Title: Gallium Complexes for Molecular Imaging of Bone Tissue Author: Bc. Jan Holub Department of Inorganic Chemistry, Faculty of Science, Charles University Supervisor: RNDr. Vojtěch Kubíček, PhD. Supervisor's Email address: kubicek@natur.cuni.cz ABSTRACT This thesis is focused on preparing new ligands for selective complexation of gallium, which might serve as potential radiopharmaceuticals for 68 Ga-PET bone imaging. Two new ligands were prepared, combining 1,4,7-triazacyclonone-1,4-diacetic acid macrocyclic skeleton and bis(phosphonate) pendant arm, bound to the remaining free nitrogen atom on the macrocycle. Macrocyclic skeleton is responsible for high kinetic and thermodynamic stability of the Ga3+ complex and the bis(phosphonate) pendant arm insures selective delivery of the complex to the bone tissue. Both new ligands were fully characterized by NMR and mass spectroscopy. Complexation of Ga3+ was studied by 31 P and 71 Ga NMR spectroscopy. Binding to bone tissue was simulated by adsorption of the complexes to hydroxoapatite. Radiochemical experiments including study of 68 Ga complexation kinetics and basic in-vivo experiments including biodistribution studies and PET examination were done in cooperation with Johannes-Gutenberg Universität Mainz in Germany. Data obtained from these experiments were...

Nitrilotriacetic Acid (NTA) is an organic ligand which has been extensively studied due to its biological significance and excellent chelating properties. Nitrilotripropionic Acid (NTPA) is a ligand that is believed to possess similar properties to NTA, but has not been as extensively studied. It has been experimentally determined that metal complexes of NTA are orders of magnitude stronger than those formed with NTPA. This is surprising, especially considering that the ligands do not differ that much from each other. NTPA contains an additional –CH2– group in each of the acid containing arms as compared to NTA. The aim of these studies were to explain, theoretically, why this is the case. Analyses were conducted with a number of software programs including, Gaussian 03, Schrödinger Maestro and AIM 2000. All Density Functional Theory (DFT) studies were conducted in solvent at the RB3LYP/6-311+G(d,p) level of theory in conjunction with a number of different solvation models. En route to explaining why the complexes differ in stability a new methodology was utilized (isodesmic reactions) in which the four stepwise protonation constants of both NTA and NTPA were successfully predicted; in fact these were the most accurate values predicted to date by DFT methods. The final step of these studies focused on predicting stability constants of metal (Zn2+ and Ni2+) complexes of NTA and NTPA. These predictions were not as accurate as those achieved for the prediction of protonation constants; however, success was achieved in predicting the trend – complexes with NTA are orders of magnitude stronger than complexes formed with NTPA. The most important observation revealed that H–clashes and C–H∙∙∙O hydrogen bonds present in M(NTPA) complexes, which are not present in M(NTA) complexes, result in the formation of additional rings which contributes to the formation of a cage. It was discovered that the H-clashes present in the M(NTPA) complexes were contributing to the overall stability of the molecule. This is completely contradictory to a previous explanation in which H-clashes, being a result of steric crowding, resulted in destabilization of a complex. If the H-clashes were not present in the M(NTPA) complexes there would not be enough stabilizing factors present in the molecule which will inevitably result in the non-existence of M(NTPA) complexes. Copyright / Dissertation (MSc)--University of Pretoria, 2010. / Chemistry / unrestricted

Slow complexation is one of the major limitations of current macrocyclic chela- tors utilized in nuclear medicine for complexation of metal radionuclides. This property can be improved by ligand design. Among metal radioisotopes, the copper ones (e.g. 60Cu, 61Cu, 62Cu, 64Cu and 67Cu) have become commonly available in recent years and cyclam-derived ligands are the most suitable ligands for Cu2+ complexation. To alter the complexation rate, bis(phosphinic acid) group is promising unit as it is able to complex metal ions in acidic solu- tions. However, geminal bis(phosphinates) represent poorly studied group of compounds and, thus, it is challenging to uncover their properties. Several simple amino-bis(phosphinates) were synthesized and its acid-base and coordi- nation properties were studied. Unlike structurally similar geminal bis(phosphonates), the title compounds showed negligible adsorption onto hydroxyapatite (commonly used model of bone tissue). The obtained knowledge dealing with geminal bis(phosphinates) was utilized in synthe- sis of two novel cyclam derivatives. The ligands (bearing either one geminal bis(phosphinate) or one geminal phosphino-phosphonate pendant arm) were synthesized by highly efficient procedure. The corresponding Cu2+ complexes are formed with very high rates and show...

New π-conjugated building blocks (unimers) for metallo-supramolecular polymers (MSPs), whose comprise: (i) substituted phosphole ring surrounded by two thiophene rings as the central block, (ii) 2,2':6',2''-terpyridine-4'-yl (tpy) end-groups as ion-selectors, and (iii) different linkers inserted between the central block and tpy end-groups, are described. Chemical and physical properties of those unimers were studied with attention on correlation between properties and structure of unimers. For example the unimer without linkers shows the UV/vis absorption maximum red shifted about 60 to 100 nm compared to bis(tpy)terthiophenes, which proves that replacing of the thiophene with phosphole unit significantly enhances the delocalization of electrons within the unimer molecule and significant area of absorption spectra can be covered. Introduction of linkers (ethynediyl, ethynediyl-thiophene-2,5-diyl, ethynediyl-1,4-phenylene) has a minor effect on the bandgap energy. All prepared unimers underwent self-assembling process with various metal ions (Co2+ , Cu2+ , Fe2+ , Ni2+ and Zn2+ ) resulting into metallo-supramolecular polymers. Three stages of the assembly of unimers into related MSPs were observed and characterized by absorption, fluorescence spectroscopy and size exclusion chromatography: 1)...

Antisense RNA (asRNA) strategies are identified as an effective and specific method for gene down-regulation at the post-transcriptional level. In this study, the major purpose is to find a correlation between the expression level and minimum free energy to enable the design of specific asRNA fragments. The thermodynamics of asRNA and mRNA hybridization were computed based on the fluorescent protein reporter genes. Three different fluorescent proteins (i) green fluorescent protein (GFP), (ii) cyan fluorescent protein (CFP) and (iii) yellow fluorescent protein (YFP) were used as reporters. Each fluorescent protein was cloned into the common pUC19 vector. The asRNA fragments were randomly amplified and the resulted antisense DNA fragments were inserted into the constructed plasmid under the control of an additional inducible plac promoter and terminator. The expression levels of fluorescent reporter protein were determined in real time by plate reader. Different results have been observed according to the fluorescent protein and the antisense fragment sequence. The CFP expression level was decreased by 50 to 78% compared to the control. However, with the GFP, the down-regulation did not exceed 30% for the different constructs used. For certain constructs, the effect was the opposite of expected and the expression level was increased. In addition, the YFP showed a weak signal compared to growth media, therefore the expression level was hard to be defined. Based on these results, a thermodynamic model to describe the relationship between the particular asRNA used and the observed expression level of the fluorescent reporter was developed. The minimum free energy and binding percentage of asRNA-mRNA complex were computed by NUPACK software. The expression level was drawn as a function of the minimum free energy. The results showed a weak correlation, but linear trends were observed for low energy values and low expression levels the CFP gene. The linear aspect is not verified for higher energy values. These findings suggest that the lower the energy is, the more stable is the complex asRNA-mRNA and therefore more reduction of the expression is obtained. Meanwhile, the non-linearity involves that there are other parameters to be investigated to improve the mathematical correlation. This model is expected to offer the chance to "fine-tune" asRNA effectiveness and subsequently modulate gene expression and redirect metabolic pathways toward the desired component. In addition, the investigation of the localization of antisense binding indicates that there are some regions that favors the hybridization and promote hence the down-regulation mechanisms. / Master of Science

Capillary zone electrophoresis (CZE) is a widely used analytical method. CZE is described theoretically very well and there are many simulation programs, which enable one to predict results of electrophoretic separations, and alternatively to study phenomena taking place during the electrophoretic separation in detail. The CZE method is not only an analytical method, but is often used for determination of many physical parameters of compounds, such as stability constants or complex mobilities. Among methods most often used for determination of complexation parameters belongs the affinity capillary electrophoresis (ACE). Its alternative is the vacancy affinity capillary electrophoresis (VACE). Whereas by the ACE method the stability constant is determined from the dependence of the analyte effiective electrophoretic mobility on the background electrolyte (BGE) composition, in the case of the VACE system peaks are used for this purpose. In this work the legitimacy of using system peaks in the VACE method for determination of stability constants was investigated. Several approaches dealing with the concentrating of complexing agent in the peak area were compared, both for the ACE and the VACE method. Two different kinds of electrophoretic systems were studied. In the first one, neutral cyclodextrin was used as...

Neste trabalho, duas técnicas de controle robusto (LQG/LTR e DML), aplicadas a um sistema elétrico de potência, são avaliadas através dos raios de estabilidade do sistema. As incertezas estruturadas do modelo nominal são consideradas nos dois controladores. Um conjunto de modelos é gerado considerando as combinações das incertezas paramétricas. Os valores singulares estruturados dos dois sistemas de controle são analisados. / In this work, two techniques of robust control (LQG/LTR) and LMI), applied to a power electric system, are available via stability radii of the system. The structured uncertainties of the nominal model are considered in both designs. A set of models is generated considering the combinations of the parametric uncertainties. The structured singular values of both systems are analysed.

Neste trabalho, duas técnicas de controle robusto (LQG/LTR e DML), aplicadas a um sistema elétrico de potência, são avaliadas através dos raios de estabilidade do sistema. As incertezas estruturadas do modelo nominal são consideradas nos dois controladores. Um conjunto de modelos é gerado considerando as combinações das incertezas paramétricas. Os valores singulares estruturados dos dois sistemas de controle são analisados. / In this work, two techniques of robust control (LQG/LTR) and LMI), applied to a power electric system, are available via stability radii of the system. The structured uncertainties of the nominal model are considered in both designs. A set of models is generated considering the combinations of the parametric uncertainties. The structured singular values of both systems are analysed.

Lors de ces travaux de thèse, des unités monomériques appelées unimères ont été synthétisées et utilisées pour le développement de polymères métallo-supramoléculaires (MSPs). Ces unités se composent (i) d’un bloc central: 2,5-dithiénylphosphole, (ii) dA’un chélate : 2,2':6',2''-terpyridine-4'-yl (tpy) et (iii) de connecteurs variés assurant la jonction entre le bloc central et le chélate. Les propriétés physico-chimiques de ces unimères ont été mesurées afin d’établir des relations structures/propriétés. Par exemple, l’unimère ne comportant pas de connecteurs entre l’unité central et le chélate présente un maximum d’absorption fortement décalé vers le rouge par rapport à l’unimère bis(tpy)terthiophène. Cette observation montre que la délocalisation électronique est accrue dans ces systèmes et permet de couvrir un large domaine spectral. L’introduction de connecteurs (éthynediyle, éthynediyle-thiophène-2,5-diyle, éthynediyle-1,4-phénylène) entre le bloc central et le chélate a un effet mineur sur l’écart HO-BV et sur la position des maxima d'absorption. Puis tous les unimères synthétisés ont été mis en présence de différents ions métalliques (Co2+, Cu2+, Fe2+, Ni2+ et Zn2+) pour former les MSPs correspondants. Ce phénomène de polymérisation a été étudié en détail en utilisant les spectroscopies d’absorption, d’émission et la chromatographie d’exclusion stérique. Ainsi, cette polymérisation présente 3 étapes : (i) la formation des dimères U-M-U, (ii) la prolongation de chaine de polymères qui atteint un une longueur maximale pour le ratio 1/1 ion métallique/unimère; (iii) terminaison réalisée avec des ions métalliques lorsque ces ions sont présent en excès. Les propriétés optiques de ces nouveaux polymères ont également été étudiées montrant qu’elles dépendent fortement de la nature de l’ion métallique utilisé. / New π-conjugated building blocks (unimers) for metallo-supramolecular polymers (MSPs), whose comprise: (i) substituted phosphole ring surrounded by two thiophene rings as the central block, (ii) 2,2':6',2''-terpyridine-4'-yl (tpy) end-groups as ion-selectors, and (iii) different linkers inserted between the central block and tpy end-groups, are described. Chemical and physical properties of those unimers were studied with attention on correlation between properties and structure of unimers. For example the unimer without linkers shows the UV/vis absorption maximum red shifted about 60 to 100 nm compared to bis(tpy)terthiophenes, which proves that replacing of the thiophene with phosphole unit significantly enhances the delocalization of electrons within the unimer molecule and significant area of absorption spectra can be covered. Introduction of linkers (ethynediyl, ethynediyl-thiophene-2,5-diyl, ethynediyl-1,4-phenylene) has a minor effect on the bandgap energy. All prepared unimers underwent self-assembling process with various metal ions (Co2+, Cu2+, Fe2+, Ni2+ and Zn2+) resulting into metallo-supramolecular polymers. Three stages of the assembly of unimers into related MSPs were observed and characterized by absorption, fluorescence spectroscopy and size exclusion chromatography: 1) formation of dimer species: U-M2+-U (U stands for unimer); 2) prolongation of polymer chain to reach the maximum length at equimolar ratio of unimer and metal ions; 3) end-capping of polymer chains and their partial decomposition at stoichiometric excess of ion couplers. Optoelectronic properties of newly formed metallo-supramolecular polymers were investigated and choice of the metal ions was shown to be of crucial importance. / V rámci této disertační práce byly připraveny stavební bloky (nazývající se unimery) pro tvorbu konjugovaných metalo-supramolekulárních polymerů (MSPs), které ve své struktuře obsahují: (i) substituovaný fosfolový kruh obklopený dvěma thiofenovými cykly jako centrální blok, (ii) 2,2':6',2''-terpyridin-4'-yl (tpy) jako koncovou skupinu pro navázání iontů, a (iii) různé spojky mezi uvedeným centrálním blokem a tpy skupinou. Chemické a fyzikální vlastnosti těchto unimerů byly prostudovány s důrazem na korelaci mezi vlastnostmi a strukturou unimeru. Například unimer bez přídavných spojek vykazuje posun UV/vis absorpčního maxima do červené oblasti o 60 až 100 nm v porovnání s bis(tpy)terthiofenem, což značí, že nahrazením thiofenu fosfolem se značně zvyšuje delokalizace elektronů v molekule unimeru a může být pokryta značná část spektra. Začlenění spojek (ethynediyl, ethynediyl-thiofen-2,5-diyl, ethynediyl-1,4-fenylen) do struktury unimeru má jen malý vliv na šířku zakázaného pásu, a tedy pozici absorpčního maxima. Všechny připravené unimery byly podrobeny procesu samo-seskupování s různými kovovými ionty (Co2+, Cu2+, Fe2+, Ni2+ a Zn2+) za vzniku organokovových polymerů. Tři stadia provázející proces samo-seskupování byla pozorována pomocí absorpční a fluorescenční spektroskopie a gelové permeační chromatografie (SEC): 1) tvorba dimerů U-M2+-U (U = unimer), 2) prodlužování polymerních řetězců a dosažení maximální délky při ekvimolárním poměru unimeru a kovových iontů, 3) vazba kovových iontů na koncové terpyridinové skupiny a rozklad polymerního řetězce na kratší při stechiometrickém přebytku kovových iontů. Optické vlastnosti nově připravených organokovových polymerů byly prozkoumány a ukázalo se, že velmi závisí na vybraném kovovém iontu.

The predominant tool for adaptation in Gram-negative bacteria is a genetic system called integron. It rearranges gene cassettes, promoting multiple antibiotic resistances, a recognized major global health threat. It is based on a unique recombination process involving a Tyrosine recombinase – called integrase IntI – and folded single-stranded DNA hairpins – called attC sites. Four recombinases and two attC sites form a macromolecular synaptic complex, which is key to the entire recombination process and the focus of our study. The bottom strand of all attC sites shows highest recombination in vivo, however, it still varies greatly and the underlying reason is unknown. We hypothesize that the difference in recombination efficiency arises from the variable mechanical stability of the synaptic complex, which in turn is affected by the attC site. Here, we established an optical tweezers force-spectroscopy assay that allows us to probe the synaptic complex stability for different DNA substrates and protein variants. We discovered a strong correlation between recombination efficiency and the mechanical stability of the synapse, indicating a regulatory mechanism from the DNA sequence to the quaternary complex structure stability. We have discovered protein residues interacting with the DNA in trans, within the synaptic complex, which reduces its stability. Furthermore, we discovered that the C-terminal helix, a conserved structural feature of tyrosine recombinases plays a key role in the stabilization of the tetramer assembly on the DNA, which upon mutation significantly destabilized the synaptic complex. Expanding upon this new understanding of synapse stability regulation we developed a novel approach for destabilizing the synaptic complex, potentially reducing the recombination efficiency. We designed α-helix mimicking peptides that would compete with the C-terminal tail of the integrase, block the interlocking interaction, and lead to synaptic complex destabilization. We have observed a prominent destabilizing effect on the synaptic complex already at 10 µM peptide concentration. Overall, our findings reveal new regulatory mechanisms in the recombination efficiency of the bacterial integron and provide first data for the active synapse destabilization mechanism. This novel understanding of the regulatory role the synaptic complex plays in the recombination efficiency of the integron system introduces a new approach to reduce the spread of antibiotic resistance among bacteria. / Das vorherrschende Anpassungsmittel bei gramnegativen Bakterien ist ein genetisches System, das Integron genannt wird. Es ordnet Genkassetten neu an und fördert so multiple Antibiotikaresistenzen, die eine globale Gesundheitsbedrohung darstellen. Es basiert auf einem einzigartigen Rekombinationsprozess, an dem eine Tyrosin-Rekombinase - Integrase IntI genannt - und gefaltete einzelsträngige DNA-Hairpins - attC-Stellen genannt - beteiligt sind. Vier Rekombinasen und zwei attC-Stellen bilden einen makromolekularen synaptischen Komplex, der für den gesamten Rekombinationsprozess entscheidend ist und im Mittelpunkt unserer Forschung steht. Der untere Strang aller attC-Stellen weist in vivo die höchste Rekombinationsrate auf, die jedoch aus unbekannten Grund stark variier. Wir vermuten, dass der Unterschied in der Rekombinationsrate auf die unterschiedliche mechanische Stabilität des synaptischen Komplexes zurückzuführen ist, die wiederum von der attC-Stelle beeinflusst wird. Hier haben wir einen Test mittels Kraft-spektroskopie mit einer optischen Pinzette entwickelt, mit dem wir die Stabilität des synaptischen Komplexes für verschiedene DNA-Substrate und Proteinvarianten untersuchen können. Wir stellten eine starke Korrelation zwischen der Rekombinationsrate und der mechanischen Stabilität der Synapse fest, was auf einen Regulationsmechanismus zwischen der DNA-Sequenz und der Stabilität der quaternären Komplexstruktur hinweist. Wir haben Proteinreste entdeckt, die innerhalb des synaptischen Komplexes mit der DNA in trans interagieren, was zu einer Verringerung dessen Stabilität führt. Darüber hinaus stellten wir fest, dass die C-terminale Helix, ein konserviertes Strukturmerkmal von Tyrosin-Rekombinasen, eine Schlüsselrolle bei der Stabilisierung des Tetramer-Aufbaus an der DNA spielt, die bei Mutation den synaptischen Komplex erheblich destabilisiert. Auf der Grundlage dieses neuen Verständnisses der Regulierung der Synapsenstabilität haben wir einen neuen Ansatz zur Destabilisierung des synaptischen Komplexes entwickelt, der die Effizienz der Rekombination verringern könnte. Wir entwarfen α-Helix-nachahmende Peptide, die mit dem C-terminalen Ende der Integrase konkurrieren, die Interlocking-Interaktion blockieren und zur Destabilisierung des synaptischen Komplexes führen. Wir haben eine deutliche destabilisierende Wirkung auf den synaptischen Komplex bereits bei einer Peptidkonzentration von 10 µM beobachtet. Insgesamt zeigen unsere Ergebnisse neue Regulationsmechanismen für die Rekombinationsleistung des bakteriellen Integrons auf und liefern erste Daten für den Mechanismus der aktiven Destabilisierung der Synapse. Dieses neue Verständnis der regulatorischen Rolle, die der synaptische Komplex bei der Rekombinationseffizienz des Integronsystems spielt, eröffnet einen neuen Ansatz zur Verringerung der Verbreitung von Antibiotikaresistenzen unter Bakterien.