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Etude des ADN glycosylases de la superfamille structurale Fpg/Nei par modélisation moléculaire, de nouvelles cibles thérapeutiques potentielles dans les stratégies anti-cancer / Study of DNA glycosylases from Fpg/Nei structural superfamilly by molecular modeling, new potential therapeutic target for anti-cancer strategiesRieux, Charlotte 20 December 2017 (has links)
L’ADN, support de l’information génétique, est constamment altéré par des agents physiques ou chimiques d’origines endogènes (métabolisme) et exogènes (UV, radiations ionisantes, produits chimiques) dont les effets sont génotoxiques. Ces modifications structurales délétères de l’ADN sont éliminées par de nombreux mécanismes de réparation. Parmi eux, le système de réparation par excision de bases (BER) est initié par les ADN glycosylases qui reconnaissent et éliminent les bases endommagées. Dans certaines stratégies anti-cancéreuses, l’utilisation de la chimiothérapie et la radiothérapie ont pour but la destruction des cellules cancéreuses en altérant leur ADN. Dans ce contexte, les ADN glycosylases réparent l’ADN des cellules traitées et induisent une résistance non désirée au traitement, faisant de ces enzymes des cibles thérapeutiques intéressantes. Le but de ces travaux est d’approfondir la compréhension des mécanismes de réparation des ADN glycosylases de la superfamille structurale Fpg/Nei grâce à la modélisation moléculaire et de pouvoir identifier et concevoir des inhibiteurs de ces enzymes. Les simulations de dynamique moléculaire (DM) nous ont permis d’étudier la « Lesion Capping Loop » (LCL) et de l’associer à la stabilisation de la base endommagée positionnée dans le site actif. Nous avons également étudié les chemins de sortie possibles de la base après coupure par l’enzyme et l’implication de la boucle LCL dans ce phénomène grâce à des simulations de DM ciblée (TMD-1). De plus, les simulations de DM couplées à un protocole d’amarrage moléculaire « aveugle » nous ont permis d’identifier 2 sites de fixations possibles majoritaires pour des petites molécules potentiellement inhibitrices. Un de ces sites correspondant au site actif de hNEIL1 a fait l’objet d’un criblage virtuel d’une partie de la base de molécules Ambinter. Ceci nous a permis d’identifier des molécules potentiellement inhibitrices dont les effets seront prochainement testés in vitro dans l’équipe sur la protéine humaine hNeil1. / The DNA, genetic information support, is frequently damaged by physical or chemical agents from endogenous (cell metabolism) and exogenous (UV, ionizing radiations, chemicals) factors whose effects are genotoxic. These deleterious DNA structural alterations are removed by many DNA repair mechanisms. Among them, the base excision repair (BER) is initiated by DNA glycosylases which recognize and remove damaged bases. In some anti-cancer strategies, the use of chemo- and radiotherapy is aimed to cancerous cells destruction by altering their DNA. In that specific context, DNA glycosylases repair the DNA of treated cells and induce unwanted resistance to treatments, making these enzymes interesting therapeutic targets. The purpose of this work is to deepen the repair mechanism knowledge of Fpg/Nei structural superfamily of DNA glycosylases using molecular modeling and designing inhibitors of these enzymes. Molecular dynamic simulations allowed us to study the « Lesion Capping Loop » (LCL) and to associate its role to substrate stabilization in the enzyme active site. We also studied some possible excision’s product release pathways and LCL implication in this phenomena by targeted molecular dynamic simulations (TMD-1). Furthermore, molecular dynamic simulations coupled to a blind molecular docking protocol allowed us to identify 2 possible main binding sites of potential inhibitiors. One of these binding sites corresponding to the hNEIL1 active site has been the object of a virtual screening of the Greenpharma database. This allowed us to identify potential inhibitors whom effects will be soon tested in vitro on the humain protein hNEIL1.
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Synthetic Approaches towards Novel Isoform Selective PI3K Inhibitors and Their Biological Activities against Prostate Cancer CellsWazeerud-Din, Idris 08 August 2018 (has links)
The development of novel imidazopyridines, which includes both tetrahydroimidazo[1,5-a]pyridine (rIMP) and imidazo[1,5-a]pyridine (IMP) was investigated using conventional and microwave induced procedures that afforded compounds at high yield of 88-96%. rIMP was synthesized using a two-step procedure that involved the microwave synthesis of IMP, then the reduction of the pyridine moiety of the fused imidazopyridine rings using 10% Pd/C and hydrazine monohydrate. The microwave synthesis of imidazopyridines involved the one pot reaction of 2-benzoylpyridine, substituted benzaldehyde and ammonium formate in acetic acid under open vessel microwave conditions, which resulted in products within 40 minutes. Novel PEG-IMP development, involved the synthesis of ethylene glycol tethered benzaldehydes and IMPs using traditional Williamson etherification synthesis, which afforded products at a high yield of 92-95%. We have then shown IMP and rIMP roles in its antiproliferative property towards PCa cells, specificity in inhibiting PI3K isoforms, and structural motif’s interaction with different residues in the kinase binding domain of the class I PI3K isoforms. The antiproliferative property towards PC3 cells shows increased activity with compounds containing pyridyl group on carbon 3 of the imidazo[1,5-a]pyridine parent moiety with signs of toxicity to PC3 within 24 hours of incubation and at 1 μM of the parent compound. Furthermore, the IMPs were tested against five prostate cellular lines: PC3, RWPE1, D145, LNCaP and LNCaP C81. IMPs showed little activity towards RWPE1 and increased activity towards PC3 cells. We determined that functionalizing the phenyl group at position 1 increased the efficacy of rIMP compared to the IMP. After showing increased toxicity to PC3 cells, it was important to investigate the mechanism in which IMP pose toxicity towards PC3 cells. The biochemical assay showed that rIMP was more effective in inhibiting PI3Kα isoform compared to both pan inhibitor wortmannin and IMP. Both IMP and rIMP inhibited more than 60% of PI3Kγ isoform activity at nanomolar concentrations. After showing IMPs affinity to PI3K isoforms, we investigated the binding interactions rIMP and IMP towards the PI3K isoforms using MOE molecular modeling software.
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Computational studies of biomoleculesChen, Sih-Yu January 2017 (has links)
In modern drug discovery, lead discovery is a term used to describe the overall process from hit discovery to lead optimisation, with the goal being to identify drug candidates. This can be greatly facilitated by the use of computer-aided (or in silico) techniques, which can reduce experimentation costs along the drug discovery pipeline. The range of relevant techniques include: molecular modelling to obtain structural information, molecular dynamics (which will be covered in Chapter 2), activity or property prediction by means of quantitative structure activity/property models (QSAR/QSPR), where machine learning techniques are introduced (to be covered in Chapter 1) and quantum chemistry, used to explain chemical structure, properties and reactivity. This thesis is divided into five parts. Chapter 1 starts with an outline of the early stages of drug discovery; introducing the use of virtual screening for hit and lead identification. Such approaches may roughly be divided into structure-based (docking, by far the most often referred to) and ligand-based, leading to a set of promising compounds for further evaluation. Then, the use of machine learning techniques, the issue of which will be frequently encountered, followed by a brief review of the "no free lunch" theorem, that describes how no learning algorithm can perform optimally on all problems. This implies that validation of predictive accuracy in multiple models is required for optimal model selection. As the dimensionality of the feature space increases, the issue referred to as "the curse of dimensionality" becomes a challenge. In closing, the last sections focus on supervised classification Random Forests. Computer-based analyses are an integral part of drug discovery. Chapter 2 begins with discussions of molecular docking; including strategies incorporating protein flexibility at global and local levels, then a specific focus on an automated docking program – AutoDock, which uses a Lamarckian genetic algorithm and empirical binding free energy function. In the second part of the chapter, a brief introduction of molecular dynamics will be given. Chapter 3 describes how we constructed a dataset of known binding sites with co-crystallised ligands, used to extract features characterising the structural and chemical properties of the binding pocket. A machine learning algorithm was adopted to create a three-way predictive model, capable of assigning each case to one of the classes (regular, orthosteric and allosteric) for in silico selection of allosteric sites, and by a feature selection algorithm (Gini) to rationalize the selection of important descriptors, most influential in classifying the binding pockets. In Chapter 4, we made use of structure-based virtual screening, and we focused on docking a fluorescent sensor to a non-canonical DNA quadruplex structure. The preferred binding poses, binding site, and the interactions are scored, followed by application of an ONIOM model to re-score the binding poses of some DNA-ligand complexes, focusing on only the best pose (with the lowest binding energy) from AutoDock. The use of a pre-generated conformational ensemble using MD to account for the receptors' flexibility followed by docking methods are termed “relaxed complex” schemes. Chapter 5 concerns the BLUF domain photocycle. We will be focused on conformational preference of some critical residues in the flavin binding site after a charge redistribution has been introduced. This work provides another activation model to address controversial features of the BLUF domain.
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Implementace logistických technologií v potravinářském průmyslu / Implementation of logistic technologies in food industryŽEMLIČKA, Kamil January 2014 (has links)
This diploma thesis focuses on proposal of possibilities when applying logistic technologies in food supply chain of the MADETA, a.s. The thesis describes material and information flow in the supply chain, including determination of key factors for successful implementation of chosen technologies. A part of the thesis deals with the proposal for a change in the way of preparing orders for customers of independent market, including stating of expected costs and savings when realizing the proposal.
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Etude structurale des aptamères peptidiques anti-Fur et de leur interaction avec leur cible / Structural study of anti-Fur peptide aptamers and their interactions with their targetCisse, Cheickna 19 January 2012 (has links)
Fur (Ferric Uptake Regulator) est un régulateur transcriptionnel spécifique des bactéries qui intervient dans le contrôle de l'homéostasie du fer, ce qui en fait une cible antibactérienne intéressante. Avant mon arrivée au laboratoire, quatre inhibiteurs interagissant spécifiquement avec Fur avaient été isolés. La partie active de ces inhibiteurs consiste en des peptides de 13 acides aminés. Au cours de cette thèse, j'ai utilisé une double-approche : théorique et expérimentale pour étudier l'interaction de ces peptides avec Fur afin de comprendre le mécanisme d'inhibition. J'ai synthétisé plusieurs séquences peptidiques, montré par des tests biochimiques que certaines inhibaient Fur et déterminé les interactions importantes à l'activité inhibitrice. J'ai obtenu des modèles théoriques des complexes Fur/peptides par amarrage moléculaire, cohérents avec les résultats expérimentaux, qui ont mis en évidence une zone d'inhibition de Fur. Des criblages in silico dans cette zone ont permis de sélectionner de petites molécules, inhibitrices potentielles de Fur et donc intéressantes pour des applications thérapeutiques. / Fur (Ferric Uptake Regulator) is a transcriptional regulator involved in the control of iron homeostasis. Specific to bacteria, Fur is an attractive antibacterial target. Before my arrival in the laboratory, four inhibitors interacting specifically with Fur had been isolated. The active part of these inhibitors consists of peptides of 13 amino acids. In this thesis I have used both theoretical and experimental approaches to study interactions of these peptides with Fur in order to understand the inhibition mechanism. I have synthesized several peptide sequences, shown through biochemical assays that some of them could inhibit Fur and I have identified residues important to the inhibitory activity. I‘ve obtained theoretical models of Fur/peptide complexes consistent with experimental results, which reveal an inhibition pocket in Fur. Small molecules have then been selected though In silico screening of this pocket, that could potentially inhibit Fur, and thus be interesting for therapeutic applications.
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Docking de compostos da família das ariloxazinas em enzimas relacionadas com a malária / Docking of arilloxazines in enzymes related to malariaCorrêa, Denis da Silva 06 August 2010 (has links)
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Previous issue date: 2010-08-06 / Universidade Federal de Minas Gerais / Malaria disease, caused mainly by Plasmodium falciparum parasite, afflicts about 500 million people and causes nearly one million deaths every year. For the development of new drugs against this disease, one possible approach is to identify an enzyme that plays a key role in P. falciparum development and presents significantly different properties from the corresponding human one. These differences can be exploited in the design of specific inhibitors of the parasite s protein, thus, three different enzymes were selected as possible targets. As there are evidences suggesting that increasing oxidative stress can effectively inhibit the growth of the malarial parasite the enzyme Glutathione Reductase of P. falciparum (PfGR), responsible for the parasite s antioxidant defense, has become a potential target for the design and development of inhibitors. The second target was the P. falciparum Dihydrofolate Reductase-Thymidylate Synthase (PfDHFR-TS), and in this case blocking its action stops the dTMP production and DNA synthesis in the parasite. The third chosen target was the P. falciparum Lactate Dehydrogenase (PfLDH), whose inhibition interrupts the ATP formation and thus causing the death of the parasite. So that a family of arilloxazines compounds, together with chloroquine and methylene blue, were studied by means of docking simulations in the binding sites of these enzymes and also in the corresponding human enzymes for comparison. The three-dimensional structures of the enzymes and of chloroquine and methylene blue were obtained from the Protein Data Bank (PDB). The structures of the arilloxazines compounds, in turn, were obtained by molecular modeling with HyperChem 6.01 and MOPAC2009 programs, using as starting models similar crystallographic structures deposited in the Cambridge Structural Database. Docking simulations were performed using GOLD 4.0.1. The docking results showed that the enzymes PfGR and PfDHFR-TS are not the preferential targets of chloroquine. For the methylene blue it was possible to elucidate its binding mode in hGR and PfGR. Regarding the arilloxazines it was possible to show that they present their higher affinity for hGR, followed by PfGR, hDHFR, PfDHFR-TS, PfLDH and hLDH. In the case of GRs, the interface site was the preferred binding site. The results suggest that if arilloxazines compounds with higher affinity for PfGR are desirable then a pentafluorophenyl should be attached at the N10 position, as in the 2e compound. When searching for arilloxazines with higher affinity for PfLDH, it seems to be desirable a carboxymethyl group at the N3 position (as in 5b) and a pentafluorophenyl group at N10 (as in 2e). Finally, the results suggest that in general the studied arilloxazines probably will present a higher affinity for hDHFR than PfDHFR-TS. All these results are an important starting point for the design of new arilloxazines ligands so that they can be used as lead compounds in the search for new drugs against malaria. / A malária, causada principalmente pelo Plasmodium falciparum, atinge cerca de 500 milhões de pessoas e causa aproximadamente um milhão de mortes todos os anos. Para o desenvolvimento de novos fármacos contra esta doença, uma das abordagens possível é identificar uma enzima que desempenhe papel vital no desenvolvimento do P. falciparum e apresente propriedades significantemente diferentes das enzimas humanas correspondentes, de modo que tais diferenças possam ser exploradas no design de inibidores específicos à proteína do parasita. Existem evidências sugerindo que aumentar o estresse oxidativo pode inibir eficientemente o crescimento do parasita causador da malária e, portanto, a enzima Glutationa Redutase do P. falciparum (GRPf), responsável por sua defesa antioxidante, tornou-se um alvo em potencial para o desenvolvimento de inibidores. Também, o bloqueio da ação da Diidrofolato Redutase-Timidilato Sintase do P. falciparum (DHFR-TSPf) interrompe a produção de dTMP e a síntese de DNA no parasita. Ainda, espera-se que a inibição da Lactato Desidrogenase do P. falciparum (LDHPf) interrompa a produção de ATP no parasita e, consequentemente, cause sua morte. Portanto, estudou-se o comportamento de compostos da família das ariloxazinas, da cloroquina e do azul de metileno nos sítios de ligação destas enzimas, além das enzimas humanas correspondentes para fins de comparação, por meio de cálculos de docking. As estruturas tridimensionais das enzimas foram obtidas no Protein Data Bank (PDB). As estruturas dos inibidores da família das ariloxazinas, por sua vez, foram obtidas por meio de modelagem molecular, utilizando os programas HyperChem 6.01 e MOPAC2009, a partir de estruturas cristalográficas semelhantes obtidas no Cambridge Structural Database; já as estruturas da cloroquina e do azul de metileno foram obtidas também no PDB. Os cálculos de docking destes compostos nos sítios de ligação das enzimas estudadas foram realizados utilizando o programa GOLD 4.0.1. Com base nos resultados de docking, sugere-se que as enzimas GRPf e DHFR-TSPf não são alvos preferenciais da cloroquina. Também, pôde-se elucidar o possível modo de ligação do azul de metileno nas enzimas GRh e GRPf. No geral, foi possível sugerir ainda que as ariloxazinas devam apresentar maior afinidade pela GRh, seguida por GRPf, DHFRh, DHFR-TSPf, LDHPf e LDHh, nesta ordem. Nas GRs, o sítio da interface foi o sítio preferencial de ligação. Para se buscar inibidores da família das ariloxazinas com maior afinidade pela GRPf, sugere-se considerar um pentafluorfenil como substituinte na posição N10, como no composto 2e. Ainda, na busca por ariloxazinas com maior afinidade pela LDHPf, sugere-se considerar um carboximetil na posição N3 (como o de 5b) e um pentafluorfenil na posição N10 (como em 2e). Por fim, foi obtido que as ariloxazinas estudadas possivelmente apresentarão, em geral, uma maior afinidade pela DHFRh do que pela DHFR-TSPf. Estes dados podem ser tomados como ponto de partida para o design de novos compostos da família das ariloxazinas, a fim de que possam atuar como compostos líderes na busca por novos fármacos contra a malária.
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Constru??o de modelos de intera??o in silico e in vitro do inibidor do tipo Kunitz de Adenanthera pavonina L. para as enzimas ciste?nicas e ser?nicasMigliolo, Ludovico 02 July 2008 (has links)
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Previous issue date: 2008-07-02 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / Serines proteinases inhibitors (PIs) are widely distributed in nature and are able to inhibit both in vitro and in vivo enzymatic activites. Seed PIs in than leguminous are
classified in seven families, Bowman-Birk and Kunitz type families that most studied representing an important role in the first line of defense toward insects pests. Some
Kunitz type inhibitors possess activities serine and cysteine for proteinases named bifunctional inhibitor, as ApTKI the inhibitor isolate from seed of Adenanthera pavonina.
The A. pavonina inhibitor presenting the uncommon property and was used for interaction studies between proteinases serine (trypsin) and cysteine (papain). In order
to determinate the in vitro interaction of ApTKI against enzymes inhibitor purification was carried cut by using chromatographic techniques and inhibition assays. The 3D model of the bifunctional inhibitor ApTKI was constructed SWISS-MODEL program by homology modeling using soybean trypsin inhibitor (STI, pdb:1ba7), as template which presented
40% of identity to A. pavonina inhibitor. Model quality was evaluated by PROCHECK program. Moreover in silico analyzes of formed complex between the enzymes and
ApTKI was evaluated by HEX 4.5 program. In vitro results confirmed the inhibitory assays, where the inhibitor presented the ability to simultaneously inhibit trypsin and
papain. The residues encountered in the inhibitor model of folder structural three-dimensional that make contact to enzymes target coud explain the specificity pattern
against serine and cysteine proteinases / Os inibidores de proteinases ser?nicas (IPs) est?o extensamente distribu?dos na natureza e inibem a atividade enzim?tica in vitro e in vivo. Estes IPs em sementes de
leguminosas compreendem sete fam?lias, no entanto as fam?lias Bowman-Birk e do tipo Kunitz s?o as mais estudadas e representam um papel importante na primeira linha de
defesa contra insetos pragas. Alguns inibidores do tipo Kunitz possuem atividades para proteinases ser?nicas e ciste?nicas sendo denominados inibidores bifuncionais, como o inibidor ApTKI da semente de Adenanthera pavonina. O inibidor de A. pavonina por apresentar essa caracter?stica incomum aos inibidores dessa fam?lia foi utilizado para o estudo da intera??o entre as proteinases ser?nica (tripsina) e ciste?nica (papa?na). Para determinar a intera??o in vitro de ApTKI e as enzimas alvo foi realizada a purifica??o do inibidor a partir de t?cnicas cromatogr?ficas e ensaios de inibi??o. O modelo 3D do
inibidor bifuncional ApTKI foi constru?do pelo programa SWISS-MODEL atrav?s da metodologia de modelagem por homologia utilizando como molde o inibidor de tripsina de soja (STI, pdb:1ba7) que apresentou 40% de identidade com a prote?na alvo. A qualidade do modelo foi avaliada pelo programa PROCHECK. Para a an?lise do complexo in silico entre as enzimas alvo e o inibidor foi utilizado o programa HEX 4.5. Estes resultados confirmaram os ensaios inibit?rios in vitro, onde ApTKI apresentou a capacidade de inibir simultaneamente tripsina e papa?na. Algumas das diferen?as
observadas nos res?duos do sitio reativo explicam a forte afinidade para tripsina e a fraca para papa?na
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Um novo protocolo in silico para a predição de complexos flexíveis entre proteínas estudo de caso para inibidores plasmáticos de fosfolipase A2 de serpentes /Matioli, Fábio Filippi. January 2016 (has links)
Orientador: Marcos Roberto de mattos Fontes / Resumo: Ainda nos dias de hoje, o envenenamento ofídico é um problema de saúde pública, afetando, sobretudo, regiões de clima tropical, subtropical, particularmente áreas rurais de países da África, Ásia, Oceania e América Latina. No Brasil, os gêneros de serpentes Bothrops e Crotalus são responsáveis por quase 95% dos acidentes ofídicos, enquanto o segundo gênero apresenta alta taxa de morbidade. O veneno das serpentes do gênero Bothrops contem fosfolipases A2 ácidas que causam uma considerada mionecrose e severas reações anticoagulantes. De outro lado, os venenos das serpentes do gênero Crotalus possuem o complexo crotoxina, o qual é formado pela crotoxina A (não catalítica) e a crotoxina B (PLA2 catalítica) que possui potente ação neurotóxica. As serpentes peçonhentas, grupo que inclui ambas as famílias citadas, utilizam esse veneno tanto para a captura de sua presa como para sua própria defesa. Inevitavelmente, essas serpentes terão contato com o seu próprio veneno, como por exemplo, na alimentação, pois as presas estarão envenenadas. Por tal fato, as serpentes peçonhentas apresentam alguns mecanismos de defesa, inclusive algumas proteínas encontradas em seu sangue que são chamadas de proteínas inibitórias de PLA2 (PLIs). Para entender melhor o mecanismo de inibição desses compostos plasmáticos, foi desenvolvido neste trabalho um novo protocolo de docking molecular que consiste em analisar as estruturas ao longo dos modos normais, docking molecular, simulação de dinâmica molecula... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Nowadays, snake envenomation is a public health issue that mostly affects tropical and subtropical regions, particularly rural areas of countries from Africa, Asia, Oceania and Latin America. In Brazil, the Bothrops and Crotalus snake genre are responsible for approximately 95% of all snake bites, and the accidents caused by the latter have a relatively high mortality rate. The venom of Bothrops snakes contains a acid phospholipases A2 that causes drastic local myonecrosis and several anticoagulant reactions. On the other hand, the Crotalus genus snake venom contains the the crotoxin complex, which is formed by crotoxin A (non-catalytic) and crotoxin B (catalytic PLA2), that have up a strong neurotoxic action. Venomous snakes, including the two afore mentioned genre, use their venoms for capturing their prey and for their own defense. These snakes will inevitably get in contact with their own venom, for example, in alimentation, for the prey itself will be poisoned. For this fact, the poison snakes features in your blood the so-called PLA2 inhibiting proteins (PLIs). In order to understand the inhibition mechanism of these plasmatic components, it has developed in this study a new molecular docking protocol that consists in analyzing the structures using normal modes, molecular docking, molecular dynamics simulation and other bioinformatics tools. The results of this work was the proposition of a new flexible molecular docking protocol between two or more proteins and your... (Complete abstract click electronic access below) / Mestre
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Computer-aided design of novel antithrombotic agents / Conception des nouveaux agents anti-thrombiques assistée par ordinateurKhristova, Tetiana 15 November 2013 (has links)
La thrombose est le plus important processus pathologique sous-jacent à de nombreuses maladies cardiovasculaires, qui sont responsables d’une mortalité élevée dans le monde entier. Dans cette thèse, la conception assistée par ordinateur de nouveaux agents antithrombotiques capables d’inhiber deux types de récepteurs situés à la surface des plaquettes a été appliquée. Le premier - αIIbβ3 - est responsable de l’interaction des plaquettes activées avec le fibrinogène pour former des caillots, tandis que le second – le thromboxane A2 – est responsable de l’activation des plaquettes par l’un des agonistes excrétés par les plaquettes activées. Afin d’atteindre cet objectif, différents types de modèles ont été développés en utilisant les informations expérimentales disponibles et la structure des complexes protéine-ligand, comprenant des modèles QSAR, des pharmacophores 3D basés sur la structure de la protéine ou du ligand, des pharmacophores 2D, des modèles basés sur la forme et sur le champ moléculaire. L’ensemble des modèles développés ont été utilisés en criblage virtuel. Cette étude a abouti sur la suggestion de nouveaux antagonistes potentiels des récepteurs αIIbβ3 et thromboxane A2. Les antagonistes de αIIbβ3 suggérés pouvant se lier soit à la forme ouverte soit à la forme fermée du récepteur ont été synthétisés et testés expérimentalement. L’expérience montre qu’ils font preuve d’une forte activité; de plus, certains des composés conçus théoriquement sont plus efficaces que le Tirofiban, qui est un médicament commercialisé. Les antagonistes recommandés du récepteur thromboxane A2 ont déjà été synthétisés mais les tests biologiques n’ont pas encore été complétés. / Thrombosis is the most important pathological process underlying many cardiovascular diseases, which are responsible for high mortality worldwide. In this theses the computer-aided design of new anti-thrombotic agents able to inhibit two types of receptors located on the surface of the platelets has been applied. The first one - αIIbβ3 - is responsible for the interaction of activated platelets with fibrinogen to form clots, whereas the second one - thromboxane A2 - is responsible for platelet activation by one of agonists excreted by activated platelets. To achieve this, different types of models have been developed using experimentally available information and structure of protein-ligand complexes. This concerns: QSAR models, structure-based and ligand-based 3D pharmacophore models, 2D pharmacophore models, shape-based and molecular field-based models. The ensemble of the developed models were used in virtual screening. This study resulted in suggestion of new potential antagonists of αIIbβ3 and thromboxane A2 receptors. Suggested antagonists of αIIbβ3 able to bind either open or closed form of the receptor have been synthesized and tested experimentally. Experiments show that they display high activity; moreover some of theoretically designed compounds are more efficient than Tirofiban – the commercialized drug molecule. The recommended antagonists of thromboxane A2 receptor have been already synthesized but biological tests have not been completed yet.
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Development of VEGFR-2 inhibitors by ynamide- based click chemistry / Developpement d'inhibiteurs de VEGFR-2 par des réactions de chimie click à partir d'ynamidesVojtickova, Margareta 27 September 2013 (has links)
Malgré d’intenses recherches, le cancer reste une des causes principales de mortalité dans le monde. Le développement de nouveaux produits actifs pour le traitement des cancers est de plus en plus nécessaire. Nous avons décidé de préparer de nouveaux composés anti-angiogéniques dérivés du composé III.1 (ligand du complexe PDB : 1Y6A) dores et déjà testé cliniquement. Cinq d’entres eux ont pu être synthétisés en utilisant une réaction Click entre un ynamide et un azide. La réaction Click catalysée au cuivre a permis de préparer cinq de nos 1,2,3-triazole cibles avec une excellente régiosélectivité. Bien que l’activité de ces composés soit bien moins importante que celle du composé oxazolique III.1 dont elles sont dérivées, nous avons montré qu’ils sont des ligands spécifiques de VEGFR-2 kinase et qu’elles représentent une nouveauté structurale intéressante dans l’espace très protégé des inhibiteurs de tyrosine kinases. / Despite to the intensively research, cancer is still a leading cause of death worldwide. There are still developed new active compounds for cancer treatment. We have decided to prepare new antiangiogenic drugs based on already clinically tested III.1 from PDB complex 1Y6A. The in Silico-designed 1,2,3-triazole analogues of III.1 were prepared using a Click chemistry approach. In order to accomplish Click reactions two key building blocks: ynamides and azides were mandatory to synthetize. Copper catalyzed Click reactions were performed in very mild condition with quantitative regioselectivity. Five predicted triazolic compounds were prepared and sent for VEGFR-2 biologicall assays. Although the activities of triazolic compounds are significantly lower than the activities of their oxazolic isosters these compounds deliver structural novelty to IP crowded space of tyrosine kinase inhibitors. / Napriek intenzívnemu výskumu, rakovina stále patrí k najčastejším príčinám úmrtia na svete. Neustále sú vyvíjané nové aktívne látky na liečbu rakoviny. Rozhodli sme sa pripraviť nové antiangiogenetické liečivá na základe klinicky testovaného III.1 z PDB komplexu 1Y6A. In Silico navrhnuté 1,2,3-triazolové III.1 analógy boli pripravené prostredníctvom Click chémie. Za účelom uskutočnenia Click reakcie, bolo nevyhnutné pripraviť dva kľúčové stavebné jednotky: ínamidy a azidy. Meďou katalyzované Click reakcie boli uskutočnené vo veľmi jemných podmienkach s kvantitatívnou regioselektivitou. Bolo pripravených päť nových triazolových látok, ktoré boli zaslané na VEGFR-2 biologické testy. Aj keď sú aktivity triazolových derivátov výrazne nižšie ako aktivity oxazolvých izostérov, tak tieto zlúčeniny vnášajú do oblasti tyrozín kinázových inhibítorov, ktorá obsahuje už rôznorodé látky, štruktúrnu originalitu.
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