Thesis (MSc. (Chemistry)) -- University of Limpopo, 2016 / 2-Benzenesulfonyloxyquinoxaline was prepared following literature procedure followed by palladium-catalysed Negishi coupling reactions to yield the corresponding, 2-mono-substituted quinoxaline derivatives, 2-phenylquinoxaline and 2-butylquinoxaline. These Negishi cross-coupled derivatives were treated with various nucleophiles, in tetrahydrofuran at room temperature, to yield a series of di-substituted quinoxaline derivatives containing; aryl-, heteroaryl-, arylalkynyl- and alkyl-substituents. Tri-substitution was successful with reaction of 6-chloro-2-benzenesulfonyloxyquinoxaline with excess phenyl-magnesium bromide to yield 2,3,6-triphenylquinoxaline. Sonogashira cross-coupled compounds were successfully synthesised by reacting 2-benzenesulfonyloxyquinoxaline, 6-nitro-2-benzenesulfonyloxyquinoxaline and 6-chloro-2-benzenesulfonyloxyquinoxaline using phenylacetylene, respectively. Nucleophilic substitution was only successful on 2-(2-phenylethynyl)quinoxaline to yield 3-butyl-2-(2-phenylethynyl)quinoxaline. The formation of carbon-nitrogen bonds was accomplished via palladium-catalysed Buchwald-Hartwig amination of 2-benzenesulfonyloxyquinoxaline with arylamines to afford N-phenylquinoxalin-2-amine and N-benzylquinoxalin-2-amine in good to high yields. N-phenylquinoxalin-2-amine was subsequently treated with iodomethane to synthesise N-methyl-N-phenylquinoxalin-2-amine. Nucleophilic substitution on Buchwald-Hartwig coupled compounds was only successful when using alkyl nucleophiles. The reaction of all these quinoxaline derivatives with various nucleophiles does not stop at the stage of α-adduct formation, but continues with the oxidation of these compounds to aromatic substitution products. All synthesised compounds were characterised by NMR, and mass spectral data as well as melting points where applicable. N-Methyl-N-phenylquinoxalin-2-amine and 2,3,6-triphenylquinoxaline showed percentage parasite viability of 42.64% and 58.12%, respectively, against the Plasmodium falciparum strain 3D7. N-Methyl-N-phenylquinoxalin-2-amine showed MIC90 of 16.4 and MIC99 of 19 μM, while 6-chloro-2-(2-phenylethynyl)quinoxalin showed MIC90 of 8.15 and MIC99 of 9.26 μM values against Mycobacterium tuberculosis (Mtb)-H37Rv strains.

No description available.

Magister Scientiae (Medical Bioscience) - MSc(MBS) / The aim of this study was to determine and evaluate the prevalence of TB infection, active TB cases and the risk factors associated with TB infection in Macassar Camp in Macassar (about 40 km from Cape Town on the False Bay coast, with a population of 369). The study design of this epidemiological study was a cross sectional study with a descriptive and an analytic component A comparison between the Mantoux, TB ELISA and X-ray screening tests was performed first. A description of the origin, discovery, characteristics and pathology associated with Mycobacterium tuberculosis as well as the development of the TB epidemic on a global, national and local level, is given. TB was first described to give a South African perspective of the TB epidemic and both the "Virgin Soil" and "Non-Virgin Soil" theory of TB was reviewed. Secondly, ~he TB infection rate in Macassar Camp and the risk factors as well as the determinants of TB infection with regards to overcrowding, ventilation, primary food subsistence level rating (PFSL), social class and employment status were evaluated The third aspect of the study compares prevalence/incidence rates of TB to clinical diagnosis with regards to the symptomatology, radiographs, sputum microscopy, bacteriology and Mantoux test. Lastly the Mantoux test was compared with the TB ELISA test with regards to diagnosis of infection, in new and past confirmed TB cases. The first part of the survey involved the measurement of openable window area and the floor area of each Camp dwelling (to determine if ventilation was within required limits), during the administration of a household questionnaire which was designed to determine the number of occupants, rooms, income, food expenditure per household in the Camp. A personal questionnaire was administered to all Macassar Camp residents to elicit information on demography, knowledge and attitudes to TB, history of past TB, TB contacts, alcohol intake and smoking habits, occupation and BCG status. The Mantoux test were performed on consenting Camp residents in addition to the collection of 5 ml of blood for the TB ELISA tests. The Camp residents heights and weights were recorded prior to the miniature mass chest radiographs being taken. The 'TB suspects' sputa were collected for the microscopy and bacteriological examination. A review of the clinical records of TB patients in the Macassar/Stellenbosch area was also undertaken. The response rate to the household questionnaire was 60 from 63 (95,2%) dwelling units. Whereas the response rate to the personal questionnaire was 296 (80,2%). As for the Mantoux and TB ELISA tests the response rate was 209 (56,6%). Of the 60 dwelling units, 43 (71,7%) were calculated (according to . Batsons Index) to be crowded and 16 (26,7%) dwelling units had an overall ventilation of less than 5% (below the required regulation). There were significantly (p<0,005) more male than female smokers and only 78 (34,2%) of the residents regarded themselves as non-smokers. A similar trend was noted with regards to the alcohol intake of the residents, where only 86 (37,7%) regarded themselves as teetotallers, with significantly more (p=0,003) male than female alcohol consumers. Females sc6red significantly (p=0,002) better than the males with regards to TB knowledge and awareness. Only 199 (67,2%), residents indicated that they had had BeG vaccination. Of the 296 residents responding to the survey, there were 83 children aged 14 years or less. And only 74 of these children were confirmed to have been vaccinated with BeG, resulting in a 89,2% BeG coverage. Two (4,7%) of the 43 children aged 14 years or less were determined to be malnourished on the basis of Z-scores (below -2SD) taking into account height for age as well as weight for height.

Tuberculosis (TB) is primarily a pulmonary disease caused by Mycobacterium tuberculosis (Mtb). Mtb is highly infectious, but studies have shown that only 5–15% of Mtb-infected individuals develop TB disease. The Bacille Calmette-Gu.rin (BCG) vaccine is the only commercially available Mtb vaccine, but its efficacy varies based on the strain used. The Mtb PhoPR-mutant variant, MTBVAC, has been tested as a possible attenuated live vaccine against Mtb. Although it has successfully conferred durable CD4+ T-cell responses in infants, it has also resulted in adverse effects. Our goal is to identify PhoPR-regulated gene(s) that mediate Mtb-induced burst size necrosis in infected cells. PhoPR is a two-component system in mycobacteria. PhoR responds to environmental cues, such as changes in pH, and phosphorylates the PhoP transcription factor, which then activates or suppresses the expression of approximately 40 Mtb genes. The Mtb PhoPR-mutant strain is able to replicate in infected macrophages, but it does not induce the horizontal spread of Mtb to other immune cells. Our lab has previously shown that virulent, cytopathic strains of Mtb, such as H37Rv, suppress early apoptosis, have faster replication rates in macrophages, and trigger cell death at a lethal load threshold of approximately 25 bacteria. Cell death of infected macrophages primarily occurs via necrosis, which involves nuclear pyknosis without DNA fragmentation and general disruption of lipid bilayer membranes. Viable bacilli are released to infect other macrophages and neutrophils recruited to the developing TB lesion. Here, we show that PhoP contributes to burst size necrosis in macrophages and that the PhoP-regulated genes, fadD21 and pks3, are potential drivers of this necrosis. FadD21 and pks3 are involved in the generation of diacyl trehalose/penta-acyl trehalose (DAT/PAT) for cell wall synthesis, suggesting that Mtb cell wall composition may determine virulence. Therefore, we have uncovered potential targets for early intervention or vaccinations to avoid granuloma formation or tissue damage in response to Mtb-induced macrophage necrosis.

Tuberkulos orsakad av Mycobacterium tuberculosis, är en av de ledande dödsorsakerna globalt sett enligt världshälsoorganisationen (WHO). M. tuberculosis ingår i Mycobacterium tuberculosis komplex (MTBC) där bland annat Mycobacterium bovis, M. bovis BCG (Bacillus Calmette-Guérin) och Mycobacterium africanum också ingår. Förutom MTBC ingår även icke-tuberkulösa mykobakterier (NTM) i genuset Mycobacterium. Fall av M. tuberculosis-infektioner rapporteras vanligtvis i utvecklingsländer medan NTM-infektioner är vanligare i västvärlden. Idag använder man sig av sputumprover för att diagnostisera vid misstanke om tuberkulos men bakterierna detekteras också från vätskor, sekret, exkret och vävnader. Odling är den vanligaste diagnostikmetoden men även mikroskopi används och molekylärbiologiska tekniker som realtids-PCR (polymerase chain reaction) vilken kan amplifiera och detektera M. tuberculosis för en snabb och säker analys. Syftet med denna studie var att utveckla en realtids-PCR-metod för att detektera NTM och särskilja dem från MTBC i formalin-fixerade paraffininbäddade vävnadsprover (FFPE). Fyra tidigare publicerade primerpar, senX3, MTC, IS6110 och IS1081, specifika för MTBC utvärderades med realtids-PCR parallellt med det kommersiella kittet AnyplexTM MTB/NTMe real-time detection med dual priming oligonukleotider (DPO). Resultaten visade att de fyra primerparen inte var specifika nog för att kunna särskilja MTBC- och NTM-stammar utan PCR-produkter av olika storlek erhölls även från NTM-stammar. Anyplex-kittet visade däremot hög specificitet och kunde gruppera samtliga testade stammar korrekt som MTBC eller NTM. Samma goda resultat erhölls vid analys av DNA-extrakt från 21 FFPE-prover. Sammanfattningsvis visar denna studie att AnyplexTM MTB/NTMe-kittet uppfyller kraven för att särskilja MTBC från NTM från FFPE-material vilket inte realtids-PCR med primers senX3, MTC, IS6110 och IS1081 gör. / Tuberculosis mainly caused by Mycobacterium tuberculosis, is one of the leading causes of death globally according to the World Health Organization (WHO). M. tuberculosis is included in the Mycobacterium tuberculosis complex (MTBC) which contains also Mycobacterium bovis, M. bovis BCG (Bacillus Calmette-Guérin) and Mycobacterium africanum. In addition to MTBC, non-tuberculous mycobacteria (NTM) are also included in the genus Mycobacterium. Cases of M. tuberculosis infections are usually reported in developing countries while NTM infections are more common in the western world. Today, sputum samples are used to diagnose tuberculosis but the bacteria can also be detected from analysis of fluids, secretions, excreta and tissues. Cultivation is a common diagnostic method but also use of microscopy and molecular biology techniques such as real-time PCR (polymerase chain reaction) which can amplify and detect M. tuberculosis for a rapid and specific analysis. The purpose of this study was to develop a real-time PCR method for detecting MTBC and distinguishing them from NTM in formalin-fixed paraffin-embedded tissue samples (FFPE). AnyplexTM MTB/NTMe real-time detection kit was compared with previously published primers senX3, MTC, IS6110 and IS1081. 21 FFPE samples were processed by DNA extraction for further analysis with real-time PCR for amplification and detection and fragment analysis for size determination. The results show that the kit meets the requirements for distinguishing MTBC from NTM both with purified strains and samples from FFPE material while the different primer combinations senX3, MTC, IS6110 and IS1081 don't. To conclude, the AnyplexTM MTB/NTMe kit can be used for diagnostics of MTBC and NTM from FFPE samples.

Au niveau mondial, la tuberculose est toujours l’une des dix premières causes de mortalité. L’un des principaux facteurs expliquant ce phénomène est l'émergence de souches du bacille tuberculeux, Mycobacterium tuberculosis, résistantes aux antibiotiques. Ainsi, l’OMS a déclaré prioritaire le développement d'une nouvelle génération d’antituberculeux qui soient efficaces contre les souches résistantes. Des études de criblage phénotypique récentes sur M. tuberculosis ont montré que des voies métaboliques de composés de l’enveloppe, telles que la biosynthèse des acides mycoliques, représentent des cibles thérapeutiques très pertinentes. Les acides mycoliques entrent dans la composition de facteurs de pathogénicité lipidiques du bacille tuberculeux. Ils portent divers types de fonctions chimiques déterminantes pour leurs rôles biologiques. Le système Fatty Acid Synthase de type II (FAS-II) impliqué dans leur biosynthèse constitue une cible thérapeutique validée. En effet, il est essentiel à la survie du bacille, possède des caractéristiques uniques, et a un rôle-clé dans sa virulence et sa persistance chez les organismes infectés. De plus, le système FAS-II est la cible de plusieurs médicaments antituberculeux tels que l’isoniazide et l’éthionamide. FAS-II est constitué d'un ensemble d'enzymes monofonctionnelles acyl carrier protein (ACP)-dépendantes. Une partie de ces protéines a été identifiée par des approches de génomique classique. Malgré cela, 20 ans après le séquençage du génome de M. tuberculosis, la composition complète de ce système ainsi que sa fonction précise restent encore à caractériser. L’objectif des travaux de recherche menés durant ma thèse est de caractériser le système FAS-II mycobactérien selon un nouvel angle d'attaque, à l'échelle du système entier. L'approche adoptée visait à i) développer et valider des méthodes expérimentales pour isoler le système FAS-II sous une forme la plus complète possible, ii) décrypter en profondeur la composition en protéines de FAS-II (collaboration équipe O. Schiltz, IPBS) ; iii) identifier de nouvelles enzymes partenaires potentielles. La 1ère partie de ce travail a consisté à mettre au point l'isolement du système FAS-II de deux mycobactéries, M. smegmatis, une espèce-modèle à croissance rapide, et M. bovis BCG, la souche vaccinale très proche de M. tuberculosis. Deux stratégies complémentaires ont été développées : la co-immunoprécipitation et la Single Step Affinity Purification (SSAP). Plusieurs enzymes du système FAS-II ont été utilisées alternativement comme appâts pour co-purifier des protéines partenaires. De nombreux paramètres ont été optimisés afin d'améliorer le taux d'enrichissement en FAS-II et de conserver le plus possible l’intégrité du système : nature de la protéine-appât, délétion du gène endogène (SSAP), conditions de lyse des bactéries, pontage chimique, étapes de purification... La 2ème partie de ma thèse a porté sur l'analyse par protéomique des fractions de purification obtenues et la 3ème partie a consisté à identifier de nouvelles enzymes partenaires. Le traitement des données a permis 1) de mettre en évidence des interactions physiques entre certaines enzymes du système FAS-II ; 2) de démontrer la présence d’une nouvelle enzyme partenaire du système : cette protéine, nommée HadD, est potentiellement impliquée dans l’une des étapes-clés de la biosynthèse des acides mycoliques nécessaire pour l’introduction des groupements fonctionnels sur ces lipides. / Globally, tuberculosis is still one of the top ten leading causes of death. In 2015, the World Health Organization (WHO) reported nearly 480,000 new cases of multidrug-resistant tuberculosis and called for the development of new antituberculosis agents. Recent phenotypic screening studies on Mycobacterium tuberculosis have shown that envelope metabolic pathways, such as mycolic acid biosynthesis, are highly relevant therapeutic targets. Mycolic acids constitute the lipid moiety of pathogenicity factors of the tubercle bacillus. They are essential mycobacterial fatty acids holding various chemical functions decisive for their biological roles. The Fatty Acid Synthase type II (FAS-II) system involved in their biosynthesis is a relevant and validated therapeutic target. Indeed, it is essential to the survival of the bacillus, has unique features, and plays a key role in its virulence and persistence in infected organisms. In addition, the FAS-II system is the target of several antituberculosis drugs such as isoniazid and ethionamide. FAS-II is made of discrete monofunctional acyl carrier protein (ACP)-dependent proteins. Some of these proteins have been identified by conventional genomic approaches. However, 20 years after the M. tuberculosis genome sequencing, the complete composition of this system and its precise function remain poorly known. The objective of my PhD project is to characterize the mycobacterial FAS-II multienzyme system with a completely new line of attack, at the scale of the entire system. The adopted approach was aimed at i) developing and validating experimental methods to isolate the FAS-II system in the most complete form, ii) deciphering the FAS-II protein composition (collaboration with O. Schiltz's team, IPBS); iii) identifying potential new partner enzymes. The first part of this work consisted of developing the isolation of the FAS-II system from two mycobacteria, M. smegmatis, a fast-growing model species, and M. bovis BCG, the vaccine strain very close to M. tuberculosis. Two complementary strategies were developed: co-immunoprecipitation and Single Step Affinity Purification (SSAP). Several enzymes of the FAS-II system were used alternatively as a bait in an attempt to co-purify partner proteins. To improve the level of FAS-II enrichment and to preserve as much as possible the integrity of the system, many parameters were optimized: nature of the bait protein, endogenous gene deletion (SSAP), bacteria lysis conditions, chemical cross-link, purification steps… The second part of my thesis focused on the proteomics analysis of the purification fractions obtained and the third part consisted in identifying new partner enzymes. The data processing allowed: 1) to demonstrate the presence of physical interactions between some FAS-II system enzymes; 2) to demonstrate the presence of a new partner enzyme of the system: this protein, called HadD, is potentially involved in one of the key steps of the mycolic acid biosynthesis pathway necessary for the introduction of functional groups on these lipids. The results obtained thanks to the optimized co-immunoprecipitation and SSAP protocols have contributed to the knowledge of the mycobacterial FAS-II system and bring promising leads for the discovery of new partner enzymes.

Chemotherapy of tuberculosis (TB), a disease caused by Mycobacterium tuberculosis (M. tuberculosis), is successful against actively-growing bacilli but ineffective against dormant/persistent organisms, found mainly in a protective lipid-laden granuloma, possibly necessitating the use of lipophilic antibiotics. In vitro, these bacilli are encased in lipid-rich biofilms. In this study, the antimycobacterial activity of one such agent, clofazimine, and its nanoparticle formulation, have been investigated against Mycobacterium smegmatis (M. smegmatis), as a surrogate for M. tuberculosis, by determining the bacteriostatic and bactericidal activities of the native (NC) and spray-dried (SDC) preparations of this agent on planktonic and biofilm populations, as well as their effects on biofilm formation and its lipid compositions, specifically free mycolic acid (FM) content. Both preparations were comparable, being bacteriostatic for rapidly-proliferating bacilli, bactericidal for slow-growing, biofilm-producing sessile bacteria, but ineffective against non-replicating, biofilm-encased M. smegmatis organisms. However, similar studies in M. tuberculosis are required. / Dissertation (MSc)--University of Pretoria, 2013. / Immunology / Unrestricted

Vitamin B1 is an indispensable co-factor for various enzymes inter alia in the Krebs cycle, pentose phosphate pathway, nucleotide and amino acid synthesis. Due to its importance in metabolism, proteins involved in the synthesis of vitamin B1 have been identified as potential drug targets. Thiamine monophosphate kinase (ThiL), catalyses the last reaction in the pathway, the ATP dependent phosphorylation of thiamine monophosphate (TMP) producing thiamine pyrophosphate (TPP) the active and co-factor form of vitamin B1. In this study, thiamine monophosphate kinase from Mycobacterium tuberculosis (MtbThiL, ~36 kDa) was produced as an N-terminally His6-tagged fusion protein, purified by affinity and size exclusion chromatography, and crystallised. Hexagonal MtbThiL crystals belonged to space group P6122. Molecular replacement revealed a symmetric homodimer with a single monomer occupying the asymmetric unit. Analysis of the structure showed that each subunit of MtbThiL has an ATP and TMP binding site and is structurally related to other ThiL enzymes. Ten lead compounds were identified from compound databases as potential ThiL inhibitors, and oxythiamine was chosen for further study. The binding affinities of oxythiamine and TMP to MtbThiL were determined by isothermal titration calorimetry and a pyruvate kinase-lactate dehydrogenase enzyme assay, which revealed that the binding affinity for oxythiamine by MtbThiL is lower than the substrate TMP. / Dissertation (MSc)--University of Pretoria, 2020. / Biochemistry / MSc / Unrestricted

Diagnosis of infectious pericardial disease has been challenging in the developing world despite improvement of treatment modalities. The diagnostic utility of pH in diagnosing infectious pericardial fluid is unknown, yet this concept is well studied in pleural fluid. This cross-sectional diagnostic study evaluated the diagnostic utility of pH in infectious compared to non-infectious pericardial effusions in a high-burden setting. Methods: Patients of 18 years with moderate to large effusion between the 1st February 2016 and 31st May2018 were enrolled at Groote Schuur Hospital in Cape Town, South Africa. After safe pericardiocentesis, pH was measured with a blood gas analyzer. Mycobacterium tuberculosis culture and/or gene Xpert for TB and/or bacteria culture and/or microscopy served as the reference standard for definite infectious pericardial effusions. We calculated sensitivity, specificity, positive and negative predictive values, negative and positive likelihood ratios for an a priori pH cut off of 7.35. Receiver operating characteristic curve analysis was used for selection of ideal pH cut off. RESULTS Using a set sensitivity of 70% we estimated that we needed to recruit a sample size of 149 subjects for a 95% confidence interval and power of 80%. We screened 200 patients, and excluded 60 because they did not meet the appropriate exclusion criteria. The prevalence of infectious pericarditis was 27.1% (n/N=34/140) as confirmed by the reference standard. We found the median pH (IQR) was 7.30(7.20-7.30) for definite infection, 7.30(7.30-7.35) for probable infection and 7.50(7.40-7.55) for non-infectious effusions p value <0.01 (test for trend). At a cut off or <7.35, the sensitivity was 89.5(95%CI: 75%.5-97.1%) and the specificity was 72.5% (95% CI: 62.8%-80.9%). The ideal ROC- determined cut off for pH that would give maximum sensitivity and specificity was ≤7.30 and the maximum sensitivity and specificity at optimum cut off are 86.8% (95% CI:71.9 - 95.6) and 86.8% (95% CI:71.9 - 95.6), respectively. The area under the curve at this cut-off point is 0.86 (95% CI 0.79 to 0.9), p<0. 001. CONCLUSION: In conclusion, pericardial PH offers diagnostic utility for infectious causes of pericardial effusions using both a PH of 7.35 and an ideal cut-off of 7.30. We recommend that given the simplicity of the test it should be adopted in evaluation of patients with pericardial effusions.

Bovine tuberculosis (BTB) is a zoonotic disease that affects domestic and wild animals, and humans. It is caused by Mycobacterium bovis (M. bovis) and has a wide host range. The effective control of BTB is of paramount importance and this can be achieved through the use of accurate and comprehensive diagnostic tests. The most widely used methods to detect BTB are the skin test and in vitro gamma interferon assay which do not detect anergic animals, but serological tests such as ELISA and fluorescence polarization assay (FPA) have been found promising in ancilliary tuberculosis diagnosis. The overall aim was to study M. tuberculosis complex (MTBC) protein, mycobacterial protein bovis 70 (MPB70) as a target for serological assays in the detection of antibodies to bovine tuberculosis. The MPB70 protein was expressed, purified and labeled with fluorescein (FITC). The mpb70 gene was fragmented into three regions without disrupting predicted epitopes. The resulting protein Fragments were expressed as fusion proteins with the monster green fluorescent protein (MGFP). The recombinant MPB70 (rMPB70) and the expressed gene fragments 2&3 were tested in immunoblots and ELISAs. The rMPB70 and fragment 2-MGFP reacted with chicken antibodies raised against rMPB70 and immune sera from BTB infected buffaloes. MPB70 peptides were synthesized as an approach to identify even smaller antigenic regions. The peptides BT1G (residues 31-45) and BT51L (residues 81-95) were recognised by anti-MPB70 chicken antibodies in the ELISA and fall within fragment 1 and 2, respectively. The tracers (rMPB70-FITC, fragment 2-MGFP fusion and peptides BT1G&BT51L) were tested in the FPA, but the results failed to distinguish between immune sera from chickens immunized with rMPB70 and negative control sera. Even though the FPA was not successful, the MPB70 fragment 2-MGFP fusion protein, which was recognized by sera from BTB infected buffaloes, was tested in an ELISA using panels of sera from uninfected and naturally M. bovis infected buffaloes and cattle. The diagnostic performance of the ELISA was, however, overall unsatisfactory and hence of very limited use as a serological test to detect antibody responses to BTB as a stand-alone assay. Sera from some of the animals gave false positive reactions indicating that MPB70 was not sufficiently specific for serodiagnosis of M. tuberculosis complex infections. / Dissertation (MSc)--University of Pretoria, 2012. / Veterinary Tropical Diseases / unrestricted