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<p>Aminoglycoside antibiotics are commonly used to treat bacterial infections but are highly susceptible to chemical modification, leading to resistance. Chemical modification can be hindered through the use of small molecule inhibitors that target bacterial enzymes involved in resistance, most notably kinases. Current methods for the discovery of small molecule inhibitors of kinases and related “kinase-like” enzymes are limited in throughput and utilize slow, tedious, and expensive assays. This thesis is focused on the development of highly versatile and scaleable kinase and “kinase-like” screening platforms for the discovery of small molecule inhibitors of these drug targets. The work begins with the validation of a matrix-assisted laser desorption/ionization tandem mass spectrometry (MALDI-MS/MS) platform utilizing phosphorylation of kanamycin, an aminoglycoside antibiotic, by aminoglycoside phosphotransferase 3ʹIIIa (APH 3ʹIIIa) as a model system. Using a product-to-substrate signal ratio as an internal standard, the assay was used to functionally screen over 200 compounds, combined into mixtures to enhance assay throughput. Moreover, the assay was used to determine inhibitory dissocation constants for newly discovered modulators. Throughput was further increased to a novel dual-kinase assay targeting a bacterial enzyme, APH 3ʹIIIa and a human kinase, protein kinase A (PKA), which was validated using the previous small molecule library. Alternative assay development platforms were also studied using imaging mass spectrometry of reaction microarrays and the fabrication of sol-gel derived bioaffinity chromatography columns. The MS-based kinase assays developed herein are highly amenable to high throughput screening, and have the potential to be extended to other important therapeutic targets.</p> / Doctor of Philosophy (PhD)

Microbial natural products have been a source for new drugs for many decades and are unrivaled in their capacity to generate not only future therapeutic agents, but also providing key agents for agricultural and industrial use. LC-MS/MS based metabolomic tools and technologies have been developed that can rapidly dereplicate nonribosomal peptides and statistically identify related congeners in an automated nontargeted process from complex natural product extracts with nanogram sensitivity. This data-base search approach is designed to handle linear, cyclic and cyclic-branched nonribosomal peptides from proteinogenic and nonproteinogenic amino acids without genomic data or traditional bioactivity directed fractionation. Chemometric work-flows combined with a comprehensive metabolomic guided discovery strategy were used to profile the chemical space of a diverse collection of understudied fungal endophytes from fruiting plants. This approach allowed for the prioritization of unique isolates and for the focused discovery, isolation and characterization of distinct outlier metabolites by LC-SPE, 1D and 2D NMR, HRMS and single crystal X-ray analysis. These metabolomic tools and strategies have led to the discovery and characterization of 35 new and over 40 known natural products, many of which are biologically active. This thesis with enabling metabolomic tools and novel discoveries has demonstrated the utility of these analytical methodologies as an effective strategy for the untargeted discovery of new natural products from bacteria and endophytic fungi. / Thesis / Doctor of Philosophy (PhD)

<p dir="ltr">In this study, we presented the discovery of the first-in-class covalent inhibitor specific to Src homology 2 domain containing phosphatase 1 (SHP1), an overlooked cancer immunotherapy target. Through high-throughput screening, we identified a chloroacetamide fragment highly selective for SHP1. This fragment was subsequently refined to yield M029, a covalent inhibitor characterized by low-micromolar potency, heightened selectivity, enhanced stability, and improved bioavailability. Notably, M029 targets a cryptic, non-conserved cysteine residue on SHP1, thereby illuminating novel avenues for future drug development focused on SHP1. This presented study also marked the first characterization of SHP1 pharmacology inhibition <i>in vivo</i> using M029 as a tool compound. Consistent to previous genetic studies, SHP1 inhibition was observed to markedly bolster anti-tumor efficacy, primarily through the activation of CD8+ T cells and NK cells, coupled with a reduction in T cell exhaustion. While no synergistic effects were noted in conjunction with anti-PD-1 treatment, M029 as a standalone therapy showcased more favorable responses compared to anti-PD-1 therapy alone, underscoring its potential for clinical application.</p><p dir="ltr">Meanwhile, we also demonstrated the effects of targeting both protein tyrosine phosphatase 1B (PTP1B), and T cell protein tyrosine phosphatase (TC-PTP) using proteolysis targeting chimeras (PROTACs). PROTACs are heterobifunctional small molecules comprising a targeted protein ligand, an E3 ligase ligand, and a linker. By recruiting an E3 ligase to the targeted proteins, PROTACs leverages the cell's ubiquitin-proteasome machinery to achieve selective target protein degradation. In contrast to traditional occupancy-based inhibitors, event-driven PROTACs show improved efficacy by promoting target protein degradation in a catalytic mode of action and greater selectivity through the obligatory formation of the target-PROTAC-E3 ternary complex, which is essential for efficient target degradation. Through optimizing the previously reported PROTAC DU-14, we acquired a cereblon (CRBN)-based PTP1B/TC-PTP dual targeting PROTAC X1 of higher bioavailability than DU-14. X1 showed enhanced efficacy than DU-14 in multiple cell lines and manifested anti-cancer efficacy <i>in vivo</i>. Additionally, employing X1 as a tool compound, we validated the anti-cancer potential of PTP1B/TC-PTP degradation in STAT3 dependent malignancies, such as non-Hodgkin’s lymphomas. Treatments with X1 or DU-14 effectively induced tumor cell apoptosis, whereas the dual inhibitor ABBV-CLS-484 failed to produce comparable outcomes.</p>

Computational methods, including homology modelling, in-silico dockings, and molecular dynamics simulations have been used to study the functional dynamics and interactions of K⁺ channels. Molecular models were built of the inwardly rectifying K⁺ channel Kir2.2, the bacterial homolog K⁺ channel KirBac3.1, and the twin pore (K2P) K⁺ channels TREK-1 and TRESK. To investigate the electrostatic energy profile of K⁺ permeating through these homology models, continuum electrostatic calculations were performed. The primary mechanism of KirBac3.1 gating is believed to involve an opening at the helix bundle crossing (HBC). However, simulations of Kir channels have not yet revealed opening at the HBC. Here, in simulations of the new KirBac3.1-S129R X-ray crystal structure, in which the HBC was trapped open by the S129R mutation in the inner pore-lining helix (TM2), the HBC was found to exhibit considerable mobility. In a simulation of the new KirBac3.1-S129R-S205L double mutant structure, if the S129R and the S205L mutations were converted back to the wild-type serine, the HBC would close faster than in the simulations of the KirBac3.1-S129R single mutant structure. The double mutant structure KirBac3.1-S129R-S205L therefore likely represents a higher-energy state than the single mutant KirBac3.1-S129R structure, and these simulations indicate a staged pathway of gating in KirBac channels. Molecular modelling and MD simulations of the Kir2.2 channel structure demonstrated that the HBC would tend to open if the C-linker between the transmembrane and cytoplasmic domain was modelled helical. The electrostatic energy barrier for K⁺ permeation at the helix bundle crossing was found to be sensitive to subtle structural changes in the C-linker. Charge neutralization or charge reversal of the PIP2-binding residue R186 on the C-linker decreased the electrostatic barrier for K⁺ permeation through the HBC, suggesting an electrostatic contribution to the PIP2-dependent gating mechanism. Multi-scale simulations determined the PIP2 binding site in Kir2.2, in good agreement with crystallographic predictions. A TREK-1 homology model was built, based on the TRAAK structure. Two PIP2 binding sites were found in this TREK-1 model, at the C-terminal end, in line with existing functional data, and between transmembrane helices TM2 and TM3. The TM2-TM3 site is in reasonably good agreement with electron density attributed to an acyl tail in a recently deposited TREK-2 structure.

The canonical Wnt signaling pathway is one of the most important pathways involved in cell proliferation and differentiation. It is highly conserved in evolution and participates not only in embryonic development but also in adult tissue homeostasis. In the intestine, Wnt signaling is closely connected to maintenance of intestinal stem cells and renewal of the epithelia. Conversely, aberrant activation of the Wnt signaling pathway underlies different types of human diseases. Its constitutive activation results in neoplasia and specifically in development of colorectal cancer, which is the third most common malignancy in western world. The aim of this thesis was to uncover various aspects of the regulatory mechanisms of the Wnt/β-catenin signaling cascade. Furthermore, I headed to find novel Wnt pathway modulators and confirm their function in vivo. The results are presented in four publications. The first study examines murine Wnt proteins processing and the sequential order of Wnt post-translational modifications which are required for the secretion and signaling activity of the ligands. Next publication focuses on the gene Troy, which we identified as negative regulator of Wnt signaling. TROY was discovered as a Wnt target gene during DNA microarray profiling of human colorectal cancer cells....

Trinucleotide repeat (TNR) instability including repeat expansions and repeat deletions is the cause of more than 40 inherited incurable neurodegenerative diseases and cancer. TNR instability is associated with DNA damage and base excision repair (BER). In this dissertation research, we explored the mechanisms of BER-mediated TNR instability via biochemical analysis of the BER protein activities, DNA structures, protein-protein interaction, and protein-DNA interaction by reconstructing BER in vitro using synthesized oligonucleotide TNR substrates and purified human proteins. First, we evaluated a germline DNA polymerase β (pol β) polymorphic variant, pol βR137Q, in leading TNR instability-mediated cancers or neurodegenerative diseases. We find that the pol βR137Q has slightly weaker DNA synthesis activity compared to that of wild-type (WT) pol β. Because of the similar abilities between pol βR137Q and WT pol β in bypassing a template loop structure, both pol βR137Q and WT pol β induces similar amount of repeat deletion. We conclude that the slightly weaker DNA synthesis activity of pol βR137Q does not alter the TNR instability compared to that of WT pol β, suggesting that the pol βR137Q carriers do not have an altered risk in developing TNR instability-mediated human diseases. We then investigated the role of DNA synthesis activities of DNA polymerases in modulating TNR instability. We find that pol βY265C and pol ν with very weak DNA synthesis activities predominantly promote TNR deletions. We identify that the sequences of TNRs may also affect DNA synthesis and alter the outcomes of TNR instability. By inhibiting the DNA synthesis activity of pol β using a pol β inhibitor, we find that the outcome of TNR instability is shifted toward repeat deletions. The results provide the direct evidence that DNA synthesis activity of DNA polymerases can be utilized as a potential therapeutic target for treating TNR expansion diseases. Finally, we explored the role of post-translational modification (PTM) of proliferating cell nuclear antigen (PCNA) on TNR instability. We find that ubiquitinated PCNA (ub-PCNA) stimulates Fanconi associated nuclease 1 (FAN1) 5’-3’ exonucleolytic activities directly on hairpin structures, coordinating flap endonuclease 1 (FEN1) in removing difficult secondary structures, thereby suppressing TNR expansions. The results suggest a role of mono-ubiquitination of PCNA in maintaining TNR stability by regulating nucleases switching. Our results suggest enzymatic activities of DNA polymerases and nucleases and the regulation of the activities by PTM play important roles in BER-mediated TNR instability. This research provides the molecular basis for future development of new therapeutic strategies for prevention and treatment of TNR-mediated neurodegenerative diseases.

This thesis deals with the device physics of organic solar cells. Organic photovoltaics (OPV) is a field of applied research which has been growing rapidly in the last decade leading to a current record value of power-conversion efficiency of 10 percent. One major reason for this boom is a potentially low-cost production of solar modules on flexible (polymer) substrate. Furthermore, new application are expected by flexible or semitransparent organic solar cells. That is why several OPV startup companies were launched in the last decade. Organic solar cells consist of hydrocarbon compounds, deposited as ultrathin layers (some tens of nm) on a substrate. Absorption of light leads to molecular excited states (excitons) which are strongly bound due to the weak interactions and low dielectric constant in a molecular solid. The excitons have to be split into positive and negative charges, which are subsequently collected at different electrodes. An effective dissociation of excitons is provided by a heterojunction of two molecules with different frontier orbital energies, such that the electron is transfered to the (electron) acceptor and the positive charge (hole) remains on the donor molecule. This junction can be realized by two distinct layers forming a planar heterojunction or by an intermixed film of donor and acceptor, resulting in a bulk heterojunction. Electrodes are attached to the absorber to collect the charges by providing an ohmic contact in the optimum case. This work focuses on the electrical processes in organic solar cells developing and employing a one-dimensional drift-diffusion model. The electrical model developed here is combined with an optical model and covers the diffusion of excitons, their separation, and the subsequent transport of charges. In contrast to inorganics, charge-carrier mobilities are low in the investigated materials and charge transport is strongly affected by energy barriers at the electrodes. The current-voltage characteristics (J-V curve) of a solar cell reflect the electrical processes in the device. Therefore, the J-V curve is selected as means of comparison between systematic series of simulation and experimental data. This mainly qualitative approach allows for an identification of dominating processes and provides microscopic explanations. One crucial issue, as already mentioned, is the contact between absorber layer and electrode. Energy barriers lead to a reduction of the power-conversion efficiency due to a decrease in the open-circuit voltage or the fill factor by S-shaped J-V curve (S-kink), which are often observed for organic solar cells. It is shown by a systematic study that the introduction of deliberate barriers for charge-carrier extraction and injection can cause such S-kinks. It is explained by simulated electrical-field profiles why also injection barriers lead to a reduction of the probability for charge-carrier extraction. A pile-up of charge carriers at an extraction barrier is confirmed by measurements of transient photocurrents. In flat heterojunction solar cells an additional reason for S-kinks is found in an imbalance of electron and hole mobilities. Due to the variety of reasons for S-kinks, methods and criteria for a distinction are proposed. These include J-V measurements at different temperatures and of samples with varied layer thicknesses. Most of the studies of this this work are based on experimental data of solar cells comprisiing the donor dye zinc phthalocyanine and the acceptor fullerene C60. It is observed that the open-circuit voltage of these devices depends on the mixing ratio of ZnPc:C60. A comparison of experimental and simulation data indicates that the reason is a changed donor-acceptor energy gap caused by a shift of the ionization potential of ZnPc. A spatial gradient in the mixing ratio of a bulk heterojunction is also investigated as a donor(acceptor)-rich mixture at the hole(electron)-collecting contact is supposed to assist charge extraction. This effect is not observed, but a reduction of charge-carrier losses at the “wrong” electrode which is seen at an increase in the open-circuit voltage. The most important intrinsic loss mechanism of a solar cell is bulk recombination which is treated at the example of ZnPc:C60 devices in the last part of this work. An examination of the dependence of the open-circuit voltage on illumination intensity shows that the dominating recombination mechanism shifts from trap-assisted to direct recombination for higher intensities. A variation of the absorption profile within the blend layer shows that the probability of charge-carrier extraction depends on the locus of charge-carrier generation. This results in a fill factor dependent on the absorption profile. The reason is an imbalance in charge-carrier mobilities which can be influenced by the mixing ratio. The work is completed by a simulation study of the influence of charge-carrier mobilities and different recombination processes on the J-V curve and an identification of a photoshunt dominating the experimental linear photocurrent-voltage characteristics in reverse bias. / Diese Dissertation beschäftigt sich mit der Physik organischer Solarzellen. Die organische Photovoltaik ist ein Forschungsgebiet, dem in den letzten zehn Jahren enorme Aufmerksamkeit zu Teil wurde. Der Grund liegt darin, dass diese neuartigen Solarzellen, deren aktueller Rekordwirkungsgrad bei 10 Prozent liegt, ein Potential für eine kostengünstige Produktion auf flexiblem (Polymer)substrat aufweisen und aufgrund ihrer Vielfältigkeit neue Anwendungsbereiche für die Photovoltaik erschließen. Organische Solarzellen bestehen aus ultradünnen (einige 10 nm) Schichten aus Kohlenwasserstoffverbindungen. Damit der photovoltaische Effekt genutzt werden kann, müssen die durch Licht angeregten Molekülzustände zu freien Ladungsträgern führen, wobei positive und negative Ladung an unterschiedlichen Kontakten extrahiert werden. Für eine effektive Trennung dieser stark gebundenden lokalisierten angeregten Zustände (Exzitonen) ist eine Grenzfläche zwischen Molekülen mit unterschiedlichen Energieniveaus der Grenzorbitale erforderlich, sodass ein Elektron auf einem Akzeptor- und eine positive Ladung auf einem Donatormolekül entstehen. Diese Grenzschicht kann als planarer Heteroübergang durch zwei getrennte Schichten oder als Volumen-Heteroübergang in einer Mischschicht realisiert werden. Die Absorberschichten werden durch Elektroden kontaktiert, wobei es für effiziente Solarzellen erforderlich ist, dass diese einen ohmschen Kontakt ausbilden, da ansonsten Verluste zu erwarten sind. Diese Arbeit behandelt im Besonderen die elektrischen Prozesse einer organischen Solarzelle. Dafür wird ein eindimensionales Drift-Diffusionsmodell entwickelt, das den Transport von Exzitonen, deren Trennung an einer Grenzfläche und die Ladungsträgerdynamik beschreibt. Abgesehen von den Exzitonen gilt als weitere Besonderheit einer organischen Solarzelle, dass sie aus amorphen, intrinsischen und sehr schlecht leitfähigen Absorberschichten besteht. Elektrische Effekte sind an der Strom-Spannungskennlinie (I-U ) sichtbar, die in dieser Arbeit als Hauptvergleichspunkt zwischen experimentellen Solarzellendaten und den Simulationsergebnissen dient. Durch einen weitgehend qualitativen Vergleich können dominierende Prozesse bestimmt und mikroskopische Erklärungen gefunden werden. Ein wichtiger Punkt ist der schon erwähnte Kontakt zwischen Absorberschicht und Elektrode. Dort auftretende Energiebarrieren führen zu einem Einbruch im Solarzellenwirkungsgrad, der sich durch eine Verringerung der Leerlaufspanung und/oder S-förmigen Kennlinien (S-Knick) bemerkbar macht. Anhand einer systematischen Studie der Grenzfläche Lochleiter/Donator wird gezeigt, dass Energiebarrieren sowohl für die Ladungsträgerextraktion als auch für die -injektion zu S-Knicken führen können. Insbesondere die Tatsache, dass Injektionsbarrieren sich auch negativ auf den Photostrom auswirken, wird anhand von simulierten Ladungsträger- und elektrischen Feldprofilen erklärt. Das Aufstauen von Ladungsträgern an Extraktionsbarrieren wird durch Messungen transienter Photoströme bestätigt. Da S-Knicke in organischen Solarzellen im Allgemeinen häufig beobachtet werden, werden weitere Methoden vorgeschlagen, die die Identifikation der Ursachen ermöglichen. Dazu zählen I-U Messungen in Abhängigkeit von Temperatur und Schichtdicken. Als eine weitere Ursache von S-Knicken werden unausgeglichene Ladungsträgerbeweglichkeiten in einer Solarzelle mit flachem Übergang identifiziert und von den Barrierefällen unterschieden. Weiterer Forschungsgegenstand dieser Arbeit sind Mischschichtsolarzellen aus dem Donator-Farbstoff Zink-Phthalozyanin ZnPc und dem Akzeptor Fulleren C60. Dort wird beobachtet, dass die Leerlaufspannung vom Mischverhältnis abhängt. Ein Vergleich von Experiment und Simulation zeigt, dass sich das Ionisationspotenzial von ZnPc und dadurch die effektive Energielücke des Mischsystems ändern. Zusätzlich zu homogenen Mischschichten werden Solarzellen untersucht, die einen Gradienten im Mischungsverhältnis aufweisen. Die Vermutung liegt nahe, dass ein hoher Donatorgehalt am Löcherkontakt und ein hoher Akzeptorgehalt nahe des Elektronenkontakts die Ladungsträgerextraktion begünstigen. Dieser Effekt ist in dem hier untersuchten System allerdings vergleichsweise irrelevant gegenüber der Tatsache, dass der Gradient das Abfließen bzw. die Rekombination von Ladungsträgern am “falschen” Kontakt reduziert und somit die Leerlaufspannung erhöht. Der wichtigste intrinsische Verlustmechanismus einer Solarzelle ist die Rekombination von Ladungsträgern. Diese wird im letzten Teil der Arbeit anhand der ZnPc:C60 Solarzelle behandelt. Messungen der Leerlaufspannung in Abhängigkeit von der Beleuchtungsintensität zeigen, dass sich der dominierende Rekombinationsprozess mit zunehmender Intensität von Störstellenrekombination zu direkter Rekombination von freien Ladungsträgern verschiebt. Eine gezielte Variation des Absorptionsprofils in der Absorberschicht zeigt, dass die Ladungsträgerextraktionswahrscheinlickeit vom Ort der Ladungsträgergeneration abhängt. Dieser Effekt wird hervorgerufen durch unausgeglichene Elektronen- und Löcherbeweglichkeiten und äußert sich im Füllfaktor. Weitere Simulationsergebnisse bezüglich des Einflusses von Ladungsträgerbeweglichkeiten und verschiedener Rekombinationsmechanismen auf die I-U Kennlinie und die experimentelle Identifikation eines Photoshunts, der den Photostrom in Rückwärtsrichtung unter Beleuchtung dominiert, runden die Arbeit ab.

Les biothérapies (anticorps monoclonaux, récepteurs solubles) ciblant les cytokines IL-6 etTNF-alpha pour le traitement des maladies inflammatoires chroniques ont constitué un succèsmajeur de l’industrie pharmaceutique. Elles présentent néanmoins des inconvénientsimportants : résistances, mode d’administration contraignant, coût élevé.Notre équipe travaille sur l’identification de petites molécules inhibant directement cescytokines, afin d’élargir l’offre thérapeutique existante. Administrées par voie orale, ellesconstitueraient une alternative particluièrement favorable aux patients.Durant ma thèse, j’ai réalisé le criblage expérimental (tests cellulaires et tests biochimiquesde liaison) des meilleurs composés identifiés par criblage virtuel d’un grande chimiothèque dediversité, ainsi que de composés dérivés de pyridazine issus d’une chimiothèque médicinale. J’aiainsi pu identifier plusieurs inhibiteurs directs du TNF-alpha et de l’IL-6. De plus, mon travail apermis d’affiner les procédures de criblage du Laboratoire.Ces travaux ouvrent de nouvelles pistes pour le développement de médicaments anti-cytokines. / Anti-cytokine biologics (monoclonal antibodies, soluble receptors) targeting TNF-alpha and IL-6in chronic inflammatory diseases have been a major success for pharmaceutical industry.However, they exhibit several drawbacks : resistance, difficult administration, high costs.Our team works on the discovery of small molecule inhibitors of cytokines suck as TNF-alphaand IL-6, in order to widen the range of therapeutic drugs. Orally active drugs would represent ahighly beneficial alternative for patients.During my PhD, I have performed an experimental screening (using cellular and biochemicalbinding testings) of the best compounds identified through virtual screening of a large chemicallibrary, and on pyridazine compounds of a medicinal chemical library. I have been able toidentify several small molecules inhibiting the interaction of TNF-! and IL-6 with their receptor.Moreover, my work will have an impact on the laboratory screening strategies.Overall, this work opens new avenues for anti-cytokine drug discovery.

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