Until recently, the standard therapy for hepatitis C treatment has been interferon and ribavirin. Such treatment has only 50% efficacy and is not well tolerated. The emergence of new drugs has increased the treatment efficacy to 90%. Despite such an achievement, the success is limited since the virus mutates rapidly, causing the emergence of drug resistant forms. In addition, most new drugs were developed to treat genotype 1 infections. Thus, development of new potent antivirals is needed and drug discovery against hepatitis C is continued. In this thesis, a FRET-based protease assay was used to evaluate new pyrazinone based NS3 protease inhibitors that are structurally different to the newly approved and currently developing drugs. Several compounds in this series showed good potencies in the nanomolar range against NS3 proteases from genotype 1, 3, and the drug resistance variant R155K. We assume that these compounds can be further developed into drug candidates that possess activity against above mentioned enzyme variants. By using SPR technology, we analyzed interaction mechanisms and characteristics of allosteric inhibitors targeting NS5B polymerases from genotypes 1 and 3. The compounds exhibited different binding mechanisms and displayed a low affinity against NS5B from genotype 3. In order to evaluate the activity and inhibitors of the NS5B polymerase, we established an SPR based assay, which enables the monitoring of polymerization and its inhibition in real time. This assay can readily be implemented for the discovery of inhibitors targeting HCV. An SPR based fragment screening approach has also been established. A screen of a fragment library has been performed in order to identify novel scaffolds that can be used as a starting point for development of new allosteric inhibitors against NS5B polymerase. Selected fragments will be further elaborated to generate a new potent allosteric drug candidate. Alternative approaches have successfully been developed and implemented to the discovery of potential lead compounds targeting two important HCV drug targets.

Hepatitis C virus (HCV) infection globally affects 130-150 million people. It causes both acute and chronic infections. Due to the severe side effects and low success rates of interferon based treatments, which formed the standard treatment for HCV, the treatment paradigm shifted to direct acting antivirals (DAAs). DAAs have revolutionized the treatment of hepatitis C virus infection. Clinical trials with combinations of DAAs have recorded >90% response with shorter treatment durations and fewer side effects than earlier treatments involving IFN. Outside the controlled setting of a clinical trial, however, response rates with DAA combinations are much lower (<70%). DAAs can fail if HCV accumulates mutations that confer drug resistance. Interestingly, the pre-existence of mutant frequency in the virus appears not to influence treatment outcome. A better predictor for DAA treatment outcome is yet to be unravelled. Surprisingly, individuals who respond poorly to IFN appear to be more likely to fail DAA treatment. IFN is a generic antiviral that improves immune responses and is expected not to have any bearing on DAA treatment outcomes. Why individuals with poor IFN sensitivity fail DAA treatment remains a mystery. In a recent study of the IFN signalling network, HCV has been shown to compromise IFN activity. It induces bistability in the network leading to distinct phenotypic responses of cells to IFN exposure. In particular, individuals who respond poorly to IFN tend to have a higher percentage of cells that are refractory to IFN; these cells allow viral persistence despite IFN exposure. We hypothesized here that in such individuals, greater ongoing replication would allow increased development of resistance and thus lead to the failure of DAAs. We constructed a model of viral dynamics that accounts for the distinct phenotypic responses of cells to IFN, viral replication and mutation, and the development of resistance to DAAs. Our model predicted that although the relative prevalence of pre- existing mutants is unaffected by IFN sensitivity, in agreement with observations, the growth of drug resistant mutants is accelerated in individuals with poor IFN sensitivity. Based on a distribution of IFN sensitivity across individuals, our model accurately described clinical observations of the response rates to different current treatment protocols. With this model, we predict that the common strategy of increasing the genetic barrier by adding more drugs to the combination was not necessary to avert the development of drug resistance. Instead, an optimised increase in DAA dosage alone or DAA+PR or PR dosage depending on the patient’s IFN sensitivity could help achieve success.

Le mécanisme d‘interaction d‘un composé xénobiotique avec la membrane est un des facteurs clés qui influence son mécanisme d‘action biologique et donc son action thérapeutique pour un principe actif. Une analyse précise des interactions intermoléculaires à l‘échelle atomique peut être obtenue par dynamique moléculaire, une méthode qui apparait plus que jamais comme une alternative élégante aux techniques expérimentales. Les simulations de dynamique moléculaire permettent d‘évaluer ces interactions avec une résolution temporelle et spatiale difficiles à atteindre avec les méthodes expérimentales. Ces informations constituent une pierre angulaire de la compréhension des mécanismes d‘action des xénobiotiques . Les résultats obtenus corrèlent généralement bien avec les données expérimentales. Dans ce travail théorique, nous avons utilisé des dynamiques moléculaires non -biaisées et biaisées (z-Contraint). Nous avons étudié les modes d‘insertion (positionnement et orientation), les coefficients de partition, et la capacité de différents xénobiotiques à traverser la bicouche lipidique (perméation passive). Plusieurs composés de différentes familles thérapeutiques ont été étudiés (antiviraux, immunosuppresseurs et antioxydants), tous étant utilisés en transplantation d‘organes ; les antioxydants sont étudiés en tant que protecteurs d‘organe contre les phénomènes d‘ischémie -reperfusion. Pour la perméation passive, les profils d‘ énergies, les coefficients de diffusion locaux et la résistance à la traversée ont été calculés pour finalement obtenir des coefficients globaux de perméabilité. Nous avons montré que ces techniques de calcul donnent une description qualitative du processus d‘insertion/perméation, montrant notamment le rôle de différentes propriétés physiques (ex., polarité, charge). Des résultats remarquables ont été obtenus pour les larges molécules. Malgré la taille, ces mol cules peuvent s‘ insérer dans la bicouche lipidique relativement facilement (faibles barrières énergétiques). Par contre, leur diffusion dans les différentes régions de la membrane peut augmenter d‘une manière signifiante. Ce travail donne une confiance accrue dans les méthodes de dynamique moléculaire pour devenir prédictive dans les années avenirs, et aide de façon concrète les pharmacologues dans la recherche de nouvelles stratégies thérapeutiques. / The mechanism of interaction between drugs or any xenobiotic and membrane is one of thekey factors that affect its biological of action, and so its therapeutic activity. A thoroughrationalization of the relationship between the intrinsic properties of the xenobiotics and theirmechanism of interaction with membranes can now be assessed with atomistic details.Molecular dynamics (MD) is a powerful research tool to study xenobiotics-membraneinteractions, which can access time and space scales that are not simultaneously accessibleby experimental methods. Semi-quantitative molecular and thermodynamic descriptions ofthese interactions can be provided using in silico model of lipid bilayers, often in agreementwith experimental measurements.The main goal of our investigation consisted to get in depth insight into the mechanisms ofinteraction/partitioning/insertion/crossing with/in/into/through membrane and drug deliveryusing MD. In this thesis, we have focused on both drugs used in renal transplantation (e.g.,antivirals, immunosuppressants) and antioxidants, which can also be used to protect organsalong the transplantation processes. We have provided a series of clues showing that MDsimulations can tackle the delicate process of drug passive permeation.Both, unbiased and biased MD (z-constraint) simulations have been used to elucidate thexenobiotics-membrane interactions (i.e., positioning and orientation) and to evaluate crossingenergies, diffusion coefficients, and permeability coefficients. These findings led us to drawqualitative structure-permeability relationships (SPR). We have carefully analyzed how thechemical and physical properties of xenobiotics affect the mechanism of interactions andthus permeability. The robustness of these MD-based methodologies has been determinedto qualitatively predict these pharmacological parameters. Hydrophobic compounds showeda favorable partitioning into the lipid bilayer and relatively low Gibbs energy of crossing thecenter of membrane (ΔGcross). Hydrophilic or charged compounds showed partitioning closeto membrane surface, in interaction with the polar head groups and water molecules; this hasbeen shown to dramatically increase ΔGcross. Amphiphilic compounds are intermediatecompounds in terms of membrane insertion/positioning/crossing. It clearly appears that theyshould be analyzed case by case, an analysis for which MD simulations could be particularlysupportive. Also the influence of size at predicting permeation has been studied (i.e.,relatively large drugs were tested). The molecular size has shown no significant influence onΔGcross whereas diffusion coefficients were significantly affected, depending on themembrane regions.

Les vascularites cryoglobulinémiques associées au virus de l'hépatite C (VC-VHC) sont caractérisées par une expansion clonale de lymphocytes B mémoires anergiques CD27+IgM+CD21-/low (Bm21-), un défaut quantitatif en lymphocytes T régulateurs (Tregs) et une polarisation Th1. Les antiviraux d'action directe sans interferon (DAAs) sont très efficaces chez les patients VC-VHC mais leur mécanisme d'action sur l'immunité cellulaire reste inconnu. Nous montrons que les DAAs normalisent la plupart des perturbations de l'homéostasie lymphocytaire B et T, en diminuant l'expansion des Bm21- et T folliculaires, et en augmentant les T régulateurs (Tregs). Nous avons étudié l'effet des Bm21- sur les sous-populations lymphocytaires T, et les réactivités de leur récepteur B. Nous montrons que les Bm21- stimulés par le CpG favorisent la sécrétion d'IFNγ par les T effecteurs et induisent leur prolifération. Inversement, les Bm21- stimulés par CpG diminuent la capacité proliférative des Tregs. Nous montrons la diversité intraclonale des IgM mutés des Bm21-, conduite par maturation d'affinité antigène dépendante. Les anticorps (Ac) des Bm21- ont une activité facteur rhumatoïde (FR) mais ne sont ni polyréactifs, ni autoréactifs contre les autoantigènes ubiquitaires. Les Ac des Bm21- ne présentent pas de réactivité croisée contre des antigènes viraux du VHC. Les Bm21- stimulés par CpG ont une signature transcriptomique révélant un phénotype non tolérogène. Ainsi, ces résultats suggèrent le rôle majeur des Bm21- dans le défaut tolérance des patients CV-VHC, à la fois par la stimulation CpG conduisant à une réactivation des Bm21- anergiques, et par l'expression clonale des IgM à activité FR. / Hepatitis C virus-associated cryoglobulinemia vasculitis (HCV-CV) is characterized by an abnormal clonal expansion of anergic CD27+IgM+CD21-/low memory B cell (Bm21-), a quantitative defect in regulatory T cells (Tregs) and Th1 profile. Interferon-free direct-acting antivirals (DAAs) proved to be very effective in patients with HCV-CV but their mechanisms of action and their effects on cellular immunity remain poorly defined. Our results indicate that DAAs effectively normalizes many of the disturbances in peripheral B- and T-lymphocyte homeostasis of HCV-CV patients, by reducting Bm21- and T follicular helper expansion and promoting Tregs. Then, we investigated the effects of Bm21- on T-cell subpopulations and study the reactivities of their B-cell receptors. We show that CpG-stimulated Bm21- promote the secretion of IFNγ by effector T cells and induce their proliferation. Conversely, stimulated Bm21- reduce the proliferative capacity of regulatory T cells. Bm21- B-cell expansions show intraclonal diversity of highly mutated IgM antibodies that were shape by an antigen-driven maturation process. Bm21- antibodies possess rheumatoid factor activity but are neither polyreactive nor recognize ubiquitous autoantigens. No crossreactivity of Bm21- antibodies against several HCV antigens was observed. We also identify a transcriptional signature in CpG-stimulated Bm21- revealing a phenotype sufficient to break the immune tolerance. Thus, these results strongly suggest a major role for Bm21- in defective tolerance of HCV-CV patients, both through CpG stimulation leading to reactivation of anergic Bm21-, and through the clonal expression of IgM antibodies with RF activity.

O objetivo principal deste estudo foi avaliar a frequência de cepas do HBV com mutações de resistência aos análogos nucleos(t)ídeos (AN) utilizados no tratamento da hepatite B entre indivíduos cronicamente infectados, não submetidos a tratamento, procedentes de diferentes regiões do Brasil. Além disso, foram avaliadas a presença de mutações que alteram a antigenicidade do HBsAg promovendo escape dos anticorpos anti-HBs; mutações nos genes pré-core/core e a associação dos diferentes subgenótipos com as mutações encontradas e características demográficas e laboratoriais dos pacientes. Foram incluídas 779 amostras de soro de pacientes com infecção crônica pelo HBV e virgens de tratamento com AN ou interferon, as quais foram coletadas no período de 2006 a 2011. Os pacientes eram procedentes dos seguintes estados brasileiros: Pará, Maranhão, Bahia, Minas Gerais, São Paulo, Paraná e Rio Grande do Sul. O DNA do HBV foi extraído das amostras de soro utilizando o Kit QIAamp DNA Blood Mini Kit (Qiagen) e posteriormente foi realizada a amplificação das regiões S/polimerase (S/P) e pré-core/core (PCC) do genoma viral por nested PCR. O fragmento amplificado foi submetido a sequenciamento direto em sequenciador automático de DNA (ABI 3500) e as sequências obtidas foram analisadas para identificação dos genótipos e subgenótipos do HBV, pesquisa de mutações na polimerase, no HBsAg e nos genes pré-core/core. A região S/Pol foi amplificada e sequenciada com sucesso em 702 amostras, as quais foram incluídas para atender aos objetivos deste estudo. Entre as 702 amostras analisadas sete genótipos e 12 subgenótipos do HBV foram identificados. O subgenótipo A1 foi o mais frequente (63,7%, 447/702), seguido pelo HBV/D3 (14,5%, 102/702). Os demais genótipos e subgenótipos encontrados e suas frequências foram as seguintes: A2 (3,3%, 23/702), A3 (0,1%, 1/702), B1 (0,1%, 1/702), B2 (0,1%, 1/702), C2 (0,9%, 6/702), D1 (0,9%, 6/702), D2 (4,6%, 32/702), D4 (5,1%, 36/702), D com subgenótipo não identificado (0,7%, 5/702), E (0,6%, 4/702), F2a (4,6%, 32/702), F4 (0,4%, 3/702), e G (0,4%, 3/702). Cepas do HBV com mutações de resistência (rtS202G, rtM204V/I, rtA194T, rtM250I, rtA181T/S, rtT184S) associadas ou não a mutações compensatórias (rtL80I, rtV173L, rtL180M, rtV207I) foram identificadas em 1,6% (11/702) das amostras analisadas. Cepas com mutações potencialmente associadas com resistência ao adefovir (rtS85A, rtL217R, rtI233V, rtN238T, rtN238D, rtN248H, rtV214A,e rtQ215S) ou ao entecavir (rtS219A) foram identificadas em 7,7% (54/702) e 2,6% (16/702) dos pacientes, respectivamente. Cinquenta e sete (8,5%) amostras apresentaram cepas do HBV com mutações na principal região hidrofílica do HBsAg previamente relacionadas com escape dos anticorpos anti-HBs ou com prejuízo na secreção do HBsAg. Foram feitas análises estatísticas para avaliar a correlação entre os subgenótipos do HBV mais frequentes na casuística (A1, A2, D1, D2, D3, D4 e F2a) e a presença de mutações nos genes PCC. Dentre as mutações nos genes PCC associadas com redução ou falha na expressão do HBeAg, as mutações A1762T/T1764A estiveram associadas aos subgenótipos A1 e F2a; G1862T e mutações nas posições 1809-1812 ao subgenótipo A1; G1896A e/ou G1899A aos subgenótipos D2, D3 e D4. Mutações associadas com evolução da doença foram detectadas e entre essas as mutações C1766T e T1768A estiveram associadas aos subgenótipos A1 e F2a, e a mutação G1888A foi associada ao subgenótipo A1. As cepas do HBV que circulam nas diferentes regiões brasileiras estudadas apresentam grande variabilidade genética e a distribuição dos genótipos e subgenótipos reflete a formação histórica de cada região e do fluxo migratório mais recente. A frequência de cepas do HBV com mutações de resistência aos AN circulando entre pacientes virgens de tratamento com esses medicamentos nas diferentes regiões do Brasil estudadas é baixa, sendo que o perfil de mutações que confere resistência total à lamivudina e parcial ao entecavir parece ser o mais disseminado. Embora tenham sido detectados casos de infecção com cepas do HBV portando mutações com grande impacto na antigenicidade dessa proteína todas as amostras apresentaram HBsAg detectável. Pacientes com HBeAg negativo foram mais frequentes na casuística estudada, independente do subgenótipo. As mutações encontradas nos genes PCC sugerem que há perfis de mutações diferentes envolvidos na negatividade do HBeAg para cada subgenótipo / The main aim of this study was to evaluate the frequency of HBV strains harboring mutations that confer resistance to nucleos(t)ide analogues (NA) used to hepatitis B treatment among treatment-naïve patients with chronic hepatitis B from different Brazilian region. Furthermore, we evaluated the presence of mutations that alter the antigenicity of HBsAg causing anti-HBs escape; mutations in genes pre-core/core and the association of different subgenotypes with the mutations detected and demographic and laboratory characteristics of the patients. Serum samples from 779 treatment-naïve patients with chronic HBV infection were included in this study. The samples were collected between 2006 to 2011 and the patients were from the following states: Pará, Maranhão, Bahia, Minas Gerais, São Paulo, Paraná and Rio Grande do Sul. HBV DNA was extracted from serum samples using the QIAamp DNA Blood Mini Kit (Qiagen) and amplification of S/polymerase (S/Pol) and pre-core/core (PCC) regions were performed by nested PCR. The amplified PCR products were submitted to sequencing in an automatic DNA sequencer (ABI 3500). The sequences obtained were analyzed to classify HBV genotypes/subgenotypes and to analyze the presence of mutations. S/Pol region was amplified and sequenced successfully from 702 samples, which were included in this study. Among these 702 samples, seven genotypes and 12 subgenotypes have been identified. HBV subgenotype A1 was the most frequent (63.7%, 447/702), followed by HBV/D3 (14.5%; 102/ 702). The remaining genotypes and subgenotypes identified and their frequencies were as follows: A2 (3.3%, 23/702), A3 (0.1%, 1/702), B1 (0.1%, 1/702), B2 (0.1%, 1/702), C2 (0.9%, 6/702), D1 (0.9%, 6/702), D2 (4.6%, 32/702), D4 (5.1%, 36/702), D unclassified subgenotype (0.7%, 5/702), E (0.6%, 4/702), F2a (4.6%, 32/702), F4 (0.4%, 3/702), and G (0.4%, 3/702). HBV strains harboring mutations conferring NA resistance alone (rtS202G, rtM204V/I, rtA194T, rtM250I, rtA181T/S, rtT184S) or combined with compensatory mutations (rtL80I, rtV173L, rtL180M, rtV207I) were identified in 1.6% (11/702) of the patients. Isolates harboring mutations potentially associated with adefovir resistance (rtS85A, rtL217R, rtI233V, rtN238T, rtN238D, rtN248H, rtV214A, and rtQ215S) or entecavir resistance (rtS219A) were identified in 7.7% (54/702) and 2.6% (16/702) of the patients, respectively. HBV with HBsAg mutations previous related with anti-HBs escape or impaired secretion were detected in 8.5% (57/702) of the samples. Statistical analyzes were performed to assess the correlation between the more frequent HBV subgenotypes found in this study (A1, A2, D1, D2, D3, D4 and F2a ) and mutations in PCC genes. Among the mutations found in these genes that were associated with reduction or failure in HBeAg synthesis, A1762T/T1764A mutations were associated to subgenotypes A1 and F2a; G1862T and mutations at positions 1809-1812 to subgenotype A1; G1896A and/or G1899A to subgenotypes D2, D3 and D4. Other mutations associated with disease progression were found: C1766T and T1768A mutations were associated with subgenotypes A1 and F2a, and the G1888A mutation was associated with subgenotype A1. HBV strains circulating in different Brazilian regions studied showed high genetic variability and distribution of genotypes and subgenotypes reflects the population formation history of each region and the occurrence of recent events of migration. The frequency of HBV strains with NA resistance mutations circulating among treatment-naive patients in different regions of Brazil studied is low and the profile of mutations that confer total resistance to lamivudine and partial resistance to entecavir is more widespread. Although some cases of infection have been detected with HBV strains carrying mutations associated with major impact on the antigenicity of this protein, all samples had detectable HBsAg. HBeAg negative cases were more frequent in the studied population, regardless of subgenotype. Different pattern of mutations were found in PCC genes, suggesting that different mechanisms are involved in HBeAg negativity for each subgenotype

Le virus de l'hépatite C (HCV) est un virus à ARN qui synthétise ses nouveaux génomes dans les cellules hôtes infectées grâce à une ARN polymérase ARN dépendante (RdRp), appelée NS5B. Cette polymérase a été pendant longtemps une cible majeure dans la recherche d'antiviraux contre l'hépatite C. Aujourd'hui, de nombreux antiviraux ont été approuvés dans le traitement de l’hépatite C ciblant différentes protéines virales, entre autre, NS5B. Le sofosbuvir qui cible le site actif de NS5B est un antiviral qui a démontré une efficacité extraordinaire dans le traitement anti-HCV.Durant ces dernières années, les recherches sur NS5B ont permis de caractériser cette protéine, à la fois structuralement et biochimiquement. La richesse des connaissances ainsi accumulées fait de NS5B un excellent modèle pour les RdRp des virus à ARN.Toutefois, peu d'études portent sur le mécanisme d’acheminement et de sélection des ribonucléotides au site actif de NS5B, et de façon générale, sur la description atomique du mécanisme de réplication assuré par NS5B, qui implique deux dications magnésium pour la catalyse comme chez toutes les polymérases de cette famille.Durant ce travail, nous avons exploité les données structurales issues de complexes ternaires (NS5B+RNA+nucleotide) obtenus en 2015 par cristallographie à l'échelle atomique. Nous avons utilisé ces structures pour mener des études de modélisation moléculaire, essentiellement par dynamique moléculaire afin d’aborder la question de l'acheminement des nucléotides vers le site actif de NS5B.Nous avons eu recours à la fois à des méthodes de dynamiques moléculaires classiques et des méthodes de dynamiques moléculaires dites biaisées telles que différentes méthodes de dynamiques moléculaires dirigées (SMD et TMD) et la dynamique moléculaire accélérée (aMD).Nos résultats indiquent que l’acheminement du nucléotide au site actif associé à un magnésium Mg(B) est contrôlé tout au long du tunnel par différents éléments de NS5B. Initialement, le nucléotide se lie à une région proche de la boucle qui surplombe le tunnel lui permettant, grâce aux interactions qu’il établit avec sa partie triphosphate, de s’orienter base en avant. Ensuite, le nucléotide atteint un point de contrôle formé essentiellement par le motif F3 (R158) et le motif F1(E143). Le nucléotide reste lié à ce site jusqu’à l’arrivée du second dication magnésium (Mg(A)) qui provoque des réarrangements structuraux, notamment au niveau du motif F3, entrainant l’avancée du nucléotide vers le site actif. Une fois ce point de contrôle passé, le nucléotide interroge alors la base du brin d’ADN matrice sans s’insérer entièrement dans le site actif.Nos simulations ont clairement établi que les dernières étapes d’entrée du nucléotide sont finement régulées par l’arrivée du second dication magnésium qui a donc un rôle de coordinateur en plus de son rôle connu dans la catalyse.Ce mécanisme d’entrée semble être spécifique aux RdRp virales et permet de comprendre pourquoi les analogues de nucléotides peuvent être aussi efficaces contre les virus à ARN. / The hepatitis C virus is an RNA virus that synthesises its new genomes in the infected host cells thanks to an RNA-dependent RNA polymerase (RdRp) termed NS5B. This polymerase has been a prime target for antiviral therapy. Numerous direct antiviral drugs are now approved in the HCV treatment and allow very high rates of treatment success. These drugs target among others the HCV NS5B RdRp with the sofosbuvir being one of the most successful drugs.Tremendous efforts have been made in the past decades to characterize NS5B, in particular structurally and biochemically. However, there is little information about the molecular mechanisms of NS5B ribonucleotides entry and selection and in general on the atomistic details of the RNA replication mechanism, although the involvement of two magnesium dications in catalysis is well established in this family of polymerases. Since 2015, structures of ternary complexes of NS5B have been resolved by crystallography offering very valuable details about the binding of nucleotides at the NS5B active site.In this work, we took advantage of these structural data to address the ribonucleotides entry and to further explore the nucleotide addition cycle in NS5B using molecular modelling and molecular dynamics simulations. We used both conventional molecular dynamics techniques and biased simulations that enhance sampling such as Steered Molecular Dynamics (SMD), Targeted Molecular Dynamics (TMD) or accelerated Molecular dynamics (aMD).Based on our modelling results, we found that the access to the active site through the nucleotides tunnel is checked by successive NS5B elements. First, the entering ribonucleotide together with an associated magnesium Mg(B) binds next to a loop that overhangs the nucleotide tunnel and interactions with its triphosphate moiety orient it base-first towards the active site. Second, the ribonucleotide encounters a checkpoint constituted by the residues of motif F3(R158) and motif F1(E143) where it is blocked until the arrival of a second magnesium ion, the Mg(A). This allowed the motif F3 to undergo small structural rearrangements leading to the advancement of the nucleotide towards the active site to interrogate the RNA template base prior to the complete nucleotide insertion into the active site.Our simulations pointed out that these dynamics are finely regulated by the second magnesium dication, thus coordinating the entry of the correct magnesium-bound nucleotide with shuttling of the second magnesium necessary for the two-metal ion catalysis. This entry mechanism is specific to viral RdRps and may explain why modified ribonucleotides can be so successful as drugs against RNA viruses.

Introduction : Le virus respiratoire syncytial (RSV) est associé à des taux élevés de morbidité et de mortalité non seulement chez les jeunes enfants, en particulier les nourrissons et ceux atteints de cardiomyopathie congénitale, mais aussi chez les personnes de tous âges immunodéprimées et chez les personnes âgées. Les options thérapeutiques actuelles se limitent à une prophylaxie par anticorps monoclonaux réservée aux nourrissons à haut risque de maladie grave associée au RSV. Le développement de nouveaux antiviraux est donc urgent. Les antiviraux ciblant les protéines de l'hôte constituent une alternative émergente aux antiviraux classiques ciblant les protéines virales qui présentent des risques de développement de résistances. L'autophagie est un mécanisme cellulaire qui peut favoriser ou limiter la réplication virale. Nos travaux en cours suggèrent que l'autophagie dans les cellules épithéliales des voies respiratoires humaines (AECs) offre une protection antivirale contre RSV. Objectif : L'objectif de cette étude est d'évaluer la capacité de divers molécules induisant l'autophagie (AID) approuvés par la FDA à inhiber la réplication du RSV dans les AECs. Méthodes : Afin de quantifier l'induction de l'autophagie, la réplication du RSV et la viabilité cellulaire à l'aide d'un système d'imagerie à haut-débit, nous avons développé un essai utilisant des cellules A549, une lignée cellulaire modèle de cellules épithéliales respiratoires, la protéine LC3-RFP comme marqueur d’autophagie, un virus RSV recombinant exprimant la protéine GFP, et un marquage avec le SYTOX-Orange et le DAPI pour évaluer la viabilité cellulaire. Résultats et discussion : En utilisant la Torin-1, un AID caractérisé qui agit de manière mTOR -dépendante, nous avons confirmé que notre essai permet de mesurer l’induction de l’autophagie. De plus, nous avons constaté que la Torin-1 diminue significativement la réplication du RSV-GFP de manière dose-dépendante. Conclusion : En résumé, notre étude a permis de mettre en place un système expérimental à haut débit pour la caractérisation de l’effet des AIDs sur l’autophagie et leur impact sur la réplication du RSV. Nos résultats permettent de montrer que l’induction de l’autophagie corrèle avec la diminution de la réplication de RSV. Ces données devront être complétées par l’utilisation d’autres AIDs pour identifier des molécules approuvées par la FDA qui présentent une activité anti-RSV in vitro. / Introduction: Respiratory syncytial virus (RSV) is associated with high rates of morbidity and mortality not only in young children, particularly infants and those with congenital cardiomyopathy, but also in immunocompromised people of all ages and in the elderly. Current treatment options are limited to monoclonal antibody prophylaxis reserved for infants at high risk of serious illness associated with RSV. The development of new antivirals is therefore urgent. Antivirals targeting host proteins are an emerging alternative to conventional antivirals targeting viral proteins that pose risks of resistance development. Autophagy is a cellular mechanism that can promote or limit viral replication. Our ongoing work suggests that autophagy in human airway epithelial cells (AECs) provides antiviral protection against RSV. Objective: The objective of this study is to evaluate the ability of various FDA-approved autophagy-inducing molecules (AIDs) to inhibit RSV replication in AECs. Methods: In order to quantify autophagy induction, RSV replication and cell viability using a high-throughput imaging system, we developed an assay using A549 cells, a cell line model of respiratory epithelial cells, the LC3-RFP protein as an autophagy marker, a recombinant RSV virus expressing the GFP protein, and labeling with SYTOX-Orange and DAPI to assess cell viability. Results and discussion: Using Torin-1, a characterized AID that acts in an mTOR-dependent manner, we confirmed that our assay can measure the induction of autophagy. Furthermore, we found that Torin-1 significantly decreases RSV-GFP replication in a dose-dependent manner. Conclusion: In summary, our study allowed to set up a high-throughput experimental system for the characterization of the effect of AIDs on autophagy and their impact on RSV replication. Our results show that the induction of autophagy correlates with the decrease in RSV replication. These data should be supplemented by the use of other AIDs to identify FDA-approved molecules that exhibit anti-RSV activity in vitro.

Estima-se que 170 milhões de pessoas no mundo estejam infectadas com o vírus da hepatite C (VHC), o que está altamente relacionado à ocorrência de hepatite crônica e carcinoma hepatocelular. A prevalência de esteatose hepática em doentes com hepatite C crônica é muito maior do que na população geral variando entre 40 a 75%. A associação entre a infecção pelo VHC e esteatose hepática é multifatorial. Duas formas de esteatose hepática são encontradas em pacientes com hepatite C crônica: esteatose metabólica (fatores de risco) e citopática relacionada ao genótipo 3a. Os lipídios são essenciais para o ciclo de replicação do VHC, eles podem exercer seu efeito em diferentes níveis como: grupos prostéticos em proteínas virais e/ou cofatores celulares na replicação de VHC, componentes especializados na estrutura do VHC onde ocorre a replicação ou como constituinte das partículas lipovirais. Trabalhos experimentais realizados anteriormente por nosso grupo relataram que a administração do composto natural Yo Jyo Hen Shi Ko (YHK) promove a inibição do desenvolvimento da esteatose, redução dos marcadores de estresse oxidativo, menor escore de inflamação, melhora nas concentrações de aminotransferases e diminuição da gordura visceral em um modelo animal de esteato-hepatite não alcoólica. A terapia padrão da hepatite C consiste em uma combinação de interferon peguilado alfa (PEG-IFN-alfa) que estimula o sistema imunológico do hospedeiro para combater a infecção e o composto antiviral ribavirina. Atualmente foram aprovados pelas agências de saúde os inibidores de protease Boceprevir, Telaprevir, Daclatasvir e Simeprevir. No entanto, sua eficiência varia entre os genótipos e as constantes mutações do vírus podem levar a resistência. A falta de uma vacina ou uma terapia definitiva faz com que diversos compostos com diferentes mecanismos de ação sejam testados como possíveis alternativas de tratamento. Tendo em vista a capacidade do YHK de reduzir a esteatose e a importância do metabolismo para a replicação do VHC, o objetivo deste trabalho foi avaliar o efeito do YHK no ciclo celular do VHC. Para isso foram utilizadas técnicas de cultura celular que permitem o estudo das diferenças fases do ciclo de replicação do VHC: entrada (VHCpp), replicação - replicons JFH1-NS3-5B e Con1, replicação e infecção- JC1-Fluc. De forma a elucidar a possibilidade de um único componente da fórmula YHK apresentar efeito sobre o VHC, foram utilizadas para comparação as substâncias ativas de seus ingredientes isoladamente: Panax pseudo ginseng - Notoginsenoside R1; Eucommia ulmoides -(±) Pinoresinol; Licorice root - Ácido Glicirrizínico. Os compostos não apresentaram efeitos na entrada, replicação e liberação de novas partículas virais. Devido à ausência de resultados bem delineados e tendo em vista os resultados das terapias anti-VHC atuais e futuras, é improvável que compostos naturais sejam utilizados ou chegarão ao desenvolvimento clínico nesta indicação / Worldwide is estimated that nearly 170 million people are infected with hepatitis C virus (HCV), highly correlated with the occurrence of chronic hepatitis and hepatocellular carcinoma. Hepatitis C patients present higher prevalence of steatosis when compared with the general population, ranging between 40% and 75%. There are two forms of steatosis in HCV infected patients: metabolic steatosis (risk factors) and cytopathic associated with genotype 3. Lipids are essential for the HCV replication cycle. It acts on different functions: as prosthetic groups into viral proteins and / or cellular cofactors in the HCV replication, as specific HCV components or as a constituent of lipovirals particles. Our group previously reported that the administration of the natural compound Yo Jyo Hen Shi Ko (YHK) inhibits steatosis development, decreases markers of oxidative stress and inflammation, improves aminotransferases concentration and decreases the visceral fat. Standard therapy for hepatitis C is a combination of pegylated interferon alpha (PEG-IFN-alfa), stimulating the host immune system to fight infection and the antiviral compound named ribavirin. Nowadays, Telaprevir, Boceprevir, Sofosbovir and Simeprevir are approved as new anti-HCV drugs; they act as protease inhibitors. Its efficiency, however, varies between genotypes, and the constant mutations of the virus can lead to resistance. The lack of vaccines, or a definitive therapy, stimulates the research of new compounds and alternative treatments. In this study, we evaluated the effect of YHK in HCV replication cycle due to the effect of YHK and the importance of lipid metabolism for HCV. For this purpose we used cell culture techniques allowing the study of different stages of HCV replication cycle: entry (HCVpp), replication - replicons JFH1 NS3-5B and Con1, also replication and infection-JC1-Fluc. We also used active compounds of its ingredients: Panax pseudo ginseng - Notoginsenoside R1; eucommia - (±) pinoresinol, Licorice root - Glycyrrhizinic Acid in order to elucidate a possible effect of a single component of the YHK formula in HCV. We could not observe any difference in HCV entry, replication and release in the presence of the four compounds. It is unlikely that natural compounds will be used or come to clinical development in this indication, due to the absence of well defined results and in view of the results of new anti-HCV therapies

A Síndrome da Imunodeficiência Adquirida (AIDS) é uma doença de amplo espectro de manifestações, sendo razão de preocupação para qualquer autoridade sanitária. A terapêutica da AIDS é complexa sendo utilizados vários medicamentos, diversas vezes ao dia. Deste modo, objetivou-se o desenvolvimento de formas farmacêuticas sólidas como comprimidos tamponados mastigáveis (CTM), comprimidos com revestimento gastro-resistentes (CRGR) e pellets (PEL) para a veiculação de didanosina (ddl). Seis especialidades farmacêuticas na forma de CTM foram estudadas quanto ao perfil de dissolução, pH do meio e capacidade neutralizante ácida (CNA). Formulações teste de CTM foram propostas visando obter CNAs e perfis de dissolução adequados. Também foram testadas formulações de comprimidos e de pellets para posterior revestimento com filme gastro-resistente derivado do ácido metacrílico. Os ensaios de dissolução das amostras de CTM revelaram diferenças nas características de liberação do fármaco. Também foram observadas diferenças relacionadas a CNA. As formulações de CTM propostas apresentaram, na maioria dos casos, adequados perfis de dissolução e CNA. As formulações CRGR que receberam revestimento gastro-resistente apresentaram perfis de dissolução de ddl adequados, entretanto os comprimidos testados intumesceram em meio ácido, indicando descontinuidade do filme polimérico sobre os comprimidos. Testes para a produção de pellets veiculando ddl mostraram-se adequados quanto à morfologia e dissolução do fármaco, o mesmo sendo observado após o revestimento com filme gastro-resistente. / The Acquired Immune Deficiency Syndrome (AIDS) is a disease that manifests itself in a myriad of ways. Because of this, the condition has been subject of concern to all sanitary authorities. The treatment of AIDS is complex and many types of medicine are used, many times a day. The objective of the present study was to develop solid pharmaceutical dosage forms such as buffered chewable tablets (CTM), gastro-resistant coating tablets (CRGR) and pellets (PEL) for the loading of didanosine (ddl). Six pharmaceutical specialties in the form of CTM were studied so as to identify the profile of the dissolution, the pH of the environment, and the neutralizing acid capacity (CNA). The use of CTM tests formulations was proposed with the objective of obtaining adequate CNA and dissolution profiles. Different compositions of tablets and pellets were tested for a later addition of gastro-resistant film derived from the methacrylic acid. The experiments on the dissolution of the sample of CTM showed differences in the characteristic of the release of the substance. Differences related to the CNA were also observed. The formulations of the CTM proposed showed to have, in the most number of the cases, both adequate dissolution behavior and CNA. The formulations of the CRGR that had received the gastro-resistant coating showed adequate profile of ddl dissolution; the tested tablets, however, swelled in the acid environment, therefore indicating a lack of continuity of the polymeric film over the tablets. The tests for the production of pellets showed adequate results as to its morphology and dissolution of ddl. The same was observed after coating the pellets with gastro-resistant film.

A Síndrome da Imunodeficiência Adquirida (AIDS) é uma doença de amplo espectro de manifestações, sendo razão de preocupação para qualquer autoridade sanitária. A terapêutica da AIDS é complexa sendo utilizados vários medicamentos, diversas vezes ao dia. Deste modo, objetivou-se o desenvolvimento de formas farmacêuticas sólidas como comprimidos tamponados mastigáveis (CTM), comprimidos com revestimento gastro-resistentes (CRGR) e pellets (PEL) para a veiculação de didanosina (ddl). Seis especialidades farmacêuticas na forma de CTM foram estudadas quanto ao perfil de dissolução, pH do meio e capacidade neutralizante ácida (CNA). Formulações teste de CTM foram propostas visando obter CNAs e perfis de dissolução adequados. Também foram testadas formulações de comprimidos e de pellets para posterior revestimento com filme gastro-resistente derivado do ácido metacrílico. Os ensaios de dissolução das amostras de CTM revelaram diferenças nas características de liberação do fármaco. Também foram observadas diferenças relacionadas a CNA. As formulações de CTM propostas apresentaram, na maioria dos casos, adequados perfis de dissolução e CNA. As formulações CRGR que receberam revestimento gastro-resistente apresentaram perfis de dissolução de ddl adequados, entretanto os comprimidos testados intumesceram em meio ácido, indicando descontinuidade do filme polimérico sobre os comprimidos. Testes para a produção de pellets veiculando ddl mostraram-se adequados quanto à morfologia e dissolução do fármaco, o mesmo sendo observado após o revestimento com filme gastro-resistente. / The Acquired Immune Deficiency Syndrome (AIDS) is a disease that manifests itself in a myriad of ways. Because of this, the condition has been subject of concern to all sanitary authorities. The treatment of AIDS is complex and many types of medicine are used, many times a day. The objective of the present study was to develop solid pharmaceutical dosage forms such as buffered chewable tablets (CTM), gastro-resistant coating tablets (CRGR) and pellets (PEL) for the loading of didanosine (ddl). Six pharmaceutical specialties in the form of CTM were studied so as to identify the profile of the dissolution, the pH of the environment, and the neutralizing acid capacity (CNA). The use of CTM tests formulations was proposed with the objective of obtaining adequate CNA and dissolution profiles. Different compositions of tablets and pellets were tested for a later addition of gastro-resistant film derived from the methacrylic acid. The experiments on the dissolution of the sample of CTM showed differences in the characteristic of the release of the substance. Differences related to the CNA were also observed. The formulations of the CTM proposed showed to have, in the most number of the cases, both adequate dissolution behavior and CNA. The formulations of the CRGR that had received the gastro-resistant coating showed adequate profile of ddl dissolution; the tested tablets, however, swelled in the acid environment, therefore indicating a lack of continuity of the polymeric film over the tablets. The tests for the production of pellets showed adequate results as to its morphology and dissolution of ddl. The same was observed after coating the pellets with gastro-resistant film.