This dissertation describes the design, synthesis and biological evaluation of novel CDK5/p25 small molecule inhibitors. Cyclin dependent kinase 5 (CDK5) is a proline directed serine/threonine kinase which plays an important role in the pathology of Alzheimer's disease (AD). CDK5/p25 has been implicated in hyperphosphorylation of tau protein which forms neurofibrillary tangles (NFTs), a contributing factor to the pathology of Alzheimer's disease (AD). Based on the deposited X-ray crystal structure of CDK5/p25 with a non-selective CDK inhibitor R-Roscovitine (PDB ID: 1UNL), eight series of novel compounds with a benzimidazole core were designed, synthesized and tested as inhibitors of CDK5/p25. An efficient synthesis of trisubtituted benzimidazoles was developed to explore the SAR at the 1-, 4-, and 6- positions of the benzimidazole core. X-ray crystal structure verification of an intermediate confirmed selective alkylation of the N-1 position of the benzimidazole scaffold. Synthesis of N-1, N-4, C6-O, C6-N, C6-C and C-2 substituted benzimidazoles were achieved via Mitsunobu coupling, Suzuki Miyaura coupling, Buchwald coupling and reductive alkylation strategies. Aminothiazole scaffolds are an established class of CDK inhibitors including CDK5. A molecular hybridization technique was applied to the design of a series of 2-, 5- disubstituted aminothiazoles incorporating structural features of both the Meriolins, natural product CDK inhibitors, and known aminothiazole scaffolds. Synthetic techniques employed included aryl lithiation, deoxygenation and acylation. / Mylan School of Pharmacy and the Graduate School of Pharmaceutical Sciences; / Medicinal Chemistry / PhD; / Dissertation;

Decreasing fossil fuel reserves and environmental concerns necessitate a shift toward biofuels. However, the chemistry of many biomass to fuel conversion pathways remains to be thoroughly studied. The future of biorefineries thus depends on developing new pathways while optimizing existing ones. Here, potential chemicals are added to create a superstructure, then an algorithm is run to enumerate every feasible reaction stoichiometry through a mixed integer linear program (MILP). An optimal chemical reaction pathway, taking into account thermodynamic, safety, and economic constraints is then found through reaction network flux analysis (RNFA). The RNFA is first formulated as a linear programming problem (LP) and later recast as an MILP in order to solve multiple alternate optima through integer cuts. A graphical method is also developed in order to show a shortcut method based on thermodynamics as opposed to the reaction stoichiometry enumeration and RNFA methods. A hypothetical case study, based on the conversion of woody biomass to liquid fuels, is presented at the end of the work along with a more detailed look at the glucose and xylose to 2-mthyltetrahydrofuran (MTHF) biofuel production pathway.

No description available.

Nuclear magnetic resonance (NMR) yields remarkably detailed structural information about virtually any molecule. However, its application to non-equilibrium systems is hampered by a lack of sensitivity. To increase the amount of signal that can be obtained from a NMR experiment, various hyperpolarization schemes have been previously introduced. One such technique is dynamic nuclear polarization (DNP), which can enhance NMR sensitivity by several orders of magnitude. The work detailed here focuses on the development of methods utilizing DNP to study non-equilibrium systems such as chemical and biochemical reactions in real-time. To work with hyperpolarized samples, we have designed and constructed a rapid injection and mixing system. This system allows samples to be transported between superconducting magnets used for polarization and for NMR spectroscopy in less than two seconds. Rapid transport is essential for successful use of samples with short spin-lattice relaxation times. For the study of reactions under non-equilibrium conditions, the system provides the additional capability for samples to be mixed with a second, unpolarized reagent. A chromogenic trypsin catalyzed ester hydrolysis reaction was used to validate the DNP-NMR technique as a tool for kinetic analysis. It is shown that the DNP-NMR method agrees with the conventional UV method within the uncertainty of the measurement. Hyperpolarization in this modality presents both challenges and opportunities, each of which motivate the development of new NMR techniques. In addition to the determination of kinetics, DNP-NMR is amenable to mechanistic analysis of a reaction. We have developed a technique based on selective inversion of spin-polarization, which allows for mapping of atoms between reactant and product of a reaction. This scheme was applied to a Grignard reaction, demonstrating applicability to organic reactions. Signal averaging, as it is applied for conventional multi-dimensional correlation spectroscopy cannot always be applied easily when using hyperpolarized sample. For the rapid measurement of heteronuclear correlation spectra, we have developed a technique utilizing the differential scaling of scalar coupling under off-resonance irradiation. Although DNP-NMR yields spectra of outstanding quality even with small quantities of sample, peak intensities are not quantitative. It is nevertheless possible to compare peak multiplets obtained from fractionally isotope labeled samples. Using biosynthetically labeled lipids from E. Coli cells, we showed that the resulting labeling patterns reflect their biosynthetic pathways. As a final case-study employing several of these newly developed methods, the uronate isomerase catalyzed isomerization of glucuronate into fructuronate was studied. The ability to follow the reaction in real-time while directly observing all anomeric forms of the reactant and product permits the independent determination of kinetics for each anomeric form of substrate and product. This study revealed the anomeric specificity of the enzyme.

SUMMARY The moenomycin-type compounds are known to inhibit selectively the enzyme penicillin binding protein 1b (PBP 1b) that catalyses the transglycosylation reaction in the biosynthesis of bacterial cell wall peptidoglycan. The moenomycins (see moenomycin A12) have been shown to interfere with this biosynthetic step interacting with the enzyme(s). The moenomycins do not induce resistance readily. A weak point in this respect may, however, be the phosphate bond to unit F. Its cleavage by a yet poorly characterized enzyme is the only enzymatic degradation reaction of the moenomycins that is known to-date. With this in mind we started a programme aimed at synthesizing trisaccharide analogues of moenomycin A12 in which the phosphate oxygen at C-1 of unit F is replaced by a CH2 group. It seemed important to retain all other functional groups in ring F as present in moenomycin since they are known to be of major importance as far as antibiotic activity is concerned. It appeared that the commercially available and cheap b-D-galactose-pentaacetate 30 would be an interesting starting material for this synthesis. In this work, the synthesis began with the introduction of the C-glycoside appendage at position 1 according to Giannis et al., thus forming the allyl C-galactopyranoside 34, a substance that represents the first C-glycosyl backbone for the synthesis of the glycosyl acceptors. The total synthesis of the glycosyl acceptors is shown in Scheme 6.1. We wanted to convert the C-allyl glycoside 34 into its propenyl analogue. Attempts to achieve this with singlet oxygen and palladium-mediated reaction proved fruitless. On the other hand, ene reaction of 34 with 4-phenyltriazolin-3,5-dione in CH2Cl2 provided 56 in 83 % yield. Ozonolysis of this alkene (-70 °C, MeOH-CH2Cl2) and subsequent quenching with dimethyl sulfide, followed by reduction of the crude aldehyde with sodium acetoxyborohydride (prepared from NaBH4 and AcOH in THF) furnished the primary alcohol 35 (85 %). This alcohol was converted into the mesylate 60 (60 %), and this in turn into the bromide 61 (80 %) by heating it at 80 °C with tetrabutylammonium bromide in toluene. The acetate groups were hydrolysed using Zemplén conditions to furnish 62 quantitatively. The primary hydroxyl group in 62 was protected as a tBuPh2Si ether 63 (85 %) on reaction with TBDPSCl in DMF at 0 °C, and as a tBuMe2Si ether 94 (87 %) on reaction with TBDMSCl in DMF at 0 °C in the presence of imidazole. PTScatalysed isopropylidenation of the 3,4-diols 63 and 94 with 2,2-dimethoxypropane in dry acetone gave the 3,4-O-acetonide derivatives 53 (88 %) and 95 (90 %), respectively. On the other hand, the glycosyl acceptor 53 was converted into the glycosyl acceptor 92. The free hydroxyl group in compound 53 was protected as an acetate group on reaction with acetic anhydride in pyridine in the presence of DMAP giving 89 (88 %). The silyl ether in 89 was cleaved with a molar solution of TBAF in THF affording compound 90 in 87 % yield. The free hydroxyl group in 90 was then subjected to an oxidation using the TEMPO method affording the aldehyde which was in turn oxidised with sodium chlorite to the corresponding acid. The acid was converted to the amide 91, making use of Staab's method, in which the acid was activated with CDI in dichloromethane to give the imidazolide, which upon reaction with ammonia furnished the amide 91 in an overall yield of 95 %. The required glycosyl acceptor 92 was obtained in quantitative yield by cleavage of the ester bond at position 5 under Zemplén conditions. Disaccharide formation was achieved employing the Jacquinet and Blatter method, which involves the use of glycosyl donor 67 and TMSOTf. No reaction was observed between this donor and acceptor 92, which may reflect the low nucleophilicity of the acceptor. On the contrary, glycosylation with acceptor 53 gave 68 (79 %). Deprotection of the silyl group in the disaccharide 68 was easily accomplished on treatment with a molar solution of TBAF in THF at RT affording 71 (89 %). Synthesis of the uronamide 72 was achieved after three major steps, in an overall yield of 98 %. Oxidation of the primary hydroxyl group in unit F to the corresponding aldehyde was accomplished with sodium hypochlorite and TEMPO. Oxidation of the crude aldehyde to the carboxylic acid with sodium chlorite followed by amide formation according to Staab gave 72. Removal of the isopropylidene group from 72 with trifluoroacetic acid (TFA) at RT furnished the diol 73 (89 %). Introduction of the carbamoyl group at C-4F position was achieved in two steps. Conversion of the diol 73 into the cyclic carbonate 76 with CDI in CH2Cl2 (84 %) and subsequent ring opening of this carbonate by bubbling a stream of gaseous ammonia into the CH2Cl2 solution at 0 °C gave 74 (62 %) as well as its isomer 77 (21 %). Dehalogenation of the N-trichloroacetyl group was intensively studied, but interactions of other functional groups in the studied substances could not be avoided. The base-labile carbonate in 76 and the carbamoyl group in urethane 74 were cleaved under the reaction conditions. Hydrolysis of 76 with 0.5 M LiOH in MeOH-THF (1:1) followed by acetylation gave 80 (73 %), while its reduction with NaBH4 in ethanol followed by acetylation gave 82 (60 °C, 85 %; RT, 83 %). On the other hand, reduction of 74 with NaBH4 in ethanol at 60 °C followed by acetylation gave 82 (78 %), while performing the reduction step at 5 °C (THF-MeOH 4:1) or at RT (ethanol or isopropanol) gave 80 in an average yield of 65 %. In a non reproducible reaction (NaBH4, EtOH, RT, then Ac2O, pyridine, RT), the desired compound 83 (42 %) was obtained accompanied by 82 (46 %) The reaction between the N-trichloroacetyl group and NaBH3CN was also fruitless. The phosphonate grouping was installed making use of Arbuzov reaction furnishing 85 (70 %). Trisaccharides could not be obtained from the oxazoline donor 42 (prepared from chitobiose octaacetate 86) through its reaction with acceptor 53. There was also no coupling product between the recently synthesized donor 88 and the acceptor 92. However, in this work, trisaccharide formation was achieved through the glycosylation reaction of donor 88 and acceptor 95 in 50 % yield (-30 °C, 1,2-dichloroethane, 3 Å, TMSOTf-TEA). Selective deprotection of the TBDMS group in compound 96 was accomplished at -10 °C with 1 eq of a molar solution of TBAF in THF. The free hydroxyl group of 97 was subjected to an oxidation using the TEMPO method affording the aldehyde. After oxidation of the aldehyde with sodium chlorite, the resulting carboxylic acid was converted according to Staab's method into the amide 93 in an overall yield of 95 % (based on 96). There were difficulties in converting the N-phthalimido group in 93 to the N-acetyl group which is necessary for biological activity of moenomycin-type compounds, since the reactions were accompanied by elimination of HBr. In conclusion, the synthetic methods employed in this work allow to prepare the di- and trisaccharides C-phosphonate analogues of moenomycin A12. / Synthese von Phosphonat-Analoga des Antibiotikums Moenomycin A12 Universität Leipzig, Dissertation Diese Arbeit enthält 130 Seiten, 73 Abbildungen, 1 Tabelle, 156 Literaturangaben Referat: Im Rahmen der vorliegenden Arbeit wurden C-Glycosid-Di- und Trisaccharid-Bausteine des Antibiotikums Moenomycin A12 ausgehend von b-D-Galactose-pentaacetat hergestellt. Das Ausgangmaterial wurde in D-Galactoheptonamid übergeführt. Die Einheit F des Disaccharidbausteins hat alle Substituenten, die die Einheit F des Moenomycins A12 hat. Der ausgearbeitete Syntheseweg sollte zur Synthese anderer Analoga geeignet sein.

Thesis (Ph. D.)--Indiana University, 2005. / Includes bibliographical references (leaves 220-228). Also available online (PDF file) by a subscription to the set or by purchasing the individual file.

Thesis (Ph.D.)--Indiana University, School of Health, Physical Education, and Recreation, 2005. / Includes bibliographical references (leaves 220-228).

Thesis (Ph.D.)--University of Melbourne, School of Chemistry, 2009. / Typescript. Includes bibliographical references.

Thesis (M.A.)--University of British Columbia, 2003. / Includes bibliographical references (leaves 154-170).

Thesis is focusing on influence of caffeine on the change of reaction time of individual. The theoretical part consists of the introduction of the specific subject and is following by information about positive and negative caffeine effect on the human body. Certain part of dissertation presents some liquid food products, where caffeine is included. The description of the reaction time of the individual before and after consumption is mentioned as well. The practical part of thesis pays attention to the experimentation with the pre-selected sample of person. The test itself was based upon usage of the reaction measurement tool with the optical stimulus for inputs. The objective of the practical part was to compare the influence of caffeine, and its specific amount, on the reaction abilities of selected individuals. Recorded data have been than statically evaluated, and prepared to final comparison. Based on receiving information the unequivocal deduction was determined.