Technetium-99m (99mTc) radiopharmaceuticals are widely used for diagnostic imaging of heart, kidney, and liver disease, and cancer. Evolution from perfusion type tracers to targeted agents however has proven difficult. 99mTc labeled antibodies for imaging specific disease biomarkers would be of great interest, however the disparity between the isotopes half-life (6 hours) and the long circulation time of most antibodies (multiple days) has been a significant barrier. Furthermore, the conjugation of bifunctional 99mTc-chelate complexes to small molecules often has a detrimental impact on targeting. The use of bioorthogonal chemistry derived from tetrazines and trans-cyclooctene derivatives, along with pretargeting has the potential to overcome these issues and create a new generation of targeted 99mTc radiopharmaceuticals. Initially, the synthesis of three generations of imidazole based tridentate chelates linked to a tetrazine was completed. These new ligands were labeled with 99mTc under mild conditions (60 °C, 20 min, pH 3.5) with modest to good radiochemical yields ranging from 31 to 83%. Biodistribution studies revealed that compound 14, which contains a polyethylene glycol 5 (PEG5) linker had the best clearance from non-target tissues. Compound 14 was also used successfully in a pretargeting strategy along with a transcyclooctene (TCO) derivative of the bone targeting bisphosphonate, alendronate (ALN). One hour following the administration of TCO-ALN to BALB/c mice, compound 14 was injected intravenously where uptake at sites of high calcium turn over (i.e. the joints) was observed. At 6 hours post injection, for example, uptake reached as high as 20.1 ± 4.91 and 16.1 ± 4.84 %ID/g in the knee and shoulder, respectively. Pretargeted imaging studies were performed subsequently with a TCO-functionalized huA33 antibody in mice bearing SW122 xenografts. The TCO-huA33 antibody was injected 24 hours before the administration of two radiolabeled tetrazines at high and low specific activities. At 6 hours post injection tumour uptake was minimal, with tumour: blood ratios <1 in all cases. Blood clearance studies determined that the tetrazines were being cleared rapidly, with a blood residence half-life of 1.3-2.1 minutes. The hypothesis is that the low concentration of the antibody (owing to its high molecular weight), combined with the rapid clearance of the tetrazine and significant off-target uptake resulted in unfavorable kinetics and low tumor binding. Studies of the clearance pathway of 14 were investigated with clinically approved hepatobiliary transport inhibitors to help understand the mechanism of clearance, which could in turn be used to optimize the pharmacokinetics of the tetrazine ligands. A range of different inhibitors of key clearance pathways were evaluated with limited success. However, co-administration of 14 with ALN resulted in a 75% decrease in gall bladder uptake of 14 (216 ± 75.9 to 33.6 ± 3.93 %ID/g). Pretargeting studies of 14 with TCO-ALN in the presence of excess ALN revealed that ALN did not hinder the uptake of TCO-ALN in the bone, with all organs and tissues having the same uptake with TCO-ALN or TCO-ALN + ALN (knee: 20.1 ± 4.91 and 14.9 ± 2.43 %ID/g, respectively). There was also a concomitant decrease in gall bladder uptake (91.5 ± 17.1 to 28.8 ± 2.63 %ID/g). Further work on improving the distribution of the tetrazine ligands involved investigating the effect of the chelate. The core chelate found in 14 without the tetrazine moiety (compound 11a) was labeled with 99mTc to produce 11b in a 31% radiochemical yield. Biodistribution studies of 11b and 14 at 6 hours post injection demonstrated that the imidazole-based 99mTc-chelate was a major factor in the rapid and significant uptake and retention in the liver and gallbladder. A new triazole based chelate with optimal clearance from Kluba and coworkers was synthesized in 45% yield and successfully labeled with 99mTc (compound 23a). Biodistribution studies were performed where at 6 hours post injection, 23a had five times lower uptake in all non-target organs compared to 11b. The synthesis of a tetrazine derivative of 23a (compound 32) unfortunately demonstrated high hepatobiliary uptake compared to the original triazole chelate (gall bladder: 228 ± 251 and 8.77 ± 0.73 %ID/g, large intestine: 85.5 ± 83.5 and 6.88 ± 0.30 %ID/g, respectively). This particular derivative had a lipophilic linker as a result of the synthetic challenges faced during the preparation of a more hydrophilic triazole-tetrazine derivative. In addition to pretargeting applications, the 99mTc-tetrazine was used as a reagent to create multimodal imaging agents. Nanoscale gas vesicle (GV) ultrasound contrast agents were functionalized with TCO via an amide coupling to lysine residues. TCO-GVs were then radiolabeled by adding compound 6 where the desired product, a new multimodal probe, was obtained in 59% radiochemical yield. SPECT imaging and biodistribution studies in mice were completed where the labeled GV’s showed uptake in the gall bladder (120 ± 29.1 %ID/g), liver (16.8 ± 7.50 %ID/g), lungs (3.26 ± 1.53 %ID/g), small intestines (14.5 ± 5.30 %ID/g), and spleen (5.47 ± 2.71 %ID/g) at 120 min post injection. In addition to radiolabelling, the TCO-GVs were also functionalized with a near IR-tetrazine dye to produce a multimodal ultrasound/photoacoustic (US/PA) imaging agent in a 68% yield. / Thesis / Doctor of Philosophy (PhD)

La radioimmunothérapie (RIT) est une stratégie théranostique associant la spécificité de reconnaissance d’anticorps monoclonaux (AcMs) (ou de formes dérivées) vis-à-vis des antigènes tumoraux et les propriétés des radionucléides (imagerie/thérapie). L’efficacité de la RIT est cependant limitée sur les tumeurs solides à cause de la lente diffusion des AcMs et de leur longue demi-vie plasmatique. Les approches de radioimmunothérapie préciblée (PRIT), qui dissocient l’injection des AcMs de celle des radioligands constituent des alternatives pertinentes envisagées pour diminuer l’hématotoxicité et améliorer l’efficacité thérapeutique de la RIT classique. Nous avons ainsi travaillé sur une stratégie de PRIT utilisant la chimie bioorthogonale par interaction entre un trans-cyclooctène (TCO) et une tétrazine (TZ), à la fois pour l’imagerie et pour la thérapie de la carcinose péritonéale (CP) d’origine colorectale (modèle A431-CEA-Luc/ AcM 35A7). Dans un premier temps nous avons évalué à la fois in vitro et in vivo dans le modèle de CP ainsi que dans un modèle sous-cutané de cancer colorectal (modèle HT29/ AcM Ts29.2) l’effet des modifications apportées aux AcMs. Nous avons ainsi montré que les modifications d’AcMs influencent l’interaction entre les TCO et la TZ, sans pour autant altérer leur immunoréactivité. L’ajout d’espaceurs PEGylés (polyéthylène glycol) entre les AcMs et les TCO induit une diminution significative de l’interaction TCO/TZ. De plus, nous avons montré que les TCO sont sujets à l’isomérisation en cis-cyclooctènes, inactifs vis-à-vis de la TZ, et que la PEGylation aggrave ce phénomène. Ces études ont ainsi montré à la fois que les AcMs-TCO ne contenant pas d’espaceur PEGylé étaient les plus favorables pour le préciblage mais également, qu’il était primordial de contrôler le taux d’isomérisation des TCO avant greffage aux AcMs pour ne pas altérer l’interaction vis-à-vis des TZ. Dans un second temps nous avons effectué avec succès la preuve de concept de l’imagerie SPECT de la CP par préciblage entre l’AcM 35A7-TCO et la TZ-PEG4-DOTA-177Lu (i.e. TZ-1). Un ciblage spécifique des tumeurs péritonéales a ainsi été obtenu, avec un très bon contraste. L’étude de PRIT effectuée avec cette même sonde TZ-1 a cependant échoué à mettre en évidence une amélioration des médianes de survie ou un ralentissement de la croissance tumorale, nous amenant ainsi à reconsidérer la structure de la TZ-1. Trois autres TZ (i.e. TZ-2-4) ont donc été évaluées par la suite, en biodistribution, afin de déterminer la meilleure pour la PRIT de la CP. Ainsi, la TZ-3, qui comporte un espaceur PEGylé plus long que la TZ-1, s’est avérée être la plus favorable dans ce type de stratégie et sera prochainement utilisée pour une nouvelle étude de thérapie. En conclusion, ces travaux de thèse ont permis de démontrer la faisabilité du concept de préciblage par chimie bioorthogonale utilisant l’interaction TCO/TZ pour l’imagerie de tumeurs disséminées dans la cavité péritonéale. Cette stratégie reste néanmoins compliquée à mettre en place du fait de l’instabilité des TCO et des problèmes de réactivité de certaines sondes TZ et nécessite encore de nombreuses optimisations avant de pouvoir envisager une application thérapeutique. / Radioimmunotherapy (RIT) consists to combine the specificity of monoclonal antibodies (mAbs), or mAbs derived structures, towards tumor antigens with the imaging/therapy properties of radionuclides, representing thus a theranostic strategy. RIT efficiency in solid tumors is limited due to both mAbs slow diffusion and long blood clearance. Pretargeted radioimmunotherapy (PRIT) appears as an alternative to circumvent hematotoxicity and improve therapeutic efficacy. We have thus worked on PRIT based on bioorthogonal click chemistry relying on the interaction between trans-cyclooctene (TCO) and tetrazine (TZ). Application of this strategy was made for imaging and therapy of peritoneal carcinomatosis (PC) from colorectal origin (A431-CEA-Luc model/ 35A7 mAb). We have first assessed the influence of mAbs modifications, in vitro and in vivo experiments made on both PC model and subcutaneous colorectal cancer (HT29 model/ Ts29.2 mAb). We thus demonstrated that mAbs modifications influence the interaction between TCO and TZ without decreasing their antigen binding capacities. Indeed, addition of PEGylated (polyethylene glycol) linkers between mAbs and TCO induced a significant decrease of TCO/TZ interaction. In addition, we also demonstrated that TCO moieties undergo severe isomerization to cis-cyclooctene (CCO) moieties which are unreactive towards TZ. Addition of PEG linkers also increased the isomerization rate of TCO to CCO. Our results highlighted that a non PEGylated mAb should represent the best structure for PRIT to avoid isomerization and consequently to control the ratio of CCO before mAbs coupling to maximize TCO/TZ interaction. In disseminated PC, we have made for the first time the proof of concept of SPECT imaging between 35A7-TCO and TZ-PEG4-DOTA-177Lu (i.e. TZ-1). We indeed obtained a specific signal corresponding to PC tumors with a very good contrast. However, a PRIT experiment using TZ-1 did not allow observing neither improvement of median survivals nor tumor growth slow down. Those disappointing results led to reconsider the TZ-1 structure and evaluate three new TZ (i.e. TZ-2-4). The TZ-3, bearing a longer PEG linker than TZ-1, appears as the most appropriate for PRIT studies and will soon be considered for a new therapy experiment. In conclusion, we demonstrated the possibility to do pretargeted imaging of peritoneal disseminated tumors using bioorthogonal click chemistry with TCO/TZ interaction. Nevertheless, this strategy is quite complicated to do due to both TCO isomerization and reactivity of radiolabelled TZ probes. Further optimizations will be mandatory before therapy can be transferred to clinic.

L'imagerie de biomolécules, et plus particulièrement des glycanes, au sein d'organismes vivants, représente un incroyable challenge. Cependant, des progrès significatifs ont été réalisés ces dix dernières années grâce au développement de la stratégie du rapporteur chimique bioorthogonal. Cette technique implique, dans un premier temps, l'incorporation d'une fonctionnalité chimique non native (rapporteur) au sein de biomolécules complexes. Ce rapporteur peut ensuite réagir sélectivement avec une sonde moléculaire spécifique permettant ainsi la détection de la biomolécule ciblée. Afin d'imager ces biomolécules en temps réel, les sondes fluorogènes, des réactifs non fluorescents qui deviennent fluorescents après réaction avec le rapporteur chimique, ont été récemment développées. Ces dernières années, la cycloaddition 1,3-dipolaire sans métaux, entre les cylooctynes et les azotures, a été élégamment employée comme réaction bioorthogonale pour l'imagerie de biomolécules au sein d'organismes vivants. Cependant, l'azoture présente certaines limitations, notamment il peut être réduit par les thiols cellulaires. En conséquence, nous avons étudié l'utilisation de 1,3-dipôles plus stables, en tant que nouveaux rapporteurs chimiques bioorthogonaux pour l'imagerie de biomolécules par fluorescence. De plus, nous avons aussi développé de nouvelles sondes fluorogènes bioorthogonales ayant de bonnes propriétés de fluorescence, telles que de hautes valeurs de rendement quantique et des longueurs d'ondes d'émission déplacées dans le rouge, pour une potentielle application chez l'animal. / Imaging biomolecules, such as glycans, in living systems remains a formidable chemical challenge. However, significant progress has been made over the past ten years, with the ground-breaking development of the bioorthogonal chemical reporter strategy. In this context, complex biomolecules are fitted with a non-native chemical functionality (reporter) that can react selectively with a complementary bioorthogonal probe for detection. In order to image these biomolecules in real time, fluorogenic probes, non fluorescent reagents that produce highly fluorescent products, have recently been developed. This last decade, the metal-free 1,3-dipolar cycloaddition between cyclooctynes and azides have been elegantly employed for biomolecules imaging in living systems. However, azides suffer from limitations such as their reduction by endogenous cellular thiols. Consequently, we have investigated the use of more stable 1,3-dipoles as new chemical reporters for fluorescent biomolecule imaging. In addition, we also developed novel bioorthogonal fluorogenic probes with improved fluorescence properties such as high quantum yields and red-shifted fluorescence emission for potential applications in living animals.

Le développement de réactions chimiques compatibles avec les milieux biologiques est un défi scientifique de taille. Les outils dont actuellement disponibles pour le marquage spécifique d’entités biologiques se sont multipliés pendant cette dernière décennie. Parmi les réactions vedettes du domaine, on trouve les réactions de Diels-Alder entre alcènes tendus et tétrazines ou encore les cycloadditions entre les cycloalcynes et les azotures (SPAAC). En revanche, les réactions de clivage bioorthogonal ont retenu une attention plus faible de la part de la communauté scientifique. Récemment notre groupe a identifié une réaction bioorthogonale entre une iminosydnone et un cycloalcyne permettant d’effectuer simultanément le clivage d’un composé et la ligation de deux entités. Ces travaux de thèse ont été entièrement dirigés vers cette nouvelle réactivité.En premier lieu, nous avons étudié la synthèse et la fonctionnalisation du partenaire iminosydnone dans le but d’obtenir une librairie de composés pour l’étude de la cinétique de la réaction de click & release avec les cycloalcynes. Dans un second temps, nous avons utilisé les outils synthétiques développés pour concevoir des sondes iminosydnones à double exaltation de fluorescence. Cela a marqué l’entrée de ces composés dans le contexte de la chimie bioorthogonale puisque la sonde la plus prometteuse a été utilisée sur des cellules vivantes.Enfin, la capacité des iminosydnones à être clivées par les cycloalcynes a été exploitée sous la forme d’espaceurs clivables dans deux applications. Nous avons tout d’abord conçu des outils pour le target-fishing. Les sondes obtenues ont permis l’immobilisation de protéines sur un support solide. La libération du support des protéines a pu être effectuée de manière quantitative tout en leur apposant une étiquette fluorescente. Le second objet exploitant les propriétés d’espaceurs clivables des iminosydnones est un ADC. Celui en développement dans cette thèse est destiné à traiter les infections bactériennes, cible atteignable uniquement en employant un espaceur clivable par un agent exogène. / The development of chemical reactions compatible with the biological medium is a major challenge. The availability of chemical tools for the specific labeling of biological entities increased dramatically during the last decade. The Diels-Alder reactions between tetrazines and strained alkenes or the Strained Promoted Azide Alkyne Cycloaddition (SPAAC) are among the most popular reactions for bioorthogonal ligations. On the other hand, moderate attention was given to bioorthogonal cleavage reactions. Recently our group identified a new bioorthogonal reaction between an iminosydnone and a cycloalkyne, enabling a cleavage and the ligation of two partners at the same time.The first aim of this PhD thesis was to study the synthesis and functionalisation of the iminosydnone partner. With the large library of compounds in our hands, we could study the kinetic properties of the click & release reaction.Next, using this transformation, we synthesized double fluorogenic iminosydnone probes. The most promising probe was then used on living cells, underlining the bioorthogonality of the reaction.Finally, we took advantage of the iminosydnone properties to use them as cleavable linkers in two applications. The first field we explored was target-fishing. The tools we developped allowed protein immobilization on a solid support. The quantitative release from the support of labeled proteins was achieved using the click & release reaction. The second object using iminosydnones as cleavable linkers we considered was an ADC. The one developped in this PhD thesis is aimed at bacteria. For treatment with ADCs, this target can only be reached using a linker cleavable with an external agent.

1 Abstract This work aims at showing synthesis and potential use of water-soluble fluorescent probes based on BODIPY. The preparation of probes containing bioorthogonal mono- and heterobifunctional functional groups was demonstrated. Ground work was done at the optimisation of reliable, scalable and fast sulfonation of BODIPY in 2,6-positions. A protocol for handling sulfonated BODIPY has been established; especially for the exchange of counterions. In counterion se- lection, their relation to synthetic pathway and biocompatibility were taken into consideration. The second part of the work shows series of water-soluble fluorescent probes, into which can be easily introduced bioactive or bioorthogonal functional groups. This can be used for click chemistry in connection with turn off/on probes or fluorescent sensing of molecules or ions. All this can be done in aqueous solution without organic solvents, which is relevant for biochemical, analytical and imaging applications. Keywords BODIPY, bifunctional, water-soluble, fluorescent probe, solubilization, biocompa- tible probes, bioorthogonal reaction, BODIPY sulfonation

In this thesis will be described research towards the development of bioorthogonal bond-cleavage reactions, and their applications in targeted drug delivery (Figure 1). The first project relates to the development of a palladium mediated bond-cleavage or "decaging" reaction which can cause a propargyl carbamate to decompose and release an amine. This was further developed by the incorporation of a protein modification handle which allowed an amine-bearing drug to be covalently ligated to a protein by a palladium-cleavable linker. This chemistry was demonstrated by the conjugation of the anticancer drug doxorubicin to a tumour targeted anti-HER2 nanobody. The drug could then be delivered to cancer cells upon addition of a palladium complex. The second project relates to the development of a platinum mediated bond-cleavage reaction. This was developed with the aim of using platinum-containing anticancer drugs - such as cisplatin - as a catalyst to cause drug release reactions in tumours. In this reaction an alkyne-containing amide can decompose to release an amine upon addition of platinum complexes, and was applied to the release of prodrugs of the cytotoxins monomethylauristatin E and 5-fluorouracil in cancer cells. A cisplatin-cleavable antibody-drug conjugate was designed and synthesised, and progress towards its biological evaluation will be discussed.

Chemical biology encompasses the study and manipulation of biological system using chemistry, often by virtue of small molecules or unnatural amino acids. Much insight has been gained into the mechanisms of biological processes with regards to protein structure and function, metabolic processes and changes between healthy and diseased states. As an ever expanding field, developing new tools to interact with and impact biological systems is an extremely valuable goal. Herein, work is described towards the synthesis of a small library of heterocyclic-containing small molecules and the mechanistic details regarding the interesting and unexpected chemical compounds that arose; an alternative set of non-toxic copper catalyzed azide-alkyne click conditions for in vivo metabolic labelling; and the synthesis of an unnatural amino acid for further chemical modification via [3+2] cycloadditions with nitrones upon incorporation into a peptide of interest. Altogether, these projects strive to supplement pre-existing methodology for the synthesis of small molecule libraries and tools for metabolic labelling, and thus provide further small molecules for understanding biological systems.

Chemical biology encompasses the study and manipulation of biological system using chemistry, often by virtue of small molecules or unnatural amino acids. Much insight has been gained into the mechanisms of biological processes with regards to protein structure and function, metabolic processes and changes between healthy and diseased states. As an ever expanding field, developing new tools to interact with and impact biological systems is an extremely valuable goal. Herein, work is described towards the synthesis of a small library of heterocyclic-containing small molecules and the mechanistic details regarding the interesting and unexpected chemical compounds that arose; an alternative set of non-toxic copper catalyzed azide-alkyne click conditions for in vivo metabolic labelling; and the synthesis of an unnatural amino acid for further chemical modification via [3+2] cycloadditions with nitrones upon incorporation into a peptide of interest. Altogether, these projects strive to supplement pre-existing methodology for the synthesis of small molecule libraries and tools for metabolic labelling, and thus provide further small molecules for understanding biological systems.

Chemical biology encompasses the study and manipulation of biological system using chemistry, often by virtue of small molecules or unnatural amino acids. Much insight has been gained into the mechanisms of biological processes with regards to protein structure and function, metabolic processes and changes between healthy and diseased states. As an ever expanding field, developing new tools to interact with and impact biological systems is an extremely valuable goal. Herein, work is described towards the synthesis of a small library of heterocyclic-containing small molecules and the mechanistic details regarding the interesting and unexpected chemical compounds that arose; an alternative set of non-toxic copper catalyzed azide-alkyne click conditions for in vivo metabolic labelling; and the synthesis of an unnatural amino acid for further chemical modification via [3+2] cycloadditions with nitrones upon incorporation into a peptide of interest. Altogether, these projects strive to supplement pre-existing methodology for the synthesis of small molecule libraries and tools for metabolic labelling, and thus provide further small molecules for understanding biological systems.

Le principal objectif de cette thèse a consisté au développement d’une méthode de screenning pour la découverte de nouvelles réactions de ligations bioorthogonales ainsi que son application sur une bibliothèque développée pour cette étude. Par conséquent, un système de screening a été conçu en trois étapes consistant au départ en une analyse HPLC, puis une évaluation basée sur la fluorescence de haute résolution et finalement un test de microscopie confocal in cellulo. Puis, nous avons standardisé toutes les analyses avec les réactions CuAAC et SpAAC. En outre, nous avons synthétisés 18 réactifs d’intérêts et effectué un screening de 58 expériences de ligation avec une évaluation par méthode HPLC. Parmi les 9 réponses positives obtenues figure 6 réactions impliquant de nouveaux réactifs et les analyses LC‐MS ont pu tous les valider comme des réactions de cycloaddition directe à l’exception d’une réaction. Finalement, nous avons pu appliquer la méthode in cellulo développée, afin d’évaluer la pertinence des réactions de chélation CuAAC pour une application sur cellules. / The main goal of this thesis was the development of a screening method for the discovery of new bioorthogonal ligation reactions as well as its application on a self‐designed library. Therefore we designed a three step screening system consisting of a preliminary HPLC assay, a high resolution fluorescence based assay and a final in cellulo confocal microscopy assay.Subsequently we standardized all assays with the highly established CuAAC and SpAAC. Furthermore, we successfully synthesized 18 reagents of interest and screened 58 ligation experiments with the help of the HPLC setup. The 9 positive hits from this screening contained 6 reactions involving novel reagents and LCMS analysis was able to validate all but one as straight forward cycloaddition reaction. Finally we were able to apply the newly developed in cellulo assay to assess the suitability of chelating CuAAC for in cell application.