The recent emergence of a number of new viral diseases as well as the re-emergence of tuberculosis (TB), indicate an urgent need for new drugs against viral and bacterial infections. Coronavirus nsp1 has been shown to induce suppression of host gene expression and interfere with host immune response. However, the mechanism behind this is currently unknown. Here we present the first nsp1 structure from an alphacoronavirus, Transmissible gastroenteritis virus (TGEV) nsp1. Contrary to previous speculation, the TGEV nsp1 structure clearly shows that alpha- and betacoronavirus nsp1s have a common evolutionary origin. However, differences in conservation, shape and surface electrostatics indicate that the mechanism for nsp1-induced suppression of host mRNA translation is likely to be different in the alpha- and betacoronavirus genera. The Modoc virus is a neuroinvasive rodent virus with similar pathology as flavivirus encephalitis in humans. The flaviviral methyltransferase catalyses the two methylations required to complete 5´ mRNA capping, essential for mRNA stability and translation. The structure of the Modoc NS5 methyltransferase domain was determined in complex with its cofactor S-adenosyl-L-methionine. The observed methyltransferase conservation between Modoc and other flaviviral branches, indicates that it may be possible to identify drugs that target a range of flaviviruses and supports the use of Modoc virus as a model for general flaviviral studies. 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) is part of the methylerythritol phosphate (MEP) pathway that produces essential precursors for isoprenoid biosynthesis. This pathway is used by a number of pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum, but it is not present in humans. Using a structure-based approach, we designed a number of MtDXR inhibitors, including a novel fosmidomycin-analogue that exhibited improved activity against P.falciparum in an in vitro blood cell growth assay. The approach also allowed the first design of an inhibitor that bridge both DXR substrate and co-factor binding sites, providing a stepping-stone for further optimization.

Since the discovery of Mycobacterium tuberculosis (Mtb) as the bacterial agent causing tuberculosis, the permanent eradication of this disease has proven challenging. Although a number of drugs exist for the treatment of tuberculosis, 1.7 million people still die every year from this infection. The current treatment regimen involves lengthy combination therapy with four different drugs in an effort to combat the development of resistance. However, multidrug-resistant and extensively drug-resistant strains are emerging in all parts of the world. Therefore, new drugs effective in the treatment of tuberculosis are much-needed. The work presented in this thesis was focused on the early stages of drug discovery by applying different hit identification and hit expansion strategies in the exploration of two new potential drug targets, glutamine synthetase (GS) and 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR). A literature survey was first carried out to identify new Mtb GS inhibitors from compounds known to inhibit GS in other species. Three compounds, structurally unrelated to the typical amino acid derivatives of previously known GS inhibitors, were then discovered by virtual screening and found to be Mtb GS inhibitors, exhibiting activities in the millimolar range. Imidazo[1,2-a]pyridine analogues were also investigated as Mtb GS inhibitors. The chemical functionality, size requirements and position of the substituents in the imidazo[1,2-a]pyridine hit were investigated, and a chemical library was designed based on a focused hierarchical design of experiments approach. The X-ray structure of one of the inhibitors in complex with Mtb GS provided additional insight into the structure–activity relationships of this class of compounds. Finally, new α-arylated fosmidomycin analogues were synthesized as inhibitors of Mtb DXR, exhibiting IC50 values down to 0.8 µM. This work shows that a wide variety of aryl groups are tolerated by the enzyme. Cinnamaldehydes are important synthetic intermediates in the synthesis of fosmidomycin analogues. These were prepared by an oxidative Heck reaction from acrolein and various arylboronic acids. Electron-rich, electron-poor, heterocyclic and sterically hindered boronic acids could be employed, furnishing cinnamaldehydes in 43–92% yield.

Made available in DSpace on 2016-06-02T19:55:39Z (GMT). No. of bitstreams: 1 5990.pdf: 3991723 bytes, checksum: 8f7428459353354f21c1db08bd391507 (MD5) Previous issue date: 2014-02-27 / Universidade Federal de Sao Carlos / The industrial production of fuel ethanol and sugar generates the main byproduct of sugarcane bagasse, which is burned in boilers for power generation. However, as a lignocellulosic material (consisting basically of three polymers: cellulose, hemicellulose and lignin), bagasse can be reused for the production of second generation bioethanol (2G), which is a renewable and environmentally friendly biofuel. For industrial 2G bioethanol production becomes economically feasible, the use of all fermentable fractions present in the bagasse is required: C6 fraction (cellulose) and C5 fraction (hemicellulose). These fractions are subjected to hydrolysis processes that generate as main sugars glucose and xylose respectively. It is important, therefore, that the microorganism employed for the production of ethanol 2G is able to utilize all the sugars generated during the hydrolysis process. In this work we chose the yeast Saccharomyces cerevisiae to be the main microorganism used in the industrial production of ethanol, although unfortunately, this yeast is unable to ferment xylose. However, while S. cerevisiae does not use xylose, can ferment xylulose obtained by isomerization of xylose by the enzyme glucose isomerase. The objective of this study was to develop and evaluate technological alternatives for the production of ethanol 2G from hexoses and pentoses using wild S. cerevisiae. In relation to the C6 fraction, in this work two important aspects have been addressed: i) study of the operation regime of a fed-batch reactor enzymatic hydrolysis of the C6 fraction of bagasse from sugarcane, yielding values of final glucose concentration of 200 g.L-1, higher than 45 g.L-1 achieved in batch reactor; ii) kinetic modeling of complex systems (enzymatic hydrolysis of lignocellulosic substrates), in which an interpolator was developed using fuzzy logic as an important tool to represent the processes of enzymatic hydrolysis of lignocellulosic materials for rugged and reliable manner. Now, in relation to the C5 fraction initially applied simple techniques of Evolutionary Engineering, leading to the selection of a different strain of S. cerevisiae, adapted to assimilate xylulose in minimal medium and characterized by reduced formation of xylitol, which demonstrated a selectivity of ~7 getanol.gxilitol -1, significantly higher than the selectivity achieved by the wild strain of ~2 getanol.gxilitol -1. The selected strain was studied in batch cultures conducted in bench scale reactor under different conditions of oxygen limitation. It was found that the production of ethanol is favored over the formation of xylitol, keeping the flow of consumed xylulose above 0,5 mmol.gMS -1.h-1 for flow of oxygen consumption of 0.1 mmol.gMS -1.h-1, reaching in this condition selectivities around 4 getanol.gxilitol -1. For zero flow of oxygen (anaerobic culture) or above 0,3 mmol.gMS -1.h-1, ethanol production is drastically reduced , regardless of the flow xylulose assimilated by the cells. / A produção industrial de etanol combustível e de açúcar gera como principal subproduto o bagaço de cana de açúcar, que é queimado nas caldeiras para geração de energia. Entretanto, por ser um material lignocelulósico (constituído basicamente por três polímeros: celulose, hemicelulose e lignina), o bagaço pode ser reaproveitado para a produção de bioetanol de segunda geração (2G), que é um biocombustível renovável e ambientalmente amigável. Para que a produção industrial de etanol 2G se torne economicamente viável, é necessário o aproveitamento de todas as frações fermentescíveis presentes no bagaço de cana: fração C6 (celulose) e fração C5 (hemicelulose). Estas frações são submetidas a processos de hidrólise que geram como principais açúcares glicose e xilose respetivamente. É importante, portanto, que o microrganismo empregado para a produção de etanol 2G seja capaz de utilizar todos os açúcares gerados no processo de hidrólise. Neste trabalho foi escolhida a levedura Saccharomyces cerevisiae por ser o principal microrganismo utilizado na produção industrial de álcool combustível, embora, infelizmente, esta levedura seja incapaz de fermentar xilose. No entanto, embora S. cerevisiae não utilize xilose, pode fermentar a xilulose obtida pela isomerização de xilose pela enzima xilose isomerase conhecida industrialmente como glicose isomerase. Assim, o objetivo do presente trabalho foi desenvolver e avaliar alternativas tecnológicas para a produção de etanol 2G a partir de hexoses e pentoses, utilizando S. cerevisiae selvagem. Em relação à Fração C6, neste trabalho foram abordados dois aspectos importantes: i) estudo da operação em regime de batelada alimentada de um reator de hidrólise enzimática da fração C6 do bagaço de cana de açúcar, obtendo-se valores de concentração final de glicose de cerca de 200 g.L-1, superiores aos 45 g.L-1 alcançados em reator operado em bateladas simples; ii) modelagem cinética de sistemas complexos (hidrólise enzimática de substratos lignocelulósicos), no qual foi desenvolvido um interpolador utilizando a lógica fuzzy como uma ferramenta importante para representar os processos de hidrólise enzimática de materiais lignocelulósicos de forma robusta e confiável. Já em relação à Fração C5, inicialmente aplicou-se técnicas simples de Engenharia Evolutiva, levando à seleção de uma linhagem diferenciada de S. cerevisiae, adaptada à assimilação de xilulose em meio mínimo e caracterizada por reduzida formação de xilitol, a qual apresentou uma seletividade de ~7 getanol.gxilitol -1, valor significativamente superior à seletividade alcançada pela linhagem selvagem, de ~2 getanol.gxilitol -1. A linhagem selecionada foi então estudada em cultivos em batelada conduzidos em biorreator de bancada, sob diferentes condições de limitação por oxigênio. Verificou-se que a produção de etanol é favorecida, em detrimento da formação de xilitol, mantendo-se o fluxo de xilulose consumida acima de 0,5 mmol.gMS -1.h-1, para fluxo de oxigênio consumido de 0,1 mmol.gMS -1.h-1, alcançando-se nessa condição seletividades em torno de 4 getanol.gxilitol -1. Para fluxos de oxigênio nulo (cultivo anaeróbio) ou acima de 0,3 mmol.gMS -1.h-1, a produção de etanol é drasticamente reduzida, independentemente do fluxo de xilulose assimilado pelas células.