Digital Commons Network^™

Metalloglycomics: Investigating The Interactions Of Metal Complexes With Heparan Mimetics, Wyatt Johnson

Theses and Dissertations

Proteoglycans containing Heparan Sulfate (HS), a sulfated glycosaminoglycan (GAG), play a major role in the cell signaling process, interacting with many different proteins. HS is over expressed on the surface of many cancer cells. Enzymatic cleavage of HS-GAGs by heparanase causes release of angiogenic growth factors leading to tumor cell migration. Heparanase is also over-expressed in tumors with significant correlation between metastatic potential and heparanase activity. Proteoglycans and their associated enzymes are thus significant drug targets of high biological relevance.

A functional consequence of strong PPC-HS binding has been shown in proof-of-concept studies confirming inhibition of the model pentasaccharide, Fondaparinux, …

Environmental Forensics Study Of Crude Oil And Petroleum Product Spills In Coastal And Oilfield Settings: Combined Insights From Conventional Gc-Ms, Thermodesorption-Gc-Ms And Pyrolysis-Gc-Ms, Michael A. Kruge, José Luis Gallego, Azucena Lara-Gonzalo, Noemi Esquinas

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

A representative set of five oil spill samples from four different regions displayed different product characteristics and different levels of weathering. Three of them were taken along shorelines affected by marine oil spill events, viz., Aboño and Prestige (Spain) and Deepwater Horizon (USA) and the other two were taken at inland oil spill sites (Angola and Kuwait). A multi-faceted environmental forensics approach revealed key molecular features. In addition to the conventional GC/MS analysis of saturated and aromatic fractions, the polar fractions also were analyzed, revealing a complex series of linear alkanones in those oil samples particularly enriched in aliphatics. Thermodesorption-GC-MS …

Progress Toward Controlled Disulfide Formation To Access Neuroactive Conotoxins, Thilini Kondasinghe

Wayne State University Dissertations

"Conotoxins are mini proteins isolated from marine snails of the Conus family. They have shown activity in the selective inhibition of various ion channels. Therefore, they present an opportunity as possible therapy for a myriad of neurological ailments. The synthesis of conotoxins would enable both biological studies and evaluation of these structures as lead targets for therapeutics. However, establishing a reliable method to consistently folding disulfide rich proteins, including conotoxin, into their native structure has been challenging over few decades. In this research project, it is shown the progress towards a mild, efficient, and broadly applicable methods to generate the …

Carbohydrate-Based Inducers Of Cellular Stress For Targeting Cancer Cell Metabolism, Fidelis Ndombera

Wayne State University Dissertations

ABSTRACT

CARBOHYDRATE-BASED INDUCERS OF CELLULAR STRESS FOR TARGETING CANCER CELL METABOLISM

by

FIDELIS TOLOYI NDOMBERA

May 2018

Advisor: Dr. Young-Hoon Ahn

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

Metabolic reprogramming and redox control of cancer cells is vital for their proliferation, but also provides selective strategies for treating cancer. Increased generation of reactive oxygen species (ROS) and an intricate control of redox status in cancer cells relative to normal cells provide a basis for designing ROS-inducing anticancer agents. In my work, I designed, synthesized and evaluated carbohydrate-based small molecules for ROS-generation, cytotoxicity and redox signaling and stress response. Our data …

Biophysical Studies Of Guanine Nucleotide-Binding Alpha Subunits, Brian Leverson

Dissertations

Guanine nucleotide-binding (G?) proteins have been intensely studied over the years due to their role as signal transduction proteins. Proper function depends on three flexible switch regions that are involved in the relatively slow hydrolysis of GTP, allowing for the proteins to act as a molecular on/off switch. The structure of a protein is essential to its biological function. Occurrences of mutations in the genes GNAS and GNAI1 to highly conserved arginine residue in the switch II region have been detected in several types of cancers.

Utilizing the combinations of temperature denaturation, kinetics assays, and molecular dynamics, we plan to …

Application Of Synthetic Organic And Medicinal Chemistry Toward Medical Advances In Cancer, Antibiotics, And Drug Delivery, Marlon Lutz

Dissertations

Cancer and bacterial infections are a great concern in our society and have affected populations worldwide. The objective of this research was to discover new therapies for treating bacterial infections and cancer, and for promoting drug delivery.

DapE is an essential component in succinylase biosynthetic pathway, which is critical to production of lysine and m-DAP which both are essential in protein synthesis and bacterial peptidoglycan cell wall construction. Synthetic approaches were developed to prepare a new substrate for the N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) enzyme enabling the discovery of new antibiotics that inhibit DapE.

MMPs are over expressed in cancer, in …

Determining Atg11'S Binding Interactions Using A Yeast Two Hybrid System And Directed Mutagenesis, Jesse Smith

Senior Honors Theses and Projects

Autophagy is a mechanism of intracellular degradation within eukaryotes. Because of its aid to a cells longevity, autophagy is believed to be important for the prevention of neurodegenerative diseases. Autophagy related protein 11 (Atg11) is a coiled-coil scaffolding protein required for selective autophagy in yeast. Atg11 is known to interact with Atg1, Atg20, and Atg29, in addition to connecting cargo molecules prApel -Atg19 to the phagophore assembly site. In addition to its many functions within yeast autophagy, Atg11 has two human homologs: Huntingtin protein and FIP200. This homology encourages us to gain a further understanding of Atg11's binding sites. In …

Synthesis And Catalytic Testing Of A Proline Functionalized Amphiphilic Block Copolymer, Eric Firestone

Master's Theses and Doctoral Dissertations

Catalysts are reagents used to reduce the amount of energy that a reaction needs to execute, allowing it to proceed at a higher rate while not being consumed. The use of catalyst functionalized amphiphilic copolymer allows easier recovery of the catalyst at the end of the synthesis and allows for the reaction. In water, under appropriate conditions, the amphiphilic block copolymers will form micelles and allow the reaction to occur on the interior of the micelle. The synthesis of amphiphilic copolymer with a hydrophobic O-methacryloyl-trans-4- hydroxy-L-proline and methyl methacrylate end and a hydrophilic acrylic acid end was characterized. The polymer …

A Lc-Ms/Ms-Based Method For The Multiplex Detection Of 24 Fentanyl Analogs And Metabolites In Whole Blood At Sub Ng Ml-1 Concentrations, Kraig Edward Strayer

Browse all Theses and Dissertations

The United States and numerous other countries worldwide are currently experiencing a public health crisis due to the abuse of illicitly manufactured fentanyl (IMF) and its analogues. This manuscript describes the development of a liquid chromatography-tandem mass spectrometry-based method for the multiplex detection of N = 24 IMF analogues and metabolites in whole blood at concentrations as low as 0.1-0.5 ng mL-1. These available IMFs were fentanyl, norfentanyl, furanyl norfentanyl, remifentanil acid, butyryl norfentanyl, remifentanil, acetyl fentanyl, alfentanil, AH-7921, U-47700, acetyl fentanyl 4-methylphenethyl, acrylfentanyl, para-methoxyfentanyl, despropionyl fentanyl (4-ANPP), furanyl fentanyl, despropionyl para-fluorofentanyl, carfentanil, (±)-cis-3-methyl fentanyl, butyryl fentanyl, isobutyryl fentanyl, sufentanil, …

Synthesis, Characterization And Molecular Dynamic Simulations Of Aqueous Choline Chloride Deep Eutectic Solvents, Sampson Asare

Electronic Theses and Dissertations

Various forms of deep eutectic solvents have been synthesized with advantages of 100% atom economy, low vapor pressure, ease of preparation, cost efficiency, low toxicity, and tunability. Though several DESs have been synthesized and characterized, including binary and ternary solvents, none of the binary DESs have been formulated with water as the sole hydrogen bond donor(HBD). This is due to a couple of opinions. First, water is disruptive to the eutectic bond in tertiary DES. Secondly, the ubiquity and concentration of water even in natural systems have led to the assertion that a solution rather than a eutectic solvent will …

A Comprehensive Analysis Of Aromatic-Proton Mediated Hydrogen Bonds, Mona S. Alshamrani

Electronic Theses and Dissertations

Hydrogen bonds play critical role in folding, structure and recognition of biological macromolecules (e.g., proteins, RNA, DNA). In addition to classical hydrogen bonds (e.g., ─OH---O=, ─OH---O─, ─NH---O─ etc.), structural analysis of protein and nucleic acids, almost a decade ago, showed that hydrogen bonds (e.g., CH---O) with hydrogen atoms on aliphatic carbon atoms (hereafter, aliphatic-protons) also play very important role in the structure and function of biomolecules. Even though, protons of aromatic ring systems (hereafter, aromatic-protons) are more polar than the aliphatic-protons, systematic analysis of hydrogen bonds of aromatic-protons have not been carried out. Therefore, I carried out a systematic analysis …

Development Of A High Performance Liquid Chromatography Method For The Analysis Of Next-Generation Cyanide Antidote, 3-Mercaptopyruvate, In Plasma, Elaf Alzhrani

Electronic Theses and Dissertations

Although the current FDA approved cyanide antidotes (i.e., sodium nitrite, sodium thiosulfate, and hydoxocoboalamine) are effective for treating cyanide poisoning, each individual antidote has major limitations, including large effective dosage, delayed onset of action, or dependence on enzymes generally confined to specific organs. To overcome these current limitations, next-generation cyanide antidotes are being investigated, including 3-mercaptopyruvate (3-MP). Analytical methods capable of detecting 3-MP from plasma are essential for the development of 3-MP as a nextgeneration cyanide antidote. Although 3-MP has been analyzed by LC-MS-MS, this instrument is not widely available. Therefore, a high performance liquid chromatography (HPLC) method with fluorescence …

Molecular Level Encapsulation Of Chromophores Using Pillar[5]Arenes For Enhanced Photostability, Manik Gudimani

Electronic Theses and Dissertations

Organic π-conjugated materials have been researched extensively for a number of applications including organic photovoltaics, electrooptic (EO) modulation, solid-state lasing, organic light emitting diodes (OLEDs), biological imaging and sensing, chemical sensing and ligands for photocatalysts. These organic optoelectronic materials have one major issue that affects its performance and lifetime—photostability. For some applications, hermetical packaging, which is expensive, is required to prevent degradation by light and oxygen. Photooxidation occurs when a material is exposed to light and causes structural and chemical changes leading to photodegradation of the material. The two primary degradation mechanisms responsible for photooxidation involve superoxide radical anion and …

An Interdisciplinary Approach To The Target Elucidation Of Novel Antibiotic 31g12, Larissa A. Walker

Graduate Student Theses, Dissertations, & Professional Papers

Staphylococcus aureus is a Gram-positive bacterial pathogen responsible for nosocomial and community-acquired infections that can quickly acquire antibiotic resistance. We have identified a novel triazole antimicrobial 31G12 based on the natural product core of nonactin isolated from the fermentation of Streptomyces griseus, that is active against many Gram-positive bacteria as well as antibiotic resistant methicillin-resistant S. aureus and vancomycin-resistant Enterococcus. The synthesis and characterization indicate that 31G12 exists as a mixture of two rotamers at room temperature and displays bacteriostatic activity against S. aureus with moderate mammalian cell toxicity. We have currently identified potential protein targets of 31G12 in …

Presence And Potential Sources Of Pharmaceutical And Personal Care Product Chemicals In Messalonskee Lake, Alyssa T. Kullberg

Honors Theses

Pharmaceuticals and personal care product chemicals (PPCPs) represent a large group of contaminants that are mostly not regulated in surface or drinking water and whose presence and environmental and health impacts are poorly understood. We investigated the presence and potential sources of 18 PPCPs in Messalonskee Lake. We collected samples four times over the summer of 2017 at 13 sites around the lake. Samples were tested for PPCPs using liquid chromatography-tandem mass spectrometry. We detected five out of the 18 PPCPs we tested for at the ng/L level: caffeine, 1,7-dimethylxanthine, acetaminophen, sulfachloropyridazine, and amphetamine. PPCPs showed a significant positive correlation …

Stable Bromine Isotope Signature Of Bromoform From Enzymatic And Abiotic Formation Pathways And Its Application In Identifying Sources Of Environmental Bromoform In The Damariscotta River, Chengyang Wang

Honors Theses

Bromoform is a major source of atmospheric bromine. Most bromoform is produced by marine organisms including macroalgae and phytoplankton, using the enzyme bromoperoxidase (BPO). Bromoform can also be a byproduct of industrial processes such as water disinfection. Identifying sources of environmental bromoform is still a challenge. A novel technique of using quadrupole mass spectrometry coupled to a gas chromatography (GCqMS) was developed and optimized for Br isotope analyses. The study shows that GCqMS in single ion monitoring (SIM) mode can measure 81Br with precision of around ±0.7‰ (60pmol bromoform injected). This study aims to investigate stable Br isotopes of bromoform …

Synthesis And Cytotoxicity Of Mansonone G Derivatives, Nhung Ngo Thi Tuyet

Chulalongkorn University Theses and Dissertations (Chula ETD)

Mansonone G (N01), a naturally occurring o-naphthoquinone was isolated from the heartwoods of Mansonia gagei Drumm. as the major component. Seventeen ether derivatives N02-N18 were successfully synthesized by the reaction of mansonone G with corresponding alkyl halide. All derivatives were characterized by 1H, 13C NMR and HRMS. Eleven of them were confirmed to be new compounds. The cytotoxic evaluation was performed against A549 and HT-29 cancer cell lines. Interestingly, all candidates displayed more potent cytotoxicity than mansonone G. The hydrophobicity was found as an important contributor to the activity. N08 displayed the most potent cytotoxicity toward the interested cells with …

Glycosylation Of 2-Nitro-1-Thioglycoside As Glycosyl Donor, Panachai Wongsrisupphakul

Chulalongkorn University Theses and Dissertations (Chula ETD)

2-Nitro thioglycosides are versatile building blocks for amino sugar synthesis. Nitro moiety at C2 position acts as stable surrogate for amino group and can be converted at late state of the synthesis. In this work, chemical glycosylation of 2-nitro thioglycoside donors were investigated. 2-nitro thioglycosides were prepared from tri-O-acetyl-D-galactal which underwent functional group manipulations and nitration to obtain 2-nitrogalactal in 47% over 4 steps. Then, Michael additions of 2-nitrogalactal with various type of S-nucleophiles were performed by using NaDTC as activator to produce 2-nitrothioglycoside donors in 46–85% yield. Glycosylation between 2-nitro thioglycoside donors and methyl 2,3,4-tri-O-benzyl-α-D-glucopyranoside as glycosyl acceptor were …

Preparaton Of Selenium Nanoparticles Stabilized By Pullulan And Derivatives, Punnida Nonsuwan

Chulalongkorn University Theses and Dissertations (Chula ETD)

The inorganic/organic selenium nanoparticles (SeNPs)/pullulan derivative hybrid material was obtained using a simple and green strategy. The chemical structure of pullulan, folic acid decorated cationic pullulan (FA-CP) was designed for stabilizing SeNPs. The SeNPs stabilized by FA-CP were observed after the addition of a cysteine hydrochloride solution into the solution mixture of Na2SeO3 and FA-CP. The results suggested that the concentrations of cysteine and stabilizer were the key factors to control the shape and morphology of SeNPs. The spherical SeNP/FA-CP was found in ratio of Na2SeO3 to cysteine was 1:1. It exhibited low toxicity against normal cells while higher toxicity …

Synthesis And Characterization Of Biomimetic Dinuclear And Tetranuclear Copper Complexes, Syed Rahmath Ullah Joy

Masters Theses

Seven new copper(II) complexes were prepared from the condensation reaction of 4-tert-butyl-2,6-diformylphenol with two equivalents of bis(pyrazolyl)ethanamine or 3,5-dimethyl-bis(pyrazolyl)ethanamine moieties in the presence of two equivalents of various copper(II) starting materials having different counter ions (i.e. acetate - AcO^-, perchlorate - CIO₄^-, tetrafluoroborate - BF₄^-, nitrate - NO₃^-, and chloride - Cl^-). The resulting copper(II) complexes were characterized in solid state by single crystal X-ray crystallography, and in solution by UV-Vis and ESI/MS spectroscopies.

X-ray crystallographic studies showed that in solid state two types of …

Pd-Based Photocatalysts For Sonogashira C-C Cross-Coupling Reactions, Komadhie Charuka Dissanayake

Masters Theses

Sonogashira C-C cross-coupling reaction has been heavily used for its simplicity, flexibility and value. Although the original Sonogashira C-C cross coupling reaction conditions entail the use of 0.5 mol% of Pd catalyst, 2 mol% of Cul as co-catalyst at room temperature, the experimental conditions used in laboratories to prepare some compounds vary substantially, especially with respect to the reaction time, temperature and loading amount of the catalysts. The most significant drawback of the conventional Sonogashira reaction is the use of Cul as it leads to the formation of homocoupling product when the reaction is exposed to air or oxidizing agents. …

Biosensing And Catalysis Applications Of Nanoporous Gold (Npg) And Platinum-Speckled Nanoporous Gold (Npg-Pt) Electrodes, Christopher J. Freeman

Theses and Dissertations

The importance of porous materials has risen substantially in the last few decades due to their ability to reduce the size and cost of bioanalytical devices and fuel cells. First, this work aims to describe the fabrication of nanoporous gold (NPG) electrodes that are resistant to electrode passivation due to fibrinogen biofouling in redox solutions. The effect on potentiometric and voltammetric experiments was seen as a deviation from ideal behavior on planar gold electrodes, whereas NPG electrodes were consistently behaving in a Nernstian fashion at low concentrations of ferri-ferrocyanide (£100 mM). An improvement in electrode behavior on NPG electrodes versus …

5-Ht2b Receptor-Mediated Cardiac Valvulopathy, Pallavi Nistala

Theses and Dissertations

5-HT_2B receptor agonism causes cardiac valvulopathy, a condition characterized by thickening of the heart valves and as a result, regurgitation of blood within the heart. The anti-obesity drug fenfluramine, which was originally prescribed as an anorectic, was withdrawn from the market due to causing cardiac valvulopathy. Fenfluramine, after metabolism by N-dealkylation, produces the metabolite norfenfluramine, which acts as a more potent valvulopathogen. The same was seen with MDMA (ecstasy), a popular drug of abuse, which is metabolized by N-dealkylation to produce MDA, a more potent valvulopathogen. Glennon and co-workers. studied a series of 2,5-dimethoxy-4- substituted phenylisopropylamines (DOX type) hallucinogens …

Fast Isotope Ratio Mass Spectrometry (Firms): A Tandem Mass Spectrometry Technique For The Rapid And Semi-Comprehensive Evaluation Of Isotope Ratios, Fredrick Ochieng

Electronic Theses and Dissertations

Isotope ratios (IRs) are a measure of the variation in abundance of light isotopes versus heavy isotopes of an element, e.g. ¹H/²H,¹²C/¹³C, and ¹⁴N/¹⁵N. Because IRs change as a molecule undergoes certain chemical and physical processes, they represent unique fingerprints that can be used to trace the source of a chemical compound. Current techniques for determination of IRs each have major limitations, such as loss of structural information, vulnerability to contamination, high cost, large sample size requirements, low precision, limited applicability, and lengthy analysis. Fast Isotope Ratio Mass Spectrometry (FIRMS) …

Electron Nuclear Dynamics Simulations Of Proton Cancer Therapy Reactions: Water Radiolysis And Proton- And Electron-Induced Dna Damage In Computational Prototypes, Erico S. Teixeira, Karthik Uppulury, Austin J. Privett, Christopher Stopera, Patrick M. Mclaurin, Jorge A. Morales

Chemistry and Occupational Health Science

Proton cancer therapy (PCT) utilizes high-energy proton projectiles to obliterate cancerous tumors with low damage to healthy tissues and without the side effects of X-ray therapy. The healing action of the protons results from their damage on cancerous cell DNA. Despite established clinical use, the chemical mechanisms of PCT reactions at the molecular level remain elusive. This situation prevents a rational design of PCT that can maximize its therapeutic power and minimize its side effects. The incomplete characterization of PCT reactions is partially due to the health risks associated with experimental/clinical techniques applied to human subjects. To overcome this situation, …

Effects Of Yoga On The Motor Skills Of A Ten-Year-Old Male With Autism Spectrum Disorder, Amber Schmitt

Senior Honors Theses and Projects

Autism Spectrum Disorder (ASD} is a neurodevelopmental disorder that is typically diagnosed in childhood due to the presence of atypical development, social interactions, and repetitive stereotypical patterns of behavior. The purpose of the present study was to examine the effects of a yoga intervention on a ten-year-old male diagnosed with ASD. It was hypothesized that the yoga intervention on select instructed poses would increase both pose duration and pose performance and that the results would generalize to longer pose duration and better pose performance on non-instructed poses. Pre-intervention assessments of motor functioning were administered, including the Movement ABC, BOT-2, TGMD, …

Addressing The Threat Of Multidrug Resistant Infectious Diseases By Synthesis Of Novel Aminoglycoside Antibiotics, Girish Chandra Sati

Wayne State University Dissertations

The ever-growing increase in multidrug resistant infectious diseases is one of the major cause of human mortality, and there is an inherent need for the development of new antibiotics. Since the discovery of streptomycin, AGAs have been playing a very important role in human therapy as highly potent broad-spectrum antibiotics and are listed as one of the critically important antimicrobials by WHO. AGAs act by inhibiting the bacterial protein synthesis and by targeting the A-site present in the small subunit of bacterial ribosome. The clinical use of AGAs is somewhat restricted due to their toxic effects (ototoxicity and nephrotoxicity) and …

Palladium-Catalyzed Carbonyl Allylation Reactions Using Tin Chloride: A Mini-Review, Armando M. Guidote Jr, Mikael John A. Baltazar, Roy Kristian C. Yanela, Noriyuki Suzuki

Chemistry Faculty Publications

The treatment of allylic alcohols as synthons of carbanions for carbonyl allylation reactions in the presence of a Pd-SnCl2 system has been one of the most interesting and most useful developments demonstrated by Yoshiro Masuyama and co-workers in the field of organic synthesis. The reaction makes use of palladium as an effective catalyst and tin (II) chloride as a low-valent reducing agent which also effectively transforms the allylic group to a nucleophilic group. The organic, as well as organometallic, chemistry of how the transformations occur and how the metals take part in the reaction is of great interest. These could …

Transplanting A Bacterial Immune System: Determining The Function Of A Novel Crispr System, Riannon Smith, Melena Garrett

Research on Capitol Hill

CRISPR (Clusters of Regularly Interspaced Short Palindromic Repeats) loci and cas (CRISPR-associated) genes provide adaptive immunity (see panel below) in bacteria and have recently been repurposed for genome editing.

Systems are structurally and functionally diverse.

• 2 classes, 6 types, 33 subtypes
• Very few have been studied experimentally
• None of the Type IV systems have been characterized

Presence Of Cofactor Nadph Slows Down The Dissociation Of Methotrexate From Dihydrofolate Reductase From Bacillus Stearothermophilus, Ryan Seamus Foley

Theses, Dissertations and Culminating Projects

The goal of this project was to study the effect of the presence or absence of the cofactor NADPH on the binding and release of ligand methotrexate (MTX) to/from Bacillus stearothermophilus (Bs) dihydrofolate reductase (DHFR). A previously developed, fluorescently-labeled Bs DHFR (C73A/S131CMDCC DHFR) was used to investigate the kinetics and protein conformational motions associated with the binding of NADPH and the binding of methotrexate to the holoenzyme. This Bs DHFR contains a distal cysteine where the fluorophore, N-[2-(1-maleimidyl)ethyl]-7-(diethylamino)coumarin-3-carboxamide (MDCC) can be covalently attached. This probe is sensitive to the local molecular environment, reporting on changes in the protein conformation associated …