Os acidentes ofídicos são considerados um grande problema de saúde pública e no Estado de São Paulo a serpente Bothrops jararaca é o agente considerado mais relevante epidemiologicamente. O antiveneno é o único medicamento oficialmente aprovado para o tratamento de picadas de serpentes e, apesar de ser eficaz em diversos aspectos, mostra-se ineficaz em relação a complicações secundárias do envenenamento, como o estresse oxidativo/nitrosativo, caracterizado por um desequilíbrio no estado redox, que pode ser extremamente deletério aos pacientes. Portanto, vê-se necessária a busca por terapias complementares que possam combater o estresse oxidativo/nitrosativo. Ademais, distúrbios da hemostasia observados em envenenamentos pela B. jararaca, tais como a plaquetopenia, a hipofibrinogenemia e o aumento da atividade do fator tissular (TF) plasmático podem ter também como causa indireta o estresse oxidativo/nitrosativo, induzido por componentes do veneno de B. jararaca (BjV). Recentemente, demonstrou-se que a regulação da atividade biológica do TF, a proteína responsável pela iniciação da cascata de coagulação in vivo, pode ser controlada pela isomerase de dissulfeto proteico (PDI) e que a atividade da PDI é inibida in vivo pela quercetina-3-rutinosídeo (rutina), um antioxidante natural encontrado em plantas e alimentos. Considerando essas premissas, o presente trabalho objetivou investigar em camundongos injetados com o veneno de B. jararaca (BjV): (a) a ocorrência de distúrbios do estado redox; (b) as alterações hematológicas e hemostáticas (em plasma e tecidos) associadas ao desequilíbrio do estado redox; (c) a atividade da rutina como agente modulador sobre essas alterações. Para isso, camundongos Swiss (30-35 g) foram divididos em 4 grupos experimentais: controle salina (salina, controle negativo), controle rutina (rutina+salina), BjV+salina (BjV+salina, controle positivo) e BjV+rutina (BjV+rutina, tratamento). Após 3, 6 e 24 h da administração dos tratamentos (via s.c.), foram coletados sangue e fragmentos de tecidos para posteriores análises. O envenenamento induziu um aumento de espécies reativas, diminuição da capacidade antioxidante total, alterações hematológicas (plaquetopenia, neutrofilia e diminuição de eritrócitos), distúrbios hemostáticos (hipofibrinogenemia, prolongamento do tempo de protrombina e aumento da atividade de TF no plasma), além de diminuir a expressão proteica de PDI no coração. A rutina não inibiu in vitro a atividade biológica de proteínas presentes no BjV (metaloproteinases, serinaproteases, fosfolipases A2 e L-aminoácido oxidases) e nem mesmo a agregação plaquetária induzida pelo veneno. No entanto, a administração do veneno incubado com rutina foi capaz de reduzir os níveis de espécies reativas, impedir a queda de eritrócitos, normalizar os níveis de fibrinogênio e o tempo de protrombina e alterar a atividade de TF e expressão proteica de TF e PDI em tecidos. Desse modo, concluímos que a rutina foi capaz de favoravelmente modular importantes alterações hemostáticas e de estado redox no envenenamento por B. jararaca, o que indica seu grande potencial como agente terapêutico complementar em envenenamentos / Snakebites are a major public health issue and in São Paulo State, and Bothrops jararaca snakes are considered the most important agents epidemiologically. Antivenom is the only officially approved treatment for snakebites and although effective in many aspects, it is ineffective in combating secondary complications induced by envenomation, e.g. oxidative/nitrosative stress (ONS), which can be extremely deleterious to patients. Therefore, it is necessary to search for new complementary therapies that could attenuate ONS. Furthermore, the hemostatic disturbances in B. jararaca envenomation - characterized by the presence of thrombocytopenia, hypofibrinogenemia and increased tissue factor (TF) activity in plasma - could be indirectly evoked by ONS induced by B. jararaca venom (BjV) components. Recently, the biological activity of TF - the protein responsible for initiating the extrinsic pathway of the coagulation cascade - was demonstrated to be regulated by protein disulfide isomerase (PDI), which in turn, can be inhibited in vivo by quercetin-3-rutinose (rutin), a natural antioxidant found in plants and diet. Based on that, the present study aimed to investigate in mice injected with BjV: (a) the alterations in redox status in plasma and tissues; (b) the hematological/hemostatic disturbances (in plasma and tissues) associated with the imbalance in redox status; (c) the activity of rutin as a modulatory agent on those alterations. Swiss mice (30-35 g) were divided in four experimental groups: saline control (saline, negative control), rutin control (rutin+saline), BjV+saline (BjV+saline, positive control) and BjV+rutin (BjV+rutin, treatment) and after 3, 6 and 24 h of the injection of treatments (s.c. route), blood and tissues were collected to further analyses. Envenomation induced an increase in reactive species, a decrease in total antioxidant capacity, hematological alterations (thrombocytopenia, neutrophilia and a decrease in red blood cell counts), hemostatic disturbances (hypofibrinogenemia, prolonged prothrombin time and an increase in the TF activity in plasma), and a decrease in protein expression of PDI in the heart. In vitro, rutin failed to inhibit the biological activity of the main BjV enzymes (metalloproteinases, serine proteases, phospholipases A2 and L-amino acid oxidases) and BjV-induced platelet aggregation. However, when the venom was incubated with rutin, there were reduced reactive species levels, less intense red blood cell drops, recovery of fibrinogen levels and prothrombin time, and alteration of TF activity and protein expression of TF and PDI in tissues. Therefore, we conclude that rutin favorably modulated important hemostatic and redox status alterations in B. jararaca envenomation, indicating its great potential as a complementary therapeutic agent for snakebites

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To unravel the mysteries of complex biological processes carried out by biomolecules it is necessary to adopt a multifaceted approach, which involves employing a wide variety of tools both computational and experimental. In order to gain a clear understanding of the function of biomolecules their three dimensional structure is required. X-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy are the only two methods capable of providing high-resolution three-dimensional structure of biomolecules. NMR has the advantage of allowing the study of structure of biomolecules in solution and is better equipped to characterize the dynamics of the protein. Protein structure determination by NMR spectroscopy consists of recombinant expression of isotopically labeled proteins, purification, data collection, data processing, resonance assignment, distance restraint and angular restraint generation, structure calculation and structure validation. Apart from 3D structure determination of biomolecules NMR has become the method of choice for studying transient protein-protein interactions, which are notoriously difficult to study at higher resolution by other methods. Mass spectrometry plays an important role in enabling rapid identification of biomolecules and their modifications. The high sensitivity and resolution mass spectrometry offers makes it the method of choice for studying post-transitional modification of proteins. Use of computers in biology has played an essential role in elucidating those structure function relationships in biomolecules that are not possible to study by experimental techniques. The first chapter of this thesis deals with the introduction of methods used in this study. A brief introduction about the theory of Nuclear Magnetic Resonance (NMR) spectroscopy is given. Protein NMR methods used for structure determination of medium sized proteins are discussed. A part of this chapter discusses about the application of mass spectrometry in biochemistry and the use of tandem MS/MS experiments in identification of proteins and peptide fragments. Finally, the last part of this chapter gives an introduction about the theory of molecular dynamics and techniques used in the post processing of MD trajectories to elucidate the dynamics of proteins. The second chapter of this thesis is concerned with NMR characterization of a novel protein-protein interaction between the glycolytic enzyme Triosephosphate isomerase and the redox protein Thioredoxin. Chemical shift perturbation studies have been done to map the binding interfaces of these proteins. The structure of the complex was then modeled using NMR restraints based docking using the known 3D structure of these proteins. The docked complex reveals crucial insights into the glutathione mediated redox regulation of Triosephosphate isomerase and the role of thioredoxin as a deglutathionylating agent. Enzyme activity assays of Triosephosphate isomerase were done to show the inhibitory effects of s-glutathionylation of Cys217 and the role of thioredoxin as a deglutathionylating agent. The third chapter of the thesis is aimed to address some important issues related to the inhibition of Plasmodium falciparum Triosephosphate isomerase by S-glutathionylation. Oxidative stress induces protein glutathionylation which is a reversible post translational modification consisting of the formation of a mixed disulfide between protein cysteines and glutathione. Mass spectrometric analysis of the kilnetics of glutathionylation along with enzyme activity assays clearly show that gluthionylation of either Cys-13 (situated in the dimmer interface) or Cys-217 (situated in Helix G) can render the enzyme inactive. Molecular dynamics simulations provide a mechanistic basis of inhibition and predict that glutathionylation at Cys217 allosterically induces loop 6 disorder. The fourth chapter of this thesis addresses the stabilizing effect of introduction of a cross-strand disulfide bond across a non-hydrogen bonded position of an antiparallel beta sheet. Multidimensional heteronuclear NMR experiments have been used to get the backbone and side-chain resonance assignments, distance and angular restraints. In addition RDC based restraints have been used to calculate the structure of oxidixed form of L79C, T89C thiroedoxin. The observation of predominantly –RH staple conformation among the NMR ensemble in typical of cross-strand disulfides. The fifth chapter of this thesis deals with the dynamics of thioredoxin using computational methods.In this chapter analysis of known complexes of thiroedoxin was done to determine binding hot spot residues using free energy calculations. The physicochemical basis for the multispecificity of thioredoxin is probed using molecular dynamics simulations. In this chapter it has been shown that conformational selection plays a very important role in thioredoxin target recognition.

A demanda por combustíveis baseados em recursos renováveis é alta nos dias de hoje e tende a aumentar bastante no futuro. No Brasil, indústrias de biocombustíveis produzem principalmente etanol a partir cana-de-açúcar. A biomassa lignocelulósica, compreendendo resíduos de culturas, resíduos florestais, sólidos urbanos, é explorada como um elevado potencial secundário na produção de biocombustíveis, mesmo na categoria de subprodutos, eliminando assim os usos competitivos. Para tornar a produção de etanol de segunda geração a partir da cana-de-açúcar economicamente sustentável, é imprescindível utilizar fração hemicelulósica da biomassa, o que corresponde de 20% a 25%, sendo a xilose seu principal componente. Saccharomyces cerevisiae não fermenta xilose, entretanto, xilulose pode ser fermentada. Portanto a busca e o estudo de enzimas que procedem com a conversão de xilose em xilulose (em condições sinérgicas às da fermentação alcoólica) se torna de extrema importância no que se refere ao aproveitamento da hemicelulose para a geração de etanol de segunda-geração. Xilose isomerases (XI) de três microorganismos diferentes (de Xanthomonas campestris pv. Campestris [Xyl_Xcc], Bifidobacterium adolescentis [Xyl_Bad] e de Lactobacillus crispatus [Xyl_LCr]) são o objeto de estudo deste projeto. A partir do conteúdo genômico desses três microorganismos, foi realizada a amplificação do gene xylA (que codifica para XI), via Clonagem Independente de Ligação/Ligase (do inglês, LIC) e clonagem em vetor de expressão pPROEX HTa adaptado para LIC, e superexpressão em Escherichia coli BL21 (DE3). As XIs foram então extraídas e purificadas por cromatografia de afinidade com metal quelado, seguida de cromatografia de exclusão molecular. Nessa etapa, as massas moleculares e raios hidrodinâmicos (RH) foram estimados, tanto por cromatografia de exclusão molecular quanto em gel nativo, revelando que Xyl_Xcc e Xyl_Bad se apresentam diméricas enquanto Xyl_LCr monomérica. Subseqüentemente, foram realizados testes de atividade em diferentes condições (pHs e temperaturas), para mapear condições ótimas de reação. A atividade ótima de ambas Xyl_Xcc e Xyl_Bad foi ao redor do pH 5,5, com temperaturas ótimas girando em torno de 60°C. Xyl_LCr se mostrou sem atividade. Além disso, o monitoramento da estabilidade térmica das XIs foi realizado através de espalhamento de raios-X a baixo ângulo (SAXS) e espectroscopia de dicroísmo circular (CD). As estabilidades térmicas da estrutura secundária e da estrutura terciária como um todo parecem aumentadas com a elevação do pH. Entretanto, isso não condiz com perfil de atividade dessas enzimas, visto que a atividade ótima se apresentou deslocada para valores de pHs ácidos. Modelos de baixa resolução obtidos por SAXS foram alinhados e sobrepostos às estruturas de alta resolução de proteínas homólogas, revelando um bom ajuste da forma tetramérica para Xyl_Bad e Xyl_Xcc e monomérica para Xyl_LCr. Portanto, levanta-se a hipótese da dissociação do tetrâmero em dímeros, possivelmente causado pela interação (mecânica) com o sistema de emaranhados do gel nativo e com os poros da coluna de exclusão molecular. Foram obtidos cristais de Xyl_Bad e Xyl_Xcc, e esses foram submetidos à difração de raios-X, revelando a presença de um domínio conservado na maioria das XIs reportadas, formado por um barril α⁄β (N-terminal). As estruturas estão em fase avançada de refinamento. Ao final, são propostos estudos futuros que complementem os resultados apresentados, e que poderão comprovar as hipóteses criadas a partir deste trabalho. / The demand for fuels based on renewable resources is high these days and tends to increase considerably in the future. In Brazil, biofuels industries mainly produce ethanol from sugarcane. The lignocellulosic biomass, including crop residues, forest residues, urban solids, is explored as a secondary high potential for biofuels production, in the same category of products, thus eliminating the competing uses. To make the production of sugarcane secondgeneration ethanol economically sustainable, it is essential to use the hemicellulose fraction of the biomass, which corresponds from 20% to 25%, the main component represented by xylose. Saccharomyces cerevisiae doesnt ferment xylose, however, xylulose may befermented. Therefore the research and study of enzymes that carry out the conversion of xylose to xylulose (in synergistic fermentation conditions) become very important with regard to the use of hemicellulose in second-generation ethanol production. Xylose isomerases (XI) from three different microorganisms (Xanthomonas campestris pv. Campestris [Xyl_Xcc], Bifidobacterium adolescentis [Xyl_Bad] and Lactobacillus crispatus [Xyl_Lcr]) are the target of this project. From the genomic content of these three organisms, gene amplification of the xylA gene (encoding XI) was performed, via Ligand / Ligation Independent Cloning (LIC) and cloning in LIC adapted pPROEX HTA expression vector , with overexpression in Escherichia coli BL21 (DE3). The XIs were then extracted and purified by affinity metal quelate chromatography, followed by size exclusion chromatography. At that time, the molecular weight and hydrodynamic radius (RH) were estimated both by size exclusion chromatography and native gel, suggesting that Xyl_Xcc and Xyl_Bad were as dimers in solution, while Xyl_Lcr as monomer. Subsequently, activity assays were performed in different conditions (pH and temperature), to find out the optimum reaction conditions. The optimal activity of both Xyl_Xcc and Xyl_Bad was around pH 5.5, with optimum temperatures hovering around 60°C. Xyl_Lcr showed no activity. Furthermore, monitoring the thermalstability of XIs was performed by small angle X-ray scattering (SAXS) and circular dichroism spectroscopy (CD). The thermal stabilities of the secondary structure and tertiary structure as a whole appear increased with increasing pH. However, this does not match with the activity profiles of these enzymes, since they showed optimal activity shifted to acidic pHs. SAXS low-resolution models were aligned and superimposed on high resolution structures of homologous proteins, revealing a concordance of the tetrameric form of Xyl_Xcc and Xyl_Bad in solution and monomeric form of Xyl_Lcr. Thus arises the possibility of dissociation of tetramer into dimers, possibly caused by interaction (mechanical) system with the tangles of native gel and pores of molecular exclusion column. Crystals were obtained from Xyl_Bad and Xyl_Xcc, and these were subjected to X-ray diffraction to generate high resolution structures, revealing the presence of a conserved domain in the most reported XIs, consisting of a α⁄ β barrel (N-terminus). The structures are in an advanced stage of refinement. Finally, future studies are proposed to complement the results presented, which may prove the hypotheses generated from this work.

A oxidação do ácido úrico (7,9-diidro-1H-purina-2,6,8(3H)-triona) pela mieloperoxidase (MPO) gera o radical de urato que, em presença do radical ânion superóxido combinam para formar o hidroperóxido de urato (HOOU). Considerando os altos níveis de MPO, ácido úrico e superóxido na placa de ateroma espera-se que o ácido úrico seja oxidado a HOOU neste microambiente inflamatório. O HOOU é um oxidante mais forte que o peróxido de hidrogênio e pode oxidar grupos tiólicos de proteínas como a proteína dissulfeto isomerase (PDI). Como consequência à oxidação da PDI, ocorre uma modulação positiva sobre a NADPH oxidase (Nox) com aumento da produção de superóxido por neutrófilos. Sendo assim, a formação do HOOU no leito vascular poderia elucidar os mecanismos moleculares pelos quais o urato colabora para a progressão da aterosclerose em pacientes com hiperuricemia. Para investigar a interação do HOOU com a PDI, padronizou-se a síntese química do HOOU através de um sistema de fotooxidação do tipo I, utilizando urato, riboflavina (fotossensibilizador) e luz UVA. Inicialmente padronizou-se o tipo de irradiação e tempo de reação com o melhor rendimento para a síntese do HOOU. O HOOU formado e seu produto de redução o álcool 5-hidroxiisourato foram separados, identificados e caracterizados através de cromatografia liquida acoplada à espectrometria de massa (LC/MS). Após a purificação, determinou-se o coeficiente de absortividade molar em 308 nm (ε308 = 6537 ± 377 M-1.cm-1) e o tempo de meia-vida, aproximadamente 41 minutos à 22°C do HOOU. O HOOU foi capaz de reagir seletivamente com o aminoácido metionina e com o tripeptídeo glutationa. Além disso, o HOOU não forma adutos estáveis com a glutationa, sendo que toda glutationa consumida foi transformada em glutationa dissulfeto. Quando incubado com a PDI (10 µM), cerca de 70 e 100% do total de HOOU (3 µM) foi consumido após 30 e 120 segundos, respectivamente, enquanto que a PDI (23 µM) teve seus grupos tiólicos oxidados após a incubação com 140 µM HOOU por 30 min a 22°C. O HOOU oxidou os resíduos de cisteína dos dois sítios catalíticos da PDI com uma constante de velocidade da reação de 1,5 ± 0,04 x 103 M-1.s-1, demonstrando uma interação favorável com essa proteína no meio biológico e um possível papel modulatório do HOOU sobre a via PDI-Nox. Interessantemente, o ácido úrico aumentou a produção de superóxido e o consumo de oxigênio de células HL-60 diferenciadas em neutrófilos (dHL-60) e ativadas com acetato de miristato de forbol (PMA). Essa regulação poderia ser mediada através da formação do HOOU durante o \"burst\" oxidativo dos neutrófilos que oxidaria a enzima PDI induzindo um consequente aumento da atividade da Nox. / The oxidation of the uric acid (7,9-dihidro-1H-purine-2,6,8(3H)-trione) by myeloperoxidase (MPO) generates the urate radical. In inflammatory conditions the superoxide reacts with urate radical to form the urate hydroperoxide (HOOU). Taking into account the high amount of MPO, urate and superoxide in the atheroma plaque, it is likely that HOOU is being formed in this inflammatory environment. The HOOU is a strong oxidizing agent and can react with thiol groups from proteins, like the protein disulfide isomerase (PDI). As a consequence of its oxidation, PDI positively modulates NADPH oxidase (Nox) and increases superoxide production by neutrophils. Therefore, the formation of HOOU in the vascular sheet would contribute to tissue damage and would explain the positive correlation between hyperuricemia and the risk for cardiovascular disease. To investigate the interaction of HOOU with PDI, we performed the chemical synthesis of the compound by the Type I photooxidation, using UVA irradiation and riboflavin as a photosensitizer. Initially, we standardized the irradiation light and the time of the reaction that produced the highest income. The HOOU and its reduced product 5-hydroxiisourate were separate, identified and characterized by liquid chromatography coupled to mass spectrometry (LC/MS). We also determine the molar extinction coefficient of HOOU at 308 nm (ε308 = 6537 ± 377 M-1.cm-1). The half-life of the compound was 41 min at 22°C. The HOOU selectively oxidized methionine and glutathione. The reaction of HOOU with glutathione did not form any stable adducts. Thus, all consumed glutathione generated glutathione disulfide. When incubated with PDI (10 µM), 70 and 100% of the total amount of HOOU (3 µM) was consumed within 30 and 120 seconds, respectively. Besides, the PDI (23 µM) had its thiol groups oxidized after incubation with 140 µM HOOU for 30 min at 22°C. The HOOU oxidized the cysteine residues from the catalytical sites of PDI with a second order rate constant of 1.5 ± 0.04 x 103 M-1.s-1. This result suggests a favorable interaction of HOOU with this protein in the biological system, as well as a possible modulatory role of HOOU on the PDI-Nox pathway. Interestingly, urate increased superoxide production and oxygen consumption by neutrophil-like cells (differentiated HL-60 cells). This effect could be mediated by the formation of HOOU during the neutrophil oxidative burst, followed by the oxidation of PDI, a positive regulation of Nox and an increase in superoxide production.

Os acidentes ofídicos são considerados um grande problema de saúde pública e no Estado de São Paulo a serpente Bothrops jararaca é o agente considerado mais relevante epidemiologicamente. O antiveneno é o único medicamento oficialmente aprovado para o tratamento de picadas de serpentes e, apesar de ser eficaz em diversos aspectos, mostra-se ineficaz em relação a complicações secundárias do envenenamento, como o estresse oxidativo/nitrosativo, caracterizado por um desequilíbrio no estado redox, que pode ser extremamente deletério aos pacientes. Portanto, vê-se necessária a busca por terapias complementares que possam combater o estresse oxidativo/nitrosativo. Ademais, distúrbios da hemostasia observados em envenenamentos pela B. jararaca, tais como a plaquetopenia, a hipofibrinogenemia e o aumento da atividade do fator tissular (TF) plasmático podem ter também como causa indireta o estresse oxidativo/nitrosativo, induzido por componentes do veneno de B. jararaca (BjV). Recentemente, demonstrou-se que a regulação da atividade biológica do TF, a proteína responsável pela iniciação da cascata de coagulação in vivo, pode ser controlada pela isomerase de dissulfeto proteico (PDI) e que a atividade da PDI é inibida in vivo pela quercetina-3-rutinosídeo (rutina), um antioxidante natural encontrado em plantas e alimentos. Considerando essas premissas, o presente trabalho objetivou investigar em camundongos injetados com o veneno de B. jararaca (BjV): (a) a ocorrência de distúrbios do estado redox; (b) as alterações hematológicas e hemostáticas (em plasma e tecidos) associadas ao desequilíbrio do estado redox; (c) a atividade da rutina como agente modulador sobre essas alterações. Para isso, camundongos Swiss (30-35 g) foram divididos em 4 grupos experimentais: controle salina (salina, controle negativo), controle rutina (rutina+salina), BjV+salina (BjV+salina, controle positivo) e BjV+rutina (BjV+rutina, tratamento). Após 3, 6 e 24 h da administração dos tratamentos (via s.c.), foram coletados sangue e fragmentos de tecidos para posteriores análises. O envenenamento induziu um aumento de espécies reativas, diminuição da capacidade antioxidante total, alterações hematológicas (plaquetopenia, neutrofilia e diminuição de eritrócitos), distúrbios hemostáticos (hipofibrinogenemia, prolongamento do tempo de protrombina e aumento da atividade de TF no plasma), além de diminuir a expressão proteica de PDI no coração. A rutina não inibiu in vitro a atividade biológica de proteínas presentes no BjV (metaloproteinases, serinaproteases, fosfolipases A2 e L-aminoácido oxidases) e nem mesmo a agregação plaquetária induzida pelo veneno. No entanto, a administração do veneno incubado com rutina foi capaz de reduzir os níveis de espécies reativas, impedir a queda de eritrócitos, normalizar os níveis de fibrinogênio e o tempo de protrombina e alterar a atividade de TF e expressão proteica de TF e PDI em tecidos. Desse modo, concluímos que a rutina foi capaz de favoravelmente modular importantes alterações hemostáticas e de estado redox no envenenamento por B. jararaca, o que indica seu grande potencial como agente terapêutico complementar em envenenamentos / Snakebites are a major public health issue and in São Paulo State, and Bothrops jararaca snakes are considered the most important agents epidemiologically. Antivenom is the only officially approved treatment for snakebites and although effective in many aspects, it is ineffective in combating secondary complications induced by envenomation, e.g. oxidative/nitrosative stress (ONS), which can be extremely deleterious to patients. Therefore, it is necessary to search for new complementary therapies that could attenuate ONS. Furthermore, the hemostatic disturbances in B. jararaca envenomation - characterized by the presence of thrombocytopenia, hypofibrinogenemia and increased tissue factor (TF) activity in plasma - could be indirectly evoked by ONS induced by B. jararaca venom (BjV) components. Recently, the biological activity of TF - the protein responsible for initiating the extrinsic pathway of the coagulation cascade - was demonstrated to be regulated by protein disulfide isomerase (PDI), which in turn, can be inhibited in vivo by quercetin-3-rutinose (rutin), a natural antioxidant found in plants and diet. Based on that, the present study aimed to investigate in mice injected with BjV: (a) the alterations in redox status in plasma and tissues; (b) the hematological/hemostatic disturbances (in plasma and tissues) associated with the imbalance in redox status; (c) the activity of rutin as a modulatory agent on those alterations. Swiss mice (30-35 g) were divided in four experimental groups: saline control (saline, negative control), rutin control (rutin+saline), BjV+saline (BjV+saline, positive control) and BjV+rutin (BjV+rutin, treatment) and after 3, 6 and 24 h of the injection of treatments (s.c. route), blood and tissues were collected to further analyses. Envenomation induced an increase in reactive species, a decrease in total antioxidant capacity, hematological alterations (thrombocytopenia, neutrophilia and a decrease in red blood cell counts), hemostatic disturbances (hypofibrinogenemia, prolonged prothrombin time and an increase in the TF activity in plasma), and a decrease in protein expression of PDI in the heart. In vitro, rutin failed to inhibit the biological activity of the main BjV enzymes (metalloproteinases, serine proteases, phospholipases A2 and L-amino acid oxidases) and BjV-induced platelet aggregation. However, when the venom was incubated with rutin, there were reduced reactive species levels, less intense red blood cell drops, recovery of fibrinogen levels and prothrombin time, and alteration of TF activity and protein expression of TF and PDI in tissues. Therefore, we conclude that rutin favorably modulated important hemostatic and redox status alterations in B. jararaca envenomation, indicating its great potential as a complementary therapeutic agent for snakebites

INTRODUÇÃO: A ativação da NADPH oxidase de neutrófilos requer o acoplamento das subunidades citosólicas p47phox, p67phox, p40phox e Rac2 ao componente de membrana citocromo b558. Em trabalhos anteriores, nós mostramos que as isoformas vasculares da oxidase são reguladas pela proteína dissulfeto isomerase (PDI), uma chaperona redox. Neste trabalho, nós utilizamos um sistema cellfree semirecombinante como ferramenta para investigar o papel da PDI na ativação da NADPH oxidase do neutrófilo. RESULTADOS: Inibidores da PDI, scrambled RNAse (100g/mL) ou bacitracina (1mM), praticamente suprimiram a geração de superóxido. Para avaliação dos efeitos do estado redox da PDI sobre a atividade da oxidase, amostras de PDI foram previamente oxidadas (H2O2; 0,5 mM) ou reduzidas (DTT; 0,5 mM). A PDI oxidada (100 nM) aumentou a produção de superóxido em aproximadamente 30%, enquanto a mesma concentração de PDI reduzida promoveu efeito inverso, inibindo a atividade do complexo. A adição de um peptídeo contendo a seqüência peptídica do sítio ativo da PDI inibiu a produção de superóxido em 70%. Dados de imunolocalização e colocalização demonstraram que a interação da PDI com a subunidade p47phox parece ser intensificada pelo estímulo com PMA e envolvem modificações do estado redox de ambas as proteínas. CONCLUSÕES: Nossos dados confirmam a associação física e funcional entre a PDI e o complexo NADPH oxidase. Além disso, sugerem que a PDI exerça um importante papel como fator de regulação redox da ativação da oxidase. / Activation of the leukocyte NADPH oxidase requires the assembly of the cytosolic subunits p47phox, p67phox and p40phox and Rac2 with the membranebound cytochrome b558. We have previously shown that the vascular oxidase is regulated by the redox chaperone protein disulfide isomerase (PDI). Taking advantage of the semirecombinant cellfree system, we sought to investigate the role of PDI in the activation of neutrophil NADPH oxidase. The PDI thiol inhibitors scrambled RNase (100g/mL) or bacitracin (1mM), almost suppressed superoxide generation. In order to investigate if the redox status of PDI thiols could modulate superoxide generation, PDI was oxidized or reduced by treatment with H2O2 (0.5mM) or DTT (1mM), respectively. Oxidized PDI increased by 30% superoxide production, while reduced PDI diminished superoxide generation also in 30%. The addition of a peptide (1M) containing PDI´s exact active site sequence inhibited superoxide production by 70 %. Immuno and colocalization data demonstrated the interaction of PDI with the subunit p47phox to be intensified by PMA stimulation and to involve redox status exchange of both proteins. Our data confirm the physical and functional association between PDI and the oxidase complex. Moreover, we show a relevant role for PDI as a redoxdependent supportive factor for NADPH oxidase activation.

Enzymatic fluorination of natural products is extremely rare. Of the 4000 halogenated natural products identified, only 13 possess a fluorine atom. The C-F bond forming enzyme from the soil bacterium, Streptomyces cattleya, remains the only native enzyme to be identified that is capable of such biochemistry. It generates 5’-fluoro-5-deoxyadenosine (5‘-FDA) from S-adenosyl-L-methionine (SAM) and F-. The “fluorinase” is the first committed step toward the biosynthesis of the two fluorometabolites, 4-fluorothreonine and fluoroacetate, via the common intermediate, fluoroacetaldehyde (FAld). The enzymatic steps responsible for the conversion of 5’-FDA to the fluorometabolites remained to be fully characterised when this project began. Previously, a purine nucleoside phosphorylase was identified that was capable of generating 5-fluorodeoxyribose-1-phosphate (5-FDRP) from 5’-FDA. 5-FDRP is subsequently isomerised to 5-fluorodeoxyribulose-1-phosphate (5-FDRulP) by an aldose-ketose isomerase enzyme. Chapter 2 describes the identification of the isomerase gene from the genomic DNA of S. cattleya and the corresponding protein product was capable of generating 5-FDRulP from 5-FDRP. The next intermediate, FAld, is generated from 5-FDRulP by a fuculose aldolase. Attempts to identify the aldolase gene from S. cattleya were unsuccessful, however a putative fuculose aldolase from Streptomyces coelicolor was isolated that could generate FAld from 5-FDRulP, which is described in Chapter 3. Following the identification and over expression of a PLP-dependant transaldolase, which generates 4-fluorothreonine (4-FT) from FAld and L-threonine in S. cattleya, Chapter 4 details the successful in vitro reconstitution of fluorometabolite biosynthesis using five over- expressed enzymes. In Chapter 5, attempts to develop a novel assay for fluorinase activity was explored. The colorimetric detection of L-methionine produced by the fluorinase in a coupled L-amino acid oxidase and horseradish peroxidase assay, leading to the oxidation of a dye substance. This was carried out with interest in developing a high-throughput assay for fluorinase mutants, generated by random mutagenesis, in order to identify those with increased activity. In the event, it proved unsuccessful.

Thesis advisor: Eranthie Weerapana / The 1,3,5-triazine is a privileged scaffold in that it is planar and has three-fold symmetry which allows for controlled modification around the ring structure with various substituents. In this thesis, we report on two modular inhibitor libraries that center around a 1,3,5-triazine core scaffolding system, which have been shown to target protein disulfide isomerase A1 (PDIA1), glutaredoxin-3 (GLRX3), and 6-phosphofructo-1-kinase (PFKP). Protein disulfide isomerase A1 (PDIA1) is a thiol-disulfide oxidoreductase localized in the lumen of the endoplasmic reticulum (ER), and is an important folding catalyst and chaperone for proteins in the secretory pathway. PDIA1 contains two active-site domains (a and a’), each containing a Cys-Gly-His-Cys (CGHC) active-site motif. Here, we synthesize a targeted library o second-generation triazine-based inhibitors to optimize the potency and selectivity of our lead compound, RB-11-ca. Characterization of this targeted library afforded an optimized PDIA1 inhibitor, KSC-34, which covalently modifies C53 in the a site of PDIA1 and demonstrates time-dependent inhibition of the reductase activity of PDIA1 in vitro with a kinact/KI = 9.66 x 103 M-1s-1. Interestingly, KSC-34 treatment demonstrated that a-site inhibition led to decreased secretion of amyloidogenic antibody light chain, thus illustrating that site-selective inhibitors like KSC-34 provide useful tools for delineating the pathological role and therapeutic potential of PDIA1. In 2014, our lab first reported on RB7, a dichlorotriazine-based electrophilic small molecule which displayed extremely high reactivity and selectivity toward lysine residues in the proteome. Herein, we further on this study by investigating the unique reactivity of RB7 through the synthesis of a second-generation small molecule electrophile library and investigating proteome-wide reactivity in vitro and in situ. This library afforded KSC-46, an RB-7 analogue with p-chlorothiophenol tuning element, which provided optimal proteome reactivity to use as a scaffold for the generation of a targeted library. To take advantage of the tuned reactivity of KSC-46, a second-generation targeted library was generated to target react residues in the proteome. This library yielded two molecules, KSC-56 and KSC-65, which were identified to target glutaredoxin-3 (GLRX3) and 6-phosphofructo-1-kinase (PFKP), respectively. GLRX3 is a cytosolic, monothiol iron-sulfur cluster chaperon protein which relies on two nucleophilic cysteine residues to bind and transfer iron clusters. PFKP is known to catalyze the first irreversible step in glycolysis and regulates the flux of glucose metabolism in the cell, which makes PFKP an attract therapeutic target. KSC-56 was further characterized to bind to Cys261 in the C-terminal glutaredoxin domain of GLRX3. / Thesis (PhD) — Boston College, 2018. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

O trabalho realizado como parte do programa de mestrado em física aplicada sub-área biomolecular, teve como objeto de estudo a enzima glicose-6-fosfato isomerase de humanas (PGI-hum). Este trabalho envolveu principalmente três áreas de estudos: biologia molecular, bioquímica e cristalografia. A parte de biologia molecular refere-se a sub-clonagem do gene da PGI-hum a partir de uma biblioteca de cDNA de cérebro de feto humano - capítulo 2 - e a expressão deste gene em bactérias Escherichia coli - capítulo 3. A parte de bioquímica envolve a purificação e caracterização de parâmetros cinéticos da enzima PGI-hum recombinante. Além dos parâmetros cinéticos, foram realizados ensaios de eficiência inibitória para quatro compostos similares ao substrato, cedidos em colaboração com o pesquisador Dr. Laurent Salmon (Lab. De Química Biorgânica e Bioinorgânica de Universidade de Paris-XI). Esta etapa encontra-se descrita nos capítulos 3 e 4. Uma vez definido o protocolo de purificação e confirmada a atividade enzimática para a PGI-hum recombinante, iniciou-se a terceira etapa do projeto: cristalização e determinação da estrutura por difração de raios-X. O primeiro passo, nesta Ultima fase do trabalho, foi determinar as condições de cristalização da PGI-hum - capítulo 5. Depois de obtidos os cristais, foram coletados dois conjuntos de dados de difração de raios-X, sendo o primeiro coletado em uma fonte convencional de raios-X e o segundo com um feixe proveniente de luz sincrotron - capítulo 6. A análise da qualidade e comparação dos conjuntos de dados - capítulo 7 - indicou qual conjunto seria utilizado nas etapas seguintes da determinação da estrutura da PGI-hum. Para resolução da estrutura cristalográfica da PGI-hum foi utilizado o método de substituição molecular com base na estrutura homóloga da PGI de coelho - capítulo 8. O refinamento estrutural da PGI resultou em uma estrutura com 2.1Å de resolução e fatores R e R free satisfatórios - capítulo 9. Uma análise estrutural preliminar é apresentada indicando uma geometria adequada para a proteína e descrevendo as principais características estruturais desta enzima em comparação com a PGI de coelho. / This work is presented as part of the Master degree requirements of the Applied Physics program, Biomolecular Physics area. The purpose of this work is the structural study by of the human glucose-6-phosphate isomerase (PGI-hum). This work has involved mainly three areas: Molecular Biology, Biochemistry and Crystallography. The Molecular Biology work was intended for the cloning of the human open reading frame of PGI-hum from a fetal human brain cDNA library - Chapter 2 - and its expression in Escherichia coli - Chapter 3. The biochemistry work has involved the PGI-hum purification and the determination of its kinetic parameters of the recombinant protein. Inhibitory efficiency measurements where made with four compounds kindly provided by Dr. Laurent Salmon (Laboratoire de Chimie Bioorganique et Bioinorganique - Universite Paris-XI - France). This work is described in Chapters 3 and 4. Once defined the expression and purification protocols and confirmed its enzymatic activity for the recombinant PGI-hum, a third phase was initiated in the project: The crystallization and structure determination by X-ray diffraction. The first step in this last phase of the project was determining the conditions for crystallization of the PGI-hum - Chapter 5. Once obtained the crystals, two data set were collected. One data set was collected \"in house\" X-ray source and a second data set was collected at the Synchrotron beam line (Laboratório Nacional de Luz Sincrotron - LNLS - Campinas) - Chapter 6. The analysis of the quality and the comparison of the two data sets, presented in Chapter 7, indicated that second data set was the best to be used at the following steps. For the resolution of the atomic structure oh the PGL-hum the method of molecular substitution based on the structure of the rabbit homologue enzyme was employed - Chapter 8. The refinement of the PGI-hum structure at 2.1Å resolution and satisfactory R and R free factors is presented in Chapter 9 of this dissertation. A preliminary structural analysis is presented indicating an adequate geometry of the protein and describing the most important structural features of the PGI-hum compared to its homologue, the rabbit PGI.