Chemical modifications of oligonucleotides provide an important tool to understand how the natural substrate works as well as how to improve their biochemical and biological properties as potential therapeutics and diagnostics. Our carba-LNA (2',4'-carba-bridged Locked Nucleic Acid) modified oligo-DNA or -RNA have been found to be useful to modulate oligo-RNA and -DNA activity. This thesis is based on four papers: Paper I (J. Org. Chem. 2010, 75, 7112-7128) deals with the synthesis of 2',4'-propylene-bridged (Carba-ENA) thymidine and its analogues. These carba-ENA nucleosides have been subsequently incorporated into 15mer antisense oligodeoxynucleotides (AON), and their affinity toward complementary mRNA and DNA, as well as their nuclease resistance and RNase H recruitment capability have been investigated in comparison with those of the native and ENA counterparts. Paper II (J. Org. Chem. 2012, 77, 6855–6872) illustrates the synthesis of dimethylbicyclo[2.2.1]heptane and a diastereomeric mixture of oxabicyclo[2.2.1]heptanes by the free-radical ring-closure reaction approach. The role of steric factors for different chair- and the boat-like transition states was evaluated involving the 5-exo radical ring closure reaction to a tethered olefin. Paper III (J. Org. Chem. 2012, 77, 9747-9755) shows an unusual strain releasing reaction of 1-mesyloxy-8,7-dimethylbicyclo[2.2.1]heptane by a base-promoted substitution at the chiral C3 followed by spontaneous concerted ring opening involving the most strained C2-C3-C4 bonds (with bond angle 94°) and the C2 bridgehead leading to anti-endo elimination of the C1-mesyloxy group by the conjugate base of adenine or thymine to give two diastereomeric C3'(S) and C3'(R) derivatives of 1-thyminyl and 9-adeninyl cyclohexene, and a mechanistic rational has been formulated. Paper IV (J. Org. Chem. 2014, 79, 7266−7276) focuses on the diastereospecific synthesis of E/Z bicyclo[2.2.1]heptane-7- and oxabicyclo[2.2.1]heptane-8-oximes and their corresponding C-nitroso derivatives. The comparative kinetic and thermodynamic studies of the conversions of the C-nitroso side products to the required oximes have been delineated leading to the synthesis of desmethyl sugar derivatives.

Part I. The syntheses of a series of stable ferrocenylsilane compounds and their corresponding polyradical cations are reported. Electron spin properties of these molecules were investigated by cyclic voltammetry, ESR, and magnetic susceptibility measurements. All the compounds presented, showed significant electronic communication (>100 mV) between the redox centers by CV. Part II. Baeyer-Villiger oxidation of (1,9-dimethyl-PCU-8,11-dione) was performed using m-chloroperoxybenzoic acid in 1:2 molar ratios. The product obtained was the corresponding dilactone 113. The structure of the reaction products was established unequivocally via single crystal X-ray diffraction methods. The reaction of the 1,9-dimethyl-PCU-8,11-dione with 1:1 molar ratio of m-chloroperoxybenzoic acid produced again the dilactone 113, and not the expected monolactone 114. Ceric ammonium nitrate (CAN) promoted oxidation reaction of 1,9-dimethyl-PCU-8,11-dione afforded a mixture of dimethylated lactones, which indicated unique reaction mechanism pathways. These individual isomers, 115 and 116, have been isolated from these mixtures via column chromatography by using silica gel as adsorbent followed by fractional recrystallization of individual chromatography fractions. Structures of these pure products have been established unequivocally by application of single crystal X-ray crystallographic methods.

In the present work, a series of 1-benzyl-2-alkylbenzenes functionalized was subjected to intramolecular cyclization reaction promoted by iron(III) chloride with diorganyl dichalcogenide allowed the synthesis of 9-(organochalcogen)-5H-benzo[7]annulenes whereas the mutual action between diorganyl dichalcogenide and iron(III) chloride in a 0.5:1.0 mole ratio was essential in order to achieve the maximal yields of the products. The cyclization reaction tolerated a variety of functional groups, such as trifluoromethyl, chloro, fluorine and methoxyl, in both 1-benzyl-2-alkynylbenzenes and diorganyl diselenides, giving the seven-membered carbocyclic exclusively via a 7-endo-dig cyclization process, it resulted in a total of 23 samples in 45-77 % yield. / No presente trabalho, uma série de 1-benzil-2-alquilbenzenos funcionalizados foi submetida à reação de ciclização intramolecular promovida por FeCl3 com dicalcogeneto de diorganoíla, permitindo a síntese de 9-(organocalcogênio)-5H-benzo[7]anulenos. Considerou-se que uma ação mútua entre o dicalcogeneto de diorganoíla e o cloreto de ferro (III), de proporções molares 0,5:1,0, é essencial para os produtos atingirem bons rendimentos. A reação de ciclização tolera uma variedade de grupos funcionais tais como trifluormetil, cloro, flúor e metoxila , em ambos os 1-benzil-2-alquilbenzenos e dicalcogeneto de diorganoíla, levando aos carbociclos de sete membros, exclusivamente por meio de um processo de ciclização 7-endo-dig, resultou-se em um total de 23 exemplos com 45 - 77% de rendimento.

This master thesis is dedicated to the preparation of fluorinated derivatives of carbocyclic nucleosides, that may serve as flaviviral replication inhibitors. Preparation of both monofluorinated as well as gem-difluorinated analogs of ribo and 2'-deoxyribonucleoside was attempted. While a suitable and reliable route for the preparation of monofluorinated compounds way found, synthesis of gem-difluorinated turned out to be rather challenging. Although most of the presented work dealt with compounds bearing adenine as a nucleobase, the universal applicability of the developed procedures, demonstrated on the preparation of a guanosine-type molecule, suggests that after slight optimization larger series of this type of compounds could be prepared.

Les virus sont au centre de problème de santé publique. En raison de l'apparition de nouveaux virus et pour certains de leur résistance aux traitements existants il est toujours d’actualité de développement de nouveaux agents antiviraux. En général, la stratégie de lutte contre les infections virales est basée sur la vaccination ou sur l'activité des petites molécules, interférant avec un ou plusieurs processus biologiques participant au cycle de vie du virus. Dans ce contexte, nous avons conçu et synthétisé des petites bibliothèques de molécules visant des propriétés anti-filovirus. Dans ce projet de recherche, nous avons mis l'accent sur le développement de composés ciblant la protéine Niemann-Pick C1, les protéases cathepsine et le processus de réplication. Lors du développement des inhibiteurs de Neimann-Pick C1 plus de 70 composés ont été synthétisés, portant le squelette pipérazine. Afin d'obtenir des inhibiteurs de cystéine cathepsines pouvant être impliqués dans la réplication du virus Ebola, nous avons synthétisé une petite bibliothèque de composés porteurs de groupement 1,3,5-triazine et possédant des activité de l’ordre du nanomolaire sur les cathepsines B, K, L et S. Enfin, pour inhiber la réplication du virus en ciblant SAH hydrolase, nous avons proposé une série de C-nucléosides carbocyclic ayant motif de 4-aza-7,9-dideazaadenosine. / The viruses cause the problem of public health. Due to the appearance of new viruses and their resistance to existing treatments there is still relevant to develop new antivirals. Generally, the strategy to combat viral infections is based on vaccination or on the activity of small molecules, interfering with one or more biological processes participating in virus life cycle. In this context, we took an effort to design and synthesize the library of small molecules possessing anti-filovirus properties. In this research project, we were focused on the developing of compounds targeting Niemann-Pick C1 protein, cathepsin proteases and replication process. In our effort into the development of the inhibitors of Neimann-Pick C1 we prepared the series of about 70 compounds, having in common the piperazine moiety. Diverse 1,4-N,N - substituents of piperazine, differencing in a size and shape were studied. In order to obtain efficient cysteine cathepsins inhibitors, we synthesized the small library of compounds bearing 1,3,5-triazine moiety. Finally, to inhibit the virus replication by targeting SAH hydrolase, we proposed the series of carbocyclic C-nucleosides having motif of 4-aza-7,9-dideazaadenosine.

Isolée d'une bactérie, Streptomyces alboniger, la puromycine est un nucléoside antibiotique naturel présentant une analogie structurale avec l'adénosine terminale de l’extrémité 3’ de l'ARNt aminoacylé. Cette similarité confère à cette molécule la faculté de pouvoir s'insérer dans le site A (actif) du ribosome et d'inhiber la synthèse des protéines. Cependant, du fait de la formation d'un produit toxique lors de sa métabolisation, la puromycine n'a jamais été employée à des fins thérapeutiques chez l'homme. Néanmoins, utilisée en tant qu'outil synthétique, elle a largement contribué à une meilleure compréhension du mécanisme du transfert peptidique. Au travers de cette thèse, six analogues carbobicycliques (deux en série ribo et quatre en série 2'-désoxy), mimant de façon optimale les conformations extrêmes nord ou sud de la puromycine, ont été synthétisés puis testés dans le ribosome. Outre confirmer que la présence d'un groupement 2'-hydroxyle améliorait l'activité inhibitrice, ces expériences in vitro ont apporté une preuve que, dans le site actif, le déplacement de l'équilibre conformationnel du ribofuranose de l'adénosine terminale de l'ARNt aminoacylé – analogue structural de la puromycine – en faveur de son conformère nord pourrait être directement impliqué dans la catalyse ribosomale du transfert peptidique. Par ailleurs, un projet annexe sur le développement de nouveaux antipaludiques potentiels a permis la synthèse, en série xylo, de la puromycine et de son métabolite naturel le puromycine aminonucléoside. Ces composés ont été testés sur les souches 3D7 et Dd2 du parasite Plasmodium falciparum. / Puromycin, a natural antibiotic nucleoside isolated from the bacterium Streptomyces alboniger, has been used to approach and to clear up the understanding of the mechanism of protein biosynthesis. In fact, its structural similarity to the 3' terminal 3'-O-aminoacyl adenylate moiety of aminoacyl-tRNA explains its activity in the ribosomal A site causing the inhibition of the protein synthesis. Since its metabolism generates a toxic product, puromycin cannot be used as therapeutical purposes for humans. During this PhD work, six carbobicyclic analogues of puromycin, conformationally restricted into the northern or southern conformations with the help of a cyclopropane moiety, were synthesized (two ribo-derivatives and four in the 2'-deoxy ribo-series) then tested for pep¬tidyl transfer efficiency in ribosomes. In addition to confirming that the 2'-hydroxyl function is necessary to improve the inhibition properties, these enzymological tests brought an evidence that the conformational switching: southern to northern, occurring in the A site, could directly be involved in the ribosomal catalysis of the peptidyl transfer. Besides, a side project on the elaboration of potential antimalarial compounds provided new xylo-analogues of puromycin and its natural metabolite PAN. These derivatives were tested on the 3D7 and Dd2 strains of the Plasmodium falciparum parasite

The PhD work "Hydroacylation and C-N coupling Reactions. Mechanistic Studies and Application in the Nucleoside Synthesis" tackle two different objectives, a) developing new methods of synthesis of nucleosides (introduction, and chapters 1 and 2) and b) to carry out a mechanistic study of the intermolecular hydroacylation and hydroiminoacylation reaction with and cationic rhodium complexes (chapter 3). Concerning the synthesis nucleosides, in chapter 1 we have explored new methods of synthesis of 2',3'-dideoxynucleosides and isonucleosides using a palladium or copper catalyzed C-N coupling reaction, aiming to overcome the stereoselectivity problems of the glycosylation reaction. The synthesis of the iodo-vinyl derivatives required as starting materials has been tried by different procedures, all of them unsuccessful. Finally, the coupling reaction has been explored in 1-iodo-glucal derivatives. Palladium catalysts were unsuccessful in coupling with benzimidazol used as model of purinic bases. Copper catalysts provided very low conversions. However, the oxidative addition of 1-iodo-glucal to palladium was proved and it was also observed that the reaction with aniline proceeds. That, suggest that the problem is in the steps involving the benzimidazol.In chapter 2, it has been developed a new method of synthesis of carbocyclic nucleosides using and enantioselective intramolecular hydroacylation reaction as a key step. This reaction leaded to the 3-hydroxymethyl-cyclopentanones in good yields and excellent enantioselectivities. When (S,S)-Me-Duphos was used the 3S-cyclopentanone was obtained, in contrast whether the (R,R)-Me-Duphos was employed the reaction proceed giving the opposite enantiomer. In both cases. The reduction of the ketone can be carried out in a stereoselective way using a hydroxyl-assited reduction with NaBH(OAc)3. Alternatively, the diastereomeric mixture obtained by a direct reduction can be resolved by using a DKR process using a combined enzyme/Ru complex catalytic system. A Mitsunobu reaction has allowed finally to link adenine to the cyclopentane moiety. In the third chapter, the mechanism of both cationic and neutral rhodium catalyst precursors in the hydroiminoacylation of alkenes was studied. The oxidative addition step was studied using both NMR and DFT techniques. Using the neutral complex, this step is a thermodynamically favoured process, as demonstrated by the isolation of the stable complex. Furthermore, DFT calculations showed the existence of an agostic intermediate on the route to the C-H activation product. In the cationic system, the oxidative addition reaction was shown by DFT calculations to be an endothermic process, hence un-favoured. This was in agreement with the NMR experiments, in which an oxidative addition product was only detected in the presence of a chloride source. Furthermore, the transition states involved in both systems were identified using DFT calculations, which proved that the presence of chloride not only stabilize the oxidative addition product but also lower the energy barrier of the overall process.Using the neutral system, it was identified the coupling product still coordinated to rhodium, which is in an enamine tautomeric form. After removal of the coupling product the stable complex [Rh(μ-Cl)(PPh3)2]2 was formed. This species was reported as a precursor for the oxidative addition step, from which the catalytic cycle can start again. However in the cationic system, the system did not yield any stable rhodium species and quickly evolved towards decomposition. / Durante la última década la terapia del SIDA ha experimentado una evolución notable. El conocimiento del modo de actuación y proliferación del virus ha permitido incrementar el número de dianas biológicas para su neutralización. Así, hoy en día se conocen compuestos que inhiben la entrada del virus en la célula, la transcripción del RNA en DNA, la integración del DNA vírico en DNA celular, la producción del envolvente proteico del virus, entre otros. Todo ello, ha permitido la realización de tratamientos dirigidos a diferentes dianas, que han neutralizado la evolución del virus mejorando la calidad de vida de los pacientes.Existen numerosas metodologías diseñadas para obtener los retrovirales mencionados anteriormente, pero en la mayoría de ellas se requieren numerosos pasos de síntesis y además en muchas de ellas se obtienen mezclas de los isómeros α/β. De este modo se pretende diseñar una alternativa sintética general para la preparación de la familia de nucleósidos arriba indicadas y al mismo tiempo que sea una alternativa práctica y eficaz a los métodos descritos hasta el momento.En el capítulo uno la obtención de isonucleosidos y 2',3'-dideoxinucleosidos se abordó utilizando como etapa clave de reacción el acoplamiento C-N entre los derivados de 4-halo-2,3-dihidrofurano y 5-halo-2,3-dihidrofurano con bases púricas y pirimidínicas, la posterior hidrogenación enantioselectiva del doble enlace nos permitiría obtener los mencionados compuestos de una forma sencilla. En el estudio realizado bajas conversiones de los productos de acoplamiento cruzado fueron detectados aunque actualmente se están intentado mejorar los resultados.Referente a la obtención de carbociclonucleosidos abordada en el capítulo 2, se ha llevado cabo una nueva metodología sintética en la que se ha aplicado la reacción de hidroacilación intramolecular enantioselectiva catalizada por rodio. Así pentenales substituidos en posición cuatro han sido convertidos en las ciclopentanonas correspondientes. En función de la quiralidad de la fosfina empleada se han obtenido tanto los enantiomeros R como S con excelentes conversiones y enantioselectividades.Con el fin de incorporar la base nitrogenada en la ciclopentanona la reducción diastereoselectiva se ha llevado a cabo dos procedimientos: a) reducción racémica de la ciclopentanona y posterior resolución cinética dinámica, b) reducción diastereoselectiva utilizando como agente reductor el triacetoxiborohidruro de sodio. En ambos casos se obtuvieron diastereoselectividades excelentes pudiendo así obtener un distereoisomero u otro en función del procedimiento y el enantiomero utilizado como material de partida. La posterior reacción de Mitsunobu sobre el alcohol y la desprotección del grupo protector nos ha permitido obtener el carbociclonucleosido con buenos rendimientos y excelentes esteroselectividades.En el capitulo tres se ha realizado un estudio sobre la reacción de hidroacilación intramolecular de alquenos cataliza por rodio, donde se ha estudiado la diferencia de comportamiento de los sistemas catiónicos y neutros de rodio en la etapa de adición oxidante. Estos estudios se han realizado utilizando técnicas espectroscópicas de resonancia magnética nuclear y cálculos teóricos mediante técnicas DFT. El estudio computacional ha mostrado que en el caso de los sistemas neutros la etapa de adición oxidante es una etapa termodinámicamente favorable hecho que se gratifica con el hecho de que el producto de adición oxidante es estable y aislable. Además se ha encontrado la existencia de un intermedio agóstico en el proceso de activación del enlace C-H. Sin embargo, en los sistemas catiónicos la etapa de adición oxidante resultó ser un proceso endotérmico. Los estados de transición encontrados no solo han demostrado que la presencia de cloruro estabiliza el producto de adición oxidante sino que también disminuye la barrera energética del proceso global. La etapa de inserción del alqueno también fue estudiada para ambos sistemas utilizando estireno como sustrato. En el sistema neutro se detectó una nueva especie de rodio la cual no había sido descrita anteriormente y fue completamente caracterizada mediante RMN multinuclear.En el sistema catiónico se consiguió detectar el hidruro correspondiente al producto de adición oxidante el cual también fue completamente caracterizado por técnicas de RMN. Sin embargo, en el estudio de la inserción del alqueno no se observó la ningún producto que indicase que el mencionado proceso se llevará acabo indicado que la inserción de alqueno es además la etapa lenta del proceso.

Ces dernières années, les analogues nucléosidiques ont eu un rôle majeur dans le traitement de maladies virales infectieuses tels le SIDA, les hépatites, l’herpès, la variole ou la grippe. Cependant, l’apparition de nouveaux virus ou de mutations virales ont renforcé la nécessité de développer des antiviraux plus efficaces et plus résistants. L’intensive recherche de dérivés nucléosidiques cliniquement actifs a permis l’émergence d’une multitude de nouvelles approches pour leurs synthèses. Parmi ce panel, les réactions catalysées par des métaux de transition tardifs font certainement partie des méthodes les plus importantes pour accéder à une large gamme de pharmacomodulations. Lors de ce projet de recherche, nous nous sommes intéressés à la conception, la synthèse et la découverte de nouveaux dérivés nucléosidiques en tant qu’antiviraux contre le virus de la variole. Pour ce faire, nous avons ciblé des 1,2,3-triazolo-carbanucléosides en série racémique ou énantiosélective ainsi que des nucléosides phosphonates acycliques. Dans un effort de développement et/ou d’amélioration de leurs méthodes de synthèse, nous avons également étudié la contribution de complexes au ruthénium et au cuivre contenant un carbène Nhétérocyclique (CNH) dans des réactions de métathèse croisée et de cycloaddition 1,3-dipolaire de Huisgen. Enfin, en vue d’obtenir des outils efficaces utilisables en synthèse nucléosidique, nous avons développés des nouveaux complexes au palladium portant un ligand CNH et testé leurs réactivités dans des réactions de Narylation de Buchwald-Hartwig et d’hydrogénation d’oléfines. / In the last decades, nucleoside analogues have played a major role in the treatment of viral infectious diseases, such as AIDS, hepatitis, herpes, smallpox or influenza. Nevertheless, the apparition of new or mutated viruses highlights the need of more potent and resistant antiviral therapeutics. The intense search for clinically useful nucleoside derivatives has resulted in a wealth of new approaches for their synthesis. Among them, latetransition metal-catalyzed reactions are certainly the most important methods to access variety of appealing pharmacomodulations. In this research project, we were interested in the conception, the synthesis and the discovery of new nucleoside derivatives as antiviral agents against smallpox viruses. Hence, we have targeted racemic or enantiomerically pure 1,2,3-triazolo-carbanucleosides as well as acyclic nucleoside phosphonates. In our effort into the development or/and the improvement of their synthetic methodologies, we have also studied the contribution of ruthenium and copper complexes bearing N-heterocyclic carbene (NHC) ligands in cross-metathesis and Huisgen 1,3-dipolar cycloaddition reactions. Finally, in order to obtain efficient tools useful in nucleoside synthesis, we have developed new NHC-containing palladium complexes and examined their reactivity in Buchwald-Hartwig N-arylation and olefins hydrogenation reactions.

Carbocyclic nucleoside analogs with norbornane moiety that have been synthesized at IOCB AS CR, represent new potential chemotherapeutic agents with significant activity against Coxsackieviruses. The main objective of this work was to study the metabolism and mechanism of action of the original analog carbocyclic nucleoside MS 254, which is characterized by its antiviral and cytostatic effects. The attention was partially paid also to the two structurally related substances (MS 255, MS 320). In this work, we determined cytotoxicity of these compounds in cell culture and the effect of MS 254 on the amount of total and oxidized glutathione, activity of glutathione-S-transferase (GST), glutathione reductase (GR) and the effect on cellular oxidative stress. The kinetics of the conjugation of MS 254 by human GST was also studied. It was found that of the three substances tested MS 255 was the most cytotoxic and MS 254 was the least cytotoxic compound. It was further found that MS 254 does not cause significant oxidative stress and that it increases the activity of GST and GR in a dose-dependent manner. Michaelis-Menten constant of the conjugation of MS 254 with the glutathione (main metabolic pathway) was determined in the milimolar range, indicating a relatively low affinity of MS 254 for GST.

Les vinylphosphonates fonctionnalisés représentent une classe importante de briques moléculaires utilisées en synthèse organique et suscitent un grand intérêt au niveau biologique. Ainsi, nous avons étudié différentes voies de synthèse pour accéder à ces composés. Il en ressort une méthode généralisable, faisant intervenir une réaction de substitution organocatalysée, à partir d’un substrat phosphoré original, et permettant d’obtenir de nombreux vinylphosphonates non décrits jusqu’ici. Par la suite, la synthèse de vinylphosphonates azahétérocycliques a été abordée en employant la réaction de métathèse cyclisante à partir de substrats adéquats, eux-mêmes obtenus par le biais de la méthodologie décrite précédemment.Nous avons enfin mis au point la première synthèse totale énantioselective de la molécule UPF 702 (vinylphosphonate cyclique comportant un motif acide aminé), connue pour ses propriétés biologiques notamment comme agoniste de récepteurs du glutamate et présentant ainsi un potentiel thérapeutique contre les maladies du système nerveux central. Deux voies de synthèses ont été imaginées, basées sur des réactions organocatalysées et de métathèse cyclisante. L’introduction de la chiralité a été réalisée via des réactions de désymétrisation ou de dédoublement enzymatiques et l’accès à l’amine par un réarrangement de Curtius. / Functionalized vinylphosphonates constitute an important class of building blocks used in organic synthesis and aroused great interest due to their various biological activities. Thus, we developed several synthetic methodologies to reach these compounds. The most general method entails an organocatalyzed substitution reaction using an original substrate, and allows the synthesis of numerous hitherto unknown vinylphosphonates.Then, the synthesis of azaheterocyclic vinylphosphonates was investigated using the ring closing metathesis from appropriate substrates which are obtained through the above methodology.Finally, we have set up the first enantioselective synthesis of UPF 702 (a cyclic vinylphosphonate including the amino acid moiety), known to exhibit agonist activity towards glutamate receptors, and thus potentially active against central nervous system diseases. Two synthetic approaches were devised, based on the organocatalyzed substitution followed by ring closing metathesis. The enantioselectivity was brought by enzymatic resolution or desymmetrisation, whereas the amino acid was prepared via a Curtius rearrangement.