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

Diss. (sammanfattning) Umeå : Univ., 2008. / Härtill 4 uppsatser.

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

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This thesis describes different aspects of protein interactions. Initially the function of peptides and their conjugates with small molecule inhibitors on the surface of Human Carbonic Anhydrase isoenzyme II (HCAII) is evaluated. The affinities for HCAII of the flexible, synthetic helix-loop-helix motif conjugated with a series of spacered inhibitors were measured by fluorescence spectroscopy and found in the best cases to be in the low nM range. Dissociation constants show considerable dependence on linker length and vary from 3000 nM for the shortest spacer to 40 nM for the longest with a minimum of 5 nM for a spacer with an intermediate length. A rationale for binding differences based on cooperativity is presented and supported by affinities as determined by fluorescence spectroscopy. Heteronuclear Single Quantum Correlation Nuclear Magnetic Resonance (HSQC) spectroscopic experiments with 15N-labeled HCAII were used for the determination of the site of interaction. The influence of peptide charge and hydrophobicity was evaluated by surface plasmon resonance experiments. Hydrophobic sidechain branching and, more pronounced, peptide charge was demonstrated to modulate peptide – HCAII binding interactions in a cooperative manner, with affinities spanning almost two orders of magnitude. Detailed synthesis of small molecule inhibitors in a general lead discovery library as well as a targeted library for inhibition of α-thrombin is described. For the lead discovery library 160 members emanate from two N4-aryl-piperazine-2-carboxylic acid scaffolds derivatized in two dimensions employing a combinatorial approach on solid support. The targeted library was based on peptidomimetics of the D-Phe-Pro-Arg showing the scaffolds cyclopropane-1R,2R-dicarboxylic acid and (4-amino-3-oxo-morpholin-2-yl)- acetic acid as proline isosters. Employing 4-aminomethyl-benzamidine as arginine mimic and different hydrophobic amines and electrophiles as D-phenylalanine mimics resulted in 34 compounds showing IC50 values for α-thrombin ranging more than three orders of magnitude with the best inhibitor showing an IC50 of 130 nM. Interestingly, the best inhibitors showed reversed stereochemistry in comparison with a previously reported series employing a 3-oxo-morpholin-2-yl-acetic acid scaffold.

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

Aquesta tesi doctoral se centra en l'estudi de l'aplicació de pèptids antimicrobians en la lluita contra agents patògens de cultius de plantes d'interès econòmic.L'estratègia sintètica s'ha portat a terme utilitzant metodologies convencionals de síntesi de pèptids en fase sòlida com l'estratègia tridimensional ortogonal Fmoc/tBut/Allyl. Ha calgut fer la recerca de les condicions òptimes per a l'eliminació del grup Allyl i la ciclació. D'entre els pèptids cíclics de 4-10 aminoacids sintetitzats, el decapèptid c(Lys-Leu-Lys-Leu-Lys-Phe-Lys-Lys-Leu-Gln) ha resultat ésser el més efectiu i s'ha pres com a base per al disseny d'una quimioteca de 56 pèptids. Dels resultats obtinguts s'ha sintetitzat una segona quimioteca basada en l'estructura general c(X1-X2-X3-X4-Lys-Phe-Lys-Lys-Leu-Gln) determinada com la que posseix el millor perfil d'activitat. Els pèptids més efectius obtinguts constituixen els primers exemples de pèptids cíclics actius contra E. amylovora i poden ser considerats com a bons candidats pel desenvolupament d'agents antimicrobians efectius en protecció vegetal. / This PhD thesis was centred on the study of the application of de novo designed head-to-tail cationic cyclic peptides as inhibitors of the plant pathogenic microorganisms responsible for diseases in plants of great economic importance.The solid-phase synthesis of the cyclopeptides was carried out using a three-dimensional orthogonal Fmoc/tBut/Allyl strategy. The optimisation study of the allyl group removal and of the head-to-tail cyclization of linear peptides on SynPhase Lanterns was required for the syntheses. From the synthesized cyclic peptides of 4 to 10 residues, the cyclodecapeptide c(Lys-Leu-Lys-Leu-Lys-Phe-Lys-Lys-Leu-Gln) was the most active and has been used as parent peptide in a using a combinatorial chemistry approach. From the results, a second library based on the structure c(X1-X2-X3-X4-Lys-Phe-Lys-Lys-Leu-Gln) has been synthesized. The best cyclodecapeptides are the first examples of cyclic peptides effective against E. amylovora and make them potential candidates for the development of antimicrobial agents for use in plant protection.