La comparaison de site peut-elle vérifier l’hypothèse: «Les origines biosynthétiques des produits naturels leurs confèrent des activités biologiques»? Pour répondre à cette question, nous avons développé un outil modélisant les propriétés accessibles au solvant des sites de liaison. La méthode a montré des aspects intéressants, mais elle souffre d’une sensibilité aux coordonnées atomiques. Cependant, des méthodes existantes nous ont permis de prouver que l’hypothèse est valide pour la famille des flavonoïdes. Afin d’étendre l’étude, nous avons développé un procédé automatique capable de rechercher des structures d’enzymes de biosynthèse de produits naturels disposant de sites actifs capables de lier une molécule de petite taille. Nous avons trouvé les structures de 117 enzymes.Les structures nous ont permis de caractériser divers modes de liaison substrat-enzyme, nous indiquant l’empreinte biologique des produits naturels ne correspond pas toujours au modèle « clé- serrure ». / Can computational binding site similarity tools verify the hypothesis: “Biosynthetic moldings give potent biological activities to natural products”? To answer this question, we designed a tool modeling binding site properties according to solvent exposure. The method showed interesting characteristics but suffers from sensitivity to atomic coordinates. However, existing methods have delivered evidence that the hypothesis was valid for the flavonoid chemical class. In order to extend the study, we designed an automated pipeline capable of searching natural products biosynthetic enzyme structures embedding ligandable catalytic sites. We collected structures of 117 biosynthetic enzymes. Finally, according to structural investigations of biosynthetic enzymes, we characterized diverse substrate-enzyme binding-modes, suggesting that natural product biological imprints usually do not agree with the “key-lock” model.

Le développement de procédés catalytiques pour la valorisation chimique du dioxyde de carbone (CO2), suscite un intérêt grandissant en termes de chimie du carbone et de développement durable. Les travaux de cette thèse portent sur l’étude de la synthèse de carbonates cycliques à partir du couplage du CO2 avec des époxydes. De nombreux catalyseurs ont été développés dont les sels d’ammoniums fournissant le nucléophile nécessaire pour initier la réaction par ouverture de l’époxyde. Notre projet propose une nouvelle approche qui consiste à augmenter la nucléophilicité du catalyseur via une chimie hôte-invité dans laquelle des récepteurs moléculaires de type cavitands viennent sélectivement encapsuler les cations ammoniums, libérant ainsi l’anion nucléophile pour une meilleure réactivité. Notre système catalytique, testé à 1 bar de CO2, a notamment démontré tout son potentiel par l’activation accrue de sels de tétraméthylammonium initialement inactifs. Des expériences effectuées sous une pression de CO2 de 10 bar, ont permis d'étudier l’influence de la structure des cavitands et de montrer qu’une double activation était possible grâce à la conception de cavitands comportant des fonctions acides de Brönsted et des propriétés d’encapsulation optimales. Une application à la catalyse hétérogène a finalement été initiée par l’immobilisation des ammoniums ou des cavitands sur des supports à base de silice pour profiter des avantages de tels procédés. / The utilization of carbon dioxide (CO2) as a key component in organic transformations has recently drawn much attention as a greener alternative to fossil fuel based resources. The objectives of this work aim at studying the synthesis of cyclic carbonates from the coupling of CO2 with epoxide. Numerous catalysts have been proposed for this reaction among which the ammonium halides providing the nucleophile to initiate the reaction by opening the epoxide. Herein, we propose a new approach based on host-guest chemistry, to improve catalytic reactivity by increasing the nucleophilicity of the halide anion. For this purpose, cavitand molecular receptors able to bind quaternary ammonium ions are used, releasing the anionic nucleophile for the initial epoxide ring-opening reaction. At CO2 atmospheric pressure, our catalytic systems demonstrated a great potential by the dramatic activation of tetramethylammonium halides, whereas when used alone, these catalysts had never shown any activity. The influence of the cavitand structure was investigated through experiments run under 10 bar of CO2 pressure, and revealed that a double activation was possible with cavitand bearing Brönsted acidic hydroxyl functions and optimal recognition properties. The heterogeneization of such catalytic systems was finally studied with the grafting of either ammoniums or cavitands on silica based materials.

Une grande partie des chimistes puisent leur inspiration auprès de la biologie. C’est le cas des chercheurs en chimie supramoléculaire, qui travaillent sur l’élaboration de récepteurs moléculaires synthétiques capables d’effectuer des reconnaissances moléculaires envers des substrats d’intérêt biologiques. Le but est ainsi de mimer l’activité des protéines naturelles, en vue d’applications cliniques.L’unité cyclotribenzylène (CTB) est une structure de symétrie C3 qui possède des propriétés complexantes intéressantes. Un CTB relié à une deuxième unité complexante par trois bras espaceurs constitue la famille des hémicryptophanes. Au cours de cette thèse, nous avons travaillé sur l’élaboration de récepteurs moléculaires basés sur cette unité CTB. Dans un premier temps nous avons développé une nouvelle méthode de synthèse d’hémicryptophane énantiopurs à l’échelle du gramme en vue d’effectuer des reconnaissances stéréosélectives de neurotransmetteurs chiraux. Nous avons ensuite développé des récepteurs CTB et hémicryptophanes combinant la chiralité du CTB et du groupement binaphtol. La configuration absolue des unités chirales ont été déterminées par une méthode de corrélation chimique. Ces récepteurs ont été utilisés pour réaliser des expériences de reconnaissance stéréosélective de saccharide et de bonnes diastéréosélectivités ont été obtenues. Enfin, nous avons travaillé sur l’élaboration d’une voie de synthèse d’hémicryptophanes fluorescents capables de subir des excitations bi-photoniques dans le but d’effectuer des expériences de suivi dans l’espace et dans le temps de substrats d’intérêt biologiques en milieu in-vivo. / Biology is an inspiration for chemists. Especially for the field of supramolecular chemistry, which one of the aim is to develop synthetic molecular receptors capable of molecular recognition to biological substrates, to mimic the activity of natural proteins for clinical applications.Cyclotribenzylene unit (CTB) is a C3-symmetry structure which present interesting recognition properties. When a CTB is connecting to another molecular unit by three spacers arms, it forms an hemicryptophane receptor. During this thesis, we worked on elaboration receptors based on CTB unit. First, a new way of enantiopure hemicryptophane synthesis on gram scale has been developed for stereoselective recognition of chiral neurotransmitters. Then receptors based on chirality of CTB and binaphthol unit has been developed. Assignment of absolute configuration of chiral unit was determined by a chemical correlation. Stereoselective recognition of carbohydrates by these receptors revealed good diastereoselectivity. Finally, a synthetic pathway leading to fluorescent hemicryptophanes was developed for bi-photonic excitation in order to realize in-vivo experiments of tracking biological substrates.

Peptides are used as synthetically available and easily derivatizable scaffold upon which it is possible to develop ligands targeting broad spectrum of biological targets. A time-tested approach to peptide binder identification is the preparation and screening of combinatorial libraries. Bypassing of this complicated procedure is possible by using biological systems for presentation, identification and selection of peptides based on the principle of in vitro evolution - i.e. display techniques. There are two complementary automated solutions for peptide binder identification described in this work. First is the SPENSER parallel peptide synthesizer, developed as a part of this diploma project, which can be used for peptide ligand discovery and optimization as well as validation of ligands identified using display techniques. Several libraries consisting of a total of 1 052 peptides have been prepared and then used to describe its potential applications. A sample of 154 preparations, representing 14.6 % analytical coverage of the prepared libraries, showed an average purity of 67 ± 19 % according to LC-MS. The libraries presented illustrate that SPENSER is a suitable tool for the parallel synthesis of linear and disulfide-cyclized peptides with limited variability, or libraries consisting of short...

Antibodies are the gold standard molecular recognition elements and a cornerstone of molecular biology. They are used in immunoassays to precisely measure a specific analyte, but certain targets are especially challenging. Difficult targets include small molecules and molecules that do not induce an immune response. Aptamers are short oligonucleotides that can form 3-dimensional structures and bind targets with high specificity. Aptamers are smaller and more flexible than antibodies and could therefore solve this problem. In contrast to antibodies, aptamers are synthetically produced, so they can have affinity for molecules that do not induce an immune response. This also makes them cheaper, faster and more ethical to produce. They are also easily modified and have the ability to renature and can therefore be reused.  Our conclusions are that aptamers can outperform antibodies, especially for small molecule targets, and that the synthetic production of aptamers gives them a further advantage over antibodies. Our report compares several different types of detection methods that use aptamers and we conclude that fluorescence-based methods are the most easy to use with basic lab equipment, can be made similar to the ELISA kits in addition to giving highly sensitive detection. We describe a variety of fluorescence-based detection strategies but the optimal method will depend on the specific aptamer and target. The report also includes an ethical analysis where antibodies and aptamers are compared. This report is commissioned by Mercodia AB, a company that develops, manufactures and distributes immunoassays for biomarkers within the field of metabolic disorders. They commissioned this report in order to give an overview of how aptamers interact with their target, and also to compare aptamer-based detection strategies with sensitivity prioritized over selectivity.  This was done by literature research.

Plants secrete peptide ligands and use receptor signaling to respond to stress and control development. Understanding the signaling mechanisms and associated molecular trafficking is key to improving plant health and productivity for food, fiber and energy applications. However, one of the challenges to elucidating communication pathways in plants is to study the trafficking of molecules and signals iteratively and non-destructively. This study focuses on using fiber-optic fluorescence microscopy to image live plants iteratively and non-destructively after delivering both labeled and unlabeled phytosulfokine (PSK) into the plant. PSK is a sulfated peptide hormone involved in the regulation of plant cell division and growth via specific receptors, PSKRs. It also plays a role in regulating how plants are able to tolerate stress conditions. The microscope provides two-color (FITC/TRITC) optics and provides high-resolution (3–5 µm) epifluorescence micrographs via a 1-m coherent imaging fiber and a GRIN objective lens. To obtain high-quality images, the fiber was mounted either to a conventional upright microscope body equipped with a leaf compressor, or to a leaf clip with 5-axis positioning (X–Y–Z plus pitch and yaw) mounted on an extensible arm. PSK and TAMRA-labelled PSK were delivered into the roots of various Arabidopsis thaliana genotypes (wt; receptor-deficient: pskr1/pskr2; and tagged receptor overproducing: PSKR1‑GFP), and their movement in roots and leaves was tracked with the fiber-optic fluorescence microscope. Peptide trafficking was successfully observed in live plants non- destructively, confirming that PSK is mobile in both wt and receptor-deficient plants. Preliminary results suggest that the level of receptor PSKR1 may change in response to PSK, and that levels of PSKR1, PSKR2 or both may impact the trafficking of PSK. Understanding how PSK is trafficked in plants will offer insights into how we can improve plants health and productivity.

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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