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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.
481

[en] SYNTHESIS AND MOLECULAR DOCKING OF 1,2,3-TRIAZOLES FOR THE TREATMENT OF CYSTIC FIBROSIS / [pt] SÍNTESE E ANCORAGEM MOLECULAR DE 1,2,3-TRIAZOIS PARA O TRATAMENTO DA FIBROSE CÍSTICA

JOYCE FERREIRA PESSANHA DA S ROCHA 20 July 2021 (has links)
[pt] Por ser uma doença genética, resultado de uma mutação em um gene específico, que gera proteínas (CFTR) defeituosas, a Fibrose Cística é uma patologia difícil de ser tratada. Os custos para os tratamentos atualmente disponíveis são altos, sem os quais, porém, a gravidade da doença tende a crescer ainda mais. Por esse motivo, novos tratamentos farmacológicos vêm surgindo, como o Trikafta (marca registrada), uma combinação tripla de fármacos com ação sinérgica (elexacaftor, ivacaftor e tezacaftor). Porém, esse medicamento ainda não é disponível no Brasil e o acesso aos tratamentos, em geral, são onerosos. Sendo assim, este trabalho visa a síntese de compostos 1,2,3-triazóis, com possível atividade biológica frente a proteína CFTR, sugerida por ancoragem molecular. Este trabalho também visa selecionar as melhores moléculas quanto aos perfis farmacocinéticos e toxicológicos, avaliados por ferramentas computacionais como swissADME e VirtualToxLab, respectivamente. Dessa forma, a estratégia sintética para a obtenção dos compostos consiste em duas etapas sintéticas. A primeira, envolve a síntese da enaminona – (E)-3-(dimetilamino)acrilaldeido (3a-d) – por organocatálise, a partir de L-prolina e DMA-DMF (1,1-dimetoxi-N,N-dimetillmetanamina) (1). A segunda etapa inclui a reação de cicloadição 1,3-dipolar onpot entre as azidas (5a-h) e as enaminonas previamente obtidas. Assim, foi possível obter 1,2,3-triazóis 1,4-substituídos (6a-k), com rendimentos de 5 a 96 por cento. Dentre eles, a molécula 6k, N-(2-(1-(4-metoxifenil)-1H-1,2,3-triazol-4-carbonil)fenil)acetamida), destacou-se quanto aos perfis toxicológicos e também pelos resultados observados nos estudos de ancoragem molecular. Os espectros de RMN de 1H e 13C RMN confirmaram a obtenção das estruturas. / [en] Because it is a genetic disease, the result of a mutation in a specific gene, which generates defective proteins (CFTR), Cystic Fibrosis is a pathology that is difficult to be treated. The costs for currently available treatments are high, without which, however, the severity of the disease tends to increase even more. For this reason, new pharmacological treatments are emerging, such as Trikafta (trademark), a triple combination of drugs with synergistic action (elexacaftor, ivacaftor and tezacaftor). However, this drug is not yet available in Brazil and access to treatments, in general, is expensive. Therefore, this work aims at the synthesis of 1,2,3-triazole compounds, with possible biological activity against the CFTR protein, proposed by molecular anchoring. This work also aims to select the best molecules in terms of pharmacokinetic and toxicological profiles, evaluated by computational tools such as swissADME and VirtualToxpot, respectively. Thus, the synthetic strategy for obtaining the compounds consists of two synthetic steps. The first involves the synthesis of enaminone - (E)-3-(dimethylamino) acrylaldehyde (3a-d) - by organocatalysis, starting from L- proline and DMA-DMF (1,1-dimethoxy-N, N-dimethylmethanamine) (1). The second stage includes the 1,3-dipolar onpot cycloaddition reaction between the azides (5a-h) and the previously obtained enaminones. Thus, it was possible to obtain 1,4-substituted 1,2,3-triazoles (6a-k), with yields of 5 to 96 percent. Among them, the molecule 6k, N- (2- (1- (4-methoxyphenyl) -1H-1,2,3-triazol-4-carbonyl) phenyl) acetamide), stood out in terms of toxicological profiles and also by results observed in molecular anchorage studies. The 1H and 13C NMR NMR spectra confirmed the structures obtained.
482

Conception et synthèse de molécules hétérocycliques comme inhibiteurs d’enzymes et médiateurs d’interaction protéine-protéine

Kiyeleko, Scarlett 08 1900 (has links)
La nature contient un grand nombre de molécules naturelles à visée thérapeutique. Depuis plusieurs années, la chimie médicinale ne cesse de s’en inspirer afin de développer de nouvelles thérapies pour améliorer le quotidien des personnes atteintes de certaines pathologies. Cette thèse traitera de la conception de molécules hétérocycliques comme inhibiteurs d’enzymes et médiateurs d’interactions protéine-protéine. Les molécules bioactives sont la pierre angulaire de la chimie thérapeutique. Depuis la découverte de l’Aspirine en 1899, elles n’ont cessé d’impacter la société à plusieurs niveaux et ont contribué à l’amélioration de la qualité de vie des patients. Il y a cependant, plusieurs pathologies pour lesquelles il n’existe à ce jour aucun remède, ce qui met en exergue les limitations de la chimie médicinale et implique le développement de nouvelles stratégies thérapeutiques. La stéato-hépatite non-alcoolique ou NASH (Non-Alcoholic Steatohepatitis) est une maladie caractérisée par une accumulation de graisses dans le foie, menant à la formation de tissus cicatriciels sur le foie. Ces derniers altèrent les fonctions hépatiques du foie et peuvent mener à la cirrhose si aucun traitement n’est administré. A ce jour, il existe aucun médicament pour guérir de NASH. La serine-thréonine kinase 25 (STK25) est une sérine-thréonine kinase, qui serait impliquée dans le développement de la maladie de NASH. Ainsi, le premier chapitre de cette thèse rapporte la synthèse de triazolo-oxazines comme inhibiteurs potentiels de STK25. Il s’agit de la première approche inhibitrice rapportée dans la littérature. Des tests biologiques ont été effectués et la modélisation moléculaire des triazolo-oxazines a été réalisée. Face au problème de pharmacorésistance et l’absence de remèdes pour certaines maladies, il y a un besoin urgent pour de nouvelles stratégies thérapeutiques est présent. Depuis quelques années, les dégradeurs ciblés de protéines suscitent un engouement. En effet, ces derniers induisent la dégradation de protéines défectueuses en recrutant les complexes de ligase E3. Cette stratégie vient pallier l’absence de sites de liaison, caractéristique de plusieurs protéines impliquées dans le développement de cancers. Parmi les dégradeurs de protéines, il y a les agrafes moléculaires et les PROTACs. Dans le second chapitre de cette thèse, la synthèse de molécules hétérocycliques comme ligand de la ligase E3 DCAF15 pour le développement éventuel de nouveaux PROTACS sera rapportée. L’outil de modélisation moléculaire a permis la sélection de molécules indoliques comportant le motif -lactame et pyrrolidine . Bien qu’ils aient été synthétisés comme un mélange racémique, des tests pour la synthèse asymétrique de ces derniers seront également discuter. Les maladies infectieuses ravagent les pays de l’Amérique latine et l’Afrique subsaharienne. Les ressources insuffisantes, les conditions sanitaires et l’instabilité des régimes politiques rendent difficile l’administration et l’acheminement de traitements. Parmi ces maladies infectieuses, il y a la leishmaniose, la trypanosomiase humaine africaine et la trypanosomiase humaine américaine lesquelles sont toutes causés par des protozoaires. Dans le troisième chapitre, des molécules hétérocycliques, comportant le motif imidazolo-oxazine seront synthétisés comme candidats potentiels pour le traitement de ces maladies infectieuses. / Nature has provided an infinite number of bioactive small molecules for therapeutic benefits. For many years, it has inspired medicinal chemistry to develop new therapies to improve the well-being of humankind. This thesis will be about the conception of heterocyclic small molecules as enzyme inhibitors and protein-protein interaction mediators. Small molecules are the cornerstone of therapeutic chemistry. Since the discovery of Aspirin in 1899, small molecules have had a significant impact on several levels and have contributed to the improvement of quality of life. Nonetheless, many diseases still have no remedy; hence there exists a need for new therapeutic strategies. Non-alcoholic steatohepatitis, (NASH) is a disease characterized by a buildup of fat in the liver, leading to the formation of scars on the liver. These scars will affect the different functions of the liver and can even lead to cirrhosis if not treated. Up until now, there is no drug for NASH. STK25 is a serine-threonine kinase, suspected to be involved in the mechanism of action of NASH. The first chapter in this thesis involves the synthesis of triazolo-oxazines as potential STK25 inhibitors for NASH treatment. It is the first example of an enzymatic approach for NASH treatment. The synthesis of potential inhibitors was designed based of molecular modeling of other inhibitors targeting CDK. In a second chapter, a new approach of small molecules degraders that recruits E3 ligases complexes for the degradation of protein is described. Among the small molecule degraders, there are molecular glues and PROTACs. This chapter will describe the design and the synthesis of heterocyclic molecules as DCAF15 ligands for the eventual development of new PROTACs. Molecular docking has been useful for the selection of the - lactams et pyrrolidines small molecules. Infectious diseases have tremendous consequences in Latin America and Africa. The lack of means, health hazards and the political instability of governments make difficult the supply and administration of treatments. Among the infectious diseases, there are Leishmaniasis, human African trypanosomiasis, human American trypanosomiasis, which are caused by bacteria. In the third chapter, imidazolo-oxazine small molecules will be synthesized as potential candidates for the treatment of these parasitic infections.
483

Design, Synthesis, and Process Chemistry Studies of Agents Having Anti-Cancer Properties

Luniwal, Amarjit 26 May 2011 (has links)
No description available.
484

Identification of Novel Ligands and Structural Requirements for Heterodimerization of the Liver X Receptor Alpha

Bedi, Shimpi 31 May 2017 (has links)
No description available.
485

Design and Synthesis of Amino Acid-based Inhibitors Against Key Enzymes

Mutthamsetty, Vinay January 2017 (has links)
No description available.
486

Structure-Based Computer Aided Drug Design and Analysis for Different Disease Targets

Kumari, Vandana 13 September 2011 (has links)
No description available.
487

Modellierung und Visualisierung von Systemen zur Beschreibung der intra- und intermolekularen Wechselwirkungen in hydrophoben Peptiden

Schneider, Alexander 11 November 2014 (has links) (PDF)
Die vorliegende Arbeit beschäftigt sich mit der Untersuchung und Beschreibung der Eigenschaften der synthetischen Dekapeptide Cetrorelix und Ozarelix durch analytische Methoden und computergestützte Modellierung. Diese Moleküle sind hydrophobe, aggregierende Antagonisten des Gonadotropin-Releasing-Hormons (GnRH). Zusätzlich wurden amyloidbildende Peptidstrukturen als Modelle für die Assoziationsprozesse in hydrophoben Peptiden untersucht und visualisiert. Die intrinsische Fluoreszenz der GnRH-Antagonisten und zusätzlich der Peptide Teverelix und D-Phe6-GnRH sowie von verkürzten Fragmenten des Cetrorelix wurde untersucht. Ein Strukturmodell für die Beschreibung der Aggregation der Dekapeptide wurde erarbeitet. Der Aufbau eines Rechenclusters durch das Einbinden der Computer am Lehrstuhl in ein Linux-System zur Verteilung von Rechenprozessen über das Netzwerk ermöglichte die Bereitstellung der notwendigen Leistung zur Realisierung der Berechnungen. Es wurden Werkzeuge zur Modellierung der solvatisierten Aggregate von Peptiden ohne eindeutige Vorzugsstruktur programmiert und in ein Docking-System für beliebige Moleküle eingebunden. Verwendet wurde das Kraftfeld MMFF94 mit einer Erweiterung durch ein Verfahren zur dynamischen Berechnung von Partialladungen in Molekülstrukturen. Solvatisierte Aggregate der Dekapeptide und von bekannten amyloidbildenden Strukturen wurden modelliert (Docking). Berechnet wurden als aggregierend beschriebene Sequenzen und entsprechende Vergleichsstrukturen des Calcitonins, des Insel-Amyloid-Polypeptides, des beta2-Mikroglobulins, des Amyloid-beta-Proteins, des Lactoferrins und weitere Modellpeptide. Die wesentlichen Wechselwirkungen während der Aggregation konnten schließlich anhand von Dynamik-Simulationen der faltblattartigen Dimere des Cetrorelix und Ozarelix beschrieben werden. So wurden die Prozesse der hydrophoben Assoziation und Stabilisierung durch Wasserstoffbrücken von Peptiden veranschaulicht und auf molekularer Ebene erfolgreich analysiert. Die Visualisierung der erhaltenen Modellierungsergebnisse erfolgt durch die Darstellung der Strukturen und Dynamik-Simulationen als interaktive 3D-Modelle in einem für diese Arbeit aufgebauten Internetauftritt. / This work discusses the analysis of the aggregation properties of the gonadotropin releasing hormone antagonists Cetrorelix, Teverelix, Ozarelix and of small amyloid forming model peptides by analytical fluorescence spectroscopy and molecular modelling. A high performance linux compute cluster was developed for calculation of molecular structures. Solvated aggregate clusters of peptides without defined secondary structure were modelled by molecular mechanics methods (forcefield mmff94) in combination with an advanced charge equilibration and docking technique. Molecular dynamics of solvated peptide dimers were implemented and the role of hydrophic association and hydrogen bond formation in hydrophobic peptide aggregates was explained. Finally, an aggregation model for the directed association of hydrophobic peptides is presented. The modelling results, 3d structures and dynamic simulations are visualized in an interactive web material.
488

Modellierung und Visualisierung von Systemen zur Beschreibung der intra- und intermolekularen Wechselwirkungen in hydrophoben Peptiden

Schneider, Alexander 08 October 2014 (has links)
Die vorliegende Arbeit beschäftigt sich mit der Untersuchung und Beschreibung der Eigenschaften der synthetischen Dekapeptide Cetrorelix und Ozarelix durch analytische Methoden und computergestützte Modellierung. Diese Moleküle sind hydrophobe, aggregierende Antagonisten des Gonadotropin-Releasing-Hormons (GnRH). Zusätzlich wurden amyloidbildende Peptidstrukturen als Modelle für die Assoziationsprozesse in hydrophoben Peptiden untersucht und visualisiert. Die intrinsische Fluoreszenz der GnRH-Antagonisten und zusätzlich der Peptide Teverelix und D-Phe6-GnRH sowie von verkürzten Fragmenten des Cetrorelix wurde untersucht. Ein Strukturmodell für die Beschreibung der Aggregation der Dekapeptide wurde erarbeitet. Der Aufbau eines Rechenclusters durch das Einbinden der Computer am Lehrstuhl in ein Linux-System zur Verteilung von Rechenprozessen über das Netzwerk ermöglichte die Bereitstellung der notwendigen Leistung zur Realisierung der Berechnungen. Es wurden Werkzeuge zur Modellierung der solvatisierten Aggregate von Peptiden ohne eindeutige Vorzugsstruktur programmiert und in ein Docking-System für beliebige Moleküle eingebunden. Verwendet wurde das Kraftfeld MMFF94 mit einer Erweiterung durch ein Verfahren zur dynamischen Berechnung von Partialladungen in Molekülstrukturen. Solvatisierte Aggregate der Dekapeptide und von bekannten amyloidbildenden Strukturen wurden modelliert (Docking). Berechnet wurden als aggregierend beschriebene Sequenzen und entsprechende Vergleichsstrukturen des Calcitonins, des Insel-Amyloid-Polypeptides, des beta2-Mikroglobulins, des Amyloid-beta-Proteins, des Lactoferrins und weitere Modellpeptide. Die wesentlichen Wechselwirkungen während der Aggregation konnten schließlich anhand von Dynamik-Simulationen der faltblattartigen Dimere des Cetrorelix und Ozarelix beschrieben werden. So wurden die Prozesse der hydrophoben Assoziation und Stabilisierung durch Wasserstoffbrücken von Peptiden veranschaulicht und auf molekularer Ebene erfolgreich analysiert. Die Visualisierung der erhaltenen Modellierungsergebnisse erfolgt durch die Darstellung der Strukturen und Dynamik-Simulationen als interaktive 3D-Modelle in einem für diese Arbeit aufgebauten Internetauftritt. / This work discusses the analysis of the aggregation properties of the gonadotropin releasing hormone antagonists Cetrorelix, Teverelix, Ozarelix and of small amyloid forming model peptides by analytical fluorescence spectroscopy and molecular modelling. A high performance linux compute cluster was developed for calculation of molecular structures. Solvated aggregate clusters of peptides without defined secondary structure were modelled by molecular mechanics methods (forcefield mmff94) in combination with an advanced charge equilibration and docking technique. Molecular dynamics of solvated peptide dimers were implemented and the role of hydrophic association and hydrogen bond formation in hydrophobic peptide aggregates was explained. Finally, an aggregation model for the directed association of hydrophobic peptides is presented. The modelling results, 3d structures and dynamic simulations are visualized in an interactive web material.
489

Stratagems for effective function evaluation in computational chemistry

Skone, Gwyn S. January 2010 (has links)
In recent years, the potential benefits of high-throughput virtual screening to the drug discovery community have been recognized, bringing an increase in the number of tools developed for this purpose. These programs have to process large quantities of data, searching for an optimal solution in a vast combinatorial range. This is particularly the case for protein-ligand docking, since proteins are sophisticated structures with complicated interactions for which either molecule might reshape itself. Even the very limited flexibility model to be considered here, using ligand conformation ensembles, requires six dimensions of exploration - three translations and three rotations - per rigid conformation. The functions for evaluating pose suitability can also be complex to calculate. Consequently, the programs being written for these biochemical simulations are extremely resource-intensive. This work introduces a pure computer science approach to the field, developing techniques to improve the effectiveness of such tools. Their architecture is generalized to an abstract pattern of nested layers for discussion, covering scoring functions, search methods, and screening overall. Based on this, new stratagems for molecular docking software design are described, including lazy or partial evaluation, geometric analysis, and parallel processing implementation. In addition, a range of novel algorithms are presented for applications such as active site detection with linear complexity (PIES) and small molecule shape description (PASTRY) for pre-alignment of ligands. The various stratagems are assessed individually and in combination, using several modified versions of an existing docking program, to demonstrate their benefit to virtual screening in practical contexts. In particular, the importance of appropriate precision in calculations is highlighted.
490

Synthesis, biological evaluation and molecular docking studies of novel indole- and benzofuran-chalcone and benzofuran-quinazoline hybrids as anticancer agents

Maluleka, Marole Maria 07 1900 (has links)
Text in English / Specially prepared 2-amino-5-bromo-3-iodoacetophenone and 5-bromo-2-hydroxy-3 iodoacetophenone were subjected to Claisen-Schmidt aldol condensation with benzaldehyde derivatives followed by sequential and/or one-pot palladium catalyzed Sonogashira cross coupling and heteroannulation of the 3-alkynylated intermediates to afford indole-chalcones and benzofuran-chalcones, respectively. The indole-chalcones derivatives were, in turn, subjected to trifluoroacetic anhydride in tetrahydrofuran under reflux to afford the corresponding 3-trifluoroacetyl substituted indole-chalcone derivatives. The coupling constant values (Jtrans) of about 16.0 Hz for the chalcone derivatives corresponding to the vinylic protons confirmed the trans geometry of the α,β-unsaturated carbonyl framework in all the cases. Their trans geometry of the chalcone derivatives was further confirmed by single crystal X-ray diffraction (XRD) analyses. Further structural elaboration of the ambident electrophilic α,β unsaturated carbonyl (chalcone) moiety of the indole-chalcones and the analogous benzofuran chalcones with 2-aminothiophenol afforded novel benzothiezapine-appended indole and benzofuran hybrids, respectively. Sonogashira cross-coupling of 5-bromo-2-hydroxy-3 iodoacetophenone with terminal acetylenes followed by heteroannulation of the intermediate 3-alkynylated 5-bromo-2-hydroxyacetophenones afforded the corresponding 7-acetyl-2-aryl-5-bromobenzofurans in a single-pot operation. The oximes derived from the 7-acetyl–substituted 2-aryl-5-bromobenzofurans were subjected to Beckmann rearrangement with triflic acid in acetonitrile under reflux. We isolated the corresponding 7-amino-2-aryl-5 bromobenzofuran derivatives formed from hydrolysis in situ of the intermediate 7-acetamide 2-aryl-5-bromobenzofurans. Amino-dechlorination of the 4-chloroquinazoline derivatives with the 7-aminobenzofurans afforded novel benzofuran 4-aminoquinazoline hybrids. The prepared compounds were characterized using a combination of nuclear magnetic resonance (1H-NMR & 13C-NMR including 19F-NMR), infrared (IR) and mass spectroscopic techniques complemented with single crystal X-ray diffraction (XRD) analyses and/or density functional (DFT) method. The benzofuran-chalcone 203a–y derivatives were evaluated for anti-growth effect against the breast cancer (MCF-7) cell line by the MTT cell viability assay. Their mode of cancer cell death (apoptosis versus necrosis) was detected by Annexin V-Cy3 SYTOX staining and caspase-3 activation. The most cytotoxic compounds 203i and 203o were also evaluated for potential to inhibit tubulin polymerization and/or epidermal growth factor receptor-tyrosine kinase (EGFR-TK) phosphorylation. The experimental results were complemented with theoretical data from molecular docking into ATP binding site of the EGFR and colchicine binding site of tubulin, respectively. The benzofuran–4-aminoquinazoline hybrids 215a–j, on the other hand, were evaluated for antiproliferative propeties in vitro against the human lung cancer (A549), epithelial colorectal adenocarcinoma (Caco-2) and hepatocellular carcinoma (C3A) cell lines. The benzofuran-aminoquinazoline hybrids were also evaluated for potential to induce apoptosis and for their capability to inhibit EGFR-TK phosphorylation complemented with molecular docking (in silico) into the ATP binding site of EGFR. Mechanistic studies demonstrated that the benzofuran-appended aminoquinazoline hybrids 215d and 215j induced apoptosis via activation of caspase-3 pathway. Moreover, compounds 215d and 215j exhibited significant and moderate inhibitory effects against EGFR (IC50 = 29.3 nM and 61.5 nM, respectively) when compared to Gefitinib (IC50 = 33.1 nM). Molecular docking of compounds 215 into EGFR-TK active site suggested that they bind to the region of EGFR like Gefitinib does. / Chemistry / D. Phil. (Chemistry)

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