Student Number : 9006831D - PhD thesis - School of Chemistry - Faculty of Science / The ligand substitution reactions of aquacobalamin are fast and hence the usual inertness of the d6 Co(III) ion has been modified. It is well established that the reactions proceed through a dissociative interchange mechanism; however, previous ligand studies were performed in a KCl medium, which led to the formation of the more substitution-inert chloro complex. The kinetics of aquacobalamin were reinvestigated with the ligands N3–, NO2–, SCN–, S2O32–, OCN– and SeCN– in a NaNO3 medium. The reactions proceeded too rapidly for saturation kinetics to be observed and hence only the second-order rate constants could be obtained. These were corrected for pH and determined as a function of temperature, from which the activation parameters were determined. The donor atom of the ambidentate ligands were investigated and correlations were found between the Mulliken population on the donor atom, the energy of the highest occupied molecular orbital (HOMO) with σ symmetry, and Δ, the enthalpy of activation, and Δ, the entropy of activation, respectively. Good correlations occurred when the donor atoms were taken to be N for SCNII‡kHII‡kS– and NO2–; S for S2O32–; O for OCN– and Se for SeCN–. The effect that changing the environment of aquacobalamin has on its kinetics was observed by determining the rate constants for the reaction of pyridine with aquacobalamin in water and 70% ethanol. The rates were faster in water and the activation parameters obtained for the reaction of aquacobalamin with pyridine in 70% ethanol are larger than they are for the reaction in water. The larger ΔH‡ arises due to less bond formation between pyridine and Co in the transition state and ΔS‡ is larger because it is dominated by the freeing of the coordinated water i.e. bond breaking is the dominant process in the transition state. The effects of a bulkier ligand than water on the kinetics of aquacobalamin were investigated. The temperature dependence of the kinetics of the substitution of I– in iodocobalamin by imidazole, N3– and S2O32– was studied. Despite the increase in size of the departing ligand there is still nucleophilic participation of the incoming ligand in the transition state and hence the reaction still proceeds via an Id mechanism. In order to probe the cis-effect of the corrin in vitamin B12 derivatives, comparative studies were undertaken of the reactions of aquacobalamin and aqua-10-Xcobalamin, X = Cl, NO, NH2, where the H at C10 was replaced with an electron-donating (Cl, NH2) or electron-withdrawing (NO) group. Formation constants were obtained for aquacobalamin and aqua-10-chlorocobalamin for the substitution of coordinated H2O with various anions (N3–, NO2–, SCN–, S2O32–, OCN–, SeCN–) and neutral N-donor ligands (CH3NH3, pyridine, imidazole). The anionic ligands bind more strongly to aqua-10-chlorocobalamin than to aquacobalamin with log K values larger by between 0.10 and 0.63 (average 0.26) larger. The converse is true for the neutral N-donor ligands, where log K is smaller by between 0.17 and 0.3 (average 0.25). Semi-empirical molecular orbital (SEMO) calculations using the ZINDO/1 model on the hydroxo complexes show that charge density is delocalised from the axial donor atom to the metal and Cl. Thus the anionic ligands bind more strongly to aqua-10-chlorocobalamin because of the ability of the metal and the Cl at C10 to accept charge density from the ligand. The cobalt ion in aqua-10-chlorocobalamin is more electron rich than it is in aquacobalamin and so it is less likely to accept further electron density from a neutral axial donor ligand. This results in the stability being lower than that of aquacobalamin. The reaction kinetics of the substitution of H2O in aqua-10-chlorocobalamin were determined for the ligands N3– and pyridine. The reaction proceeds via a dissociative interchange mechanism since saturation was seen for pyridine and not for N3–. The activation parameters, ΔH‡ and ΔS‡, are lower for aqua-10-chlorocobalamin than aquacobalamin and hence it can be deduced that bond breaking between the coordinated water and the cobalt atom is more dominant in aquacobalamin. The rates of reaction are faster for aquacobalamin than they are for aqua-10-chlorocobalamin. SEMO calculations show that as the Co–O bond is stretched, the charge density on Co in aquacobalamin is always lower than that on aqua-10-chlorocobalamin, suggesting that aquacobalamin is a better electrophile towards the incoming ligand, thereby explaining the faster kinetics. Aqua-10-nitrosocobalamin was synthesised and characterised by FAB(MS), NMR and UV-vis spectroscopy. The strongly electron-withdrawing NO group has deactivated the metal ion towards ligand substitution, with neither 1.2 M pyridine nor 0.7 M N3– showing any spectroscopic evidence for the displacement of the axial H2O ligand. This provides further evidence that the electronic structure of the corrin ring can directly influence the ligand-binding properties of the metal. Aqua-10-aminocobalamin was synthesised from aqua-10-nitrosocobalamin but is unstable in solution. Hence, only a preliminary UV-vis study could be undertaken with the compound. This study shows that the shifts in the bands occur towards longer wavelengths than that of aqua-10-chlorocobalamin, suggesting that the amino group at the C10 position donates more electron density to the cobalt centre than the chloro group.

African trypanosomes are protozoan blood parasites that infect both humans and livestock. BALB/c mice are highly susceptible to experimental infections by Trypanosoma congolense while C57BL/6 mice are relatively resistant, as measured by degree and pattern of parasitemia and survival time. Rapid death observed in highly susceptible BALB/c mice is due to a systemic inflammatory response syndrome (SIRS). A small subset of pathogenic, MHC class II-restricted CD4+ T cells, activated during the course of T. congolense infections, mediates early mortality in infected highly susceptible BALB/c mice via excessive synthesis of the cytokine IFN-gamma. Since these pathogenic T cells are matrixadherent, they could be distinguished from conventional Th1 cells. There is a possibility that this subpopulation of T cells has unique surface markers.<p> The complement system is highly activated in African trypanosomiasis, leading to persistent hypocomplementemia. Amplification of the alternative pathway of complement is faster in BALB/c mice than in C57BL/6 mice and the degradation of complement component C3b to complement component C3d, during the amplification of the alternative pathway of complement, proceeds faster in BALB/c than in C57BL/6 mice (Ogunremi et al., 1993). T. congolense-infected BALB/c mice have more immune complexes containing trypanosomal variant surface glycoprotein (VSG) than C57BL/6 mice in their plasma (Pan & Tabel, unpublished). T. congolense-infected BALB/c mice might have more VSG-C3d immune complexes than infected C57BL/6 mice. The receptor for complement component C3d is the cell surface molecule CR2, also referred to as CD21. It is known that CR2 is widely expressed on B lymphocytes and follicular dendritic cells. There is also some evidence that CR2 is expressed on a subpopulation of activated T cells. Binding of VSG-C3d immune complexes to the complement receptor CR2 might costimulate the CR2+ T cells to produce IFN-ã. I hypothesize that IFN-ã-producing T cells in T. congolense-infected BALB/c mice are CR2+ and that the CR2+ T cells increase in numbers in experimental murine T. congolense infections.<p> Kinetic studies were carried out by staining spleen cells of T. congolense-infected BALB/c mice for the presence of CR2 on T cells (CD3+ cells). Total numbers of spleen cells showed a 5-fold increase with progressive T. congolense infections. The total numbers of T cells in the spleen showed a 7-fold increase at day 8 post infection. The total numbers of CR2+ T cells in the spleen showed a 3 to 7-fold increase with progressive infection. Parallel studies on B lymphocytes (CD19+ cells) showed that absolute numbers of B cells in the spleen had a 5 to 6-fold increase with progressive infection. Absolute numbers of CR2+ B cells in the spleen showed a 4-fold increase at day 7 post infection. The total numbers of CR2+ cells in the spleen showed an increase while the mean numbers of CR2 molecules per cell showed a reduction with progressive infection.<p> These results show that CR2+ T cells in the spleen increase in numbers with progressive T. congolense infections in BALB/c mice. I suggest that CD4+CR2+ T cells might play a role in the pathogenesis of T. congolense infections.

African trypanosomes are protozoan blood parasites that infect both humans and livestock. BALB/c mice are highly susceptible to experimental infections by Trypanosoma congolense while C57BL/6 mice are relatively resistant, as measured by degree and pattern of parasitemia and survival time. Rapid death observed in highly susceptible BALB/c mice is due to a systemic inflammatory response syndrome (SIRS). A small subset of pathogenic, MHC class II-restricted CD4+ T cells, activated during the course of T. congolense infections, mediates early mortality in infected highly susceptible BALB/c mice via excessive synthesis of the cytokine IFN-gamma. Since these pathogenic T cells are matrixadherent, they could be distinguished from conventional Th1 cells. There is a possibility that this subpopulation of T cells has unique surface markers.<p> The complement system is highly activated in African trypanosomiasis, leading to persistent hypocomplementemia. Amplification of the alternative pathway of complement is faster in BALB/c mice than in C57BL/6 mice and the degradation of complement component C3b to complement component C3d, during the amplification of the alternative pathway of complement, proceeds faster in BALB/c than in C57BL/6 mice (Ogunremi et al., 1993). T. congolense-infected BALB/c mice have more immune complexes containing trypanosomal variant surface glycoprotein (VSG) than C57BL/6 mice in their plasma (Pan & Tabel, unpublished). T. congolense-infected BALB/c mice might have more VSG-C3d immune complexes than infected C57BL/6 mice. The receptor for complement component C3d is the cell surface molecule CR2, also referred to as CD21. It is known that CR2 is widely expressed on B lymphocytes and follicular dendritic cells. There is also some evidence that CR2 is expressed on a subpopulation of activated T cells. Binding of VSG-C3d immune complexes to the complement receptor CR2 might costimulate the CR2+ T cells to produce IFN-ã. I hypothesize that IFN-ã-producing T cells in T. congolense-infected BALB/c mice are CR2+ and that the CR2+ T cells increase in numbers in experimental murine T. congolense infections.<p> Kinetic studies were carried out by staining spleen cells of T. congolense-infected BALB/c mice for the presence of CR2 on T cells (CD3+ cells). Total numbers of spleen cells showed a 5-fold increase with progressive T. congolense infections. The total numbers of T cells in the spleen showed a 7-fold increase at day 8 post infection. The total numbers of CR2+ T cells in the spleen showed a 3 to 7-fold increase with progressive infection. Parallel studies on B lymphocytes (CD19+ cells) showed that absolute numbers of B cells in the spleen had a 5 to 6-fold increase with progressive infection. Absolute numbers of CR2+ B cells in the spleen showed a 4-fold increase at day 7 post infection. The total numbers of CR2+ cells in the spleen showed an increase while the mean numbers of CR2 molecules per cell showed a reduction with progressive infection.<p> These results show that CR2+ T cells in the spleen increase in numbers with progressive T. congolense infections in BALB/c mice. I suggest that CD4+CR2+ T cells might play a role in the pathogenesis of T. congolense infections.

The enzyme carbonic anhydrase (CA), catalysing the interconversion between CO2 and HCO3', has long been known to be present in plants as well as in animals. Several of the animal isozymes, but none of the plant CAs, have been extensively studied. When the first plant CA cDNA sequences were published in 1990, it was obvious that the animal and plant CAs represent evolutionarily distinct families with no significant sequence homology between the families. Pea CA is synthesised as a precursor and subsequently processed at the import into the chloroplast. When we purified CA from pea leaves two oligomeric forms with molecular masses around 230 kDa were obtained. One form was homogenous while the other form contained subunits of two different sizes. The larger subunit has an acidic and highly charged N-terminal extension, consisting of 37 residues. We propose that the sequence that precedes the cleavage site resulting in the large subunit represents the functional transit peptide, directing CA to the chloroplast. Neither the transit peptide nor the acidic 37-residue peptide were found to affect the folding, activity or oligomerisation of pea CA. Kinetic investigations showed that pea CA requires a reduced environment and high concentrations of buffer for maximal catalytic activity. High buffer concentrations result in a faster turnover of the enzyme (kcat) while the efficiency (kcatlKm) is not affected. This is consistent with a ping-pong mechanism with the buffer as the second substrate. Both kcat and kcatlKm increase with pH but the dependences cannot be described by simple titration curves. SCN' is an uncompetitive inhibitor at high pH and a noncompetitive inhibitor at neutral and low pH. This is in accordance with the mechanistic model, previously proposed for human CAM, involving a zincbound water molecule as a catalytic group. In this model, the carbon dioxide - bicarbonate interconversion, reflected by kcatlKm, is temporally separated from a rate limiting proton-transfer step. At high pH, solvent hydrogen isotope effects obtained for pea CA agree with this scheme, while they do not fit at neutral and low pH. Site-specific mutations of cysteine residues at positions 165, 269 and 272 were difficult to study, either because strong deviations from Michaelis-Menten kinetics were observed, or because the mutants were found in inclusion bodies. However, the mutant H208A was found to be a very efficient enzyme with the highest kcatlKm value obtained for any CA so far, 2.9-108 M'1s '1. With the H208A mutant an increased dependence on high buffer concentrations at low pH was obtained. At high pH, the mutant is more efficient than the unmutated enzyme. The H208A mutant is also more prone to oxidation than the wild-type enzyme. / <p>Diss. (sammanfattning) Umeå : Umeå universitet, 1994, härtill 4 uppsatser</p> / digitalisering@umu

With the increasing realization of their involvement in numerous biological processes, synthetic oligosaccharides present promising potential in drug and vaccine discovery. Selective functionalization of hydroxy groups in polyols represent a long-standing goal in chemistry since the chemical synthesis of O-glycosides often requires extensive protecting group manipulation. Organoboron catalysis is a recent strategy for regioselective activation of the equatorial hydroxy group of cis-vicinal diols. Following the initial findings that diarylborinic acid catalyzes the regioselective acylation of carbohydrate derivatives, kinetic studies were conducted to obtain better insight on the mechanism. Thereafter, the ability of diarylborinic acid to catalyze the regioselective alkylation of carbohydrates was demonstrated. Finally, investigations in the capability of diarylborinic acid to influence regiochemical outcome of glycosylation reactions were explored. Similarly, kinetic experiments were devised to shed light on the mechanism of the reaction.

With the increasing realization of their involvement in numerous biological processes, synthetic oligosaccharides present promising potential in drug and vaccine discovery. Selective functionalization of hydroxy groups in polyols represent a long-standing goal in chemistry since the chemical synthesis of O-glycosides often requires extensive protecting group manipulation. Organoboron catalysis is a recent strategy for regioselective activation of the equatorial hydroxy group of cis-vicinal diols. Following the initial findings that diarylborinic acid catalyzes the regioselective acylation of carbohydrate derivatives, kinetic studies were conducted to obtain better insight on the mechanism. Thereafter, the ability of diarylborinic acid to catalyze the regioselective alkylation of carbohydrates was demonstrated. Finally, investigations in the capability of diarylborinic acid to influence regiochemical outcome of glycosylation reactions were explored. Similarly, kinetic experiments were devised to shed light on the mechanism of the reaction.

Addition reactions of ten neutral nucleophiles and seven anionic nucleophiles with the pentaosmium pentadecacarbonyl carbido cluster Os5C(CO)15 have been kinetically studied and several important reactivity trends have been established. The calculated activation parameters support an associative mechanism involving the attack of nucleophiles on the parent cluster in the rate-limiting step. Decarbonylation reactions of neutral arachno clusters Os5C(CO)15L have also been kinetically studied and different reactivity trends have been observed. Reactions of Os5C(CO)15 with both neutral and anionic nucleophiles produce corresponding arachno clusters in good yield. Neutral arachno clusters decarbonylate when heated to yield corresponding nido clusters. All studied anionic arachno clusters are resistant to decarbonylation, but most of them readily react with organic acids to form corresponding hydrido clusters. Reactions of anionic arachno clusters with methyl triflate yielded several new clusters. Exploration of metal-ligand bond lengths in the respective pairs of arachno and nido clusters yielded a valuable conclusion with regard to steric effects prevalent in these molecules. The mechanisms for polyhedral structural rearrangements between arachno and nido derivatives of the pentaosmium carbido cluster have been proposed. Thermolysis of cluster Ru3[Ph2PCH(Me)PPh2](CO)10 in the presence of diphenylacetylene yields alkyne-substituted clusters Ru3(PhCCPh)[Ph2PCH(Me)PPh2](CO)8 and Ru3(PhCCPh)[Ph2PCH(Me)PPh2](CO)7 as the major products. The backbone-modified diphosphine in both clusters has facilitated the growth of single crystals suitable for X-ray crystallography. The kinetics for the conversion between two clusters have been investigated and the calculated activation parameters were found to be inconsistent with a rate-limiting step involving a dissociative loss of CO.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: see full text for abstract. / AFRIKAANSE OPSOMMING: Sien volteks vir die opsomming.

Ce travail présente une nouvelle application des alcoxyamines en chimie thérapeutique et notamment pour lutter contre le parasite plasmodium falciparum, responsable du paludisme.Cette idée repose sur l'utilisation de la chimie radicalaire. A ce jour un traitement de choix met en œuvre l'artémisinine. Le mode d'action est la destruction du parasite par la formation de radicaux libres. L'artémisinine est activée par le Fe(II) de l'hème libéré lors de la digestion de hémoglobine par le parasite. L'activation conduit à la production de radicaux alkyles qui déclenchent l'apparition d'un stress oxydatif entrainant la mort du parasite.Dans ce travail, nous avons synthétisé des alcoxyamines inédites possédant des structures chimiques particulières. Ces alcoxyamines sont activables par protonation ou par complexation par des ions métalliques tels que le Fe(II) afin de produire de façon rapide et ciblée des radicaux capable d'induire un stress oxydatif. Des études cinétiques des molécules préparées dans ce manuscrit ont aussi été effectuées. Celles-ci ont montré une réduction drastique des énergies d'activation et des temps de demi-vie des alcoxyamines activées permettant de produire des radicaux rapidement et de manière sélective. Ce travail a permis d'obtenir des alcoxyamines modèles pour valider le concept d'alcoxyamines anti-paludéens. / This work presents a new application of alkoxyamines in therapeutics chemistry, in order to fight the parasite plasmodium falciparum, a parasite responsible for malaria.This idea is based on a mechanism similar to that of artemisinin, a standard drug used for malaria. Artemisinin is activated by iron(II) of heme, released during hemoglobin digestion by the parasite. Activation leads to the formation of radicals which trigger oxidative stress leading to the death of the parasite.In this work, we have synthesized new alkoxyamines with particular chemical structures. These alkoxyamines, upon protonation or metal-complexation, produce radicals able to afford oxydative stress. Moreover kinetic studies showed a drastic reduction of the activation energies and half-lives of activated alkoxyamines in oder to produce quickly radicals, which makes it possible to obtain model alkoxyamines with anti-malarial activities.

Bacteria have exhibited a remarkable capacity to become resistant to commonly used antibacterial compounds obliging the researchers to find new target to kill them. Peptidoglycan, a polymer which is completely specific to the bacterial world and the enzymes, is an ideal target. Peptidoglycan is formed by linear glycan chains composed of alternating N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) residues cross-linked by short peptides. Among the multitude of enzymes of degradation of the peptidoglycane, the N-acetylmuramyl-L-alanine amidase have the capacity to break the bond between the peptide and the lactyl grouping of MurNAc wearing this peptide. The subject of this work was to study AmiD, a N-acetylmuramyl-L-alanine amidase from E.coli. For that purpose, two carbohydrates 1,6-anhMurNAc with a protective group at the fourth position have been synthesised on gram scale in seven steps. After that, we have realized a structural study at the level of the peptide chain by miming the structure of the peptidoglycane. First, different amide compounds have been prepared. In a second time, we have synthesised carbohydrate compounds with one, two and three amino acids in the peptide chain. Finally, two carbohydrates with a triazole in the peptide chain have been prepared by click chemistry from a synthesised azoture precursor. All compounds have been synthesised with a chromatic group at the end of the peptide chain in order to facilitated the HPLC detection of the residue after hydrolysis by AmiD. Substrates studies, inhibition studies and kinetic studies have been realised with these carbohydrates. This work present also the first results of the synthesis of 1,6-anhydro-4-fluoroMurNAc, a possible inhibitor of bacterial growth. If the peptide chain contains a minimum of dipeptide residue (L-Ala--D-Glu), our results pointed that AmiD is able to cleave the amide bond between the lactyl group of the MurNAc and the -amino group of L-Ala. In the presence of a tripeptide chain (L-Ala--D-Glu-L-Lys) higher hydrolysis rates have been observed. Furthermore, the m-A2pm found in the natural substrate of AmiD can be replaced by L-Lys which facilitates the synthesis of the MurNAc derivatives.