Computer modeling of enzymes is a valuable complement to experiments. Quantum chemical studies of enzymatic reactions can provide a detailed description of the reaction mechanism and elucidate the roles of various residues in the active site. Different reaction pathways can be analyzed, and their feasibility be established based on calculated energy barriers. In the present thesis, density functional theory has been used to study the active sites and reaction mechanisms of three different enzymes, cytosine deaminase (CDA) from Escherichia coli, ω-transaminase from Chromobacterium violaceum (Cv-ωTA) and dinitrogenase reductase-activating glycohydrolase (DraG) from Rhodospirillum rubrum. The cluster approach has been employed to design models of the active sites based on available crystal structures. The geometries and energies of transition states and intermediates along various reaction pathways have been calculated, and used to construct the energy graphs of the reactions. In the study of CDA (Paper I), two different tautomers of a histidine residue were considered. The obtained reaction mechanism was found to support the main features of the previously proposed mechanism. The sequence of the events was established, and the residues needed for the proton transfer steps were elucidated. In the study of Cv-ωTA (Paper II and Paper III), two active site models were employed to study the conversion of two different substrates, a hydrophobic amine and an amino acid. Differences and similarities in the reaction mechanisms of the two substrates were established, and the role of an arginine residue in the dual substrate recognition was confirmed. In the study of DraG (Paper IV), two different substrate-binding modes and two different protonation states of an aspartate residue were considered. The coordination of the first-shell ligands and the substrate to the two manganese ions in the active site was characterized, and a possible proton donor in the first step of the proposed reaction mechanism was identified. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

Dynamic systems for screening, control and identification of different protein-ligand interactions are presented. Dynamic chemistry is used to produce new compounds/constituents in situ that can interact with a target molecule. Several entities can be introduced at the same time and interact with one another. These molecules make a dynamic combinatorial library (DCL) which is used in dynamic combinatorial chemistry (DCC). DCC is a recently introduced approach to generate dynamically interchanging libraries of compounds. These libraries are made of different building blocks that reversibly interact with one another and spontaneously assemble to encompass all possible combinations. If a target molecule, for instance a receptor is added to the system and one or more molecules show affinity to the target species, these compounds will, according to Le Châtelier´s principle, be amplified on the expense of the other non-bonding constituents. To further advance the technique, especially when biological systems are targeted, new reaction types and new screening methods are necessary. This thesis describes the development of different reversible reactions, thiol/disulfide interchange, transthiolesterification and the nitroaldol (Henry) reaction as means of generating reversible covalent bond reactions. Two different types of target proteins are used, enzymes belonging to the hydrolase family and the plant lectin Concanavalin A. Dynamic combinatorial resolution (DCR) is presented. This new concept relies on the consecutive kinetic resolution of dynamic combinatorial libraries, leading to complete amplification and control of dynamically interchangeable processes. By applying a kinetically controlled step to a thermodynamically controlled system, complete transformation and amplification can be obtained. The concept has been demonstrated by developing transthiolesterification and nitroaldol exchange reactions to generate diversity, forming libraries under thermodynamic control, and used in one-pot processes with kinetically controlled enzyme-mediated resolution. The results demonstrate that the reaction types are useful for the generation of dynamic libraries, and that the dynamic combinatorial resolution concept is highly valuable for efficient substrate identification, asymmetric synthesis, and library screening. The thesis also describes three other dynamic chemistry protocols. The first one describes dynamic kinetic resolution (DKR) of nitroaldol adducts by combined lipase catalysis. The second one describes finding lectin inhibitors from a glycodisulfide library and the third one describes finding an inhibitor of acetylcholinesterase using a tandem driven dynamic self-inhibition approach. / <p>QC 20100818</p>

<p>An introduction to bacterial polysaccharides and the methods for structural determination are described in the first two parts of the thesis.</p><p>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. </p><p>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 <i>Streptococcus thermophilus</i> and the other a homopolysaccharide produced by <i>Propionibacterium freudenreichii</i>. 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 <i>Escherichia coli</i> strain 180/C3 and O5 is discussed and investigated. Finally, interaction studies of an octasaccharide derived from the <i>Salmonella enteritidis</i> O-antigen and a bacteriophage are described which were performed with NMR experiments.</p>

<p>The Autumn gum moth, <em>Mnesampela privata </em>(Lepidoptera: Geometridae) is an endemic Australian moth whose larvae feed upon species of <em>Eucalyptus.</em> The moths favorite host plants are <em>E. globulus </em>and<em> E. nitens</em> 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 <em>M. privata</em>.</p><p>The carrot psyllid, <em>Trioza apicalis </em>(Homoptera: Psylloidea), is one of the major pests of carrot (<em>Daucus carota</em>) 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.</p><p>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.</p><p>From analysis of abdominal tip extracts of <em>M. privata</em> females from Tasmania a blend of (3<em>Z</em>,6<em>Z</em>,9<em>Z</em>)-3,6,9-nonadecatriene and (3<em>Z,6Z,9Z</em>)-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.</p><p>In the analysis of carrot leaf extracts we found a compound, α-<em>cis</em>-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.</p>

<p>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.</p><p>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 <i>p</i>-methoxybenzylidene acetals was obtained.</p><p>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.</p><p>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</p>

<p>New techniques and approaches for organic synthesis, purification and biological testing are enabling pharmaceutical industries to produce and test increasing numbers of compounds every year. Surprisingly, this has not led to more new drugs reaching the market, prompting two questions – why is there not a better correlation between their efforts and output, and can it be improved? One possible way to make the drug discovery process more efficient is to ensure, at an early stage, that the tested compounds are diverse, representative and of high quality. In addition the biological evaluation systems have to be relevant and reliable. The diversity of the tested compounds could be ensured and the reliability of the biological assays improved by using Design Of Experiments (DOE) more frequently and effectively. However, DOE currently offers insufficient options for these purposes, so there is a need for new, tailor-made DOE strategies. The aim of the work underlying this thesis was to develop and evaluate DOE approaches for diverse compound selection and efficient assay optimisation. This resulted in the publication of two new DOE strategies; D-optimal Onion Design (DOOD) and Rectangular Experimental Designs for Multi-Unit Platforms (RED-MUP), both of which are extensions to established experimental designs.</p><p>D-Optimal Onion Design (DOOD) is an extension to D-optimal design. The set of possible objects that could be selected is divided into layers and D-optimal selection is applied to each layer. DOOD enables model-based, but not model-dependent, selections in discrete spaces to be made, since the selections are not only based on the D-optimality criterion, but are also biased by the experimenter’s prior knowledge and specific needs. Hence, DOOD selections provide controlled diversity.</p><p>Assay development and optimisation can be a major bottleneck restricting the progress of a project. Although DOE is a recognised tool for optimising experimental systems, there has been widespread unwillingness to use it for assay optimisation, mostly because of the difficulties involved in performing experiments according to designs in 96-, 384- and 1536- well formats. The RED-MUP framework combines classical experimental designs orthogonally onto rectangular experimental platforms, which facilitates the execution of DOE on these platforms and hence provides an efficient tool for assay optimisation.</p><p>In combination, these two strategies can help uncovering the crossroads between biology and chemistry in drug discovery as well as lead to higher information content in the data received from biological evaluations, providing essential information for well-grounded decisions as to the future of the project. These two strategies can also help researchers identify the best routes to take at the crossroads linking biological and chemical elements of drug discovery programs.</p>

<p>Rheumatoid arthritis (RA) is an autoimmune disease affecting approximately 1% of the population in the western world. It is characterised by a tissue specific attack of cartilage in peripheral joints. Collagen induced arthritis (CIA) is one of the most commonly used animal models for (RA), with similar symptoms and histopathology. CIA is induced by immunisation of mice with type II collagen (CII), and the immunodominant part was previously found to be located between residues 256-270. This thesis describes the interaction between the MHC molecule, glycopeptide antigens from CII and the T cells that is essential in development of CIA. The glycopeptide properties for binding to the mouse MHC molecule Aq have been studied, as well as interaction points in the glycopeptide that are critical for stimulation of a T-cell response.</p><p>The thesis is based on five studies. In the first paper the minimal glycopeptide core, that is required for binding to the Aq molecule while still giving a full T cell response was determined. The second paper studied the roles of amino acid side-chains and a backbone amide bond as T-cell contact points. In the third paper the hydrogen bond donor-acceptor characteristics of the 4-OH galactose hydroxyl group of the glycopeptide was studied in detail. In the fourth paper we established a structure activity relationship (QSAR model) for (glyco)peptide binding to the Aq molecule. Finally, the stereochemical requirements for glycopeptide binding to the Aq molecule and for T-cell recognition was studied in the fifth paper.</p><p>The study was performed using collagen glycopeptide analogues, which were synthesised on solid phase. Amide bond and hydroxyl group isosteres were introduced for study of hydrogen bond donor-acceptor characteristics. Statistical methods were used to design a representative peptide test set and in establishing a QSAR model.</p><p>The results give a deeper understanding of the interactions involved in the ternary MHC-glycopeptide-T cell complex. This information contributes to research directed towards finding new treatments for RA.</p>

<p>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). </p><p>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.</p><p>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.</p>

<p>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.</p><p>In the first part of this thesis, we focused on post-translational modifications of a class of unnatural oligomers known as <i>β</i>-peptides. Through the design and synthesis of a glycosylated <i>β</i>³-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 <i>β</i>³-peptides was synthesized with the aim to optimize the helical stability in water.</p><p>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.</p><p>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 <i>all</i>-<i>β</i>³-peptides were investigated for this purpose. In a subsequent paper, a completely different strategy was employed; herein, the ability of a single <i>β</i>²-amino acid to restrict the conformational freedom of a cyclic α-peptide was studied. </p><p>In the third part of this thesis, we synthesized and investigated the folding propensities of novel backbone modified oligomers, i.e. <i>β</i>-peptoids (<i>N</i>-substituted <i>β</i>-Ala) with α-chiral side chains.</p><p>The collective results of these studies have established the procedures required for synthesis of glycosylated <i>β</i>-peptides and deepened our understanding of the factors governing folding among such oligomers. Moreover, it was established that <i>β</i>-amino acids can be a useful tool to increase conformational stability of cyclic peptides.</p>

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