BACKGROUND: Prostate cancer (PCa) is the most commonly diagnosed solid tumor and the second leading cancer death in the United States, and also one of the major cancer-related deaths in Chinese. Androgen deprivation therapy (ADT) is the first line treatment for metastatic PCa. PCa ultimately relapses with subsequent ADT treatment failure and becomes castrate-resistant (CR). It is important to develop effective therapies with a surrogate marker towards CR PCa. METHOD: Histone deacetylase (HDAC) inhibitors were examined to determine their effects in androgen receptor (AR)/ cellular prostatic acid phosphatase (cPAcP)-positive PCa cells, including LNCaP C-33, C-81, C4-2 and C4-2B and MDA PCa2b androgen-sensitive and androgen-independent cells, and AR/cPAcP-negative PCa cells, including PC-3 and DU 145 cells. Cell growth was determined by cell number counting. Western blot analyses were carried out to determine AR, cPAcP and PSA protein levels. RESULTS: cPAcP protein level was increased by HDAC inhibitor treatment. Valproic acid, a HDAC inhibitor, suppressed the growth of AR/cPAcP-positive PCa cells by over 50% in steroid-reduced conditions, higher than on AR/cPAcP-negative PCa cells. Further, HDAC inhibitor pretreatments increased androgen responsiveness as demonstrated by PSA protein level quantitation. CONCLUSION: Our results clearly demonstrate that HDAC inhibitors can induce cPAcP protein level, increase androgen responsiveness, and exhibit higher inhibitory activities on AR/cPAcP-positive PCa cells than on AR/cPAcP-negative PCa cells. Upon HDAC inhibitor pretreatment, PSA level was greatly elevated by androgens. This data indicates the potential clinical importance of cPAcP serving as a useful biomarker in the identification of PCa patient sub-population suitable for HDAC inhibitor treatment.

Bone metastases are a frequent clinical complication associated with cancer. The aim of this PhD thesis was to set up a model system for the study of tumour cell – bone cell interactions in vitro, ex vivo and in vivo and to use this system to test the efficacy of a novel therapeutic agent for the treatment of osteolytic bone disease. Co-culture or conditioned medium studies using human or mouse cancer cell lines were used to develop an in vitro model system of tumour cell – bone cell interactions. This showed that osteolytic tumour cells enhance osteoclast formation, fusion and resorption through the production of various factors that act directly on osteoclasts and their precursors. And in addition, that osteolytic tumour cells also enhance osteoclastogenesis indirectly via increasing the production of RANKL in osteoblasts. Other effects on osteoblasts included reductions in differentiation, migration and adhesion. Successful ex vivo and in vivo models for the study of tumour – induced osteolysis were created using adapted organ cultures and intratibial injection techniques respectively. IGF-1 and its receptor are known to play important roles in both bone metabolism and breast cancer. Therefore a study of the effects of IGF-1 receptor inhibition on tumour cell – bone cell interactions was performed. In vitro studies showed that the novel IGF-1 receptor tyrosine kinase inhibitor PQIP significantly inhibited IGF-1 and breast cancer enhanced osteoclast formation. Western blot analysis suggested this may be due to the inhibition of both IGF-1 and cancer conditioned medium induced PI3k/Akt activation. Moreover, treatment of osteoblasts with PQIP inhibited cancer cell conditioned medium induced increases in RANKL production. Ex vivo studies using human MDA-MB-231 – mouse calvarial organ co-cultures demonstrated that MDA-MB-231 cells caused osteolysis and this was completely prevented by PQIP without affecting cancer cell viability. Furthermore, once daily oral administration of PQIP significantly decreased trabecular bone loss and reduced the size of osteolytic bone lesions following mouse 4T1 breast cancer cell intratibial injection in mice. Quantitative histomorphometry showed a significant reduction in breast cancer-induced osteoclast number and activity. Consistent with the significant inhibition of osteoblast differentiation, spreading, migration and bone nodule formation observed in vitro, PQIP also inhibited osteoblast number and bone formation in vivo. No inhibition of in vivo tumour volume was observed. These findings clearly suggest that oral PQIP treatment reduced the rate of cancer associated bone turnover. In conclusion, this thesis successfully demonstrates a model system for investigating tumour cell-bone cell interactions in vitro, ex vivo and in vivo. Using this model system I showed that pharmacologic inhibition of IGF-1 receptor kinase activity using PQIP inhibits osteoclast and osteoblast changes induced by breast cancer cells in vitro and in vivo and prevents osteolysis ex vivo and in vivo. This indicates that PQIP and its novel derivatives which are now in advanced clinical development may be of value in the treatment of osteolytic bone disease associated with breast cancer.

The Pim family of serine/threonine protein kinases (Pim 1, 2, and 3) contribute to cellular transformation by regulating glucose metabolism, protein synthesis, and mitochondrial oxidative phosphorylation. Drugs targeting the Pim protein kinases are being tested in phase I/II clinical trials for the treatment of hematopoietic malignancies. The goal of these studies was to identify Pim substrate(s) that could help define the pathway regulated by these enzymes and potentially serve as a biomarker of Pim activity. To identify novel substrates, bioinformatics analysis was carried out to identify proteins containing a consensus Pim phosphorylation site. This analysis identified the insulin receptor substrate 1 and 2 (IRS1/2) as potential Pim substrates. Experiments were carried out in tissue culture, animals, and human samples from phase I trials to validate this observation and define the biologic readout of this phosphorylation. Our study demonstrates in both malignant and normal cells using either genetic or pharmacological inhibition of the Pim kinases or overexpression of this family of enzymes that human IRS1S1101 and IRS2S1149 are Pim substrates. In xenograft tumor experiments and in a human phase I clinical trial, a pan-Pim inhibitor administered in vivo to animals or humans decreased IRS1S1101 phosphorylation in tumor tissues. This phosphorylation was shown to have effects on the half-life of the IRS family of proteins, suggesting a role in insulin or IGF signaling. These results demonstrate that IRS1S1101 is a novel substrate for the Pim kinases and provide a novel marker for evaluation of Pim inhibitor therapy.

Thesis (PhD)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: Pantothenate kinase (PanK) enzymes catalyze the first reaction in the five step biosynthesis of the essential cofactor coenzyme A. Enzymes representing each of the three identified PanK types have been studied and characterized and these PanK types exhibits a unique diversity between different organisms, therefore highlighting them as potential drug targets. In this study the type III PanK of specifically pathogenic bacteria were characterized with the goal of developing type-specific inhibitors. Several questions about the activity of the Mycobacterium tuberculosis enzyme was answered, which addresses the contradicting results achieved in related PanK studies performed to date. Furthermore the first inhibitors, that are competitive to the pantothenate binding site, were designed, synthesized and tested against the Pseudomonas aeruginosa enzyme. This resulted in the discovery of the most potent inhibitors of the type III PanKs to date. / AFRIKAANSE OPSOMMING: Pantoteensuurkinase-ensiem (PanK) kataliseer die eerste stap in die vyf stap biosintese van die lewens belangrike en essensiële kofaktor, koënsiem A (KoA). Die meerderheid patogeniese bakterieë, waaronder die organisme wat tuberkulose veroorsaak, besit ‘n unieke vorm van die PanK-ensiem. Gevolglik word hierdie ensieme as belangrike teikens vir die ontwikkeling van antibakteriële middels beskou. In hierdie studie is die aktiwiteit van die Mycobacterium tuberculosis ensiem gekarakteriseer wat verskeie teenstrydige bevindings oor hierdie ensiem beantwoord het. Verder is nuwe inhibitore vir die Pseudomonas aeruginosa ensiem ontwerp, gesintetiseer en getoets. Die beste inhibitore van hierdie tipe ensiem tot op hede is sodoende geïdentifiseer.

Eukaryotic protein kinases are one of the most important classes of human proteins, and a great deal of research has focused on the development of small molecule inhibitors as biological probes for the determination of their cellular function or as therapeutics for the treatment of disease, such as cancer. The need for new selective inhibitors and a better understanding of the selectivities of existing small molecules is readily apparent. Towards the goal of better understanding protein kinases and the molecules that inhibit them, I have developed a split-protein-based approach for the investigation of these kinase-small molecule interactions. Employing split-firefly luciferase as a reporter domain, we engineered a three-hybrid system capable of determining kinase inhibition through competitive interactions between an active site-directed ligand and a small molecule of interest. This method measures luciferase activity as a function of ligand binding, as opposed to the more traditional assays which quantify kinase activity directly, and alleviates the laborious process of protein purification. The model kinase PKA and the promiscuous ligand staurosporine were used in an initial test case to successfully validate the general design principles of our assay. The modular nature inherent to the assay's design enabled us to adapt it to roughly 300 additional protein kinases and two different ligands. We were able to establish a protocol for rapidly ascertaining the inhibition of a kinase by a library of 80 commercially available kinase inhibitors in a 96-well, high-throughput format. This protocol was then systematically applied to the AGC group of kinases to observe patterns of inhibition across similarly related kinases. We have further shown how these results might be correlated with the sequence identity between kinases to better anticipate inhibitor promiscuity. Finally, we were able to illustrate how a kinase-centric approach could be applied to correlate alterations to the kinase domain with changes in luminescence. This has use for the interrogation of different modes of inhibition as well as in identifying the specific determinants of inhibitor binding. In total, these efforts represent the optimization of a new, general platform for determining kinase inhibitor selectivity across the kinome, and it could potentially be applied universally to the interrogation of protein-ligand interactions.

Microsomal prostaglandin E synthase-1 (mPGES-1) is the terminal enzyme following cyclooxygenase-2 (COX-2) for the production of prostaglandin E₂(PGE₂), and has been identified as a novel therapeutic target for cancers. From an in silico screen aimed at developing novel small molecule inhibitors of mPGES-1, a 2-aminothiazole compound PGE0001 was identified from 13 putative hits based on its ability to reduce cellular PGE₂ and minimal COX-2 inhibition in vitro. Utilizing drug design strategies based on a 4-point pharmacophore model, we also discovered a new series of compounds exhibiting superior potency without inhibiting COX-2, as exemplified by compound PGE0056. In multiple cancer cell lines, both PGE0001 and PGE0056 reduced cytokine-stimulated PGE₂ release with submicromolar EC₅₀ values, although the two compounds exhibited differential kinetics. Importantly, these compounds showed promising anti-tumor effects in xenograft mouse models. Mice injected with the compounds also had reduced PGE₂ in serum. Surprisingly, none of the compounds inhibited mPGES-1 in cell-free assays, except for MK-886, a reported mPGES-1 inhibitor. In order to determine the mechanisms of action of PGE0001 and PGE0056, the PGE₂ synthesis cascade was extensively examined. Immunoblotting analysis suggested that the PGE₂ reduction in a short time frame was not due to alteration of the protein level of enzymes involved in PGE₂ synthesis/metabolism. So far, we have excluded upstream COX-1/2, phospholipase A₂, and other PGE synthases (mPGES-2 & cytosolic PGES) as major targets for PGE0001 or PGE0056. Interestingly, these compounds were found to inhibit a number of kinases implicated in cancer, presumably due to their structural feature. Although these alternative kinase targets may not sufficiently explain the mechanisms responsible for PGE₂ reduction, inhibition of them may strengthen the therapeutic potential of our compounds. We also implemented a target pull-down approach using biotinylated derivatives of these compounds, followed by proteomic analysis to isolate targets to which these compounds bind. As a result, we identified a couple of other enzymes involved in the arachidonic acid metabolic pathway, which need to be further validated. In summary, we identified novel classes of anti-inflammatory compounds with anti-tumor activity, although the mechanisms of action remain to be clarified.

New approaches are needed for the treatment of patients with T-cell acute lymphoblastic leukemia (T-ALL) who fail to achieve remission with chemotherapy. Analysis of the effects of pan-PIM protein kinase inhibitors on human T-ALL cell lines demonstrated that the sensitive cell lines expressed higher PIM1 protein kinase levels, whereas T-ALL cell lines with NOTCH mutations tended to have lower levels of PIM1 kinase and were insensitive to these inhibitors. NOTCH-mutant cells selected for resistance to gamma secretase inhibitors developed elevated PIM1 kinase levels and increased sensitivity to PIM inhibitors. Gene profiling using a publically available T-ALL dataset demonstrated overexpression of PIM1 in the majority of early T-cell precursor (ETP)-ALLs and a small subset of non-ETP ALL. While the PIM inhibitors blocked growth, they also stimulated ERK and STAT5 phosphorylation, demonstrating that activation of additional signaling pathways occurs with PIM inhibitor treatment. To block these pathways, Ponatinib, a broadly active tyrosine kinase inhibitor (TKI) used to treat chronic myelogenous leukemia, was added to this PIM-inhibitor regimen. The combination of Ponatinib with a PIM inhibitor resulted in synergistic T-ALL growth inhibition and marked apoptotic cell death. Treatment of mice engrafted with human T-ALL with these two agents significantly decreased the tumor burden and improved the survival of treated mice. This dual therapy has the potential to be developed as a novel approach to treat T-ALL with high PIM expression.

ABSTRACT MOLECULAR MECHANISMS AND GENE SIGNATURES INVOVLED IN CALCINEURIN INHIBITOR NEPHROTOXICITY IN KIDNEY ALLOGRAFT By Huong Le Diem Nguyen, M.S. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Physiology at Virginia Commonwealth University. Virginia Commonwealth University, 2011. Major Director: Valeria Mas, Ph.D. Associate Professor, Department of Surgery and Pathology Director of Molecular Transplant Research Laboratory, Division of Transplant Calcineurin inhibitors (CNI), cyclosporin A and tacrolimus, are potent immunosuppressive agents but induce toxicities causing damages and graft dysfunction, and have been suggested to contribute to late-term loss of graft in kidney transplant recipients. Even though insights on mechanism of CNI nephrotoxicity have been uncovered, prevention and treatment of these toxicities remain a major challenge in the clinical administration of CNI due to low dose-toxicity correlation, difficulty in establishing a differential patho-histological diagnosis, and varying individual susceptibility. We hypothesize that CNI nephrotoxicity follows distinct disease pathways and is characterized by significant gene signatures that differentiate it from other conditions such as acute rejection and chronic allograft dysfunction. Moreover, we postulate that CNI-induced toxicity profiles contribute to the IF/TA signatures. Microarray analysis and gene annotation were done on the study database included of tissues diagnosed with CNI nephrotoxicity (n = 9), interstitial fibrosis/tubular atrophy (IF/TA, n=10), and normal allografts (NA, n = 8). All samples were histologically classified based on the revised Banff ‘07 criteria for renal allograft pathology. Top-scored biological networks in CNI tissues were related to metabolic disease, cellular development, renal necrosis, apoptosis cell-death, immunological disease, inflammatory disease, and many others. Canonical pathway analysis emphasized oxidative stress response mediated by NRF2 and various cell-death signaling pathways including 14-3-3 signaling pathway, p53 signaling pathway, and TGF-β signaling pathway. Profiling of differentially expressed genes was done based on their statistical significance and biological relevance to the unique pathology of CNI nephrotoxicity. Among these, three genes RGS1, CXCR4, and TGIF1 were further quantitatively evaluated using real time-PCR. Between CNI group and normal allograft, t-test results showed only RGS1 gene expression level was statistically significant. Between IF/TA group in normal allograft, both RGS1 and CXCR4 showed statistical significance. The calculated relative fold changes revealed an up-regulated pattern of RGS1 and CXCR4 expression in association with pathological groups (CNI and IF/TA). We did not, however, find any association between the expression of TGIF1 in either CNI group or IF/TA group.

The haloacid dehalogenase (HAD) family of phosphatases is an ancient, ubiquitous group of enzymes, and their emerging role in human health and disease make them attractive targets for detailed analyses. This thesis comprises the biochemical and structural characterization of chronophin, an HAD-type phosphatase, which has been shown to act on Ser3-phosphorylated cofiln-1, a key regulator of actin dynamics, and on the Ser/Thr-phosphorylated steroid receptor co-activator 3 (SRC-3). Besides being a specific phosphoprotein phosphatase, chronophin also acts on the small molecule pyridoxal 5'-phosphate (PLP, vitamin B6), implying that chronophin serves as a regulator of a variety important physiological pathways. The analysis of chronophin was performed on different levels, ranging from intrinsic regulatory mechanisms, such as the allosteric regulation via dimerization or the characterization of specificity determinants, to modes of extrinsic modulation, including the association with putative interacting proteins or the generation of chronophin-specific inhibitors. The association of the previously identified putative chronophin interactors calcium- and integrinbinding protein 1 (CIB1) and calmodulin was investigated using recombinantly expressed and purified proteins. These studies revealed that the interaction of chronophin with CIB1 or calmodulin is mutually exclusive and regulated by calcium. Neither CIB1 nor calmodulin had an effect on the in vitro chronophin phosphatase activity towards PLP or phospho-cofilin-1, but might regulate other functions of this important phosphatase. The role of chronophin dimerization was studied by generating a constitutively monomeric variant, which showed reduced PLP hydrolyzing activity. X-ray crystallographic studies revealed that dimerization is essential for the positioning of the substrate specificity loop in chronophin, unraveling a previously unknown mechanism of allosteric regulation through a homophilic interaction. This mechanism potentially applies to other enzymes of the C2a subfamily of HAD-type phosphatases, as all structurally characterized members show a conserved mode of dimerization. The general determinants of substrate specificity in the C2a subfamily of HAD phosphatases were investigated by performing domain swapping experiments with chronophin and its paralog AUM and subsequent biochemical analyses of the hybrid proteins. The X-ray crystallographic structure determination of the chronophin catalytic domain equipped with the AUM capping domain revealed the first partial structure of AUM. This structural information was then used in subsequent studies that analyzed the divergent substrate specificities of AUM and chronophin in an evolutionary context. Finally, a set of four chronophin inhibitors were generated based on the structure of PLP and characterized biochemically, showing moderate inhibitory effects with IC50-values in the micromolar range. These compounds nevertheless constitute valuable tools for future in vitro experiments, such as studies concerning the structure-function relationship of chronophin as a PLP phosphatase. In addition, the crystal structure of one inhibitor bound to chronophin could be solved. These results provide the basis for the further development of competitive chronophin inhibitors with increased specificity and potency. / HAD Phosphatasen gehören zu einer phylogenetisch alten Proteinfamilie, die in allen drei Domänen des Lebens vertreten ist. Enzyme dieser vergleichsweise wenig charakterisierten Familie von Phosphatasen erweisen sich zunehmend als biomedizinisch interessante Zielmoleküle, da immer mehr Krankheiten identifiziert werden, bei denen HAD Phosphatasen eine Rolle spielen. In der hier vorliegenden Doktorarbeit wurde die HAD Phosphatase Chronophin biochemisch und strukturell charakterisiert. Bisher konnte gezeigt werden, dass Chronophin die Proteine Cofilin-1, ein Schlüsselprotein in der Regulation des Aktin-Zytoskeletts, und den Steroidrezeptor Coaktivator 3 (SRC-3) dephosphoryliert. Darüberhinaus ist bekannt, dass Chronophin eine spezifische Pyridoxal 5'-Phosphat (PLP, Vitamin B6) Phosphatase ist, und somit an der Regulation verschiedenster Signalwege beteiligt ist. Die hier beschriebene Analyse von Chronophin beinhaltet die Untersuchung intrinsischer Regulationsmechanismen, wie z.B. Determinanten der Substratspezifität, die allosterische Regulation über Dimerisierung, bis hin zur Kontrolle durch extrinsische Faktoren wie interagierende Proteine oder Inhibitoren. Die Interaktion von Chronophin mit den kürzlich in unserer Arbeitsgruppe identifizierten Interaktionspartnern CIB1 (Kalzium- und Integrin-bindendes Protein 1) und Calmodulin wurde mit Hilfe rekombinant exprimierter und gereinigter Proteine untersucht. Dabei kam heraus, dass sich die Assoziation von CIB1 und Calmodulin an Chronophin gegenseitig ausschließt, und dass dieser Prozess durch Kalzium reguliert wird. Dabei beeinflusst weder die Bindung an CIB1 noch an Calmodulin die Phosphataseaktivität von Chronophin gegenüber den Substraten PLP oder phosphoryliertem Cofilin-1. Möglicherweise regulieren die beiden interagierenden Proteine die Funktion von Chronophin auf eine andere, hier nicht weiter untersuchte Art und Weise. Der Einfluss der Chronophin-Dimerisierung wurde untersucht, indem wir eine konstitutiv monomere Variante des üblicherweise dimeren Chronophins geschaffen haben. Diese monomere Variante des Enzyms wies eine deutlich reduzierte Aktivität gegenüber PLP auf. Durch röntgenkristallographische Analysen des wild-typischen Proteins und der monomeren Variante konnten wir zeigen, dass die Dimerisierung von Chronophin notwendig ist, um ein Strukturelement, welches wichtig für die Substratspezifität ist, in einer korrekten Position zu halten. Dieser allosterische Mechanismus zur Aufrechterhaltung der Substratspezifität war bisher unbekannt, und trifft möglicherweise auf alle Proteine der C2a Unterfamilie von HAD Phosphatasen zu, die strukturell mit Chronophin verwandt sind. Die Faktoren, welche auf die Substratspezifität von Chronophin Einfluss nehmen wurden untersucht, indem einzelne Proteindomänen mit dem paralogen Protein AUM ausgetauscht, und die so geschaffenen Protein-Hybride biochemisch untersucht wurden. Durch das Lösen der röntgenkristallographischen Struktur eines Protein-Hybrids, bestehend aus der katalytischen Domäne von Chronophin und der capping-Domäne von AUM, konnte die die erste partielle Struktur von AUM untersucht werden. Mit Hilfe dieser strukturellen Information und durch bioinformatische Analysen konnten anschließend die unterschiedliche Substratspezifitäten der beiden paralogen Phosphatasen Chronophin und AUM in einem evolutionsbiologischen Kontext untersucht werden. Zusätzlich wurden vier mögliche Chronophin-Inhibitoren auf der Basis der PLP-Struktur synthetisiert. Die biochemische Analyse der Substanzen als Chronophin-Hemmer ergab moderate inhibitorische Eigenschaften mit IC50-Werten im micromolaren Bereich. Jedoch stellen die hier charakterisierten Inhibitoren nützliche Werkzeuge für die Untersuchung der Struktur-Wirkungsbeziehungen von Chronophin als PLP-Phosphatase dar. Die röntgenkristallographische Struktur von Chronophin mit einem der Inhibitoren liefert außerdem eine wichtge Grundlage für die zukünfitige Verbesserung der Inhibitoren bezüglich Effektivität und Spezifität.

The involvement of the pro-inflammatory cytokine, tumour necrosis factor alpha (TNF-α) and the sympathetic nervous system in the development of delayed-onset muscle soreness has not been established. I assessed the effect of etanercept, a TNF- α inhibitor, and atenolol, a β1-receptor antagonist, on DOMS induced in the quadriceps muscle. Thirteen male subjects reported to the exercise laboratory on three separate occasions, 6-15 weeks apart. In a randomised, double-blind cross-over format, I administered etanercept (25mg), atenolol (25mg) or placebo, one hour before the exercise. Subjects then completed four sets of 15 repetitions at 80% of their one repetition maximum (1RM) on a 45° inclined leg press machine. Muscle strength changes were detected by remeasuring the subject’s 1RM 24h, 48h and 72h after the exercise. Sensitivity to pressure of the quadriceps muscle was measured using a pressure algometer before and 24h, 48h and 72h after exercise. The subject’s perception of the pain was measured with the visual analogue scale and McGill Pain Questionnaire. Muscle tumour necrosis factor-alpha concentration was measured before exercise and then 2h and 24h after exercise in four subjects. Muscle strength was impaired 24h and 48h after exercise regardless of agent administered (P < 0.001). At 72h after exercise, muscle strength was significantly improved (P < 0.01) in subjects receiving etanercept and atenolol compared to those receiving placebo. The subject’s were significantly more sensitive to pressure applied to the quadriceps 24h, 48h and 72h after exercise compared to before exercise, regardless of agent administered (P < 0.001). The VAS was elevated significantly at all three time intervals, with no difference after etanercept or atenolol administration compared to that of placebo. There was no significant difference in the muscle TNF-α concentration between any of the time intervals or between subjects receiving placebo and etanercept (P=0.065). The administration of atenolol and etanercept, at the regimen used, had no effect on the soreness associated with DOMS.