Investigation of additive effects in enantioselective copper-catalysed C-H insertion and aromatic addition reactions of α-diazocarbonyl compounds

Significant enhancements in enantioselectivities and reaction efficiencies in asymmetric copper-catalysed C-H insertion and aromatic addition reactions of α-diazocarbonyl compounds in the presence of various group I salts are reported. For the first time in carbenoid chemistry, evidence for the critical role of the metal cation is described.

Structural and Biochemical Dissection of the Trehalose Biosynthetic Complex in Pathogenic Fungi

Trehalose is a non-reducing disaccharide essential for pathogenic fungal survival and virulence. The biosynthesis of trehalose requires the trehalose-6-phosphate synthase, Tps1, and trehalose-6-phosphate phosphatase, Tps2. More importantly, the trehalose biosynthetic pathway is absent in mammals, conferring this pathway as an ideal target for antifungal drug design. However, lack of germane biochemical and structural information hinders antifungal drug design against these targets.

In this dissertation, macromolecular X-ray crystallography and biochemical assays were employed to understand the structures and functions of proteins involved in the trehalose biosynthetic pathway. I report here the first eukaryotic Tps1 structures from Candida albicans (C. albicans) and Aspergillus fumigatus (A. fumigatus) with substrates or substrate analogs. These structures reveal the key residues involved in substrate binding and catalysis. Subsequent enzymatic assays and cellular assays highlight the significance of these key Tps1 residues in enzyme function and fungal stress response. The Tps1 structure captured in its transition-state with a non-hydrolysable inhibitor demonstrates that Tps1 adopts an “internal return like” mechanism for catalysis. Furthermore, disruption of the trehalose biosynthetic complex formation through abolishing Tps1 dimerization reveals that complex formation has regulatory function in addition to trehalose production, providing additional targets for antifungal drug intervention.

I also present here the structure of the Tps2 N-terminal domain (Tps2NTD) from C. albicans, which may be involved in the proper formation of the trehalose biosynthetic complex. Deletion of the Tps2NTD results in a temperature sensitive phenotype. Further, I describe in this dissertation the structures of the Tps2 phosphatase domain (Tps2PD) from C. albicans, A. fumigatus and Cryptococcus neoformans (C. neoformans) in multiple conformational states. The structures of the C. albicans Tps2PD -BeF3-trehalose complex and C. neoformans Tps2PD(D24N)-T6P complex reveal extensive interactions between both glucose moieties of the trehalose involving all eight hydroxyl groups and multiple residues of both the cap and core domains of Tps2PD. These structures also reveal that steric hindrance is a key underlying factor for the exquisite substrate specificity of Tps2PD. In addition, the structures of Tps2PD in the open conformation provide direct visualization of the conformational changes of this domain that are effected by substrate binding and product release.

Last, I present the structure of the C. albicans trehalose synthase regulatory protein (Tps3) pseudo-phosphatase domain (Tps3PPD) structure. Tps3PPD adopts a haloacid dehydrogenase superfamily (HADSF) phosphatase fold with a core Rossmann-fold domain and a α/β fold cap domain. Despite lack of phosphatase activity, the cleft between the Tps3PPD core domain and cap domain presents a binding pocket for a yet uncharacterized ligand. Identification of this ligand could reveal the cellular function of Tps3 and any interconnection of the trehalose biosynthetic pathway with other cellular metabolic pathways.

Combined, these structures together with significant biochemical analyses advance our understanding of the proteins responsible for trehalose biosynthesis. These structures are ready to be exploited to rationally design or optimize inhibitors of the trehalose biosynthetic pathway enzymes. Hence, the work described in this thesis has laid the groundwork for the design of Tps1 and Tps2 specific inhibitors, which ultimately could lead to novel therapeutics to treat fungal infections.

Design of Antibacterial Prochelators to Target Drug-Resistant Bacteria

Transition metals such as iron and copper are valued in biology for their redox activities because they are able to access various oxidation states. However, these transition metals are also implicated in a number of human disease states and play a role in bacterial infections. The ability to manipulate and monitor metal ions has vast implications on the fields of biology and human health. As such, the research described here covers two related goals: to manipulate metals in specific biological circumstances and to visualize this disturbance in cellular metal homeostasis.

Antibiotic resistance necessitates the development of drugs that exploit new mechanisms of action such as the disruption of metal homeostasis. In order to manipulate metals at the site of bacterial infection, two prochelators were developed around a β-lactam core such that the active chelator is released in the presence of bacteria that produce the resistance-causing β-lactamase enzyme. Both prochelators display enhanced activity toward resistant bacteria compared to clinical antibiotics.

Fluorescent sensors are a powerful tool for detecting small concentrations of biological analytes. Two analogs of a ratiometric fluorescent sensor were designed and synthesized to monitor cellular concentrations of copper and iron. These sensors were found to operate as designed in vitro; however the fluorescence intensity necessary for quantification of cellular metal pools has not yet been achieved.

Discovery and Characterization of a Novel Fatty Acid Synthase Inhibitor with Antineoplastic Activity against Breast Cancer

During oncogenesis, cancer cells go through metabolic reprogramming to maintain their high growth rates and adapt to changes in the microenvironment and the lack of essential nutrients. Several types of cancer are dependent on de novo fatty acid synthesis to sustain their growth rates by providing precursors to construct membranes and produce vital signaling lipids. Fatty acid synthase (FASN) catalyze the terminal step of de novo fatty acid synthesis and it is highly expressed in many types of cancers where it’s up-regulation is correlated with cancer aggressiveness and low therapeutic outcome. Many FASN inhibitors were developed and showed potent anticancer activity however, only one inhibitor advanced to early stage clinical trials with some dose limiting toxicities. Using a modified fluorescence-linked enzyme chemoproteomic strategy (FLECS) screen, we identified HS-106, a thiophenopyrimiden FASN inhibitor that has anti-neoplastic activity against breast cancer in vitro and in vivo. HS-106 was able to inhibit both; purified human FASN activity and cellular fatty acid synthesis activity as evaluated by radioactive tracers incorporation into lipids experiments. In proliferation and apoptosis assays, HS-106 was able to block proliferation and induce apoptosis in several breast cancer cell lines. Several rescue experiment and global lipidome analysis were performed to probe the mechanism by which HS-106 induces apoptosis. HS-106 was found to induce several changes in lipids metabolism: (i) inhibit fatty acids synthesis. (ii) Inhibit fatty acids oxidation as indicated by the ability of inhibiting Malonyl CoA accumulation to block HS-106 induced apoptosis and the increase in the abundance of ceramides. (iii) Increase fatty acids uptake and neutral lipids formation as confirmed 14C Palmitate uptake assay and neutral lipids staining. (iv)Inhibit the formation of phospholipids by inhibiting de novo fatty acid synthesis and diverting exogenous fatty acids to neutral lipids. All of these events would lead to disruption in membranes structure and function. HS-106 was also tested in Lapatinib resistant cell lines and it was able to induce apoptosis and synergizes Lapatinib activity in these cell lines. This may be due the disruption of lipid rafts based on the observation that HS-106 reduces the expression of both HER2 and HER3. HS-106 was found to be well tolerated and bioavailable in mice with high elimination rate. HS-106 efficacy was tested in MMTV neu mouse model. Although did not significantly reduced tumor size (alone), HS-106 was able to double the median survival of the mice and showed potent antitumor activity when combined with Carboplatin. Similar results were obtained when same combinations and dosing schedule was used in C3Tag mouse model except for the inability of HS-106 affect mice survival.

From the above, HS-106 represent a novel FASN inhibitor that has anticancer activity both in vivo and in vitro. Being a chemically tractable molecule, the synthetic route to HS-106 is readily adaptable for the preparation of analogs that are similar in structure, suggesting that, the pharmacological properties of HS-106 can be improved.

Amélioration des propriétés pharmacocinétiques de peptides par différentes alkylations N-terminales

Modélisations moléculaires réalisés avec le logiciel HyperChem 8.

Rockmagnetic investigations of IODP Site U1302-U1303

Integrated Ocean Drilling Program (IODP) Sites U1302-U1303, drilled on the SE flank of Orphan Knoll (Labrador Sea), preserve a record of detrital layers and other proxies of hydrographic change that extend the record of ice-sheet/ocean interactions through most of the Brunhes Chron. The age model is built by tandem matching of relative paleointensity (RPI) and oxygen isotope data (d18O) from Neogloboquadrina pachyderma (sin.) to reference records, indicating a mean Brunhes sedimentation rate of 14 cm/kyr. Sedimentation back to marine isotope stage (MIS) 18 is characterized by detrital layers that are detected by higher than background gamma-ray attenuation (GRA) density, peaks in X-ray fluorescence (XRF) indicators for detrital carbonate (Ca/Sr) and detrital silicate (Si/Sr), and an ice-rafted debris (IRD) proxy (wt.% >106 µm). The age model enables correlation of Site U1302/03 to IODP Site U1308 in the heart of the central Atlantic IRD belt where an age model and a similar set of detrital-layer proxies have already been derived. Ages of Heinrich (H) layers H1, H2, H4, H5 and H6 are within ~2 kyr at the two sites (H0, H3 and H5a are not observed at Site U1308), and agree with previous work at Orphan Knoll within ~3 kyr. At Site U1308, Brunhes detrital layers are restricted to peak glacials and glacial terminations back to marine isotope stage (MIS) 16 and have near-synchronous analogs at Site U1302/03. Detrital layers at Site U1302/03 are distributed throughout the record in both glacial and most interglacial stages. We distinguish Heinrich-like layers associated with IRD from detrital layers marked by multiple detrital-layer proxies (including Ca/Sr) but usually not associated with IRD, that may be attributed to lofted sediment derived from drainage and debris-flow events funneled down the nearby Northwest Atlantic Mid-Ocean Channel (NAMOC). The prominent detrital layers at Sites U1302/03 and U1308 can be correlated to millennial scale features in the Chinese speleothem (monsoon) record over the last 400 kyr, implying a link between monsoon precipitation and Laurentide Ice Sheet (LIS) instability. The detrital-layer stratigraphy at Site U1302/03 provides a long record of LIS dynamics against which other terrestrial and marine records can be compared.

Lithic grain and mineral composition of sand and sandstones from the North Pacific Ocean and the Bering Sea (Table 3)

Sand and sandstone compositions from different types of basins reflect provenance terranes governed by plate tectonics. One hundred and one thin sections of Upper Miocene to Holocene sand-sized material were examined from DSDP/IPOD Sites in the North Pacific Ocean and the Bering Sea. The Gazzi-Dickinson point-counting method was used to establish compositional characteristics of sands from different tectonic settings. Continental margin forearc sands from the western North America continental margin arc system are clearly different from backarc/marginal-sea sands from the Aleutian intraoceanic arc system. The forearc sands have average QFL percentages of 29-42-29, LmLvLst percentages of 32-34-34, 3 Fmwk%M and 0.82 P/F. Aleutian backarc sands have average QFL percentages of 8-22-69. LmLvLst percentages of 9-85-6, 0.5 Fmwk%M and 0.96 P/F. A trend of increasing QFL%Q and decreasing LmLvLst%Lv westward in the backarc region of the Aleutian Ridge reflects the influence of the Asiatic continental margin. Aleutian backarc sands without continental influence have average QFL percentages of 1-20-79, LmLvLst percentages of 1-98-1, 0 Fmwk%M and 0.99 P/F. Of the continental margin forearc samples, sands on the Astoria Fan (west of the Oregon-Washington trench) contain the highest LmLvLst%Lv and lowest P/F; sands from mixed transform-fault and trench settings (Delgada Fan and Gulf of Alaska samples) have slightly higher Qp/Q (0.03); and sands from the Pacific-Juan de Fuca-North America triple junction have the highest Fmwk%M. Delgada Fan and Gulf of Alaska sands have average QFL percentages of 27-38-35, LmLvLst percentages of 37-26-37, 2 Fmwk%M and 0.86 P/F. Astoria Fan sands have average QFL percentages of 35-41-24, LmLvLst percentages of 30-47-23, 3 Fmwk%M and 0.74 P/F. The triple-junction sands have average QFL percentages of 28-59-13, LmLvLst percentages of 25-26-49, 9 Fmwk%M and 0.87 P/F. The petrologic data from the modern ocean basins examined in this study can provide useful analogs for interpretation of ancient oceanic sequences. Our data suggest some refinements of, but generally substantiate, existing petrologic models relating sandstone composition to tectonic setting.

THE DESIGN AND SYNTHESIS OF SILOXANE PRECURSORS FOR CHIRAL PERIODIC MESOPOROUS ORGANOSILICA MATERIALS

The development of cost-effective and reliable methods for the synthesis and separation of asymmetric compounds is paramount in helping to meet society’s ever-growing demand for chiral small molecules. Of these methods, chiral heterogeneous supports are particularly appealing as they allow for the reuse of the chiral source. One such support, based on the synergy between chiral organic units and structurally stable inorganic silicon scaffolds are periodic mesoporous organosilicas (PMOs). In the work described herein, I examine some of the factors governing the transmission of chirality between chiral dopants and prochiral bulk phases in chiral PMO materials. In particular, the exploration of 1,1’-binaphthalene-bridged chiral dopants with a focus on the point of attachment into the materials. Moreover, the effects of ordering in the materials are examined and reveal that chirality transfer is more facile in materials with molecular-scale order then those containing amorphous walls. Secondly, the issues surrounding the synthesis and purification of aryl-triethoxysilanes as siloxane precursors are addressed. Both the introduction of a two-carbon linker and the direct attachment of allyl and mixed allyldiethoxysilane species are explored. This work demonstrates that allyldiethoxysilanes are ideal, in that they are stable enough to permit facile synthesis, while still being able to hydrolyze completely to produce well-ordered materials. Lastly, the production of new bulk phases for chiral PMO materials is examined by introducing new prochiral nitrogen-containing siloxane precursors. Biphenyldiamine and bipyridine-bridged siloxane precursors are readily synthesized on reasonable scales. Their use as the bulk siloxane precursor in the production of PMO materials however, is precluded by insufficient gelation and additional siloxane precursors are necessary for the production of ordered materials. In addition to the research detailed above that forms the body of this thesis, two short works are appended. The first details the production of polythiophene assemblies mediated through coordination nanospaces, while the second explores the production of N-heterocyclic carbene functionalized gold nanoparticles through ligand exchange.

Design and Implementation of Tools for STM Studies in UHV and at the Solid-Liquid Interface

This thesis presents details of the design and development of novel tools and instruments for scanning tunneling microscopy (STM), and may be considered as a repository for several years' worth of development work. The author presents design goals and implementations for two microscopes. First, a novel Pan-type STM was built that could be operated in an ambient environment as a liquid-phase STM. Unique features of this microscope include a unibody frame, for increased microscope rigidity, a novel slider component with large Z-range, a unique wiring scheme and damping mechanism, and a removable liquid cell. The microscope exhibits a high level of mechanical isolation at the tunnel junction, and operates excellently as an ambient tool. Experiments in liquid are on-going. Simultaneously, the author worked on designs for a novel low temperature, ultra-high vacuum (LT-UHV) instrument, and these are presented as well. A novel stick-slip vertical coarse approach motor was designed and built. To gauge the performance of the motor, an in situ motion sensing apparatus was implemented, which could measure the step size of the motor to high precision. A new driving circuit for stick-slip inertial motors is also presented, that o ffers improved performance over our previous driving circuit, at a fraction of the cost. The circuit was shown to increase step size performance by 25%. Finally, a horizontal sample stage was implemented in this microscope. The build of this UHV instrument is currently being fi nalized. In conjunction with the above design projects, the author was involved in a collaborative project characterizing N-heterocyclic carbene (NHC) self-assembled monolayers (SAMs) on Au(111) films. STM was used to characterize Au substrate quality, for both commercial substrates and those manufactured via a unique atomic layer deposition (ALD) process by collaborators. Ambient and UHV STM was then also used to characterize the NHC/Au(111) films themselves, and several key properties of these films are discussed. During this study, the author discovered an unexpected surface contaminant, and details of this are also presented. Finally, two models are presented for the nature of the NHC-Au(111) surface interaction based on the observed film properties, and some preliminary theoretical work by collaborators is presented.

Anticipating climate-induced changes to forest cover in Ontario and the implications for future bioenergy development

Climate change is expected to have marked impacts on forest ecosystems. In Ontario forests, this includes changes in tree growth, stand composition and disturbance regimes, with expected impacts on many forest-dependent communities, the bioeconomy, and other environmental considerations. In response to climate change, renewable energy systems, such as forest bioenergy, are emerging as critical tools for carbon emissions reductions and climate change mitigation. However, these systems may also need to adapt to changing forest conditions. Therefore, the aim of this research was to estimate changes in forest growth and forest cover in response to anticipated climatic changes in the year 2100 in Ontario forests, to ultimately explore the sustainability of bioenergy in the future. Using the Haliburton Forest and Wildlife Reserve in Ontario as a case study, this research used a spatial climate analog approach to match modeled Haliburton temperature and precipitation (via Fourth Canadian Regional Climate Model) to regions currently exhibiting similar climate (climate analogs). From there, current forest cover and growth rates of core species in Haliburton were compared to forests plots in analog regions from the US Forest Service Forest Inventory and Analysis (FIA). This comparison used two different emission scenarios, corresponding to a high and a mid-range emission future. This research then explored how these changes in forests may influence bioenergy feasibility in the future. It examined possible volume availability and composition of bioenergy feedstock under future conditions. This research points to a potential decline of softwoods in the Haliburton region with a simultaneous expansion of pre-established hardwoods such as northern red oak and red maple, as well as a potential loss in sugar maple cover. From a bioenergy perspective, hardwood residues may be the most feasible feedstock in the future with minimal change in biomass availability for energy production; under these possible conditions, small scale combined heat and power (CHP) and residential pellet use may be the most viable and ecologically sustainable options. Ultimately, understanding the way in which forests may change is important in informing meaningful policy and management, allowing for improved forest bioenergy systems, now and in the future.

Lipoprotein-associated phospholipase A2 (Lp-PLA2) as a therapeutic target to prevent retinal vasopermeability during diabetes

Lipoprotein-associated phospholipase A2 (Lp-PLA2) hydrolyses oxidized low-density lipoproteins into proinflammatory products, which can have detrimental effects on vascular function. As a specific inhibitor of Lp-PLA2, darapladib has been shown to be protective against atherogenesis and vascular leakage in diabetic and hypercholesterolemic animal models. This study has investigated whether Lp-PLA2 and its major enzymatic product, lysophosphatidylcholine (LPC), are involved in blood-retinal barrier (BRB) damage during diabetic retinopathy. We assessed BRB protection in diabetic rats through use of species-specific analogs of darapladib. Systemic Lp-PLA2 inhibition using SB-435495 at 10 mg/kg (i.p.) effectively suppressed BRB breakdown in streptozotocin-diabetic Brown Norway rats. This inhibitory effect was comparable to intravitreal VEGF neutralization, and the protection against BRB dysfunction was additive when both targets were inhibited simultaneously. Mechanistic studies in primary brain and retinal microvascular endothelial cells, as well as occluded rat pial microvessels, showed that luminal but not abluminal LPC potently induced permeability, and that this required signaling by the VEGF receptor 2 (VEGFR2). Taken together, this study demonstrates that Lp-PLA2 inhibition can effectively prevent diabetes-mediated BRB dysfunction and that LPC impacts on the retinal vascular endothelium to induce vasopermeability via VEGFR2. Thus, Lp-PLA2 may be a useful therapeutic target for patients with diabetic macular edema (DME), perhaps in combination with currently administered anti-VEGF agents.

Biallelic ATM inactivation significantly reduces survival in patients treated on the United Kingdom Leukemia Research Fund Chronic Lymphocytic Leukemia 4 trial.

PURPOSE: The prognostic significance of ATM mutations in chronic lymphocytic leukemia (CLL) is unclear. We assessed their impact in the context of a prospective randomized trial. PATIENTS AND METHODS: We analyzed the ATM gene in 224 patients treated on the Leukemia Research Fund Chronic Lymphocytic Leukemia 4 (LRF-CLL4) trial with chlorambucil or fludarabine with and without cyclophosphamide. ATM status was analyzed by denaturing high-performance liquid chromatography and was related to treatment response, survival, and the impact of TP53 alterations for the same patient cohort. RESULTS: We identified 36 ATM mutations in 33 tumors, 16 with and 17 without 11q deletion. Mutations were associated with advanced disease stage and involvement of multiple lymphoid sites. Patients with both ATM mutation and 11q deletion showed significantly reduced progression-free survival (median, 7.4 months) compared with those with ATM wild type (28.6 months), 11q deletion alone (17.1 months), or ATM mutation alone (30.8 months), but survival was similar to that in patients with monoallelic (6.7 months) or biallelic (3.4 months) TP53 alterations. This effect was independent of treatment, immunoglobulin heavy chain variable gene (IGHV) status, age, sex, or disease stage. Overall survival for patients with biallelic ATM alterations was also significantly reduced compared with those with ATM wild type or ATM mutation alone (median, 42.2 v 85.5 v 77.6 months, respectively). CONCLUSION: The combination of 11q deletion and ATM mutation in CLL is associated with significantly shorter progression-free and overall survival following first-line treatment with alkylating agents and purine analogs. Assessment of ATM mutation status in patients with 11q deletion may influence the choice of subsequent therapy.

Lead: Inorganic Chemistry

The article covers basic inorganic chemistry of lead. As an introduction, the properties and historical uses of metallic lead are discussed, followed by aspects of lead toxicity, including the toxicity origins and effects of lead poisoning. Properties of lead as a heavy p-block element are discussed, with emphasis on the modern view of the so-called “inert pair effect”, including its origin, the influence on stability of lead oxidation states, and on the coordination chemistry of lead(II), viz., “sterically active lone pair”. This is followed by an overview of lead inorganic compounds, including halides, pseudohalides, oxides and chalcogenides, hydroxides and their chalcogenide analogs, alkoxides, oxoacids, O-donors, S- and Se-donors, Group 15 donors, compounds with lead-transition metal bonds, and finally metallic clusters (Zintl phases). This is by no means a comprehensive review, rather compounds representative for each class were presented. In most sections, structural aspects of each class of compounds are discussed, followed by applications, with the focus on modern uses in material science.

Electrophysiological effects of guanosine and MK-801 in a quinolinic acid-induced seizure model

TORRES, F ; FILHO, M.S. ; ANTUNES, C. ; KALININE, E. ; ANTONIOLLI, E. ; PORTELA, Luis Valmor ; SOUZA, Diogo Onofre ; TORT, A. B. L. . Electrophysiological effects of guanosine and MK-801 in a quinolinic acid-induced seizure model. Experimental Neurology , v. 221, p. 296-306, 2010

Développement d'une méthode de prédiction de l'orientation et de l'insertion des protéines dans une membrane modèle

Les protéines membranaires intégrales jouent un rôle indispensable dans la survie des cellules et 20 à 30% des cadres de lectures ouverts codent pour cette classe de protéines. La majorité des protéines membranaires se trouvant sur la Protein Data Bank n’ont pas une orientation et une insertion connue. L’orientation, l’insertion et la conformation que les protéines membranaires ont lorsqu’elles interagissent avec une bicouche lipidique sont importantes pour la compréhension de leur fonction, mais ce sont des caractéristiques difficiles à obtenir par des méthodes expérimentales. Des méthodes computationnelles peuvent réduire le temps et le coût de l’identification des caractéristiques des protéines membranaires. Dans le cadre de ce projet de maîtrise, nous proposons une nouvelle méthode computationnelle qui prédit l’orientation et l’insertion d’une protéine dans une membrane. La méthode est basée sur les potentiels de force moyenne de l’insertion membranaire des chaînes latérales des acides aminés dans une membrane modèle composèe de dioléoylphosphatidylcholine.