Chemistry Theses Copyright (c) 2013 Georgia State University All rights reserved. http://digitalarchive.gsu.edu/chemistry_theses Recent documents in Chemistry Theses en-us Mon, 06 May 2013 08:01:10 PDT 3600 Discovery of Novel Cross-Talk between Protein Arginine Methyltransferase Isoforms and Design of Dimerization Inhibitors http://digitalarchive.gsu.edu/chemistry_theses/58 http://digitalarchive.gsu.edu/chemistry_theses/58 Mon, 29 Apr 2013 06:25:43 PDT Protein arginine methyltransferase, PRMT, is a family of epigenetic enzymes that methylate arginine residues on histone and nonhistone substrates which result in a monomethylation, symmetric dimethylation or asymmetric dimethylation via the transfer of a methyl group from S-adenosyl-L-methionine (SAM). We discovered a novel interaction between two PRMT isoforms: PRMT1 interacts and methylates PRMT6. In this study site-directed mutagenesis was performed on selected arginines identified from tandem mass spectrometric analysis to investigate major methylation sites of PRMT6 by PRMT1. In combination with radiometric methyltransferase assays, we determined two major methylation sites. Methylations at these sites have significant effects on the nascent enzymatic activity of PRMT6 in H4 methylation. PRMTs have the ability to homodimerize which have been linked to methyltransferase activity. We designed dimerization inhibitors (DMIs) to further investigate the need for dimerization for enzyme activity. Preliminary results suggest that the monomeric form of PRMT1 retains methyltransferase activity comparable to that of the uninhibited PRMT1.

]]> Brandon S. Canup Unsymmetrical Trimethine Cyanine Dyes: Synthesis, Optical Properties, and Evaluations as Inhibitors of Protein Arginine Methyl Transferases http://digitalarchive.gsu.edu/chemistry_theses/57 http://digitalarchive.gsu.edu/chemistry_theses/57 Fri, 26 Apr 2013 13:05:57 PDT Carbocyanine dyes are a class of organic compounds that possess two nitrogen containing heterocycles that act as electron donors and acceptors connected by a conjugated methine bridge. This thesis will present the synthetic methodology of symmetrical and unsymmetrical trimethine cyanine dyes in three chapters. The first chapter is a review on the synthesis and application of unsymmetric cyanine dyes. The second will describe the synthesis of unsymmetrical trimethine cyanine dyes and how their optical properties differ from symmetrical dyes. The third chapter will not only discuss the synthetic procedure for synthesis of symmetrical trimethine cyanine dyes, but also will show how varying the N-alkyl substituents and hydrophobicity of the heterocycles affects the dyes interaction with and ability to be used as inhibitors for protein arginine methyltransferases (PRMTs). Several synthesized compounds have displayed lower IC50 values for the inhibition of PRMT1 and PRMT5 comparable to that of current inhibitors.

]]> Andrew R. Levitz Effects of Temperature on the Kinetic Isotope Effects for Proton and Hydride Transfers in the Active Site Variant of Choline Oxidase Ser101Ala http://digitalarchive.gsu.edu/chemistry_theses/56 http://digitalarchive.gsu.edu/chemistry_theses/56 Fri, 26 Apr 2013 13:05:55 PDT Choline oxidase catalyzes the oxidation of choline to glycine betaine. The reaction includes betaine aldehyde as an intermediate. FAD is reduced by the alcohol substrate, betaine aldehyde intermediate and oxidized by molecular oxygen to give hydrogen peroxide. In this study, the Ser101Ala variant of choline oxidase was prepared to elucidate the contribution of the hydroxyl group of Ser101 in the proton and hydride transfer reactions for proper preorganization and reorganization of the active site towards quantum mechanical tunneling. The thermodynamic parameters associated with the enzyme-catalyzed OH and CH bond cleavages and the temperature dependence of the associated solvent and substrate kinetic isotope effects were investigated using a stopped-flow spectrophotometer. The proton and hydride transfer have been shown to be occurring via quantum tunneling in CHO-S101A enzyme.

]]> Rizvan C. Uluisik Synthesis of Novel Fluorescent Benzothiazole Cyanine Dyes as Potential Imaging Agents http://digitalarchive.gsu.edu/chemistry_theses/55 http://digitalarchive.gsu.edu/chemistry_theses/55 Tue, 04 Dec 2012 07:50:56 PST Near-infrared (NIR) fluorescence imaging has emerged as an attractive non-invasive approach for direct visualization of diseases which depends on the development of stable, highly specific and sensitive optical probes. The NIR region of the electronic spectrum offers a reduction in the background autofluorescence and an increase in the tissue penetration depth. Cyanine dyes have often been considered promising contrast optic agents owing to their photophysical properties.

Herein the synthesis of various penta- and heptamethine benzothiazole cyanine dyes has been described and their in vivo imaging efficacy was determined. Varying functionalities on the benzothiazole aromatic ring and changing substituents on the benzothiazolium nitrogen atom reflected subsequent changes in the imaging pattern and have resulted in the development of promising brain targeting agents.

]]> Shirish Paranjpe Nanoprecipitation in Quartz Nanopipettes and Application in the Crystallization of Inorganic Salts http://digitalarchive.gsu.edu/chemistry_theses/54 http://digitalarchive.gsu.edu/chemistry_theses/54 Thu, 19 Jul 2012 11:01:10 PDT The high surface to volume ratio which is a property of nanoscale devices means the interfacial effects from these devices on the mass transport of analyte can be significant. Quartz nanopipette effect on the mass transport behavior of inorganic monovalent salts such as potassium chloride is shown to differ from those of conical nanopore. Quartz nanopipettes demonstrate a more significant interfacial impact on the mass transport behavior of inorganic salts. This is evidenced by significant impacts on ionic transport even at high electrolyte concentration where nanopore interfacial effects do not significantly impact the ion transport. Nanopipettes have been use to precipitate salts such as lithium chloride in bulk concentrations three orders of magnitude below the saturation concentration. These novel interfacial interactions have opened new avenues for crystallization of more complex organic biomolecules using inorganic systems as model systems on which to base the approach for these more complex systems.

]]> Warren D. Brown Studying the DNA Binding and Conformation of Metal-Binding Site Mutations in Pirin http://digitalarchive.gsu.edu/chemistry_theses/53 http://digitalarchive.gsu.edu/chemistry_theses/53 Thu, 19 Jul 2012 08:25:10 PDT The transcription factor NF-κB interacts with many other co-regulator proteins that modulate its binding and transcriptional activity. One of these co-regulators, Pirin, is an iron-dependent metalloprotein that has been shown to enhance the DNA binding of NF-κB homodimers. Here, we characterize the interactions between Pirin and its known NF-κB binding partners and examined the role of Bcl-3, a protein that is required for Pirin’s interaction with p50. In addition, we use site-directed mutagenesis to alter conserved residues within Pirin’s metal binding environment and observed how it affected the DNA binding and conformation of the Pirin-NF-κB complex. These studies show that, while a similar enhancing effect on DNA binding is observed, the interactions of Pirin with different NF-κB members are distinct from each other and could possibly have different physiological purposes.

]]> Imran J. Rehmani Design and Synthesis of Thiamine Analogs as Anti-Cancer Therapeutics http://digitalarchive.gsu.edu/chemistry_theses/52 http://digitalarchive.gsu.edu/chemistry_theses/52 Tue, 17 Jul 2012 06:58:58 PDT Cancer is one of the leading causes of death. There have been many investigations into therapeutic ways to prevent and reverse cancerous growth. We report a new approach in this thesis, which is to investigate the functions of Vitamin B1 (thiamine) in cancerous cells and their regulation. A number of thiamine analogs were synthesized to carry out the structure-activity relationship (SAR) studies with two transporters THTR1 and THTR2. Initial results show that the modifications of thiazole reduced the uptake of thiamine.

]]> Hieu T. Dinh Two-site DNA Minor Groove Binding Compounds http://digitalarchive.gsu.edu/chemistry_theses/51 http://digitalarchive.gsu.edu/chemistry_theses/51 Mon, 16 Jul 2012 11:51:16 PDT DNA minor groove binding compounds have had limited therapeutic uses, in part due to problems with sequence specificity. A two-site model has been developed to enhance specificity, in which compounds bind to two short AT sites separated by one or two GC base pairs. Using thermal melting, heterocyclic dications with this capability were tested with various oligonucleotides for binding affinity and specificity. Compounds of interest were further probed using circular dichroism, mass spectrometry, biosensor-SPR, and molecular modeling. Several compounds were found to “jump” a GC base pair, binding to AT sites in the minor groove of DNA with a two-site recognition mode. One compound was also found to recognize a single intervening GC base pair. Compounds with terminal, non-polar amidine extensions were found to have increased DNA binding compared to analogs with terminal amidines. This unique, two-site DNA recognition mode offers novel design principles to recognize entirely new DNA motifs.

]]> Shelby Diane Sheldon Deuser Synthetic Development of the Tri- and Pentamethine Cyanine Chromophore for Biomolecular Interactions http://digitalarchive.gsu.edu/chemistry_theses/50 http://digitalarchive.gsu.edu/chemistry_theses/50 Thu, 19 Apr 2012 09:22:41 PDT The synthetic methodology of tri- and pentamethine carbocyanines and their interactions with biomolecules will be discussed in two chapters. The first chapter describes the preparation of halogenated carbocyanine dyes that display multiple charges; furthermore, these particular compounds were examined for their ability to bind G-quadruplex DNA with selectivity over duplex DNA and have potential for developing novel chemotherapeutic agents. The second section discusses the synthetic methods utilized to prepare trimethine cyanine fluorophores. This chapter will show how varying the N-indolenyl substituients’ hydrophobicity from ethyl to phenylpropyl influences the binding to Human Serum Albumin (HSA); additionally, alternating the terminal heterocyclic moieties of the cyanine dye has a direct quantitative effect on the biomolecular interaction. These identical compounds were recognized to be structurally analogous to agents that commonly interact with Protein Arginine Methyl Transferase (PRMT) and these compounds display low IC50 values toward inhibition of PRMT1 with unique NIR imaging properties.

]]> Eric A. Owens Synthesis of Chiral N-Heterocyclic Carbene Precursors and Key Intermediates for Catalytic Enantioselective Cyclizations of Conjugated Trienes http://digitalarchive.gsu.edu/chemistry_theses/49 http://digitalarchive.gsu.edu/chemistry_theses/49 Thu, 19 Apr 2012 09:22:38 PDT Cocatalyzed reactions using Brønsted acids and chiral N-heterocyclic carbenes to yield highly enantioselective products have been reported recently in many journals. The development of new chiral N-heterocyclic carbenes is a competitive field among synthetic chemist. In a recent study we found that conjugated trienes could be cyclized using Brønsted acids and chiral N-heterocyclic carbenes. The synthesis of novel chiral N-heterocyclic carbene precursors, and the precursors to novel conjugated trienes are reported herein.

]]> Phillip D. Wilkerson Synthesis of Coupling Substrates for Use in a Highly Enantioselective Conjugated Triene Cyclization Enabled by a Chiral N-Heterocyclic Carbene http://digitalarchive.gsu.edu/chemistry_theses/48 http://digitalarchive.gsu.edu/chemistry_theses/48 Tue, 17 Apr 2012 09:40:12 PDT The ability to generate chiral building blocks is of paramount importance to organic chemists. This problem presents itself most notably at the interface of chemistry and biology, where molecules of only a single enantiomer can induce function to many biological systems. In this context, recent developments in the field of organocatalysis, most notably the employment of chiral N-heterocyclic carbenes (NHCs) have shown much promise.

Our group has recently shown that one possible chiral NHC catalyzed Stetter cyclization product of a conjugated triene, a highly functionalized cyclopentenone, contains both a chiral center and an adjacent conjugated diene. This structure can be easily elaborated to a bicyclic structural motif present in some biologically active natural products from the ginkgolide family, and is difficult to access by other means. The synthesis of novel vinyl stannanes and other coupling substrates involved in the development of the aforementioned reaction discovery are described in this report.

]]> Christopher A. Toth Spectroscopic Studies of Carbocyanine and 2,4,6- Trisubstituted Pyridine Dyes for Bioanalytical and pH Indicating Applications http://digitalarchive.gsu.edu/chemistry_theses/47 http://digitalarchive.gsu.edu/chemistry_theses/47 Wed, 30 Nov 2011 05:57:58 PST In part A, the effect of varying short-chain alkyl substitution on the spectroscopic properties of cyanine dyes was examined. Molar absorptivities and quantum yields were determined for groups of pentamethine and heptamethine dyes for which the substitution of the indole nitrogen was varied. For both sets of dyes, increasing alkyl chain length did not significantly change quantum yield or molar absorptivity. These results may be useful in designing new cyanine dyes.

In part B, the effect of structure on the suitability of 2,4,6-trisubstituted pyridines as color pH indicators was studied by determining spectral effects of protonation, molar absorptivities, pKa values, and the structural origin of the spectral behavior. Good color indicating properties result from aniline substitution at the 4 position of pyridine and electron donating substitution at the 2 and 6 positions of pyridine, which provide a strong red shift in the spectra and greater red shifted peak absorptivity, respectively.

]]> Gala M. Chapman Arylboronic Acids With Strong Fluorescence Intensity Changes Upon Sugar Binding http://digitalarchive.gsu.edu/chemistry_theses/46 http://digitalarchive.gsu.edu/chemistry_theses/46 Tue, 29 Nov 2011 07:43:37 PST Boronic acids play an important role in the design and synthesis of chemosensors for carbohydrates due to their ability to reversibly bind with diol-containing compounds. Along this line, the availability of boronic acids that change fluorescence upon sugar binding is critical to a successful sensor design effort. Here, two boronic acids that show strong fluorescent intensity changes upon sugar binding are reported: isoquinoline-7-boronic acid (7-IQBA) and phenoxathiin-4-boronic acid (4-POBA).

]]> Sarah R. Laughlin Synthesis of Selective 5-HT7 Receptor Antagonists http://digitalarchive.gsu.edu/chemistry_theses/45 http://digitalarchive.gsu.edu/chemistry_theses/45 Mon, 28 Nov 2011 09:10:00 PST The 5-HT7 receptor is the most recent addition to the 5-HT receptor family and has been linked to a variety of physiological and pathophysiological processes. Well established antide-pressant pharmaceuticals have recently been found to activate the 5-HT7 receptor, supporting the role of the 5-HT7 receptor in the antidepressant mechanism. The synthesis of potent selec-tive 5-HT7 receptor antagonists could afford a greater understanding of the 5-HT7 receptor function as well as lead to potential drug candidates.

The synthesis of unfused biheteroaryl derivatives as 5-HT7 receptor ligands has been de-scribed within. These compounds have been tested for biological activity on the 5-HT6 and 5-HT7 receptors. 4-(3’-Furyl)-2-(N-substituted-piperazino)pyrimidines were found to be potent 5-HT7 receptor ligands. 4-(2’-Furyl)-2-(N-substituted-piperazino)pyrimidines have shown high se-lectivity for the 5-HT7 receptor over the 5-HT6 receptor.

]]> Adam Ehalt Synthesis and Characterization of Metal Nanoclusters Stabilized by Dithiolates http://digitalarchive.gsu.edu/chemistry_theses/44 http://digitalarchive.gsu.edu/chemistry_theses/44 Tue, 22 Nov 2011 09:15:04 PST Rapidly expanding research in nanotechnology has led to exciting progress in a versatile array of applications from medical diagnostics to photocatalytic fuel cells. Such success is due to the ability of researchers to manipulate the desired properties of nanomaterials by controlling their size, shape, and composition. Among the most thriving areas of nanoparticle research has been the synthesis and characterization of stable metallic nanoclusters capped by thiolate ligands. Our group has extended this research to study copper, silver, and gold clusters with remarkable stability and energetics, which was achieved by using dithiolates as the ligand stabilizers. In addition to the enhanced stability offered by the chelate effect, the use of dithiolate ligands instead of monothiolates is proposed to provide an alternate interfacial bond structure that is shown to strongly influence energetic properties of nanoclusters, with strong evidence of metal-ligand charge transfer. Energetic properties were characterized by spectroscopic and electrochemical methods.

]]> Donald A. Robinson III Interactions of Metals and Radicals: A Biochemical Perspective in Tryptophan Dioxygenase http://digitalarchive.gsu.edu/chemistry_theses/43 http://digitalarchive.gsu.edu/chemistry_theses/43 Mon, 18 Jul 2011 06:02:48 PDT An intriguing mystery about tryptophan 2, 3-dioxygenase is its hydrogen peroxide-triggered enzyme reactivation from the resting ferric oxidation state to the catalytically active ferrous form. In this study, we found that such an odd Fe(III) reduction by an oxidant depends on the presence of L-Trp, which ultimately serves as the reductant for the enzyme. In the peroxide reaction with tryptophan 2, 3-dioxygenase, a previously unknown catalase-like activity was detected. A ferryl species (δ = 0.055 mm/s and ΔEQ = 1.755 mm/s) and a protein-based free radical (g = 2.0028 and 1.72 millitesla linewidth) were characterized by Mössbauer and EPR spectroscopy, respectively. This is the first compound ES-type of ferryl intermediate from a heme-based dioxygenase characterized by EPR and Mössbauer spectroscopy. Density functional theory calculations revealed the contribution of secondary ligand sphere to the spectroscopic properties of the ferryl species. A Trp-Trp dimer and a monooxygenated L-Trp were both observed as the enzyme reactivation by-products by mass spectrometry. Together, these results lead to the unraveling of an over 60-year old mystery of peroxide reactivation mechanism.

]]> Kednerlin Dornevil Optimization of Expression and Purification Methods for the Study of Protein-Based Magnetic Resonance Imaging Contrast Agents http://digitalarchive.gsu.edu/chemistry_theses/42 http://digitalarchive.gsu.edu/chemistry_theses/42 Fri, 15 Jul 2011 09:17:38 PDT Magnetic Resonance Imaging instruments rely on a contrast agent to provide high-resolution images of tissues in vivo. However, current clinical contrast agents are hindered by low relaxivity and fast correlation time, necessitating high injection dosages. These concerns, among others, have driven the development of a class of protein-based contrast agents (ProCAs), by design of lanthanide binding sites into a scaffold protein. ProCA1 has a higher reported relaxivity and dosage efficiency than current contrast agents. In this study, expression and Glutathione-S-Transferase purification procedures were optimized, and a refolding method for rapid production of ProCA1 has been developed to enable studies of conformation, metal binding, relaxivity, and in vivo applications. Several ProCA1 variants with 4-5 charged ligand residues were shown to have strong gadolinium binding affinity (Kd of 10-12 M) and metal selectivity. Several options to improve ProCA1 have been explored, including addition of a polyethylene chain or a bombesin tag.

]]> Natalie White Binding of Bisbenzamidines with AT Rich DNA: A Thermodynamic Study http://digitalarchive.gsu.edu/chemistry_theses/41 http://digitalarchive.gsu.edu/chemistry_theses/41 Thu, 14 Jul 2011 12:12:36 PDT Diamidines are small molecules that generally possess antiparasitic properties and bind preferentially to the minor groove of AT rich DNA. With the goal of getting a better understanding of the thermodynamic driving forces and binding affinities, a series of pentamidine analogs were investigated with various AT rich DNA by ITC, UV-Vis and fluorescence spectroscopic methods. Findings suggest that the substitution of the linker oxygen of pentamidine to a nitrogen slightly improves the binding affinity. All of the investigated compounds are entropically driven at 25 oC with non-alternating AT DNA. Additionally, the increased fluorescence of the nitrogen and sulfur linked analogs will enable future work to be done with fluorescence microscopy to help determine if and where these compounds accumulate in the target organism.

]]> Nancy A. Kilpatrick Novel Rhein Analogues as Potential Anicancer Agents and a Novel Metal Free Synthesis of 6H-ISOINDOLO[2,1-A]INDOL-6-ONE http://digitalarchive.gsu.edu/chemistry_theses/40 http://digitalarchive.gsu.edu/chemistry_theses/40 Tue, 12 Jul 2011 11:29:44 PDT The first section of this work describes the synthesis of a library of novel rhein analogues that are potential anticancer agents. The design of these compounds takes advantage of the ability for rhein to intercalate into DNA and as the incorporation of an alkylating agent, which serves to covalently modify DNA. In three cell lines, these compounds showed potent cytotoxicity with IC50 in the low to mid-μM range. The second project was focused on the development of an efficient synthesis of 6H-Isoindolo[2,1-α]indol-6-one (24), a core structure for a number of biologically active compounds. The approach is metal-free and uses a Beckmann rearrangement followed by an intramolecular cyclization.

]]> Alexander B. Draganov DNA Photocleavage by 9-Aminomethylanthracene Dyes at pH 7.0: Ionic Strength Effects http://digitalarchive.gsu.edu/chemistry_theses/39 http://digitalarchive.gsu.edu/chemistry_theses/39 Fri, 08 Jul 2011 06:37:04 PDT DNA photosensitizers are compounds that are capable of binding in to DNA strands through groove binding, intercalation, or electrostatic interactions. Excitation of these agents by light generates reactive oxygen species which causes extensive photo-oxidative damage to genomic DNA. Physiological concentrations of NaCl and KCl are ~ 150 mM and 260 mM within the cell nucleus where DNA is contained. Unfortunately, the ability of most photosensitizers to bind to double-helical DNA is reduced and photocleavage yields are diminished as concentrations of salt increase. The aim of this project is to observe the photocleavage of pUC19 plasmid DNA induced by N1,N1-bis(9-anthrymethyl)triethylenetetraamine tetrahydrochloride (AL-VIII 23) 1 or N,N-dimethyl-N’-(9-methylanthracenyl)ethylenediamine (NMEA) 2 in presence of salt. Spectroscopic titrations and DNA melting assays were used to study binding modes and affinities of both dyes to the helix upon the addition of salt.

]]> Blessing D. Deeyaa