<p>This thesis examines the isolation and characterisation (biological and chemical) of polypeptides from plants. A fractionation protocol was developed and applied on 100 plant materials with the aim of isolating highly purified polypeptide fractions from small amounts of plant materials. The polypeptide fractions were analysed and evaluated for peptide content and biological activities. A multitarget functional bioassay was optimised as a method for detecting substances interacting with the inflammatory process of activated neutrophil granulocytes. In this assay, the neutrophil was challenged with an inflammatory mediator, <i>N</i>-formyl methionyl-leucyl-phenylalanine (fMLP), or with platelet activating factor (PAF), to induce exocytotic release of the enzyme elastase, which then was quantified by photometric determination of the product p-nitroanilide (pNA) formed from a chromogenic substrate for elastase. Of the tested extracts, 41% inhibited pNA formation more than 60%, and 3% stimulated formation.</p><p>Phoratoxin B and four new peptides, phoratoxins C-F, were isolated from <i>Phoradendron tomentosum</i>. In addition, the cardiac glycoside digitoxin was isolated from <i>Digitalis purpurea</i>. All these substances expressed cytotoxicity and a neutrophil challenging activity.</p><p>Phoratoxins C-F were similar to earlier described phoratoxins A and B, which belong to the group of thionins. All the peptides were evaluated for cytotoxicity in a human cell line panel. Phoratoxin C was the most potent towards the cell lines (mean IC₅₀: 160 nM), and was therefore investigated further on tumour cells from patients. Correlation analysis of the log IC₅₀ values indicated a mechanism of action different from clinically used archetypal cytotoxic drugs. Phoratoxin C also showed selective toxicity to the solid tumours when compared to the haematological cancer types. The phoratoxin C was 18 times more potent towards the solid tumour samples from breast cancer cells (87 nM) compared to the tested haematological malignancies.</p><p>The structure-activity relationship concerning cytotoxicity was evaluated for digitoxin and related cardiac glycosides. Digitoxin was shown to be potent, with the average IC₅₀ 37 nM being within the therapeutic concentration used for cardiac congestion (13-45 nM). Digitoxin expressed selective toxicity towards solid tumours from patients compared to haematological malignancies.</p>

Thromboxane A2 (TXA2) is an important mediator metabolized from arachidonic acid through the cyclooxygenase pathway, mainly in platelets and macrophages. It is a potent inducer of platelet aggregation and smooth muscle contraction. Its overproduction has been detected in pathologies such as stroke, asthma, myocardial infarction or atherosclerosis. The action of TXA2 is mediated by a specific G-protein coupled receptor (TP) of which two alternative spliced isoforms, TPalpha and TPbeta, have been described. The exact role of these two isoforms is not clearly understood. However, recent studies have described their implications in vascular physiology and pathology. The inhibition of the action of TXA2 on platelets and blood vessels would be interesting as original therapies against cardiovascular diseases. Consequently, the design of TP receptor antagonists remains of great interest in cardiovascular medicine. In the laboratory of medicinal chemistry (University of Liège, Belgium), several nitrobenzenesulfonylureas, derived from torasemide (a loop diuretic), have been previously described as TP receptor antagonists. Two compounds, BM573 and BM613 were among the most interesting molecules identified in that previous work. The present project is divided in two parts. First, we have determined the pharmacological properties of BM573 and BM613 as thromboxane synthase inhibitors and TP receptor antagonists, in vitro and in vivo. In our assays, these two compounds were proved to have high affinity for both TPalpha and TPbeta, to be potent antiplatelet agents, to inhibit thromboxane synthase and TP-mediated smooth muscle contraction. Additionally, they significantly reduced the size of the thrombus in a rat model of ferric chloride-induced arterial thrombosis. Consequently, we demonstrated that the TP receptor antagonists BM573 and BM613, belonging to the chemical family of nitrobenzenesulfonylureas, could be regarded as antiplatelet and antithrombotic agents potentially useful in thromboxane-related diseases such as stroke or myocardial infarction. Secondly, given the interesting pharmacological profile of BM573 and BM613, we have designed and synthesized several series of compounds derived from these two agents. We have evaluated the binding properties (affinity) of the first generation (+/- 35 original derivatives) of compounds on either TPalpha or TPbeta, transiently expressed in COS-7 cell lines. Additionally, we have measured the ability of our drugs to inhibit the intracellular calcium mobilization upon TPalpha or TPbeta stimulation. To confirm our results, we also assessed the antiplatelet properties of our drugs by means of determination of inhibition of human platelet aggregation. On the basis of the results obtained with these in vitro assays, we have synthesized and evaluated a second generation of derivatives (+/- 35 original compounds) and improved the selectivity of several original compounds for TP receptor isoforms. The originality of this work was to evaluate a large library of synthetic compounds on both TP receptor isoforms, using specific pharmacological tests. By means of structure-activity relationship studies, we were able to identify chemical groups implicated in selectivity and to propose lead compounds for development of highly specific TPalpha or TPbeta antagonists. Besides, we have identified an in vivo drug candidates for prevention of thrombosis and pathological platelet aggregation./Le thromboxane A2 (TXA2) est un métabolite de la cascade de lacide arachidonique (AA) par la voie des cyclooxygénases et de la thromboxane synthase, principalement formé dans les plaquettes et les macrophages. Le TXA2 est un puissant inducteur de lagrégation plaquettaire et de la contraction des muscles lisses vasculaires et bronchiques. Par ailleurs, une augmentation des taux en TXA2 a été constatée dans différentes pathologies : l'infarctus du myocarde, l'atherosclérose, les accidents vasculaires cérébraux, ou encore l'asthme. Laction du TXA2 sur les tissus résulte de la stimulation dun récepteur appartenant à la famille des récepteurs couplés aux protéines G. Ce récepteur au TXA2 (TP) présente deux isoformes générées par épissage alternatif, TPalpha et TPbeta. Le rôle physiologique exact de ces deux isoformes n'est pas encore connu. Cependant, de récents travaux ont mis en évidence leur importance, notamment dans la physiologie vasculaire et dans certaines pathologies. Linhibition de laction du TXA2 au niveau des plaquettes et des vaisseaux sanguins pourrait donc être une stratégie thérapeutique innovante pour traiter et prévenir les maladies cardiovasculaires. En conséquence, le développement dantagonistes des récepteurs TP reste dun grand intérêt en médecine cardiovasculaire. Des études de pharmacomodulation avaient permis au Laboratoire de Chimie Pharmaceutique (Université de Liège, Belgique) d'identifier des nitrobenzènesulfonylurées, dérivées du torasémide (un diurétique de lanse), présentant un puissant antagonisme des récepteurs TP. Parmi ceux-ci, deux composés, le BM573 et le BM613, faisaient parties des molécules les plus intéressantes identifiées au cours de ces précédentes recherches. Ce projet est divisé en deux parties. Premièrement, nous avons déterminé les propriétés pharmacologiques du BM573 et du BM613 en tant quinhibiteurs de la thromboxane synthase et antagonistes des récepteurs TP, in vitro et in vivo. Au cours de nos expériences, ces deux composés se sont révélés posséder une grande affinité pour TPalpha et TPbeta, être de puissants agents antiplaquettaires, des inhibiteurs de la thromboxane synthase et de la contraction des muscles lisses induite par le TXA2. En outre, lutilisation de ces produits dans un modèle de thrombose artérielle induite par le chlorure ferrique chez le rat a provoqué une réduction significative du thrombus formé. En conséquence, nous avons démontré que le BM573 et le BM613, appartenant à la famille chimique des nitrobenzenesulfonylurées, pouvaient être considérés comme des agents antiplaquettaires et antithrombotiques, potentiellement utiles en tant quagents thérapeutiques dans des pathologies associées au TXA2 telles que linfarctus du myocarde ou laccident vasculaire cérébral. Ensuite, nous nous sommes concentrés sur l'activité de cette famille de composés (les nitrobenzènesulfonylurées) vis-à-vis des deux isoformes du récepteur au thromboxane. Pour ce faire, nous avons conçu et synthétisé de nombreuses séries de composés dérivés du BM573 et du BM613. Nous avons tout dabord évalué laffinité de la première génération de composés (+/- 35 dérivés) sur des lignées cellulaires (COS-7) exprimant sélectivement soit TPalpha soit TPbeta. De plus, nous avons mesuré la capacité de ces composés à inhiber la mobilisation de calcium intracellulaire ([Ca2+]i) induite par la stimulation des deux isoformes TPalpha et TPbeta séparément. Nos résultats ont été confirmés sur agrégation plaquettaire humaine. Sur la base des résultats obtenus avec cette première génération de produits, nous avons synthétisé une seconde génération (+/- 35 dérivés) de composés, et avons réussi à augmenter la sélectivité en faveur de TPbeta pour certains produits. Loriginalité de ce travail réside dans le fait que nous avons évalué un nombre de produits importants sur TPalpha et TPbeta, au moyen de tests pharmacologiques spécifiques. Grâce à des études de relation structure-activité, nous avons identifié des groupements chimiques impliqués dans la sélectivité entre les deux isoformes. Nous pouvons donc proposer des structures "chef de file" pouvant être utiles pour le développement de composés hautement sélectifs, soit pour TPalpha, soit pour TPbeta. Par ailleurs, nous avons identifié in vivo des candidats pour le développement dagents thérapeutiques pour la prévention des thromboses et des autres pathologies provoquées par une activation plaquettaires excessive.

This thesis examines the isolation and characterisation (biological and chemical) of polypeptides from plants. A fractionation protocol was developed and applied on 100 plant materials with the aim of isolating highly purified polypeptide fractions from small amounts of plant materials. The polypeptide fractions were analysed and evaluated for peptide content and biological activities. A multitarget functional bioassay was optimised as a method for detecting substances interacting with the inflammatory process of activated neutrophil granulocytes. In this assay, the neutrophil was challenged with an inflammatory mediator, N-formyl methionyl-leucyl-phenylalanine (fMLP), or with platelet activating factor (PAF), to induce exocytotic release of the enzyme elastase, which then was quantified by photometric determination of the product p-nitroanilide (pNA) formed from a chromogenic substrate for elastase. Of the tested extracts, 41% inhibited pNA formation more than 60%, and 3% stimulated formation. Phoratoxin B and four new peptides, phoratoxins C-F, were isolated from Phoradendron tomentosum. In addition, the cardiac glycoside digitoxin was isolated from Digitalis purpurea. All these substances expressed cytotoxicity and a neutrophil challenging activity. Phoratoxins C-F were similar to earlier described phoratoxins A and B, which belong to the group of thionins. All the peptides were evaluated for cytotoxicity in a human cell line panel. Phoratoxin C was the most potent towards the cell lines (mean IC50: 160 nM), and was therefore investigated further on tumour cells from patients. Correlation analysis of the log IC50 values indicated a mechanism of action different from clinically used archetypal cytotoxic drugs. Phoratoxin C also showed selective toxicity to the solid tumours when compared to the haematological cancer types. The phoratoxin C was 18 times more potent towards the solid tumour samples from breast cancer cells (87 nM) compared to the tested haematological malignancies. The structure-activity relationship concerning cytotoxicity was evaluated for digitoxin and related cardiac glycosides. Digitoxin was shown to be potent, with the average IC50 37 nM being within the therapeutic concentration used for cardiac congestion (13-45 nM). Digitoxin expressed selective toxicity towards solid tumours from patients compared to haematological malignancies.

Una de les àrees més prometedores en recerca biomèdica i farmacèutica és el disseny molecular computacional, que intenta establir relacions entre propietats físico-químiques i activitat biològica. L'èxit d'aquestes tècniques depen críticament de la qualitat de la descripció molecular. En aquest sentit, metodologies basades en potencials d'interacció molecular (MIP) són eines útils per la comparació de compostos que presenten comportaments biològics semblants. Aquest projecte desenvolupa eines per comparar molècules basades en la caracterització de llurs MIPs. El programa de similaritat molecular MIPsim ha estat desenvolupat i aplicat a diferents problemes biològics. Aquesta tesi consisteix en quatre estudis científics que mostren l'ús del MIPSim en aliniament molecular, catalisi enzimàtica, en acoratge de molècules dins el lligand i en estudis 3D-QSAR. / One of the most promising areas in biomedical and pharmaceutical research is computer assisted molecular design, which tries to stablish relationships between physicochemical properties and biological activity. The success of these techniques depends critically on the quality of the molecular description. In this sense, methodologies based on molecular interaction potentials (MIP) are useful tools for the comparison of compounds displaying related biological behaviours. This project aims to develop tools to compare 'molecules based on the characterization 'of their MIPs. To this end, the molecular similarity program MIPSim has been further developed and applied to different biological problems. This thesis consists on four scientific studies showing the use of MIPSim for molecular alignment, enzymatic catalysis, ligand-protein docking and 3D-QSAR analyses.

The budding yeast Saccharomyces cerevisiae has been an invaluable model organism in contributing to the current understanding of cellular biology, owing mainly to its highly tractable genetic system and the completion of its genome sequencing in 1996. Indeed, these bolstered the development of novel methods that have provided great insights into genetic and protein networks in human cells. With the large collection of datasets, S. cerevisiae also became an ideal platform for investigating the mechanism of action of novel compounds. The first part of my thesis uses a validated chemogenomic assay to investigate the mechanism of action of structurally related novel DNA-damaging agents, delineating valuable structure-activity relationship in the process. The second part describes the development of a method that uses drug-induced wild-type growth dynamic to characterize novel compounds, which, in combination with the chemogenomic assay, may complement existing high throughput screening experiments to improve the current drug development process.

The budding yeast Saccharomyces cerevisiae has been an invaluable model organism in contributing to the current understanding of cellular biology, owing mainly to its highly tractable genetic system and the completion of its genome sequencing in 1996. Indeed, these bolstered the development of novel methods that have provided great insights into genetic and protein networks in human cells. With the large collection of datasets, S. cerevisiae also became an ideal platform for investigating the mechanism of action of novel compounds. The first part of my thesis uses a validated chemogenomic assay to investigate the mechanism of action of structurally related novel DNA-damaging agents, delineating valuable structure-activity relationship in the process. The second part describes the development of a method that uses drug-induced wild-type growth dynamic to characterize novel compounds, which, in combination with the chemogenomic assay, may complement existing high throughput screening experiments to improve the current drug development process.

Chapter 1 gives background information on proteases and discusses the concept of protease inhibition as a therapeutic strategy for humans. It introduces the key concept that conformation defines biological activity. It also outlines how proteases almost universally bind their substrate/inhibitors in an extended β-strand conformation. The use of calpain as a prototype protease for the testing of β-strand mimics synthesised later in the thesis is also discussed. Chapter 2 describes how molecular modeling was used to rationalise the structure based activity relationships (SAR) of known calpain inhibitors. Molecular modeling was then used to successfully design a number of acyclic β-strand mimics. The synthesis and testing of eight such inhibitors is described. The most potent β-strand mimic prepared was 2.13. This was determined to have an IC₅₀ of 30 nM against calpain II. Chapter 3 outlines the history and application of ring closing metathesis (RCM) to the synthesis of cyclic compounds. The attempted synthesis of an eight membered cyclic nitrogen to nitrogen conformationally constrained dipeptide is described. The synthesis of a conformationally constrained β-amino acid calpain inhibitor (3.73) is also described. A novel calpain inhibitor motif was designed in Chapter 4. On the basis of this an in-silico combinatorial library of two hundred and eighty eight possible β-strand templates was prepared. Conformational analysis of this library was performed and from this a number of excellent β-strand templates were identified and selected for synthesis. The preparation of ten β-strand templates is described. New microwave irradiation methodology was developed to achieve this. vii The formation of a six-membered catalyst deactivating chelate is also proposed to explain why some dienes fail to undergo RCM. Two methods to circumvent the formation of such a chelate are outlined. The addition of Lewis acid chloro-dicyclohexyl borane to the RCM reaction mixture and chain length alteration are investigated. Chapter 5 describes the design of macrocyclic β-strand mimics using induced fit molecular modelling. The physicochemical properties of these were calculated in-silico. From this analysis a number of Tyr-XX-Gly based and Tyr-XX-Cys based macrocyclic calpain inhibitors were selected for synthesis. The preparation and testing of these are described. In the Tyr-XX-Gly macrocyclic system a number of variables were investigated and numerous SAR implications concluded. Aldehyde 5.14 was identified as the best electrophilic warhead macrocyclic calpain inhibitor with an IC₅₀ against calpain II of 27 nM. The best non-electrophilic warhead macrocycle (5.13) had an IC₅₀ against calpain II of 704 nM. Chapter 6 describes synthetic optimisation for the preparation of calpain inhibitors 2.13, 5.14 and 5.17. Multi-gram quantities of each were prepared. Aldehydes 2.13 and 5.14 were evaluated as anti-cataract agents using in-vivo cataract sheep model. Both of these β-strand mimics were demonstrated to retard cataract development. Macrocycle 5.14 was found to be the most effective, decreasing the rate of cataract development between forty four and forty nine per cent relative to control. Chapter 7 outlines the attempted development of RCM methodology for the chiral synthesis of α-α disubstituted amino acid lactams. In addition, methodology for the stereoselective incorporation of a C-N constrained β-amino acid carbocycle into a peptide or peptidomimetic is described.

Les homéoprotéines sont des facteurs de transcription importants au cours du développement des organismes vivants, capables notamment de voyager de cellule en cellule. Ces protéines comportent une longue extrémité N-terminale désordonnée, suivie de trois hélices α séparées par une boucle et un tour. Des études de relations structure-activité ont montré que des domaines cationiques (riches en K et R) particuliers dans ces protéines sont responsables de ces propriétés de transfert cellulaire leur permettant d’être secrétées et internalisées dans les cellules. Ces processus impliquent que ces protéines hydrophiles soient capables de franchir la membrane plasmique composée d'un coeur hydrophobe. La membrane plasmique est en effet composée d’une bicouche lipidique, dans laquelle sont insérées de nombreuses protéines, telles que les protéoglycanes portant des ramifications de glycosaminoglycanes (GAG), polysaccharides anioniques. Dans le but de comprendre au niveau moléculaire le processus d'entrée des homéoprotéines dans des cellules eucaryotes, différentes constructions protéiques ont été produites et étudiées : le peptide pénétrant les cellules correspondant à l'hélice 3 (H3), la séquence correspondant à l'homéodomaine (HD), l'homéodomaine étendu d'une séquence putative de liaison aux GAG (NLS-HD) et la protéine entière (En2). La quantification absolue de l’entrée de ces constructions dans des cellules CHO-K1 par spectrométrie de masse a mis en évidence une efficacité d'entrée meilleure pour H3 > NLS-HD > HD, ainsi que l’importance des GAG de surface dans le processus et plus particulièrement celui des héparanes sulfates (HS). Des expériences complémentaires d’ITC, de dichroïsme circulaire et de RMN ont permis d'identifier deux sites d’interaction avec l’héparine (un site principal de haute affinité et un site secondaire de plus basse affinité), interagissant principalement avec le polysaccharide par interactions électrostatiques. In fine, ces études conduisent à une meilleure compréhension moléculaire du processus d'internalisation des homéoprotéines dans des cellules eucaryotes. / Homeoproteins are important transcription factors during the development of living organisms, and are able to travel from cell to cell. These proteins contain a long N-terminal extremity structurally disordered, followed by three α helices separated by a U-turn. Structure-activity relation studies have shown that in these proteins, some cationic domains (rich in K and R) confer them the cellular transfer properties, allowing them to be secreted by and internalized into cells. These processes imply that the hydrophilic proteins are able to cross plasma membrane. Indeed, the plasma membrane possess a hydrophobic heart and is composed by a lipidic bilayer, in which numerous proteins are inserted, such as proteoglycans carrying glycosaminoglycan (GAG) ramifications, that belong to anionic polysaccharids. In order to understand the entry process of homeoproteins into eukaryotic cells at a molecular level, different proteic constructions have been produced and studied: the cell penetrating peptide corresponding to the third α helix (H3), the sequence corresponding to its homeodomain (HD), the homeodomain with an added putative GAG-binding domain (NLS-HD), and the wild-type protein Engrailed 2 (En2). The absolute mass spectrometry quantification of the peptide and proteins in cells shows a range of internalization efficiency as follows: H3 > NLS - HD > HD. It also highlights the importance of cell-surface GAGs in the internalization and more particularly that of heparan sulfates (HS). Complementary experiments of ITC, circular dichroism and NMR have shown two interaction sites for the heparin (one principal site of high affinity and a secondary site showing a lower affinity) both interacting mainly with polysaccharidic residues using electrostatic interactions. In fine, these studies lead to a better molecular understanding of homeoproteins internalization process in eukaryotic cells.

L'ulcère de Buruli est une maladie nécrosante de la peau et des tissus mous accompagnée d'ulcères de grandes tailles, causée par une mycobactérie. L’Organisation Mondiale de la Santé a lancé en 1998 une initiative mondiale contre cette maladie tropicale négligée, présente notamment en Afrique et en Australie. L'infection est causée par Mycobacterium ulcerans, mycobactérie faisant partie de la même famille que les mycobactéries responsables de la tuberculose et de la lèpre. Mycobacterium ulcerans sécrète une toxine nommée mycolactone, responsable de cette infection. Cette toxine a des propriétés cytotoxiques et immunosuppressives. Le projet de recherche développé dans l'équipe concerne la synthèse et l'évaluation biologique des mycolactones A et B et de leurs analogues. A l'heure actuelle, la première étude relation structure-activité conduisant à une meilleure compréhension du mode d'action des mycolactones a été établie. La stratégie de synthèse choisie implique plusieurs réactions de couplage catalysées par des métaux (fer, cuivre, palladium) pour la création de liaisons carbone-carbone. La stéréochimie des sept alcools secondaires a quant à elle été contrôlée par des réactions d'allyl-et crotylboration asymétrique ainsi que par des réactions de dihydroxylation catalytique et asymétrique. Au cours de ce travail de thèse, 12 analogues ont ainsi été obtenus en appliquant cette voie de synthèse. / Buruli ulcer, a severe necrotizing skin disease caused by Mycobacterium ulcerans, is one of the most neglected tropical diseases. The World Health Organization has started in 1998 a Global Initiative against this disease. The pathogen belongs to the same family as the mycobacteria responsible for tuberculosis and leprosy and 6000 new cases are registered each year. Infection leads to extensive destruction of the skin and soft tissues with the formation of large ulcers usually on the legs or the arms and can caver up 15% of the skin surface. These effects are due to the presence of the bacterial toxins mycolactones, secreted by M ulcerans. Mycolactones are the first polyketides isolated from a human pathogen. Deciphering their functional interactions is of fundamental importance for the understanding and ultimately the control of this devastating mycobacterial infection. A Diverted Total Synthesis approach of mycolactones analogues has been developed and provides the first insights into their structure-activity relationship based on cytopathic assays on L929 fibroblasts.

No description available.