Functional Dendritic Structures from Bile Acids: Supramolelcular Hosts, Light Harvesters and Drug Carriers Chapter 1. An Overview of Functional Dendrimers. Dendrimers are welldefined, hyperbranched macromolecules that are prepared by highly controlled iterative methodologies. The ability to modulate the size, molecular weight, chemical functionalities and the position and number of functional groups in dendrimers make them promising candidates for a wide variety of applications. In this chapter, three areas 1) hostguest chemistry 2) light harvesting and 3) drug delivery, where dendrimers are increasingly finding applications, are discussed with selected examples. Chapter 2. Hydroxyl Terminated Dendritic Oligomers from Bile Acids: Synthesis and Properties. Bile acids are excellent building blocks for dendritic construction because of their many interesting features. They are readily available, chiral, facial amphiphiles with complementary functionalities. Moreover, due to the large size of the bile acid units, a dendritic structure consisting of only a few such repeat units can have an extended structure with multiple functionalizable groups. (figure 1) The high reactivity of the chloroacetyl group has been exploited for the synthesis of bile acid based first and second-generation dendrons with glycolate linkers and multiple hydroxyl groups. The synthesis involves only a few steps and avoids the use of protecting groups for the terminal hydroxyl groups. The synthesis of a bile acid tetramer is shown here as an example (Figure 1). Carboxyl protected cholic acid was reacted with chloroacetylchloride to generate the trischloroacetylated derivative. This compound on reaction with excess of sodium cholate generated the tetramer with nine hydroxyl groups via displacement of the chlorides. In order to synthesize higher generation dendritic structures, perchloroacetylated firstgeneration dendrons were first synthesized. These were subsequently reacted with excess of sodium deoxcholate to generated secondgeneration dendrons with multiple hydroxyl groups (Figure 2). All the compounds were characterized by H NMR, C NMR, IR, ESIMS/MALDI-TOF, HPLC and elemental analysis(wherever possible) Figure 2. Structure of tridecamer. These dendritic structures with facially amphiphilic bile acid backbones on the periphery were able to solubilize cresol red, a hydrophilic dye, in a nonpolar solvent, thus exhibiting reverse micellar characteristics. Chapter 3. Multiple Naproxen Appended Bile Acid Dendrimers as Light Harvesters and Drug Carriers. Part I. Synthesis and Characterization. Using the same synthetic strategy as in Chapter 2, bile acid based dendritic structures appended with multiple bioactive (S)naproxens were generated as potential drug carriers. The construction of these dendrimers was accomplished using per(chloroacetylated) bile acid dendrons and conveniently displacing all the chlorides with naproxen units. Since naproxen is photoactive with a high fluorescence quantum Figure 3. Structures of secondgeneration dendrimers and a monomer with multiple naproxens. yield, the photophysical properties of these multichromophoric dendrimers could be further explored (Figure 3). By functionalizing the carboxyl group on the side chain with an anthracenyl moiety the energy transfer properties of these dendrimers could be studied. In this section the synthesis of first and secondgeneration dendritic structures with multiple naproxen units at the periphery and benzyl/anthracenyl moiety on the side chain are described (Figure 3). Model compounds using monomeric bile acid units were synthesized for comparison with the dendritic structures. All the compounds were characterized by H NMR, C NMR, IR, ESIMS/MALDITOF, HPLC and elemental analysis (wherever possible). Part II: Absorption, Fluorescence and Intramolelcular Energy Tranfer Studies. Absorption studies showed that the molar extinction coefficients increase linearly with increasing number of naproxen units and the absorption spectra of anthracenyl moiety remain unchanged in all the dendritic systems. These indicated the absence of ground state interaction between the chromophores. In the 275-290 nm absorption region, the molar extinction coefficient of naproxen is much greater than that of the 9-anthracenylmethyl chromophore. Hence excitation in this region would mainly excite the naphthalene chromophore. Upon excitation at 275 nm, there was predominant emission from the anthracenyl moiety in the dendritic structures (containing both chromophores) and the fluorescence intensity increased with increasing number of naproxens(Figure4). This indicated that the dendrimers act as efficient light harvesters with energy transfer from naproxen to anthracene (intramolecular nature of the energy transfer was confirmed through control experiments). (Figure 4: Refer PDF File) The fluorescence and energy-transfer properties were further investigated by time-resolved fluorescence spectroscopy. The presence of fast decay component(s) in the naproxen decay in dendritic structures (containing both chromophores) indicates that its fluorescence is quenched in the presence of anthracene due to energy transfer ((λex 275 nm, λem 350 nm (Figure 5). This was further confirmed by monitoring the fluorescence of the sensitized anthracenyl chromophore (λex 275 nm, λem 436 nm) which exhibited a fast rise comparable to he quenched naproxen lifetime(s). The efficiency of energy transfer was estimated by donor quenching by both steadystate and timeresolved techniques. The dendritic structures exhibited high energy transfer efficiencies (~ 70 – 90 %) with the net efficiency decreasing from the first to second-generation. Part III. In vitro Study of Hydrolysis of Naproxen Appended Bile Acid Prodrugs by Chemical and Enzymatic Methods. The naproxen appended bile acid dendrimers consist of hydrolyzable ester and glycolate linkers. Hence the chemical stability and enzymatic degradation with possible release of naproxen was studied. Two compounds, monomer appended with two naproxens and trimer with four naproxens have been used for the initial investigations (Figure 6). The compounds were found to be highly stable towards chemical hydrolysis and did not show any hydrolysis in phosphate buffer, pH = 7.4 even after 7 days. Since the compounds were not soluble in water, Arabic gum and TritonX were used for emulsification. Figure 6. Structures of monomer and trimer. (Refer PDF File) The enzymatic hydrolysis of the compounds was then studied using Candida Rugosa Lipase. In both cases, there was slow hydrolysis of the substrate and intermediates were formed (with release of free naproxen) which were detected by HPLC (reverse phase column with a UV detector). The trimer underwent much slower hydrolysis compared to the monomer. The intermediates were characterized by absorption and mass (ESIMSQTOF) spectrometry.

Part I of this thesis describes the development of bioactive small molecules of relevance to the study of the apicomlexan parasite Toxoplasma gondii into useful chemical tools. The research includes the target identification and validation studies, using both chemical and biological methods. Chapter 1 provides an overview of chemical genetics with a particular emphasis on methods for the identification of the protein targets of bioactive small molecules. The concept of biochemical protein target identification techniques was introduced with a detailed discussion of interesting applications from the literature. Chapter 2 focuses on the development of a tetrahydro-β-carboline based lead molecule into a chemical tool through target identification studies. The structure activity relationship (SAR) data associated with this core structure, the design of a chemical inducer of dimerisation (CID) and the synthesis of this CID are discussed in detail. Chapter 3 described work done to identify the potential protein target(s) of Conoidin A. Experiments to assess whether Conoidin A can inhibit a proposed target in vitro are also included. Further optimisation of this structural class to develop more potent inhibitors is discussed in the second part of this chapter. Part II of this thesis describes the development of methods for the synthesis of medium-sized ring containing compounds using oxidative fragmentation and rearrangement strategies. Chapter 5 provides an overview of the existing oxidative fragmentation methodology, with an emphasis on the use of oxidative fragmentation reactions for the synthesis of medium-sized ring systems (8-11 ring atoms). Chapter 6 focuses on using the established oxidative fragmentation method in the oxizino carbazolone system to investigate the diasteroselectivity of this reaction. Possible mechanisms for this transformation are investigated and discussed using both chemical and computational methods. An interesting rearrangement reaction has also been observed during this study. Chapter 7 focuses on developing an asymmetric oxidative fragmentation method, for use in the diazabenz[e]aceathrylenes system. Asymmetric oxidative fragmentation reactions using [Ru(pybox)(pydic)] catalysts are discussed. Attempts to optimise the enantiomeric excesses of the reaction by varying reaction conditions and substituents in the substrate are also included.

Rheumatoid arthritis (RA) is an autoimmune inflammatory disease that leads to degradation of cartilage and bone mainly in peripheral joints. In collagen-induced arthritis (CIA), a mouse model for RA, activation of autoimmune CD4+ T cells depends on a molecular recognition system where T-cell receptors (TCRs) recognize a complex between the class II MHC Aq protein and CII259-273, a glycopeptide epitope from type II collagen (CII). Interestingly, vaccination with the Aq/CII259-273 complex can relieve symptoms and cause disease regression in mice. This thesis describes the use of modified glycopeptides to explore interactions important for binding to the Aq protein and recognition by autoimmune T-cell hybridomas obtained from mice with CIA. The CII259-273 glycopeptide was modified by replacement of backbone amides with different amide bond isosteres, as well as substitution of two residues that anchor the glycopeptide in prominent pockets in the Aq binding site. A three-dimensional structure of the Aq/glycopeptide complex was modeled to provide a structural basis for interpretation of the modified glycopeptide’s immunological activities. Overall, it was found that the amide bond isosteres affected Aq binding more than could be explained by the static model of the Aq/glycopeptide complex. Molecular dynamics (MD) simulations, however, revealed that the introduced amide bond isosteres substantially altered the hydrogen-bonding network formed between the N-terminal 259-265 backbone sequence of CII259-273 and Aq. These results indicated that the N-terminal hydrogen-bonding interactions follow a cooperative model, where the strength and presence of individual hydrogen bonds depended on the neighboring interactions. The two important anchor residues Ile260 and Phe263 were investigated using a designed library of CII259-273 based glycopeptides with substitutions by different (non-)natural amino acids at positions 260 and 263. Evaluation of binding to the Aq protein showed that there was scope for improvement in position 263 while Ile was preferred in position 260. The obtained SAR understanding provided a valuable basis for future development of modified glycopeptides with improved Aq binding. Furthermore, the modified glycopeptides elicited varying T-cell responses that generally could be correlated to their ability to bind to Aq. However, in several cases, there was a lack of correlation between Aq binding and T-cell recognition, which indicated that the interactions with the TCRs were determined by other factors, such as presentation of altered epitopes and changes in the kinetics of the TCR’s interaction with the Aq/glycopeptide complex. Several of the modified glycopeptides were also found to bind well to the human RA-associated DR4 protein and elicit strong responses with T-cell hybridomas obtained from transgenic mice expressing DR4 and the human CD4 co-receptor. This encourages future investigations of modified glycopeptides that can be used to further probe the MHC/glycopeptide/TCR recognition system and that also constitute potential therapeutic vaccines for treatment of RA. As a step towards this goal, three modified glycopeptides presented in this thesis have been identified as candidates for vaccination studies using the CIA mouse model.

New strategies are needed to counter the growing problem of bacterial resistance to antibiotics. One such strategy is to design compounds that target bacterial virulence, which could work separately or in concert with conventional bacteriostatic or bactericidal antibiotics. Pilicides are a class of compounds based on a ring-fused 2-pyridone scaffold that target bacterial virulence by blocking the chaperone/usher pathway in E. coli and thereby inhibit the assembly of pili. This thesis describes the design, synthesis, and biological evaluation of compounds based on the pilicide scaffold with the goal of improving the pilicides and expanding their utility. Synthetic pathways have been developed to enable the introduction of substituents at the C-2 position of the pilicide scaffold. Biological evaluation of these compounds demonstrated that some C-2 substituents give rise to significant increases in potency. X-ray crystallography was used to elucidate the structural basis of this improved biological activity. Furthermore, improved methods for the preparation of oxygen-analogues and C-7 substituted derivatives of the pilicide scaffold have been developed. These new methods were used in combination with existing strategies to decorate the pilicide scaffold as part of a multivariate design approach to improve the pilicides and generate structure activity relationships (SARs). Fluorescent pilicides were prepared using a strategy where selected substituents were replaced with fluorophores having similar physicochemical properties as the original substituents. Many of the synthesized fluorescent compounds displayed potent pilicide activities and can thus be used to study the complex interactions between pilicide and bacteria. For example, when E. coli was treated with fluorescent pilicides, it was found that the compounds were not uniformly distributed throughout the bacterial population, suggesting that the compounds are primarily associated to bacteria with specific properties. Finally, by studying compounds designed to inhibit the aggregation of Aβ, it was found that some compounds based on the pilicide scaffold inhibit the formation of the functional bacterial amyloid fibers known as curli; these compounds are referred to as 'curlicides'. Some of the curlicides also prevent the formation of pili and thus exhibit dual pilicide-curlicide activity. The potential utility of such 'dual-action' compounds was highlighted by a study of one of the more potent dual pilicide-curlicides in a murine UTI model were the compound was found to significantly attenuate virulence in vivo.

My PhD study 'Educational application of models of complex biochemical processes' discusses the possibility of integrating simple bioorganic teaching experiments, modelling complex biochemical processes in living systems into a curriculum of secondary schools, and universities, and even elementary schools in some cases. The aim of these experiments is simplified, but illustrative and appropriate for approaching complex problems of biochemical processes in a transparent experiment, running in spite of conditions comparable to real natural clauses in a living system. The theoretical part is divided into three thematic circuits: biochemistry and bioorganic chemistry, bioorganic models and their characteristics and selected specific forms of applying bioorganic models into teaching chemistry. The next part dealing with bioorganic models and their characteristics is further divided on the base of some specific models. These are consisted of models of enzymes and their catalytic activity, models of biochemical reactions and antidotal and toxic substances affecting life-forms and their carcinogenic efficiency. The practical part contains methodic treatment of six selected models that demonstrate specific biochemical processes or structure of complex organic compounds. These models include modeling biuret...

Indiana University-Purdue University Indianapolis (IUPUI) / Spore photoproduct lyase (SPL) is a radical SAM (S-adenosylmethionine) enzyme that is responsible for the repair of the DNA UV damage product 5-thyminyl-5,6-dihydrothymine (also called spore photoproduct, SP) in the early germination phase of bacterial endospores. SPL initiates the SP repair process using 5'-dA• (5'-deoxyadenosyl radical) generated by SAM cleavage to abstract the H6proR atom which results in a thymine allylic radical. These studies provide strong evidence that the TpT radical likely receives an H atom from an intrinsic H atom donor, C141 in B. subtilis SPL. I have shown that C141 can be alkylated in native SPL by iodoacetamide treatment indicating that it is accessible to the TpT radical. Activity studies demonstrate a 3-fold slower repair rate of SP by C141A which produces TpTSO2 - and TpT simultaneously with no lag phase observed for TpTSO2- formation. Additionally, formation of both products shows a Dvmax kinetic isotope effect (KIE) of 1.7 ± 0.2 which is smaller than the DVmax KIE of 2.8 ± 0.3 for the WT SPL reaction. Removal of the intrinsic H atom donor by this single mutation disrupts the rate-limiting process in the enzyme catalysis. Moreover, C141A exhibits ~0.4 turnover compared to the > 5 turnovers in the WT SPL reaction. In Y97 and Y99 studies, structural and biochemical data suggest that these two tyrosine residues are also crucial in enzyme catalysis. It is suggested that Y99 in B. subtilis SPL uses a novel hydrogen atom transfer pathway utilizing a pair of cysteinetyrosine residues to regenerate SAM. The second tyrosine, Y97, structurally assists in SAM binding and may also contribute to SAM regeneration by interacting with radical intermediates to lower the energy barrier for the second H-abstraction step.

Die Entwicklung von enzymfreien, isothermen Nachweisverfahren für Nukleinsäuren, die mit der PCR konkurrieren können, ist seit langem ein Ziel. Eine potenzielle Strategie besteht darin, Nukleinsäure-templierte Reaktionen zu verwenden, bei denen das Templat (Analyt) als Katalysator fungiert und das Signal verstärkt. Die derzeitig verwendeten Strategien, wie Ligations- oder Transferreaktionen, sind jedoch in ihrer Empfindlichkeit aufgrund des Effekts der Produktinhibierung begrenzt. Um dies zu überwinden, müssen die Reaktanten nicht nur sequenzspezifisch an die DNA oder RNA binden, sondern die Produkte müssen sich auch von der DNA oder RNA wieder lösen können. Diese Arbeit stellt ein neues Paradigma für Nukleinsäure templierte Reaktionen vor: Das Loss-of-Affinity Prinzip. In diesem Prinzip werden Produkte generiert, die eine geringere Affinität zum Templat aufweisen als die Reaktanten. Dadurch wird die Produktinhibierung verhindert. Im ersten Teil dieser Arbeit wurde das Loss-of-Affinity Prinzip mit triplexbildenden, spaltbaren bis-PNA Sonden untersucht. Diese erfuhren eine C-O-Bindungsspaltung, ausgelöst durch die katalytische Photoreduktion eines Rutheniumkomplexes. Nach mehreren Optimierungsrunden zeigte eine 10-mer bis-PNA Sonde eine beeindruckende katalytische Effizienz. Diese Ergebnisse zeigen, dass das Loss-of-Affinity Prinzip zur Überwindung der Produktinhibierung genutzt werden kann. Die verwendeten bis-PNAs zeigten jedoch eine stark unspezifische Bindung. Im zweiten Teil dieser Arbeit wurden die bis-PNA Sonden gegen PNA- und GPNA-Spermin Sonden ausgetauscht, um das Problem der unspezifischen Bindung zu überwinden. Die PNA- und GPNA Spermin Sonden zeigten die wahrscheinlich effizientesten, bisher bekannten Nukleinsäure templierten Reaktionen, welchee die meisten natürlichen Enzyme übertrafen. Darüber hinaus zeigten sie eine ausgezeichnete Sequenzspezifität. / Developing enzyme-free isothermal detection methods of nucleic acids that can challenge PCR has been a long-standing goal. One potential strategy revolves around nucleic acid-templated reactions, in which the template (analyte) can act as a catalyst and amplify the signal. However, current strategies such as ligation reactions or functional group interconversions are plagued by product inhibition, which limits the sensitivity. To overcome this, the reactants must not only bind to DNA or RNA in a sequence-specific manner, but the products must also be able to detach from the DNA or RNA. This work introduces a new paradigm to nucleic acid-templated reactions, the loss-of-affinity principle, which yields products that have a lower template affinity than the reactants. This prevents product inhibition. In the first part of this work, the loss-of-affinity principle was explored with triplex-forming immolative bis-PNA probes that underwent a C-O bond cleavage upon catalytic photoreduction using a ruthenium complex. After several rounds of optimization, a 10-mer bis-PNA demonstrated an impressive catalytic efficiency. These results demonstrate that the loss-of-affinity principle can be used to overcome product inhibition. However, the bis-PNAs demonstrated highly non-specific binding. In the second part of this work, the bis-PNAs were replaced with PNA- and GPNA-spermine probes to address the issue of non-specific binding. The PNA- and GPNA-spermine probes exhibited probably the most efficient nucleic acid-templated reactions to date, outperforming most natural enzymes. In addition, they demonstrated excellent sequence specificity.

To study the functions of glycoconjugates in biological systems reliable and efficient protocols for glycoconjugate synthesis are needed. To reach this goal we have developed methods for solid-phase synthesis of glycoconjugates that can be monitored with gel-phase 19F spectroscopy using fluorinated linkers, building blocks, and protecting groups. We have developed a new fluorine containing linker suitable for solid-phase synthesis of glycoconjugates. The linker was more acid-labile than similar linkers in order to enable cleavage under mild conditions of the target compound from the linker resin.  A carbamate-based strategy has been applied to attach a spacer carrying an amino group to a fluorinated Wang linker for synthesis of amino-functionalized glycoconjugates using thioglycoside donors with fluorinated protective groups. Cleavage from the solid support was performed with trifluoroacetic acid and subsequent protecting group removal gave the target compound. The terminal amine was conjugated with didecyl squarate and this derivative can be attached to various proteins and solid surfaces carrying primary or secondary amines. To evaluate this methodology we have immobilized glycoconjugates in amino-functionalized microtiter plates and successfully probed them with lectin. In addition, a novel fluorine containing protecting group has been designed, synthesized and evaluated. The protecting group was used for protection of the unreactive 4-OH in a galactose building block that was applied in the synthesis of 6-aminohexyl galabioside and was removed with TBAF in THF. Adenovirus serotype 8 (Ad8), Ad19, and Ad37 cause the severe ocular infection, epidemic keratoconjunctivities (EKC). During infection, the adenoviruses interact with sialic acid containing glycoconjugates on the epithelial cells via fiber structures extending from the viral particles. The virus particle most likely binds to the host cell in a multivalent way by simultaneously using multiple fiber proteins and binding sites. Multivalent sialic acid containing conjugates could efficiently inhibit Ad37 cell attachment and subsequent infection of human corneal epithelial (HCE) cells. Three compact tri- and tetravalent sialic acid conjugates were prepared and evaluated as inhibitors of adenoviral host cell attachment and subsequent infection and all conjugates were potent as anti-adenoviral agents. The conjugates can readily be synthesized from accessible starting materials. A crystal structure of the Ad37 fiber knob protein and the trivalent sialic acid conjugate showed that the three binding sites were all occupied by one sialic acid residue each.