La voie de synthèse des acides aminés ramifiés est présente chez les plantes, les bactéries et les champignons mais est absente chez les mammifères. C’est pourquoi il est intéressant de cibler cette voie métabolique par des inhibiteurs spécifiques des enzymes qui la compose afin de développer des herbicides non sélectifs. Une famille d’herbicide déjà commercialisée agit sur la première enzyme de cette chaine enzymatique. Néanmoins des cas de mauvaises herbes résistantes à ces composés sont apparus et leur incidence continue d’augmenter. Il apparait donc important de cibler une autre enzyme de la voie de synthèse de ces acides aminés ramifiés afin de contourner ce problème de résistance.L’enzyme cétoacide réductoisomérase (KARI) intervient également dans la voie métabolique citée précédemment. Deux inhibiteurs IpOHA et Hoe 704 ont été développés dans les années 1980, mais malheureusement n’ont pas montré d’activité lors de traitements en plein champ. Cependant ils restent tous les deux, les références en tant qu’inhibiteurs in vitro.L’analyse de la diffraction par rayons X de KARI cristallisée avec un des inhibiteurs ou son substrat naturel montre que les groupements fonctionnels portés par ces derniers viennent complexer deux cations métalliques au sein du site actif. De plus la comparaison des structures des inhibiteurs ou des états de transition du substrat permet de dégager une structure générale pour le développement de nouvelles molécules potentiellement actives. Ainsi trois sous-structures doivent être présentes avec une double pince complexante, un groupement lipophile et un groupement accepteur de liaison hydrogène.Dans ce contexte, différents groupements comme des oxydes de diorganylphosphines, des dihydropyrimidinediones, des dérivés d’acides carboxyliques ou hydroxamiques peuvent être modifiés et utilisés comme motifs complexants. Les fonctions et groupements fonctionnels cités ont déjà prouvé leur efficacité lors du développement d’autres inhibiteurs de métalloenzymes. / The branched-chain amino acids metabolic pathway is present in many living beings such as plants, bacteria and fungi but not in mammals. This is why it has been interesting to target this enzymatic pathway with specific inhibitors in order to develop non-selective herbicides. The main non-selective herbicides commercialised inhibit the first enzyme of this metabolic route. However more and more cases of resistant weed appeared and spread. Thus it raises the interest and importance of designing new compounds targeting another enzyme from the biological pathway in order to circumvent the resistance issue.The Ketolacid Reductoisomerase (KARI) protein also intervenes in the aforementioned enzymatic pathway. Although two inhibitors, IpOHA and Hoe 704, were synthesised during the 80s they have not proven active enough in field treatment. Nonetheless both inhibitors remain as references for in vivo biological activity.The X-ray diffraction representations of KARI including each inhibitor or its natural substrate show that the functional groups borne by the latter chelate two metal cations within the active site. Moreover the comparison between inhibitor structures and the substrate transition states reveals a general pattern in order to design and develop new potential biologically active compounds. For that purpose three major substructure units have to be considered: a double chelating pincer, a lipophilic group and a hydrogen bond accepting moiety.In this context different functional groups such as diorganylphosphine oxides, dihydropyrimidinediones, carboxylic acid or hydroxamic acid derivatives could be modified and used as chelating motifs. The functional groups listed have already proven their efficacy as part of other metalloenzyme inhibitors.

The post-translational modification of histones and their interaction with transcription factors is essential to gene regulation. Furthermore, these targets would greatly benefit from probe molecules to fully elucidate their biological actions and to potentially lead to therapeutics. However, these protein-protein interactions have been considered difficult to inhibit and few high-quality chemical probes currently exist for the study of epigenetic biological systems in particular.

Understanding the specific mechanisms regulating chemotherapeutic drug anti-cancer activities will uncover novel strategies to enhance the efficacy of these drugs in clinical settings. Activating Transcription Factor 3 (ATF3) is a stress inducible gene whose expression has been associated with survival outcomes in cancer models. This study characterizes the chemotherapeutic drugs, cisplatin and Histone Deacetylase Inhibitor (HDACi), M344 as novel inducers of ATF3 expression. Cisplatin is a DNA damaging agent widely used in various tumour types including lung, head and neck, and ovarian carcinomas. The HDAC inhibitor, SAHA, has recently been approved as a single agent in the treatment of subcutaneous T-cell lymphoma and HDACis themselves show potential for synergistic anti-cancer effects when used in combination with established chemotherapeutic drugs, including cisplatin. This study evaluates the mechanisms by which cisplatin and HDACi induce ATF3, as well as the role ATF3 plays as a mediator of cisplatin-induced cytotoxicity and the enhanced cytotoxicity between HDACi and cisplatin in combination. In this study, we demonstrate that cytotoxic doses of cisplatin and carboplatin consistently induced ATF3 expression in a panel of human tumour derived cell lines. Characterization of this induction revealed a p53, BRCA1, and integrated stress response (ISR) independent mechanism, all previously implicated in stress mediated ATF3 induction. Analysis of MAPKinase pathway involvement in ATF3 induction by cisplatin revealed a MAPKinase dependent mechanism. Cisplatin treatment, in combination with specific inhibitors to each MAPKinase pathway (JNK, ERK and p38) resulted in decreased ATF3 induction at the protein level. MAPKinase pathway inhibition led to decreased ATF3 mRNA expression and a reduction in the cytotoxic effects of cisplatin as measured by MTT cell viability assay. In A549 lung carcinoma cells, targeting ATF3 with specific shRNAs also attenuated the cytotoxic effects of cisplatin. Similarly, ATF3 -/- MEFs were shown to be less sensitive to cisplatin induced cytotoxicity as compared with ATF3+/+ MEFs. Taken together, we identified cisplatin as a MAPKinase pathway dependent inducer of ATF3 whose expression regulates in part cisplatin’s cytotoxic effects. Furthermore, we demonstrated that the HDAC inhibitor M344 was also an inducer of ATF3 expression at the protein and mRNA level in the same human derived cancer cell lines. Combination treatment with M344 and cisplatin lead to increased induction of ATF3 compared with cisplatin alone. Utilizing the MTT cell viability assay, M344 treatment was also shown to enhance the cytotoxic effects of cisplatin in these cancer cell lines. Unlike cisplatin, the mechanism of ATF3 induction by M344 was found to be independent of MAPKinase pathways. Utilizing ATF4 heterozygote (+/-) and knock out (-/-) mouse embryonic fibroblast (MEF) M334 induction of ATF3 was shown to depend on the presence of ATF4, a known regulator of ATF3 expression as part of the ISR pathway. HDACi treatment did not affect the level of histone acetylation associated with the ATF3 promoter as determined through Chromatin immunoprecipitation (ChIP) analysis, suggesting that ATF3 induction was not a direct effect of HDACi mediated histone acetylation. We also demonstrated that ATF3 regulates the enhanced cytotoxicity of M344 in combination with cisplatin as evidenced by attenuation of cytotoxicity in shRNAs targeting ATF3 expressing cells. This study identifies the pro-apoptotic factor, ATF3 as a novel target of M344, as well as a mediator of the co-operative effects of cisplatin and M344 induced tumour cell cytotoxicity.

The inhibitor of apoptosis (IAP) proteins traditionally regulate programmed cell death by binding to and inhibiting caspases. Recent studies have uncovered a variety of alternate cellular roles for several IAP family members. The cellular inhibitor of apoptosis 1 (cIAP1) protein, for instance, regulates different axes of the NF-κB signalling pathway. Given the extensive functions of NF-κB signalling in muscle differentiation and regeneration, I asked if cIAP1 also plays critical roles in skeletal muscle myogenesis. In a primary myoblast cell-culture system, genetic and pharmacological approaches revealed that loss of cIAP1 dramatically increases the fusion of myoblasts into myotubes. NF-κB signalling occurs along a classical and an alternative pathway, both of which are highly active in cIAP1-/- myoblasts. Suppression of the alternative pathway attenuates myotube fusion in wildtype and cIAP1-/- myoblasts. Conversely, constitutive activation of the alternative pathway increases myoblast fusion in wildtype myoblasts. cIAP1-/- mice have greater muscle weight and size than wildtypes, as well as an increased number of muscle stem cells. These results identify cIAP1 as a regulator of myogenesis through its modulation of classical and alternative NF-κB signalling pathways. Loss of the structural protein dystrophin in the mdx mouse model of Duchenne muscular dystrophy leads to chronic degeneration of skeletal muscle. The muscle pathology is strongly influenced by NF-κB signaling. Given the roles demonstrated for cIAP1 in cell culture and in vivo, I asked whether loss of cIAP1 would influence muscle pathology in the mdx mouse. To address this question, double-mutant mice were bred lacking both cIAP1 and dystrophin (cIAP1-/-;mdx). Histological analyses revealed that double-mutant mice exhibited reduced indications of damage on several measures, as compared to single-mutant (cIAP1+/+;mdx) controls. Unexpectedly, these reductions were seen in the “slow-twitch” soleus muscle but not in the “fast-twitch” extensor digitorum longus (EDL) muscle. The improvements in pathology of double-mutant solei were associated with reductions in muscle infiltration by CD68-expressing macrophages. Finally, the double-mutant mice exhibited improved endurance and resistance to damage during treadmill-running exercise. Taken together, these results suggest that loss of cIAP1, through its multiple regulatory functions, acts to improve myogenesis and increase muscle resistance to damage.

The discovery of stem and progenitor cells capable of ongoing neurogenesis in the adult mammalian brain has raised hope that we will one day be able to harness their intrinsic regenerative capacity following injury. Development of such therapeutic strategies relies on a comprehensive understanding of the underlying regulation of the neurogenic process. To this end, I show, in this thesis, that cultured post-natal hippocampal neural progenitor cells (NPCs) express a specific repertoire of connexins (Cx), a family of channel forming proteins critical for communication prior to the development of functional chemical synapses. I show that this pattern of Cx expression, specifically Cx43 and Cx45, is modulated by interaction with the extracellular matrix component laminin providing evidence of extracellular matrix-cell interaction in the regulation of intrinsic Cx expression and function in postnatal NPCs. In adult brain, I show, for the first time, that Cx45 localizes to all cell types of the neuronal lineage with the exception of the type 3 doublecortin (DCX)-positive NPCs. Using a loss of function approach, I show that this expression is required for the normal proliferation of type 1 nestin and glial fibrillary acidic protein-positive stem like NPCs but not for the differentiation or survival of their progeny in the adult hippocampus. With respect to exogenous pharmacological cues that influence hippocampal neurogenesis, this thesis also demonstrates that chronic treatment with a sub-set of selective serotonin reuptake inhibitor antidepressants, fluoxetine and escitalopram, increases the proliferation but not the survival of adult NPCs in healthy, non-depressed mice. Further, standard post-operative analgesia with the opiate buprenorphine inhibits the proliferation of DCX-positive adult NPCs and increases the survival of their progeny. Finally, over the course of the research for this thesis, it became clear that exposing research animals to even very subtle environmental changes can influence the basal neurogenic process. Ultimately this work further highlights the exquisite sensitivity of the regulation of what is already recognized to be a highly dynamic process and provides important insight into the neurogenic process that can be used to inform future therapeutic development and application.

With the increasing threat of multidrug resistant bacteria, there is a growing need to invent new drug classes that combat untreatable infections. Small molecule antibiotics have been successful in the past, but humanity is now losing the arms race against previously treatable pathogens. However, the number of clinically approved drugs targeting traditionally undruggable targets in bacteria remains low. New targets of complex protein-target interactions must be targeted for future pharmacological development. In an effort to create clinically viable biologics, the Verdine lab has developed a class of therapeutics called hydrocarbon stapled α-helical peptides; these peptides are known to affect protein-protein interactions by retaining secondary structure in vivo. Although this class of molecules has been extensively researched in cancer and viral therapies, there has been little work in bacteria due to the proposed endocytic method of entry. Moreover, DNA-binding stapled peptides have not been extensively investigated due the complexities in designing a peptide with gene selectivity. In an attempt to study peptides in bacteria, two stapled peptides based on the RpoN domain of σ54 and the FtsZ C-terminus have been synthesized. σ 54 is a DNA-binding co-factor of RNA polymerase (RNAP) and has been shown to regulate virulence and nitrogen and carbon metabolism. FtsZ is the structural unit of the contractile Z-ring that induces cell division. By designing stapled α-helical peptides to target these untraditional PPIs, we anticipate that these molecules may be used for future antimicrobial pharmacological development that treat multidrug resistant bacteria.

The number of known monogenic rare diseases (~7000) exceeds the number of effective treatments (~500) by more than an order of magnitude underlining the pressing need for generalizable therapeutic approaches for this class of conditions. In this regard, the majority of recessive and x-linked recessive disorders are caused by missense mutations encoding proteins that frequently have residual function but are rapidly degraded by the 26S proteasome. Bortezomib is a small molecule that inhibits the 26S proteasome and has been approved for use in patients for an unrelated condition; multiple myeloma. Previous work has shown that, for a small number of disorders, bortezomib can inhibit the degradation of the mutant protein, thereby increasing the protein level and activity, holding out the promise of a beneficial therapeutic effect by the repurposing of this agent. We present here a high level western blot based survey of nine recessive disorders to characterize the general effectiveness of such an approach. Thirteen patient fibroblast cell lines comprising 9 different diseases with 19 known mutations were selected on the basis of missense mutations protein expression data when available. The cell lines were incubated with bortezomib (10 nM and 50 nM; 24 hrs) and levels of the mutated protein were quantified by western blot. Unfortunately, no consistent, appreciable increase was observed for any of the conditions tested. The general therapeutic value of re-purposing bortezomib for recessive and x-linked diseases appears limited at best. The few reported cases of bortezomib successfully working in increasing mutated protein levels appear to be the exceptions and not the norm. Moreover successes are more often limited to cell lines carrying a transgene expressing the mutated protein rather than endogenous mutated protein in patient cell lines.

Le cancer est un problème très présent dans nos sociétés modernes. En effet en 2010 il touchait plus de 10 millions de personnes dans le monde. Aujourd'hui cette maladie est la première cause de mortalité dans les pays industrialisés.Malheureusement, les thérapies envisagées restent fréquemment insuffisantes et possèdent de nombreux effets secondaires qui ternissent les bienfaits du traitement. Pour éviter justement cette toxicité auprès des cellules saines, la recherche développe depuis quelques années des traitements ciblés. La plupart des médicaments antimitotiques actuellement sur le marché présentent de forts effets secondaires notamment cardiologiques, hématologiques et neurotoxiques.Nous nous sommes donc intéressés à une autre cible thérapeutique intervenant toujours au niveau de la mitose mais provoquant moins d'effets néfastes et pouvant être surexprimée dans les cellules cancéreuses: la kinésine humaine Eg5.La kinésine humaine Eg5 est indispensable au bon fonctionnement de la mitose. Elle possède un rôle essentiel dans les premières étapes du cycle cellulaire et est requise pour la séparation des centrosomes à chaque pôle de la cellule.La suppression ou l'inhibition d'Eg5 bloque la cellule en pré-métaphase avec un fuseaumonoastral caractéristique formé de deux centrioles non séparés entourés des chromosomes et des microtubules. Le maintien de ce type de fuseau provoque l'activation des checkpoints du cycle cellulaire et provoque l'apoptose.Notre travail consiste en la synthèse de composés susceptibles d'inhiber la kinésine humaine Eg5 et de bloquer ainsi le développement des cellules cancéreuses.Le recherche de nouveaux ligands potentiels de la kinésine Eg5 est effectué selon un mode de conception rationnel fondé sur l'analyse de la structure tridimensionelle des complexes protéines/ligands ou "structure-based drug design". Ces travaux sont réalisés en utilisant les outils de modélisation moléculaire par la mise en oeuvre de méthode "de novo".L'ensemble des informations recueilli au travers de logiciels très performants permet l'obtention d'un modèle statistiquement significatif destiné à la conception et à la prédiction des activités biologiques.Ces travaux associés à l'expertise chimique du laboratoire, ont permis la conception de trois nouvelles familles, potentielles ligand d'Eg5, de structure: triazoloquinazolinone, triazolométhylquinazolinone, dihydroimidazoquinazolinone. / Cancer is a real problem in our civilization. Indeed, in 2010, it affected more than 10 million people in the world. Today, this disease is the first cause of death in industrialized countries.Unfortunately, the proposed therapies remain frequently insufficient and lead to side effects which remove the benefits of the medical treatment. In order to avoid the toxicity to safe cells, since a few years, researches have been done to develop targeted therapies. Most of the anti-mitotic drugs actually available on the market lead to important side effects such as cardiological, hematological and neurotoxic problems.Thus, we interested to another therapeutic target which still acts at the level of the mitosis but causing fewer side effects and can be overexpressed into the cancer cells: the mitotic kinesin Eg5.The mitotic kinesin Eg5 plays an important role in the early stages of mitosis and is one of the most attractive target enzymes in antimitotic drug development. The modulation of the Eg5 activity has been shown to cause aberrant mitotic spindle formation, cell cycle arrest during mitosis and the inhibition of proliferation of tumor cells in culture. With regard to the potential of Eg5 modulators in the treatment of human cancers, we report the design, synthesis and biological studies of quinazolinone derivatives as mitotic kinesin Eg5 inhibitors. We developed three series of molecules derived from quinazolin-4-one scaffold following a “de novo drug design” strategy.

Heparan sulphate (HS) is critical for embryonic development with involvement in a myriad of biological processes, centrally mediating morphogenic movements and facilitating the specification and differentiation of tissues. Complicated by its structural micro-heterogeneity along with expression on numerous different proteoglycan cores, the plethora of roles for HS in biology and their underlying mechanisms have not yet been fully defined. The discovery and characterisation of new reagents and methods for modification of HS expression and/or structure will aid efforts in elucidating the structure and activity of this glycosaminoglycan. Until now, azido sugars have been utilised as labelling reagents for various types of glycosylation, including N-glycans, O-linked mucin-type glycosylation and O-GlcNAcetylation of proteins. Incorporation of the unnatural azido sugar into the glycan of interest inserts a chemically reactive abiotic azide for subsequent detection via Staudinger ligation or click chemistries. However, to our knowledge, application of these azido sugars has not been explored for glycosaminoglycans. A metabolic labelling approach using Ac4GalNAz yields UDP-GalNAz and UDP-GlcNAz (Boyce et al., 2011), ready to target CS/DS and HS, respectively. We hypothesised that HS synthesis might be altered in the presence of UDP-GlcNAz due to the location of the azide on the acetyl group and the potential for interference with endogenous N-deacetylase-N-sulphotransferase biosynthetic enzyme activity. In mammalian cell culture (Chinese hamster ovary cells), treatment with Ac4GalNAz led to a decrease in total HS abundance accompanied by significant increases in 6-O-sulphation within the chains. Incorporation of a radiolabelled metabolic precursor revealed that average HS chain length was decreased in azido sugar-treated CHO cells. The modifications to HS were dose-dependent and HS inhibition was transient. Following removal of Ac4GalNAz from cell culture, HS expression returned to baseline levels within 24 hours. Previous work from the Bertozzi group has demonstrated the utility of Ac4GalNAz for visualising GalNAc- and O-GlcNAc-modified proteins in vivo. Using Xenopus, we were able to show that treatment of fertilised eggs with Ac4GalNAz decreased the abundance of HS in a similar way to that seen in vitro, with an associated impact on embryonic development. Embryonic axial elongation was impaired, with defective myotomal development and aberrant axonal patterning along the trunk and tail. Posterior somite cell nuclei were disorganised, with loss of distinct chevron patterning and skeletal muscle development was impaired with muscle fibres spanning some of the somite boundaries. Removal of the inhibitor partially rescued tail extension defects, as well as muscle development, but not axonal patterning. Therefore, these experiments illustrate a novel application for Ac4GalNAz as a soluble and reversible inhibitor of HS synthesis for in vitro and in vivo studies. The observed potential for control of inhibition via time- and dose-dependent effects enables targeted and selective inhibition of HS and potentially provides a powerful new inhibitor for the study of HS-mediated events.

This study investigated the corrosion processes at the top and bottom of carbon steel pipelines transporting wet gases, and studied possible chemical mitigation strategies. First, immersion tests were carried out using carbon steel to study the effects of de-aeration with high purity nitrogen gas on the corrosion rate. Secondly, the corrosion rate was assessed for varying chloride ion concentrations in an aerated environment. In general, increasing de-aeration time changes the corrosion mechanism from mass transfer oxygen reduction to water reduction reaction. However, oxygen solubility controlled the corrosion process in aerated solution containing different chloride ion concentrations. A special two-electrode cell was designed for the top of the line corrosion (TLC) electrochemical measurements but a conventional three electrode cell was used for the bottom of the line corrosion (BLC) measurements. The TLC rate increases with temperature, and X-Ray Diffraction (XRD) confirmed the presence of chukanovite {Fe2(CO3)(OH)2}and possibly ferrous carbonate corrosion products at 40oC and 60oC respectively. However, for the BLC, the cementite phase remained on the metal surface after preferential dissolution of the ferrite phase in the carbon steel. Addition of acetic acid (HAc) locally dissolved the initially FeCO3 film formed on the metal surface, causing local corrosion damage. Addition of methyl di ethanol amine (MDEA) as a pH stabiliser reduced TLC and BLC rates due to enhanced stability of FeCO3 at pH 5.7-6.3. When Zn2+ ions were added as ZnCl2, both Fe2O3 and ZnCO3 were formed at reduced corrosion rate. Whenever FeCO3 film was damaged/dissolved by HAc addition of neither pH stabiliser; MDEA nor hydrate preventer; mono ethylene glycol (MEG) could not re-establish a protective film on the metal surface. The following organic inhibitors were investigated as potential mitigators of TLC: 2-mercaptobenzimidazole (2MBI), 2-amino-5-ethyl-1,3,4-thiodiazole (AETDA), 2-phenyl-2-imidazoline (2PI), dicyclohexylamine (DHA), and a commercial inhibitor formulation (CI-A). The inhibition efficiency (IE%) was found to increase in the order CI-A > 2MBI > AETDA > DHA. Their efficiency increases (except DHA) with inhibitor concentrations both at top and bottom of the line. 2MBI and CI-A behaved as mixed inhibitors but AETDA behaved as cathodic inhibitor, all were best fitted to a simple Langmuir adsorption isotherm. However, IE% of DHA decreased at higher inhibitor concentrations. Surprisingly, 2PI inhibitor increased the corrosion rate, and the corrosion rate further increased with increase inhibitor concentrations. Weight loss measurements results of TLC are also presented which showed lower inhibition efficiency for all the inhibitors investigated compared with electrochemical measurements in similar environments. The free energy of adsorption (∆Goads values for 2MBI and AETDA are around -36kJ.mol-1 while for CI-A the value was -15kJ.mol-1 (-7kJ.mol-1 in the presence of HAc). This is evidence for adsorption of 2MBI and AETDA on the metal surface by chemisorption with CI-A by physisorption. XPS analysis confirmed the presence of FeCO3 and FeOOH as corrosion products in the brine solution in the absence and presence of HAc containing different corrosion inhibitors.