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Méthodes de criblage virtuel in silico : importance de l’évaluation et application à la recherche de nouveaux inhibiteurs de l’interleukine 6. / In silico virtual screening methods : importance of evaluation and application to the search of new interleukin 6 inhibitorsLagarde, Nathalie 29 October 2014 (has links)
Le criblage virtuel est largement employé pour la recherche de nouveaux médicaments.La sélection de structures pour les méthodes de criblage virtuel basées sur la structure reste problématique. Nous avons montré que les propriétés physico-chimiques du site de liaison, critères simples et peu coûteux en temps de calcul, pouvaient être utilisées pour guider celle-ci.L’évaluation des méthodes de criblage virtuel, critique pour vérifier leur fiabilité, repose sur la qualité de banques d’évaluation. Nous avons construit la NRLiSt BDB, n’incluant que des données vérifiées manuellement et prenant en compte le profil pharmacologique des ligands. Une étude à l’aide du logiciel Surflex-Dock montre qu’elle devrait devenir la base de données de référence, pour l’évaluation des méthodes de criblage virtuel et pour rechercher de nouveaux ligands des récepteurs nucléaires. L’application d’un protocole hiérarchique de criblage in silico/in vitro, a permis d’identifier de nouveaux composés inhibiteurs de l’IL-6, potentiellement utilisables dans le traitement de la polyarthrite rhumatoïde. Les résultats in vitro devront être confirmés par des tests in vivo. / Virtual screening is widely used in drug discovery processes.Structure selection in structure-based virtual screening methods is still problematic. We showed that simple and “low cost” binding site physico-chemical properties could be used to guide structure selection.The evaluation of virtual screening methods, necessary to ensure their reliability, relies on benchmarking databases quality. We created the NRLiSt BDB, gathering only manually curated data and taking into account ligands pharmacological profiles. A study using Surflex-Dock showed that the NRLiSt BDB should become the reference, both for the evaluation of virtual screening methods and for the identification of new ligands of the nuclear receptors.The use of a in silico/invitro hierarchical approach screening allowed to identify new IL-6 inhibitors, that could be used in rheumatoid arthritis treatment. In vitro results should be confirmed in vivo.
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Planification des opérations de cross-docking : prise en compte des incertitudes opérationelles et de la capacité des ressources internes / Scheduling cross-docking operations : Integration of operational uncertainties and resource capacitiesLadier, Anne-Laure 21 November 2014 (has links)
Dans une plateforme de cross-docking, les produits sont déchargés descamions entrants, triés puis directement rechargés dans les camions sortants– chaque produit passe moins de 24 heures sur la plateforme.L’analyse des écarts entre la littérature et les observations réalisées sur leterrain permet de dégager deux axes de recherche : la prise en compte desincertitudes opérationnelles d’une part, et de la capacité des ressourceshumaines de la plateforme d’autre part.Le problème de planification des camions entrants et sortants avec fenêtrede temps est modélisé par un programme linéaire et résolu par troisheuristiques différentes. La robustesse des plannings obtenus est ensuitetestée à l’aide d’un modèle de simulation à événements discrets, qui permetd’évaluer plusieurs reformulations robustes du modèle initial.Le problème de planification des employés sur la plateforme est traité àl’aide de trois programmes linéaires mixtes, résolus de façon séquentielle.La combinaison des deux modèles permet d’obtenir un modèle d’aide àla décision pour une plateforme de cross-docking. / In a cross-docking platform, goods are unloaded from inbound trucks,sorted and directly reloaded in outbound trucks – each product typicallystays less than 24 hours in the platform.By analyzing the gaps between the literature and on-field observations,we highlight two research directions: accounting for operational uncertainties,and for the human resource capacity in the platform.A truck scheduling problem with time windows for the inbound andoutbound trucks is modeled with an integer program and solved withthree different heuristics. The robustness of the schedules obtained is thentested with a discrete-event simulation model, which enables to evaluateseveral robust reformulations of the initial model.The employee timetabling and rostering problem in the platform is addressedwith three mixed integer linear problems solved sequentially. Thetwo models can be combined to serve as a decision-support tool for across-docking platform.
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Développement et validation du logiciel S4MPLE : application au docking moléculaire et à l'optimisation de fragments assistée par ordinateur dans le cadre du fragment-based drug design / Development and validation of molecular modeling tool S4MPLE : application to in silico fragment-based drug design, using molecular docking and virtual optimisation of fragment-like compoundsHoffer, Laurent 03 June 2013 (has links)
Cette thèse a pour but de développer le pendant in silico des étapes clés du Fragment-Based Drug Design (FBDD), et ce dans le cadre plus général du développement de l'outil S4MPLE. Le FBDD génère des ligands drug-like à partir de petites molécules (fragments). Après une étape de validation de S4MPLE et de sa fonction d’énergie, un recentrage autour du FBDD est réalisé, à travers le docking puis l'optimisation virtuelle de fragments par growing ou linking (G/L). Cette stratégie reposesur 1) la création d’une chimiothèque focalisée en connectant un ou deux fragment(s) avec des linkers pré-générés, et 2) l’échantillonnage avec S4MPLE des composés chimères dans le site avec des contraintes. Des simulations de G/L plus ou moins ambitieuses (site flexible, ajout de H2O libres) permettent de valider cette approche avec des études rétrospectives basées sur des données expérimentales. La dernière phase de la thèse a consisté à appliquer ce protocole in silico à un projet de l’entreprise. / This work aims to develop in silico methods targeting the key stages of Fragment-Based Drug Design (FBDD), participating to the development of the molecular modeling tool S4MPLE. Briefly, FBDD generates ıdrug-likeı ligands from small organic molecules called fragments. After a validation step of S4MPLE and its energy function, the work focused on FBDD: molecular docking of fragments and their subsequent virtual optimization. The latter mimics standard evolution strategies in FBDD(growing and linking). This in silico approach involves among other two key stages 1) building of a focused library by plugging in pre-generated linkers into reference fragments using rules and 2) sampling of these new compounds under atomic and binding site constraints. Validation simulations, relying on known experimental data, included ıclassicalı growing / linking and more challenging ones (site flexibility, free waters). Finally, this strategy is applied to one project of the company.
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Méthodes de criblage virtuel in silico : importance de l’évaluation et application à la recherche de nouveaux inhibiteurs de l’interleukine 6. / In silico virtual screening methods : importance of evaluation and application to the search of new interleukin 6 inhibitorsLagarde, Nathalie 29 October 2014 (has links)
Le criblage virtuel est largement employé pour la recherche de nouveaux médicaments.La sélection de structures pour les méthodes de criblage virtuel basées sur la structure reste problématique. Nous avons montré que les propriétés physico-chimiques du site de liaison, critères simples et peu coûteux en temps de calcul, pouvaient être utilisées pour guider celle-ci.L’évaluation des méthodes de criblage virtuel, critique pour vérifier leur fiabilité, repose sur la qualité de banques d’évaluation. Nous avons construit la NRLiSt BDB, n’incluant que des données vérifiées manuellement et prenant en compte le profil pharmacologique des ligands. Une étude à l’aide du logiciel Surflex-Dock montre qu’elle devrait devenir la base de données de référence, pour l’évaluation des méthodes de criblage virtuel et pour rechercher de nouveaux ligands des récepteurs nucléaires. L’application d’un protocole hiérarchique de criblage in silico/in vitro, a permis d’identifier de nouveaux composés inhibiteurs de l’IL-6, potentiellement utilisables dans le traitement de la polyarthrite rhumatoïde. Les résultats in vitro devront être confirmés par des tests in vivo. / Virtual screening is widely used in drug discovery processes.Structure selection in structure-based virtual screening methods is still problematic. We showed that simple and “low cost” binding site physico-chemical properties could be used to guide structure selection.The evaluation of virtual screening methods, necessary to ensure their reliability, relies on benchmarking databases quality. We created the NRLiSt BDB, gathering only manually curated data and taking into account ligands pharmacological profiles. A study using Surflex-Dock showed that the NRLiSt BDB should become the reference, both for the evaluation of virtual screening methods and for the identification of new ligands of the nuclear receptors.The use of a in silico/invitro hierarchical approach screening allowed to identify new IL-6 inhibitors, that could be used in rheumatoid arthritis treatment. In vitro results should be confirmed in vivo.
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Recherche d'inhibiteurs de l'interaction Lutheran-Laminine par des techniques de modélisation et de simulation moléculaires / Investigation of Lutheran-Laminin Interaction Inhibitors Using Molecular Modeling and Simulation TechniquesMadeleine, Noelly 28 September 2017 (has links)
La drépanocytose est une maladie génétique qui se caractérise par des globules rouges en forme de faucille. Chez les personnes atteintes de drépanocytose, ces globules rouges (GR) adhèrent à l’endothélium vasculaire et provoquent ainsi une vaso-occlusion. Ce phénomène s’explique par la surexpression de la protéine Lutheran (Lu) à la surface des globules rouges falciformes qui se lie fortement à la Laminine (Ln) 511/521 exprimée par l’endothélium vasculaire enflammé. Le but de cette étude est d’identifier un inhibiteur d’interaction protéine-protéine (PPI) qui possède une forte probabilité de liaison à Lu afin d’inhiber l’interaction Lu-Ln 511/521. Un criblage virtuel de 1 295 678 composés ciblant la protéine Lu a été réalisé. La validation préalable d’un protocole de scoring a été envisagée sur la protéine CD80 qui présente un site de liaison avec des caractéristiquestopologiques et physico-chimiques similaires au site de liaison prédit sur Lu ainsi que plusieurs ligands avec des constantes d’affinité connues. Ce protocole contient différentes étapes de sélection basées sur les affinités calculées (scores), des simulations de dynamique moléculaire et les propriétés moléculaires. Un protocole de scoring fiable a été validé sur CD80 avec le programme de docking DOCK6 et les fonctions de scoring XSCORE et MM-PBSA ainsi qu’avec la méthode decalcul FMO. L’application de ce protocole sur Lu a permis d’obtenir deux ligands validés par des tests in vitro qui font l’objet d’un dépôt de brevet. La fonction de scoring XSCORE a permis d’identifier neuf autres ligands qui semblent aussi être des candidats prometteurs pour inhiber l’interaction Lu-Ln 511/521. / Drepanocytosis is a genetic blood disorder characterized by red blood cells that assume an abnormal sickle shape. In the pathogenesis of vaso-occlusive crises of sickle cell disease, red blood cells bind to the vascular endothelium and promote vaso-occlusion. At the surface of these sickle red blood cells, the overexpressed protein Lutheran (Lu) strongly interacts with the Laminin (Ln) 511/521.The aim of this study was to identify a protein-protein interaction (PPI) inhibitor with a highprobability of binding to Lu for the inhibition of the Lu-Ln 511/521 interaction. A virtual screening was performed with 1 295 678 compounds that target Lu. Prior validation of a robust scoring protocol was considered on the protein CD80 because this protein has a binding site with similar topological and physico-chemical characteristics and it also has a series of ligands with known affinity constants. This protocol consisted of multiple filtering steps based on calculated affinities (scores), molecular dynamics simulations and molecular properties. A robust scoring protocol was validated on the protein CD80 with the docking program DOCK6 and the scoring functions XSCORE and MM-PBSA and also with the FMO method. This protocol was applied to the protein Lu and we found two compounds that were validated by in vitro studies. The protection of these ligands by a patent is under process. Nine other compounds were identified by the scoring functionXSCORE and seem to be promising candidates for inhibiting the Lu-Ln 511/521 interaction.
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ESTUDOS TEÓRICOS E DE MODELAGEM MOLECULAR IN SILICO APLICADOS À INTERAÇÃO ENTRE A ENZIMA DELTA-AMINOLEVULINATO DESIDRATASE E DISSELENETOS DE DIARILA / IN SILICO THEORETICAL AND MOLECULAR MODELING STUDIES APPLIED TO THE BINDING AFFITY OF DIARYL DISELENIDES TO DELTA-AMINOLEVULINIC ACID DEHYDRATASE ENZYMESaraiva, Rogério de Aquino 06 May 2013 (has links)
Conselho Nacional de Desenvolvimento Científico e Tecnológico / Delta-aminolevulinic acid dehydratase (δ-ALA-D) is an essential metalloprotein found in several biological processes, since it is able to catalyze the formation of porphobilinogen (PBG), a precursor monopyrol of tetrapyrroles (heme and chlorophyll). This enzyme is sensible to heavy metals and other pro-oxidant agents and, consequently, it has been classically used as a protein marker for lead intoxication. Both in vitro and in vivo studies has shown that the organochalcogen diphenyl diselenide [(PhSe)2] could be a promising drug due to present antioxidant, neuroprotective, anti-inflammatory, anti-atherosclerotic and other activities. Contrariwise, (PhSe)2 could also be toxic because it can inhibit the activity of important sulfhydryl enzymes, including δ-ALA-D. Regarding some experimental data, it has been speculated that mammalian δ-ALA-D inhibition can occur via the oxidation of two vicinal thiols located in it active center site. However, no molecular model had been proposed in order to explain this interaction with details. Thus, we aimed to get a further understanding about the interaction involving δ-ALA-D and diselenides using in silico molecular modeling methods, which are consisted in theoretical methods applied in to represent or mimic the behavior and interaction of ligands and enzymes from their structural and thermodynamic information. Docking simulations indicated an important role for π-π interactions involving Phe208 and cation-π interactions involving Lys199 and Arg209 residues with the aromatic ring of (PhSe)2 and analogs bis 4-(clorophenyl) diselenide, bis 4-(methoxyphenyl)diselenide and bis 3-(trifluorometil(phenyl)diselenide. These interactions allowed an approximation between Se atoms and SH of Cys124 (3.3 3.5 Å). The analogs interacted similarly with the active site of δ-ALAD. According to the quantum method MFCC (Molecular Fractionation with Conjugated Caps), interactions involving (PhSe)2 could occur up to 8.5 Å distance from the centroid of active site. Phe208, Phe79, Cys122, Cys124, Pro125, Asp120, Lys199, Lys252 and Cys132 displayed strong attraction energy to (PhSe)2. The representative molecular model is in accordance with in vitro assays and gives mechanistic support to previous speculative mechanism of inhibition. Phenyl moieties in (PhSe)2 can be strongly attracted by aromatic and positive charged residues from δ-ALA-D active site. This allows the approximation of the reactive electrophile moiety Se-Se to the nucleophile S- groups from Cys122, Cys124 and Cys132, facilitating the release of coordinated Zn(II), thiol oxidation and formation of 2 molecules of phenylselenol (PhSeH). In conclusion, the presence of aromatic moieties in (PhSe)2 and its reactive electrophile moiety Se-Se are crucial to δ-ALA-D inhibition, which leads to thiol oxidation and consequent impairment of its activity. / A enzima δ-aminolevulinato desidratase (δ-ALA-D) é uma metaloproteína essencial em vários processos biológicos, uma vez que é responsável por catalisar a formação de porfobilinogênio (PBG), um precursor dos tetrapirrólicos (heme, clorofila). Esta enzima é sensível a metais pesados e outros pró-oxidantes e, dessa forma, tem sido classicamente usada como um marcador na intoxicação por chumbo. Estudos in vitro e in vivo têm demonstrado que o organocalcogênio disseleneto de difenila [(PhSe)2] pode ser um fármaco promissor por demonstrar várias atividades biológicas, incluindo antioxidante, neuroprotetora, anti-inflamatória, anti-aterosclerótica e outras. Por outro lado, o (PhSe)2 e análogos também são tóxicos por inibir a atividade de enzimas sulfidrílicas, incluindo a δ-ALA-D. Baseados em dados experimentais, tem-se especulado que a inibição da δ-ALA-D de mamíferos pode ocorrer via oxidação de dois tióis vizinhos localizados no centro ativo da enzima. No entanto, não se tinha conhecimento de nenhum estudo baseado em modelagem molecular com o intuito de explicar esta interação de forma mais detalhada. Diante disso, objetivamos compreender essas interações a partir da modelagem molecular in silico, que consiste em métodos teóricos aplicados para representar ou mimetizar o comportamento e interação de ligantes e enzimas a partir de informações sobre os requisitos estruturais e termodinâmicos essenciais. Os estudos de docking molecular indicaram um papel importante das interações π-π envolvendo Phe208 e cátion-π envolvendo Lys199 e Arg209 e anéis aromáticos do (PhSe)2 e análogos bis 4-(clorofenil) disseleneto, bis 4-(metoxifenil) disseleneto e bis 3-[trifluorometil(fenil)] disseleneto. Estas interações permitem uma aproximação entre átomos de Se do composto e SH da Cys124 (3.3 3.5 Å). Os análogos também interagem de forma semelhante com o sítio ativo da δ-ALA-D. De acordo com o método MFCC (Fracionamento Molecular com Capas Conjugadas), foi possível observar interações envolvendo o (PhSe)2 e resíduos posicionados até uma distância de 8,5 Å do centroide do ligante. Phe79, Cys122, Cys124, Pro125, Asp120, Lys199, Lys252 e Cys132 demonstraram as maiores energia de interação (atrativa) com o (PhSe)2. O modelo molecular representado está em conformidade com ensaios in vitro e fornece informações importantes que reforçam o mecanismo de inibição especulado. Os grupos fenil do (PhSe)2 são fortemente atraídos por resíduos aromáticos e carregados positivamente presentes no sítio ativo da δ-ALA-D. Dessa forma, permite-se a aproximação da porção eletrófila Se Se ao grupos nucleófilos S dos resíduos Cys122, Cys124 e Cys132, facilitando a liberação de Zn(II), a oxidação dos tiolatos e a formação de duas moléculas de fenilselenol (PhSeH), levando a consequente inibição da atividade da enzima.
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Formação de complexos entre compostos híbridos pirrolbenzodiazepinas-cumarinas com DNA por estudos de docking molecular / Complex formation between pirrolbenzodizepinescoumarins hybrids with DNA by molecular docking studiesRodrigues, Sergio Ricardo Pizano 24 March 2011 (has links)
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Previous issue date: 2011-03-24 / Financiadora de Estudos e Projetos / Compounds of the pirrolbenzodiazepine (PBD) family are known for their promising antitumor activity. Among these, the hybrids, those that have a portion PDB a chain spacer and another functional group, such as the coumarins of this work, have been extensively explored. It is also known that these compounds bind to DNA, but there is no structural data showing how it occurs. To overcome this lack of information molecular docking calculations were performed to study the formation of complexes between these PBD-hybrids and DNA. The compounds were modeled and the coordinates of complexes DNA-receptors with different ligands were obtained from the Protein Data Bank. The redocking served to validate the conditions of the experiments and the scores were used as the parameter to evaluate the complexes formed. The analysis of the intermolecular interactions, an essential knowledge for understanding the obtained structures were analyzed using high-resolution molecular imaging. The results of the in silico experiments showed the formation of complexes in the mixed-mode with the PBD ligand moiety intercalating between the DNA bases and the coumarin portion occupying the minor groove, and a preference for intercalation between GG bases. Moreover, it is possible to postulate that the complex becomes an adduct with the formation of a covalent bond between the intercalated portion PBD and a nucleotide base G. Finally, a correlation between the docking results and the biological activities of the studied compounds was established. / Compostos da família das pirrolbenzodiazepinas (PBD) são conhecidos por apresentarem atividade antitumoral promissora. Dentre elas, as chamadas híbridas que possuem uma porção PDB uma cadeia espaçadora e outro grupo funcional, como as cumarinas deste trabalho, têm sido muito exploradas. Sabe-se que estes compostos se ligam ao DNA, mas não há dados estruturais mostrando como a ligação ocorre. Para suprir esta falta de informação foram realizados cálculos de docking molecular para estudar a formação de complexos entre estas PBDs híbridas e o DNA. Os compostos estudados foram modelados e as coordenadas de complexos DNA-receptores com diferentes ligantes foram obtidas do Protein Data Bank. O redocking serviu para validar as condições dos experimentos e os escores foram utilizados como parâmetro de avaliação dos complexos formados. A análise das interações intermoleculares, conhecimento essencial para o entendimento das estruturas obtidas, foi feita utilizando visualização molecular de alta resolução. Os resultados dos experimentos in silico mostraram a formação de complexos no modo de ligação misto, com os ligantes intercalando a porção PBD entre bases do DNA e a porção cumarina ocupando o sulco menor, mostrando ter preferência pela intercalação entre bases GG. Mais ainda, é possível postular que o complexo se torne um aduto com a formação de uma ligação covalente entre a porção PBD intercalada e uma base nucleotídica G. Finalmente foi estabelecida uma correlação entre os resultados do docking e as atividades biológicas dos compostos estudados.
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Docking molecular aplicado ao estudo da formação de complexos entre análogos de resveratrol e derivados de 1,2,3-triazol e a enzima COX-2 / Molecular docking applied to the study of complexes formation between resveratrol analogues and 1,2,3-triazole derivatives and the COX-2 enzymeCastilho, Luis Nelson Prado 14 December 2011 (has links)
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Previous issue date: 2011-12-14 / Prostaglandin H synthases (PGHS), or cyclooxygenases (COX), are known to exist in at least two isoforms, COX-1 and COX-2, encoded by different genes. COX s play a central role in the inflammatory cascade by converting arachidonic acid, released from membrane phospholipids, into bioactive prostanoids. Non-steriodal anti-inflammatory drugs (NSAIDs) represent an important therapeutic category related to the reduction of inflammation, pain and fever, however, can cause gastric and kidney failure. Selective inhibition of COX-2 by NSAIDs known as coxibs leads to a significant reduction of these side effects in addition reduce fatal thrombotic events and act in controlling some types of cancer and progression of Alzheimer's disease, when used for a long period. This study, based on molecular docking, describes the search for the most favorable poses in the formation of complexes between COX-2 and resveratrol analogues and 1,2,3-triazole derivatives. The three dimensional structure of the enzyme, 1cx2, was obtained from the Protein Data Bank (PDB). The structures of the ligands were obtained by molecular modeling. The docking calculations were carried out with the program GOLD 4.1.2. Analyses of the docking results show that interactions with residues of the side pocket of COX are important for the stabilization of the complexes, in particular His90, Arg120, Ser353, Tyr355 and Arg513 should be mentioned. The ligands studied locate, preferably, between α-helices 13 and 26 of the isoenzyme, and the interaction with the serine 353 residue seems to be related to the activity presented by ligands with low IC50 values, a characteristics that can be exploited in rational design of new leader molecules or in the optimization of selective ligands that should occupy the side pocket of the cyclooxygenase active site of COX-2. / Prostaglandinas H sintases (PGHS), ou ciclooxigenases (COX), existem em pelo menos duas isoformas, COX-1 e COX-2, codificadas por genes diferentes. A COX desempenha um papel central no processo inflamatório através da conversão do ácido araquidônico, liberado a partir dos fosfolipídios da membrana, em prostanóides bioativos. Anti-inflamatórios não esteroides (AINEs) representam uma importante categoria terapêutica relacionada à redução de inflamação, dor, e febre, no entanto, podem causar insuficiência renal e gástrica. A inibição seletiva da COX-2 pelos AINEs conhecidos como coxibs leva a uma redução significativa desses efeitos colaterais, além de reduzir eventos trombóticos fatais e agir no controle de alguns tipos de câncer e na progressão do mal de Alzheimer, quando utilizados de forma prolongada. Este estudo, baseado em docking molecular, descreve a busca das poses mais favoráveis para a formação dos complexos entre a COX-2 e ligantes análogos do resveratrol e derivados de 1,2,3-triazol. A estrutura tridimensional da enzima 1cx2 foi obtida do Protein Data Bank (PDB). As estruturas dos ligantes foram obtidas por modelagem molecular. Os cálculos de docking foram realizados utilizando o programa GOLD 4.1.2. As análises dos resultados de docking mostram que as interações com os resíduos do bolso lateral presente na COX são importantes para a estabilização dos complexos, especialmente, His90, Arg120, Ser353, Tyr355 e Arg513. Os ligantes estudados se localizam, preferencialmente, entre as α- hélices 13 e 26 da isoenzima, sendo que a interação com o resíduo serina 353 demonstra estar relacionada com a atividade apresentada por ligantes com baixos valores de IC50, característica que pode ser explorada racionalmente no desenho de novas moléculas lideres ou na otimização de ligantes seletivos que ocupem o bolso lateral do sítio ativo ciclooxigenase da COX-2.
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Contribuição ao conhecimento químico e biológico de espécies da flora paraibana: Xylopia langsdorffiana e Maytenus distichophyllaEsmeraldo, Paula Ferreira dos Santos 23 February 2015 (has links)
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Previous issue date: 2015-02-23 / Phytochemical studies with Xylopia langsdorffiana (Annonaceae), have described isolation of
trachylobane, atisane, kaurane, and labdane diterpenes, from the leaves, fruits, stems and roots
of the species. Maytenus distichophylla (Celastraceae), popularly known as espinheira santa –
(sacred thorn bush), is used in folk medicine to treat stomach ulcers, and data from the literature
report the isolation of triterpenoids friedelane, and pyrimidine sesquiterpene alkaloids.
Computer aided drug design brings optimizing techniques that facilitate the discovery of new
drugs, offering features that allow the connection of compounds to known proteins in three
dimensions, and the resulting models are able to predict reliable experimental values for
biologically active molecules, making the search for biologically active compounds more
efficient. Our work associated experimental tests and computational investigations based on
plants selected from the Paraiban flora: X. langsdorffiana, M. distichophylla, and other
Maytenus species. We report the experimental tests performed with roots and stems of
Maytenus distichophylla that enabled extraction and structural determination of flavonoids,
steroids, and friedelane and lupane triterpenoids. Parallel studies were developed using
computational docking, PLS, and hydrophobicity, with 15 triterpenoids isolated from Maytenus
species (including M. distichophylla), and 17 diterpenes isolated from X. langsdorffiana.
Further, we determined chemical compositions (by GC-MS and NMR), and modulation activity
against multi-resistant bacteria. Essential oils of three X. langsdorffiana specimens were
analyzed by Principal Component Analysis (PCA). Three compounds were isolated from stems
of M. distichophylla by chromatographic techniques: 3-oxo-12α-hydroxyfriedelane, 30-
hydroxyfriedelan-3one and 29-hydroxyfriedelan-3-one. Another four compounds were isolated
from the roots: β-sitosterol, 11α-hydroxyglochidone, rigidenol and 4’-Omethylepigallocatechin,
this being the first report in the species of the latter three. In the
docking study, the diterpenes ent-atisan-7α-acetoxy-16α-ol, labdorfianic C acid e labdorfianic
B acid had the lowest formation energy values when respectively complexed with cruzaine,
CYP2C9, and COX. The triterpenoids with the lowest formation energy values when
complexed with these enzymes were, 3β-hydroxy-9,12-en-ursane (cruzaine), 3,4-secofriedelan-
3-oic acid (CYP2C9) and 3-oxo-12α-hydroxyfriedelane (COX). In predicting
antitumor activity, as calculated from the constructed PLS model, the diterpene labdorfianic C
acid, and triterpene 3β-hydroxyfriedelane, showed the best predicted values. The majority
compounds identified in the essential oils were: ent-atisan-16α-ol, germacrene D, limonene and
β-pinene. The monoterpenes, β-pinene and limonene, were identified in all analyzed essential
oils in different percentages. Through analysis of the essential oil of the X. langsdorffiana stem
(specimen A), NMR (¹H and ¹³C) were able to identify ent-atisan-16α-ol, the first time reported
for this species. Some essential oils from specimen A when modulated with oxacillin against S.
aureus, decreased concentration of the antibiotic by 99%. Principal component analysis (PCA)
performed with the essential oil of three X. langsdorffiana specimens allowed identifying a
similarity between the chemical species A and B, and a difference in C compared to A and/or
B. This result may be related to the age or size of the specimens, since they share the same
geographic coordinates. The models obtained in the CADD studies of were satisfactory and
generated predictive results. / Estudos fitoquímico com Xylopia langsdorffiana (Annonaceae), descrevem o isolamento de
diterpenos do tipo traquilobano, atisano, caurano e labdano, das folhas, frutos, caule e raízes da
espécie. Maytenus distichophylla (Celastraceae), conhecida popularmente como espinheira
santa, é utilizada na medicina popular para o tratamento de ulceras estomacais, e dados da
literatura relatam o isolamento de triterpenos do tipo friedelano e alcaloides sesquiterpênicos
pirimidínicos. O planejamento de fármacos auxiliado por computador, vem otimizando técnicas
que facilitam na descoberta de novos fármacos, oferecendo recursos que permitem o
acoplamento de compostos à proteínas tridimensionalmente conhecidas e originando modelos
capazes de predizer valores experimentais confiáveis para moléculas biologicamente ativas,
tornando a busca por compostos biologicamente ativos mais eficiente. Este trabalho associou
ensaios experimentais e investigações computacionais baseadas nas plantas extraídas da flora
Paraibana: X. langsdorffiana, M. distichophylla, e outras espécies do gênero Maytenus.
Reportaremos os testes experimentais realizados com raízes e caule de Maytenus distichophylla
que possibilitaram a extração e determinação estrutural de flavonoide, esteroide e, triterpenos
do tipo friedelano e lupano. Paralelamente realizamos estudos computacionais de docking, PLS
e hidrofobicidade, com 15 triterpenos isolados de espécies do gênero Maytenus (incluindo M.
distichophylla) e, 17 diterpenos isolados de X. langsdorffiana. Além disso, determinamos a
composição química (por CG-EM e RMN), e atividade moduladora frente a bactérias
multirresistentes. Os óleos essenciais das 3 espécimes de X. langsdorffiana foram analisadas
pela Análise de Componente Principal (PCA). Três compostos foram isolados do caule de M.
distichophylla por técnicas cromatográficas: 3-oxo-12α-hidroxifriedelano, 30-hidroxifriedelan-
3ona e 29-hidroxifriedelan-3-ona. Outros quatro compostos foram isolados das raízes: β-
sitosterol, 11α-hidroxigloquidona, rigidenol e 4’-O-metilepigalocatequina, sendo os três
últimos relatados pela primeira vez na espécie. No estudo de docking, os diterpenos ent-atisan-
7α-acetoxi-16α-ol, ácido labdorfiânico C e ácido labdorfiânico B apresentaram os menores
valores de energia de formação quando complexados com a cruzaína, CYP2C9 e COX,
respectivamente. Os triterpenos que apresentaram os menores valores de energia de formação
complexados com essas enzimas foram, 3β-hidroxi-9,12-en-ursano (cruzaína), ácido 3,4-secofriedelan-
3-óico (CYP2C9) e 3-oxo-12α-hidroxifriedelano (COX). Na predição da atividade
antitumoral, calculada a partir do modelo PLS construído, o diterpeno ácido labdorfiânico C, e
o triterpeno 3β-hidroxifriedelano, apresentaram os melhores valores preditos. Os compostos
majoritários identificados nos óleos essenciais foram: ent-atisan-16α-ol, germacreno D,
limoneno e β-pineno. Os monoterpenos, β-pineno e limoneno, foram identificados em todos os
óleos essenciais analisados, com diferentes porcentagens. Através da análise do óleo essencial
do caule (espécime A) de X. Langsdorffiana, por RMN (¹H e ¹³C) foi possível identificar o entatisan-
16α-ol, relatado pela primeira vez na espécie. Alguns óleos essenciais do espécime A,
quando modulados com oxacilina frente a S. aureus, diminuíram a concentração do antibiótico
em 99%. A análise de componente principal (PCA) realizada com o óleo essencial de três
espécimes de X. langsdorffiana, permitiu identificar uma similaridade química entre os
espécimes A e B, e uma diferença em C, quando comparados com A e/ou B. Este resultado
pode estar relacionado a idade ou porte dos espécimes, já que os mesmos se encontram na
mesma coordenada geográfica. Os modelos obtidos nos estudos de CADD foram satisfatórios
e geraram resultados preditivos.
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170 |
Triagem virtual de metabólitos secundários com potencial atividade antimicrobiana do gênero solanum e estudo fitoquimico de solanum Capsicoides allBarros, Renata Priscila Costa 13 February 2017 (has links)
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Previous issue date: 2017-02-13 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / The human body has a large bacterial flora, but when these bacteria, the principle of
commensal character, become part of site other than it's natural, they can cause some
severe diseases. Researches that are based either on the search of new drugs from plants
or on the improvement of phytotherapics are in prominence and continue to play an
important role nowadays. In this perspective, the aim was to carry out a phytochemical
study of Solanum capsicoides All. fruits to isolate and characterize the chemical
substances of this species and to use in silico studies to carry out investigations of new
molecules potentially active for methicillin resistant Staphylococcus aureus (MRSA) and
Escherichia coli using a database created with secondary metabolites isolated from
Solanum genus. The phytochemical study of Solanum capsicoides All. fruits resulted in
the isolation of three substances: carpesterol, acetylated glucose and 4-hydroxybenzaldehyde.
A review of the literature led to the creation of a database with 421
different secondary metabolites isolated from the Solanum genus. Two databases from
CHEMBL were selected. The first one with activity against MRSA and another against
E. coli. The compounds were classified according to the pIC50 values to generate and
validate the model using "Random Forest"(RF). The structure of six new target proteins
against S. aureus obtained from the PDB (Protein database) were used for virtual
screening of the based on the receptor structure using docking studies by the Molegro
Virtual Docker, reaching to select Solanum database molecules capable of interacting in
the binding sites of proteins. The RF prediction model for MRSA obtained a percent
accuracy of 81%, area under the Receiver Operating Characteristic (ROC) curve of 0.885,
selecting 8 molecules with an active potential above 60%. The prediction model for
Escherichia coli obtained an accuracy rate of 88%, area under ROC curve of 0.932,
selecting 4 molecules with potential probability above 84%. The study of the coupling of
six target enzymes to S. aureus selected an average of 50 molecules from the bank of 421
isolated molecules of the genus Solanum with an ability to interact with on active site of
each enzyme. In addition, it was possible to obtain 1 molecule with active potential and
interaction capacity with 5 enzymes studied, 7 molecules interacting with 3 enzymes and
6 with 2 enzymes of S. aureus. The rutin, a molecule potentially active in the in silico
study for S. aureus and E. coli, together with carpesterol, were tested in vitro against these
bacteria. Microbiological tests have shown that carpesterol has no antimicrobial activity
for the studied strains, and that the rutin has activity only for E. coli. An interaction study
with strains of S. aureus ATCC 25923, a standard strain sensitive to all antibiotics, and
SAM-01, a multidrug resistant strain, was designed. There was interaction only between
rutin and oxacillin, one of the three antibiotics studied in the interaction, for a strain SAM-
01, reducing the resistance of this strain. / O ser humano possui uma vasta flora bacteriana que é comensal, mas quando essas
bactérias, a princípio de caráter comensal, passam a fazer parte de outro sítio que não o
seu natural, podem causar graves patogenias. Pesquisas que se fundamentam na busca por
novos medicamentos a partir de plantas ou no melhoramento de fitoterápicos já existentes
vem se destacando e continuam a desempenhar um papel importante nos dias de hoje.
Nessa perspectiva objetivou-se realizar um estudo fitoquímico dos frutos de Solanum
capsicoides All. para isolar e caracterizar substâncias químicas desta espécie e, utilizando
estudos in silico, realizar investigações de novas moléculas potencialmente ativas para
Staphylococcus aureus resistente a meticilina (MRSA) e Escherichia coli, utilizando um
banco de dados criado com metabólitos secundários isolados do gênero Solanum. O
estudo fitoquímico dos frutos de Solanum capsicoides All. resultou no isolamento de três
substancias: carpesterol, glicose acetilada e 4-hidroxi-benzaldeído. A revisão de literatura
levou à criação de um banco de dados com 421 diferentes metabólitos secundários
isolados do gênero Solanum. Foram selecionados dois bancos de dados obtidos a partir
do CHEMBL. O primeiro com atividade contra S. aureus multirresistente (MRSA) e o
outro contra E. coli. Os compostos foram classificados de acordo com valores de pIC50
para gerar e validar o modelo utilizando “Random Forest”(RF). A estrutura de seis novas
proteínas alvo contra S. aureus obtidas do Protein Data Bank (PDB) foram utilizadas para
triagem virtual baseada na estrutura do receptor utilizando estudos de “docking” com o
software Molegro Virtual Docker, a fim de selecionar moléculas do banco de dados de
Solanum com potencial capacidade de interagir nos sítios de ligação dessas proteínas. O
modelo RF de predição para S. aureus multirresistente obteve uma porcentagem de acerto
de 81%, área sob a curva Receiver Operating Characteristic (ROC) de 0,885,
selecionando 8 moléculas com potencial ativo superior a 60%. O modelo de predição para
Escherichia coli obteve taxa de acerto de 88%, área sob curva ROC de 0,932,
selecionando 4 moléculas com probabilidade de potencial ativo superior a 84%. O estudo
do docking das seis enzimas alvo para S. aureus selecionou uma média de 50 moléculas
do banco de 421 moléculas isoladas do gênero Solanum com a capacidade de interagir no
sitio ativo de cada enzima. Analisando moléculas multitarget, foi possível obter 1
molécula com potencial ativo e capacidade de interação com 5 das 6 enzimas estudadas,
7 moléculas interagindo com 3 enzimas e 6 com 2 enzimas de S. aureus. A rutina, uma
molécula potencialmente ativa no estudo in silico para S. aureus e E. coli, juntamente
com o carpesterol, foram testadas in vitro contra essas bactérias. Os testes
microbiológicos mostraram que o carpesterol não possui atividade antimicrobiana para as
cepas estudadas, e que a rutina possui atividade apenas para a cepa de E. coli. Foi
realizado ainda estudo de interação com as cepas de S. aureus ATCC 25923, uma cepa
padrão sensível a todos os antibióticos, e SAM-01, uma cepa multirresistente. Houve
interação apenas entre a rutina e a oxacilina, um dos três antibióticos estudados na
interação, para a cepa SAM-01, diminuindo a resistência dessa cepa.
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