The cellular slime mold, Dictyostelium discoideum, provides an ideal model system to study eukaryotic development, cell differentiation, and aging. A crucial developmental event in Dictyostelium is glycogen degradation. The degradation of glycogen provides glucose monomers that are used to synthesize structural components necessary for cellular differentiation. Glycogen degradation is catalyzed by glycogen phosphorylase, and two developmentally regulated glycogen phosphorylase activities have been discovered in Dictyostelium. Glycogen phosphorylase 1 (gp-1) activity is predominant early in development, and is dependent upon 5’ AMP as a positive allosteric modifier; glycogen phosphorylase 2 (gp-2) activity peaks late in development and is independent of 5° AMP. I showed that these two glycogen phosphorylase activities are associated with unique proteins that are the products of two distinct, but related, genes. Both genes were observed to be typical Dictyostelium genes in a number of respects. The gp-1 and gp-2 enzymes were also found to be similar to glycogen phosphorylases from other organisms. I also examined the developmental expression of these genes and found that both mRNAs are developmentally regulated; gp-1 mRNA levels fluctuate during development, while gp-2 mRNA levels increase late in development. The expression of the gp-1 and gp-2 genes is regulated by exogenous cAMP. Exogenous cAMP enhances the level of gp-1 mRNA, apparently through a mechanism that requires intracellular cAMP signaling. Specific DNA sequence elements appear to be required for maximal vegetative and late developmental expression of gp-1. Exogenous cAMP induces the appearance of gp-2 mRNA via a mechanism that appears to be independent of intracellular cAMP signaling. Repeated TA-rich sequences located between nucleotides 193 and 305 upstream of the transcriptional start site are necessary for maximal cAMP induction of gp-2. I also examined the cell type specific expression of gp-1 and gp-2. gp-1 is expressed predominantly in pre-stalk cells. gp-2 1s expressed in both cell types in a temporally regulated fashion; this type of expression has not been reported for other Dictyostelium genes, but, given the importance of glycogen degradation in both stalk and spore cells, it is not inconceivable that such regulation 1s necessary. / Ph. D.

A la suite des nombreux travaux sur l’inhibition de la glycogène phosphorylase (GP) menés au laboratoire et au travers de diverses collaborations, cette thèse décrit en cinq chapitres suivis d’une partie expérimentale détaillée, les dernières avancées en termes de synthèse et d’évaluation biologique des inhibiteurs du site catalytique de la GP. La chapitre I de ce manuscrit est consacrée à la présentation des diabètes et plus particulièrement du diabète de type II dont le traitement, motivation première de ce projet, repose sur la connaissance des mécanismes complexes régulant la glycémie. Les différents inhibiteurs synthétisés sont classés par famille selon leur structure qui associe un aglycone hétérocyclique, susceptible d’affinité pour le canal β proche du site actif de l’enzyme, avec un motif glycopyranosidique, ou glycopyranosylidène dans le cas des motifs spiro. Le chapitre II est consacré aux inhibiteurs spiro-bicycliques tels que les glucopyranosylidène-spiro-1,4,2-oxathiazoles et les glucopyranosylidène-spiro-isoxazolines. Le chapitre III décrit la synthèse de C- et N-glycosyles hétérocycles, principalement des glycopyranosyl-1,2,3-triazoles. Enfin le chapitre IV décrit la fonctionnalisation de 5-halogéno-1,2,3-triazoles 4-substitués par couplages pallado-catalysés qui ont constitué un développement imprévu mais original des travaux. Pour terminer, le chapitre V décrit l’évaluation des molécules préparées en tant qu’inhibiteurs de la glycogène phosphorylase. Les expériences et résultats d’enzymologie, de cristallographie ainsi que les tests cellulaires in vitro et in vivo sur le rat sont présentés / Following many studies lead on the inhibition of glycogen phosphorylase (GP) in our laboratory an trough several collaborations, this thesis describes in five chapters and a detailed experimental section, the most recent advances in the areas of synthesis and biological evaluation of GP’s catalytic site inhibitors. Chapter I is dedicated to the description of diabetes and especially type 2 diabetes of which treatment, the main goal of this project, requires knowledge of the complex mechanisms that regulates glycemia. Synthesized inhibitors are broken down into families according to their structure which associates an heterocyclic aglycon, prone to binding in the β pocket lining the active site, with a glycopyranoside or glycopyranosylidene moiety in the case of spiro compounds. Chapter II focuses on spiro-bicyclic inhibitors such as glucopyranosilidene-spiro-1,4,2-oxathiazoles and glucopranosylidene-spiro-isoxazolines. Chapter III describes the synthesis of C- and N-glycosyl-heterocycles, mainly glycopyranosyl-1,2,3-triazoles. Finally, chapter IV studies the palladium-mediated cross coupling fonctionalization of 4-substituted-5-halogenated-1,2,3-triazoles that represents an unexpected but interesting development of the project. To conclude, chapter V gathers the evaluation of synthesized molecules as GP inhibitors. Enzymology and crystallography as well as in vitro and in vivo experiments are presented

Branched chain sugars display a varied and valuable range of biological activities. This thesis concerns the synthesis of 3,5-di-C-methyl-D-glucose, a potential inhibitor of glycogen phosphorylase (GP), and therefore a proposed therapeutic agent for type 2 diabetes. Chapter 1 looks at the occurrence of branched sugars in the natural world and current therapies for type 2 diabetes. Inhibition of GP is explored, and the molecular modelling studies which led to the design of the project target. Chapter 1 also looks into the development of new foodstuffs, the chemistry and biochemistry of imino sugars and branched hydroxy proline analogues. In Chapter 2, a range of different approaches to 3,5-di-C-methyl-D-glucose are investigated. Most of the initial investigations were carried out on the L-enantiomer, a readily available test system deriving from 2-C-methyl-D-ribono lactone. 2-C-Methyl-D-ribono lactone is synthesised rapidly from D-glucose in a one-pot reaction; as the key starting material for this work, the scalability of this process was investigated. One of the attempted syntheses of di-C-methyl glucose lead to the development of a route towards 3,5-di-C-methyl fructose, a novel dibranched ketose sugar. It was envisaged that through an enzymatic transformation, it might be possible to produce 3,5-di-C-methyl glucose stereoselectively. Synthesis of both enantiomers of 3,5-di-C-methyl glucose and mannose are reported, alongside results of GPb inhibition studies. Analysis of the preferred ring size of a range of di-C-methyl branched sugars and sugar lactones generated in this work is also presented. Chapter 3 explores the chemistry of 2,4-di-C-methyl-L-arabinono lactone, a key intermediate in the synthesis of 3,5-di-C-methyl-L-glucose. From this lactone a novel deoxy sugar, 2-deoxy-2,4-di-C-methyl-L-arabinono lactone, was generated. Routes towards a selection of imino sugars were explored, resulting in the synthesis of a methyl branched isofagomine analogue. A substituted aziridine was synthesised, from which a route to a di-C-methyl branched piperidine was proposed, and a pyrrolidine. Also presented is a synthesis of a dihydroxy di-C-methyl branched proline analogue. Detailed NMR analysis of several of the sugars generated in this work was carried out by Dr M. Wormald, of the University of Oxford Biochemistry department. The results of these investigations are presented in the Appendix. Throughout this work, the presence of quaternary centres has posed a problem with the assignment of relative configuration. As a result, this work has been greatly supported by X-ray crystallography, and the structures shown herein were wholly generated by me. Several other crystals were run during the course of this work, not all pertaining to these projects, and are provided in the CD appendix.

The current energy crisis is exponentially growing and widening the chasm between demand and supply. Biofuels such as ethanol not only provide greener alternatives to fossil fuels but have been shown to reduce emissions from vehicles, improving air etc. Biofuel production from sources such as cellulose is believed to be more sustainable due to its low cost, vast availability in nature and sources such as industrial plant waste can be put to good use. However, due to the absence of a low-cost technology to overcome its recalcitrance, a concept called Consolidated Bioprocessing (CBP) has been put forward which proposes to integrate the production of saccharolytic enzymes, hydrolysis of the carbohydrate components to sugar molecules, and the fermentation of hexose and pentose sugars to biofuels into a single process. The present study involves development of cellulolytic E. coli strains towards cellodextrin assimilation by employing an energy-saving strategy in cellulose metabolism through the phosphorolytic cleavage of cellodextrin mixture produced as cellulosic degradation products.

Made available in DSpace on 2014-06-11T19:22:54Z (GMT). No. of bitstreams: 0 Previous issue date: 2005-08-18Bitstream added on 2014-06-13T20:29:19Z : No. of bitstreams: 1 silva_don_me_sjrp.pdf: 1054782 bytes, checksum: 832047dd271670cc0bc6debdbd5dc8d8 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A Purina Nucleosídeo Fosforilase (PNP) catalisa a fosforólise de nucleosídeos de purina para suas respectivas bases e açucares (ribose ou desoxirribose) 1-fosfato. A PNP desempenha uma função central no metabolismo das purinas, normalmente operando na via de recuperação do DNA das células. Mais ainda, a PNP cliva ligações glicosídicas com inversão da configuração para produzir a-ribose 1-fosfato. Acredita-se que no organismo do Mycobacterium tuberculosis a PNP desempenha tarefas similares, o que levanta o interesse em desenvolver ciência que dê suporte para o desenvolvimento de drogas baseadas na estrutura desta proteína. A proteína é um homotrímero simétrico com um arranjo triangular das subunidades, similar às PNPs triméricas de mamíferos. Cada monômero consiste de um enovelamento a/ß formado por onze fitas ß circundadas por oito hélices a. O estudo desta PNP visa proporcionar comparações com outras estruturas, na intenção de identificar as bases estruturais de possíveis diferenças ou similaridades funcionais entre esta e outras PNPs, num esforço para desenvolver pesquisa que dê suporte para o desenho de novas drogas mais seletivas e poderosas contra a tuberculose. / The Purine nucleoside phosphorylase (PNP) catalyses the phosphorolysis of purine nucleosides to corresponding bases and ribose 1-phosphate. PNP plays a central role in purine metabolism, normally operating in the purine salvage pathway of cells. Moreover, PNP cleaves glycosidic bond with inversion of configuration to produce á-ribose 1-phosphate. It is believed that in the MtPNP is responsible for the same labor in the Mycobacterium tuberculosis organism, which arouses the interest in developing science for giving support to the development of structure based drugs. The protein is a symmetrical homotrimer with triangular arrangement of the subunits, similar to the trimeric mammalian PNPs. Each monomer consist of a á/â folding formed by eleven â sheet surrounded by eight á helices. The study of this PNP aims the possibility of caring out comparisons with other structures, in order to identify the structural basis of possible differences or functional similarities between this and other PNPs, in an effort to develop research which gives support to the design of more selective and powerful new drugs against tuberculosis.

Orientador: Mário Tyago Murakami / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-20T16:32:04Z (GMT). No. of bitstreams: 1 Martins_NadiaHelena_D.pdf: 33217097 bytes, checksum: 6cbd9ad5dcfddd06e2357b3c680cd3f6 (MD5) Previous issue date: 2011 / Resumo: A enzima purina nucleosídeo fosforilase hexamérica de Bacillus subtilis (BsPNP233) c uma nucleosídeo fosforilase do tipo 1 , responsável pela catalise reversível da reação de guebra de urn nucleosídeo em base nitrogenada e ribose-1-fosfato na via de salvação de purinas. Essa enzima possui interesses biomédicos e biotecnológicos devido ao uso na terapia gênica em canceres sólidos e na biossíntese de análogos de nucleosídeos...Observação: O resumo, na íntegra, poderá ser visualizado no texto completo da tese digital / Abstract: The hexamcric purine nucleoside phosphorylase from Bacillus subtilis (BsPNP233) is a nucleoside phosphorylase typc-1 involved in purine salvage pathway by the nucleoside phosphorolysis resulting in purine base and ribose-1-phosphatc. The interest about this enzyme involves gene therapy application in solid cancers treatment and nucleoside analogs biosynthesis...Note: The complete abstract is available with the full electronic document / Doutorado / Genetica de Microorganismos / Doutor em Genetica e Biologia Molecular

The study of enzyme binding sites is an essential but rather demanding process of increased complexity since the amino acids lining these areas are not rigid. At the same time, the minimization of side effects and the specificity of new ligands is a great challenge in the structure-based drug design approach. Using glycogen phosphorylase - a validated target for the development of new antidiabetic agents - as a case study, this project focuses on the examination of side-chain conformations of amino acids that play a key role in the catalytic site of the enzyme. Specifically, different rotamers of each amino acid were collected to build a dataset of different conformations of the catalytic site. The rotamers were filtered by their probability of occurrence and subsequently, all rotamers that create steric clashes were rejected. Then, these conformations were clustered based on their similarity. Three different clustering algorithms and multiple numbers of clusters were tested using the silhouette scores evaluation for the clustering process. In order to measure the similarity, the Euclidean metric was used which due to the correspondence of the coordinates between the conformations was very similar to the cRMSD metric. Two-level clustering was applied to the dataset for more in-depth observations. According to the clustering results, specific aminoacids with major geometrical variations in their rotamers play the most important role in the separation of the clusters. Additionally, all rotamers of an amino acid can be grouped based on their structure, something that was confirmed using “Chimera” software as a visualization tool. To this end, the ultimate aim of this study is to examine whether the clustering of conformations produces clusters with points geometrically similar to each other, in order to identify near neighbors, i.e. conformations that are quite similar in structure but do not play a determinant role in the function and those that are quite diverse and could be further exploited.

Development of multicellular organisms is one of the most fundamental but least understood biological processes. Due to its simple life cycle, the lower eukaryote Dictyostelium has been used as a model system to study several basic biological problems, such as cell differentiation, cell motility, cell adhesion, signal transduction, and especially gene regulation. Glycogen phosphorylase is the enzyme that initiates one of the key biochemical pathways, glycogen degradation, during Dictyostelium discoideum development. Two forms of glycogen phosphorylase, gpl and gp2, exist in D. discoideum with gp1 being active in vegetative cells and gp2 in differentiating cells. Study of glycogen phosphorylase gene regulation clearly will provide insight into the molecular mechanism of D. discoideum development and facilitate understanding of development in general. Two distinct genes that encode the two forms of glycogen phosphorylase were cloned. The nucleotide sequence analysis of the gp2 gene revealed an open reading frame of 2976 bp, that consists of three exons separated by two introns. An interesting feature in the gene is a 45 bp sequence in the second exon that contains 11 CAA trinucleotide repeats. The entire 5' and 3' non-coding regions of the gp2 gene and the whole 5' noncoding region of the gp1 gene have also been cloned. The regulation of the gp2 gene by Dictyostelium developmental signals was studied. Both cyclic AMP (cAMP) and Differentiation Inducing Factor (DIF) were discovered to induce gp2 gene expression during differentiation. DIF was also found to inhibit the cAMP responsiveness of the gene. Both cAMP and DIF induction of the gene were repressed by NH₃. Another developmental signalling molecule, adenosine, was involved in gp2 gene regulation through the inhibition of the DIF-mediated expression. The cell-type-specificity of the gp2 gene were also investigated. The gene was found to be expressed in both prestalk/stalk and prespore/spore cells. This is in agreement with the cAMP and DIF inducibility of the gene since the former molecule is a spore-cell morphogen, while the latter is a stalk-cell morphogen. A model of gp2 gene regulation during development is proposed, based on these findings. The two gp? introns and the 45 bp CAA repeat were studied by deletion of these elements. However, there were no alterations of gp2 gene expression observed after these deletions. Also investigated was genomic structural alteration in gp1- mutants that were obtained through homologous recombination and antisense RNA. Southern analysis revealed that the normal gp1 gene was disrupted in all homologous recombination transformants and in half of the antisense RNA transformants. Finally, for the first time, an extrachromosomal luciferase reporter vector has been established for the study of cis-acting regulatory elements in D. discoideum. / Ph. D.

La toxoplasmose est une anthropozoonose ubiquitaire causée par Toxoplasma gondii. Malgré de nombreuses recherches, l'arsenal thérapeutique reste très restreint. L'objectif des travaux présentés dans ce mémoire est la synthèse de carbazolequinones et l'évaluation de leur efficacité sur T. gondii. Les carbazolequinones naturelles comme les calothrixines ont des propriétés antiparasitaires et cytotoxiques. La synthèse de para- et ortho-quinones de type benzo-, isoxazolo- et triazolo-carbazolequinones a été réalisée par application des réactions de cycloaddition [4+2] ou 1,3-dipolaires régiosélectives. La stratégie de synthèse à partir de dipolarophiles monobromés permet en effet, d'accéder sélectivement au régioisomère souhaité. Les attributions de structure des régiosiomères ont été confirmées par RMN 1H NOE et par une étude des corrélations 1H -13C HMBC. Concernant l'évaluation biologique in vitro, les composés inhibent la croissance de T. gondii comme la sulfadiazine et la pyriméthamine, avec une cytotoxicité sur les cellules myélomonocytiques THP1. Aucun des composés synthétisés n'inhibent la PNP, enzyme clé de la voie de sauvetage des purines, seule voie d'accès pour le parasite aux bases puriques. L'inhibition de la croissance de T. gondii par nos composés n'est pas liée directement liée à l'inhibition de la PNP.

La protéine tyrosine phosphatase 1B (PTP 1B) et la glycogène phosphorylase (GP) sont des nouveaux cibles thérapeutiques pour le traitement du diabète (type II) et l'obésité. Dans l'objective de trouver des inhibiteurs actives et sélectives de ces enzymes, des aryl C glycosides tels que les C glycosyl 1,4 naphthaquinones, les 6 O benzoyl C glycosyl benzoquinone /naphthaquinones, les dérivés quinone d'acides glycuroniques et d'amides carboxylés ainsi que les inhibiteurs bidentates C glycosyl quinones ont été conçus et synthétisés. En tout, 178 composés ont été préparés. Le mécanisme et les facteurs d'influence de la réaction de C aryl glycosylation ont également été étudiés. Les essais préliminaires montrent que certaines molécules présentent des activités biologiques très intéressantes. Des études biologiques plus approfondies seront réalisées par la suite.