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.

Nous avons développé de nouveaux accès pour la construction de molécules comportant les motifs Csp3-CF3 et Csp3-SCF3. Deux réactions de transfert d'hydrure sur des composés trifluorométhylés par catalyse avec des métaux de transition ont été réalisées : 1) l'isomérisation catalytique d'alcools allyliques trifluorométhylés par des complexes de fer (II); 2) le transfert d'hydrogéne énantiosélectif de céto-imines trifluorométhylées par des complexes chiraux de ruthénium en utilisant l'isopropanol comme source d'hydrure pour obtenir des amines trifluorométhylées optiquement actives avec de hauts rendements et de hautes énantiosélectivités. La trifluorométhylthiolation allylique nucléophile de dérivés de Morita-Baylis-Hillman a été étudiée. L'accès régio- et stéréosélectif aux produits SCF3 thermodynamiques a été réalisé par la combinaison de S8/CF3SiMe3/KF/DMF avec de bons rendements. Le produit cinétique a été obtenu en utilisant le réactif de Zard. / We have developed new accesses for the construction of molecules featuring Csp3-CF3 and Csp3-SCF3 motifs. Two atom-economical hydride transfer reactions of trifluoromethylated compounds by transition-metal catalysis were realized: 1) the isomerization of trifluoromethylated allylic alcohols by iron (II) complexes; 2) the enantioselective transfer hydrogenation of trifluoromethylated ketimines by a chiral complex of ruthenium and isopropanol as hydride source for the preparation of optically pure trifluoromethylated amines in high yields and high enantioselectivities. The nucleophilic allylic trifluoromethylthiolation of Morita-Baylis-Hillman derivatives was investigated. The regio- and stereoselective access to thermodynamic trifluoromethylthiolated products has been achieved by combination of S8/KFfMe3SiCF3/DMF in good yields. The kinetic trifluoromethylthiolated products were obtained by using Zard's trifluoromethylthiolating reagent.

Yes / Platinum complexes are the most widely used anticancer drugs; however, new generations of agents are needed. The organoiridium(III) complex [(η5-Cpxbiph)Ir(phpy)(Cl)] (1-Cl), which contains π-bonded biphenyltetramethylcyclopentadienyl (Cpxbiph) and C^N-chelated phenylpyridine (phpy) ligands, undergoes rapid hydrolysis of the chlorido ligand. In contrast, the pyridine complex [(η5-Cpxbiph)Ir(phpy)(py)]+ (1-py) aquates slowly, and is more potent (in nanomolar amounts) than both 1-Cl and cisplatin towards a wide range of cancer cells. The pyridine ligand protects 1-py from rapid reaction with intracellular glutathione. The high potency of 1-py correlates with its ability to increase substantially the level of reactive oxygen species (ROS) in cancer cells. The unprecedented ability of these iridium complexes to generate H2O2 by catalytic hydride transfer from the coenzyme NADH to oxygen is demonstrated. Such organoiridium complexes are promising as a new generation of anticancer drugs for effective oxidant therapy. / We thank the ERC (247450), SNSF (PA00P2_145308 for N.P.E.B.), IAS (for I.R.C.), BBSRC (for J.M.H.), Science City (AWM and ERDF), and the EPSRC for support, and Prof. Timothy Bugg and members of EC COST Action CM1105 for stimulating discussions. We also thank Professor Pat Unwin, Mike Snowden, and Rob Lazenby for their help with the electrochemical experiments and the National Cancer Institute for NCI-60 human tumor cell panel screening.

D-Arginine dehydrogenase (DADH) catalyzes the oxidation of D-arginine to imino arginine using FAD as the cofactor. The enzyme is part of a recently discovered two-enzyme complex from Pseudomonas aeruginosa involved in arginine utilization. Function of the enzyme within the organism is unknown. Work on this enzyme has been undertaken to understand the structure as well as its reaction mechanism so as to eventually assign a function to the enzyme within the physiological context. In the reductive half-reaction 2 e- and 1 H+ are transferred from the amino acid substrate to FAD cofactor. In the oxidative half-reaction the reducing equivalents from the FAD cofactor are passed to an electron acceptor that is yet to be discovered. The enzyme has been established to have no reactivity with O2. Choline oxidase (CHO) from Arthrobacter globiformis is a well characterized member of Glucose-Methanol-Choline Superfamily that reacts with molecular O2. It catalyzes the oxidation of choline to glycine betaine mediated by betaine aldehyde intermediate using FAD as the cofactor and O2 as the oxidant to regenerate oxidized FAD for further reaction. Glycine betaine, the product of the reaction is an important osmolyte that regulates nutrients for plants under stressful conditions. Therefore it is of commercial interest to genetically engineer crops that do not typically possess competent pathways for glycine betaine synthesis. In this dissertation molecular details concerning the reductive half-eaction of DADH and oxidative half-reaction of CHO have been studied using a combination of steady state kinetics, rapid kinetics, pH, multiple substrates, mutagenesis, substrate deuterium and solvent isotope effects, viscosity effects or computational approaches. In DADH, the oxidation of amino acid substrate by FAD has been shown to most likely proceed via hydride transfer mechanism in the reductive half-reaction with Glu87, Tyr53, Tyr249 and His48 emerging as key players in substrate binding, catalysis or for up keeping the integrity of the FAD cofactor. In CHO, the oxidative half-reaction proceeds without stabilization of any reaction intermediates with H atom from reduced FAD and H+ from solvent or solvent exchangeable site occurring in the same kinetic step.

京都大学 / 新制・課程博士 / 博士(人間・環境学) / 甲第23991号 / 人博第1043号 / 新制||人||245(附属図書館) / 2022||人博||1043(吉田南総合図書館) / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)教授 藤田 健一, 教授 小松 直樹, 教授 津江 広人, 教授 大江 洋平 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DFAM

Choline oxidase catalyzes the four-electron oxidation of choline to glycine betaine, a limited number of compounds that accumulate to high levels in cytoplasm to prevent dehydration and plasmolysis in adverse hyperosmotic environments. With this respect, the study of choline oxidase has potential for the development of therapeutic agents that inhibit the biosynthesis of glycine betaine, thereby rendering pathogenic bacteria susceptible to either conventional treatments or the immune system. In this study, the highly GC rich codA gene encoding for choline oxidase was cloned, expressed. The resulting enzyme was purified to high levels, allowing for detailed biochemical, mechanistic and structural characterizations. A chemical mechanism for the reaction catalyzed by choline oxidase was established by using kinetic isotope effects and viscosity effects as probes, in which the choline hydroxyl proton is not in flight in the transition state for CH bond cleavage. Furthermore, these experiments indicated that chemical steps of flavin reduction by choline and betaine aldehyde are rate limiting for the overall turnover of the enzyme. Further mechanistic characterization clearly suggested a hydride transfer mechanism that is fully quantum mechanical. The structure of choline oxidase was resolved at 1.86 Å resolution in collaboration with the group of Dr. Allen O. Orville, at the Georgia Institute of Technology, providing a structural framework that is consistent with the mechanistic studies. The results of these studies will be presented and discussed in the context of the Glucose-Methanol-Choline oxidoreductase enzyme superfamily, of which choline oxidase is a member. Previous structural and mechanistic studies of alcohol- and aldehyde-oxidizing enzymes with different cofactors, as well as the biotechnological and biomedical relevance of choline oxidase are presented in Chapter 1. Chapter 3-8 illustrate my studies on choline oxidase, including cloning, expression, purification and preliminary characterizations (Chapter 3), spectroscopic and steady state kinetics (Chapter 4), the determination of the chemical mechanism for alcohol oxidation and the investigation of the involvement of quantum mechanical tunneling (Chapter 5 and 6), the study of aldehyde oxidation (Chapter 7), and the structural determination of choline oxidase by x-ray crystallography (Chapter 8). Chapter 9 presents a general discussion of the data presented.

Choline oxidase catalyzes the flavin-dependent, two-step oxidation of choline to glycine betaine via the formation of an aldehyde intermediate. The oxidation of choline includes two reductive half-reactions followed by oxidative half-reactions. In the first oxidation reaction, the alcohol substrate is activated to its alkoxide via proton abstraction and oxidized via transfer of a hydride from the alkoxide α-carbon to the N(5) atom of the enzyme-bound flavin. In the wild-type enzyme, proton and hydride transfers are mechanistically and kinetically uncoupled. The role of Ser101 was investigated in this dissertation. Replacement of Ser101 with threonine, alanine, cysteine, or valine demonstrated the importance of the hydroxyl group of Ser101 in proton abstraction and in hydride transfer. Moreover, the kinetic studies on the Ser101Ala variant have revealed the importance of a specific residue for the optimization of the overall turnover of choline oxidase. The UV-visbible absorbance of Ser101Cys suggests Cys101 can form an adduct with the C4a atom of the flavin. The mechanism of formation of the C4a-cysteinyl adduct has been elucidated. D-arginine dehydrogenase (DADH) catalyzes the oxidation of D-amino acids to the corresponding imino acids, which are non-enzymatically hydrolyzed to α-keto acids and ammonia. The enzyme is strick dehrogenase and deoesnot react with molecular oxygen. Steady state kinetic studies wirh D-arginine and D-histidine as a substrate and PMS as the electron acceptor has been investigated. The enzyme has broad substrate specificity for D-amino acids except aspartate, glutamate and glycine, with preference for arginine and lysine. Leucine is the slowest substrate in which steady state kinetic parameters can be obtained. The chemical mechanism of leucine dehydrogenation catalyzed by DADH was explored with a combination of pH, substrate and solvent kinetic isotope effects (KIE) and proton inventories by using rapid kinetics in a stopped-flow spectrophotometer. The data are discussed in the context of the crystallographic structures at high resolutions (<1.3 Å) of the enzyme in complex with iminoarginine or iminohistidine.

The amine oxidase family of enzymes has been the center of numerous mechanistic studies because of the medical relevance of the reactions they catalyze. This study describes transient and steady-state kinetic analyses of two flavin amine oxidases, mouse polyamine oxidase (PAO) and human lysine specific demethylase (LSD1), to determine the mechanisms of amine oxidation. PAO is a flavin adenine dinucleotide (FAD)-dependent enzyme that catalyzes the oxidation of N1-acetylated polyamines. The pH-dependence of the kcat/Kamine indicates that the monoprotonated form of the substrate is required for catalysis, with the N4 nitrogen next to the site of CH bond cleavage being unprotonated. Stopped-flow spectroscopy shows that the pH-dependence of the rate constant for flavin reduction, kred, displays a pKa of 7.3 with a decrease in activity at acidic pH. This is consistent with an uncharged nitrogen being required for catalysis. Mutating Lys315 to methionine has no effect on the kcat/Kamine-pH profile with the substrate spermine, and the kred value only shows a 1.5-fold decrease with respect to wild-type PAO. The mutation results in a 30- fold decrease in kcat/KO2. Solvent isotope effects and proton inventories are consistent with Lys315 accepting a proton from a water molecule hydrogen-bonded to the flavin N5 during flavin oxidation. Steady-state and transient kinetic studies of para-substituted N,N'-dibenzyl-1,4- diaminobutanes as substrates for PAO show that the kred values for each correlate with the van der Waals volume (VW) and the value. The coefficient for VW is the same at pH 8.6 and 6.6, whereas the p value increases from -0.59 at pH 8.6 to -0.09 at pH 6.6. These results are most consistent with a hydride transfer mechanism. The kinetics of oxidation of a peptide substrate by human lysine specific demethylase (LSD1) were also studied. The kcat/KM pH-profile is bell-shaped, indicating the need for one unprotonated nitrogen next to the site of CH bond cleavage and another protonated nitrogen. The kcat and kred values are equal, and identical isotope effects are observed on kred, kcat, and kcat/KM, indicating that CH bond cleavage is rate-limiting with this substrate.

Ordered mesoporous silicas have been shown to have a variety of useful applications ranging from adsorbents for containments to supports for catalysts. While these materials have received a good deal of attention in the literature there is still much opportunity for new technologies. We present research describing a novel approach to incorporate functionality onto the pore surfaces of these materials as well as a highly active catalyst for the Suzuki-Miyaura reaction. Our approach to selectively graft functionality on to the pore walls of the mesoporous silicas SBA-15 and MCM-41 involves treating the materials loaded with a structure directing agent (SDA), with hexamethyldisilazane that passivates the external surface through silylation. Once the SDA is removed the mesopores can be functionalized selectively using standard methods. A test designed to look at the passivation layer is also described. The catalyst developed is designated Pd-SBA-15-SH(g) and it is active for the Suzuki-Miyaura reaction. The activity, recyclability and leaching of Pd-SBA-15-SH(g) was found to be superior to related materials. A mechanistic analysis suggests the catalyst is a reservoir for soluble Pd metal. A key challenge that is holding back wide scale application of ammonia borane (NH3BH3) as a hydrogen storage material for mobile applications is the dearth of regeneration strategies. Presented are our forays into the development of an organic hydride based regeneration strategy. The first phase of the project focused on the reaction between Hantzsch esters and B(C6F5)3. N-substituted Hantzsch esters were found to transfer hydride to boron in >90 % yield. Mechanistic analysis of the reaction suggests either a SET mechanism or a highly asynchronous transition state. A novel hydride transfer equilibrium promoted by B(C6F5)3 was observed and it operated at temperatures below -10 ºC. N,N-ditertbutyl-dihydroimidazole is also an effective hydride donor to B(C6F5)3 as well as other Lewis acids that are more relevant mimics to those invoked in regeneration schemes. When the redistribution of B(SPh)3 is carried out with N,N-ditertbutyl-dihydroimidazole in the presence of NEt3 and CH2Cl2 at 50 ºC, BH2(NEt)3(SPh) is formed. CH2Cl2 functions as a thiol scavenger under the reaction conditions. 1-Octene trapping experiments provided indirect evidence for the formation of diborane, a critical component in the regeneration of NH3BH3. / Thesis (Ph.D, Chemistry) -- Queen's University, 2011-09-09 14:51:54.697

Enzymes direct chemical reactions with precision and speed, making life as we know it possible. How they do this is still not completely understood, but the relatively recent discovery of subpicosecond protein motion coupled to the reaction coordinate has provided a crucial piece of the puzzle. This type of motion is called a rate-promoting vibration (RPV) and has been seen in a number of different enzymatic systems. It typically involves a compression of the active site of the enzyme which lowers the barrier for the reaction to occur. In this work we present a number of studies that probe these motions in two dehydrogenase enzymes, yeast alcohol dehydrogenase (YADH) and homologs of lactate dehydrogenase (LDH). The goal of the study on the reaction of YADH was to probe the role of the protein in proton tunneling in the enzyme, which was suggested to occur from experimental kinetic isotope effect studies. We did this using transition path sampling (TPS), which perturbatively generates ensembles of reactive trajectories to observe transitions between stable states, such as chemical reactions. By applying a quantum method that can account for proton tunneling, centroid molecular dynamics, and generating reactive trajectory ensembles with and without the method, we were able to observe the change in barrier to proton transfer upon application of the tunneling method. We found that there was little change in the barrier, showing that classical over-the-barrier transfer is dominant over tunneling in the proton transfer in YADH. We also applied the knowledge of RPVs to identify a new class of allosteric molecules, which modulate enzymatic reaction not by changing a binding affinity, but by disrupting the reactive motion of enzymes. We showed, through design of a novel allosteric effector for human heart LDH, applying TPS to a system with and without the small molecule bound, and analysis of the reaction coordinate of the reactive trajectory ensemble, that the molecule was able to disrupt the motion of the protein such that it was no longer coupled to the reaction. We also examined the subpicosecond motions of two other LDHs, from Plasmodium falciparum and Cryptosporidium parvum, which evolved separately from previously studied LDHs. We found, using TPS and reaction coordinate identification, that while the LDH from C. parvum had similar dynamics to the earlier LDHs, the LDH from P. falciparum had a earlier transition-state associated with proton transfer, not hydride transfer. This is likely due to this LDH having a larger active site pocket, increasing the amount of motion necessary for proton transfer, and, thus, the barrier to proton transfer. More work is necessary in this system to determine whether the protein is coupled with the search for the reactive conformation for proton transfer. Protein motion coupled to the particle transfer in dehydrogenases plays an important role in their reactions and there is still much work to be done to understand the extent and role of RPVs.