This thesis describes bioanalytical methods for generating fingerprints of biological systems for extracting relevant information with (protein) drugs in focus. Similarities and differences between samples can reveal the hidden relevant information, which can be used to optimize the production and facilitate the quality control of such protein drugs during their development and manufacture. Metabolic fingerprinting and multivariate data analysis (MVDA) can also facilitate early diagnosis of diseases and the effects and toxicity of drugs. Currently, several protein drugs are available on the global market. Nevertheless, despite, the success of such biotherapeutics significant challenges remain to be overcome in maintaining their stability and efficacity throughout their production cycle and long-term storage. The native structure and functional activity of therapeutic proteins is affected by many variables from production to delivery, incl. variables assoc. with conditions in bioreactors, purification, storage and delivery. Thus, part of the work underlying this thesis focused on structural analysis of a protein drug using chemical labeling, peptide mapping, and evaluation of the charge state distributions of the whole protein generated by ESI. The other part focuses on non-targeted metabolomics with a view to optimizing the cell cultivation process and assessment of the drug’s toxicity. A combination of appropriate analytical methods and MVDA is needed to find markers that can facilitate optimization of the cultivation system and expression of the target proteins in early stages of process development. Rapid methods for characterizing the protein drugs in different stages of the process are also required for quality control. In order to obtain high quality fingerprints analytical separation techniques with high resolution (such as HPLC or UHPLC) and sensitive analytical detection techniques (such as ESI, quadrupole or TOF MS) have been used, singly or in combination. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript.

The pathogenesis of Alzheimer’s disease (AD), the most common senile dementia, is a complex process. A crucial event in AD is the aggregation of amyloid-β protein (Aβ), a cleavage product from the Amyloid Precursor Protein (APP). Aβ40, a common component in amyloid plaques found in patients, aggregates in vitro at concentrations, much higher than the one found in vivo. But in the presence of charged lipid membranes, aggregations occurs at much lower concentration in vitro compared to the membrane-free case. This can be understood due to the ability of Aβ to get electrostatically attracted to target membranes with a pronounced surface potential. This electrostatically driven process accumulates peptide at the membrane surface at concentrations high enough for aggregation while the bulk concentration still remains below threshold. Here, we elucidated the molecular nature of this Aβ-membrane process and its consequences for Aβ misfolding by Circular Dichroism Spectroscopy, Differential Scanning Calorimetry and Nuclear Magnetic Resonance Spectroscopy. First, we revealed by NMR that Aβ40 peptide does indeed interact electrostatically with membranes of negative and positive surface potential. Surprisingly, it even binds to nominal neutral membranes if these contain lipids of opposite charge. Combined NMR and CD studies also revealed that the peptide might be shielded from aggregation when incorporated into the membrane. Moreover, CD studies of Aβ40 added to charged membranes showed that both positively and negatively membranes induce aggregation albeit at different kinetics and finally that macromolecular crowding can both speed up and slow down aggregation of Aβ.

Interactions between light and a molecule can result in reversible or irreversible changes in properties of both the light and the molecule. Of the many known interactions, nonlinear absorption is a process in which an intense light signal, for instance from a laser, can be moderated. This can be manifested either in a marked lowering of the light’s intensity or in reductions in fluctuations of its intensity. Such an effect is often termed ‘optical power limiting’ (OPL). High power lasers can be very dangerous since their high intensity can damage or destroy eyes and optical sensors. However, there are currently no adequate protective measures against lasers that cover the entire visible region and there is an increasing demand for new or improved OPL materials. Some of the most promising optical power limiting materials are substances that combine nonlinear optical properties with high transparency in normal light, but after activation by a laser beam, their light transmittance falls extremely rapidly via so-called self-activating mechanisms. The platinum(II) acetylides comprise one class of compounds with such properties. In this study, various OPL Pt(II) acetylides were synthesized and their nonlinear optical properties were characterized. The emphasis of the work was on preparation of the compounds, but in order to design organoplatinum chromophores for OPL, attempts were also made to obtain insight into the mechanisms of nonlinear absorption. The work was divided into two main parts. In the first the goal was to find compounds that are good optical limiters in solution. The possibility of isolating the chromophore site by dendron shielding and the effects of incorporating a thiophene ring into the organic molecular system were also explored. In addition, a new route for synthesizing these compounds was developed. The second part was focused on incorporating the most interesting compounds into solid materials. The preparation and characterization of Pt(II) acetylides with molecular groups for covalent attachment to a silica matrix via the solution gel approach is described.

Skin pigmentation is an important issue in most cultures. Until recently we have not understood the most important elements of pigmentation regarding detailed chemical structure. The synthesis of melanin is very complex, and although core enzymes, other important proteins, and parts of the melanin structure have been identified much information in this context awaits disclosure. The function of the melanocyte and the deposition of melanin pigments into the keratinocytes are very important in the protection against UV light. Melanin pigments consist of high-molecular structures often described as brown to black eumelanin and yellow to red pheomelanin. Eumelanin is photoprotective, whereas pheomelanin is believed to be carcinogenic after UV radiation. There is strong evidence that people of fair complexion with freckles who tan poorly are at higher risk of developing melanoma. These people have a higher pheomelanin to eumelanin ratio in their skin. Melanoma, one of the most widely spread cancers, is derived from melanocytes. There is accumulating evidence that pigment constitution is highly involved in the development of melanoma. We found that patients with advanced melanoma secrete substantial amounts of pigment structures into the urine, in particular those with diffuse melanosis. In subsequently performed experiments we purified these pigments and subjected the product to chemical degradation by either hydrogen peroxide oxidation or hydriodic hydrolysis. Several new chromatographic methods were developed for the structural analysis of these products. Structural analysis of new chromatographic peaks was performed. In conclusion, complex pheomelanin structures as well as low molecular weight pigments and free benzothiazoles have been identified in the urine of patients with melanoma and diffuse melanosis. The present thesis provides new insight into melanogenesis and melanoma progression. This opens the doorway to further approaches to the investigation of melanins and can help to understand fundamental problems about the structure and biosynthesis of natural melanins.

Synchrotron-based spectroscopic techniques enable investigations of the many important biological and environmental functions of the ubiquitous element sulfur. In this thesis the methods for interpreting sulfur K-edge X-ray absorption near edge structure (XANES) spectra are developed and applied for analyses of functional sulfur groups. The influence of coordination, pH, hydrogen bonding, etc., on the sulfur 1s electronic excitations is evaluated by transition potential density functional theory. Analyses have been performed of reduced sulfur compounds in marine-archaeological wood from historical shipwrecks, including the Vasa, Stockholm, Sweden and the Mary Rose, Portsmouth, U.K.. The accumulation of sulfur as thiols in lignin-rich parts of the wood on the seabed is also a probable pathway in the natural sulfur cycle for how reduced sulfur enters fossil fuels via humic matter in anaerobic marine sediments. Sulfur K-edge XANES spectra for several biochemical model compounds and for coexisting isomeric sulfur species in cysteine and sulfite(IV) aqueous solutions have been analyzed with the aid of theoretical calculations. Cysteine derivatives are important for biochemical detoxification, and mercury(II) cysteine complexes in solution have been structurally characterized by means of Extended X-ray Absorption Fine Structure (EXAFS), Raman and 199Hg NMR spectroscopy. Lanthanoid(III) ions were found to coordinate eight dimethyl sulfoxide oxygen atoms in a distorted square antiprism in the solid state and in solution, by combining crystallography, EXAFS, XANES and vibrational spectroscopy. The mean M-O bond distances for the disordered crystal structures are in good agreement with those from the lattice-independent EXAFS studies. The different sulfur K-edge XANES spectra for the dimethyl sulfoxide ligands in the hexasolvated complexes of the trivalent group 13 metal ions, Tl(III), In(III), Ga(III) and Al(III), were interpreted by theoretical calculations.

This thesis describes the development and mechanistic studies of carbocyclization reactions of allene-substituted olefins and 1,3-dienes, catalyzed by palladium(0) and palladium(II). These reactions results in the formation of [n,3,0] bicyclic systems (n = 3-5) with high stereoselectivity and in good to excellent yields. The first carbocyclization presented is a novel palladium(0)-catalyzed cyclo- isomerization of allene-substituted olefins. Secondly an efficient aerobic biomimetic system has been developed for a Pd(II)-catalyzed allylic oxidative carbocyclization of allene-substituted olefins. Additionally, during the studies of palladium-catalyzed carbocyclizations of allene-substituted olefins, it was found that in the absence of palladium a mild thermal ene-reaction occurs. In this manner stereodefined, functionalized bicyclic compounds are obtained with good regioselectivity and in high yields. The third and fourth carbocyclization developed are a palladium(II)-catalyzed oxidation and a palladium(0)-catalyzed intramolecular telomerization of allene-substituted 1,3-dienes. A mechanistic study of the palladium(II)-catalyzed oxidation of allene-substituted 1,3-dienes was made, and reaction intermediates could be isolated. The stereochemistry of the reaction intermediates was assigned, and this made it possible to suggest a mechanism for the reaction. The presented mechanism is a trans carbopalladation of the 1,3-diene, where the allene act as the carbon nucleophile. Due to different stereochemical outcomes of the stoichiometric and catalytic reactions, this mechanism could only explain the stoichiometric reaction. Another mechanism for the catalytic reaction was suggested, which rationalizes both the regio- and stereochemistry of the products.

Carbohydrates play important roles in biological processes. Their function is closely related to their conformation. In this thesis, conformational studies of carbohydrates by NMR spectroscopy and molecular dynamics computer simulations are described. The first two papers discuss the anomalous solubility of β-cyclodextrin compared to other cyclodextrins. Time correlation functions revealed flexibility in all cyclodextrins. Molecular dynamics computer simulations showed that the glycosidic linkages were rather rigid and the flexibility was suggested to be macrocyclic. From spatial distribution functions β-cyclodextrin was found to have greater ability to order the surrounding water than the other cyclodextrins. Paper III deals with some of the difficulties of conformational studies. In Paper IV, a new method, Additative Potential Maximum Entropy, APME, is applied to a disaccharide. Conformational distribution functions are derived from NOEs, J-couplings and residual dipolar couplings and calculated from computer simulations. All distribution functions were found to be in good agreement. In papers V and VI oligosaccharides from human milk are studied. Residual dipolar coupling, J-couplings and cross relaxation rates were measured by NMR spectroscopy and molecular dynamics computer simulations were carried out. Both oligosaccharides showed high flexibility for the β-D-GlcpNAc-(1→3)-β-D-Galp linkage.

This PhD thesis presents structural investigations of amorphous inorganic materials: oxide and oxynitride glasses and mesoporous bioactive glasses (MBGs), by solid-state Nuclear Magnetic Resonance (NMR). Lanthanum oxide and oxynitride [La-Si-(Al)-O-(N)] glasses have a large number of potential applications due to their physical properties. In our work we have studied, compared to previous investigations, significantly expanded ranges of glass compositions (for oxynitride glasses, including samples of very high nitrogen content, up to 53 % out of the anions). We have estimated local environments of 29Si and 27Al structural units (their coordination, polymerization degree and number of N incorporated into tetrahedral units) in the materials. We have suggested a random Al/Si distribution along with almost uniform non-bridging oxygen atoms distribution in aluminosilicate glasses. Silicon nitride was used as precursor in the oxynitride glass synthesis. We studied both α- and β-modifications of silicon nitride, 15N-enriched, as well as fully (29Si, 15N)-enriched samples. We have shown that the linewidths of 15N NMR spectra are dominated by J(29Si-15N) coupling in 29Si315N4 sample. Mesoporous bioactive glasses in the CaO-SiO2-P2O5 system show superior bioactivity (the ability to form a hydroxycarbonate apatite layer on the glass surface when exposed to body fluids) compared to conventional bioactive glasses due to their large surface area and uniform pore-size distribution. Previous studies suggested a homogeneous cation distribution over the MBG samples on a 10−20 nm length-scale. From our results, on the other hand, we may conclude that Si and P is not intimately mixed. We propose a structural model, in which the pore walls of MBGs are composed of a silica network, and a phosphate phase is present as nanometer-sized clusters that are dispersed on the pore wall.

Amyotrophic lateral sclerosis (ALS) is a devastating disease that affects people in their late mid-life, with fatal outcome usually within a few years. The progressive degeneration of neurons responsible for muscle movement (motor neurons) throughout the central nervous system (CNS) leads to muscle wasting and paralysis, and eventually affects respiratory function. Most cases have no familial background (sporadic) whereas about 10% of cases have relatives affected by the disease. A substantial number of familial cases are caused by mutations in the gene encoding superoxide dismutase-1 (SOD1). Since the initial discovery of this relationship about 17 years ago, numerous workers have tried to identify the pathogenicity of mutant SOD1 but without any final agreement or consensus regarding mechanism. The experiments in this thesis have been aimed at finding common pathogenic mechanisms by analyzing transgenic mouse models expressing mutant SOD1s with widely different properties.     Mitochondrial pathology and dysfunction have been reported in both ALS patients and murine models. We used density gradient ultracentrifugation for comparison of mitochondrial partitioning of SOD1 in our transgenic models. It was found that models with high levels of mutant protein, overloaded mitochondria with high levels of SOD1-protein whereas models with wild type-like levels of mutant protein did not. No significant association of the truncation mutant G127X with mitochondria was found. Thus, if mitochondrial dysfunction and pathology are fundamental for ALS pathogenesis this is unlikely to be caused by physical association of mutant SOD1 with mitochondria.     Density gradient ultracentrifugation was used to study SOD1 inclusions in tissues from an ALS patient with a mutant SOD1 (G127X). We found large amounts in the ventral horns of the spinal cord but also in the liver and kidney, although at lower levels. This showed that such signs of the disease can also be found outside the CNS.     This method was used further to characterize SOD1 inclusions with regard to the properties of mutant SOD1 and the presence of other proteins. The inclusions were found to be complex detergent-sensitive structures with mutant SOD1 reduced at disulfide C57-C146 being the major inclusion protein, constituting at least 50% of the protein content. Ten co-aggregating proteins were isolated, some of which were already known to be present in cellular inclusions. Of great interest was the presence of several proteins that normally reside in the endoplasmic reticulum (ER), which is in accordance with recent data suggesting that the unfolded protein response (UPR) has a role in ALS.     To obtain unbiased information on the pathogenesis of mutant SOD1, we performed a total proteome study on spinal cords from ALS transgenic mice. By multivariate analysis of the 1,800 protein spots detected, 420 (23%) were found to significantly contribute to the difference between transgenic and control mice. From 53 proteins finally identified, we found pathways such as mitochondrial function, oxidative stress, and protein degradation to be affected by the disease. We also identified a previously uncharacterized covalent SOD1 dimer.    In conclusion, the work described in this thesis suggests that mutant SOD1 affects the function of mitochondria, but not mainly through direct accumulation of SOD1 protein. It also suggests that SOD1 inclusions, present in both the CNS and peripheral tissues, mainly consist of SOD1 but they also trap proteins involved in the UPR. This might be deleterious as motor neurons, unable to renew themselves, are dependent on proper protein folding and degradation.

Nitrogen rich glasses in the systems Ca-Si-O-N, Sr-Si-O-N and AE-Ca-Si-O-N (AE = Mg, Sr and Ba) have been prepared using a novel glass-synthesis route. The limits of the glass forming regions in the Ca and Sr systems and substitution limits in the AE-Ca-Si-O-N systems have been determined and physical properties of the glasses measured. Transparent glasses were obtained for a few specific compositions in the Ca-Si-O-N and Mg-Ca-Si-O-N systems. All other glasses were found to be translucent gray to opaque black, with the coloration of the glasses depending on the modifier. Small inclusions of Ca/Sr silicides and, in much smaller amounts, elemental Si are believed to be responsible for their poor transparency. A large glass forming region was found for the Ca-Si-O-N system, with glasses retaining up to 58 e/o N and 42 e/o Ca. In comparison, a more narrow glass forming region was found for the corresponding Sr system, with glasses retaining up to 45 e/o N and 39 e/o Sr. The glass formation was found to depend on reaction kinetics and precursors used. A strong exothermic reaction was observed at temperatures 650–1000oC, providing improved conditions for reaction kinetics upon further heating. Physical property measurements for the Ca and Sr glasses showed that glass transition and crystallization temperatures, viscosity, hardness, Young’s modulus and shear modulus depend strongly on the nitrogen content and that these properties increase approximately linearly with increasing nitrogen content. Glass density and refractive index are also dependent on the modifier element and content, in particular for the Sr glasses. Glasses AE-Ca-Si-O-N, with approximately constant (Ca/AE): Si:O:N ratios, showed that mixed modifier glass properties, such as density, molar volume, glass transition temperature, hardness, refractive index can be related to the effective cation field strength of the modifiers.