The pathogenic bacterium Mycobacterium tuberculosis (Mt) is the causative agent of tuberculosis, a widespread and fatal infectious disease. Today, treatment against tuberculosis involves a combination of drugs, which need to be taken for at least six months and which often causes severe side effects. Therefore, new drugs that are more effective and that give fewer side effects are needed. A characteristic feature of the Mt bacterium is its very complex and thick cell wall, which prevents many potential drug molecules from penetrating it. Inhibiting any one of the enzymes that are involved in its biosynthesis would therefore seem to be a good strategy for eliminating the Mt bacteria. The aim of this study was to characterize four enzymes involved in Mt cell wall biosynthesis. In order to do that, they were produced recombinantly in E. coli and purified. Crystallization experiments were set up in order to produce diffracting crystals, with the aim of structure determination and drug design.

Mycobacterium tuberculosis (Mtb), a pathogenic bacterium, is the causative agent in the vast majority of human tuberculosis (TB) cases. Nearly one-third of the world’s population has been affected by TB and annually two million deaths result from the disease. Because of the high cost of medication for a long term treatment with multiple drugs and the increase of multidrug-resistant Mtb strains, faster-acting drugs and more effective vaccines are urgently demanded. Several metabolic pathways of Mtb are attractive for identifying novel drug targets against TB. Hence, a high quality genome-scale metabolic network of Mtb (HQMtb) was reconstructed to investigate its whole metabolism and explore for new drug targets. The HQMtb metabolic network was constructed using an unbiased approach by extracting gene annotation information from various databases and consolidating the data with information from literature. The HQMtb consists of 686 genes, 607 intracellular reactions, 734 metabolites and 471 E.C. numbers, 27 of which are incomplete. The HQMtb was compared with two recently published Mtb metabolic models, GSMN-TB by Beste et al. and iNJ661 model by Jamshidi and Palsson. Due to the different reconstruction methods used, the three models have different characteristics. The 68 new genes and 80 new E.C. numbers were found only in the HQMtb and resulting in approximately 52 new metabolic reactions located in various metabolic pathways, for example biosynthesis of steroid, fatty acid metabolism, and TCA cycle. Through a comparison of HQMtb with a previously published human metabolic network (EHMN) in terms of protein signatures, 42 Mtb metabolic genes were proposed as new drug targets based on two criteria: (a) their protein functional sites do not match with any human protein functional sites; (b) they are essential genes. Interestingly, 13 of them are found in a list of current validated drug targets. Among all proposed drug targets, Rv0189c, Rv3001c and Rv3607c are of interest to be tested in the laboratory because they were also proposed as drug target candidates from two research groups using different methods.

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Introduction: In recent years, there has been growing interest in regulation of gene expression by small non-coding RNA (sRNA). The first sRNA discovered in 1960s was 6S RNA from E. coli (length ~184 nt). It took ~ 30 years to obtain meaningful insights into its function. 6S RNA binds during stationary phase to RNA polymerase (RNAP) containing sigma factor 70 (primary sigma factor), thereby preventing transcription from σ70 - dependent promoters. In our laboratory we discovered a small RNA (length ~300 nt) in stationary phase of growht in Mycobacterium smegmatis. This sRNA was named Ms 1. The function of Ms 1 is uknown and preliminary experiments indicated that Ms 1may bind to RNAP that lacks σ factor (σA ). Goals: The aim of this Diploma project is to contribute to the characterization of Ms 1. Approaches: First, by molecular cloning, affinity chromatography and in vitro transcription I prepared the tools for subsequent experiments in vitro: RNAP, σA , Ms 1 and its mutated variants. Next, these tools were used for binding experiments on native gels and for transcription experiments. Results: RNAP, σA , Ms 1 and its variants were prepared. In vitro binding assays showed that wt Ms 1 but not a mutated variant of Ms 1 binds to RNAP. Using this assays were identified areas of Ms 1 that are important...

Charles University in Prague Faculty of Pharmacy in Hradec Králové Department of Biochemical Sciences Candidate: Kateřina Šedivá Supervisor: Mgr. Eva Novotná, Ph.D. Title of diploma thesis: Cloning, expression and purification of mycobacterial dihydrofolate reductase Dihydrofolate reductase is an enzyme essential for the metabolism of folic acid - it catalyzes the reduction of dihydrofolate to tetrahydrofolate. Tetrahydrofolate is an important cofactor involved in one-cabron transfer reactions. Dihydrofolate reductase plays a key role in the synthesis of DNA, RNA and proteins. Dihydrofolate reductase was also found in M. tuberculosis. This bacterium is the most common causative agent of tuberculosis in humans. Thus dihydrofolate reductase could be a potential target for the design of new antituberculotics. The recombinant protein dihydrofolate reductase was prepared in several steps. The coding sequence of the protein was first amplified by polymerase chain reaction. A recombinant plasmid, obtained by the ligation of an amplified segment of DNA with plasmid pET-28b(+), was transformed into competent cells E. coli strain BH101 by the heat shock method. Cells E. coli strain BL21(DE3) were used for the protein expression. The expression was induced by the addition of isopropyl-β-D-...

Describe la epidemiologia molecular de las cepas circulantes de Mycobacterium tuberculosis mediante PCR en tiempo real y análisis de alta resolución en especímenes clínicos del Hospital Nacional Arzobispo Loayza.

Doctor of Philosophy / Department of Chemistry / Stefan H. Bossmann / Porin A from Mycobacterial smegmatis (MspA) is an octameric trans-membrane channel protein and is one of the most stable porins known to date. MspA has been successfully isolated and purified to obtain liquid extracts and crystals using a modified extraction procedure. A full analytical assessment has been carried out to authenticate its’ structure, including gel electrophoresis, spectroscopy (fluorescence, UV, FTIR, NMR), HPLC, Bradford protein assay, dynamic light scattering and X-ray crystallography. Nanoscopic vesicle formation of MspA molecules in aqueous media has been thoughroughly investigated. Temperature dependent dynamic light scattering experiments reveal that size of such vesicles is dependent on temperature but is independent of ionic strength of the medium. Zeta potential measurements reveal a steady build up of positive charge on the vesicle surface with increasing temperature. For the first time, wild type (WT) MspA has been utilized as a channel forming agent. This phenomenon has future potential in DNA sequencing and the development of antimycobacterial drugs. Channel activity of WT MspA and mutant A96C MspA has been investigated and has shown to form stable channels across DPhPC lipid bilayers. Blocking of the channel current via external molecules (i.e. channel blocking) is an extremely important process, which helps to evaluate the biosensor ability of the pore. In this regard, two Ruthenium based compounds, Ru(QP-C2)38+ (i.e. RuC2) and Ru(bpy)32+have been successfully employed as channel blocking agents. Both compounds show evidence for channel blocking of WT MspA. However, these results are not reproducible. Three dimensional aggregation behavior of RuC2-MspA vesicles have been thoughroughly investigated. It is evident that addition of RuC2 significantly increases vesicle size and polydispersity of MspA aggregates in solution. The results provide explanations onto the lack of channel blocking ability of MspA by RuC2. Development of a ‘greener’ dye sensitized solar cell with the use of MspA as an electron carrier is investigated for the first time. A series of Ru(II)-phenanthroline-based dyes have been synthesized as non-toxic dyes in this regard. Chemical binding between the dyes and MspA has been achieved successfully. Two types of solar cell prototypes, i.e. TiO2-based (Grätzel type) and FTO-based have been developed and tested. Significant current generation and conversion efficiencies have been achieved for both cell types. This marks the first development of a protein-based photovoltaic device, which has the potential to be developed as a new class of “hybrid soft solar cells”.

Tuberculosis (TB) is a deadly infectious lung disease caused by the pathogenic bacterium Mycobacterium tuberculosis (Mtb). The identification of macrophage signaling proteins exploited by Mtb during infection will enable the development of alternative host-directed therapies (HDT) for TB. HDT strategies will boost host immunity to restrict the intracellular replication of Mtb and therefore hold promise to overcome antimicrobial resistance, a growing crisis in TB therapy. Protein Kinase R (PKR) is a key host sensor that functions in the cellular antiviral response. However, its role in defense against intracellular bacterial pathogens is not clearly defined. Herein, we demonstrate that expression and activation of PKR is upregulated in macrophages infected with Mtb. Immunological profiling of human THP-1 macrophages that overexpress PKR (THP-PKR) showed increased production of IP-10 and reduced production of IL-6, two cytokines that are reported to activate and inhibit IFNy-dependent autophagy, respectively. Indeed, sustained expression and activation of PKR reduced the intracellular survival of Mtb, an effect that could be enhanced by IFNy treatment. We further demonstrate that the enhanced anti-mycobacterial activity of THP-PKR macrophages is mediated by a mechanism dependent on selective autophagy as indicated by increased levels of LC3-II that colocalize with intracellular Mtb. Consistent with this mechanism, inhibition of autophagolysosome maturation with bafilomycin A1 abrogated the ability of THP-PKR macrophages to limit replication of Mtb, whereas pharmacological activation of autophagy enhanced the anti-mycobacterial effect of PKR overexpression. As such, PKR represents a novel and attractive host target for development of HDT for TB, and our data suggest value in the design of more specific and potent activators of PKR.

Master of Science - Molecular Medicine and Haematology / The completion of the genome sequence of Mycobacterium tuberculosis strain H37Rv revealed that 10% of the coding capacity is devoted to two, large multigene families that are characterised by repeat sequences. These are the PE and PPE families that code for acidic, glycine rich proteins. A subgroup of the PE family is the polymorphic GC rich sequence (PGRS) gene subfamily. Genome comparisons of clinical isolates of M. tuberculosis have confirmed the polymorphic character of some of these genes suggesting they may be analogous to the contingency loci found in other pathogenic bacteria. Certain PE-PGRS proteins play a direct role in virulence in M. marinum, other PE-PGRS genes are cell surface associated, and some PE-PGRS proteins are variable surface antigens, supporting a potential role in host pathogen interactions. A reporter assay designed to investigate mutations in a PE-PGRS repeat-containing sequence was used to assess mutation rates in various M. smegmatis host strains by fluctuation analysis. A wide spectrum of mutations was observed and the evidence suggests that slipped-strand mispairing between proximal and distal PGRS sequences located in cis is the predominant type of mutational event at such loci. Moreover, slipped-strand mispairing at such loci occurs at a moderately higher rate than base substitution mutagenesis and is mediated by the normal replicative polymerase.

Considerando o grave quadro das doenças negligenciadas, no Brasil e no mundo, e as limitações do tratamento empregado, na atualidade, torna-se urgente a pesquisa de novos fármacos, que sejam mais ativos e seguros. Para tanto, a busca de moléculas-protótipo, a partir de espécies vegetais, tem sido importante estratégia. Neste contexto, foi realizado o estudo de Annona crassiflora Mart. (Annonaceae), cujos alcalóides totais (AT) demonstraram promissora atividade antiprotozoária in vitro, em estudo anterior. Em paralelo, outras espécies de Annona mostraram atividade antimicobacteriana in vitro, igualmente, tendo motivado o presente estudo. Cinco das vinte frações alcaloídicas obtidas, por cromatografia em coluna, a partir dos AT das folhas, apresentaram atividade anti-Leishmania in vitro, tendo causado 100% de morte das formas promastigotas de Leishmania (L.) infantum chagasi. Além disto, três delas foram ativas frente ao Mycobacterium tuberculosis. O isolamento de dois alcalóides noraporfínicos foi realizado, por fracionamento biomonitorado em coluna cromatográfica, seguido de cromatografia líquida de alta eficiência (CLAE) semipreparativa. As estruturas dos compostos isolados foram elucidadas empregando-se as análises espectroscópicas de ressonância magnética nuclear, mono e bidimensionais, e por CLAE acoplada à espectrometria de massas (CLAEIES-EM2). Um dos alcalóides foi identificado pela primeira vez, nesta espécie, sendo que o outro apresentou estrutura inédita. Ambos demonstraram significativa atividade anti-Leishmania in vitro (CE50≤ 10 µ g/ mL) frente às formas promastigotas de L. (L.) infantum chagasi [MHOM/BR/1972/LD]. O primeiro teve maior índice de seletividade (IS: 7,4), em relação à citotoxicidade em células do tecido conjuntivo NCTC Clone 929 de camundongos. Frente ao Mycobacterium tuberculosis (ATCC 27294) e ao M. smegmatis (ATCC 35798), os alcalóides isolados foram inativos (CIM ≥ 128 µg/ mL). O óleo volátil das folhas foi analisado por cromatografia gasosa acoplada à espectroscopia de massas (CG-EM), tendo sido identificados 41 constituintes, prevalecendo os sesquiterpenos (81,7%) em relação aos monoterpenos (0,8%). Entre os compostos majoritários encontrados no óleo, citam-se os sesquiterpenos α-amorfeno (43,6%), E-cariofileno (17,7%) e o germacreno (5,3%). Nos testes de atividade anti-Leishmania in vitro frente às formas promastigotas de quatro espécies do parasita, o óleo foi mais ativo em L. (L.) infantum chagasi (CE50: 25,97 µg/ mL). Nas formas tripomastigotas do Trypanosoma cruzi mostrou atividade 8,5 vezes superior àquela do fármaco-padrão benznidazol (CE50: 5,31 µg/ mL). Os resultados obtidos ratificaram a importância da prospecção da flora, em particular de A. crassiflora, como fonte potencial de compostos bioativos, que venham a constituir novos fármacos, como alternativa à restrita terapêutica existente para o tratamento das doenças negligenciadas. / Neglected diseases are a serious health problem in Brazil and worldwide. The available drugs are limited in effectiveness with a high toxicity. There is an urgent need of more safe and bioactive compounds. The search of new molecules from plant species is a well known and important strategy to achieve this goal. In a previous work, Annona crassiflora Mart. (Annonaceae) showed a promising antiprotozoal activity. Beside this, other Annona species presented an interesting antimicobacterial action. In this bio-guided study, after the column fractionation of the leaves total alkaloids, in vitro tests were performed and five from twenty fractions were highly active (100% deaths) against promastigotes of Leishmania (L.) infantum chagasi, and only three were active against Mycobacterium tuberculosis. After purification of the bioactive fractions, two noraporphine alkaloids were isolated by HPLC and identified by the usual mono and bidimensional spectroscopic techniques. One of them was isolated from the first time from this species. The other one is a novel chemical entity. Both compounds presented anti- Leishmania activity (CE50 ≤ 10 µg/ mL) against L. (L.) infantum chagasi [MHOM/BR/1972/LD]. The first one showed a higher selectivity index (SI: 7.4) considering its mice connective tissue cells toxicity [NCTC Clone 929]. However, both were inactive against Mycobacterium tuberculosis (ATCC 27294) and M. smegmatis (ATCC 35798) (CIM ≥ 128 µg/ mL). In the leaves volatile oil 41 compounds were identified. The sesquiterpenes were in majority (81.7%), followed by monoterpenes (0.8%). The sesquiterpenes α-amorphene (43.6%), E-caryophyllene (17.7%) and germacrene (5.3%) were the main constituents. The oil was little effective against the four tested Leishmania species and slightly more active against L. (L.) infantum chagasi (CE50: 25.97 µg/ mL). However, it was highly active against the trypomastigotes of Trypanosoma cruzi (CE50: 5.31 µg/ mL) showing to be 8.5 times more active than benznidazol. These results stimulate a deeper investigation of those alkaloids as antiprotozoal agents, confirming the importance of the plant species metabolites as a source of new bioactive molecules and their potential as future drugs.