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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
41

Computational High Throughput Screening Targeting DNA Repair Proteins To Improve Cancer Therapy

Barakat, Khaled H. Unknown Date
No description available.
42

Structure Based Ligand Design for Monoamine Transporters and Mitogen Activated Kinase 5

Manepalli, Sankar 15 March 2012 (has links)
Depression is a major psychological disorder that affects a person's mental and physical abilities. The National Institute of Mental Health (NIMH) classified it as a serious medical illness. It causes huge economic, as well as financial impact on the people, and it is also becoming a major public health issue. Antidepressant drugs are prescribed to mitigate the suffering caused by this disorder. Different generations of antidepressants have been developed with dissimilar mechanisms of action. According to the Center for Disease Control, the usage of antidepressants has skyrocketed by 400 percent increase over 2005- 2008 survey period. This dramatic rise in usage indicates that these are the most prescribed drugs in the US. Even with the FDA mandated "black box" warning of increased suicidal thoughts upon use of selected antidepressants, these drugs are still being used at a higher rate. <br>All classes of antidepressants are plagued by side effects with mainly sexual dysfunction common among them. To avoid the adverse effects, an emphasis is to discover novel structural drug scaffolds that can be further developed as a new generation of antidepressants. The importance of this research is to discover structurally novel antidepressants by performing in silico virtual screening (VS) of chemical databases using the serotonin transporter (SERT). In the absence of a SERT crystal structure, a homology model was developed. The homology model was utilized to develop the first structure-based pharmacophore for the extracellular facing secondary ligand binding pocket. The pharmacophore captured the necessary drug-SERT interaction pattern for SERT inhibitory action. This pharmacophore was employed as one of the filters for VS of candidate ligands. The ten compounds identified were purchased and tested pharmacologically. Out of the ten hits, three structurally novel ligands were identified as lead compounds. Two of these compounds exhibited selectivity towards SERT; the remaining lead compound was selective towards the dopamine transporter and displayed cocaine inhibition. The two SERT selective compounds will provide new opportunities in the development of novel therapeutics to treat depression. <br>For dopamine transporter (DAT), the study was based on recently developed structurally diverse photo probes. In an effort to better understand the binding profile similarities among these different scaffolds, the photo probes were docked into DAT. The finger print analysis of the interaction pattern of docked poses was performed to identify the inhibitor-binding sites. <br>For mitogen activated protein kinase 5 (MEK5), given the lack of structural information, a homology model of MEK5 was developed to guide the rational design of inhibitors. Docking of known MEK5 inhibitors into the homology model was performed to understand the inhibitory interaction profile. Several series of analogues were designed utilizing the generated interaction profile. / Bayer School of Natural and Environmental Sciences / Chemistry and Biochemistry / PhD / Dissertation
43

Recherche de nouveaux antipaludiques par bioinformatique structurale et chémoinformatique : application à deux cibles : PfAMA1 et PfCCT / Identification of new antimalarial molecules by structural bioinformatics and cheminformatics : application to two targets : PfAMA1 and PfCCT

Pihan, Émilie 02 July 2013 (has links)
Le paludisme est causé par cinq espèces du genre Plasmodium, P. falciparum étant le plus mortel. Des résistances de certaines souches du parasite ont été rapportées pour tous les médicaments mis sur le marché. Les moustiques vecteurs du parasite sont résistants aux insecticides et aucun vaccin n'est disponible. Cette maladie est un problème économique et de santé publique pour les pays en voie de développement. Mes travaux de thèses visent à identifier de nouveaux traitements contre le paludisme, en ciblant deux nouvelles protéines. Les Apicomplexes ont développé un mécanisme unique d'invasion, impliquant une interaction forte entre la cellule hôte et la surface du parasite, appelée jonction mobile. La caractérisation structurale et fonctionnelle du complexe AMA1-RON2 a ouvert la voie à la découverte de petites molécules capables d'empêcher l'interaction AMA1-RON2 et de ce fait, l'invasion. Le parasite a aussi besoin de phospholipides pour construire sa membrane durant le cycle érythrocytaire. Il y a six fois plus de phospholipides dans les érythrocytes infectés que dans les érythrocytes sains. Notre stratégie est d'inhiber la voie de synthèse de novo Kennedy et plus précisément, son étape limitante catalysée par la PfCCT. Des filtres basés sur le ligand (LBVS) et sur la structure (SBVS) ont été utilisés pour tester virtuellement les chimiothèques commerciales que j'ai préparées. Pour chaque projet, des molécules ont été sélectionnées pour leurs scores de docking et les interactions qu'elles établissent avec les résidus clés de la protéine. En combinant la bioinformatique structurale et la chémoinformatique, nous avons identifié des inhibiteurs potentiels des deux cibles protéiques. / Human malaria is caused by five parasitic species of the genus Plasmodium, P. falciparum being the most deadly. Drug resistance of some parasite strains has been reported for commercial drugs. Vector mosquitoes are resistant to perythroid insecticides and no successful vaccine is available. This disease is a public and economic health issue for developing countries. My PhD projects investigate new treatments for malaria, by targeting two new proteins. Apicomplexa parasites have developed a unique invasion mechanism involving a tight interaction formed between the host cell and the parasite surfaces called Moving Junction. The structural and functional characterization of the AMA1-RON2 complex pave the way for the design of low molecular weight compounds capable of disrupting the AMA1-RON2 assembly and thereby invasion. The parasite also needs phospholipids to build its membrane during the erythrocytic cycle. There are six times more phospholipids in infected erythrocytes compared to healthy ones. Our strategy is to inhibit the de novo Kennedy pathway and more precisely its rate-limiting step catalysed by the enzyme PfCCT. Filters were used for ligand-based (LBVS) and structure-based virtual screening (SBVS) of commercial chemical databases that I have prepared. For each project, molecules were selected in terms of their docking scores and their interactions with key active site residues. By combining structural bioinformatics and cheminformatics, we identified potential inhibitors of the two protein targets.
44

Identificação de novos inibidores da enzima aldolase de Trypanosoma brucei / Identification of novel inhibitors of aldolase from Trypanosoma brucei

Leonardo Luiz Gomes Ferreira 23 April 2013 (has links)
As doenças tropicais negligenciadas, que atingem as populações mais carentes do mundo, representam em termos humanitários e socioeconômicos uma grande preocupação global. As tripanossomíases estão entre as doenças parasitárias mais importantes, e, particularmente, a tripanossomíase africana, ou doença do sono, destaca-se como uma grave condição de saúde, causada pelo parasita unicelular Trypanosoma brucei. Dentre os principais alvos metabólicos considerados para o desenvolvimento de novos fármacos para o tratamento das tripanossomíases, a glicólise recebe especial atenção em função de seu papel vital no processo de produção de ATP para o parasita que vive na corrente sanguínea. Esta tese de doutorado tem como objetivo identificar novos candidatos a inibidores da enzima aldolase (EC 4.1.2.13) da via glicolítica de T. brucei. Considerando-se que o alvo macromolecular em questão é validado para o planejamento de fármacos, inibidores desta enzima são candidatos a novos agentes quimioterápicos. Este trabalho explora a integração de métodos experimentais e computacionais através de estratégias de planejamento de fármacos baseado na estrutura do receptor (SBDD, na sigla inglesa para structure-based drug design) e na estrutura do ligante (LBDD, na sigla inglesa para ligand-based drug design) para a identificação de inibidores da enzima alvo. Foram produzidos resultados significativos, tais como a identificação através de triagens virtuais em larga escala de novas moléculas capazes de inibir a atividade da aldolase. Adicionalmente, destaca-se a obtenção de protocolos de expressão, purificação e cristalização para a enzima alvo. Como parte da estratégia de identificação de novos inibidores da aldolase, foram desenvolvidos modelos de QSAR 2D e 3D e estudos de dinâmica molecular. / Neglected tropical diseases, which affect the poorest populations across the developing world, are a major global concern. The trypanosomiases are amongst the most serious neglected tropical diseases, and particularly, African trypanosomiasis (sleeping sickness), caused by the unicellular parasite Trypanosoma brucei, appears as a fatal condition. The glycolytic pathway emerges as a promising target among the metabolic pathways for the development of new drugs, due to its essential role in the ATP generating process in the bloodstream form of the parasite. The goal of this work is to identify new inhibitors for the glycolytic enzyme aldolase (EC 4.1.2.13) from Trypanosoma brucei. Inhibitors of this enzyme are drug candidates with high potential for clinical development, as the respective target enzyme was validated as a molecular target for the therapy of trypanosomiasis. The strategy employed in this study includes the integration of SBDD (structure-based drug design) and LBDD, (ligand-based drug design) for the identification of inhibitors of the target enzyme, through the combination of computational and experimental methodologies. Significant results were obtained, such as the identification of new small molecule inhibitors of the aldolase enzyme through high-throughput virtual screening. Additionally, it is highlighted the standardization of expression, purification and crystallization protocols for the target enzyme. As a component of the strategy for the identification of novel aldolase inhibitors, 2D and 3D QSAR models were developed, as well as molecular dynamics studies.
45

Prospecção de inibidores para a enzima malato sintase do Paracoccidioides brasiliensis: uma avaliação por triagem virtual e dinâmica molecular / Prospecting for inhibitors malate synthase ensyme the Paracoccidoides brasiliensis: an evaluation by virtual screening and molecular dynamics

Costa, Fausto Guimarães 16 April 2015 (has links)
Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2015-11-03T12:46:00Z No. of bitstreams: 2 Disssertação - Fausto Guimarães Costa - 2015.pdf: 7717372 bytes, checksum: 0c97192720a82947f88e00adcc4dc90b (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2015-11-03T12:47:31Z (GMT) No. of bitstreams: 2 Disssertação - Fausto Guimarães Costa - 2015.pdf: 7717372 bytes, checksum: 0c97192720a82947f88e00adcc4dc90b (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2015-11-03T12:47:31Z (GMT). No. of bitstreams: 2 Disssertação - Fausto Guimarães Costa - 2015.pdf: 7717372 bytes, checksum: 0c97192720a82947f88e00adcc4dc90b (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2015-04-16 / Paracoccidioidomycose / A Paracoccidioidomicose...
46

Busca In Silico de Inibidores de Fosfolipase A2 de Apis mellifera com validação In Vitro e In Vivo / In Silico search of Phospholipase A2 Inhibitors of Apis mellifera with In Vitro and In Vivo Validation

Daniel Macedo de Melo Jorge 09 May 2013 (has links)
A Apis mellifera é um inseto pertencente à ordem Himenóptera, família Apidae, possui ocorrência cosmopolita e grande importância ecológica, econômica e médica. As subespécies hibridas que ocorrem no Brasil possuem características predominantemente africanas e passaram a ser conhecidas como abelhas africanizadas. As principais características das abelhas africanizadas são o comportamento agressivo, boa resistência a doenças, alta produção de mel e o aumento da frequência de enxameamentos, que tem causado preocupação por estar acompanhado, de aumento no número de acidentes. A agressividade e o aumento da frequência do exameamento fazem com que elas estejam repetidamente envolvidas em ataques massivos a humanos e animais, tornando esse tipo de envenenamento um problema de saúde pública. A busca de tratamento para o envenenamento tem sido alvo de diversas pesquisas. De uma forma geral, os tratamentos atuam sobre os efeitos causados pelo veneno (medicamentos) ou sobre os componentes do veneno (soros e inibidores). Os principais componentes do veneno são a fosfolipase A2 (PLA2) e a melitina. A PLA2 é uma das principais proteínas do veneno, que degrada a membrana plasmática das células e tem o seu efeito potencializado pela presença da melitina. A PLA2 da Apis mellifera possui a estrutura protéica determinada e sítio ativo identificado. Essas características qualificam a PLA2 como potencial alvo de estudos de planejamento de fármacos. A estratégia de planejamento de fármacos tem como objetivo acelerar o processo de identificação de ligantes, contribuindo para o processo da descoberta de fármacos. Este trabalho teve como objetivo identificar in silico potenciais inibidores contra a PLA2 de Apis mellifera, avaliar in vitro e in vivo a potencial atividade inibitória dos compostos selecionados e identificar a citotoxicidade in vitro dos compostos. A estrutura da PLA2 foi obtida da base de dados (PDB) e a busca de compostos feita das bibliotecas Maybridge e Chembridge. A triagem virtual foi realizada com o auxilio do programa GOLD. Os compostos identificados (22 da Maybridge e 68 da Chembridge) pelos programas GOLD foram filtrados com o uso das ferramentas computacionais para seleção dos compostos com melhores interações no sítio ativo. Os parâmetros utilizados como filtros foram as análises das ligações químicas e os campos de interação molecular. Os compostos selecionados (20 da Maybridge e 29 da Chembridge) foram submetidos a um grupo de programas computacionais para predição de características físico-químicas (drug-like), toxicidade e atividade biológica dos ligantes. Os resultados das predições sugeriram que os compostos da Chembridge fossem utilizados nas análises experimentais. Os compostos da biblioteca Chembridge foram adquiridos (29 do total de 49 compostos). Os compostos tiveram as suas potenciais atividades inibitórias avaliadas in vitro e in vivo. A atividade fosfolipásica foi avaliada para os 29 compostos e 11 apresentaram atividade inibitória contra PLA2. Os 11 compostos foram avaliados in vivo com o experimento de indução de edema e 5 compostos conseguiram reduzir o edema. Os compostos foram avaliados em relação a citoxicidade que poderiam causar. A citotoxicidade in vitro foi calculada para 3 compostos dos 5 inibidores obtidos. O resultado do experimento identificou 2 compostos como citotóxicos e 1 com menor citotoxicidade. Apesar da citotoxicidade identificada, mais estudos devem ser realizados para determinar a concentração inibitória não tóxica. Portanto, o trabalho identificou 5 potenciais inibidores específicos contra a PLA2 de Apis mellifera. / Apis mellifera is an insect belonging to the order Hymenoptera , Apidae family , has cosmopolitan occurrence and major ecological , economic, and medical . The hybrid subspecies that occur in Brazil have predominantly African features and came to be known as Africanized bees . The main characteristics of Africanized bees are aggressive behavior , good disease resistance, high honey production and increased frequency of enxameamentos , which has caused concern to be monitored , the increase in the number of accidents . The aggressiveness and increased frequency of exameamento cause they are repeatedly involved in massive human and animal attacks , making this kind of poisoning a problem of public health. The search for treatments for poisoning has been the subject of several studies . In general , treatments act on the effects caused by poison ( drug ), or the components of poison ( sera and inhibitors) . The main components of the venom are A2 ( PLA2 ) and phospholipase melittin . PLA2 is a major venom proteins , which degrades the plasma membrane of the cells and its effect is potentiated by the presence of melittin . The Apis mellifera PLA2 has determined the protein structure and active site identified . These characteristics qualify PLA2 as a potential target for drug design studies . The strategy for drug design aims to accelerate the identification of ligands , contributing to the process of drug discovery . This study aimed to identify in silico potential inhibitors of PLA2 Apis mellifera , in vitro and in vivo the potential inhibitory activity of selected compounds and identify the in vitro cytotoxicity of the compounds . The structure of PLA2 was obtained from the database (PDB ) and the search for compounds made from Maybridge Chembridge and libraries. The virtual screening was done with the aid of the GOLD program. The identified compounds ( 22 and 68 of the Maybridge Chembridge ) by GOLD programs were filtered with the use of computational tools for the selection of compounds with better interactions in the active site . The parameters used were as filters analyzes of chemical bonds and the fields of molecular interaction. The selected compounds ( 20 and 29 of the Maybridge Chembridge ) were submitted to a group of computer programs for the prediction of physico- chemical characteristics ( drug -like) , toxicity and biological activity of the ligands . The results of the predictions suggest that the compounds of Chembridge were used in experimental analysis . The compounds were obtained from Chembridge library (29 of 49 compounds). The compounds had their potential inhibitory activity evaluated in vitro and in vivo . The phospholipase activity was assessed for compounds 29 and 11 showed inhibitory activity against PLA2 . The 11 compounds were evaluated in vivo experiment with the induction of edema and 5 compounds were able to reduce edema . The compounds were evaluated for cytotoxicity that could cause . The in vitro cytotoxicity was calculated for three of the compounds obtained 5 inhibitors . The result of the experiment identified as cytotoxic compounds 2 and 1 with lower cytotoxicity . Despite the cytotoxicity identified , further studies should be conducted to determine the non-toxic inhibitory concentration . Therefore, the study identified 5 potential specific inhibitors of PLA2 Apis mellifera.
47

Planejamento racional de novos agentes quimioterápicos: Identificação e estudos cinéticos de novos inibidores da gliceraldeído-3-fosfato desidrogenase glicossomal de Trypanosoma cruzi / Rational design of new chemotherapeutic agents: identification and kinetic studies of new inhibitors of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi

Aderson Zottis 26 March 2009 (has links)
As doenças negligenciadas são conseqüências marcantes do subdesenvolvimento que atinge diversas regiões do planeta. Dentre estas, destaca-se a Doença de Chagas, causada pelo parasita Trypanosoma cruzi, a qual afeta aproximadamente um quarto da população da América Latina e para qual os fármacos utilizados apresentam baixa eficácia, toxidez e sérios efeitos colaterais. Este quadro é agravado pela emergência de cepas resistentes, o que indica a grande necessidade de desenvolvimento de novos agentes quimioterápicos contra esta doença. A enzima gliceraldeído-3-fosfato desidrogenase (GAPDH) da via glicolítica do T. cruzi é um alvo macromolecular interessante devido ao seu papel essencial no metabolismo de tripanossomatídeos. Constitui o objetivo desta tese o desenvolvimento, a padronização e a validação de ensaios enzimáticos para a realização de extensivas triagens bioquímicas de modo a contribuir para a identificação de novos inibidores da GAPDH pertencentes a diversas classes químicas. Os compostos estudados são provenientes de síntese orgânica e de complexos inorgânicos de Rutênio, bem como de origem natural. Paralelamente, a realização do ensaio virtual em larga escala a partir de uma base de dados dirigida e da estrutura da GAPDH de T. cruzi resultou na identificação de um inibidor inédito da proteína alvo. Estudos do mecanismo de ação enzimático levaram à elucidação da modalidade de alguns inibidores identificados nesse estudo. / Parasitic diseases are a major global cause of illness, long-term disability, and death, with severe socio-economic consequences for millions of people worldwide. In Latin America, nearly one fourth of the population is infected by Trypanosoma cruzi, the causative agent of Chagas disease. The limited existing drug therapies suffer from a combination of drawbacks including poor efficacy, resistance and serious side effects. Therefore, there is an urgent need for new drugs that can overcome resistance and are safe and effective for use in human. The crucial dependence on glycolysis as a source of energy makes the glycolytic parasite enzymes promising targets for drug design. In this context, the enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was identified as an attractive target for drug design. The development of standard enzymatic assays combined with extensive biological screening was the aim of this work and it has been contributing for the identification of novel GAPDH inhibitors. These compounds belong to several chemical classes from different sources, including organic synthesis, inorganic complexes and natural products. In addition, a virtual screening approach was applied in a focused database, previously filtered by drug-like properties, in order to identify new hits. This strategy resulted in the discovery of a novel scaffold with significant inhibitory activity against T. cruzi GAPDH. Kinetic and inhibition assays were conducted to shed light on the mechanism of action of the promising inhibitors.
48

Drug design in silico : criblage virtuel de protéines à visée thérapeutique

Elkaïm, Judith 20 December 2011 (has links)
Les processus qui mènent à la découverte de nouveaux médicaments sont longs et fastidieux, et les taux de succès sont relativement faibles. L’identification de candidats par le biais de tests expérimentaux s’avère coûteuse, et nécessite de connaître en profondeur les mécanismes d'action de la protéine visée afin de mettre en place des essais efficaces. Le criblage virtuel peut considérablement accélérer ces processus en permettant une évaluation rapide de chimiothèques de plusieurs milliers de molécules afin de déterminer lesquelles sont les plus susceptibles de se lier à une cible. Ces dernières années ont ainsi été témoins de quelques success stories dans ce domaine.Le premier objectif de ce travail était de comparer différents outils et stratégies couramment utilisés dans le criblage virtuel “structure-based”, puis de les appliquer à des cibles protéiques à visée thérapeutique, en particulier dans le cadre du cancer.La protéine kinase GSK3 et un test set de ligands connus ont servi de modèle pour différentes études méthodologiques ayant pour but d’évaluer les programmes de docking et de scoring à notre disposition. En particulier, l’utilisation de plusieurs structures relaxées du récepteur ou l’insertion de torsions sur certains résidus du site actif pendant le docking ont permis d’évaluer l’influence de la flexibilité de la protéine. L’utilité et la pertinence d’outils permettant de générer automatiquement les structures 3D des ligands et de méthodes de consensus scoring ont également été étudiées.Un criblage virtuel de la Pontine, une ATPase impliquée dans la croissance tumorale pour laquelle aucun inhibiteur n’était connu, a permis la sélection de candidats issus de banques de données commerciales. Ces molécules ont été testées dans un essai enzymatique par le biais d’une collaboration, et quatre d’entre elles se sont révélées capable d’inhiber l’activité ATPase de la Pontine. Le criblage de bases de ligands synthétisés et imaginés dans l’équipe a également fourni un inhibiteur original. Au contraire, l’étude de la sPLA2-X humaine, une phospholipase dont l’activité catalytique est dépendante d’un atome de Ca2+ localisé au sein du site actif, a montré les limites de nos outils de docking qui n’ont pas été capables de gérer cet ion métallique et mis en évidence la nécessité de mettre en place d’autres outils. / The process of drug discovery is long and tedious. Besides, it is relatively inefficient in terms of hit rate. The identification of candidates through experimental testing is expensive and requires extensive data on the mechanisms of the target protein in order to develop efficient assays. Virtual screening can considerably accelerate the process by quickly evaluating large databases of compounds and determining the most likely to bind to a target. Some success stories have emerged in the field over the last few years.The objectives of this work were first, to compare common tools and strategies for structure-based virtual screening, and second, to apply those tools to actual target proteins implied notably in carcinogenesis.In order to evaluate the docking and scoring programs available, the protein kinase GSK3 and a test set of known ligands were used as a model to perform methodological studies. In particular the influence of the flexibility of the protein was explored via relaxed structures of the receptor or the insertion of torsions on the side chains of residues located in the binding site. Studies concerning the automatic generation of 3D structures for the ligands and the use of consensus scoring also provided insights on the usability of these tools while performing a virtual screening.Virtual screening of the human protein Pontin, an ATPase implied in tumor cell growth for which no inhibitors were known, allowed the prioritization of compounds from commercial databases. These compounds were tested in an enzymatic assay via a collaboration, and led to the identification of four molecules capable of inhibiting the ATPase activity of Pontin. Additional screens of in-house oriented databases also provided at least one innovative inhibitor for this protein. On the contrary, a study of the human PLA2-X, a phospholipase that requires a Ca2+ atom to bind to its active site in order to catalyze the hydrolysis of its substrate, revealed the limits of our docking tools that could not handle the metal ion and the need for new tools.
49

Computer-aided drug design of broad-spectrum antiviral compounds / Conception assistée par ordinateur de composés antiviraux à large spectre

Klimenko, Kyrylo 14 March 2017 (has links)
De nouveaux antiviraux à large spectre, agissant comme intercalant d'acides nucléiques, ont été identifiés par criblage virtuel et grâce à des cartes de l’espace chimique. La 1ère partie de la thèse présente le modèle QSPR pour la solubilité aqueuse des molécules organiques dans une grande gamme de températures. Ce modèle a été utilisé pour l'évaluation de la solubilité des composés antiviraux. Dans la 2ème partie de cette thèse, les filtres structuraux, les modèles QSAR et pharmacophores sont présentés. Leur utilisation pour cribler une base de données contenant plus de 3,2 M de composés est ensuite décrite. Cette étape a conduit à sélectionner 55 touches qui ont été synthétisées et testées expérimentalement. Parmi eux, deux composés ont révélé une activité élevée contre le Vaccinia virus et une faible toxicité. Dans la 3ème partie de la thèse, l'approche par Cartes Topographiques Génératives (GTM) a été utilisée pour construire des cartes 2D de l'espace chimique des composés antiviraux. Les structures chimiques et les données expérimentales des composés antiviraux, présents dans la base de données ChEMBL, ont été extraites de la base, examinées et annotées avec les principaux Genus des virus. Ce jeu de données a été utilisé pour construire des cartes sur lesquels tous les autres composés de la base de données ChEMBL ont été projetés. L'analyse de ces cartes révèle des motifs structuraux caractérisant des types particuliers d'antiviraux. / Virtual screening and cartography of chemical space approaches have been used for design of broad-spectrum antivirals acting as nucleic acids intercalators. The 1st part of thesis reports QSPR model for aqueous solubility of organic molecules within the wide temperature range. This model was later used for solubility assessment of antiviral compounds. In the second part of work, structural filters, QSAR and pharmacophore models were developed then used to screen a database containing some 3.2 M compounds. This resulted in 55 hits which were synthesized and experimentally tested. Two lead compounds displayed high activity against Vaccinia virus and low toxicity. In the 3d part of the thesis, Generative Topographic Mapping (GTM) approach was used to build 2D maps of chemical space of antiviral compounds. Experimental data on antiviral compounds were extracted from ChEMBL database, curated and annotated by major virus Genus. Selected dataset was used to build maps on which all other ChEMBL compounds were projected. Analysis of the maps revealed structural motifs characterizing particular types of antivirals.
50

Computational Modelling in Drug Discovery : Application of Structure-Based Drug Design, Conformal Prediction and Evaluation of Virtual Screening

Lindh, Martin January 2017 (has links)
Structure-based drug design and virtual screening are areas of computational medicinal chemistry that use 3D models of target proteins. It is important to develop better methods in this field with the aim of increasing the speed and quality of early stage drug discovery. The first part of this thesis focuses on the application of structure-based drug design in the search for inhibitors for the protein 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), one of the enzymes in the DOXP/MEP synthetic pathway. This pathway is found in many bacteria (such as Mycobacterium tuberculosis) and in the parasite Plasmodium falciparum. In order to evaluate and improve current virtual screening methods, a benchmarking data set was constructed using publically available high-throughput screening data. The exercise highlighted a number of problems with current data sets as well as with the use of publically available high-throughput screening data. We hope this work will help guide further development of well designed benchmarking data sets for virtual screening methods. Conformal prediction is a new method in the computer-aided drug design toolbox that gives the prediction range at a specified level of confidence for each compound. To demonstrate the versatility and applicability of this method we derived models of skin permeability using two different machine learning methods; random forest and support vector machines.

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