Platinum-based drugs are an important group of alkylating-like agents which are used in cancer chemotherapy treatment. Cisplatin and oxaliplatin in particular are still commonly used today and are the focus of this thesis. As with most chemotherapy drugs, the efficacy of these drugs are limited by toxicity as well as tumour resistance, and therefore by increasing our understanding of these areas it is hoped to one day achieve personalised chemotherapy. The use of ICP-MS in the study of bio-sciences is still relatively new, however it has the ability to provide robust, fast and accurate methods for the quantification of platinum in biological samples. The research presented here utilised mass spectrometry in the study of the formation of Pt-DNA adducts in the clinical samples, the binding of oxaliplatin to short peptides and the effect of selenium supplementation on oxaliplatin in colorectal cancer cell lines. A comparison in the number of Pt-DNA adducts in saliva and leukocyte samples obtained from patients undergoing Pt-based chemotherapy demonstrated a lack of correlation between the two sample types. Samples were taken pre- and post-treatment and analysed via SF-ICP-MS and significant inter-patient variability was observed as expected. In both leukocyte and saliva samples, not only was Pt from previous chemotherapy cycles observed, but Pt was detected in the DNA in both sample types 1 hour after treatment. However a lack of correlation between platinum levels seen in the blood and saliva, combined with unexpected difficulties obtaining patient adherence to the saliva sampling protocol, indicated that saliva does not at present offer a reliable alternative to leukocytes for this assay. The binding of oxaliplatin to short nitrogen and sulfur rich peptides was investigated. Platinum binding to the peptides was observed and no significant differences in the level of binding were observed between the range of N and S rich peptides studied in this investigation. Partly due to the inability to reproduce biological conditions in this study, oxaliplatin was observed as a whole molecule, and furthermore dimers and multimers were also observed. The effect of selenium supplementation on the total cellular uptake of platinum was investigated in cultured cells via ICP-MS and LA-ICP-MS. It was observed that selenium decreased the amount of Pt taken up by the cancer cells. This was seen in analysis of populations of cells as well as by single cell analysis. Furthermore, while problems were encountered measuring selenium in subcellular experiments, the effect of selenium on the subcellular distribution of platinum as well as the number of Pt-DNA adducts could be determined.

Small molecule Zn(II) complexes containing N- and S- donor environments may serve as appropriate models for mimicking Zn protein sites, and thus, their reactions with heavy metal ions such as Pt(II) and W(0) may provide insight into possible adduct formation and zinc displacement. To study such possible interactions between zinc finger proteins and platinum-bound DNA, the ZnN2S2 dimeric complex, N,N?-bis(2- mercaptoethyl)-1,4-diazacycloheptane zinc (II), [Zn-1?]2, has been examined for Znbound thiolate reactivity in the presence of Pt(II) nitrogen ? rich compounds. The reactions yielded Zn/Pt di- and tri- nuclear thiolate-bridged adducts and metalexchanged products, which were initially observed via ESI-mass spectrometry (ESI-MS) analysis of reaction solutions, and ultimately verified by comparison to the ESI-MS analysis, 195Pt NMR spectroscopy, and X-ray crystallography of directly synthesized complexes. The isolation of Zn-(?-SR)-Pt-bridged [(Zn(bme-dach)Cl)(Pt(dien))]Cl adduct from these studies is, to our knowledge, the first Zn-Pt bimetallic thiolatebridged model demonstrating the interaction between Zn-bound thiolates and Pt(II). Additional derivatives involving Pd(II) and Au(III) have been explored to parallel the experiments executed with Pt(II). The [Zn-1?]2 was then modified by cleavage with Na+[ICH2CO2]- to produce (N- (3-Thiabutyl)-N?-(3-thiapentaneoate)-1,4-diazacycloheptane) zinc(II), Zn-1?-Ac or ZnN2SS?O, and 1,4-diazacycloheptane-1,4-diylbis(3-thiapentanoato) zinc(II), Zn-1?-Ac2 or ZnN2S?2O2, monomeric complexes (where S = thiolate, S? = thioether). The [Zn-1?]2 di- and Zn-1?-Ac mono-thiolato complexes demonstrated reactivity towards labile-ligand tungsten carbonyl species, (THF)W(CO)5 and (pip)2W(CO)4, to yield, respectively, the [(Zn-1?-Cl)W(CO)4]- complex and the [(Zn-1?-Ac)W(CO)5]x coordination polymer. With the aid of CO ligands for IR spectral monitoring, the products were isolated and characterized spectroscopically, as well as by X-ray diffraction and elemental analysis. To examine the potential for zinc complexes (or zinc-templated ligands) to possibly serve as a toxic metal remediation agents, Zn-1?-Ac and Zn-1?-Ac2 were reacted with Ni(BF4)2. The formation of Zn/Ni exchanged products confirmed the capability of ?free? Ni(II) to displace Zn(II) within the N-, S-, and O- chelate environment. The Zn/Ni exchanged complexes were analyzed by ESI-MS, UV-visible spectroscopy, IR spectroscopy of the acetate regions, and X-ray crystallography. They serve as foundation molecules for more noxious metal exchange / zinc displacement products.

[pt] Ferramentas BLAST são normalmente utilizadas para efetuar comparações entre sequências de DNA, RNA e proteínas. No entanto, face ao crescimento exponencial das bases biológicas, existe uma preocupação quanto ao desempenho do BLAST, mesmo considerando os equipamentos de grande capacidade computacional hoje existente. Considerando tal fato, algumas ferramentas capazes de executar o BLAST em ambientes distribuídos, tais como clusters e grids, vêm sendo desenvolvidas de modo a acelerar consideravelmente a sua execução. No entanto, até o presente momento, não foi constatado, na literatura existente, nenhum estudo com o objetivo de comprar o desempenho entre essas ferramentas. A avaliação de desempenho dessas ferramentas é normalmente efetuada de forma isolada, considerando apenas o tempo de execução (elapsed time), em situações diversas, como, por exemplo, variando o número de nós em que a ferramenta BLAST é executada.. Almejando uma investigação mais detalhada, principalmente no que diz respeito a avaliação de desempenho do BLAST em ambientes distribuídos, a presente dissertação tem como um dos seus objetivos efetuar um estudo detalhado sobre como comparar o desempenho do BLAST em um ambiente distribuído, considerando para tal, a avaliação de três ferramentas BLAST, dentre elas balaBLAST, desenvolvida no Laborátorio de Bioinformática da PUC-RIO. O segundo objetivo é verificar a eficácia do balanceamento de carga efetuada pela ferramenta balaBLAST. / [en] BLAST tools are typically used to make comparisons between sequences of DNA, RNA and proteins. However, given the exponential growth of the biological databases, there is concern about the performance of BLAST, even considering the equipment of large computing power that exists today. Considering this fact, some tools to run BLAST in distributed environments such as clusters and grids, have been developed to greatly accelerate its performance. However, until now, has not been found in existing literature, no study in order to compare the performance between these tools. The performance evaluation of these tools is usually done in isolation, considering only the execution time (elapsed time) in different situations, for example, varying the number of nodes in the tool BLAST runs. Craving a more detailed investigation, especially with regard to performance evalution of BLAST in distributed environments, this dissertation has as one of your goals make a detailed study to compare the performance of BLAST in a distributed enviroment, considering for such the evaluation of three tools BLAST, among them the balaBLAST developed in the Bioinformatics Laboratory of PUC-Rio. The second objective is to verify the effectiveness of load balancing performed by the tool balaBLAST.

[pt] Na busca de novos quimioterápicos diferentes dos clássicos derivados de cisplatina, ligantes derivados aroíl-hidrazônicos e complexos de cobre(II) aparecem como compostos promissores. Esta tese relata o desenvolvimento e a síntese de uma nova combinação desses compostos a partir de oito ligantes bases de Schift aroíl-hidrazônicos inéditos e seus Cu2-complexos derivados de sais de perclorato ou acetato 1‒14. Os complexos de cobre(II) obtidos contêm em suas estruturas modelos estruturais de sítios ativos de algumas metaloenzimas. Os compostos foram amplamente caracterizados utilizando várias técnicas espectroscópicas e analíticas. As análises por difração de raios X de quatro ligantes e cinco complexos são descritas em detalhes nessa tese. A estabilidade dos compostos foi estudada em meio celular e sua atividade biológica foi analisada. Os resultados incluem um estudo da interação de dois ligantes derivados de tiofeno (H3L1) ou furano (H3L2) e seus respectivos complexos 1 e 2 (primeiro conjunto de compostos) com uma proteína e DNA do timo de vitelo (calf thymus DNA), com o objetivo de medir a afinidade de ligação à albumina sérica bovina e ao DNA usando as técnicas de absorção de UV/Visível e/ou fluorescência. Adicionalmente, foi visto através de técnicas de espalhamento de luz que a interação entre os compostos e a proteína é reversível. Uma importante contribuição do presente trabalho foi analisar a capacidade de clivagem do DNA plasmidial de dois complexos 1 e 2 usando a técnica de espalhamento de luz dinâmico. Neste trabalho são estudadas as alterações do raio hidrodinâmico do DNA plasmidial causada pelo corte nas hélices resultante da presença dos complexos. Ensaios de citotoxicidades em algumas células cancerígenas, revelaram a alta capacidade dos ligantes (H3L1 and H3L2) e dos complexos (1 e 2) de induzir a morte celular. Ademais, as muitas propriedades biológicas, incluindo a atividade anticancerígena do fragmento isoxazol, motivaram sua inclusão na estrutura dos ligantes H3L3 and H2L4 e complexos 3‒6 (segundo conjunto de compostos). A combinação dessas estruturas pode vir a ser promissora na procura de novos medicamentos contra o câncer. A interação dos derivados dos ligantes isoxazol-aroíl-hidrazônicos com o DNA foi diretamente estudada por espectroscopia na absorbância e fluorescência, usando as propriedades luminescentes apresentadas pelos ligantes. No caso dos complexos, o ensaio de deslocamento de brometo de etídio revelou uma afinidade importante através da intercalação nos ácidos nucleicos da sequência do DNA. Adicionalmente, este trabalho conseguiu demostrar que ligantes e complexos contendo um braço fenólico no lugar de um braço piridínico melhoram a citotoxicidade in vitro em células de câncer de mama epitelial humano, alcançando a faixa nanomolar. A capacidade de metalação e transmetalação dos ligantes binucleares H3L3 e H2L4 e seus complexos de cobre 3‒6 com Fe(II), Fe(III) e Zn(II) provenientes do meio biológico foi verificada como uma estratégia adicional para induzir a morte de células cancerígenas. Além disso, para estudar a interação dos compostos com o sistema biológico e/ou para demostrar a permeabilidade celular dos compostos, os ligantes (H3L5‒H3L7) e complexos (7‒12) foram funcionalizados com fluoróforos potentes como pireno (H3L5) (conjunto três de compostos), benzopiranotiofeno (H3L6) ou borodipirrometeno (H3L7) (conjunto quatro de compostos) associados aos fragmentos hidrazônicos. Estudos de microscopia de fluorescência do ligando H3L7 comprovaram sua presença dentro de células de câncer. Também, análises de co-localização para organelas mostraram a afinidade dos ligantes com a mitocôndria. Finalmente, motivada pelas propriedades biológicas da molécula isoniaziada e seu uso em tratamentos de quimioterapia, esta tese mostra de forma general a síntese, caracterização e citotoxicidade de um novo ligante isoniazídico (H2L8) e seus complexos de perclorato ou acetato de cobre(II) 13 e 14 (conjunto cinco de compostos) visando realizar um pedido de patente. / [en] On the search of new chemotherapeutic agents differing from the classic cisplatin family drugs, aroylhydrazonic derivatives and their copper(II) complexes appear as promising compounds. This thesis reports on the design and syntheses of a novel combination of them through eight new aroylhydrazones and their fourteen perchlorate and/or acetate Cu2-complexes 1‒14. The obtained bioinspired copper(II) complexes constitute structural models for the active sites of some type 3 copper enzymes. The compounds were fully characterized using various spectroscopic and analytical techniques. X-ray diffraction structures for four ligands and five complexes are described in detail. Compounds stability was studied in cellular medium and their biological activity was examined. The results include a large study on the interaction of two thiophene (H3L1) or furan (H3L2) ligand derivatives and their respective μ-hydroxo dicopper complexes 1 and 2 (first set of compounds) respectively, with bovine serum albumin protein and calf thymus DNA using different spectroscopic techniques, which include the binding affinity to BSA and DNA using UV/Visible and/or fluorescence techniques. Additionally, scattering techniques revealed that the interaction between the compounds and BSA induces reversible aggregation of the biomolecules. As an important contribution of the present work, the plasmid DNA cleavage ability of the complexes 1 and 2 was studied by Dynamic Light Scattering. The changes of hydrodynamic radius values of pBR322 plasmid DNA are correlated to the nick induced by the complexes in the helices. Cytotoxic assays on some cancer cells revealed the high ability of H3L1 and H3L2, and complexes 1 and 2 to induce cell death. On the other hand, the many biological properties, including anticancer activity, of the isoxazole molecule, motivated the inclusion of this moiety in two ligands H3L3 and H2L4 and four complexes 3‒6 (second set of compounds). Interaction of these isoxazole-aroylhydrazonic ligand derivatives with DNA was directly studied by absorbance and fluorescence spectroscopy, as a result of the fluorescence properties displayed by the ligands. In the case of the isoxazole-aroylhydrazonic complexes-DNA interaction, the ethidium bromide displacement assay revealed significant affinity by intercalation binding mode of the nucleic acid in the DNA sequence. Additionally, this work successfully demonstrated that ligands and complexes containing a phenol pendant arm instead of a pyridine one improve the in vitro cytotoxicity on human epithelial breast cancer cells, attaining nanomolar range. Metal chelation and transmetallation ability of binucleating ligands H3L3 and H2L4 and their copper complexes 3‒6 with Fe(II), Fe(III) and Zn(II) from the biological medium was verified as an additional cell death induction anticancer strategy. Moreover, to study the interaction of the compounds with the biological system and to demonstrate their cell permeability, ligands (H3L5‒H3L7) and complexes (7‒12) were functionalized in their hydrazone moieties with potent fluorophores, such pyrene (H3L5) (set three of compounds), benzopyranothiophene (H3L6), or boron-dipyrromethene (H3L7) derivatives (set four of compounds). Fluorescence microscopy studies proved the presence of ligand H3L7 inside cancer cells, proving its ability to pass through the cell membrane. Besides, co-localization analysis for organelles showed the affinity of this ligand for the mitochondria. Finally, motived by the wide spectrum of biological properties of the isoniazid molecule and its use in chemotherapy, this thesis reports the syntheses, characterization and cytotoxicity studies on cancer cells of a new isonicotinoyl hydrazone ligand (H2L8) and its perchlorate or acetate copper(II) complexes 13 and 14 (set five of compounds), which are involved in a patent request.