Tuberculosis affects millions of people worldwide every year. The current treatment for TB is divided into a regimen of both first- and second-line drugs, where first-line treatments are more tolerated and require shorter treatment lengths. With rising levels of resistance, alternative treatment regimes are urgently needed to fight this disease. Ethionamide, a second-line drug is administered as a prodrug which is activated in vivo by the enzyme EthA, which is in turn regulated by EthR. The disruption of the action of EthR could lead to novel therapeutics which could enhance the efficacy of ethionamide, and raise it to a first-line treatment. The work reported in this thesis examines the elaboration of three chemical scaffolds using fragment-based approaches to develop novel inhibitors capable of disrupting the EthR-DNA interaction. The first scaffold, 5-(furan-2-yl)isoxazole was investigated by fragment-merging approaches and produced compounds with the best of these having a KD of 7.4 uM. The second scaffold, an aryl sulfone was elaborated using fragment-merging strategies. This led to several modifications of the fragment, leading to several variants with KDs around 20 uM. With both of these series the affinity could not be improved below 10 uM and due to the synthetic complexity a further scaffold was prioritised. The third scaffold was explored was a 4-(4-(trifluoromethyl)phenyl)piperazine using fragmentgrowing from the NH of the piperazine to probe deeper into the EthR binding pocket. In addition to this, SAR around the 4-(trifluoromethyl)phenyl group was assessed to explore the interactions with EthR. These modifications led to compounds with nanomolar IC50s. A range of compounds were then screened by REMAssay to determine the boosting effect on ethionamide, and this identified compounds with up to 30 times boosting in the ethionamide MIC. The final chapter examines a concept where compounds were designed to exploit the dimeric nature of EthR by linking two chemical warheads with a flexible linker. These compounds are examined using mass spectrometry to investigate the stoichiometry of the interaction to provide insight into the binding of these extended compounds and exploring an alternative strategy to inhibit EthR. The work in this thesis demonstrated the successful use of fragment-based approaches for development of novel EthR inhibitors which showed significant ethionamide boosting effects.

This study aims at tackling some of the problems often encountered in photostability testing and liquid formulation development. Three anti-cancer drugs will be employed as models; Dacarbazine (DBZ) has well established photostability issues, Axitinib (AXI) and Sunitinib (SUT) are two new drugs only commercially available in solid dosage forms. In ethanol, the photokinetics of these drugs were well described by the newly proposed Φ-order kinetic mathematical model. This has confirmed the photoreversible character of AXI and SUT’s and unimolecular photoreaction of DBZ’s photodegradations. Also, the Φ-order kinetics is proven to describe them better than the usually used classic thermal reaction orders. In aqueous solution, the drugs were found to undergo thermal and photochemical complex degradations, involving at least 3 photoproducts. A new photokinetic approach has been proposed in this work to solving and unravelling the attributes of such complex mechanisms. For the first time, the quantum yields (QY) of the three drugs were determined and found to increase with irradiation wavelength. SUT’s QY were comparable in ethanol and water (QY460 = 0.02), DBZ was found to be more photoefficient in water (QY330 = 0.04 and 0.1, respectively) and AXI in water (QY330 = 0.06 and 0.03). Φ-order kinetics’ potential for the development of reliable actinometers of the three drugs, without prior knowledge of unknown reaction parameters, has also been established. A general equation to describe the isotherm of a (Gn:Hm) guest-host multicomponent complex was proposed in this work to palliate the lack of a strategy for characterising nanosponge-drug complexes. It provides information on both stiochiometry and association constant of the complex. The results indicate that hydrophobic AXI forms a 1:0.8 complex, indicating the possibility of multiple association sites and/or different types of binding. The newly developed AXI/nanosponge liquid formulation has significantly increased solubility (5000-fold) and thermal stability. Furthermore, the photostability of DBZ and SUT were considerably improved by using a strategy based on light-absorption competitors. Their initial velocities reduced from 10 and 3 s-1 (respectively) to 1 and 0.13 s-1. The successful application of these methods to the model anti-cancer drugs has set out new approaches that might be found useful for future treatments of photodegradation data, development of drug-actinometers and liquid formulations of drugs.

[pt] As fluorquinolonas constituem uma importante classe de agentes antimicrobianos sintéticos utilizados clinicamente por mais de 30 anos. Além da atividade antibacteriana, algumas fluorquinolonas, assim como seus complexos metálicos, mostraram ter atividade citotóxica, sendo, portanto, promissores como agentes antitumorais. Neste trabalho, obtivemos complexos de Au(III), Cu(II) e Bi(III) com as seguintes fluorquinolonas: norfloxacina, levofloxacina e esparfloxacina. Esses novos complexos foram caracterizados por diversas técnicas, tais como: análise elementar, condutimetria, espectroscopia na região do infravermelho, ressonância paramagnética eletrônica (RPE), ressonância magnética nuclear (RMN) de 1H e 13C, espectroscopia UV-Vis, fluorescência estacionária e resolvida no tempo. Atividades biológicas foram realizadas para todos os complexos. Usualmente, as fluorquinolonas coordenam-se aos íons metálicos de modo bidentado, através da carbonila do ácido carboxílico e da carbonila cetônica. Esta coordenação foi confirmada para os complexos de Cu(II), entretanto, para os complexos de Au(III) e Bi(III), os resultados de infravermelho e do RMN de 1H e 13C mostraram que a coordenação foi feita através dos nitrogênios do anel piperazina, uma coordenação não encontrada usualmente para as fluorquinolonas. Os complexos de Au(III) mostraram ser ativos frente às linhagens tumorais A20 (Linfoma murino), B16-F10 (Melanoma murino) e K562 (Leucemia mielóide humana). Os complexos de Cu(II) mostraram significativa atividade antiparasitária, enquanto os complexos de Bi(III), mostraram atividade antibacteriana. / [en] The fluoroquinolones are an important class of synthetic antimicrobial agents clinically used for over 30 years. In addition to antibacterial activity, some fluoroquinolones, as well as their metal complexes, presented cytotoxic activity and are therefore promising as antitumor agents. In order to obtain new complexes of Au (III) and other metal ions that have biological activity, this work had the objective to synthesize new complexes using ligands of the group of fluoroquinolones. These new complexes were characterized by various techniques such as elemental analysis, conductometry, infrared spectroscopy, electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR) of 1H and 13C NMR, UV-Vis, stead state and time-resolved fluorimetry studies. Biological activities were analized for all complexes. Usually, the fluoroquinolones coordinate to the metal ions as bidentate through the carbonyl and carboxylic acid ketonic carbonyl group. This was confirmed Cu(II) complex, however, for Au(III) and Bi (III) complexes, the results of IR and 1H and 13C NMR showed that the coordination was trough the nitrogen using the piperazine ring, a coordination not usually found for fluoroquinolones. The complexes of Au(III) shown to be active against the A20 tumor cell lines (murine lymphoma), B16-F10 (murine melanoma) and K562 (human myeloid leukemia). Complexes of Cu(II) showed significant antiparasitic activity, whereas complexes of Bi(III) have shown antibacterial activity.

Lactobacillus kunkeei is one of the most abundant bacteria within the honey crop of the honey bee. Genome sequencing of L. kunkeei isolated from honey bees all over the world showed several genes unique for L. kunkeei. Among these orphan genes, an array of four to five highly conserved genes coding for giant extracellular proteins were found. Cryogenic electron microscopy imaging of a giant-protein preparation from L. kunkeei A00901 showed an overall structure similar to a long string with a knot at the end. Further analysis showed high similarity between the different giants at the N-terminus, and secondary structure predictions showed that the same region was rich in β-sheets.  These results, combined with the knowledge of other large extracellular proteins, led to the hypothesis that the “knot” domain is located at the N-terminus and that these proteins are used by the cell to latch on to the intestine lining or other cells in the honey crop. In this study, predictions were made to locate the N-terminal domains of two of these giant proteins. Four different constructs were made for each protein, where three constructs were designed for expression and purification of the N-terminal domain with different end-positions, and one construct was for a predicted β-solenoid domain located downstream from the N-terminal domain. The protein constructs were recombinantly produced in E. coli, and three of the N-terminal constructs from both proteins were purified. Thermal stability was tested using nano differential scanning fluorimetry (nanoDSF), Thermofluor, and circular dichroism (CD), which all showed characteristic melting curves at low melting temperatures, ranging from 33 °C to 44 °C, for all three constructs. During CD measurements, all three constructs showed refolding after thermal denaturation and a higher abundance of antiparallel β-sheets over α-helices. Looking at the protein structure, small angle X-ray scattering data indicated that all three proteins formed elongated structures. These results indicate that a folded domain has been found for both proteins. Although, further analysis will be required to determine the boundaries of the N-terminal domains, and to elucidate if these domains have anything to do with ligand binding and the L. kunkeei ability to latch onto the honey crop.

The N-methyl-D-aspartate receptor (NMDAR) hypofunctional hypothesis is believed to explain one of the contributing factors to schizophrenia. This hypothesis suggests the dysregulation of NMDAR, a protein responsible for receiving signals from the synapses between neurons, is the cause of some of the symptoms seen in schizophrenia. The post synaptic density protein 95 (PSD95) uses its PDZ-domains to help facilitate the received signal from NMDAR to α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) which in turn transmits the signal through the neuron. One way to increase the function of NMDAR could be to increase its affinity towards PDZ-domains of PSD95 using a small molecule. Fragment based drug design (FBDD) is one way to screen for molecules that modulates the NMDAR-PDZ interaction. This work describes the development of differential scanning fluorimetry (DSF) and surface plasmon resonance (SPR) assays using a fusion protein to screen for molecules that potentiate the interaction between NMDAR and AMPAR as well as methods assisting in the prioritization of hits based on both affinity, selectivity, and mechanism. The developed assays were used to screen a library containing 768 compounds. Screen positives and other compounds of interest were triaged and evaluated based on affinity, selectivity, and ability to modulated peptide binding resulting in eight confirmed hits that interacts with the two PDZ-domains of PSD95 investigated. As part of this work, the dissociation constant (KD) was determined for a panel of peptides representing versions of the truncated NMDAR GluN2b-subunit C-terminal towards PDZ1 and 2 of PSD95.

Although the etiology and pathogenesis of inflammatory bowel disease (IBD) is not fully understood, it is generally accepted that the inflammation results from aberrant immune responses to antigens of gut microbiota in genetically susceptible individuals (Sartor et al., 2006). Alteration in intestinal microbiota has been found in IBD patients with increased abundance of certain bacteria and decreased abundance of others. Due to the complexity of the disease, multifaceted interactions between genetic factors, host immune response, gut microbiota and environment factors need to be taken into account. In this thesis, the pathogenesis of IBD was first reviewed in respect with the four factors mentioned above. Then we concentrated on the interaction between IBD-associated bacteria and mucosal immune system. We investigated the ability of mucosal-associated bacteria (MAB) from IBD patients to induce spontaneous colitis in germ-free (GF) mice and the impact of those bacteria on the development of dextran sulfate sodium (DSS)-colitis. Together with the analysis of the composition of gut microbiota of MAB colonized mice, we demonstrated the potential deleterious microbes were able to increase the susceptibility to DSS-colitis once they found a suitable niche. We revealed the mechanism of an E.coli strain...