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Remdesivir is the only FDA-approved drug for the treatment of COVID-19 patients. The active form of remdesivir acts as a nucleoside analog and inhibits the RNA-dependent RNA polymerase (RdRp) of coronaviruses including SARS-CoV-2. Remdesivir is incorporated by the RdRp into the growing RNA product and allows for addition of three more nucleotides before RNA synthesis stalls. Here we use synthetic RNA chemistry, biochemistry and cryoelectron microscopy to establish the molecular mechanism of remdesivir-induced RdRp stalling. We show that addition of the fourth nucleotide following remdesivir incorporation into the RNA product is impaired by a barrier to further RNA translocation. This translocation barrier causes retention of the RNA 3ʹ-nucleotide in the substrate-binding site of the RdRp and interferes with entry of the next nucleoside triphosphate, thereby stalling RdRp. In the structure of the remdesivir-stalled state, the 3ʹ-nucleotide of the RNA product is matched and located with the template base in the active center, and this may impair proofreading by the viral 3ʹ-exonuclease. These mechanistic insights should facilitate the quest for improved antivirals that target coronavirus replication.
The SARS virus is the etiological agent of the severe acute respiratory syndrome, a deadly disease that caused more than 700 causalities in 2003. One of its viral proteins, the SARS coronavirus main protease, is considered as a potential drug target and represents an important model system for other coronaviruses. Despite extensive knowledge about this enzyme, it still lacks an effective anti-viral drug. Furthermore, it possesses some unusual features related to its active-site region. This work gives atomistic insights into the SARS coronavirus main protease and tries to reveal mechanistic aspects that control catalysis and inhibition. Thereby, it applies state-of-the-art computational methods to develop models for this enzyme that are capable to reproduce and interpreting the experimental observations. The theoretical investigations are elaborated over four main fields that assess the accuracy of the used methods, and employ them to understand the function of the active-site region, the inhibition mechanism, and the ligand binding. The testing of different quantum chemical methods reveals that their performance depends partly on the employed model. This can be a gas phase description, a continuum solvent model, or a hybrid QM/MM approach. The latter represents the preferred method for the atomistic modeling of biochemical reactions. A benchmarking uncovers some serious problems for semi-empirical methods when applied in proton transfer reactions. To understand substrate cleavage and inhibition of SARS coronavirus main protease, proton transfer reactions between the Cys/His catalytic dyad are calculated. Results show that the switching between neutral and zwitterionic state plays a central role for both mechanisms. It is demonstrated that this electrostatic trigger is remarkably influenced by substrate binding. Whereas the occupation of the active-site by the substrate leads to a fostered zwitterion formation, the inhibitor binding does not mimic this effect for the employed example. The underlying reason is related to the coverage of the active-site by the ligand, which gives new implications for rational improvements of inhibitors. More detailed insights into reversible and irreversible inhibition are derived from in silico screenings for the class of Michael acceptors that follow a conjugated addition reaction. From the comparison of several substitution patterns it becomes obvious that different inhibitor warheads follow different mechanisms. Nevertheless, the initial formation of a zwitterionic catalytic dyad is found as a common precondition for all inhibition reactions. Finally, non-covalent inhibitor binding is investigated for the case of SARS coranavirus main protease in complex with the inhibitor TS174. A novel workflow is developed that includes an interplay between theory and experiment in terms of molecular dynamic simulation, tabu search, and X-ray structure refinement. The results show that inhibitor binding is possible for multiple poses and stereoisomers of TS174.
In this study, a double-donor concept is used to improve the performance of thermally evaporated merocyanine(s)/C60 bulk heterojunction (BHJ) solar cells. It is shown that the co-evaporation of two merocyanine dyes with absorption bands at ~ 500 nm (SW dye) and ~ 650 nm (LW dye), respectively, together with C60 fullerene results in an improvement of open-circuit voltage (VOC), short-circuit current (JSC) as well as total power conversion efficiency (PCE) compared to the best single-donor cell. The enhancement of JSC is attributed to a higher photon harvesting efficiency of the mixed-donor devices due to a better spectral coverage.
Merocyanine Dyes as Organic Semiconductors for Vacuum-processed Solar Cell and Transistor Devices
(2015)
The present thesis comprises the synthesis of new functional merocyanine dyes, the study of their electro-optical properties as well as solid state packing and their application as p-type semiconductor materials in transistor and solar cell devices. The absorption properties of the obtained compounds could be modified by variation of the donor unit, the introduction of electron-withdrawing substituents in the acceptor unit or elongation of the polymethine chain. For a particular dye, the absorption band could be shifted by more than 160 nm by increasing the solvent polarity due to a conformational switch between a merocyanine-like and a cyanine-like structure. Single crystal analyses revealed that the studied dyes tend to pack either in an antiparallel fashion forming dimers with no overall dipole moment or in a staircase-like pattern where the dipole moments point to the same direction and are only balanced by another staircase oriented in the opposite direction (stair dimer). With respect to application as semiconductor materials, the latter packing arrangement resulted most favorable for charge carrier mobility. We concluded that this packing motif is preserved in the solar cell devices, where the selenium-containing dye afforded the highest performance of this series for an optimized planar-mixed heterojunction solar cell (6.2 %).
The technology of organic photovoltaics offers the possibility of low-cost devices due to easy fabrication procedures and low material consumption and at the same time high flexibility concerning the applied substrates or design features such as the color palette. Owing to these benefits, this research field is highly active, being reflected by the continuously rising number of publications. Chapter 1 gives an extensive overview of a part of these reports, namely the field of solution-processed BHJ organic solar cells using small molecules as electron-donating materials. In the early years of this research area (2006-2008), well known hole transporting materials such as triphenylamine based chromophores, oligothiophenes and polyaromatic hydrocarbons were applied. However, many of these dyes lacked absorption at longer wavelengths and were therefore limited in their light harvesting qualities. Later, chromophores based on low band gap systems consisting of electron-donating and electron-accepting units showing internal charge transfer overcame this handicap. Today, donor-substituted diketopyrrolopyrroles (D-A-D chromophores), squaraines (D-A-D chromophores) and acceptor substituted oligothiophenes (A-D-A chromophores) are among the most promising dyes for small molecule based organic solar cells with PCEs of 4-5%. This work is based on the findings of the groups of Würthner and Meerholz, which tested merocyanine dyes for the first time in organic BHJ solar cells.4 According to the Bässler theory85, the high dipolarity of these dyes should hamper the charge transport, but the obtained first results with PCE of 1.7% proved the potenital of this class of dyes for this application. Merocyanine dyes offer the advantages of facile synthesis and purification, high tinctorial strength and monodispersity. Additionally, the electronic structure of the dyes, namely the absorption as well as the electrochemical properties, can be adjusted by using the right combination of donor and acceptor units. For these reasons, this class of dye is highly interesting for the application in organic solar cells. It was the aim of the thesis to build more knowledge about the potential and limitations of merocyanines in BHJ photovoltaic devices. By screening a variety of donor and acceptor groups a comprehensive data set both for the molecular materials as well as for the respective solar devices was generated and analyzed. As one focus, the arrangement of the chromophores in the solid state was investigated to gain insight about the packing in the solar cells and its relevance for the performance of the latter. To do so, X-ray single crystal analyses were performed for selected molecules. By means of correlations between molecular properties and the characteristics of the corresponding solar cells, several design rules to generate efficient chromophores for organic photovoltaics were developed. The different donor and acceptor moieties applied in this work are depicted in the following ...
Metabolic glycoengineering enables a directed modification of cell surfaces by introducing target molecules to surface proteins displaying new features. Biochemical pathways involving glycans differ in dependence on the cell type; therefore, this technique should be tailored for the best results. We characterized metabolic glycoengineering in telomerase-immortalized human mesenchymal stromal cells (hMSC-TERT) as a model for primary hMSC, to investigate its applicability in TERT-modified cell lines. The metabolic incorporation of N-azidoacetylmannosamine (Ac\(_4\)ManNAz) and N-alkyneacetylmannosamine (Ac\(_4\)ManNAl) into the glycocalyx as a first step in the glycoengineering process revealed no adverse effects on cell viability or gene expression, and the in vitro multipotency (osteogenic and adipogenic differentiation potential) was maintained under these adapted culture conditions. In the second step, glycoengineered cells were modified with fluorescent dyes using Cu-mediated click chemistry. In these analyses, the two mannose derivatives showed superior incorporation efficiencies compared to glucose and galactose isomers. In time-dependent experiments, the incorporation of Ac\(_4\)ManNAz was detectable for up to six days while Ac\(_4\)ManNAl-derived metabolites were absent after two days. Taken together, these findings demonstrate the successful metabolic glycoengineering of immortalized hMSC resulting in transient cell surface modifications, and thus present a useful model to address different scientific questions regarding glycosylation processes in skeletal precursors.
Liquid crystal (LC) shape‐amphiphiles with a disc tethered to a fullerene have been intensely studied for the application in photovoltaics, and helical nanosegregation of C\(_{60}\) has been claimed around the π‐stacking disks based on X‐ray results. The most promising materials reported to date have been resynthesized and studied comprehensively by XRS, density measurements, modelling, and electron density reconstruction. In contrast to previous reports, the results indicate that metal phthalocyanine−fullerene mesogens pack in lamellar columnar phases with p2gm symmetry. Fullerenes assemble in layers and are flanked by phthalocyanine columns, thus explaining the balanced charge carrier mobility of electrons and holes. Such variable donor−acceptor structures are promising for organic electronic applications.
A series of bis‐(4’‐pyridylethynyl)arenes (arene=benzene, tetrafluorobenzene, and anthracene) were synthesized and their bis‐N‐methylpyridinium compounds were investigated as a class of π‐extended methyl viologens. Their structures were determined by single crystal X‐ray diffraction, and their photophysical and electrochemical properties (cyclic voltammetry), as well as their interactions with DNA/RNA were investigated. The dications showed bathochromic shifts in emission compared to the neutral compounds. The neutral compounds showed very small Stokes shifts, which are a little larger for the dications. All of the compounds showed very short fluorescence lifetimes (<4 ns). The neutral compound with an anthracene core has a quantum yield of almost unity. With stronger acceptors, the analogous bis‐N‐methylpyridinium compound showed a larger two‐photon absorption cross‐section than its neutral precursor. All of the dicationic compounds interact with DNA/RNA; while the compounds with benzene and tetrafluorobenzene cores bind in the grooves, the one with an anthracene core intercalates as a consequence of its large, condensed aromatic linker moiety, and it aggregates within the polynucleotide when in excess over DNA/RNA. Moreover, all cationic compounds showed highly specific CD spectra upon binding to ds‐DNA/RNA, attributed to the rare case of forcing the planar, achiral molecule into a chiral rotamer, and negligible toxicity toward human cell lines at ≤10 μM concentrations. The anthracene‐analogue exhibited intracellular accumulation within lysosomes, preventing its interaction with cellular DNA/RNA. However, cytotoxicity was evident at 1 μM concentration upon exposure to light, due to singlet oxygen generation within cells. These multi‐faceted features, in combination with its two‐photon absorption properties, suggest it to be a promising lead compound for development of novel light‐activated theranostic agents.
Despite significant progress in the synthesis of covalent organic frameworks (COFs), reports on the precise construction of template-free nano- and microstructures of such materials have been rare. In the quest for dye-containing porous materials, a novel conjugated framework DPP-TAPP-COF with an enhanced absorption capability up to λ=800 nm has been synthesized by utilizing reversible imine condensations between 5,10,15,20-tetrakis(4-aminophenyl)porphyrin (TAPP) and a diketopyrrolopyrrole (DPP) dialdehyde derivative. Surprisingly, the obtained COF exhibited spontaneous aggregation into hollow microtubular assemblies with outer and inner tube diameters of around 300 and 90 nm, respectively. A detailed mechanistic investigation revealed the time-dependent transformation of initial sheet-like agglomerates into the tubular microstructures.