Depuis les années 1990, la chimie combinatoire dynamique permet la découverte et la préparation de nouveaux récepteurs synthétiques à partir de briques moléculaires simples sous contrôle thermodynamique. Dans ce contexte, nous avons récemment décrit une nouvelle famille de para-cyclophanes dynamiques: les dyn[n]arènes. Ces macrocycles, composés de briques moléculaires 1,4-bisthiophénoliques fonctionnalisées, ont pu être obtenus à l'échelle du gramme à partir d'une procédure simple ne mettant pas en jeu de purification par chromatographie. Cette accessibilité synthétique a rendu possible une étude structurale permettant la rationalisation des forces motrices mises en jeu lors des processus d'auto-assemblage, mais aussi de leurs propriétés de reconnaissance moléculaire vis-à-vis de molécules ioniques. A partir de données expérimentales et de calculs réalisés en chimie théorique, les phénomènes physiques responsables de la sélectivité et de l'affinité remarquables observées entre l'un des membres de cette famille, un dyn[4]arène poly anionique, et une série d'a,?-alkyle-diamines ont été étudiés. Finalement, au cours de cette étude, nous avons redécouvert une voie de synthèse simple menant à une famille de molécules encore peu étudiée : les dithiocines. La fonctionnalisation de ces objets a été explorée dans le but d'obtenir une plateforme multifonctionnelle pour des applications biologiques / Since the 1990s, dynamic combinatorial chemistry has allowed the discovery and preparation of new synthetic receptors from simple building blocks under thermodynamic control. In this context, we have recently described a new family of dynamic para cyclophanes, the so-called dyn[n]arenes. These macrocycles, made from functionalized 1,4-bisthiophenolic building blocks, could be obtained on a gram scale from a simple purification procedure, and without any chromatography. Their synthetic accessibility allows us to study the driving forces behind their self-assembly, as well as their molecular recognition properties towards ionic guest molecules. Experimental and computational experiments were also conducted to reveal the subtle physical phenomena that are responsible for the remarkable selectivity and affinity observed between a poly-anionic dyn[4]arene and a series of a,?-alkyl-diamines. During these previous studies, we rediscovered a simple synthetic route towards a family of molecules that is unexploited so far: the dithiocins. The functionalization of these molecular objects has been explored in order to generate versatile platforms for biological applications

The research work reported in the thesis deals with the development of dynamic covalent systems and their applications in evaluation and screening of protein-ligands and enzyme inhibitors, as well as in synthetic methodologies. The thesis is divided into four parts as described below. In part one, synthetic methodologies to access 3-functionalized phthalides and 3-thioisoindolinones using the concept of cascade reactions are demonstrated. Efficient syntheses of the target products are designed and performed in one-pot process under mild reaction conditions.  In part two, phosphine-catalyzed disulfide metathesis for the generation of dynamic carbohydrate system in aqueous solution is demonstrated. In the presence of biological target (Concanavalin A), the optimal dynamic ligand is successfully identified in situ by the 1H STD-NMR spectroscopy. In part three, lipase-catalyzed resolutions of dynamic reversible systems using reversible cyanohydrin and hemithioacetal reactions in one-pot processes are demonstrated. The dynamic systems are generated under thermodynamic control in organic solution and subsequently resolved by lipase-mediated resolution under kinetic control. The resolution processes resulted in the lipase-selected substrates with high structural and stereochemical specificities. In the last part, dynamic fragment-based strategy is presented using β-galactosidase as a model target enzyme. Based on our previous study, the best dynamic inhibitor of β-galactosidase was identified using 1H STD-NMR technique from dynamic hemithioacetal systems. The structure of the dynamic inhibitor is tailored by fragment linking and optimization processes. The designed inhibitor structures are then synthesized and tested for inhibition activities against β-galactosidase. / QC 20110526

Le présent travail de recherche vise à mieux connaître les interactions au sein d'auto-assemblages petites molécules – ADN dans le but de faciliter la conception de futurs ligands ou vecteurs de l'ADN. Pour se faire, des composés guanidiniums, sélectionnés pour leur capacité d'interaction avec les oxoanions – incluant les phosphodiesters de l'ADN – ont été bisfonctionnalisés pour sonder l'importance des interactions secondaires dans les auto-assemblages petites molécules - ADN. Deux approches différentes, rationnelle et combinatoire dynamique, ont été utilisées pour étudier les interactions au sein des auto-assemblages formés le long du squelette phosphodiester.Avec l'approche rationnelle, des guanidiniums bisfonctionnalisés avec des groupements aromatiques de taille variable ont démontré leur capacité à s'auto-assembler avec l'ADN en solution aqueuse via la reconnaissance du squelette phosphodiester. Les expériences de compétition montrent l'importance des interactions d'empilement π-π dans la stabilisation de ces auto-assemblages.Dans le cadre de l'approche combinatoire dynamique, un guanidinium comportant deux terminaisons aldéhyde a été utilisé pour générer, par amination réductrice, des bibliothèques combinatoires dynamiques basées sur la liaison imine. La génération de bibliothèques avec différentes amines en absence et en présence d'oligo(dT) sur cellulose met en évidence des effets de matrice caractérisés par des changements constitutionnels. Les résultats montrent ainsi que les constituants aux groupements cationiques et aromatiques sont sélectivement retenus contrairement aux constituants portant des substituants anioniques. Les informations structurales obtenues par ces deux approches pourront à l'avenir être utilisées pour la conception de nouveaux ligands de l'ADN.Parallèlement à ces études des interactions petites molécules – ADN, des polymères covalents dynamiques poly-acylhydrazones combinant des moitiés cationiques et de courts groupements d'éthylène glycol au sein de leur chaîne principale ont été conçus. Ces matériaux, capables de s'auto-assembler sous forme d'oligomères par polycondensation à haute concentration, complexent efficacement l'ADN double brin dans les médias biologiques et sont dégradables en milieu acide. L'association de ces deux caractéristiques les rend donc intéressants pour une application en tant que vecteurs « intelligents » pour la délivrance de gènes. / The present research work aims to learn more about the interactions inside small-molecules – DNA self-assemblies in order to facilitate the conception of future DNA ligands or vectors. To achieve this goal, guanidinium compounds, selected for their recognized ability to interact with oxoanions – DNA phosphodiesters – were bisfunctionnalized to probe the importance of secondary interactions in the small-molecules – DNA self-assemblies. Two different approaches, rational and dynamic combinatorial, were used to study the interactions inside the self-assemblies formed along the phosphodiester backbone.With the rational approach, guanidiniums bisfunctionnalized with aromatic groups of varying size demonstrated the ability to self-assemble with DNA in aqueous solution via phosphodiester recognition. The competition experiments show the importance of the π-π stacking interactions in the stabilisation of these self-assemblies.Within the framework of the dynamic combinatorial approach, a guanidinium bearing two aldehyde terminations was used to generate, by reductive amination, dynamic combinatorial libraries based on the imine bond. The generation of libraries with different amines in absence and in presence of oligo(dT) on cellulose shows templating effects that are characterized by constitutional changes. The results thus show that constituents with cationic or aromatic groups are selectively retained on DNA while those featuring anionic groups are not.The structural information gained by these two approaches could be used in the future to design new DNA ligands.In parallel to these studies of the small-molecules – DNA interactions, dynamic covalent polymers combining cationic moieties and short ethylene glycol groups in their principal chain have been designed. These materials are able to self-assemble as oligomeres by polycondensation performed at high concentration and effectively complex double-stranded DNA in biological media and are degradable in acidic conditions. The association of these two characteristics make them interesting for an application as “smart” vectors for gene delivery.

La reconnaissance de biomolécules dans des milieux biologiques complexes est un réel défi pour les chimistes et les biologistes, associé à des enjeux médicaux majeurs. Face à cette problématique, le chimiste peut choisir d’utiliser des molécules désignées par ses soins, ou encore de sélectionner et d’utiliser directement des structures commerciales ou naturelles. Suivant cette dernière approche, les dendrigrafts de lysines (DGL) ont montré une neutralisation des héparines de différentes tailles supérieures à l’action de la protamine, le seul médicament autorisé en cas de surdosage de l’anticoagulant. Une étude par dynamique moléculaire a permis de mettre en avant le mécanisme d’interaction entre les héparines d’une part, et les DGLs et la protamine d’autre part. Par ailleurs, suivant la première approche de design et synthèse, nous avons utilisé la chimie combinatoire dynamique pour obtenir des nouveaux récepteurs synthétiques à partir de brique moléculaires diverses de type 1,4-dithiphénols. Des études à la fois théorique, en DFT et dynamique moléculaire, et expérimentale, ont été menés pour comprendre les phénomènes régissant l’auto-assemblage de ces briques en oligomères cycliques et la complexation de ces cavitands avec des biomolécules d’intérêt / The recognition of biomolecules in complex biological media is a challenge associated with various therapeutic applications. The chemist can address this issue following two approaches: either he designs him-self and synthesises its molecules or he selects a commercially available or natural molecule and directly uses it for its properties. Following the last strategy, dendrigraft of lysine (DGL) efficiently neutralised all classes of the anticoagulant heparin, with a superior effect compared to protamine, the only FDA-approved drug in case of heparin overdosage. A study by molecular dynamic revealed the mechanism of binding between heparins and DGL and protamine respectively. At the opposite of this approach, we used dynamic combinatorial chemistry in order to obtain disulfide bridged cyclophanes from the self-assembly of various 1,4-bisthiophenols by oxidation of thiols into disulfide bonds. By a combination of theoretical (DFT and molecular dynamic) and experimental studies, we investigated the driving forces and the influences of fundamental concepts such as solvation and steric effects for the self-assembly of these polythiols and the binding of the corresponding cavitands with therapeutic biomolecules

This thesis deals with the design, formation and evaluation of dynamic systems constructed by means of sulfur-containing reversible reactions, in organic and aqueous media and under mild conditions. In a first part, the synthesis of thioglycoside derivatives, constituting the biologically relevant starting components of the dynamic systems, is described. In addition, the pD-profile of the mutarotation process in aqueous media for a series of 1-thioaldoses is reported and revealed an astonishing beta-anomeric preference for all the carbohydrate analogs under acidic or neutral conditions. In a second part, the phosphine-catalyzed or -mediated disulfide metathesis for dynamic system generation in organic or aqueous media is presented, respectively. The direct in situ 1H STD-NMR resolution of a dynamic carbohydrate system in the presence of a target protein (Concanavalin A) proved the suitability and compatibility of such disulfide metathesis protocols for the discovery of biologically relevant ligands. In a third part, hemithioacetal formation is demonstrated as a new and efficient reversible reaction for the spontaneous generation of a dynamic system, despite a virtual character of the component associations in basic aqueous media. The direct in situ 1H STD-NMR identification of the best dynamic beta-galactosidase inhibitors from the dynamic HTA system was performed and the results were confirmed by inhibition studies. Thus, the HTA product formed from the reaction between 1-thiogalactopyranose and a pyridine carboxaldehyde derivative provided the best dynamic inhibitor. In a fourth and final part, a dynamic drug design strategy, where the best inhibitors from the aforementioned dynamic HTA system were used as model for the design of non-dynamic (or “static”) beta-galactosidase inhibitors, is depicted. Inhibition studies disclosed potent leads among the set of ligands. / QC 20100621

This thesis is divided into six parts, all centered around the development of dynamic (i.e., reversibly interacting) systems of molecules and their applications in dynamic combinatorial chemistry (DCC) and organic synthesis. Part one offers a general introduction, as well as a more detailed description of DCC, being the central concept of this thesis. Part two explores the potential of the nitroaldol reaction as a tool for constructing dynamic systems, employing benzaldehyde derivatives and nitroalkanes. This reaction is then applied in part three where a dynamic nitroaldol system is resolved by lipase-catalyzed transacylation, selecting two out of 16 components. In part four, reaction and crystallization driven DCC protocols are developed and demonstrated. The discovery of unexpected crystalline properties of certain pyridine β-nitroalcohols is used to resolve a dynamic system and further expanded into asynthetic procedure. Furthermore, a previously unexplored tandem nitroaldol-iminolactone rearrangement reaction between 2-cyanobenzaldehyde and primarynitroalkanes is used for the resolution of dynamic systems. It is also coupled with diastereoselective crystallization to demonstrate the possibility to combine several selection processes. The mechanism of this reaction is investigated and a synthetic protocol is developed for asymmetric synthesis of 3-substituted isoindolinones. Part five continues the exploration of tandem reactions by combining dynamic hemithioacetal or cyanohydrin formation with intramolecular cyclization to synthesize a wide range of 3-functionalized phthalides. Finally, part six deals with the construction of a laboratory experiment to facilitate the introduction of DCC in undergraduate chemistry education. The experiment is based on previous work in our group and features an acetylcholinesterase-catalyzed resolution of a dynamic transthioacylation system. / QC 20100628

The fast development of DNA-encoded chemical libraries (DECL) in the past 10 years has received great attention from pharmaceutical industries. It applies the selection approach for small molecular drug discovery. Because of the limited choices of DNA-compatible chemical reactions, most DNA-encoded chemical libraries have a narrow structural diversity and low synthetic yield. There is also a poor correlation between the ranking of compounds resulted from analyzing the sequencing data and the affinity measured through biochemical assays. By combining DECL with dynamical chemical library, the resulting DNA-encoded dynamic library (EDCCL) explores the thermodynamic equilibrium of reversible reactions as well as the advantages of DNA encoded compounds for manipulation/detection, thus leads to enhanced signal-to-noise ratio of the selection process and higher library quality. However, the library dynamics are caused by the weak interactions between the DNA strands, which also result in relatively low affinity of the bidentate interaction, as compared to a stable DNA duplex. To take advantage of both stably assembled dual-pharmacophore libraries and EDCCLs, we extended the concept of EDCCLs to heat-induced EDCCLs (hi-EDCCLs), in which the heat-induced recombination process of stable DNA duplexes and affinity capture are carried out separately. To replace the extremely laborious and repetitive manual process, a fully automated device will facilitate the use of DECL in drug discovery. Herein we describe a novel lab-on-a-chip platform for high throughput drug discovery with hi-EDCCL. A microfluidic system with integrated actuation was designed which is able to provide a continuous sample circulation by reducing the volume to a minimum. It consists of a cooled and a heated chamber for constant circulation. The system is capable to generate stable temperatures above 75 °C in the heated chamber to melt the double strands of the DNA and less than 15 °C in the cooled chamber, to reanneal the shuffled library. In the binding chamber (the cooled chamber) specific retaining structures are integrated. These hold back beads functionalized with the target protein, while the chamber is continuously flushed with library molecules. Afterwards the whole system can be flushed with buffer to wash out unspecific bound molecules. Finally the protein-loaded beads with attached molecules can be eluted for further investigation

Discipline récente, la chimie supramoléculaire est l'un des domaines les plus fertiles de la recherche chimique. Motivé par le défi que représente la reconnaissance moléculaire sur mesure d'édifices complexes, un grand intérêt est apparu pour la conception et la synthèse des récepteurs macrocycliques polyfonctionnalisés. Nous avons récemment décrit une nouvelle classe de récepteurs moléculaires accessibles et polyvalents: les Dyn[n]arenes. Cette nouvelle classe est obtenue à partir de briques moléculaires 1,4-dithiophénols fonctionnalisés en position ortho assemblées par des liaisons disulfures. Cette stratégie de macrocyclisation contrôlée thermodynamiquement permet de produire de grandes quantités de produit final avec un moindre coût synthétique. Des récepteurs sur-mesure pour la reconnaissance d'anions, de cations et de zwitterions ont été obtenus par cette approche polyvalente. En particulier, le Dyn[4]arene octacarboxylate a montré la capacité de reconnaître sélectivement des dérivés de la lysine par via un ajustement induit asymétrique du récepteur lors de l'association. L'utilisation de ce récepteur pour reconnaître des peptides et protéines portant en position N-terminale une lysine a été étudiée. Enfin, la post-fonctionnalisation de ces Dyn[4]arenes a été explorée afin d'améliorer leur solubilité et leur propriétés de reconnaissance vis-à-vis de cibles biologiquement actives, ainsi que pour étudier la possibilité de leur greffage sur phase solide et leur utilisation en chromatographie d'affinité / As a recent discipline, supramolecular chemistry is one of the most active and fast-growing fields of chemical research. Driven by the challenge that tailored molecular recognition of complex molecules represents, a large interest has grown for the design and synthesis of multi-functionalized macrocyclic receptors. We recently described a new class of accessible and versatile molecular receptors: Dyn[n]arenes. This new class is obtained from 1,4-dithiophenols units functionalized in ortho position and assembled by disulfide linkages. This strategy of thermodynamically controlled macrocyclization allows producing large amounts of final product with a low synthetic cost. On demand receptors for anions, cations and zwitterions were obtained by this versatile approach. Particularly, the octacarboxylate-bearing dyn[4]arene showed the ability to selectively recognize Lysine derivatives via an asymmetric induced adjustment of the receptor upon the complexation. The use of this receptor to recognize N-terminal Lysine tagged peptides and proteins have been investigated. Finally, post-functionalization of Dyn[4]arenes have been explored to improve their solubility and recognition properties toward biologically active target and to investigate their solid phase grafting to be implemented in affinity chromatography