Real-time monitoring of protein conformational changes using a nano-mechanical sensor.

Proteins can switch between different conformations in response to stimuli, such as pH or temperature variations, or to the binding of ligands. Such plasticity and its kinetics can have a crucial functional role, and their characterization has taken center stage in protein research. As an example, Topoisomerases are particularly interesting enzymes capable of managing tangled and supercoiled double-stranded DNA, thus facilitating many physiological processes. In this work, we describe the use of a cantilever-based nanomotion sensor to characterize the dynamics of human topoisomerase II (Topo II) enzymes and their response to different kinds of ligands, such as ATP, which enhance the conformational dynamics. The sensitivity and time resolution of this sensor allow determining quantitatively the correlation between the ATP concentration and the rate of Topo II conformational changes. Furthermore, we show how to rationalize the experimental results in a comprehensive model that takes into account both the physics of the cantilever and the dynamics of the ATPase cycle of the enzyme, shedding light on the kinetics of the process. Finally, we study the effect of aclarubicin, an anticancer drug, demonstrating that it affects directly the Topo II molecule inhibiting its conformational changes. These results pave the way to a new way of studying the intrinsic dynamics of proteins and of protein complexes allowing new applications ranging from fundamental proteomics to drug discovery and development and possibly to clinical practice.

Validation of a spectrophotometric method to estimate the adsorption on nanoemulsions of an antimalarial oligonucleotide

This study describes the validation of a spectrophotometric method to estimate oligonucleotides association with cationic nanoemulsions. Phosphodiester and phosphorothioate oligonucleotides targeting Plasmodium falciparum topoisomerase II were analyzed at 262 nm. Linear response (r > 0.998) was observed from 0.4 to 1.0 nmol/mL, the relative standard deviation values for the intra- and inter-days precision were lower than 2.6% and the recovery ranged from 98.8 to 103.6% for both oligonucleotides. The association efficiency was estimated based on an ultrafiltration/centrifugation method. Oligonucleotides recovery through 30 kDa-membranes was higher than 92%. The extent of oligonucleotides association (42 to 98%) varied with the composition of nanoemulsions

Aplysfistularine: a novel dibromotyrosine derivative isolated from Aplysina fistularis

The new dibromotyrosine derivative 3,5-dibromo-4-[3'dimethylamonium]propoxyphenyl]-N,N,N-trimethylethanamonium, here referred to as aplysfistularine (1), was isolated from the marine sponge Aplysina fistularis along with 2-(3,5-dibromo-4methoxyphenyl)-N,N,N-trimethylethanamonium (2), aplysterol (3) and 24,28-didehydroaplysterol (4). Their identification was performed by mass spectrometry, infrared, ¹H and 13C NMR, and by comparison with literature data. Compound 2 and the mixture of 3 and 4 were tested in vitro (inhibitory activity) with supercoiled DNA relaxation techniques, and showed inhibitory activity on human DNA topoisomerase II-α. Compound 1 was not tested due to paucity of the material.

Un criblage ciblant de nouveaux facteurs impliqués dans l’assemblage mitotique des chromosomes dans le nématode C. elegans

La division cellulaire est un processus fondamental des êtres vivants. À chaque division cellulaire, le matériel génétique d'une cellule mère est dupliqué et ségrégé pour produire deux cellules filles identiques; un processus nommé la mitose. Tout d'abord, la cellule doit condenser le matériel génétique pour être en mesure de séparer mécaniquement et également le matériel génétique. Une erreur dans le niveau de compaction ou dans la dynamique de la mitose occasionne une transmission inégale du matériel génétique. Il est suggéré dans la littérature que ces phénomènes pourraient causé la transformation des cellules cancéreuses. Par contre, le mécanisme moléculaire générant la coordination des changements de haut niveau de la condensation des chromosomes est encore incompris. Dans les dernières décennies, plusieurs approches expérimentales ont identifié quelques protéines conservées dans ce processus. Pour déterminer le rôle de ces facteurs dans la compaction des chromosomes, j'ai effectué un criblage par ARNi couplé à de l'imagerie à haute-résolution en temps réel chez l'embryon de C. elegans. Grâce à cette technique, j'ai découvert sept nouvelles protéines requises pour l'assemblage des chromosomes mitotiques, incluant la Ribonucléotide réductase (RNR) et Topoisomérase II (topo-II). Dans cette thèse, je décrirai le rôle structural de topo-II dans l'assemblage des chromosomes mitotiques et ces mécanismes moléculaires. Lors de la condensation des chromosomes, topo-II agit indépendamment comme un facteur d'assemblage local menant par la suite à la formation d'un axe de condensation tout au long du chromosome. Cette localisation est à l'opposé de la position des autres facteurs connus qui sont impliqués dans la condensation des chromosomes. Ceci représente un nouveau mécanisme pour l'assemblage des chromosomes chez C. elegans. De plus, j'ai découvert un rôle non-enzymatique à la protéine RNR lors de l'assemblage des chromosomes. Lors de ce processus, RNR est impliqué dans la stabilité des nucléosomes et alors, permet la compaction de haut niveau de la chromatine. Dans cette thèse, je rapporte également des résultats préliminaires concernant d'autres nouveaux facteurs découverts lors du criblage ARNi. Le plus important est que mon analyse révèle que la déplétion des nouvelles protéines montre des phénotypes distincts, indiquant la fonction de celles-ci lors de l'assemblage des chromosomes. Somme toute, je conclus que les chromosomes en métaphase sont assemblés par trois protéines ayant des activités différentes d'échafaudage: topoisomérase II, les complexes condensines et les protéines centromériques. En conclusion, ces études prouvent le mécanisme moléculaire de certaines protéines qui contribuent à la formation des chromosomes mitotiques.

Structural Chromosomal Alterations Induced by Dietary Bioflavonoids in Fanconi Anemia Lymphocytes

Introduction Fanconi anemia is an autosomal recessive disease characterized by a variety of congenital abnormalities, progressive bone marrow failure, increased chromosomal instability and higher risk to acute myeloid leukemia, solid tumors. This entity can be considered an appropriate biological model to analyze natural substances with possible genotoxic effect. The aims of this study were to describe and quantify structural chromosomal aberrations induced by 5 flavones, 2 isoflavones and a topoisomerase II chemotherapeutic inhibitor in Fanconi anemia lymphocytes in order to determine chromosomal numbers changes and/ or type of chromosomal damage. Materials and methods Chromosomes stimulated by phytohaemagglutinin M, from Fanconi anemia lymphocytes, were analysed by conventional cytogenetic culture. For each chemical substance and controls, one hundred metaphases were evaluated. Chromosomal alterations were documented by photography and imaging analyzer. To statistical analysis was used chi square test to identify significant differences between frequencies of chromosomal damage of basal and exposed cell cultured a P value less than 0.05. Results There were 431 chromosomal alterations in 1000 metaphases analysed; genistein was the more genotoxic bioflavonoid, followed in descendent order by genistin, fisetin, kaempferol, quercetin, baicalein and miricetin. Chromosomal aberrations observed were: chromatid breaks, chromosomal breaks, cromatid and chromosomal gaps, quadriratials exchanges, dicentrics chromosome and complex rearrangements. Conclusion Bioflavonoids as genistein, genistin and fisetin, which are commonly present in the human diet, showed statistical significance in the number of chromosomal aberrations in Fanconi anemia lymphocytes, regarding the basal damage.

Effect of the anti-neoplastic drug doxorubicin on XPD-mutated DNA repair-deficient human cells

Doxorubicin (DOX), a member of the anthracycline group, is a widely used drug in cancer therapy. The mechanisms of DOX action include topoisomerase II-poisoning, free radical release, DNA adducts and interstrand cross-link (ICL) formation. Nucleotide excision repair(NER) is involved in the removal of helix-distorting lesions and chemical adducts, however, little is known about the response of NER-deficient cell lines to anti-tumoral drugs like DOX. Wild type and XPD-mutated cells, harbouring mutations in different regions of this gene and leading to XP-D, XP/CS or TTD diseases, were treated with this drug and analyzed for cell cycle arrest and DNA damage by comet assay. The formation of DSBs was also investigated by determination of gamma H2AX foci. Our results indicate that all three NER-deficient cell lines tested are more sensitive to DOX treatment, when compared to wild type cells or XP cells complemented by the wild type XPD cDNA, suggesting that NER is involved in the removal of DOX-induced lesions. The cell cycle analysis showed the characteristic G2 arrest in repair-proficient MRC5 cell line after DOX treatment, whereas the repair-deficient cell lines presented significant increase in sub-G1 fraction. The NER-deficient cell lines do not show different patterns of DNA damage formation as assayed by comet assay and phosphorylated H2AX foci formation. Knock-down of topoisomerase II alpha with siRNA leads to increased survival in both MRC5 and XP cells, however, XP cell line still remained significantly more sensitive to the treatment by DOX. Our study suggests that the enhanced sensitivity is due to DOX-induced DNA damage that is subject to NER, as we observed decreased unscheduled DNA synthesis in XP-deficient cells upon DOX treatment. Furthermore, the complementation of the XPD-function abolished the observed sensitivity at lower DOX concentrations, suggesting that the XPD helicase activity is involved in the repair of DOX-induced lesions. (C) 2009 Elsevier B.V. All rights reserved.

Efeitos citotóxicos do teniposide, um derivado semi-sintético das epipodofilotoxinas, sobre linhagens celulares de carcinoma renal humano

O câncer renal corresponde a aproximadamente 3% dos tumores malignos do adulto, sendo a terceira malignidade urológica mais comum. Os tratamentos sistêmicos disponíveis para pacientes portadores de carcinoma renal avançado são, via de regra, pouco eficazes e sem um impacto definido na sobrevida. Portanto, torna-se imperioso que novos agentes e/ou estratégias terapêuticas para esta enfermidade sejam desenvolvidas. O derivado das epipodolofilotoxinas, etoposide, tem sido utilizado com sucesso no tratamento de vários tipos de tumores sólidos e hematológicos. Este agente exerce a sua ação antitumoral através da inibição da enzima nuclear topoisomerase II. Estudos recentes demonstraram que o efeito citotóxico in vitro deste agente é bem mais pronunciado quando as linhagens tumorais são expostas à droga por um tempo mais prolongado. Isto vem sendo confirmado em estudos clínicos, nos quais foi documentado um aumento significativo no percentual de respostas tumorais objetivas em pacientes com câncer avançado tratados com etoposide em doses repetidas diárias de forma continuada, comparativamente a pacientes que receberam pulsos de doses altas da droga a intervalos mais longos. Infelizmente, estudos iniciais com etoposide não revelaram uma atividade antitumoral significativa em pacientes com câncer renal avançado. Por esta razão, os estudos preliminares explorando o potencial terapêutico de seu análogo teniposide nesta doença também não receberam a devida atenção na literatura. Entretanto, este análogo possui potenciais vantagens terapêuticas em relação ao etoposide, uma vez que apresenta um tempo de retenção intracelular mais prolongado em linhagens de tumores sólidos in vitro. Estas observações nos estimularam a reconsiderar o estudo do potencial citotóxico do teniposide em modelos experimentais de câncer renal avançado. Nesta dissertação, foram estudados vários protocolos de administração de teniposide em linhagens de câncer renal humano, uma vez que esta neoplasia carece de drogas ativas disponíveis no armamentário terapêutico. Foram utilizadas as linhagens celulares RXF-393, A-498 e TK-10, as quais foram incubadas com teniposide em concentrações pré-determinadas e tempos de incubação variáveis. Além disto, foram feitos experimentos em que protocolos de administração de teniposide como agente único foram comparados a protocolos em que o mesmo foi combinado com agentes que bloqueiam a ação da glicoproteína P, responsável pelo efluxo ativo da droga do interior da célula tumoral. Além disso, foram também estudados protocolos incluindo a associação de teniposide com agentes que interferem com a síntese do DNA. Para os estudos de avaliação de citotoxicidade dos agentes quimioterápicos, os mesmos foram pré-incubados por 24 h na ausência ou presença do inibidor da DNA polimerase α afidicolina glicinada (0,2 µM) ou do inibidor da ribonucleotídeo redutase hidroxiuréia (200 µM) e após incubados por diferentes tempos de exposição com diluições seriadas de teniposide. Os efeitos citotóxicos foram avaliados através do método colorimétrico com sulforodamina B (SRB). Os protocolos de exposição prolongada das células ao teniposide mostraram um aumento significativo na sua citotoxicidade nas linhagens RXF-393, A-498 e TK-10, sugerindo que a citotoxicidade do teniposide é dependente de tempo de administração. Neste sentido, uma maior taxa de dano no DNA foi observada nas células expostas ao teniposide por tempos de administração mais prolongados. Curiosamente, os diferentes tempos de exposição ao teniposide não influenciaram de forma clara na formação de complexos DNA-topoisomerase II, nem nas medidas da atividade desta enzima. O uso concomitante de agentes moduladores da glicoproteína P como o verapamil, a ciclosporina A e o tamoxifeno não produziu potencialização do efeito antiproliferativo do teniposide. Por sua vez, os tratamentos com agentes que interferem na síntese de DNA, como a afidicolina glicinada ou a hidroxiuréia, potencializaram a citotoxicidade do teniposide em todas as linhagens estudadas, seguindo as características intrínsecas de cada linhagem. Em conclusão, os resultados apresentados nesta dissertação sugerem que o teniposide apresenta um maior efeito citotóxico em protocolos de administração prolongada em combinação com agentes inibidores da síntese de DNA. Frente a estes resultados iniciais, o teniposide será testado nos protocolos de administração acima mencionados em um painel contendo um maior número de linhagens tumorais in vitro. Uma vez confirmadas as observações acima descritas, serão iniciados estudos em modelos tumorais in vivo. Estes estudos servirão de base nas decisões quanto à reavaliação clínica do teniposide em ensaios de fase I em pacientes com neoplasias avançadas refratárias.

Late morfofunctional alterations of the Sertoli cell caused by doxorubicin administered to prepubertal rats

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Design and synthesis of peptides from bacterial ParE toxin as inhibitors of topoisomerases

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Screening of Brazilian plants for antimicrobial and dnadamaging activities: I. Atlantic rain forest . Ecological station juréia-itatins

(Triagem de plantas nativas do Brasil para atividades antimicrobiana e de Danos no DNA I. Mata Atlântica . Estação Ecológica Juréia-Itatins). Oitenta e oito espécies nativas do estado de São Paulo foram coletadas numa região de Mata Atlântica e ensaiadas quanto a sua atividade antimicrobiana e capacidade de causar danos no DNA. Dos 114 extratos submetidos aos ensaios para atividade antibacteriana, apenas os extratos de folhas e galhos de Aspidosperma ramiflorum (Apocynaceae) apresentaram uma atividade fraca contra Escherichia coli. No ensaio antifúngico com Candida albicans, não foram observados extratos ativos. Por outro lado, no ensaio de bioautografia com Cladosporium sphaerospermum e C. cladosporioides 12% dos extratos apresentaram atividade. Contudo, nesse ensaio, somente o extrato dos ramos de Psychotria mapoureoides (Rubiaceae) inibiu fortemente o crescimento de ambas espécies do fungo. O ensaio para danos no DNA com cepas mutantes de Saccharomyces cerevisiae apresentou 17.5 % de extratos ativos. A maioria dos extratos ativos (55 %) apresentou resultados seletivos para danos dependentes da topoisomerase II como mecanismo de reparo do DNA e somente 20 % foram seletivos para o mecanismo da topoisomerase I.

Screening for antifungal, DNA-damaging and anticholinesterasic activities of Brazilian plants from the Atlantic Rainforest: Ilha do Cardoso State Park

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Alterations of spermatogenesis in etoposide-treated rats: A stereological study

The etoposide is an anticancer drug that interacts with topoisomerase II. Thirty-day-old rats received intraperitonially 2mg/kg of etoposide for 30 consecutive days. Their testes were analyzed in the adult phase under light microscopy according to histomorphometric and stereological parameters. Random 3mum-thick-paraplast sections of testis were stained with periodic acid-Schiff reaction and Harris' hematoxylin method. Serum testosterone level and reproductive performance were also investigated. The results showed an accentuated decrease in the frequency of germinal lineage cell types and differentiated spermatogonia were the most affected cell types. Morphometric and stereological testicular parameters exhibited highly, significant reductions in adult etoposide-treated rats. Their reproductive performance diminished but their serum testosterone level was not significantly altered. The mortality frequency of the progenies was 100%.

Peptídeos derivados da toxina ParE: síntese, estrutura e estudos de inibição de DNA topoisomerases

Pós-graduação em Biotecnologia - IQ

Estrutura e função da proteína YacG de Klebsiella pneumoniae e seus derivados peptídicos

Pós-graduação em Biotecnologia - IQ

Gene Expression Profile in Response to Doxorubicin-Rapamycin Combined Treatment of HER-2-Overexpressing Human Mammary Epithelial Cell Lines

HER-2-positive breast cancers frequently sustain elevated AKT/mTOR signaling, which has been associated with resistance to doxorubicin treatment. Here, we investigated whether rapamycin, an mTOR inhibitor, increased the sensitivity to doxorubicin therapy in two HER-2-overexpressing cell lines: C5.2, which was derived from the parental HB4a by transfection with HER-2 and SKBR3, which exhibits HER-2 amplification. The epithelial mammary cell line HB4a was also analyzed. The combined treatment using 20 nmol/L of rapamycin and 30 nmol/L of doxorubicin arrested HB4a and C5.2 cells in S to G(2)-M, whereas SKBR3 cells showed an increase in the G(0)-G(1) phase. Rapamycin increased the sensitivity to doxorubicin in HER-2-overexpressing cells by approximately 2-fold, suggesting that the combination displayed a more effective antiproliferative action. Gene expression profiling showed that these results might reflect alterations in genes involved in canonical pathways related to purine metabolism, oxidative phosphorylation, protein ubiquitination, and mitochondrial dysfunction. A set of 122 genes modulated by the combined treatment and specifically related to HER-2 overexpression was determined by finding genes commonly regulated in both C5.2 and SKBR3 that were not affected in HB4a cells. Network analysis of this particular set showed a smaller subgroup of genes in which coexpression pattern in HB4a cells was disrupted in C5.2 and SKBR3. Altogether, our data showed a subset of genes that might be more robust than individual markers in predicting the response of HER-2-overexpressing breast cancers to doxorubicin and rapamycin combination. Mol Cancer Ther; 11(2); 464-74. (C) 2011 AACR.