The RET receptor tyrosine kinase has essential roles in cell survival, differentiation, and proliferation. Oncogenic activation of RET causes the cancer syndrome multiple endocrine neoplasia type 2 (MEN 2), and is a frequent event in sporadic thyroid carcinomas. Multiple endocrine neoplasia 2B (MEN 2B), a subtype of MEN 2, is caused primarily by a methionine to threonine substitution of residue 918 in the kinase domain of the RET receptor (2B-RET), however the molecular mechanisms that lead to the disease phenotype are unclear. In this study, we show that the M918T mutation causes a 10 fold increase in ATP binding affinity, and leads to a more stable receptor-ATP complex, relative to the wildtype receptor. We also show that 2B-RET can dimerize and become autophosphorylated in the absence of ligand. Our data suggest that multiple distinct but complementary molecular mechanisms underlie the MEN 2B phenotype and provide potential targets for effective therapeutics for this disease. In the second part of the study, we identified a novel β-catenin-RET kinase signaling pathway which is a critical contributor to the development and metastasis of human thyroid carcinoma. We show that RET binds to, and tyrosine phosphorylates, β-catenin and demonstrate that the interaction between RET and β-catenin can be direct and independent of cytoplasmic kinases, such as SRC. As a result of RET-mediated tyrosine phosphorylation, β-catenin escapes cytosolic downregulation by the APC/Axin/GSK3 complex and accumulates in the nucleus, where it can stimulate β-catenin-specific transcriptional programs in a RET-dependent fashion. We show that downregulation of β-catenin activity decreases RET-mediated cell proliferation, colony formation, and tumour growth in nude mice. Finally, we used a structure guided approach to identify and characterize a novel, non-ATP competitive, RET inhibitor; SW-01. We show that SW-01 provides significant RET inhibition in an in vitro kinase assay using purified RET. Moreover, RET phosphorylation is blocked, or dramatically reduced, in vivo in cells overexpressing active RET. We observe a significant decrease in cell proliferation and colony formation in RET-expressing cells in the presence of SW-01. Together, our data suggest that SW-01 has potential as a novel RET kinase inhibitor with clinical utility. / Thesis (Ph.D, Pathology & Molecular Medicine) -- Queen's University, 2008-09-15 16:20:59.976

Heme oxygenases (HO) catalyze the degradation of heme into biliverdin, carbon monoxide (CO) and free iron. The two major isoforms, HO-2 (constitutive) and HO-1 (inducible by various stressors such as heavy metals and reactive oxygen species) are involved in a variety of physiological functions, including anti-inflammation, antiapoptosis, neuromodulation, and vascular regulation. Major tools used in exploring these actions have been metalloporphyrin analogs of heme that inhibit the HOs. However, these tools are limited by their lack of selectivity; they affect other heme-dependent enzymes, such as cytochromes P450 (CYPs), soluble guanylyl cyclase (sGC), and nitric oxide synthase (NOS). Our laboratory has been able to successfully synthesize a series of small molecule non-porphyrin HO inhibitors (QC-xx) that have had little or no effect against sGC and NOS; however, their effects on various CYP isoforms has yet to be fully elucidated. In order to determine the effects on CYP enzyme activity, microsomal preparations of two CYP isoforms (2E1 and 3A1/3A2) were incubated with varying concentrations of HO inhibitor and the activity was determined via spectrophotometric analysis. Results indicated that some QC compounds demonstrated little to no inhibition of CYP2E1 and/or CYP3A1/2, while some others did inhibit these CYP isoforms. Four regions of interest were analyzed further and several structural changes were identified as conferring increased HO inhibition and decreased effect on both CYP2E1 and 3A1/2. Based on the information obtained, three putative compounds were designed and it is hypothesized that these compounds will be selective inhibitors for HO-1 over HO-2 and will display little effect on either CYP2E1 or 3A1/2 activities. / Thesis (Master, Pharmacology & Toxicology) -- Queen's University, 2008-11-20 11:19:48.841

This work presents the investigation of fungal AdoMet-dependent methyltransferases. The first part of the dissertation focuses on two distinct methyltransferases with previously unknown functions in the budding yeast Saccharomyces cerevisiae and the human fungal pathogen Candida albicans. To characterize these enzymes I used a combinatorial approach that exploits contemporary high-throughput techniques available in yeast (chemical genetics, expression, lipid profiling and genetic interaction analysis) combined with rigorous biological follow-up. First, I showed that S. cerevisiae CRG1 (ScCRG1) is a small molecule methyltransferase that methylates cytotoxic drug cantharidin and is important for maintaining lipid homeostasis and actin cytoskeleton integrity in response to small-molecule cantharidin in the baker’s yeast. Similarly to ScCRG1, orf19.633 in the human fungal pathogen C. albicans (CaCRG1) methylates cantharidin and is important for GlcCer biosynthesis. I also demonstrated that CaCrg1 is a ceramide- and PIP-binding methyltransferase involved in Candida’s morphogenesis, membrane trafficking and fungal virulence. Together, the analysis of two genes in yeast illuminated the important roles of the novel small molecule methyltransferases in coupling drug response to lipid biosynthesis and fungal virulence. In the second part of my dissertation, I present the systematic characterization of the genetic architecture of the yeast methyltransferome by examining fitness of double-deletion methyltransferase mutants in standard and under environmental stress conditions. This analysis allowed me to describe specific properties of the methyltransferome network and to uncover functional relationships among methyltransferases inspiring multiple hypotheses and expanding the current knowledge of this family of enzymes.

This work presents the investigation of fungal AdoMet-dependent methyltransferases. The first part of the dissertation focuses on two distinct methyltransferases with previously unknown functions in the budding yeast Saccharomyces cerevisiae and the human fungal pathogen Candida albicans. To characterize these enzymes I used a combinatorial approach that exploits contemporary high-throughput techniques available in yeast (chemical genetics, expression, lipid profiling and genetic interaction analysis) combined with rigorous biological follow-up. First, I showed that S. cerevisiae CRG1 (ScCRG1) is a small molecule methyltransferase that methylates cytotoxic drug cantharidin and is important for maintaining lipid homeostasis and actin cytoskeleton integrity in response to small-molecule cantharidin in the baker’s yeast. Similarly to ScCRG1, orf19.633 in the human fungal pathogen C. albicans (CaCRG1) methylates cantharidin and is important for GlcCer biosynthesis. I also demonstrated that CaCrg1 is a ceramide- and PIP-binding methyltransferase involved in Candida’s morphogenesis, membrane trafficking and fungal virulence. Together, the analysis of two genes in yeast illuminated the important roles of the novel small molecule methyltransferases in coupling drug response to lipid biosynthesis and fungal virulence. In the second part of my dissertation, I present the systematic characterization of the genetic architecture of the yeast methyltransferome by examining fitness of double-deletion methyltransferase mutants in standard and under environmental stress conditions. This analysis allowed me to describe specific properties of the methyltransferome network and to uncover functional relationships among methyltransferases inspiring multiple hypotheses and expanding the current knowledge of this family of enzymes.

There is a need for new antiviral drugs. Especially for the treatment of adenovirus infections, since no approved anti-adenoviral drugs are available. Adenovirus infections in healthy persons are most often associated with respiratory disease, diarrhea and infections of the eye. These infections can be severe, but are most often self-limiting. However, in immunocompromised patients, adenovirus infections are associated with morbidity and high mortality rates. These patients are mainly stem cell or bone marrow transplantation recipients, however solid organ transplantation recipients or AIDS patients may be at risk as well. In addition, children are at higher risk to develop disseminated disease. Due to the need for effective anti-adenoviral drugs, we have developed a cell based screening assay, using a replication-competent GFP expressing adenovirus vector based on adenovirus type 11 (RCAd11GFP). This assay facilitates the screening of chemical libraries for antiviral activity. Using this assay, we have screened 9800 small molecules for anti-adenoviral activity with low toxicity. One compound, designated Benzavir-1, was identified with activity against representative types of all adenovirus species. In addition, Benzavir-1 was more potent than cidofovir, which is the antiviral drug used for treatment of adenovirus disease. By structure-activity relationships analysis (SAR), the potency of Benzavir-1 was improved. Hence, the improved compound is designated Benzavir-2. To assess the antiviral specificity, the activity of Benzavir-1 and -2 on both types of herpes simplex virus (HSV) was evaluated. Benzavir-2 displayed better efficacy than Benzavir-1 and had an activity comparable to acyclovir, which is the original antiviral drug used for therapy of herpes virus infections. In addition, Benzavir-2 was active against acyclovir-resistant clinical isolates of both HSV types. To expand our search for compounds with antiviral activity, we turned to the natural products. An ethyl acetate extract library was established, with extracts derived from actinobacteria isolated from sediments of the Arctic Sea. Using our screening assay, several extracts with anti-adenoviral activity and low toxicity were identified. By activity-guided fractionation of the extracts, the active compounds could be isolated. However, several compounds had previously been characterized with antiviral activity. Nonetheless, one compound had uncharacterized antiviral activity and this compound was identified as a butenolide. Additional butenolide analogues were found and we proposed a biosynthetic pathway for the production of these compounds. The antiviral activity was characterized and substantial differences in their toxic potential were observed. One of the most potent butenolide analogues had minimal toxicity and is an attractive starting point for further optimization of the anti-adenoviral activity. This thesis describes the discovery of novel antiviral compounds that targets adenovirus and HSV infections, with the emphasis on adenovirus infections. The discoveries in this thesis may lead to the development of new antiviral drugs for clinical use.

While hundreds of papers have been published on frustrated Lewis pairs (FLPs) – the combination of bulky Lewis acids and bases which cannot form adducts – few of these use aluminum-based Lewis acids. The research outlined in this thesis expands the small molecule activation chemistry of FLPs to include Al.Combinations of bulky phosphines and AlX3 (X = halide or C6F5) with CO2 leads to the rapid activation to form the complexes R3P(CO2)(AlX3)2 (R = otol, Mes). Subsequent treatment with ammonia borane (AB) results in the rapid reduction of the CO2 fragment to methanol after water quench. Subsequent reactivity studies have established that AB adducts of AlX3, which react with CO2, are key intermediates in this chemistry. Further studies with Mes3P(CO2)(AlX3)2 revealed that these can reduce exogenous CO2 to CO, along with the generation of Mes3P(C(OAlX2)2O)(AlX3) and [Mes3PX][AlX4]. Detailed experimental and theoretical mechanistic investigations outline a possible mechanism involving direct CO2 insertion into free AlX3, followed by nucleophilic attack by PMes3 resulting in the expulsion of CO. Reactions with olefins were also investigated. While addition products of the type R3P(CH2CH2)AlX3 could be obtained with ethylene, C–H bond activation occurred with bulkier olefins. The resulting allyl species underwent subsequent C–C bond forming reactions with other olefins or CO2. Hydrogen was also activated using PR3/AlX3 FLPs to form species of the general formula, [R3PH][(H)(AlX3)2] (X = I, C6F5). These were found to reduce unactivated olefins, generating the redistributed products [R3PH][AlX4] and RAlX2 (R = alkyl). Attempts to circumvent this redistribution and favour alkyl protonation, thus generating a catalytic hydrogenation catalyst, are also discussed. Finally, the activation of N2O was also examined. While addition products could be formed, unexpected aromatic or benzylic C–H bond activation chemistry occurred in the presence of excess Al. A radical reaction pathway is proposed

Three classes of bifunctional compounds related to frustrated Lewis pair chemistry were studied. The first class, alkynyl-linked phosphonium borates, was strategically synthesized and the corresponding neutral alkynyl-linked phosphine boranes generated in solution. They were reacted with THF, alkenes and alkynes to undergo either ring-opening or multiple bond addition reactions, giving rise to zwitterionic macrocycles. In two select alkynyl-linked phosphonium borates, thermolysis resulted in unique rearrangements transforming the phosphino- and boryl-substituted alkynyl moieties into C4 chains. The alkynyl-linked phosphine boranes were further demonstrated to coordinate as η3-BCC ligands in Ni(0) complexes. The rigid nature of the coordination was confirmed by dimerization without cleavage of the Ni–B interaction upon the addition of acetonitrile or carbon monoxide. Moreover, reactions with Al-, Zn- and B-based Lewis acids prompted hydride transfer within the alkynyl-linked phosphonium borate and interesting functional group transfer reactions. The second class of the bifunctional systems, a series of gem-substituted bis-boranes, was subjected to reactions with tBu3P and CO2. The O-linked bis-borane was shown to coordinate the phosphino-carboxylate moiety with one B, while the methylene-linked bis-boranes were demonstrated to chelate the carboxyl group. The third bifunctional system class, vinyl-group tethered boranes, was examined to elucidate the mechanism of the frustrated Lewis pair addition reaction to olefins. Using a bis(pentafluorophenyl)alkylborane, the close proximity of the olefinic protons and the ortho-fluorine nuclei were evident by both NOE measurements and DFT calculations. Moreover, its reactions with phosphine bases suggested that an initial interaction between the highly electrophilic borane and the olefinic fragment precedes such frustrated Lewis pair addition reaction. Furthermore, a bis(pentafluorophenyl)alkoxyborane was synthesized and reacted with P-, N-, C- and H-based nucleophiles, demonstrating the wide range of Lewis bases that can be applied in olefin addition reactions with complementary regioselectivity.

While hundreds of papers have been published on frustrated Lewis pairs (FLPs) – the combination of bulky Lewis acids and bases which cannot form adducts – few of these use aluminum-based Lewis acids. The research outlined in this thesis expands the small molecule activation chemistry of FLPs to include Al.Combinations of bulky phosphines and AlX3 (X = halide or C6F5) with CO2 leads to the rapid activation to form the complexes R3P(CO2)(AlX3)2 (R = otol, Mes). Subsequent treatment with ammonia borane (AB) results in the rapid reduction of the CO2 fragment to methanol after water quench. Subsequent reactivity studies have established that AB adducts of AlX3, which react with CO2, are key intermediates in this chemistry. Further studies with Mes3P(CO2)(AlX3)2 revealed that these can reduce exogenous CO2 to CO, along with the generation of Mes3P(C(OAlX2)2O)(AlX3) and [Mes3PX][AlX4]. Detailed experimental and theoretical mechanistic investigations outline a possible mechanism involving direct CO2 insertion into free AlX3, followed by nucleophilic attack by PMes3 resulting in the expulsion of CO. Reactions with olefins were also investigated. While addition products of the type R3P(CH2CH2)AlX3 could be obtained with ethylene, C–H bond activation occurred with bulkier olefins. The resulting allyl species underwent subsequent C–C bond forming reactions with other olefins or CO2. Hydrogen was also activated using PR3/AlX3 FLPs to form species of the general formula, [R3PH][(H)(AlX3)2] (X = I, C6F5). These were found to reduce unactivated olefins, generating the redistributed products [R3PH][AlX4] and RAlX2 (R = alkyl). Attempts to circumvent this redistribution and favour alkyl protonation, thus generating a catalytic hydrogenation catalyst, are also discussed. Finally, the activation of N2O was also examined. While addition products could be formed, unexpected aromatic or benzylic C–H bond activation chemistry occurred in the presence of excess Al. A radical reaction pathway is proposed

One of the largest problems in current medicine is the shortage of organs for transplant due to technological limitations in the storage of organs for any length of time. A possible solution to this problem would involve cryopreservation. However, current cryopreservatives such as sucrose or DMSO have concerning cytotoxic issues that limit their possible applications. A major cause of cryoinjury is the uncontrolled recrystallization of inter and intra-cellular ice crystals that occurs during the thawing process leading to mechanical damage and dehydration. The Ben lab has thus been interested in the design of compounds that are capable of inhibiting this process but do not possess other undesirable properties found in the native compounds. These synthetic analogues have been shown to increase cellular viability post-thaw. A series of mixed α/β glycopeptides are prepared and analyzed for antifreeze properties. The results of this study imply that it is not the gross conformation of the glycopeptide that is responsible for activity, but rather that intramolecular relationships may be responsible for disrupting the reorganization of ice. A technique was devised for the incorporation of triazoles into the analogues to investigate the importance of the linker and to greatly simplify the synthesis of a library of glycoconjugates. It was found that the IRI activity of glycopeptides is very sensitive to the distance between carbohydrate and peptide backbone. The electron density at the anomeric oxygen is an important parameter with respect to intramolecular networks. A series of substituted galactosides is presented that modify the electronics of the anomeric oxygen. The results demonstrate that decreasing electron density at this position appears to improve IRI activity in a predictable manner. To better understand the remarkable IRI activity of a key analogue, it was systematically truncated. This study led to the serendipitous discovery of a series of very highly IRI active analogues that do not contain a peptide backbone. These compounds represent the first non-glycopeptides that can show very significant IRI activity even at very low concentrations. The final portion of the thesis reports the efforts towards the preparation of a carbasugar analogue of AFGP-8.

The thesis topic entitled above involves the use of small molecules as a general means to drive nucleic acid assembly and structural transitions. We have shown that coralyne, a crescent-shaped small molecule, can assemble homo-adenine DNA and RNA sequences into anti-parallel duplexes at neutral pH, a structure containing putative purine-purine (A*A) base pairs that is otherwise unstable. The importance of the structure of the small molecule in the recognition and stabilization of A*A base pairing has been established by experimental evidence. We further provide structural evidence for the putative A*A base pairing that is stabilized by coralyne and molecules of similar size and shape. Our hypothesis that planar molecules that are slightly too large to intercalate Watson-Crick base pairs might intercalate the larger purine-purine base pairs has led to the design of a new class of small molecules that tightly bind purine-purine duplexes with excellent selectively. We have demonstrated that azacyanines can exhibit strong and selective association with a human telomeric sequence that forms a unimolecular G-quadruplex in solution. The synthetic accessibility of azacyanines makes this class of molecules amenable to library preparation for high-throughput screening. Together, the findings reported in this thesis provide further evidence for the robust and versatile nature of selective small molecule recognition of nucleic acids, especially purine-purine duplexes.