Thesis (M.Sc.)--University of Adelaide, Dept. of Physiology, 1977.

Rats fed diets which contained 15% of casein and 0.620% of methionine with 0.0002, 0.02 and 0.42% of dietary inorganic sulfate had a dietary sulfate-related change in methionine metabolism. Rats fed the diets low in sulfate (0.0002%) had a 35% increase in methionine metabolism compared to rats fed the diets high in sulfate (0.42%). In contrast, rats fed the diet low in sulfate (0.0002%) had the lowest level of tissue S-adenosyl-methionine and the highest activity of phenylethanolamine-N-methyltransferase activity. Those animals fed the diet normal with respect to sulfate (0.02%) had intermediate levels of S-adenosylmethionine and phenylethanolamine-N-methyl transferase activity. Rats fed the diet high in sulfate (0.42%) had the highest level of tissue S-adenosyl-methionine and the lowest phenylethanol-amine-N-methyl transferase activity. Due to the inverse relationship between S-adenosylmethionine and phenylethanolamine-N-methyl transferase activity, it appears that the catecholamines may function as a methyl sink for the increase in the metabolism of methionine required to provide sulfate for rats fed diets low in sulfate.

B. braunii is a green alga that has attracted attention as a potential renewable fuel source due to its high oil content and the archeological record of its unique contribution to oil and coal shales. Three extant chemotypes of B. braunii have been described, namely race A, race B, and race L, which accumulate alkadienes and alkatrienes, botryococcene and squalene and their methylated derivatives, and lycopadiene, respectively. The methylated triterpenes, particularly botryococcenes, produced by race B can be efficiently converted to high quality combustible fuels and other petrochemicals; however, botryococcene biosynthesis has remained enigmatic. It has been suggested that botryococcene biosynthesis could resemble that of squalene, arising from an initial condensation of two molecules of farnesyl diphosphate (FPP) to form pre-squalene diphosphate (PSPP), which then undergoes a reductive rearrangement to form squalene, or in an alternative reductive rearrangement, botryococcene. Based on the proposed similarities, we predicted that a botryococcene synthase would resemble squalene synthase and hence, isolated squalene synthase-like genes from B. braunii race B. While B. braunii does harbor at least one typical squalene synthase, none of the other three squalene synthase-like (SSL) genes encode for botryococcene biosynthesis directly. SSL-1 catalyzes the biosynthesis of PSPP and SSL-2 the biosynthesis of bisfarnesyl ether and to a lesser extent squalene, while SSL-3 does not appear able to directly utilize FPP as a substrate. However, when SSL-1 is combined with either SSL-2 or SSL-3, in vivo and in vitro, robust squalene or botryococcene biosynthesis was observed, respectively. These findings were unexpected because squalene synthase, an ancient and likely progenitor to the other Botryococcus triterpene synthases, catalyzes a two-step reaction within a single enzyme unit without intermediate release, yet in B. braunii, these activities appear to have separated and evolved inter-dependently for specialized triterpene production. Expression of various configurations of the SSL genes in TN-7 yeast demonstrates that botryococcene can be efficiently produced in a heterologous host. Additionally, three triterpene methyltransferase (TMTs) were isolated which efficiently catalyze the transfer of a methyl group from S-adenosyl methionine (SAM) to either squalene (TMT-1 and TMT-2) or botryococcene (TMT-3) in vivo and in vitro. Co-expression of the various TMT genes with either squalene synthase or botryococcene synthase in TN-7 yeast resulted in the accumulation of C31 and C32 methyl derivatives of squalene or botryococcene, demonstrating their potential for heterologous production. The methylation sites were determined by NMR spectroscopy to be identical to C31 and C32 methyl-derivatives of squalene or botryococcene observed in B. braunii race B. Expression studies of various heterologous squalene synthase genes in S. cerevisiae corroborated an earlier but surprising observation reported in the literature. While the squalene synthase gene of S. cerevisiae was able to complement an erg9 (squalene synthase) knockout in yeast, squalene synthase genes from plants and animals were not. Chemical profiles revealed that squalene accumulated to significant levels in yeast expressing the squalene synthase of plant, animal, or S. cerevisiae. This suggested that it was not the ability of these heterologous synthase enzymes to produce squalene, but their inability to feed squalene into the native sterol biosynthetic pathway that prevented them from restoring normal ergosterol biosynthesis in S. cerevisiae. By examining the ability of chimera squalene synthase enzymes to complement the erg9 mutation, a discrete sequence of amino acids near the C-terminus of the enzyme was identified which is necessary and sufficient for allowing any squalene synthase to restore normal sterol metabolism.

>Magister Scientiae - MSc / Anxiety, resilience and childhood trauma can be categorized as functional behavioural categories, with a wealth of research behind each. The research approach adopted for each, in most cases, is either from a genetic or neuropsychological standpoint, with few studies combining both to better understand all three functional behavioural categories as a multidimensional construct A number of candidate genes have been identified as markers for anxiety, resilience and childhood trauma, of which Catechol-methyl-transferase (COMT) and several respective single nucleotide polymorphisms (SNPs) are included. Although COMT SNPs have been linked to at least one of the functional categories, with a handful of haplotypes identified, to our knowledge no study has investigated the combination of SNPs selected for this study (rs6269, rs4818, rs4680, rs4633, rs737865, rs2075507) as a possible haplotype, specifically in a South African population. The use of SNaPshot for the genotyping of genes is an efficient and reliable means of identifying genotype frequencies and haplotypes in large sample groups, yet when selecting more than two SNPs of interest, the development of a multiplex assay is ideal. The first aim of the study was to design and optimize a multiplex assay to genotype several COMT SNPs. The primer design, multiplex optimization and SNaPshot conditions used showed good working parameters that can be utilized and further improved by optimization. Self-report measures are widely used to measure psychiatric disorders, such as anxiety, and has also been used for the measurement of resilience and childhood trauma. With each functional behavioural category well investigated in its respective domain, there is a need to investigate all three as a collective in a South African population due to the high rate of anxiety and childhood trauma exposure in communities. The second aim of the study was to investigate the prevalence of anxiety, resilience and childhood as functional behavioural categories in the full South African sample group; and the role of sex, through established self-report measures and respective normative data. Additionally, this carried over into investigating the correlation between anxiety, resilience and childhood trauma as a multidimensional construct in both the full South African sample and between sexes. There is a clear relationship which exists between all three functional behavioural categories, as they show a correlation in various dimensions independent of one another. Higher anxiety levels amongst females were reported, with no difference between sexes for resiliency. The empirical data collected from both COMT SNP and self-report measures for male and female where explored and reviewed against current literature for better understanding and insight into the association of COMT SNPs with anxiety, resilience and childhood trauma in a South African population. The results of this study to understand the complexity and association of all three functional behavioural categories as a multidimensional construct will be invaluable and may assist in the identification of possible risk factors which are essential for the promotion of better mental health in society.

Although the tremendous catalytic power of enzymes is widely recognized, their exact mechanisms of action are still a source of debate. In order to elucidate the origin of their power, it is necessary to look at individual residues and atoms, and establish their contribution to ligand binding, activation, and reaction. Given the present limitations of experimental techniques, only computational tools allow for such detailed analysis. During my PhD studies I have applied a variety of computational methods, reviewed in Chapter 2, to the study of two enzymes: DfrB dihydrofolate reductase (DHFR) and methyltetrahydrofolate: corrinoid/iron-sulfur protein methyltransferase (MeTr). ¶ The DfrB enzyme has intrigued microbiologists since it was discovered thirty years ago, because of its simple structure, enzymatic inefficiency, and its insensitivity to trimethoprim. This bacterial enzyme shows neither structural nor sequence similarity with its chromosomal counterpart, despite both catalysing the reduction of dihydrofolate (DHF) using NADPH as a cofactor. As numerous attempts to obtain experimental structures of an enzyme ternary complex have been unsuccessful, I combined docking studies and molecular dynamics simulations to produce a reliable model of the reactive DfrB•DHF•NADPH complex. These results, combined with published empirical data, showed that multiple binding modes of the ligands are possible within DfrB. ¶ Comprehensive sequence and structural analysis provided further insight into the DfrB family. The presence of the dfrB genes within integrons and their level of sequence conservation suggest that they are old structures that had been diverging well before the introduction of trimethoprim. Each monomer of the tetrameric active enzyme presents an SH3-fold domain; this is a eukaryotic auxiliary domain never found before as the sole domain of a protein, let alone as the catalytic one. Overall, DfrB DHFR seems to be a poorly adapted catalyst, a ‘minimalistic’ enzyme that promotes the reaction by facilitating the approach of the ligands rather than by using specific catalytic residues. ¶ MeTr initiates the Wood-Ljungdahl pathway of anaerobic CO2 fixation. It catalyses the transfer of the N5-methyl group from N5-methyltetrahydrofolate (CH3THF) to the cobalt centre of a corrinoid/iron-sulfur protein. For the reaction to occur, the N5 position of CH3THF is expected to be activated by protonation. As experimental studies have led to conflicting suggestions, computational approaches were used to address the activation mechanism. ¶ Initially, I tested the accuracy of quantum mechanical (QM) methods to predict protonation positions and pKas of pterin, folate, and their analogues. Then, different protonation states of CH3THF and active-site aspartic residues were analysed. Fragment QM calculations suggested that the pKa of N5 in CH3THF is likely to increase upon protein binding. Further, ONIOM calculations which accounted for the complete protein structure indicated that active-site aspartic residues are likely to be protonated before the ligand. Finally, solvation and binding free energies of several protonated forms of CH3THF were compared using the thermodynamic integration approach. Taken together, these preliminary results suggest that further work with particular emphasis on the protonation state of active-site aspartic residues is needed in order to elucidate the protonation and activation mechanism of CH3THF within MeTr.

Recent years have seen the emergence of Mycobacterium abscessus, a highly drug-resistant non-tuberculous mycobacterium, which causes life-threatening infections in people with chronic lung conditions like cystic fibrosis. This opportunistic pathogen is refractory to treatment with standard anti-tuberculosis drugs and most currently available antibiotics, often resulting in accelerated lung function decline. This project aims to use a structure-guided fragment-based drug discovery approach to develop effective drugs to treat M. abscessus infections. During the early stage of the project, three bacterial targets were identified, based on analysis of the structural proteome of M. abscessus and prior knowledge of M. tuberculosis drug targets, followed by gene knockout studies to determine target essentiality for bacterial survival. The three targets from M. abscessus were then cloned, expressed and purified and suitable crystallization conditions were identified leading to the determination of high resolution structures. Further, a large number of starting fragments that hit the three target proteins were determined, using a combination of biophysical screening methods and by defining crystal structures of the complexes. For target 3, PPAT (Phosphopantethiene adenylyl transferase), a chemical linking of two fragments followed by iterative fragment elaboration was carried out to obtain two compounds with low micromolar affinities in vitro. However, these compounds afforded only low inhibitory activity on M. abscessus whole cell. All starting fragments of target 2, PurC (SAICAR synthase), occupied the ATP indole pocket. Efforts were then made to identify further fragment hits by screening diverse libraries. Sub-structure searches of these initial fragment hits and virtual screening helped to identify potential analogues amenable to further medicinal chemistry intervention. While fragment hits of target 1, TrmD (tRNA-(N1G37) methyl transferase), were prioritized, whereby two chemical series were developed using fragment growing and merging approaches. Iterative fragment elaboration cycle, aided by crystallography, biophysical and biochemical assays led to the development of several potential lead candidates having low nano-molar range of in vitro affinities. Two such compounds afforded moderate inhibition of M. abscessus and stronger inhibition of M. tuberculosis and S. aureus cultures. Further chemical modifications of these compounds as well as others are now being done, to optimize cellular and in vivo activities, to be ultimately presented as early stage clinical candidates.

A azatioprina e a 6 mercaptopurina (6-MCP) são drogas muito utilizada no tratamento das doenças inflamatórias intestinais (DII), porém estão associadas a vários efeitos colaterais. A determinação prévia do genótipo da tiopurina metiltransferase (TPMT) pode identificar pacientes de maior risco de toxicidade a droga. Os objetivos deste estudo foram avaliar a prevalência dos polimorfismos do gene da TPMT em pacientes com DII acompanhados no Hospital Universitário Pedro Ernesto (HUPE) da UERJ, comparando com a prevalência em outras populações e correlacionar a presença desses polimorfismos com a toxicidade às drogas. Foram avaliados 146 pacientes com doença de Crohn (DC) e 73 com retocolite ulcerativa idiopática (RCUI). A pesquisa dos principais genótipos da TPMT (*2, *3, *3C) foi realizada por técnicas de PCR (alelo específico e RFLP). Os achados clínicos foram correlacionados com a genotipagem e avaliados por análises multivariadas. Dentre os pacientes que estavam em uso de azatioprina, 14 apresentaram pancreatite ou elevação de enzimas pancreáticas, 6 apresentaram hepatoxicidade e 2 evoluíram com neutropenia. Os polimorfismos do gene da TPMT foram observados em 37 dos 219 pacientes (8 foram heterozigotos para o genótipo *2, 11 heterozigotos para *3A e 18 foram heterozigotos para o polimorfismo *3C). Não foi observado nenhum homozigoto polimórfico. Uma correlação positiva foi observada entre a elevação de enzimas pancreáticas e os genótipos *2 e *3C. A prevalência dos polimorfismos neste estudo (16,89%) foi maior que a descrita para população caucasiana e em outros estudos brasileiros. Apesar do predomínio do genótipo *3C, não houve ocorrência exclusiva de um polimorfismo, conforme observado em outras populações. A população brasileira devido à sua miscigenação têm características genotípicas próprias diferentes do outros países do mundo. Dois polimorfismos da TPMT (*2 e *3C) estiveram associados à toxicidade ao uso da azatioprina em pacientes com DII no sudeste do Brasil. O teste genético pode auxiliar na escolha da melhor droga e na dose ideal para os pacientes portadores de DII antes do início do tratamento. / Although azathioprine is commonly used for treating patients with inflammatory bowel disease (IBD), there is still concern about potential severe side effects. Determining the Thiopurine-Methyl-Transferase (TPMT) genotype is expected to identify patients predisposition in respect of toxicity prior to azathioprine administration. The aim of this study was to analyze the prevalence of TPMT genotypes and association with drug toxicity in IBD patients from south-eastern Brazil, constituted by a heterogeneous population. We analyzed 146 Crohns disease (CD) and 73 ulcerative colitis (UC) patients, for the presence of the major TPMT genetic variants (TPMP*2, *3A, *3C) by means of specific allele and RFLP PCR. Clinical data were systematically recorded and correlated with the genotype results, and analyzed in multivariate models. Among the side effects recorded from patients taking azathioprine, 14 presented pancreatitis and/or elevation of pancreatic enzymes, while 6 had liver toxicity, and 2 had neutropenia. TPMT polymorphisms were detected in 37/219 patients (8 heterozygous for *2, 11 heterozygous for *3A and 18 heterozygous for *3C). No homozygotic polymorphisms were found. A positive correlation was found between the elevation of pancreatic enzymes and either TPMT*2 or TPMT*3C. The prevalence of polymorphisms in this study (16,89%) was greater than described with caucasian population or other Brazilian studies. Despite the prevalence of genotype *3C, it was not the only polymorphism shown as observed in other populations. Two genetic variants of TPMT gene (*2 and *3C) are associated with azathioprine toxicity in IBD patients from a south-eastern Brazilian population. Genetic testing may help in the selection of the most appropriate medication prior to treatment initiation.

A azatioprina e a 6 mercaptopurina (6-MCP) são drogas muito utilizada no tratamento das doenças inflamatórias intestinais (DII), porém estão associadas a vários efeitos colaterais. A determinação prévia do genótipo da tiopurina metiltransferase (TPMT) pode identificar pacientes de maior risco de toxicidade a droga. Os objetivos deste estudo foram avaliar a prevalência dos polimorfismos do gene da TPMT em pacientes com DII acompanhados no Hospital Universitário Pedro Ernesto (HUPE) da UERJ, comparando com a prevalência em outras populações e correlacionar a presença desses polimorfismos com a toxicidade às drogas. Foram avaliados 146 pacientes com doença de Crohn (DC) e 73 com retocolite ulcerativa idiopática (RCUI). A pesquisa dos principais genótipos da TPMT (*2, *3, *3C) foi realizada por técnicas de PCR (alelo específico e RFLP). Os achados clínicos foram correlacionados com a genotipagem e avaliados por análises multivariadas. Dentre os pacientes que estavam em uso de azatioprina, 14 apresentaram pancreatite ou elevação de enzimas pancreáticas, 6 apresentaram hepatoxicidade e 2 evoluíram com neutropenia. Os polimorfismos do gene da TPMT foram observados em 37 dos 219 pacientes (8 foram heterozigotos para o genótipo *2, 11 heterozigotos para *3A e 18 foram heterozigotos para o polimorfismo *3C). Não foi observado nenhum homozigoto polimórfico. Uma correlação positiva foi observada entre a elevação de enzimas pancreáticas e os genótipos *2 e *3C. A prevalência dos polimorfismos neste estudo (16,89%) foi maior que a descrita para população caucasiana e em outros estudos brasileiros. Apesar do predomínio do genótipo *3C, não houve ocorrência exclusiva de um polimorfismo, conforme observado em outras populações. A população brasileira devido à sua miscigenação têm características genotípicas próprias diferentes do outros países do mundo. Dois polimorfismos da TPMT (*2 e *3C) estiveram associados à toxicidade ao uso da azatioprina em pacientes com DII no sudeste do Brasil. O teste genético pode auxiliar na escolha da melhor droga e na dose ideal para os pacientes portadores de DII antes do início do tratamento. / Although azathioprine is commonly used for treating patients with inflammatory bowel disease (IBD), there is still concern about potential severe side effects. Determining the Thiopurine-Methyl-Transferase (TPMT) genotype is expected to identify patients predisposition in respect of toxicity prior to azathioprine administration. The aim of this study was to analyze the prevalence of TPMT genotypes and association with drug toxicity in IBD patients from south-eastern Brazil, constituted by a heterogeneous population. We analyzed 146 Crohns disease (CD) and 73 ulcerative colitis (UC) patients, for the presence of the major TPMT genetic variants (TPMP*2, *3A, *3C) by means of specific allele and RFLP PCR. Clinical data were systematically recorded and correlated with the genotype results, and analyzed in multivariate models. Among the side effects recorded from patients taking azathioprine, 14 presented pancreatitis and/or elevation of pancreatic enzymes, while 6 had liver toxicity, and 2 had neutropenia. TPMT polymorphisms were detected in 37/219 patients (8 heterozygous for *2, 11 heterozygous for *3A and 18 heterozygous for *3C). No homozygotic polymorphisms were found. A positive correlation was found between the elevation of pancreatic enzymes and either TPMT*2 or TPMT*3C. The prevalence of polymorphisms in this study (16,89%) was greater than described with caucasian population or other Brazilian studies. Despite the prevalence of genotype *3C, it was not the only polymorphism shown as observed in other populations. Two genetic variants of TPMT gene (*2 and *3C) are associated with azathioprine toxicity in IBD patients from a south-eastern Brazilian population. Genetic testing may help in the selection of the most appropriate medication prior to treatment initiation.