This study illustrates the utility of click chemistry in functionalizing triazabutadienes by allowing access to various applications both biological and material based. Triazabutadienes have been shown to trigger the release of highly reactive diazonium species in a pH dependent way when placed in acidic conditions. Electron-rich phenyl systems such as tyrosine residues have been shown to react with diazonium compounds to form stable azo bonds. Modification of these triazabutadiene motifs can functionalize them as linkers or impact solubility; which can allow for target specificity and mild cleavage of linker in order to liberate diazonium near site of interest. Incorporation of azide-alkyne cycloadditions onto these molecules will allow chemical functionalization and cross-linking properties. The 1,2,3-triazole triazabutadiene derivatives are synthesized via Huisgen 1,3-dipolar cycloaddition from alkynyl modifications on the triazabutadiene that are reacted with various azides that show substrate diversity.

This work details the attachment of dendrimers to proteins, peptides and single stranded DNA (ssDNA). Dendrimers based on melamine satisfy many of the synthetic demands in the field of bioconjugate chemistry including: monodispersity, synthetic flexibility and scalability. The solution-phase syntheses of both ssDNA-dendrimer and peptide-dendrimer bioconjugates is described, and thorough characterization by matrix-assisted laser desorption ionization/ time-of-flight (MALDI-TOF) mass spectrometry, UV-vis spectroscopy, fluorescence spectroscopy, and polyacrylamide gel electrophoresis is discussed. Non-covalent DNA-dendrimer complexes have been shown to facilitate antisense gene delivery, but are vulnerable to dissociation and subsequent enzymatic degradation within the cell. In an effort to prepare biocompatible antisense agents capable of effectively shielding ssDNA from intracellular nuclease digestion, disulfide-linked ssDNA-dendrimers were prepared and rigorously characterized to rule out the possibility of an electrostatic-based interaction. Hybridization assays were performed to determine if the covalently-attached dendrimer affected the ability of the attached ssDNA strand to anneal with a complementary sequence to form double-stranded DNA (dsDNA)-dendrimers. Results indicate that ssDNA-dendrimer conjugates readily anneal to complementary ssDNA strands either in solution or attached to gold surfaces. Nuclease digestions of conjugates in solution suggested that enzymatic manipulation of dsDNA-dendrimers is possible, offering promise for DNA-based computation and other fields of DNA-nanotechnology. Much larger bioconjugates consisting of dendrimers, proteins and peptides were prepared with the goal of obtaining molecular weights sufficient for enhanced permeability and retention (EPR) in tumors. While the dendrimer provides the advantages of a purely synthetic route for drug delivery, the protein portion of the bioconjugate provides a monodisperse, macromolecular scaffold for the non-covalent self-assembly of the dendrimers. The strategy presented herein is based on the strong interaction between biotin and the 60 kD tetrameric protein streptavidin. Each monomer of streptavidin is capable of binding 1 biotin molecule, thus when biotin functionalized peptide-dendrimers are added to streptavidin they bind to form a cluster of dendrimers, or a megamer. The biotinylated peptides that link the dendrimers to the streptavidin core provide a way to actively target specific cell types for drug delivery. Megamer formation through the addition of tetrameric streptavidin was successful as indicated by MALDI-TOF, UV-vis titration and gel electrophoresis assays.

Artificial ribonucleases (ARs) are recognised as a potential strategy to selectively target and cleave biologically significant RNA in cells. However, in order to work as true enzymes they must exhibit catalytic turnover. Many of the reported ARs incorporate metal-containing centres (e.g. dysprosium, copper) in order to induce substantial phosphodiester cleavage, which is not amenable to use in vivo. Therefore, new strategic directions employing metal-independent ARs, such as peptidyl-oligonucleotide conjugates (POCs), need to be investigated. Previous work has shown that poor or non-complementary POCs demonstrate catalytic turnover of a HIV-1 substrate; however, sequence specificity is an issue. For POCs to be useful from a therapeutic standpoint they must only cleave specific RNA molecules and do so in a catalytic fashion, therefore removing the requirement for stoichiometric drug delivery and binding. Consequently, novel POC design strategies are required that allow selective RNA targeting but promote dissociation of the POC following phosphodiester cleavage. In this research, three types of different peptidyl-oligonucleotide conjugate designs have been implemented with the attempt to find an appropriate balance between selectivity and catalytic turnover.(i) Selective targeting and quantitative cleavage (97-100%) of a tRNAPhe target was achieved through phosphoramidate attachment of a 17-mer TΨC-targeting oligonucleotide to catalytic amphiphilic peptide sequences containing leucine, arginine and glycine. Although the half-life of tRNAPhe was less than 1 h on exposure to some of these POCs, hybridisation studies reveal that the POCs bind too tightly to their target RNA sequences and thus an excess of POC is required for efficient cleavage activity. The effect of peptide and oligonucleotide sequence variations as well as the role of enhanced conformational freedom via incorporating an abasic deoxyribose linker between the oligonucleotide targeting motif and catalytic peptide is also investigated. (ii) Most of ‘Dual’ peptidyl-oligonucleotide conjugates containing an amphiphilic RNA-cleaving peptide placed between two RNA recognition motifs directed towards the TΨC loop and 3’ acceptor stem of tRNAPhe demonstrate marked RNA binding and cleavage activities. Interestingly, those dual conjugates which showed poor or negligible binding ability in electrophoresis assays, demonstrated sufficient RNA cleavage (70%) within the vicinity of the 65GACAC61 target region. Therefore, weak POC:RNA complexes may exist which could facilitate substrate turnover. (iii) Finally, POCs were designed which induce bulge-loops in their target RNA region upon hybridisation. By introducing regions of non-complementarity into the oligonucleotide sequences, 2- to 5- membered bulges sizes were formed. Via attachment of a catalytic peptide to an internally modified oligonucleotide residue, catalytic peptides were placed directly adjacent to single-stranded RNA regions to promote cleavage by nuclease mimics. Through probing the hybridised complexes with RNase H, the presence of bulges were confirmed for all bulge-loop sizes, which will be followed by cleavage experiments to assess the possibility for reaction catalytic turnover. In conclusion, a variety of POCs have been synthesised, characterised and partially tested for their RNA cleaving and turnover activity. Based on the encouraging results presented POCs could be further developed to target disease specific RNA sequences such as micro- or messenger RNAs.

Controlling interactions in synthetic polymers as precisely as in proteins would have a strong impact on polymer science. Advanced structural and functional control can lead to rational design of, integrated nano- and microstructures. To achieve this, properties of monomer sequence defined oligopeptides were exploited. Through their incorporation as monodisperse segments into synthetic polymers we learned in recent four years how to program the structure formation of polymers, to adjust and exploit interactions in such polymers, to control inorganic-organic interfaces in fiber composites and induce structure in Biomacromolecules like DNA for biomedical applications. / Die Kontrolle von Wechselwirkungen in synthetischen Polymersystemen mit vergleichbarer Präzision wie in Polypeptiden und Proteinen hätte einen dramatischen Einfluss auf die Möglichkeiten in den Polymer- und Materialwissenschaften. Um dies zu erreichen, werden im Rahmen dieser Arbeit Eigenschaften von Oligopeptiden mit definierter Monomersequenz ausgenutzt. Die Integration dieser monodispersen Biosegmente in synthetische Polymere erlaubt z. B. den Aufbau von Peptid-block-Polymer Copolymeren. In solchen sogenannten Peptid-Polymer-Konjugaten sind die Funktionalitäten, die Sekundärwechselwirkungen und die biologische Aktivität des Peptidsegments präzise programmierbar. In den vergangen vier Jahren konnte demonstriert werden, wie in Biokonjugatsystemen die Mikrostrukturbildung gesteuert werden kann, wie definierte Wechselwirkungen in diesen Systemen programmiert und ausgenutzt werden können und wie Grenzflächen zwischen anorganischen und organischen Komponenten in Faserkompositmaterialien kontrolliert werden können. Desweiteren konnten Peptid-Polymer-Konjugate verwendet werden, um für biomedizinische Anwendungen DNS gezielt zu komprimieren oder Zelladhäsion auf Oberflächen zu steuern.

Les pénicillines font partie des molécules chimiques les plus fréquemment impliquées dans l’allergie médicamenteuse. Selon l’hypothèse de l’haptène, les molécules chimiques de petite taille doivent se lier aux protéines pour êtres immunogènes. Cependant, très peu est connu sur le processus d’immunisation des patients aux bioconjugués pénicilline-protéine. Notre groupe a récemment synthétisé des bioconjugués albumine sérique humaine-benzylpénicilline (HSA-BP) et a démontré l'existence de lymphocytes T CD4+ naïfs spécifiques du bioconjugué HSA-BP chez des donneurs sains. L'objectif de ce travail de thèse est d'identifier des séquences peptidiques issus de la HSA hapténisées avec la BP, impliquées dans l’activation des cellules T naïves ainsi que l’immunisation des patients allergiques et par conséquent les manifestations cliniques. Notre stratégie combine la spectrométrie de masse, la modélisation moléculaire et le criblage virtuel, la synthèse chimique orientée et la validation biologique sur des lignées de cellules T de longues durées chez les donneurs sains, et à l’aide du test de transformation lymphocytaire ainsi que les lignées de cellules T de courte durée chez les patients allergiques. Cette étude a permis: (1) l’identification des résidus lysine présents sur la HSA hapténisés par la BP par spectrométrie de masse, (2) la sélection par une approche in silico des peptides de 15-mer potentiellement immunogènes, (3) la synthèse orientée de ces peptides-BP à l’aide d’un monomère lysine-BP, (4) l’identification des épitopes reconnus par les cellules T naïves de donneurs sains, (5) la validation de deux épitopes situés sur les lysines 159 et 525 chez les patients allergiques aux pénicillines et (6) confirmation de la HSA comme un bon modèle pour l’hapténisation de la BP. / Penicillins are among the most prevalent drug-inducing allergy. According to the hapten hypothesis small chemical molecules needs to bind to proteins to be immunogenic. However, little is known on the process of patients immunization to penicillin-protein conjugates. Our group has recently synthesized benzylpenicillin-human serum albumin (BP-HSA) bioconjugate and demonstrated the existence of naïve CD4+ T lymphocytes specific to BP-HSA in healthy donors. The objective of this work was to identify peptides sequences from HSA haptenized with BP involved in naïve T-cells activation, immunization of patients and consequently the clinical manifestations. Our strategy combines mass spectrometry, molecular modeling and virtual screening, chemical oriented synthesis and biological validation using long-term T-cell lines in healthy donors and the lymphocyte transformation test as well as short-term T-cell lines in allergic patients. This study allowed: (1) the identification of lysine residues involved in the BP binding to HSA using mass spectrometry, (2) the selection of BP-peptides containing the lysine residues likely to induce immune response using an in silico approach, (3) the synthesis of the selected BP-15 mer peptide bioconjugates using a lysine-BP monomer, (4) the identification of epitopes recognized by naïve T cells from healthy donors, (5) the validation of two epitopes located on lysines 159 and 525 in allergic patients to penicillins and (6) the confirmation of HSA as a good model for BP haptenation.