Open Access

Promiscuous acyltransferases enable transesterification reactions in bulk water by preferentially catalyzing acyl transfer over hydrolysis. Until recently, only a small number of promiscuous acyltransferases have been described in the literature, exhibiting several limitations in terms of acyltransferase efficiency and applicability. This work focuses on the discovery of novel promiscuous acyltransferases and the engineering of promiscuous acyltransferases via rational design. Several promiscuous acyltransferases in the bacterial hormone-sensitive lipase family and family VIII carboxylesterases have been identified, demonstrating that promiscuous acyltransferase activity is not a rare phenomenon. Moreover, the efficiency and applicability of the enzymes could be improved via protein engineering in terms of acyltransferase activity, enantioselectivity, and substrate scope.

Free radicals are known to induce significant structural and functional modifications to the cell membrane and its components. Biophysical quantification of such changes using single molecule studies highlight the role of these individual biomolecules. In this PhD work, we focus on nitric oxide radical and try to understand how they influence interaction of different biomolecules with lipid membranes by using biomimetic systems. In specific we try to answer how cell membrane permeability and bilayer thickness would be influenced by the nitric oxide radical with different phospholipids compositions (i.e. on planar supported lipid bilayers). Later we tested, interaction of transmembrane protein integrin αiibβ3 incorporated into the bilayer (i.e. nanodiscs) with nitric oxide. Finally, how to overcome the negative effects encountered by the phospholipids and proteins using biopolymer coated gold nanoparticles as delivery system. The study involved use of atomic force microscopy and quartz-crystal microbalance with dissipation as primary investigation tools complemented with other relevant biophysical and biochemical techniques.

Unter promiskuitiver Acyltransferase-Aktivität versteht man die Eigenschaft bestimmter Hydrolasen, in wässriger Lösung bevorzugt Acyltransfer statt Hydrolyse zu katalysieren. Bis vor Kurzem waren nur wenige promiskuitive Acyltransferasen literaturbekannt. Dies führte zu der allgemeinen Annahme, dass diese Aktivität ein seltenes Phänomen in Hydrolasen ist. Diese Arbeit zeigt jedoch, dass promiskuitive Acyltransferase-Aktivität in der Familie der bakteriellen hormonsensitiven Lipasen und Carboxylesterasen der Familie VIII weit verbreitet ist. Detaillierte Struktur-Funktions-Analysen ermöglichen die sequenzbasierte Vorhersage und Optimierung der Acyltransferase-Aktivität in beiden Enzymfamilien. Insbesondere die Carboxylesterasen der Familie VIII überschreiten die Grenzen des bisher für möglich Gehaltenen, indem sie gute Enantioselektivität bei der kinetischen Racematspaltung sekundärer Alkohole zeigen und darüber hinaus die irreversible Bildung von Amiden und Carbamaten in Wasser katalysieren können. Die biokatalytische Acylierung von Zuckern in Wasser galt lange Zeit als unerreichtes Ziel der Biokatalyse. In dieser Arbeit wurde jedoch gezeigt, dass natürlich vorkommende und modifizierte Carboxylesterasen der Familie VIII die regioselektive Acetylierung von Glucose, Maltose und Maltotriose in Wasser mit hoher Effizienz katalysieren können.

S-adenosyl-L-methionine- (SAM) dependent methyltransferases (MTs) catalyse methylation of halide ions and the C, O, N, S, Se, and As atoms of biomolecules ranging from biopolymers to small molecules. They display different chemo-, regio- and stereoselectivity according to their specific functions. This thesis focuses on the engineering of O-methyltransferases (OMTs) and halide methyltransferases (HMTs) through rational design and directed evolution to study their structure-function relationship and to explore their catalytic promiscuity. The influence of substrate binding residues on the substrate scope and regioselectivity of a plant OMT against various phenolic substrates (Article I) and flavonoids (Article II) has been investigated. Article III describes the directed evolution of an HMT for the biocatalytic synthesis of diverse SAM analogues. With the evolved HMT, regioselective alkylation of phenolic compounds and flavonoids, as well as the SAM analogue regeneration, were achieved through an HMT-MT cascade reaction. Article I Specific residues expand the substrate scope and enhance the regioselectivity of a plant O-methyltransferase. It was reported in literature that an isoeugenol 4-OMT (IeOMT) can be engineered to a caffeic acid 3-OMT (CaOMT) by replacing three consecutive residues. In this article, we investigated the effect of these residues on substrate preference and regioselectivity of IeOMT. The triple mutant T133M/A134N/T135Q and the respective single mutants were constructed and tested against a series of phenolic compounds. The variant T133M had a universal effect to improve enzymatic activities against all tested substrates while the mutant A134N had enhanced regioselectivity. The triple mutant T133M/A134N/T135Q benefits from these two mutations, which not only expanded the substrate scope, but also enhanced the regioselectivity of IeOMT. On the basis of this work, regiospecific methylated phenolics can be produced in high purity by different IeOMT variants. Article II Influence of substrate binding residues on the substrate scope and regioselectivity of a plant O-methyltransferase against flavonoids Flavonoid OMTs (FOMTs), isoflavonoid OMTs (IOMTs) and phenylpropanoid OMTs (POMTs) display different substrate preferences. Sequence comparison showed that the substrate binding residues at positions 322 and 326 are different between these OMT groups and might be critical for the substrate discrimination. Residues at positions 322 and 326 in IeOMT (a POMT) were mutated to the commonly presented residues in FOMT and IOMT. The introduced mutants, in cooperation with the variant T133M, have improved or brought novel activities and regioselectivity against the tested flavonoids eriodictyol, naringenin, luteolin, quercetin, and also the isoflavonoid genistein compared to the wild-type IeOMT. On the basis of this work, methylated flavonoids that are rare in nature were produced in high purity. Article III Directed evolution of a halide methyltransferase enables biocatalytic synthesis of diverse SAM analogs Biocatalytic alkylations to obtain chemo‐, regio‐ and stereoselectively alkylated compounds can be achieved by MTs with the supply of SAM analogues. It was recently discovered that SAM can be directly synthesized from S adenosyl-L homocysteine (SAH) and methyl iodide, catalysed by an HMT. To explore the promiscuity of HMT in the synthesis of SAM analogues, we performed directed evolution of the Arabidopsis thaliana HMT based on a sensitive, colorimetric iodide assay. The identified variant V140T displayed activities against ethyl‐, propyl‐, and allyl iodides to produce the corresponding SAM analogues. With this HMT variant, regioselective ethylation of luteolin and allylation of 3,4‐dihydroxybenzaldehyde, as well as the SAM analogue regeneration, were achieved through this HMT-MT one-pot cascade reaction.

The synthesis of several bioactive compounds and active pharmaceutical ingredients relies on the development of general and efficient methods to prepare optically pure amines. Transaminases are industrially relevant enzymes and are useful for synthesizing a large number of compounds that contain a chiral amine functionality. Although the immense potential associated to the use of these biocatalysts, the equilibrium position is often unfavorable for amine synthesis. The use of an excess of amine donor, compared to the ketone substrate, combined with selective removal of the formed product, can help in overcoming this limitation. This work mainly focused on broadening the application of membrane-based in situ product recovery (ISPR) techniques for the transaminase-catalyzed synthesis of chiral amines. The overall work was designed around the implementation of amine donors, possessing considerably larger molecular ‘size’ compared to commonly used amine donors. To clearly distinguish these molecules from traditional donor amines, we designate them as High Molecular Weigh amine donors. With a molecular weight between 400 and 1500 g/mol, in contrast to traditional donor amines, HMW amine donors enable a size-based separation between amine donor and amine product molecules. HMW amines, provided in excess for thermodynamic equilibrium shifting can thus be simply retained by a size-exclusion mechanism by commercial membranes, while the smaller product amines are permeated. Therefore, a selective recovery of the desired chiral amine product is possible. The implementation of ISPR techniques using HMW amine donors can theoretically lead to (i) equilibrium shifting, (ii) alleviation of product inhibition, and (iii) a highly pure product stream. The feasibility of using HMW amine donors in aqueous, organic solvent and solvent-free media for the transaminase-catalyzed synthesis of 1-methyl-3-phenylpropylamine (MPPA) was proven in this thesis. The latter two approaches were investigated with the aim to achieve higher product concentrations. Along with that, we demonstrated two membrane-assisted ISPR proof of concepts. Specifically, nanofiltration was coupled with the enzymatic reaction performed in aqueous media (Article I), while liquid-liquid (L-L) extraction in a contactor was applied for transamination in organic solvent media (Article II). As an alternative to membrane-based strategies we also designed a spinning reactor concept for the integrated chiral amine synthesis (in organic solvent) and recovery (Article III).

Abstract Certain hydrolases preferentially catalyze acyl transfer over hydrolysis in an aqueous environment. However, the molecular and structural reasons for this phenomenon are still unclear. Herein, we provide evidence that acyltransferase activity in esterases highly correlates with the hydrophobicity of the substrate‐binding pocket. A hydrophobicity scoring system developed in this work allows accurate prediction of promiscuous acyltransferase activity solely from the amino acid sequence of the cap domain. This concept was experimentally verified by systematic investigation of several homologous esterases, leading to the discovery of five novel promiscuous acyltransferases. We also developed a simple yet versatile colorimetric assay for rapid characterization of novel acyltransferases. This study demonstrates that promiscuous acyltransferase activity is not as rare as previously thought and provides access to a vast number of novel acyltransferases with diverse substrate specificity and potential applications.

In modern-day organic synthesis, transitional metal catalysis has become an essential tool-kit to access the biologically significant complex organic scaffolds. The activation profile of these sophisticated catalytic systems in cross-coupling chemistry and ring-closing processes has been well appreciated and frequently employed by the scientific community. The present thesis is describing the results of interdisciplinary research involving medicinal chemistry and transitional metal homogeneous catalysis. A molybdenum mediated process was employed to access 32 unprecedented heterocyclic fused poly sulfur ring containing pentathiepins in moderate to good yields as a part of medicinal chemistry. Biologically significant, such as quinoxaline, pyrazine, pyridine, nicotinamide, quinoline, imdazo-pyrazine, pyrrolo-pyrazine, purine, and pyridine sulfonamide scaffolds were functionalized with pentathiepin unit via multi-step organic synthesis. Essentially, the Sonogashira cross-coupling and(Et4N)2[MoO(S4)2] mediated ring-closing steps were commonly employed in all pentathiepin syntheses. The analytically pure samples were characterized by 1H, 13C, 19F-NMR, FTIR, ESI-MS, CHNS, and X-ray single-crystal diffraction analysis. Notably, all pentathiepins exhibited an ABX3 multiplet pattern between δ: 4.2-4.5 ppm with the integration of 2H for the ethoxy functional group's methylene protons substituted on the five-membered ring of pentathiepin, which was later considered as a fingerprint for pentathiepin formation. The mechanistic investigations via control experiments suggest that the tetra sulfur ring Mo(IV) precursor (Et4N)2[MoO(S4)2] is vital along with elemental sulfur for the pentathiepin formation, and the Mo(IV) complex regenerates in the reaction. Furthermore, For the first time, the GPx1 enzyme inhibitor properties of novel fused heterocyclic pentathiepins were established, where these probes exhibited 9-12 folds higher potency than mercaptosuccinic acid. Notably, <1 µM concentration of quinoxaline, pyrazine, and quinoline fused pentathiepins were potent enough to inhibit 50% of GPx1 enzyme activity. Additionally, cytotoxicity, antimicrobial and antifungal studies were conducted for all pentathiepins. In anticancer investigations, the IC50 concentrations for all pentathiepins were ranging between 0.22 to 4.7 µM. The second half of the thesis introduces a novel water-soluble Pd/PTABS as a potent catalyst for C-X (X = N, O, and S) cross-coupling chloroheteroarenes and halonucleosides. The novel, mild and efficient Pd/PTABS catalytic system was successfully employed at low catalytic loadings (1 mol%) for the amination (C−N), etherification (C−O), and thioetherification (C−S) of chloroheteroarenes at ambient to moderate temperatures. The Pd/PTABS catalyst is well-tolerating various heterocyclic scaffolds, and under the optimized catalytic conditions, various secondary amines, electron-rich or electron-poor phenols, thiophenols, and alkylthiols, were efficiently employed as nucleophilic coupling partners. Notably, the catalyst offered tremendous regio and chemoselectivity with excellent temperature control. Besides, novel sulfones and sulfoximines were prepared from the thioethers obtained via Pd/PTABS. The catalyst was employed efficiently for synthesizing biologically significant known drugs or drug candidates such as alogliptin (anti-diabetic agent), XRK 469 (antitumor agent), and Imuran-Azathioprine (immunosuppressive) in competitive yields. Preliminary DFT investigations were performed, and based on the DFT analysis, the electropositive character of the phosphorous atom in quaternary ammonium salts of PTABS supports the heteroatom directed C−Cl activation hypothesis.

Abstract Biocatalysis has found numerous applications in various fields as an alternative to chemical catalysis. The use of enzymes in organic synthesis, especially to make chiral compounds for pharmaceuticals as well for the flavors and fragrance industry, are the most prominent examples. In addition, biocatalysts are used on a large scale to make specialty and even bulk chemicals. This review intends to give illustrative examples in this field with a special focus on scalable chemical production using enzymes. It also discusses the opportunities and limitations of enzymatic syntheses using distinct examples and provides an outlook on emerging enzyme classes.

Abstract This work presents a stepwise reversible two‐electron transfer induced hydrogen shift leading to the conversion of a bis‐pyrrolinium cation to an E‐diaminoalkene and vice versa. Remarkably, the forward and the reverse reaction, which are both reversible, follow two completely different reaction pathways. Establishing such unprecedented property in this type of processes was possible by developing a novel synthetic route towards the starting dication. All intermediates involved in both the forward and the backward reactions were comprehensively characterized by a combination of spectroscopic, crystallographic, electrochemical, spectroelectrochemical, and theoretical methods. The presented synthetic route opens up new possibilities for the generation of multi‐pyrrolinium cation scaffold‐based organic redox systems, which constitute decidedly sought‐after molecules in contemporary chemistry.

Abstract The bidirectional force transmission process of integrin through the cell membrane is still not well understood. Several possible mechanisms have been discussed in literature on the basis of experimental data, and in this study, we investigate these mechanisms by free and steered molecular dynamics simulations. For the first time, constant velocity pulling on the complete integrin molecule inside a dipalmitoyl‐phosphatidylcholine membrane is conducted. From the results, the most likely mechanism for inside‐out and outside‐in signaling is the switchblade model with further separation of the transmembrane helices.

Abstract Halide assays are important for the study of enzymatic dehalogenation, a topic of great industrial and scientific importance. Here we describe the development of a very sensitive halide assay that can detect less than a picomole of bromide ions, making it very useful for quantifying enzymatic dehalogenation products. Halides are oxidised under mild conditions using the vanadium‐dependent chloroperoxidase from Curvularia inaequalis, forming hypohalous acids that are detected using aminophenyl fluorescein. The assay is up to three orders of magnitude more sensitive than currently available alternatives, with detection limits of 20 nM for bromide and 1 μM for chloride and iodide. We demonstrate that the assay can be used to determine specific activities of dehalogenases and validate this by comparison to a well‐established GC‐MS method. This new assay will facilitate the identification and characterisation of novel dehalogenases and may also be of interest to those studying other halide‐producing enzymes.

Abstract A device for the transaminase‐catalysed synthesis combined with continuous recovery of chiral amines was designed. The system enabled the separation of the reaction components in three liquid phases: a reaction phase, an organic solvent phase (where the poorly water soluble ketone substrate was supplied), and an aqueous extraction phase for continuous product recovery. The transaminase‐mediated asymmetric synthesis of (S)‐1‐methyl‐3‐phenylpropylamine was employed as model reaction. Factors influencing the performance of the system, such as reactor geometry, working volumes and operating parameters, were investigated. Specifically, reaction yield and product recovery were enhanced by i) reducing the thickness of the reaction phase, while continuously stirring and ii) reducing the volume of the extraction phase. Under the optimal condition tested, 85 % of the product formed was extracted and a product concentration value of 9 g/L was reached. However, co‐extraction of the unreacted amine donor (17 %) was observed. Advantages and drawbacks of this process compared to existing technologies, as well as possible optimization strategies are discussed.

Septic arthritis is a medical emergency associated with high morbidity and mortality, yet hardly any novel advances exist for its clinical management. Despite septic arthritis being a global health burden, experimental data uncovering its etiopathogenesis remain scarce. In particular, any interplay between septic arthritis and preceding joint diseases are unknown as is the contribution of the synovial membrane to the onset of inflammation. Using C57BL/6 mice as a model to study sepsis, we discovered that Group A Streptococcus (GAS) – an important pathogen causing septic arthritis - was able to invade the articular microenvironment. Bacterial invasion resulted in the infiltration of immune cells and detrimental inflammation. In vitro infected fibroblast-like synoviocytes induced the expression of chemokines (Ccl2, Cxcl2), inflammatory cytokines (Tnf, Il6), and integrin ligands (ICAM-1, VCAM-1). Apart from orchestrating immune cell attraction and retention, synoviocytes also upregulated mediators impacting on bone remodeling (Rankl) and cartilage integrity (Mmp13). Using collagen-induced arthritis in DBA/1 × B10.Q F1 mice, we could show that an inflammatory joint disease exacerbated subsequent septic arthritis which was associated with an excessive release of cytokines and eicosanoids. Importantly, the severity of joint inflammation controlled the extent of bone erosions during septic arthritis. In order to ameliorate septic arthritis, our results suggest that targeting synoviocytes might be a promising approach when treating patients with inflammatory joint disease for sepsis.

The definition of Green Chemistry was first formulated at the beginning of the 1990s – 30 years ago and states as follows: “design of chemical products and processes to reduce or eliminate the use and generation of hazardous substances” (Poliakoff et al. 2002). Biocatalysis is one of the examples of “green” chemistry as it is relying on natural or modified enzymes. Today, biocatalysis is a standard technology for the production of chemicals (Straathof et al. 2002). In this PhD thesis, the implications of biocatalysis using different class of enzymes are discussed: two cytochrome P450 monoxygenases, two kinases and one lyase are shown as tools for the production of bioactive compounds. The P450 enzymes have a central role in the oxidative metabolism of a wide variety of compounds including the synthesis of endogenous substrates such as steroids and fatty acids. Moreover, P450s catalyze the hydroxylation of non-activated carbon atoms in a regio- and stereospecific fashion avoiding use of protecting groups and several, time-consuming chemical steps. Here, the recombinant expression and biocatalytic characterization of bacterial CYP107D1 for the regio- and stereoselective hydroxylation of two steroid compounds is reported. Since the natural electron transfer partners of these P450s are unknown, PdX and PdR from P. putida were employed to supply CYP107D1 with the necessary electrons for catalysis. This three-component system was used in bioconversions of two bile acids: LCA and DCA. P450 CYP107D1 exhibits high regio- and stereoselectivity for the tested steroids, giving 6β-hydroxylated products. The properties of the CYP107D1 make this multifaceted P450 monooxygenase an attractive enzyme for the production of novel drug metabolites. Moreover, the crystal structure of the enzyme is known, which provides the basis for developing a protein-engineering strategy aimed at catalytic properties of the CYP107D1 The second enzyme described in the thesis is the self-sufficient cytochrome P450 monooxygenase from Fusarium graminarium (FG067). From the overall structure, it resembles the well investigated CYP102 from Bacillus megaterium (CYP BM3) and the P450 from Fusarium oxysporum (CYPfoxy). In this study, two different strategies to recombinantly produce the fungal P450 monooxygenase P450-FG067, namely (a) producing in E. coli and (b) producing in P. pastoris were investigated. The P450 FG_067 from Fusarium graminarium was successfully overexpressed in P. pastoris. The enzyme was functionally active, converted fatty acid substrates of carbon chain length C10-16 with regiospecificity of the hydroxylating position ω -1, ω - 2 and ω-3, with the highest affinity for capric acid. The hydroxylation at different positions of the fatty acid chain is needed for different chemical industries. For example, ω-HFAs can be used as starting materials for the synthesis of polymers, with high resistance to heat or chemicals (Xiao et al. 2018). Therefore, the application of recombinant enzyme such as self-sufficient P450 FG_067 for a commercial production of HFAs is in high industrial demand. In this thesis, two kinases were used for the producton of phosphorylated metabolites. Kinases catalyzing N-phosphorylation, which are of synthetic interest because of tedious chemical procedures in selective chemical N-phosphorylations. A highly active and stabile arginine kinase, obtained by cloning and expressing the argK gene from Limulus polyphemus in E. coli, was used in the one-step synthesis of Nω-phospho-L-arginine using the phosphoenolpyruvate/pyruvate kinase system for ATP regeneration. Applying arginine kinase in biocatalysis opens up new opportunities for the selective biocatalytic N-phosphorylation of interesting low-molecular-weight compounds and metabolites. Another kinase investigated in this thesis was shikimate kinase. The highly active and stable shikimate kinase AroL was achieved by synthesizing the codon-optimized aroL gene and expressing it in high yield in E. coli. Next, shikimate kinase was used in an one-step synthesis of shikimate-3-phosphate using the phosphoenolpyruvate/pyruvate kinase system for ATP regeneration. Development of the described biocatalytic preparation of shikimate-3-phosphate is a superior route incomparison to a tedious multi-step and low yield classical synthesis of this compound. The biocatalytic phosphorylation is of great interest for a commercial production of metabolites and metabolite-like structures. The last investigeted enzyme in this PhD thesis was argininosuccinate lyase from Saccharomyces cerevisiae. The argininosuccinate lyase was cloned and overexpressed in E. coli as a highly active and stable biocatalyst. A simple and straightforward biocatalytic asymmetric Michael addition reaction has been established for the synthesis of the key metabolite N-(([(4S)-4-amino-4-carboxybutyl]amino)imino methyl)-L-aspartic acid, commonly referred to as L-argininosuccinate. This one-step addition reaction was developed by running part of the urea cycle in reverse. The use of this argininosuccinate lyase and reaction monitoring by NMR enabled the development of a biocatalytic asymmetric Michael addition reaction as a novel green chemistry route with high molecular economy for the synthesis of this important metabolite at gram scale. Recent advances in the field of scientific research have helped to understand the structure and functional activities of enzymes, which has in turn led to an increase in their stability, activity and substrate specificity. Nowadays, biocatalysis provide more sustainable, efficient, and less polluting methods for the production of fine chemicals and advanced pharmaceutical intermediates. The biocatalysts used in this thesis are introduced as a technology for the efficient synthesis of biologically active compounds, which is greener, reduces pollution and costs compared to chemical synthesis. In summary, the pharmaceutical industry should use the advantage of the progress of biochemistry to obtain biocatalysts in the production of fine chemicals on an industrial scale, improving the quality of end products and saving costs.

Proteostasis is critical for cells to maintain the balance between protein synthesis, quality control, and degradation. This is particularly important for myeloid cells of the central nervous system as their immunological function relies on proper intracellular protein turnover by the ubiquitin-proteasome system. Accordingly, disruption of proteasome activity due to, e.g., loss-of-function mutations within genes encoding proteasome subunits, results in systemic autoinflammation. On the molecular level, pharmacological inhibition of proteasome results in endoplasmic reticulum (ER) stress-activated unfolded protein response (UPR) as well as an induction of type I interferons (IFN). Nevertheless, our understanding as to whether and to which extent UPR signaling regulates type I IFN response is limited. To address this issue, we have tested the effects of proteasome dysfunction upon treatment with proteasome inhibitors in primary murine microglia and microglia-like cell line BV-2. Our data show that proteasome impairment by bortezomib is a stimulus that activates all three intracellular ER-stress transducers activation transcription factor 6, protein kinase R-like endoplasmic reticulum kinase and inositol-requiring protein 1 alpha (IRE1α), causing a full activation of the UPR. We further demonstrate that impaired proteasome activity in microglia cells triggers an induction of IFNβ1 in an IRE1-dependent manner. An inhibition of the IRE1 endoribonuclease activity significantly attenuates TANK-binding kinase 1-mediated activation of type I IFN. Moreover, interfering with TANK-binding kinase 1 activity also compromised the expression of C/EBP homologous protein 10, thereby emphasizing a multilayered interplay between UPR and type IFN response pathway. Interestingly, the induced protein kinase R-like endoplasmic reticulum kinase-activation transcription factor 4-C/EBP homologous protein 10 and IRE1-X-box-binding protein 1 axes caused a significant upregulation of proinflammatory cytokine interleukin 6 expression that exacerbates STAT1/STAT3 signaling in cells with dysfunctional proteasomes. Altogether, these findings indicate that proteasome impairment disrupts ER homeostasis and triggers a complex interchange between ER-stress sensors and type I IFN signaling, thus inducing in myeloid cells a state of chronic inflammation.

Das klarzellige Nierenzellkarzinom (ccRCC) ist eine von vielen Krebserkrankungen. Viele Patienten weisen eine Mutation im Von-Hippel-Lindau-Gen (VHL) auf und/ oder zeigen eine Überexpression des Enzyms Nicotinamid-N-Metyltransferase (NNMT). Es wurden insgesamt fünf etablierte Zelllinien verwendet, die embryonale Nierenzelllinie HEK-293 und vier ccRCC-Zelllinien (Caki-1, Caki-2, 769-P, 786-O), welche sich in ihrer Expression der Proteine NNMT und VHL unterscheiden. Zudem wurde eine stabile Zelllinie aus den Caki-2 Zellen generiert, die durch ein Doxycyclin induzierbares Tet-On-System NNMT vermehrt exprimiert (C2NNMTs). Es wurden sowohl molekularbiologische als auch biochemische Methoden zur Analyse angewendet. Die Zelllinien wurden für Transfektionsstudien zur Überexpression oder zum Knockdown von NNMT genutzt, um die Einflussnahme auf die Enzyme Nikotinamid-phosphoribosyltransferase (NAMPT), Sirtuin 1 (SIRT1), Methioninadenosyltransferase-2 β-Untereinheit (MAT2B) und Aldehydoxidase (AOX1) zu analysieren. Da SAM (S-Adenosylmethionin) der Methyldonor von NNMT ist, wurde auch der Einfluss der Methioninkonzentration betrachtet. Viele der bisherigen publizierten Versuche wurden bei 100 µM Methionin durchgeführt, was jedoch nicht der humanen Serumkonzentration entspricht, welche bei 20 µM Methionin liegt. Umfangreiche massenspektrometrische Analysen führten zur Identifizierung weiterer Proteine, welche durch die NNMT-Modulation beeinflusst wurden. Die Identifikation einer Vielzahl veränderter Targets verdeutlichte den Einfluss auf den Energiemetabolismus bis hin zur Apoptose. Es zeigten sich unterschiedliche Regulationen von Glykolyse-, Respirations-, Citratzyklus-, Pentosephosphatweg- und Lipidsyntheseproteinen. Insgesamt ergaben sich individuelle, zellspezifische Regulierungen, welche auf die Sirtuine zurückzuführen sind. Weiterhin wurden Untersuchungen zur erhöhten Expression von NNMT unter Einfluss von Nikotinamid (NAM) sowie Interleukin-6 (IL-6) durchgeführt. Die Analysen zeigten, dass zwischen der Pseudohypoxie und der Erhöhung der NNMT-Expression ein Zusammenhang besteht, denn IL-6 phosphoryliert ERK (engl. Extracellular-signal Regulated Kinases) und STAT3 (engl. Signal transducer and activator of transcription 3), welche beide benötigt werden, um die Transkription des NNMT-Gens zu beeinflussen und die NNMT-Proteinexpression zu fördern. Die Ergebnisse dieser Untersuchungen sollen dazu dienen, die biochemischen Zusammenhänge einer veränderten Expression von NNMT besser zu verstehen und damit neue diagnostische Ansätze zu ermöglichen.

In contrast to its terrestrial counterpart, the metabolic degradation of marine polysaccharides is underexplored. This work aimed to functionally characterize ulvan- and xylan-degrading enzymes from marine Bacteroidetes in order to clarify the metabolic degradation pathway. For the provision of a broad polysaccharide substrate spectrum, ulvan from several different algal sources was extracted to be used in further characterization experiments. The structural differences of these ulvans could be demonstrated by enzymatic degradation with ulvan-active enzymes. In order to clarify the synergistic catalytic effects of polysaccharide sulfatases with GHs in the degradation process of ulvan, several putative sulfatases from F. agariphila were produced recombinantly in E. coli. For that, a coexpression with an FGE encoding gene was required. It could be demonstrated that several glycoside hydrolases are inhibited, if their substrate is sulfated at the cleavage position and that a previous desulfation using one of the sulfatases enabled the further degradation. Some of the sulfatases showed an endolytic or exolytic cleavage behavior like reported for several GHs. With the combined catalytic activities, it was possible to successfully elucidate the complex ulvan degradation mechanism for the first time, which enables the use of ulvan as a biotechnological source for the production of fine chemicals and pharmaceuticals. This degradation mechanism was shown to be complemented by an alternative pathway that helps with the degradation of uronic acid-containing oligosaccharides. Here, the synergistic effects of a multimodular enzyme containing a sulfatase and rhamnosidase domain were demonstrated. Furthermore, the first dehydratase participating in the degradation of oligosaccharides was revealed. The functional characterization of putative xylan-targeting PULs from two Flavobacteriia revealed the existence of marine endolytic and exolytic xylanases. The enzymes of these PULs were produced recombinantly in E. coli and were used in biocatalysis reactions on xylan from beechwood, xylan from P. palmata or commercial xylooligosaccharide standards. Further side chain-active GHs were found to exclusively be active on either standards or xylan. The great variation of genetic equipment was demonstrated by comparing the enzyme activities of these PUL structures assuming different ecological adaptations of these organisms especially, because these PULs do not code for any putative sulfatases, which is uncommon for PULs targeting xylan. A different degradation behavior of the investigated enzymes suggested a preferred conversion of β-1,4-linked xylan, potentially present in some microalgae. The acquired insight of the metabolic ulvan and xylan utilization greatly expands the scientific knowledge about the ecologic interplays in marine environments concerning the polysaccharide utilization. It indicates the necessity of backup mechanisms for metabolic processes in order to get access to complex marine carbon sources in nature. Several small degradation cascades complement each other to break down substrate compounds to monomeric level for the use of structurally diverse polysaccharides. This expands the insights into the metabolic processes in the degradation of marine polysaccharides, which are an important part of the understanding of the ecological interactions in aquatic habitats and the ocean’s carbon cycle. The characterization of ulvan- and xylan-active enzymes and the clarification of their substrate scopes allow to use these enzymes in future production of carbohydrate-derived chemical products for many industrial applications, making it possible to use algal waste for recycling to high value materials with even beneficial effect for the environment.

Das Gram-positive Bakterium Streptococcus pneumoniae ist ein humanspezifisches Pathogen des oberen Respirationstraktes. Der opportunistische Krankheitserreger kann jedoch mehrere Organe befallen und tiefer in den Körper vordringen, was zu lokalen Entzündungen wie Sinusitis und Otitis media oder zu lebensbedrohlichen Infektionen wie Pneumonie, Meningitis oder Sepsis führen kann. Für das Bakterium S. pneumoniae wurden bisher kaum Metabolom-Daten erhoben. Daher war das Ziel dieser Dissertation eine umfassende Charakterisierung des Metaboloms von S. pneumoniae. In dieser Dissertation wurden als analytische Methoden die Gaschromatografie (GC) und Flüssigkeitschromatografie (LC) jeweils gekoppelt mit Massenspektrometrie (MS) sowie die Kernspinresonanzspektroskopie (NMR) verwendet, um die Metaboliten zu analysieren. Es sind mehrere Analysetechniken erforderlich, um den Großteil des Metaboloms mit seinen chemisch verschiedenen Metaboliten zu erfassen. Artikel I fasst die Literatur zu Untersuchungen des Metabolismus von S. pneumoniae in den letzten Jahren zusammen. Um eine Momentaufnahme des biologischen Systems zum jeweiligen Zeitpunkt zu erhalten, ist neben dem reproduzierbaren Wachstum während der Kultivierung auch die exakte Probenahme zu beachten. Aus diesem Grund wurde in dieser Dissertation ein Probenahmeprotokoll für das Endometabolom von S. pneumoniae etabliert (Artikel II). Mithilfe des optimierten Protokolls wurde eine umfassende Metabolomanalyse in einem chemisch definierten Medium durchgeführt (Artikel II). Um S. pneumoniae in einer Umgebung ähnlich der im Wirt zu untersuchen, wurde in einem modifizierten Zellkulturmedium kultiviert. Intermediate zentraler Stoffwechselwege von S. pneumoniae wurden analysiert. Das intrazelluläre Stoffwechselprofil wies auf einen hohen glykolytischen Flux hin und bot Einblicke in den Peptidoglykan-Stoffwechsel. Darüber hinaus widerspiegelten die Ergebnisse die biochemische Abhängigkeit von S. pneumoniae von aus dem Wirt stammenden Nährstoffen. Ein umfassendes Verständnis der Stoffwechselwege von Pathogenen ist wichtig, um Erkenntnisse über die Anpassungsstrategien während einer Infektion zu gewinnen und so neue Angriffspunkte für Wirkstoffe zu identifizieren. Die zunehmende Verbreitung von resistenten S. pneumoniae-Stämmen zwingt zur Suche nach neuen antibiotisch wirksamen Substanzen. Im Zuge dessen wurde in Artikel III die metabolische Reaktion von S. pneumoniae während des Wachstums unter dem Einfluss antibakterieller Substanzen mit dem Ziel der Identifizierung metabolischer Anpassungsprozesse untersucht. Dabei wurden Antibiotika mit unterschiedlichen Wirkmechanismen verwendet, wie die Beeinflussung der Zellwandbiosynthese (Cefotaxim, Teixobactin-Arg10), der Proteinbiosynthese (Azithromycin) sowie Nukleotidsynthese (Moxifloxacin). Es konnten keine Wirkmechanismus-spezifischen Marker-Metaboliten identifiziert werden. Jedes Antibiotikum verursachte weitreichende Veränderungen im gesamten Metabolom von S. pneumoniae. Die Nukleotid- und Zellwandsynthese waren am stärksten betroffen. Besonders vielversprechend sind Antibiotika mit zwei Wirkorten wie Teixobactin-Arg10 und Kombinationen aus zwei Antibiotika. In dieser Dissertation wurde das erste Mal das synthetisch hergestellte Teixobactin-Arg10 mittels einer der modernen OMICS-Techniken untersucht. Die vorliegende umfassende Metabolom-Studie bietet wertvolle Erkenntnisse für Forscher, die an der Identifizierung neuer antibakterieller Substanzen arbeiten. Insgesamt tragen die Ergebnisse der Dissertation zu einem besseren Verständnis der bakteriellen Physiologie bei.

Aufgrund der extremen Instabilität des Molybdän Cofaktors (MoCo) ist eine genauere Untersuchung der aktiven Zentren der lebenswichtigen MoCo-abhängigen Enzyme allein durch biochemische Methoden fast unmöglich. Hierfür liefert eine chemische Modellierung des Cofaktors die einzige Möglichkeit einen tieferen Einblick in seine Struktur und Funktion. Die vorliegende Dissertation ermöglicht einen weitaus tieferen Einblick in Struktur-Funktionsbeziehung des Molybdän-Cofaktors hinsichtlich des zentralen Metalls und des Molybdopterin-Liganden. Zunächst wurde die Rolle des Molybdänzentrums in den Modellverbindungen detailliert analysiert. Hierfür wurde in den synthetisierten Modellen Molybdän mit Rhenium, ausgetauscht. Die erhaltenen Komplexe wurden zuerst umfangreichend durch verschiedene Methoden Kristallstrukturanalyse, IR-, Raman-, NMR-, 2D-NMR-Spektroskopie, temperaturabhängige Elektrochemie und quantenchemischen Berechnungen analysiert und auf Analogien und Unterschiede verglichen. Dabei wurde auf der Suche eines MoCo-Modells, das die richtige Balance zwischen katalytischer Aktivität und Stabilität besitzt, untersucht, ob Rhenium eine potenzielle Alternative zu Molybdän darstellen kann. Um einen tieferen Einblick in die Chemie des Pterin-Strukturabschnitts von MoCo zu erschaffen, beschäftigt sich diese Arbeit mit der Feinabstimmung von Chinoxalin- und Pterin-Dithiolen-Liganden sowie mit der Entwicklung deren Molybdän-Komplexen. Dazu konnten neuartige Chinoxalin- und Pterin-Dithiolen-Liganden synthetisiert werden, die als Modell-Liganden für die Erforschung der Biosynthese des MoCos fungieren können. Hierin wird die Synthese und die vollständige Charakterisierung eines neuartigen Oxo-Bis(pterin)dithiolen-Molybdän-Komplexes beschrieben. Durch 2D-NMR Spektroskopie konnte die Struktur des erhaltenen Komplexes in Lösung detailliert analysiert werden. Schließlich wurden im Rahmen der vorliegenden Arbeit erstmals durchgeführte Untersuchungen zur Bindung von chemisch synthetisierten MoCo-Modellen mit dem Apoenzym der Trimethylamin-N-Oxid-Reduktase unternommen. Dabei konnte die essenzielle Rolle des Pterin-Gerüstes für die richtige Platzierung des Cofaktors in der Bindungstasche des Apoenzyms etwas näher aufgeklärt werden. Zukünftig könnten noch strukturell genauere MoCo-Modelle den Weg für die Synthese einer semi-artifiziellen Sulfitoxidase, die als eine Behandlungsmöglichkeit der Molybdän-Cofaktor-Defizienz (MoCoD) und der isolierten Sulfitoxidase-Defizienz (iSOD) eingesetzt werden, eröffnen.

Über 40% der derzeit verwendeten Arzneimittel beinhalten Amine als Wirkstoff. Vor allem die Chiralität dieser Moleküle stellt eine immer größere Bedeutung dar. Chirale Moleküle unterscheiden sich in der räumlichen Anordnung der Atome um das chirale Zentrum. Nicht selten besitzen Naturstoffe ein solches chirales Zentrum und sind asymmetrisch aufgebaut. In diesem Zusammenhang ist es nicht verwunderlich, dass die in der Medizin eingesetzten Wirkstoffe einen unterschiedlichen Wirkungsgrad je nach chiraler Konfiguration aufweisen. Ziel dieser Arbeit war es neue Methoden zur stereoselektiven Synthese chiraler Amine zu untersuchen. Im Gegensatz zu herkömmlichen chemischen Synthesen, die beispielsweise auf Übergangsmetalle als Katalysatoren setzen, stellen Enzyme als Katalysatoren eine interessente Alternative dar. Stereo-, Regio- und Chemoselektivität ist Enzymen oft von Natur aus gegeben. Im Mittelpunkt der enzymatischen asymmetrischen Synthese optisch aktiver Amine standen bisher Amintransaminasen (ATA), die eine Aminogruppe von einem Amin (Aminodonor) auf ein Keton (Aminoakzeptor) transferieren. Diese Enzyme sind jedoch auf die Synthese primärer Amine beschränkt, sekundäre und tertiäre Amine sind nicht zugänglich. Eine Alternative hierzu stellen Iminreduktasen (IREDs) dar. Dabei handelt es sich um NADPH-abhängige Enzyme, die eine Reduktion von Iminsubstraten zu optisch aktiven Aminen katalysieren. Vor allem die IRED-katalysierte reduktive Aminierung steigerte das Interesse dieser Enzymklasse. In einer reduktiven Aminierung wird nicht das Imin selbst als Substrat eingesetzt, sondern eine prochirales Keton. Dieses formt mit einem Aminsubstrat (Nukleophil) ein Imin und wird anschließend reduziert. Durch diesen Reaktionsweg sind IREDs nicht nur auf zyklische Substrate beschränkt, auch instabile azyklische Imine werden zugänglich. Die reduktive Aminierung mittels Iminreduktase wurde erstmalig im Jahr 2014 beschrieben und war zu Beginn dieser Arbeit nur als "Proof of Concept" gezeigt worden. Im Rahmen dieser Promotionsarbeit konnte gezeigt werden, dass diese Enzyme die Möglichkeit bieten, optisch aktive Amine mit hohen Umsätzen und Enantiomeren- bzw. Diastereomerenüberschüssen zu synthetisieren.