Powerful tools have emerged in the past few years to allow the sensing, imaging and modulation of biological processes in living systems. Bioorthogonal organometallic reactions are transformations catalysed by transition metals, which are compatible within a biological environment. Palladium-mediated cross-coupling and decaging reactions, for example, have been successfully applied to catalyse non-natural chemical transformations within a biological milieu. Up until now, copper-catalysed cycloaddition reactions have been used extensively for the conjugation, immobilisation, and purification of biomolecules, but their further application in vivo has been limited by the inherent toxicity of copper. Herein, different transition metal catalysts were designed and applied in cellular and in vivo manipulations. Polymeric solid supports were functionalised with palladium nanoparticles and used as biocompatible, heterogeneous catalysts in selective decaging and cross-coupling reactions to activate fluorescent probes and synthesise cytotoxic anticancer drugs in situ. In order to gain tumour selectively, targeting functionalities were incorporated into the particles to allow the spatial control of the selective activation of labelling probes. The simultaneous synthesis of two different anticancer agents intracellularly, by two totally different mechanisms (in situ synthesis and decaging), is reported. The cellular toxicity of copper was addressed by entrapping copper nanoparticles on a polymeric solid support, allowing the activation of labelling probes, as well as the synthesis of an anticancer agent from two benign components through the well-known copper catalysed azide-alkyne cycloaddition. The biocompatibility of the copper catalysts in vivo was shown by implantation in zebrafish embryos.

The recovery of the selected biological material in affinity-based separations relies on reversing the biological interaction responsible for the binding. General elution methods which are independent of the bioaffinity interaction have attracted increasing attention. The first three chapters of this thesis describe the development of a novel “click” functionalised azobenzene-based linker for affinity-independent elution protocols and the preliminary affinity studies using this linker. Ligands functionalised with a bioorthogonal propargyl label were readily attached to the terminal azide of the linker using the copper(I) catalysed Huisgen cycloaddition (or "click" reaction). Following separation, the linker was cleaved under mild non-denaturing conditions using Na2S2O4. In the last three chapters a novel approach towards the synthesis of the 4-methyl proline fragment of the cytotoxic natural product bisebromoamide (a potential affinity target) is proposed. For the pyrrolidine ring construction an enamide-olefin ring-closing metathesis (RCM) approach has been attempted. The installation of the required absolute stereochemistry has been achieved using a phase-transfer catalyst for the enantioselective alkylation of Schiff bases derived from glycine esters.

The need for chemoselective bond formation within complex biological systems has driven much research in chemical biology and chemical medicine and has allowed control over the structure and biological properties of a range of chemical entities. Reactions that are highly biocompatible, selective and occur at low concentration are classified as being bioorthogonal. Although bioorthogonal reactions have been successfully applied to bioconjugation and imaging in living systems, only a few examples exist of bioorthogonal reactions being utilised for the activation of prodrugs. The tetrazine mediated inverse electron demand Diels-Alder reaction is characterized by excellent reaction rates and high biocompatibility in both in vitro and in vivo applications. To date, this chemistry has found only limited application in prodrug activation or drug release strategies. Herein, a series of tetrazine-trigger systems are reported in which an active drug is liberated from its inactive form upon triggering with tetrazine. It is shown that the release of encapsulated and conjugated drugs from polymeric nanoparticles can be triggered by tetrazines providing an on-demand release within biological systems. In a totally new approach that fully complies with the principle of bioorthogonality by avoiding the generation of any by-products, tetrazine was utilised as a prodrug scaffold leading to symbiotic and traceless dyadic prodrug activation. The simultaneous formation of two active drugs (here the anticancer drug camptothecin and a known micro RNA inhibitor) was confirmed and validated within a biological environment. The use of tetrazines as a trigger to activate or release an active drug will open new directions in the field of chemical biology/medicine.

Over the past decade, bioorthogonal chemistry has emerged as powerful tools used for tracking biomolecules within living systems. Despite the vast number of organic transformations in the literature, only select few reactions meet the stringent requirements of bioorthogonality. There is increasing demands to develop biocompatible reactions that display high specificity and exquisitely fast kinetics under physiological conditions. With the goal of increasing reaction rates as a means for reducing the concentrations of labelling reagents used for bioconjugation, we have developed metal-catalyzed and metal-free alkyne-nitrone cycloadditions as alternatives to azide-alkyne cycloadditions and demonstrate their applications for imaging cell surface proteins. The copper(I)-catalyzed alkyne-nitrone cycloaddition, also known as the Kinugasa reaction, is typically conducted with a Cu(I) catalyst in the absence of air. We have developed highly efficient micelle promoted multicomponent Kinugasa reactions in aqueous media to make the reaction faster and more efficient. Despite good product yields, the slow kinetics, limited substrate scope and competing side-reaction pathways precludes its practical applicability for biological labelling. We have designed and synthesized β-lactam alkyne probes obtained from these reactions for activity-based protein profiling of the activities of membrane proteins. Additionally, we report that alkyne tethered β-lactams serve as surface enhanced Raman spectroscopy (SERS) reporters bound to silver nanoparticles, and demonstrated that alkyne bound silver nanoparticles can be used for SERS imaging cell surface proteins. The strain-promoted alkyne-nitrone cycloaddition (SPANC) was also explored as a rapid alternative bioorthogonal reaction. We found that the reaction proceeded in high yield within aqueous media, and displayed rate enhancements that were 1-2 orders of magnitude faster than analogous reactions involving azides. The scope and kinetics of SPANC was evaluated in model reactions of various nitrones (acyclic and cyclic) with cyclooctynes, with the purpose of identifying stable nitrones that displayed intrinsically faster kinetics than azides in strain-promoted cycloadditions with cyclooctynes. Cyclic nitrones displayed good stability and exceptionally fast reactivity in these reactions. The SPANC reaction exhibited high selectivity in the presence of biological nucleophilic amino acid side chains and the presence of biological media did not adversely affect the reaction. We have utilized SPANC for highly specific labelling of proteins in vitro and for imaging ligand-receptor interactions on the surfaces of live cancer cells. The high selectivity, fast reaction rate, and aqueous compatibility of SPANC makes the reaction suitable for a variety of in vivo biological imaging applications.

Over the past decade, bioorthogonal chemistry has emerged as powerful tools used for tracking biomolecules within living systems. Despite the vast number of organic transformations in the literature, only select few reactions meet the stringent requirements of bioorthogonality. There is increasing demands to develop biocompatible reactions that display high specificity and exquisitely fast kinetics under physiological conditions. With the goal of increasing reaction rates as a means for reducing the concentrations of labelling reagents used for bioconjugation, we have developed metal-catalyzed and metal-free alkyne-nitrone cycloadditions as alternatives to azide-alkyne cycloadditions and demonstrate their applications for imaging cell surface proteins. The copper(I)-catalyzed alkyne-nitrone cycloaddition, also known as the Kinugasa reaction, is typically conducted with a Cu(I) catalyst in the absence of air. We have developed highly efficient micelle promoted multicomponent Kinugasa reactions in aqueous media to make the reaction faster and more efficient. Despite good product yields, the slow kinetics, limited substrate scope and competing side-reaction pathways precludes its practical applicability for biological labelling. We have designed and synthesized β-lactam alkyne probes obtained from these reactions for activity-based protein profiling of the activities of membrane proteins. Additionally, we report that alkyne tethered β-lactams serve as surface enhanced Raman spectroscopy (SERS) reporters bound to silver nanoparticles, and demonstrated that alkyne bound silver nanoparticles can be used for SERS imaging cell surface proteins. The strain-promoted alkyne-nitrone cycloaddition (SPANC) was also explored as a rapid alternative bioorthogonal reaction. We found that the reaction proceeded in high yield within aqueous media, and displayed rate enhancements that were 1-2 orders of magnitude faster than analogous reactions involving azides. The scope and kinetics of SPANC was evaluated in model reactions of various nitrones (acyclic and cyclic) with cyclooctynes, with the purpose of identifying stable nitrones that displayed intrinsically faster kinetics than azides in strain-promoted cycloadditions with cyclooctynes. Cyclic nitrones displayed good stability and exceptionally fast reactivity in these reactions. The SPANC reaction exhibited high selectivity in the presence of biological nucleophilic amino acid side chains and the presence of biological media did not adversely affect the reaction. We have utilized SPANC for highly specific labelling of proteins in vitro and for imaging ligand-receptor interactions on the surfaces of live cancer cells. The high selectivity, fast reaction rate, and aqueous compatibility of SPANC makes the reaction suitable for a variety of in vivo biological imaging applications.

Ce travail est composé de trois projets. Le premier projet a pour objectif de découvrir de nouveaux métabolites de la vitamine A. Il a consisté en la synthèse d’un analogue du rétinaldéhyde, portant une fonction azoture et permettant de suivre son devenir in vivo. Le second projet a consisté en l’élaboration de la sonde ATPP permettant l’analyse de l’ensemble des métabolites aldéhydiques d’un échantillon. La sonde permet un gain de sensibilité en LS-MS². Une analyse de sa biodistribution a été faite, et montre que la sonde ATPP, après injection intrapéritonéale, est distribuée in vivo. Concernant le troisième projet, un réactif de couplage homobifonctionnel « thiol-thiol » a été élaboré. Les produits du couplage ont montré une excellente stabilité plasmatique. Le réactif a d’abord été appliqué avec succès au couplage de petites molécules, puis au couplage d’un oligonucléotide modifié et d’un peptide. / This work consists of three projects. The first project aims to discover new metabolites of vitamin A. An analog of retinaldehyde, carrying an azide function was synthesized. It would allow to follow its fate in vivo. The second project consisted in the development of a probe allowing the analysis of all the aldehyde metabolites in a sample. The probe provides sensitivity gain in LS-MS². An analysis of its biodistribution has been done, and showed the ATPP probe is distributed after an intraperitoneal injection. Concerning the third project, a homobifunctional coupling reagent "thiol-to-thiol" has been developed. The coupling products showed excellent plasma stability. The reagent was first successfully applied to the coupling of small molecules and then to the coupling of a modified oligonucleotide and a peptide.

Chemotherapeutics are potent molecules capable of systematically treating cancer. As healthy tissues contain features also inherent to cancer cells, treatment often results in unwanted sideeffect. As chemotherapeutic side-effect produces significant harm and often limits optimal drug dosing, new strategies must be developed to improve treatment selectivity. A prodrug strategy provides one option to improve the selectivity of an established chemotherapeutic. By modifying a pharmaceutically active drug, interaction with biology may be functionally masked. Subsequent ‘un-masking’ the prodrug exclusively at the intended treatment site may direct treatment only to where the anticancer effect is required. This thesis progresses the novel approach of bioorthogonal organometallic (BOOM) prodrug activation. A metal catalyst and masked chemotherapeutic constitute reaction partners to provide a new strategy for intratumoural prodrug activation. Whereby the prodrug and metal catalyst are independently non-cytotoxic, in combination the prodrug undergoes catalytic activation to deliver an anticancer affect. By positioning the metal catalyst within a tumour (i.e. by microsurgery), an administered masked prodrug sensitive to catalyst-mediated activation could allow for ‘targeted’ chemotherapy localised to the tumour site. The design, synthesis and study of new BOOM prodrug candidates are reported herein. Novel protecting groups are developed to enhance drug masking to biology and subsequent catalyst-mediated activation. Prodrug screening studies are carried out in cancer cell culture models, with zebrafish and in ex vivo rodent model tumour explants. The catalyst, a palladium (Pd0) functionalised bead system, is optimised for enhanced activation, drug release and in vivo implantation. The potentially infinite generation of active chemotherapeutics exclusively in tumour would increase the efficacy of treatment whilst reducing harmful effect on healthy tissue.

Chemotherapy is widely used to treat various forms of cancer. However, some chemotherapeutic drugs, due to their antineoplastic properties, also act upon healthy cells which normally replicate rapidly causing a plethora of undesirable side effects. One rising and promising therapeutic strategy is the development of prodrugs. Prodrugs are derivatives of the pharmaceutically active drugs but require an enzymatic or biochemical transformation within a certain biological space in order for it to become activated and capable of exerting the desired pharmacological effect. As a novel prodrug approach, this thesis describes the pioneering use of a bioorthogonal organometallic (BOOM) activation strategy to develop spatially-controlled anticancer treatments. Bioorthogonal reactions are selective chemical processes between two abiotic reagents in a biological system that do not interfere with the system’s biotic components. In BOOM reactions, one of the reagents is a metal catalyst, which if immobilized, could in principle allow for the local transformation of a continuous flow of a bioorthogonal chemo-substrate indefinitely. To exploit the benefits of this paradigm in anticancer therapy, this thesis reports the design, synthesis and screening of a set of prodrugs masked with bioorthogonal protecting groups sensitive to activation by a catalysts-based “activating device”. Specifically, it describes the synthesis of palladium (Pd0) functionalized resins (the activating device) capable of activating cytotoxic pyrimidine analogue prodrugs masked with Pd0-labile protecting groups. Both the Pd0 functionalized resins and the BOOM-activated prodrugs are independently non-cytotoxic. However, once in combination together, the Pd0 is capable of mediating the removal of the masking groups in situ and rendering the drugs in their cytotoxic state with comparable antiproliferative properties to the unmodified parental drugs in vitro. The Pd0 resins also display biocompatibility and local catalytic activity inside zebrafish embryos. This approach is intended to generate a more targeted therapeutic treatment regime while minimizing harm to normal healthy tissues through the local generation of prodrugs which are not dependent on intrinsic biological activators but by an external activating device, thus reducing the systemic presence of the drug.

Over the past decade, bioorthogonal chemistry has emerged as powerful tools used for tracking biomolecules within living systems. Despite the vast number of organic transformations in the literature, only select few reactions meet the stringent requirements of bioorthogonality. There is increasing demands to develop biocompatible reactions that display high specificity and exquisitely fast kinetics under physiological conditions. With the goal of increasing reaction rates as a means for reducing the concentrations of labelling reagents used for bioconjugation, we have developed metal-catalyzed and metal-free alkyne-nitrone cycloadditions as alternatives to azide-alkyne cycloadditions and demonstrate their applications for imaging cell surface proteins. The copper(I)-catalyzed alkyne-nitrone cycloaddition, also known as the Kinugasa reaction, is typically conducted with a Cu(I) catalyst in the absence of air. We have developed highly efficient micelle promoted multicomponent Kinugasa reactions in aqueous media to make the reaction faster and more efficient. Despite good product yields, the slow kinetics, limited substrate scope and competing side-reaction pathways precludes its practical applicability for biological labelling. We have designed and synthesized β-lactam alkyne probes obtained from these reactions for activity-based protein profiling of the activities of membrane proteins. Additionally, we report that alkyne tethered β-lactams serve as surface enhanced Raman spectroscopy (SERS) reporters bound to silver nanoparticles, and demonstrated that alkyne bound silver nanoparticles can be used for SERS imaging cell surface proteins. The strain-promoted alkyne-nitrone cycloaddition (SPANC) was also explored as a rapid alternative bioorthogonal reaction. We found that the reaction proceeded in high yield within aqueous media, and displayed rate enhancements that were 1-2 orders of magnitude faster than analogous reactions involving azides. The scope and kinetics of SPANC was evaluated in model reactions of various nitrones (acyclic and cyclic) with cyclooctynes, with the purpose of identifying stable nitrones that displayed intrinsically faster kinetics than azides in strain-promoted cycloadditions with cyclooctynes. Cyclic nitrones displayed good stability and exceptionally fast reactivity in these reactions. The SPANC reaction exhibited high selectivity in the presence of biological nucleophilic amino acid side chains and the presence of biological media did not adversely affect the reaction. We have utilized SPANC for highly specific labelling of proteins in vitro and for imaging ligand-receptor interactions on the surfaces of live cancer cells. The high selectivity, fast reaction rate, and aqueous compatibility of SPANC makes the reaction suitable for a variety of in vivo biological imaging applications.

Gas filled microbubbles (MBs) stabilized by a shell (e.g. lipids) are commonly used as ultrasound (US) contrast agents. Attaching biomolecules to the surface of MBs allows for molecular US imaging of various diseases. With the increased interest in targeted US imaging, new platforms to prepare disease-targeted MBs are necessary. Furthermore, attaching signaling agents to MBs creates multi-modal imaging opportunities, enhancing visualization and quantification of disease biomarkers. In this thesis, MBs labeled with 99mTc and/or rhodamine dye by taking advantage of the strong interaction between biotin and streptavidin are reported. Radiolabeling of MBs was achieved in good radiochemical yield (~ 30%). 99mTc-labeled MBs were targeted to vascular endothelial growth factor receptor 2 (VEGFR2) using an anti-VEGFR2 antibody and to prostate specific membrane antigen (PSMA) using small-molecule based PSMA inhibitors. In vitro evaluations showed successful binding of MBs to the target while in vivo targeting assessments were unsuccessful. New strategies to target MBs to the site of interest were then developed through the use of the bioorthogonal reaction between tetrazine (Tz) and trans-cyclooctene (TCO). A biotinylated derivative of Tz was loaded on streptavidin coated MBs to create a Tz-derivatized MB (MBTz). Targeting MBTz to extracellular markers of cancer such as VEGFR2, PSMA and urokinase plasminogen activator receptor (uPAR) in vitro was achieved using TCO-conjugated antibodies. In vivo targeting was successful for VEGFR2 and PSMA, but not uPAR. Translating the new strategy to other US contrast agents was then investigated. Gas vesicles (GVs) produced in halobacteria were conjugated with TCO using amide-coupling chemistry. A 99mTc-labeled derivative of Tz was loaded on TCO-GVs (RCY= 59%) and their distribution assessed by SPECT/CT imaging and ex vivo tissue counting. Having established a convenient platform to conjugate molecules to GVs and MBs, future work focuses on developing a new generation of human compatible molecular US imaging probes. / Dissertation / Doctor of Philosophy (PhD)