The main theme of this thesis is to develop a fluorescent probe for imaging the subcellular distribution of kinetically labile copper pools that might play a critical role in copper homeostasis. Various copper-selective sensors were designed by combining 1,3,5-triaryl-2-pyrazoline fluorophores with polythioethers as receptor moieties. A series of donor-substituted 1,3,5-triaryl-2-pyrazoline fluorophores were synthesized and characterized in terms of their photophysical and electrochemical properties. Interestingly, the aryl substituents attached to the 1- and 3-position of the pyrazoline ring influence the photophysical properties of the fluorophore in distinctly different ways. The excited-state equilibrium energy is primarily influenced by changes of the substituent in the 1-position, whereas the reduction potential of the fluorophore is determined by the 3-aryl group. Results from computational analyses agree well with the experimental data. A pyrazoline fluorophore library was synthesized, and their photophysical and electrochemical properties were studied. The compounds cover a broad range of excited state energies and reduction potentials, and allow for selective and differential tuning of these two parameters. A series of thiazacrownethers and tripodal aniline copper(I) receptors were synthesized and their copper binding stoichiometries, stability constants, and copper-self-exchange kinetics were investigated. The measured self-exchange activation parameters revealed for all studied ligands a negative activation entropy, suggesting a predominant associative exchange mechanism. With detailed knowledge of the fluorophore platform and copper receptors, sensor CTAP-1 was designed, synthesized and characterized. The probe shows a 4.6-fold emission enhancement and reaches a quantum yield of 14% upon saturation with Cu(I). The sensor exhibits excellent selectivity towards Cu(I) and is insensitive towards millimolar concentrations of Mg(II) or Ca(II). Mouse fibroblast cells (3T3) incubated with the sensor produced a copper-dependent perinuclear staining pattern, which colocalizes with the subcellular location of the mitochondria and the Golgi apparatus. The subcellular topography of copper was further determined by synchrotron-based x-ray fluorescence (SXRF) microscopy. Furthermore, microprobe x-ray absorption measurements at various subcellular locations showed a near-edge feature that is characteristic for low-coordinate monovalent copper. The data provide a coherent picture with evidence for a kinetically labile copper pool, which is predominantly localized in the mitochondria and the Golgi apparatus.

We have designed and synthesized boradiazaindacene (BODIPY) derivatives, appropriately functionalized for metal ion mediated supramolecular polymerization. Thus, ligands for 2- and 2,6-terpyridyl and bipyridyl functionalized BODIPY dyes were synthesized through Sonogashira couplings. These new fluorescent building blocks are responsive to metal ions in a stoichiometry dependent manner. Octahedral coordinating metal ions such as Zn(II), result in polymerization at a stoichiometry which corresponds to two terpyridyl ligands to one Zn(II) ion. However, at increased metal ion concentrations, the dynamic equilibria are re-established in such a way that, monomeric metal complex dominates. The position of equilibria can easily be monitored by 1H NMR and fluorescence spectroscopy. As expected, open shell Fe(II) ions while forming similar complex structures, quench the fluorescence emission of all four functionalized BODIPY ligands.

The design of chromophores targets materials with optoelectronic properties necessary for advanced applications. Organic materials possess properties which emerge from the collective impact of the constituent backbone and substituents as well as their connectivity (i.e. molecular architecture), necessitating the exploration of novel conjugated architectures. This thesis chronicles our examination of 1,4-distyryl-2,5-bis(arylethynyl)benzenes (cruciforms, XFs). Electronic substitution of this 'X-shaped' cross-conjugated scaffold tunes both the energy levels and the spatial distribution of the frontier molecular orbitals (FMOs) in XFs. The resulting fluorophores exhibit FMO separation, imbuing XFs with desirable properties for sensory applications. Using model analytes, we examine how the underlying FMO arrangement and the nature of analyte interaction elicit observable responses. These studies provide a foundation for future access of functional responsive ratiometric cores. This case study demonstrates the importance and unique potential of FMO-separated fluorophores.

Flora and fauna from terrestrial and marine environments provide libraries of natural compounds for drug discovery. The last four decades have seen major advances in ocean exploration that have allowed chemists and biologists to explore previously inaccessible and rare marine organisms. The study of under-explored marine organisms can result in the discovery of structurally novel and unusual natural products with drug potential. Prior to 2005, no natural products had been reported from the Fijian red macroalgae Callophycus serratus or Neurymenia fraxinifolia. As a result of the work described in this thesis and others in the same research group, 33 unique brominated meroditerpenes have been isolated and elucidated alpha-pyrone natural products were discovered from N. fraxinifolia, enriching the natural product library for drug development. Several natural products isolated from C. serratus exhibited sub-micromolar inhibition against the human malaria parasite Plasmodium falciparum, including a drug-resistant strain. Derivatization of the natural product bromophycolide A into fluorescent probes allowed the determination of a non-enzymatic mechanism of action against the human malaria parasite P. falciparum. Through a combination of detailed SAR mapping, molecular fluorescent imaging of live cells, UV-vis spectroscopic analyses, and protein affinity techniques, the mechanism of action of bromophycolide A against P. falciparum was determined to involve inhibition of heme crystallization. These studies identify a new class of natural products that target heme detoxification in both drug-sensitive and drug-resistant P. falciparum and suggest an avenue to circumvent drug resistance.

Fluorescence microscopy is a powerful analytical tool for visualizing biological processes at the subcellular level. In this regard, 1,3,5-triarylpyrazoline based fluorescent probes which act as "turn-on" probes, have been extensively researched. These probes achieve their fluorescence "turn-on" response by inhibition of fluorescence quenching by acceptor-excited photoinduced electron transfer upon binding of an analyte. It has been recently shown that some fluorescent probes used in biological research form colloids composed of nanoparticles, due to their hydrophobic character. This hydrophobic character can also lead to partitioning of the probe into cellular membranes. Colloid formation and membrane partitioning may affect the probes' photophysical properties such as absorption and emission wavelength and quantum yields. Recently, a series of 1,3,5-triarylpyrazolines synthesized in our group by M. T. Morgan, showed no formation of aggregates in aqueous buffer. Surprisingly, these probes increased their fluorescence intensity in the presence of liposomes. The photoinduced electron transfer process is greatly affected by the polarity of the medium in which the probe is used. In this study, the effect of membrane proximity on the photoinduced electron transfer process for pyrazoline based "turn-on" probes has been investigated. A series of water soluble 1,3,5-triarylpyrazolines have been synthesized in which a N,N-dialkylaniline moiety acts as an electron donor and a proton acceptor and an alkylated sulfonamide moiety acts as a molecular anchor for interaction with neutral and anionic liposomes.

Mitochondrial gene expression in trypanosomatid pathogens requires extensive post transcriptional modification called RNA editing. This unique molecular mechanism, catalyzed by a multiprotein complex (the editosome), generates translatable transcripts for essential components of parasite respiratory complex. How editosome proteins are assembled and perform RNA editing is not fully understood. Moreover, previous studies have shown that editosome proteins are essential for parasite survival, which makes editosome as a suitable target for drug discovery. Currently, researchers use radio-labeled based assays to monitor RNA editing process. However, these assays are not suitable for high throughput screening of editosome inhibitors, have low detection limits, and cannot monitor RNA editing in real time. / Therefore, to develop a sensitive high throughput RNA editing assay, we have designed a sensitive hammerhead ribozyme-based fluorescence assay. Ribozyme structure was remodeled by adding or removing uridylate in its conserved catalytic core to make an inactive ribozyme. In the presence of the editosome, inactive ribozyme is edited to an active ribozyme. Consequently, hammerhead ribozyme activity can be measured by cleaving its fluorescently labeled substrate. We have shown that higher sensitivity is achieved using fluorescent based assay than conventional radio-labeled assay. Moreover, we can use this assay for rapid identification and characterization of the editosome inhibitors against RNA editing activities in trypanosomatids.

Kinases play a crucial role in regulating cellular signaling cascades, making them therapeutic targets for several human diseases. In human cancers, mis-regulation and mutations of kinases such as EGFR (epidermal growth factor receptor) have been found to drive malignant transformation. Due to the conserved structural elements of protein kinases, the majority of kinase inhibitors available have a tendency to inhibit multiple targets. The biological impact of this promiscuity is insufficiently defined and the prevalence of cellular compensatory mechanisms additionally varies the clinical responses to drug treatment. In order to understand the relationship between selectivity and efficacy, prior to clinical trials, it is essential to characterize how inhibitors interact with the kinome within a cellular context. Monitoring inhibitor-target interactions generally involves in vitro assaying with purified proteins or protein domains, which compromises the native integrity of the kinases. Cellbased assays either gain outcomes from bulk populations that average out cell variance or phenotypic assays that lack molecular resolution. To obtain information on drug interactions on a single cell level, we have developed a method to measure the direct binding of kinase inhibitors to their targets in situ and in vivo. Kinase inhibitors are chemically tagged with fluorophores that serve as acceptors to genetically tagged donor fluorophores on the enzyme and the interaction is measured using FRET-FLIM. With epidermal growth factor receptor (EGFR) and irreversible EGFR inhibitors as the model system, this approach has been applied to image inhibitor-kinase interactions in live and fixed cells. Using this method, a small panel of tyrosine kinase targets, and labeled inhibitors, we were able to investigate the cross-specificity within the panel. Additionally it was found that the specificity of inhibitors for specific kinase conformations enables the distinction between EGFR in the active and inactive conformation by the inhibitor-probes. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2011.

Copper is an essential trace element and required for various biological processes, but free copper is toxic. Therefore, copper is tightly regulated in living cells and disruptions in this homeostatic machinery are implicated in numerous diseases. The current understanding of copper homeostasis is substantial but incomplete, particularly in regard to storage and exchange at the subcellular level. Intracellular copper is primarily present in the monovalent oxidation state. Therefore, copper(I) selective fluorescent probes can be utilized for imaging exchangeable copper ions in live cells, but these probes are often lipophilic and hence poorly water soluble. To address this problem, water-soluble fluorescent probes with greatly improved contrast ratio and fluorescence quantum yield are characterized in this work. This work also describes a novel application of water-soluble fluorescent probes, in-gel detection of copper proteins with solvent accessible Cu(I) sites under non-denaturing conditions. Knowledge of copper(I) stability constants of proteins is important to elucidate the mechanisms of cellular copper homeostasis. Due to the high affinity of most Cu(I)-binding proteins, the stability constants cannot be determined directly by titration of the apo-protein with Cu(I). Therefore, accurate determination of Cu(I) stability constants of proteins critically depends on the Cu(I) affinity standards. However, the previously reported binding affinity values of the frequently used Cu(I) affinity standards are largely inconsistent impeding reliable data acquisition for the Cu(I) stability constants of proteins. To solve this problem, a set of water-soluble ligands are developed in this work that form colorless, air-stable copper(I)-complexes with 1:1 stoichiometry. These ligands can be applied as copper(I) buffering agents and affinity standards in order to study copper biochemistry. Copper(I) binding proteins are an integral part of the copper homeostatic machinery and they work in conjunction to regulate copper uptake, distribution, and excretion. However, available evidence indicates the existence of putative copper-binding proteins that are yet to be characterized. Therefore, several proteomics-based methods are developed in this work by employing the strategy to label Cu(I)-binding cysteines in a copper-dependent manner which lays the foundation for the identification of new copper proteins from cellular extracts.

Sistemas nanocarreadores de moléculas orgânicas têm emergido como promissores sistemas para aplicação na terapêutica e/ou diagnóstico. No presente trabalho foram desenvolvidas nanocápsulas poliméricas contendo, em seus diferentes domínios, sondas fluorescentes capazes de fornecer imagem quando analisadas em microscópio de fluorescência confocal, mostrando as potencialidades do sistema como agente para imagem ótica. Uma importante característica de moléculas propostas como marcadores fluorescentes, é que não haja sobreposição dos espectros de absorção e emissão de fluorescência. Para tanto, foi utilizado um corante sintético do grupo dos benzoxazólicos (HBO-C8) para marcação do núcleo lipofílico, e os polímeros PCL e quitosana foram ligados covalentemente aos corantes rodamina B e alaranjado de acridina, respectivamente. As formulações desenvolvidas e caracterizadas com dois ou três marcadores apresentaram caráter nanotecnológico e as fotomicrografias de transmissão revelaram que as nanopartículas contendo HBO-C8 e PCL-Rho (sem quitosana), preservou a morfologia da nanopartícula. Adicionalmente, o HBO-C8 foi quantificado na formulação contendo HBO-C8 e PCL-Rho, onde verificou-se que 98% do corante está internalizado na nanopartícula, alcançando assim, o objetivo proposto de usá-lo como sonda para marcação do núcleo lipofílico. Por meio da microscopia de fluorescência confocal, foram obtidas imagens dos marcadores fluorescentes colocalizados, para as formulações contendo dois ou três domínios fluorescentes, demonstrando que essas nanocápsulas podem ser propostas como uma plataforma promissora para serem empregadas como sondas para imagem ótica. / Nanocarriers systems of organic molecules have emerged as promising systems for application in therapy and diagnosis. In the present study polymeric nanocapsules containing fluorescent probes in their different domains, capable of providing image when analyzed in confocal fluorescence microscope, showing the potential of the system as an agent for optical imaging. An important feature of proposed molecules as fluorescent probes, there is no overlap of the spectra of absorption and fluorescence emission. Thus, a group of synthetic dye benzoxazólicos (HBO-C8) to mark the lipophilic core, and PCL and chitosan polymers were covalently linked to dye rhodamine B and acridine orange , respectively. The formulations developed and characterized with two or three markers showed nanotechnological character and transmission photomicrographs showed that nanoparticles containing PCL-Rho and HBO-C8 (without chitosan) preserved morphology of the nanoparticle. Additionally, the HBO-C8 was was quantified on formulation contained HBO-C8 and PCL-Rho, where it was found that 98% of the dye is internalized in the nanoparticle thus reaching the purpose proposed to use as a probe for marking the lipophilic core . By images of confocal fluorescence microscopy were obtained the colocalized of fluorescent markers to formulations containing two or three fluorescent domains, demonstrating that these nanocapsules can be proposed as a promising platform to be used as probes for optical image.

Sistemas nanocarreadores de moléculas orgânicas têm emergido como promissores sistemas para aplicação na terapêutica e/ou diagnóstico. No presente trabalho foram desenvolvidas nanocápsulas poliméricas contendo, em seus diferentes domínios, sondas fluorescentes capazes de fornecer imagem quando analisadas em microscópio de fluorescência confocal, mostrando as potencialidades do sistema como agente para imagem ótica. Uma importante característica de moléculas propostas como marcadores fluorescentes, é que não haja sobreposição dos espectros de absorção e emissão de fluorescência. Para tanto, foi utilizado um corante sintético do grupo dos benzoxazólicos (HBO-C8) para marcação do núcleo lipofílico, e os polímeros PCL e quitosana foram ligados covalentemente aos corantes rodamina B e alaranjado de acridina, respectivamente. As formulações desenvolvidas e caracterizadas com dois ou três marcadores apresentaram caráter nanotecnológico e as fotomicrografias de transmissão revelaram que as nanopartículas contendo HBO-C8 e PCL-Rho (sem quitosana), preservou a morfologia da nanopartícula. Adicionalmente, o HBO-C8 foi quantificado na formulação contendo HBO-C8 e PCL-Rho, onde verificou-se que 98% do corante está internalizado na nanopartícula, alcançando assim, o objetivo proposto de usá-lo como sonda para marcação do núcleo lipofílico. Por meio da microscopia de fluorescência confocal, foram obtidas imagens dos marcadores fluorescentes colocalizados, para as formulações contendo dois ou três domínios fluorescentes, demonstrando que essas nanocápsulas podem ser propostas como uma plataforma promissora para serem empregadas como sondas para imagem ótica. / Nanocarriers systems of organic molecules have emerged as promising systems for application in therapy and diagnosis. In the present study polymeric nanocapsules containing fluorescent probes in their different domains, capable of providing image when analyzed in confocal fluorescence microscope, showing the potential of the system as an agent for optical imaging. An important feature of proposed molecules as fluorescent probes, there is no overlap of the spectra of absorption and fluorescence emission. Thus, a group of synthetic dye benzoxazólicos (HBO-C8) to mark the lipophilic core, and PCL and chitosan polymers were covalently linked to dye rhodamine B and acridine orange , respectively. The formulations developed and characterized with two or three markers showed nanotechnological character and transmission photomicrographs showed that nanoparticles containing PCL-Rho and HBO-C8 (without chitosan) preserved morphology of the nanoparticle. Additionally, the HBO-C8 was was quantified on formulation contained HBO-C8 and PCL-Rho, where it was found that 98% of the dye is internalized in the nanoparticle thus reaching the purpose proposed to use as a probe for marking the lipophilic core . By images of confocal fluorescence microscopy were obtained the colocalized of fluorescent markers to formulations containing two or three fluorescent domains, demonstrating that these nanocapsules can be proposed as a promising platform to be used as probes for optical image.