Neste trabalho foi investigado o potencial de modelos metaloporfirínicos em mimetizar a ação do citocromo P450 na oxidação de um herbicida, a atrazina. Foram utilizadas as metaloporfirinas comerciais de segunda geração solúveis em solvente orgânico, cloreto de 5,10,15,20-tetrakis(2,6-diclorofenil)porfirina metal(III) [M(TDCPP)Cl] e cloreto de 5,10,15,20-tetrakis(pentafluorofenil) porfirina metal(III) [M(TFPP)Cl] (metal = ferro e manganês), tanto em solução homogênea como suportadas em montmorilonita K-10 aminofuncionalizadas; e metaloporfirinas solúveis em água, como a cloreto de 5,10,15,20-tetrakis-(N-metil-4-piridil) porfirina ferro(III), [Fe(TMPy)Cl], e cloreto de [5,10,15,20-tetra(4-carboxifenil)porfirina] ferro(III), [Fe(TCPP)Cl]. Os oxidantes testados foram iodosilbenzeno, ácido metacloroperbenzóico e peróxido de hidrogênio em água, metanol e acetonitrila. Os produtos de oxidação da atrazina foram identificados por cromatografia líquida de alta eficiência (CLAE). Os resultados mostraram que as metaloporfirinas foram capazes de oxidar a atrazina, um herbicida com características de persistência no meio ambiente, e mimetizar a ação da enzima in vivo e in vitro com formação de dois metabólitos: DEA e DIA, resultado da N-desalquilação das cadeias etila e propila do substrato, respectivamente. O DEA correspondeu a um dos principais produtos da reação, e formou-se apenas traços de DIA, mostrando a preferência das metaloporfirinas em oxidar a cadeia etila da atrazina. Verificou-se também a formação de cinco produtos desconhecidos, sendo possível a identificação de apenas um deles por espectrometria de massas, devido à baixa concentração dos demais, o qual corresponde à formação de uma amida na cadeia etila da atrazina (COA). Esse composto correspondeu ao produto de maior rendimento na maioria das reações. O monitoramento das reações em diferentes intervalos de tempo e a variação nas condições reacionais mostraram que os principais produtos de oxidação do herbicida, DEA e COA, são formados por mecanismos independentes e por espécies catalíticas distintas. O DEA é formado via espécie ativa Me(V)OP [Mn(V)OP ou Fe(IV)OP+], enquanto o COA é originado via Me(IV)OP [Mn(IV)OP ou Fe(IV)OP]. Estudos de intermediários por UV-Vis e EPR mostraram que a espécie ferril predomina como intermediário de reação para os sistemas Fe(TFPP)Cl/ACN com os dois oxidantes, iodosilbenzeno e ácido metacloroperbenzóico. Para as metaloporfirinas Fe(TCPP)Cl e Fe(TMPy)Cl o estudo da oxidação do herbicida ficou comprometido devido à baixa solubilidade da atrazina em água, o que provocava sua precipitação e destruição do catalisador. Para as metaloporfirinas suportadas em montmorilonita K-10 aminofuncionalizada também não foi observada formação de produtos, resultado atribuído à dificuldade do substrato, considerado bastante inerte, atingir o sítio catalítico. Todos esses resultados mostraram o potencial de aplicação desses modelos biomiméticos em estudos que buscam elucidar o metabolismo de herbicidas in vivo, tendo em vista a dificuldade de se trabalhar com as enzimas in vitro, e resultaram na proposição de um esquema de reação da oxidação da atrazina catalisada pelas metaloporfirinas nas condições estudadas. / In this work we investigated the ability of metalloporphyrin model systems to mimic the action of cytochrome P450 in the oxidation of a herbicide, atrazine. To this end, we employed the second generation commercially available metalloporphyrins metal (III) 5,10,15,20-tetrakis(2,6-dichlorophenyl)porphyrin chloride [M(TDCPP)Cl] and metal (III) 5,10,15,20- tetrakis(pentafluorophenyl)porphyrin chloride [M(TFPP)Cl] (metal = iron or manganese), all soluble in organic solvents, as well as the water soluble metalloporphyrins iron (III) 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin chloride [Fe(TMPy)Cl] and iron (III) 5,10,15,20-tetrakis(4-carboxyphenyl)porphyrin chloride [Fe(TCPP)Cl]. These metalloporphyrins were used both in homogeneous solution and supported on montmorillonite K-10. Iodosylbenzene, metachloroperbenzoic acid, and hydrogen peroxide were tested as oxidants, using one of the following reaction media: water, methanol, and acetonitrile. Products generated during atrazine oxidation were identified by high performance liquid chromatography. Our results show that the metalloporphyrins are able to oxidize atrazine, a highly persistent herbicide in the environment, as well as mimic the action of P450 enzymes both in vivo and in vitro, with formation of two metabolites, namely DEA and DIA, which result from the N-dealkylation of the ethyl and propyl chains of the substrate, respectively. We also detected the formation of five unknown products, and we were able to identify only one of them by means of mass spectrometry, which corresponds to the formation of an amide on the atrazine ethyl chain (COA) and was the compound obtained in highest yields in most of the reactions. The other four unknown products were obtained in very low concentrations, which prevented us from determining their structures. By monitoring the reactions at different time intervals and varying the reactional conditions, we were able to see that the main herbicide oxidation products, DEA and COA, are generated via distinct mechanisms and different active catalytic species. DEA is formed via the species Me(V)OP [Mn(V)OP or Fe(IV)OP.+], while COA results from the action of the species Me(IV)OP [Mn(IV)OP or Fe(IV)OP]. Studies of the reaction intermediates by UV-VIS and EPR showed that the ferryl species is the main reaction intermediate in the case of Fe(TFPP)Cl/ACN systems and the oxidants, iodosylbenzene and metachloroperbenzoic acid. Studies of herbicide oxidation were difficult to carry out in the case of the metalloporphyrins Fe(TCPP)Cl and Fe(TMPy)Cl due to the low solubility of atrazine in water, which led to its precipitation and catalyst destruction. With respect to the metalloporphyrins supported on montmorillonite K-10, no reaction products were obseved because of the difficult diffusion of the inert substrate into the catalytic site. All these results demonstrate the potential application of these biomimetic model systems in studies that pursue the elucidation of herbicide metabolism in vivo, especially when one bears in mind the difficulty in working with enzymes in vitro. Our data enabled the proposition of a scheme for metalloporphyrin-catalyzed atrazine oxidation under the conditions used herein.

The process of in vitro-in vivo extrapolation (IVIVE) can be used to predict pharmacokinetics of drugs in patients using data from in vitro systems. This process relies on the use of experimentally obtained scaling factors, such as abundances of different drug-metabolising enzymes and microsomal protein content (MPPGL). The use of simulators is dependent on abundances and activities of pharmacokinetically relevant enzymes. The incorporation of inter-individual variability in abundances of enzymes, correlations between enzyme expression patterns, and relationships between genetic, physiological, and environmental factors and enzyme expression and activity can make predictions using IVIVE and simulations of pharmacokinetic experiments in virtual populations more accurate and realistic. Incorporation of variability and correlations can also assist in predicting extreme cases where drug therapy may be ineffective or may cause adverse effects. A meta-analysis of 52 studies was carried out to assess the reported abundances of cytochrome P450 and uridine glucuronosyltransferase (UGT) enzymes in adult Caucasian subjects. Some heterogeneity was found between studies and the weighted means and overall coefficients of variation were calculated. Some strong enzyme expression correlations were identified; CYP3A4/CYP3A5*1/*3 (rs = 0.66, p < 0.0001, n = 37), CYP3A4/CYP2C8 (rs = 0.79, p < 0.0001, n = 107), and CYP2C8/CYP2C9 (rs = 0.71, p < 0.0001, n = 72). A quantitative protocol based on targeted proteomics was used to quantify cytochrome P450 and UGT enzymes in adult liver samples (n = 24). The QconCAT standard used for quantification was successfully expressed in-house after optimisation of the expression protocol, and the utility of two strategies in expressing recalcitrant QconCAT proteins was highlighted; the use of a fusion partner and reshuffling the order of peptides in the sequence. The enzymes quantified in this study were CYP1A2, 2A6, 2B6, 2C8, 2C9, 2C18, 2D6, 2J2, 3A4, 3A5, 3A7, 3A43, and 4F2, and UGT1A1, 1A3, 1A4, 1A6, 1A9, 2B4, 2B7, and 2B15. Correlations of expression identified in the meta-analysis were confirmed and new correlations were demonstrated between UGT enzymes and between enzymes from the two families. Correlations between UGT enzymes were particularly strong and statistically significant. Relationships between enzyme expression levels and genotype, age, sex, smoking, and alcohol consumption were investigated. A significant effect of genotype on expression was seen for CYP3A5 (p < 0.0001). An overall moderate decline of expression with age was observed for all the enzymes under study; however, this relationship was not statistically significant in most cases. Gender did not have a considerable effect on expression, although some differences in expression were observed between male and female donors. Smoking seemed to induce the expression of all enzymes; however, statistically significant induction was demonstrated only in the cases of CYP2A6, CYP3A4, CYP3A7, and UGT1A1 (p < 0.05). Alcohol consumption was not shown to have a considerable effect on enzyme expression. Two pig livers were used to optimise some aspects of the experimental protocol including solubilisation and digestion of proteins. Pig MPPGL was measured and relative hepatic contents of drug-metabolising cytochrome P450 enzymes in pig liver were established using label-free quantification.

Mycobacterium tuberculosis (Mtb) causes tuberculosis (TB) and poses a global threat to human health. A third of the world’s population is infected with Mtb. Multi-drug resistant and extensively drug resistant Mtb strains are widespread and development of new drugs is urgently needed to treat drug resistant TB. This thesis focuses on the Mtb cytochrome P450 (P450) enzymes CYP126A1 and CYP143A1. P450s are heme-binding enzymes that catalyse activation of molecular oxygen and the oxidation of substrates bound close to the heme. CYP126A1 and CYP143A1 are “orphans” in terms of their functional characterization, but potential drug targets in view of ability of azole-based P450 inhibitors to inhibit growth and viability of Mtb. The CYP126A1 and CYP143A1 genes were cloned and expressed in Escherichia coli. Expression conditions and strains were optimised to maximise soluble protein production and methods were developed to purify the P450s using affinity, ion exchange and size exclusion chromatography. Both P450s were shown to bind heme b, and heme was shown to be axially coordinated by a cysteine thiolate and a water molecule in both cases using UV-visible and electron paramagnetic resonance (EPR) spectroscopy. Both P450s bound carbon monoxide (CO) in their reduced forms to produce heme Fe2+-CO complexes with absorption maxima at ~450 nm – characteristic of P450s. CYP126A1 and CYP143A1 bound avidly to a range of inhibitors, including several azole drugs. As examples, binding constant (Kd) values of 13.8 µM and 21.9 µM were determined for clotrimazole and econazole with CYP143A1; while ketoconazole bound CYP126A1 with a Kd of 0.20 µM. Each of these drugs is very effective in inhibiting Mtb growth. EPR confirmed inhibitory coordination of both P450s by azole drug nitrogen atoms; though indirect coordination via a retained axial water ligand may also occur in some cases. Extinction coefficients were determined as έ420 = 125 mM-1 cm-1 (CYP126A1) and έ415 = 105 mM-1 cm-1 (CYP143A1). CYP126A1’s heme iron redox potential was shown to be unusually positive (E°’ = -80 mV). Light scattering studies showed CYP126A1 to be a monodisperse, monomeric protein. CYP143A1 is also mainly a monomer, but with a small proportion of an oligomeric form. Despite its polydispersity, CYP143A1 was crystallized and its structure solved by X-ray diffraction to a resolution of 1.9 Å, using molecular replacement with the Mtb P450 CYP142A1. A limited compound screen of typical P450 substrates failed to provide “hits” to identify CYP143A1 substrate selectivity, but the presence of polyethylene glycol in the CYP143A1 active site in crystals suggests fatty acids as potential substrates. CYP126A1 was crystallized for studies to identify binding modes of small molecules (“fragments”) identified to interact with CYP126A1 by NMR. Crystal structures of CYP126A1 in complex with two such fragments (NMR401 and NMR343) were determined to ~2.0 Å resolution in ongoing research to build Mtb P450 isoform-specific inhibitors. Compounds identified as CYP126A1 substrates/inhibitors identified by high-throughput screening were validated by UV-visible titrations with the P450, and binding modes and affinity established. In conclusion, this thesis provides novel insights into the biochemical, biophysical and structural properties of two novel Mtb P450s that are potential targets for new anti-TB drugs.

Orientador: Paulo Eduardo Martins Ribolla / Resumo: Introdução: O desenvolvimento de estratégias para redução no custo do sequenciamento de genoma completo (WGS) é importante para projetos que demandam por grandes quantidades de amostras. Uma estratégia de baixo custo é o sequenciamento de baixa cobertura aliado a técnicas de imputação para genotipagem eficiente e de confiabilidade adequada. A malária é uma das principais doenças transmitidas por artrópodes no mundo e o Brasil é considerado um país com alta incidência de malária, principalmente na região Amazônica, sendo principal vetor o mosquito Anopheles darlingi. Objetivo: O objetivo do presente estudo foi desenvolver estratégia para analisar dados de WGS de baixa cobertura de mosquitos Anopheles darlingi coletados no município de Mâncio Lima no Acre e verificar associação entre dados genéticos e dados de importância epidemiológica, tais como comportamento de picada, horário de atividade e distanciamento em escala microgeográfica. Materiais e métodos: Amostras de mosquitos Anopheles darlingi foram coletadas no município de Mâncio Lima - AC, entre 2016 e 2017. As bibliotecas foram preparadas com Nextera™ XT e sequenciadas no NextSeq500 da Illumina. Foi realizado genotipagem por sequenciamento e aplicado imputação. Estudos de associação ampla do genoma foram realizados com comportamento de picada e horário de atividade. Sinais de estratificação na população foram investigados por FST amplo no genoma e teste de permutação para significância. Resultados: Sinais fracos porém si... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Introduction: Strategy development to reduce the cost of whole genome sequencing (WGS) is important for projects that demand large quantities of samples. A low-cost strategy is low-coverage sequencing combined with imputation techniques for efficient genotyping and sufficient confiability. Malaria is one of the main diseases transmitted by arthropods in the world and Brazil is considered a country with a high incidence of malaria, especially in the Amazon region with the main vector being the Anopheles darlingi mosquito. Objective: The objective of the present study was to develop a strategy to analyze low-coverage WGS data from Anopheles darlingi mosquitoes collected in the municipality of Mâncio Lima in Acre State and verify associations between genetic data and data of epidemiological importance, such as biting behavior, time of activity and distance on a microgeographic scale. Materials and methods: Samples of Anopheles darlingi mosquitoes were collected in the municipality of Mâncio Lima - AC, between 2016 and 2017. The libraries were prepared with Nextera ™ XT and sequenced on Illumina's NextSeq500. Genotyping by sequencing was performed and imputation was applied. Genome wide association studies were performed with biting behavior and time of activity. Population stratification signals were investigated by genome-wide FST and permutation test applied for significance. Results: Weak but significant stratification signals were identified considering distances of 2 to 3 k... (Complete abstract click electronic access below) / Mestre

Tumour-related diseases are the second most common cause of death in the Czech Republic, right after cardiovascular diseases. Nanomedicine - a novel scientific discipline - shows captivating potential in anticancer treatment with help of so called nanotranporters - nanoparticles capable of transporting other molecules. Encapsulation of a cytostatic drug into a nanoparticle improves its pharmacokinetical and pharmacodynamical properties which helps to reduce adverse side effects on non-tumour healthy tissue. In the scope of this diploma thesis apoferritin - apo-form of ferritin - was studied, since this nanotransporter shows promise for clinical use in anticancer treatment. Effect of hepatic microsomes from premedicated and control rats on biotransformation of doxorubicin cytostatic (Dox) in free and apoferritin nanoparticle-bound forms was investigated at pH 7,4. Over the course of biotransformation two types of metabolites - M1 and M2 - were observed. Regardless of the employed inductor all studied microsomes have exhibited similar metabolism of free doxorubicin and its apoferritin encapsulated form (ApoDox). Our results also imply that doxorubicin can be metabolically processed by rat hepatic microsomes in both free and ApoDox form with similar efficiency. We have also studied biotransformation...

Cytochromes P450 form a large family of hemoproteins. Some of them are responsible for the metabolism of endogenous substrates, but their major role is in detoxification of exogenous substrates (xenobiotics), some of them are activated to reactive species forming covalent adducts with DNA and increasing intracellular oxidative stress. Cytochrome P450 are considered by very promiscuous in terms of their substrate specificity, thus one enzyme can typically oxidize many substrates. Cytochrome P450 1A1 prefers a planar aromatic compounds (e.g. polycyclic aromatic hydrocarbons, azo dyes, etc.). Cytochrome P450 1A2 elicits similar substrate specificity, but prefers slightly basic aromatic derivatives, for example caffeine. This work focuses on (i) the preparation of expression vectors containing genes encoding human cytochromes P450 1A1 and 1A2, (ii) their consequent expression in heterologous system followed by (iii) isolation of corresponding proteins. The genes coding both proteins were modified and transferred from older vectors to the more efficient to expression plasmids pET-22b. However, the new constructs did not produce stable native proteins. The modified genes were therefore transferred to the original expression plasmids pCW. The problem with the incorporation of native human form of...

Malaria, a disease caused by parasites of the Plasmodium genus, infects over 220 million people annually, resulting in over 400,000 deaths. Most of these deaths occur in Africa in children < 5 years of age. Artemisia annua L., an ancient Chinese medicinal herb, is known for its foremost phytochemical constituent, artemisinin (AN). Semisynthetic derivatives of AN form the primary component of artemisinin combination therapies (ACTs), the frontline treatment for malaria worldwide. However, ACTs have several drawbacks including cost and availability. Thus, cheaper, more readily available antimalarials are needed. Recent clinical data suggested dried leaves of A. annua (DLA) administered orally as a tea infusion may be as efficacious as ACTs despite a significantly lower AN dose delivered. In mice, AN plasma concentration was improved when administered as DLA compared to pure AN. I therefore hypothesized that phytochemicals within DLA enhanced the oral bioavailability of AN. To investigate this hypothesis, here I examined the effects of DLA on the underlying mechanisms that govern oral bioavailability. Using an in vitro human digestion model, I showed that AN solubility was greater when delivered as DLA, largely due to essential oil in the plant. Furthermore, AN intestinal permeability was enhanced in a Caco-2 cell model of the intestinal epithelium. Extracts, teas, and phytochemicals produced by Artemisia also inhibited the activity of CYP2B6 and CYP3A4, the enzymes responsible for first-pass AN metabolism in the liver. Additionally, AN tissue distribution was improved when delivered as DLA and AN accumulation in tissues was higher in female vs. male rats. Finally, I showed that DLA was a more efficacious anti-inflammatory than pure AN in rats, potentially due to enhanced AN bioavailability. Taken together, these results shed light on the mechanisms behind enhanced oral bioavailability afforded by DLA and demonstrate the potential for DLA to be used as a therapeutic for malaria and other diseases.

Alteration in diet and knockdown of detoxification genes impacts the response of C. elegans to oxygen deprivation stress. I hypothesized that feeding worms a vitamin D3-supplementation diet would result in differential oxygen deprivation stress response. We used a combination of wet lab and transcriptomics approach to investigate the effect of a vitamin-D3 supplemented diet on the global gene expression changes and the anoxia response phenotype of C. elegans (Chapter 2). C. elegans genome consists of 143 detoxification genes (cyp and ugt). The presence of a significant number of genes in these detoxification families was a challenge with identifying and selecting specific cyp and ugt genes for detailed analysis. Our goal was to understand the evolution, phylogenetic, and expression of the detoxification enzymes CYPs and UGTs in C. elegans (Chapter 3). We undertook a phylogenetic and bioinformatics approach to analyze the C. elegans, detoxification family. Phylogenetic analysis provided insight into the association of the human and C. elegans xenobiotic/endobiotic detoxification system. Protein coding genes in C. elegans have been predicted to be human orthologs. The results of this work demonstrate the role of C. elegans in the identification and characterization of vitamin D3 induced alterations in gene expression profile and anoxia response phenotypes and the identification of human orthologs for the detoxification enzymes and provides insight into the gene expression pattern.

Yes / Structural features from the anticancer prodrug nemorubicin (MMDX) and the DNA-binding molecule DRAQ5™ were used to prepare anthraquinone-based compounds, which were assessed for their potential to interrogate cytochrome P450 (CYP) functional activity and localisation. 1,4-disubstituted anthraquinone 8 was shown to be 5-fold more potent in EJ138 bladder cancer cells after CYP1A2 bioactivation. In contrast, 1,5-bis((2-morpholinoethyl)amino) substituted anthraquinone 10 was not CYP-bioactivated but was shown to be fluorescent and subsequently photo-activated by a light pulse (at a bandwidth 532–587 nm), resulting in punctuated foci accumulation in the cytoplasm. It also showed low toxicity in human osteosarcoma cells. These combined properties provide an interesting prospective approach for opto-tagging single or a sub-population of cells and seeking their location without the need for continuous monitoring.

Yes / Epidemiological studies have shown that head and neck cancer (HNC) is a complex multistage process that in part involves exposure to a combination of carcinogens and the capacity of certain drug-metabolising enzymes including cytochrome P450 (CYP) to detoxify or activate such carcinogens. In this study, CYP1A1, CYP1B1 and CYP2W1 expression in HNC was correlated with potential as target for duocarmycin prodrug activation and selective therapy. In the HNC cell lines, elevated expression was shown at the gene level for CYP1A1 and CYP1B1 whereas CYP2W1 was hardly detected. However, CYP2W1 was expressed in FaDu and Detroit-562 xenografts and in a cohort of human HNC samples. Functional activity was measured in Fadu and Detroit-562 cells using P450-Glo™ assay. Antiproliferative results of duocarmycin prodrugs ICT2700 and ICT2706 revealed FaDu and Detroit-562 as the most sensitive HNC cell lines. Administration of ICT2700 in vivo using a single dose of ICT2700 (150 mg/kg) showed preferential inhibition of small tumour growth (mean size of 60 mm3) in mice bearing FaDu xenografts. Significantly, our findings suggest a potential targeted therapeutic approach to manage HNCs by exploiting intratumoural CYP expression for metabolic activation of duocarmycin-based prodrugs such as ICT2700. / The authors would like to thank Bradford Institute for Health Research for funding a PhD studentship to DP through a competitive scheme and Yorkshire Cancer Research programme Grant (B381PA) for supporting our cytochrome P450-focused drug discovery research.