Artificial Siderophores with a Trihydroxamate-DOTAM Scaffold Deliver Iron and Antibiotic Cargo into the Bacterial Pathogen Escherichia coli

Infections with multidrug-resistant Gram-negative bacteria constitute a silent pandemic threat that is increasing globally. A major technical and scientific hurdle hampering the development of efficient antibiotics against Gram-negative species is the low permeability of their outer membrane that prevents the entry of most small molecules into the cells. This can be overcome by targeting active iron transport systems of the pathogens in a Trojan-Horse strategy that makes use of drug-loaded artificial siderophores. While we utilized catechols as iron-binding motifs in previous work, this study reports the design, synthesis and characterization of siderophores with a DOTAM scaffold that was substituted with three hydroxamate arms allowing for a hexacoordination of iron. Their iron-chelating capabilities were shown colorimetrically, and the ability of compound 1 to deliver iron into Escherichia coli in a chelation-specific manner was proven by a growth recovery assay. A covalent siderophore-ciprofloxacin conjugate exerted antibiotic effects against E. coli, albeit it was less potent than the free drug. The study qualifies artificial DOTAM siderophores with hydroxamate binders as scaffolds for bacterial Trojan Horses. This contribution for honoring my mentor Helmut Schwarz echoes two motifs of my work with him: Hydroxylamin, the topic of my first paper ever, and the fascinating properties of iron ions, studied in the gas phase during my Ph.D. Thesis, became a core subject of our current chemical biology research on antiinfectives

Bioassays to Monitor Taspase1 Function for the Identification of Pharmacogenetic Inhibitors

Background: Threonine Aspartase 1 (Taspase1) mediates cleavage of the mixed lineage leukemia (MLL) protein and leukemia provoking MLL-fusions. In contrast to other proteases, the understanding of Taspase1's (patho)biological relevance and function is limited, since neither small molecule inhibitors nor cell based functional assays for Taspase1 are currently available. Methodology/Findings: Efficient cell-based assays to probe Taspase1 function in vivo are presented here. These are composed of glutathione S-transferase, autofluorescent protein variants, Taspase1 cleavage sites and rational combinations of nuclear import and export signals. The biosensors localize predominantly to the cytoplasm, whereas expression of biologically active Taspase1 but not of inactive Taspase1 mutants or of the protease Caspase3 triggers their proteolytic cleavage and nuclear accumulation. Compared to in vitro assays using recombinant components the in vivo assay was highly efficient. Employing an optimized nuclear translocation algorithm, the triple-color assay could be adapted to a high-throughput microscopy platform (Z'factor = 0.63). Automated high-content data analysis was used to screen a focused compound library, selected by an in silico pharmacophor screening approach, as well as a collection of fungal extracts. Screening identified two compounds, N-[2-[(4-amino-6-oxo-3H-pyrimidin-2-yl)sulfanyl]ethyl]benzenesulfonamideand 2-benzyltriazole-4,5-dicarboxylic acid, which partially inhibited Taspase1 cleavage in living cells. Additionally, the assay was exploited to probe endogenous Taspase1 in solid tumor cell models and to identify an improved consensus sequence for efficient Taspase1 cleavage. This allowed the in silico identification of novel putative Taspase1 targets. Those include the FERM Domain-Containing Protein 4B, the Tyrosine-Protein Phosphatase Zeta, and DNA Polymerase Zeta. Cleavage site recognition and proteolytic processing of these substrates were verified in the context of the biosensor. Conclusions: The assay not only allows to genetically probe Taspase1 structure function in vivo, but is also applicable for high-content screening to identify Taspase1 inhibitors. Such tools will provide novel insights into Taspase1's function and its potential therapeutic relevance

Identifizierung chemischer Transportinhibitoren zur Modulation (patho)biologischer Genprodukte

Die intrazelluläre Lokalisation von Proteinen und Makromolekülen unterliegt in Eukaryoten einer strengen Regulation. Insbesondere erlaubt die Kompartimentierung eukaryotischer Zellen in Zellkern und Zytoplasma den simultanen Ablauf räumlich getrennter biochemischer Reaktionen, und damit die unabhängige Regulation zellulärer Programme. Da trotz intensiver Forschungsbemühungen bis dato die molekularen Details sowie die (patho)biologische Bedeutung von Kern-Zytoplasma-Transportprozessen noch immer nicht vollkommen verstanden sind, wurde im Rahmen der vorliegenden Arbeit ein Fokus auf die Identifizierung von chemischen Transportinhibitoren gelegt. Das zu diesem Zweck entwickelte Translokations-Biosensor-System basiert auf der Kombination von autofluoreszierenden Proteinen, sowie spezifisch ausgewählten Kernexport- und Kernimportsignalen. Nach Etablierung geeigneter Zellmodelle, die effizient und stabil die Translokations-Biosensoren exprimieren, wurde die 17 000 Substanzen umfassende Bibliothek der ChemBioNet-Initiative nach Kernexportinhibitoren mittels einer Fluoreszenzmikroskopie-basierten Hochdurchsatzanalyse-Plattform durchmustert. Zunächst wurden Translokations-Algorithmen, welche eine zuverlässige automatisierte Erkennung von Zellkern und Zytoplasma erlauben, optimiert. Im Folgenden konnten acht neue niedermolekulare Kernexport-Inhibitoren identifiziert werden, die sich in der Stärke, der Geschwindigkeit, sowie in der Beständigkeit der vermittelten Inhibition unterscheiden. Die Aktivität der Inhibitoren konnte auf den isolierten nukleären Exportsignalen (NES) von HIV-1 Rev und Survivin als auch auf den entsprechenden Volllängeproteinen mittels Mikroinjektionsexperimenten sowie durch umfassende in vitro und biochemische Methoden bestätigt werden. Zur Untersuchung der funktionellen Einheiten der Inhibitoren wurden homologe Substanzen auf Ihre Aktivität hin getestet. Dabei konnten für die Aktivität wichtige chemische Gruppen definiert werden. Alle Substanzen stellen neue Inhibitoren des Crm1-abhängigen Exports dar und zeigen keine nachweisbare NES-Selektivität. Interessanterweise konnte jedoch eine zytotoxische und Apoptose-induzierende Wirkung auf verschiedene Krebszellarten festgestellt werden. Da diese Wirkung unabhängig vom p53-Status der Tumorzellen ist und die Inhibitoren C3 und C5 die Vitalität nicht-maligner humaner Zellen signifikant weniger beeinträchtigen, wurden diese Substanzen zum internationalen Patent angemeldet. Da der nukleäre Export besonders für Tumorzellen einen wichtigen Überlebenssignalweg darstellt, könnte dessen reversible Hemmung ausgenutzt werden, um besonders in Kombination mit gängigen Krebstherapien eine therapeutisch relevante Tumorinhibition zu erzeugen. Eine weitere Anwendungsmöglichkeit der neuen Exportinhibitoren ist auf dem Gebiet der Infektionskrankheiten zu sehen, da auch die Aktivität des essentiellen HIV-1 Rev-Proteins inhibiert wird. Zusätzlich konnte in der Arbeit gezeigt werden, dass der zelluläre Kofaktor des Crm1-abhängigen Exports des HIV-1 Rev-Proteins, die RNA-Helikase DDX3, ein eigenes NES enthält. Der Nachweis einer direkten Interaktion des HIV-1 Rev- mit dem DDX3-Protein impliziert, dass multiple Angriffstellen für chemische Modulatoren hinsichtlich einer antiviralen Therapie gegeben sind. Da die Vielfalt des chemischen Strukturraums es unmöglich macht diesen experimentell vollständig zu durchmustern, wurden im Rahmen dieser Arbeit auch Naturstoffe als vielversprechende Wirkstoffquelle untersucht. Um zukünftig umfassend bioaktive Substanzen aus diesen hochkomplexen Stoffgemischen experimentell identifizieren zu können, wurde eine Fluoreszenzmikroskopie-basierte Hochdurchsatzanalyse-Plattform am Mainz Screening Center (MSC) etabliert. Damit konnte bereits ein weiterer, bisher unbekannter Exportinhibitor aus Cyphellopsis anomala identifiziert werden. Neben einer Anwendung dieser Substanz als chemisches Werkzeug zur Aufklärung der Regulation von Transportvorgängen, stellt sich auch die evolutionsbiologisch relevante Frage, wie es dem Pilzproduzenten gelingt die Blockierung des eigenen Kernexports zu umgehen. Weiterführende Projekte müssen sich neben der Aufklärung der molekularen Wirkmechanismen der gefundenen Substanzen mit der Identifizierung spezifischer chemischer „Funktionseinheiten“ beschäftigen. Neben einem verbesserten mechanistischen Verständnis von Transportvorgängen stellen die erarbeiteten Transportinhibitoren Vorstufen zur Weiterentwicklung möglicher Wirkstoffe dar. Die im Rahmen dieser Arbeit etablierte Technologie-Plattform und molekularen Werkzeuge stellen darüber hinaus eine wichtige Voraussetzung dar, um eine systematische Suche nach möglichen Wirkstoffen im Forschungsfeld der „Chemischen Biomedizin“ voranzutreiben.In eukaryotes the intracellular localization of proteins and macromolecules is tightly regulated. The compartmentalization of eukaryotic cells into nucleus and cytoplasm allows the simultaneous flow of biochemical reactions and thus independent regulation of cellular programs. As the molecular details and (patho)biological relevance of nucleocytoplasmic transport remain unsolved, despite intensive effort in investigation, it was the aim of this thesis to identify chemical transport inhibitors. The translocation biosensor system is based on a combination of autofluorescent proteins and specific nuclear localization and export signals. This system was specifically developed to identify compounds interfering with nuclear transport. For screening the 17 000 compounds of the ChemBioNet collection, cell lines efficiently and stably expressing the translocation biosensors were established. Evaluation of inhibitory effect was performed using a microscope based high throughput platform. Translocation algorithms were optimized for a reliable and automated analysis of nucleus and cytoplasm. Eight novel low molecular weight compounds inhibiting nuclear export were identified. Those compounds differ in speed and consistency of mediated inhibition. The novel inhibitors show activity on isolated nuclear export signals (NES) of HIV-1 Rev and Survivin as well as on the respective full length proteins, as proven by microinjection experiments and extensive in vitro and biochemical methods. In order to define functional units of these inhibitors, homologous compounds were tested for activity. Chemical groups important for activity were identified. All compounds are inhibitors of Crm1-dependent nuclear export, without possessing any NES selectivity. Interestingly a cytotoxic and apoptosis-inducing effect on several cancer cells was discovered. This effect was independent of p53-status of the tumor cells. As the inhibitors C3 und C5 significantly less affect viability of non-malignant human cells, those compounds were applied for international patent. Nuclear export is an essential survival pathway for tumor cells. Thus its reversible inhibition could be used to create a therapeutically relevant tumor inhibition in combination with current cancer therapeutics. Infectious disease is another possible field of application of the novel export inhibitors, as HIV-1 Rev activity is also inhibited. Additionally it was shown in this thesis, that DDX3, a cellular cofactor of Crm1-dependent export of HIV-1 Rev, has an internal NES. The confirmation of a direct interaction between HIV-1 Rev and DDX3 implies, that there are multiple areas of attack for chemical modulators concerning antiretroviral therapy. rnDue to its diversity, it is not possible to screen the whole chemical space in an experiment. Thus, natural compounds were tested as a promising source of active agents in this thesis. For identifying bioactive compounds from complex compound mixtures in the future, a microscope based high throughput platform was established at the Mainz Screening Center (MSC). Therewith, a novel to date unknown export inhibitor was identified from Cyphellopsis anomala. Beside using this compound as a chemical tool for elucidating the regulation of transport processes the question remains, in which way the fungal producer avoids inhibition of its own nuclear export. Continuative projects have to elucidate the molecular mechanism of action of the novel compounds but also their functional units have to be identified. Beside an improved mechanistic understanding, the novel transport inhibitors may be precursors for further development as potential therapeutics. The technology platform and the molecular tools established in this thesis are prerequisite for systematically search for novel active substances in the field of ‘chemical biology’

An update on the pathobiological relevance of nuclear receptors for cancers of the head and neck

Cancers of the head and neck are among the most common neoplasms worldwide, characterized by local tumor aggressiveness, high rate of early recurrence, development of metastasis and second primary tumors. Although disease management of head and neck cancer has improved significantly, overall survival-rates remained largely unchanged over the last decades. Thus, in addition to modern chemo-radiation treatment strategies combined with sophisticated surgery, there is still a need for molecular markers and key regulatory factors exploitable for chemoprevention and targeted therapies. A critical event in carcinogenesis is the uncontrolled modulation of genetic programs, mediated by deregulated signaling cascades, together with downstream transcriptional modulators. Hence, nuclear receptors, belonging to a superfamily of transcription factors implicated in a broad spectrum of physiological and pathophysiological processes, have also been associated with HNC. Enhanced expression of several nuclear receptors has been shown in head and neck cancer cells, and strategies targeting these molecules have been developed and tested in the clinics. In particular, the effects of retinoids targeting nuclear receptors of the thyroid hormone receptor-like receptor subfamily have been vigorously examined in large clinical chemoprevention trials. This review seeks to provide a general overview of nuclear receptors’ molecular functions and summarizes their prognostic/therapeutic relevance, as well as the (pre)clinical studies targeting nuclear receptors in HNC

Article Translocation Biosensors – Cellular System Integrators to Dissect CRM1-Dependent Nuclear Export by Chemicogenomics

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xCELLanalyzer: A Framework for the Analysis of Cellular Impedance Measurements for Mode of Action Discovery

Mode of action (MoA) identification of bioactive compounds is very often a challenging and time-consuming task. We used a label-free kinetic profiling method based on an impedance readout to monitor the time-dependent cellular response profiles for the interaction of bioactive natural products and other small molecules with mammalian cells. Such approaches have been rarely used so far due to the lack of data mining tools to properly capture the characteristics of the impedance curves. We developed a data analysis pipeline for the xCELLigence Real-Time Cell Analysis detection platform to process the data, assess and score their reproducibility, and provide rank-based MoA predictions for a reference set of 60 bioactive compounds. The method can reveal additional, previously unknown targets, as exemplified by the identification of tubulin-destabilizing activities of the RNA synthesis inhibitor actinomycin D and the effects on DNA replication of vioprolide A. The data analysis pipeline is based on the statistical programming language R and is available to the scientific community through a GitHub repository

Subcellular Quantification of Uptake in Gram-Negative Bacteria.

Infections by Gram-negative pathogens represent a major health care issue of growing concern due to a striking lack of novel antibacterial agents over the course of the last decades. The main scientific problem behind the rational optimization of novel antibiotics is our limited understanding of small molecule translocation into, and their export from, the target compartments of Gram-negative species. To address this issue, a versatile, label-free assay to determine the intracellular localization and concentration of a given compound has been developed for Escherichia coli and its efflux-impaired ΔTolC mutant. The assay applies a fractionation procedure to antibiotic-treated bacterial cells to obtain periplasm, cytoplasm, and membrane fractions of high purity, as demonstrated by Western Blots of compartment-specific marker proteins. This is followed by an LC-MS/MS-based quantification of antibiotic content in each compartment. Antibiotic amounts could be converted to antibiotic concentrations by assuming that an E. coli cell is a cylinder flanked by two half spheres and calculating the volumes of bacterial compartments. The quantification of antibiotics from different classes, namely ciprofloxacin, tetracycline, trimethoprim, and erythromycin, demonstrated pronounced differences in uptake quantities and distribution patterns across the compartments. For example, in the case of ciprofloxacin, a higher amount of compound was located in the cytoplasm than in the periplasm (592 ± 50 pg vs 277 ± 13 pg per 3.9 × 1

Multivalent Siderophore-DOTAM Conjugates as Theranostics for Imaging and Treatment of Bacterial Infections.

There is a strong need to better diagnose infections at deep body sites through noninvasive molecular imaging methods. Herein, we describe the synthesis and characterization of probes based on siderophore conjugates with catechol moieties and a central DOTAM scaffold. The probes can accommodate a metal ion as well as an antibiotic moiety and are therefore suited for theranostic purposes. The translocation of the conjugates across the outer and inner cell membranes of E. coli was confirmed by growth recovery experiments with enterobactin-deficient strains, by the antibacterial activity of ampicillin conjugates, and by confocal imaging using a fluorogen-activating protein-malachite green system adapted to E. coli. The suitability of the probes for in vivo imaging was demonstrated with a Cy5.5 conjugate in mice infected with P. aeruginosa