Le traitement du virus de l'hépatite C (VHC) a connu une révolution récente, rapide et exemplaire grâce à l'arrivée des agents antiviraux directs (AAD) en plusieurs vagues depuis 2011, détrônant ainsi la bithérapie interféron-pégylé/ribavirine. Ces nouveaux traitements ont été rapidement confrontés à des limites concernant leur efficacité et leur tolérance notamment à leurs débuts avec les inhibiteurs de la protéase NS3/4A de première génération. L'arrivée de nouveaux AAD sur le marché lors d'une 2ème vague en 2014 a permis toutefois de surpasser celles-ci et de devenir le traitement de référence du VHC.Leur efficacité remarquable a laissé naître l'idée d'une potentielle élimination du VHC grâce à l'utilisation universelle de ces traitements. Cependant, leur coût élevé et les comportements à risque observés dans des sous-groupes de population (utilisateurs de drogues intraveineuses et homosexuels) restent encore des problématiques cruciales à surmonter pour espérer atteindre les objectifs fixés par l'Organisation Mondiale de la Santé en 2030 concernant l'élimination du VHC. De plus ces traitements, permettant l'élimination virale quasi-systématique et donc consécutivement une diminution du risque de complications hépatiques, ont été récemment confrontés à une polémique concernant un potentiel risque de récidive précoce de carcinome hépatocellulaire (CHC) suite à une exposition à ces derniers.Le travail présenté dans cette thèse s'articule autour de trois problématiques ayant toutes pour objectif principal d'optimiser l'utilisation de ces traitements dans l'optique de contrôler l'histoire naturelle de la maladie à l'échelle individuelle et à l'échelle populationnelle par l'intermédiaire de diverses méthodes statistiques.Nos résultats ont permis de montrer au sein d’une première problématique ayant exploré l'efficacité et la tolérance de ces traitements antiviraux à l’échelle individuelle: (i) une efficacité antivirale moindre que celle annoncée dans les essais de phase III des inhibiteurs de protéase de première génération(télaprévir et bocéprévir), (ii) un effet indésirable significatif des inhibiteurs de protéase de première génération sur la fonction rénale, (iii) une tolérance moins bonne de ces premières molécules que lors du traitement par bithérapie avec une incidence accrue d'anémie probablement liée à un surdosage en ribavirine induit par les inhibiteurs de protéase et (iv) une efficacité antivirale remarquable des AAD arrivés depuis 2014 sans impact des caractéristiques du patient ni des dosages pharmacologiques sur la réponse virologique. Dans un second temps, la problématique d'un risque de récidive de CHC accru après un traitement par AAD a également été explorée par l'analyse d'une cohorte locale, celle-ci ayant conclu à l'absence de risque accru comparé à un groupe de patients non exposés. Enfin, nos travaux basés sur la modélisation de la transmission du VHC en France dans la population coinfectée VIH-VHCont montré qu'un taux annuel de traitement par AAD de 50% était nécessaire dans la population homosexuelle ayant des pratiques à haut-risque de transmission pour contrer l'épidémie actuellement observée.Nos travaux ont donc permis d'apporter des données pour optimiser l'utilisation des nouveaux traitements anti-VHC par l'intermédiaire de diverses approches statistiques et ont apporté des éléments de réponse aux grandes problématiques actuelles. L'efficacité exemplaire et la tolérance quasi-parfaite des dernières molécules antivirales permettent une utilisation universelle de ces traitements dans toutes les populations de patients. Des études complémentaires robustes sont cependant nécessaires pour apporter des arguments à la question de la récidive du CHC. Des efforts sont également attendus concernant l'accès au traitement, la diminution des coûts associés et un dépistage renforcé du VHC pour espérer pouvoir éradiquer un jour cette maladie. / The arrival of direct-acting antivirals agents (DAAs) has spurred a rapid revolution in the treatment of hepatitis C virus (HCV), supplanting the previous standard of care, i.e. pegylated interferon and ribavirin. These new treatments are associated with an increased rate of virological response however they rapidly faced some limits more particularly at the beginning with the first generation NS3/4A protease inhibitors. From 2014 on the second wave of DAA was available for treatment of chronic HCV infection and surpassed previous encountered limits. These treatments are nowadays the gold standard for HCV treatment in high-income countries.The idea of HCV eradication recently emerged since DAA treatment are highly effective. However, their associated high cost and recent high-risk behaviors associated with an increased risk of HCV transmission (among intravenous drug users and homosexuals) have been reported. These issues need therefore to be addressed in order to achieve the objectives of the World Health Organization for 2030 of an HCV eradication. Moreover, these treatments allow a sustained virological response in almost all patients and consequently reduce the risk of liver-related complications, but a recent controversy regarding a potential increased risk of hepatocellular carcinoma after DAA treatment has been raised.Three issues will be extensively discussed in this manuscript regarding how these treatments can be used to optimize their effect on HCV natural history at the individual and population level through different statistical approaches.As regards the first issue, this project allowed us to demonstrate regarding the tolerance and efficacy of DAA treatment: (i) a lower antiviral efficacy than previously reported in the phase III trials for first generationprotease inhibitor regimen (telaprevir and boceprevir), (ii) impairment of renal function during first generation protease inhibitor treatment, (iii) an increased rate of reported side effects during first-generation protease inhibitor treatment and more particularly anemia, potentially related to an increased ribavirin biodisponibility induced by protease inhibitor intake and (iv) a remarkable antiviral efficacy of second generation DAAs without impact of patients' characteristics norpharmacology on virological response rate. The recent issue regarding a higher risk of HCC recurrence after DAA treatment was also explored through a local cohort study and no impact of DAA treatment was observed when comparing DAA-exposed vs non DAA-exposed patients. Finally, we conducted amodelling study on HCV transmission in the coinfected HIV-HCV French population and our results suggested that an annual DAA treatment coverage rate of 50% was required in the homosexual population with high-risk behaviors to counter the recent observed epidemic in this population.Our different works provide new insights on how to optimize the use of DAA treatment through several statistical approaches and bring new elements for discussion on the recent controversy. The new DAA have an excellent efficacy and tolerance profile and should be universally used in all populations without restriction. However, further studies are required to explore on a deeper level the question regarding HCC recurrence after DAA treatment. Efforts are also still needed regarding DAA treatment access, associated costs and HCV screening to reach the objective of HCV eradication

Les nucléosides modifiés représentent aujourd'hui une famille incontournable dans la chimiothérapie antivirale. Leur développement progressif au cours de ces 50 dernières années a permis d'endiguer de nombreuses épidémies et d'apporter des traitements efficaces contre de nombreux virus tels que les herpès, les hépatites ou encore le VIH. Toutefois, les infections virales continuent de représenter un problème de santé publique majeur en raison de l'émergence de souches virales résistante aux traitements existants ainsi que l'apparition de nouveaux virus. A ce titre, le développement de nouveaux antiviraux plus actifs, plus sûrs et/ou possédant des modes d'action alternatifs reste plus que jamais d‘actualité. Ce manuscrit, divisé en deux grandes parties, présente d'abord la synthèse métallo-catalysée de nouvelles familles de dérivés nucléosidiques (acycliques et osidiques) puis s'étend ensuite à la préparation de dérivés hétérocycliques à visée anti-VIH. Ainsi, dans une première partie, l'utilisation de réactions de métathèses croisées, catalysées au Ru et activées par les ultrasons, ainsi que l'emploi de lipases dans des réactions de protections/déprotections régiosélectives nous ont permis d'élaborer deux nouvelles familles de nucléosides acycliques alkényles. D'autre part, des réactions d'hétérocouplages acétyléniques catalysées au Ni/Cu ont été réalisés dans le cadre de la synthèse d'une bibliothèque de 2'-déoxyuridines portant un motif 1,3-diyne en position C5. Dans une deuxième partie, la réaction multicomposante de Biginelli a été utilisée dans le développement d'une série de dérivés de dihydropyrimidines β-dicétoacides à visée anti-VIH par inhibition de l'intégrase virale. / Modified nucleosides represent the cornerstone of antiviral chemotherapy. Their progressive development over the last 50 years permitted to contain many epidemics and provided effective treatments against many viruses such as herpes, hepatitis or HIV. However, viral infections remain a major public health problem due to the emergence of resistant strains to existing treatments and the appearance of new viruses. As such, the development of new antivirals, most active and safer and/or acting through alternative mechanisms remains, more than ever, necessary. In this context, the work presented in this manuscript are part of the effort to design and synthesize new molecules with antiviral activities. This manuscript, divided in two parts, firstly focus on the metallo-catalyzed synthesis of new families of nucleoside derivatives (acyclic and osidic) and continue with the synthesis of heterocyclic structures targeting anti-HIV activity. Thus, the use of Ru-catalyzed metathesis reactions under ultrasonic activation and the lipases-catalyzed regioselective protection/deprotection reactions allowed us to develop two new families of alkenyl acyclic nucleosides. The synthesis and antiviral evaluation of C5-(1,3-diyne)-2'-deoxyuridine derivatives, prepared by Ni/Cu-mediated alkyne C-H heterocoupling reaction, are also described. In the second part, the multicomponent Biginelli reaction has been used to develop a series of dihydropyrimidine derivatives bearing a β-diketoacids unit targeting anti-HIV activity by inhibition of the viral integrase.

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.

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

L’identification d’antiviraux à large spectre est un des défis majeurs de la rechercheactuelle en virologie. Une des stratégies les plus prometteuses consiste à cibler une interactionvirus/hôte conservée. Ainsi, avec la technique d’AlphaScreen® et le modèle d’interactionprotéine VI de l’Adénovirus (AdV)/Nedd4-2, nous avons réalisé un criblage biochimique àhaut débit contre l’interaction virus/hôte [LP]PxY/Nedd4, commune à différentes familles devirus. Nous avons trouvé des candidats inhibiteurs issus d’une banque de composés approuvéspar les agences de santé. Nous les avons testés, caractérisés et validé leur effet antiviral surdeux familles de virus totalement différentes. Ainsi, les composés C9 (Sulconazole) et C4(Flunarizine) que nous avons identifiés diminuent la réplication de l’AdV, un virus à ADNenveloppé et du virus de Marburg, un virus à ARN, non enveloppé de la famille desFiloviridae. Ces résultats ont permis de valider l’interaction [LP]PxY/Nedd4 comme unecible idéale d’un antiviral à large spectre et de proposer un repositionnement de ces moléculesC9 et C4 comme antiviraux potentiels. Nous avons également synthétisé de nouvellesmolécules analogues du composé C9 et démontré qu’elles étaient tout aussi efficaces que lecomposé lui-même sur la réplication de l’AdV. Ces résultats nous ont permis de présenter laclasse des dérivés imidazolés comme structure de base pour l’élaboration de nouveauxantiviraux, potentiellement à large spectre. / Broad-spectrum antiviral identification is considered as one of the major aims of theactual virology research and one strategy consists in targeting virus/host interaction. Using theAlphaScreen® technology and the adenoviral model protein VI/Nedd4-2, we performed highthroughputbiochemical screening targeting the [LP]PxY/Nedd4 interaction, a commoninteraction of different virus families. We identified candidate inhibitors from a librarycompound approved by health agencies. We tested, characterized and validated the antiviraleffect of those compounds on two very different virus families. Indeed, compounds C9(Sulconazole) and C4 (Flunarizine) decrease replication of the adenovirus, a DNA nonenvelopedvirus and the replication of the Marburg virus, an RNA enveloped virus from theFilovirus family. Taken together, those results permit us to validate the [LP]PxY/Nedd4interaction as good target for a broad spectrum antiviral and to propose the “repositioning” ofcompounds C4 and C9 as antivirals. Moreover, we have synthesized new analogues from C9showing similar effect on AdV replication compared to the original molecule (C9). Inconclusion, our work on developing new broad-spectrum antivirals highlights the possibilityto use imidazole derivatives as a new class of antiviral compounds.

Hepatitis C virus (HCV), a blood-borne pathogen, is a small enveloped RNA virus belonging to the Hepacivirus genus of the Flaviviridae family. HCV infection represents one of the major health concerns affecting approximately 170 million people globally. Patients with chronic HCV infection are at risk of developing hepatic fibrosis, cirrhosis and hepatocellular carcinoma. No protective anti-HCV vaccine is available yet. Until recently, standard therapy based on pegylated interferon plus ribavirin, was inadequate in treating all the patients as it results in a sustained virological response in only 40 to 50 percent of patients infected with the most common genotype (gt 1). Advances in understanding host-HCV interactions have helped developing newer anti-HCV agents such as telaprevir and boceprevir. However, treatment success is still limited due to different factors including genotype specificity, high cost, potential drug-drug interactions, substantial side effects etc. The positive-sense single-stranded RNA genome of HCV is approximately 9.6kb long which is flanked by highly structured and conserved 5’ and 3’ untranslated regions (UTRs) at both ends. Unlike cap-dependent translation of host cell mRNAs, HCV translation is mediated by an internal ribosomal entry site (IRES) present majorly within the 5’UTR. Several reports have demonstrated the interaction of different cellular proteins with HCV-5’UTR and/or 3’UTR, which include human La protein, polypyrimidine tract binding protein (PTB), poly (rC)-binding protein 2 (PCBP2) etc. These interactions of trans-acting factors with the UTRs may be important for HCV translation and/or replication. Earlier study from our laboratory revealed the importance of interaction of human La protein, by its central RNA recognition motif (RRM), with the HCV IRES around a tetranucleotide sequence GCAC near initiator AUG in influencing HCV translation. However, the role of this interaction, if any, in HCV RNA replication was not known. In the first part of the thesis, we characterized the interaction between human La protein and the GCAC to understand its role in HCV replication. We incorporated mutation, which altered the binding of La, in the GCAC motif in HCV monocistronic replicon and checked HCV RNA replication by reverse transcriptase polymerase chain reaction (RT-PCR). The mutation drastically inhibited HCV replication. Interestingly, overexpression of La could reverse the effect of this mutation and significantly enhanced HCV RNA levels. Using a bicistronic replicon, we observed that decrease in replication was independent of translation inhibition. Furthermore, mutation at the GCAC motif reduced the association between La and viral polymerase, NS5B as seen in co-immunoprecipitation assays. Moreover, this mutation affected translation to replication switch regulated by the interplay between HCV-NS3 protease and human La protein. Our analyses of point mutations, based on RT-PCR and luciferase assays, revealed distinct roles of each nucleotide of the GCAC motif in HCV replication and translation. Finally, 5’-3’ crosslink assays revealed that specific interaction of the GCAC motif with human La protein is important for linking 5’ and 3’ends of HCV genome. Results clearly demonstrate the mechanism of regulation of HCV replication by interaction of cis-acting element GCAC within the HCV IRES with human La protein. HCV is highly species-specific. Under natural conditions, HCV infects only humans and chimpanzees. This restricted host-tropism has prevented the development of a small animal model to study HCV infection in vivo. Although several human-specific entry factors have been identified to be responsible for this species selectivity, full multiplication of the HCV in animals (other than humans and chimpanzees) is still not possible. In the second part of the thesis, we showed that a post-entry host factor –‘La protein’ may also contribute in determining HCV host tropism. We aligned La protein sequences from different species and interestingly we found that HCV RNA interacting beta-turn sequence (KYKETDL) in central RRM (residues 112-184) is conserved only in human and chimpanzee. Earlier, it was shown from our laboratory that a heptameric peptide comprising of this sequence (derived from human La) could inhibit HCV translation by competing with La interaction with the IRES element. However, in the current study, another peptide corresponding to the mouse La sequence (KYKDTNL) was unable to inhibit HCV RNA translation. Similarly, wild-type mouse La (mLa) failed to stimulate HCV IRES function, but addition of chimeric mouse La protein bearing human beta-turn sequence (mLahN7) significantly increased HCV IRES mediated translation in vitro. Also, exogenous supplementation of mLahN7 enhanced HCV translation in cell culture system. Moreover, quantitative as well as tagged RT-PCR analyses showed an enhanced HCV replication upon overexpression of mLahN7. The findings obtained in this part raise a possibility of creating HCV mouse model using human specific cellular entry factors and a humanized form of La protein. Hepatitis C has emerged as a major challenge to the medical community. Developing more potent and safe anti-HCV regimens is need of the hour. As described above, a linear hepatapeptide (KYKETDL) was synthesized and shown to reduce HCV translation. However, this linear peptide was stable only for a shorter time scale. Therefore, in the third part of the thesis, effect of a more stable cyclic form of this peptide has been described. NMR spectroscopy suggested that the beta turn conformation is preserved in cyclic peptide as well. Also, using in vitro bicistronic reporter assay, we demonstrated that cyclic peptide inhibits HCV translation in a dose dependent manner. In fact, due to its higher stability, cyclic peptide reduced HCV translation and replication more efficiently than the corresponding linear peptide at longer post-treatment time point. Additionally, we observed that cyclic peptide is non-toxic in cell culture system. Our results suggest that cyclic peptide might emerge as a promising lead compound against hepatitis C. Due to availability of only partially effective liver protective drugs in modem medicine, complementary and alternative medicine approach, based on plant derived compounds, is also being utilised against HCV. Plant derived compounds have advantages of having high chemical diversity, drug-likeliness properties and ability of being metabolized by the body with little or no toxicity than synthetic ones. Different studies have shown that phytochemicals may exert anti-HCV activities by acting as direct-acting antivirals and play a potential therapeutic role in treating HCV infection. Also, from our laboratory, it was shown that methanolic extract of Phyllanthus amarus (P. amarus) plant inhibited HCV replication. The fourth part of the thesis describes the study on the anti-HCV properties of several bioactive components from P. amarus extract. Using a fluorimetric assay, we demonstrated that two principal components of this extract, phyllanthin and corilagin reduced the HCV NS3 protease activity significantly in vitro. We also observed a sharp reduction in HCV negative sense RNA levels in cell culture system. Structural knowledge-based molecular docking studies showed interactions of phyllanthin and corilagin with the amino acid residues of the catalytic triad of NS3 protease. Further, these compounds were found to be non-toxic in cell culture. Also, phyllanthin and corilagin displayed antioxidant properties by blocking HCV induced oxidative stress generated by reactive oxygen species suggesting their hepatoprotective nature. More importantly, our in vivo toxicity analyses and pharmacokinetics studies proved their safety, tolerability, metabolic stability, and systemic oral bioavailability and support their potential as novel anti-HCV therapeutic candidates. Altogether, the study deciphers mechanistic details of translation and replication of HCV RNA and demonstrates novel antiviral agents targeting these important viral processes.

Antiviral drug resistance is a major problem in the treatment of viral infections, including influenza and hepatitis C virus (HCV). Influenza neuraminidase (NA) is a viral sialidase on the surface of the influenza virion and a primary antiviral target in influenza. Two subtypes of NA predominate in humans, N1 and N2, but different patterns of drug resistance have emerged in each subtype. To provide a framework for understanding the structural basis of subtype specific drug resistance mutations in NA, we used molecular dynamics simulations to define dynamic substrate envelopes for NA to determine how different patterns of drug resistance have emerged in N1 and N2 NA. Furthermore, we used the substrate envelope to analyze HCV NS3/4A protease inhibitors in clinical development. In addition, influenza hemagglutinin (HA) is a primary target of neutralizing antibodies against influenza. Novel broadly neutralizing antibodies (BnAbs) against the stem region of HA have been described and inhibit several influenza viral subtypes, but antibody neutralization escape mutations have emerged. We identified potential escape mutations in broadly neutralizing antibody F10 that may impact protein dynamics in HA that are critical for function. We also solved crystal structures of antibody fragments that are important for understanding the structural basis of antibody binding for influenza BnAbs. These studies can inform the design of improved therapeutic strategies against viruses by incorporating an understanding of structural elements that are critical for function, such as substrate processing and protein dynamics, into the development of novel therapeutics that are robust against resistance.

Charles University Faculty of Pharmacy in Hradec Králové Department of Pharmacology & Toxicology Student: Dominika Bezděková Supervisor: doc. PharmDr. Lukáš Červený, Ph.D. Title of diploma thesis: IN VITRO STUDY OF DRUG-DRUG INTERACTIONS OF HIV PROTEASE INHIBITOR DARUNAVIR ON EFFLUX ABC TRANSPORTERS Abstract: Darunavir is a drug used in the therapy of HIV belonging to the group of protease inhibitors. These protease inhibitors are used as a part of the combination antiretroviral therapy. For the increase of bioavailability, darunavir is always used in combination with ritonavir or cobicistat. As the CYP3A4 and ABCB1 (P-glycoprotein) transporter substrate, darunavir is a drug with a high potential to drug interactions. Considering the amount of adverse effects that can be caused by darunavir, it is necessary to know these drug interactions for the safety of therapy. Inhibition of the intestinal ABCB1 by the co-administrated drugs could also lead to the increased bioavailability of darunavir and to reduction of frequency of administration leading to a cheaper therapy. This thesis studies the drug-drug interactions of darunavir with in vitro methods using two cell lines - MDCKII and Caco-2 cells. The results from the transport of darunavir across the MDCKII cell monolayer indicates that darunavir is a ABCB1...

Charles University Faculty of Pharmacy in Hradec Králové Department of Pharmacology & Toxicology Student: Veronika Halodová Supervisor: doc. PharmDr. Lukáš Červený, Ph.D. Title of diploma thesis: In vitro and ex vivo study of drug-drug interactions of antivirals on intestinal membrane transporters Tenofovir (TFV) is the first-line agent in the treatment of hepatitis B virus (HBV) infection for patients aged over 12 years and one of the first-line choices for the combination antiretroviral therapy (cART) of infections caused by human immunodeficiency virus (HIV). Two commercially available prodrugs have been developed for oral administration of TFV, tenofovir disoproxil fumarate (TDF) and tenofovir alafenamide fumarate (TAF). These prodrugs increase TFV membrane permeability and oral bioavailability. One of the factors that can affect the bioavailability of orally administrated drugs is active transport mediated by efflux transporters, mainly by P-glycoprotein (ABCB1, P-gp) and Breast cancer resistance protein (ABCG2, BCRP). It has been already proved that TDF and TAF are substrates of both of these transporters. The goal of this diploma thesis was to use in vitro and ex vivo models of intestinal barrier to assess the impact of the efflux transporters on TDF and TAF transport in the intestine and on their...

Le virus de l’hépatite C (VHC) est un agent causateur de maladies du foie important responsable d’une pandémie affectant près de 180 millions d’individus mondialement. L’absence de symptômes dans les premières années d’infection entraîne des diagnostics tardifs qui empêchent la prise en charge rapide des patients avant l’apparition d’une fibrose et, dans près de 16 % des cas d’infection, d’une cirrhose. En exploitant les interactions protéine-protéine membranaires, des essais utilisant la technologie BRET, dans les cellules vivantes, ont été précédemment optimisés afin d’établir le réseau complet des interactions du VHC. En utilisant les fondements de cette étude, un essai à haut débit dans les cellules vivantes a été réalisé pour identifier de nouveaux composés anti-VHC ciblant une nouvelle interaction NS3/4A-NS3/4A. Approximativement 110,000 petites molécules ont été criblées pour leurs effets sur l’homodimérization de NS3/4A et ont été classées par rapport à leur spécificité et à leur puissance contre le VHC. Au terme de cette étude, UM42811 a été identifié comme un activateur potentiel de l’interaction NS3/4A-NS3/4A offrant une activité antivirale prometteuse dotant une excellente fenêtre thérapeutique. Par la suite, un séquençage exhaustif des virus, soumis à un traitement de UM42811, a permis d’établir le profil de résistance du VHC contre ce composé. Grâce à cette fine cartographie, il a été possible d’identifier un nouveau mécanisme d’inhibition de NS3/4A qui est indépendant de son activité protéase. En utilisant les données de notre groupe sur les interactions VHC-hôte, il a été possible de continuer la caractérisation fonctionnelle du composé UM42811 en étudiant son effet sur les interactions potentiellement bénéfiques à la persistance virale. Pour ce faire, les protéines associées au transport nucléaire et mitochondriale qui sont des interactants de choix de NS3/4A ont été priorisées. Parmi ces facteurs de l’hôte, l’étude de karyopherin subunit beta 1 (KPNB1) et de heat shock protein 60 (HSP60) a été priorisée. De façon intéressante, les expériences de co-immunoprécipitation ont démontré que UM42811 était capable de prévenir l’interaction KPNB1-NS3/4A ainsi que l’interaction HSP60-NS3/4A. De plus, les études ii fonctionnelles et les analyses d’immunobuvardage de type western ont démontré que l’interaction KPNB1-NS3/4A avait des effets délétères sur l’induction des gènes stimulés par l’interféron (ISG). Finalement, il a été démontré que KPNB1 est possiblement clivé par NS3/4A suggérant la présence potentielle d’un mécanisme de subversion ou d’échappement. En bref, cette étude démontre la puissance des stratégies impliquant les interactions protéine-protéine dans les cellules vivantes pour l’identification de nouveaux composés inhibiteurs, caractérise un nouveau mécanisme d’inhibition anti-VHC et révèle la possibilité d’un nouveau mécanisme d’évasion du système immunitaire. / Hepatitis C virus (HCV) is an important causative agent for liver diseases and is responsible for a worldwide pandemic affecting roughly 180 million individuals worldwide. Late diagnosis following the progression to fibrosis and to cirrhosis, in nearly 16% of chronic infections, is attributed to the absence of symptoms in the first years of infection. By exploiting membrane protein-protein interactions (PPI), live cell assays using bioluminescence resonance energy transfer (BRET) technology have previously been optimized to complete a comprehensive hepatitis C virus (HCV) protein interaction network. Using the groundwork laid by this network study, a high-throughput assay (HTS) cell-based assay was implemented to identify novel inhibitory compounds targeting an unreported NS3/4A-NS3/4A interaction. Approximately 110,000 compounds from a small-molecule collection were screened to monitor modulation of NS3/4A homodimerization and were discriminated based on specificity and potency. UM42811 was identified as a potential NS3/4A-NS3/4A interaction activator and found to have a promising antiviral activity boasting an excellent therapeutic window. Combined deep sequencing and mutation mapping have yielded a resistance profile based on statistical and functional probability pointing towards a novel inhibitory mechanism targeting the HCV NS3/4A independent from protease activity inhibition. Data from an HCV to host protein interaction network generated by our group was used to analyze alternative effects of UM42811 on interactions which potentially benefit viral persistence. NS3/4A-specific host interactors were heavily associated with nuclear and mitochondrial transport based on Gene Ontology (GO). Among these specific interactors, karyopherin subunit beta 1 (KPNB1) and heat shock protein 60 (HSP60) were selected for further study. Interestingly, co-immunoprecipitation experiments revealed that UM42811 was able to prevent both KPNB1-NS3/4A and HSP60-NS3/4A interactions. Moreover, functional and western analysis revealed the KPNB1-NS3/4A interaction to have deleterious effects on iv interferon stimulated gene (ISG) induction. Unexpectedly, analysis revealed a putative NS3/4A mediated cleavage of KPNB1. Overall, this study demonstrates the strength of cell-based PPI strategies in the identification of novel HCV antiviral compounds, characterizes a novel inhibitory mechanism for HCV and reveals a potentially novel viral immune evasion mechanism.