O vírus linfotrópico de células T humanas do tipo 1 (HTLV-1) é um retrovírus associado a duas manifestações clínicas principais: i) mielopatia associada ao HTLV- 1/paraparesia espástica tropical (HAM/TSP) e a ii) leucemia/linfoma de células T do adulto (ATL). Devido à ausência de tratamentos específicos e efetivos, faz-se necessário o desenvolvimento de novas drogas para o tratamento das doenças associadas ao HTLV-1. Nesse sentido, nosso objetivo foi realizar a triagem de compostos químicos para identificar indutores de apoptose e/ou bloqueadores da proliferação celular em linhagem celular infectada pelo HTLV-1 (MT-2), bem como drogas com efeito sobre a atividade de Tax viral. Inicialmente, foi estabelecido um ensaio baseado em células, o qual permitiu realizar a triagem de compostos pelo método de redução da resazurina. A partir de 26 derivados 1,2,3-triazólicos, oito compostos (hits) apresentaram atividade >= 70% por reduzirem de forma significativa a atividade metabólica da MT-2. Tais hits foram selecionados para as etapas de validação. O composto 61 foi o único a induzir uma parada na fase S do ciclo celular, enquanto os compostos 48, 49, 65 e 66 induziram a apoptose da linhagem MT-2. Na avaliação do efeito dos compostos sobre a atividade da proteína viral Tax, uma linhagem repórter com a expressão induzida de Tax foi estabelecida. Verificamos que apenas os compostos 48 e 49 foram capazes de reduzir a expressão de GFP, e consequentemente, interferir na atividade de Tax. Uma biblioteca de 707 compostos do NIH também foi avaliada neste estudo. A partir da triagem primária, 34 compostos (hits) com atividade >= 50% foram obtidos, enquanto na triagem secundária, apenas cinco hits foram confirmados. Entretanto, apenas dois destes foram selecionados para as futuras etapas de validação (dissulfiram e bromidrato de galantamina). Por fim, exceto os compostos 65 e 66, os demais hits não interferiram na viabilidade da linhagem hepática Huh-7. Os resultados deste estudo mostraram que os compostos 48, 49, 61, dissulfiram e bromidrato de galantamina deveriam ser explorados como novas abordagens terapêuticas das doenças associadas ao HTLV-1. / Human T-cell lymphotropic virus type 1 (HTLV-1) is a retrovirus associated with two main clinical manifestations: i) HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and ii) adult T cell leukemia/lymphoma (ATL). Due to the lack of a specific and an effective therapy, the development of new drugs for treatment of HTLV-1 associated diseases is urgently required. Thus, our aim was to perform a drug screening for identification of apoptosis inducers and/or cell proliferation inhibitors in a HTLV-1-infected cell line (MT-2), as well as drugs with effect on activity of viral Tax. First, it was established a cell-based assay in order to perform a drug screening by resazurin reduction method. From 26 1,2,3-triazole derivatives, eight compounds (hits) presented >= 70% of activity, since they significantly reduced the metabolic activity of MT-2. These hits were selected for the further validation steps. Compound 61 was the only one that induced an S phase cell cycle arrest, while compounds 48, 49, 65 and 66 promoted apoptosis of MT-2. In the evaluation of the effect of these compounds on activity of Tax viral protein, an inducible-tax reporter cell line was established. We verified that only compounds 48 and 49 were able to reduce GFP expression and, then, get involved on the Tax activity. A NIH library of 707 compounds was also assessed in this study. From a primary screening, 34 compounds (hits) with activity >= 50% were obtained, while in secondary screening, five hits were confirmed, of which two of them were selected for future validation steps (disulfiram and galantamine hydrobromide). Finally, except for compounds 65 and 66, other hits did not interfere in cellular viability of hepatic cell line, Huh-7. The results of this study showed that compounds 48, 49, 61, disulfiram and galantamine hydrobromide should be explored as new therapeutic approaches of HTLV-1-associated diseases.

O vírus linfotrópico de células T humanas do tipo 1 (HTLV-1) é um retrovírus associado a duas manifestações clínicas principais: i) mielopatia associada ao HTLV- 1/paraparesia espástica tropical (HAM/TSP) e a ii) leucemia/linfoma de células T do adulto (ATL). Devido à ausência de tratamentos específicos e efetivos, faz-se necessário o desenvolvimento de novas drogas para o tratamento das doenças associadas ao HTLV-1. Nesse sentido, nosso objetivo foi realizar a triagem de compostos químicos para identificar indutores de apoptose e/ou bloqueadores da proliferação celular em linhagem celular infectada pelo HTLV-1 (MT-2), bem como drogas com efeito sobre a atividade de Tax viral. Inicialmente, foi estabelecido um ensaio baseado em células, o qual permitiu realizar a triagem de compostos pelo método de redução da resazurina. A partir de 26 derivados 1,2,3-triazólicos, oito compostos (hits) apresentaram atividade >= 70% por reduzirem de forma significativa a atividade metabólica da MT-2. Tais hits foram selecionados para as etapas de validação. O composto 61 foi o único a induzir uma parada na fase S do ciclo celular, enquanto os compostos 48, 49, 65 e 66 induziram a apoptose da linhagem MT-2. Na avaliação do efeito dos compostos sobre a atividade da proteína viral Tax, uma linhagem repórter com a expressão induzida de Tax foi estabelecida. Verificamos que apenas os compostos 48 e 49 foram capazes de reduzir a expressão de GFP, e consequentemente, interferir na atividade de Tax. Uma biblioteca de 707 compostos do NIH também foi avaliada neste estudo. A partir da triagem primária, 34 compostos (hits) com atividade >= 50% foram obtidos, enquanto na triagem secundária, apenas cinco hits foram confirmados. Entretanto, apenas dois destes foram selecionados para as futuras etapas de validação (dissulfiram e bromidrato de galantamina). Por fim, exceto os compostos 65 e 66, os demais hits não interferiram na viabilidade da linhagem hepática Huh-7. Os resultados deste estudo mostraram que os compostos 48, 49, 61, dissulfiram e bromidrato de galantamina deveriam ser explorados como novas abordagens terapêuticas das doenças associadas ao HTLV-1. / Human T-cell lymphotropic virus type 1 (HTLV-1) is a retrovirus associated with two main clinical manifestations: i) HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and ii) adult T cell leukemia/lymphoma (ATL). Due to the lack of a specific and an effective therapy, the development of new drugs for treatment of HTLV-1 associated diseases is urgently required. Thus, our aim was to perform a drug screening for identification of apoptosis inducers and/or cell proliferation inhibitors in a HTLV-1-infected cell line (MT-2), as well as drugs with effect on activity of viral Tax. First, it was established a cell-based assay in order to perform a drug screening by resazurin reduction method. From 26 1,2,3-triazole derivatives, eight compounds (hits) presented >= 70% of activity, since they significantly reduced the metabolic activity of MT-2. These hits were selected for the further validation steps. Compound 61 was the only one that induced an S phase cell cycle arrest, while compounds 48, 49, 65 and 66 promoted apoptosis of MT-2. In the evaluation of the effect of these compounds on activity of Tax viral protein, an inducible-tax reporter cell line was established. We verified that only compounds 48 and 49 were able to reduce GFP expression and, then, get involved on the Tax activity. A NIH library of 707 compounds was also assessed in this study. From a primary screening, 34 compounds (hits) with activity >= 50% were obtained, while in secondary screening, five hits were confirmed, of which two of them were selected for future validation steps (disulfiram and galantamine hydrobromide). Finally, except for compounds 65 and 66, other hits did not interfere in cellular viability of hepatic cell line, Huh-7. The results of this study showed that compounds 48, 49, 61, disulfiram and galantamine hydrobromide should be explored as new therapeutic approaches of HTLV-1-associated diseases.

<p>Proximity ligation is a recently established technique that can provide answers to questions about the concentration, localization, interactions, modifications and functions of proteins. The method enables sensitive protein measurements with a detection limit in the low femtomolar range in complex biological samples. In proximity ligation, the challenge of detecting specific proteins is converted to the analysis of specific DNA sequences. Proximity probes containing oligonucleotide extensions are designed to bind pairwise to target proteins, and to form amplifiable tag sequences upon ligation when brought in proximity. Protocols for the conversion of monoclonal or polyclonal antibodies into proximity probes through the attachment of oligonucleotide sequences are described in the thesis. In addition, the thesis describes the adaptation of the proximity ligation technology for detection of microbial pathogens, analysis of interactions between proteins and nucleic acids, and of inhibition of receptor-ligand interactions. </p><p>Nucleic acid amplification allows specific detection of pathogens with single-copy sensitivity. There are many circumstances, however, when analysis of pathogen surface antigens or the antibody response can provide increased diagnostic value. Proximity ligation reactions were used to measure numbers of virus and bacteria by detection of viral or bacterial surface proteins. Detection sensitivities similar to those of nuclear acid-based detection reactions were achieved directly in infected samples for a parvovirus and for an intracellular bacterium. </p><p>Biological processes are orchestrated by interactions of proteins with molecules in their environment, and investigations of interactions between proteins and other biomolecules are thus of great importance. Protocols were established for very specific and sensitive homogeneous-phase analysis of interactions between proteins and specific nucleic acid sequences. Finally, the proximity ligation mechanism was used to monitor interactions between VEGF-A and two of its receptors, VEGFR-1 and VEGFR-2, and to characterize the effects of agents disrupting this interaction.</p>

Proximity ligation is a recently established technique that can provide answers to questions about the concentration, localization, interactions, modifications and functions of proteins. The method enables sensitive protein measurements with a detection limit in the low femtomolar range in complex biological samples. In proximity ligation, the challenge of detecting specific proteins is converted to the analysis of specific DNA sequences. Proximity probes containing oligonucleotide extensions are designed to bind pairwise to target proteins, and to form amplifiable tag sequences upon ligation when brought in proximity. Protocols for the conversion of monoclonal or polyclonal antibodies into proximity probes through the attachment of oligonucleotide sequences are described in the thesis. In addition, the thesis describes the adaptation of the proximity ligation technology for detection of microbial pathogens, analysis of interactions between proteins and nucleic acids, and of inhibition of receptor-ligand interactions. Nucleic acid amplification allows specific detection of pathogens with single-copy sensitivity. There are many circumstances, however, when analysis of pathogen surface antigens or the antibody response can provide increased diagnostic value. Proximity ligation reactions were used to measure numbers of virus and bacteria by detection of viral or bacterial surface proteins. Detection sensitivities similar to those of nuclear acid-based detection reactions were achieved directly in infected samples for a parvovirus and for an intracellular bacterium. Biological processes are orchestrated by interactions of proteins with molecules in their environment, and investigations of interactions between proteins and other biomolecules are thus of great importance. Protocols were established for very specific and sensitive homogeneous-phase analysis of interactions between proteins and specific nucleic acid sequences. Finally, the proximity ligation mechanism was used to monitor interactions between VEGF-A and two of its receptors, VEGFR-1 and VEGFR-2, and to characterize the effects of agents disrupting this interaction.

Docking is one of the methods in virtual screeing. Studies from around 1980 to now, many docking software have been developed, but these software have many short comings. The software currently used for docking have many disadvantage: poor efficiency, rigid structure of the proteins and the ligands, poor accuracy, without the polarization after binding, leading virtual screening is still stuck in a supporting role. Our experiment with new method improves those shortcomings of docking. With this new method, we obtain the following improvements in docking process: better efficiency, flexible structure of the proteins and the ligands, better accuracy. In the depression-related protein docked with traditional Chinese medicine test. We change the conformations of ligands with the shapes of active sites before posing, this makes the conformation of complex much more reasonable, even more complicated, large ligands. In the experiment of random sites docking, we found a possible path for compounds traveling into active sites. We illustrate a docking area by linking all possible docking sites. The lead compound may not successfully travel into active site when this area is occupied by other proteins or ligands. In the docking experiment with side-chain rotation, we rotate the torsion angle to make side chains relax. We obtained a similar result with molecular dynamics, and saved a lot of time.

Ricin is a potent cytotoxin easily purified in large quantities. It presents a significant public health concern due to its potential use as a bioterrorism agent. For this reason, extensive efforts have been underway to develop antidotes against this deadly poison. The catalytic A subunit of the heterodimeric toxin has been biochemically and structurally well characterized, and is an attractive target for structure-based drug design. Aided by computer docking simulations, several ricin toxin A chain (RTA) inhibitors have been identified; the most promising leads belonging to the pterin family. To date, the most potent RTA inhibitors developed using this approach are only modest inhibitors with apparent IC50 values in the 10-4 M range, leaving significant room for improvement. This thesis discusses the development of a subset of inhibitors belonging to the pterin family in which amino acids have been utilized as building blocks. Inhibitors in this family have achieved a significant increase in potency, and have provided valuable structural information for further development. / text

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2006. / Härtill 3 uppsatser.

Hereditary non-polyposis colon cancer syndrome (HNPCC) is associated with an increased risk of developing several types of cancer and is the most common cause of hereditary ovarian cancer after BRCA1 and BRCA2 mutations. HNPCC results from a germline mutation in one of the DNA mismatch repair (MMR) genes: MLH1, MSH2, PMS1, PMS2, MSH6, MSH3 and MLH3. While there has been extensive investigation of MMR deficiency in colorectal cancer, MMR in ovarian cancer is relatively under-investigated. The goal of this project was to study MMR deficiency in ovarian cancer at both the clinical and molecular level. The first aim was to examine the frequency of MMR loss in a large patient cohort and investigate the clinical consequences of MMR deficiency. The second aim was to describe the molecular characteristics of MMR deficiency in ovarian cancer cell lines and establish an in vitro cell line model of MMR deficiency in ovarian cancer. The third aim was to identify synthetic lethal strategies for the treatment of ovarian cancer to maximise cytotoxicity in a MMR-deficient background. In order to characterise the clinical consequences of MMR deficiency, a large patient cohort was studied with regard to MMR status. Three tissue microarrays consisting of 581 ovarian tumours were constructed, and expression of the four most frequently lost MMR proteins: MLH1, MSH2, PMS2 and MSH6 were detected by immunohistochemistry. Afterwards, MMR status and histology subtypes were analysed in combination with the associated clinical data. The overall incidence of MMR deficiency (loss of any MMR protein) was 15.7%, with PMS2 being the most frequently lost protein (9.7%). In addition, MMR deficiency tended to appear in a grouped fashion: MLH1 with PMS2; MSH2 with MSH6. Patients with non-serous subtypes of ovarian cancer, clear cell or mucinous especially, had higher incidence of MMR deficiency compared to patients with serous ovarian cancer. Overall MMR deficient patients were more likely to be diagnosed at early stages compared with MMR proficient patients, and this is probably due to the association between MMR deficiency and non-serous histology. However, platinum-based treatment for patients with MMR deficiency gives no advantage over those without MMR deficiency. Therefore better treatments for this subgroup of patients may be needed. The features of MMR deficiency in ovarian cancer were also characterized at the molecular level. After quantifying mRNA and protein expression of MMR genes in 19 ovarian cell lines, three cell lines (SKOV3, TOV21G and IGROV1) were found to have a defect in MLH1 expression at both the mRNA and protein level. Interestingly, the three cell lines also carried a defect in PMS2 expression at the protein level but not at the mRNA level, which is consistent with our clinical data demonstrating that MLH1 protein and PMS2 protein are paired in loss. In addition, across the 19 cell lines, MLH1 and PMS2 showed positive correlation at both the mRNA level (R=0.53, p=0.02) and protein level (R=0.72, p=0.0006). In order to study co-expression of MLH1 and PMS2, a plasmid encoding the cDNA for MLH1 was transfected into the three MLH1 deficient cell lines; and conversely siRNA targeting MLH1 was transfected into the MMR proficient cell line A2780 and expression of MLH1 protein and PMS2 protein was quantified. The results showed that re-introduction of MLH1 into MLH1 deficient cells resulted in increased expression of PMS2 protein, while knocking down MLH1 in MMR proficient cells leads to decreased PMS2 protein expression. This indicates that MLH1 may play a crucial role in regulating PMS2 protein expression. As the three MLH1 and PMS2 protein deficient cell lines all express PMS2 mRNA, the regulation of PMS2 expression by MLH1 is likely to be at the translational or post-translational level. However, the expression of PMS2 protein was not increased in the absence of MLH1, even when the proteasomal and lysosomal protein degradation pathways were blocked (as seen with SKOV3 cells), suggesting decreased PMS2 protein expression is not due to rapid degradation in the absence of MLH1. Therefore MLH1 may play a role in regulating the synthesis of PMS2 protein at the translational level, rather than preventing the degradation of PMS2. Thus, to investigate the mechanism by which PMS2 protein levels are regulated by MLH1, future work should focus on translational regulation of PMS2. In order to identify synthetic lethal strategies to target MMR deficiency in ovarian cancer, an isogenic cell line model of MMR deficiency was established by stable transfection of a plasmid for MLH1 and its corresponding empty vector into SKOV3 cells. The MLH1+ cell line SAC-1 and MLH1- cell line SN-5 were selected for drug screening based on their phenotype and growth rate. The AlamarBlue assay, with z’ above 0.5, was chosen for drug screening and a kinase inhibitor library containing 362 drugs of known target was screened. Two drugs with similar structures that targeted PLK1 showed greater growth inhibition of SN-5 compared with SAC-1. When the two cell lines were treated with another PLK1 inhibitor, BI2536, with different structure, a 2-fold difference in growth inhibition between SAC-1 and SN-5 was also observed, suggesting PLK1 is a potential synthetic lethal target for MLH1 deficiency in ovarian cancer. Together these data demonstrate that clinically, MMR deficiency is associated with non-serous subtypes of ovarian cancer and specific MMR proteins are paired in loss. While current standard therapy offers no selective benefit to ovarian cancer patients with MMR deficiency, inhibiting PLK1 activity may confer selective benefit.

Amyloid $\beta$ (1-42) (A$\beta$42) is a seminal neuropathic agent in Alzheimer’s disease (AD), a multifaceted neurodegenerative disorder for which no preventative measures or disease modifying therapies currently exist. Aggregation of this peptide plays a key role in the synaptic dysfunction and neuronal death associated with the disease. Perturbing the aggregation process, therefore, represents a key strategy for the development of new AD therapeutics. A variety of issues with current screening methods, including lack of reproducibility, high reagent consumption and spectral interference from the test molecules, can limit efforts to identify new small molecule inhibitors. Furthermore, the lack of robust, time- and cost-efficient methods for screening compounds in cellular or in vivo models limits the throughput with which seemingly active small molecules can be validated and prioritised. Herein, this thesis describes efforts to overcome such limitations through the development of a unified in vitro to in vivo assay system, in which hits identified in the ‘nanoFLIM’ microfluidic-based assay can quickly be tested in cellular and whole organism disease models. The assay platform designed relies on the use of an amyloid aggregation fluorescence lifetime sensor. A$\beta$42 aggregation is monitored by changes in the fluorescence lifetime of an attached fluorophore, which is significantly quenched upon amyloid formation. To take advantage of the benefits associated with miniaturisation, an in vitro microfluidic platform was employed. A microfluidic chip capable of trapping 110 precisely ordered droplets was designed, allowing for increased sample size and greatly lowering reagent consumption relative to conventional assay formats. Optimisation of the lifetime sensor technique permitted real-time compound screening in SH-SY5Y neuroblastoma cells, as well as in disease model Caenorhabditis elegans (C. elegans). To demonstrate the potential of this assay, a selection of novel chemical libraries developed in the Spring research group was screened, resulting in the identification of a key library of interest. The inhibitory activity of the lead compound from this collection was validated using a variety of biophysical tests, and was also shown to suppress amyloid aggregation in the live cell fluorescence lifetime sensor assay, as well as in whole organism disease model C. elegans. Whilst assay development was underway, additional screening of structurally diverse chemical libraries was performed using a conventional Thioflavin T spectroscopic assay. Such work identified another molecular scaffold capable of exerting a strong inhibitory effect against A$\beta$42 aggregation. A selection of analogues was synthesised to improve the in vivo profile of this library, giving rise to a second lead inhibitory compound. The activity of this compound was subsequently validated in biophysical and cellular tests, and was also tested in disease model Drosophila melanogaster. The aggregation of A$\beta$42 lies at the root of Alzheimer’s disease. In light of the relatively few drug candidates in clinical trials for this disorder, the development of improved translational screening approaches and continued screening of novel chemical libraries is necessary to identify new potential therapeutics. In this study, an in vitro to in vivo fluorescence lifetime imaging assay has been established. Using this assay system and conventional screening approaches, two A$\beta$42 aggregation inhibitors have been identified and validated. These represent promising candidates for the development of new AD therapeutic agents, or for use as molecular probes to further dissect the mechanisms underlying this devastating disease.

Tumour dissemination is a major reason for failure of therapy for many tumour types therefore there is a requirement for novel targets & therapies. The αIIbβ3 and αvβ3 integrins have been demonstrated to have significant involvement at many stages of the tumour dissemination process including, tumour cell adhesion, migration, metastasis and angiogenesis, and thus the β3 integrins are a potential target for therapeutic antagonism with small molecules. Because of the clear interaction between the different integrin types, targeting integrins as a therapeutic strategy requires targeting more than one integrin type. Consequently, the ICT is developing a group of novel new αIIbβ3 and αvβ3 integrin dual antagonists. One of the main challenges is having a relevant, validated experimental model that expresses these integrins. The aim of the work presented here is to develop and validate an in vitro αIIbβ3 and αvβ3 integrin expressing assay of tumour cell invasion. The spheroid invasion assay has the advantage over standard monolayer transwell chamber invasion assays of being a 3-dimensional assay, and thus mimics better the cell-cell interactions and architecture that are present in a tumour compared to the monolayer-based assay. A panel of human cancer cell lines known to express one of the molecular targets of interest, αvβ3 integrin was evaluated for the ability to form spheroids and to invade through collagen matrices. One glioma cell line, U87-MG, demonstrated consistent spheroid formation and invasion and was thus selected for further studies. Optimum conditions were established for use of U87-MG in the invasion assay, and the assay was validated using a known inhibitor of invasion, LiCl and known β3 antagonist, cRGDfV. Subsequently a group of novel small molecule β3 antagonists were evaluated at nontoxic concentrations using the assay. Both LiCl and cRGDfV inhibited spheroid invasion through the gel in a dose-dependent manner, thus validating the assay. Furthermore, when the novel small molecule β3 antagonists were evaluated using the model, a dose and time dependent reduction in U87-MG spheroids invasion in collagen was observed. In further work initial steps were taken to construct a cell line which expresses both αIIbβ3 and αvβ3 integrin to use in the model to assess for dual integrin antagonism. In conclusion, this work has established a validated assay which has been utilised for some compounds to evaluate a group of novel small molecule β3 integrin antagonists with encouraging results.