L'activation de molécules inertes telles que les alcanes constitue l'un des défis les plus difficiles en catalyse, du fait de la grande stabilité de la liaison C-H. Pour répondre aux principes de la chimie verte, les méthodes de fonctionnalisation doivent respecter un certain nombre d'exigences, telles que l'utilisation de solvants et de réactifs non toxiques, la réduction des apports énergétiques, en association avec une activité élevée. Afin de satisfaire ces conditions, nous nous sommes dirigés vers l'utilisation d'un système enzymatique. En effet, les liaisons C-H non activées peuvent être fonctionnalisées en conditions douces par des monooxygénases, telles que les cytochromes P450, mais leur activité est relativement faible. Dans le but de disposer de cytochromes P450 plus actifs sur les alcanes, nous décrivons la fusion entre un membre de la famille des CYP153 et un partenaire donneur d'électrons. Cette protéine de fusion a été caractérisée, et ses propriétés catalytiques étudiées. Nous avons montré que la fusion augmente de manière considérable l'activité alcane hydroxylase. Nous avons, dans un second temps, continué d'exploiter le fort potentiel de ce biocatalyseur en tentant de réduire le volume de son site actif par mutagénèse dirigée, en vue de l'hydroxylation des alcanes gazeux, notamment le méthane. Enfin, différentes modifications des conditions réactionnelles nous ont permis d'atteindre une activité non égalée pour l'hydroxylation terminale de l'octane. / Activation of inert molecules such as alkanes is considered as one of the most difficult challenges in catalysis, due to the high stability of the C-H bond. To comply with the principles of green chemistry, functionalization methods must respect multiple requirements, such as the use of non-toxic solvents and reagents, in addition to reducing energy usage whilst maintaining maximal activity. To satisfy these conditions, we decided to focus on the use of an enzymatic system. Indeed, unactivated C-H bonds can be functionalized under mild conditions by monooxygenases, such as cytochrome P450s, but their activity is relatively limited. In order to have cytochrome P450s more active on alkanes, we describe the fusion between a member of the CYP153 family and an electron donor partner. This fusion protein has been characterized and its catalytic properties studied. We have shown that the fusion increases significantly the alkane hydroxylase activity. Our second step was to continue to exploit the potential of this biocatalyst by attempting to reduce the volume of its active site using site-directed mutagenesis for the hydroxylation of gaseous alkanes, including methane. Finally, various modifications of the reaction conditions allowed us to achieve the terminal hydroxylation of octane with a previously unequalled activity.

La pourriture grise est une maladie qui affecte de nombreuses cultures dont la vigne. Elle est provoquée par un complexe de deux espèces fongiques, l’espèce majoritaire Botrytis cinerea et l’espèce minoritaire Botrytis pseudocinerea. Les deux espèces se distinguent par leur sensibilité à certains fongicides notamment au fenhexamid, inhibiteur de la 3-cétoréductase des stérols. Ce fongicide a un spectre d’action restreint aux espèces phylogénétiquement proches du genre Botrytis (Sclerotinia et Monilinia fructicola). Son utilisation a conduit à la sélection de souches résistantes parmi lesquelles on distingue trois phénotypes : le phénotype HydR1 correspond à l’espèce B. pseudocinerea naturellement résistante ; les phénotypes HydR2 et HydR3 correspondent à l’espèceB. cinerea ayant acquis la résistance suite à l’introduction du fongicide. L’objet de cette thèse est l’étude des phénotypes HydR1 et HydR2 présents à de faibles, voire très faibles fréquences dans des populations de pourriture grise.Chez B. pseudocinerea (HydR1), nous avons identifié une monooxygénase à cytochrome P450 nommée Cyp684 responsable de la résistance au fenhexamid. Le gène cyp684 montre des polymorphismes (structure et séquence nucléotidique) entre les espèces ainsi qu’une induction par le fenhexamid chez B. pseudocinerea. La comparaison de la séquence du gène cyp684 chez plusieurs espèces de Botrytis et de leurs niveaux de résistance au fenhexamid indique que les acides aminés polymorphes de la protéine Cyp684 sont responsables de la résistance au fenhexamid chez B. pseudocinerea. Le rôle connu des monooxygénase à cytochrome P450 dans la métabolisation des xénobiotiques et la synergie entre le fenhexamid et des inhibiteurs de monooxygénases à P450 suggèrent que Cyp684 soit impliqué dans la métabolisation du fenhexamid. Concernant le phénotypeHydR2 de B. cinerea, le mécanisme de résistance reste à identifier. Les souches HydR2 se distinguent par leur phénotype rose dû à un métabolite secondaire nommé bikavérine. Le génotypage réalisé sur les descendantes d’un croisement entre une souche HydR2 et une souche sensible a mis en évidence un lien physique entre le gène ou l’allèle hydR2 et le cluster bikavérine. Afin d’identifier la niche écologique et de comprendre l'épidémiologie de B. pseudocinerea, nous avons développé une méthode de qPCR espèce spécifique, nommée « B. pseudocinerea allele specific PCR » (BpASP). Cet outil permettra de détecter et de quantifier l’espèce B.pseudocinerea dans les populations de Botrytis, selon la saison, la région géographique et les plantes hôtes. / Grey mold is a fungal disease affecting many crops including grapevine. It is generated by a species complex of two fungal species, the major one, Botrytis cinerea, and the minor species, Botrytis pseudocinerea. Both species differ by their sensitivity to several fungicides, in particular to fenhexamid, a potent inhibitor of sterol 3-ketoreductase. This fungicide has a narrow spectrum of activity limited to species closely related to the genus Botrytis (e.g., Sclerotinia and Monilinia fructicola). Fenhexamid applications have led to the selection of resistant strains with three different phenotypes: the HydR1 phenotype corresponds to the naturally resistant species B. pseudocinerea; HydR2 and HydR3 phenotypes correspond to B. cinerea strains that acquired resistance after the introduction of fenhexamid. The topic of this thesis is the study of the phenotypes HydR1 andHydR2 present at low or even very low frequencies in grey mold populations. We identified a cytochrome P450 monooxygenase named Cyp684 responsible for resistance to fenhexamid in B.pseudocinerea (HydR1). The cyp684 gene differs between both species in its gene structure, nucleotide sequence (polymorphisms) and expression. The comparison of cyp684 sequences among different Botrytis species and their resistance levels to fenhexamid indicate the polymorphic amino acids of the Cyp684 protein to be responsible for fenhexamid resistance in B. pseudocinerea. The known involvement of cytochrome P450s in xenobiotic metabolisation and synergy between fenhexamid and P450-inhibitors suggest that Cyp684 could be involved in fenhexamid metabolisation. Concerning the B. cinerea HydR2 phenotype, the resistance mechanism remains to be identified. HydR2 strains have a specific purple pigmentation due to the secondary metabolite bikaverin. Genotyping of progeny derived from a cross between a HydR2 and a sensitive strain revealed aphysical link between the hydR2 gene or allele and the gene cluster involved in bikaverin biosynthesis. In order to identify the ecological niche of B. pseudocinerea and its epidemiological behavior we developed a species-specific qPCR method named “B. pseudocinerea allele specific PCR” (BpASP). This tool will allow detecting and quantifying the species B. pseudocinerea in natural Botrytis populations, collected according to season, geographic origin or plant hosts.

Cette thèse a été consacrée à l'évolution du transcriptome de Drosophila simulans, et à son rôledans l'adaptation et la spéciation. L'étude a comporté deux parties. La première utilisant des pucesà ADN pour comparer les transcriptomes de populations de D. simulans, de son espèce jumelleD. sechellia, et de leurs hybrides. La seconde basée sur la quantification des transcrits par séquen-çage haut débit pour comparer une population de la zone d'origine (Afrique), et une populationd'une zone récemment envahie (France métropolitaine). Ces analyses ont mis en évidence plusieursgroupes ou familles de gènes montrant des variations d'expression.Un résultat majeur est l'implication prépondérante de la famille des cytochromes P450 dansl'adaptation. Cette superfamille composée de 85 gènes chez D. simulans est notamment importantepour la détoxi_cation des xénobiotiques. L'expression de plusieurs gènes de cette famille estfortement réduite chez D. sechellia, probablement à cause de la spécialisation de cette espèce surla plante Morinda citrifolia (plante toxique pour les autres drosophiles). On peut s'attendre alorsà un relâchement des contraintes de sélection sur cette famille de gènes, dû à une forte réductionde la diversité des toxines auxquelles cette espèce est exposée.Ces gènes sont également impliqués dans la différenciation entre les populations de la zoneancestrale de D. simulans et les populations dérivées. La zone ancestrale, en Afrique de l'est etdans les îles de l'Océan Indien occidental, est encore peu anthropisée. A contrario, la plupartdes populations dérivées, comme ici notre population de la vallée du Rhône, sont exposées à descontraintes chimiques sous la forme de pesticides utilisés massivement sur les grandes cultures.Ces pesticides contraignent les populations dérivées à s'adapter, ce qui peut se réaliser par uneaugmentation de l'expression. Nous avons détecter une augmentation de l'expression de treizeP450, dont un gène très bien connu pour ses fonctions de détoxifcation : Cyp6g1. Ce gène montreune augmentation d'expression corrélée à une résistance aux pesticides et à l'insertion d'élémentstransposables en 5' ; ceci a été montré en détail chez D. melanogaster, et dans une moindre mesurechez D. simulans. Nous avons mis en évidence chez cette dernière espèce un nouvel évènementd'insertion.Nos résultats montrent également que d'autres familles de gènes impliqués dans les détoxi_-cations sont concernées par ces augmentations d'expression liées à l'anthropisation des milieux,notamment les Glutathion transfèrases (GST).Nous avons également examiné la plasticité d'expression liée au changement de ressource, enélevant une partie de nos populations sur la ressource d'origine (fruits), et une autre partie sur lemilieu axénique, milieu d'élevage standard de laboratoire (stérile). Les drosophiles élevées sur unmilieu "naturel" montrent une forte activation du système immunitaire, et notamment une forteinduction des gènes effecteurs de l'immunité innée, codant les peptides anti-microbiens. Cela estprobablement dû à la présence de microorganismes sur ce milieu (ici, la banane). En conclusion,cette thèse a révélé des familles de gènes fortement impliquées dans les différenciations d'expressionentre populations, espèces, et ressources, posant les jalons d'une meilleure compréhension desmécanismes d'adaptation du transcriptome. / The topic of this thesis was the evolution of the transcriptome of Drosophila simulans, andits role in adaptation and speciation. First, we used microarrays to compare transcriptomes ofpopulations of D. simulans, its sister species D. sechellia and their hybrids. Second, we useda RNA-seq like approach to quantify gene expression of a population from the ancestral range(Africa) on the one side, and a population from a recently invaded zone (France) on the other side.These analyses revealed several gene groups or families showing gene expression variations.One main result is the major involvement of the cytochrome P450 gene family in adaptation.This superfamily is composed of 85 genes in D. simulans, and is notably important in detoxificationof xenobiotics. The expression of several genes of this family is strongly reduced in D. sechellia,likely due to the specialization of this species on Morinda citrifolia (a plant toxic for any otherdrosophila). This specialization may strongly reduce the diversity of toxines this species is exposedto, thus relaxing selective constraints on this gene family.These genes are also involved in the differentiation between populations of the ancestral range ofD. simulans and derived populations. The ancestral range, in eastern Africa and in the occidentalislands of the Indian Ocean, is not highly anthropized yet. Contrasting with this pattern, manyderived populations (here our population from the Rhône valley) are exposed to chemical pressuresdue to the massive use of pesticides on agricultural zones. These pesticides force derived populationsto adapt, which can happen via increased expression in genes such as the very famous exampleof Cyp6g1. This gene shows a strong increase in expression correlated with pesticide resistance aswell as the insertion of transposable elements upstream of the gene ; this was described in detailsin D. melanogaster, and to some extent in D. simulans. We have shown a novel insertion event inthe latter species.Our results also reveal the involvement of other gene families in detoxification linked withanthropized environment via increase of gene expression, notably the Glutathione transferases(GST).We also examined expression plasticity linked with resource change, raising half our _ies ontheir natural food resource (fruits), and the other half on axenic medium (standard sterile laboratorymedium). Drosophila raised on their natural medium show a strong activation of their immunesystem, and notably an induction of the effectors of teir innate immunity, the anti-microbial peptides.This observation can be explained by the presence of microorganisms on this medium (here,banana). To conclude, this thesis revealed gene families strongly involved in expression differentiationamong populations, species and food resources, paving the way of a better understanding ofmechanisms of adaptation of the transcriptome.

La schizophrénie est une pathologie sévère et fréquente. Elle constitue un problème majeur de santé publique. Les traitements disponibles présentent des problèmes de tolérance non négligeables et leur efficacité reste modérée. La recherche en pharmacogénétique des antipsychotiques a pour objectif d’aider les prescripteurs à choisir les traitements de façon plus rationnelle. Les carences méthodologiques des premières études réalisées expliquent sans doute le peu de résultat répliqué à ce jour. Dans une cohorte de patients schizophrènes caucasiens traités par olanzapine ou rispéridone et évaluée prospectivement pour l’efficacité et la tolérance du traitement, nous avons d’abord recherché des critères cliniques permettant de prédire la réponse au traitement. L’age précoce de début des troubles et la durée de la maladie sont des prédicteurs individuels de la mauvaise réponse au traitement. Nous avons également étudié l’implication de variants génétiques du transporteur de la noradrénaline dans l’efficacité des traitements. Nous avons observé l’implication de deux polymorphismes dans la décroissance des symptômes positifs sous traitement. L’analyse de l’impact du variant C825T de la GNB3 dans la prise de poids sous antipsychotique n’a pas retrouvé d’association significative. Enfin, nous avons étudié l’ensemble des variants alléliques du cytochrome P450 2D6 dans cette cohorte de patients schizophrènes comparée à des témoins. L’allèle CYP2D6*2 était associé à un effet protecteur vis à vis de la schizophrénie. Les associations retrouvées devraient aider à mieux comprendre les mécanismes physiopathologiques impliqués dans la schizophrénie et la réponse au traitement / Schizophrenia is a frequent and severe disease. It constitutes a major public health problem. All the available treatments however, have significant adverse side-effects and their efficacy remains moderate. The aim of pharmacogenetic research is to help practitioners to choose treatments in a more rational way. The methodological limits of the first published studies probably explain the lack of replication of such studies. In a prospective study of a sample of Caucasian schizophrenic patients treated with olanzapine or risperidone, clinical criteria were assessed as factors that may predict drug response. Early onset and duration of the disease, individually predicted an unfavourable drug response. We also studied genetic variants of the norepinephrine transporter to see how they may affect antipsychotic drug efficacy. Two polymorphisms were associated with a reduction in positive symptoms in treated schizophrenic patients. No association between the GBN3 C825T variant and weight gain in patients treated by antispychotic drugs was observed. Finally, we genotyped all the cytochrome P450 2D6 allelic variants in the same Caucasian schizophrenic sample and a Caucasian origin control cohort. The CYP2D6*2 allele was strongly associated with protection towards schizophrenia. The two observed associations may help to better understand the still unwell known physiopathological mechanisms implicated in schizophrenia aetiology and antipsychotic drug response

The cytochrome P450 enzyme system is a multicomponent electron-transfer chain composed of a haem-containing monooxygenase cytochrome P450 (CYP) and one or more redox partners. Eukaryotic CYPs and their redox partner NADPH-dependent cytochrome P450 oxidoreductase (CPR) are involved in many biological processes. Each protein has one N- terminal membrane anchor domain for location within the endoplasmic reticulum (ER). In mammals, CYPs and CPR are especially abundant in liver cells, where they play important roles in the metabolism of steroids, fatty acids, and xenobiotic compounds including numerous drugs of pharmaceutical importance. Incorporation into lipid membranes is an important aspect of CYP and CPR function, influencing their kinetic properties and interactions. In this thesis, soluble nanometer-scale phospholipid bilayer membrane discs, "nanodiscs", were used as a reconstitution system to study the influence of lipid membrane composition on the activities of the abundant human CYP3A4 and human CPR. Both enzymes were expressed and purified from bacteria, and assembled into functionally active membrane-bound complexes in nanodiscs. Nanodisc assembly was assessed by a combination of native and denaturing gel electrophoresis, and a fluorimetric assay was developed to study CYP3A4 reaction kinetics using 7-benzyloxyquinoline as substrate. Kinetic properties were investigated with respect to different lipid membrane compositions: phosphatidyl choline; a synthetic lipid mixture resembling the ER; and natural lipids extracted from liver microsomes. Full activity of the CYP3A4 system, with electron transfer from NADPH via CPR, could only be reconstituted when both CYP3A4 and CPR were membrane-bound within the same nanodiscs. No activity was observed when CPR and CYP3A4 were each incorporated seperately into naodiscs then mixed together, or when soluble forms of CPR were mixed with pre-assembled CYP3A4-nanodiscs. Thus, assembly of the two proteins within the same membrane was shown to be essential for the function of the CPR-CYP3A4 electron transfer system. Comparison of the reaction kinetics in different membrane compositions revealed liver microsomal lipid to have an enhancing effect both on the activity of the assembled CPR-CYP3A4 nanodisc complex, and on the activity of CPR alone incorporated in nanodiscs, when compared either to the synthetic lipid mixture or to phosphatidyl choline alone. Thus, natural lipids appear to possess properties or include components important for the catalytic function of the CYP system, which are absent from synthetic lipid. Input of electrons, measured by NADPH consumption, exceeded product formation rate by the CPR-CYP3A4 complex in nanodiscs, indicating "leakage" in the electron flow, possibly due to uncoupling of the two enzymes. Uncoupling was shown to occur by developing a novel fluorimetric method using the dye MitSOX to detect superoxide production. The significance of this, and to what extent control of coupling could be a natural means of regulation of the CPR-CYP system, remains to be determined. Thus, phospholipid bilayer nanodiscs prove a powerful tool to enable detailed analysis of the reaction kinetics of membrane-reconstituted CPR-CYP systems, and to allow pertinent questions to be addressed concerning the integral significance of the membrane environment.

Les cytochromes P450 (CYPs) jouent un rôle essentiel dans le métabolisme oxydatif de nombreux composés endogènes et exogènes. L’expression de CYPs est extrêmement variable en fonction de facteurs physiopathologiques, génétiques et environnementaux. Le métabolisme des xénobiotiques par les CYPs dépend en partie de la nature, de la quantité et de l’activité d’isoformes des CYPs impliqués. L'analyse quantitative de l'expression de CYP dans les organes du métabolisme, tels que le foie, sont d'une importance particulière étant donné que la biotransformation réalisée par les CYPs est souvent un facteur critique qui affecte l'efficacité, la disponibilité et la toxicité des médicaments chez l'homme. La technique actuelle de dosage la plus courante est l’immunoquantification par Western Blot. Cette technique est limitée par la disponibilité et la spécificité de l'anticorps. Les techniques de protéomique par spectrométrie de masse, permettant d’analyser de très faibles quantités de protéines en mélange, sont les méthodes de choix pour l’identification et la quantification des CYPs dans différents organes. Nous avons développé et validé une méthode pour doser 6 CYPs (1A2, 2C9, 2D6, 2J2, 3A4 et 3A5) par spectrométrie de masse en couplage chromatographique. Cette méthode, simple, rapide de sensibilité satisfaisante et peu coûteuse, a été validée dans différents types de matrices biologiques (lignées cellulaires hépatiques et neuronales, baculosomes). Ensuite, elle a été appliquée à grande échelle pour l’analyse de 50 foies humains (microsomes et mitochondries) afin d’étudier la relation phénotype/génotype pour les CYPs. Cette méthode pourra être appliquée à d’autres CYPS, est un outil utile qui permettra d’améliorer la compréhension et la prédiction pharmacocinétique et toxique de médicaments et d’autres produits chimiques. / Cytochromes P450 (CYPs) play a key role in the oxidative metabolism of many endogenous and exogenous compounds. The expression of CYPs is extremely variable depending on patho-physiological, genetic and environmental factors. The metabolism of xenobiotics by CYPs depends on the nature the quantity and the activity of CYP isoforms involved. Quantitative analysis of CYP expression in organs such as liver, are of particular importance since the biotransformation performed by CYPs is often a critical factor that affects the efficiency, availability and drug toxicity in humans. The most common technique is the immune-quantitation (Western Blot). This technique is limited by the availability and specificity of the antibody. Mass spectrometry-based proteomics, able to analyze very small amounts of protein in a mixture, are the methods of choice for identification and quantification of CYPs in different organs. We developed and validated a method for dosing 6 CYPs (1A2, 2C9, 2D6, 2J2, 3A4 and 3A5) by liquid chromatography coupled with mass spectrometry. This simple, rapid, low-cost method has an adequate sensitivity, and has been validated in different types of biological matrices (liver and neuronal cell lines, baculosomes). It has been applied at large-scale to analyze these 6 CYPs in 50 human livers samples (microsomes and mitochondria) to study the phenotype/genotype relationship. This method, which could easily be applied to other CYPs, provides an important tool to improve the understanding and prediction of pharmacokinetics and toxicity profile of drugs and other chemicals.

Les thérapies anticancéreuses ont connu ces dernières années un développement important ayant pour conséquence une amélioration dans la qualité de vie des patients. Cependant la survenue de résistances et la part significative de cancer sans traitement efficace nous oblige à envisager le développement de nouvelles stratégies anticancéreuses. Nous avons développé une nouvelle technique basée sur le principe du gène suicide en utilisant le gène du cytochrome P450 2B6 associé au cyclophosphamide (CPA). Cette technique qui consiste au transfert d’un gène métabolisant une prodrogue anticancéreuse dans la tumeur permet une sensibilisation des tumeurs à cette prodrogue. Le premier objectif de ce travail a consisté à améliorer le métabolisme de la prodrogue en construisant un gène muté du CYP2B6 en fusion avec la réductase, partenaire indispensable du CYP. Dans un deuxième temps nous avons transféré le gène CYP2B6TM-RED dans des cellules tumorales qui sont devenues sensibles au CPA entrainant une éradication des tumeurs. Ces résultats ont été confirmés in vivo sur des modèles de souris immunocompétentes. Nous avons, en plus de l’effet cytotoxique, mis en évidence un important effet bystander et le développement d’une immunité antitumorale spécifique. Ceci nous laisse penser que cette méthode peut permettre de protéger contre les récidives et les métastases. Les bons résultats obtenus dans le développement de cette nouvelle stratégie anticancéreuse, nous laissent espérer d’un futur passage en clinique. Pour cela de nouveaux modèles animaux devront être mis au point pour optimiser le transfert du transgène dans les tumeurs. / Anticancer therapies had, in recent years, an important development that results in an improvement in the quality of life of patients. However, the occurrence of resistance and the significant proportion of untreated cancer force us to consider the development of new anticancer strategies. We have developed a new technique based on the principle of suicide gene using the gene of cytochrome P450 2B6 associated with cyclophosphamide (CPA). This technique involves the transfer of a gene metabolizing an anticancer prodrug within the tumor allowing tumors sensitization to this prodrug. The first objective of this work was to improve the metabolism of the prodrug in building a mutated CYP2B6 fused with the reductase gene essential partner of CYP. In a second step we transferred the CYP2B6TM-RED gene in tumor cells that have been significantly sensitized. These results were confirmed on in vivo models of immunocompetent mice. In addition to the cytotoxic effect, mice were able to develop a specific anti-tumor immunity. This suggests to us that this method can protect against recurrence and metastasis. The good results obtained in the development of this new anticancer strategy, let us hope for a future transition into clinic. For this, new animal models will be developed to definitively validate the method.

Master of Science / Department of Entomology / Kun Yan Zhu / Cytochrome P450 monooxygenases (P450s) are important enzymes involved in the metabolism of a variety of xenobiotics, including insecticides and plant allelochemicals, and endogenous compounds, including juvenile hormones, ecdysteroids and fatty acids, in insects. Despite rapid advances in revealing various P450 genes in insects, our knowledge on the role of these genes in detoxification of insecticides is very limited. This research was to perform a genome-wide analysis of P450 genes and evaluate the role of selected P450 genes in detoxification of three commonly used pyrethroid insecticides in the yellow fever mosquito (Aedes aegypti). Our genome-wide analysis of revealed 159 P450 genes that can be classified into 18 families and 63 subfamilies. These genes are distributed in four clans, including 11 genes in the CYP2 clan, 80 in the CYP3 clan, 58 in the CYP4 clan and 10 in the mitochondrial CYP clan. The largest families are CYP6, CYP9, CYP4 and CYP325. The intron-exon organization of the genes is very diverse among the gene families, and the highest conservation of gene structures was observed in the CYP6 and CYP9 families predominantly containing single-intron genes. The phylogenetic analysis suggested that the CYP6 and CYP9 families might be derived from a common ancestor. The expression patterns of five transcripts including three individual genes (CYP6AA5, CYP6AL1 and CYP9J32) and two alternative splicing variants (CYP4J16A and CYP4J16B) of CYP4J16 were investigated in various tissues and at different developmental stages of the mosquito. Our results indicated differential expressions of these transcripts in different tissues and at different developmental stages examined. Furthermore, the exposure of the mosquitoes (larvae and adults) to each of three pyrethroid insecticides (permethrin, cypermethrin and deltamethrin) resulted in either down or up-regulation of these transcripts. Functional analyses of the selected P450 transcripts were conducted by using RNA interference (RNAi) followed by insecticide bioassay. RNAi was achieved by feeding mosquito larvae with chitosan/double stranded RNA (dsRNA) nanoparticles or injecting dsRNA to the adults. For the larvae, we obtained relatively low repressions of the P450 transcripts but the repressions were sufficient for carrying out our functional studies. Our study showed increased mortalities by 41.2% to cypermethrin when CYP6AA5 was silenced and 46.0% to permethrin when CYP9J32 was silenced. Similarly, the injection of dsRNAs in adults resulted in significant repressions of the P450 transcripts, and subsequent insecticide exposures led to a 29.3% increase in the adult mortality to cypermethrin when CYP6AA5 was silenced. Our further analysis of the nuclear receptor HR96 in the up-regulation of the P450 genes showed that when HR96 was silenced by RNAi, the up-regulation of CYP4J16B by cypermethrin was reduced by 10.1-fold but silencing HR96 did not affect the up-regulation of other P450 genes examined. These results suggest that HR96 is likely involved in regulating the expression of CYP4J16B in Ae. aegypti. However, different regulatory mechanism (s) may be involved in the up-regulation of other P450 genes examined. Model structure of CYP6AA5 was created by homology modeling and insecticides substrates were docked into the active site of this protein. Our results indicate that all three insecticides can fit into the catalytic pocket. The interaction distances between the heme iron and the putative aromatic hydroxylation site were 9.2, 9.4 and 7.2 Å for permethrin, cypermethrin and deltamethrin, respectively, whereas for aliphatic hydroxylation site these distances were 5.3, 2.8 and 2.9 Å. These results showed that CYP6AA5 may be able to metabolize cypermethrin and deltamethrin preferentially by aliphatic hydroxylation as indicated by the close interaction with the heme iron.

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Introduction Earlier studies have shown the popularity of herbal products among people as traditional, complementary or alternative medication. One of the major clinical risks in the concomitant administration of herbal products and prescription medicine is pharmacokinetic herb-drug interaction (HDI). This is brought about by the ability of phytochemicals to inhibit or induce the activity of metabolic enzymes and transport proteins. The aim of this study was to investigate the potential of the crude extracts of popular medicinal herbs used in South Africa to inhibit major cytochrome P450 (CYP) enzymes and transport proteins through in vitro assessment. Methods Medicinal herbs were obtained from traditional medical practitioners and 15 were selected for this study. The selected herbal products were extracted and incubated with human liver microsomes to monitor the following reactions as markers for the metabolic activities of the respective CYP: phenacetin O-deethylation (CYP1A2), diclofenac 4‟-hydroxylation (CYP2C9), S-mephenytoin 4‟- hydroxylation (CYP2C19) and testosterone 6β-hydroxylation (CYP3A4). In addition, the influence of Lessertia frutescens (formerly Sutherlandia frutescens) and Hypoxis hemerocallidea was investigated on more isozymes: coumarin 7-hydroxylation (CYP2A6), bupropion hydroxylation (CYP2B6), paclitaxel 6α-hydroxylation (CYP2C8), bufuralol 1‟-hydroxylation (CYP2D6), chlorzoxazone 6- hydroxylation (CYP2E1) and midazolam 1‟-hydroxylation (CYP3A4/5). The generation of the CYPspecific substrates/metabolites were monitored and quantified with the aid of LC-MS/MS. The metabolic clearance of midazolam using cryopreserved hepatocytes was monitored in the presence of Lessertia frutescens and Hypoxis hemerocallidea. The potential of both to inhibit human ATP-binding cassette (ABC) transporter activity was assessed using recombinant MDCKII and LLC-PK1 cells overexpressing human breast cancer resistant protein (BCRP) and human P-glycoprotein (P-gp), respectively. Similarly, the potential for interactions with human organic anion transporting polypeptide (OATP1B1 and OATP1B3) was assessed using recombinant HEK293 cells over-expressing OATP1B1 and OATP1B3, respectively. Results Bowiea volubilis, Kedrostis Africana, Chenopodium album, Lessertia frutescens (methanolic extract), Hypoxis hemerocallidea, Spirostachys africana and Lessertia frutescens (aqueous extract), in ascending order of potency demonstrated strong inhibition of CYP1A2 activity (IC50 = 1-100 g/mL). Similarly, Emex australis, Alepidea amatymbica, Pachycarpus concolor, Lessertia frutescens, Capparis sepiaria, Kedrostis africana and Pentanisia prunelloides inhibited CYP2C9 with IC50 less than 100 g/mL. The following demonstrated strong inhibition of CYP2C19 with IC50 values less than 100 g/mL: Acacia karroo, Capparis sepiaria, Chenopodium album, Pachycarpus concolor, Ranunculus multifidus, Lessertia frutescens and Zantedeschia aethiopica. CYP3A4 was inhibited by Lessertia frutescens, Hypoxis hemerocallidea, Spirostachys Africana, Bowiea volubilis, Zantedeschia aethiopica, Chenopodium album, Kedrostis Africana, Acacia karroo, Emex australis, Pachycarpus concolor, Ranunculus multifidus, Capparis sepiaria and Pentanisia prunelloides. Time-dependent (irreversible) inhibition of CYP3A4/5 (KI = 296 μg/mL, kinact = 0.063 min-1) and delay in the production of midazolam metabolites in the human hepatocytes, leading to a 40% decreased midazolam upscaled in vivo clearance, was observed with Lessertia frutescens. Further, Lessertia frutescence inhibited the activity of P-gp (IC50 = 324.8 μg/mL), OATP1B1 (IC50 = 10.4 μg/mL) and OATP1B3 (IC50 = 6.6 μg/mL). Hypoxis hemerocallidea inhibited the activity of OATP1B1 (IC50 = 118.7 μg/mL) and OATP1B3 (IC50 = 290.1 μg/mL) with no potent inhibitory effects on P-gp. None of the two inhibited the activity of BCRP within the tested concentrations. Conclusion The result indicates the potential for HDI between the selected medicinal herbs and the substrates of the enzymes investigated in this study, if sufficient in vivo concentrations are achieved. / AFRIKAANSE OPSOMMING: Inleiding Vroeëre studies het aangedui dat die gebruik van plantaardige produkte as tradisionele, aanvullende en alternatiewe medikasie baie gewild is. Een van die grootste kliniese risiko‟s geassosieer met die gelyktydige gebruik van plantaardige produkte met voorskrifmedikasie is farmakokinetiese kruiegeneesmiddel interaksies (HDI). Hierdie interaksies word veroorsaak deur die vermoë van plantchemikalieë om die aktiwiteit van metaboliese ensieme en transportproteïene te inhibeer of te induseer. Die doel van hierdie studie is om ondersoek in te stel na die moontlikheid van onsuiwer ekstrakte van gewilde Suid-Afrikaanse medisinale kruie om die belangrikste sitochroom P450 (CYP)- ensieme en transportproteïene te inhibeer. Hierdie ondersoek sal plaasvind deur middel van in vitrostudies. Metodes Medisinale kruie is verkry vanaf tradisionele genesers, waaruit ʼn totaal van 15 kruie geselekteer is vir gebruik tydens hierdie studie. Die geselekteerde kruie is geëkstraheer en met menslike lewermikrosome geïnkubeer om die volgende reaksies as merkers vir die metaboliese aktiwiteit van die onderskeie CYP-ensieme te moniteer: fenasetien-O-deëtilasie (CYP1A2), diklofenak-4‟- hidroksilasie (CYP2C9), S-mefenitoïen-4‟-hidroksilasie (CYP2C19) en testosteroon-6β-hidroksilasie (CYP3A4). Afgesien van die voorafgaande, is ook die invloed van Lessertia frutescens en Hypoxis hemerocallidea op verskeie ander iso-ensieme ondersoek. Hierdie iso-ensieme is soos volg: koumarien-7-hidroksilasie (CYP2A6), bupropioonhidroksilasie (CYP2B6), paklitaksiel-6α-hidroksilasie (CYP2C8), bufuralol-1‟-hidroksilasie (CYP2D6), chloorsoksasoon-6-hidroksilasie (CYP2E1) en midasolaam-1‟- hidroksilasie (CYP3A4/5). Die produksie van CYP-spesifieke substrate/metaboliete is gemoniteer en deur middel van LC-MS/MS-analises gekwantifiseer. Die metaboliese opruiming van midasolaam deur middel van krio-gepreserveerde hepatosiete is gemoniteer in die teenwoordigheid van Lessertia frutescens en Hypoxis hemerocallidea. Die moontlikheid van beide om menslike ATPbindingskasset (ABC)-transporteerderaktiwiteit te inhibeer is bepaal deur die gebruik van rekombinante MDCKII- en LLC-PK1-selle wat onderskeidelik menslike borskanker-weerstandige proteïen (BCRP) en menslike P-glikoproteïen (P-gp) potensieel. Op ʼn soortgelyke wyse is die moontlikheid vir interaksies met menslike organiese anion-transportpolipeptiede (OATP1B1 en OATP1B3) bepaal deur rekombinante HEK293-selle te gebruik wat onderskeidelik OATP1B1 en OATP1B3 potensieel. Resultate Bowiea volubilis, Kedrostis Africana, Chenopodium album, Lessertia frutescens (metanol-ekstrak), Hypoxis hemerocallidea, Spirostachys africana en Lessertia frutescens (water-ekstrak), in toenemende potensie, het sterk inhibisie van CYP1A2-aktiwiteit (IC50 = 1-100 g/mL) getoon. In ooreenstemming met die voorafgaande resultate het Emex australis, Alepidea amatymbica, Pachycarpus concolor, Lessertia frutescens, Capparis sepiaria, Kedrostis africana en Pentanisia prunelloides CYP2C9 met IC50–waardes van minder as 100 g/mL geïnhibeer. Die volgende het sterk inhibisie van CYP2C19 met IC50-waardes van minder as 100 g/mL getoon: Acacia karroo, Capparis sepiaria, Chenopodium album, Pachycarpus concolor, Ranunculus multifidus, Lessertia frutescens en Zantedeschia aethiopica. CYP3A4 is deur Lessertia frutescens, Hypoxis hemerocallidea, Spirostachys Africana, Bowiea volubilis, Zantedeschia aethiopica, Chenopodium album, Kedrostis Africana, Acacia karroo, Emex australis, Pachycarpus concolor, Ranunculus multifidus, Capparis sepiaria en Pentanisia prunelloides geïnhibeer. Tydafhanklike (onomkeerbare) inhibisie van CYP3A4/5 (KI = 296 μg/mL, kinact = 0.063 min-1) en vertraging in die produksie van midasolaammetaboliete in menslike hepatosiete wat aanleiding gee tot ʼn 40% afname in midasolaam bepaal in vivo opruiming, is waargeneem met Lessertia frutescens. Lessertia frutescens het ook die aktiwiteit van P-gp (IC50 = 324.8 μg/mL), OATP1B1 (IC50 = 10.4 μg/mL) en OATP1B3 (IC50 = 6.6 μg/mL) geïnhibeer. Hypoxis hemerocallidea het die aktiwiteit van OATP1B1 (IC50 = 118.7 μg/mL) en OATP1B3 (IC50 = 290.1 μg/mL) geïnhibeer met geen betekenisvolle effekte op P-gp nie. Geen een van die twee het die aktiwiteit van BCRP geïnhibeer binne die konsentrasies waarin getoets is nie. Gevolgtrekking Die resultate van hierdie studie dui aan dat wanneer voldoende in vivo-konsentrasies bereik word, die moontlikheid vir kruie-geneesmiddel interaksies tussen die geselekteerde medisinale kruie en ensiemsubstrate ʼn werklikheid word.

Tuberculosis (TB) affects nearly a third of the world’s population and has been termed a ‘Global Emergency’ by the WHO. The emergence of multi/extensively drug resistant (M/XDR) strains of Mycobacterium tuberculosis (Mtb), the causative agent of TB, and the increasing incidences of azole drug resistant sterol demethylases (CYP51) from pathogenic fungi has propelled studies to understand mechanisms of azole drug resistance on the drug target CYP51. Since Mtb is devoid of a sterol biosynthetic pathway, the presence and study of CYP51B1 and 19 other Cytochrome P450s in its genome is important to clarify host-pathogen mechanism of infection and the potential of using azole drugs to treat TB. In this study, CYP51B1 from Mtb was used as the model enzyme to study CYP51 mutants from Candida albicans fluconazole-resistant clinical strains. By protein engineering methods, F89H, L100F, S348F, G388S and R391K CYP51B1 mutants were made and azole drug binding properties were investigated using stopped-flow kinetics and static equilibrium methods. Dissociation constant (Kd) values were derived for a range of commercially available azole drugs by fitting the equilibrium binding data to a hyperbolic equation. Kd values for stopped-flow kinetics were derived by plotting observed binding rates (kobs) across different azole drug concentrations against time, followed by fitting multiple kobs data to a linear equation to derive azole drug de-binding (koff) and binding (kon) rate constants – the Kd was obtained by koff/kon. Extinction coefficient for heme b content in mutants and Wild Type (WT) CYP51B1 were an average of ɛ419 = 96.1 mM-1 cm-1. Biochemical characterisation of the mutants were carried out using established experiments on CYP51 – reduction of Fe(III)-heme to Fe(II)-heme, NO binding to Fe(III)-heme, rates of CO-Fe(II) adduct formation and rates of collapse of the P450 to P420 species in the presence of CO and estriol with redox partners from Mtb. In order to elucidate the effects of the above mutations on the iron-heme catalytic region, electron paramagnetic resonance (EPR) experiments were carried out with and without azole drugs. Circular dichroism (CD), differential scanning calorimetry (DSC) and multi-angled laser light scattering (MALLS) analysis confirmed that F89H, R391K and L100F mutants were stable and homogeneous. Crystallogenesis was successful for the above mentioned mutants and atomic structures were obtained for all mutants and WT CYP51B1 (in ligand-bound and substrate-free forms), except for S348F and G388S mutants which were expressed as inclusion bodies and 60% holoenzyme, respectively. Reconstituted catalytic assays to determine the sterol demethylating propensity of the mutants were carried out using redox partners from Mtb or E. coli, and with lanosterol and dihydrolanosterol as the surrogate substrates. Redox potentiometry showed similar potentials to WT for all mutants except for the G388S mutant which was relatively positive (–102 mV). Redox cycling experiments followed by EPR analysis for mutants and WT resulted in a novel P450 high-spin species at g value 5.84 (80 %) which gradually collapsed to the initial low spin state over 48 h. Expression trials were concurrently carried out on two other Mtb P450 genes – CYP123 (Rv0744c) and CYP136 (Rv3059) products of which may have similar functions to CYP51B1 or may share similar redox partners. CYP123 is located on the same operon as CYP51B1 while CYP136 has a 29% sequence identity to another CYP51 from a marine slime bacterium. Although further work is necessary, in this study CYP123 was expressed totally as inclusion bodies while CYP136 was expressed as soluble apoprotein fused with trigger factor chaperone.