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Description
Small molecules have proven to be very important tools for exploration of biological systems including diagnosis and treatment of lethal diseases like cancer. Fluorescent probes have been extensively used to further amplify the utilization of small molecules. The manipulation of naturally occurring biological targets with the help of synthetic compounds is the focus of the work described in this thesis.
Bleomycins (BLMs) are a class of water soluble, glycopeptide-derived antitumor antibiotics consisting of a structurally complicated unnatural hexapeptide and a disaccharide, clinically used as an anticancer chemotherapeutic agent at an exceptionally low therapeutic dose. The efficiency of BLM is likely achieved both by selective localization within tumor cells and selective binding to DNA followed by efficient double-strand cleavage. The disaccharide moiety is responsible for the tumor cell targeting properties of BLM. A recent study showed that both BLM and its disaccharide, conjugated to the cyanine dye Cy5**, bound selectively to cancer cells. Thus, the disaccharide moiety alone recapitulates the tumor cell targeting properties of BLM. Work presented here describes the synthesis of the fluorescent carbohydrate conjugates. A number of dye-labeled modified disaccharides and monosaccharides were synthesized to study the nature of the participation of the carbamoyl moiety in the mechanism of tumor cell recognition and uptake by BLM saccharides. It was demonstrated that the carbamoylmannose moiety of BLM is the smallest structural entity capable for the cellular targeting and internalization, and the carbamoyl functionality is indispensible for tumor cell targeting. It was also confirmed that BLM is a modular molecule, composed of a tumor cell targeting moiety (the saccharide) attached to a cytotoxic DNA cleaving domain (the BLM aglycone). These finding encouraged us to further synthesize carbohydrate probes for PET imaging and to conjugate the saccharide moiety with cytotoxins for targeted delivery to tumor cells.
The misacylated suppressor tRNA technique has enabled the site-specific incorporation of noncanonical amino acids into proteins. The focus of the present work was the synthesis of unnatural lysine analogues with nucleophilic properties for incorporation at position 72 of the lyase domain of human DNA polymerase beta, a multifunctional enzyme with dRP lyase and polymerase activity.
Bleomycins (BLMs) are a class of water soluble, glycopeptide-derived antitumor antibiotics consisting of a structurally complicated unnatural hexapeptide and a disaccharide, clinically used as an anticancer chemotherapeutic agent at an exceptionally low therapeutic dose. The efficiency of BLM is likely achieved both by selective localization within tumor cells and selective binding to DNA followed by efficient double-strand cleavage. The disaccharide moiety is responsible for the tumor cell targeting properties of BLM. A recent study showed that both BLM and its disaccharide, conjugated to the cyanine dye Cy5**, bound selectively to cancer cells. Thus, the disaccharide moiety alone recapitulates the tumor cell targeting properties of BLM. Work presented here describes the synthesis of the fluorescent carbohydrate conjugates. A number of dye-labeled modified disaccharides and monosaccharides were synthesized to study the nature of the participation of the carbamoyl moiety in the mechanism of tumor cell recognition and uptake by BLM saccharides. It was demonstrated that the carbamoylmannose moiety of BLM is the smallest structural entity capable for the cellular targeting and internalization, and the carbamoyl functionality is indispensible for tumor cell targeting. It was also confirmed that BLM is a modular molecule, composed of a tumor cell targeting moiety (the saccharide) attached to a cytotoxic DNA cleaving domain (the BLM aglycone). These finding encouraged us to further synthesize carbohydrate probes for PET imaging and to conjugate the saccharide moiety with cytotoxins for targeted delivery to tumor cells.
The misacylated suppressor tRNA technique has enabled the site-specific incorporation of noncanonical amino acids into proteins. The focus of the present work was the synthesis of unnatural lysine analogues with nucleophilic properties for incorporation at position 72 of the lyase domain of human DNA polymerase beta, a multifunctional enzyme with dRP lyase and polymerase activity.
ContributorsBhattacharya, Chandrabali (Author) / Hecht, Sidney M. (Thesis advisor) / Moore, Ana (Committee member) / Gould, Ian R (Committee member) / Arizona State University (Publisher)
Created2014
Description
Mitochondria are crucial intracellular organelles which play a pivotal role in providing energy to living organisms in the form of adenosine triphosphate (ATP). The mitochondrial electron transport chain (ETC) coupled with oxidative phosphorylation (OX-PHOS) transforms the chemical energy of amino acids, fatty acids and sugars to ATP. The mitochondrial electron transport system consumes nearly 90% of the oxygen used by the cell. Reactive oxygen species (ROS) in the form of superoxide anions (O2*-) are generated as byproduct of cellular metabolism due to leakage of electrons from complex I and complex III to oxygen. Under normal conditions, the effects of ROS are offset by a variety of antioxidants (enzymatic and non-enzymatic).
Mitochondrial dysfunction has been proposed in the etiology of various pathologies, including cardiovascular and neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease, ischemia-reperfusion (IR) injury, diabetes and aging. To treat these disorders, it is imperative to target mitochondria, especially the electron transport chain. One of the methodologies currently used for the treatment of mitochondrial and neurodegenerative diseases where endogenous antioxidant defenses are inadequate for protecting against ROS involves the administration of exogenous antioxidants.
As part of our pursuit of effective neuroprotective drugs, a series of pyridinol and pyrimidinol analogues have been rationally designed and synthesized. All the analogues were evaluated for their ability to quench lipid peroxidation and reactive oxygen species (ROS), and preserve mitochondrial membrane potential (Δm) and support ATP synthesis. These studies are summarized in Chapter 2.
Drug discovery and lead identification can be reinforced by assessing the metabolic fate of orally administered drugs using simple microsomal incubation experiments. Accordingly, in vitro microsomal studies were designed and carried out using bovine liver microsomes to screen available pyridinol and pyrimidinol analogues for their metabolic lability. The data obtained was utilized for an initial assessment of potential bioavailability of the compounds screened and is summarized fully in Chapter 3.
Mitochondrial dysfunction has been proposed in the etiology of various pathologies, including cardiovascular and neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease, ischemia-reperfusion (IR) injury, diabetes and aging. To treat these disorders, it is imperative to target mitochondria, especially the electron transport chain. One of the methodologies currently used for the treatment of mitochondrial and neurodegenerative diseases where endogenous antioxidant defenses are inadequate for protecting against ROS involves the administration of exogenous antioxidants.
As part of our pursuit of effective neuroprotective drugs, a series of pyridinol and pyrimidinol analogues have been rationally designed and synthesized. All the analogues were evaluated for their ability to quench lipid peroxidation and reactive oxygen species (ROS), and preserve mitochondrial membrane potential (Δm) and support ATP synthesis. These studies are summarized in Chapter 2.
Drug discovery and lead identification can be reinforced by assessing the metabolic fate of orally administered drugs using simple microsomal incubation experiments. Accordingly, in vitro microsomal studies were designed and carried out using bovine liver microsomes to screen available pyridinol and pyrimidinol analogues for their metabolic lability. The data obtained was utilized for an initial assessment of potential bioavailability of the compounds screened and is summarized fully in Chapter 3.
ContributorsAlam, Mohammad Parvez (Author) / Hecht, Sidney M. (Thesis advisor) / Gould, Ian R (Committee member) / Moore, Ana (Committee member) / Arizona State University (Publisher)
Created2014
Description
Increasing concentrations of carbon dioxide in the atmosphere will inevitably lead to long-term changes in climate that can have serious consequences. Controlling anthropogenic emission of carbon dioxide into the atmosphere, however, represents a significant technological challenge. Various chemical approaches have been suggested, perhaps the most promising of these is based on electrochemical trapping of carbon dioxide using pyridine and derivatives. Optimization of this process requires a detailed understanding of the mechanisms of the reactions of reduced pyridines with carbon dioxide, which are not currently well known. This thesis describes a detailed mechanistic study of the nucleophilic and Bronsted basic properties of the radical anion of bipyridine as a model pyridine derivative, formed by one-electron reduction, with particular emphasis on the reactions with carbon dioxide. A time-resolved spectroscopic method was used to characterize the key intermediates and determine the kinetics of the reactions of the radical anion and its protonated radical form. Using a pulsed nanosecond laser, the bipyridine radical anion could be generated in-situ in less than 100 ns, which allows fast reactions to be monitored in real time. The bipyridine radical anion was found to be a very powerful one-electron donor, Bronsted base and nucleophile. It reacts by addition to the C=O bonds of ketones with a bimolecular rate constant around 1* 107 M-1 s-1. These are among the fastest nucleophilic additions that have been reported in literature. Temperature dependence studies demonstrate very low activation energies and large Arrhenius pre-exponential parameters, consistent with very high reactivity. The kinetics of E2 elimination, where the radical anion acts as a base, and SN2 substitution, where the radical anion acts as a nucleophile, are also characterized by large bimolecular rate constants in the range ca. 106 - 107 M-1 s-1. The pKa of the bipyridine radical anion was measured using a kinetic method and analysis of the data using a Marcus theory model for proton transfer. The bipyridine radical anion is found to have a pKa of 40±5 in DMSO. The reorganization energy for the proton transfer reaction was found to be 70±5 kJ/mol. The bipyridine radical anion was found to react very rapidly with carbon dioxide, with a bimolecular rate constant of 1* 108 M-1 s-1 and a small activation energy, whereas the protonated radical reacted with carbon dioxide with a rate constant that was too small to measure. The kinetic and thermodynamic data obtained in this work can be used to understand the mechanisms of the reactions of pyridines with carbon dioxide under reducing conditions.
ContributorsRanjan, Rajeev (Author) / Gould, Ian R (Thesis advisor) / Buttry, Daniel A (Thesis advisor) / Yarger, Jeff (Committee member) / Seo, Dong-Kyun (Committee member) / Arizona State University (Publisher)
Created2015
Description
Cellular redox phenomena are essential for the life of organisms. Described here is a summary of the synthesis of a number of redox-cycling therapeutic agents. The work centers on the synthesis of antitumor antibiotic bleomycin congeners. In addition, the synthesis of pyridinol analogues of alpha-tocopherol is also described. The bleomycins (BLMs) are a group of glycopeptide antibiotics that have been used clinically to treat several types of cancers. The antitumor activity of BLM is thought to be related to its degradation of DNA, and possibly RNA. Previous studies have indicated that the methylvalerate subunit of bleomycin plays an important role in facilitating DNA cleavage by bleomycin and deglycobleomycin. A series of methylvalerate analogues have been synthesized and incorporated into deglycobleomycin congeners by the use of solid-phase synthesis. All of the deglycobleomycin analogues were found to effect the relaxation of plasmid DNA. Those analogues having aromatic C4-substituents exhibited cleavage efficiency comparable to that of deglycoBLM A5. Some, but not all, of the deglycoBLM analogues were also capable of mediating sequence-selective DNA cleavage. The second project focused on the synthesis of bicyclic pyridinol analogues of alpha-tocopherol. Bicyclic pyridinol antioxidants have recently been reported to suppress the autoxidation of methyl linoleate more effectively than alpha-tocopherol. However, the complexity of the synthetic routes has hampered their further development as therapeutic agents. Described herein is a concise synthesis of two bicyclic pridinol antioxidants and a facile approach to their derivatives with simple alkyl chains attached to the antioxidant core. These analogues were shown to retain biological activity and exhibit tocopherol-like behaviour.
ContributorsCai, Xiaoqing (Author) / Hecht, Sidney M. (Thesis advisor) / Gould, Ian R (Committee member) / Hartnett, Hilairy E (Committee member) / Arizona State University (Publisher)
Created2011
Description
Mitochondria are energy-producing organelles present in eukaryotic cells. Energy as adenosine triphosphate (ATP) is produced at the end of a series of electron transfers called the electron transport chain (ETC). Such a highly coordinated and regulated series of electron transfer reactions give rise to a small percentage of electron leakage which, by the subsequent reduction of molecular oxygen, produce superoxide anions (O2.-). These anions initiate the production of additional highly reactive oxygen-containing radicals commonly known as reactive oxygen species (ROS). Although cells are equipped with endogenous antioxidant systems to minimize ROS accumulation, these endogenous defense systems become inadequate when ROS generation is increased. When ROS production occurs in excess, the cell is said to be under oxidative stress. Unchecked ROS production causes damage to cellular macromolecules, which in turn leads to cell death. Dysfunctional mitochondria and subsequent cell degeneration are a common cause of neurodegenerative diseases such as Friedreich’s ataxia (FRDA) and Alzheimer’s disease (AD). Therefore, targeting the mitochondria by neuroprotective drugs is imperative for the treatment of such diseases. In Chapter 1, the functioning of the ETC is described. Moreover, excessive ROS production and its consequences are also described.
FRDA is a progressive neurodegenerative disease caused by insufficient expression of frataxin (FXN). FXN is instrumental in the assembly of iron-sulfur clusters, which in turn are critical for the functioning of the ETC enzyme complexes. Therapeutic agents which, in addition to being antioxidants also increase FXN, can be good drugs to counter FRDA. In Chapter 2, the synthesis of phenothiazine analogues are described. Moreover, their efficacy as antioxidants and their ability to increase FXN are described. Finally, the synthesis of a reduced salt form of one analogue and its ability to cross the blood brain barrier (BBB) in mouse models of the disease is also described.
In Chapter 3, to discover potent neuroprotective drugs, a pair of regioisomeric benzoquinone analogues has been synthesized. The compounds were tested for their efficacy as antioxidants. Additionally, two pyrimidinol based redox cores were analyzed electrochemically to enable a better understanding of the mechanism of action of the multifunctional radical quencher (MRQ) class of antioxidants.
FRDA is a progressive neurodegenerative disease caused by insufficient expression of frataxin (FXN). FXN is instrumental in the assembly of iron-sulfur clusters, which in turn are critical for the functioning of the ETC enzyme complexes. Therapeutic agents which, in addition to being antioxidants also increase FXN, can be good drugs to counter FRDA. In Chapter 2, the synthesis of phenothiazine analogues are described. Moreover, their efficacy as antioxidants and their ability to increase FXN are described. Finally, the synthesis of a reduced salt form of one analogue and its ability to cross the blood brain barrier (BBB) in mouse models of the disease is also described.
In Chapter 3, to discover potent neuroprotective drugs, a pair of regioisomeric benzoquinone analogues has been synthesized. The compounds were tested for their efficacy as antioxidants. Additionally, two pyrimidinol based redox cores were analyzed electrochemically to enable a better understanding of the mechanism of action of the multifunctional radical quencher (MRQ) class of antioxidants.
ContributorsBandyopadhyay, Indrajit (Author) / Hecht, Sidney M. (Thesis advisor) / Gould, Ian R (Committee member) / Trovitch, Ryan (Committee member) / Arizona State University (Publisher)
Created2019
Description
The field of Ionic Liquid (IL) research has received considerable attention during the past decade. Unique physicochemical properties of these low melting salts have made them very promising for applications in a many areas of science and technology such as electrolyte research, green chemistry and electrodeposition. One of the most important parameters dictating their physicochemical behavior is the basicity of their anion. Using four sets of Protic Ionic Liquids (PILs) and spectroscopic characterization of them, a qualitative order for anion basicity of ILs is obtained.
Protic Ionic Liquids are made by proton transfer form a Brønsted acid to a base. The extent of this transfer is determined by the free energy change of the proton transfer process. For the cases with large enough free energy change during the process, the result is a fully ionic material whereas if the proton transfer is not complete, a mixture of ions, neutral molecules and aggregates is resulted. NMR and IR spectroscopies along with electrochemical and mechanical characterization of four sets of PILs are used to study the degree of ionicity.
Protic Ionic Liquids are made by proton transfer form a Brønsted acid to a base. The extent of this transfer is determined by the free energy change of the proton transfer process. For the cases with large enough free energy change during the process, the result is a fully ionic material whereas if the proton transfer is not complete, a mixture of ions, neutral molecules and aggregates is resulted. NMR and IR spectroscopies along with electrochemical and mechanical characterization of four sets of PILs are used to study the degree of ionicity.
ContributorsHasani, Mohammad (Author) / Angell, C. Austen (Thesis advisor) / Yarger, Jeffrey L (Committee member) / Gould, Ian R (Committee member) / Arizona State University (Publisher)
Created2016
Description
Hydrothermal environments are important locales for carbon cycling on Earth and elsewhere in the Universe. Below its maximum temperature (~73 °C), microbial photosynthesis drives primary productivity in terrestrial hydrothermal ecosystems, which is thought to be performed by bacterial phototrophs in alkaline systems and eukaryotic algae in acidic systems, yet has received little attention at pH values intermediate to these extremes. Sequencing of 16S and 18S rRNA genes was performed at 12 hot springs with pH values 2.9-5.6 and revealed that cyanobacteria affiliated with the genus Chlorogloeopsis and algae of the order Cyanidiales coexisted at 10 of the sites. Cyanobacteria were present at pH values as low as 2.9, which challenges the paradigm of cyanobacteria being excluded below pH 4. Presence of the carotenoid β-cryptoxanthin in only 2 sites and quantitative PCR data suggest that algae were inactive at many of the sites when sampled. Spatial, but perhaps not temporal, overlap in the habitat ranges of bacterial and eukaryal microbial phototrophs indicates that the notion of a sharp transition between these lineages with respect to pH is untenable.
In sedimentary basins, biosphere-derived organic carbon is subjected to abiotic transformations under hydrothermal conditions. Benzaldehyde was experimentally evaluated as a model to assess the chemistry of aldehydes under these conditions. It was first demonstrated that gold, a traditional vessel material for hydrothermal experiments, caused catalysis of benzaldehyde degradation. Experiments in silica tubes were performed at 250, 300, and 350 °C yielding time-dependent data at several starting concentrations, which confirmed second-order kinetics. Therefore, disproportionation was expected as a major reaction pathway, but unequal yields of benzoic acid and benzyl alcohol were inconsistent with that mechanism. Consideration of other products led to development of a putative reaction scheme and the time dependencies of these products were subjected to kinetic modeling. The model was able to reproduce the observed yields of benzoic acid and benzyl alcohol, indicating that secondary reactions were responsible for the observed ratios of these products. Aldehyde disproportionation could be an unappreciated step in the formation of carboxylic acids, which along with hydrocarbons are the most common organic compounds present in natural systems.
In sedimentary basins, biosphere-derived organic carbon is subjected to abiotic transformations under hydrothermal conditions. Benzaldehyde was experimentally evaluated as a model to assess the chemistry of aldehydes under these conditions. It was first demonstrated that gold, a traditional vessel material for hydrothermal experiments, caused catalysis of benzaldehyde degradation. Experiments in silica tubes were performed at 250, 300, and 350 °C yielding time-dependent data at several starting concentrations, which confirmed second-order kinetics. Therefore, disproportionation was expected as a major reaction pathway, but unequal yields of benzoic acid and benzyl alcohol were inconsistent with that mechanism. Consideration of other products led to development of a putative reaction scheme and the time dependencies of these products were subjected to kinetic modeling. The model was able to reproduce the observed yields of benzoic acid and benzyl alcohol, indicating that secondary reactions were responsible for the observed ratios of these products. Aldehyde disproportionation could be an unappreciated step in the formation of carboxylic acids, which along with hydrocarbons are the most common organic compounds present in natural systems.
ContributorsFecteau, Kristopher Michael, 1986- (Author) / Shock, Everett L (Thesis advisor) / Gould, Ian R (Committee member) / Hartnett, Hilairy E (Committee member) / Arizona State University (Publisher)
Created2016
Description
The addition of aminoalkyl-substituted 2,6-bis(imino)pyridine (or pyridine diimine, PDI) ligands to [(COD)RhCl]2 (COD = 1,5-cyclooctadiene) resulted in the formation of rhodium monochloride complexes with the general formula (NPDI)RhCl (NPDI = iPr2NEtPDI or Me2NPrPDI). The investigation of (iPr2NEtPDI)RhCl and (Me2NPrPDI)RhCl by single crystal X-ray diffraction verified the absence of amine arm coordination and a pseudo square planar geometry about rhodium. Replacement of the chloride ligand with an outer-sphere anion was achieved by adding AgBF4 directly to (iPr2NEtPDI)RhCl to form [(iPr2NEtPDI)Rh][BF4]. Alternatively, this complex was prepared upon chelate addition following the salt metathesis reaction between AgBF4 and [(COD)RhCl]2. Using the latter method, both [(NPDI)Rh][BF4] complexes were isolated and found to exhibit κ4-N,N,N,N-PDI coordination regardless of arm length or steric bulk. In contrast, the metallation of PPDI chelates featuring alkylphosphine imine substituents (PPDI = Ph2PEtPDI or Ph2PPrPDI) resulted in the formation of cationic complexes featuring κ5-N,N,N,P,P-PDI coordination in all instances, [(PPDI)Rh][X] (X = Cl, BF4). Adjusting the metallation stoichiometry allowed the preparation of [(Ph2PPrPDI)Rh][(COD)RhCl2], which was characterized by multinuclear NMR spectroscopy and single crystal X-ray diffraction.
ContributorsLevin, Hagit Ben-Daat (Author) / Trovitch, Ryan J (Thesis advisor) / Gould, Ian R (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2016