Submitted by Haroudo Xavier Filho (haroudo.xavierfo@ufpe.br) on 2016-04-05T17:59:08Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) TESE_SINARA MONICA VITALINO DE ALMEIDA_FINAL UNIFICADO BIBLIOTECA.pdf: 9803056 bytes, checksum: 68bd08234fdac2b45bf400b3ebd62957 (MD5) / Made available in DSpace on 2016-04-05T17:59:08Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) TESE_SINARA MONICA VITALINO DE ALMEIDA_FINAL UNIFICADO BIBLIOTECA.pdf: 9803056 bytes, checksum: 68bd08234fdac2b45bf400b3ebd62957 (MD5) Previous issue date: 2015-07-23 / CAPES, CNPq / O câncer é, sem sombra de dúvidas, a doença mais temida pela população, em razão da sua alta incidência e elevadas taxas de mortalidade para determinados tipos da doença. Nas últimas décadas, os pesquisadores têm obtido avanços significativos no entendimento da patogênese, nas características e nas terapias do câncer. A quimioterapia é frequentemente o tratamento escolhido para muitos tipos de câncer e por este motivo a pesquisa por novos agentes quimioterápicos constitui um dos alicerces na luta contra o câncer. Os intercaladores orgânicos são compostos poliaromáticos que podem se inserir entre pares de bases adjacentes da dupla fita de DNA e inibir a síntese de ácido nucléico in vivo, essa propriedade é comumente observada em drogas anticâncer usadas na terapia clínica. Por isto, a descoberta de novos intercaladores do DNA tem sido considerada uma abordagem prática e um número expressivo de moléculas tem sido avaliado quanto às suas propriedades intercaladoras. Neste trabalho foram sintetizados novos agentes anticâncer tendo como molécula de partida o anel acridina. Foram sintetizados e caracterizados oito novos derivados da série 2-acridin-9-il-metileno-N-fenil-hidrazina-carbotioamida (3a-3h) com diferentes substituintes na porção fenil (não substituídos ou com substituintes elétrondoadores ou elétron-retiradores) e dois novos derivados da série 3-(acridin-9-il)-n-benzilideno-2- cianoacrilohidrazidas (AMTAC-01 e AMTAC-02). Os compostos foram avaliados quanto às suas propriedades intercaladoras ao ctDNA in vitro e atividades antiproliferativas contra linhagens de células tumorais de mama (MCF-7), ovário resistente a múltiplas drogas (NCI-ADR/RES), pulmão (NCI-H460), próstata (PC-3), cólon (HT29), ovário (OVCAR-03), rim (786-0), leucemia (K562) e glioma (U251). Foram investigadas alterações morfológicas induzidas por tratamento de células MCF-7 com o composto mais ativo da série 2-acridin-9-il-metileno-N-fenil-hidrazinacarbotioamida (3a) através de microscopias eletrônicas de transmissão, varredura e da análise de exposição de fosfatidilserina e fragmentação de DNA. Além disso, a atividade de inibição da topoisomerase IIa dos derivados 3-(acridin-9-il)-n-benzilideno-2-cianoacrilohidrazidas foi verificada e a ligação com ctDNA foi estudada por meio de espectroscopia de absorção em fluorescência. Todos os derivados produzidos das duas séries apresentaram interação com o DNA. Após o contato com DNA foram verificados efeitos hipercrômicos e hipocrômicos, bem como mudanças para o vermelho ou azul nos espectros de absorbância. Essas modificações são preditivas de formação de complexo entre DNA e derivado. As constantes de ligação calculadas estão entre 1.74 x 104 e 1.0 x 106 M-1 para os derivados 3a-3h e entre 2.3-2.5 x 106 M-1 para os AMTAC’s. Estes valores indicam alta afinidade pelos pares de base do DNA. Da série 2-acridin- 9-il-metileno-N-fenil-hidrazina-carbotioamida o composto mais eficiente para ligação in vitro com o DNA foi o derivado cloro-substituído (3f), enquanto o composto mais ativo no teste antiproliferativo foi o derivado não substituído na porção tiossemicarbazona (3a). Os valores de concentração letal para 50 % do número inicial de células para o derivado 3a contra as linhagens NCI-H460, MCF-7, U251, NCI-ADR/RES, HT-29 e PC-3 foram 43.41, 60.26, 68.93, 70.2, 70.24 e 72.95 μM, respectivamente. As análises por microscopias eletrônicas de varredura e transmissão de células MCF-7 tratadas com 60 μM do derivado 3a demonstraram alterações ultramorfológicas indicativas de autofagia: vacúolos com dupla membrana. Além disso, os derivados AMTAC-01 e AMTAC-02 foram mais ativos contra as linhagens tumorais de próstata e melanoma, respectivamente. Ambos os derivados apresentaram atividade inibidora topoisomerase IIa na concentração de 50 μM. Os resultados indicam que uma ligação eficiente ao DNA é uma condição necessária para atividade antitumoral e que os novos derivados híbridos de acridina apresentaram promissoras atividades antiproliferativa, ligadora do DNA e inibição da topoisomerase. / People fear cancer more than any other serious illness which can be explained by the high incidence and mortality rates for some types of cancer. In the last decades, significant advances were obtained regarding cancer pathogenesis, features and therapies. Chemotherapy is often the treatment of choice for many types of cancer and the search for new chemotherapeutic agents still plays a major role in the fight against cancer. Organic intercalators are poliaromatic compounds that are able to insert into DNA double strands and inhibit in vivo acid nucleic synthesis. This characteristic is, in general, observed in anticancer drugs, hence the discovery and development of new DNA intercalators has been considered a practical approach and a number of intercalators have been recently reported. In this work, new anticancer agents were synthetized based on acridine nucleus for structural modification using substituted thiosemicarbazide moieties. It were synthetized eight new (Z)-2-(acridin-9- ylmethylene)-N-phenylhydrazinecarbothioamide derivatives (3a-3h) presenting different substituents on phenyl ring (non-substituted and electron-donating or -withdrawing) and two new 3-(acridin-9-yl)-N-benzylidene-2-cyanoacrilohydrazide derivatives (AMTAC-01 and AMTAC-02). In vitro ctDNA interaction was assayed and antiproliferative activity was evaluated against cancer cell lines of glioma (U251), breast (MCF-7), ovary expressing phenotype multiple drugs resistance (NCI-ADR/RES), kidney (786–0), lung (NCI-H460), prostate, (PC-3), ovary (OVCAR-03), colon adenocarcinoma (HT-29) and chronic myeloid leukemia (K-562). It was investigated ultramorphological changes induced by 3a treatment on MCF-7 cells by transmission and scanning electron microscopies, besides the evaluation of phosphatidylserine externalization and DNA fragmentation. Topoisomerase IIa inhibitory activity of AMTAC’s was evaluated. ctDNA binding properties were performed with calf thymus DNA (ctDNA) by electronic absorption and fluorescence spectroscopies. Both hyperchromic and hypochromic effects, as well as red or blue shifts were demonstrated by addition of ctDNA to the derivatives. These spectroscopic alterations indicated formation of derivative-DNA complex. The calculated binding constants ranged from 1.74 x 104 to 1.0 x 106 M-1 for 3a-3h derivatives and 2.3-2.5 x 106 M-1 for AMTAC’s compounds. These values mean that the new acridine derivatives have high affinity to ctDNA. From (Z)-2-(acridin-9- ylmethylene)-N-phenylhydrazinecarbothioamide serie, the most efficient compound in in vitro binding to ctDNA was 3f, while the most active compound in antiproliferative assay was 3a. Regarding lethal concentration (LC50), compound 3a was lethal to NCI-H460, MCF-7, U251, NCI-ADR/RES, HT-29 and PC-3 cells on the respective concentrations: 43.41, 60.26, 68.93, 70.2, 70.24 and 72.95 μM. Scanning and transmission electron microscopies revealed that treatment with 60 μM of 3a induces morphological changes in MCF-7 cells indicating autophagy, such as vacuole with double membrane. On the other hand, antiproliferative assay demonstrated that AMTAC-01 and AMTAC-02 were most active against prostate and melanoma tumor cell lines, respectively. Both derivatives displayed potent topoisomerase IIα inhibitory activity at 50 μM. Taking together, these results indicates that an efficient binding is a necessary condition for antiproliferative activity. The new acridine hybrid derivatives showed promising DNA binding, antiproliferative against cancer cells and inhibitory topoisomerase activity.

Orientador: Marcelo Brocchi / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-25T03:27:50Z (GMT). No. of bitstreams: 1 Cordeiro_TamiresFernandaVilasBoas_M.pdf: 3029203 bytes, checksum: 69ac5762ed6eaafac425a284455352cf (MD5) Previous issue date: 2014 / Resumo: Salmonella enterica é um dos patógenos de origem alimentar mais prevalente. É uma bactéria gram-negativa, pertencente à família Enterobacteriaceae, intracelular facultativa, não formadora de esporo, anaeróbia facultativa, capaz de infectar animais incluindo o homem. Geralmente é adquirida por meio de alimentos contaminados com tal micro-organismo e pode causar em humanos gastroenterite e bacteremia. O presente trabalho propõe a construção de linhagens mutantes de S. enterica Typhimurium para genes codificadores de proteínas associadas ao nucleóide (NAPs ¿ Nucleoid-Associated Proteins). Tais proteínas auxiliam no enovelamento do DNA, permitindo que o cromossomo bacteriano seja compactado, além disso também influenciam na regulação transcricional de genes, em especial daqueles que respondem a mudanças ambientais. As NAPs são numerosas e o estudo desse grupo é bastante importante, pois vários esclarecimentos ainda precisam ser feitos a respeito de grande parte dessas proteínas. Dados recentes do nosso grupo de pesquisa têm demonstrado que mutantes nulos de S. enterica Typhimurium para genes codificadores de NAPs são atenuados quanto à virulência e capazes de induzir proteção no modelo murino de infecção. Esses resultados demonstram o importante papel de tais proteínas na virulência bacteriana. Assim, o presente estudo tem como objetivo a construção de mutantes nulos para dois genes codificadores de NAPs (stpA e ybaB) em S. enterica Typhimurium e a avaliação do fenótipo desses mutantes. Não há dados na literatura sobre o papel de tais NAPs com relação à virulência bacteriana. No caso de YbaB, não existem dados na literatura sobre o papel desta NAP em enterobactérias. Foi utilizado o sistema de recombinação ? Red para obtenção dos mutantes. Para observação do fenótipo de tais linhagens, foram feitos experimentos in vitro e in vivo. Os resultados observados nos experimentos in vitro mostram fenótipos interessantes das linhagens mutantes em comparação com as respectivas linhagens selvagens. No caso da mutação ?stpA, foi observada maior sobrevivência de células com essa deleção a certas situações de estresse em comparação com a linhagem selvagem. Já para a mutação ?ybaB, nossos ensaios de motilidade sugerem que a deleção desse gene teve efeito sobre a motilidade das células mutantes. Quanto à virulência dos mutantes construídos, tais mutações não afetaram a patogenicidade de S. enterica de modo considerável. Assim, as linhagens mutantes obtidas no presente trabalho não apresentam potencial de serem aplicadas como vacinas, mas lançam perspectivas para estudos futuros a respeito do papel biológico de YbaB em S. enterica / Abstract: Salmonella enterica is one of the most prevalent foodborne pathogens. It is a gram- negative bacterium, belonging to the Enterobacteriaceae family, intracellular facultative, non-spore forming, anaerobic facultative, capable of infecting animals, including man. It¿s usually acquired through foods contaminated with such microorganism and can cause gastroenteritis and bacteremia in humans. This study proposes the construction of mutant strains of S. enterica Typhimurium for genes encoding nucleoid-associated proteins (NAPs). These proteins help on folding of DNA, allowing the bacterial chromosome to be compressed, also influencing the transcriptional regulation of genes, especially those that respond to environmental changes. The NAPs are numerous and the study of this group is very important, because several explanations still have to be made regarding most of these proteins. Recent data from our research group has shown that null mutants of S. enterica Typhimurium for genes encoding NAPs are attenuated for virulence and capable of inducing protection in a murine model of infection. These results demonstrate the important role of these proteins in bacterial virulence. Thus, the present study aims at the construction of null mutants for two genes encoding NAPs (stpA and ybaB) in S. enterica Typhimurium and at the evaluation of the phenotype of these mutants. There are no data in the literature about the role of such NAPs regarding bacterial virulence. For the YbaB, there are no data in the literature about the role of this NAP in enterobacteria. The ? Red recombination system was used to obtain the mutants. For observation of the phenotype of such strains, in vitro and in vivo experiments were performed. The results obtained in in vitro experiments showed interesting phenotypes of mutant strains compared to their wild-type strains. In the case of ?stpA mutation, increased cell survival was observed on certain stress situations compared to the wild-type strain. For the ?ybaB mutation, our studies suggest that deletion of this gene had effect on motility of mutant cells. For virulence of the constructed mutants, these mutations did not affect the pathogenicity of S. enterica considerably. Thus, the mutant strains obtained in this study have no potential to be applied as vaccines, but this work provides prospects for future studies on the biological role of YbaB in S. enterica / Mestrado / Genetica de Microorganismos / Mestra em Genética e Biologia Molecular

Abstract Gene products that are only expressed in one tissue or cell type are useful models for investigating the biochemical and molecular mechanisms of tissue/cell-specific gene regulation. The regulatory regions of such genes are also practical tools in gene therapy. In this work, prostate-specific and androgen-dependent gene regulation was investigated by using human prostatic acid phosphatase (hPAP) and rat probasin (rPB) as models. In DNase I footprinting, a protected 12 bp region was found in the PB gene between the nucleotides -251 and -240 only with nuclear extracts of prostatic origin. The sequence of this area was GAAAATATGATA. Weak interaction could be detected between the DNA-binding domain of AR and the prostatic transcription factor. The results also suggested that the prostatic regulatory protein makes AR binding to its response element more effective and concomitantly magnifies the effect of androgen. A hPAP construct containing the sequence between the nucleotides -734 and +467 in front of the CAT reporter gene was highly expressed in the prostate of transgenic mice. Five homologues (A-E) for our previously identified prostate-specific GAAAATATGATA DNA-binding site were found in the area where the sites C and E could bind the regulatory protein in EMSA. The prostatic transcription factor complex bound to the GAAAATATGATA site was purified and characterized from a suspension-adapted mass culture of PC-3 prostate cancer cells by using sequence-specific DNA affinity chromatography, mass spectrometry and supershifts. Several potential transcription factors were identified, but only USF2 was confirmed to be part of the transcription factor complex. Two PC-3 cell line variants (anchorage-dependent and suspension-adapted, anchorage-independent variants) were used as a model for advanced, androgen-independent prostate cancer. Genes that were overexpressed in a suspension-adapted PC-3 cell line were further investigated, since they can be considered as putative markers of metastatic activity. The macrophage inhibitory cytokine-1 (MIC-1) gene, which was overexpressed in the suspension-adapted PC-3 cell line, was further investigated in order to clarify the mechanism behind aggressive cell growth and androgen-independent gene regulation. In patient specimens, MIC-1 had no or low expression in benign prostatic hyperplasia and normal prostate but high in prostatic cancer and therefore it could be a useful marker for aggressive prostate cancer. Indomethacin increased the expression of MIC-1 in PC-3 cells, and apoptosis was also induced in this cell line but not in saPC-3 cell line suggesting a block in MIC-1 inducible apoptosis pathway.

Natural products continue to be a major chemical lead matter for drug discovery due to their diverse chemical structures and bioactivities. Clinically significant natural products include anti-cancer and anti-infective compounds and while many more of these compounds show promising bioactivity, their clinical relevance is often limited by toxicity or poor solubility. Combinatorial biosynthesis can be employed to modify existing chemical scaffolds towards reducing these limitations. To fully take advantage of these biochemical tools, it is important to understand the biosynthesis and mechanism of action of the molecules. Saccharides in glycosylated natural products provide specific interactions with cellular targets and are often crucial for a compound’s bioactivity. Genetic engineering of sugar pathways can modify glycosylation patterns leading to the diversification of natural products. Saquayamycins (SQN) H and I are cytotoxic angucycline antibiotics containing five deoxyhexoses including the rare amino sugar rednose. Elucidating the biosynthetic pathway of rednose could add to the arsenal of combinatorial biosynthesis tools for drug development. Our research goal of investigating the rednose biosynthetic pathway was pursued through two specific aims: the identification of the Streptomyces sp. KY 40-1 gene cluster involved in the biosynthesis of SQN H and I (sqn) (specific aim 1), and the validation of the proposed L-rednose biosynthetic pathway up to the glycosyl transfer through enzymatic synthesis of NDP-3,6-dideoxy-L-idosamine (specific aim 2). The sqn gene cluster revealed deoxysugar biosynthetic genes that could be used to alter glycosylation patterns to generate novel compounds while the enzymatic synthesis afforded novel genetic engineering tools to generate novel TDP-deoxysugars that could be used to diversify compounds such as aminoglycosides to circumvent resistance mechanisms. The first step to generate TDP-glucosamine enzymatically was accomplished, however later steps were unsuccessful. The aureolic acid mithramycin (MTM) was recently tested in clinical trials for Ewing sarcoma following the discovery of MTM as a potent inhibitor of the oncogenic transcription factor EWS-FLI1 present only in Ewing sarcoma cells It is understood that MTM binds the minor groove of G/C rich DNA as an Mg2+-coordinated dimer disrupting transcription of proto-oncogenes; however, the DNA recognition rules were not completely understood, making further interrogation of MTM’s DNA binding preferences necessary. This research goal of further understanding the mechanism of action for MTM was approached through two specific aims: the investigation of the dimerization of MTM (specific aim 3), and the investigation of MTM’s DNA binding preferences (specific aim 4). This work established that MTM and its biosynthetic precursor premithramycin B (PreMTM B), and several MTM analogues with modified 3-side chains: mithramycin SDK (MTM SDK), mithramycin SA tryptophan (MTM SA-Trp), and mithramycin SA alanine (MTM SA-Ala) dimerize even in the absence of DNA under physiologically relevant conditions. The study also demonstrated that modification of the 3-side chain modulates DNA binding affinity of MTM analogues, established a minimum MTM binding site on DNA, and revealed MTM DNA recognition is driven by direct (sequence) and not indirect (conformation) readout laying the foundation for subsequent research based on the interaction between MTM, DNA, and the oncogenic transcription factor EWS-FLI1 in the rational design of new MTM analogues for the treatment of Ewing sarcoma.

No description available.

The thesis entitled “Benzimidazole based Novel Ligands for Specific Recognition of Duplex and G-Quadruplex DNA” deals with the design, synthesis and modeling of several benzimidazole based molecules and their interaction with duplex and G-quadruplex DNA structures. It also elucidates the inhibition effect of the ligands on the activity of Topoisomerase I and Telomerase. The work has been divided into six chapters. Chapter 1. DNA Interacting Small Organic Molecules: Target for Cancer Therapy This first chapter presents an overview on the various types of small molecules that interact with duplex and G-quadruplex structures of DNA or interfere with the activity of DNA targeted enzymes like topoisomerase and telomerase. The importance of such molecules as chemotherapeutic agents is highlighted. Chapter 2. DNA Recognition: Conformational Switching of Duplex DNA by Mg2+ ion Binding to Ligand Bis-benzimidazoles like Hoechst 33258 are well known ligands that bind to duplex DNA (ds-DNA) minor grooves. Here a series of dimeric bisbenzimidazole based ligands in which two Hoechst units are connected via oxyethylene based hydrophilic [Ho-4ox-Ho (1), Ho-3ox-Ho (2)] or via hydrophobic oligomethylene [Ho-(CH2)8-Ho (3)](Figure 1) spacers have been synthesized. The aim of this investigation is to examine the binding property of these dimers on the ds-DNA to explore whether the variation in the length of the spacer has any effect on DNA binding properties particularly in presence of selected metal ions. The changes of individual dimers in DNA binding efficiency was studied in detail by fluorescence, circular dichroism spectral titrations and thermal denaturation experiment with selected duplex DNA formed from appropriate oligonucleotides. We have also examined the changes that occur in geometry of the molecules from linear to hairpin motif in presence of Mg2+ ion. A large difference was observed in [ligand]/ [DNA] ratio and binding efficiency with ds-DNA upon change in the ligand geometry from linear to hairpin motif. The experimental results were then substantiated using docking and molecular dynamics simulations using a model ds-DNA scaffold. Both experimental and theoretical studies indicate that the DNA binding is highly dependent on the spacer type and length between the two monomeric Hoechst units. The spacer length actually helps to achieve shape complimentarity with the double-helical DNA axis. Figure1: Chemical structures of the dimeric ligands Ho-4ox-Ho, Ho-3ox-Ho, Ho-(CH2)8-Ho and Hoechst 33258 (Ho) used in this study. Chapter 3. DNA Binding and Topoisomerase I Inhibiting Properties of New Benzimidazole Substituted Polypyridyl Ruthenium (II) Mixed-Ligand Complexes In this study, we have synthesized and fully characterized three new Ru(II) based polypyridyl and benzimidazole mixed complexes: (1) [Ru(bpy)2(PMI)], 2+ (2) [Ru(bpy)2(PBI)]2+ and (3) [Ru(bpy)2(PTI)]2+ (Figure 2) . The affinities of these complexes toward duplex DNA were investigated. In addition, the photocleavage reaction of DNA and topoisomerase I inhibition properties of these metal complexes were also studied. The DNA binding efficiency of individual complexes was studied in detail by absorbance, fluorescence spectral titrations and thermal denaturation experiment using natural calf-thymus DNA. Upon irradiation at 365 nm, all three Ru(II) complexes were found to promote the cleavage of plasmid DNA from negatively supercoiled to nicked circular and subsequently to linear DNA. The inhibition of topoisomerase I mediated by these Ru(II) complexes was also examined. These experiments demonstrate that each complex serves as an efficient inhibitor toward topoisomerase I and such inhibition activity is consistent with interference with the DNA religation step catalyzed by topoisomerase. Figure 2. Chemical structures of the metal complexes used in this present study. Chapter 4. Synthesis and Evaluation of a Novel Class of G-Quadruplex-Stabilizing small molecules based on the 1,3-Phenylene-bis (piperazinyl benzimidazole) syatem Achieving stabilization of telomeric DNA in the G-quadruplex conformation by various organic compounds is an important goal for the medicinal chemists seeking to develop new anticancer agents. Several compounds are known to stabilize the G-quadruplexes. However, relatively few are known to induce their formation and/or alter the topology of the pre-formed G-quadruplex DNA. Herein, four compounds having the 1,3-phenylene-bis(piperazinyl benzimidazole) (Figure 3) unit as a basic skeleton have been synthesized, and their interactions with the 24-mer telomeric DNA sequences from Tetrahymena thermophilia d(T2G4)4 have been investigated using high-resolution techniques such as circular dichroism (CD) spectropolarimetry, CD melting, emission spectroscopy, and polyacrylamide gel electrophoresis. The data obtained, in the presence of one of three ions (Li+, Na+ or K+), indicate that all the new compounds have a high affinity for G-quadruplexDNA, and the strength of the binding with G-quadruplex depends on (i) phenyl ring substitution, (ii) the piperazinyl side chain, and (iii) the type of monovalent cation present in the buffer. Results further suggest that these compounds are able to abet the conversion of the intramolecular G-quadruplex DNA into parallel stranded intermolecular G-quadruplex DNA. Notably, these compounds are also capable of inducing and stabilizing the parallel stranded G-quadruplex DNA from randomly structured DNA in the absence of any stabilizing cation. The kinetics of the structural changes induced by these compounds could be followed by recording the changes in the CD signal as a function of time. Figure 3. Chemical structures of the ligands used in this study. Chapter 5A. The Spacer Segment in the Dimeric 1,3-phenylene-bis (piperazinyl benzimidazole) has a Dramatic Influence on the Binding and Stabilization of Human Telomeric G-Quadruplex DNA Ligand-induced stabilization of G-quadruplex structures formed by human telomeric DNA is an active area of basic and clinical research. The compounds which stabilize the G-quadruplex structures lead to suppression of telomerase activity. Herein, we present the interaction of a series of monomeric and dimeric compounds having 1,3-phenylene-bis(piperazinyl benzimidazole) (Figure 4) as basic pharmacophore unit with G-quadruplex DNA formed by human telomeric repeat d[(G3T2A)3G3]. These new compounds provide an excellent stabilization property to the pre-formed G-quadruplex DNA in the presence of one of three ions (100 mM Li+, Na+ or K+ ions). Also the G-quadruplex DNA formed in the presence of low concentrations of ligands in 100 mM K+, adopts a parallel-stranded conformation which attains an unusual thermal stability. The dimeric ligands having oxyethylene based spacer provide much higher stability to the pre-formed G-quadruplex DNA and the G-quadruplexes formed in presence of the dimeric compounds than the corresponding monomeric counterparts. Consistent with the above observation, the dimeric compounds exert significantly higher telomerase inhibition activity than the monomeric compounds. The ligand induced G-quadruplex DNA complexes were further investigated by computational molecular modeling, which provide useful information on their structure-activity relationship. Figure 4. Chemical structures of the monomeric and dimeric ligands used in this study. Chapter 5B. Role of Spacer in Symmetrical Gemini bisbenzimidazole based Ligands on the Binding and Stabilization of Dimeric G-Quadruplex DNA derived from Human Telomeric Repeats The design and development of anticancer agents that act via stabilization of the telomeric G-quadruplex DNA is an active area of research because of its importance in the negative regulation of telomerase activity. Several classes of G-quadruplex DNA binding ligands have been developed so far, but they mainly act on the DNA sequences which are capable of forming a single Gquadruplex unit. In the present work, we have developed few new dimeric (Gemini) bisbenzimidazole ligands (Figure 5), in which the spacer joining the two bisbenzimidazole units have been varied using oligooxyethylene units of different length. Herein we show the interaction of each of these ligands, with the G-quadruplex DNA, derived from oligodeoxynucleotides d(T2AG3)4 and d(T2AG3)8, which fold into a monomeric and dimeric (having two folded G-tetrad units) G-quadruplex DNA, respectively. We also present evidence that the G-quadruplex DNA structure formed by these sequences in K+ solution in presence of the ligands is parallel, with unusual stability, and the spacer length between the two bisbenzimidazole units has critical role on the G-quadruplex stability, particularly on the G-quadruplex structures formed by the 48-mer sequence. The computational aspects of the ligand-G-quadruplex DNA association have also been analyzed. Interestingly, the gemini ligand having longer spacer was highly potent in the inhibition of telomerase activity than the corresponding gemini ligands having shorter spacer or the monomeric ligand. Also, the dimeric ligands are more cytotoxic toward the cancer cells than normal cells. Figure 5. Chemical structures of the monomeric and gemini ligands used in this study. Chapter 6. Stabilization and Structural Alteration of G-Quadruplex DNA made from Human Telomeric Repeat Mediated by Novel Benzimidazole Derivatives based on Tröger’s Base Ligand-induced stabilization of G-quadruplex formation by the telomeric DNA single stranded 3'-overhang is a nice strategy to inhibit telomerase from catalyzing telomeric DNA synthesis and form capping telomeric ends. Herein we present the first report of the interactions of two novel bisbenzimidazoles (TBBz1 and TBBz2)(Figure 6) based on the Tröger’s base skeleton with the G-quadruplex DNA. These molecules stabilize the G-quadruplex DNA derived from a human telomeric sequence. Significantly strong binding affinity of these molecules to G-quadruplex DNA relative to duplex DNA was observed by CD spectroscopy, thermal denaturation and UV-vis titration studies. The above results obtained are in excellent agreement with the biological activity, measured in vitro using a modified TRAP assay. Additionally exposure of cancer cells to these compounds showed a remarkable decrease in the population growth. Also, it has been observed that the ligands are selectively more cytotoxic toward the cancerous cells than the corresponding noncancerous cells. To understand further, the ligand-G-quadruplex DNA complexes were investigated by computational molecular modeling. This provided additional insights on the structure activity relationship. Computational studies suggest that the adaptive scaffold not only allows these ligands to occupy the G-quartet but also binds with the grooves of the G-quadruplex DNA. Figure 6. Chemical structures of the ligands, TBBz1 and TBBz2 used in this study, (For structural formula pl see the abstact.pdf file.)

京都大学 / 0048 / 新制・課程博士 / 博士(エネルギー科学) / 甲第22087号 / エネ博第395号 / 新制||エネ||76(附属図書館) / 京都大学大学院エネルギー科学研究科エネルギー基礎科学専攻 / (主査)教授 森井 孝, 教授 木下 正弘, 教授 片平 正人 / 学位規則第4条第1項該当 / Doctor of Energy Science / Kyoto University / DGAM

AG to A transition at position -76 in the promoter region of the apoAI gene was previously identified, and the A-76 has been shown to be associated with high apoAI levels. The functional significance of the point mutation was assessed by analysing the DNA-protein binding and promoter activities of the different alleles. This data would suggest that the point mutation alters the function of the apoAI promoter as gel retention assays revealed that the G fragment (-140 to +10) formed an extra DNA-protein complex compared to the A fragment (-140 to +10). Concurrent with the altered DNA-protein interaction between the G and the A fragments, the transcriptional activities of the apoAI gene were found to also be altered. CAT assays have indicated a 1.91 fold increase in promoter activity of the A fragment as compared to the G fragment (-256 to +397). The difference in promoter activity was, however, highly dependent on the particular fragment used, as no difference was observed between the alleles when a fragment {-256 to +68) was used. In this study elements were identified in the region +68 to +397 that causes a reduction in the promoter activity of the G allele by 3.6 fold, whilst reducing the A allele activity by 2 fold. This data would suggest that the point mutation functionally alters the apoAI promoter activity via its interaction with other sequences especially in the region +68 to +397.

For nearly five decades, the simple eukaryote Saccharomyces cerevisiae has been used as a model for understanding the eukaryotic cell cycle. One vein of this research has focused on understanding how chromosome structure is regulated in relation to the cell cycle. This work characterizes a new mechanism that modulates the chromatin organizing condensin complex, in hopes of furthering the understanding of chromosome structure regulation in eukaryotes. During mitosis, chromosomes are condensed to facilitate their segregation through a process mediated by the condensin complex. Upon interphase onset, condensation is reversed, allowing for efficient transcription and replication of chromosomes. This work demonstrates that Ycg1, the Cap-G subunit of budding yeast condensin, is cell-cycle regulated with levels peaking in mitosis and decreasing as cells enter G1 phase. The cyclical expression of Ycg1 is unique amongst condensin subunits, and is established by a combination of cell cycle-regulated transcription and constitutive proteasomal degradation. Interestingly, when cyclical expression of Ycg1 is disrupted, condensin formation and chromosome association increases, and cells exhibit a delay in cell-cycle entry. These results demonstrate that Ycg1 levels limit condensin function, and suggest that regulating the expression of an individual condensin subunit helps to coordinate chromosome conformation with the cell cycle. These data, along with recent corroborating results in Drosophila melanogaster suggest that condensin regulation through limiting the expression of a single condensin subunit may be broadly conserved amongst eukaryotes.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第20940号 / 理博第4392号 / 新制||理||1631(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)教授 杉山 弘, 教授 三木 邦夫, 教授 秋山 芳展 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM