In humans and most eukaryotes, thymidylate synthase (TSase) serves as a key enzyme that catalyzes the reductive methylation of deoxyuridine monophosphate (dUMP) to synthesize deoxythymidine monophosphate (dTMP), a key component of DNA. The N5, N10- methylene-5,6,7,8-tetrahydrofolate (MTHF) serves as both the methylene donor and the hydride donor while generating dihydrofolate (H2folate) as the byproduct. However, in 2002, Myllykallio reported the discovery of flavin-dependent thymidylate synthase (FDTS) that also functions to maintain the dTMP pool, although the mechanism is different. Since then, considerable progress was made in characterizing this enzyme. It was found that structurally FDTS is substantially different from TSase both with respect to structure and with respect to the mechanistic pathway of catalysis. In the FDTS-catalyzed methylation of dUMP, MTHF serves only as the methylene donor, generating tetrahydrofolate (H4folate), unlike TSase, and FDTS utilizes NADPH as a reductant. Activity of the enzyme depends on the presence of the noncovalently bound prosthetic group, flavin adenine dinucleotide (FAD). Interestingly, the enzyme FDTS is present in several human pathogens that cause diseases including syphilis, tuberculosis, anthrax poisoning, typhus, botulism, peptic ulcers and more, but is absent in humans; thus, it poses an attractive target for antibiotics. In the modern world, antibiotic resistance is a menace; consequently, new targets for new antibiotics are being sought. Hence, elucidating the chemical mechanism of FDTS is of paramount interest, as we and others believe this could allow for rational design of drugs that selectively target these pathogens with minimal human toxicity. Although several chemical mechanisms for FDTS catalysis have been put forward, complete understanding has still not been achieved. One of the primary concerns was the role of FAD in catalysis, and we found – as described in Chapter II and III – that FAD is a methylene carrier rather than just a hydride donor, as previously postulated. Secondly, all mechanisms proposed so far predict the presence of a noncovalently bound putative exocyclic methylene intermediate (an isomer of dTMP) occurring in the catalytic pathway of FDTS. However, direct evidence to prove its existence was lacking. Recently, we have been able to synthesize this intermediate, as described in Chapter IV. As shown in Chapter V and VI, we used steady-state kinetics, isotopic substitution and NMR studies to test this intermediate with FDTS. We believe our findings will greatly improve the understanding of this enzyme and will impact drug design by government agencies, pharmaceutical companies, and academic laboratories.

Transglutaminases (protein-glutamine:amine y-glutamyl- transferase, EC 2.3.2.13) are a family of calcium-dependent enzymes which catalyze an acyl transfer between glutamine residues and a wide variety of primary amines. When lysine acts as the acyl-acceptor substrate, α-glutamyl lysine isopeptide bond is formed. Isopeptide catalyzation results in protein cross-linkage which is prevalent throughout biological processes. Microbial transglutaminase (mTG) is a bacterial variant of the transglutaminase family, distinct by virtue of its calcium-independent catalysis of the isopeptidic bond. Furthermore, mTGs promiscuity in donor substrate preference highlights its biocatalytic potential. To realize the potential of the enzyme, a high-reactivity tag was necessary for protein labelling. To address this, an enzyme-coupled assay was developed to characterize peptides in the hopes of developing orthogonal substrates to facilitate mTG-mediated labelling and biocatalysis. The discovery of high-reactivity peptide tags allowed the realization of in vitro protein labelling- facilitated by mTG. The 7M48 peptide was fused to a test protein, where it was subsequently propargylated with propargyl amine to fluorescently label or immobilize a test protein. Although there are endless possibilities for in vitro bio-conjugation through mTG, proteolytic activation limits any in-cell labelling strategies with this enzyme. To circumvent this issue, development of an alternative bacterial enzyme, Bacillus subtilis transglutaminase (bTG), was chosen to replace mTG. bTG maintains the advantages associated with mTG but is expressed in its active form. Unlike mTG, there is limited preliminary research associated with the enzyme or its substrate scope. To better understanding substrate reactivity, a FRET-based assay was developed allows for the discovery of new high-reactivity peptides for bTG. These peptides were then used in labelling strategies to demonstrate the potential bTG-mediated bioconjugation. This strategy includes the added advantage of potential for in-cellulo labelling.

No / We report on a supramolecular self-assembly system that displays coupled light switching, biocatalytic condensation/hydrolysis and gelation. The equilibrium state of this system can be regulated by light, favouring in situ formation, by protease catalysed peptide synthesis, of self-assembling trans-Azo-YF-NH2 in ambient light; however, irradiation with UV light gives rise to the cis-isomer, which readily hydrolyzes to its amino acid derivatives (cis-Azo-Y + F-NH2) with consequent gel dissolution.

Les enzymes sont des biocatalyseurs de plus en plus utilisés pour la transformation de molécules organiques (chimie fine, bioconversions, dépollution, chimie du pétrole) car elles possèdent de très bonnes sélectivité et réactivité, générant rapidement de larges quantités de produit. Cependant, la fragilité des enzymes, notamment en solution, limite souvent leur utilisation. Il est donc crucial de les immobiliser et de les stabiliser dans des supports adaptés. Une grande variété de matrices d’immobilisation (organiques ou inorganiques) a déjà étudiée, mais aucune ne satisfait pleinement aux critères nécessaires pour le développement de bio-réacteurs (accessibilité au site actif de l’enzyme, relargage de l’enzyme, diffusion des réactifs, recyclabilité, stabilité..). En outre, la majorité de ces matrices présente une porosité désordonnée, inadaptée pour une immobilisation homogène. L’utilisation de matériaux hybrides, cristallins et poreux de type Metal-Organic Frameworks (MOFs) a été récemment proposée comme alternative avec des applications en biocatalyse et en biodétection.Le travail de cette thèse a consisté à associer des matériaux de type Metal-Organic Frameworks à une mini-enzyme, la microperoxidase 8 (MP8), afin d’obtenir des matériaux multifonctionnels. Dans une première partie, le MOF mésoporeux, MIL-101(Cr), a été utilisé pour encapsuler la MP8, ce qui a conduit à une amélioration de son activité catalytique dans des conditions qui ne sont pas adéquates pour l’activité enzymatique (conditions acides, forte concentration en H2O2), démontrant ainsi le rôle protecteur du MOF vis-à-vis de l’enzyme. De plus, il a été possible de recycler le biocatalyseur. Cette approche a également permis d’améliorer considérablement la sélectivité de la MP8 pour la dégradation d’un colorant organique toxique négativement chargé, le méthyl orange, grâce à son adsorption sélective par interaction électrostatique avec les particules de MIL-101(Cr). La seconde partie a été consacrée à l’utilisation de matériaux MIL-101(Cr) fonctionnalisés. Tout d’abord, l’influence de la fonctionnalisation du ligand (avec un groupement –NH2 ou –SO3H) sur l’encapsulation de la MP8 ainsi que sur son activité catalytique pour des réactions de sulfoxydation a été étudiée. Il a été montré que l’activité catalytique et la réactivité de la MP8 sont affectées par le microenvironnement spécifique des pores du MOF, notamment pour des réactions de sulfoxydation mettant en jeu des dérivés thioanisole. Ensuite, un MOF à métal mixte (MIL-101(Cr/Fe)) choisi pour ses propriétés catalytiques stables, a été synthétisé et caractérisé. Enfin, la dernière partie de cette thèse a été consacrée à la synthèse in-situ d’un MOF (le microporeux MIL-53(Al)-FA) en présence de biomolécules (BSA) dans des conditions compatibles avec la préservation de la structure protéique (en solution aqueuse à température ambiante). Les matériaux hybrides obtenus ont été caractérisés en couplant de nombreuses techniques. Cette méthode d’encapsulation a conduit à des taux d’immobilisation extrêmement élevés. Une étude préliminaire a été initiée avec l’enzyme, Horseradish Peroxidase , qui conserve son activité catalytique après immobilisation. / The use of enzymes in biocatalytic processes has been a challenging goal over the years. While enzymes present exceptional catalytic properties, their fragility hinders their industrial application. Their stabilization and protection are therefore of paramount importance. This can be effectively addressed through their immobilization within host solid matrices. Traditional materials (silica, clays, polymers, biopolymers, porous carbons…) have been widely studied as supports. Their pure organic or inorganic nature often requires a compromise between affinity with enzymes and robustness of the matrix. Besides, most of them have non-ordered porosity, with non-homogenous pore size distributions, unsuitable for homogeneous immobilization. Metal-Organic Frameworks (MOFs) have been recently introduced as alternative supports, thanks to their hybrid nature and their crystalline and highly porous structures.The aim of this PhD was to combine Metal-Organic Frameworks (highly porous and chemically stable polycarboxylate MOFs) and a mini-enzyme, microperoxidase 8 (MP8) to obtain multifunctional biocatalysts. In a first part, the mesoporous MIL-101(Cr) was used as a host matrix to encapsulate MP8. The encapsulation led to an increased catalytic activity under conditions (acidic conditions, high concentration of H2O2) detrimental to the catalytic activity of MP8, thereby demonstrating the protecting effect of MIL-101(Cr) matrix. The biocatalyst was also efficiently recycled. The selectivity of MP8 for the degradation of the harmful negatively charged organic dye methyl orange was also enhanced, thanks to the charged-based selective adsorption of the dye in MIL-101(Cr) porosity. A second part of the work was devoted to the use of functionalized MIL-101(Cr) analogs. First, functionalized ligands (bearing –NH2 and –SO3H groups) were used, and their influence on MP8 encapsulation was evaluated. The catalytic activity toward sulfoxidation reactions was also studied. The successful encapsulation of MP8 was strongly dependent on charge matching between the enzyme and the MOFs particles, while its catalytic activity was affected by the specific microenvironment of the pores. The MOF frameworks also modified the reactivity of MP8 toward different thioanisole derivatives. Then, a mixed metal MOF (MIL-101(Cr/Fe)), selected for its stable catalytic properties, was synthesized and characterized. Finally, the last part was devoted to the in-situ synthesis of MOFs (microporous MIL-53(Al)-FA) in presence of biomolecules (BSA) under compatible conditions with the preservation of the protein’s quaternary structure (aqueous media and room temperature). The resulting hybrid materials were thoroughly characterized and presented high loadings of BSA. A preliminarily study was performed with the enzyme, Horseradish Peroxidase, which retained its catalytic activity after immobilization.