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Xenocoumacin (Xcn) 1 and 2 are the major antibiotics produced by the insect-pathogenic bacterium Xenorhabdus nematophila. Although the antimicrobial activity of Xcns has been explored, research regarding their action on mammalian cells is lacking. We aimed to investigate the action of Xcns in the context of inflammation and angiogenesis. We found that Xcns do not impair the viability of primary endothelial cells (ECs). Particularly Xcn2, but not Xcn1, inhibited the pro-inflammatory activation of ECs: Xcn2 diminished the interaction between ECs and leukocytes by downregulating cell adhesion molecule expression and blocked critical steps of the NF-κB activation pathway including the nuclear translocation of NF-κB p65 as well as the activation of inhibitor of κBα (IκBα) and IκB kinase β (IKKβ). Furthermore, the synthesis of pro-inflammatory mediators and enzymes, nitric oxide (NO) production and prostaglandin E2 (PGE2), inducible NO synthase (iNOS), and cyclooxygenase-2 (COX-2), was evaluated in leukocytes. The results showed that Xcns reduced viability, NO release, and iNOS expression in activated macrophages. Beyond these anti-inflammatory properties, Xcn2 effectively hindered pro-angiogenic processes in HUVECs, such as proliferation, undirected and chemotactic migration, sprouting, and network formation. Most importantly, we revealed that Xcn2 inhibits de novo protein synthesis in ECs. Consequently, protein levels of receptors that mediate the inflammatory and angiogenic signaling processes and that have a short half-live are reduced by Xcn2 treatment, thus explaining the observed pharmacological activities. Overall, our research highlights that Xcn2 exhibits significant pharmacological in vitro activity regarding inflammation and angiogenesis, which is worth to be further investigated preclinically.
The formation of amyloid-β oligomers plays a key role in the onset of Alzheimer’s disease. We investigated the aggregation of amyloid-β oligomers by mass spectrometry and ion mobility spectrometry, revealing those structural properties, which lead to the formation of mature fibrils. We can show that the arrangement of the first oligomers is crucial for the topology of the resulting species, leading to the formation of non-toxic aggregates or fibrils.
The family of phytochrome photoreceptors contains proteins with different domain architectures and spectral properties. Knotless phytochromes are one of the three main subgroups classified by their distinct lack of the PAS domain in their photosensory core module, which is in contrast to the canonical PAS-GAF-PHY array. Despite intensive research on the ultrafast photodynamics of phytochromes, little is known about the primary kinetics in knotless phytochromes. Here, we present the ultrafast Pr ⇆ Pfr photodynamics of SynCph2, the best-known knotless phytochrome. Our results show that the excited state lifetime of Pr* (~200 ps) is similar to bacteriophytochromes, but much longer than in most canonical phytochromes. We assign the slow Pr* kinetics to relaxation processes of the chromophore-binding pocket that controls the bilin chromophore’s isomerization step. The Pfr photoconversion dynamics starts with a faster excited state relaxation than in canonical phytochromes, but, despite the differences in the respective domain architectures, proceeds via similar ground state intermediate steps up to Meta-F. Based on our observations, we propose that the kinetic features and overall dynamics of the ultrafast photoreaction are determined to a great extent by the geometrical context (i.e., available space and flexibility) within the binding pocket, while the general reaction steps following the photoexcitation are most likely conserved among the red/far-red phytochromes.
Despite a high clinical need for the treatment of colorectal carcinoma (CRC) as the second leading cause of cancer-related deaths, targeted therapies are still limited. The multifunctional enzyme Transglutaminase 2 (TGM2), which harbors transamidation and GTPase activity, has been implicated in the development and progression of different types of human cancers. However, the mechanism and role of TGM2 in colorectal cancer are poorly understood. Here, we present TGM2 as a promising drug target.
In primary patient material of CRC patients, we detected an increased expression and enzymatic activity of TGM2 in colon cancer tissue in comparison to matched normal colon mucosa cells. The genetic ablation of TGM2 in CRC cell lines using shRNAs or CRISPR/Cas9 inhibited cell expansion and tumorsphere formation. In vivo, tumor initiation and growth were reduced upon genetic knockdown of TGM2 in xenotransplantations. TGM2 ablation led to the induction of Caspase-3-driven apoptosis in CRC cells. Functional rescue experiments with TGM2 variants revealed that the transamidation activity is critical for the pro-survival function of TGM2. Transcriptomic and protein–protein interaction analyses applying various methods including super-resolution and time-lapse microscopy showed that TGM2 directly binds to the tumor suppressor p53, leading to its inactivation and escape of apoptosis induction.
We demonstrate here that TGM2 is an essential survival factor in CRC, highlighting the therapeutic potential of TGM2 inhibitors in CRC patients with high TGM2 expression. The inactivation of p53 by TGM2 binding indicates a general anti-apoptotic function, which may be relevant in cancers beyond CRC.
Fatty acid and polyketide synthases (FASs and PKSs) synthesize physiologically and pharmaceutically important products by condensation of acyl building blocks. The transacylation reaction catalyzed by acyl transferases (ATs) is responsible for the selection of acyl-CoA esters for further processing by FASs and PKSs. In this study, the AT domains of different multidomain (type I) PKS systems are kinetically described in their substrate selectivity, AT−Acyl carrier protein (ACP) domain-domain interaction and enzymatic kinetic properties. We observe that the ATs of modular PKSs, intricate protein complexes occurring in bacteria and responsible for the biosynthesis of bioactive polyketides, are significantly slower than ATs of mammalian FASs, reflecting the respective purpose of the biosynthetic pathways within the organism and their metabolic context. We further perform a mutational study on the kinetics of the AT−ACP interaction in the modular PKS 6-deoxyerythronolide B synthase (DEBS) and find a high plasticity in enzyme properties, which we explain by a high plasticity in AT−ACP recognition. Our study enlarges the understanding of ATs in its molecular properties and is similarly a call for thorough AT-centered PKS engineering strategies.
Die vorliegende Arbeit Zeitaufgelöste NMR-spektroskopische Untersuchung konformationeller Dynamiken in DNA G-Quadruplexen befasst sich mit der detaillierten biophysikalischen Untersuchung wichtiger strukturdynamischer Eigenschaften von nicht-kanonischen Nukleinsäure Sekundärstrukturelementen.
Im Genom aller eukaryotischer Lebewesen, insbesondere dem menschlichen Genom finden sich DNA-Sequenzabschnitte, die überdurchschnittlich Guanosin (G)-reich sind. Diese poly-G Abschnitte sind nicht zufällig im Genom verteilt, sondern häufen sich vermehrt in Genabschnitten, die besonders wichtig für die Regulation der Genexpression sind. G-reiche DNA-Sequenzen können unter geeigneten Umständen alternative Sekundärstrukturen ausbilden, die von der doppelsträngigen, kanonischen Watson-Crick Konformation abweichen. In Anwesenheit monovalenter Kationen können sich G-Nukleotide in einer Tetrade über Hoogsteen Interaktionen anlagern. Diese Tetraden können sich stapeln und dadurch sogenannte G-Quadruplexe (G4) ausbilden. Das menschliche cMYC Gen wird typischerweise als proto-Onkogen bezeichnet. Es kodiert für einen unspezifischen Transkriptionsfaktor, der bei einer Vielzahl von systematischen und soliden Tumorerkrankungen stark überexprimiert wird. Die zelluläre Konzentration des Genprodukts kann zu 90% über ein G4 cis-Element in der Promotorregion reguliert werden. Der cMYC G4 hat die Möglichkeit verschiedene Konformationen einzunehmen. Im Falle des cMYC G4 kann man zusätzliche, nicht-konventionelle Formen der konformationellen Isomerie finden. Zum einen gibt es die Möglichkeit, dass bei einem G4, der aus drei Tetraden und vier intramolekularen Strangabschnitten (dreistöckiger G4) besteht, einzelne Strangabschnitte mehr als drei konsekutive G-Nukleotide besitzen. Dadurch können sich Faltungs-Isomere bilden, die sich durch Verschieben des Strangs relativ zum verbleibenden dreistöckigen Tetradengerüst ergeben. Man spricht von G-Register Isomeren. Eine zweite Möglichkeit der Strukturisomerie ergibt sich, wenn in einer Nukleotidsequenz mehr als vier G-reiche Strangabschnitte aufeinander folgen. Jeweils vier dieser Strangabschnitte können in unterschiedlicher Weise kombiniert werden, um ein G4 Isomer auszubilden. In jedem dieser so zustande gekommenen G4 verbleibt ein (oder mehrere) G-reicher Strangabschnitt, der im konkreten Isomer nicht zur Faltung verwendet wird. Diese zusätzlichen G-Stränge werden daher auch Ersatzräder (engl. spare-tires) genannt; man erhält spare-tire Isomere.
Obwohl diese Formen des Polymorphismus, deren biologischer Kontext und die biophysikalischen Konsequenzen in Arbeiten von C. Burrows (2015) und A. Mittermaier (2016) erstmals umfassend beschrieben wurden, gab es bis zum Ausgangspunkt dieser Arbeit keine Kenntnisse über deren strukturelle Dynamik, den Faltungswegen und den zugrundeliegenden molekularen Mechanismen. Zeitaufgelöste Kernspinresonanz (engl. nuclear magnetic resonance, NMR) Spektroskopie ist eine bestens geeignete Methode, um die Dynamik von Biomakromolekülen mit atomarer Auflösung zu studieren. Um solche Experimente durchführen zu können, braucht es geeignete Herangehensweisen für die Präparation eines Nicht-Gleichgewichtszustands. In dieser Arbeit wird eine neu erarbeitete Strategie vorgestellt, die es erlaubt, Einblick in die Faltungs- und Umfaltungskinetiken eines dynamischen Konformations-Ensembles nicht-konventioneller Strukturisomere der cMYC G4 DNA-Sequenz zu erhalten.
Hierzu wurden photolabile Schutzgruppen (engl. Photocages) positionsspezifisch an bestimmten G-Nukleobasen (O6-(R)-NPE) angebracht. Die Schutzgruppen blockieren die Basenpaar-Interaktionen des Nukleotids, wodurch dieses sich nicht mehr an einer Tetradenbildung beteiligen kann. Die Photocages wurden jeweils an den Nukleotiden eingeführt, die nur in jeweils einem der G-Register Isomere an der Tetradenbildung beteiligt sind. Durch diese gezielte Destabilisierung konnten die Isomere getrennt und im gefalteten Zustand isoliert werden. Die so erhaltenen Konformationen wurden umfassend spektroskopisch charakterisiert. Der Ansatz, das konformationelle Gleichgewicht durch Photocages transient zu stören, wurde daraufhin weiterentwickelt. Mehrere Photocages wurden an Nukleobasen in zentraler Position einzelner G-Strangabschnitte angebracht. Dadurch konnte eine ausreichende Destabilisierung erreicht werden, die die Faltung jedweder G4 Strukturen unterbindet. Somit wurde ein ungefalteter Zustand erzeugt, der unter ansonsten frei wählbaren, physiologischen Bedingungen besteht. Durch in situ Photolyse der Schutzgruppen konnte so die Licht-induzierte G4 Faltung unter konstanten Puffer- und Temperaturbedingungen untersucht werden. Dieser Ansatz wurde auf die Untersuchung der Faltungswege, die zu verschiedenen spare-tire Isomeren führen, fokussiert.
Zusammenfassend kann festgestellt werden, dass es insgesamt erstmalig gelungen ist, die Kinetiken der wesentlichen Faltungs- und Umfaltungswege entlang der konformationellen Energielandschaft des cMYC G4 Elements zu untersuchen. Das komplexe, dynamische Zusammenspiel aller relevanten, nicht-konventionellen isomeren G4 Strukturen konnte entworren und umfassend experimentell beschrieben werden. Der dafür weiterentwickelte Ansatz über konformationelle Selektion mit Hilfe photolabiler Schutzgruppen hat dabei experimentelle Einblicke erlaubt, die bislang nicht zugänglich waren. Die Strukturen und Faltungszustämde, die mit den chemisch modifizierten Oligonukleotiden erhalten und isoliert wurden, sind umfassend spektroskopisch untersucht worden. Die Anwendung verschiedener spektroskopischer Ansätze und deren Kombination mit weiteren biophysikalischen Methoden hat eine Methoden-unabhängige Validierung der erhaltenen kinetischen und thermodynamischen Daten ermöglicht.
Thermally stable and highly conductive SAMs on Ag substrate — the impact of the anchoring group
(2021)
Self-assembled monolayers (SAMs) on metal substrates are an important part of modern interfacial chemistry and nanotechnology. The robustness of SAMs strongly depends on their thermal stability, which, together with electric conductivity, crucial for their applications in molecular/organic electronics. In this context, using a multidisciplinary approach, the structure, stability, and conductivity properties of conjugated aromatic SAMs featuring the naphthalene backbone and S, Se, or COO group, mediating bonding to the Ag substrate are addressed. Whereas thermal stability of these SAMs exhibits a strong dependence on anchoring group, their conductivity is similar, which is rationalized by tentative model considering redistribution of charge density along the molecular framework. The thermal stability of model naphthalenethiol SAM, emphasized by desorption energy of ≈1.69 eV, is better than that of typical N-heterocyclic carbene (NHC) monolayers considered currently as the most stable SAMs on metal substrates. However, in contrast to NHC SAMs, which are highly insulating, the naphtalene-based SAM, with S, Se or COO anchoring groups, are highly conductive, even in comparison with analogous oligophenyl SAMs (by a factor of 10). A unique combination of the ultimate thermal stability and superior conductivity for the naphthalenethiol SAM on Ag makes it highly attractive for applications.
In recent years, the incidence of infected wounds is steadily increasing, and so is the clinical as well as economic interest in effective therapies. These combine reduction of pathogen load in the wound with general wound management to facilitate the healing process. The success of current therapies is challenged by harsh conditions in the wound microenvironment, chronicity, and biofilm formation, thus impeding adequate concentrations of active antimicrobials at the site of infection. Inadequate dosing accuracy of systemically and topically applied antibiotics is prone to promote development of antibiotic resistance, while in the case of antiseptics, cytotoxicity is a major problem. Advanced drug delivery systems have the potential to enable the tailor-made application of antimicrobials to the side of action, resulting in an effective treatment with negligible side effects. This review provides a comprehensive overview of the current state of treatment options for the therapy of infected wounds. In this context, a special focus is set on delivery systems for antimicrobials ranging from semi-solid and liquid formulations over wound dressings to more advanced carriers such as nano-sized particulate systems, vesicular systems, electrospun fibers, and microneedles, which are discussed regarding their potential for effective therapy of wound infections. Further, established and novel models and analytical techniques for preclinical testing are introduced and a future perspective is provided.
The new class of microbial rhodopsins, called xenorhodopsins (XeRs),[1] extends the versatility of this family by inward H+ pumps.[2–4] These pumps are an alternative optogenetic tool to the light-gated ion channels (e.g. ChR1,2), because the activation of electrically excitable cells by XeRs is independent from the surrounding physiological conditions. In this work we functionally and spectroscopically characterized XeR from Nanosalina (NsXeR).[1] The photodynamic behavior of NsXeR was investigated on the ps to s time scale elucidating the formation of the J and K and a previously unknown long-lived intermediate. The pH dependent kinetics reveal that alkalization of the surrounding medium accelerates the photocycle and the pump turnover. In patch-clamp experiments the blue-light illumination of NsXeR in the M state shows a potential-dependent vectoriality of the photocurrent transients, suggesting a variable accessibility of reprotonation of the retinal Schiff base. Insights on the kinetically independent switching mechanism could furthermore be obtained by mutational studies on the putative intracellular H+ acceptor D220.
The new class of microbial rhodopsins, called xenorhodopsins (XeRs),[1] extends the versatility of this family by inward H+ pumps.[2–4] These pumps are an alternative optogenetic tool to the light-gated ion channels (e.g. ChR1,2), because the activation of electrically excitable cells by XeRs is independent from the surrounding physiological conditions. In this work we functionally and spectroscopically characterized XeR from Nanosalina (NsXeR).[1] The photodynamic behavior of NsXeR was investigated on the ps to s time scale elucidating the formation of the J and K and a previously unknown long-lived intermediate. The pH dependent kinetics reveal that alkalization of the surrounding medium accelerates the photocycle and the pump turnover. In patch-clamp experiments the blue-light illumination of NsXeR in the M state shows a potential-dependent vectoriality of the photocurrent transients, suggesting a variable accessibility of reprotonation of the retinal Schiff base. Insights on the kinetically independent switching mechanism could furthermore be obtained by mutational studies on the putative intracellular H+ acceptor D220.
The assembly of a specific polymeric ubiquitin chain on a target protein is a key event in the regulation of numerous cellular processes. Yet, the mechanisms that govern the selective synthesis of particular polyubiquitin signals remain enigmatic. The homologous ubiquitin-conjugating (E2) enzymes Ubc1 (budding yeast) and Ube2K (mammals) exclusively generate polyubiquitin linked through lysine 48 (K48). Uniquely among E2 enzymes, Ubc1 and Ube2K harbor a ubiquitin-binding UBA domain with unknown function. We found that this UBA domain preferentially interacts with ubiquitin chains linked through lysine 63 (K63). Based on structural modeling, in vitro ubiquitination experiments, and NMR studies, we propose that the UBA domain aligns Ubc1 with K63-linked polyubiquitin and facilitates the selective assembly of K48/K63-branched ubiquitin conjugates. Genetic and proteomics experiments link the activity of the UBA domain, and hence the formation of this unusual ubiquitin chain topology, to the maintenance of cellular proteostasis.
The stress-dependent dynamics of Saccharomyces cerevisiae tRNA and rRNA modification profiles
(2021)
RNAs are key players in the cell, and to fulfil their functions, they are enzymatically modified. These modifications have been found to be dynamic and dependent on internal and external factors, such as stress. In this study we used nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS) to address the question of which mechanisms allow the dynamic adaptation of RNA modifications during stress in the model organism S. cerevisiae. We found that both tRNA and rRNA transcription is stalled in yeast exposed to stressors such as H2O2, NaAsO2 or methyl methanesulfonate (MMS). From the absence of new transcripts, we concluded that most RNA modification profile changes observed to date are linked to changes happening on the pre-existing RNAs. We confirmed these changes, and we followed the fate of the pre-existing tRNAs and rRNAs during stress recovery. For MMS, we found previously described damage products in tRNA, and in addition, we found evidence for direct base methylation damage of 2′O-ribose methylated nucleosides in rRNA. While we found no evidence for increased RNA degradation after MMS exposure, we observed rapid loss of all methylation damages in all studied RNAs. With NAIL-MS we further established the modification speed in new tRNA and 18S and 25S rRNA from unstressed S. cerevisiae. During stress exposure, the placement of modifications was delayed overall. Only the tRNA modifications 1-methyladenosine and pseudouridine were incorporated as fast in stressed cells as in control cells. Similarly, 2′-O-methyladenosine in both 18S and 25S rRNA was unaffected by the stressor, but all other rRNA modifications were incorporated after a delay. In summary, we present mechanistic insights into stress-dependent RNA modification profiling in S. cerevisiae tRNA and rRNA.
Leukemia patients bearing t(6;11)(q27;q23) translocations can be divided in two subgroups: those with breakpoints in the major breakpoint cluster region of MLL (introns 9–10; associated mainly with AML M1/4/5), and others with breakpoints in the minor breakpoint cluster region (introns 21–23), associated with T-ALL. We cloned all four of the resulting fusion genes (MLL-AF6, AF6-MLL, exMLL-AF6, AF6-shMLL) and subsequently transfected them to generate stable cell culture models. Their molecular function was tested by inducing gene expression for 48 h in a Doxycycline-dependent fashion. Here, we present our results upon differential gene expression (DGE) that were obtained by the “Massive Analyses of cDNA Ends” (MACE-Seq) technology, an established 3′-end based RNA-Seq method. Our results indicate that the PHD/BD domain, present in the AF6-MLL and the exMLL-AF6 fusion protein, is responsible for chromatin activation in a genome-wide fashion. This led to strong deregulation of transcriptional processes involving protein-coding genes, pseudogenes, non-annotated genes, and RNA genes, e.g., LincRNAs and microRNAs, respectively. While cooperation between the MLL-AF6 and AF6-MLL fusion proteins appears to be required for the above-mentioned effects, exMLL-AF6 is able to cause similar effects on its own. The exMLL-AF6/AF6-shMLL co-expressing cell line displayed the induction of a myeloid-specific and a T-cell specific gene signature, which may explain the T-ALL disease phenotype observed in patients with such breakpoints. This again demonstrated that MLL fusion proteins are instructive and allow to study their pathomolecular mechanisms.
Leukemia patients bearing t(6;11)(q27;q23) translocations can be divided in two subgroups: those with breakpoints in the major breakpoint cluster region of MLL (introns 9–10; associated mainly with AML M1/4/5), and others with breakpoints in the minor breakpoint cluster region (introns 21–23), associated with T-ALL. We cloned all four of the resulting fusion genes (MLL-AF6, AF6-MLL, exMLL-AF6, AF6-shMLL) and subsequently transfected them to generate stable cell culture models. Their molecular function was tested by inducing gene expression for 48 h in a Doxycycline-dependent fashion. Here, we present our results upon differential gene expression (DGE) that were obtained by the “Massive Analyses of cDNA Ends” (MACE-Seq) technology, an established 3′-end based RNA-Seq method. Our results indicate that the PHD/BD domain, present in the AF6-MLL and the exMLL-AF6 fusion protein, is responsible for chromatin activation in a genome-wide fashion. This led to strong deregulation of transcriptional processes involving protein-coding genes, pseudogenes, non-annotated genes, and RNA genes, e.g., LincRNAs and microRNAs, respectively. While cooperation between the MLL-AF6 and AF6-MLL fusion proteins appears to be required for the above-mentioned effects, exMLL-AF6 is able to cause similar effects on its own. The exMLL-AF6/AF6-shMLL co-expressing cell line displayed the induction of a myeloid-specific and a T-cell specific gene signature, which may explain the T-ALL disease phenotype observed in patients with such breakpoints. This again demonstrated that MLL fusion proteins are instructive and allow to study their pathomolecular mechanisms.
Leukemia patients bearing the t(4;11)(q21;q23) translocations can be divided into two subgroups: those expressing both reciprocal fusion genes, and those that have only the MLL-AF4 fusion gene. Moreover, a recent study has demonstrated that patients expressing both fusion genes have a better outcome than patients that are expressing the MLL-AF4 fusion protein alone. All this may point to a clonal process where the reciprocal fusion gene AF4-MLL could be lost during disease progression, as this loss may select for a more aggressive type of leukemia. Therefore, we were interested in unraveling the decisive role of the AF4-MLL fusion protein at an early timepoint of disease development. We designed an experimental model system where the MLL-AF4 fusion protein was constitutively expressed, while an inducible AF4-MLL fusion gene was induced for only 48 h. Subsequently, we investigated genome-wide changes by RNA- and ATAC-Seq experiments at distinct timepoints. These analyses revealed that the expression of AF4-MLL for only 48 h was sufficient to significantly change the genomic landscape (transcription and chromatin) even on a longer time scale. Thus, we have to conclude that the AF4-MLL fusion protein works through a hit-and-run mechanism, probably necessary to set up pre-leukemic conditions, but being dispensable for later disease progression.
The prevalence and specificity of local protein synthesis during neuronal synaptic plasticity
(2021)
To supply proteins to their vast volume, neurons localize mRNAs and ribosomes in dendrites and axons. While local protein synthesis is required for synaptic plasticity, the abundance and distribution of ribosomes and nascent proteins near synapses remain elusive. Here, we quantified the occurrence of local translation and visualized the range of synapses supplied by nascent proteins during basal and plastic conditions. We detected dendritic ribosomes and nascent proteins at single-molecule resolution using DNA-PAINT and metabolic labeling. Both ribosomes and nascent proteins positively correlated with synapse density. Ribosomes were detected at ~85% of synapses with ~2 translational sites per synapse; ~50% of the nascent protein was detected near synapses. The amount of locally synthesized protein detected at a synapse correlated with its spontaneous Ca2+ activity. A multifold increase in synaptic nascent protein was evident following both local and global plasticity at respective scales, albeit with substantial heterogeneity between neighboring synapses.
Treatment of hexachloropropene (Cl2C[double bond, length as m-dash]C(Cl)–CCl3) with Si2Cl6 and [nBu4N]Cl (1 : 4 : 1) in CH2Cl2 results in a quantitative conversion to the trisilylated, dichlorinated allyl anion salt [nBu4N][Cl2C[double bond, length as m-dash]C(SiCl3)–C(SiCl3)2] ([nBu4N][1]). Tetrachloroallene Cl2C[double bond, length as m-dash]C[double bond, length as m-dash]CCl2 was identified as the first intermediate of the reaction cascade. In the solid state, [1]− adopts approximate Cs symmetry with a dihedral angle between the planes running through the olefinic and carbanionic fragments of [1]− of C[double bond, length as m-dash]C–Si//Si–C–Si = 78.3(1)°. One-electron oxidation of [nBu4N][1] with SbCl5 furnishes the distillable blue radical 1˙. The neutral propene Cl2C[double bond, length as m-dash]C(SiCl3)–C(SiCl3)2H (2) was obtained by (i) protonation of [1]− with HOSO2CF3 (HOTf) or (ii) H-atom transfer to 1˙ from 1,4-cyclohexadiene. Quantitative transformation of all three SiCl3 substituents in 2 to Si(OMe)3 (2OMe) or SiMe3 (2Me) substituents was achieved by using MeOH/NMe2Et or MeMgBr in CH2Cl2 or THF, respectively. Upon addition of 2 equiv. of tBuLi, 2Me underwent deprotonation with subsequent LiCl elimination, 1,2-SiMe3 migration and Cl/Li exchange to afford the allenyl lithium compound Me3Si(Li)C[double bond, length as m-dash]C[double bond, length as m-dash]C(SiMe3)2 (Li[4]), which is an efficient building block for the introduction of Me, SiMe3, or SnMe3 (5) groups. The trisilylated, monochlorinated allene Cl3Si(Cl)C[double bond, length as m-dash]C[double bond, length as m-dash]C(SiCl3)2 (6), was obtained from [nBu4N][1] through Cl−-ion abstraction with AlCl3 and rearrangement in CH2Cl2 (1˙ forms as a minor side product, likely because the system AlCl3/CH2Cl2 can also act as a one-electron oxidant).
Chronic inflammation is characterized by persisting leukocyte infiltration of the affected tissue, which is enabled by activated endothelial cells (ECs). Chronic inflammatory diseases remain a major pharmacotherapeutic challenge, and thus the search for novel drugs and drug targets is an ongoing demand. We have identified the natural product vioprolide A (vioA) to exert anti-inflammatory actions in vivo and in ECs in vitro through inhibition of its cellular target nucleolar protein 14 (NOP14). VioA attenuated the infiltration of microglia and macrophages during laser-induced murine choroidal neovascularization and the leukocyte trafficking through the vascular endothelium in the murine cremaster muscle. Mechanistic studies revealed that vioA downregulates EC adhesion molecules and the tumor necrosis factor receptor (TNFR) 1 by decreasing the de novo protein synthesis in ECs. Most importantly, we found that inhibition of importin-dependent NF-ĸB p65 nuclear translocation is a crucial part of the action of vioA leading to reduced NF-ĸB promotor activity and inflammatory gene expression. Knockdown experiments revealed a causal link between the cellular target NOP14 and the anti-inflammatory action of vioA, classifying the natural product as unique drug lead for anti-inflammatory therapeutics.
We investigated the folding kinetics of G-quadruplex (G4) structures by comparing the K+-induced folding of an RNA G4 derived from the human telomeric repeat-containing RNA (TERRA25) with a sequence homologous DNA G4 (wtTel25) using CD spectroscopy and real-time NMR spectroscopy. While DNA G4 folding is biphasic, reveals kinetic partitioning and involves kinetically favoured off-pathway intermediates, RNA G4 folding is faster and monophasic. The differences in kinetics are correlated to the differences in the folded conformations of RNA vs. DNA G4s, in particular with regard to the conformation around the glycosidic torsion angle χ that uniformly adopts anti conformations for RNA G4s and both, syn and anti conformation for DNA G4s. Modified DNA G4s with 19F bound to C2′ in arabino configuration adopt exclusively anti conformations for χ. These fluoro-modified DNA (antiTel25) reveal faster folding kinetics and monomorphic conformations similar to RNA G4s, suggesting the correlation between folding kinetics and pathways with differences in χ angle preferences in DNA and RNA, respectively.
The deubiquitinase USP32 regulates non-proteolytic ubiquitination in the endosomal-lysosomal system
(2021)
The regulation of essential cellular processes requires tightly controlled and directed transport of proteins and membranes. The highly dynamic endosomal and lysosomal system forms the key network for exchange and trafficking of molecules with its early endosomes, recycling endosomes, late endosomes, lysosomes, and additionally autophagosomes.
In this system, the small GTPase Rab7 has an essential role at the late endosomal stage regulating vesicle transport, tethering, and fusion, and retromer mediated receptor recycling back to the trans-Golgi network (TGN). Thus, Rab7 is also important for autophagosomes and lysosomes.
Lysosomes do not only represent the end point of the degradation pathway with several feeder pathways. But these organelles are also a dynamic signaling hub for a variety of metabolic processes. The ever-important regulator of cellular biosynthetic pathways mTORC1 dynamically associates with lysosomes where it is activated. mTORC1 activation is a complex multi-step process where a series of signaling events converge in dependence of amino acid levels thereby enabling interactions between the lysosomal v-ATPase, Ragulator complex (consisting of LAMTOR1-5), and Rag GTPases.
Ubiquitin signals are involved in almost all cellular processes. With this, their regulatory mechanism is also described for the endosomal-lysosomal system as well as mTORC1 signaling. Deubiquitinases (DUBs) release conjugated ubiquitin from proteins and thereby maintain the dynamic state of the cellular ubiquitinome.
The ubiquitin-specific protease 32 (USP32) is a poorly characterized DUB with only emerging cellular function. However, its predicted domain structure includes two unique domains within the entire DUB family. It has been linked to the development of breast cancer and small cell lung cancer. Furthermore, overexpressed GFP-USP32 was localized at the TGN, and a global mass spectrometry-based DUB interactome study suggested an interaction with the retromer complex. Based on these data, USP32 was a very interesting candidate to study its cellular function in this PhD project.
To investigate the function without disease background, a polyclonal USP32 knockout (USP32KO) RPE1 cell line was generated using the CRISPR/Cas9 technology. First experiments revealed different protein expression levels in various cell lines, and a subcellular localization of USP32 at membranes of the Golgi and lysosomal compartments. In a subsequent SILAC-based ubiquitinome analysis potential substrates of USP32 were identified. Interestingly, various proteins of the endosomal-lysosomal system were detected with enriched non-proteolytic ubiquitination upon USP32 depletion.
The further characterization of Rab7 as USP32 substrate confirmed the USP32-sensitive ubiquitination of Rab7 at lysine (K) residues 191 and 194. The ubiquitination in USP32KO cells did not change the subcellular localization of Rab7, but enhanced the interaction with the effector protein RILP. This implied that Rab7 was either more active or RILP had higher affinity to ubiquitinated Rab7. The subsequent results verified this theory. The retromer mediated recycling of CI-M6PR back to the TGN was faster or more efficient in USP32-depleted cells.
Accompanying this, levels of hydrolases were enriched in lysosomes isolated from USP32KO cells. Notably, USP32 had no direct effect on expression level or assembly of the retromer complex itself.
The observed lysosomal phenotypes connected another identified substrate to the function of USP32 in the endosomal-lysosomal system: LAMTOR1. LAMTOR1 is a component of the Ragulator complex and thus involved in the activation of mTORC1 at the lysosomal surface. Similar as for Rab7, the first experiments to characterize LAMTOR1 as USP32 substrate confirmed the USP32-sensitive ubiquitination at K20 independent of amino acid availability. However, ubiquitination of LAMTOR1 decreased its lysosomal localization in untreated and amino acid starved USP32KO cells. The following label-free interactome study detected a reduced interaction of LAMTOR1 and subunits of the lysosomal v-ATPase upon loss of USP32. This resulted in a shifted subcellular localization of mTOR (subunit of mTORC1) away from lysosomes. Furthermore, direct substrates of mTORC1 were less or slower re-phosphorylated after long amino acid starvation and re-activation of mTORC1 in USP32KO cells indicating a reduced mTORC1 activity.
Both USP32-dependent regulations of Rab7 and LAMTOR1/Ragulator converged in enhanced autophagic processes analyzed by increased LC3 levels upon amino acid starvation and USP32 depletion.
In summary, the presented thesis described the diverse role of USP32 in the endosomal and lysosomal system, and contributes to the understanding of novel ubiquitin signals in this context.
The desensitized channelrhodopsin-2 photointermediate contains 13 -cis, 15 -syn retinal Schiff base
(2021)
Channelrhodopsin-2 (ChR2) is a light-gated cation channel and was used to lay the foundations of optogenetics. Its dark state X-ray structure has been determined in 2017 for the wild-type, which is the prototype for all other ChR variants. However, the mechanistic understanding of the channel function is still incomplete in terms of structural changes after photon absorption by the retinal chromophore and in the framework of functional models. Hence, detailed information needs to be collected on the dark state as well as on the different photointermediates. For ChR2 detailed knowledge on the chromophore configuration in the different states is still missing and a consensus has not been achieved. Using DNP-enhanced solid-state MAS NMR spectroscopy on proteoliposome samples, we unambiguously determined the chromophore configuration in the desensitized state, and we show that this state occurs towards the end of the photocycle.
B-cell acute lymphoblastic leukaemia (B-ALL) is characterized by the overproduction of lymphoblasts in the bone marrow (BM), and it is the most common cancer in children while being comparatively uncommon in adults. On the other hand, in chronic myeloid leukaemia (CML), 70% of cases are found in patients older than 50 years, making it uncommon in children. All CML cases and up to 3% of paediatric B- ALL (and 25% of adult B-ALL) cases are due to fusion gene BCR-ABL1, which gives rise to the cytoplasmatic, constitutively active oncoprotein, tyrosine kinase BCR-ABL1 through a reciprocal translocation between chromosomes 9 and 22. The constitutively active BCR-ABL tyrosine kinase leads to deregulation of different signal transduction pathways such as cell growth, proliferation and cell survival. The role of the bone marrow microenvironment (BMM) can mediate disease initiation (only in mice), progression, therapy resistance, and relapse, as has been increasingly recognized over the last two decades. In general, the BMM is a very complex arrangement of various cell types such as osteoblasts, osteoclasts, endothelial cells, adipocytes, mesenchymal stromal cells, macrophages and several others. In addition, the BMM is composed of multiple chemical and mechanical factors and extra cellular matrix (ECM) proteins which contribute to the BMM’s features influencing leukaemia behaviour. Considering the incidence of B-ALL and CML in children and in adults respectively, we hypothesized that the young and/or an aged BMM might also play a previously unrecognized role in the aggressiveness of B-ALL and CML. We proposed that BM, transduced with BCR-ABL1-expressing retrovirus in the murine transduction/transplantation model of B-ALL, transplanted into young versus old recipient mice would lead to a more aggressive disease in young mice, and similarly CML would be more aggressive in old recipient mice. In close recapitulation with the human incidence, induction of CML led to a significantly shorted survival in old recipient mice. On the other hand, induction of B-ALL showed a shortened survival in young compared to old syngeneic mice, as well as in a xenotransplantation model. Among the highly heterogenous composition of the BMM, we implicate young BM macrophages as a supportive niche for B-ALL cells. The results were found to be mostly due to potential soluble factors differentially secreted from young and old macrophages. Therefore, we hypothesized that the chemokine CXCL13, which has been demonstrated to play a role in B cell migration and act as a diagnostic marker in the cerebrospinal fluid of patients with neuroborreliosis, might be responsible for the observed phenotype. CXCL13 was found to be more highly expressed in healthy and leukaemic young mice as well as in conditioned medium of young macrophages. Using a variety of in vitro experiments, CXCL13 showed to significantly increase the proliferation and the migration of leukaemia cells when exposed to young macrophages, and the phenotype was rescued while using a CXCL13 neutralizing antibody. The CXCL13 role was also confirmed in vivo, since macrophage ablation led to a prolongation of survival in young mice and a reduction of CXCL13 levels. The use of an additional mouse model, leukaemia cells with CXCR5 deficiency, led to a significant prolongation of survival of young mice, confirming the importance of the CXCL13-CXCR5 axis in B-ALL. In line with our murine results, we found that human macrophages and CXCL13 levels were higher in pediatric B-ALL patients than in adults. Consistent with our murine data, the expression level of CXCR5 may act as a prognostic marker in B-ALL, as well as a predictive marker for central nervous system relapse in human B-ALL. The overall findings show that a young BMM, and in particular macrophages, influences B-ALL progression. We specifically identified CXCL13, secreted by young macrophages, as a promoter of proliferation of B-ALL cells, influencing survival in B-ALL via CXCR5. The CXCR5-CXCL13 axis may be relevant in human B-ALL, and higher CXCR5 expression in human B-ALL may act as a predictive marker.
Lead-optimization strategies for compounds targeting c-Myc G-quadruplex (G4) DNA are being pursued to develop anticancer drugs. Here, we investigate the structure-activity- relationship (SAR) of a newly synthesized series of molecules based on the pyrrolidine-substituted 5-nitro indole scaffold to target G4 DNA. Our synthesized series allows modulation of flexible elements with a structurally preserved scaffold. Biological and biophysical analyses illustrate that substituted 5-nitroindole scaffolds bind to the c-Myc promoter G-quadruplex. These compounds downregulate c-Myc expression and induce cell-cycle arrest in the sub-G1/G1 phase in cancer cells. They further increase the concentration of intracellular reactive oxygen species. NMR spectra show that three of the newly synthesized compounds interact with the terminal G-quartets (5′- and 3′-ends) in a 2 : 1 stoichiometry.
Die Autophagie ist ein in Eukaryonten evolutionär konservierter Prozess, bei dem es zu einem lysosomalen Abbau von cytosolischen Bestandteilen kommt. Die dabei entstehenden biochemischen Bausteine stehen anschließend erneut zum Aufbau benötigter Strukturen zur Verfügung. Verschiedene Stimuli, wie beispielsweise Nährstoffmangel, können die Aktivität der Autophagie erhöhen und ermöglicht Zellen dadurch die Aufrechterhaltung der Zellhomöostase, selbst unter Stressbedingungen. Im Verlauf der Autophagie bildet sich eine tassenförmige Doppelmembran-Struktur, das sogenannte Phagophor. Dieses wächst, um das abzubauende Material zu umschließen und wird dabei von sogenannten Atg-Proteinen (autophagy-related genes) prozessiert. Nach der Schließung spricht man vom Autophagosom, welches letztlich mit einem Lysosom verschmilzt und das Autophagolysosom bildet, welches wiederum die eingeschlossenen Bestandteile zerlegt und die recycelten Bausteine freigibt. Die einzelnen Schritte während der Autophagie sind hochgradig durch die Atg-Proteine reguliert. Eines dieser Atg-Proteine, das Atg8, ist an einigen entscheidenden Schritten wie dem Phagophor-Wachstum, der Autophagosom-Reifung sowie der Schließung beteiligt. Während es in Hefen nur ein einziges Atg8-Protein gibt, so zeigt sich in höheren Eukaryonten meist eine gewisse Diversität. So codiert beispielsweise das humane Genom mindestens sechs Atg8-Homologe. Neben den drei Proteinen der LC3-Familie (A, B, C) zählen auch GABARAP, GABARAPL1 und GABARAPL2 dazu. Die Gründe für diese Diversität sind noch nicht vollständig aufgeklärt, weshalb es wichtig ist, möglichst selektive Modulatoren zu entwickeln, um so die Aufgaben der einzelnen Homologen entschlüsseln zu können. Eine weitere wichtige Aufgabe übernimmt Atg8 beim Binden des abzubauenden Materials über sogenannte Autophagie-Rezeptoren, wie beispielsweise p62. Der Bindevorgang beruht dabei auf der Interaktion von p62 mit ubiquitinierten Zellbestandteilen auf der einen Seite und der Interaktion zwischen p62 und LC3 auf der anderen Seite. Letztgenannte beruht auf dem Binden des LIR-Motivs (LC3-interagierende Region) von p62 an die LDS (LIR-docking site) des LC3-Proteins. Das LIR-Motiv zeichnet sich durch Aminosäure-Sequenz D-D-D-W/F/Y-X1-X2-L/I/V aus. Währende die aromatische Seitenkette (W/F/Y) die hydrophobe Tasche 1 (HP1) der LDS besetzt, ragt die aliphatische Seitenkette (L/I/V) in die HP2 hinein. Damit sollte es möglich sein, die LIR-LC3-Interaktion, durch das Besetzen der LDS zu stören bzw. zu inhibieren. Solche Inhibitoren könnten zum einen der weiteren Aufklärung der Prozesse, an denen die Autophagie beteiligt ist, dienen, zum anderen jedoch auch die Untersuchung fehlerhafter Autophagie ermöglichen. Ausgangspunkt für diese Arbeit stellt die Verbindung Novobiocin dar, die im Rahmen eines Mitteldurchsatz-Screenings als potenzieller Inhibitor der LIR-LC3-Interaktion identifiziert und mittels ITC, TSA und 1H-15N-HSQC verifiziert werden konnte. Die Struktur des Novobiocins setzt sich aus dem 3-Amino-4-hydroxy-8-methylcoumarin-Kern, der über eine Amidbindung an 3-iso-Prenyl-4-Hydroxybenzoesäure gebunden ist, sowie einer O-glykosidischen Bindung in Position C7 des Coumarins mit L-Noviose zusammen. Da es sich bei Novobiocin (XL6) um ein verhältnismäßig komplexes Molekül handelt, wurde der Einfluss einzelner funktionellen Gruppen des Moleküls auf die Bindungsaffinität hin untersucht. Hierfür wurden Synthesestrategien sowohl für die Coumarin-Gerüste als auch verschiedene Benzoesäuren entwickelt. Die erhaltenen Verbindungen wurden mittels ITC und TSA untersucht. Dabei wurde die Verbindung MH507 als geeigneter Ausgangspunkt für die Untersuchung der Struktur-Aktivitätsbeziehungen (SAR) bezüglich der Benzamid-Seite identifiziert. Im Rahmen einer ersten SAR-Untersuchung wurden neben verschiedenen 3-Alkyl-benzoesäuren, auch verschiedene divalente Isostere (-O-, -S-, -NHSO2-) der benzylischen Methylengruppe synthetisiert. Diese, sowie kommerzielle Aminosäuren, wurden mit 3-Amino-4,7-dihydroxycoumarin zu den entsprechenden Endverbindungen gekuppelt. Ergänzend dazu wurden auch eine Verbindung mit umgekehrter Konstitution der Amidbindung dargestellt, um den Einfluss der Reihenfolge zu verifizieren. In einer weiteren SAR-Studie wurden Derivate synthetisiert, die zusätzlich eine Funktionalisierung am C7 des Coumarin-Gerüstes über Amidkupplung, Sulfonamid-Bildung bzw. Suzuki-Reaktion erlauben und somit eine Interaktion mit der HP1 ermöglichen könnten. Dafür wurde eine weitere Synthesestrategie zur Darstellung von 7-Nitro- bzw. 7-Brom-3-amino-4-hydroxycoumarinen ausgearbeitet und eine Reihe von Endverbindungen dargestellt. Neben den Coumarin-Derivaten wurden auch vier Peptidomimetika synthetisierten. Hierfür wurde, basierend auf den Interaktionen zwischen dem LIR-Motiv und der LC3 Proteinoberfläche, ein Pharmakophor-Modell erstellt. Neben einem Pentapeptid wurden auch drei Verbindungen dargestellt, die ein 5-Amino 2-methoxybenzohydrazid-Gerüst besitzen. Um die synthetisierten Verbindungen auf ihre inhibitorische Aktivität auf LC3A bzw. LC3B gegenüber dem LIR-Motiv von p62 hin untersuchen zu können, wurde ein HTRF-basierter Verdrängungsassay entwickelt. Dabei diente ein mit dem LIR-Motiv modifiziertes sGFP als FRET-Akzeptor, während das jeweilige Terbium-Kryptat-gelabelte SNAP-LC3-Fusionsprotein als FRET-Donor fungierte. Neben den Titrationsexperimenten zur Bestimmung der IC50-Werte wurden auch die jeweiligen Dissoziationskonstanten (Kd) von LC3A und LC3B gegenüber dem LIR-sGFP-Fusionsprotein bestimmt, um die IC50-Werte in inhibitorische Konstanten (Ki) zu überführen, da diese untereinander besser vergleichbar sind.
Die Verbindung MH209 zeigte die höchste Aktivität auf LC3A bzw. LC3B und besitzt aufgrund der Noviose-Einheit eine gute Wasserlöslichkeit, weshalb sie für die weiteren Untersuchungen ausgewählt wurde. Im Zuge von Kristallisationsexperimenten gelang die Isolierung und Vermessung eines Co-Kristalls von LC3A mit Verbindung MH209. Durch die Kristallstruktur wurden wichtige Einblicke in die intermolekularen Wechselwirkungen der 4-Hydroxycoumarine mit der LC3A- bzw. LC3B-Proteinoberfläche gewonnen und die Bindungsmode aufgeklärt. Diese Erkenntnisse passen gut zu den Ergebnissen aus den durchgeführten TSA-, ITC- und HTRF-Assays, wie beispielsweise der korrekten Konstitution der Amidbindung am C3 des Coumarin-Gerüstes. Mittels ITC wurde die Verbindung MH209 auf ihre Bindungsaffinität gegenüber den anderen humanen Homologen der Atg8-Proteinfamilie hin untersucht. Dabei zeigte sich, dass MH209 abgesehen von LC3A und LC3B keinerlei Aktivität auf den humanen Atg8-Homologen besitzt. Diese Selektivität ist nützlich, um die biologische Bedeutung der Diversität von Atg8-Homologen in höheren Eukaryonten zu untersuchen und Prozesse, in die diese involviert sind, aufzuklären.
Release of neuropeptides from dense core vesicles (DCVs) is essential for neuromodulation. Compared to the release of small neurotransmitters, much less is known about the mechanisms and proteins contributing to neuropeptide release. By optogenetics, behavioral analysis, electrophysiology, electron microscopy, and live imaging, we show that synapsin SNN-1 is required for cAMP-dependent neuropeptide release in Caenorhabditis elegans hermaphrodite cholinergic motor neurons. In synapsin mutants, behaviors induced by the photoactivated adenylyl cyclase bPAC, which we previously showed to depend on acetylcholine and neuropeptides (Steuer Costa et al., 2017), are altered like in animals with reduced cAMP. Synapsin mutants have slight alterations in synaptic vesicle (SV) distribution, however, a defect in SV mobilization was apparent after channelrhodopsin-based photostimulation. DCVs were largely affected in snn-1 mutants: DCVs were ∼30% reduced in synaptic terminals, and not released following bPAC stimulation. Imaging axonal DCV trafficking, also in genome-engineered mutants in the serine-9 protein kinase A phosphorylation site, showed that synapsin captures DCVs at synapses, making them available for release. SNN-1 co-localized with immobile, captured DCVs. In synapsin deletion mutants, DCVs were more mobile and less likely to be caught at release sites, and in non-phosphorylatable SNN-1B(S9A) mutants, DCVs traffic less and accumulate, likely by enhanced SNN-1 dependent tethering. Our work establishes synapsin as a key mediator of neuropeptide release.
Translational riboswitches are cis-acting RNA regulators that modulate the expression of genes during translation initiation. Their mechanism is considered as an RNA-only gene-regulatory system inducing a ligand-dependent shift of the population of functional ON- and OFF-states. The interaction of riboswitches with the translation machinery remained unexplored. For the adenine-sensing riboswitch from Vibrio vulnificus we show that ligand binding alone is not sufficient for switching to a translational ON-state but the interaction of the riboswitch with the 30S ribosome is indispensable. Only the synergy of binding of adenine and of 30S ribosome, in particular protein rS1, induces complete opening of the translation initiation region. Our investigation thus unravels the intricate dynamic network involving RNA regulator, ligand inducer and ribosome protein modulator during translation initiation.
Specialized transporter proteins facilitate controlled uptake and extrusion of molecules across biological membranes that would otherwise be impermeable to them. The superfamily of solute carriers (SLC) comprises the second largest group of membrane proteins in humans, acting on a variety of small polar and non-polar molecules and ions. Because of their central role in metabolism, malfunctioning of these proteins often is pathogenic. The interest in SLC transporters as drug targets – as well as for drug delivery – has therefore increased in the past years. For many SLC subfamilies, however, structural and functional information remains scarce to date.
The here presented data provides important insights into different aspects of the transport mechanism of the SLC23 and SLC26 protein families. Importantly, we show that SLC23 nucleobase transporters, in contrast to what was been previously reported, work as uniporters rather than as proton-coupled symporters. In order to do so, we developed the first and only in vitro transport assay for the SLC23 family, which enables investigation of protein function in a defined environment. Moreover, we provide a hypothesis on the role of the extremely conserved negative charged substrate binding site residue found not only in the SLC23, but also SLC4 and SLC26 families. Based on a detailed analysis of binding and transport we conclude that this conserved negative charged has a relevance for protein stability rather than for substrate binding, which explains its conservation for all three protein families that otherwise differ in their substrate specificities and modes of transport. Lastly, we investigated the relevance of oligomerization for the SLC23 and SLC26 families, highlighting the importance of the STAS domain for forming active dimers in the SLC26 anion transporter family.
Salt-inducible kinases (SIKs) are key metabolic regulators. Imbalance of SIK function is associated with the development of diverse cancers, including breast, gastric and ovarian cancer. Chemical tools to clarify the roles of SIK in different diseases are, however, sparse and are generally characterized by poor kinome-wide selectivity. Here, we have adapted the pyrido[2,3-d]pyrimidin-7-one-based PAK inhibitor G-5555 for the targeting of SIK, by exploiting differences in the back-pocket region of these kinases. Optimization was supported by high-resolution crystal structures of G-5555 bound to the known off-targets MST3 and MST4, leading to a chemical probe, MRIA9, with dual SIK/PAK activity and excellent selectivity over other kinases. Furthermore, we show that MRIA9 sensitizes ovarian cancer cells to treatment with the mitotic agent paclitaxel, confirming earlier data from genetic knockdown studies and suggesting a combination therapy with SIK inhibitors and paclitaxel for the treatment of paclitaxel-resistant ovarian cancer.
A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called ‘PDF-Global-Fit’ and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross-correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF-Global-Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF-Global-Fit is in excellent agreement with the published crystal structure data.
Dysfunction of YEATS-domain-containing MLLT1, an acetyl/acyl-lysine dependent epigenetic reader domain, has been implicated in the development of aggressive cancers. Mutations in the YEATS domain have been recently reported as a cause of MLLT1 aberrant reader function. However, structural basis for the reported alterations in affinity for acetyled/acylated histone has remained elusive. Here, we report the crystal structures of both insertion and substitution present in cancer, revealing significant conformational changes of the YEATS-domain loop 8. Structural comparison demonstrates that such alteration not only altered the binding interface for acetylated/acylated histones, but the sequence alterations in the T1 loop may enable dimeric assembly consistent inducing self-association behavior. Nevertheless, we show that also the MLLT1 mutants can be targeted by developed acetyllysine mimetic inhibitors with affinities similarly to wild type. Our report provides a structural basis for the altered behaviors and potential strategy for targeting oncogenic MLLT1 mutants.
In this thesis, we characterized megasynthases such as fatty acid synthases (FASs) and polyketide synthases. The obtained insights into structure and function were used to engineer such systems to produce new-to-nature compounds.
The in vitro characterization of megasynthases requires reproducible access to these enzymes in high quality. Therefore, we established purification strategies for the yeast FAS and the methylsalicylic acid synthase (MSAS) from Saccharopolyspora erythraea (SerMSAS) and applied the latter one on MSAS from Penicillium patulum (PenPaMSAS) and on 6-deoxyerythronolide B synthase (DEBS) module 6. With the purified samples, we were able to obtain initial structural data for SerMSAS and solve the complete structure of the yeast FAS (PDB: 6TA1). On the example of the yeast FAS, we could show that the sample can suffer from adsorption to the water-air interface during the grid preparation for electron microscopy and presented how the use of graphene-based grids can overcome this problem. The combined structural and functional analysis of the yeast FAS showed that the structural domains trimerization module and dimerization module 2 are not essential for the assembly of the whole system. Therefore, they can potentially be used for domain exchange approaches. The in-depth functional analysis of SerMSAS revealed that not SerMSAS itself releases the product, but a 3-oxoacyl-(acyl-carrier protein) synthase like enzyme within the gene cluster transfers 6-methyl salicylic acid from SerMSAS to another carrier protein for subsequent modifications. In contrast, we showed that PenPaMSAS can release its product by hydrolysis and that non-native substrates can be incorporated although at significantly slower turnover rates compared to the native starter substrate. Our further investigation demonstrated that the substrate specificity of the acyltransferase (AT) is a critical factor for the incorporation of non-native substrates.
With the insight from the functional and structural characterization, we engineered megasynthases for the biosynthesis of natural product derivatives. We targeted the AT of PenPaMSAS for active site mutagenesis and discovered a mutant which can transfer non-native substrates significantly faster (~200-300%). Additionally, the malonyl/acetyl transferase (MAT) of the mammalian FAS was used as a promising target for protein engineering because of its previously reported properties including polyspecificity, fast transfer kinetics, robustness, and plasticity. We showed that the MAT can transfer fluorinated substrates and accept the acyl carrier protein of DEBS module 6. By exchanging the substrate specific AT of DEBS with the polyspecific MAT of the mammalian FAS, we demonstrated an efficient DEBS/FAS hybrid and an optimal truncation site for the applied ATs. In contrast to the wild type system, the DEBS/FAS enzyme was able to synthesize demethylated and fluorinated derivatives. The production and purification of a fluoro-methyl-disubstituted polyketide was of particular interest, as it has a high potential for the generation of new drugs and shows the potential of protein engineering. Furthermore, the incorporation of the disubstituted substrate had important implication in the mechanistic details of the ketosynthase-mediated C-C bond formation.
Cytochrome c oxidases are among the most important and fundamental enzymes of life. Integrated into membranes they use four electrons from cytochrome c molecules to reduce molecular oxygen (dioxygen) to water. Their catalytic cycle has been considered to start with the oxidized form. Subsequent electron transfers lead to the E-state, the R-state (which binds oxygen), the P-state (with an already split dioxygen bond), the F-state and the O-state again. Here, we determined structures of up to 1.9 Å resolution of these intermediates by single particle cryo-EM. Our results suggest that in the O-state the active site contains a peroxide dianion and in the P-state possibly an intact dioxygen molecule, the F-state may contain a superoxide anion.
The nsP3 macrodomain is a conserved protein interaction module that plays essential regulatory roles in host immune response by recognizing and removing posttranslational ADP-ribosylation sites during SARS-CoV-2 infection. Thus, targeting this protein domain may offer a therapeutic strategy to combat the current and future virus pandemics. To assist inhibitor development efforts, we report here a comprehensive set of macrodomain crystal structures complexed with diverse naturally-occurring nucleotides, small molecules as well as nucleotide analogues including GS-441524 and its phosphorylated analogue, active metabolites of remdesivir. The presented data strengthen our understanding of the SARS-CoV-2 macrodomain structural plasticity and it provides chemical starting points for future inhibitor development.
Upon antibiotic stress Gram-negative pathogens deploy resistance-nodulation-cell division-type tripartite efflux pumps. These include a H+/drug antiporter module that recognizes structurally diverse substances, including antibiotics. Here, we show the 3.5 Å structure of subunit AdeB from the Acinetobacter baumannii AdeABC efflux pump solved by single-particle cryo-electron microscopy. The AdeB trimer adopts mainly a resting state with all protomers in a conformation devoid of transport channels or antibiotic binding sites. However, 10% of the protomers adopt a state where three transport channels lead to the closed substrate (deep) binding pocket. A comparison between drug binding of AdeB and Escherichia coli AcrB is made via activity analysis of 20 AdeB variants, selected on basis of side chain interactions with antibiotics observed in the AcrB periplasmic domain X-ray co-structures with fusidic acid (2.3 Å), doxycycline (2.1 Å) and levofloxacin (2.7 Å). AdeABC, compared to AcrAB-TolC, confers higher resistance to E. coli towards polyaromatic compounds and lower resistance towards antibiotic compounds.
In this report, we perform structure validation of recently reported RNA phosphorothioate (PT) modifications, a new set of epitranscriptome marks found in bacteria and eukaryotes including humans. By comparing synthetic PT-containing diribonucleotides with native species in RNA hydrolysates by high-resolution mass spectrometry (MS), metabolic stable isotope labeling, and PT-specific iodine-desulfurization, we disprove the existence of PTs in RNA from E. coli, S. cerevisiae, human cell lines, and mouse brain. Furthermore, we discuss how an MS artifact led to the initial misidentification of 2′-O-methylated diribonucleotides as RNA phosphorothioates. To aid structure validation of new nucleic acid modifications, we present a detailed guideline for MS analysis of RNA hydrolysates, emphasizing how the chosen RNA hydrolysis protocol can be a decisive factor in discovering and quantifying RNA modifications in biological samples.
Herein, we present a multi-cycle chemoenzymatic synthesis of modified RNA with simplified solid-phase handling to overcome size limitations of RNA synthesis. It combines the advantages of classical chemical solid-phase synthesis and enzymatic synthesis using magnetic streptavidin beads and biotinylated RNA. Successful introduction of light-controllable RNA nucleotides into the tRNAMet sequence was confirmed by gel electrophoresis and mass spectrometry. The methods tolerate modifications in the RNA phosphodiester backbone and allow introductions of photocaged and photoswitchable nucleotides as well as photocleavable strand breaks and fluorophores.
Serine-ubiquitination regulates Golgi morphology and the secretory pathway upon Legionella infection
(2021)
SidE family of Legionella effectors catalyze non-canonical phosphoribosyl-linked ubiquitination (PR-ubiquitination) of host proteins during bacterial infection. SdeA localizes predominantly to ER and partially to the Golgi apparatus, and mediates serine ubiquitination of multiple ER and Golgi proteins. Here we show that SdeA causes disruption of Golgi integrity due to its ubiquitin ligase activity. The Golgi linking proteins GRASP55 and GRASP65 are PR-ubiquitinated on multiple serine residues, thus preventing their ability to cluster and form oligomeric structures. In addition, we found that the functional consequence of Golgi disruption is not linked to the recruitment of Golgi membranes to the growing Legionella-containing vacuoles. Instead, it affects the host secretory pathway. Taken together, our study sheds light on the Golgi manipulation strategy by which Legionella hijacks the secretory pathway and promotes bacterial infection.
SixGey alloys are emerging materials for modern semiconductor technology. Well-defined model systems of the bulk structures aid in understanding their intrinsic characteristics. Three such model clusters have now been realized in the form of the SixGey heteroadamantanes [0], [1], and [2] through selective one-pot syntheses starting from Me2GeCl2, Si2Cl6, and [nBu4N]Cl. Compound [0] contains six GeMe2 and four SiSiCl3 vertices, whereas one and two of the GeMe2 groups are replaced by SiCl2 moieties in compounds [1] and [2], respectively. Chloride-ion-mediated rearrangement quantitatively converts [2] into [1] at room temperature and finally into [0] at 60 °C, which is not only remarkable in view of the rigidity of these cage structures but also sheds light on the assembly mechanism.
SixGey alloys are emerging materials for modern semiconductor technology. Well-defined model systems of the bulk structures aid in understanding their intrinsic characteristics. Three such model clusters have now been realized in the form of the SixGey heteroadamantanes [0], [1], and [2] through selective one-pot syntheses starting from Me2GeCl2, Si2Cl6, and [nBu4N]Cl. Compound [0] contains six GeMe2 and four SiSiCl3 vertices, whereas one and two of the GeMe2 groups are replaced by SiCl2 moieties in compounds [1] and [2], respectively. Chloride-ion-mediated rearrangement quantitatively converts [2] into [1] at room temperature and finally into [0] at 60 °C, which is not only remarkable in view of the rigidity of these cage structures but also sheds light on the assembly mechanism.
Nuclear magnetic resonance (NMR) spectroscopy is a powerful and popular technique for probing the molecular structures, dynamics and chemical properties. However the conventional NMR spectroscopy is bottlenecked by its low sensitivity. Dynamic nuclear polarization (DNP) boosts NMR sensitivity by orders of magnitude and resolves this limitation. In liquid-state this revolutionizing technique has been restricted to a few specific non-biological model molecules in organic solvents. Here we show that the carbon polarization in small biological molecules, including carbohydrates and amino acids, can be enhanced sizably by in situ Overhauser DNP (ODNP) in water at room temperature and at high magnetic field. An observed connection between ODNP 13C enhancement factor and paramagnetic 13C NMR shift has led to the exploration of biologically relevant heterocyclic compound indole. The QM/MM MD simulation underscores the dynamics of intermolecular hydrogen bonds as the driving force for the scalar ODNP in a long-living radical-substrate complex. Our work reconciles results obtained by DNP spectroscopy, paramagnetic NMR and computational chemistry and provides new mechanistic insights into the high-field scalar ODNP.
2-Aminobenzimidazole 10, although a weak catalyst in the monomeric state, is a successful building block for effective artificial ribonucleases. In an effort to identify new building blocks with improved catalytic potential, RNA cleavage by a variety of heterocyclic amidines and guanidines has been studied. In addition to pKa values and steric effects, the energy difference between tautomeric forms seems to be another important parameter for catalysis. This information is available from quantum chemical calculations on higher levels, but semiempirical methods are sufficient to get a first estimate. According to this assumption, imidazoimidazol 18, characterized by isoenergetic tautomeric forms, is superior to 2-aminoimidazol 6, the best candidate among the simple compounds. By far the largest effects are seen with 2-aminoperimidine 24, which rapidly cleaves RNA even in the micromolar concentration range. The impressive reactivity, however, is related to a tendency of compound 24 to form polycationic aggregates which are the actual catalysts.
2-Aminobenzimidazole 10, although a weak catalyst in the monomeric state, is a successful building block for effective artificial ribonucleases. In an effort to identify new building blocks with improved catalytic potential, RNA cleavage by a variety of heterocyclic amidines and guanidines has been studied. In addition to pKa values and steric effects, the energy difference between tautomeric forms seems to be another important parameter for catalysis. This information is available from quantum chemical calculations on higher levels, but semiempirical methods are sufficient to get a first estimate. According to this assumption, imidazoimidazol 18, characterized by isoenergetic tautomeric forms, is superior to 2-aminoimidazol 6, the best candidate among the simple compounds. By far the largest effects are seen with 2-aminoperimidine 24, which rapidly cleaves RNA even in the micromolar concentration range. The impressive reactivity, however, is related to a tendency of compound 24 to form polycationic aggregates which are the actual catalysts.
Diversity-oriented synthesis (DOS) is a rich source for novel lead structures in Medicinal Chemistry. In this study, we present a DOS-compatible method for synthesis of compounds bearing a free thiol moiety. The procedure relies on Rh(II)-catalyzed coupling of dithiols to diazo building blocks. The synthetized library was probed against metallo-β-lactamases (MBLs) NDM-1 and VIM-1. Biochemical and biological evaluation led to identification of novel potent MBL inhibitors with antibiotic adjuvant activity.
Photoactivatable compounds for example photoswitches or photolabile protecting groups (PPGs, photocages) for spatiotemporal light control, play a crucial role in different areas of research. For each application, parameters such as the absorption spectrum, solubility in the respective media and/or photochemical quantum yields for several competing processes need to be optimized. The design of new photochemical tools therefore remains an important task. In this study, we exploited the concept of excited-state-aromaticity, first described by N. Colin Baird in 1971, to investigate a new class of photocages, based on cyclic, ground-state-antiaromatic systems. Several thio- and nitrogen-functionalized compounds were synthesized, photochemically characterized and further optimized, supported by quantum chemical calculations. After choosing the optimal scaffold, which shows an excellent uncaging quantum yield of 28 %, we achieved a bathochromic shift of over 100 nm, resulting in a robust, well accessible, visible light absorbing, compact new photocage with a clean photoreaction and a high quantum product (ϵ⋅Φ) of 893 M−1 cm−1 at 405 nm.
Photoactivatable compounds for example photoswitches or photolabile protecting groups (PPGs, photocages) for spatiotemporal light control, play a crucial role in different areas of research. For each application, parameters such as the absorption spectrum, solubility in the respective media and/or photochemical quantum yields for several competing processes need to be optimized. The design of new photochemical tools therefore remains an important task. In this study, we exploited the concept of excited-state-aromaticity, first described by N. Colin Baird in 1971, to investigate a new class of photocages, based on cyclic, ground-state-antiaromatic systems. Several thio- and nitrogen-functionalized compounds were synthesized, photochemically characterized and further optimized, supported by quantum chemical calculations. After choosing the optimal scaffold, which shows an excellent uncaging quantum yield of 28 %, we achieved a bathochromic shift of over 100 nm, resulting in a robust, well accessible, visible light absorbing, compact new photocage with a clean photoreaction and a high quantum product (ϵ⋅Φ) of 893 M−1 cm−1 at 405 nm.
Redirection of the transcription factor SP1 to AT rich binding sites by a synthetic adaptor molecule
(2021)
The ubiquitous transcription factor SP1 binds to a GC rich consensus sequence. Here we describe an adaptor molecule that mediates binding of SP1 to a non-cognate DNA site rich in AT. The adaptor is comprised of a Dervan-type hairpin polyamide with high affinity to an AT rich hexamer duplex. It also carries a 27mer DNA that contains the SP1 consensus sequence. The synthesis and purification of the polyamide-DNA conjugate is reported. Pulldown experiments and western blot analysis demonstrate adaptor mediated binding of SP1 to the hexamer duplex TTGTTA.
Resistant microbes are a growing concern. It was estimated that about 33,000 of people die because of the infections caused by multidrug resistant bacteria each year in Europe (ECDC, 2018, https://www.ecdc.europa.eu/). Bacteria can acquire resistance against toxic compounds via different mechanisms and intrinsic active efflux is one of the first mechanisms deployed by bacterial cells. The membrane-localized efflux pumps catalysing this reaction, extract toxic compounds from the interior of the cell and transport these to the outside, thereby maintaining sub-lethal toxin levels in the cytoplasm, periplasm and membranes. Gram-negative three-component efflux pumps, analysed in this study, are composed of an inner membrane protein, a member of the Resistance-Nodulation cell Division (RND) superfamily, an Outer Membrane Factor (OMF) protein and a Membrane Fusion Protein (MFP) that connects the two afore mentioned components into an active efflux pump. The pumps described in this work, AcrAB-TolC and EmrAB-TolC, are drug efflux pumps belonging to the RND and MFS superfamilies, respectively, while CusCBA is an efflux pump that belongs to the RND heavy metal efflux family. Another efflux pump that was used as a model for the design of an in vitro assay for the silver ion transport studies, CopA, belongs to the P-type ATPase superfamily. All pumps analysed in this study are part of the resistance system of Escherichia coli, which is a highly clinically relevant pathogen.
In order to examine the AcrAB-TolC, CopA and CusA efflux pumps, the individual components were separately produced in E. coli, purified to monodispersity and reconstituted in large unilamellar vesicles, LUVs. Means for the optimized production and adequate conditions for efficient reconstitution were presented in this study. The activity of AcrB in LUVs was detected using fluorescence quenching of the dye 8-hydroxy-1,3,6 pyrenetrisulfonate (pyranine), which is incorporated inside the proteoliposomes and is sensitive to the pH changes in its surrounding. The inactive AcrB variant with a substitution in the proton relay network, D407N, showed no activity in proteoliposomes, which correlates with the measurements done in empty liposomes. When AcrA was co-reconstituted with AcrB D407N proteoliposomes it did not restore protein activity. To test the assembly of the AcrAB-TolC pump out of its single components, an in vitro assay was established where the complex assembly was tested with AcrAB- and TolC-containing liposomes. These experiments showed putative AcrAB-TolC formation in the presence or absence of a pump substrate, taurocholate, as well as in the presence of the pump inhibitor, MBX3132. The assembly appeared stable over time and results were invariant in the presence or absence of a pH gradient across the AcrAB-containing membrane.
After determination of the ATPase activity of the P-type ATPase, CopA, in detergent micelles, the protein was reconstituted in LUVs. Quenching of the Ag+-sensitive dye Phen Green SK (PGSK), present on the inside of the CopA-containing proteoliposomes, was observed in presence of ATP and Ag+. Under the same conditions, but in absence of Ag+-ions, quenching was reduced by 80 % after 300 seconds. No PGSK-quenching was observed in control liposomes in the presence of ATP and Ag+. The additional presence of sodium azide led to minimal reduction of the PGSK-quenching as expected since sodium azide is not an inhibitor of P-type ATPases, but the quenching rate was similar to that of the same experimental condition with control liposomes.
The RND superfamily member CusA, as part of the tripartite CusCBA efflux pump, has been proposed to sequester Ag+ or Cu+ from either the cytoplasmic or periplasmic side of the inner membrane. The periplasmic transport of silver ions was implied from an in vitro assay where the quenching of a pH sensitive dye, 9-amino-6-chloro-2-methoxyacridine (ACMA), indicates acidification of the lumen of the proteoliposomes containing CusA when an inwardly directed pH was imposed. The same experiment with the CusA D405N variant, which was previously reported to be an inactive variant, also led to ACMA quenching, although at a slightly lower rate. Under application of an inwardly directed pH and a (negative inside), CusA-containing proteoliposomes showed a strong quenching of the incorporated PGSK dye, suggesting strong Ag+ influx.
The Major Facilitator Superfamily-(MFS-) type EmrAB-TolC pump has an analogous structural setup as the RND-type AcrAB-TolC pump. To examine the efflux of one of its substrates, carbonyl - cyanide m-chlorophenylhydrazone (CCCP), a plate-based susceptibility assay was used. The presence of the EmrAB-TolC pump confers lower susceptibility levels towards CCCP in E. coli, compared to cells not expressing the pump or cells expressing only the MFS component, indicating that EmrAB-TolC extrudes CCCP.
The work done in this study opens up a path towards investigation of drug and metal resistance in vitro. The methodologies to obtain proteoliposomal samples of multicomponent efflux pumps and subsequent measurements of drug/metal ion and H+ fluxes, as well as the determination of pump assembly are crucial for the future research on pump catalysis and transport kinetics. The in vivo drug-plate assays done in this work provide initial insights for future investigations of the drug susceptibility of E. coli expressing the MFS-type tripartite efflux pumps.
In dieser Arbeit werden die Ergebnisse quantenchemischer Untersuchungen von verschiedenen Siliciumverbindungsklassen vorgestellt, die in weiten Teilen als Begleitung zu experimentellen Arbeiten durchgeführt wurden. Das erste Hauptkapitel befasst sich mit den Chloridkomplexen von Perchlorsilanen, zu denen die inversen Sandwichkomplexe und die Silafullerane mit endohedralem Gast gehören. Der Fokus liegt dabei auf den Bindungseigenschaften zwischen Ligand und Silan. Weiterhin werden thermodynamische Untersuchungen zu Aufbaureaktionen und Eigenschaften der Verbindungen vorgestellt. Mit den durchgeführten Rechnungen kann gezeigt werden, dass durch Wahl geeigneter Substituenten am Siliciumatom ein Wechsel in den Chloridkomplexen von einem hyperkoordinierten Siliciumatom hin zu einem Siliciumatom mit ausgebildeter Tetrelbindung erreicht werden kann. Bei den inversen Sandwichkomplexen sind beide Bindungsmodi möglich, von denen die Tetrelbindung die stärkere darstellt. Neben Chloridionen können hier auch Nitrile und Chlorsubstituenten am eigenen Silangerüst als Liganden fungieren. Die stärksten Tetrelbindungen können bei den endohedral funktionalisierten Silafullerankomplexen gefunden werden. Hier stellt das experimentell isolierte Strukturmotiv mit zwölf äußeren Trichlorsilylsubstituenten das thermodynamisch stabilste Substitutionsmuster dar. Im folgenden Kapitel werden die generellen physikalischen Ursachen für die beobachteten thermodynamischen Trends zwischen Perchlorsilanisomeren sowie Disproportionierungsreaktionen behandelt und ein direkter Vergleich mit Alkanhomologen angestellt. Bei den Perchlorsilanen und den meisten Homologen ist bei den untersuchten Systemen eine energetische Präferenz von verzweigteren Strukturen zu erkennen. Die Ursache hierfür liegt hauptsächlich bei stärkeren attraktiven Wechselwirkungen durch Korrelationseffekte, Hyperkonjugation sowie elektrostatische Effekte, welche stärkere repulsive Wechselwirkungen wie die Pauli-Repulsion überkompensieren. Im letzten Kapitel kommen zu den bisher behandelten Reaktionen unter Si-Cl- und Si-Si-Bindungsbeteiligung noch Reaktionen unter Si-C-Bindungsbeteiligungen hinzu. Dort werden die auch wegen ihrer Elektronentransporteigenschaften interessanten Silacyclopentadiene (Silole) hinsichtlich ihrer Isomerisierung, Dimerisierung und weiteren pericyclischen Reaktivität untersucht. Gegenüber dem verwandten Cyclopentadien zeigen diese eine deutlich erhöhte Reaktivität, was zu verschiedenen Dimerisierungsreaktionen führt, solange keine Abfangreagenzien im Überschuss zugegen sind.
Photoacids attract increasing scientific attention, as they are valuable tools to spatiotemporally control proton-release reactions and pH values of solutions. We present the first time-resolved spectroscopic study of the excited state and proton-release dynamics of prominent merocyanine representatives. Femtosecond transient absorption measurements of a pyridine merocyanine with two distinct protonation sites revealed dissimilar proton-release mechanisms: one site acts as a photoacid generator as its pKa value is modulated in the ground state after photoisomerization, while the other functions as an excited state photoacid which releases its proton within 1.1 ps. With a pKa drop of 8.7 units to −5.5 upon excitation, the latter phenolic site is regarded a super-photoacid. The 6-nitro derivative exhibits only a phenolic site with similar, yet slightly less photoacidic characteristics and both compounds transfer their proton to methanol and ethanol. In contrast, for the related 6,8-dinitro compound an intramolecular proton transfer to the ortho-nitro group is suggested that is involved in a rapid relaxation into the ground state.
Probing the photointermediates of light-driven sodium ion pump KR2 by DNP-enhanced solid-state NMR
(2021)
KR2 is a light-driven sodium ion pump found in marine flavobacterium Krokinobacter Eikastus. The protein belongs to the microbial rhodopsin family, which is characterized by seven transmembrane helices and a retinal cofactor covalently bound to a conserved lysine residue through a Schiff base linkage. Specific features of KR2 and other sodium pumping rhodopsins are the NDQ motif, the N-terminal helix capping the protein at the extracellular side, and the sodium ion bound at the protomer interface in the pentameric structure. The ability to pump sodium ions was a surprising discovery since the positive charge at the Schiff base was long thought to hinder the transport of non-proton cations and the Grotthuss mechanism could not be applied to explain the Na+ transport. The photocycle of KR2 revealed by flashed photolysis and ultrafast femtosecond absorption spectroscopy consists of consecutive intermediates, named K, L, M, and O.
Here, DNP-enhanced ssNMR was used to analyze various aspects of these intermediate states. The K/L-state can be generated and trapped by in-situ illumination inside the magnet at 110 K. The trapping of L-state together with the K-state at this temperature is unexpected as this usually leads to the trapping of only K-state in bacteriorhodopsin (BR), proteorhodopsin (PR), and channelrhodopsin 2 (ChR2). This observation suggests a lower energy barrier between K- and L-state in KR2. For the O-state, the intermediate was generated by illuminating outside the magnet, followed by rapid freezing in liquid nitrogen and transfer to the magnet. Based on these procedures, the retinal conformation, and the electrostatic environment at the Schiff base in KR2 dark, K-, L- and O-intermediates were probed using 13C-labeled retinals bound to 15N-labeled KR2 by both 1D and 2D magic angle spinning (MAS) NMR experiments.
The obtained data show an all-trans retinal conformation with the distortion of 150° at H-C14-C15-H in the dark state whereas the retinal has a 13-cis, 15-anti conformation in the K- and L-state after light activation. Differences between K- and L-intermediates were observed. The retinal chemical shifts of the K-state show a large deviation from the model compound behavior between the middle and end part of the polyene chain. In the L-state, these differences are much less pronounced. These observations indicate that the light energy stored in the K-state dissipates into the protein in the subsequent photointermediate states. Furthermore, an additional shielding observed for C14 in L-state indicates the slight rotation toward a more compact 13-cis, 15-syn conformation. The distortion of the H-C14-C15-H angle in the L-state (136°) is larger than in the dark state. This twist of the retinal in the L-state would play an important role in lowering the pKa of the Schiff base, which is a prerequisite for the proton transfer from the Schiff base to the proton acceptor (D116). The electrostatic environments at the Schiff base in K- and L-states cause a de-shielding of the 15N nitrogen compared to the dark state. This indicates a stepwise stronger interaction with the counterion as the Schiff base proton moves away from the Schiff base and comes closer to the D116 in the transition from K- to L-state and approaches the proton transfer step during the M-state formation. In the O-state, the retinal was found to be in the all-trans conformation but differed to the dark state in the C13, C20, and Schiff base nitrogen chemical shifts. The largest effect (9 ppm) was observed for the Schiff base nitrogen, which could be explained by the effect of the positive charge of bound Na+ near the Schiff base in the O-state, coordinated by N112 and D116 as observed in the O-state crystal structure in the pentameric form.
The structural change at the opsin followed the retinal isomerization and the energy transfer from the chromophore to the surrounding were also investigated in this thesis using various amino acids labeling schemes. Moreover, 1H-13C hNOE in combination with CE-DNP was applied to probe the dynamics of retinylidene methyl groups and 23Na MAS NMR was employed to detect the bound sodium ion at the protomer interface in KR2 dark state.
Intrinsische und extrinsische Faktoren wie die Darreichungsform, Komedikation und genetische Polymorphismen können einen signifikanten Einfluss auf die Exposition des Wirkstoffes haben und in der Folge zu Veränderungen in der Wirksamkeit oder Sicherheit eines Wirkstoffes führen. Die Fähigkeit die Auswirkungen solcher Faktoren auf die Exposition und die pharmakologische Aktivität eines Wirkstoffes zu quantifizieren und zu extrapolieren, repräsentiert einen Meilenstein bei der Bestimmung der erforderlichen Dosisanpassungen und der Umsetzung von Risikomanagementstrategien in der klinischen Pharmakologie. Unter dem Blickwinkel der modellbasierten Arzneimittelforschung und -entwicklung (engl. model-informed drug discovery and development (MID3)) können dynamisch mechanistische Modelle, wie z. B. whole-body PBPK/PD-Modelle, für die Vorhersage des Effekts sowie der Wechselwirkung mehrerer Faktoren auf PK und PD nützlich sein und könnten daher als Orientierung für die Wahl der Formulierung und für klinische Dosierungsempfehlungen dienen.
Obwohl PBPK-Modelle in der Pharmabranche inzwischen routinemäßig zur internen Entscheidungsfindung und zur Unterstützung der regulatorischen Bewertung eingesetzt werden, bleibt das Vertrauen Waiver von speziellen klinischen pharmakologischen Studien für biopharmazeutische Anwendungen durch PBPK- Modellanalysen zu stützen eher gering. Andererseits hat sich die virtuelle Bioäquivalenz im Zusammenhang mit der Simulation klinischer Studien als ein vielversprechendes, aber noch unterentwickeltes Feld erwiesen, mit dessen Hilfe der Anwendungsbereich der PBPK-Modellierung in der Biopharmazeutik erweitert werden kann. So werden beispielsweise BCS-basierte Biowaiver für Wirkstoffe der BCS-Klassen II und IV derzeit von den Gesundheitsbehörden nicht akzeptiert. In einigen Fällen hat die PBPK-Modellierung durch Verknüpfung der In-vitro-Freisetzung mit der In-vivo-Performance der Formulierung jedoch gezeigt, dass ein solcher Ansatz unter Umständen wissenschaftlich gerechtfertigt sein könnte. Auf ähnliche Weise können PBPK-Modellierung und VBE verwendet werden, um klinisch relevante Spezifikationen für die Wirkstofffreisetzung festzulegen und den "safe space" der Freisetzung zu definieren (oder zu erweitern). Doch selbst bei Wirkstoffen, die Unterschiede im Umfang und in der Rate der Absorption außerhalb der Bioäquivalenzgrenzen aufweisen, was bedeutet, dass sie nicht als bioäquivalent und damit austauschbar angesehen werden können, kann die therapeutische Äquivalenz beibehalten werden, sofern dies durch eine Expositions-Wirkungs-Analyse und/oder eine Expositions-Sicherheits-Analyse unter Verwendung empirischer, halb- oder vollmechanistischer PK/PD-Modelle angemessen begründet wird.
Wie bereits erwähnt bieten PK/PD- und insbesondere PBPK/PD-Modelle einen mechanistischen Ansatz, der die Gewebekonzentrationen am Wirkort des Wirkstoffes mit der pharmakologischen Wirkung verknüpft. Im Rahmen dieser Arbeit wird zunächst ein Überblick über bestehende PK/PD-Modelle und deren mathematischen Umsetzung vorgestellt. Darüber hinaus sind wirkstoffspezifische Fallbeispiele mit einer offensichtlichen Entkopplung von PK und PD von besonderem Interesse, bei denen Expositionsschwankungen weniger kritisch, wenn nicht gar irrelevant für die pharmakologische Reaktion sind (Publikation 1).
In diesem Zusammenhang bietet PBPK Modellierung und Simulation die Möglichkeit die oben genannten wissenschaftlichen Überlegungen zu untersuchen, ungetestete Szenarios zu erforschen und schließlich evidenzbasiert und arzneimittelspezifische Empfehlungen für Bioäquivalenzprüfungen zu erteilen. Daher bestand das Hauptziel darin PBPK/PD-Modelle zu entwicklen, zu validieren und anzuwenden sowie virtuelle Trials zu simulieren, um den relativen Effekt der In-vitro/ In-vivo-Freisetzung, PK-Charakteristiken (z.b. die Halbwertszeit) und die intraindividuelle Variabilität bei der In-vivo-Arnzeimittelwirkung von BCS Klasse II schwach sauren Verbindungen zu beurteilen und einen PBPK-IVIVE integrierten Arbeitsablauf vorzuschlagen, um virtuelle Bioäquivalenzstudien durchzuführen.
Es wurden drei BCS Klasse II schwach saure Wirkstoffe (Naproxen, Flurbiprofen, Ibuprofen) mit ähnlicher Disposition und ähnlichen metabolischen Eigenschaften zur Untersuchung ausgewählt. Allgemein sind alle drei Wirkstoffe stark an Plasmaproteine gebunden und haben daher ein niedriges Verteilungsvolumen, niedrigen First-Pass-Effekt, niedrige systemische Clearance und eine nahezu vollständige Bioverfügbarkeit (F>0.9). Allerdings unterscheiden sie sich signifikant in ihrer Halbwertszeit: Für Naproxen beträgt t1/2≃20-24 h, für Flurbiprofen t1/2≃7 h und für Ibuprofen t1/2≃2 h, was moderate bis lange, moderate und kurze Halbwertszeiten widerspiegelt.
Für alle drei Wirkstoffe wurde ein systematischer Arbeitsablauf erstellt einschließlich: i) Charakterisierung von in vitro biopharmazeutischen Eigenschaften (z.b. Löslichkeit, Freisetzung) gefolgt von modellbasierten Analysen von In-vitro-Ergebnissen, ii) Entwicklung und umfassende Validierung von PBPK/PD-Modellen und iii) Simulierung und Risikoeinschätzung von Bioäquivalenzstudien. Die Fallstudien von Naproxen (Publikation 2) und Ibuprofen (Publikation 3) konzentrieren sich auf bewährte Verfahren der IVIVE für biopharmazeutische Parameter, Risikoabschätzung und Simulation von Bioäquivalenzstudien mit PBPK-Modellen, welche die inter-occasion Variabilität miteinbeziehen. Das Beispiel von Flurbiprofen (Publikation 4) hebt die Wichtigkeit des Verständnisses des relativen Einflusses von intrinsischen (z.b. genetische Polymorphismen) und extrinsischen (z.b. Komedikationen) Faktoren auf die PK und PD des Wirkstoffes hervor, wenn Empfehlungen für die Bioäquivalenz und die therapeutische Gleichwertigkeit gemacht werden. Alle drei Fallbeispiele liefern mechanistische Erkenntnisse über die Freisetzungssgrenzen, die für die In-vivo-Arneimittelwirksamkeit kritisch ist, unter Berücksichtigung der PK-Eigenschaften des Wirkstoffes und der physiologischen Variabilität mit dem Ziel den Status quo des aktuellen BCS-basierten Biowaiveransatzes in Frage zu stellen und integrierte In-vitro-, In-vivo- und In-silico-Paradigma der Risikobewertung für Waiver von In-vivo-Bioäquivalenzstudien einzuführen.
In dem letzten Teil der Arbeit werden Herausforderungen, Kenntnislücken und Möglichkeiten von PBPK/PD-Modellierung zur Unterstützung von Waivern von in vivo klinischen Studien im Bereich von oralen Biopharmazeutika diskutiert (Publikation 5).
Im Großen und Ganzen schlägt diese Dissertation biorelevante In-vitro-Methoden für die Vorhersage von In-vivo-Formulierungsperformance und neue PBPK/PD-Methoden vor, um Daten von in vitro biopharmazeutischen Experimenten zu den In-vivo-Bedingungen zu extrapolieren. Außerdem ist dies das erste Mal nach unserem Kenntnisstand, dass PBPK/PD-Ansätze zur Durchführung virtueller Bioäquivalenzstudien vorgeschlagen werden, die auch die inter-occasion Variabilität der Pharmakokinetik berücksichtigen. Desweiteren hebt diese Arbeit die Bedeutung von pharmakokinetischen Eigenschaften auf Bioäquivalenz-Ergebnissen hervor und stellt ein neues Konzept zur Risikoeinschätzung von Bioäquivalenz vor, in welchem die Bewertung des Bedarfs eines Waivers von einer In-vivo-Bioäquivalenzstudie sowohl auf biopharmazeutischen als auch pharmakokinetischen Wirkstoffeigenschaften basiert und quantitativ mit PBPK/PD-Modellierung bewertet wird.
In dieser Arbeit wird sowohl das Potenzial von molekularen Photoschaltern als lichtempfindliche Komponenten für photopharmakologische Anwendungen als auch das von künstlichen RNA-Aptameren als regulatorische Schalteinheiten für die Entwicklung von funktionellen Riboschaltern untersucht. Verschiedene wesentliche Aspekte beider Anwendungs-felder wurden eingehend einzeln untersucht und die beiden Schaltsysteme schließlich durch das Design eines synthetischen RNA-Aptamers kombiniert, dessen Ligandbindung durch licht-induzierte Isomerisierung seines Photoschalterliganden reguliert werden kann.
Molekulare Photoschalter wie Azobenzole und Spiropyrane haben sich als vielversprechende photochemische Werkzeuge erwiesen, um lichtgesteuert reversible und biochemisch nutzbare Effekte erzeugen. Spiropyrane bergen aufgrund der drastischen Veränderungen ihrer molekularen Eigenschaften infolge der Photoisomerisierung zum Merocyanin (MC) ein enormes Anwendungs-potenzial. Von den hier untersuchten wasserlöslichen Pyridin- (Py-) und Nitro-BIPS-Derivaten zeigt insbesondere die Py-BIPS-Verbindung 2 ein außerordentlich vielseitiges Verhalten. Im Vergleich zu anderen Vertretern dieser Photoschalterklasse wird ein deutlich höherer MC-Anteil von etwa 50% thermisch innerhalb von wenigen Minuten akkumuliert. Durch lichtinduzierten Ringschluss zum reinen Spiropyran (SP) und thermische Wiederherstellung des Gleichgewichts, kann diese hohe Schaltamplitude über mehrere Zyklen ohne signifikante Zersetzung beibehalten werden. Der Einsatz von schädlichem UV-Licht kann somit vermieden werden, was zusätzlich sehr vorteilhaft für einen möglichen Einsatz in einem biochemischen Kontext ist.
Verbindung 2 weist zudem mehrere Protonierungsstellen auf, die ihr in Abhängigkeit des pH-Wertes faszinierende photosaure Eigenschaften verleihen. Das einfach protonierte HMC Isomer ermöglicht eine lichtstimulierte reversible Kontrolle des pH-Wertes in einem Bereich von etwa 4,5 bis 7,5, mit möglichen pH-Sprüngen von bis zu 1,5 Einheiten. Durch transiente Absorptionsstudien wurde ein Mechanismus für die Protonenfreisetzung nachgewiesen, der lediglich auf der Veränderung des pKs-Wertes der N-protischen Position infolge des lichtinduzierten Ringschlusses beruht. Im Gegensatz dazu wird das phenolische Proton des doppelt protonierten HMCH Isomers innerhalb von 1-2 Pikosekunden nach Anregung aus dem angeregten Zustand an das Lösemittel übertragen. Durch eingehende Ultrakurzzeitmessungen der Freisetzung des phenolischen Protons, konnten die protonierten Spezies der Py- und Nitro-Merocyanine als Superphotosäuren etabliert werden. Sie können somit als ultraschnelle Auslöser für protonenvermittelte Prozesse eingesetzt werden, die zu den fundamentalsten Reaktionen in der Natur gehören.
Was potenzielle pharmakologische Zielsysteme betrifft, so dürfte RNA eine große Zukunft bevorstehen, da sie einfach zu synthetisieren ist und Zugang zu verschiedenen Ebenen zellulärer Regulationsmechanismen bietet. Insbesondere RNA-Aptamere, die in der Lage sind, niedermolekulare Liganden mit außergewöhnlich hoher Affinität und Spezifität zu binden, sind für die Entwicklung von künstlichen Riboschaltern hoch interessant. Während künstliche Aptamere für beliebige Liganden durch einen in vitro Selektionsprozess generiert werden können, ist nicht zur Gänze geklärt warum nur wenige von ihnen als aktive in vivo Riboschalter funktionieren. Die vorliegenden Ergebnisse zeigen die Bedeutung der konformationellen Aptamerdynamik während der Ligandenbindung für das Regulationspotential. Die Mg2+-abhängigen Bindungsstudien des hochfunktionellen Tetrazyklin (TC) -Aptamers zeigen, dass zweiwertige Kationen nicht nur für die korrekte Vorfaltung des Aptamers wichtig sind, sondern auch an der Ligandenbindung und RNA-Strukturanpassung selbst beteiligt sein können. Nach der Assoziation von TC an die Bindungstasche pflanzt sich eine Konformationsanpassung zur entfernten Dreifachhelixregion fort, wo Mg2+ zusätzlich für die Ausbildung endgültig gebundenen Zustandes benötigt wird.
Neben dem Einfluss von Mg2+, zeigen zeitaufgelöste Ligandenbindungsstudien von drei Ciprofloxacin (CFX) -Aptameren eine klare Korrelation zwischen der Kinetik des Struktur-anpassungsschrittes der RNA an den Liganden und dem beobachteten Regulationspotenzial in parallel durchgeführten in vivo Assays. Es wird geschlussfolgert, dass eine beschleunigte und irreversible RNA-Anpassung auf eine Konformationsänderung hindeutet, die ausgeprägt genug ist, um eine Aktivität als Riboschalter zu ermöglichen. Diese Erkenntnisse werden durch die berichteten Ligandenbindungskinetiken von anderen künstlichen Aptameren und auch von natürlichen Riboschaltern bestätigt und sollten weitreichende Implikationen für die Optimierung von Selektionsprotokollen für funktionelle Aptamere haben.
Schließlich wird ein lichtempfindliches RNA-Aptamer vorgestellt, dessen Ligand auf dem Antibiotikum Chloramphenicol (Cm) basiert, welches synthetisch mit einem Azobenzolfragment versehen wurde (azoCm). Durch systematische Optimierung von in vitro Selektionsprotokollen und die erfolgreiche Implementierung eines Belichtungsschrittes zur Isomerisierung des Liganden konnten Aptamere erhalten werden, die spezifisch an die trans-Form von azoCm binden. Bindungsaffinitätsstudien bestätigen diese Selektivität und durch Zirkulardichroismusstudien konnte zudem eine lichtinduzierte reversible Dissoziation des von cis-azoCm gezeigt werden. Damit wird hier eine erfolgreiche Entwicklungsstrategie für lichtabhängige RNA-Aptamer – Ligandsysteme dargelegt, welche wiederum fundamental neuartige Ansätze für die Erschließung lichtstimulierter biologischer Regulationswege zugänglich machen.
RNA ist vor allem als Vermittler von Erbinformationen bekannt. Doch neben der Translation in Proteine ist sie auch maßgeblich an regulatorischen Prozessen in der Zelle beteiligt. So kommen in vielen Organismen Argonautenproteine vor, die zusammen mit microRNA einen Komplex bilden, der in der Lage ist, mRNA zu spalten oder auf andere Weise deren Translation zu unterdrücken. Da die Deregulierung von microRNA bei verschiedenen Krankheiten wie Krebs, Parkinson oder Alzheimer auftritt, wurden in dieser Arbeit Alkylanzien entwickelt, die zur besseren Inhibierung von microRNA beitragen sollen.
Als Alkylierungsmittel wurden ortho-Chinonmethide verwendet, die zunächst in geschützter Form synthetisiert wurden und nach Aktivierung mit einer Nukleobase reagieren können. Für die Erkennung der miRNA-Sequenz wurden diese zu einem Konjugat mit Peptid-Nukleinsäuren (PNAs) verbunden. Es wurden zwei Arten von Chinonmethid-Präkursoren hergestellt: Mit o Nitrobenzyl photolabil geschützte, die sich mit Licht der Wellenlänge 365 nm aktivieren lassen, und über ein Disulfid geschützte, die mithilfe eines Reduktionsmittels aktiviert werden. Die photolabil geschützten Derivate lassen sich damit gezielt örtlich und zeitlich aktivieren. Vom reduktiv aktivierbaren Präkursor wurden drei Derivate mit sterisch unterschiedlichen Resten am Disulfid (Benzyl-, Isopropyl- oder tert-Butyl-Rest) hergestellt, die einen Einfluss auf die Kinetik der Entschützung haben. Diese Derivate können nach Eintritt in eine Zelle durch die dort vorherrschende hohe Glutathion-Konzentration aktiviert werden, während sie extrazellulär unreaktiv sind.
Zunächst wurde die Kinetik eines photolabil geschützten Konjugats ohne RNA untersucht. Hier kommt es nach Bestrahlung zur Selbstalkylierung, bei der die Nukleobasen der PNA angegriffen werden. Bei 37 °C erfolgte dies mit einer Halbwertszeit von 0.43 h unter Annahme einer Reaktion 1. Ordnung. Die Kinetik der Alkylierung der komplementären RNA ließ sich durch zwei parallel ablaufende Reaktionen 1. Ordnung abbilden. Die Schnelle hatte eine Halbwertszeit von 0.42 h und die Langsame 11 h mit einer Ausbeute von 73 % nach 168 h. Bei Bestrahlung des Konjugats und erst anschließender Zugabe der RNA wurde ebenfalls eine Halbwertszeit von 11 h bei einer einzelnen Reaktionen 1. Ordnung erhalten. Dies lässt sich mit der Reversibilität mancher Reaktionsprodukte erklären. Die schnelle Reaktion entspricht der direkten Reaktion des Chinonmethids mit der RNA, die langsame entsteht durch Umlagerung von reversiblen Addukten.
Die Analyse der RNA-Alkylierung erfolgte mithilfe von denaturierender Polyacrylamid-Gelelektrophorese, bei der in Abhängigkeit der Gel-Temperatur scheinbar unterschiedliche Kinetiken gemessen wurden. Dies ist ebenfalls eine Folge der Reversibilität. Bei 57 °C kann ein Teil der Bindungen zwischen RNA und den Konjugaten brechen und es wird am Anfang der Reaktion eine geringere Ausbeute gemessen als bei 25 °C Geltemperatur. Die Ausbeute nach 168 h änderte sich jedoch nicht, da im Verlauf der Reaktion die reversiblen Addukte in irreversible umgewandelt werden.
Mit miRNA-20a als Ziel wurden mit einem 10mer Konjugat zunächst nur 13 % Ausbeute nach 72 h und mit einem 15mer Konjugat 41 % nach 75 h erreicht. Durch internen Einbau des Chinonmethid-Präkursors in die PNA, sodass es einem Adenosin der RNA gegenübersteht, konnte die Ausbeute auf 75 % nach 72 h gesteigert werden, da Adenosin bevorzugt alkyliert wird.
Bei den reduktiv aktivierbaren Chinonmethid-Präkursoren waren alle synthetisierten Konjugate in Puffer ohne Glutathion (GSH) stabil. Die Reihenfolge der Reaktionsgeschwindigkeit der Disulfidspaltung war bei 0.5 mM und 10 mM GSH: Benzyl > Isopropyl > tert-Butyl. Die Halbwertszeit bei 10 mM GSH betrug weniger als 5 min (Benzyl-Konjugat) bis 2 h (t Butyl Konjugat). Jedoch bildeten sich mit allen Konjugaten bei 10 mM GSH auch Addukte mit GSH.
Die Reaktivitätsreihenfolge blieb bei der Alkylierung von RNA erhalten. Allein das Benzyl-Konjugat erreichte bei einer GSH-Konzentration von 0.5 mM schon die gleiche Reaktionsgeschwindigkeit wie das photolabil geschützte Chinonmethid. Bei 10 mM GSH erreichten die Derivate zwar nach wenigen Stunden ihre maximale Ausbeute, diese betrug jedoch nur 23 % (tert-Butyl-Konjugat) bis 43 % (Benzyl-Konjugat), da die Chinonmethide auch durch GSH als Nukleophil abgefangen werden.
Mit einem Konjugat, das ein photolabiles Chinonmethid sowie Biotin trägt, wurde ein Fluoreszenzpulldown mit Cy5-markierter RNA durchgeführt. Hier zeigte die bestrahlte Probe eine deutlich höhere Fluoreszenz (6.8x), als eine unbestrahlte Vergleichsprobe. Bei einem Pulldown-Versuch mit miRNA-20a bzw. mit RISCs aus HeLa-Zelllysat konnte das Argonautenprotein jedoch nicht eindeutig mittels Westernblot nachgewiesen werden.
Anhand des reduktiv aktivierbaren Benzyl-Konjugats konnte gezeigt werden, dass sich das Konjugat in Zelllysat zersetzt und nur ein Teil zu Addukten mit Nukleobasen reagiert. Die Ursache wurde in der hydrolyselabilen Abgangsgruppe gesehen, sodass weitere photolabil geschützte Derivate mit Dimethylamino-, Trimethylammonium-, Pivaloylester- und Benzoylestergruppe synthetisiert wurden. Von diesen war nur das Benzoylester-Konjugat in der Lage, RNA mit 72 % Ausbeute nach 48 Stunden zu alkylieren. Zudem war es für mindestens 1 h in Zelllysat stabil.
A highly diastereoselective one-pot synthesis of the 1,3-diamino-2-alcohol unit bearing three continuous stereocenters is described. This method utilizes 2-oxyenamides as a novel type of building block for the rapid assembly of the 1,3-diamine scaffold containing an additional stereogenic oxygen functionality at the C2 position. A stereoselective preparation of the required (Z)-oxyenamides is reported as well.
Glutathione has long been suspected to be the primary low molecular weight compound present in all cells promoting the oxidative protein folding, but twenty years ago it was found “not guilty”. Now, new surprising evidence repeats its request to be the “smoking gun” which reopens the criminal trial revealing the crucial involvement of this tripeptide.
Osteopontin levels in human milk are related to maternal nutrition and infant health and growth
(2021)
Background: Osteopontin (OPN) is a glycosylated phosphoprotein found in human tissues and body fluids. OPN in breast milk is thought to play a major role in growth and immune system development in early infancy. Here, we investigated maternal factors that may affect concentrations of OPN in breast milk, and the possible associated consequences for the health of neonates. Methods: General characteristics, health status, dietary patterns, and anthropometric measurements of 85 mothers and their babies were recorded antenatally and during postnatal follow-up. Results: The mean concentration of OPN in breast milk was 137.1 ± 56.8 mg/L. Maternal factors including smoking, BMI, birth route, pregnancy weight gain, and energy intake during lactation were associated with OPN levels (p < 0.05). Significant correlations were determined between body weight, length, and head circumference, respectively, and OPN levels after one (r = 0.442, p = < 0.001; r = −0.284, p = < 0.001; r = −0.392, p = < 0.001) and three months (r = 0.501, p = < 0.001; r = −0.450, p = < 0.001; r = −0.498, p = < 0.001) of lactation. A negative relation between fever-related infant hospitalizations from 0–3 months and breast milk OPN levels (r = −0.599, p < 0.001) was identified. Conclusions: OPN concentrations in breast milk differ depending on maternal factors, and these differences can affect the growth and immune system functions of infants. OPN supplementation in infant formula feed may have benefits and should be further investigated.
Background and Purpose: The cyclic nucleotides cAMP and cGMP are ubiquitous second messengers regulating numerous biological processes. Malfunctional cNMP signalling is linked to diseases and thus is an important target in pharmaceutical research. The existing optogenetic toolbox in Caenorhabditis elegans is restricted to soluble adenylyl cyclases, the membrane-bound Blastocladiella emersonii CyclOp and hyperpolarizing rhodopsins; yet missing are membrane-bound photoactivatable adenylyl cyclases and hyperpolarizers based on K+ currents.
Experimental Approach: For the characterization of photoactivatable nucleotidyl cyclases, we expressed the proteins alone or in combination with cyclic nucleotide-gated channels in muscle cells and cholinergic motor neurons. To investigate the extent of optogenetic cNMP production and the ability of the systems to depolarize or hyperpolarize cells, we performed behavioural analyses, measured cNMP content in vitro, and compared in vivo expression levels.
Key Results: We implemented Catenaria CyclOp as a new tool for cGMP production, allowing fine-control of cGMP levels. We established photoactivatable membrane-bound adenylyl cyclases, based on mutated versions (“A-2x”) of Blastocladiella and Catenaria (“Be,” “Ca”) CyclOp, as N-terminal YFP fusions, enabling more efficient and specific cAMP signalling compared to soluble bPAC, despite lower overall cAMP production. For hyperpolarization of excitable cells by two-component optogenetics, we introduced the cAMP-gated K+-channel SthK from Spirochaeta thermophila and combined it with bPAC, BeCyclOp(A-2x), or YFP-BeCyclOp(A-2x). As an alternative, we implemented the B. emersonii cGMP-gated K+-channel BeCNG1 together with BeCyclOp.
Conclusion and Implications: We established a comprehensive suite of optogenetic tools for cNMP manipulation, applicable in many cell types, including sensory neurons, and for potent hyperpolarization.
The ribosomal S1 protein (rS1) is indispensable for translation initiation in Gram-negative bacteria. rS1 is a multidomain protein that acts as an RNA chaperone and ensures that mRNAs can bind the ribosome in a single-stranded conformation, which could be related to fast recognition. Although many ribosome structures were solved in recent years, a high-resolution structure of a two-domain mRNA-binding competent rS1 construct is not yet available. Here, we present the NMR solution structure of the minimal mRNA-binding fragment of Vibrio Vulnificus rS1 containing the domains D3 and D4. Both domains are homologues and adapt an oligonucleotide-binding fold (OB fold) motif. NMR titration experiments reveal that recognition of miscellaneous mRNAs occurs via a continuous interaction surface to one side of these structurally linked domains. Using a novel paramagnetic relaxation enhancement (PRE) approach and exploring different spin-labeling positions within RNA, we were able to track the location and determine the orientation of the RNA in the rS1–D34 bound form. Our investigations show that paramagnetically labeled RNAs, spiked into unmodified RNA, can be used as a molecular ruler to provide structural information on protein-RNA complexes. The dynamic interaction occurs on a defined binding groove spanning both domains with identical β2-β3-β5 interfaces. Evidently, the 3′-ends of the cis-acting RNAs are positioned in the direction of the N-terminus of the rS1 protein, thus towards the 30S binding site and adopt a conformation required for translation initiation.
Metabolic syndrome (MetS) is a highly prevalent disease cluster worldwide. It requires polypharmacological treatment of the single conditions including type II diabetes, hypertension, and dyslipidemia, as well as the associated comorbidities. The complex treatment regimens with various drugs lead to drug-drug interactions and inadequate patient adherence, resulting in poor management of the disease. Multi-target approaches aim at reducing the polypharmacology and improving the efficacy. This review summarizes the medicinal chemistry efforts to develop multi-target ligands for MetS. Different combinations of pharmacological targets in context of in vivo efficacy and future perspective for multi-target drugs in MetS are discussed.
In this thesis, molecular dynamics (MD) simulations are used to study the interaction of different proteins with lipid bilayers. MD simulations can be used as a “computational microscope” to gain atomistic insights into the interactions between proteins and lipids that can barely be accessed in such detail by experimental methods. The different chapters of this thesis address the lipid sensing functionality of amphipathic helices (AHs) when bound to membranes, the folding of AHs at lipid-water interfaces as well as the conformational dynamics of the HIV-1 Env glycoproteins in viral-like and experimental bilayers. In the last chapter the possibilities to enhance the performance of MD simulations are explored, leading to a more efficient usage of computational resources.
Acinetobacter baumannii is a worldwide opportunistic pathogen responsible for nosocomial infections. One of the main factors contributing to multidrug resistance in A. baumannii is the upregulation of various chromosomally encoded or acquired efflux pumps, which expel toxic compounds out of the cells with high efficiency.
The resistance-nodulation-cell division (RND)-type efflux pump gene deletion strains ∆adeAB, ∆adeFG or ∆adeIJ and the major facilitator superfamily (MFS) chloramphenicol efflux pump gene deletion strain ∆craA of A. baumannii ATCC 19606 were created and a differential gene expression study was conducted via RT-qPCR. The expression of efflux pump genes adeB, adeG, adeJ, craA, and the outer membrane protein ompA were examined in the absence and presence of chloramphenicol. No significant up- or downregulation of these genes for any of these deletion strains in comparision to the wild-type strain in absence of the drug chloramphenicol.
In contrast, craA was significantly up-regulated in A. baumannii exposed to chloramphenicol, emphasizing the importance of CraA in chloramphenicol resistance. CraA is widely present in clinical isolates of A. baumannii. It is homologous to the well-studied multiple-drug efflux transporter MdfA from Escherichia coli (61% similarity), but surprisingly reported to be acting as a specific chloramphenicol transporter of A. baumannii (Roca et al., 2009).
The drug susceptibility assay done with A. baumannii ATCC 19606 ΔcraA showed that CraA could confer resistance towards phenicols (chloramphenicol, thiamphenicol, and florfenicol), which was in line with the previous report. CraA was heterologously overproduced in E. coli BW25113 ∆emrE∆mdfA and its substrate specificity was determined by drug susceptibility assays and whole cell fluorescent dye uptake experiments. We observed that the substrate specificity of craA overexpressed in E. coli was more diverse and resembling that of the E. coli MdfA homolog. Apart from resistance towards phenicols (chloramphenicol, thiamphenicol, and florfenicol), CraA also confer resistance towards monovalent cationic drugs (benzalkonium, TPP+, and ethidium), long dicationic drugs (dequalinium and chlorhexidine), fluoroquinolones (norfloxacin and ciprofoxacin) and anticancer drugs (mitomycin C). We showed that CraA is a drug/H+ antiporter by ACMA quenching in inverted CraA or CraA variant containing membrane vesicles.
To address the molecular determinants for multidrug binding and transport, 45 mostly single Ala-substitution variants of CraA were created. These include substitution variants for membrane-embedded proton-titratable residues (E38, D46, and E338) and residues predicted to be important for binding and transport of drug, as inferred from docking experiments on basis of a MdfA-derived CraA model. The combined results indicated a high degree of functional similarities between MdfA and CraA. The conserved titratable residues E26 and D34 (E38 and D46 in CraA) are important for transport in both these homologs. The CraA variant E38A is inactive against all tested drugs, but D46A is only inactive for some drugs, suggesting that only E38 is involved in H+-transport.
Another focus of this thesis is the three tetracycline transporters of A. baumannii strain AYE, TetA, TetG and TetA(A). Susceptibility assays involving tetracycline, minocycline, doxycycline and the last-resort antibiotic tigecycline were conducted on E. coli BW25113 ∆emrE∆mdfA overexpressing these transporters. TetA(A) was excluded from further study due to toxicity of the cells caused by protein overexpression. Both TetA and TetG confer resistance against tetracycline, minocycline and doxycycline. Although tigecycline was reported not to be recognized by tetracycline efflux pumps, we surprisingly found that TetA is able to transport tigecycline. The role of TetA in tigecycline efflux in A. baumannii was confirmed by conducting tigecycline susceptibility assays on A. baumannii.
We speculate that TetA embedded in the inner membrane acts in cooperation with RND-type tripartite systems that span the inner and outer membrane to extrude tigecycline from the periplasm across the outer membrane. A. baumannii ATCC 19606 ∆adeAB were indeed sensitive to tigecycline in comparison to wild-type strain. Deletion of adeIJ also leads to sensitivity to tigecycline, but less so compared to the DadeAB phenotype, while A. baumannii ATCC 19606 ∆adeFG did not show any difference compared to wild-type strain in tigecycline susceptibility. Differential gene expression analysis of the RND efflux pumps (adeB, adeG and adeJ) and tetA of A. baumannii strain AYE showed that the expression of tetA expression is significantly upregulated when tigecycline is present in the growth medium.
We conclude that craA encodes a broad-spectrum efflux pump rather than a specific chloramphenicol transporter. In A. baumannii, the synergistic effects with the outer membrane and/or the presence of other transporters could result in the discrepancy observed. Thus, the possibility of CraA in conferring multidrug resistance should not be overlooked, especially when it is up-regulated under antibiotic stress conditions.
T-cell development is a highly dynamic and stepwise process comprimising T lineage commitment, T-cell receptor (TCR) gene rearrangements and subsequent selection. From a quantitative point of view, only a few hundred progenitor cells migrate from the bone marrow into the thymus. Developing thymocytes (termed double negative (DN), CD4-CD8-) can be further divided into DN1-4 cells based on the expression of CD25 and CD44. These developmental events are interspersed by proliferative bursts which ultimately lead to the generation of millions of double positive (DP, CD4+CD8+) thymocytes that then undergo selection. As a consequence, a proportion of naïve T-cells evolves to ensure adaptive, but not autoreactive immunity.
Previous studies of our lab focused on the quantification of thymus colonization and identified thymus entry to be dependent on expression of the chemokine receptors CCR7 and CCR9 (Krueger et al., 2010; Ziętara et al., 2015). CCR7/9 double knockout (DKO) mice are almost completely devoid of the most immature thymocyte populations (DN1 and DN2), but show near normal DN3 cellularity. Interestingly, a similar defect during early development but a virtually complete recovery of later stages and total thymocyte numbers was also observed in thymi of miR-17~92 deficient mice. Here, a failure of prethymic IL-7 signaling dampens early T-cell development (Regelin et al., 2015). For this reason, we hypothesized a tight regulation of thymocyte population size through alterations in the underlying cell cycle kinetics.
In this thesis, we employed in vivo single- and dual-nucleoside pulse labeling combined with determination of DNA replication over time in different WT thymocyte subsets at steady-state. Based on this, we assessed alterations in cell cycle kinetics of CCR7/9 and miR-17~92 defcicient mice and identified compensatory mechanisms of thymocytes on the level of cell cycle phase distribution and cell cycle speed. In addition, single-cell RNA sequencing helped to obtain information on cell cycle dynamics of early thymocyte subsets, exemplarily shown for WT and CCR7/9 DKO mice. Lastly, we performed cell cycle analyses in a model of endogenous thymic repair upon sublethal total body irradiation which provided insight into intrathymic cell cycle regulation as an adjustable system to re-establish normal thymus cellularity.
In the second part of the thesis, we addressed the role of miR-21 in the thymus. In various studies, we and others identified miRNAs as key posttranscriptional regulators of the immune system and especially for T-cell development (Regelin et al. 2015; Mildner et al. 2017; Li et al. 2007; Ebert et al. 2009; Ziętara et al. 2013; Schaffert et al. 2015). The dynamic expression of miR-21 during T-cell development (Neilson et al. 2007; Kirigin et al. 2012; Kuchen et al. 2010) prompted us to hypothesize that miR-21 has a regulatory function in the thymus. A miR 21-knockout mouse model allowed us to study the role of this miRNA for the development of T-cells in the thymus and the maintenance of T-cells in the periphery. In addition, we performed competitive bone marrow chimera experiments in the context of miR-21 deficiency and overexpression. Further insights were provided by exploring the function of miR-21 in negative selection in vivo as well as in T-cell differentiation in coculture experiments in vitro. To unravel implications of miR-21 to regulate cellular stress responses, we assessed the contribution of miR-21 in a model of endogenous regeneration of the thymus after sublethal irradiation. We could not provide evidence for a prominent role for miR-21 during T-cell development. Together, our experiments revealed that miR-21 is largely dispensable for physiologic T-cell development despite high and dynamic expression in the thymus (Kunze Schumacher et al., 2018). The apparent discrepancy between dynamic expression but lack of a regulatory function in the thymus led us to conclude that miR-21 is rather fine tuning T-cell responses than controlling a developmental event.
Polyketides are highly valuable natural products, which are widely used as pharmaceuticals due to their beneficial characteristics, comprising antibacterial, antifungal, immunosuppressive, and antitumor properties, among others. Their biosynthesis is performed by large and complex multiproteins, the polyketide synthases (PKSs). This study solely focuses on the class of type I PKSs, which arrange all their enzymatic domains on one or more polypeptides. Despite their high medical value, little is known about mechanistic details in PKSs.
One central domain is the acyl transferase (AT), which is present in all PKSs and channels small acyl substrates into the enzyme. More precisely, the AT loads the substrates onto the essential acyl carrier protein (ACP), which subsequently shuttles the substrates and all intermediates for condensation and modification to additional domains to build the final polyketide.
Some PKSs use their domains several times during biosynthesis and work iteratively – these are called iterative PKSs. Others feature several sets of domains, each being used only once during biosynthesis – these PKSs are called modular PKSs. All PKSs or PKS modules consist of minimum three essential domains to connect the acyl substrates. Three modifying domains are optional and can enlarge the minimal set. According to the domain composition, the acyl substrate is fully reduced, partly reduced, or not reduced at all. This variation of modifying domains accounts for the huge structural and therefore functional variety of polyketides.
Even though the structure of fatty acids is not exactly reminiscent of polyketides, their biosynthetic pathways are closely related. Fatty acid biosynthesis is carried out by fatty acid synthases (FASs), which share many similarities with PKSs. Both megasynthases feature the same domains, performing the same reactions to connect and modify small acyl substrates. In contrast to PKSs, FASs always contain one full set of modifying domains which is used iteratively, leading to fully reduced fatty acids.
The present thesis extensively analyzes the AT of different PKSs in its substrate selectivity, AT-ACP domain-domain interaction, and enzymatic kinetic properties. The following key findings are revealed through comparison: 1.) ATs of PKSs appear slower than the ones of FASs, which may reflect the different scopes of biosynthetic pathways. Fatty acids as essential compounds in all organisms are needed in high amounts for physiological functions, whereas polyketides as secondary metabolites only require basal concentrations to take effect. 2.) The slower ATs from modular PKSs do not load non-native substrates even in absence of the native substrates. This is different to the faster ATs from iterative PKSs and FASs, which indicates high substrate specificity solely for the ATs from modular PKSs and emphasizes their role as gatekeepers in polyketide synthesis. 3.) The substrate selectivity can emerge in either the first or the second step of the AT-mediated ACP loading and is not assured by a hydrolytic proofreading function.
Moreover, a mutational study on the AT-ACP interaction in the modular PKS 6-deoxyerythronolide B synthase (DEBS) shows that single surface point mutations can influence AT-mediated reactions in a complex manner. Data reveals high enzyme kinetic plasticity of the AT-ACP interaction, which was also recently demonstrated for the interaction in a type II FAS.
Based on these findings, the mammalian FAS is engineered towards a modular PKS-like as- sembly line with the long-term goal to rationally synthesize new products. Basically, three important aspects need to be considered: 1.) AT’s loading needs to be splitted in specific loading of a priming substrate by a priming AT and in specific loading of an elongation substrate by an elongation AT. 2.) FAS-based elongation modules need to be designed with varying domain compositions for introducing functional groups in the product. 3.) Covalent and non-covalent linkers need to be designed for connection of priming and elongation modules.
This study focuses on the first aspect, splitting loading of priming and elongation substrates. An elongation substrate-specific AT is installed in the mammalian FAS via domain swapping. Since ATs from modular PKSs were proven to be substrate specific, these are used to exchange the mammalian FAS AT. This work demonstrates that it is extremely challenging to create stable and functional chimeras, but first essential steps are taken. Proper domain boundaries for AT swapping are established and a stable chimera with 70 % wild type AT activity is created. However, this chimera is only of limited value for application in an elongation module due to the intrinsic slow turnover rate of the wild type AT. Using another PKS AT, a stable elongation module is designed and analyzed in its activity in combination with a priming module. These experiments demonstrate that the loading of priming substrates are successfully suppressed in the elongation module, but nonetheless only minor turnover rates are detected in the assembly line.
...
Mixed-valence compounds as polarizing agents for overhauser dynamic nuclear polarization in solids
(2021)
Herein, we investigate a novel set of polarizing agents—mixed-valence compounds—by theoretical and experimental methods and demonstrate their performance in high-field dynamic nuclear polarization (DNP) NMR experiments in the solid state. Mixed-valence compounds constitute a group of molecules in which molecular mobility persists even in solids. Consequently, such polarizing agents can be used to perform Overhauser-DNP experiments in the solid state, with favorable conditions for dynamic nuclear polarization formation at ultra-high magnetic fields.
Komplexe biologische Phänotypen resultieren aus einem koordinierten Zusammenspiel von einer Vielzahl von Genen. Um zu verstehen, wie Krankheiten durch genetische Dysfunktionen
entstehen können, ist es unabdingbar die genetischen Interaktionsnetzwerke in menschlichen Zellen zu entschlüsseln. Eine Identifizierung von Kontext-abhängigen genetischen Interaktionen kann bedeutende Erkenntnisse über die Beziehung von Phänotyp und Genotyp liefern und erklären, wie synergistische Gen-Funktionen die Entstehung von komplexen Krankheiten bedingen.
Gepoolte, kombinatorische CRISPR (kurz für: clustered regularly interspaced short palindromic repeats) Screens stellen eine wirkungsvolle Methode zur simultanen Untersuchung potentieller Interaktionen von einer großen Anzahl von Genen dar. Mit sogenannten multiplex CRISPR
gRNA Bibliotheken werden im Rahmen großangelegter Screens vielzählige kombinatorische Gen-Knockouts in Zellen generiert. Diese multiplex CRISPR gRNA Bibliotheken können aus bis zu hunderttausenden Plasmiden bestehen, die jeweils für eine andere gRNA-Kombination kodieren und auf ein spezifisches Gen-Paar abzielen. Im Gegensatz zu CRISPR Screens für Einzel-Knockouts gehen multiplex CRISPR Screens zur Identifizierung von genetischen Interaktionen mit zusätzlichen Herausforderungen einher: Zum einen wächst der verbundene Arbeitsaufwand für die Konstruktion der multiplex CRISPR gRNA Bibliotheken proportional mit der Anzahl der gewünschten Ziel-Gene, welche die Diversität der Bibliothek bestimmt. In einer idealen gRNA-Bibliothek wären alle gRNA-Sequenzen gleich häufig vorhanden. Jedoch weisen
gRNA-Bibliotheken aufgrund von technischen Beschränkungen gRNA-Sequenzen mit höherer, beziehungsweise niedriger Abundanz auf. Konventionelle Methoden zur Herstellung von
gRNA-Bibliotheken basieren beispielsweise auf iterativen, gepoolten Klonierungsschritten mit PCR-amplifizierten Oligonucleotiden, welche zu einer Ungleichverteilung oder zum Verlust von gRNA-Sequenzen führen können. Daher bieten Methoden zur gRNA-Bibliotheken-Generierung Optimierungspotenzial. Da die Reproduzierbarkeit der Screen-Ergebnisse durch die sogenannte Screening Coverage sichergestellt werden muss, erfordert eine Erhöhung der
Bibliotheks-Diversität gleichzeitig auch eine Vergrößerung des Versuchsmaßstabs und ist mit umfangreichem Zellkultur-Arbeitsaufwand verbunden. Die Screening Coverage gibt die
durchschnittliche Abundanz der einzelnen gRNA-Sequenzen in der Zellpopulation während des Screens an. Aktuelle Richtlinien empfehlen eine Screening Coverage, die zwischen dem 200- bis 1000-fachen Wert der Bibliotheks-Diversität liegt, allerdings fehlen bisher genaue Angaben die auf die verwendete gRNA Bibliothek abgestimmt sind. Deshalb stellt die benötigte Screening Coverage bisher einen limitierenden Faktor dar, der die Anzahl der möglichen Ziel-Gene-Kombinationen in einem Screen beschränkt.
In der vorliegenden Arbeit stellen wir eine neue Methode zur Generierung von multiplex gRNA Bibliotheken mit hohen Diversitäten vor. Die Methode, genannt 3Cs (covalently-closed circular-synthesized) Multiplexing, umgeht iterative, gepoolte Klonierugsschritte mit Restriktionsenzymen und PCR-Amplifikation von gRNA-kodierenden Oligonucleotiden. Wir
zeigen, dass 3Cs Multiplexing auf robuste Weise zur Herstellung von gleichmäßig verteilten multiplex gRNA Bibliotheken verwendet werden kann. Der Verteilungs-Skew, auch Skew-Ratio oder Bibliotheksbreite genannt, ist ein Maß zur Ermittlung der Gleichverteilung der gRNA-Sequenzen in der Bibliothek. Wir zeigen, dass 3Cs multiplex Bibliotheken typischerweise einen Verteilungs-Skew von 2.5 aufweisen, was unter den üblichen Werten von Einzel-gRNA Bibliotheken liegt.
Wir nahmen an, dass die gRNA-Bibliotheksverteilung die Robustheit von gepoolten CRISPR Screens beeinflussen könne und deshalb bei der Auswahl einer geeigneten Screening
Coverage berücksichtigt werden müsse. Um den Einfluss der gRNA-Bibliotheksverteilung auf die Screen-Qualität in Abhängigkeit von der verwendeten Screening Coverage zu untersuchen, generierten wir zwei künstlich fehlverteilte multiplex gRNA-Bibliotheken. Diese wurden, zusätzlich zu einer nahezu gleichverteilten multiplex gRNA-Bibliothek, jeweils mit einer 20- und 200-fachen Screening Coverage in einem kombinatorischen Proliferationsscreen angewandt.
Dadurch konnten wir die gRNA-Bibliotheksverteilung als den bestimmenden Parameter für die benötigte Screening Coverage identifizieren. Zusätzlich konnten wir zeigen, dass 3Cs multiplex gRNA-Bibliotheken auf Grund ihrer gleichmäßigen Verteilung mit minimierter Screening Coverage eingesetzt werden können, was zu einer 10-fachen Reduktion des assoziierten Arbeitsaufwands führt. Während bisherige Richtlinien für gepoolte CRISPR Screens die initiale
gRNA-Bibliotheksverteilung nicht berücksichtigen, empfehlen wir die Screening Coverage an dieser auszurichten.
Autophagie ist ein streng regulierter zellulärer Prozess, der den Lysosomen Abbau von intrazellulärem Material steuert und im Zusammenhang mit zahlreichen menschlichen Erkrankungen steht. Da Autophagie in eine Vielzahl von Signalwegen integriert ist, bietet es außerdem therapeutische Ansatzpunkte zur Behandlung von Krankheiten. Die Identifizierung von synergistischen Funktionen zwischen Autophagie-Genen könnte unser Verständnis über die molekularen Mechanismen, die der Regulation der Autophagie zu Grunde liegen, erweitern und dadurch neuartige Behandlungen ermöglichen.
Um genetische Interaktionen von Autophagie-Genen zu untersuchen haben wir eine 3Cs multiplex gRNA Bibliothek generiert, die auf menschliche Autophagie-Genkombinationen
abzielt. In dieser Arbeit demonstrieren wir die Funktionalität der 3Cs Autophagie multiplex gRNA Bibliothek unter Anwendung minimierter Screening Coverage in zwei verschiedenen Screen-Ausführungen: In einem Proliferationsscreen konnten wir Geninteraktionen
identifizieren, deren Verlust zu einer gesteigerten oder verringerten Zellproliferation führt. Unter diesen resultierte der Knockout von WDR45B-PIK3R4 zur stärksten Suppression der Proliferation, während die Depletion von ATG7-KEAP1 zu extrem verstärkter Proliferation beitrug. Unter Einsatz eines Autophagie-Reporters konnten wir in einem Autophagie Screen genetische Interaktionen aufdecken, die essentiell für Autophagie sind, darunter die
Interaktionen zwischen ATG2A-ATG2B , GABARAPL2-WIPI2 und ULK4-SQSTM1.
Wir glauben, dass 3Cs Multiplexing in Zukunft breite Anwendung in verschiedenen biologisch relevanten Feldern finden kann und die Entschlüsselung von kontext-abhängigen genetischen Interaktionen voranbringen und so das Verständnis für die Entstehung von komplexen pathologischen Phänotypen erweitern wird.
Biomoleküle, insbesondere Membranproteine (MPs), sind oftmals sehr sensitiv gegenüber ihrer chemischen Umgebung, wie pH-Wert, Puffer, Salzkonzentration und vielen weiteren Faktoren. MPs stabil und funktional in Lösung zu halten ist nicht trivial. Sie stellen deshalb eine besondere Herausforderung bei der Analyse von biologischen Systemen dar. Aus diesem Grund wurden und werden nach wie vor sogenannte membrane mimicking-(MM-) Systeme, wie beispielsweise Nanodiscs (NDs) oder styrene-maleic acid lipid particles (SMALPs), untersucht und entwickelt, um MPs eine naturähnliche Umgebung in Form einer Lipid-Doppelschicht zu bieten und sie so in ihrer natürlichen Konformation und natürlichen Funktionsweise/Aktivität in Lösung zu halten.
Laser induced liquid bead ion desorption (LILBID) Massenspektrometrie (MS) hat sich als hervorragende analytische Methode herausgestellt, um MPs in Kombination mit MM-Systemen zu untersuchen. LILBID-MS bietet nicht nur die Möglichkeit Proteine an sich zu identifizieren, sondern ermöglicht ebenfalls eine zerstörungsfreie Analyse von nicht-kovalent gebundenen Proteinkomplexen, sowie die Detektion einzelner Subkomplexe eines Proteinkomplexes. Auch die Analyse von Protein-Ligand-Wechselwirkungen ist möglich. Bei der LILBID-Ionisationsmethode werden kleine Tröpfchen erzeugt, die einen wässrig gelösten Analyt enthalten. Die Analyt-Tröpfchen werden anschließend mittels IR-Laser bestrahlt, wodurch der Analyt freigesetzt und massenspektrometrisch analysiert werden kann.
Diese Dissertation beschäftigt sich zum einen mit der Analyse des Lyse-Proteins ΦX174-E der Bakteriophage ΦX174, zum anderen mit Untersuchungen zur Histidinkinase SpaK aus B. subtilis in Kombination mit MMs. Weiterhin wird die Frage geklärt, ob und wie gut sich LILBID-MS zur Analyse von Saposin-Nanopartikel-(SapNPs)-solubilisierten MPs eignet. Darüber hinaus wird in dieser Dissertation die Darstellung von SapNP-solubilisierten MPs mittels zellfreier Proteinsynthese näher charakterisiert und untersucht welche Parameter aus präparativer Sicht optimiert werden können.
In vorausgegangenen Analysen von ND-solubilisierten MPs mittels LILBID-MS zeigte sich, dass manche in Verbindung mit NDs genutzten Lipide unerwünschte Signale im Spektrum zur Folge haben, die aus massiven Lipid-Anhaftungen am MSP oder dem Analyten resultieren. Überlappungen der m/z-Signale verschiedener Analyt- und/oder Komplexkomponenten mit diesen Lipid-Cluster-Signalen kann wiederum zum Verlust von Informationen führen. Daher beschäftigt sich ein weiterer Teil dieser Arbeit mit der Frage, ob durch den Einsatz von UV-schaltbaren Lipiden der Anwendungsbereich und/oder die Auflösung von LILBID-MS erweitert und verbessert werden kann.
Um biologische Prozesse zu verstehen ist es ebenfalls wichtig die zeitlichen/kinetischen Aspekte einer Reaktion zu untersuchen/kennen, sowie molekulare Prozesse gezielt zu kontrollieren. Licht hat sich hierbei als ein hervorragendes Werkzeug in der Analytik, sowie in der molekularen Prozesskontrolle etabliert. Licht bietet den Vorteil sehr selektiv eingesetzt werden zu können und sowohl orts- als auch zeitaufgelöst Informationen liefern zu können. Das gezielte Triggern einer Reaktion oder einer Protein-Protein-Interaktion kann beispielsweise durch sog. photo-cleaving von photolabilen Schutzgruppen ermöglicht werden. Bisweilen bietet die native MS nur wenig Möglichkeiten schnelle Reaktionen zu analysieren und kinetische Informationen zu gewinnen. Daher beschäftigt sich ein weiterer Teil dieser Dissertation damit zu untersuchen, ob und wie sich lichtgesteuerte Reaktionen im LILBID-Ionisationsprozess induzieren und gegebenenfalls auch zeitlich analysieren und charakterisieren lassen können.
2D NOESY plays a central role in structural NMR spectroscopy. We have recently discussed methods that rely on solvent-driven exchanges to enhance NOE correlations between exchangeable and non-exchangeable protons in nucleic acids. Such methods, however, fail when trying to establish connectivities within pools of labile protons. This study introduces an alternative that also enhances NOEs between such labile sites, based on encoding a priori selected peaks by selective saturations. The resulting selective magnetization transfer (SMT) experiment proves particularly useful for enhancing the imino–imino cross-peaks in RNAs, which is a first step in the NMR resolution of these structures. The origins of these enhancements are discussed, and their potential is demonstrated on RNA fragments derived from the genome of SARS-CoV-2, recorded with better sensitivity and an order of magnitude faster than conventional 2D counterparts.
Chronic rhinosinusitis (CRS) is often treated by functional endoscopic paranasal sinus surgery, which improves endoscopic parameters and quality of life, while olfactory function was suggested as a further criterion of treatment success. In a prospective cohort study, 37 parameters from four categories were recorded from 60 men and 98 women before and four months after endoscopic sinus surgery, including endoscopic measures of nasal anatomy/pathology, assessments of olfactory function, quality of life, and socio-demographic or concomitant conditions. Parameters containing relevant information about changes associated with surgery were examined using unsupervised and supervised methods, including machine-learning techniques for feature selection. The analyzed cohort included 52 men and 38 women. Changes in the endoscopic Lildholdt score allowed separation of baseline from postoperative data with a cross-validated accuracy of 85%. Further relevant information included primary nasal symptoms from SNOT-20 assessments, and self-assessments of olfactory function. Overall improvement in these relevant parameters was observed in 95% of patients. A ranked list of criteria was developed as a proposal to assess the outcome of functional endoscopic sinus surgery in CRS patients with nasal polyposis. Three different facets were captured, including the Lildholdt score as an endoscopic measure and, in addition, disease-specific quality of life and subjectively perceived olfactory function.
Sphingosin 1 Phosphat (S1P) ist ein wichtiger Lipidmediator, der über G Protein gekoppelte Rezeptoren und intrazelluläre Wirkungen vielfältige Wirkungen auslöst und eine Rolle bei der Lymphozytenzirkulation, der Erhaltung der endothelialen Barriere, bei Entzündungsprozessen und Tumorwachstum spielt. Die S1P Lyase (Sgpl1) katalysiert den irreversiblen Abbau von S1P und damit den letzten Schritt des Sphingolipidkatabolismus‘. Ein Fehlen der Sgpl1 bewirkt eine Akkumulation von S1P und anderen Sphingolipiden im Blut und Gewebe, was multiple Organschäden zur Folge hat. Menschen mit S1P Lyase Insuffizienz Syndrom (SPLIS) leiden insbesondere unter steroidresistentem nephrotischem Syndrom, Nebennierenrinden-insuffizienz und neurologischen Störungen. Weitere mögliche Symptome sind Lymphopenie, Hautveränderungen und Dyslipidämien. S1P Lyase defiziente Mäuse weisen sehr ähnliche Organschädigungen auf.
An Sgpl1 Knockoutmäusen war zuerst die massive Akkumulation nicht nur von Sphingolipiden, sondern auch von Cholesterin und Triglyceriden in Blut und Leber aufgefallen. Auch bei SPLIS Patienten wurde eine Hypercholesterinämie beobachtet. Um die Kreuzregulation des Sphingolipid- und Cholesterinmetabolismus besser zu verstehen, sollte die Rolle der Sgpl1 in der Leber, dem Hauptort des Lipidmetabolismus, untersucht werden. Hierzu sollte ein Mausmodell mit einem hepatozytenspezifischen Sgpl1 Knockout (Sgpl1HepKO) etabliert und charakterisiert werden. Dies wurde durch Kreuzen von Sgpl1fl/fl-Mäusen mit Mäusen, welche die Cre-Rekombinase unter dem Albuminpromoter exprimierten, erreicht. Die basale Charakterisierung zeigte, dass diese Mäuse im Gegensatz zu globalen Sgpl1 Knockoutmäusen sowohl im Alter von acht Wochen, als auch im Alter von acht Monaten einen unauffälligen Phänotyp aufwiesen. Das äußere Erscheinungsbild inklusive Leber und Körpergewicht, das Blutbild, die Leberenzyme sowie die Histologie der Leber waren unverändert. Die Analyse der Leberlipide mit Hilfe von Hochleistungsflüssigkeits-chromatographie gekoppelt mit einer Tandem Massenspektrometrie zeigte eine signifikante Akkumulation (≈1,5 2 fach) von S1P, Sphingosin und Ceramiden, aber nicht von Glucosylceramiden und Sphingomyelin in der Leber. Messungen im Plasma zeigten eine Erhöhung mehrerer Ceramide, während der S1P Spiegel normal war. Ferner zeigten Untersuchungen der Galle signifikant erhöhte Konzentrationen an S1P, Dihydro S1P und Glucosylceramiden, jedoch unveränderte Ceramide. Die Ergebnisse legen folgende Schlussfolgerungen nahe: 1. In der Leber kann mit Hilfe von Ceramidsynthasen akkumulierendes Sphingosin in Ceramide umgewandelt werden, welche anschließend ins Blut sezerniert und letztendlich vermutlich von anderen Zellen verstoffwechselt werden. Außerdem ist nicht ausgeschlossen, dass S1P ebenfalls ins Blut sezerniert und dort effektiv abgebaut wird, so dass die S1P Konzentration im Plasma unverändert bleibt. 2. S1P sowie Glucosylceramide werden an die Galle abgegeben und ausgeschieden. 3. Die Sgpl1 in der Leber ist nicht essentiell für die Regulation des Plasma S1Ps, was zuvor vermutet worden war
Eine Analyse der Sterole zeigte in Sgpl1HepKO Mäusen erhöhte Spiegel an Cholesterin und Desmosterol in der Leber. In Übereinstimmung mit der erhöhten Proteinexpression des low density lipoprotein (LDL ) Rezeptors und erniedrigten Konzentrationen des LDL Cholesterins im Plasma, deuten diese Daten auf eine erhöhte Aufnahme von LDL Cholesterin durch die Leber hin. Untersuchungen in der Leber sowie mit primären Hepatozyten zeigten im Gegensatz zu globalen Sgpl1 Knockoutmäusen keine Veränderungen der Peroxisomen-Proliferator-aktiviertem Rezeptor γ Expression. Weitere Gene mit zentraler Rolle wie der Liver X receptor oder die Fettsäuresynthase, waren ebenfalls nicht reguliert. Dieser im Vergleich zu globalen Sgpl1-Knockoutmäusen milde Phänotyp lässt sich durch die deutlich geringere Akkumulation von Sphingolipiden aufgrund der oben beschriebenen Kompensations-mechanismen in Sgpl1HepKO Mäusen erklären.
In weiteren Untersuchungen sollten die Auswirkungen einer Sgpl1-Defizienz an Fibroblasten untersucht werden. Hierzu standen embryonale Fibroblasten aus Sgpl1 Knockoutmäusen zur Verfügung (Sgpl1-/- MEFs). In einer Kooperation mit Dr. Janecke von der Universität Innsbruck standen außerdem humane Fibroblasten eines SPLIS Patienten zur Verfügung.
An Sgpl1-/- MEFs war zuvor eine gestörte Calciumhomöostase festgestellt worden, welche sich durch eine erhöhte zytosolische Calciumkonzentration und vermehrte Calciumspeicherung im Endoplasmatischen Retikulum und in Lysosomen auszeichnete. Die Plasmamembran-Calcium ATPase (PMCA) trägt an Fibroblasten entscheidend zur Regulation der zytosolischen Calciumkonzentration bei. Ihre Expression auf Proteinebene war jedoch in Sgpl1-/- MEFs nicht verändert. Im Rahmen dieser Arbeit wurde durch eine Immunfärbung erstmals festgestellt, dass die PMCA in Sgpl1-/- MEFs nicht vollständig an der Plasmamembran lokalisiert war. Dies könnte der Grund für die erhöhte zytosolische Calciumkonzentration in den Zellen sein. ...
Antigen presentation via major histocompatibility complex class I (MHC I) molecules is essential to mount an adaptive immune response against pathogens and cancerous cells. To this end, the transporter associated with antigen processing (TAP) delivers snippets of the cellular proteome, resulting from proteasomal degradation, into the ER lumen. After peptide loading and editing by the peptide-loading complex (PLC), stable peptide-MHC I complexes are released for cell surface presentation. Since the process of MHC I trafficking is poorly defined, we established an approach to control antigen presentation by introduction of a photo-caged amino acid in the catalytic ATP-binding site of TAP. By optical control, we initiate TAP-dependent antigen translocation, thus providing new insights into TAP function within the PLC and MHC I trafficking in living cells. Moreover, this versatile approach has the potential to be applied in the study of other cellular pathways controlled by P-loop ATP/GTPases.
The repertoire of natural products offers tremendous opportunities for chemical biology and drug discovery. Natural product-inspired synthetic molecules represent an ecologically and economically sustainable alternative to the direct utilization of natural products. De novo design with machine intelligence bridges the gap between the worlds of bioactive natural products and synthetic molecules. On employing the compound Marinopyrrole A from marine Streptomyces as a design template, the algorithm constructs innovative small molecules that can be synthesized in three steps, following the computationally suggested synthesis route. Computational activity prediction reveals cyclooxygenase (COX) as a putative target of both Marinopyrrole A and the de novo designs. The molecular designs are experimentally confirmed as selective COX-1 inhibitors with nanomolar potency. X-ray structure analysis reveals the binding of the most selective compound to COX-1. This molecular design approach provides a blueprint for natural product-inspired hit and lead identification for drug discovery with machine intelligence.
The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium’s collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.
Lack of efficacy of a partial adenosine A1 receptor agonist in neuropathic pain models in mice
(2021)
Previous studies suggest that adenosine A1 receptors (A1R) modulate the processing of pain. The aim of this study was to characterize the distribution of A1R in nociceptive tissues and to evaluate whether targeting A1R with the partial agonist capadenoson may reduce neuropathic pain in mice. The cellular distribution of A1R in dorsal root ganglia (DRG) and the spinal cord was analyzed using fluorescent in situ hybridization. In behavioral experiments, neuropathic pain was induced by spared nerve injury or intraperitoneal injection of paclitaxel, and tactile hypersensitivities were determined using a dynamic plantar aesthesiometer. Whole-cell patch-clamp recordings were performed to assess electrophysiological properties of dissociated DRG neurons. We found A1R to be expressed in populations of DRG neurons and dorsal horn neurons involved in the processing of pain. However, administration of capadenoson at established in vivo doses (0.03–1.0 mg/kg) did not alter mechanical hypersensitivity in the spared nerve injury and paclitaxel models of neuropathic pain, whereas the standard analgesic pregabalin significantly inhibited the pain behavior. Moreover, capadenoson failed to affect potassium currents in DRG neurons, in contrast to a full A1R agonist. Despite expression of A1R in nociceptive neurons, our data do not support the hypothesis that pharmacological intervention with partial A1R agonists might be a valuable approach for the treatment of neuropathic pain.
Ziel dieser Doktorarbeit war es, die Bedeutung der Kristallstrukturbestimmung aus Pulverdaten (SDPD) herauszuarbeiten und etwaige Grenzen durch neue Methodenentwicklungen zu erweitern, insbesondere bei Analyse der Paarverteilungsfunktion (PDF).
Die Effizienz der SDPD konnte anhand der erfolgreich gelösten Kristallstruktur von Carmustin (1,3 Bis-2-chlorethyl-1-nitrosoharnstoff, C5H9Cl2N3O2) aufgezeigt werden. [CS01]
Die Grenzen der SDPD wurden ausgelotet und erfolgreich erweitert. Nach weit verbreiteter kristallographischer Meinung ist die Strukturlösung mittels des simulierten Temperns (simulated annealing, SA) bei mehr als 25 zu bestimmenden Parametern problematisch oder unmöglich. Die pharmazeutischen Salze Lamivudin-Camphersulfonat (LC) und Aminogluthethimid-Camphersulfonat (AC) konnten, trotz ihrer hohen Anzahl an Freiheitsgraden von 31 für LC bzw. 37 für AC erfolgreich bestimmt werden. Die Strukturlösung von AC war herausfordernd und nicht direkt bei Anwendung der SA-Methode möglich. Nach einer intensiven Fehleranalyse stellte sich heraus, dass nicht die Grenzen der SA-Methode ausschlaggebend für das anfängliche Scheitern der Strukturlösung waren, sondern falsch extrahierte Intensitäten des vorangegangenen Pawley-Fits. Nach Behebung dieser Fehlerquelle war die Strukturlösung von AC problemlos. [CS02]
Mittels SDPD kann die absolute Konfiguration chiraler Verbindungen nicht direkt bestimmt werden. Durch Kristallisation der zu bestimmenden chiralen Verbindung mit einem chiralen Gegenion bekannter Konformation in einer simplen Säure-Base-Reaktion zu einem diastereomeren Salz und nachfolgender SDPD konnte eine neue Methode entwickelt werden, um die Konfigurationsbestimmung aus Pulverdaten zu ermöglichen. Diese Methode wurde anhand der drei pharmazeutischen Salze (R)-Flurbiprofen-(R)-Chinin (FQ), (2R5S)-Lamivudin-(R)-Camphersulfonat (LC) und (R)-Aminogluthethimid-(R)-Camphersulfonat (AC) aufgezeigt: In allen drei Fällen konnte die korrekte Konfiguration des pharmazeutischen Wirkstoffes mit den hierfür entwickelten Kriterien erfolgreich bestimmt werden. [CS03, CS04]
Durch Kombination der klassischen SDPD mit neuen methodischen Ansätzen konnten die Kristallstrukturen der schlecht kristallinen organischen Pigmente 2-Monomethylchinacridon (MMC, C21H14N2O2) und 4,11-Difluorchinacridon (DFC, C20H10N2O2F2) bestimmt werden, obwohl aufgrund ihrer geringen Kristallqualität keine sinnvolle Indizierung möglich war.
Für die Kristallstrukturbestimmung von DFC lieferte der neu entwickelte Global-Fit des Programms FIDEL mögliche Strukturmodelle mit ähnlich guter Übereinstimmung an das experimentelle Pulverdiagramm. Die Rietveld-Verfeinerung der Strukturmodelle in Kombination mit der Anpassung der Kristallstruktur an die PDF-Daten und kraftfeldbasierter Gitterenergieminimierung konnte einen geeigneten Strukturrepräsentanten von DFC liefern. [CS05, CS06]
Im Fall von MMC war eine Kombination der Methoden von Rietveld-Verfeinerung, Verfeinerung an die PDF-Daten und Gitterenergieminimierung zielführend zur Bestimmung der Orientierungs-Fehlordnung von MMC im Kristall. MMC ist hierbei die erste organische Verbindung, deren Fehlordnung durch Anpassung an die PDF bestimmt werden konnte. [CS07]
Große Erfolge konnten bei der Methodenentwicklung der PDF-Analyse erzielt werden. Die Bestimmung von Kristallstruktur organischer Verbindungen durch Anpassung an die PDF ohne vorherige Kenntnis der Gitterparameter oder Raumgruppe wurde durch die Entwicklung des PDF-Global-Fits erreicht. Lediglich die PDF-Kurve und eine Molekülstruktur werden als Input benötigt. Die Strukturlösung beruht auf einem globalen Optimierungs-Ansatz, bei welchem in ausgewählten Raumgruppen Zufallsstrukturen erzeugt werden. Die Zufallsstrukturen werden mit den experi¬mentellen Daten verglichen und entsprechend ihres Ähnlichkeitsindexes, basierend auf der Kreuz-Korrelation, sortiert. [CS08, CS09] Die vielversprechendsten Kandidaten werden in einem einge¬schränkten simulierten annealing-Ansatz an die experimentelle PDF angepasst. Eine nachfolgende Strukturverfeinerung der besten Strukturmodelle liefert die korrekte Kristallstruktur. Der Erfolg des PDF-Global-Fits wurde am Beispiel der Barbitursäure aufgezeigt: Ausgehend von 300 000 Zufallsstrukturen konnte die korrekte Kristallstruktur von Barbitursäure bestimmt werden. Barbitursäure ist hierdurch die erste organische Verbindung, deren Lokalstruktur durch Anpassung an die PDF bestimmt wurde, ohne Input oder Vorgabe von Gitterparametern oder Raumgruppe.[CS10]
Im Rahmen dieser kumulativen Dissertation konnte eine Methode mitentwickelt werden, die die Bestimmung der absoluten Konfiguration pharmazeutischer Verbindungen aus Röntgenpulverbeugungsdaten ermöglicht. Die Methode basiert auf der Bildung von Salzen. Die notwendige Herstellung dieser Salze mit Salzbildnern bekannter Konfiguration wurde hinsichtlich einer minimalen Ansatzgröße optimiert und erlaubt ein Arbeiten mit Mengen von unter zehn Mikrogramm. Die Kristallisation konnte sogar direkt in den Kapillaren für die Aufnahme der Pulverdiagramme durchgeführt werden. Die absolute Konfiguration einiger als Testfälle gewählter pharmazeutischer Wirkstoffe konnte auf diese Art erfolgreich bestimmt werden. Dies stellt eine erfolgreiche Erweiterung bisher verfügbarer Methoden dar.
1,1,3,3-Tetraethyl-5-nitroisoindolin (TENI) und 1,1,3,3-Tetraethyl-5-nitroisoindolin-2-oxyl (TENO) sind Zwischenstufen in der Synthese von RNS-Spinlabeln für die EPR-Spektroskopie. Die Kristallstrukturen beider Verbindungen konnten aus Einkristallbeugungsdaten bestimmt werden. TENI hat einen Schmelzpunkt nahe der Raumtemperatur. TENO hat dagegen einen wesentlich höheren Schmelzpunkt, obwohl das Molekül nur ein Sauerstoffatom zusätzlich hat. Die Kristallstruktur liefert die Erklärung für dieses Phänomen: In der Kristallstruktur von TENI findet sich als stärkste intermolekulare Wechselwirkung eine einzelne schwache, sehr lange Wasserstoffbrückenbindung.
6-Amino-2-iminiumyl-4-oxo-1,2,3,4-tetrahydropyrimidin-5-aminiumsulfat, ein Edukt der Synthese von Leukopterin konnte als Hydrat erhalten werden. Die Kristallstruktur dieses Monohydrats konnte problemlos bestimmt werden, ebenso wie die von synthetisiertem 4-Amino-2,6-dimethylpyrimidin.
Natriumethanolat wurde nach einer 180 Jahre alten Vorschrift von Liebig synthetisiert. Wie die Röntgenpulverdiagramme zeigen, bilden sich dabei jedoch Gemische von verschiedenen Phasen. Die Kristallstruktur von reinem NaOEt konnte aus Pulverdaten bestimmt werden. Ebenfalls wurden ein Diethanolsolvat sowie zwei weitere Phasen identifiziert. Vom Diethanolsolvat NaOEt · 2 HOEt konnten Einkristalle hergestellt und die Kristallstruktur aus diesen bestimmt werden. Die Kristallstrukturen von Natrium-n-propanolat (NaOnPr), Natrium-n-butanolat (NaOnBu) und Natrium-n-amylat (NaOnAm) konnten ebenfalls aus Pulverdaten aufgeklärt werden. Sie weisen ein ähnliches Na-O-Gitter wie Natriumethanolat auf, allerdings kristallisieren sie in der Raumgruppe P 4/n m m. Die abweichende Raumgruppe des NaOEt (P -4 21 m) liegt am sterischen Anspruch der Ethylgruppe. Die längeren Alkylgruppen sind hochgradig fehlgeordnet und somit im Mittel zylinderförmig. Die Ethylgruppe dagegen hat einen weniger symmetrischen Raumbedarf. Die Solvate der Alkalialkoholate wurden mit zunehmender Länge der Alkylketten instabiler. Nichtsdestotrotz konnten drei verschiedene Solvate hergestellt werden: NaOnPr · 2 HOnPr, NaOiPr · 5 HOiPr und NaOtAm · HOtAm. Ihre Kristallstrukturen konnten aus Einkristallbeugungsdaten bestimmt werden. In diesen Strukturen zeigen sich sehr unterschiedliche Strukturmotive, die teilweise die mögliche Existenz weiterer Solvatstufen andeuten.
Die industriellen Rotpigmente Pigment Red 52 und Pigment Red 48 wurden im Labor unter verschiedenen Bedingungen synthetisiert. Dabei wurden neben den kommerziell verfügbaren Phasen einige neue Phasen identifiziert. Erstmals konnten Kristallstrukturen von P.R.52 und P.R.48 bestimmt werden. Von Pigment Red 52 konnte ein bisher unbekanntes Mononatriumsalz hergestellt werden. Von diesem Salz konnte ein DMSO-Solvat-Monohydrat kristallisiert werden. Aus erhaltenen Einkristallen konnte die Struktur bestimmt werden. Von Pigment Red 48 konnte ebenfalls ein bisher nicht literaturbekanntes Mononatriumsalz isoliert werden. Von zwei Hydratstufen dieser Verbindung konnten Einkristalle hergestellt und ihre Kristallstrukturen bestimmt werden. Eine weitere Phase wurde als Anhydrat identifiziert. Vom Di-Natriumsalz des P.R.52 sowie von seinem Calciumsalz wurden insgesamt fünf verschiedene Hydratstufen gefunden. Die Kristallstrukturen dieser Hydrate konnten aus Röntgenpulverbeugungsdaten bestimmt werden. Von einer Hydratstufe konnte ebenfalls ein Einkristall erhalten und die Struktur bestätigt werden. Eine Veröffentlichung ist in Vorbereitung.
Die Isomere des Orangepigments Perinon werden nach gemeinsamer Synthese industriell durch Überführung in „Trennsalze“ getrennt. Weder die Molekülkonstitution der Trennsalz-Ionen, noch die chemische Zusammensetzung der Feststoffe, noch deren Kristallstrukturen waren bisher bekannt. Die industrielle Form des „trans-Trennsalzes“ konnte im Labor hergestellt werden. Eine weitere Phase des trans-Perinontrennsalzes konnte hergestellt und identifiziert werden. Durch die nachfolgende Einkristallstrukturanalyse zeigte sich, dass die Trennsalze eine völlig andere Molekülkonstitution haben, als in der Literatur beschrieben war: Statt eines planaren Perinongerüsts enthält das Trennsalz ein verdrehtes Bis(benzimidazolat)naphthalindicarboxylat-tetraanion, dessen Ladung durch Kalium-Kationen kompensiert wird. Das bisher nie als Feststoff beschriebene cis-Perinontrennsalz wurde hergestellt und kristallisiert. Es konnten Einkristalle hergestellt und die Kristallstruktur aus diesen bestimmt werden. Alle Perinontrennsalze enthalten im Kristallgitter eine beträchtliche Anzahl Wasser- und Ethanolmoleküle. Durch Festkörper-NMR-Spektroskopie konnte gezeigt werden, dass das Wasser-Ethanol-Netzwerk stark dynamisch ist. Bei der Hydrolyse der Trennsalze entstehen wieder die ursprünglichen, wasser- und lösungsmittelfreien Perinonpigmente.
Die Synthese und Charakterisierung von neuartigen metallorganischen Koordinationsverbindungen hat in den vergangenen Jahrzehnten einen wahren Aufschwung erlebt. Aufgrund ihrer außerordentlichen strukturellen Vielfalt eröffnen sich zahlreiche Anwendungsmöglichkeiten über alle naturwissenschaftlich-technischen Domänen hinweg. Daher besteht ein allgemeines Interesse nicht nur in der Entwicklung neuer Verbindungen und Untersuchungen von Struktur-Eigenschafts-Beziehungen, sondern auch in einer Verbesserung ihrer Darstellungsmethoden.
Diese Dissertation beschäftigt sich mit Koordinationspolymeren und -netzwerken, die aus zweiwertigen 3d-Übergangsmetallhalogeniden (MX2, wie bspw. MnCl2 oder FeBr2) und Pyridin (py) bzw. Pyridinderivaten (CNpy, wie bspw. 3-Cyanopyridin) aufgebaut sind. Die Darstellung der Koordinationsverbindungen erfolgte in erster Linie über gewöhnliche Kristallisationsexperimente in alkoholischer Lösung, bei denen Phasen der Stöchiometrie [MX2(CNpy)4] oder [MX2(CNpy)2]n anfielen. Diese wurden anschließend systematisch erhitzt (“getempert“), was in der Regel zu einer stufenweisen und irreversiblen Abgabe eines Teils der Liganden führte, also bspw. von [MX2(CNpy)2]n zu [MX2(CNpy)1]n. Für diesen sog. „thermischen Abbau“ hat sich die Verwendung eines DTA-TG-Gerätes bewährt. Da die Zielverbindungen als mikrokristalline Pulver anfielen, erfolgte die Bestimmung ihrer Kristallstrukturen auf Basis von Röntgenpulverdaten.
Insgesamt wurden im Rahmen dieser Arbeit 41 neue Phasen synthetisiert und deren Kristallstrukturen aus Röntgenpulverdaten bestimmt. Zusammenfassend ist für die verschiedenen Pyridinderivate folgendes zu konstatieren:
3-Cyanopyridin
Im Falle der MBr2-Serie wurden für M = Mn, Fe, Co und Ni Koordinationsverbindungen der Stöchiometrie [MBr2(3-CNpy)4] erhalten, deren Kristallstrukturen aus diskreten Komplexmolekülen bestehen. Derart ligandenreiche Verbindungen konnten bei keiner der übrigen Serien erhalten werden. Alle Kristallstrukturen der Zusammensetzung [MX2(3-CNpy)2]n zeigen bei M = Mn, Fe, Co, Ni und Cu eine Kettenstruktur, in der die Halogenatome als µ2-Brückenliganden fungieren. Die Ketten weisen eine Fischgrät-Anordnung auf. Im Falle von [ZnX2(3-CNpy)2] werden ausschließlich diskrete Komplexmoleküle beobachtet. In allen Kristallstrukturen der [MCl2(3-CNpy)1]n-Serie liegen Doppelketten mit µ2- und µ3-verbrückenden Cl-Atomen vor. Hingegen weisen die Verbindungen der [MBr2(3-CNpy)1]n-Serie Netzwerkstrukturen auf, in denen, zusätzlich zu µ2-Cl-Atomen, über NCN-Atome gebrückt wird.
3,5-Dicyanopyridin
Aufgrund der umfassenden Erkenntnislage bei [NiCl2(CNpy)x]n und [NiCl(py)x]n- Verbindungen wurde NiCl2 für erste Experimente mit 3,5-Dicyanopyridin als neuem, bifunktionalem Liganden ausgewählt. Erwartungsgemäß führte deren Umsetzung zur Bildung von [NiCl2(3,5-CNpy)2]n, dessen Kristallstruktur das hinlänglich bekannte charakteristische Kettenmotiv aufweist. Thermischer Abbau von [NiCl2(3,5-CNpy)2]n führt indes nicht zur Bildung von [NiCl2(3,5-CNpy)1]n (bzw. grundsätzlich zu [NiCl2(3,5-CNpy)x<2]n (mit bi- oder gar tridentatem Liganden), sondern unmittelbar zur vollständigen Zersetzung in NiCl2 und 3,5-CNpy. Daher sollten weitere Experimente mit NiBr2 als Edukt durchgeführt werden, da in [NiBr2(CNpy)1]n neben Npy auch NCN an Ni-Atome zu koordinieren vermag, wodurch ja deren Netzwerkstrukturen resultieren.
4-Cyanopyridin
Alle Kristallstrukturen der Zusammensetzung [MX2(4-CNpy)2]n zeigen bei M = Mn, Fe, Co, Ni und Cu ebenfalls eine Kettenstruktur, in der die Halogenatome als µ2-Brückenliganden fungieren. Auch in diesen Kristallstrukturen liegt eine Fischgrät-Anordnung der Ketten vor. Im Falle von [ZnX2(4-CNpy)2] werden ausschließlich diskrete Komplexmoleküle beobachtet. In allen Kristallstrukturen der [MX2(4-CNpy)1]n-Serie liegen Netzwerkstrukturen vor, in denen die Metallatome über µ2-Halogenatome und NCN-Atome verbrückt werden. Alle Kristallstrukturen der [MBr2(4-CNpy)1]n-Serie sind charakteristisch fehlgeordnet, da die Orientierung der 4-CNpy-Liganden invertiert wird („Kopf-Schwanz“-Fehlordnung).
The knob-associated histidine-rich protein (KAHRP) plays a pivotal role in the pathophysiology of Plasmodium falciparum malaria by forming membrane protrusions in infected erythrocytes, which anchor parasite-encoded adhesins to the membrane skeleton. The resulting sequestration of parasitized erythrocytes in the microvasculature leads to severe disease. Despite KAHRP being an important virulence factor, its physical location within the membrane skeleton is still debated, as is its function in knob formation. Here, we show by super-resolution microscopy that KAHRP initially associates with various skeletal components, including ankyrin bridges, but eventually colocalizes with remnant actin junctions. We further present a 35 Å map of the spiral scaffold underlying knobs and show that a KAHRP-targeting nanoprobe binds close to the spiral scaffold. Single-molecule localization microscopy detected ~60 KAHRP molecules/knob. We propose a dynamic model of KAHRP organization and a function of KAHRP in attaching other factors to the spiral scaffold.
The knob-associated histidine-rich protein (KAHRP) plays a pivotal role in the pathophysiology of Plasmodium falciparum malaria by forming membrane protrusions in infected erythrocytes, which anchor parasite-encoded adhesins to the membrane skeleton. The resulting sequestration of parasitized erythrocytes in the microvasculature leads to severe disease. Despite KAHRP being an important virulence factor, its physical location within the membrane skeleton is still debated, as is its function in knob formation. Here, we show by super-resolution microscopy that KAHRP initially associates with various skeletal components, including ankyrin bridges, but eventually colocalizes with remnant actin junctions. We further present a 35 Å map of the spiral scaffold underlying knobs and show that a KAHRP-targeting nanoprobe binds close to the spiral scaffold. Single-molecule localization microscopy detected ~60 KAHRP molecules/knob. We propose a dynamic model of KAHRP organization and a function of KAHRP in attaching other factors to the spiral scaffold.
The vascular endothelium is a monolayer of endothelial cells that builds the inner lining of the blood vessels and constitutes a regulatory organ within the physiological system to sustain homeostasis. Endothelial cells participate in physiological processes including inflammation and angiogenesis. Dysregulation of these processes, however, can evoke or maintain pathological disorders, including cardiovascular and chronic inflammatory diseases or cancer. Although pathological inflammation and angiogenesis represent treatable conditions, current pharmacotherapeutic approaches are frequently not satisfying since their long-term application can evoke therapy resistance and thus reduced clinical efficacy. Consequently, there is an ongoing demand for the discovery of new therapeutic targets and drug leads. Considering that endothelial cells play a critical role in both angiogenesis and inflammation, the vascular endothelium represents a promising target for the treatment of diseases.
Vioprolide A is a secondary metabolite isolated from the myxobacterium Cystobacter violaceus Cb. vi35. Recently, vioprolide A was identified to interact with NOP14, a nucleolar protein involved in ribosome biogenesis. Ribosome biogenesis is an indispensable cellular event that ensures adequate homeostasis. Abnormal alterations in the ribosome biogenesis, referred to as ribosomopathies, however, can lead to an overall increase in the risk of developing cancer. Accordingly, several studies have outlined the involvement of NOP14 in cancer progression and metastasis, and vioprolide A has been demonstrated to exert anti-cancer effects in vitro. However, the impact of vioprolide A and NOP14 on the endothelium has been neglected so far, although endothelial cells are crucially involved in inflammation and angiogenesis under both physiological and pathological conditions.
In the present study, the effect of vioprolide A on inflammatory and angiogenic actions was analysed. In vivo, the laser-induced choroidal neovascularization (CNV) assay outlined a strong inhibitory effect of vioprolide A on both inflammation and angiogenesis. Furthermore, intravital microscopy of the cremaster muscle in mice revealed that vioprolide A strongly impaired the TNF-induced leukocyte-endothelial cell interaction in vivo.
In further experiments, the specific effect of vioprolide A on activation processes of primary human umbilical vein endothelial cells (HUVECs) was examined. According to the in vivo results, vioprolide A decreased the leukocyte-endothelial cell interaction in vitro through downregulating the cell surface expression and total protein expression of ICAM-1, VCAM-1 and E-selectin. Vioprolide A evoked its anti-inflammatory actions via a dual mechanism: On the one hand, the expression of pro-inflammatory proteins, including TNFR1 and cell adhesion molecules, was lowered through a general downregulation of de novo protein synthesis. The inhibition of de novo protein synthesis is most likely linked to the interaction with and inhibition of NOP14 by vioprolide A in HUVECs. On the other hand, the natural product prevented the nuclear translocation and promotor activity of the pro-inflammatory transcription factor NF-ĸB. Interestingly, most anti-inflammatory compounds that interfere with the NF-ĸB signaling pathway prevent NF-ĸB nuclear translocation through recovering or stabilizing the inhibitory IĸB proteins. Vioprolide A, however, decreased rather than stabilized the IĸB proteins and prevented NF-ĸB nuclear translocation through interfering with its importin-dependent nuclear import. By performing siRNA-mediated knockdown experiments, we evaluated the role of NOP14 in inflammatory processes in HUVECs and could establish a causal link between the anti-inflammatory actions of vioprolide A and the deletion of NOP14.
Besides exerting anti-inflammatory actions, we found that vioprolide A potently decreased the angiogenic key features proliferation, migration and sprouting of endothelial cells. Mechanistically, the natural product interfered with pro-angiogenic signaling pathways. Vioprolide A reduced the protein level of growth factor receptors, including VEGFR2, which is the most prominent receptor responsible for angiogenic signaling in endothelial cells. This effect was based on the general inhibition of de novo protein synthesis by the natural product. Downregulation of growth factor receptors impaired the activation of downstream signaling intermediates, including the MAPKs ERK, JNK and p38. To our surprise, however, activation of Akt, another downstream effector of VEGFR2, was increased rather than decreased. Furthermore, vioprolide A lowered the nuclear translocation of the transcriptional coactivator TAZ, which is regulated by the evolutionary conserved Hippo signaling pathway. Interestingly, however, and in contrast to NF-ĸB, TAZ nuclear translocation in mammalian cells seems to be independent of importins. In this context, we found that vioprolide A reduced both the protein level and nuclear localization of MAML1, which is needed to retain TAZ in the nucleus after its successful translocation.
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Internationale Fachkonferenz im Hybrid-Format : Nachbericht zur Frankfurt Cancer Conference 2021
(2021)
Polymorphic G-quadruplex (G4) secondary DNA structures have received increasing attention in medicinal chemistry owing to their key involvement in the regulation of the maintenance of genomic stability, telomere length homeostasis and transcription of important proto-oncogenes. Different classes of G4 ligands have been developed for the potential treatment of several human diseases. Among them, the carbazole scaffold with appropriate side chain appendages has attracted much interest for designing G4 ligands. Because of its large and rigid π-conjugation system and ease of functionalization at three different positions, a variety of carbazole derivatives have been synthesized from various natural or synthetic sources for potential applications in G4-based therapeutics and biosensors. Herein, we provide an updated close-up of the literatures on carbazole-based G4 ligands with particular focus given on their detailed binding insights studied by NMR spectroscopy. The structure-activity relationships and the opportunities and challenges of their potential applications as biosensors and therapeutics are also discussed. This review will provide an overall picture of carbazole ligands with remarkable G4 topological preference, fluorescence properties and significant bioactivity; portraying carbazole as a very promising scaffold for assembling G4 ligands with a range of novel functional applications.
In vivo inducible reverse genetics in patients' tumors to identify individual therapeutic targets
(2021)
High-throughput sequencing describes multiple alterations in individual tumors, but their functional relevance is often unclear. Clinic-close, individualized molecular model systems are required for functional validation and to identify therapeutic targets of high significance for each patient. Here, we establish a Cre-ERT2-loxP (causes recombination, estrogen receptor mutant T2, locus of X-over P1) based inducible RNAi- (ribonucleic acid interference) mediated gene silencing system in patient-derived xenograft (PDX) models of acute leukemias in vivo. Mimicking anti-cancer therapy in patients, gene inhibition is initiated in mice harboring orthotopic tumors. In fluorochrome guided, competitive in vivo trials, silencing of the apoptosis regulator MCL1 (myeloid cell leukemia sequence 1) correlates to pharmacological MCL1 inhibition in patients´ tumors, demonstrating the ability of the method to detect therapeutic vulnerabilities. The technique identifies a major tumor-maintaining potency of the MLL-AF4 (mixed lineage leukemia, ALL1-fused gene from chromosome 4) fusion, restricted to samples carrying the translocation. DUX4 (double homeobox 4) plays an essential role in patients’ leukemias carrying the recently described DUX4-IGH (immunoglobulin heavy chain) translocation, while the downstream mediator DDIT4L (DNA-damage-inducible transcript 4 like) is identified as therapeutic vulnerability. By individualizing functional genomics in established tumors in vivo, our technique decisively complements the value chain of precision oncology. Being broadly applicable to tumors of all kinds, it will considerably reinforce personalizing anti-cancer treatment in the future.
The concept of using precipitation inhibitors (PIs) to sustain supersaturation is well established for amorphous formulations but less in the case of lipid-based formulations (LBF). This study applied a systematic in silico–in vitro–in vivo approach to assess the merits of incorporating PIs in supersaturated LBFs (sLBF) using the model drug venetoclax. sLBFs containing hydroxypropyl methylcellulose (HPMC), hydroxypropyl methylcellulose acetate succinate (HPMCAS), polyvinylpyrrolidone (PVP), PVP-co-vinyl acetate (PVP/VA), Pluronic F108, and Eudragit EPO were assessed in silico calculating a drug–excipient mixing enthalpy, in vitro using a PI solvent shift test, and finally, bioavailability was assessed in vivo in landrace pigs. The estimation of pure interaction enthalpies of the drug and the excipient was deemed useful in determining the most promising PIs for venetoclax. The sLBF alone (i.e., no PI present) displayed a high initial drug concentration in the aqueous phase during in vitro screening. sLBF with Pluronic F108 displayed the highest venetoclax concentration in the aqueous phase and sLBF with Eudragit EPO the lowest. In vivo, the sLBF alone showed the highest bioavailability of 26.3 ± 14.2%. Interestingly, a trend toward a decreasing bioavailability was observed for sLBF containing PIs, with PVP/VA being significantly lower compared to sLBF alone. In conclusion, the ability of a sLBF to generate supersaturated concentrations of venetoclax in vitro was translated into increased absorption in vivo. While in silico and in vitro PI screening suggested benefits in terms of prolonged supersaturation, the addition of a PI did not increase in vivo bioavailability. The findings of this study are of particular relevance to pre-clinical drug development, where the high in vivo exposure of venetoclax was achieved using a sLBF approach, and despite the perceived risk of drug precipitation from a sLBF, including a PI may not be merited in all cases.
The Corona pandemic has painfully taught us the threat of new pathogens in a globalized world and how vital modern vaccines are. Platform technologies play an important role in the discovery of new vaccines as reducing the time for the development dramatically — time that saves lives. Here, we present the protein Dodecin and how it may be utilized as a versatile platform technology to produce cheap and robust new vaccines for everyone in all parts of the world.
Age-related multifactorial diseases, such as the neurodegenerative Alzheimer’s disease (AD), still remain a challenge to today’s society. One mechanism associated with AD and aging in general is mitochondrial dysfunction (MD). Increasing MD is suggested to trigger other pathological processes commonly associated with neurodegenerative diseases. Silibinin A (SIL) is the main bioactive compound of the Silymarin extract from the Mediterranean plant Silybum marianum (L.) (GAERTN/Compositae). It is readily available as a herbal drug and well established in the treatment of liver diseases as a potent radical scavenger reducing lipid peroxidation and stabilize membrane properties. Recent data suggest that SIL might also act on neurological changes related to MD. PC12APPsw cells produce low levels of human Aβ and thus act as a cellular model of early AD showing changed mitochondrial function. We investigated whether SIL could affect mitochondrial function by measuring ATP, MMP, as well as respiration, mitochondrial mass, cellular ROS and lactate/pyruvate concentrations. Furthermore, we investigated its effects on the mitochondrial membrane parameters of swelling and fluidity in mitochondria isolated from the brains of mice. In PC12APPsw cells, SIL exhibits strong protective effects by rescuing MMP and ATP levels from SNP-induced mitochondrial damage and improving basal ATP levels. However, SIL did not affect mitochondrial respiration and mitochondrial content. SIL significantly reduced cellular ROS and pyruvate concentrations. Incubation of murine brain mitochondria with SIL significantly reduces Ca2+ induced swelling and improves membrane fluidity. Although OXPHOS activity was unaffected at this early stage of a developing mitochondrial dysfunction, SIL showed protective effects on MMP, ATP- after SNP-insult and ROS-levels in APPsw-transfected PC12 cells. Results from experiments with isolated mitochondria imply that positive effects possibly result from an interaction of SIL with mitochondrial membranes and/or its antioxidant activity. Thus, SIL might be a promising compound to improve cellular health when changes to mitochondrial function occur.
The prevention of tau protein aggregations is a therapeutic goal for the treatment of Alzheimer's disease (AD), and hydromethylthionine (HMT) (also known as leucomethylthioninium-mesylate [LMTM]), is a potent inhibitor of tau aggregation in vitro and in vivo. In two Phase 3 clinical trials in AD, HMT had greater pharmacological activity on clinical endpoints in patients not receiving approved symptomatic treatments for AD (acetylcholinesterase (AChE) inhibitors and/or memantine) despite different mechanisms of action. To investigate this drug interaction in an animal model, we used tau-transgenic L1 and wild-type NMRI mice treated with rivastigmine or memantine prior to adding HMT, and measured changes in hippocampal acetylcholine (ACh) by microdialysis. HMT given alone doubled hippocampal ACh levels in both mouse lines and increased stimulated ACh release induced by exploration of the open field or by infusion of scopolamine. Rivastigmine increased ACh release in both mouse lines, whereas memantine was more active in tau-transgenic L1 mice. Importantly, our study revealed a negative interaction between HMT and symptomatic AD drugs: the HMT effect was completely eliminated in mice that had been pre-treated with either rivastigmine or memantine. Rivastigmine was found to inhibit AChE, whereas HMT and memantine had no effects on AChE or on choline acetyltransferase (ChAT). The interactions observed in this study demonstrate that HMT enhances cholinergic activity in mouse brain by a mechanism of action unrelated to AChE inhibition. Our findings establish that the drug interaction that was first observed clinically has a neuropharmacological basis and is not restricted to animals with tau aggregation pathology. Given the importance of the cholinergic system for memory function, the potential for commonly used AD drugs to interfere with the treatment effects of disease-modifying drugs needs to be taken into account in the design of clinical trials.
Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a 1-MDa membrane protein complex with a central role in energy metabolism. Redox-driven proton translocation by complex I contributes substantially to the proton motive force that drives ATP synthase. Several structures of complex I from bacteria and mitochondria have been determined, but its catalytic mechanism has remained controversial. We here present the cryo-EM structure of complex I from Yarrowia lipolytica at 2.1-Å resolution, which reveals the positions of more than 1600 protein-bound water molecules, of which ~100 are located in putative proton translocation pathways. Another structure of the same complex under steady-state activity conditions at 3.4-Å resolution indicates conformational transitions that we associate with proton injection into the central hydrophilic axis. By combining high-resolution structural data with site-directed mutagenesis and large-scale molecular dynamic simulations, we define details of the proton translocation pathways and offer insights into the redox-coupled proton pumping mechanism of complex I.
The specific and precise arrangement of proteins and biomolecules in 3D is an important prerequisite for the study of cell migration, cellular signal transduction and the production of artificial tissue. In a variety of research approaches, proteins have been immobilized on rigid surfaces such as glass or gold to observe protein-protein or protein-cell interactions. While these commonly used analytical platforms offer advantages such as rapid washing steps and easy use, due to their rigidity and two-dimensionality, they cannot replicate the extracellular matrix (ECM) the native environment of cells. This severe deviation from the natural environment results in significant changes in cell structure and cellular processes such as the polarization of the cell, its morphology, and signal transduction. In order to maintain the functionality of the immobilized proteins, it is also enormously important that the proteins are oriented and anchored in the material under mild conditions.
An immobilization strategy that makes this possible is bioaffinity. For this, the specific interaction of a biomolecule with an interaction partner anchored on a surface is used to immobilize the biomolecule. Such an interaction is for example the nitrilotriacetic acid (NTA)/His-tag binding. NTA is a chelator molecule that, when bound to divalent metal ions such as Ni(II), forms an octahedral complex with oligohistidines. The oligo histidine-tag can be competed out of the complex by free histidine or imidazole due to structural similarity. This is exploited in immobilized metal affinity chromatography (IMAC). The binding of a monoNTA/His-tag complex (KD=10 µM) is not stable enough to be used for immobilizations. Therefore, multivalent variants of the chelator were developed, like trisNTA which has a high affinity for His6 tagged proteins (KD= 10 nM). The PA-trisNTA developed in a preliminary work was the first light-activatable system based on the trisNTA chelator head.
The aim of this work was to synthesize a new two-photon (2P) activatable trisNTA (TPA trisNTA) interaction molecule, to analyze its photophysical characteristics and to apply it for two- and three dimensional (2D/3D) biomolecule patterning. The final goal was to use TPA trisNTA for cellular applications in order to manipulate membrane protein organization. Therefore, TPA trisNTA was designed to maintain a stable autoinhibition enabling the immobilization of proteins under physiological conditions with high precision in the x/y, as well as z dimension only upon light activation. 2P activation brings some outstanding advantages: i) the use of near-infrared (NIR) light is less harmful to cells compared to ultraviolet (UV) light, ii) the longer wavelength allows the radiation to penetrate deeper into tissues, iii) the precision of focal irradiation is more accurate because only a focal volume (about 1 fL) is excited and, unlike UV light, scattered light does not lead to activation.
Several backbones for TPA-trisNTA were considered as 2P cleavable groups due to their 2P absorption ability and small size: 3 nitrodibenzofuran (NDBF), 6 bromo 7 hydroxycoumarin (Bhc), and 7 diethylaminocoumarin (DEAC). Initially, suitable synthetic routes were developed for the respective carbaldehydes, since these represented an important intermediate for both the construction of amino acid (aa) derivatives as well as ß hydroxy acids. ß Hydroxy acids were important intermediates because their photocleavage differs from aa derivatives. To establish the conversion from carbaldehydes to hydroxy acids via Reformatsky reaction, commercially available carbaldehydes of the nitroveratral (NV) or nitropiperonal (NP) group were used in addition. The conversion of NDBF, NV, NP proved to be difficult, whereas the ß-hydroxy acid was successfully synthesized from Bhc as well as from DEAC.
Starting from DEAC ß hydroxy acid, a Fmoc protected amino acid derivative was synthesized. To ensure high cleavage efficiency, the DEAC ß hydroxy acid was linked to monoFmoc ethylenediamine through a carbamate linker. Subsequently, the photocleavable group was successfully incorporated into the linker of TPA-trisNTA by solid-phase peptide synthesis (SPPS).
The functional principle of TPA-trisNTA, similar to PA-trisNTA, is based on the autoinhibition of the multivalent chelator head trisNTA, which is linked to an intramolecular oligohistidine sequence by a peptide linker. In presence of Ni(II) ions, trisNTA forms a metal ion-mediated complex with histidine, causing TPA-trisNTA to self-inactivate. The cleavage site is the DEAC based photocleavable amino acid. In contrast to PA-trisNTA, the incorporation of two photocleavable amino acids was omitted. Instead, only one photocleavable DEAC was incorporated in front of the His tag. To avoid a second DEAC group within the His tag, a His5 tag was used instead of an His6 tag. It is known from preliminary work that a His5 tag is sufficient to maintain autoinhibition in the presence of His6-tagged proteins of interest (POIs), but can be displaced from the complex after light-driven cleavage of the peptide backbone. Placement of a cysteine in the peptide linker between the trisNTA and the DEAC group allowed for permanent surface anchoring after photocleavage of the linker.
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Herpes simplex virus type 1 (HSV-1) is a widespread neurotropic virus. Primary infection of HSV-1 in facial epithelium leads to retrograde axonal transport to the central nervous system (CNS) where it establishes latency. Under stressful conditions, the virus reactivates, and new progeny are transported anterogradely to the primary site of infection. During the late stages of neuronal infection, axonal damage can occur, however, the impact of HSV-1 infection on the morphology and functional integrity of neuronal dendrites during the early stages of infection is unknown. We previously demonstrated that acute HSV-1 infection in neuronal cell lines selectively enhances Arc protein expression - a major regulator of long-term synaptic plasticity and memory consolidation, known for being a protein-interaction hub in the postsynaptic dendritic compartment. Thus, HSV-1 induced Arc expression may alter the functionality of infected neurons and negatively impact dendritic spine dynamics. In this study we demonstrated that HSV-1 infection induces structural disassembly and functional deregulation in cultured cortical neurons, an altered glutamate response, Arc accumulation within the somata, and decreased expression of spine scaffolding-like proteins such as PSD-95, Drebrin and CaMKIIβ. However, whether these alterations are specific to the HSV-1 infection mechanism or reflect a secondary neurodegenerative process remains to be determined.
Viele Studien konnten nachweisen, dass die Produktion von cGMP eine entscheidende Funktion im nozizeptiven System einnimmt. Hierbei wurde vor allem die cGMP-Produktion über lösliche Guanylatzyklasen untersucht. Welche Rolle die partikulären Guanlyatzyklasen bei der Entstehung von Schmerzen haben ist weitgehend ungeklärt. Die vorliegende Arbeit zeigte, dass die partikuläre Guanylatzyklase NPR2 stark in DRG-Neuronen exprimiert wird und dort mit cGKI-alpha sowie CRP4 colokalisiert ist. Aktiviert wird NPR2 über den Peptidliganden CNP. Hervorzuheben ist, dass CNP nicht in primär afferenten Neuronen, dafür jedoch vermehrt im Dorsalhorn des Rückenmarks gebildet wird. Tierexperimentelle Untersuchungen zeigten, dass SNS-Npr2-/--Mäuse ein verringertes Schmerzverhalten bei thermischer Stimulation aufwiesen. Während sie im Capsaicin-Test keinen Phänotyp zeigten, wiesen sie in Phase II des Formalin-Modells ein signifikant reduziertes Leckverhalten auf. Diese Ergebnisse liefern Hinweise für eine Beteiligung des CNP/NPR2/cGKI Signalwegs an der Detektion von Hitzeschmerz und an der TRPA1-vermittelten Schmerzantwort. Dabei scheint NPR2 eine pronozizeptive Funktion zu besitzen. CRP4 als Zielprotein scheint hingegen eine antinozizeptive Wirkung zu haben. Zudem kann die Hypothese aufgestellt werden, dass CNP über einen retrograden Transport aus dem Rückenmark die Aktivierung von NPR2 auslösen könnte. Zusammengefasst zeigen die Daten dieser Arbeit, dass eine cGMP-abhängige Aktivierung durch NPR2 primär für die Detektion thermischer Reize zuständig ist, während die Literatur Hinweise darauf gibt, dass lösliche Guanylatzyklasen vor allem an inflammatorischen und neuropathischen Prozessen beteiligt sind. Daher scheinen partikuläre und lösliche Guanylatzyklasen unterschiedliche Eigenschaften im nozizeptiven System zu besitzen.
Protein ubiquitination is a post-translational modification that typically involves the conjugation of ubiquitin to substrate proteins via a three-enzyme cascade and regulates a wide variety of cellular processes. Recent studies have revealed that SidE family of Legionella effectors such as SdeA catalyzes novel phosphoribosyl-linked ubiquitination (PR-ubiquitination) of serines in host substrate proteins utilizing NAD+, without the need of E2, E3. The catalytic core of SdeA comprises a mono-ADP-ribosyltransferase (mART) domain that functions to ADP-ribosylate ubiquitin, and a phosphodiesterase (PDE) domain that processes ADP-ribosylated ubiquitin and transfers the resulting phosphoribosylated ubiquitin to serines of substrates.
To date, extensive efforts have been made to study the function of SdeA and mechanism of SdeA mediated PR-ubiquitination, however, the cellular effects of this novel ubiquitination and phosphoribosylation of ubiquitin remained poorly understood. In our study, using biochemical and cell biological approaches, we explored the biological effect of phosphoribosylation of ubiquitin caused by SdeA in cells. We found that phosphoribosylated ubiquitin is not available for conventional ubiquitination, thereby phosphoribosylation of ubiquitin impairs numerous classical ubiquitination related cellular processes including mitophagy, TNF-α signaling and proteasomal degradation.
The precise temporal regulation of the functions of bacterial effectors during Legionella infection by other effectors with antagonizing activities has been well studied so far. Not surprisingly, PR-ubiquitination catalyzed by SidE family effecters is tightly controlled as well, it has been long known that effector SidJ counteracts the toxicity of SdeA to yeast cells. Interestingly, in an experiment for verifying the activity of SidJ, we found that Legionella lysate lacking SidJ was still able to remove ubiquitin from PR-ubiquitinated substrates. Using biochemical approach we identified DupA and DupB, two Legionella bacterial effectors that specifically reverse the novel serine PR-ubiquitination catalyzed by SdeA. We found that DupA and DupB possess a highly homologous PDE domain that removes ubiquitin from PR-ubiquitinated substrates by cleaving the phosphodiester bond between the phosphoribosylated-ubiquitin and serines of substrates. Catalytically deficient mutant DupA H67A strongly binds to PR-ubiquitinated proteins but not capable of cleaving PR-ubiquitin, using it as a trapping bait we identified over 180 substrates of PR-ubiquitination, including a number of ER and Golgi proteins.
In particular, we found that exogenously expressed SdeA localizes to the Golgi apparatus via its C-terminal region and disrupts the Golgi. We validated the identified potential substrates of SidE effectors and found that SdeA modifies Golgi tethering proteins GRASP55 and GRASP65. Using mass spectrometry analyses we identified four serine targets (S3, S408, S409, S449) of GRASP55 PR-ubiquitinated by SdeA in vitro. Ubiquitination of GRASP55 serine mutant in cells co-expressing SdeA or infected with Legionella was markedly decreased, compared with that of the wild-type GRASP55. In addition, with co-immunoprecipitation analyses we found that SdeA-catalyzed ubiquitination regulates the function of GRASP55. PR-ubiquitinated GRASP55 exhibited reduced self-interaction compared to unmodified GRASP55, expression of GRASP55 serine mutant in cells in part rescued Golgi damage caused by SdeA. Furthermore, our study reveals that Golgi structure disruption caused by SdeA does not result in the recruitment of Golgi membranes to the Legionella-containing vacuoles. Instead, it affects cellular secretory pathway including cytokine secretion in cells.
Taken all together, this work expands the understanding of this unconventional PR-ubiquitination catalyzed by Legionella effectors and sheds light on the functions of PR-ubiquitination by which Legionella regulates the Golgi function and secretion pathway during bacterial infection.
Therapeutic oligonucleotides interact with a target RNA via Watson-Crick complementarity, affecting RNA-processing reactions such as mRNA degradation, pre-mRNA splicing, or mRNA translation. Since they were proposed decades ago, several have been approved for clinical use to correct genetic mutations. Three types of mechanisms of action (MoA) have emerged: RNase H-dependent degradation of mRNA directed by short chimeric antisense oligonucleotides (gapmers), correction of splicing defects via splice-modulation oligonucleotides, and interference of gene expression via short interfering RNAs (siRNAs). These antisense-based mechanisms can tackle several genetic disorders in a gene-specific manner, primarily by gene downregulation (gapmers and siRNAs) or splicing defects correction (exon-skipping oligos). Still, the challenge remains for the repair at the single-nucleotide level. The emerging field of epitranscriptomics and RNA modifications shows the enormous possibilities for recoding the transcriptome and repairing genetic mutations with high specificity while harnessing endogenously expressed RNA processing machinery. Some of these techniques have been proposed as alternatives to CRISPR-based technologies, where the exogenous gene-editing machinery needs to be delivered and expressed in the human cells to generate permanent (DNA) changes with unknown consequences. Here, we review the current FDA-approved antisense MoA (emphasizing some enabling technologies that contributed to their success) and three novel modalities based on post-transcriptional RNA modifications with therapeutic potential, including ADAR (Adenosine deaminases acting on RNA)-mediated RNA editing, targeted pseudouridylation, and 2′-O-methylation.
G-quadruplexes (G4), found in numerous places within the human genome, are involved in essential processes of cell regulation. Chromosomal DNA G4s are involved for example, in replication and transcription as first steps of gene expression. Hence, they influence a plethora of downstream processes. G4s possess an intricate structure that differs from canonical B-form DNA. Identical DNA G4 sequences can adopt multiple long-lived conformations, a phenomenon known as G4 polymorphism. A detailed understanding of the molecular mechanisms that drive G4 folding is essential to understand their ambivalent regulatory roles. Disentangling the inherent dynamic and polymorphic nature of G4 structures thus is key to unravel their biological functions and make them amenable as molecular targets in novel therapeutic approaches. We here review recent experimental approaches to monitor G4 folding and discuss structural aspects for possible folding pathways. Substantial progress in the understanding of G4 folding within the recent years now allows drawing comprehensive models of the complex folding energy landscape of G4s that we herein evaluate based on computational and experimental evidence.