The human kallikrein family is a family of proteolytic enzymes, classified as serine proteases, that derive from chromosome 19, locus 13.3-13.4. These enzymes are widespread in pathophysiological processes such as cancer and neurodegenerative diseases; hence studies of catalytic sites and inhibitors are important in relation to the longer term of design of therapeutic drugs. One member of the family, human kallikrein 4 (hK4) which is thought to carry out crucial functions in the prostate, was expressed in this study as a secreted protein in a baculovirus expression system, bearing a His-tag and V5-epitope that were used for purification and detection respectively. Its mass was estimated to be 35kDa, ~2kDa less than the equivalent product expressed in monkey kidney cells. The protein was purified to 50-90% purity with a yield of 0.93mg/L-4.8mg/L based on methods derived from computational prediction of its properties, such as pI. Computational analysis was extended by applying high-performing computing techniques, such as molecular dynamics, and flexible ligand docking, to predict antigenic regions, the likely substrate specificity and putative inhibitors. These results show that hK4 has a loop, between Leu83-Ser94 that shows promise as a specific segment that can be exploited for generation of antibodies. Preferred substrates were also predicted to bear hydrophobic residues at the P'-region of the scissile bond and amphiphilic residues at the P-region. At the S-region, hK4 potentially involves its unique PLYH-motif in recognizing the P4/P5 position from the substrate. Flexible ligand-docking studies indicate that hK4 can be inhibited by inhibitors that carry a modified bulky hydrophobic sidechain with a guanidinium group at the P1-position and its own putative autoactivation region residues at the P2, P1' and P2' position. The computational study was extended to other members of the kallikrein family, predicting distinctions between these that could be used for future studies. These results show that 8 of the fifteen kallikrein members are very homologous in terms of specificity bearing typical trypsinlike activity and specificity, except for hK2, hK3, hK4, hK5, hK7, hK9, hK15 that retain certain distinct signatures in the binding pocket in terms of secondary specificity. The principles of substrate-specificity analysis that were developed were further applied on three metzincins, MMP-3, ADAM-9 and ADAM-10. These three enzymes are metalloproteases, which are involved in tissue remodeling, intracellular signalling and cell-to-cell mediation. The substrate-specificity analysis was carried out on all three metzincins using the structure of a crystallized complex of the MMP-3 enzyme with the TIMP-1 natural inhibitor as template. In this specific enzyme-substrate complex, the challenge was to model and suggest a possible orientation of the P-region, which is not known. The interactions on the P/S-region are therefore unclear and need to be clarified. In order to suggest the arrangement of the enzyme-substrate complex and the undefined S-subsites, four new residues were added in an extended beta-sheet conformation to the P1' residue (derived originally from the TIMP-1 inhibitor) to create a full-length modeled substrate spanning P4'-P4. This new modeled region, in particular, was bound through backbone H-bonds with the enzyme at position 169 (MMP nomenclature) suggesting a new crucial residue for substrate binding, and satisfied steric and chemical restraints in the S'-region of the enzyme. This modeling approach also indicated a putative presence of an S2/S3-pocket on these metzincins which is composed of different residues for MMP-3, ADAM-9 and ADAM-10, and which could prove useful for future drug design projects. Furthermore, the data argue against the involvement of a polarizable water molecule in catalysis, a mechanism that has been postulated by various groups. A new catalytic mechanism is suggested to involve an oxyanion anhydride transition state. This study is a demonstration of the power of combining bioinformatics with wet-lab biochemistry.

This PhD aimed to elucidate the mechanisms by which polymorphisms may alter androgen-induced transactivation of androgen receptor (AR) target genes which may be important in prostate cancer aetiology. The second aspect of this PhD focused on identifying and characterising functional polymorphisms that may have utility as predictive risk indicators for prostate cancer and which may aid in earlier therapeutic intervention and better disease management. Analyses were carried out on the kallikrein-related peptidase 3 (KLK3), also known as the prostate specific antigen (PSA), gene and the kallikrein-related peptidase 4 (KLK4) gene. The PSA and KLK4 genes are part of the serine protease family that have trypsin or chymotrypsin like activity and are thought to play a role in the development of hormone-dependent cancers in tissues such as those in the prostate, breast, endometrium and ovaries. In the prostate, PSA is regulated by androgens and three androgen response elements (AREs) have been described in the promoter and upstream enhancer region. The PSA ARE I harbours a polymorphism at -158 bp from the transcription initiation site (TIS) that results in a G to A transition (G-158A). This PhD investigated the functional significance of the PSA G-158A polymorphism which has been reported to be associated with prostate cancer risk. Electromobility shift assays (EMSAs) investigating the interaction of ARE I variants with the AR DNA binding domain (AR-DBD) demonstrated that the A allele had a two-fold increased binding affinity for the AR-DBD when compared with the G allele. This was confirmed with endogenous AR in limited proteolysis-EMSA experiments. The limited proteolysis-EMSA experiments also demonstrated differential sensitivities of PSA ARE I alleles to trypsin digestion, which suggests that the G-158A polymorphism has an allosteric effect on the AR that alters AR/ARE I complex stability. Furthermore, Chromatin Immunoprecipitation (ChIP) assays suggest that the A allele more readily recruited the AR in vivo when compared with the G allele and is consistent with the in vitro binding data. Luciferase reporter assays carried out in both LNCaP and 22Rv1 prostate cancer cells, and using the natural (dihydrotestosterone; DHT) ligand demonstrated that the A allele was more responsive to androgens in LNCaP cells. Hence, this study has elucidated the potential mechanisms by which the G-158A polymorphism may differentially regulate PSA expression (of which up-regulation of PSA is thought to be important in prostate cancer development and progression). KLK4 has similar tissue-restricted expression as PSA and is up-regulated by steroid hormones in many endocrine cells including those in the prostate. A putative ARE (KLK4-pARE) located at -1,005 to -1019 relative to the more predominantly used transcription initiation site, TIS3, was initially found in supershift assays using AR antibodies to interact with endogenous AR. However, subsequent EMSA analysis using purified AR-DBD suggest that KLK4-pARE may be interacting with the AR indirectly. To investigate this hypothesis, a tandem construct of KLK4-pARE was cloned into the pGL3-Promoter vector for hormone-induced reporter assays. However, reporter assays did not demonstrate any responsiveness of KLK4-pARE to androgens, estradiol or progestins. Consequently, Real-Time PCR was carried out to reassess the hormonal regulation of KLK4 at the mRNA level. Consistent with the literature, data from this study suggests that KLK4 may be up-regulated by androgens, progestins and estradiol in a cyclical manner. Hormone-induced luciferase reporter assays were then carried out on seven promoter constructs that span 2.8 kb of the KLK4 promoter from TIS3. However, none of the seven promoter constructs demonstrated any significant responsiveness to androgens, estradiol or progestins. This study suggests that hormone response elements (HREs) that may drive the hormonal regulation of KLK4 in prostate cancer may be located further upstream from the promoter region investigated in this PhD, or alternatively, may lie 3' of TIS3. The characterisation of KLK4 promoter polymorphisms and their flanking sequences were also carried out in parallel to the functional work with the intent to assess the functional significance of any polymorphisms that may be located within HREs. In total 19 polymorphisms were identified from the public databases and from direct sequencing within 2.8 kb of the KLK4 promoter from TIS3. However, the functional and clinical significance of these 19 polymorphisms were not further pursued given the negative findings from the functional work. The PSA AR enhancer region was also assessed for potential polymorphisms that may be associated with prostate cancer risk. A total of 12 polymorphisms were identified in the PSA enhancer of which two (A-4643G and T-5412C) have been reported to alter functionality of the enhancer region and thus, prioritised for further analysis. Association analysis for prostate cancer risk was then carried out on these PSA enhancer polymorphisms as none of the KLK4 promoter polymorphisms were found in functional HREs. No significant association for either the A-4643G or T-5412C polymorphism with prostate cancer risk was found at the P = 0.05 level. However, under an age-adjusted dominant model a 1.22- (95% CI = 1.16-1.26) and 1.23-fold (95% CI = 1.17-1.29) increased risk for prostate cancer was found for the A-4643G or T-5412C polymorphisms, respectively. Both polymorphisms were also assessed for association with tumour grade and stage and PSA levels. Genotypes were significantly different for the A-4643G and T-5412C polymorphisms with tumour stage and PSA levels, respectively. However, these results are likely to be biased by the case population which consist primarily of men who presented with incidental (pT1) and organ-confined (pT2) tumours. To summarise, the A-4643G and T-5412C polymorphisms are unlikely to be associated with prostate cancer risk, PSA levels or stage/grade of disease. However, further analyses in a larger cohort is warranted given that these polymorphisms alter androgen responsiveness of the PSA enhancer and that elevated PSA levels are indicative of men with prostate cancer. To summarise, this PhD has elucidated the functional significance of the PSA G-158A polymorphism in prostate cancer and which may be important in prostate cancer patho-physiology. This PhD has also furthered the understanding of the hormonal regulation of KLK4 in prostate cancer cells. Finally, this PhD has carried out a pilot study on two functional PSA enhancer polymorphisms (A-4643G and T-5412C) with prostate cancer risk.