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Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Targeted therapy for prostate cancer may offer potential improvement over current conventional therapies because of its specificity. Although conventional treatments are effective, they are not curative and have several limitations. In prostate cancer, activation of both the epidermal growth factor receptor (EGFR) and the phosphatidylinositol 3 – kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway have been implicated in tumorigenesis and resistance to both conventional and targeted anticancer therapies. Having a better understanding of the molecular mechanisms involved in PCa development, progression and resistance to therapy, could assist in the design of novel therapeutic strategies. The objective of this study was to inhibit key molecular targets of the human epidermal growth factor receptor signalling pathway and expose prostate cell lines to doses of radiation, so as to establish potential therapeutic targets that may be amenable to combined modality therapy, and formulate a cocktail of inhibitors to evaluate its radiosensitising capability. The EGFR/PI3K/mTOR pathway plays an important role in the radiosensitivity of the human prostate carcinoma cell line (DU145) and the normal cell line (1542N). In our study we have shown that AG-1478, an EGFR inhibitor, and BEZ-235, a dual inhibitor of the PI3K/mTOR pathway, singly or in combination, at low and relatively high radiation doses, resulted in radiosensitisation of DU145 cells. Radio-protection was achieved in 1542N cells. AG-1478 had no effect on radiosensitivity. / AFRIKAANSE OPSOMMING: Geteikende terapies wens hul spesifisiteit teenoor konvensionele terapies vir prostaat kanker, mag potensieel verbetering offer. Konvensionele behandeling is wel effektief maar nie genesend nie wens ‘n aantal beperkings, sowel as die toksisiteit vir normale selle. In prostaat kanker is die aktivering van beide die epidermiese groei faktor reseptor (EGFR) en fosfatidielinositol 3-kinase/Akt/soogdier teiken vir rapamisien (mTOR) seingewing baan sterk betrek by tumor groeisel en weerstand teen konvensionele en geteikende anti-kanker terapies. Beter begrip van die molekulêre meganismes betrokke by prostaat kanker ontwikkeling, bevordering en weerstand teen terapie, kan die ontwerp van nuwe terapeutiese strategies ondersteun. Die doelwit van hierdie studie was om sleutel molekulêre teikens van die epidermiese groei faktor reseptor seingewing baan te inhibeer en om prostaat selle bloot te stel aan dosisse bestraling, om potensiële terapeutiese teikens te vestig wat vatbaar is vir gekombineerde modaliteit terapie, om ‘n mengsel van stremmiddels te formuleer, en om die straling gevoeligmaking bekwaamheid daarvan te evalueer. Die EGFR/PI3K/mTOR seingewingbaan speel ‘n belangrike rol in the radiosensitiwiteit van die menslike prostaat kanker sellyn (DU145) en die normale prostaat sellyn (1542N). Die studie bevind dat AG-1478, ‘n EGFR stremmer, en BEZ-235, ‘n tweevoudige beperker van die fosforinositied 3-kinase (PI3K) en soogdier teiken vir rapamisien (mTOR) seingewingbaan, enkel of in kombinasie die DU145 selle radiosensitiseer vir straling dosisse van 2 en 6 Gy. Stralings beskerming was verkry met die 1542N sellyn. AG-1478 het geen effek getoon op radiosensitiwiteit nie.

The spliceosome is a complex, dynamic ribonucleoprotein (RNP) complex that undergoes numerous conformational changes during its assembly, activation, catalysis and disassembly. Defects in spliceosome assembly are thought to trigger active dissociation of faulty splicing complexes. A yeast genetic screen was performed to identify components of the putative discard pathway. This study found that weak mutant alleles of SPP382 suppress defects in several proteins required for spliceosome activation (Prp38p, Prp8p and Prp19p) as well as substrate mutations (weak branch point mutants). This evolutionary conserved protein had been found in both yeast and mammalian splicing complexes. However, its role in splicing had not been elucidated. This study focused on understanding the cellular role of Spp382p in splicing and particularly in the discard pathway. Spp382p was found to be essential for normal splicing and for efficient intron turnover. Since Spp382p binds Prp43p and is required for intron release in vitro, spp382 mediated suppression of splicing factor mutations might reflect lowered Prp43p activity. In agreement with this, we find that prp43 mutants also act as suppressors. This leads us to propose a model in which defects in spliceosome assembly, like those caused by prp38-1, prompt Spp382p-mediated disassembly of the defective complex via Prp43p Bolstering this theory, we find that Spp382p is specifically recruited to defective complexes lacking the 5 exon cleavage intermediate and spp382 mutants suppress other splicing defects. I show by stringent proteomic and two-hybrid analyses that Spp382p interacts with Cwc23p, a DnaJ-like protein present in the spliceosome and co-purified the Prp43p-DExD/H-box protein. In this study, I also show that Cwc23p is itself essential for splicing and normal intron turnover. Enhanced expression of another protein, Sqs1p, structurally related to Spp382p and also found associated with Prp43p is inhibitory to both growth and splicing. Synthetic lethal and dosage suppression studies bolster a functional linkage between Spp382p, Cwc23p, Sqs1p and Prp43p and together, the data support the existence of a Spp382p -dependent spliceosome integrity (SPIN) complex acting to remove defective spliceosomes.

Kynurenine 3-monooxygenase is a FAD-dependent aromatic hydroxylase (FAH) which is a widely suggested therapeutic target for controlling the balance of bioactive metabolite levels produced by the mammalian kynurenine pathway (KP). Prior to starting this work no structural information was known for the enzyme, with studies of the human form complicated by the presence of a C-terminal transmembrane helix. The bacterial Pseudomonas fluorescens enzyme (PfKMO) lacks the transmembrane region and has been previously characterised by Crozier-Reabe and Moran [1, 2]. Therefore PfKMO, which shares 32 % sequence identity with the human enzyme, was selected as a target for structure solution. Initial substrate bound PfKMO crystals showed poor X-ray diffraction. Subsequent growth optimisation and the generation of a C252S/C461S PfKMO mutant (dm2) yielded crystals suitable for structure solution. Selenomethioninelabelled substrate bound dm2 crystals were used to solve the first structure to a resolution of 3.40 Å. With just one protein molecule per asymmetric unit, a high solvent content was responsible for the poor diffraction properties of this crystal form. The overall fold resembled that of other FAH enzymes with a Rossmann-fold based FADbinding domain above a buried substrate binding pocket. Interestingly PfKMO possesses an additional, novel C-terminal domain that caps the back of the substrate-binding pocket on the opposite side to the flavin. Residues proposed to be involved in substrate binding were identified and shown to be highly conserved among mammalian KMO sequences. Subsequently single crystals of substrate-free dm2 PfKMO were obtained and showed significantly stronger diffraction due to new lattice packing in an orthorhombic space group bearing four molecules per asymmetric unit. The structure was solved to a resolution of 2.26 Å and revealed a clear conformational change of the novel C-terminal domain. This movement opens a potential route of substrate/product exchange between bulk solvent and the active site. The investigation of a set of C-terminal mutants further explored the relevance and mechanics of the conformational change. In addition the presence of chloride ions in the substrate-free crystal growth solution caused a small number of localised subtle alterations to the structure, with a potential chloride binding site identified adjacent to the flavin cofactor. This may have relevance for the observed inhibition of PfKMO activity by monovalent anions – a feature widely common to FAH enzymes [3]. The first discovered KMO inhibitors were analogues of the substrate L-Kyn, however one such compound (m-NBA) was recently shown to instigate uncoupled NADPH oxidation leading to the release of cytotoxic hydrogen peroxide [1]. A set of substrate analogues were tested and characterised for inhibition of PfKMO. The picture was shown to be complex as some substrate analogues completely inhibited the enzyme whilst the binding of some still stimulated low-levels of NADPH oxidation. Crystallographic studies with m-NBA and 3,4-dichlorobenzoylalanine (3,4-CBA) bound revealed indistinguishable structures from that of substrate-bound PfKMO. These studies suggest that the analogue 3,4CBA is a potent PfKMO inhibitor whose therapeutic potential may be re-visited. The previous most potent KMO inhibitor whose structure was not analogous to the substrate was Ro 61-8048 [4], which unfortunately did not pass pre-clinical safety tests. A novel series of 1,2,4-oxadiazole amides based on the structure of Ro 61-8048 was created by Gavin Milne (PhD, University of St Andrews) and tested on PfKMO. Rounds of refinement led to the discovery and refinement of low nanomolar competitive inhibitors of the bacterial enzyme. PfKMO was co-crystallised with each of the four most potent compounds forming a third different lattice arrangement, which yielded structures to resolutions of 2.15-2.40 Å. The structures displayed conformational changes resembling the substrate-free fold possibly caused by displacement of a crucial substrate-binding residue, R84. Overall the wealth of structural data obtained may be transferable to predictions about the structural features of human KMO and to the rational design of therapeutic inhibitors. The potent novel inhibitors tested may additionally present a new exciting development for the therapeutic inhibition of human KMO.

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