Rhomboids are a family of intramembrane serine proteases that cleave transmembrane protein substrates within the lipid membrane. They are involved in a wide range of biological processes, including signal transduction, parasite invasion, bacterial quorum sensing and apoptosis. While previous X-ray crystal structures and functional studies have provided some detailed insights into the mechanism of intramembrane hydrolysis, it is still not clear how the transmembrane substrate can gain access into the active site from the lipid environment. While several modes of action have been suggested, one hypothesis proposes a lateral movement of the fifth transmembrane helix, causing a displacement that would allow transmembrane substrates to enter the rhomboid active site. A powerful method that has the potential to yield insights into rhomboid dynamics is solution NMR; however, the large size of rhomboid protease samples has complicated conventional methods typically used to assess protein structure and dynamics. ¹⁹F NMR could allow the study of rhomboid conformational dynamics by providing a simplified spectrum with high sensitivity to changes in local chemical environments. In this thesis various methods of ¹⁹F incorporation were evaluated for utility in studying rhomboid conformational dynamics, focusing on the GlpG rhomboid from E. coli. First, GlpG samples were prepared with ¹⁹F incorporated into tryptophan sidechains, and 1D ¹⁹F NMR spectra were acquired. While spectra with decent spectral dispersion were obtained, the assignment process was complicated by low signal-to-noise, and multiple changes in the spectrum introduced by the mutation. Chemoselective labelling of cysteine residues with probes containing a trifluoromethyl group was also investigated and found to give rise to well resolved ¹⁹F NMR spectra with promising characteristics. In addition, protocols for incorporation of trifluoromethyl-phenylalanine using unnatural amino acid incorporation at introduced amber codon sites were also explored, since one of the long-term goals of this work is to study ¹⁹F-labelled GlpG in its native lipid environment. For this purpose, some protocol development was also performed to introduce GlpG into lipid nanoparticles using styrene maleic acid co-block polymers. However, low expression yields of trifluoromethyl-phenylalanine-labelled GlpG and the large size of the lipid nanoparticles are not yet compatible with solution NMR. Nonetheless, this thesis lays the groundwork for further development of these samples to allow the future study of conformational exchange of GlpG in native lipid membranes.

Le protéasome 26S est une macromolécule impliquée dans la dégradation de la majorité des protéines cellulaires. Parmi ces protéines, il y a les différents régulateurs de processus cruciaux tels que les protéines responsables de la progression du cycle cellulaire, de l’apoptose, des réponses inflammatoires, de l’activation de NF-B, de la présentation antigénique et de la différenciation cellulaire. Par conséquent, les inhibiteurs du protéasome sont des agents thérapeutiques dans des pathologies tels que le cancer, l’inflammation et les maladies auto-immunes. En effet, les inhibiteurs du protéasome sont connus pour induire la mort sélective des cellules cancéreuses tout en les rendant plus sensibles aux autres traitements anticancéreux existants (chimiothérapie, radiothérapie…). L’objectif de notre laboratoire est de développer des inhibiteurs non covalents du protéasome de structures peptidomimétiques fluorés ou non fluorés, et de montrer l’intérêt du fluor en chimie médicinale. Mon projet de thèse s’inscrit dans ce cadre. Dans un premier temps nous avons mis en évidence la grande diversité et la quantité des inhibiteurs du protéasome montrant ainsi l’importance de cette macromolécule comme cible dans le traitement du cancer. D’ailleurs, deux de ces inhibiteurs sont utilisés dans le traitement du myélome multiple et du lymphome du manteau et, plusieurs composés sont en études cliniques pour différents cancers. Nous avons aussi mis en évidence le bénéfice apporté par l’incorporation de groupement fluoré sur une molécule bioactive en particulier dans les structures peptidomimétiques. En revanche, ce rappel bibliographique a aussi montré que les peptidomimétiques contraints et fluorés sont peu décrits dans la littérature et le seul exemple à notre connaissance est l’analogue contraint et fluoré de la substance P contenant le motif (Z)-fluoroalcène.La deuxième partie de ces travaux de thèse s’est focalisée sur la conception, la synthèse et l’évaluation biologique d’inhibiteurs originaux du protéasome. Nous avons mis au point une synthèse facile et efficace de pseudopeptides possédant les motifs α et β-hydrazino acides et le motif β-hydrazino acide trifluorométhyle (schéma 1). Ces molécules inhibent de manière efficace le site CT-L du protéasome du lapin avec une IC50 de l’ordre du submicromolaire. Nous avons ainsi démontré que l’activité biologique est maintenue en remplaçant un α-amino acide par un scaffold α ou β-hydrazino acide. La pharmacomodulation effectuée autour de ces motifs nous a permis d’établir des relations structure-activité. Nous avons aussi mis au point un modèle de docking assez fiable qui va nous permettre de prédire le potentiel inhibiteur de nos futures molécules.Enfin, nous avons déterminé l’IC50 de nos molécules en utilisant la technique du FABS en RMN du 19F. Schéma1: voies d’accès aux peptidomimétiques contenant les motifs α et β-hydrazino acide et le motif β-hydrazino acide trifluorométhyl.Ces travaux de thèses ont été complétés par une méthodologie de synthèse portant sur le développement de nouveaux synthons contraints fluorés dans le but de les incorporer dans nos inhibiteurs de protéasome. Les cyclopropanes trifluorométhyles ont été obtenus en utilisant la réaction tandem de Michael, addition nucléophile suivie de cyclisation avec une excellente diastéréosélectivité pour certaines réactions. Les cyclopropanes obtenus ont été fonctionnalisés en amino acides ce qui faciliterait leur incorporation dans nos pseudopeptides. Les N-aminoaziridines fluorés ont été synthétisés à partir d’oléfines fluorés et de précurseurs de nitrène en présence de diacétate d’iodobenzène (PhI(OAc)2. L’incorporation de ces nouveaux scaffolds dans la structure de nos inhibiteurs de protéasome est en cours de réalisation dans le laboratoire. / The proteasome is a multicatalytic protease complex that is responsible for the ubiquitin-dependent turnover of cellular proteins. Proteasome substrates include misfolded or misassembled proteins as well as short-lived components of signaling cascades that regulate cell proliferation and survival pathways. Inhibition of the proteasome leads to an accumulation of substrate proteins and results in cell death. The proteasome consists of a 20S proteolytic core and two 19S regulatory caps that assemble with the core at either end to form a 26S complex. Clinical validation of the proteasome as a therapeutic target in oncology has been provided by bortezomib, a dipeptide boronic acid, which is approved for the treatment of patients with multiple myeloma1and mantle cell lymphoma. In the first part of my PhD, I designed (by the help of molecular modeling) and synthesized an original series of proteasome inhibitors introducing fluorinated peptidomimetics. Fluorine atom is able to favour hydrogen bond and to increase hydrophobicity and metabolic stability of the molecules. I also synthesized a series of non fluorinated peptidomimetics containing hydrazino acid moieties as proteasome inhibitors. Thereby, we designed and synthesized a library of 50 molecules that allowed us to establish a structure-activity relationship. The biological evaluation showed that half of these compounds have a micromolar IC50 (inhibitor concentration giving 50% inhibition). Then we decided to test the inhibitor activity of our synthesized molecules by 19F NMR using the FABS technique. So we developed a fluorine substrate for screening and determination of IC50 of our potential protéasome inhibitors. In order to increase the activity of our molecules and according to encouraging observation by molecular modelling, we decided to introduce constrained scaffolds such as trifluoromethyl cyclopropane or trifluoromethyl N-aminoaziridine scaffolds in our peptidomimetics structures. So we needed trifluoromethyl cyclopropane and trifluoromethyl N-aminoaziridine amino acids that could be easily incorporate in peptidic structure. To our knowledge there is no precedent on the synthesis of fluorinated N-aminoaziridines or trifluoromethyl cyclopropane β-amino acids which allowed us to develop a new synthesis methodology of these scaffolds. First, I synthesized different trifluoromethyl N-Aminoaziridine with several protective groups. The reaction of N-Aminoaziridine was performed in DCM with K2CO3 as base and (Diacetoxyiodo)benzene. For the synthesis of trifluomethyl cyclopropane β-amino acid, we used the cyclopropanation of Michael acceptors (tandem Michael Additions-Nucleophilic Cyclization (MA-NC)). Encouraged by this result and in order to develop different scaffolds trifluoromethyl cyclopropanes, we screened other nucleophiles. These scaffolds have been functionalized to amino acid in order to introduce it in peptidic structure.

Palicourea marcgravii St. Hil. (Rubiaceae) vulgarmente conhecida como \"erva de rato\" é uma planta tóxica brasileira de grande interesse econômico na pecuária, por provocar, em bovinos, convulsões, arritmias cardíacas e \"morte súbita\" em elevado número de animais. No presente trabalho, as folhas dessecadas e moídas de P. marcgravii foram extraídas com etanol 95 %, a temperatura ambiente, por percolação; o extrato resultante foi fracionado por partição com acetato de etila e butanol saturado com água. Os resíduos obtidos foram testados \"per os\" em ratos, buscando-se investigar nos mesmos, a presença do princípio ativo tóxico. O resíduo aquoso foi o único que produziu convulsões e morte dos animais. A existência do monofluoroacetato (MF A) no resíduo aquoso foi comprovada biologicamente através do paralelismo entre as retas refetentes às funções dose/porcentagem de letalidade e dose/latência para a 1ª convulsão que foram construídas para o resíduo aquoso e padrão de referência (monofluoroacetato de sódio). O MFA foi também identificado quimicamente através da RMN19F e da cromatografia em camada delgada. Os resultados obtidos comprovaram a presença de MF A nas folhas de P.marcgravii, responsabilizando-o pelos efeitos tóxicos produzidos. Também foram levantadas algumas hipóteses na tentativa de explicar a sintomatologia dos animais intoxicados. / Palicourea marcgravii St. Hil. (Rubiaceae) is one of the most economica1ly important poisonous plants for Brazilian livestock, since it induces not only seizures, cardiac arrythmias, but also \"sudden death\" of large number of the intoxicated animals. ln the present paper, the dissected and grounded leaves of P.marcgravii were extracted with ethanol 95 %, at room temperature, by percolation; the resultant extract was fractionized by partition in ethyl acetate and butanol saturated with water. The obtained residues were administered \"per os\" to rats, trying to look for the presence of the active toxic principIe. The aqueous residue was the only that induced seizures and death to the animals. The presence of monofluoroacetate (MFA) in the aqueous residue was biologica1ly confirmed by the correlation shown in the sodium monofluoroacetate and the aqueous residue dose-response and dose effect curves. MFA was also identified through NMR19F and thin layer chromatography. The obtained results confirmed the presence of MF A in the P.marcgravii leaves; they also suggest that the toxic effects induced by this plant are a consequence of the presence of MFA in its leaves. Further, some hypothesis were also perfomed, in an attempt to better explain the symptoms induced by the plant leaves.

Palicourea marcgravii St. Hil. (Rubiaceae) vulgarmente conhecida como \"erva de rato\" é uma planta tóxica brasileira de grande interesse econômico na pecuária, por provocar, em bovinos, convulsões, arritmias cardíacas e \"morte súbita\" em elevado número de animais. No presente trabalho, as folhas dessecadas e moídas de P. marcgravii foram extraídas com etanol 95 %, a temperatura ambiente, por percolação; o extrato resultante foi fracionado por partição com acetato de etila e butanol saturado com água. Os resíduos obtidos foram testados \"per os\" em ratos, buscando-se investigar nos mesmos, a presença do princípio ativo tóxico. O resíduo aquoso foi o único que produziu convulsões e morte dos animais. A existência do monofluoroacetato (MF A) no resíduo aquoso foi comprovada biologicamente através do paralelismo entre as retas refetentes às funções dose/porcentagem de letalidade e dose/latência para a 1ª convulsão que foram construídas para o resíduo aquoso e padrão de referência (monofluoroacetato de sódio). O MFA foi também identificado quimicamente através da RMN19F e da cromatografia em camada delgada. Os resultados obtidos comprovaram a presença de MF A nas folhas de P.marcgravii, responsabilizando-o pelos efeitos tóxicos produzidos. Também foram levantadas algumas hipóteses na tentativa de explicar a sintomatologia dos animais intoxicados. / Palicourea marcgravii St. Hil. (Rubiaceae) is one of the most economica1ly important poisonous plants for Brazilian livestock, since it induces not only seizures, cardiac arrythmias, but also \"sudden death\" of large number of the intoxicated animals. ln the present paper, the dissected and grounded leaves of P.marcgravii were extracted with ethanol 95 %, at room temperature, by percolation; the resultant extract was fractionized by partition in ethyl acetate and butanol saturated with water. The obtained residues were administered \"per os\" to rats, trying to look for the presence of the active toxic principIe. The aqueous residue was the only that induced seizures and death to the animals. The presence of monofluoroacetate (MFA) in the aqueous residue was biologica1ly confirmed by the correlation shown in the sodium monofluoroacetate and the aqueous residue dose-response and dose effect curves. MFA was also identified through NMR19F and thin layer chromatography. The obtained results confirmed the presence of MF A in the P.marcgravii leaves; they also suggest that the toxic effects induced by this plant are a consequence of the presence of MFA in its leaves. Further, some hypothesis were also perfomed, in an attempt to better explain the symptoms induced by the plant leaves.

Abstract The present thesis exploits advanced liquid and gas NMR methods for the characterization of various interesting materials. The methods used to study the structural properties of thermally modified wood, ionic liquids, cements, shales, and porous organic cages include MRI, NMR cryoporometry, Laplace NMR, multidimensional Laplace NMR, as well as ¹²⁹Xe and ¹⁹F NMR. The commonality factor in all the studies is the usage of either inherent or introduced liquid or gas molecules to probe the topical materials. The MRI method was utilized to visualize the water absorption phenomena in the thermally modified pine wood. High-resolution images made it possible to observe the spatial distribution of free water and the changes in the rate of absorption of water in wood samples modified at different temperatures. The images also helped to resolve the individual resin channels. T₂ maps enabled us to observe the changes in the relaxation values of free water in thermally modified wood as compared to their unmodified reference wood samples. The multidimensional Laplace NMR methods were exploited to study the structural and dynamical properties of a novel halogen-free, boron-based ionic liquid (hf-BIL). NMR self-diffusion (D) experiments showed the presence of two coexisting dynamic phases in hf-BIL. Multidimensional D − T₂ correlation experiments made it possible to determine the T₂ relaxation times of the slow and fast diffusing phases. T₂ − T₂ relaxation exchange measurements allowed quantifying the exchange rates of anions and cations between the phases. Moreover, the theoretical modeling of the experimental data revealed that the slow diffusing phase was composed of anion-cation aggregates, while the fast diffusing phase was comprised of free anions and cations. ¹²⁹Xe NMR analysis of the xenon adsorbed in the cements and shales helped us to determine their porous structures. The method exploits the high sensitivity of the chemical shift of ¹²⁹Xe to its local environment. The chemical shift value of ¹²⁹Xe enabled us to estimate the size of the mesopores in the cement samples. The exchange spectroscopy (EXSY) measurements were used to determine the exchange rates between the free gas and mesopores of the cement samples. ¹²⁹Xe NMR spectra of the shale samples provided information about pore sizes and paramagnetic compounds. ¹H NMR cryoporometry measurements of the shale samples immersed in acetonitrile made it possible to analyze the pore size distribution ranging from 10 to over 100 nm. Moreover, T₂ − T₂ exchange measurements helped us to quantify the exchange rates of acetonitrile in the shale samples. Xenon and SF₆ were used as internal reporters to gain versatile information on adsorption phenomena in the cage and window cavities of the crystalline porous organic cages. ¹²⁹Xe NMR analysis of the adsorbed xenon helped us to determine the diffusion coefficients and activation energy of diffusion as well as thermodynamic parameters. With the help of T₂ relaxation time values, it was possible to estimate the exchange rates between cage and window cavities. Chemical exchange saturation transfer (CEST) experiments resolved a window cavity site, which arises from crystal defects in porous organic cages. In addition, ¹⁹F NMR analysis made it possible to estimate the relaxation rates and diffusion coefficients of SF₆ gas in porous organic cages. Modelling of the T₁, T₂ and diffusion data confirmed that the cage to window exchange is the completely dominating mechanism for ¹²⁹Xe T₂ relaxation. T₁ relaxation is dominated by diffusion modulated dipole-dipole relaxation (DDinter) and chemical shift anisotropy (CSA) relaxation due to local cavity mobility. Whereas, in case of SF₆ T₂ data, the dominating mechanism is diffusion modulated dipole-dipole relaxation and for T₁ the local tumbling of SF₆ in cage cavity is the key dynamics behind the dipole-dipole and CSA mechanisms. / Original papers The original publications are not included in the electronic version of the dissertation. Javed, M. A., Kekkonen, P. M., Ahola, S., & Telkki, V.-V. (2015). Magnetic resonance imaging study of water absorption in thermally modified pine wood. Holzforschung, 69(7), 899–907. https://doi.org/10.1515/hf-2014-0183 Javed, M. A., Ahola, S., Håkansson, P., Mankinen, O., Aslam, M. K., Filippov, A., … Telkki, V.-V. (2017). Structure and dynamics elucidation of ionic liquids using multidimensional Laplace NMR. Chem. Commun., 53(80), 11056–11059. https://doi.org/10.1039/c7cc05493a http://jultika.oulu.fi/Record/nbnfi-fe2017102750335 Javed, M. A., Komulainen, S., Daigle, H., Zhang, B., Vaara, J., Zhou, B., & Telkki, V.-V. (2019). Determination of pore structures and dynamics of fluids in hydrated cements and natural shales by various ¹H and ¹²⁹Xe NMR methods. Microporous and Mesoporous Materials, 281, 66–74. https://doi.org/10.1016/j.micromeso.2019.02.034 http://jultika.oulu.fi/Record/nbnfi-fe2019041712678 Komulainen, S., Roukala, J., Zhivonitko, V. V., Javed, M. A., Chen, L., Holden, D., … Telkki, V.-V. (2017). Inside information on xenon adsorption in porous organic cages by NMR. Chemical Science, 8(8), 5721–5727. https://doi.org/10.1039/C7SC01990D http://jultika.oulu.fi/Record/nbnfi-fe201709288804 Håkansson, P., Javed, M. A., Komulainen, S., Chen, L., Holden, D., Hasell, T., … Telkki, V.-V. (2019). NMR relaxation and modelling study of the dynamics of SF₆ and Xe in porous organic cages. Manuscript.