This thesis describes stereoselective syntheses of four amino acids, three of which are C-glycosidic analogues of glycosylated amino acids. The overall goal of the project was to probe the interactions between MHC molecules, glycopeptide antigens and T cell receptors, that are essential for development of collagen induced arthritis. Collagen induced arthritis is a frequently used mouse model for rheumatoid arthritis, an autoimmune disease that attacks joint cartilage and leads to a painful and eventually crippling condition. The thesis is based on four studies. The first study describes the synthesis of hydroxylysine, an amino acid that is found in collagen and is an important constituent of the glycopeptide proposed as an antigen in collagen induced arthritis. During the synthesis of hydroxylysine some new insight into the mechanism of the reductive opening of p-methoxybenzylidene acetals was obtained. The remaining three studies deals with the synthesis of C-glycosidic analogues of glycosylated amino acids, hydroxy norvaline, threonine and hydroxylysine.The synthesis of each amino acid required control of several stereogenic centra and utilizes a variety of approaches such as use of stereoselective reactions, chiral auxilaries, chiral templates and asymmetric catalysis. The C-glycosidic analogues of galactosylated hydroxynorvaline and hydroxylysine were incorporated in glycopeptides from type II collagen and evaluated in T cell response assays. It was found that the T cells were stimulated by the C-glycopeptides, but that higher concentrations were required than for the native O-glycopeptide

Carbohydrates are abundant in nature and have functions ranging from energy storage to acting as structural components. Analysis of carbohydrate structures is important and can be used for, for instance, clinical diagnosis of diseases as well as in bacterial studies. The complexity of glycans makes it difficult to determine their structures. NMR spectroscopy is an advanced method that can be used to examine carbohydrates at the atomic level, but full assignments of the signals require much work. Reliable automation of this process would be of great help. Herein studies of Escherichia coli O-antigen polysaccharides are presented, both a structure determination by NMR and also research on glycosyltransferases which assemble the polysaccharides. The computer program CASPER has been improved to assist in carbohydrate studies and in the long run make it possible to automatically determine structures based only on NMR data. Detailed computer studies of glycans can shed light on their interactions with proteins and help find inhibitors to prevent unwanted binding. The WaaG glycosyltransferase is important for the formation of E. coli lipopolysaccharides. Molecular docking analyses of structures confirmed to bind this enzyme have provided information on how inhibitors could be composed. Noroviruses cause gastroenteritis, such as the winter vomiting disease, after binding human histo-blood group antigens. In one of the projects, fragment-based docking, followed by molecular dynamics simulations and binding free energy calculations, was used to find competitive binders to the P domain of the capsid of the norovirus VA387. These novel structures have high affinity and are a very good starting point for developing drugs against noroviruses. The protein targets in these two projects are carbohydrate binding, but the techniques are general and can be applied to other research projects. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Submitted. Paper 5: Manuscript. Paper 6. Manuscript.

This thesis summarizes the results of studies on two aspects of nucleic acids. Chemically modified antisense oligonucleotides (AONs) have been evaluated with regards to their suitability for mRNA targeting in an antisense approach (Paper I – III). The chemically modified nucleotidic units 2'-O-Me-T, 2'-O-MOE-T, oxetane-T, LNA-T, azetidine-T, aza-ENA-T, carbocyclic-ENA-T and carbocyclic-LNA-T were incorporated into 15-mer AONs and targeted against a 15-mer RNA chosen from the coding region of SV-40 large T antigen. The comparative study showed that a single modified nucleotide in the AON with North-East locked sugar (oxetane-T and azetidine-T) lowered the affinity for the complementary RNA whereas North locked sugars (LNA-T, aza-ENA-T, carbocyclic-ENA-T, and carbocyclic-LNA-T) significantly improved the affinity. A comparative RNase H digestion study showed that modifications of the same type (North-East type or North type) in different sequences gave rise to similar cleavage patterns. Determination of the Michaelis-Menten parameters by kinetic experiments showed that the modified AONs recruit RNase H resulting in enhanced turnover numbers (kcat) although with weaker enzyme-substrate binding (1/Km) compared to the unmodified AON. The modified AONs were also evaluated with regards to resistance towards snake venom phosphodiesterase and human serum to estimate their stability toward exonucleases. The aza-ENA-T and carbocyclic-ENA-T modified AONs showed improved stability compared to all other modified AONs. In general, the modified AONs with North type nucleotides (except LNA-T) were found to be superior to the North-East type as they showed improved target affinity, comparable RNase H recruitment capability and improved exonuclease stability. The second aspect studied in this thesis is based on physicochemical studies of short RNA molecules utilizing NMR based pH titration and alkaline hydrolysis reactions (Paper IV – V). The NMR based (1H and 31P) pH titration studies revealed the effect of guaninyl ion formation, propagated electrostatically through a single stranded chain in a sequence dependent manner. The non-identical electronic character of the internucleotidic phosphodiesters was further verified by alkaline hydrolysis experiments. The internucleotidic phosphodiesters, which were influenced by guaninyl ion formation, were hydrolyzed at a faster rate than those sequences where such guaninyl ion formation was prevented by replacing G with N1-Me-G.

The Autumn gum moth, Mnesampela privata (Lepidoptera: Geometridae) is an endemic Australian moth whose larvae feed upon species of Eucalyptus. The moths favorite host plants are E. globulus and E. nitens which are the most important species used in commercial plantations of the Australian pulpwood industry. The autumn gum moth has become one of the most significant outbreak insects of eucalyptus plantations throughout Australia. As a consequence great financial losses to the forest industry occur. Today insecticides such as pyrethroids are used for control of eucalyptus defoliators as M. privata. The carrot psyllid, Trioza apicalis (Homoptera: Psylloidea), is one of the major pests of carrot (Daucus carota) in northern Europe. The psyllid causes curling of the carrot leafs and reduction of plant growth. Today the carrot crops are protected with the pyrethroid insecticide cypermethrin, which is toxic to aquatic organisms and is, from 2010, prohibited for use in Sweden by the Swedish Chemicals Inspectorate. An alternative to insecticides is to protect the seedlings with semiochemicals, a chemical substance or mixture of them that carries a message. This thesis describes the identification and the syntheses of semiochemicals from the above mentioned insect species. From analysis of abdominal tip extracts of M. privata females from Tasmania a blend of (3Z,6Z,9Z)-3,6,9-nonadecatriene and (3Z,6Z,9Z)-3,6,9-heneicosatriene was identified as the sex pheromone of this species. The identification of the C19- and C21-trienes was confirmed by synthesis. In the analysis of carrot leaf extracts we found a compound, α-cis-bergamotene, that induces antennal response in the carrot psyllid. This is just the beginning of the studies of trying to manipulate this psyllid with semiochemicals instead of insecticides.

An introduction to bacterial polysaccharides and the methods for structural determination are described in the first two parts of the thesis. In a structural elucidation of bacterial polysaccharides NMR experiments are important as is component analysis. A short description of immunochemical methods such as enzyme immunoassays is included. Two NMR techniques used for interaction studies, trNOE and STD NMR, are also discussed. The third part of the thesis discusses and summarizes the results from the included papers. The structures of the exopolysaccharides produced by two lactic acid bacteria are determined by one- and two dimensional NMR experiments. One is a heteropolysaccharide produced by Streptococcus thermophilus and the other a homopolysaccharide produced by Propionibacterium freudenreichii. The structure of an acidic polysaccharide from a marine bacterium with two serine residues in the repeating unit is also investigated. The structural and immunological relationship between two O-antigenic polysaccharides from Escherichia coli strain 180/C3 and O5 is discussed and investigated. Finally, interaction studies of an octasaccharide derived from the Salmonella enteritidis O-antigen and a bacteriophage are described which were performed with NMR experiments.

Transition metals have played an important role in synthetic organic chemistry for more than a century, and offer catalytic transformations that would have been impossible with classical chemistry. One of the most useful and versatile of the transition metals is palladium, which over the years has catalyzed many important carbon-carbon forming reactions. Popular cross-coupling reactions such as the Suzuki, Stille and the Heck reaction are all catalyzed by palladium, or more correctly, by palladium in its ground state, Pd(0). Recently, interest in palladium(II)-catalyzed transformations has started to grow, partly due to the development of the vinylic substitution reaction, commonly called the oxidative Heck reaction, presented in this thesis. This Pd(II)-catalyzed, ligand-modulated reaction occurs under air at room temperature, and for the first time a general protocol employing a wide range of olefins and arylboronic acids was obtained. Ligand screening showed that the bidentate nitrogen ligand, 2,9-dimethyl-1,10-phenanthroline (dmphen), was the most suitable ligand. Dmphen is believed to facilitate regeneration of active Pd(II), increase catalytic stability and improve the regioselectivity in the reaction. A mechanistic investigation was conducted using electrospray ionization mass spectrometry (ESI-MS), making it possible to observe cationic intermediates in a productive oxidative Heck arylation. The results obtained are in agreement with the previously proposed catalytic cycle. The emerging discipline of high-speed synthesis is making contributions to society’s growing demand for new chemical entities. This inspired the development of two ultrafast, microwave-accelerated carbonylation reactions with dicobalt octacarbonyl acting both as an in situ carbon monoxide supplier and reaction mediator. A wide range of symmetrical benzophenones was produced in only 6 to 10 s, using aryl iodides as the substrate. The second carbonylation reaction provided symmetrical and unsymmetrical ureas in process times ranging from 10 s to 40 minutes using primary and secondary amines.

The beauty of the wide functionality of proteins and peptides in Nature is determined by their ability to adopt three-dimensional structures. This thesis describes artificial molecules developed to mimic secondary structures similar to those found crucial for biological activities. In the first part of this thesis, we focused on post-translational modifications of a class of unnatural oligomers known as β-peptides. Through the design and synthesis of a glycosylated β3-peptide, the first such hybrid conjugate was reported. In this first report, a rather unstable 314-helical structure was found. Subsequently, a collection of six new glycosylated β3-peptides was synthesized with the aim to optimize the helical stability in water. The ability of natural proteins, i.e. lectins, to recognize the carbohydrate residue on these unnatural peptide backbones was investigated through a biomolecular recognition study. The second part of this thesis concerns the design of conformationally homogeneous scaffolds, which could be of importance for biomedical applications. In paper V, four- and five-membered cyclic all-β3-peptides were investigated for this purpose. In a subsequent paper, a completely different strategy was employed; herein, the ability of a single β2-amino acid to restrict the conformational freedom of a cyclic α-peptide was studied. In the third part of this thesis, we synthesized and investigated the folding propensities of novel backbone modified oligomers, i.e. β-peptoids (N-substituted β-Ala) with α-chiral side chains. The collective results of these studies have established the procedures required for synthesis of glycosylated β-peptides and deepened our understanding of the factors governing folding among such oligomers. Moreover, it was established that β-amino acids can be a useful tool to increase conformational stability of cyclic peptides.

Mechanistic studies on three different ruthenium-based catalysts have been performed. The catalysts have in common that they have been employed in hydrogen transfer reactions involving alcohols and ketones, amines and imines or both. Bäckvall’s catalyst, η5-(Ph5C5)Ru(CO)2Cl, finds its application as racemization catalyst in dynamic kinetic resolution, where racemic alcohols are converted to enantiopure acetates in high yields. The mechanism of the racemization has been investigated and both alkoxide and alkoxyacyl intermediates have been characterized by NMR spectroscopy and in situ FT-IR measurements. The presence of acyl intermediates supports a mechanism via CO assistance. Substantial support for coordination of the substrate during the racemization cycle is provided, including exchange studies with both external and internal potential ketone traps. We also detected an unexpected alkoxycarbonyl complex from 5-hydroxy-1-hexene, which has the double bond coordinated to ruthenium. Shvo’s catalyst, [Ru2(CO)4(μ-H)(C4Ph4COHOCC4Ph4)] is a powerful catalyst for transfer hydrogenation as well as for dynamic kinetic resolution. The mechanism of this catalyst is still under debate, even though a great number of studies have been published during the past decade. In the present work, the mechanism of the reaction with imines has been investigated. Exchange studies with both an external and an internal amine as potential traps have been performed and the results can be explained by a stepwise inner-sphere mechanism. However, if there is e.g. a solvent cage effect, the results can also be explained by an outer-sphere mechanism. We have found that there is no cage effect in the reduction of a ketone containing a potential internal amine trap. If the mechanism is outer-sphere, an explanation as to why the solvent cage effect is much stronger in the case of imines than ketones is needed. Noyori’s catalyst, [p-(Me2CH)C6H4Me]RuH(NH2CHPhCHPhNSO2C6H4-p-CH3), has successfully been used to produce chiral alcohols and amines via transfer hydrogenation. The present study shows that the mechanism for the reduction of imines is different from that of ketones and aldehydes. Acidic activation of the imine was found necessary and an ionic mechanism was proposed.

Mucin is a term used to describe a large family of heavily glycosylated proteins which are present on the surfaces of secretory epithelial cells and are overexpressed by many carcinomas. Membrane-bound mucin MUC1 is of special interest. Its backbone consists of repeating units of twenty amino acids with five potential glycosylation sites. These sites are expanded to structures like the T (Galβ(1->3)GalNAcα-Ser/Thr) and Tn (GalNAcα-Ser/Thr) antigens by the action of various glycosyltransferases. In different types of carcinomas these epitopes are being terminated by sialic acid residues to form among others: 2,3-sialyl-T and sialyl-Tn structures due to the elevated levels of different sialyltransferases. Solid-phase synthesis of the selected antigens derived from the mucin MUC1 has been developed and optimized. A chemoenzymatic approach has been used to effectively prepare 2,3-sialyl-T and 2,6-sialyl-Tn glycopeptides. The formation of intramolecular sialic acid lactones in presence of acetic acid was investigated. The stability of lactones formed from 2,3-sialyl-T towards water was studied using NMR spectroscopy and it appeared that 1''->2' lactone displayed remarkable strength to hydrolysis and it was suggested as a candidate for cancer vaccine. Gel-phase 19F NMR spectroscopy is known to be a very good tool to characterize resin-bound products using fluorinated protecting groups and linker molecules. The hydrophobic peptide LLLLTVLTV, which is a fragment from the MUC1 signal sequence, was prepared using solid-phase synthesis according to a modified Fmoc protocol with more active coupling reagent, stronger base, and the isopropylidene dipeptide Fmoc-Leu-Thr-(ΨMe,Mepro)-OH. Gel-phase 19F NMR spectroscopy was used to evaluate peptide chain aggregation and coupling and deprotection efficiency. A carbamate linker strategy proved to be effective in solid-phase synthesis of serine-based neoglycolipids with terminal amino functionality. Neoglycolipids were covalently bound to secondary amines in microtiter plates using squaric acid ester methodology. These arrays have potential to study the interactions between carbohydrates and e.g. proteins and microbes. The new fluorinated α-amino protective group [1-(4-(4-fluorophenyl)-2,6-dioxocyclohexylidene)ethyl] Fde was developed. This group is cleaved with hydrazine in DMF solution. By using amino acids protected with this group, it was possible to quantify the efficiency of peptide coupling using gel-phase 19F NMR spectroscopy.

In this thesis a computational complement to experimental observables will be presented. Computational tools such as molecular dynamics and quantum chemical tools will be used to aid in the interpretation of experimentally (NMR) obtained structural data. The techniques are applied to study the dynamical features of biologically important carbohydrates and their interaction with proteins. When evaluating conformations, molecular mechanical methods are commonly used. Paper I, highlights some important considerations and focuses on the force field parameters pertaining to carbohydrate moieties. Testing of the new parameters on a trisaccharide showed promising results. In Paper II, a conformational analysis of a part of the repeating unit of a Shigella flexneri bacterium lipopolysaccharide using the modified force field revealed two major conformational states. The results showed good agreement with experimental data. In Paper III, a trisaccharide using Langevin dynamics was investigated. The approach used in the population analysis included a least-square fit technique to match T1 elaxation parameters. The results showed good agreement with experimental T-ROE build-up curves, and three states were concluded to be involved. In Paper IV, carbohydrate moieties were used in the development of prodrug candidates, to “hide” peptide opioid receptor agonists. Langevin dynamics and quantum chemical methods were employed to elucidate the structural preference of the compound. The results showed a chemical shift difference between hydrogens across the ring for the two isomers as well as a difference in the coupling constant, when taking the dynamics into account. In Paper V, the interaction of the Salmonella enteritidis bacteriophage P22 with its host bacterium, involves an initial hydrolysis of the O-antigenic polysaccharide (O-PS). Docking calculations were used to examine the binding between the Phage P22 tail-spike protein and the O-PS repeating unit. Results indicated a possible active site in conjunction with NMR measurements.