, the highest concentration being in the caudate-putamen in brain, where it has an important role in neuronal signaling with this region and potential involvement in neurologic disease of extrapyramidal origin.A2a antagonism was shown to be a promising pharmacological target for neurodegenerative diseases such as Parkinson’s disease (PD) and Alzheimer disease (AD). Currently, only three compounds are still in clinical phase for PD treatment. Even if they show good affinities for the receptor, there is still a need for improving their ADME properties by keeping their selectivity towards other adenosine receptors.At the beginning of this project, a Tic-hydantoin derivative was identified as a new ligand with a good affinity for the A2a receptor. Based on the recently published crystalline structure of the A2A receptor complexed with the selective and high-affinity antagonist ZM241385 and a pharmacophoric model, we identified the missing features needed for a good affinity in our molecule. We designed and evaluated in silico many pharmacomodulations around the heterocyclic ring and Tic-guanidin substructure was proposed to present favorable hydrogen bound with Asn253 of the A2a binding site. This structure was obtained after optimization of a new synthetic pathway. Moreover, 1700 molecules were originally designed and evaluated in silico. Among potential interesting families, two of them, quinolizidinones and amino-imidazopyridines were synthesized and evaluated in vitro toward their affinity for A2a receptor and their cytotoxicity towards neuronal cells.

A modelagem das interações entre macromoléculas e ligantes ainda se depara com diversos desafios na área de desenho de fármacos assistidos por computador. Apesar do crescimento da área, temas como a flexibilidade do receptor, funções de pontuação e solvatação ainda têm sido alvo de intensa investigação na comunidade científica. Com o objetivo de analisar a interação em milhares ou milhões de complexos, é imprescindível uma boa harmonização entre o custo computacional e a acurácia dos métodos computacionais que permitem a classificação de ligantes de acordo com a energia de interação. O LiBELa (Ligand Binding Energy Landscape) é um programa de docagem molecular com abordagem híbrida, ou seja, utiliza informações do ligante e do receptor durante o processo de docagem. Inicialmente, as características estéricas e eletrostáticas de um ligante de referência (cristalográfico, por exemplo) são utilizadas nos cálculos de similaridade e sobreposição, obtendo assim uma conformação inicial pré-otimizada do ligante testado. Em seguida, a energia de interação é minimizada no sítio ativo de receptor a partir de potenciais energéticos. Quatro funções de pontuação baseadas em campo de força foram testadas e otimizadas, compostas por potenciais de van der Waals, de Coulomb, e uma função empírica de solvatação denominada função de Stouten-Verkhivker (SV). A flexibilidade do sistema foi tratada através da geração de confôrmeros que amostram os graus de liberdade dos ligantes descritos como semi-rígidos e através de potenciais atenuados que suavizam a superfície de energia de interação, permitindo interações em distâncias interatômicas antes repulsivas. Como ponto de partida, os métodos implementados no programa LiBELa demonstraram resultados satisfatórios nos testes de cross- e self-docking, mostrando ser uma ferramenta eficiente em encontrar os modos de ligação cristalográficos de forma equivalente ou até melhor às dos programas comparados. Através de testes de enriquecimento nos conjuntos de dados DUD, DUDE e CM-DUD, foram otimizadas de forma sistemática as constantes dielétrica, do termo de solvatação, e dos termos de atenuação. Também foi realizado um paralelo entre as funções de pontuação, incluindo a atenuação e o termo de solvatação. Estes mesmos testes mostraram resultados superiores do LiBELa de 39% e 15% em comparação com um programa baseado puramente no receptor (DOCK 6.6), relativo à média da área sob a curva em escala semi-logarítmica nas bases de dados DUDE e DUD respectivamente. Apesar da função de solvatação SV implementada no LiBELa apresentar boa correlação com dados experimentais (r=0,72) e com o modelo Zou GB de solvatação (r=0,88), não apresentou correlação significativa com os métodos GB e PB implementados no pacote de programas disponível no AmberTools. Comparadas às funções de pontuação do LiBELa, as funções com correção para solvatação apresentaram pior enriquecimento, salvo alguns alvos específicos. Por fim, foram realizados ensaios de docagem molecular utilizando como alvo uma enzima β-galactosidase da família GH42, cuja estrutura fora resolvida em nosso grupo. Os resultados permitiram conclusões acerca de como o modo de ligação interfere na preferência de ligação entre dissacarídeos de ligações glicosídicas distintas, consistentes com dados experimentais de ensaios cinéticos de ligação. / Modeling the interactions between macromolecules and ligands still faces several challenges in the computer-aided drug design area. Despite the growth in the area, subjects such as receptor flexibility, scoring functions and solvation still have been widely explored in the scientific community. In order to analyze the interaction for thousands or millions of complexes, a good harmonization between the computational cost and the accuracy of the calculation methods in molecular docking programs is essential. LiBELa (Ligand Binding Energy Landscape) is a hybrid approach program that uses both ligand and receptor information for ligand docking. Initially, the steric and electrostatic characteristics from a reference binder (crystallographic, for example) are used to similarity and overlay calculations, thus obtaining an initial conformation of the ligand tested. Then, within the receptor´s active site, the interaction energy is minimized using energetic potentials. Four force field-based scoring functions were tested and optimized, composed of van der Waals and Coulomb potentials and an empirical solvation function called Stouten-Verkhivker (SV). Concerning the system flexibility, besides the confomers generation that sample the degrees of freedom for semi-rigid ligands, attenuated potentials smooth the energy surface allowing interactions between previously repulsive interatomic distances. As a starting point, LiBELa performed satisfactorily in the cross- and self-docking tests, showing that is an eficient tool to reproduce crystallographic binding modes equivalently to or even better than reference programs. Through enrichment of DUD, DUDE and CM-DUD datasets, the dielectric constant, solvation and softening terms were systematically optimized. It also allowed a parallel between scoring functions, including attenuation and solvation term. Finally, it revealed the LiBELa showed an enhancement of 39% and 15% as compared to the purely receptor-based program DOCK 6.6, relative to the mean of the area under the curve on a semi-logarithmic scale in the DUDE and DUD databases respectively. Although the SV solvation function implemented in LiBELa showed good correlations with experimental data (r = 0.72) and with the Zou GB / SA solvation method implemented in DOCK6 (r = 0.88), it did not show significant correlation with the GB/SA and PB/SA methods implemented in AmberTools. Comparing all the LiBELa tested scoring functions, those including solvation correction showed worse enrichments, except for some specific targets. Finally, molecular docking experiments using LiBELa were conducted with a β-galactosidase from GH42 family, whose structure was solved in our group. The results allowed conclusions concerning how the binding mode interferes the preference for some disaccharides of distinct glycosidic bonds, consistent with experimental data from kinetic assays.

O uso de programas de computador para simular a formação de complexos entre proteínas é uma abordagem importante para melhor compreensão de como estas moléculas interagem. A representação paramétrica e a representação em polinômios tridimensionais de Zernike são ambas descrições compactas de superfícies moleculares baseadas em harmônicos esféricos utilizadas para visualização e comparação de superfícies moleculares e para atracamento de proteínas. Entretanto, apresentam limitações como restrição à topologia da superfície e dificuldade de representação de funções arbitrárias. Neste estudo, procurou-se refinar a capacidade de representação destes métodos para obtenção de elevada qualidade de reprodução e aplicabilidade a superfícies de topologia arbitrária. Através da análise de diversos algoritmos de suas etapas, foi possível identificar os estágios de cálculo de malha triangular de superfície molecular e de mapeamento esférico como os mais influentes na qualidade da representação paramétrica em harmônicos esféricos, e a alta sensibilidade a mudança de valores nas funções projetadas na qualidade da representação em Zernike 3D. A incorporação de um método de cálculo de superfícies que gera uma malha com elevada regularidade, aliado a um moderno algoritmo de mapeamento esférico garantiu baixo nível de distorções e obtenção de superfícies reconstruídas de alta qualidade. Uma técnica de detecção de similaridade entre superfícies de diferentes conformações de um ensemble permitiu compartilhamento de partes da descrição entre várias superfícies, com correspondente redução de volume de dados e de demanda por processamento, e com influência controlável nas distorções introduzidas. Um modo diferente de organização dos dados de entrada causou melhoria na qualidade de reconstrução de funções gerais em Zernike 3D, embora com a introdução de um mapa para restauração da função. Os resultados obtidos indicam aplicação promissora dos métodos em docking de proteínas com alto nível de detalhes. / Using computer programs to simulate protein complex formation is an important approach for better comprehension of the interaction mechanisms of such molecules. The parametric representation and the Zernike polynomial method are both compact representations of molecular surfaces based on spherical harmonics, used for visualization and comparison of molecules and for protein-protein docking. They pose, however, limitations regarding surface topology and difficulty in representing arbitrary functions. In this study, the representation capacity of such methods were refined to attain high quality reproductions and applicability to arbitrary topologies. Throughout the analysis of several algorithms, the stages of surface mesh calculation and spherical mapping were identified as highly influential on the quality of the spherical harmonics parametric representation, while high sensibility to changes in the function values were identified as an influential factor for projections in 3D Zernike. A surface calculation method that generates a highly regular mesh was adopted and paired with a modern spherical mapping algorithm to yield reconstructions with low level of distortions and high quality surfaces. Similarity among surfaces from different structures in a conformational ensemble were detected to allow sharing of portions of the description among several surfaces, with corresponding reduction in data volume and processing demand and controllable influence of distortions. A new input data organization method improved the reconstruction quality of general functions in 3D Zernike, although introducing a map to restore the function. Results indicate promising application of the methods in highly detailed protein-protein docking.

The thesis focuses on optimization of inbound and outbound truck scheduling with thegoal of minimizing total operation time of cross docking. A model of cross docking isdeveloped; two different methods are applied on the model in order to find an optimaldocking sequence for receiving and shipping trucks and their assignment to receiving andshipping docks, and product routing from receiving to shipping trucks.The two methods used were mathematical modeling and heuristic algorithm. For the firstmethod, a mixed integer programming model was developed to minimize total operationtime; AMPL modeling language is used for the mathematical modeling for small sizedproblems. For the second method, a heuristic algorithm was developed to find nearoptimal solutions fast and was used for problems of larger size. In order to examine theperformance of heuristic algorithm, small problems were solved by both mathematicalmodel and the heuristic algorithm.The results from the mathematical model and the heuristic algorithm are very close withslight differences in receiving and shipping truck docking sequence, and in productrouting between these two methods. In addition, the heuristic algorithm also calculatesnumber of products transferring from receiving trucks to the temporary storage as well asthe number of products transferring from the temporary storage to shipping truck incontrary to the mathematical model. Total number of units of products passing throughthe temporary storage calculated by heuristic algorithm is presented and it can be seenthat the heuristic algorithm transfers to the temporary storage as few products as possible.Furthermore, in cases that receiving and shipping trucks are divided into groups orclusters in the cross docking operation, heuristic algorithm can be used to calculateoptimal number of receiving and shipping docks based on preferences of total operationtime or total number of products passing through the temporary storage.Another issue which is focused on is the problem of dock door assignment. Closeshipping docks to each receiving dock are determined and the percentage of productstransferred from a receiving dock to its close shipping docks is calculated as a method tomeasure the performance of the dock assignment solution.

Orientador: Karina Alves de Toledo / Banca: Aripuanã Sakurada Aranha Watanabe / Banca: Luciane Alarcão Dias-Melício / Resumo: O Vírus Sincicial Respiratório Humano (hRSV) atua como um dos principais agentes etiológicos das mais de 15 milhões de infecções do trato respiratório inferior em crianças e idosos anualmente. A despeito de décadas de inúmeras pesquisas em busca de compostos anti-hRSV, atualmente não existem vacinas ou medicamentos eficazes contra esta infecção viral. Dentre os leucócitos presentes nas vias aéreas de indivíduos acometidos por hRSV, os neutrófilos são predominantes e se mostram em estado de ativação, incluindo a indução da liberação das NETs. As NETs, compostas por DNA e proteínas granulares/nucleares tem sido descritas como eficientes na captura e eliminação de diversos microrganismos. Em relação ao hRSV, o vírus induz a liberação das NETs no tecido pulmonar de indivíduos infectados, mas as consequências desse evento ainda não foram elucidadas. O objetivo deste trabalho foi investigar se as NETs possuem algum efeito anti-hRSV. Para tanto, foram realizados ensaios in vitro e in silico. NETs geradas a partir do estímulo com PMA e avaliadas por eletroforese apresentaram longos fragmentos de DNA e proteínas de peso molecular próximos daqueles determinados para elastase, catepsina G, mieloperoxidase e histonas. As NETs apresentaram índices de citotoxicidade celular abaixo de 50%, com uma CC50 >67μg/mL. Ensaio virucida realizado com diferentes MOIs (0.1, 0.5 e 1.0), mostraram eficiência das NETs (CE50 ≅ 1 e IS ≅ 66). As interações obtidas in silico demonstram forte interação entre... / Abstract: Annualy the Human Respiratory Syncytial Virus (hRSV) acts as one of the main etiological agents of more than 15 million infections in the lower respiratory tract of children and elderly. Despite decades of extensive research in search of anti-hRSV compounds, there are currently no vaccines or effective drugs against this viral infection. Among the present leukocytes in the airways of individuals affected by hRSV, the neutrophils are predominant and are shown in activation state, including the induction of the release of NETs. NETs, composed by DNA and glanular/nuclear proteins have been described as efficient in capturing and eliminating several microorganisms. Regarding hRSV, the virus induces the release of NETs in the lung tissue of infected individuals, but the consequences of this event have not yet been elucidated. The goal of this study was to investigate whether the NETs have some anti-hRSV effect. For that purpose, assays were performed in vitro and in silico. NETs generated from the stimulation with PMA and evaluated by electrophoresis showed long DNA fragments and proteins of molecular weight close to those determined for elastase, cathepsin G, myeloperoxidase, and histones. The NETs presented cellular cytotoxicity indices below 50%, with CC50 >67µg/mL. Virucide assay performed with different MOIs (0.1, 0.5 and 1.0), showed efficiency of the NETs (CE50 ≅ 1 and IS ≅ 66). The interactions obtained in silico demonstrate strong interaction between elastase and histone proteins with the F-hRSV protein, pre and postfusion, in important regions for the infection/replication of the virus. The data obtained up to date indicate that the NETs have a promising antiviral role and this effect may be related to its direct action in the capture of viral particles and/or interference of the fusion activity of F protein. In conclusion, our results associated with previous literature ... / Mestre

As plantas medicinais são consideradas importantes fontes de compostos biologicamente ativos. Para muitas doenças crônicas, como as neurodegenerações, substâncias que apresentam atividades simultâneas em mais de um alvo relacionado à etiopatologia dessas desordens, constituem potenciais agentes terapêuticos. Nesse contexto, os objetivos deste trabalho foram a avaliação química e biológica de três espécies de samambaias de ocorrência no sul do Brasil: Blechnum binervatum, B. brasiliense e B. occidentale. O isolamento bioguiado foi utilizado para a identificação da(s) substância(s) com potencial atividade em modelos in vitro e in silico relacionados às desordens neurodegenerativas. A avaliação dos extratos e frações permitiu destacar a fração acetato de etila de B. brasiliense como a mais ativa na estabilização de radicais hidroxila (CI50: 12,5 μg/mL) e na inibição da lipoperoxidação (CI50: 10,4 μg/mL), sendo uma das mais ativas frente ao óxido nítrico (CI50: 55,6 μg/mL). Adicionalmente, na inibição da isoforma A da enzima monoamina oxidase (MAO), esta fração foi a que apresentou menor valor de CI50 (28,6 μg/mL). As frações diclorometano também apresentaram bons resultados na inibição da MAO-A, sendo algumas ativas igualmente como antioxidantes. Frente à MAO-B, os extratos e frações das três espécies vegetais demonstraram menores efeitos e foram inativos frente às enzimas acetil e butiril colinesterase, não demonstrando toxicidade em células polimorfonucleares (PMN) de ratos Wistar, na concentração de 1 mg/mL. Utilizando células-tronco cultivadas, os extratos e frações selecionadas, nas concentrações de 100 a 500 μg/mL, não afetaram a viabilidade celular e não apresentaram efeitos tóxicos. Análises químicas por cromatografia líquida de alta eficiência, acoplada a detector de arranjo de diodos e espectrometria de massas, permitiram a identificação de isômeros dos ácidos cafeoil quínico e cafeoil chiquímico nos extratos das três espécies estudadas. B. binervatum apresentou, ainda, ácido cafeico glicosilado, ácido isosalvianólico A e ácido rosmarínico sulfatado. Ácido salvianólico F foi identificado em B. binervatum e B. occidentale, bem como isômeros do ácido brainico. Ácido rosmarínico foi caracterizado em B. binervatum e B. brasiliense. Quercetina 3-O-glicosídeo e vicenina-2 também foram identificadas. As análises por cromatografia gasosa, acoplada à espectrometria de massas demonstraram que o diterpeno neofitadieno foi o composto majoritário nas frações diclorometano de Blechunm e nas frações hexano de B. occidentale e B. binervatum. Para a fração hexano de B. brasiliense, β-sitosterol foi o principal componente. A partir da fração acetato de etila de B. brasiliense foi isolado o ácido rosmarínico, o qual se mostrou ativo nos ensaios de atividade antioxidante, na inibição da catecol-O-metil transferase (CI50: 26,7 μM) e da MAO-A (CI50: 50,1 μM), sendo proposto mecanismo reversível de inibição desta enzima. Nos estudos de docking foram verificadas as interações moleculares entre o composto e as enzimas MAO-A e COMT, por ligações de hidrogênio e interações hidrofóbicas nos sítios ativos enzimáticos. O composto não apresentou efeitos tóxicos em células PMN de roedores, nas concentrações de 0,5 e 5 mM. Os ácidos rosmarínico e clorogênico isolados do extrato de B. binervatum não influenciaram na viabilidade celular e não induziram efeito tóxico sobre células-tronco (100 a 500 μM), sendo que o ácido rosmarínico foi capaz, ainda, de induzir proliferação celular. Capacidade protetora contra danos celulares causados por H2O2 (1400 μM) foi observada para ambas as substâncias, nas concentrações de 10-100 μM, sendo os resultados corroborados pelas imagens de microscopia celular. O ácido rosmarínico apresentou melhores respostas quando comparado ao ácido clorogênico, sendo mais efetivo na inibição dos danos por H2O2. O conjunto dos resultados obtidos ressalta a importância dos estudos associados químico-biológico de espécies vegetais e aponta para as potencialidades de samambaias como fontes de produtos bioativos, capazes de atuar sobre múltiplos alvos enzimáticos e não-enzimáticos relacionados a doenças neurodegenerativas. / Medicinal plants are considered important sources of biologically active compounds. For many chronic diseases, such as neurodegenerations, substances that present simultaneous activities in more than one target related to the etiopathology of these disorders are considered potential therapeutic agents. In this context, the aims of the study were the chemical and biological evaluation of three fern species, occurring in south Brazil: Blechnum binervatum, B. brasiliense and B. occidentale. The bioguided isolation was employed to identify compound(s) with potential activities at in vitro and in silico models associated to neurodegenerative disorders. The biological evaluation of extracts and fractions allowed to highlight the ethyl acetate fraction of B. brasiliense, which was the most active in the stabilization of hydroxyl radicals (IC50: 12.5 μg/mL) and on lipoperoxidation inhibition (IC50: 10.4 μg/mL), being one of the most active sample against nitric oxide (IC50: 55.6 μg/mL). Furthermore, on the inhibition of isoform A from monoamine oxidase (MAO), this fraction showed the lowest IC50 value (28.6 μg/mL). The dichloromethane fractions also presented good results in the MAO-A inhibition, being some of them active as antioxidants, too. Against MAO-B, extracts and fractions of the three species demonstrated reduced effects and all samples were inactive in the acetyl and butyryl cholinesterase inhibition, showing no toxic effects to polymorphonuclear cells (PMN) from Wistar rats, at 1 mg/mL. Using cultured stem cells, the selected extracts and fractions at 100 to 500 μg/mL did not affect cell viability and absence of cytotoxic effects was observed. The chemical analysis by high performance liquid chromatography, coupled to photodiode array detector and mass spectrometry, allowed the identification of caffeoyl quinic acid and caffeoyl shikimic acid isomers in the three studied fern species. B. binervatum presented also glycosilated caffeic acid, isosalvianolic acid A and sulphated rosmarinic acid. Salvianolic acid F was identified in B. binervatum and B. occidentale, as well as, brainic acid isomers. Rosmarinic acid was characterized in B. binervatum and B. brasiliense. Quercetin 3-O-glycoside and vicenin-2 were also found. Analysis by gas chromatography with mass spectrometry showed the diterpene neophytadiene was the major compound in dichloromethane fractions of Blechunm and in hexane fractions of B. occidentale and B. binervatum. For the hexane fraction from B. brasiliense, β-sitosterol was majority. From the ethyl acetate fraction of B. brasiliense was isolated rosmarinic acid, which was shown to be active in antioxidant assays, in the inhibition of catechol-O-methyltransferase (IC50: 26.7 μM) and MAO-A (IC50: 50.1 μM), being suggested a reversible inhibition mechanism against this enzyme. In docking studies were observed molecular interactions between the compound and MAO-A and COMT enzymes, via hydrogen bonds and hydrophobic interactions in enzyme active sites. The compound did not induce toxic effects to rodent PMN cells, at concentrations of 0.5 and 5 mM. The rosmarinic and chlorogenic acids, isolated from B. binervatum extract, did not influence cell viability and did not induce toxicity to stem cells (100 to 500 μM), the rosmarinic acid was also capable to induce cell proliferation. Protective ability against H2O2-induced cell damage (1400 μM) was observed for both substances at concentrations of 10-100 μM, and the results were supported by cellular microscopy images. Rosmarinic acid presented better responses compared with chlorogenic acid, being powerful inhibitor against H2O2-induced damage. The overall results highlights the importance of associated chemical-biological studies of plant species and points at the potential of ferns as sources of bioactive compounds, capable of modulating multiple enzymatic and non-enzymatic targets related to neurodegenerative diseases.

Orientador: Luis Paulo Barbour Scott. / Dissertação (mestrado) - Universidade Federal do ABC. Programa de Pós-Graduação em Engenharia da Informação.

Orientador: Luis Paulo Barbour Scott. / Dissertação (mestrado) - Universidade Federal do ABC. Programa de Pós-Graduação em Engenharia da Informação.

Orientadora: Profa. Dra. Káthia Maria Honório / Dissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Ciência & Tecnologia - Química, 2014. / Este trabalho propoe o uso de tecnicas de modelagem molecular para entender os principais fatores relacionados com a interacao entre um conjunto de ligantes bioativos e o receptor TGF-¿À tipo 1 (ALK5), alvo biologico envolvido no desenvolvimento de doencas como cancer e fibrose. Para entender essas interacoes, foram utilizadas tecnicas computacionais de modelagem molecular que sao utilizadas para quantificar essas interacoes. Dentre as metodologias utilizadas neste trabalho, foram empregadas tecnicas de acoplamento molecular e analises das relacoes quantitativas tridimensionais entre estrutura quimica e atividade biologica (QSAR 3D). Dessa forma, foi estudado um conjunto de dados contendo 70 moleculas empregando tecnicas de QSAR 3D (CoMFA e CoMSIA). Os modelos CoMFA obtidos apresentaram significativos valores de validacao interna (r2 = 0,979 e q2LOO = 0,882) e externa (conjunto de predicao - r2pred = 0,998 e potencial preditivo externo . r2m= 0,998) e os modelos obtidos da analise CoMSIA tambem apresentaram valores significativos de validacao interna (r2 = 0,913 e q2LOO = 0,822) e validacao externa (conjunto de predicao - r2pred = 0,975 e potencial preditivo externo . r2m = 0,975. A analise dos mapas de contribuicoes estereoquimicas e eletrostaticas (CoMFA) e dos mapas de contribuicoes eletrostaticas e dos grupos doadores de ligacao de hidrogenio (CoMSIA) para o composto mais ativo e menos ativo foi capaz de indicar caracteristicas importantes para a inibicao do alvo biologico em estudo. Portanto, o emprego de metodologias computacionais foi de fundamental importancia para o entendimento sobre os principais fatores envolvidos na interacao entre os ligantes estudados e o receptor ALK5. / This study proposes the use of molecular modeling techniques to understand the main factors related to the interaction between a set of ligands and bioactive TGF-â receptor type 1 (ALK5), biological target involved in the development of diseases such as cancer and fibrosis. To understand these interactions, computational molecular modeling techniques were used, which are used to quantify these interactions. Among the methodologies used in this study, techniques of molecular docking and analyses of three-dimensional quantitative relations between chemical structure and biological activity (3D QSAR) were performed with the goal of understanding the main physico-chemical features related to the biological activity. Thus, we studied a data set containing 70 molecules and 3D QSAR analyses (CoMFA and CoMSIA) were carried out. The CoMFA models have good statistical parameters (r2 =0.979 and q2LOO =0.882) and a significant predictive power (r2pred=0.998 and r2m = 0.998). The CoMSIA models also showed significant values for the internal validation (r2=0.913 and q2LOO =0.822) and the external validation (r2pred=0.975 and r2m=0.975). The analysis of the steric and electrostatic contributions (CoMFA), as well as the electrostatic contributions and donor groups for hydrogen bonding (CoMSIA) for the most active and least active compounds was able to indicate important characteristics of inhibiting the biological target under study. Therefore, the use of computational methodologies was of fundamental importance to understand the main factors involved in the interaction between the studied ligands and the ALK5 receptor.