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The human African trypanosomiasis is a neglected tropical disease, which is caused by the protozoan Trypanosoma brucei and transmitted by the bite of the tsetse fly. An untreated infection leads to death. However, only a few drugs with significant drawbacks are currently available for treatment. In this thesis, quinolone amides with an antitrypanosomal activity were synthesized and their biological and physicochemical properties were measured. New structure-activity relationships and a promising lead structure were discovered.
As central components of life, DNA and RNA encode the genetic information. However, RNA performs several functions that exceed the competences stated in the ‘central dogma of life‘. RNAs undergo extensive post-transcriptional processing like chemical modifications. Among all classes of RNA, tRNAs are the most extensively modified. Their modifications are chemically diverse and vary from simple methylations (e.g. m3C, m6A) to more complex residues, like isopentenyl group (e.g. i6A, hypermodifications: e.g. ms2i6A) or even amino acids (e.g. t6A). Depending on their location within the overall structure, modifications can have an impact on tRNA stability and structure, as well as affinity for the ribosome and translation efficiency and fidelity. Given the importance of tRNA modifications new tools are needed for their detection and to study their recognition by proteins and enzymatic transformations.
The chemical synthesis of these naturally occurring tRNA modifications as phosphoramidite building blocks is a prerequisite to incorporate the desired modification via solid-phase synthesis into oligonucleotides. With the help of the m3C, (ms2)i6A, and t6A oligonucleotides, the importance and impact of tRNA modifications was investigated in this thesis. To this end, the role of METTL8 as the methyltransferase responsible for the installation of the methyl group at C32 for mt-tRNAThr and mt-tRNASer(UCN) was resolved. Thereby, the respective adenosine modification on position 37 is essential for the effectiveness of the enzyme. Besides, by means of NMR analysis, CD spectroscopy, thermal denaturation experiments, and native page separation, the impact of m3C32 on the structure of the tRNA ASLs was shown. The modification appeared to fine-tune the tRNA structure to optimize mitochondrial translation. To investigate the regulation of the dynamic modification pathway of m3C, demethylation assays were performed with the modified tRNA-ASLs and the (α-KG)- and Fe(II)-dependent dioxygenase ALKBH1 and ALKHB3. A demethylation activity of ALKBH3 on the mt-tRNAs was observed, even though it has so far only been described as a cytoplasmic enzyme. Whether this is physiologically relevant and ALKBH3 present a mitochondrial localization needs further validation. In addition, ALKBH1 was confirmed to not be able to demethylate m3C on mt-tRNAs, but indications for a deprenylation and exonuclease activity were found. Furthermore, the aforementioned naturally occurring modifications were utilized to find analytical tools that can determine the modification levels by DNAzymes, which cleave RNA in the presence of a specific modification. Selective DNA enzymes for i6A, as well as the three cytidine isomers m3C, m4C, and m5C have been identified and characterized.
Besides the naturally occurring tRNA modifications, the investigation on artificially modified nucleosides is also part of this thesis. Nucleosides with specific properties for desired applications can be created by modifying the scaffold of native nucleosides.
During the pandemic, the potential of antiviral nucleoside analogues was highlighted for the treatment of the SARS-CoV-2 infection. For examinations of the potential drug-candidate Molnupiravir, the N4-hydroxycytidine phosphoramidite building block was synthesized and incorporated into several RNA oligonucleotides. A two-step model for the NHC-induced mutagenesis of SARS-CoV-2 was proposed based on RNA elongation, thermal denaturation, and cryo-EM experiments using the modified RNA strands with the recombinant SARS-CoV-2 RNA-dependent RNA polymerase. Two tautomeric forms of NHC enable base pairing with guanosine in the amino and with adenosine in the imino form, leading to error catastrophe after the incorporation into viral RNA. These findings were further corroborated by thermal melting curve analysis and NMR spectroscopy of the NHC-containing Dickerson Drew sequence. In conclusion, the anti-amino form in the NHC-G base pair was assigned by NMR analysis using a 15N-labeld NHC building block incorporated into the Dickerson Drew sequence.
This thesis also addressed the synthesis of a 7-deazaguanosine crosslinker with a masked aldehyde as a diol linker for investigations of DNA-protein interactions. The diol functional group can be unmasked to release the reactive aldehyde, which can specifically form a covalent bond with amino acids Lys or Arg within the protein complex condensin. The incorporation of the synthesized phosphoramidite and triphosphate building blocks were shown and the functionality of the PCR product containing the crosslinker was demonstrated by oxidation and the formation of a covalent bond with a fluorescein label.
The development of assays that detect changes in this methylation pattern of m6A could provide new insights into important biological processes. In the last project of this thesis, the influence of RNA methylation states on the structural properties of RNA was analyzed and a fluorescent nucleoside analog (8-vinyladenosine) as molecular tools for such assays was developed. Initial experiments with the fluorescent nucleoside analog N6-methyl-8-vinyladenosine (m6v8A) were performed and revealed a strong fluorescence enhancement of the free m6v8A nucleoside by the installation of the vinyl moiety at position 8.
Overall, this thesis contributes to various research topics regarding the application of naturally occurring and artificial nucleoside analogues. Starting with the chemical synthesis of RNA and DNA modifications, this thesis has unveiled several open questions regarding the dynamic (de-)methylation pathway of m3C and the mechanism of action of molnupiravir through in-depth analysis and provided the basis for further investigations of the protein complex condensin, and a new fluorescent nucleoside analog m6v8A.
The 1st chapter provides a detailed review of the development of synthetic approaches to triarylboranes from their first report nearly 135 years ago to the present. In the 2nd chapter, a novel and convenient methodology is reported for the one-pot synthesis of sterically-congested triarylboranes, using bench-stable aryltrifluoroborates as the boron source. The new procedure gives access to symmetrically- and unsymmetrically-substituted triarylboranes. The borylated triarylboranes are suggested as building blocks for the design of functional materials. In the 3rd chapter, four luminescent tetracationic bis-triarylborane DNA and RNA sensors that show high binding affinities, in several cases even in the nM range, are investigated. The molecular structures of two of the neutral precursors reveal some structural flexibility for these compounds in the solid state. The compounds were found to be highly emissive even in water and DNA and RNA binding affinities were found to be dependent on linker length and flexibility. Strong SERS responses for three of the four compounds demonstrate the importance of triple bonds for strong Raman activity in molecules of this compound class. In chapter 4, the compound class of water-soluble tetracationic bis-triarylborane chromophores is extended by EDOT-linked compounds and those are compared to their thiophene-containing analogs. Absorption and emission are significantly red-shifted in these compounds, compared to their thiophene-containing analogs and, due to a large Stokes shift, one of the reported compounds exhibits the most bathochromically shifted emission, observable well into the near infrared region, of all tetracationic water-soluble bis-triarylborane chromophores reported to date. Long-lived excited states, completely quenched by oxygen, were observed for the water-stable compounds of this study via transient absorption spectroscopy and a quantum yield for singlet oxygen formation of 0.6 was determined for one of them.
Tribenzotriquinacene (TBTQ) is a polycyclic aromatic framework with a particularly rigid, C3v symmetrical, bowl-shaped core bearing three mutually fused indane wings. It has been discussed as a defect center for a nanographene by Kuck and colleagues. Therefore, extended TBTQ structures are promising models for saturated defect structures in graphene and graphene like molecules and could be used to investigate the role of defects for the electronic properties of graphene. With this motivation, three different pi-extended TBTQ derivatives have been synthesized in this work. Several different Scholl reaction conditions were tried to obtain fully annulated product of hexaphenyl substituted TBTQ. The desired benzannulated TBTQ derivative could not be obtained due to unfavourable electron density in the respective positions of the molecule and increased reactivity of the bay position of the precursor. As an another method for benzannulation is the on-surface synthesis of graphene flakes and can be carried out using electron beams e.g. in a tunneling microscope (STM). According to our previous research, the parent system TBTQ and centro-methyl TBTQ on silver and gold surfaces showed that the gas phase deposition of these molecules gives rise to the formation of highly ordered two-dimensional assemblies with unique structural features. This shows the feasibility for the formation of defective graphene networks starting from the parent structures. Therefore, the same deposition technique was used to deposit Me-TBTQ(OAc)3Ph6, and investigate the molecular self-assembly properties directly on the surface of Cu (111). In summary, the substrate temperature dependent self-assembly of Me-TBTQ(OAc)3Ph6 molecules on Cu(111), shows the following evolution of orientations. At room temperature, molecules form dimers, which construct a higher-coverage honeycomb lattice. Furthermore, one of the acetyl group located in the bay positions of the TBTQ core is cleaved and the remaining two induce the metal-molecule interaction. It was presumed that by increasing the temperature to 393 K, the remaining acetyl and methyl groups would beeliminated from the molecular structure.In addition, the smaller TBTQ-Ph6 molecules preferably lie flat on Cu(111) crystal and allowing the molecules to settle into a C3-symmetry and form a dense hexagonal structure.
A series of monomeric chirally substituted indolenine squaraine monomers were successfully synthesized and utilized for the construction of various oligo- and polymers, in order to study their chiroptical properties in terms of exciton chirality. The quaternary carbon atom at the 3-position of the indolenine subunit, as well as the alkyl side chain attached to the indolenine nitrogen were selected as the most suitable site for chiral functionalization.
For the C(3)-chiral derivatives, two synthetic routes depending on the desired substitution at the stereogenic center were established. The chiral side chains were prepared via Evans asymmetric alkylation where the resulting branching point at the 2 position constituted the chiral center. While the chiral substitution only had minor effects on the linear optical properties and geometric structure of the chromophore, all compounds exhibited a distinct and measurable CD signal that correlated with the distance of the chiral center to the central chromophore.
Polymers bearing chiral side chains exhibited a solvent- and temperature-dependent helix-coil equilibrium, which was influenced by the type of side chain used. CD spectroscopy revealed the helical conformation to possess a preferred twist sense, and temperature-dependent measurements showed the degree of homohelicity to be nearly complete in certain cases. Furthermore, a CPL signal was able to be obtained for the helical conformer of one polymer.
Various (co)oligo- and polymers comprising the C(3)-chiral monomers only displayed a solvent-independent J-type absorption behavior and thus did not form helical conformations in solution. CD spectroscopy revealed a solvent-dependent adoption of quasi-enantiomeric conformers, which was elucidated by quantum chemical TDDFT calculations.
The aim of this work was the selective functionalisation of tribenzotriquinacene (TBTQ) in order to extend the aromatic system and tune the electronic properties. The synthesised molecules could be starting materials for a model system of a defective graphene fragment. The “triple cyclisation pathway” by Hopf et al. was adapted and fluorinated tribenzotriquinacenes were synthesised for the first time.
Phenanthrene groups were also introduced in other model systems and the crystal structures of phenanthrene functionalised TBTQs were compared with the parent molecules.
In addition, the arrangement of TBTQ and centro methyl functionalised TBTQ was investigated on a Ag(111) surface for the first time using scanning transmission microscopy (STM). Different arrangements were observed, depending on the coverage of the surface.
The insights gained about the interaction between TBTQs as well as their synthesis provide a foundation for further work and potential applications as components in organic electronic devices.
In this thesis, the synthesis and photophysics of a great variety of squaraine dyes are presented. This variety is based on four parent squaraines containing either indolenine or quinoline heterocycles. By a suitable choice of the donor and acceptor unit, the optical properties can already be adapted to the properties desired on the stage of the monomer.
To promote a further derivatisation of these dyes, diverse functional groups are attached to the monomers using transition metal-catalysed C-C coupling reactions. However, this has to be preceded by the synthesis of bromine-functionalised derivatives as a direct halogenation of squaraine dyes is not feasible. Therefore, the halogen function is already introduced in precursor molecules giving rise to a molecular building block system containing bromine-, boronic ester-, and alkyne-functionalised monomer units, which pave the way to a plethora of squaraine oligomers and polymers.
The indolenine homopolymer pSQB-1 as well as the corresponding small molecular weight oligomers dSQB-1 and tSQB were synthesized applying Ni-mediated Yamamoto and Pd-catalysed Suzuki coupling methodologies, respectively. The motivation for this project relied on the fundamental investigations by Völker et al. on pSQB-V. A progressive red-shift of the lowest energy absorption maximum from the dimer to the polymer was observed in CHCl3 compared to the monomer. With increasing number of monomer units, the exciton coupling decreases from the dimer to the polymer. In addition, the shape of the absorption band manifold shows a strong dependence on the solvent, which was also observed by Völker et al. J-type aggregate behavior is found in chlorinated solvents such as CHCl3 and DCM, whereas H-type aggregates are formed in acetone. Temperature-dependent absorption studies in PhCN reveals a reversible equilibrium of diverse polymer conformers, which manifests itself in a gradual change from H-aggregate behavior to a mixture with a more pronounced J-aggregate behavior upon raising the temperature. It isassumed that both characteristic aggregate bands correlate in borderline cases with two polymer structures which can be assigned to a zig-zag and a helical structure. As no experimental evidence for these structures could hitherto be provided by NMR, TD-DFT computations on oligomers (22-mers) can reproduce very closely the characteristic features of the spectra for the two conformational isomers.
The subsequent chapters are motivated by the goal to influence the optical properties through a control of the superstructure and thus of the intramolecular aggregate formation.
On the one hand, bulky groups are implemented in the 3-position of the indolenine scaffold to provoke steric repulsion and thus favoring J-aggregate behavior at the expense of helical arrangements. The resulting homopolymer pDiPhSQB bearing two phenyl groups per indolenine exhibits J-type aggregate behavior with red-shifted absorption maxima in all considered solvents which is explained to be caused by the formation of elongated zig-zag structures. Furthermore, single-crystal X-ray analysis of monomer DiPhSQB-2-Br2 reveals a torsion of the indolenine moieties as a consequence of steric congestion. The twist of the molecular geometry and the resulting loss of planarity leads to a serious deterioration of the fluorescence properties, however a significant bathochromic shift of ca. 1 200 cm-1 of the lowest absorption band was observed compared to parent SQB, which is even larger than the shift for dSQB-1 (ca. 1 000 cm-1).
On the other hand, a partial stiffening of the polymer backbone is attempted to create a bias for elongated polymer chains. In this respect, the synthetic approach is to replace every second biarylaxis with the rigid transoid benzodipyrrolenine unit. Despite a rather low average degree of polymerization < 10, exclusively red-shifted absorption maxima are observed in all solvents used.
In order to complete the picture of intramolecular aggregates through the selective design of H-aggregates, a squaraine-squaraine copolymer was synthesised containing the classic cisoid indolenine as well as the cisoid quinoline building block. Taking advantage of the highly structure directing self-assembly character of the quinoline moiety, the copolymer pSQBC indeed showes a broad, blue-shifted main absorption band in comparison with the monomer unit dSQBC. The shape of the absorption band manifold solely exhibited a minor solvent and temperature dependence indicating a persistent H-aggregate behaviour. Hence, as a proof of concept, it is shown that the optical properties of the polymers (H- and J-aggregate) and the corresponding superstructure can be inherently controlled by an adequate design of monomer precursors.
The last chapter of this work deals, in contrast to all other chapters, with intermolecular aggregates. It is shown that the two star-shaped hexasquarainyl benzenes hSQA-1 and hSQA-2 exhibit a strong propensity for self-organisation. Concentration- and temperature-dependent studies reveal a great driving force for self-assembly in acetone. While the larger hSQA-2 instantaneously forms stable aggregates, the aggregates of hSQA-1 shows a pronounced kinetic stability. Taking advantage of the kinetic persistency of these aggregates, the corresponding kinetic activation parameters for aggregation and deaggregation can be assessed. The absorption spectra of both hexasquarainyl benzenes in the aggregated state reveal some striking differences. While hSQA-1 features an intensive, very narrow and blue-shifted absorption band, two red-shifted bands are observed for hSQA-2, which are closely located at the monomer absorption. The very small bandwidth of hSQA-1 are interpreted to be caused by exchange narrowing and pointed towards highly ordered supramolecular aggregates. The concentration-dependent data of the two hexasquarainyl benzenes can be fitted to the dimer-model with excellent correlation coefficients, yielding binding constants in excess of 10^6 M-1, respectively. Such high binding constants are very surprising, considering the unfavourable bulky 3,3-dimethyl groups of the indolenine units which should rather prevent aggregation. Joint theoretical and NMR spectroscopic methods were applied to unravel the supramolecular aggregate structure of hSQA-1, which is shown to consist of two stacked hexasquarainyl benzenes resembling the picture of two stacked bowls.
Several lines of evidence implicate a dysregulation of tryptophan hydroxylase (TPH)-dependent serotonin (5-HT) synthesis in emotions and stress and point to their potential relevance to the etiology and pathogenesis of various neuropsychiatric disorders. However, the differential expression pattern of the two isoforms TPH1 and TPH2 which encode two forms of the rate-limiting enzyme of 5-HT synthesis is controversial. Here, a comprehensive spatio-temporal analysis clarifies TPH1 and TPH2 expression during pre- and postnatal development of the mouse brain and in adult human brain as well as in peripheral organs including the pineal gland. Four different methods (real time PCR, in situ hybridization, immunohistochemistry and Western blot analysis) were performed to systematically control for tissue-, species- and isoform-specific expression on both the pre- and posttranslational level. TPH2 expression was consistently detected in the raphe nuclei, as well as in fibres in the deep pineal gland and in the gastrointestinal tract. Although TPH1 expression was found in these peripheral tissues, no significant TPH1 expression was detected in the brain, neither during murine development, nor in mouse and human adult brain. Also under conditions like stress and clearing the tissue from blood cells, no changes in expression levels were detectable. Furthermore, the reuptake of 5-HT into the presynaptic neuron by the serotonin transporter (SERT) is the major mechanism terminating the neurotransmitter signal. Thus, mice with a deletion in the Sert gene (Sert KO mice) provide an adequate model for human affective disorders to study lifelong modified 5-HT homeostasis in interaction with stressful life events. To further explore the role of TPH isoforms, Tph1 and Tph2 expression was studied in the raphe nuclei of Sert deficient mice under normal conditions as well as following exposure to acute immobilization stress. Interestingly, no statistically significant changes in expression were detected. Moreover, in comparison to Tph2, no relevant Tph1 expression was detected in the brain independent from genotype, gender and treatment confirming expression in data from native animals. Raphe neurons of a brain-specific Tph2 conditional knockout (cKO) model were completely devoid of Tph2-positive neurons and consequently 5-HT in the brain, with no compensatory activation of Tph1 expression. In addition, a time-specific Tph2 inducible (i) KO mouse provides a brain-specific knockdown model during adult life, resulting in a highly reduced number of Tph2-positive cells and 5-HT in the brain. Intriguingly, expression studies detected no obvious alteration in expression of 5-HT system-associated genes in these brain-specific Tph2 knockout and knockdown models. The findings on the one hand confirm the specificity of Tph2 in brain 5-HT synthesis across the lifespan and on the other hand indicate that neither developmental nor adult Tph2-dependent 5-HT synthesis is required for normal formation of the serotonergic system, although Tph1 does not compensate for the lack of 5-HT in the brain of Tph2 KO models. A further aim of this thesis was to investigate the expression of the neuropeptide oxytocin, which is primarily produced in the hypothalamus and released for instance in response to stimulation of 5-HT and selective serotonin reuptake inhibitors (SSRIs). Oxytocin acts as a neuromodulator within the central nervous system (CNS) and is critically involved in mediating pain modulation, anxiolytic-like effects and decrease of stress response, thereby reducing the risk for emotional disorders. In this study, the expression levels of oxytocin in different brain regions of interest (cortex, hippocampus, amygdala, hypothalamus and raphe nuclei) from female and male wildtype (WT) and Sert KO mice with or without exposure to acute immobilization stress were investigated. Results showed significantly higher expression levels of oxytocin in brain regions which are involved in the regulation of emotional stimuli (amygdala and hippocampus) of stressed male WT mice, whereas male Sert KO as well as female WT and Sert KO mice lack these stress-induced changes. These findings are in accordance with the hypothesis of oxytocin being necessary for protection against stress, depressive mood and anxiety but suggest gender-dependent differences. The lack of altered oxytocin expression in Sert KO mice also indicates a modulation of the oxytocin response by the serotonergic system and provides novel research perspectives with respect to altered response of Sert KO mice to stress and anxiety inducing stimuli.
The design of ligands is one of the most important and simultaneously challenging fields of research in modern inorganic chemistry. The aim is to synthesise ligands that can serve as coordination units for a broad variety of metal fragments and different purposes. The ligands have to be very flexible concerning their donating behaviour and geometrical prerequisites in order to correspond to the required metal fragments.