<p>The proteasome is a multi-subunit protease complex responsible for most of the non-lysosomal protein turnover in eukaryotic cells. This degradation process can be conducted dependent or independent of ubiquitination as different isoforms with different substrate preferences coexist in the cell. Proteasomal activity declines during aging due to a decreased expression of proteasome subunits, complex disassembly, and oxidative stress. This malfunction leads to protein accumulation, subsequent aggregation, and ultimately diseased states. Considering the shared feature of aggregation and accumulation of intrinsically disordered proteins (IDPs) in age-related diseases, and the substrate preference of the 20S isoform for misfolded proteins, enhancing the proteolytic activity of the 20S proteasome has arisen as an attractive strategy to minimize the burden associated with this increased protein load. Recently, we identified the FDA-approved drug miconazole (MO) as a stimulator of the 20S isoform and validated its activity profile in biochemical and cell-based assays. Given its FDA-approved drug status, we considered that to successfully repurpose it, information regarding its binding location within the 20S and network of binding partners, as well as its value in protein homeostasis in age-related diseases are necessary. Herein, we (1) conduct SAR studies to determine MO’s key features responsible for proteasomal activation and obtain molecules with enhanced ability to activate the 20S proteasome; next, using the developed SAR model, we (2) design a diazirine-based photoreactive probe that allows for the identification of MO’s binding partners and location within the 20S proteasome. Lastly, we (3) explore the use of MO to restore the activity of impaired proteasomes by Parkinson’s disease-associated toxic oligomers. This work expands upon previous research avenues by using newer approaches to study this enzymatic complex, and describes methods that can be further used to better establish the role of the 20S proteasome in age-related diseases.</p>

The performance of artificial nerve guidance conduits (NGC) in peripheral nerve regeneration can be improved by providing structures with multiple small channels instead of a single wide lumen. 3D-printing is a strategy to access such multi-channeled structures in a defined and reproducible way. This study explores extrusion-based 3D-printing of two-component hydrogels from a single cartridge printhead into multi-channeled structures under aseptic conditions. The gels are based on a platform of synthetic, anhydride-containing oligomers for cross-linking of gelatinous peptides. Stable constructs with continuous small channels and a variety of footprints and sizes were successfully generated from formulations containing either an organic or inorganic gelation base. The adjustability of the system was investigated by varying the cross-linking oligomer and substituting the gelation bases controlling the cross-linking kinetics. Formulations with organic N-methyl-piperidin-3-ol and inorganic K2HPO4 yielded hydrogels with comparable properties after manual processing and extrusion-based 3D-printing. The slower reaction kinetics of formulations with K2HPO4 can be beneficial for extending the time frame for printing. The two-component hydrogels displayed both slow hydrolytic and activity-dependent enzymatic degradability. Together with satisfying in vitro cell proliferation data, these results indicate the suitability of our cross-linked hydrogels as multi-channeled NGC for enhanced peripheral nerve regeneration.

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Pharmaceutical companies and FDA (Federal Drug Administration) rules rely heavily on crystalline active pharmaceutical ingredients delivered as tablets and powders in the form of neutral compounds, salts and solvates of neutral compounds and salts. About half of all drugs sold in the market are in the form of salts which are held together by ionic bonds along with some other forces. Recently, Ionic liquids (ILs) an interesting class of chemical compounds have offered potential opportunity for exploration as novel drug ionic liquid salts, particularly in the field of transdermal/topical drug delivery. Due to the multifunctional nature of these salts they could allow generation of new pathway to manipulate the transport and deposition behaviour of the drug molecule. It is this modular approach of IL that forms the basis of the research presented here, in which pharmaceutically acceptable compounds are combined with selected drugs with known problems. IL salts were generated by combining at least one drug molecule with FDA approved compounds and were assessed for physicochemical properties, skin deposition and permeation studies. Skin deposition data suggested that these systems exhibit high skin retention, which was found to correlate with the molecular weight. On the other hand, permeation data displayed an inverse relationship between flux values and molecular weight of the permeant. Similar work was extended with ILs with mixed anions containing two drugs. The benzalkonium-sulfacetamide ILs were investigated for synergism and the biological studies data display no synergistic effect. It was also illustrated that in-situ IL based ibuprofen hydrogels systems could be manipulated via IL approach for topical application. These findings suggest the potential applicability of IL based formulations for topical delivery of drugs.

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Alzheimer’s disease is an incurable neurodegenerative disorder linked to the amyloid β (Aβ) peptide, a 38-43 residue peptide. The detailed molecular disease mechanism(s) is (are) unknown, but oligomeric Aβ structures are proposed to be involved. In common for the papers in this thesis is interactions; interactions between Aβ(1-40) and selected molecules and metal ions. The purpose has been to find out more about the structural states that Aβ can adopt, in particular the β-sheet state, which probably is linked to the oligomeric structures. The methods used have been nuclear magnetic resonance (NMR), circular dichroism (CD) and fluorescence spectroscopy using Thioflavin T (ThT). Upon addition of SDS/LiDS detergent or Congo red (CR) to Aβ(1-40), the initial random coil/PII-helix state was transformed into β-sheet and, in the case of detergent, a final α-helical state. In contrast to SDS/LiDS and CR, the dimeric Affibody molecule locks monomeric Aβ(1-40) in a β-hairpin state. It was found that by truncating the flexible N-terminal end of the Affibody molecule its affinity to Aβ was improved. The aggregation of Aβ(1-40) was further studied in the presence of a β-cyclodextrin dimer by a kinetic assay using ThT. Although having a weak dissociation constant in the millimolar range, the β-cyclodextrin dimer modified the aggregation pathways of Aβ. Finally Aβ(1-40) was studied in presence of Cu2+ and Zn2+ at physiological and low pH. Cu2+ was observed to maintain its specific binding to Aβ when decreasing the pH to 5.5 while Zn2+ behaved differently. This could be of importance in the Alzheimer’s disease brain in which the environment can become acidic due to inflammation.        In conclusion the results show that Aβ(1-40) is very sensitive to its environment, responding by adopting different conformations and aggregating in aqueous solutions. The β-sheet state is induced by varying molecules with different properties, properties that govern the final Aβ state. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Manuscript. Paper 5: Manuscript.

The conversion of the native monomeric cellular prion protein (PrPC) into an aggregated pathological β-oligomeric (PrPβ) and an infectious form (PrPSc) is the central element in the development of prion diseases. The structure of the aggregates and the molecular mechanisms of the conformational change involved in this conversion are still unknown. My research hypothesis was that a specific structural rearrangement of normal PrPC monomers leads to the formation of new inter-subunit interaction interfaces in the prion aggregates, leading to aggregation. My approach was to use constraints obtained by structural proteomic methods to create a 3D model of urea-acid induced recombinant prion oligomers (PrPβ). My hypothesis was that this model would explain the mechanism of the conformational change involved in the conversion, the early formation of the β-structure nucleation site, and would describe the mode of assembly of the subunits within the oligomer. I applied a combination of limited proteolysis, surface modification, chemical crosslinking and hydrogen/deuterium exchange (HDX) with mass spectrometry for the differential characterization of the native and the urea-acid converted prion β-oligomer structures to get an insight into the mechanism of the conversion and aggregation. Using HDX, I detected a region of the protein in which backbone amides become more protected from exchange in PrPβ compared to PrPC. In order to obtain the inter-residue distance constraints to guide the assembly of the oligomer model, I then applied zero-length and short-range crosslinking to an equimolar mixture of 14N/15N-metabolically labeled β-oligomer thereby enabling the classification of the crosslinks as either intra-protein or inter-protein. Working with the Dokholyan group at the University of North Carolina at Chapel Hill, I was able to assemble a structure of the β-oligomer based on the combination of constraints obtained from all methods. By comparing the structures before and after the conversion, I was able to deduce the conformational change, that occurs during the conversion as the rearrangement and disassembly of the beta sheet 1– helix 1 – beta sheet 2 (β1-H1-β2) region from the helix 2 – helix 3 (H2-H3) core, forming new β-sheet nucleation site and resulting in the exposure of hydrophobic residues patches leading to formation of inter-protein contacts within aggregates. / Graduate / 2018-06-14

Non-fullerene Acceptors (NFAs) have gathered a great deal of interest for use inorganic photovoltaics (OPVs) due to recent breakthroughs in their power conversion efficiency and other advantages they offer over their Fullerene-based counterparts. In this work, a new promising non-fullerene polymer acceptor, PF5-Y5, have been studied using density functional theory and time-dependent density functional theory; and the effects that oligomer length, geometry relaxation and exchange-correlation interaction has on the exciton binding energies (the difference between optical and fundamental energy gaps) have been investigated. Both the fundamental and optical gaps are significantly affected by the choice of functional (i.e., the description of the exchange-correlation interaction). However, it does not appear to significantly impact obtained exciton binding energies as the effects of the fundamental and optical gaps cancel each other out. Both the fundamental and optical energy gap are shown to slightly reduce as a function of the oligomer length (~0.1 - 0.3 𝑒𝑉 reduction for each repeated monomer). As both gaps are reduced by a similar amount per repeated monomer, they counteract each other and the total effect that oligomer length has on the exciton binding energy is very low. Geometry relaxation and thermal effects showed the largest impact on the fundamental gap and exciton binding energy, with their combined effect resulting in a ~0.5 𝑒𝑉 reduction in binding energy. / Non-Fullerene Acceptorer (NFAs) har rönt stort intresse för användning i organiska solceller (OPVs) på grund av genombrott på senare tid gällande deras effektomvandlingsverkningsgrad och en mängd andra fördelar som de erbjuder jämfört med sina fullerene-baserade motsvarigheter. I det här arbetet har en ny lovande polymer-acceptor, PF5-Y5, studerats med hjälp av täthetsfunktionalteori (DFT) och tidsberoende täthetsfunktionsteori (TD-DFT). Effekterna som oligomerlängd, geometri-avslappning och utbytes-korrelations-interaktion har på exciton-bindningsenergin (skillnaden mellan optiska ochfundamentala energigapen) har även undersökts.  Både erhållna värden för det fundamentala och optiska gapet påverkas avsevärt av valet av funktional (dvs. beskrivningen av utbytes-korrelations-interaktionen). Valet av funktional verkar dock inte nämnvärt påverka erhållna värden för excitonbindningsenergin då effekterna från det fundamentala och optiska gapen till stor del tar ut varandra.  Både det fundamentala och optiska energigapet minskar som en funktion av oligomerlängden (~0.1 - 0.3 𝑒𝑉 minskning för varje upprepad monomer). Eftersom båda energigapen minskar ungefär lika mycket för varje upprepad monomer så motverkar de till stor grad varandra; och den totala effekten som oligomerlängd har på exciton-bindningsenergin förblir låg. Strukturell relaxation (eng: geometry relaxation) och termiska effekter visade sig ha störst påverkan på det fundamentala energigapet och exciton-bindningsenergin, och deras sammanlagda effekt ledde till en ~0,5 𝑒𝑉 reduktion i bindningsenergi.

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