<p>Malaria is a widespread disease caused by parasites of the genus <i>Plasmodium</i>. Each year 500 million clinical cases are reported resulting in over one million casualties. The most lethal species, <i>P. falciparum</i>, accounts for ~90% of the fatal cases and has developed resistance to chloroquine. The resistant strains are a major problem and calls for novel drugs.</p><p>In this thesis, the process of computational inhibitor design is illustrated through the development of <i>P. falciparum</i> aspartic protease inhibitors. These proteases, called plasmepsins, are part of the hemoglobin degradation chain. The hemoglobin is degraded during the intraerythrocytic cycle and serves as the major food source. By inhibiting plasmepsins the parasites can be killed by starvation.</p><p>Novel inhibitors with very high affinity were found by using a combination of computational and synthetic chemistry. These inhibitors were selective and did not display any activity on human cathepsin D. The linear interaction energy (LIE) method was utilized in combination with molecular dynamics (MD) simulations to estimate free energies of binding. The MD simulations were also used to characterize the enzyme–inhibitor interactions and explain the binding on a molecular level.</p><p>The influence of the partial charge model on binding free energy calculations with the LIE method was assessed. Two semiempirical and six <i>ab initio</i> quantum chemical charge derivation schemes were evaluated. It was found that the fast semiempirical charge models are equally useful in free energy calculations with the LIE method as the rigorous <i>ab initio</i> charge models.</p>

Malaria is a widespread disease caused by parasites of the genus Plasmodium. Each year 500 million clinical cases are reported resulting in over one million casualties. The most lethal species, P. falciparum, accounts for ~90% of the fatal cases and has developed resistance to chloroquine. The resistant strains are a major problem and calls for novel drugs. In this thesis, the process of computational inhibitor design is illustrated through the development of P. falciparum aspartic protease inhibitors. These proteases, called plasmepsins, are part of the hemoglobin degradation chain. The hemoglobin is degraded during the intraerythrocytic cycle and serves as the major food source. By inhibiting plasmepsins the parasites can be killed by starvation. Novel inhibitors with very high affinity were found by using a combination of computational and synthetic chemistry. These inhibitors were selective and did not display any activity on human cathepsin D. The linear interaction energy (LIE) method was utilized in combination with molecular dynamics (MD) simulations to estimate free energies of binding. The MD simulations were also used to characterize the enzyme–inhibitor interactions and explain the binding on a molecular level. The influence of the partial charge model on binding free energy calculations with the LIE method was assessed. Two semiempirical and six ab initio quantum chemical charge derivation schemes were evaluated. It was found that the fast semiempirical charge models are equally useful in free energy calculations with the LIE method as the rigorous ab initio charge models.

O câncer de mama é a doença maligna mais comum e a principal causa de morte entre as mulheres. Sua complexa etiologia envolve múltiplos fatores de risco, a maioria deles relacionada aos níveis cumulativos de exposição da mama aos estrógenos. A maioria de suas ações é mediada pela ligação a seus receptores ER e ER que são fatores de transcrição. Outro fator que exerce um controle extraordinário no comportamento celular, regulando a transcrição gênica e influenciando diversos processos biológicos, e que, quando alterado, é associado ao processo de tumorigênese da mama é a matriz extracelular. A laminina, um dos principais componentes da matriz extracelular, interage com as células através das integrinas e está relacionada ao fenótipo maligno, atuando na adesão, migração, proliferação, diferenciação e sobrevivência celular. Nosso grupo identificou diversos genes diferencialmente expressos em células de câncer de mama ER+ na presença ou ausência de uma monocamada de laminina utilizando a técnica DDRT-PCR. Dois dos genes identificados, DDEF2 e PHLDA1, estão associados à adesão; DDEF2 envolvido na sinalização das integrinas e PHLDA1 relacionado com apoptose por perda de adesão. Nosso objetivo foi investigar os efeitos do 17-estradiol e da laminina na regulação da expressão dos genes DDEF2 e PHLDA1 nas linhagens celulares MCF-7, MDA-MB-231 e posteriormente S30, utilizando a técnica RT-PCR em tempo real. O gene PHLDA1 foi induzido pelo E2 via ER nas células MCF-7 e pela laminina nas células S30, e o gene DDEF2 foi reprimido pelo E2 e induzido pela laminina nas células S30 / The breast cancer is the most common malignant disease and the leading cause of death among women. Its complex etiology involves multiple risk factors, most of them related to the levels of cumulative breast exposure to estrogen. Most of its actions is mediated by binding to its receptor ER and ER that are transcription factors. Another factor that has a tremendous control in cell behavior, regulating the gene transcription and influencing various biological processes, which when altered, is attached to the process of tumorigênese of the breast is the extracellular matrix (ECM). The laminin, one of the main components of the ECM, interacts with the cells through integrins and is related to the malignant phenotype, acting in adhesion, migration, proliferation, differentiation and cell survival. Our group identified several genes diferentialy expressed in breast cancer cells ER + in the presence or absence of a laminin monolayer using the technique DDRT-PCR. Two of the genes identified, DDEF2 and PHLDA1, are associated with adhesion; DDEF2 is involved in the integrins signaling and PHLDA1 is related with apoptosis by loss of adhesion. Our goal was to investigate the effects of 17-estradiol and laminin in regulating the expression of the genes DDEF2 and PHLDA1 in MCF-7, MDA-MB-231 and later S30 cell lines, using the real time RT-PCR technique. The gene PHLDA1 was induced by E2 via ER in MCF-7 cells and the laminin in S30 cells, and the gene DDEF2 was suppressed by E2 and induced by laminin in S30 cells

O câncer de mama é a doença maligna mais comum e a principal causa de morte entre as mulheres. Sua complexa etiologia envolve múltiplos fatores de risco, a maioria deles relacionada aos níveis cumulativos de exposição da mama aos estrógenos. A maioria de suas ações é mediada pela ligação a seus receptores ER e ER que são fatores de transcrição. Outro fator que exerce um controle extraordinário no comportamento celular, regulando a transcrição gênica e influenciando diversos processos biológicos, e que, quando alterado, é associado ao processo de tumorigênese da mama é a matriz extracelular. A laminina, um dos principais componentes da matriz extracelular, interage com as células através das integrinas e está relacionada ao fenótipo maligno, atuando na adesão, migração, proliferação, diferenciação e sobrevivência celular. Nosso grupo identificou diversos genes diferencialmente expressos em células de câncer de mama ER+ na presença ou ausência de uma monocamada de laminina utilizando a técnica DDRT-PCR. Dois dos genes identificados, DDEF2 e PHLDA1, estão associados à adesão; DDEF2 envolvido na sinalização das integrinas e PHLDA1 relacionado com apoptose por perda de adesão. Nosso objetivo foi investigar os efeitos do 17-estradiol e da laminina na regulação da expressão dos genes DDEF2 e PHLDA1 nas linhagens celulares MCF-7, MDA-MB-231 e posteriormente S30, utilizando a técnica RT-PCR em tempo real. O gene PHLDA1 foi induzido pelo E2 via ER nas células MCF-7 e pela laminina nas células S30, e o gene DDEF2 foi reprimido pelo E2 e induzido pela laminina nas células S30 / The breast cancer is the most common malignant disease and the leading cause of death among women. Its complex etiology involves multiple risk factors, most of them related to the levels of cumulative breast exposure to estrogen. Most of its actions is mediated by binding to its receptor ER and ER that are transcription factors. Another factor that has a tremendous control in cell behavior, regulating the gene transcription and influencing various biological processes, which when altered, is attached to the process of tumorigênese of the breast is the extracellular matrix (ECM). The laminin, one of the main components of the ECM, interacts with the cells through integrins and is related to the malignant phenotype, acting in adhesion, migration, proliferation, differentiation and cell survival. Our group identified several genes diferentialy expressed in breast cancer cells ER + in the presence or absence of a laminin monolayer using the technique DDRT-PCR. Two of the genes identified, DDEF2 and PHLDA1, are associated with adhesion; DDEF2 is involved in the integrins signaling and PHLDA1 is related with apoptosis by loss of adhesion. Our goal was to investigate the effects of 17-estradiol and laminin in regulating the expression of the genes DDEF2 and PHLDA1 in MCF-7, MDA-MB-231 and later S30 cell lines, using the real time RT-PCR technique. The gene PHLDA1 was induced by E2 via ER in MCF-7 cells and the laminin in S30 cells, and the gene DDEF2 was suppressed by E2 and induced by laminin in S30 cells