Thesis advisor: Charles S. Hoffman / The biological roles of the most recently discovered mammalian cyclic nucleotide phosphodiesterase (PDE) family, PDE11, are poorly understood, in part due to the lack of selective inhibitors. To address this need for such compounds I completed a ~200,000 compound high throughput screen (HTS) for PDE11 inhibitors using a yeast-based growth assay. Further characterization of lead candidates using both growth-based assays in the fission yeast Schizosaccharomyces pombe and in vitro enzyme assays identified four potent and selective PDE11 inhibitors. I examined the effect of these compounds on human adrenocortical cells, where PDE11 is believed to regulate cortisol levels. One compound, along with two structural analogs, elevates cAMP levels and cortisol production through PDE11 inhibition, thus phenocopying the behavior of adrenocortical tumors associated with Cushing syndrome. These compounds can be used as research tools to study the biological function of PDE11, and can also serve as leads to develop therapeutic compounds for the treatment of adrenal insufficiencies. This study further validates the yeast-based HTS platform as a powerful tool for the discovery of potent, selective and biologically-active PDE inhibitors. / Thesis (PhD) — Boston College, 2012. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

No description available.

Thesis advisor: Charles Hoffman / The second messenger cyclic 3’-5’ adenosine monophosphate (cAMP) signaling pathway plays an important physiological role in many organisms. Cyclic nucleotide phosphodiesterases (PDEs) regulate signal transduction by catalyzing the hydrolysis of cAMP and cGMP allowing for the downregulation of cyclic nucleotide levels. Human PDEs are encoded by 21 genes grouped into 11 families. The biological role of the most recently discovered PDE family (PDE11) remains poorly understood partly due to the lack of selective inhibitors. Mutations in the PDE11A gene have been linked to a wide range of diseases, such as Cushing Syndrome, which is a result of inactivating mutations expressed in adrenocortical tumors. Meanwhile, PDE11 levels are seen to increase in the ventral hippocampus as a function of aging, and is associated with a loss of social memory. Thus, the development of a selective PDE11 inhibitor could provide a potential therapeutic benefit to patients receiving long-term corticosteroid treatment by stimulating cortisol production by the adrenal gland, as well as to aging adults to maintain social memory. To address these needs, candidate PDE11 inhibitors related to a compound discovered by the Hoffman lab in a high throughput screen for PDE11 inhibitors are being synthesized by the Rotella laboratory. I have been evaluating these compounds using two fission yeast-based growth assays in complement with in vitro enzyme assays carried out by Dr. Jeremy Eberhard. Here I describe my role in the project, leading to the identification of a compound, SMQ2-57, which is a selective inhibitor of the PDE11 enzyme whose potency has been confirmed through both yeast-based assays and in vitro enzyme assays. In addition, I have taken both a forward and reverse genetic approach to identify PDE11A4 mutant alleles that confer resistance to inhibitor compounds as such knowledge could guide a rational drug design approach to produce more effective PDE11 inhibitors. Based on our results, SMQ2-57 could serve as a useful tool in understanding the biological role of PDE11. Meanwhile, data from my study of compound resistant mutant PDE11 alleles should allow for the characterization of the physical interaction between PDE11 and its inhibitors in an effort to guide a medicinal chemistry program to develop a more potent and drug-like PDE11 inhibitor. / Thesis (BS) — Boston College, 2023. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Scholar of the College. / Discipline: Biology.

Breast cancers with overexpression or amplification of the HER2 tyrosine kinase receptor are more aggressive, resistant to chemotherapy, and associated with a worse prognosis. Currently, these breast cancers are treated with the monoclonal antibody trastuzumab (Herceptin®). Unfortunately, not all patients respond to trastuzumab drug therapy; some patients show de novo resistance, while others acquire resistance during treatment. This thesis describes our RNAi studies to identify novel regulators of the HER2 signaling pathway in breast cancer. Three kinome-wide siRNA screens were performed on five HER2 amplified and seven HER2 non-amplified breast cancer cell lines, two normal breast cell lines, as well as two HER2-positive breast cancer cell lines with acquired trastuzumab resistance and their isogenic trastuzumab-sensitive controls. To understand the main kinase drivers of HER2 signaling, we performed a comprehensive screen that selected against growth inhibitors of the non-HER2 amplified breast cancer cell lines. This screen identified the loss of the HER2/HER3 heterodimer as the most prominent selective inhibitor of HER2-amplified breast cancers. In a trastuzumab sensitization screen on five trastuzumab-treated breast cancer cell lines, we identified several siRNA against the PI3K pathway as well as various other signaling pathways that inhibited proliferation. Finally, in a screen for acquired trastuzumab resistance, PKCη and its downstream targets were identified. Loss of PKCη resulted in a decrease in G1/S transition and upregulation of the cyclin dependent kinase inhibitor p27. Initial data suggest that PKCη promotes p27 ubiquitination and degradation. Taken together, these studies provide novel insight into the complex signaling of HER2-positive breast cancers and the mechanisms of resistance to trastuzumab therapy. This work describes how various kinases can modulate cell proliferation, and points to possible novel drug targets for the treatment of HER2-positive breast cancers.

The budding yeast S. cerevisiae is widely used as a model organism to study biological processes that are conserved among eukaryotes. Di fferent genomic approaches have been applied successfully to interrogate the mode of action of small molecules and their combinations. In this thesis, these technologies were applied to di fferent sets of chemical compounds in the context of two collaborative projects. In addition to insight into the mode of action of these molecules, novel approaches for analysis of chemical-genetic pro files to integrate GO annotation, genetic interactions and protein complex data have been developed. The fi rst project was motivated by a pressing need to design novel therapeutic strategies to combat infections caused by opportunistic fungal pathogens. Systematic screens of 1180 FDA approved drugs identifi ed 148 small molecules that exhibit synergy in combination with uconcazole, a widely used anti-fungal drug (Wright lab, McMaster University, Canada). Genome-wide chemical-genetic profiles for 6 of these drugs revealed two di fferent modes of action of synergy. Five of the compounds a ffected membrane integrity; these chemical-genetic interactions were supported by microscopy analysis and sorbitol rescue assays. The sixth compound targets a distinct membrane-associated pathway, sphingolipid biosynthesis. These results not only give insight into the mechanism of the synergistic interactions, they also provide starting points for the prediction of synergistic anti-fungal combinations with potential clinical applications. The second project characterised compounds that aff ected melanocytes in a chemical screen in zebra fish (Patton lab, Edinburgh). Chemical-genetic screens in S.cerevisiae enabled us to show that melanocyte pigmentation reducing compounds do so by interfering with copper metabolism. Further, we found that defects in intracellular AP1 and AP3 trafficking pathways cause sensitivity to low copper conditions. Surprisingly, we observed that the widely-used MAP-kinase inhibitor U0126 a ffects copper metabolism. A nitrofuran compound was found to speci fically promote melanocyte cell death in zebrafi sh. This enabled us to study off -target eff ects of these compounds that are used to treat trypanosome infections. Nifurtimox is a nitrofuran prodrug that is activated by pathogen-specifi c nitroreductases. Using yeast and zebra fish we were able to show that nitrofurans are also bioactivated by host-specifi c aldehyde dehydrogenases suggesting that a combination therapy with an aldehyde dehydrogenase inhibitor might reduce side e ffects associated with nifurtimox.

No description available.

eEF-2K, also known as CaM kinase-III, is an atypical protein kinase which negatively regulates the global rate of protein synthesis through the phosphorylation and inactivation of its substrate eEF-2. Recently eEF-2K has been validated as a novel target for anti-cancer therapy. However, a detailed understanding of the role of eEF-2K in cancer biology is unavailable. Mechanistic studies can often provide an understanding of enzyme function. Therefore, we determined the kinetic mechanism of eEF-2K using a peptide substrate (Acetyl-RKKYKFNEDTERRRFL-amide). We found that eEF-2K adopts a ternary-complex, steady state ordered mechanism, with ATP binding required before the peptide substrate. A good cellular inhibitor is required for elucidating the role of eEF-2K in cancer biology. To date, NH125 is the only inhibitor used to investigate the activity of eEF-2K in cells. Although it is reported as a specific inhibitor of eEF-2K, its exact mode of action has not been reported. Through in-vitro assays and cellular studies, we found that NH125 is a non-specific inhibitor of eEF-2K that blocks eEF-2 phosphorylation in cells. There is a great demand for specific inhibitors of eEF-2K. We developed a fluorescence high throughput assay system for eEF-2K. The assay utilizes the peptide substrate labeled with a Sox moiety whose phosphorylation can be monitored at 485 nm in the presence of magnesium. We also validated the assay in a screen of 30,000 compounds in 384 well plates. We found the assay to be robust and identified a relatively specific inhibitor of eEF-2K and determined its mechanism of action. We found it behaved as a slowly reversible inhibitor of eEF-2K with a two step inhibition mechanism - fast initial binding at the enzyme active site, followed by a slower inactivation step. We propose that the nitrile group on the compound binds to the active site thiol in the enzyme covalently forming a reversible thioimidate adduct to inactivate the enzyme. / text

Breast cancers with overexpression or amplification of the HER2 tyrosine kinase receptor are more aggressive, resistant to chemotherapy, and associated with a worse prognosis. Currently, these breast cancers are treated with the monoclonal antibody trastuzumab (Herceptin®). Unfortunately, not all patients respond to trastuzumab drug therapy; some patients show de novo resistance, while others acquire resistance during treatment. This thesis describes our RNAi studies to identify novel regulators of the HER2 signaling pathway in breast cancer. Three kinome-wide siRNA screens were performed on five HER2 amplified and seven HER2 non-amplified breast cancer cell lines, two normal breast cell lines, as well as two HER2-positive breast cancer cell lines with acquired trastuzumab resistance and their isogenic trastuzumab-sensitive controls. To understand the main kinase drivers of HER2 signaling, we performed a comprehensive screen that selected against growth inhibitors of the non-HER2 amplified breast cancer cell lines. This screen identified the loss of the HER2/HER3 heterodimer as the most prominent selective inhibitor of HER2-amplified breast cancers. In a trastuzumab sensitization screen on five trastuzumab-treated breast cancer cell lines, we identified several siRNA against the PI3K pathway as well as various other signaling pathways that inhibited proliferation. Finally, in a screen for acquired trastuzumab resistance, PKCη and its downstream targets were identified. Loss of PKCη resulted in a decrease in G1/S transition and upregulation of the cyclin dependent kinase inhibitor p27. Initial data suggest that PKCη promotes p27 ubiquitination and degradation. Taken together, these studies provide novel insight into the complex signaling of HER2-positive breast cancers and the mechanisms of resistance to trastuzumab therapy. This work describes how various kinases can modulate cell proliferation, and points to possible novel drug targets for the treatment of HER2-positive breast cancers.

Palmitoylation refers to the covalent attachment of fatty acids, such as palmitate, onto the cysteine residues of proteins. This process may subsequently alter their localization and function. Nearly all of the enzymes that catalyze palmitoylation, zDHHC protein acyl transferases (PATs), are implicated in neurological disorders, infectious diseases, and cancer in humans. Of particular interest to those who study palmitoylation are Ras family GTPas and zDHHC9-GCP16, the zDHHC PAT that palmitoylates Ras proteins. Erf2-Erf4 is the zDHHC PAT that palmitoylates Ras proteins in Saccharomyces cerevisiae. Currently, there are no methods to therapeutically target palmitoylation for the treatment of disease. One of the barriers to identifying a modulator of palmitoylation is the lack of a reliable high-throughput screening system. To date, few assay systems have been developed to examine the kinetics and mechanism of that palmitoylation reaction. This lab has developed a fluorescence-based coupled assay to gain insight into the enzymology, biochemical mechanism, and kinetics of the palmitoylation reaction. This assay may be used to identify specific inhibitors of autopalmitoylation. In the first step of this reaction, the palmitoyl-moiety from palmitoyl-CoA is transferred to the zDHHC9 PAT cysteine side chain to form a palmitoyl:enzyme intermediate. The second step of palmitoylation is the subsequent transfer of the palmitoyl-moiety from the palmitoyl:enzyme intermediate to the cysteine residue of the substrate protein. This fluorescence-based coupled assay was utilized to screen a natural products library and a unique synthetic compound library for inhibitors of Erf2 autopalmitoylation. These screens led to the identification of fungal metabolite extracts and ten bis-cyclic piperazine compounds that inhibit Erf2 autopalmitoylation in the low micromolar range. This effect is similar to known inhibitors of palmitoylation that lack specificity for the palmitoylation reaction itself.

Arenaviruses cause an estimated 300,000 – 500,000 infections annually. Currently there is no arenavirus-specific antiviral drug available to treat these infections. This study sought to use the non-pathogenic New World arenavirus Tacaribe virus (TCRV) as a model for the pathogenic Junin virus (JUNV) and Machupo virus (MACV) that cause haemorrhagic fevers in South America. TCRV was used to explore three different approaches in the search for an antiviral drug against arenavirus infection targeted specifically against the viral nucleoprotein (NP). Of the four expressed arenaviral proteins, NP is the most abundant and is thought to be of multifunctional nature involved in viral replication, suppression of the innate immune system and viral egress. The approaches to find targets for broad-spectrum anti-arenaviral drugs were high throughput screens (HTS) with purified NP using thermal shift assays, exploring the virus interactions with the innate immune system and identifying virus- host protein-protein interactions. HTS resulted in the identification of two small- molecule compounds, [5-(2-Furyl)thien-2-yl]methanol and cyclosporine A (CsA), showing broad-spectrum activity against arenaviruses. Interferon-stimulated genes (ISGs), such as IFIT3, were identified to reduce viral titres and potential 202 protein- interactions between NP and host cell proteins were identified, of which the interaction with apoptosis-inducing factor 1 (AIF1) was described further. To characterise the importance of these interactions as potential drug targets further, a TCRV reverse genetics system was constructed.