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New functionalized nucleic acids for application in chemical biology
Kielkowski, Pavel ; Hocek, Michal (advisor) ; Stiborová, Marie (referee) ; Moravcová, Jitka (referee)
4 Abstract This work is focused on the synthesis of the modified 2'-deoxyribonucleoside triphosphates, their incorporation into DNA and use in chemical biology applications. The synthetic routes to the double-headed nucleosides and nucleotide triphosphates in which the two nucleobases were connected via ethynyl or propargyl linker has been developed. (Cytosin-5-yl)ethynyl, 3-(cytosin-1-yl)prop-1-yn-1-yl and 3-(5-fluorocytosin-1-yl)prop-1-yn- 1-yl derivatives of pyrimidine and 7-deazaadenine 2'-deoxyribonucleosides and nucleoside triphosphates were prepared by aqueous palladium-catalyzed cross-coupling reactions. The double-headed modified nucleoside triphosphates were good substrates for DNA polymerases suitable for primer extension and PCR construction of DNA bearing linked cytosine or 5- fluorocytosine in the major groove mimicking the flliped-out nucleotide. The assay for the testing of the inhibition of DNA methyltransferases was developed. Next, the transient protection of DNA against cleavage by restriction endonucleases (REs) using (trialkylsilyl)ethynyl modified DNA was developed. A series of 7-(trialkylsilyl)ethynyl-7- deaza-2'-deoxyadenosine triphosphates was prepared and they were shown to be incorporated into DNA by primer extension and/or PCR using KOD XL polymerase. The deprotection conditions...
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Mechanisms of anticancer drug action in neuroblastomas
Groh, Tomáš ; Stiborová, Marie (advisor) ; Levová, Kateřina (referee) ; Vališ, Karel (referee)
Cancer cells are able to adapt to different stress factors such as hypoxia, which is caused by insufficient tumor vascularization. An increased acetylation status of histones H3 and H4 in UKF-NB-3 and UKF-NB-4 neuroblastoma cell lines was found to be a mechanism of adaptation of these cells to hypoxia. An increase in acetylation of histones H3 and H4 is suggested to cause changes in the structure of chromatin that lead to activation of gene transcription. In addition, cultivation of tested neuroblastoma cells under hypoxic conditions changes expression of proteins of a transcription factor N-myc, which is essential for development of neuroblastomas. This transcription factor is also responsible for a metabolic adaptation of neuroblastoma cells, increases their aggressiveness and its expression leads to a worse prognosis of the disease. Inhibitors of histone deacetylases (HDAC) are suggested to be the promising agents exhibiting various anticancer effects. They can induce cell cycle arrest, differentiation or programmed cell death in sensitive tumors. In this study, the effect of one of inhibitors of HDACs, valproate, on expression of proteins of transcription factors N-myc and hypoxia inducible factor 1α (HIF-1α) was investigated. Valproate decreases protein levels of both transcription factors in...
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Mechanism of enzymatic activation of carcinogens and drugs by the system of cytochrome P450
Indra, Radek ; Stiborová, Marie (advisor) ; Souček, Pavel (referee) ; Koblihová, Jitka (referee)
13 Abstract An environmental pollutant and a human carcinogen benzo[a]pyrene (BaP) is after its activation with cytochrome P450 (CYP) able to covalently bind to DNA. In the thesis, one of the target was to investigate an influence of individual components of mixed function monooxygenase (MFO) system on metabolism of benzo[a]pyrene and generation of adducts of activated BaP with DNA. The study was particularly focused to increase our knowledge on the effect of cyt b5 on metabolism of BaP by cytochrome P450 1A1 (CYP1A1) and its potential to serve as a donor of electrons during the reaction cycle of this cytochrome P450. The effect of cyt b5 on generation of BaP metabolites and adducts of BaP with DNA was investigated. In addition the effect of two different expression systems for cytochrome P450 1A1 (prokaryotic and eukaryotic) was also studied. The influence of cyt b5 on oxidation another xenobiotic compound, a plant alkaloid ellipticine that exhibit antitumor activities, was also investigated. Its pharmacological efficiency, as well as side effects depends on its metabolic activation by cytochrome P450. CYP3A4 is very important for ellipticine activation and therefore this enzyme was used in our experiments. Furthermore, a suitability of rat as a model organism mimicking the metabolic fate of BaP...
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Impact of isolate deficiency of F1FO-ATP syntthase on other complexes of oxidative phosphorylation in skin fibroblasts depending on cullture conditions
Kedrová, Kateřina ; Stiborová, Marie (advisor) ; Poljaková, Jitka (referee)
Isolated deficiency of F1FO-ATPsynthase is a soubgroup of mitochondrial diseases caused by mutations in nuclear and mitochondrial-encoded structural subunits, or nuclear-encoded assembly factors of F1FO-ATPsynthase. The most often mutations are found in a MTATP6 gene localized in the mitochondrial DNA and a TMEM70 gene, localized in the nuclear DNA. A MTATP6 gene encodes subunit a of F1FO-ATPsynthase and its mutation usually leads to reduced phosphorylation activity of F1FO-ATPsynthase. A TMEM70 gene encodes a 21 kDa mitochondrial protein of the inner mitochondrial membrane of not completely explained function and its mutation results in the decrease in a content of fully assembled F1FO- ATPsynthase. The aim of this thesis was to investigate the impact of isolated F1FO- ATPsynthase deficiency on the oxidative phosphorylation system (complex I-IV), other selected mitochondrial proteins, and mitochondrial network in two cell lines of primary human skin fibroblasts with an isolated deficiency of F1FO-ATPsynthase (mutation m.8851T>C in MTATP6 and mutation c.317-2A>G in TMEM70) during the first days of their cultivation in media containing galactose or glucose as a carbohydrate source with a presence or absence of L-glutamine. The control cell line was found to have higher amounts of respiratory chain...
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Insulin analogues with A-chain extended by the D-domain of IGF-1 and IGF-2
Povalová, Anna ; Stiborová, Marie (advisor) ; Dračínská, Helena (referee)
Insulin and insulin-like growth factors (IGF-1 and -2) together with their receptors take part in a complex system, which affects both basal metabolism of carbohydrates, lipids and proteins as well as cell growth, proliferation, differentiation and apoptosis. Defects in action of insulin or IGFs can lead to serious diseases such as diabetes or cancer. Both of these disorders represent nowadays one of the biggest health threats to the world's population. Insulin and IGFs induce different biological effects through their cognate receptors; two isoforms of the insulin receptor (IR-A and IR-B) and the receptor for IGF-1 (IGF-1R). These receptors bind insulin and IGFs with different affinities and induce different but partially overlapping signalling events leading towards metabolic (especially insulin) or mitogenic responses (IGFs and insulin). To understand the mechanism of action of insulin and IGFs it is important to specify which structural domains of these hormones are responsible for binding to the receptors and exerting specific effects. One region that is missing in insulin is the D-domain of IGF-1 and -2. For this reason, we decided to prepare insulin analogues with the A-chain extended by either the whole D-domain of IGF-1 or IGF-2, or by fragments of the IGF-1 D-domain in order to define the...
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Tandemová hmotnostní spektrometrie sfingolipidů s aplikací pro metabolické studie a diagnostiku sfingolipidos
Kuchař, Ladislav ; Ledvinová, Jana (advisor) ; Stiborová, Marie (referee) ; Holčapek, Michal (referee)
In recent years, mass spectrometry (MS) become the dominant technology in lipidomic analysis and widely influenced research and diagnosis of diseases of lipid metabolism, e.g. lysosomal storage disorders (LSD) characterized by impairment of the lysosomal functions. Defects in lysosomal processing of sphingolipids SFL belong to the category of sphingolipidoses. This condition has severe and even fatal clinical outcome. The primary aim of this work was to establish quantitative and qualitative methods of SFL analysis useful for research and diagnosis of LSD. At first, semisynthesis of mass labeled lipid standards utilizing immobilized sphingolipid ceramide N-deacylase was performed. Established methods of quantitative analysis were then used to prove the increased excretion of urinary SFL in LSD with characteristic storage in the kidney. Determination of excreted urinary SFL was found useful for differential diagnosis of prosaposin and saposin B deficiences for which routine enzymology is failing. MS also enabled monitoring of individual molecular species (isoforms) of SFL, which led to the finding that their urinary pattern is changing in some LSD. This resulted in the development of new screening method in dry urinary samples based on isoform profile evaluation. Another MS application referred to...
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Synthesis of nucleosides, nucleotides and nucleic acids bearing bipyridine-type ligands
Kalachová, Ľubica ; Hocek, Michal (advisor) ; Stiborová, Marie (referee) ; Rosenberg, Ivan (referee)
An efficient methodology of construction of base-modified nucleosides bearing oligopyridine ligands, based on the Sonogashira or Suzuki cross-coupling reaction of halogenated nucleosides, was developed. This methodology was then successfully employed in construction of base-modified DNA bearing oligopyridine ligands which were studied in post-synthetic complexation with labile transition metals. The first step in construction of modified DNA is the synthesis of deoxynucleoside triphosphate (dNTPs) bearing various metal chelating groups, which are in second step enzymatically incorporated into DNA by primer extension experiment. The first task was the synthesis of dNTPs bearing different oligopyridine ligands, which could be done by aqueous phase cross-coupling reaction with suitable building blocks or by triphosphorylation of oligopyridine-modified deoxynucleosides. Both ways were successfully used. Aqueous phase Sonogashira cross-coupling was used for synthesis of dNTPs bearing oligopyridine ligands attached via short and rigid acetylene tether, while classical triphosphorylation of modified nucleosides was used for construction of dNTPs bearing oligopyridine ligands attached via long and flexible octadiyne linker. Sonogashira cross-coupling reaction was also used for preparation of both types of...
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The role of Hippo Signalling pathway in tumor cell metabolism
Lettlová, Sandra ; Stiborová, Marie (advisor) ; Dračínská, Helena (referee)
Vitamine E analogues α-tocopheryl succinate (α-TOS) and mitochondrially targeted vitamine E succinate (MitoVES) are anti-cancer agents from the group of "mitocans", the compounds acting via mitochondria which present a promising invariant target for cancer cell therapy. α-TOS and MitoVES induce apoptosis selectively in various cancer cell types involving generation of reactive oxygen species (ROS). Generated superoxid anion radicals in response to α-TOS and MitoVES are believed to be converted into hydrogen peroxide that is known to activate Mammalian sterile 20-like kinase (Mst1), the central component of Hippo signalling pathway, that presents an universal size control mechanism in all metazoans and its deregulation is linked to tumourigenesis. MitoVES and α-TOS were both reported to activate Mst1 that phosphorylates Forkhead box O1 (FoxO1) transcription factor resulting in its transport to nucleus where induce the expression of pro-apoptotic genes, including NOXA, and thus promote apoptosis. The target of Hippo signalling pathway is transcriptional co- activator Yes-associated protein (Yap) which was found in Drosophila melanogaster to regulate the expression of transcription factor c-Myc which is known as the most prominent human oncogene. This thesis focused on involvement of Hippo signalling...
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Star polymeric carriers of drugs for targeting and pH-dependent release of drugs
Bittner, Matyáš ; Stiborová, Marie (advisor) ; Liberda, Jiří (referee)
This diploma thesis brings new data about design, synthesis, physico-chemical characterisation and biological efficacy of the novel star-like HPMA-based conjugates intended for treatment of solid tumors. Recently, many different water-soluble drug delivery systems based on N-(2- hydroxypropyl)methacrylamide (HPMA) copolymers have been described. Here, we report synthesis and physico-chemical characterisation of high molecular weight star-like HPMA- based polymer carriers with low polydispersity prepared by controlled grafting of HPMA copolymers onto PAMAM dendrimer core. With the aim to keep the polydispersity of drug delivery system as low as possible, reversible Addition-Fragmentation Chain Transfer (RAFT) polymerisation was used for HPMA-based polymer precursor preparation. The end groups of the polymer presursors was afterwards used for grafting using carbodidimide condensation reaction or copper free click chemistry on polyamidoamine (PAMAM) dendrimers resulting in a formation of star-like high-molecular-weight (HMW) drug carriers. Described synthetic procedure provided preparation of star-like HMW drug carriers with Mw between 1.105 - 3.105 g/mol and narrow distribution of Mw. The model drug, doxorubicin (Dox), was attached to the hydrazide group containing polymer cariers by pH- sensitive...
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Molecular mechanism of carcinogenicity of aristolochic acid
Levová, Kateřina ; Stiborová, Marie (advisor) ; Ryšlavá, Helena (referee) ; Souček, Pavel (referee)
Aristolochic acids (AA) are carcinogenic and nephrotoxic alkaloids from Aristolochia species. Aristolochic acid I (AAI), the major component of AA, causes the development of Aristolochic acid nephropathy (AAN) and Balkan endemic nephropathy (BEN). These two diseases cause total renal failure and urothelial malignancies. The fact that these diseases have not been developed in all persons, who have been exposed to their action, might be causd by different activities and protein levels of the enzymes metabolizing AAI. Thus, the identification of enzymes involved in the metabolism, and detailed knowledge of their expression and catalytic specifities is a major importance. Aristolochic acid I (AAI) can be metabolized by several types of reactions. Like most nitroaromatics, the main activation pathway of AAI is reduction of its nitro group to form a cyclic acylnitrenium ion, which can bind to the purine bases, thereby forming AAI-DNA adducts. The detoxication pathway of AAI is its oxidative demethylation by cytochromes P450 forming detoxication metabolite 8-hydroxyaristolochic acid Ia (AAIa). In the present thesis, using rat and human enzymes and as well as several mice models, the metabolism of AAI in vitro and in vivo was investigated. The first model has deleted gene for NADPH:cytochrome P450...
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