Antibiotic resistance has been a developing problem for mankind in recent decades and multi-drug resistant bacteria are now encountered that are resistant to all treatment options available. In 2014, the World Health Organization announced that this problem is driving us towards a “post-antibiotic era” that will change the face of modern medicine as we know it. If lack of novel antibiotic development and FDA approval continues, by the year 2050, 10 million people will die each year to an antimicrobial resistant bacterial infection. With lack of pharmaceutical industry involvement in developing novel antibiotics, the responsibility now lies within the academic institutions to identify potential novel therapeutics to fuel the antibiotic drug discovery pipeline. Combinatorial chemistry is one technique used to expedite the discovery process by assessing a large chemical space in a relatively short time when compared to traditional screening approaches. Combinatorial libraries can be screened using multiple approaches and has shown successful application towards many disease states. We initially discovered broad spectrum antibacterial bis-cyclic guanidines using combinatorial libraries and expanded on the knowledge of the physiochemical attributes necessary to inhibit Gram negative bacterial pathogens. Following this success, we continued to assess the combinatorial libraries for adjunctive therapeutics that potentiate the activity of obsolete clinical antibiotics. The polyamine efflux pump inhibitors discovered in this subsequent study prove the benefits of using the large chemical space provided in the combinatorial libraries to identify a variety of therapeutics. Our studies always begin with identifying an active compound and active compounds undergo hit-to-lead optimization. This optimization studies are of utmost importance in developing a novel antibacterial agent for therapeutic applications. Our medicinal chemistry work described here is proof of the success of careful structure activity analyses to optimize a hit scaffold to create a more effective antibacterial agent. Overall, our work described here reveals the potential role of academic institutions in fending off the impending “post-antibiotic era”.

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Accurate, timely replication of a DNA molecule is a pivotal moment in the life cycle of every living organism. Any temporal or spatial defect putting the fine-tuned replication machinery off balance causes the so-called replication stress. As the replication machinery consists mainly of enzymes and other proteins, it is not surprising that many of the obstacles most severely blocking the replication machinery progress are of protein origin. Therefore, specialized proteases responsible for relieving replication stress matured during evolution. However, neither the full repertoire of proteolytic enzymes and their particular substrates taking place in countering the DNA replication stress nor detailed molecular mechanisms involved remain unknown. This thesis describes how conserved putative aspartic proteases of the Ddi1-like family engage in countering DNA replication stress via a proteolysis dependent mechanism. We structurally and biophysically characterized yeast and human members of the Ddi1-like family, explored their interactions with ubiquitin and polyubiquitin chains, and identified hypersensitivity to DNA replication inhibitor hydroxyurea in a yeast strain double deleted for DDI1 gene together with a DNA dependent metalloprotease WSS1. Detailed analysis of the DDI1 role in hydroxyurea...

RNA is essential for the transfer of genetic information, as the central dogma of biology dictates. The role of RNA, however, is not limited to serving as an information shuttle between DNA and fully functional protein. Indeed, RNA has experienced a surge of interest in the field of chemical biology for its other critical roles in biology including those in control of transcription, translation, splicing, genetic replication, and catalysis. RNA has proven to be a difficult and complex target for the design of small molecular ligands because of its structural heterogeneity and conformational flexibility. Yet, the highly folded tertiary structures of these oligomers present unique scaffolds which designed ligands should be able to selectively target. To that end, two branched peptide libraries ranging in size from 4,096–46,656 unique sequences were screened for their ability to bind HIV-1 related RNA structures, the transactivation response element (TAR) and the Rev response element (RRE). In addition to discovering a mid-nanomolar branched peptide ligand for TAR, the first branched boronic acid peptide library designed to target RNA was screened for binding to RRE. Each of these efforts resulted in the identification of selective binders to their respective RNA targets, and the unnatural branching of these compounds was demonstrated to provide a multivalent binding interaction with the RNA. Furthermore, these compounds were shown to be cell permeable and displayed little to no cytotoxicity in HeLa and A2780 cells. / Ph. D.

Les travaux réalisées lors de cette thèse s'intéressent aux dynamiques de mouvement, de réaction et de constitution des fonctions imines. Les aldéhydes les plus réactives pour cette réaction de condensation ont été identifiées. Un processus d'échange intramoléculaire aléatoire rapide a été observé entre le salicylaldéhyde et l'éthylènediamine dont la vitesse est contrôlée par les substituants, la longueur de la chaîne amine, le solvant et la température. Cette observation conduità l'élaboration de mouvements de déplacement d'abord non-directionnels puis développés pour devenir directionnels. Une sélectivité dynamique réactionnelle a été introduite sur des mélanges d'aldéhydes et d'amines. Elle a été baptisée simpléxité et est utilisée pour de la protection de fonctions. Enfin, la nature dynamique de l'imine a été étudiée à l'interface solide-liquide parmicroscopie à effet tunnel et montre une accélération et une amplification des produits formées sur la surface. / This thesis reports on the intertwined motional, reactional and constitutional dynamics of imines. It goes from acquiring the basic data about the reaction to applications in various fields of Chemistry. The most reactive aldehydes for the reaction were identified and their reactivities were explained by physical-organic chemistry methods. An intramolecular motion was observed for simple diamines. This observation led to introduction of a non-directional small molecule walking, and eventually to development of a directional walker. A representation of dynamic combinatorial libraries was proposed and then was used for analysis of aldehyde-amine libraries, which exhibit selective amplification of a given species due to the complexity of its composition. This phenomenon was called simplexity. The simplexity example was then used as a concept for dynamic selective protecting groups in acylation of amines. Also, the dynamic imine linkage was also studied on the solid-liquid interface. It was found that the reactions taking place at the graphite surface are largely accelerated and that the formation of the largest molecules is amplified due to the surface.

Photoschalter sind Moleküle, die eine reversible lichtgesteuerte Umwandlung zwischen zwei Zuständen mit unterschiedlichen Eigenschaften durchlaufen. In den letzten zehn Jahren hat der Einbau dieser photochromen Moleküle in intelligente, auf Stimuli ansprechende Materialien zunehmende Aufmerksamkeit erregt, da sie die einzigartige Fähigkeit bieten, makroskopische Eigenschaften mit einem externen optischen Stimulus reversibel zu verstärken und zu verändern. Die begrenzte Leistung von Photoschaltern in festen Medien bleibt eine Herausforderung. In diesem Zusammenhang werden in dieser Arbeit zwei wichtige Aspekte näher untersucht. Erstens der Prozess der Entwicklung neuer Photoschalter mit maßgeschneiderten Eigenschaften und zweitens die Implementierung von Photoschaltern in feste Materialien und die damit verbundenen Herausforderungen. Im ersten Teil dieser Arbeit wurde Dynamisch-kovalente Chemie (DCC) verwendet, um die Entdeckung und Entwicklung einer neuartigen Klasse von Photoschaltern mit drei Zuständen zu beschleunigen. Die dynamische Natur der zentralen Doppelbindung von α-Cyanodiarylethenen wurde genutzt, um ein thermodynamisches Gleichgewicht mit anderen Arylacetonitrilen herzustellen. Die entwickelte Methode kombiniert eine schnelle Diversifizierung mit einer Rasterung auf spezifische Eigenschaften, die durch einen externen Stimulus aufgedeckt werden, und ermöglicht die effiziente Untersuchung der Beziehung zwischen Struktur und den zugehörigen Eigenschaften. Im zweiten Teil der Arbeit wird die Entwicklung und die Synthese eines Zweikomponenten-Kern-Schale-MOFs mit einem internen nicht-funktionalisierten Kompartiment, das von einer dünnen photoschaltbaren Außenschale bedeckt ist, vorgestellt. Diese Strategie ermöglicht ein effizientes Schalten des Chromophors und die resultierende dünne „intelligente“ Schale fungiert als modulare kinetische Barriere für die molekulare Gastdiffusion in das Material, die durch Licht gesteuert werden kann. / Photoswitches are molecules that undergo a reversible light-triggered conversion between two states with different properties. In the past decade, the incorporation of these photochromic molecules in smart stimuli-responsive materials has gained increased attention as it offers the unique ability to reversibly amplify and change macroscopic properties with an external optical stimulus. The limited performance of photoswitches in solid mediums remains a challenge. In this context two important aspects are studied in more detail in this thesis. First, the process of developing new photoswitches with tailored properties and second, the implementation of photoswitches in solid materials and the challenges associated with it. In the first part of this thesis dynamic covalent chemistry (DCC) was used to accelerate the discovery and development of a novel three-state photoswitch class. The dynamic nature of the central double bond of α-cyanodiarylethenes was exploited to establish a thermodynamic equilibrium with other arylacetonitriles. The developed DCC tool combines fast and efficient diversification with screening for specific photochemical properties revealed by an external stimulus, enabling the rapid study of the relationship between structure and the associated properties. The second part of this thesis summarizes the design and synthesis of a two-component core-shell MOF with an internal non-functionalized compartment covered by a thin photoswitchable outer shell. This strategy allows efficient switching of the chromophore and the resulting thin “smart” shell acts as a modular kinetic barrier for molecular guest diffusion into the material that can be controlled by light.