Genetic material of bacteria is subject to damage due to multitudinous factors, both extrinsic and intrinsic in origin. Mechanisms for the maintenance of genomic integrity are thus essential for a bacterium to survive. Bacterium also requires appropriate minor changes in the genetic material so as to adapt to the changing environments. Structural and related studies of two proteins from mycobacteria, one involved in recombinational DNA repair (RecA) and the other involved in SOS response which helps in adaptation to stress (LexA) form the subject matter of the thesis. The available literature on structural and related studies on RecA and LexA are reviewed in the introductory chapter. The action of RecA involves transition to an active filament formed in association with DNA and ATP, from an inactive filament in the absence of DNA. The structure of the inactive filament was first established in E. coli RecA (EcRecA). The interaction of RecA with non-hydrolysable ATP analogues and ADP were thoroughly characterised and the DNA binding loops were visualised in this laboratory using the crystal structures involving the proteins from Mycobacterium tuberculosis (MtRecA) and Mycobacterium smegmatis (MsRecA). A switch residue, which triggers the transformation of the information on ATP binding to the DNA binding regions, was identified. The 20 residue C-terminal stretch of RecA, which is disordered in all other relevant crystal structures, was defined in an MsRecA-dATP complex. The ordering of the stretch is accompanied by the generation of a new nucleotide binding site which can communicate with the original nucleotide binding site of an adjacent molecule in the filament. The plasticity of MsRecA and its mutants involving the switch residue was explored by studying crystals grown under different conditions at two different temperatures and, in one instance, at low humidity. The structures of these crystals and those of EcRecA and Deinococcus radiodurans RecA (DrRecA) provide information on correlated movements involving different regions of the molecule. MtRecA has an additional importance as an adjuvant drug target in Mycobacterium tuberculosis. Apart from recombination, another important property of RecA is its coprotease activity whereby it stimulates the inherent cleavage of a certain class of proteins. One of the substrates for the coprotease activity of RecA is LexA. LexA is a transcriptional repressor involved in SOS response in bacteria. LexA performs its function through an autoproteolysis stimulated by RecA, resulting in the derepression of the genes under its control. Structural studies on LexA from E. coli have shown that it has an N-terminal domain involved in binding to DNA and a C-terminal domain involved in catalysis and dimerisation. LexA mediated SOS response in bacteria has been shown in many cases to be responsible for the resistance gained by bacteria on treatment with antibiotics. In that respect, LexA is considered to be a potential drug target in Mycobacterium tuberculosis. Structures of crystals of Mycobacterium tuberculosis RecA, grown and analysed under different conditions and reported in the thesis, provide insights into hitherto underappreciated details of molecular structure and plasticity (Chapter 2). In particular, they yield information on the invariant and variable features of the geometry of the P-loop, whose binding to ATP is central for all the biochemical activities of RecA. The strengths of interaction of the ligands with the P-loop reveal significant differences. This in turn affects the magnitude of the motion of the ‘switch’ residue, Gln195 in M. tuberculosis RecA, which triggers the transmission of ATP-mediated allosteric information to the DNA binding region. M. tuberculosis RecA is substantially rigid compared with its counterparts from M. smegmatis and E. coli, which exhibit concerted internal molecular mobility. Details of the interactions of ligands with the protein, characterised in the structures, could be useful for design of inhibitors against M. tuberculosis RecA. Eleven independent simulations, each involving three consecutive molecules in the RecA filament, carried out on the protein from M. tuberculosis, M. smegmatis and E. coli and their ATP complexes, provide valuable information which is complementary to that obtained from crystal structures, in addition to confirming the robust common structural frame work within which RecA molecules from different eubacteria function (Chapter 3). Functionally important loops, which are largely disordered in crystal structures, appear to adopt in each simulation subsets of conformations from larger ensembles. The simulations indicate the possibility of additional interactions involving the P-loop which remains largely invariant. The phosphate tail of the ATP is firmly anchored on the loop while the nucleoside moiety exhibits substantial structural variability. The most important consequence of ATP binding is the movement of the ‘switch’ residue. The relevant simulations indicate the feasibility of a second nucleotide binding site, but the pathway between adjacent molecules in the filament involving the two nucleotide binding sites appears to be possible only in the mycobacterial proteins. As described in Chapter 4, full length LexA, the N-terminal and C-terminal segments defined by the cleavage site, two point mutants involving changes in active site residues (S160A and K197A) and another involving change at the cleavage site (G126D) were cloned, expressed and purified. The wild type protein cleaves at basic pH. The mutants do not autocleave at basic pH even after incubation for 12 hours. The wild type and the mutant protein dimerise and bind DNA with equal facility. The C-terminal segment also dimerises, but has a tendency to form tetramer as well. The full length proteins including the mutants and the C-terminal segment crystallised. The structure of the crystals obtained for mutant G126D could not be solved. Each of the other crystals, four in number, contained only the catalytic core and a few residues preceding it, indicating that the full length proteins underwent cleavage, at the canonical cleavage site or elsewhere, during the long period involved in the formation of the crystals. Crystals obtained from the solutions of the wild type protein and the C-terminal segment contains dimers of the catalytic core. Crystals obtained using the active site mutants appear to contain different type of tetramers. One of them involves the swapping of the peptide segment preceding the catalytic core. Models of tetramerisation of the full length protein similar to those observed for the catalytic core are feasible. A model of a complex of MtLexA with M. tuberculosis SOS box could be readily built. In this complex, the mutual orientation of the two N-domains of the dimer is different from that in the EcLexA-DNA complex.

La tuberculose continue d’être une cause majeure de morbidité et de mortalité dans le monde, principalement dans les pays en voie de développement, bien qu’elle soit une maladie curable. Le diagnostic rapide et précis de la TB active est essentiel pour l’initiation rapide du traitement et le contrôle de la maladie. Le développement de nouveaux tests rapides de diagnostic de TB active représente un véritable challenge pour l’optimisation du diagnostic.L’objectif principal de nos travaux de thèse était de développer et d’évaluer des approches de PCR en temps réel ciblant la séquence d’insertion IS6110 pour la détection de l’ADN de MTB dans les expectorations.Nous avons tout d’abord développé une PCR en temps réel ciblant la séquence répétée IS6110 pour la quantification de l’ADN de MTB. L’évaluation des étapes d’optimisation de la sensibilité de la PCR IS6110 a permis de préciser les performances analytiques et le gain de sensibilité comparativement à une PCR ciblant le gène unique senX3. Au terme d’une comparaison de six protocoles de lyse/ extraction la méthode Chelex® s’est avérée être la plus efficace dans la récupération de l’ADN. La performance diagnostique de la PCR optimisée a été évaluée et comparée avec la PCR automatisée Xpert MTB/RIF sur un panel de 62 échantillons respiratoires.Dans un deuxième temps, nous avons comparé la performance diagnostique de la PCR IS6110 optimisée, le test Xpert MTB/RIF et la version ultrasensible récemment commercialisée du test PCR leader Xpert MTB/RIF Ultra pour la détection de l’ADN de MTB dans des expectorations ayant une faible charge bacillaire.Enfin, à partir de 203 LCR collectés dans le cadre du diagnostic de méningites aseptiques au Burkina Faso, nous avons évalué la performance de la PCR en temps réel multiplexe (IS6110, HSV1, HSV2) combinée à l’extraction par la méthode Chelex® pour la détection de l’ADN de MTB et d’Herpès. / TTuberculosis continues to be a major cause of morbidity and mortality worldwide, mainly in developing countries, despite being a curable disease. The rapid and accurate diagnosis of active TB is essential for rapid initiation of treatment and disease control. The development of new rapid diagnostic tests for active TB represents a real challenge for the optimization of the diagnosis.The main objective of our thesis work was to develop and evaluate real-time PCR approaches targeting the IS6110 insertion sequence for the detection of sputum MTB DNA. We first developed a real-time PCR targeting the IS6110 repeat sequence for the quantification of MTB DNA. The evaluation of the sensitivity optimization steps of the IS6110 PCR made it possible to specify the analytical performances and the sensitivity gain compared to a PCR targeting the single gene senX3. After a comparison of six lysis / extraction protocols, the Chelex® method proved to be the most efficient in the recovery of DNA. The diagnostic performance of optimized PCR was evaluated and compared with automated Xpert MTB / RIF PCR on a panel of 62 respiratory specimens.In a second step, we compared the diagnostic performance of the optimized IS6110 PCR, the Xpert MTB / RIF test and the highly marketed ultra-sensitive version of the Xpert MTB / RIF Ultra leader PCR assay for the detection of sputum MTB DNA. having a low bacillary load.Finally, from 203 LCR collected in the context of the diagnosis of aseptic meningitis in Burkina Faso, we evaluated the performance of the multiplexed real-time PCR (IS6110, HSV1, HSV2) combined with extraction by the Chelex® method for the detection of MTB and Herpes DNA.

Apesar da incidência per capita da tuberculose (TB) ter se mantido estável em 2005, o número de novos casos que surgem a cada ano continua a aumentar no mundo todo. De acordo com a Organização Mundial de Saúde, foram estimados 9,4 milhões de novos casos de TB em 2008, dos quais 1,4 milhões eram HIV - positivos, e com 1,8 milhões de mortes - o equivalente a 4.500 mortes por dia. Fatores como migração, privação sócio-econômica, co-infecção TB-HIV e o aparecimento de cepas resistentes contribuíram para o aumento do número de casos de TB no mundo, principalmente nos países onde a TB já foi considerada erradicada, e criaram a necessidade do desenvolvimento de novas terapêuticas. Alvos moleculares específicos, que são essenciais para o patógeno, e ausentes no hospedeiro, como as enzimas da via do ácido chiquímico são alvos atraentes para o desenvolvimento de novas drogas antituberculose. Essa via leva à síntese de compostos aromáticos, como aminoácidos aromáticos, e é encontrada em plantas, fungos, bactérias e parasitas do phylum Apicomplexa, mas está ausente em humanos. No ano de 2000, foi comprovada a essencialidade dessa via para a viabilidade do bacilo, tornando todas essas enzimas alvos validados para estudo. A segunda enzima da via, deidroquinato sintase (DHQS), catalisa a conversão de 3-deoxi-D-arabino heptulosonato-7-fosfato em 3-deidroquinato, o primeiro composto cíclico. Neste trabalho, são descritos o requerimento de metais divalentes na reação e a determinação do mecanismo cinético da DHQS. Os parâmetros cinéticos verdadeiros foram determinados e, juntamente com os experimentos de ligação, o mecanismo rápido-equilíbrio aleatório foi proposto. O tratamento com EDTA aboliu completamente a atividade de DHQS, sendo que a adição de Co+2 e Zn+2 levam a recuperação total e parcial da atividade enzimática, respectivamente. O excesso de Zn+2 inibe a atividade DHQS, e os dados de ITC indicaram a presença de dois sítios seqüenciais de ligação, o que é consistente com a existência de um sítio secundário inibitório. O protocolo de cristalização foi estabelecido e experimentos em andamento proporcionarão a elucidação da estrutura tridimensional da DHQS, que irá beneficiar tanto o desenho de novos inibidores como uma análise detalhada dos rearranjos do domínio da proteína. Em conjunto, estes resultados representam um passo essencial para o desenho racional de inibidores específicos que podem fornecer uma alternativa promissora para um novo, eficaz, e mais curto de tratamento para TB. / Although the estimated per capita tuberculosis (TB) incidence was stable in 2005, the number of new cases arising each year is still increasing globally. According with World Health Organization, there were estimated 9.4 million new TB cases in 2008, from which 1.4 million were HIV-positive, with 1.8 million deaths total – equal to 4500 deaths a day. Migration, socio-economic deprivation, HIV co-infection and the emergence of extensively-resistance strains, have all contributed to the increasing number of TB cases worldwide, mainly in countries where it was once considered eradicated, and have created an urgent need for the development of new therapeutics against TB. Specific molecular targets, that are essential to the pathogen, and absent in the host, like the enzymes of the shikimate pathway, are attractive targets to development of new antitubercular drugs. This pathway leads to the biosynthesis of aromatic compounds, including aromatic amino acids and it is found in plant, fungi, bacteria and Apicomplexa parasites, but is absent in humans. In 2000, this pathway was proved to be essential to the viability of the pathogen, which validates all its enzymes as potential targets. The second enzyme of this pathway, dehydroquinate synthase (DHQS), catalyzes the conversion of 3-deoxy-D-arabinoheptulosonate 7-phosphate in 3-dehydroquinate, the first cyclic compound. In this work, we described the metal requirement and kinetic mechanism determination of the dehydroquinate synthase. The determination of the true kinetic parameters was performed, and, in addition to ligand binding experiments, the rapid-equilibrium random mechanism was determined. The treatment with EDTA abolished completely the activity of DHQS, and the addition of Co+2 and Zn+2 leads to full and partial recovery of enzyme activity, respectively. Excess of Zn+2 inhibits the DHQS activity, and the ITC data revealed two sequential binding sites, which is consistent with the existence of a secondary inhibitory site. The crystallization protocol was established and ongoing experiments will provide the three-dimensional structure of mtDHQS, which will benefit both the design of novel inhibitors as well as detailed analysis of domain rearrangements of protein. Taken together, these results represent an essential step for the rational design of specific inhibitors that can provide a promising alternative to a new, effective, and shorter treatment for TB.

Apesar da incidência per capita da tuberculose (TB) ter se mantido estável em 2005, o número de novos casos que surgem a cada ano continua a aumentar no mundo todo. De acordo com a Organização Mundial de Saúde, foram estimados 9,4 milhões de novos casos de TB em 2008, dos quais 1,4 milhões eram HIV - positivos, e com 1,8 milhões de mortes - o equivalente a 4.500 mortes por dia. Fatores como migração, privação sócio-econômica, co-infecção TB-HIV e o aparecimento de cepas resistentes contribuíram para o aumento do número de casos de TB no mundo, principalmente nos países onde a TB já foi considerada erradicada, e criaram a necessidade do desenvolvimento de novas terapêuticas. Alvos moleculares específicos, que são essenciais para o patógeno, e ausentes no hospedeiro, como as enzimas da via do ácido chiquímico são alvos atraentes para o desenvolvimento de novas drogas antituberculose. Essa via leva à síntese de compostos aromáticos, como aminoácidos aromáticos, e é encontrada em plantas, fungos, bactérias e parasitas do phylum Apicomplexa, mas está ausente em humanos. No ano de 2000, foi comprovada a essencialidade dessa via para a viabilidade do bacilo, tornando todas essas enzimas alvos validados para estudo. A segunda enzima da via, deidroquinato sintase (DHQS), catalisa a conversão de 3-deoxi-D-arabino heptulosonato-7-fosfato em 3-deidroquinato, o primeiro composto cíclico. Neste trabalho, são descritos o requerimento de metais divalentes na reação e a determinação do mecanismo cinético da DHQS. Os parâmetros cinéticos verdadeiros foram determinados e, juntamente com os experimentos de ligação, o mecanismo rápido-equilíbrio aleatório foi proposto. O tratamento com EDTA aboliu completamente a atividade de DHQS, sendo que a adição de Co+2 e Zn+2 levam a recuperação total e parcial da atividade enzimática, respectivamente. O excesso de Zn+2 inibe a atividade DHQS, e os dados de ITC indicaram a presença de dois sítios seqüenciais de ligação, o que é consistente com a existência de um sítio secundário inibitório. O protocolo de cristalização foi estabelecido e experimentos em andamento proporcionarão a elucidação da estrutura tridimensional da DHQS, que irá beneficiar tanto o desenho de novos inibidores como uma análise detalhada dos rearranjos do domínio da proteína. Em conjunto, estes resultados representam um passo essencial para o desenho racional de inibidores específicos que podem fornecer uma alternativa promissora para um novo, eficaz, e mais curto de tratamento para TB. / Although the estimated per capita tuberculosis (TB) incidence was stable in 2005, the number of new cases arising each year is still increasing globally. According with World Health Organization, there were estimated 9.4 million new TB cases in 2008, from which 1.4 million were HIV-positive, with 1.8 million deaths total – equal to 4500 deaths a day. Migration, socio-economic deprivation, HIV co-infection and the emergence of extensively-resistance strains, have all contributed to the increasing number of TB cases worldwide, mainly in countries where it was once considered eradicated, and have created an urgent need for the development of new therapeutics against TB. Specific molecular targets, that are essential to the pathogen, and absent in the host, like the enzymes of the shikimate pathway, are attractive targets to development of new antitubercular drugs. This pathway leads to the biosynthesis of aromatic compounds, including aromatic amino acids and it is found in plant, fungi, bacteria and Apicomplexa parasites, but is absent in humans. In 2000, this pathway was proved to be essential to the viability of the pathogen, which validates all its enzymes as potential targets. The second enzyme of this pathway, dehydroquinate synthase (DHQS), catalyzes the conversion of 3-deoxy-D-arabinoheptulosonate 7-phosphate in 3-dehydroquinate, the first cyclic compound. In this work, we described the metal requirement and kinetic mechanism determination of the dehydroquinate synthase. The determination of the true kinetic parameters was performed, and, in addition to ligand binding experiments, the rapid-equilibrium random mechanism was determined. The treatment with EDTA abolished completely the activity of DHQS, and the addition of Co+2 and Zn+2 leads to full and partial recovery of enzyme activity, respectively. Excess of Zn+2 inhibits the DHQS activity, and the ITC data revealed two sequential binding sites, which is consistent with the existence of a secondary inhibitory site. The crystallization protocol was established and ongoing experiments will provide the three-dimensional structure of mtDHQS, which will benefit both the design of novel inhibitors as well as detailed analysis of domain rearrangements of protein. Taken together, these results represent an essential step for the rational design of specific inhibitors that can provide a promising alternative to a new, effective, and shorter treatment for TB.

Emergence of drug resistance is a major problem in the treatment of many diseases including tuberculosis. To tackle the problem, it is essential to obtain a global perspective of the molecular mechanisms by which bacteria acquire drug resistance. Systems biology approaches therefore become necessary. This work aims to understand pathways to drug resistance and strategies for inhibition of the resistant strains by using a combination of experimental genomics and computational molecular systems approaches. Laboratory evolution of Mycobacterium smegmatis MC2 155 by treatment with isoniazid (INH), a front-line anti-tubercular drug, resulted in a drug-resistant strain (4XR), capable of growth even at about 10-times the minimum inhibitory concentration of the drug. Whole genome sequence of the 4XR was determined, which indicated only 31 variations in the whole genome, including 3 point mutations, 17 indels and 11 frame-shifts. Two mutations were in proteins required for the pharmacological action of the drug, albeit in regions distant from the drug binding site. The variations however were insufficient to explain the observed resistance to isoniazid. For a better understanding of the global changes associated with drug resistance, whole genome-wide gene expression data was obtained for the resistant strain and compared with that of the WT strain. 716 genes were found to be differentially regulated in 4XR, spanning different biochemical, signaling and regulatory pathways. From this, some explanations for the emergence of drug resistance were obtained, such as the up-regulation of the enzymes in the mycolic acid biosynthesis pathway and also of the drug efflux pumps. In addition, enrichment analysis indicated that up-regulated genes belong to functional categories of response to stress, carbohydrate metabolism, oxidation-reduction process, ion transport, signaling as well as lipid metabolism. The differential gene regulations seemed to be partially responsible for conferring the phenotype to the organism. Alterations in the metabolic pathways in 4XR were characterized using the phenotypic microarray technology, which experimentally scanned the respiratory ability of the resistant bacteria under 280 different nutrient conditions and 96 different inhibitors. Phenotypic gain, where the resistant strain grows significantly better than the wild type and phenotypic loss, where the growth of the resistant strain is compromised as compared to the sensitive strains were derived from the comparison of the phenotypic responses. Differences in survival ability and growth rates in different nutrient sources in the resistant phenotype as compared to the wild type were observed, suggesting rewiring in the metabolic network of the drug-resistant strain. In particular, the pathways of central carbon metabolism and amino acid biosynthesis exhibit significant differences. The strain-specific metabolic pathway differences may guide in devising strategies to tackle the drug-resistant strains selectively and in a rational manner. Scanning electron microscopy indicated the morphology of the drug-resistant strains to be significantly altered, as compared to the control drug-sensitive strain. It is well-known that isoniazid acts by inhibiting mycolic acid biosynthesis. The pathway turns out to be a target for many other anti-tubercular drugs also, since mycolic acids are major components of the cell wall. It is therefore important to understand what changes occur in the mycolic acid and the associated pathways in the drug-resistant variety so that strategies to tackle the latter can be chosen more judiciously. The lipidome of the cell wall was therefore quantitatively characterized by mass spectrometric analyses, which indeed confirmed that the 4XR strain has a significantly different composition profile. Among the six categories of lipids, the members of the glycerophospolipids category were abundant while the fatty acyls, polyketides and saccharolipids were lower in the 4XR strain as compared to the WT. The lipidomic data derived from the cell wall of INH-resistant strain shows that it results in the mycolic acid pathway function restoration, which would otherwise be lost upon drug exposure in the sensitive strain. Understanding the precise changes that occur in the lipidome in the drug-resistant strains is expected to be useful in developing new ways to tackle resistance. Next, to understand the implications of altered gene expression profiles, protein-protein interaction networks are constructed at a genome-scale that captures various structural and functional associations mediated by proteins in the mycobacterial cell. Using transcriptome data of 4XR, a response network is computed. Using an algorithm previously developed in the laboratory, the networks have been mined to identify highest differential activity paths and possible mechanisms that are deployed by the cells leading to drug resistance. Known resistance mechanisms such as efflux, cytochromes, SOS, are all seen to constitute the highest activities for achieving drug resistance in 4XR. Interestingly, such paths are seen to form a well-connected subnet, indicating such differential activities to be orchestrated. This clearly shows that multiple mechanisms are simultaneously active in the 4XR and may together generate drug resistance. Mechanisms of detoxification and antioxidant responses are seen to predominate in the 4XR subnet. Overall the analysis provides a shortlist of strategies for targeting the drug resistant strain. Next, the phenotypic microarray platform was used for screening for growth in Msm in the presence of various drugs. Data analysis and clustering resulted in identification of conditions that lead to phenotypic gain or loss in the 4XR as well as those that lead to differential susceptibility to various drugs. Drugs such as cephalosporins, tobramycin, aminotriazole, phenylarsine oxide, vancomycin and oxycarboxin were also found to inhibit growth in the resistant strain selectively. In other words, the 4XR is found to be collaterally sensitive to these drugs. The top-net formed by the highest differential activity paths, identified from the network described earlier has already indicated the involvement of proteins that generate antioxidant responses. Insights from the two methods, first from the targeted approach and second, from the phenotypic discovery approach were combined together to select only those compounds to which the 4XR strain was collaterally sensitive and targeted proteins responsible for antioxidant responses. These compounds are vancomycin, phenylarsine oxide, ebselen and clofazimine. These were further tested against the virulent M. tuberculosis H37Rv strain in a collaborator‘s laboratory. 3 of these compounds such as vancomycin, ebselen and phenylarsine oxide were found to be highly active in combinations with isoniazid against all tested Mtb strains, showed high levels of inhibition against H37Rv and 3 different single drug resistant, MDR and XDR strains. Moreover, they were observed to be highly potent when given in combinations. Clofazimine on the other hand, in combination with isoniazid showed activity but no significant synergy in the virulent drug-resistant strains of M. tuberculosis though synergistic to the sensitive strain. Thus, experiments with M. tuberculosis provide empirical proof that four different compounds, all capable of blocking antioxidant responses, are capable of inhibiting growth of single-, multiple- and extremely-drug-resistant clinical isolates of M. tuberculosis. Using transcriptome data from literature for M. tuberculosis exposed to six different drugs, similar drug specific response networks were constructed. These networks indicate differences in the cellular response to different drugs. Interestingly, the analysis suggests that different drug targets and hence different drugs could trigger drug resistance to various extents, leading to the possibility of prioritizing drug targets based on their resistance evolvability. An earlier study from the laboratory suggested the concept of target-co-target pairs, where-in the co-target could be a key protein in mediating drug resistance for that particular drug and hence for its target protein. Top ranked hubs in multiple drug specific networks such as PolA, FadD1, CydA, a monoxygenase and GltS, can possibly serve as co-targets. Simultaneous inhibition of the co-target along with the primary target could lower the chances of emergence of drug resistance. Such analyses of drug specific networks provide insights about possible routes of communication in the cell leading to drug resistance and strategies to inhibit such communication to retard emergence of drug resistance. Since mutations in the target proteins are known to form an important mechanism by which resistant strains emerge, an understanding of the nature of mutations in different drug targets and how they achieve resistance is crucial. Sequence as well as structural bases for the resistance from known drug-resistant mutants in different drug targets is deciphered and then positions amenable to such mutations are predicted in each target. Mutational indices of individual residues in each target structure are computed based on sequence conservation. Saturated mutagenesis is performed in silico and structural stability analysis of the target proteins has been carried out. Critical insights were obtained in terms of which amino acid positions are prone to acquiring mutations. This in turn suggests interactions that are not desirable, thus can be translated into guidelines for modifying the existing drugs as well as for designing new drugs. Finally, the work presented here describes application of the systems biology approaches to understand the underlying mechanisms of drug resistance, which has provided insights for drug discovery on multiple fronts though target identification, target prioritization and identification of co-targets. In particular, the work has led to a rational exploration of collateral drug sensitivity and cross-resistance of the drug-resistant strain to other compounds. Combinations of such compounds with isoniazid were first identified in the M. smegmatis model system and later tested to hold good for the virulent M. tuberculosis strain, in a collaborative study. The combinations were found to be active against three different clinical drug-resistant isolates of M. tuberculosis. Therefore, this study not only reveals the global view of resistance mechanisms but also identifies synergistic combinations of promising drug candidates based on the learnt mechanisms, demonstrating a possible route to exploring drug repurposing. The combinations are seen to work at a much reduced dosage as compared to the conventional tuberculosis drug regimens, indicating that the toxicity and any associated adverse effects may be greatly reduced, suggesting that the combinations may have a high chance to succeed in the next steps of the drug discovery pipeline.

A biodiversidade de microrganismos encontrados nos ecossistemas constitui excelentes fontes para a descoberta de moléculas farmacologicamente ativas. Neste estudo, 32 isolados de actinobactérias coletadas do solo e 51 isolados de fungos de manguezais da costa brasileira foram avaliados quanto à ação antifúngica, antimicobacteriana, leishmanicida e tripanossomicida. Extratos orgânicos obtidos a partir do sobrenadante da cultura dos isolados foram testados e cinco apresentaram concentrações inibitórias mínimas iguais ou inferiores a 400 mg/mL sobre fungos patogênicos e dois demonstraram expressiva ação contra a forma tripomastigota de Trypanosoma cruzi. Para a forma promastigota de Leishmania amazonensis e Mycobacterium tuberculosis H37Rv, os extratos não foram efetivos. Os resultados indicam que fungos isolados de manguezais representam boas perspectivas na investigação de novos agentes antimicrobianos. / The biodiversity of microorganisms found in the ecosystems provide excellent perspectives for the discovery of pharmacologically active molecules. In this study, 32 actinobacteria from the soil and 51 fungi from the mangrove swamps of the Brazilian coast were analyzed with respect to their antifungal, antimycobacterial, leishmanicidal and trypanocidal actions. Organic extracts from the supernatant of the culture of the microorganisms were analyzed and five extracts presented MICs equal or less than 400 mg/mL over the pathogenic fungi and two presented significant action against the trypomastigote of Trypanosoma cruzi. The results indicate that fungi from mangrove swamps present promising perspectives for the research of new antimicrobial agents.

Considerando que os meios de cultura e as condições de incubação são os principais fatores para o sucesso do primo isolamento, além do método de descontaminação, quatro meios de cultura e três condições de incubação foram investigados. Noventa e sete amostras de lesões granulomatosas foram submetidas ao método de descontaminação com cloreto de 1-hexadecilpiridinio (HPC) a 1,5%, e semeadas em dois meios a base de ovo, Stonebrink e Löwenstein-Jensen com piruvato de sódio, e em dois meios a base de ágar, B83 e Middlebrook 7H11. Cada meio foi incubado a 37ºC por 90 dias em três condições de incubação, atmosfera com 10% de CO2, atmosfera normal e atmosfera com suposta tensão de CO2 obtida pela queima do algodão hidrófobo e fechamento do tubo com rolha de cortiça. O tipo de condição de incubação utilizado teve influência nos meios a base de ovo apenas no inicio da incubação (30 dias), mas nenhuma nos meios a base de ágar. A incubação em atmosfera com 10% de CO2 diminuiu o tempo de aparecimento da primeira colônia e aumentou o número de UFC. O meio B83 foi mais rápido no aparecimento das colônias e teve o maior sucesso de isolamento aos 30 dias, mas não houve diferença com os meios Stonebrink e Löwenstein-Jensen com piruvato, no sucesso de isolamento e número de UFC aos 60 e 90 dias. De acordo com os dados, em sete oportunidades houve isolamento de M. bovis apenas no meio de Stonebrink e em quatro apenas no B83, assim, sugere-se a utilização desses dois meios de cultura em paralelo, incubados em atmosfera com acréscimo de CO2 / Considering that the culture media and the incubation conditions are the main factors for the success of primary isolation, besides the decontamination procedure, four culture media and three incubation conditions were investigated. Ninety-seven samples of granulommatous lesions were submitted to the decontamination procedure by 1-hexadecylpyridinium chloride at 1,5% w/v, and inoculated on two egg-based media, Stonebrink and Löwenstein-Jensen with sodium pyruvate, and two agar-based media, B83 and Middlebrook 7H11. Each medium was incubated at 37ºC for 90 days in three incubation conditions, in air containing 10% CO2, in air, and in air with a supposed higher CO2 tension created by burning the hydrophobic cotton used to close the tubes and subsequently closing with a cork. The type of incubation condition used had influence on the egg-based media only at the beginning of incubation (30 days), but none on the agar-based media. The incubation in air containing 10% CO2 decreased the time to first appearance of colonies and increased the number of colonies. B83 medium showed a faster growth and detected more isolates at 30 days of incubation. However, there was no difference between B83, Stonebrink and Löwenstein-Jensen with pyruvate at 60 and 90 days of incubation. According to the data, seven M. bovis isolates grew only on Stonebrink and four only on B83, therefore, the use of both media, in parallel, incubated in air containing CO2 is suggested.

A legislação permite o uso de leite cru para fabricar queijos com maturação superior a 60 dias em temperatura acima de 5°C, mas falta comprovação científica sólida sobre a eficácia desse processo quanto à inativação de importantes patógenos que podem estar presentes no leite, como o Mycobacterium bovis; além disso, não há metodologia oficial para pesquisa deste agente em alimentos. Desta forma, este trabalho se propôs a estabelecer um protocolo para estudar a curva de inativação do Mycobacterium bovis durante a cura do queijo. Foram fabricadas três partidas de queijo do tipo parmesão com leite pasteurizado e contaminado com uma cepa de Mycobacterium bovis isolada de bovinos abatidos no estado de São Paulo. O queijo foi curado a 18°C e analisado semanalmente até o 63ºdia. As amostras foram submetidas à diluição decimal seriada, semeadas em duplicata em meio Stonebrink-Leslie, acrescido de antibióticos, e incubadas a 37°C por 45 dias. Os resultados de um queijo foram perdidos por contaminação por fungos. O valor D18°C médio, ponderado pelas incertezas, foi de 37,5 dias ± 5,3 dias. Esse resultado indica a necessidade de outros estudos para ampliar o número de queijos estudados e obter, portanto, um resultado mais representativo do efeito da cura sobre o decaimento da população de M. bovis. Há também necessidade de melhorar o poder inibitório do meio de cultura para evitar perdas devido ao crescimento de fungos. / The legislation that regulates the specific conditions for the consumption of food allows the use of raw milk to produce cheese matured over 60 days at temperatures above 5°C; however, the effectiveness of this process in the inactivation of important pathogens that may be present in milk, such as Mycobacterium bovis, lacks solid scientific evidence. In addition, there is no official methodology for the research of this pathogen in foods. Considering that context, this study proposes to establish a protocol to study the inactivation curve of Mycobacterium bovis during cheese curing. Three matches were made with parmesan cheese and pasteurized milk contaminated with a strain of Mycobacterium bovis isolated from cattle slaughtered in the state of São Paulo. The cheese was cured at 18°C and analyzed weekly until the 63th day. The samples were submitted to decimal serial dilution, plated in duplicate in the Middle Stonebrink-Leslie, plus antibiotics, and incubated at 37° C for 45 days. The results of a single cheese were lost to fungal contamination. The value D 18°C average, weighted by the uncertainties, was 37.5 days ±5.3 days. This result indicates the need for further studies to expand the number of cheeses studied and to therefore obtain a more representative result of the effect of healing on the decay of the population of M. bovis. There is also the need to improve the inhibiting power of the culture medium to avoid losses due to fungal growth.

Made available in DSpace on 2014-08-20T13:32:45Z (GMT). No. of bitstreams: 1 tese_daniela_fernandes_ramos.pdf: 1004504 bytes, checksum: d8fd2e285277928c8af06e08c3527471 (MD5) Previous issue date: 2012-11-30 / Bovine tuberculosis (BTB) caused by Mycobacterium bovis is an infectious disease of zoonotic which mainly affects cattle and buffaloes, and cause economic losses in the production of meat and milk in many countries. In Brazil, the official rates are at 1.3% of the national herd infected, corresponding to approximately 2.5 million animals. To contribute to the control of BTB, many molecular techniques have been developed in order to differentiate isolates and establish epidemiological correlations between them. Among these techniques, the most used are the Restriction Fragment Lenght Polymorphism (RFLP), Polymorphic Guanine-cytosine-Rich Sequence [1], Spoligotyping [2], Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeat (MIRU-VNTR) and Exact Tandem Repeat [3]. The spoligotyping and MIRU-VNTR are today considered standard methods of molecular techniques for typing of M. bovis. Both are based on PCR techniques that evaluate polymorphism in the number of repeat sequences present in the genome. Taking into account that the molecular characterization enables to increase our knowledge on the epidemiology of M. bovis and in tuberculosis control, this study aimed at the molecular characterization of isolates of M. bovis in the north and south of the Brazil, by isolating agent, identification of M. bovis by amplification of the region RD7 Multiplex PCR and genotyping using the techniques of spoligotyping, MIRU-VNTR and ETR. Nine-nine lymph nodes were collected from beef cattle in the north of the region and 162 dairy cattle in southern Brazil, and only 10 samples were positive for M. bovis in the north and 85 in the south region. Through analysis of molecular combination of spoligotyping and VNTR was possible to identify different genotypic patterns in the regions studied demonstrating the genetic diversity of M. bovis in our country. / A tuberculose bovina (BTB) causada pelo Mycobacterium bovis é uma doença infecto-contagiosa de caráter zoonótico que acomete principalmente bovinos e bubalinos, e causa prejuízos econômicos na produção de carne e leite em muitos países. No Brasil, os índices oficiais estão em 1,3% do rebanho nacional infectado, correspondendo a, aproximadamente, 2,5 milhões de animais. Visando contribuir para o controle da BTB, muitas técnicas moleculares vêm sendo desenvolvidas com o objetivo de diferenciar isolados e estabelecer correlações epidemiológicas entre eles. Dentre essas técnicas, as mais usadas são o Restriction Fragment Lenght Polymorphism (RFLP), Polymorphic Guanine-cytosine-Rich Sequence [1], Spoligotyping [2], Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeat (MIRU-VNTR) e Exact Tandem Repeat [3]. O spoligotyping e MIRU-VNTR são, hoje, considerados métodos padrões de técnicas moleculares para tipagem de M. bovis. Ambas são técnicas baseadas em PCR que avaliam o polimorfismo do número de sequências repetidas presentes no genoma. Levando em conta que a caracterização molecular possibilita aumentar nosso conhecimento na epidemiologia do M. bovis e no controle da tuberculose, este trabalho teve como objetivo a caracterização molecular de isolados de M. bovis da região norte e sul do Brasil, através do isolamento do agente, identificação de M. bovis pela amplificação da região RD7 por PCR Multiplex e genotipagem usando as técnicas de spoligotyping, MIRU-VNTR e ETR. Foram coletadas 99 linfonodos de bovinos de corte da região norte e 162 de bovinos de leite da região sul do Brasil, sendo que apenas 10 amostras foram positivas para M. bovis no norte e 85 na região sul. Através da análise molecular da combinação de spoligotyping e VNTR foi possível identificar diferentes padrões genotípicos nas regiões estudas demonstrando a diversidade genética de M. bovis no nosso país.

Submitted by Jaqueline Silva (jtas29@gmail.com) on 2014-10-23T20:48:04Z No. of bitstreams: 2 Dissertação - Fábio Muniz de Oliveira - 2014.pdf: 12287155 bytes, checksum: 58eb4d1e227a17283f27cf610577402a (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Jaqueline Silva (jtas29@gmail.com) on 2014-10-23T20:49:02Z (GMT) No. of bitstreams: 2 Dissertação - Fábio Muniz de Oliveira - 2014.pdf: 12287155 bytes, checksum: 58eb4d1e227a17283f27cf610577402a (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-10-23T20:49:02Z (GMT). No. of bitstreams: 2 Dissertação - Fábio Muniz de Oliveira - 2014.pdf: 12287155 bytes, checksum: 58eb4d1e227a17283f27cf610577402a (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-02-28 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / For hundreds years tuberculosis (TB), a contagious disease caused by Mycobacterium tuberculosis (Mtb), has been a global public health problem. Even after the development of the vaccine BCG, in 1921, tuberculosis control continues on slow pace. This comes to be as a result of the variable efficacy (from 0 to 80%) presented by the vaccine in the protection against TB in adults. Therefore, the development of a new vaccine against TB is necessary. In this study, it was evaluated a recombinant vaccine composed of Mycobacterium smegmatis expressing the CMX fusion protein (mc2- CMX), formed from three antigen epitopes of Mtb: Ag85C, MPT51 and HspX. M. smegmatis mc2 155 was transformed with pLA71-CMX by electroporation, and the presence of the CMX protein was confirmed by imuno blotting. BALB/c mice were distributed in four groups: saline, infection, BCG and mc2-CMX. The groups were immunized with their respective vaccines in two moments with an interval of fifteen days and the animal blood was collected fifteen days after the last immunization. Thirty days after the last immunization, the animals were challenged with Mtb H37Rv (intravenously) and thirty days after the challenge, the blood was collected to perform ELISA test. Seventy days after the challenge, the lungs from all mice were collected to obtain cells for flow-cytometry, histological analysis and also to determine the bacillary burden. The immunization with mc2-CMX induced higher levels of antibodies of IgG1 (1,910±0,70) and IgG2a (0,139±0,020) class anti-CMX when compared with BCG group (0,646±0,19 and 0,413±0,24; respectively, p<0,05). These results demonstrated the relevance of CMX antigen in the immunogenicity of the recombinant vaccine. Seventy days after the challenge, the amount of T CD4 cells in the lung producing Th1- type cytokines was assessed. It was observed a significant increase in the percentage of T CD4 cells positive for IFN-γ and TNF-α in the immunized mice with mc2-CMX vaccine, when compared with the group immunized with BCG. Mice challenged with Mtb presented significant higher percentage of IL-2 producer cells when compared with the non-immunized group. However, only the mice immunized with the vaccine mc2- CMX presented significant higher percentage when compared with the infection group. The immune response induced by the vaccine was effective in the control of Mtb infection, confirmed by the histological analysis and the bacillar burden determined. The groups vaccinated with mc2-CMX and BCG presented a significant reduction of the lung lesion induced by the Mtb infection, and also lung bacterial load, when compared with the infection group. Thus, the recombinant vaccine mc2-CMX presents potential characteristics to be used in the prevention of TB. / Há séculos a tuberculose (TB), doença infectocontagiosa causada por Mycobacterium tuberculosis (Mtb), vem sendo um problema de saúde pública mundial. Mesmo após o surgimento da vacina BCG em 1921, o controle da tuberculose continua a passos lentos. Isso se deve à eficácia variável de 0 a 80% apresentada pela vacina na proteção contra TB em indivíduos adultos. Deste modo, o desenvolvimento de uma nova vacina contra a TB é necessário. Neste estudo, avaliou-se uma vacina recombinante composta por Mycobacterium smegmatis expressando a proteína de fusão CMX (mc2-CMX), formada por três antígenos do Mtb: Ag85C, MPT51 e HspX. M. smegmatis mc2 155 foi transformado com pLA71-CMX por eletroporação, sendo a expressão da proteína CMX confirmada por imunoblot. Camundongos BALB/c foram distribuídos em quatro grupos: salina, infecção, BCG e mc2-CMX. Os grupos foram imunizados com suas respectivas vacinas em dois momentos com intervalos de 15 dias, e o sangue de todos os animais coletado quinze dias após a última imunização. Trinta dias após a imunização, os animais foram desafiados com Mtb H37Rv (via endovenosa) e trinta dias após o desafio, o sangue foi coletado para realização de ELISA. Setenta dias após desafio, o pulmão e o baço de todos os camundongos foi coletado para obtenção de células para realização de citometria, histopatológico e determinação da carga bacilar. A imunização com o mc2-CMX induziu níveis maiores de anticorpos da classe IgG1 (1,910±0,70) e IgG2a (0,139±0,020) anti-CMX quando comparado com o grupo BCG (0,646±0,19 e 0,413±0,24, respectivamente, p<0,05). Estes resultados demonstram a relevância do antígeno CMX na imunogenicidade da vacina recombinante. Após setenta dias do desafio, a quantidade de células T CD4 produtoras de citocinas do tipo Th1 foi analisada no pulmão. Foi observado um aumento significativo na porcentagem de células T CD4 positivas para IFN-γ e TNF-α nos camundongos imunizados com vacina mc2-CMX, quando comparado com o grupo BCG. Camundongos desafiados com Mtb apresentaram porcentagens maiores de células produtoras de IL-2, quando comparado com o grupo não desafiado. Todavia, somente os camundongos imunizados com a vacina mc2-CMX apresentaram porcentagens significativamente maiores em comparação ao grupo infecção. A resposta imune observada foi efetiva no controle da infecção por Mtb, sendo isto confirmado quando os pulmões dos camundongos foram analisados histologicamente e a carga bacilar determinada. Os grupos vacinados com as vacinas mc2-CMX e BCG apresentaram uma redução significativa da lesão pulmonar induzida pela infecção por Mtb, e também da carga bacilar no pulmão, quando comparados com o grupo infecção. Conclui-se que mc2-CMX tem um bom potencial para ser explorado como vacina contra a TB.