In evolution alternative genetic trajectories can potentially lead to similar phenotypic outcomes. However, certain trajectories are preferred over others. These preferences bias the genomes of living organisms and the underlying processes can be observed in ongoing evolution. We have studied a variety of biases that can be found in bacterial chromosomes and determined the selective causes and functional consequences for the cell. We have quantified codon usage bias in highly expressed genes and shown that it is selected to optimise translational speed. We further demonstrated that the resulting differences in decoding speed can be used to regulate gene expression, and that the use of ‘non-optimal’ codons can be detrimental to reading frame maintenance. Biased gene location on the chromosome favours recombination between genes within gene families and leads to co-evolution. We have shown that such recombinational events can protect these gene families from inactivation by mobile genetic elements, and that chromosome organization can be selectively maintained because inversions can lead to the formation of unstable hybrid operons. We have used the development of antibiotic resistance to study how different bacterial lifestyles influence evolutionary trajectories. For this we used two distinct pairs of antibiotics and disease-causing bacteria, namely (i) Mycobacterium tuberculosis that is treated with rifampicin and (ii) Escherichia coli that is treated with ciprofloxacin. We have shown that in the slow-growing Mycobacterium tuberculosis, resistance mutations are selected for high-level resistance. Fitness is initially less important, and over time fitness costs can be ameliorated by compensatory mutations. The need for rapid growth causes the selection of ciprofloxacin resistance in Escherichia coli not only to be selected on the basis of high-level resistance but also on high fitness. Compensatory evolution is therefore not required and is not observed. Taken together, our results show that the evolution of a phenotype is the product of multiple steps and that many factors influence which trajectory is the most likely to occur and be most beneficial. Over time, selection will favour this particular trajectory and lead to biased evolution, affecting genome sequence and organization.

Thesis (PhD)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: The prevalence of multi-drug resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis has been increasing to alarming levels globally. This has been exacerbated by tuberculosis (TB) co-infection with HIV where the epidemic is endemic. South Africa as a developing country is hit hard by TB and efforts to develop TB drugs that are compatible with anti-retroviral medication and also effective against MDR/XDR, could help shorten the treatment duration of the current TB treatment regimens. This thesis presents the identification and characterisation of a novel furanone based compound (F1082) and its derivatives as leads for anti-TB drug development. Furanones are generally known for an array of biological activities ranging from antibacterial, antifungal and antitumor. F1082 has an aromatic benzene structure and was identified from screening synthetic compounds against M. tuberculosis. It is potent against M. tuberculosis at minimum inhibitory concentration (MIC) of 8 μg/ml. It is selective for mycobacteria since it did not inhibit the growth of Gram-positive and Gram-negative bacteria at concentrations five times the MIC for M. tuberculosis. F1082 is generally bacteriostatic around MIC concentrations in its effects against M. tuberculosis however; it may be bactericidal at higher concentrations. It is as effective against MDR, XDR and clinical isolates of M. tuberculosis at the same concentration as the M. tuberculosis H37Rv reference strain. This suggests that F1082 may have a different mechanism of action compared to current TB drugs. It has been shown to have no antagonistic effect with the first-line anti-TB drugs and it has been shown to synergize with rifampicin by reducing the MIC of rifampicin. A drawback of F1082 is that it is cytotoxic to human cell lines, but this is presently being addressed through the synthesis of analogues that have shown improved activity and less cytotoxicity. The synthesis of more than 40 analogues has led to identification of 4 compounds that have more than five times higher activity and more than 100 times less cytotoxicity against human cell-lines. Microarray analyses have identified possible metabolic pathway/s in M. tuberculosis that is/are affected by F1082. One subset of genes which showed the most prominent alteration encodes the siderophores, which are involved with iron homeostasis in the M. tuberculosis bacillus. Of these genes, 7 were of interest (mbtB, mbtC, mbtD, mbtE, mbtF, mbtH and bfrB) as they all fall in the same cluster and are involved in iron acquisition. Due to the involvement of iron we also show that F1082 generates oxidative stress that is metal (iron) dependent. From the results we conclude that F1082 is a promising antituberculosis lead compound with unique target properties and also specificity against mycobacteria. / AFRIKAANSE OPSOMMING: Die voorkoms van veelvuldige middelweerstandige M.tuberculosis (MDR) en uiters middelweerstandige M.tuberculosis (XDR) is besig om toe te neem teen ‘n kommerwekkende tempo wêreldwyd. Hierdie situasie word vererger met die ko-infektering van M.tuberculosis en HIV. Suid- Afrika, as ontwikkelende land, word sleg benadeel met tuberkulose siekte. Antituberkulose middels wat kan saamwerk met bestaande antiretrovirale middels en ook effektief is teen MDR en XDR stamme, kan alles meewerk om die behandelingstyd van tuberkulose te verkort. In hierdie tesis identifiseer en karakteriseer ons ‘n furanoon-gebaseerde verbinding (F1082) en derivate daarvan as voorloper-middels vir anti-tuberkulose middelontwikkeling. Furanone is algemeen bekend vir ‘n verskeidenheid van biologiese aktiwiteite insluitende antibakteriële-, antifungale- en antitumor aktiwiteite. F1082 bevat ‘n aromatiese benseenstruktuur en is oorspronklik geïdentifiseer gedurende die skandering van sintetiese middels teen M.tuberculosis. Dit het ‘n sterk werking teen M.tuberculosis met ‘n minimum inhibitoriese konsentrasie (MIC) van 8ug/ml. Dit is baie selektief vir mikobakterieë aangesien dit nie gram-positiewe of gram-negatiewe bakterieë teen 5 maal die MIC, soos vir M.tuberculosis, geïnhibeer het nie. F1082 is bevind om, by laer konsentrasies, bakteriostaties te wees in sy aktiwiteit teen M.tuberculosis maar by hoër konsentrasies word ‘n meer bakteriosidiese effek waargeneem. F1082 is effektief teen MDR, XDR en kliniese isolate van M.tuberculosis en teen dieselfde konsentrasie soos vir die M. tuberculosis H37Rv verwysingstam waargeneem is. Dit impliseer dat F1082 dalk ‘n alternatiewe meganisme van werking het in vergelyking met die van die huidige TB teenmiddels. F1082 toon geen antagonistiese werking in kombinasie met die voorste anti- TB middels nie, maar toon wel sinergistiese werking in kombinasie met rifampisien. F1082 toon nog sitotoksiese aktiwiteit teenoor menslike sellyne, maar die sintese van derivate van F1082 toon tot dusvêr groter anti-TB aktiwiteit en verminderde sitotoksisiteit. Die sintese van meer as 40 homoloë het gelei tot die identifisering van vier verbindings met vyf keer hoër anti-TB aktiwiteit en honderd keer verminderde sitotoksisiteit teen menslike sellyne as F1082 self. “Microarray” ontledings het ‘n aantal metabolise paaie geïdentifiseer waar F1082 ‘n effek kan uitoefen. Een stel gene wat die mees uitstaande effek toon kodeer vir siderofore wat betrokke is by yster homeostase in M.tuberculosis. Van hierdie gene was daar sewe van belang omdat hulle in dieselfde groep voorkom en almal betrokke is by ysteropname (mbtB, mbtC, mbtD, mbtE, mbtF, mbtH, bfrB). Weens die rol wat F1082 in ysterhomeostase speel, toon ons ook dat F1082 intrasellulêre oksidatiewe stres bevorder wat yster afhanklik is. Al ons resultate dui daarop dat F1082 ‘n belowende ant-TB voorloper verbinding is met spesifisiteit teen M.tb en unieke teikeneienskappe in M. tuberculosis.

Thesis (MScMedSc)--Stellenbosch University, 2012. / Bibliography / ENGLISH ABSTRACT: Evidence suggests that biological mechanisms, such as energy dependant efflux pumps, in addition to the rpoB gene mutations, define the level of rifampicin (RIF) resistance in drug resistant Mycobacterium tuberculosis (M. tuberculosis) strains with similar genetic backgrounds. Additionally, proteomic studies showed up-regulation of components of F1F0-ATP synthase enzyme, encoded by the atpBEFHAGDC operon which is responsible for ATP production, in response to RIF. The hypothesis of the current study is that the exposure of a multi-drug resistant (MDR) M. tuberculosis strain to RIF leads to the initiation of a signalling cascade of events. This results in the increased expression of F1F0-ATP synthase leading to an increase in energy production and subsequent activation of efflux pumps. RIF will thus be actively extruded from the cell, increasing the level of RIF resistance. This study aims to identify genetic regions responsible for the regulation of expression of the atpBEFHAGDC operon. Additionally we aim to identify other novel mechanisms contributing to the level of RIF resistance in M. tuberculosis. A specialised reporter vector was constructed to monitor the expression of atpBEFHAGDC, with the use of a fluorescent protein. Subsequently a library of random knockouts was created by transposon mutagenesis in order to identify possible regulators, as well as novel mechanisms contributing to RIF resistance. Two hypothetical proteins, Rv2005c and Rv2417c, were identified in M. tuberculosis transposon mutants showing decreased fluorescence correlating to decreased expression of atpBEFHAGDC. Rv2005c encodes a universal stress protein, suggesting its potential role in a signalling cascade initiated upon RIF exposure. In a model pathway of regulation we propose that the product of Rv2005c is responsible for releasing a repressor protein, Rv1049, thereby stimulating a cascade of signalling events resulting in the up-regulation of atpBEFHAGDC. This increase in ATP production thereby fuels the extrusion of RIF from the cell via efflux pumps. In addition, it was found that disruptions in Rv2524c (fatty acid synthase), Rv1048c (hypothetical protein) and Rv3163c (probable conserved secreted protein) resulted in an increase in the level of RIF resistance in a RIF resistant clinical isolate. Interestingly, Rv2524c also showed to have a potential role in regulation of atpBEFHAGDC, whereby it ensures the repression of atpBEFHAGDC. Another gene identified to be involved in the increase in RIF resistance, Rv0260c, is annotated as a possible transcriptional regulator. This study was successful in identifying possible regulatory proteins involved in regulation of the F1F0-ATP synthase in response to RIF, and highlights the complexity of the regulatory events that occur in response to RIF in a MDR M. tuberculosis strain. This study was also successful in identifying candidates for functional analysis to determine novel mechanisms contributing to the level of RIF resistance in M. tuberculosis. Together these findings demonstrate that RIF resistance in M. tuberculosis is more complex than originally thought. Considering that anti-Tuberculosis (TB) drug TMC207 targets the F1F0-ATP synthase, a key enzyme in the production of energy in mycobacteria, the newly identified regulatory genes of F1F0-ATP synthase may represent ideal targets for novel anti-TB drug design. / AFRIKAANSE OPSOMMING: Huidige dogma toon dat mutasies in die rpoB geen vir rifampicin (RIF) weerstandigheid in Mycobacterium tuberculosis (M. tuberculosis) verantwoordelik is. Onlangs is egter bevind dat ander biologiese meganismes, soos energie afhanklike membraanpompe, saam met mutasies in hierdie geen, die verskillende vlakke van RIF weerstandigheid in M. tuberculosis isolate met soortgelyke genetiese agtergrond kan verklaar. Addisionele proteïen studies het gewys dat die komponente van die F1F0-ATP sintase ensiem, wat verantwoordelik vir ATP sintese is en gekodeer word deur die atpBEFHAGDC operon, opgereguleer word na RIF blootstelling. Die hipotese van hierdie studie is dat blootstelling van ‘n multi-middelweerstandige M. tuberculosis isolaat aan RIF aanleiding sal gee tot ʼn aanvanklike sein wat dan verskeie ander biologiese paaie sal aanskakel. Hierdie gebeure sal dan lei tot ‘n verhoging in geenuitdrukking van die F1F0-ATP sintase operon met gevolglike verhoging in energie produksie, wat uiteindelik energie afhanklike membraan pompe sal aanskakel. Die aktiewe uitpomp van RIF uit die sel sal dan ʼn verhoging in die vlak van RIF weerstandigheid veroorsaak. Die eerste doel van hierdie studie is om genetiese areas te identifiseer wat verantwoordelik is vir die regulering van geenuitdrukking van die atpBEFHAGDC operon. Die tweede doel is om nuwe meganismes te identifiseer wat verskille in die vlakke van RIF weerstandigheid in verskillende nou verwante kliniese isolate sal verklaar. ʼn Gespesialiseerde vektor wat die geenuitdrukking van die atpBEFHAGDC operon sal monitor is suksesvol ontwikkel met die gebruik van ʼn fluoresserende proteïen. Daarna is van die transposon mutagenese metode gebruik gemaak om ʼn biblioteek van ewekansige geenuitlatings te maak en hierdie biblioteek is dan gebruik om nuwe meganismes van RIF weerstandigheid te ondersoek. Hierdie studie het twee hipotetiese proteïene, Rv2005c en Rv2417c, in M. tuberculosis transposon mutante geïdentifiseer wat verantwoordelik is vir verlaagde fluoressensie. Dit korreleer met die verwagte verlaagde geenuitdrukking van atpBEFHAGDC. Die geen Rv2005c kodeer vir ʼn universele spanningsproteïen en die resultaat voorspel dat Rv2005c ʼn potensiële rol het om ʼn netwerk van seine in die bakterium aan te skakel direk na blootstelling aan RIF. In ʼn voorgestelde model van regulerende paaie voorspel ons dat die produk van Rv2005c verantwoordelik is vir die vrystelling van ʼn onderdrukker proteïen, Rv1049. Dit lei dan tot die stimulering van ʼn netwerk van intrasellulêre seine wat aanleiding gee tot die opregulering van atpBEFHAFDC. Die opregulering van atpBEFHAFDC sal dan aanleiding gee tot ʼn verhoging in ATP produksie wat die uitpomp van RIF uit die sel sal versnel met die gebruik van energie afhanklike membraan pompe. Dit is verder gevind dat uitskakeling van die gene Rv2524c (vetsuur sintase), Rv1048c (hipotetiese proteïen) en Rv3163c (moontlike konserwatiewe uitskei proteïen) aanleiding gegee het tot die verhoging in die vlakke van RIF weerstandigheid in ʼn RIF weerstandige kliniese isolaat. In die studie is ook bewys dat Rv2524c ʼn potensiële rol in die regulering van atpBEFHAGDC het deurdat dit die onderdrukking van atpBEFHAGDC verseker. Rv0260c is voorheen gelys as ʼn moontlike transkripsionele reguleerder wat betrokke is by die verhoging van RIF weerstandigheid. Hierdie studie was suksesvol in die identifisering van moontlike gene en proteïne wat betrokke is in die regulering van die F1F0-ATP sintase in reaksie tot RIF blootstelling. Dit beklemtoon die kompleksiteit van die regulerende gebeurtenisse wat plaasvind in reaksie tot RIF blootstelling in ʼn multi-middelweerstandige M. tuberculosis isolaat. Verder was daar suksesvol kandidaat gene en ʼn reguleerder geïdentifiseer wat in toekomstige studies ondersoek kan word vir hulle funksionele bydrae om nuwe meganismes te vind wat die varierende vlakke van RIF weerstandigheid in M. tuberculosis sal verklaar. Opsommend demonstreer hierdie studie dat RIF weerstandigheid meer kompleks is as wat voorheen aangeneem was. Die nuwe baie belowende teen-Tuberkulose middel, TMC207, se aanslag is gemik op die belangrike ensiem (F1F0-ATP sintase) wat in hierdie studie ondersoek was. Dus kan nuut geïdentifiseerde proteïene wat betrokke is by die regulering van hierdie ensiem beskou word as ideale kandidate vir die ontwikkeling van nuwe teen -Tuberkulosemiddels. / The National Research Foundation and the Department of Biomedical Sciences

Thesis (MScMedSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Anti-tuberculosis drugs target specific essential cellular processes and structural components. The first line drug, rifampicin (RIF) is a RNA polymerase inhibitor which targets the β-subunit and subsequently inhibits the initiation of transcription. Previous proteomic and transcriptomic analyses have shown that exposure to RIF for 24hrs significantly increased the abundance of proteins involved in energy metabolism in clinical isolates. No studies have been done to describe the transcriptional responses to RIF in an in vitro RIF resistant M. tuberculosis isolate. Application of in vitro mutants is novel since it will exclude most of the confounding factors which may be present in clinical isolates obtained from patients where the bacterium may have been incubated for several weeks or even years. This study aimed to determine the effect of prolonged exposure to RIF and the effect of the rpoB Ser531Leu mutation on the expression of energy metabolism genes, sigma factors and a regulator in RIF mono-resistant in vitro mutants with different levels of RIF resistance (minimum inhibitory concentration (MIC): 40μg/ml and 70μg/ml). RIF mono-resistant in vitro mutants were generated from a pan susceptible Beijing cluster 208 progenitor using the Luria Delbruck assay. In vitro RIF mono-resistant mutants harbouring the Ser531Leu rpoB mutation and which displayed different levels of RIF resistance were selected. To assess the effect of prolonged RIF exposure on the expression of candidate genes, the in vitro mutants were cultured in liquid media and exposed to RIF for 1, 7 and 14 days. High quality RNA was extracted from these cultures at each time point and Real-Time Quantitative Polymerase Chain Reaction (RT-qPCR) was done on the selected candidate genes. The results indicate that limited expression of energy metabolism genes and sigma factors was observed after prolonged RIF exposure. In addition, the activity of the regulator (Rv1846c) was down-regulated in the presence of RIF explaining the up-regulated state of energy metabolism genes. To assess the effect of the rpoB Ser531Leu mutation on the candidate genes, RNA was extracted from the RIF unexposed culture at mid-log phase. RT-qPCR was done for each in vitro mutant in addition to the wild-type progenitor isolate. These results show that energy metabolism genes and sigma factors were significantly up-regulated in the RIF resistant mutantss harbouring an rpoB Ser531Leu mutation. This suggests that the mutation had a significant effect on the cellular energy cost due to the up-regulated state of the energy metabolism genes. In addition, an increase in the expression of sigma factors may be required to compensate for the rpoB mutation by enforcing the binding of the RNA polymerase and sigma factors to the promoter for transcription to be initiated. It is therefore important to assess these candidate genes for their potential as novel candidates for future drug design as this is an important aspect to influence tuberculosis control. / AFRIKAANSE OPSOMMING: Teen-tuberkulose middels teiken essensiële sellulêre prosesse en strukturele komponente. Die eerste linie teen-tuberkulose middel, rifampisien (RIF) is ʼn RNS polimerase inhibeerder wat die β-subeenheid teiken en daarna die inisiasie van transkripsie onderdruk. Vorige proteomiese en transkriptomiese analises het getoon dat blootstelling aan RIF vir 24 uur beduidende styging in sekere protiene wat verband hou met energie metabolisme in kliniese isolate veroorsaak. Die huidige studie poog om die effek van langdurige RIF blootstelling, asook die effek van die rpoB Ser531Leu mutasie op die uitdrukking van energie metabolisme gene, sigma faktore en reguleerders op RIF-enkel weerstandige in vitro mutante by verskillende vlakke van RIF weerstandigheid (Minimum Inhiberende Konsentrasie (MIK): 40μg/ml en 70μg/ml) te ondersoek. RIF-enkelweerstandige in vitro mutante isolate is gegenereer van ʼn sensitiewe Beijing 208 stamfamilielid deur die Luria Delbruck metode. In vitro RIF enkelweerstandige mutante met die rpoB Ser531Leu mutasie en verskillende vlakke van RIF weerstandigheid is geselekteer. Om die langdurige effek van RIF blootstelling op kandidaat geen uitdrukking te ondersoek, is in vitro mutante isolate gegroei in vloeibare medium en blootgestel aan RIF vir 1, 7 en 14 dae. Goeie kwaliteit RNS is geëkstraheer van hierdie kulture by elke tydpunt om Werklike-tyd Kwantitatiewe Polimerase Ketting Reaksie (RT-qPCR) op die kandidaat gene uit te voer. Die resultate toon dat ʼn beperkte aantal energie metabolisme en sigma faktor gene uitgedruk was na RIF blootstelling. Verder is die uitdrukking van die reguleerder (Rv1846c) af gereguleer in die teenwoordigheid van RIF en dit verduidelik die op gereguleerde energie metaboliese geen patroon. Om die effek van die rpoB Ser531Leu mutasie op die kandidaat gene te evalueer, is RNS geëkstraheer van ʼn weerstandige en RIF sensitiewe kultuur wat nie blootgestel was aan RIF nie. RT-qPCR is uit gevoer op elke in vitro mutante isolaat asook op ʼn sensitiewe isolaat sonder ʼn mutasie. Hierdie resultate toon dat energie metabolisme gene en sigma faktore beduidend opreguleer word in die isolate met ʼn rpoB Ser531Leu mutasie. Dit dui daarop dat die mutasie ʼn beduidende effek op die sellulêre energie koste het, omdat die energie metabolisme gene op gereguleer is. Verder kan ʼn toename in die uitdrukking van sigma faktore benodig word om die effek van die rpoB mutasie te oorkom deur binding van die RNS polimerase en die sigma faktore aan die promotor om transkripsie inisiasie te forseer. Dit is daarom belangrik om hierdie kandidaat gene verder te ondersoek vir toekomstige ontwikkeling van teenmiddels teen tuberkulose.

Tuberculosis is an ancient infectious disease and a leading cause of death globally. Preclinical research is important for defining drugs and regimens which should be carried forward to human studies. This thesis aims to characterize the population pharmacokinetics and exposure-response relationships of anti-tubercular drugs alone and in combinations, and to suggest experimental designs for preclinical settings. The population pharmacokinetics of rifampicin, isoniazid, ethambutol and pyrazinamide were described for the first time in two mouse models. This allowed for linking the population pharmacokinetic model to the Multistate Tuberculosis Pharmacometric (MTP) model for biomarker response, which was used to characterize exposure-response relationships in monotherapy. Pharmacodynamic interactions in combination therapies were quantitatively described by linking the MTP model to the General Pharmacodynamic Interaction (GPDI) model, which provided estimates of single drug effects together with a quantitative model-based evaluation framework for evaluation of pharmacodynamic interactions among drugs in combinations. Synergism (more than expected additivity) was characterized between rifampicin and ethambutol, while antagonism (less than expected additivity) was characterized between rifampicin and isoniazid in combination therapies. The new single-dose pharmacokinetic design with enrichened individual sampling was more informative than the original design, in which only one sample was taken from each mouse in the pharmacokinetic studies. The new oral zipper design allows for informative pharmacokinetic sampling in a multiple-dose administration scenario for characterizing pharmacokinetic-pharmacodynamic relationships, with similar or lower bias and imprecision in parameter estimates and with a decreased total number of animals required by up to 7-fold compared to the original design. The optimized design for assessing pharmacodynamic interactions in the combination therapies, which was based on EC20, EC50 and EC80 of the single drug, provided lower bias and imprecision than a conventional reduced four-by-four microdilution checkerboard design at the same total number of samples required, which followed the 3Rs of animal welfare. In summary, in this thesis the population pharmacokinetic-pharmacodynamic models of first-line drugs in mice were characterized through linking each population pharmacokinetic model to the MTP model. Pharmacodynamic interactions were quantitatively illustrated by the MTP-GPDI model. Lastly, experimental designs were optimized and recommended to both pharmacokinetic and pharmacodynamic studies for preclinical settings.

With approximately nine million new cases and the attributable cause of death of an estimated two millions people every year there is an urgent need for new and effective drugs and treatment regimens targeting tuberculosis. The tuberculosis drug development pathway is however not ideal, containing non-predictive model systems and unanswered questions that may increase the risk of failure during late-phase drug development. The aim of this thesis was hence to develop pharmacometric tools in order to optimize the development of new anti-tuberculosis drugs and treatment regimens. The General Pulmonary Distribution model was developed allowing for prediction of both rate and extent of distribution from plasma to pulmonary tissue. A distribution characterization that is of high importance as most current used anti-tuberculosis drugs were introduced into clinical use without considering the pharmacokinetic properties influencing drug distribution to the site of action. The developed optimized bronchoalveolar lavage sampling design provides a simplistic but informative approach to gathering of the data needed to allow for a model based characterization of both rate and extent of pulmonary distribution using as little as one sample per subject. The developed Multistate Tuberculosis Pharmacometric model provides predictions over time for a fast-, slow- and non-multiplying bacterial state with and without drug effect. The Multistate Tuberculosis Pharmacometric model was further used to quantify the in vitro growth of different strains of Mycobacterium tuberculosis and the exposure-response relationships of three first line anti-tuberculosis drugs. The General Pharmacodynamic Interaction model was successfully used to characterize the pharmacodynamic interactions of three first line anti-tuberculosis drugs, showing the possibility of distinguishing drug A’s interaction with drug B from drug B’s interaction with drug A. The successful separation of all three drugs effect on each other is a necessity for future work focusing on optimizing the selection of anti-tuberculosis combination regimens. With a focus on pharmacokinetics and pharmacodynamics, the work included in this thesis provides multiple new methods and approaches that individually, but maybe more important the combination of, has the potential to inform development of new but also to provide additional information of the existing anti-tuberculosis drugs and drug regimen.

La tuberculose est une maladie d'urgence dans le monde, l'apparition de souches résistantes au traitement a produit l'utilisation de produits naturels comme alternative. Des études ont montré que les extraits de Leucophyllum frutescens présentaient un effet antimicrobien, mais l'inconvénient est que les extraits sont récupérés dans un véhicule qui contient des solvants organiques. La préparation de nanoparticules polymériques (NP) implique l'élimination du solvant dans lequel l'actif est solubilisé, ce qui permet les utiliser comme véhicules pour l'administration des extraits. Par conséquent, le but de cette étude a été design et développer des formulations de NP avec un extrait de L. frutescens et de la rifampicine (RIF), afin d'évaluer l'activité biologique in vitro contre M. tuberculosis. Premièrement, l'extrait méthanolique de feuilles et de racines de L. frutescens et ses fractions a été obtenu. L'activité contre M. tuberculosis a été déterminée, l'extrait de racines (EMR) et ses fractions hexanique (FHR et RF1) ont été les plus actives avec une CMI de 100, 40 et 40 μg/mL, respectivement. RIF, EMH, FHR et RF1 ont été incorporés dans NP par nanoprécipitation. Des NP de ≈180 nm avec une distribution de taille homogène ont été obtenus. Les NP ont été évaluées sur M. tuberculosis, les formulations de NP-PLGA-RIF (CMI=0,10 μg/mL) et NP-PLGA-RF1 (CMI=80 μg/mL) ont montré la meilleure activité. Finalement, l'activité des formulations combinées contre M. tuberculosis a été évaluée, la combinaison de RIF avec NP-PLGA-RF1 a produit le meilleur comportement, réduisant la CMI des deux sans montrer un effet toxique. Les études réalisées dans ce travail ont montré l'utilisation potentielle d'une formulation de NP contient une fraction végétale de L. frutescens en combinaison avec le RIF comme alternative contre M. tuberculosis / Tuberculosis is an emergency disease worldwide, the emergence of resistant strains to the treatment has produced the use of natural products as alternative. Studies have shown that Leucophyllum frutescens extracts present antimicrobial effect, but the disadvantage is that the extracts are recovered in a vehicle that contains organic solvents. The preparation of polymeric nanoparticles (NP) involves the elimination of the solvent in which the active is solubilized, which makes possible to use them as vehicles for the administration of the extracts. Therefore, the aim of this study was to design and develop formulations of NP with an extract of L. frutescens, and rifampicin (RIF), in order to evaluate the in vitro biological activity against M. tuberculosis. Firstly, the methanolic extract of leaves and roots of L. frutescens and its fractions were obtained. The anti-M. tuberculosis activity was determined, being the root extract (EMR) and its hexane fractions (FHR and RF1) the most actives with a MIC of 100, 40 and 40 μg/mL, respectively. RIF, EMH, FHR and RF1 were incorporated into NP by nanoprecipitation. NP of ≈180 nm with homogeneous size distribution were obtained. The NP were evaluated on M. tuberculosis, being the formulation of NP-PLGA-RIF (MIC=0.10 μg/mL) and NP-PLGA-RF1 (CMI=80 μg/mL) with better activity. Finally, the anti-M. tuberculosis activity of the combined form formulations was evaluated, the combination of RIF with NP-PLGA-RF1 produced better behavior, reducing the MIC of both without showing toxic effect. The studies carried out in this work showed the potential use of an NP formulation contains a vegetable fraction of L. frutescens in combination with RIF as an alternative against M. tuberculosis

Parkinsons sjukdom (PD) är ett tillstånd som ger en försvårad och försämrad livskvalité. I dagsläget finns det endast symtomatiska läkemedel men ingen bot med vilken sjukdomen upphör eller som bromsar förloppet. Pågående forskningsarbete utgår bland annat från att ta fram nya läkemedel men även också undersöka om redan befintliga läkemedel går att använda som behandling av PD. Många av de redan befintliga läkemedlen som testas är de som har förmågan att påverka proteinet α-synuklein (α-syn) och dess aggregering, som visats vara en central orsak till uppkomsten av PD. I föreliggande litteraturstudie undersöktes på vilket sätt en del läkemedel vars indikation är PD och även andra sjukdomstillstånd såsom astma, påverkar (ex. påskyndar eller inhiberar) in-vitro aggregering av α-syn. Därutöver genomfördes en detaljerad analys av de utvalda läkemedlen och deras effekt på α-syn aggregering utifrån deras kemiska egenskaper med avseende på löslighet (hydrofila, lipofila, amfifila) och inbindning till α-syn. Här kunde det visas att aggregering av α-syn inhiberades av alla utvalda läkemedel förutom dexametason, som istället påskyndade aggregeringskinetiken för proteinet. Dessutom uppvisade fasudil, ceftriaxon, dopamin, entakapon och tolkapon inbindning till delar av (hydrofila, hydrofoba eller amfifila) vilka delade samma fysikalkemiska egenskaper som α-syn. Därtill uppvisade utvalda läkemedel med till viss del plana strukturer (ex. aromatiska ringar) direkt inbindning till α-syn, vilka också rapporterats ha en något högre grad av transport över blod-hjärnbarriären, dock måste dessa fynd mer noggrant undersökas. Sammanfattningsvis visade alla utvalda läkemedel förutom dexametason anti-aggregeringsegenskaper (hämmande) mot α-syn genom att antingen indirekt eller direkt binda till proteinet och därmed hindra proteinet från att börja binda till sig själv. Mer studier måste genomföras för att studera effekten av läkemedelsexponering på α-syn för att identifiera viktiga segment av proteinet som kan utgöra läkemedelsmål för inhibering av α-syn aggregering. / Parkinson's disease (PD) is a condition that leads to an aggravated and worsened quality of life. At present, there are only symptomatic drugs for PD but no cure that eradicate the disease nor halter the disease progression have been found. Current research is being carried out to develop new drugs, but efforts also investigate whether existing drugs can be used as treatment for PD. Many of the already existing drugs being tested are those that have the ability to interact with a protein called α-synuclein (α-syn), that has been implicated to be a major player for onset of PD. In the present literature study, it was investigated in what way some drugs, whose indication is PD but also other diseases such as asthma, affect (i.e. propagate or inhibit) the in-vitro aggregation kinetics of αsyn. Additionally, a detailed analysis of the investigated drugs and their effect on the aggregation pathway was made to characterize common chemical features of the selected drugs based upon choice of solvents and binding to α-syn. Here, it could be shown that aggregation of α-syn is inhibited upon exposure to all selected drugs except dexametason which instead propagated aggregation of α-syn. In addition, fasudil, ceftriaxone, dopamine, entacapone and tolcapone was found to bind to parts (hydrophilic, hydrophobic or amphiphilic) of α-syn similar to their solubility features. Moreover, the selected drugs that were found to bind to α-syn seemed to exhibit planar in structure (i.e. aromatic rings) and also be associated to pass the blood-brain barrier to a greater extent, however these findings need to be more thoroughly investigated. In summary, all drugs but dexametason were shown to inhibit aggregation of α-syn invitro by either indirectly or directly affecting the aggregation of the protein. Further investigations need to be carried out to study the effect of drug exposure on α-syn aggregation in order to propose key segments of α-syn that can act as drug targets for inhibition of protein aggregation.

A permeabilidade através do epitélio intestinal tem se tornado um importante aspecto a ser determinado nas avaliações biofarmacotécnicas envolvendo fármacos e medicamentos. A técnica mais empregada para essa determinação in vitro é aquela que utiliza a cultura de células Caco-2. Entretanto, ainda são discutíveis as condições para a realização desses experimentos, uma vez que a padronização das mesmas é fator fundamental para a confiabilidade dos resultados. Nesta tese, foram avaliadas as condições para realização dos estudos de permeabilidade através de membranas de células Caco-2 para a rifampicina, principal fármaco utilizado no tratamento da tuberculose. Para tanto, foram investigados fatores tais como a citotoxicidade da rifampicina em diferentes concentrações, a influência da concentração do fármaco sobre a permeabilidade, do pH de realização dos experimentos e da presença de proteínas do muco intestinal, além da influência de proteínas plasmáticas. Foi também investigado o potencial indutor da rifampicina sobre a expressão da glicoproteína-P (Pgp) e seu impacto na permeabilidade da própria rifampicina. Os estudos foram desenvolvidos utilizando membranas de células Caco-2 provenientes da American Type Culture Collection (ATCC) cultivadas em placas Transwel®, a quantificação da fração permeada foi por cromatografia líquida de alta eficiência com métodos validados. A análise da indução da expressão da Pgp foi realizada por PCR-RT. Demonstrou-se que as concentrações da rifampicina (10,0; 25,0 e 50,0 µg/mL) não ocasionaram danos às células Caco-2 no estudo de citotoxicidade pela técnica que emprega o sal do brometo de 3-(4,5-dimetil-2-tiazoli)-2,5-difenil-2H-tetrazólio (MTT). As concentrações de rifampicina (5,0; 10,0 e 25,0 µg/mL) não resultaram em valores estatisticamente diferentes de permeabilidade aparente (Papp) em células Caco-2 nas condições do estudo. A rifampicina apresentou valor de Papp significativamente maior em pH 6,8 dentre os valores de pH avaliados (5,8 ; 6,8; 7,4). A presença de muco simulado e de soro fetal bovino não resultou em valores de permeabilidade significativamente distintos do resultado obtido sem a sua adição ao experimento. A expressão da Pgp em células Caco-2 é induzida pela adição da rifampicina (10µg/mL), ocasionando diminuição da sua permeabilidade por mecanismo de efluxo. Pelos resultados de permeabilidade obtidos em todas as condições avaliadas, a rifampicina pode ser considerada um fármaco de alta permeabilidade de acordo com o Sistema de Classificação Biofarmacêutica. / The permeability through the intestinal epithelium has become an important aspect to be determined in evaluations involving drugs and pharmaceutical products. The most common technique for this determination in vitro is one that uses the culture of Caco-2 cells. Nevertheless, the conditions for carrying out such experiments are still questionable, since the standardization of them is essential to the reliability of the results. In this thesis, we evaluate the conditions for the studies of permeability of rifampicin through membranes of Caco-2 cells, the main drug used in the treatment of tuberculosis. To this end, we examined factors such as cytotoxicity of rifampicin at different concentrations, the influence of drug concentration on the permeability, as well as the pH of the experiments, the presence of proteins of intestinal mucus, and the influence of plasma proteins. It was also investigated the potential of rifampicin on the expression of P-glycoprotein (Pgp) and its impact on the permeability of rifampicin itself. The studies were developed using membranes of Caco-2 cells from American Type Culture Collection (ATCC) grown on plates Transwel®, and the quantification of the fraction of drug permeated was obtained by high performance liquid chromatography with validated methods. The analysis of induction of expression of Pgp was performed by RT-PCR. It was demonstrated that the concentrations of rifampicin (10,0; 25,0 and 50,0 µg/mL) did not cause damage to Caco-2 cells in the study of the cytotoxicity technique that uses a bromide salt of 3 - (4,5-dimethyl-2 - thiazol) -2,5-diphenyl-2H-tetrazolium (MTT). The concentrations of rifampicin (5,0; 10,0 and 25,0 &#181g/mL) did not result in statistically different values of apparent permeability (Papp) in Caco-2 cells under the conditions of the study. Rifampicin showed a value of Papp significantly higher at pH 6.8 in comparison with other measured pH values (5,8 and 7,4). The presence of mucus simulated and fetal calf serum did not result in permeability values significantly different from the result obtained without its addition to the experiment. The expression of P-gp in Caco-2 cells is induced by the addition of rifampicin (10 µg/ml), decreasing its permeability by efflux mechanism. Taking into account the results of permeability obtained in all conditions, the rifampicin can be considered a high permeability drug according to the biopharmaceutical classification system.

Instead of planktonic growth in nature, many species of bacteria form biofilm to survive in harsh conditions. Although many chronic bacterial infections are caused by bacterial species in a biofilm lifestyle, previous research has focused on studying antibiotic resistance in planktonic growth. Here we used a modified MBEC assay, i.e. biofilm growth on pegs, to determine Escherichia coli biofilm inhibitory concentrations (BIC) of ciprofloxacin, streptomycin and rifampicin and to study the minimal selective concentration (MSC) for ciprofloxacin in E. coli biofilm. We could observe high inhibitory concentrations for all antibiotics in the biofilm pre-formed in media without antibiotics compared to the biofilm formed in antibiotics. We also show preliminary result indicating that sublethal concentrations of ciprofloxacin lead to the selection of ciprofloxacin resistant mutants in biofilm and that the selection level is lower than what was observed in planktonic growing E. coli. With more knowledge in how the biofilm formation precedes in different antibiotic settings, the treatment for chronic biofilm infections used today could be evaluated and changed so that the infections could be eradicated.