Orientador: Jesus Aparecido Ferro / Coorientador: Marcelo Luiz de Laia / Banca: Agda Paula Facincani / Banca: José Belasque Junior / Banca: Haroldo Alves Pereira Junior / Banca: Eliana Gertrudes de Macedo Lemos / Resumo: O cancro cítrico é uma das principais doenças da cultura do citros, provocando lesões nas folhas, ramos e frutos, tendo como consequência a queda dos frutos e folhas, o que leva à perdas significativas na produção. A partir do sequenciamento completo do genoma da bactéria gram-negativa Xanthomonas citri subsp. citri (Xac), agente causal do cancro cítrico, abriu-se a possibilidade da utilização de estratégias de análise genômica funcional no estudo da função de genes da bactéria relacionados com a infecção na planta e com o desenvolvimento da doença. Uma das estratégias utilizadas foi a obtenção de mutantes de Xac contendo genes relacionados à patogenicidade e virulência interrompidos pelo método de mutagênese insercional aleatória utilizando o transposon Tn5 (LAIA et al., 2009). No presente trabalho a técnica de microarranjos de DNA foi utilizada para avaliar a expressão global de genes de dois mutantes de Xac 72 h após a infecção in planta. Em um dos mutantes (8B7) o gene interrompido foi o xrvA, um regulador de virulência, e no outro mutante (18D6) o gene interrompido codifica uma histidina quinase híbrida sensora que faz parte de um sistema de transdução de sinal de dois componentes. Os resultados das hibridizações revelaram um total de 553 genes diferencialmente expressos para os dois mutantes estudados quando comparado com o genótipo selvagem (Xac 306), sendo 323 no mutante 8B7 e 230 no mutante 18D6. Esses genes foram divididos em diferentes categorias funcionais e uma análise funcional comparativa revelou que eles podem desempenhar um papel importante no processo de patogenicidade / Abstract: Citrus canker is a major disease affecting citrus crops worldwide, causing lesions on leaves, branches and fruits that results in the falling of fruit and leaves, leading to significant losses in orange production. The complete genome sequencing of Xanthomonas citri subsp. citri (Xac), a Gram-negative bacteria and the causal agent of citrus canker, allowed the possibility of using functional genomic strategies to study the function of genes related to plant infection and disease development in this bacteria. One strategy was to produce mutants for phatogenicity and virulence genes by random insertional mutagenesis using Tn5 Transposon (LAIA et al., 2009). In the present work DNA microarray analysis was used to evaluate the global gene expression profile of two Xac mutants after 72 hours of plant infection. One mutant (8B7) carry a mutation in the xrvA gene (XAC1495), a virulence regulator, and the other (18D6) carry a mutation in a hybrid histidine quinase sensor of a two-component signal transduction system. The results revealed a total of 553 differentially expressed genes for the two mutant strains compared with Xac wild type, with 323 in the mutant 8B7, and 230 in the mutant 18D6. These genes were allocated into several functional categories and a comparative functional analysis showed that they can play an important role in the pathogenicity and virulence of Xac / Doutor

abstract: Molecular dynamics (MD) simulations provide a particularly useful approach to understanding conformational change in biomolecular systems. MD simulations provide an atomistic, physics-based description of the motions accessible to biomolecular systems on the pico- to micro-second timescale, yielding important insight into the free energy of the system, the dynamical stability of contacts and the role of correlated motions in directing the motions of the system. In this thesis, I use molecular dynamics simulations to provide molecular mechanisms that rationalize structural, thermodynamic, and mutation data on the interactions between the lac repressor headpiece and its O1 operator DNA as well as the ERK2 protein kinase. I performed molecular dynamics simulations of the lac repressor headpiece - O1 operator complex at the natural angle as well as at under- and overbent angles to assess the factors that determine the natural DNA bending angle. I find both energetic and entropic factors contribute to recognition of the natural angle. At the natural angle the energy of the system is minimized by optimization of protein-DNA contacts and the entropy of the system is maximized by release of water from the protein-DNA interface and decorrelation of protein motions. To identify the mechanism by which mutations lead to auto-activation of ERK2, I performed a series of molecular dynamics simulations of ERK1/2 in various stages of activation as well as the constitutively active Q103A, I84A, L73P and R65S ERK2 mutants. My simulations indicate the importance of domain closure for auto-activation and activity regulation. My results enable me to predict two loss-of-function mutants of ERK2, G83A and Q64C, that have been confirmed in experiments by collaborators. One of the powerful capabilities of MD simulations in biochemistry is the ability to find low free energy pathways that connect and explain disparate structural data on biomolecular systems. An extention of the targeted molecular dynamics technique using constraints on internal coordinates will be presented and evaluated. The method gives good results for the alanine dipeptide, but breaks down when applied to study conformational changes in GroEL and adenylate kinase. / Dissertation/Thesis / Ph.D. Chemistry 2011

Orientador: Julio Wilson Dos-Santos / Banca: Camila Buonani da Silva / Banca: João Paulo Borin / Resumo: O futebol é um esporte com ações de alta intensidade, implicando em aumento de dano tecidual, que pode ser mensurado pela análise de marcadores bioquímicos, como a creatina quinase (CK), lactato desidrogenase (LDH) e mioglobina (Mb). Os testes físicos mais utilizados para determinar a aptidão física dos jogadores são: teste aeróbio intermitente de Yo-yo, velocidade de 10 e 30 metros, corridas repetidas anaeróbias (RSA, 6 x 20-20 m) e impulsão vertical squat e contra movimento (IVSQUAT e IVCMV). Entretanto, a relação entre o nível de aptidão física do jogador, seu desgaste durante a partida com a intensidade na qual ele joga e com as ações técnicas é pouco estudada. Diante disso, o presente estudo tem como objetivo: verificar se os jogadores que apresentam melhor desempenho nos testes físicos também têm maior participação com a bola e jogam em maior intensidade; verificar quais indicadores de dano muscular no jogo se relacionam com a aptidão física, as ações técnicas e a intensidade do jogo de futebol; bem como, verificar a relação entre CK, LDH e Mb com a intensidade do jogo. O presente estudo contou com 11 jogadores de futebol de uma equipe participante do Campeonato Paulista da primeira divisão. Os jogadores passaram por avaliação antropométrica e avaliação das capacidades físicas (Yo-yo, RSA, 10 e 30 metros e IV). A FC do jogo foi monitorada durante duas partidas oficiais para determinar a carga do jogo, pelo impulso de treinamento (TRIMP). Duas horas antes do início e apó... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Soccer is a sport with high intensity actions, involving an increase in tissue damage, which can be measured by the analysis of biochemical markers such as creatine kinase (CK), lactate dehydrogenase (LDH) and myoglobin (Mb). The physical tests most used to determine the physical fitness of the players are: Yo-yo intermittent aerobic test, 10 and 30 meters speed, repeated anaerobic races (RSA, 6 x 20-20 m) and vertical squat and counter-movement (IVSQUATand IVCMV). However, therelationship between the level of physical fitness of the player, his wear during the match with the intensity in which he plays and the technical actionsis little studied. Therefore, the present study has as objective: to verify if the players that present better performance in the physical tests also have higherparticipation with the ball and play in higherintensity; to verifywhich indicators of muscle damage in matches relate to physical fitness, technical actions and intensity of the soccermatch; as well as,toverifythe relationship amongCK, LDH and Mb with the intensity of the match. The present study had 11 soccer players from a team participating in the First Division Paulista Championship. The players underwent anthropometric evaluation and assessment of physical abilities (Yo-yo, RSA, 10 and 30 meters and IV). The HFof the game was monitored during two official matches to determine the loading of the game by the training impulse (TRIMP). Two hours before and after the game blood samples (5 mL) w... (Complete abstract click electronic access below) / Mestre

Traditionally, drug discovery programs have focused on prioritising compounds by their affinity to a specific target in isolation, which was hypothesised to be the cause of a particular disease. Through chemical inhibition, the disease could, thus, be prevented or at the very least, controlled. These hypotheses require significant validation before drug screening can begin which relates to lengthy and expensive programs. Furthermore, drug screening against a single target in isolation is not a realistic model of cellular behaviour and is not appropriately tailored to more complex diseases such as cancer. Phenotypic drug discovery, on the other hand, bypasses any involvement of known targets, instead focusing on the desired outcome – the phenotype. In this way, drugs are biased by their potency on the phenotype and not against any particular targets. The molecular mechanism of action need not be known at all, however, it can be useful to later reveal the target(s) involved by various deconvolution methods. This thesis describes a cooperative ligand based phenotypic drug discovery approach, undertaken in order to develop more suitable small molecule drugs for cancer treatment. For this purpose, the promiscuous pyrazolopyrimidine inhibitor PP1 was chosen as a starting model compound. Modification of PP1 on the N1 position allowed a series of water solubilising groups to be incorporated into the pyrazolopyrimidine scaffold which created an initial 12-membered library. Testing against MCF7 breast cancer cells and looking at phenotypic end points such as cell proliferation, cell mobility and cell cycle, generated early target-agnostic structure/anti-proliferative activity relationships. These early results, along with compounds published in recent literature, were used to generate further libraries. Profiling lead compounds against a selection of 18 kinases known to be targeted by PP1, showed the compounds were inhibiting either SRC family or mTOR kinases which enabled the creation of two, structure specific, groups of inhibitors. Further lead optimisation led to the rapid discovery of preclinical candidates with excellent drug-like properties and potencies in both cellular assays and against their respective targets. Compounds also showed improved selectivity profiles compared to PP1 and commonly known inhibitors of SRC and mTOR kinases. Reported, herein, is the discovery of the first sub-nanomolar SRC inhibitor which does not inhibit the kinase ABL and shows excellent properties suitable for further preclinical development.

Made available in DSpace on 2014-06-11T19:23:25Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-08-12Bitstream added on 2014-06-13T18:09:34Z : No. of bitstreams: 1 aizemberg_r_me_arafcf.pdf: 685654 bytes, checksum: d058342c2d66649275266dc34dcb968d (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Universidade Estadual Paulista (UNESP) / A levedura Pichia pastoris vem sendo largamente utilizada como um eficiente sistema de expressão para a produção de proteínas heterólogas, pois é um sistema seguro, fácil e mais barato que sistemas de expressão de outros eucariotos. Neste trabalho, a enzima de interesse é a glicerol quinase (GK), que cataliza a transferência do fosfato terminal do ATP para o glicerol originando glicerol-3-fosfato e ADP. Esta reação pode ser utilizada na determinação da concentração de glicerol, subproduto da fermentação alcoólica. A leitura do consumo de glicerol é realizada pela determinação espectrofotométrica do NADH gerado na reação de oxido-redução catalizada pela enzima glicerol-3-fosfato desidrogenase. Este estudo de indução foi realizado em diferentes condições de crescimento da levedura Pichia pastoris. Os resultados mostraram a seleção do melhor clone da levedura Pichia pastoris para a expressão extracelular da enzima glicerol quinase, e a determinação das melhores condições do meio de cultura para a produção da enzima de interesse foram: concentração do meio de cultura BMMY (20 vezes), densidade inicial de célula (0,1 mg/mL), concentração de metanol na fase de indução (1%), natureza do tampão (fosfato de potássio), pH (6,0), suplementação de glicerol no meio BMMY (1%), peptona (marca Difco), sem adição de sulfato de amônio, caseína e glicina, uso do meio BMMY e liofilização do mesmo. Estudos de parâmetros cinéticos foram realizados e a atividade máxima da GK foi obtida em pH 9,8, a 50ºC e 2,5 μM de substrato, por metodologia clássica, além da presença de sulfato de magnésio e diluição da enzima de 30 vezes. A enzima apresentou alta estabilidade térmica ― a atividade foi completamente... / The yeast Pichia pastoris has been widely used as an efficient expression system for production of heterologous proteins because it is a safe, easy and cheaper than expression systems in other eukaryotes.In this studie, the enzyme of interest is glycerol kinase (GK), which catalizes the transfer of terminal phosphate from ATP to glycerol resulting glycerol-3-phosphate and ADP. This reaction can be used in determining the concentration of glycerol, a byproduct of fermentation. The reading of the consumption of glycerol is carried out by spectrophotometric determination of NADH generated in the redox reaction catalyzed by the enzyme glycerol-3-phosphate dehydrogenase. This study of induction was performed in different conditions of growth of the yeast Pichia pastoris. The results show that selecting the best clone of the yeast Pichia pastoris for the expression of extracellular enzyme glycerol kinase, and determining the best conditions of the culture medium for producing the enzyme of interest were: concentration of the culture medium BMMY (20 times), initial cell density (0.1 mg/mL), methanol concentration in the induction phase (1%), nature of buffer (potassium phosphate), pH (6.0), glycerol supplementation in BMMY medium (1%), peptone (Difco), without addition of ammonium sulfate, casein and glycine in BMMY and lyophilized medium. Studies of kinetic parameters were conducted and the GK maximum activity was obtained at pH 9.8 at 50°C and 2.5 μM substrate by conventional method, besides the presence of magnesium sulfate and diluting the enzyme 30 times. The enzyme showed high thermal stability - the activity was fully maintained up to 50°C for one hour - and at pH 7.0 for 7 days and kept under refrigeration, freeze-dried extract showed a decrease in enzymatic activity. Calculated by... (Complete abstract click electronic access below)

I. A phosphoglycerate kinase (PGK) deficient variant cell line, R1.1.7, derived from the Chinese hamster ovary cell line, CHO-K1, is used as a recipient in the development of a DNA-mediated transfection system designed for the study of in vivo expression of exogenous PGK gene sequences. II. Several PGK DNA sequences are detected in the Chinese hamster genome by hybridisation of genomic DNA digests with a human PGK cDNA probe. A number of these sequences are shown to be X-linked. Four of the PGK sequences observed in the blot hybridisations are isolated from a CHO-K1 DNA genomic library and analysed by probing with different regions of the PGK cDNA, heteroduplex mapping and DNA sequencing. One of these sequences is a 572 bp exon from the functional X-linked PGK gene (PGK-1) which is expressed in all somatic cells. The three remaining PGK sequences are intronless pseudogenes which were apparently derived independently, from an ancestral Chinese hamster PGK gene, within the last 50 million years. They exhibit features typical of 'processed' pseudogenes which are generated via an mRNA intermediate and integrated into breaks in the chromosomal DNA.

There is a growing body of interest to understand the regulation of allosteric proteins. Allostery is a phenomenon of protein regulation whereby binding of an effector molecule at a remote site affects binding and activity at the protein‟s active site. Over the years, these sites have become popular drug targets as they provide advantages in terms of selectivity and saturability. Both experimental and computational methods are being used to study and identify allosteric sites. Although experimental methods provide us with detailed structures and have been relatively successful in identifying these sites, they are subject to time and cost limitations. In the present dissertation, Molecular Dynamics Simulations (MDS) and Principal Component Analysis (PCA) have been employed to enhance our understanding ofallostery and protein dynamics. MD simulations generated trajectories which were then qualitatively assessed using PCA. Both of these techniques were applied to two important trypanosomatid drug targets and controlling enzymes of the glycolytic pathway - pyruvate kinase (PYK) and phosphofructokinase (PFK). Molecular Dynamics simulations were first carried out on both the effector bound and unbound forms of the proteins. This provided a framework for direct comparison and inspection of the conformational changes at the atomic level. Following MD simulations, PCA was run to further analyse the motions. The principal components thus captured are in quantitative agreement with the previously published experimental data which increased our confidence in the reliability of our simulations. Also, the binding of FBP affects the allosteric mechanism of PYK in a very interesting way. The inspection of the vibrational modes reveals interesting patterns in the movement of the subunits which differ from the conventional symmetrical pattern. Also, lowering of B-factors on effector binding provides evidence that the effector is not only locking the R-state but is also acting as a general heat-sink to cool down the whole tetramer. This observation suggests that protein rigidity and intrinsic heat capacity are important factors in stabilizing allosteric proteins. Thus, this work also provides new and promising insights into the classical Monod-Wyman-Changeux model of allostery.

La résistance à la chimiothérapie constitue un frein majeur à son efficacité. Notre équipe a récemment pu montrer que le masitinib, un nouvel inhibiteur de protéines tyrosine kinases, possède une activité de resensibilisation des cellules tumorales résistantes à la chimiothérapie lorsqu'il est combiné à certaines chimio-drogues. L'objectif des travaux de cette thèse est de déterminer les voies de signalisation, modulées par l'action du masitinib, qui sont impliquées dans la resensibilisation aux chimiothérapies et amélioration de l'activité anti-tumorale.Dans la première partie de la thèse, nous avons pu identifier la nucléoside kinase dCK (désoxycytidine kinase), protéine activatrice d'un grand nombre de chimiothérapies, comme nouvelle cible du masitinib. Cette première étude nous a permis de mettre en évidence un nouveau concept thérapeutique: le masitinib, un composé chimique de type inhibiteur de protéines tyrosine kinases, peut jouer en même temps le rôle d'activateur de nucléoside kinase.Nous avons pu mettre en évidence dans la deuxième partie de la thèse que le traitement combiné entre l'épi-drogue décitabine et le masitinib peut être plus efficace pour la réexpression de certains gènes non ou peu induits par la décitabine seule.En conclusion, ces travaux nous ont permis de mettre en évidence l'interaction entre un inhibiteur de protéine tyrosine kinases et une nucléoside kinase, dans un concept d'activation enzymatique qui pourra certainement servir de base pour l'élaboration de nouvelles petites molécules chimiques spécifiques de l'activation de dCK ou d'autres nucléosides kinases nécessaires à l'activation des drogues de chimiothérapie. / Resistance to chemotherapy is considered as one of the major blockers of its efficacy. Recently, our team demonstrated that masitinib, a new tyrosine kinases inhibitor, possesse a resensitization activity of cell lines resistant to chemotherapy when associated with chemodrugs.The aim of this work is to determine signaling pathways, modulated by masitinib action, that could explain the resensitization to chemotherapy and improvement of anti-tumoral activity.In the first part of this work, we identified the nucleoside kinase dCK (deoxycytidine kinase), a chemotherapy activating protein, as a new target of masitinib. In summary, this first part of the work allowed us to describe a new and never described concept: masitinib, a small molecule belonging to tyrosine kinases group, can also play a role as nucleoside kinase activator.We were able to demonstrate through the second part of the work that the combined treatment of the epidrug decitabine and masitinib can be more effective than decitabine treatment for the re-expression of some genes non or weakly induced by decitabine when used alone.In conclusion, These data allowed us to introduce an interaction between a tyrosine kinases inhibitor and a nucleoside kinase, as an enzymatic activation new concept. This could be used as a base for the design of new small chemical molecules specific for dCK or other nucleoside kinases essential for the activation of chemodrugs. This concept will obviously help to imagine and evaluate more potential therapeutic combinations of chemodrugs and small chemical molecules to overcome the resistance to chemotherapy dependent on nucleoside kinases.

Master of Science in Biomedical Sciences / Department of Clinical Sciences / Mary Lynn Higginbotham / This study evaluated sixteen canine nasal carcinoma and five normal nasal epithelium samples for expression and phosphorylation of known targets of toceranib [vascular endothelial growth factor receptor-2 (VEGR2), platelet derived growth factor alpha (PDGFR-[alpha]), platelet derived growth factor receptor beta (PDGFR-[beta]), and stem cell factor receptor (c-KIT)] and epidermal growth factor receptor 1 (EGFR1) using immunohistochemistry, RT-PCR and a receptor tyrosine kinase (RTK) phosphorylation panel. Protein for VEGFR2 was expressed in neoplastic cells of all carcinomas, PDGFR-[alpha] was noted in 15/16, whereas PDGFR-[beta] was detected in 3/16 samples, but showed primarily stromal staining. Protein expression for c-KIT was present in 4/16 and EGFR1 was noted in 14/16 samples. Normal tissue showed variable protein expression of the RTKs. Messenger RNA for VEGFR2, PDGFR-[beta], and c-KIT were noted in all samples. Messenger RNA for PDGFR-[alpha] and EGFR1 were detected in 15/16 samples. All normal nasal tissue detected messenger RNA for all RTKs of interest. Constitutive phosphorylation of VEGFR2, PDGFR-[alpha], PDGFR-[beta] and c-KIT was not observed in any carcinoma or normal nasal sample, but phosphorylation of EGFR1 was noted in 10/16 carcinoma and 3/5 normal samples. The absence of major phosphorylated RTK targets of toceranib suggests the clinical effect of toceranib may occur through inhibition of alternative and currently unidentified RTK pathways in canine nasal carcinomas. The observed protein and message expression and phosphorylation of EGFR1 in the nasal carcinoma samples merits further inquiry into EGFR1 as a therapeutic target for this cancer.

Class of 2015 Abstract / Objectives: Two characterized peptide substrates were assayed with human Polo-like kinase 4 to determine phosphorylation activity. A pilot library of Type-II kinase inhibitors designed to fit into the ATP-binding pocket will be screened to determine HsPlk4 inhibition activity, which will help characterize a novel drug compound. Methods: Two peptide substrates of varying concentrations (2 uM, 1 uM, and 0.5 uM) were each combined with serial dilutions of HsPlk4 (1.25 uM, 0.625 uM, 0.313 uM, 0.156 uM, 0.078 uM, and 0.039 uM). EZ Reader detected phosphorylation activity by measuring fluorescence of both substrate and product, which separated at respective time points based on electrophoresis. The subsequent part of the experiment will be to inhibit the kinase activity with molecular inhibitors. Results: The results showed HsPlk4 activity with the modified PLKtide, (5FAM)KKKTPSDSLYDDGLSKK(CONH2). All reactions with the various concentrations of substrate 1 and HsPlk4 showed phosphorylation activity. The reaction started within the first 10 minutes, quickly reaching maximal phosphorylation of substrate. No p-values were calculated due to lack of data. Conclusions: No overall conclusions can be drawn based on the current results. Results showed the reaction reached its saturation point, so methods need to be refined to obtain data within the first 10 minutes. HsPlk4 phosphorylation of PLKtide confirmed the presumption that PLK family is a conserved family of Ser/Thr kinases. There are practical limitations for obtaining good kinetics data depicting enzyme activity, such as having EZ Reader quickly sample the reaction.