Orientador: Eduardo Mello de Capitani / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas / Made available in DSpace on 2018-08-05T04:22:55Z (GMT). No. of bitstreams: 1 Nunes_ElizabeteAbrantes_D.pdf: 12821896 bytes, checksum: 69c5877e5bd28eeddfa61b9e06a31e01 (MD5) Previous issue date: 2005 / Resumo: A tuberculose, a resistência aos medicamentos antituberculose e o HIV são hoje em dia três grandes endemias, com tendências similares e com prejuízos incalculáveis para a humanidade, em particular nos países de baixos recursos. Obiectivos do trabalho: Determinar o padrão de resistência aos medicamentos antituberculose, em pacientes HIV positivos, portadores de doença pulmonar por micobactéria tuberculosa e micobactéria não tuberculosa na região de Maputo e a prevalência de MOTT nesta população. População e métodos: estudo elaborado em dois hospitais da cidade de Maputo, Moçambique. Foram estudados 503 doentes com tuberculose pulmonar e HIV+. Obteve-se 282 amostras da expectoração e ou lavagem brônquica nas quais foi solicitado; baciloscopia, cultura de BK, cultura de micobactérias nào tuberculosas e teste de sensibilidade para os antibacilares. Foram também avaliadas as características clínicas, radiográficas, a contagem de CD4 e o perfil hematológico. Resultados: Em 229 (98,7%) dos isolados, o M tuberculosis foi a principal micobactéria identificada. As micobactérias não tuberculosas, surgiram em apenas 3 (1,3%) casos, identificadas na expectoração e com clínica compatível. Dos 282 doentes, 232 (82%) apresentaram sensibilidade aos medicamentos antituberculose (MAT) e 50 (17%) resistência a qualquer MAT. Quanto ao padrão de resistência 27 (13,6%) eram casos novos e 21 (26,6%) casos previamente tratados. Resistências mais observadas a qualquer MAT, foram de 13,6% nos CN e 26,6% nos PT. As resistências gerais aos diferentes MAT foram: 10 H- 14,9%, 20 S- 7,8%, 30 R - 6,4%. A resistência à R foi aumentada tanto nos CN como nos PT. A tuberculose multiresistente combinada, foi de 5,7%, sendo nos CN, 3% e PT, 11,4%. Factores de risco de resistência e de TB-MR, foram identificados: tratamento anterior de TB e CD4<200. Estes doentes apresentaram mediana de CD4 de 151 cels/mm3, mediana de Hgb de 7,8g1dl e de CTL 1140. Do ponto de vista radiológico o padrão atípico foi o mais frequente e cavidades foram observadas num grupo reduzido, predominando nos PT e nos casos que apresentaram poliresistência aos MAT.O sarcoma de kaposi pulmonar surgiu em 4,8% dos doentes e as infecções fiíngicas/bacterianas em 27,9% Conclusões: A tuberculose multiresistente (TB-:MR)apresentou níveis elevados pelo que se deve reduzir o risco de transmissão da TB com medidas de controle da transmissão nosocomial e na comunidade e ampliar a DOTS estratégia a um maior número de população. Face à resistência elevada à H, aconselhamos a introdução de um 30MAT na fase de manutenção no regime de tratamento dos CN, teste de sensibilidade aos MAT no início dos retratamentos. A profilaxia com H em HIV+ na prevenção de TB e tratamento de infecção latente deverá ser analisada com cuidado devido á elevada resistência à H. Uso de cotrimoxazol para redução das causas de morte associadas ao HIV!TB. Tratamento antiretroviral e aconselhamento para teste voluntário de HIV em todos os doentes TB / Abstract: Tuberculosis, multidrug-resistant tuberculosis and mv are, today, the three greatest endemics with similar trends and immeasurable impairment to humanity,particularin low resources countries. Obiectives: Determine the resistance pattern to anti-tuberculosis drugs (ATD) in mv positive patients with pulmonary disease by mycobacteria tuberculosis and mycobacteria non tuberculosis in the Maputo region and the prevalence of MOTT in this population. Population and methods: the study was conducted in 503 patients with pulmonary tuberculosis and mv positive in two hospitaIs of Maputo City, Mozambique. Two hundred and eighty two (282) sputum samples and/or bronchial wash were submitted for testing of baciloscopy, BK culture, MOTT and Drug Susceptibility Testing (DST) for ATD. Clinical and radiographic characteristics, CD4 counting and hematological profile were also evaluated. Results: M tuberculosis was the main organism identified in 229 (98,7%) of the isolated samples. Non-tuberculosis mycobacteria were identified in sputum of only 3 (1,3%) of the cases with compatible clinic. Drug sensitivity was observed in 232 (82%) patients and resistance in 50 (17%) of the 282 sampled cases. In relation to the drug resistance pattems, 27 (13,6%) were in New Cases (NC) and 21 (26,6%) in Previously Treated cases (PT). More observed resistance to ATD was recorded in 13,6% in NC and 26,6% in PT. General resistant to different ATD was: 1° H- 14,9%, 2° S- 7,8%, 3° R- 6,4%. The resistance to R increased both in the NC as in PT. Overall, the MDR-TB was 5,7%, being 3% in NC and 11,4% in PT. The risk factors identified for resistance and MDR-TB were: previous treatment to TB and CD4 <200. These patients presented a median CD4 of 151 cells/mm3, a median of Hgb of 7,8 g/dl and of CTL 1140. From a radiological point ofview, the atipic pattem was the most frequent and cavities were observed in a small group predominant1yin PT and in-the cases that presented poliresistance to ATD. The pulmonary Kaposi sarcoma was observed in 4,8% ofthe patients and the fungall bacterial infections in 27,9%. Conclusions: The high levels of MDR-TB recorded in this study suggests that the risk of TB transmission should be reduced through control measures of nosocomial transmission and in the community and amplify the DOTS strategy to a greater population number. As a result of the high resistance to H, it is advised to introduce one of the 3o ATDin the maintenance phase of the treatment regime of NC, and sensitivity tests to ATD in the beginning of retreatment. Prophylaxis with H in HIV positive for TB prevention and latent infection treatment should be analyzed carefully, due to the high resistance to H. The use of cotrimoxazol to reduce the death causes associated to lllV/TB. Anti-Retroviral Treatment (ATRV) is important and also counceling for HIV voluntary testing in all TB patients / Doutorado / Clinica Medica / Doutor em Clínica Médica

South Africa currently has the highest incidence of TB per 100 000 people in the world. In 2007 alone 112 000 people died of TB in South Africa, of which 94 000 were co-infected with HIV. Although TB treatments exist, poor patient compliance and drug resistance are challenges to TB management programs worldwide. Here, this challenge was addressed by the development of a polymeric anti-TB nanodrug delivery system for anti-TB drugs that could enable entry, targeting and sustained release for longer periods, hence reducing the dose frequency and simultaneously improve patient compliance. The aim was to prepare functionalised polymeric nano drug delivery vehicles to target TB infected macrophage cells. Successful nano encapsulation of anti-TB drugs was achieved and uptake of the antibiotics in the cells, demonstrated. A possible targeting agent, mycolic acids (MA) from M. tuberculosis was explored. The MA incorporated into nanoparticles could possibly serve as a ligand for cholesterol-rich areas, due to the cholesteroid nature of MA and the fact that MA is attracted to cholesterol. In another targeting scenario, MA incorporated into nanoparticles may interact with the anti-mycolic acid antibodies that are anticipated to be present in higher concentrations at the infected areas. The cholesteroid nature of MA was confirmed and how it related to the fine structure of the MA. The prepared MA containing nanoparticles were shown in vitro to be taken up in macrophage cell lines, without the MA hindering the uptake of the particles. In terms of toxicity, nanoparticles with or without MA were found to be acceptable for use, although MA did affect the viability of the cells more than poly, DL, lactic-coglycolic acid particles alone in in vitro studies. This paves the way for testing MA as a ligand to target anti-TB drugs to the sites of infection in human TB patients. / Thesis (PhD)--University of Pretoria, 2010. / Biochemistry / unrestricted

Thesis (MScMedSc)--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), infects one third of the world’s population and kills 1.7 million people per year. The increasing prevalence of multi- and extensively drug resistant M. tuberculosis strains means that there is an urgent need to develop new anti-TB drugs. The genome of M. tuberculosis has five copies of the ESAT-6 gene clusters (ESX-1, -2, -3, -4 and -5), which are essential for the survival (ESX-3) and pathogenicity (ESX-1 and ESX-5) of the bacterium. The ESX clusters encode for proteins which form a novel secretion system which has been shown to secreted small T-cell antigens of the esx gene family, as well as other proteins such as the PE and PPE’s. The mycosins are a family of genes situated in the ESX clusters which encode for putative subtilisin-like serine proteases. These proteins are the most conserved proteins within the five clusters. Apart from their conserved protein sequence, mycosin-3 is also an essential protein specific to the mycobacteria, which makes it an attractive potential drug target. Identifying the substrate(s) of mycosin-3 could help to understand the function of this enzyme and discover novel inhibitors from which new drugs could be designed. We hypothesize that the secreted products of the ESX system could be potential substrates for the mycosins. Specifically, we hypothesize that PE5, PPE4, esxG and esxH (all found in ESX-3) might be the substrates for mycosin-3. Mycosin-3, PE5, PPE4, esxG and esxH were thus cloned, expressed and purified respectively. The four substrates were used for protease assays using mycosin-3 as the protease. The protease-substrate mixture were subsequently separated on 2-D SDS-PAGE gels to check whether there were any cleavage of the four substrates. Although all the target fusion proteins were cloned and expressed successfully, the protease assay results showed no cleavage for any of the four substrates. Possible explanations for the failure of cleavage were: (1) impure enzyme and substrate(s); (2) inappropriate buffer conditions; (3) the hypothesized substrates might not be the substrates of mycosin-3; and (4) incorrect folding or modification of the target fusion proteins might have taken place. Future research will aim to address these possible limitations in order to fully elucidate the function and substrate specificity of mycosin-3 and to use this information for the design of novel drugs against M. tuberculosis. / AFRIKAANSE OPSOMMING: Mycobacterium tuberculosis, die organisme wat tuberkulose (TB) veroorsaak, infekteer `n derde van die wêreld se bevolking en veroorsaak die dood van 1.7 miljoen mense per jaar. Die verhoogde voorkoms van multi- en ekstensiewe middelweerstandige stamme van M. tuberculosis beteken dat daar `n ernstige nodigheid is om nuwe anti-TB middels te ontwikkel. Die genoom van M. tuberculosis het vyf kopieë van die ESAT-6 geengroepe (ESX-1, -2, -3, -4 en -5), wat essensieel is vir die oorlewing (ESX-3) en patogenisiteit (ESX-1 and ESX-5) van die bakterium. Die ESX groepe enkodeer vir proteïene wat `n nuwe uitskeidingssisteem vorm wat bewys is om klein T-sel antigene van die esx geenfamilie, sowel as ander proteïene soos die PE en PPE proteïene uit te skei. Die mycosins is `n familie gene wat in die ESX geengroepe voorkom en wat waarskynlik enkodeer vir subtilisin-agtige serine proteases. Hierdie proteïene is die mees gekonserveerde proteïene in die vyf geengroepe. Mycosin-3 is `n essensiële protein wat spesifiek in die mikobakteriëe voorkom, sodat dit `n aantreklike teiken vir die ontwikkeling van middels is. Die identifisering van die substrate van mycosin-3 kan moontlik help om die funksie van die ensiem te verstaan en om nuwe inhibeerders vir die ensiem te ontdek, wat kan lei tot die onwikkeling van nuwe middels. Ons hipotese is dat die uitgeskeide proteïene van die ESX sisteem moontlik die substrate van die mycosin proteïene kan wees. Meer spesifiek, ons hipnotiseer dat die proteïene PE5, PPE4, esxG en esxH (wat almal in ESX-3 voorkom) die substrate vir mycosin-3 kan wees. Mycosin-3, PE5, PPE4, esxG en esxH is afsonderlik gekloneer, uitgedruk en gesuiwer. Die vier substrate is gebruik vir protease proewe met mycosin-3 as die protease. Die protease-substraat mengsel is hierna deur middel van 2-D SDS-PAGE geanaliseer om te kyk of daar enige kliewing van die vier substrate voorgekom het. Alhoewel al die teiken fusieproteïene suksesvol gekloneer, uitgedruk en gesuiwer is, het die protease proewe geen kliewing getoon vir enige van die vier potensiële substrate nie. Moontlike verklarings vir hierdie negatiewe resultaat is die volgende: (1) ensiem en substrate was moontlik onsuiwer; (2) bufferkondisies was moontlik nie korrek nie; (3) gehipotiseerde substrate mag moontlik nie substrate van mycosin-3 wees nie; en (4) nie-korrekte vouing of modifisering van die teiken proteïene kon moontlik plaasgevind het. Toekomstige navorsing sal daarop gemik wees om hierdie beperkinge aan te spreek om sodoende die funksie en substrate van mycosin-3 te kan ontdek en nuwe middels teen M. tuberculosis te ontwerp.

The aim of this research was to develop and fully investigate a novel method of antibiotic drug delivery to the lung that will address problems with current therapeutic regimens for treatment of airway infections. To demonstrate the performance of prepared formulations, the design of suitable characterization methods were also aimed. A novel dissolution method for evaluating the in vitro dissolution behavior of inhalation formulations was developed. The membrane holder was designed to enclose previously air-classified formulations so that they could be uniformly tested in the dissolution apparatus. Dissolution procedures, the apparatus, the dose collection, the medium, and test conditions were developed and the dissolution behaviors of test compounds were evaluated by experimental and mathematical analysis. It was proved that the aerodynamic separation of formulation prior to dissolution assessment have a significant influence on the dissolution profiles. The optimized test method using the membrane holder was applied to evaluate in vitro dissolution profiles of the manufactured formulations of rifampicin (RF). The carrier/excipient-free RF dry powder formulation was investigated. The rifampicin dihydrate (RFDH) powders having MMAD of 2.2 um were prepared using a simple recrystallization process. The RFDH powders have a thin flaky structure, and this unique morphology provides improved aerosolization properties at maximal API loading. The manufactured RFDH formulation showed 80% drug release within 2 hours. To retard the release rate of RF, the prepared RFDH crystals were coated with hydrophobic polymer, PLA or PLGA, using spray-dryer equipped with multi-channel spray nozzles. The multi-channel spray nozzle used in this study has two separate nozzles for aqueous solution and one for gas fluid. The RFDH crystals and the coating solutions were sprayed through the two separate liquid nozzles at the same time. The coated RFDH formulations were prepared using multi-channel spray nozzles. The coated formulations contained at least 50% w/w of RF with no change of their flaky morphology. The initial RF release was lowered by coating; the lowest initial RF release was observed from the coated powders with PLA polymer as 32% among the coated formulations. Overall, the 80% of RF was released within 8 hours. The RFDH and coated RFDH formulations delivered via the pulmonary route would be anticipated to provide higher local (lung) drug concentrations than that of orally delivered powders. Particularly, the coated RFDH powders deposited in the alveolar region may prolong the drug residence time in the site of infections. Additionally, it was proved that the RFDH and coated RFDH formulations provided much better stability than the amorphous RF. / text

En 1993, l’Organisation Mondiale de la Santé déclarait que la tuberculose était « une urgence de santé publique mondiale ». Plus de 20 ans après, cette maladie infectieuse causée par Mycobacterium tuberculosis, reste toujours un problème à l’échelle de la planète. Malgré des progrès très importants enregistrés dans la lutte contre la tuberculose dans le monde, l’OMS estime que 9 millions de personnes ont contracté cette maladie en 2013 et que 1,5 million sont morts durant cette même année. De plus, l'émergence de la tuberculose multirésistante nécessite le développement de nouveaux outils et de nouvelles stratégies thérapeutiques. Récemment, deux nouveaux composés, bedaquiline et delamanid ont reçu une autorisation temporaire d’utilisation dans le but de renforcer l’arsenal thérapeutique. Néanmoins, il existe toujours la possibilité que la bactérie puisse rapidement développer des résistances liées au mécanisme d’action de ces nouveaux médicaments. C’est pour toutes ces raisons que l’arsenal thérapeutique doit être renforcé. Ce travail de thèse repose sur la découverte et l'optimisation de nouveaux composés antituberculeux selon des approches dont le point de départ commun est le criblage de petites molécules appelées fragments.La première partie de ce manuscrit présente la continuité d’un travail démarré au cours de la thèse de Baptiste Villemagne et qui a pour but de potentialiser l’activité de l'éthionamide, un médicament antituberculeux utilisé pour le traitement de seconde intention. Le répresseur transcriptionnel EthR a été validé comme élément clé dans la bioactivation de l’éthionamide. Les inhibiteurs de cette cible, développés selon une approche par fragments ont permis de potentialiser l'activité de l'éthionamide in vitro. Cependant, la faible stabilité microsomale de ces composés a limité leur utilisation in vivo. L’étude de la métabolisation du composé tête de série et la modification structurale de ce dernier a permis le développement des nouveaux inhibiteurs d’EthR présentant des propriétés pharmacocinétiques et physico-chimiques désormais acceptables pour la réalisation de tests in vivo.La deuxième partie de cette thèse s’est concentrée sur la synthèse d’inhibiteurs de MabA, une &#946;-cétoacyl-ACP réductase mycobactérienne participant à la synthèse des acides gras à longue chaîne, précurseurs des acides mycoliques qui sont les constituants majeurs de la paroi mycobactérienne. Cette enzyme a été montrée comme étant indispensable à la survie de la bactérie mais aucun inhibiteur à ce jour n’a été identifié. Le criblage d’une chimiothèque de fragments sur MabA a été réalisé via deux tests différents (un test d’affinité pour la cible (TSA) et un test enzymatique). Les hits ainsi identifiés ont été resynthétisés et testés dans un test fonctionnel. Les étapes d’optimisation de l’activité des hits reconfirmés sont ainsi décrites. Ces résultats ont permis de développer des composés présentant des activités de l’ordre du micromolaire. Dans la troisième partie, un travail de conception et de synthèse de nouveaux fragments, visant à compléter la chimiothèque actuelle a été effectué. Les fragments originaux contenant un motif isoxazoline ont été synthétisés à partir d’alcènes et d’aldoximes utilisés en tant que synthons de départ, selon une réaction de cycloaddition 1,3-dipolaire. L’analyse conformationnelle de ces fragments a permis de montrer que ces structures venaient enrichir l’espace de la diversité, notamment par l’introduction d'un motif permettant le déploiement des substituants dans les trois dimensions de l’espace. La solubilité expérimentale de ces fragments a été également mesurée et nous avons pu montrer que ces molécules étaient adaptées au criblage. / In 1993, the World Health Organization (WHO) declared Tuberculosis (TB) as a global public health emergency. Over 20 years later, this infectious disease caused by Mycobacterium tuberculosis, remains a major public health problem. Despite the significant progress in the fight against TB worldwide, WHO estimates that 9 million people contracted the disease in 2013 and 1.5 million died in that year. In addition, the emergence of multidrug-resistant tuberculosis (MDR-TB) requires the development of new tools and new therapeutic strategies. Recently, two new compounds, bedaquiline and delamanid were approved in MDR-TB treatment in order to strengthen the actual MDR-TB chemotherapy. Nevertheless, there is always the possibility that the tubercle bacillus can quickly develop resistance related to the mechanism of action of these new drugs. Therefore, the actual therapeutic arsenal must be strengthened. This thesis is based on the discovery and optimization of new anti-TB compounds starting from the screening of small molecules called fragments.The first part of this thesis is the continuation of the research project which was started during the thesis of Baptiste Villemagne. This work aims to develop compounds that can boost the activity of ethionamide, a second-line drug used to treat MDR-TB. The transcriptional repressor EthR has been validated as a key element in the bioactivation of ethionamide. EthR inhibitors were identified using a fragment-based approach and were optimized to potentiate the activity of ethionamide in vitro. However, the low microsomal stability of the lead compound has limited its use in vivo. The metabolism study of the lead compound and key structural modifications allowed a development of new potent EthR inhibitors having acceptable pharmacokinetic and physico-chemical properties for in vivo testing.The second part of this thesis focused on the synthesis of MabA inhibitors. MabA is a mycobacterial &#946;-ketoacyl-ACP reductase involved in the synthesis of long-chain fatty acids, precursors of mycolic acids, which are major constituents of the mycobacterial cell wall. This enzyme has been shown to be essential for the survival of the bacteria but until now no inhibitor has been identified. Screening of a library of fragment molecules on MabA was performed via two different assays (affinity assay using TSA and an enzymatic assay). The identified hits were re-synthesized and tested in a functionnal assay. The optimization steps to improve the activity of the hits are also described. Compounds with activity in the micromolar range were discovered.In the third part, a design and synthesis of new fragments is described. The aim of this project is to build a collection of original fragments showing a 3D-structure scaffold amenable for rapid derivatization. The fragments that contain an original isoxazoline motif were synthesized from alkenes and aldoxime as starting building-blocks by using 1,3-dipolar cycloaddition. The conformational analysis of these structures has shown that they were, as expected, able to deploy substituents in the 3D space. The experimental solubility of these fragments was also measured and the results demonstrated that these molecules are suitable for the screening against new biological targets to help kick-start hit discovery program.

Thesis (MScMedSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: BACKGROUND: The emergence of mycobacterium tuberculosis resistance to first line drugs has renewed interest in second-line anti-tuberculosis drugs. Generally, Paraaminosalicylic acid (PAS) is less potent and frequently more toxic than the first line drugs. Furthermore, the pharmacokinetics of PAS in children has not been well characterized. AIMS: The aims of the present study were (1) to determine the pharmacokinetics of PAS in pediatric patients, (2) to describe the discrepancy between children and adult pharmacokinetics and the appropriate dosing regimen of PAS and (3) to investigate the potential of the second-line anti-tuberculosis drugs PAS, terizidone and ethionamide (often used as first-line drug in children) to inhibit the catalytic activities of CYP450 1A2 and 2C9. PATIENTS: Twenty two patients with drug resistant tuberculosis were included in the study. Ten patients were children with mean age of 4.2 years (range: 1 to 12 years). Twelve patients were adults with mean age of 31.3 years (range: 18 to 53). 4 children (40%) and 4 adults (33.3%) were HIV positive and were on ART. METHODS: Children received 75 mg/kg twice daily on the first visit and after two weeks they received 150 mg/kg once. Adults received a standard 4 g twice daily. Blood samples were taken at different time points after the dose. In the additional study, the inhibitory effects of PAS, ethionamide and terizidone on phenacetin O-deethylation, a marker substrate of CYP1A2 and diclofenac 4’-hydroxylation, a marker substrate of CYP2C9, were studied using human liver microsomes. RESULTS: For the 75 mg/kg dose, the mean AUC was 233.3 =g•h/ml and the mean CL was 10.4 l/h/kg. The mean of the observed Cmax of the drug was 45.4 =g/ml and the mean Tmax was 4.8 hrs. For the 150 mg/kg dose, the mean AUC of PAS was 277.9 =g•h/ml and the mean CL was 47.1 l/h/kg. The mean of the observed Cmax of the drug was 56.5 =g/ml and the mean Tmax was 4.8 hrs. On the first visit the mean AUC was 368 =g•h/ml and the mean CL was 13.2 l/h/kg. The mean of the observed Cmax of PAS was 51.3 =g/ml and the mean Tmax was 5.2 hrs. On the second visit the mean AUC was 230 =g•h/ml and the mean CL was 23.9 l/h/kg. The mean of the observed Cmax of PAS was 37.6 =g/ml and the mean Tmax was 5.2 hrs. The comparisons between pharmacokinetics profile of PAS and patients characteristics e.g. age, indicated no statistically significant differences between children (both treatment regimens) and adult patients as well as HIV positive and negative patients. In the in vitro study, all drugs demonstrated no inhibition potency towards the investigated CYP450 enzymes. CONCLUSIONS:The dose of 75 mg/kg twice daily in children appears to be appropriate to achieve serum concentration above the PAS minimum inhibitory concentration of approximately 1 =g/ml. PAS, ethionamide and terizidone are unlikely to affect the metabolism of concomitantly administered medications that are metabolized by either CYP450 1A2 and/or 2C9 isoenzymes. / AFRIKAANSE OPSOMMING: AGTERGROND: Die opkoming van eersteliniemiddel-weerstandige mycobacterium tuberculosis het opnuut belangstelling in tweedelinie-antituberkulosemiddels aangewakker. Oor die algemeen is para-aminosalisielsuur (PAS) minder kragtig en dikwels ook meer toksies. Verder is die farmakokinetika van PAS in kinders nog nie goed vasgestel nie. DOELSTELLINGS: Die doelstellings van hierdie studie was (1) om die farmakokinetika van PAS in pediatriese pasiënte vas te stel, (2) om die diskrepansie tussen kinder- en volwasse-farmakokinetika, sowel as die toepaslike doseringskedule, van PAS te beskryf en (3) om die potensiaal van die tweedeline-antituberkulosemiddels PAS, terisidoon en etioonamied (gereeld gebruik as eerste linie middels in kinders) te ondersoek wat betref hul vermoë om die katalitiese werking van CYP450 1A2 en 2C9 te inhibeer. PASIËNTE: Twee-en-twintig pasiënte met middelweerstandige tuberkulose is in hierdie studie ingesluit. Tien pasiënte was kinders met ‘n gemiddelde ouderdom van 4.2 jaar (reeks: 1 tot 12 jaar). Twaalf pasiënte was volwassenes met ‘n gemiddelde ouderdom van 31.3 jaar (reeks: 18 tot 53 jaar). 4 kinders (40%) en 4 volwassenes (33.3%) was MIV positief en was op TRM’s. METODES: Kinders het 75 mg/kg twee maal daaliks gedurende die eerste besoek ontvang en 150 mg/kg een maal ná twee weke ontvang. Volwassenes het ‘n standaarddosis van 4 g twee maal daagliks ontvang. Bloedmonsters is op verskillende tye ná die dosering geneem. In die addisionele studie is in die inhiberende effekte van PAS, etioonamied en terisidoon op fenasetien-O-deëtilering, ‘n merkersubstraat van CYP1A2 en diklofenak-4’-hidroksilasie, ‘n merkersubstraat van CYP2C9, ondersoek deur gebruik te maak van menslike lewermikrosome. RESULTATE: Vir die 75 mg/kg dosis was die gemiddelde area-onder-die-kurwe (AOK) 233.3 =g•h/ml en die gemiddelde middelopruiming (CL) 10.4 l/h/kg. Die gemiddelde geobserveerde Cmaks van die middel was 45.4 =g/ml en die gemiddelde Tmaks was 4.8 h. Vir die 150 mg/kg dosering was die gemiddelde AOK van PAS 277.9 =g•h/ml en die gemiddelde CL 47.1 l/h/kg. Die gemiddelde geobserveerde Cmaks van die middel was 56.5 =g/ml en die gemiddelde Tmaks was 4.8 h. Gedurende die eerste besoek was die AOK 368 =g•h/ml en die gemiddelde CL was 13.2 l/h/kg. Die gemiddelde geobserveerde Cmaks van PAS was 51.3 =g/ml en die gemiddelde Tmaks was 5.2 h. Gedurende die tweede besoek was die gemiddelde AOK 230 =g•h/ml en die gemiddelde CL 23.9 l/h/kg. Die gemiddelde geobserveerde Cmaks van PAS was 37.6 =g/ml en die gemiddelde Tmaks was 5.2 h. Die vergelyking van PAS-farmakokinetika en eienskappe van die pasiënte het geen statisties beduidende verskille in die gemiddelde AOK tussen kinders (op albei doserings) en volwassenes getoon nie. Met die in vitrostudie het geen van die middels inhibisie-werking teenoor die CYP450-ensieme wat ondersoek is, getoon nie. GEVOLGTREKKINGS: Die gevolgtrekking kan gemaak word dat die dosering van 75 mg/kg twee maal daagliks voldoende is om serumkonsentrasies wat bo PAS se minimum inhiberende konsentrasie van 1 =g/ml te bereik. Dit is onwaarskynlik dat PAS, etioonamied en terisidoon die metabolisme van gelyktydig-toegediende medikasies, wat op hul beurt deur die CYP240-isoënsieme 1A2 en/of 2C9 gemetaboliseer word, sal affekteer. / Division of Pharmacology, Stellenbosch University / National Research Foundation (NRF) grant generously offered by Professor Donald Grant

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.

Thesis (M.A.)--Indiana University, 2010. / Title from screen (viewed on June 4, 2010). Department of History, Indiana University-Purdue University Indianapolis (IUPUI). Advisor(s): William H. Schneider, Robert G. Barrows, Stephen J. Jay. Includes vitae. Includes bibliographical references (leaves 107-112).

La tuberculose (TB), provoquée par Mycobacterium tuberculosis, est une des trois maladies prioritaires dans le monde. Les TB multi-résistantes (MDR) et ultra-résistantes (XDR-TB) représentent des obstacles majeurs pour la lutte antituberculeuse. Dans les pays à MDR-TB élevée, comme le Vietnam, la détection insuffisante de la résistance aux antibiotiques est un des facteurs principaux qui favorisent la transmission des souches résistantes. De plus, dans ces pays, encore très peu de choses sont connues sur la résistance à la pyrazinamide et aux antibiotiques de seconde ligne et sur les déterminants génétiques liés à ces résistances. Dans ce contexte, ce travail vise donc à acquérir des connaissances sur la résistance aux antibiotiques au Vietnam et à étudier comment M. tuberculosis évolue de l’état sensible à l’état ultra-résistant.260 isolats cliniques collectés au Vietnam entre 2005 et 2009 ont été inclus. Diverses techniques et analyses ont été utilisées: tests de sensibilité aux médicaments (développement d'un test à temps réduit), spoligotypage et MIRU-VNTR (24 loci) et séquençage de gènes. Les données ont été analysées par des analyses statistiques et phylogénétiques. Ce travail s’est d’abord focalisé sur la caractérisation d’isolats hautement résistants et sur la résistance à la pyrazinamide. Une forte proportion d'isolats quadruple résistants aux antibiotiques de première ligne a été identifiée comme pré-XDR et XDR et en majorité appartenant à la famille Beijing. L'analyse moléculaire a également révélé une forte proportion d'isolats, en particulier MDR, quadruple résistants et de la famille Beijing, portant des mutations associées à la résistance à la pyrazinamide.L'analyse génétique et phylogénétique globale a ensuite montré une grande diversité de profils de mutations dans chaque famille et chaque cluster MIRU-VNTR. Ces données suggèrent que M. tuberculosis peut suivre des chemins évolutifs variés pour devenir ultra-résistant. La prédominance de mutations et de combinaisons de mutations associées à un haut niveau de résistance et à un faible coût en termes de fitness suggère un effet cumulatif des mutations et un rôle de l’épistasie dans l'acquisition de la résistance multiple. De plus, une fréquence élevée de mutations compensatoires associées à la résistance à la rifampicine a été détectée chez les isolats très résistants. Ces processus semblent donc influencer fortement l'évolution de la résistance dans notre échantillon. Il est à noter que les mutations liées à des niveaux de résistance élevée et à de faibles coûts en termes de fitness, ainsi que les mutations compensatoires étaient plus particulièrement associées à la famille Beijing.En conclusion, ce travail fournit des connaissances uniques sur la résistance aux antibiotiques chez M. tuberculosis au Vietnam. En particulier, ces données prédisent une évolution de la résistance vers une situation de plus en plus préoccupante. Premièrement, la famille Beijing, en cours d’invasion au Vietnam, apparaît associée à de hauts niveaux de résistance, de faible coût en termes de fitness et aux mutations compensatoires. Deuxièmement, le risque élevé de résistance à la pyrazinamide remet en question son efficacité et son utilisation dans les traitements contre la MDR et la XDR-TB. Troisièmement, les données suggèrent une évolution de M. tuberculosis vers un potentiel de résistance plus élevé par effet cumulatif des mutations associés à la résistance et l’existence de phénomènes d’épistasie. Comme les échantillons étudiés dans ce travail ont été collectés, l’étape suivante est de valider nos hypothèses sur des données actualisées.Enfin, ce travail avec les données déjà publiées a permis d’établir, pour la première fois, un inventaire des mutations associées à la résistance aux antibiotiques chez M. tuberculosis au Vietnam. Cette base de données sera utilisée pour le développement d'une puce à ADN pour la détection rapide de la résistance aux antibiotiques au Vietnam. / Tuberculosis (TB) is one of the deadliest infectious diseases worldwide, mainly caused by Mycobacterium tuberculosis. Multidrug resistant (MDR) and extensively drug resistant (XDR) TB are currently main challenges for TB control. In high MDR-TB burden countries like Vietnam, one of the main factors of drug resistant strain spread is the insufficient capacity of drug resistance detection. Besides, still little is known in these countries about the resistance to second line and pyrazinamide drugs (key drugs in the MDR-TB treatment) and the genetic determinants linked to these resistances. In this context, this work aimed to acquire knowledge on drug resistance in Vietnam and to understand how M. tuberculosis evolved from sensitive to highly drug resistance form by molecular analysis.260 clinical isolates collected in Vietnam between 2005 and 2009 were included. Various techniques and analyses were used: drug susceptibility testing (development of a test with a reduced turn-around time), spoligotyping and 24-MIRU-VNTR typing and gene sequencing. The data were analyzed by statistical and phylogenetic analyses.First, this work was focused on highly drug resistant M. tuberculosis clinical isolates and pyrazinamide resistance. A high proportion of quadruple first-line drug resistant isolates (resistant to isoniazid, rifampicin, streptomycin and ethambutol) have been characterized as pre-XDR and XDR isolates, belonging especially to Beijing family. The molecular analysis revealed also high proportion of drug resistant isolates carrying highly confident pyrazinamide resistance-associated mutations, particularly in MDR and quadruple resistant isolates and in Beijing family.Second, the genetic and phylogenetic analyses showed high diversity of mutation patterns within each family and each MIRU-VNTR cluster suggesting various evolutionary trajectories towards first and second-line drug resistance. The predominance of specific mutations and combinations of mutations associated with high level of resistance and low fitness cost suggests a cumulative effect of mutations and a role for epistasis in multiple-drug resistance acquisition. In addition, high frequency of fitness-compensatory mutations associated with rifampicin resistant mutations was detected in highly drug resistant isolates. These processes may drive the evolution of drug resistance in this sample and lead to a successful spread of highly drug resistant strains. It is worth noting that Beijing family was specifically linked to high-level drug resistance and low fitness cost mutations and to compensatory mutations.In conclusion, this work provides knowledge on the resistance to the first and second-line anti-TB drugs in clinical M. tuberculosis samples collected in Vietnam between 2005 and 2009. These data predict an evolution towards a more problematic situation in terms of drug resistance. First, because the Beijing family, which is currently invading Vietnam, is associated with highly drug resistance, mutations linked to high-level drug resistance and low fitness cost and compensatory mutations. Second, the high risk of pyrazinamide resistance in our sample challenges the efficacy and the use of this drug in MDR-TB treatment. Third, our data suggest an evolution of M. tuberculosis towards a higher potential of drug resistance because of a probable cumulative effect of drug resistant mutations and epistatic interactions. Since the samples under study were collected between 2005-2009, the next step is to test our hypotheses on a recent sampling. Finally, this study together with published data allowed making, for the first time, an inventory of the drug resistance associated mutations in M. tuberculosis isolates from Vietnam.

Tee PhD thesis presents the study of the response of Mycobacterium tuberculosis, the causative agent of tuberculosis, upon prolonged exposure to lethal concentrations of the first line anti-tuberculosis drug, rifampicin. The study shows that prolonged exposure to lethal concentration of rifampicin causes cell death initially by several log orders of cells, followed by a persistence phase, from where rifampicin resisters emerge carrying mutation in the RRDR locus of the rpoB gene. This phenomenon was found to occur even when the drug concentration is well above MBC levels. Luria-Delbruck experiment, in a modified format, showed that the resisters emerged as fresh mutants, and not due to the growth of pre-existing natural resisters to rifampicin. The per sister cells, which showed high levels of hydroxyl radical generation, were found to have thickened outer layer, unlike the mid-log phase cells, which restricts the permeability of a fluorescent-conjugate of rifampicin, 5-FAM-rifampicin, 10-fold less in per sister cells, as compared to mid-log phase cells. The thickened outer layer has high negative surface charge and is hydrophilic in nature. It is proposed that the hydrophilic-natured thickened outer layer might have restricted the permeability of lethal concentrations of hydrophobic-natured rifampicin. This, in turn, might have ensured the presence of sub-lethal concentration rifampicin inside the per sisters, which in turn might have generated the hydroxyl radical that caused mutagenesis to generate rifampicin resisters. The Chapter 1 is the Introduction to the thesis presented in 4 parts – Part 1.1, 1.2, 1.3 and 1.4, introducing briefly the history of antibiotics, antibiotic resistance, antibiotic persistence and a brief history of tuberculosis respectively. It is concluded with a rationale behind the present study. The Chapter 2 presents the entire Materials and Methods used in the experiments described in the thesis. The Chapter 3 presents the data on the response of M. tuberculosis to rifampicin upon extended exposure. Rifampicin exposure of susceptible M. tuberculosis H37Ra cells showed a decrease in their CFU/ml followed by a persistence phase wherein the CFU/ml remained constant. However, prolonged exposure of rifampicin even at higher concentrations showed regrowth in the culture, which was found to be due to the emergence of rifampicin-resistant bacteria. Screening of rifampicin-resistant mutants showed point mutations in the rifampicin resistance determining region (RRDR) of the rpoB gene in all the mutants. In parallel, using trans formants of M. tuberculosis expressing unstable GFP under the respective native ribosomal RNA promoter, the metabolic status of the per sister cells was determined. When actively growing highly fluorescing cells were exposed to lethal concentration of rifampicin, their metabolism diminished, as illustrated by the decrease in their fluorescence during persistence phase, followed by the emergence of a sub-population of bacteria which were again metabolically active. In order to verify whether the rifampicin resisters are freshly formed mutants or have come from the naturally existing resisters, Luria-Delbruck fluctuation test was performed in a modified manner. The number of rifampicin resisters that emerged from the persistent phase was found to vary amongst different cultures from different days and different times of exposure, showing fluctuation. However, the addition of theorem before persistence phase almost abolished the generation of the rifampicin-resistant bacilli, indicating the role of hydroxyl radical in the emergence of rifampicin resisters. The generation of hydroxyl radical in mycobacteria exposed to rifampicin was confirmed using electron para-magnetic resonance spectrometry (EPR), with the spin trap agent, 5,5- Dimethyl-1-pyrroline N-oxide (DMPO) specific for hydroxyl radical. An increase in the formation DMPO-OH adduct in the persistence phase cells was observed, in comparison to mid-log phase cells. Exposure to theorem significantly diminished the adduct formation. The persistence phase cells also showed significantly high levels of signal specific to the hydroxyl-specific fluorescent dye, hydroxyphenyl fluorescein (HPF), as compared to the mid-log phase cells. In addition we have determined the oxidative stress in the bacilli upon rifampicin exposure using a redox biosensor (Mrx1-roGFP) which also showed high oxidative stress in the persistent phase. These observations confirmed the presence of high levels of oxidative stress and hydroxyl radical in the rifampicin persistent cells, in comparison with mid-log phase cells. Whole genome sequencing of the four independently isolated rifampicin resistant M. tuberculosis showed genome wide mutations having less common mutations with respect to the wild type genome, indicative of the occurrence of random mutagenesis. In addition mutation frequencies were comparable between the samples with respect to the wild type sample. About 69% of the mutations were A-C or T-G, followed by A-T or T-A, which is known to be due to oxidative stress in the cells. Variations in the colony morphology were also observed on the persistent phase cells, indicating the occurrence of mutagenesis in the bacterial genome during rifampicin treatment. The Chapter 4 is on the morphological and ultrastructural studies on rifampicin-exposed M. tuberculosis cells. Transmission electron micrographs of rifampicin per sisters showed significant thickening of the outermost capsular layer (OL), as compared to the mid-log phase cells. This observation was verified by staining the cells with ruthenium red, which specifically stains anionic polysaccharide of the OL. Zeta potential (ZP) measurement of the surface charge of the persistent cells showed high negative ZP, as compared to the mid-log phase cells. The negative ZP value was found to gradually increase during the course of rifampicin treatment and to decrease during the regrowth phase. Hexadecane assay showed larger proportion of per sister cells being retained in the aqueous phase, as compared to the mid-log phase cells. This indicated the higher hydrophilicity of the per sister cells, which was in agreement with the higher surface negative charge of the cells. The permeability of rifampicin per sister cells to 5-FAM-rifampicin (rifampicin conjugated to 5-carboxy fluorescein, which is as hydrophobic as rifampicin) was found to be 10-fold less than that of the mid-log phase cells. However, removal of the thick OL by bead beating (BB) with 4 mm glass beads significantly improved the permeability of per sister cells to 5-FAM-rifampicin. On the contrary, no difference in the 5-FAM-rifampicin uptake was observed in mid-log phase cells, with or without BB. These observations implied that the thick hydrophilic-natured OL with high negative surface charge may be playing a significant role in limiting the permeability of hydrophobic-natured rifampicin entry into the persisted cells. This in turn may ensure the presence of sub-lethal concentration of rifampicin inside the persisted cells that are exposed to lethal concentration of the antibiotic. Exposure of bacteria to sub-lethal concentration of antibiotics has been reported to generate oxidative stress in the bacteria, leading to mutagenesis. A model has been proposed based on these observations in which the persistent mycobacteria are protected from lethal concentrations of the rifampicin by the thick OL which in turn ensures sub-lethal intracellular antibiotic concentration, leading to the generation of hydroxyl radical mediated mutagenesis and thereby emergence of rifampicin resisters. This thesis is concluded with the list of salient findings, publications and references.