Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-04-27T19:41:04Z No. of bitstreams: 1 gustavosenragoncalvesdecarvalho.pdf: 7312351 bytes, checksum: 619ab5b1846a289b3dd2a2d56e459c0c (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-05-13T13:06:35Z (GMT) No. of bitstreams: 1 gustavosenragoncalvesdecarvalho.pdf: 7312351 bytes, checksum: 619ab5b1846a289b3dd2a2d56e459c0c (MD5) / Made available in DSpace on 2017-05-13T13:06:35Z (GMT). No. of bitstreams: 1 gustavosenragoncalvesdecarvalho.pdf: 7312351 bytes, checksum: 619ab5b1846a289b3dd2a2d56e459c0c (MD5) Previous issue date: 2011-07-16 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Este trabalho tratou da pesquisa para a descoberta de potenciais fármacos contra doenças negligenciadas e foi divido em três partes. A primeira parte apresenta uma nova metodologia para síntese de ciclo-nucleosídeos, a partir de carboidratos (D-glicose e D-xilose), mais especificamente análogos N3,2’-ciclo-nucleosídeos até então inéditos na literatura. Essa metodologia desenvolvida foi aplicada na obtenção de um análogo da 5’-metil-tioadenosina (MTA), um importante regulador metabólito, controlador da 5’-metil-tioadenosina/S-adenosilhomocisteína (MTA/SAH) nucleosidase. A segunda parte deste trabalho trata, da síntese de bioisósteros do resveratrol, um importante metabólito encontrado em plantas superiores. Desde a descoberta de seus efeitos como cardioprotetor e antioxidantes, várias pesquisas associam este composto a novas potencialidades medicinais. Desta forma utilizando-se da ferramenta do isosterismo clássico, onde a ligação C=C entre os anéis foi substituída por uma ligação C=N, sintetizou-se uma série de análogos do resveratrol. O terceiro e último assunto tratado neste trabalho foi a preparação e avaliação biológica de compostos heterocíclicos contendo o nitrogênio como heteroátomo. Realizou-se a síntese de três séries distintas de heterociclos nitrogenados, mais especificamente imidazolidinas, hexahidropirimidinas e benzimidazóis que foram obtidos através de sínteses rápidas e eficientes. Os compostos obtidos foram caracterizados por diferentes técnicas espectroscópicas, a saber, infravermelho, RMN 1D e 2D, espectrometria de massas de alta resolução e análise elementar e foram submetidos a ensaios biológicos com o intuito de se testar seus potenciais como leishmanicida, antibacteriano, antitubercular, antioxidante, antimalárico e antichagásico. / This work deals with the research for discovery of potential drugs against neglected diseases and has been divided into three parts. The first part presents a new methodology for synthesis of cyclo-nucleosides from carbohydrate (D-glucose and D-xylose) analogues specifically N3, 2'-cyclo-nucleosides until then unpublished in literature. This methodology was applied to obtain an analogue of 5'-methyl-tioadenosina (MTA), an important metabolite regulator, controller of 5'-methyl-tioadenosine/Sadenosylhomocysteine (MTA / SAH) nucleosidase. The second part of this work concerns the synthesis of resveratrol bioisosters, a major metabolite found in higher plants. Since the discovery of its cardioprotective and antioxidants effects and several research associates this compound for new potential medicines. Thus, using the tool of classical isosteric, where C=C bond between the rings is replaced by a C=N bond, summed up a series of analogues of resveratrol. The third and final issues addressed in this work were the preparation and biological evaluation of heterocyclic compounds containing nitrogen as heteroatom. We carried out the synthesis of three distinct series of nitrogen heterocycles, specifically imidazolidines, hexahydropyrimidines and benzimidazole were obtained through rapid and efficient syntheses. The compounds were characterized by different spectroscopic techniques, namely infrared, 1D and 2D NMR, high resolution mass spectrometry and elemental analysis and were bioassayed in order to test their potential as antileishmanial, antibacterial, antitubercular, antioxidant, antimalarial and anti-Chagas agents.

Trypanosoma brucei is a causative agent of African sleeping sickness. It is an extracellular parasite which circulates in the blood, lymph and eventually invades the central nervous system. There is a great need for new medicines against the disease and specific properties of nucleoside kinases in the pathogen can be exploited as targets for chemotherapy.  T. brucei contains a gene where two thymidine kinase sequences are fused into a single open reading frame. These types of tandem thymidine kinases were found only in different types of parasites, which made us to believe that it might be beneficial for them. Each thymidine kinase sequence in these tandem enzymes are here referred to as a domain. By cloning and expressing each domain from T. brucei separately, we found that domain 1 was inactive and domain 2 was as active as the full-length enzyme. T. brucei thymidine kinase phosphorylated the pyrimidine nucleosides thymidine and deoxyuridine and to some extent purine nucleosides like deoxyinosine and deoxyguanosine. Human thymidine kinase increases the affinity to its substrates when it forms oligomers. Similarly, the T. brucei two thymidine kinase sequences, which can be viewed as a pseudodimer, had a higher affinity to its substrates than domain 2 alone.  T. brucei lacks de novo purine biosynthesis and it is therefore dependent on salvaging the required purine nucleotides for RNA and DNA synthesis from the host. Purine salvage is considered as a target for drug development. It has been shown that in the presence of deoxyadenosine in the growth medium, the parasites accumulate high levels of dATP and the extensive phosphorylation of deoxyadenosine leads to depleted ATP pools. Initially, we wondered if deoxyadenosine could be used as a drug against T. brucei. However, we found that T. brucei is partially protected against deoxyadenosine because it was cleaved by the enzyme methylthioadenosine phosphorylase (MTAP) to adenine and ribose-1-phosphate. At higher concentration of deoxyadenosine, 3 the formed adenine was not efficiently salvaged into ATP and started to inhibit MTAP instead. The deoxyadenosine was then instead phosphorylated by adenosine kinase leading to accumulation of dATP. The MTAP reaction makes deoxyadenosine itself useless as a drug and instead we focused on finding analogues of deoxyadenosine or adenosine that were cleavage-resistant and at the same time good substrates of T. brucei adenosine kinase. Our best hit was then 9-(2-deoxy-2-fluoro-ß-D-arabinofuranosyl) adenine (FANA-A). An additional advantage of FANA-A as a drug was that it was taken up by the P1 nucleoside transporter family, which makes it useful also against multidrug resistant parasites that often have lost the P2 transporter function and take up their purines solely by the P1 transporter. In parallel with our study of nucleoside metabolism in T. brucei, we also have a collaboration project where we screen essential oils from plants which are used in traditional medicine. If the essential oils are active against the trypanosomes, we further analyze the different components in the oils to identify new drugs against African sleeping sickness. One such compound identified from the plant Smyrnium olusatrum is isofuranodiene, which inhibited T. brucei proliferation with an IC50 value of 3 μM.

Environ un tiers des cancers est dû à la dérégulation du facteur de transcription c-Myc. Les mécanismes par lesquels ce facteur de transcription est impliqué dans le processus de cancérogenèse commencent à être mieux compris grâce notamment à l'identification de ses gènes cibles. Parmi eux a été identifié, à la fin des années 2000, le gène dnph1 codant pour une protéine surexprimée dans de nombreux cancers. Cependant, à ce jour, le rôle et la fonction biologiques de cette nouvelle cible thérapeutique restent méconnus. Cette protéine a été caractérisée au laboratoire comme étant une 2'-désoxyribonucléoside 5'-monophosphate N-hydrolase, activité jamais décrite jusqu'alors. Si les 2'-désoxyribonucléosides 5'-monophosphates sont substrats de cette enzyme, il a été montré que les ribonucléotides puriques canoniques sont des inhibiteurs compétitifs. Au cours de ces travaux de thèse, nous avons entrepris différentes études de relation structure-activité autour d'analogues ribonucléosidiques 5'-monophosphates dans le but d'identifier des inhibiteurs plus affins. Une première famille d’analogues modifiés en position 6 de la purine par différents groupements de taille et fonction variables a été synthétisée et les premiers inhibiteurs micromolaires de DNPH1 ont ainsi pu être identifiés. La co-cristallisation de certains composés avec l'enzyme a guidé la conception d'inhibiteurs de deuxième génération, modifiés en positions 6 et 2. Un léger effet additif sur les constantes d’inhibition a alors été observé et des inhibiteurs sub-micromolaires ont été identifiés. Des tests in vitro sur des lignées cellulaires cancéreuses surexprimant DNPH1 ont montré une activité cytotoxique micromolaire de certains des composés synthétisés. D'autres modifications portant sur la partie ribose-phosphate et le squelette purique ont été abordées dans le but de renforcer l'affinité et la stabilité biologique des inhibiteurs. L'ensemble de ces travaux a permis d'une part de mieux caractériser cette nouvelle cible et d'autre part d'identifier les premiers inhibiteurs micromolaires cytotoxiques. Ces résultats ouvrent des perspectives pour la conception de molécules plus efficaces. / About one third of the cancers is due to the deregulation of the transcription factor c-Myc. The gene dnph1 was identified a decade ago as a target gene of the c-Myc oncoprotein and encodes for a protein which is frequently over-expressed in several cancers. However, its biological role remains still unknown. It was recently shown that DNPH1 is a novel 2'-deoxyribonucleoside 5'-monophosphate N-hydrolase and that natural purine ribonucleotides act as competitive inhibitors. The aim of this thesis was the synthesis of strong inhibitors in order to study this new potential cancer target DNPH1. Several structure-activity relationships were built around ribonucleoside 5'-monophosphate derivatives. A first series of compounds modified at the 6 position of the purine core has been synthesized and enabled us to identify the first micromolar inhibitiors. Thanks to these inhibitors, X-ray structures of DNPH1 in interaction with inhibitors have been resolved and led us to the development of a new generation of analogues modified at the 6 and 2 positions. A slight additional effect on the inhibitory potency was noticed and some sub-micromolar inhibitors were identified. Among the synthesized compounds, several have shown micromolar cytotoxic effects against human cancer cells over-expressing DNPH1. Other modifications on the ribose-phosphate and the purine moieties have also been considered in order to increase both biological stability and affinity of the inhibitors. This work allowed a better characterization of the enzyme active site as well as the identification of new cytotoxic compounds. These results pave the way for the design of more potent inhibitors.

Dans le premier chapitre de cette thèse, nous nous sommes intéressés aux virus de l'immunodéficience humaine et des hépatites B et C ainsi qu'aux thérapies utilisées dans le traitement de ces affections. Nous avons introduit l'importance des nucléosides fluorés, et nous avons donné quelques exemples de nucléosides fluorés utilisés en chimiothérapie antivirale et antitumorale. Dans le second chapitre, nous avons présenté une synthèse rapide de 2',3'-didésoxy-3'-fluoro-beta-D-thréo-nucléosides portant les bases pyrimidiques naturelles et substituées en position N3 par un groupement nitro ou amino. Les composés obtenus ont été évaluées contre divers virus à ADN et ARN (y compris le VIH) dans des expériences de culture cellulaire. Dans le troisième chapitre, nous nous somme intéressés à la synthèse de différents 2',3'-didésoxy-2'-fluoro-3'-(N-hydroxyimino), (N-methoxyimino) and (hydroxyl-amino) nucléosides en série pyrimidine. Les composés obtenus ont été évaluées contre divers virus à ADN et ARN dans des expériences de culture cellulaire. / In the first chapter, we presented the human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV), as well as the therapies used to treat these diseases. In a second part, we discussed about the importance of the incorporation of fluorine atom into nucleoside analogues, and in a third part of this chapter, we presented the recent literature sources of the synthesis and biological activity of fluorinated nucleosides. In the second chapter, we designed and synthesized a series of 2',3'-dideoxy-3'-fluoro-threo-pyrimidine nucleosides by direct and rapid methodology and evaluated them for their inhibitory effects on a number of RNA and DNA viruses in cell culture experiments. None of these nucleoside derivatives showed any antiretroviral activity nor cytotoxicity. In the third chapter of this manuscript, we synthesized a new series of 2',3'-dideoxy-2'-fluoro-3'-(N-hydroxyimino),(N-methoxyimino) and (hydroxylamino)pyrim idine nucleosides and also evaluated for their inhibitory effects on a number of RNA and DNA viruses, without finding any activity or cytotoxicity.

De par leur grande diversité chimique et leur implication dans de nombreux mécanismes biologiques, les molécules phosphorées font l'objet de nombreuses recherches scientifiques. Depuis près de 30 ans, plusieurs composés phosphorés ont été développés et utilisés pour leurs propriétés médicinales ou phytosanitaires. Les dérivés de type phosphinates ou phosphonates se sont révélés être des composés de choix, grâce à leur grande stabilité chimique et enzymatique. Par ailleurs, les sucres et leurs analogues ont largement démontré leur potentiel biologique en raison de leur implication dans de nombreux processus biologiques. Dans ce contexte, il a été envisagé de développer des analogues de sucres phosphorés possédant un atome de phosphore endocyclique. Il s'agit de structures totalement inédites obtenues à partir de précurseurs phosphorés simples et par des réactions de type : P-alkylation, Pudovik, ouverture d'époxyde, cyclisation par transacétalisation ou transestérification. Grâce à des synthèses en 4 à 7 étapes, deux familles de phosphinosucres ont été préparées ainsi qu'une famille de phosphonosucres en tant qu'analogues de sucre. En parallèle, la synthèse d'analogues de nucléosides phosphorés a également été étudiée par introduction de nucléobases sur les analogues de sucres phosphorés précédemment cités. Ces travaux ont mis en jeu des réactions issues à la fois de la chimie de nucléosides mais également de la chimie du phosphore, permettant d'accéder à des analogues de nucléosides totalement inédits dont l'activité antivirale a pu être évaluée. Enfin, une nouvelle famille de phosphonates nucléosidiques acycliques a été synthétisée en 6 ou 7 étapes en série pyrimidique. Deux prodrogues dérivées de la cytosine et de l'uracile ont également été préparées avec des groupements enzymolabiles de type Bis-(S-acyl-2-thioéthyle). L'ensemble des analogues de nucléotides synthétisés ont été évalués pour leurs propriétés antivirales contre les virus de l'hépatite C et du SIDA. Ainsi, à travers ce projet, trois grandes familles de nouvelles molécules phosphorées ont été développées : les hétérocycles phosphorés oxygénés en tant qu'analogues de sucres, des analogues de nucléosides phosphorés, une nouvelle classe de phosphonates nucléosidiques acycliques. / According to their wide chemical diversity and their implication in many biological processes, phosphorus compounds are intensively studied by organic chemists. Since 30 years, many phosphorus molecules have been developed and used for their biological properties in medicine or agrochemistry. Chemically and enzymatically stable compounds, phosphonates and phosphoninates are potential derivatives for drug design. Besides, sugars are an important biological family involved in numerous biological pathways which have widely revealed a high therapeutic potential. In this context, the first objective of these works was to develop sugar analogues with an endocyclic phosphorus atom (phosphasugars) to synthesize unpublished families of phosphinosugars and phosphonosugars. Their synthesis were carried out in 4 to 7 steps, using as key reactions : P-alkylation, Pudovik, epoxyde ring-opening reaction, cyclisation by transacetalisation or transesterification. Moreover, these phosphasugars were extended to the synthesis of new nucleoside analogues by introducing nucleobase on phosphasugar moiety. The antiviral activity of these new compounds was evaluated. Finally, a new class of acyclic nucleoside phosphonates was prepared in pyrimidinyl series. Different nucleotide analogues and prodrugs were synthesized in 6-7 steps with uracil, thymine and cytosine and evaluated against HCV and HIV.

Dans un premier chapitre, nous avons présenté un historique succinct de la chimiothérapie antivirale et l'utilisation d'analogues nucléos(t)idiques. Nous nous sommes focalisés en particulier sur les nucléosides phosphonates acycliques (ANP) en tant qu'antiviraux potentiels. Dans un second chapitre, nous avons décrit la synthèse de β-céto, β-hydroxylamino et β-O-(benzyl)hydroxylamino ANP dérivés de l'adénine et de la cytosine. Les isomèrs (R) et (S)-β-hydroxy-ANP ont été préparés par dédoublement du racémique correspondant avec le (S)-MPA et l'attribution des configurations absolues a été effectuée par RMN et calculs de modélisation moléculaire. Nous avons aussi développé une méthodologie de synthèse de β-azido-ANP, ces derniers étant utilisés pour la préparation de β-amino-ANP par hydrogénation catalytique. Dans un troisième chapitre, nous avons présenté la synthèse des 2H-azirine et cis-aziridne-ANP et examiné lʹ ouverture de cycle comme voie d'accès à des ANP α,β-fonctionnalisés. Les propriétés biologiques de ces nouveaux ANP ont été évaluées en culture cellulaire sur un certain nombre de virus à ADN et ARN. / In the first chapter, we presented a brief history of antiviral chemotherapy and use of nucleos(t)ide analogues, especially acyclic nucleoside phosphonates as potential antiviral agents. In the chapter-II we have successfully synthesized ¦Â-keto, ¦Â-hydroxylamino and ¦Â-O-(benzyl)hydroxylamino ANPs of adenine and cytosine derivatives. Then (R) and (S)-¦Â-hydroxy-ANPs were prepared via chiral resolution of racemic ¦Â-hydroxy-ANPs with (S)-MPA and assignment of absolute configuration was achieved using NMR and molecular modeling studies. We also developed a methodology for the synthesis of ¦Â-azido-ANPs and those were used for the preparation of ¦Â-amino-ANPs by catalytic hydrogenation. In third chapter, we synthesized 2H-azirine and cis-aziridine-ANPs and explored their ring opening to functionalized ¦Á,¦Â-ANPs. The novel ANPs obtained during this study were evaluated for their inhibitory effect on a number of DNA and RNA viruses in cell culture experiments.

Foram determinadas por meio de difração de raios x as estruturas de cinco compostos azaçúcares. Foram estudadas as interações envolvidas na formação das redes cristalinas em cada um dos compostos analisados. Foi encontrado que nos compostos azaçúcares estudados, as interações principais são as ligações de hidrogênio do tipo C-H···O e C-H···π. Este comportamento foi verificado usando ferramentas como as superfícies de Hirshfeld e os gráficos de impressão digital. Realizou-se o estudo de docking molecular dos compostos azaçúcares com respeito à enzima purina nucleosídeo fosforilase (PNP). Foi determinado que estes compostos têm a capacidade de entrar no sitio ativo da PNP. O estudo das interações dos cinco azaçúcares com a PNP mostrou que estes compostos apresentam as mesmas interações presentes em inibidores da PNP já reportados. / Structures of five azasugars were determined by X-ray diffraction. Crystal network interactions were analyzed for each compound. The main interaction found for these azasugar compounds is hydrogen bond as C-H···O e C-H···π. This behavior was verified by tools as Hirshfeld surface and 2D finger print plots. Molecular docking was performed for azasugar compounds in Purine Nucleoside phosphorylase (PNP). This study confirmed that these compounds are available to enter to the PNP active site. Interactions exploration showed the same interactions for the azasugars studied and for already known PNP inhibitors.

Delta subunit of bacterial RNA pol and its role in regulation of gene expression in B. subtilis. In this work I focus on regulation of eubacterial gene expression. First, I describe recent knowledge about a key stage of gene expression - transcription, focusing on regulation of trancription iniciation via small effector molecules (guanosine tetraphosphate, initiating nucleoside triphosphate) that are important for the regulation of ribosomal RNA. Second, in the experimental part of my work, I focus on the role of the _ protein, a subunit of RNA polymarase in gram positive bacteria, in transcription iniciation and its effects on regulation of RNA polymerase by the concentration of initiating nucleoside triphosphates.

Nucleoside 5'-Diphosphate Kinase (NdPK EC 2.7.4.6) is an enzyme (phosphotransferase) with extraordinary characteristics due to its unique ability to transfer phosphor groups to interconvert all nucleoside di- and triphosphates as a part of the DNA synthesis. Due to Biovica International AB's use of signaling and complementing enzymes in their in vitro diagnostic (IVD) test assays for Thymidine Kinase activity, an investigation was proposed to evaluate NdPK, which is a complementing enzyme in the assay. The aim of the study was to evaluate the enzymatic turnover of the enzyme NdPK with a spectrophotometric assay to obtain the specific activity (Units/mg solid protein). To determine the specific activity, enzyme kinetic methodology was applied, including the Michaelis-Menten model. In this study, the method is proposed as a general internal control procedure for the company, as a tool for function control of the different purchased enzymes used in their products in development. Results from the study reflects the different methods used to gain the specific activity for NdPK, where they were compared with the already specified specific activity from the manufacturing company. The results were auspicious, but before the method's authorization as an internal quality procedure, a few amendments are in mind. For instance, determining a method for the graphical readings, validating the method for quality control, and investigating if the method is applicable to other complementing enzymes. In conclusion, the method for determining the specific activity of the enzyme NdPK can be done, by executing the procedure of colorimetric enzyme assay.

Les analogues de nucléosides ont joué, et continuent de jouer, un rôle crucial dans le traitement des maladies virales et cancéreuses. Les travaux de recherche ont permis d’élargir les connaissances sur le mécanisme d’action des analogues de nucléosides. Cependant, certaines zones d’ombre demeurent. Le développement de nouveaux analogues de nucléosides est essentiel à la compréhension de leur mécanisme en vue de synthétiser des analogues beaucoup plus efficaces, moins toxiques, possédant une meilleure biodisponibilité et stabilité métabolique au sein de l’organisme humain. Le laboratoire du Pr Yvan Guindon a développé et breveté plusieurs familles d’analogues de nucléosides à centre quaternaire carboné stéréogénique pour leur utilisation en tant qu’agent antiviral, chimiothérapeutique ou bien dans le contexte de traitement de l’insuffisance cardiaque. Le sujet de ce mémoire présente l’étude de la synthèse d’analogues de nucléosides portant un centre quaternaire C3’ et un groupement hydroxyle en C2’. Pour ce faire, une stratégie de synthèse acyclique est employée afin de contrôler les différents stéréocentres. La réaction énantiosélective de Mukaiyama et la réaction diastéréosélective de transfert d’atomes par catalyse photo-rédox sont des étapes clés de cette voie de synthèse. L’introduction diastéréoselective de la nucléobase sur un précurseur acyclique suivit de la cyclisation intramoléculaire S1’→C4’ permet la formation de l’analogue de nucléoside L-1’,2’-cis-4’-thio. Le développement d’une nouvelle stratégie de synthèse du L-1’,2’-cis-4’-thio est étudié. La réaction radicalaire diastéréosélective de transfert d’atomes développée au laboratoire passe par un intermédiaire oxasilolane bromé qui est peu stable. L’objectif est d’exploiter sa stéréochimie tout en formant le centre quaternaire afin d’obtenir une voie de synthèse beaucoup plus courte et efficace. / Nucleoside analogues have an important role in the treatment of viral and carcinogenic diseases. Although the research has greatly expanded the knowledge of nucleoside analogue synthesis and their mechanisms of action, the development of new analogues remains essential to discovering more effective and less toxic analogues with improved bioavailability and metabolic stability. The laboratory of Professor Yvan Guindon has developed and patented several novel families of nucleoside analogues bearing a stereogenic all-carbon quaternary center for their use as antivirals, chemotherapeutic compounds or in the context of heart failure. The subject of the dissertation is the synthesis of such nucleoside analogues bearing a quaternary center at the C3’ position and a C2’ hydroxyl group. The key steps in the synthetic pathway involve an enantioselective Mukaiyama reaction followed by a diastereoselective group transfer using photoredox catalysis and blue light to generate the stereogenic quaternary center. Diastereoselective introduction of the nucleobase onto an acyclic precursor followed by a subsequent intramolecular S1’-to-C4’ SN2-like cyclization allows for the formation of novel L-1’,2’-cis-4’-thionucleoside analogues. Alternatively, modifications of the key diastereoselective radical atom transfer reaction, typically involving a brominated methylester, have been investigated. Formation and subsequent transformation of a thiolated oxasilolane intermediate will reduce the number of steps to synthesize these novel L-1’,2’-cis-4’-thionucleoside analogues.