Introdução: A Organização Mundial da Saúde estima que cerca de 71 milhões de pessoas estejam vivendo infectadas pelo vírus da hepatite C (HCV), o que corresponde a 1% da população mundial. A infecção crônica pelo HCV é uma das principais causas de cirrose hepática e carcinoma hepatocelular. O tratamento farmacológico visa a erradicação do vírus e melhora da atividade inflamatória. Em 2015, três fármacos de ação direta (DAA), simeprevir (SMV), sofosbuvir (SOF) e daclatasvir (DCV), foram incluídos no protocolo brasileiro de tratamento da hepatite C crônica. Estudos demonstram que o uso destes medicamentos está associado a elevadas taxas de resposta ao tratamento e a menor incidência de reações adversas em relação às terapias baseadas no uso do interferon e de inibidores de protease de primeira geração. Outros trabalhos indicam que pode haver associação entre a presença de determinadas mutações de resistência viral com a resposta ao tratamento farmacológico. Objetivos: Verificar a efetividade e a segurança dos esquemas de tratamento da hepatite C crônica que envolvem os DAA e analisar se a presença das mutações de resistência impacta negativamente na resposta ao tratamento. Casuística e Métodos: Trata-se de um estudo quase experimental de braço único realizado no Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto. Foram incluídos indivíduos maiores de 18 anos, infectados pelo genótipo 1 do HCV, que iniciaram tratamento com esquema que continha SOF em associação com DCV ou SMV. Foram coletados dados sociodemográficos, antropométricos, clínicos e realizou-se levantamento da ocorrência de reações adversas durante o tratamento, por meio do sistema informatizado do hospital. A coleta de sangue, para verificação da presença de mutações de resistência viral, foi realizada em até 15 dias antes do início do tratamento. O principal desfecho considerado foi a RVS12, definida como a ausência de carga viral detectável na 12ª semana após o fim do tratamento. Resultados: 262 indivíduos foram incluídos no estudo, dos quais 58,0% eram do sexo masculino e 79,4% foram classificados como brancos. A média de idade calculada para a amostra foi 55 anos, com desvio padrão de 10 anos. Quanto aos esquemas de tratamento propostos, 49,6% dos pacientes receberam tratamento com SOF e DCV e 50,4% fizeram uso de SOF e SMV. A taxa global de RVS12 foi de 92,7% (93,9% para SOF + DCV e 91,7% para SOF + SMV). Não foram identificados fatores associados a RVS, segundo a análise estatística. As reações adversas mais comuns foram anemia, náuseas, cefaleia e fadiga. Não foi encontrada evidência de associação entre a presença de mutações associadas a resistência ao tratamento e a falha no tratamento. Conclusão: O uso de esquemas de tratamento compostos por SOF e DCV ou SOF e SMV apresentou alta taxa de RVS e bom perfil de tolerabilidade em pacientes com genótipo 1 do HCV. / Background: The World Health Organization estimates that about 71 million people are living with hepatitis C virus (HCV), which accounts for 1% of the world population. Chronic HCV infection is one of the major causes of liver cirrhosis and hepatocellular carcinoma. The pharmacological treatment aims to eradicate the virus and improve inflammatory activity. In 2015, three direct-acting antivirals (DAA), simeprevir (SMV), sofosbuvir (SOF) and daclatasvir (DCV) were included in the brazilian protocol for the treatment of chronic hepatitis C. Studies have shown that the use of these drugs is associated with higher rates of response to treatment and to lower incidence of adverse reactions, compared to therapies based on the use of interferon and first-generation protease inhibitors. Other studies indicate that there may be an association between the presence of certain viral resistance mutations and the response to pharmacological treatment. Aims: To verify the effectiveness and safety of chronic hepatitis C treatment regimens involving DAA and to analyze whether the presence of resistance mutations negatively affects SVR rates. Methods: It is an almost experimental single-arm study performed at the Clinics Hospital of the Ribeirão Preto Medical School. We included individuals older than 18 years old, infected with HCV genotype 1, who started treatment with a regimen containing SOF in combination with DCV or SMV. Sociodemographic, anthropometric and clinical data were collected and the occurrence of adverse reactions during the treatment was investigated through the computerized system of the hospital. Blood collection for search for viral resistance mutations was performed within 15 days prior to initiation of treatment. The main outcome was SVR12, defined as the absence of detectable viral load at the 12th week after the end of treatment. Results: 262 subjects were included in the study, of which 58.0% were male and 79.4% were white. The mean age calculated for the sample was 55 years, with standard deviation of 10 years. Regarding the treatment regimens, 49.6% of the patients received SOF and DCV and 50.4% used SOF and SMV. The SVR12 rate was 92.7% (93.9% for SOF + DCV and 91.7% for SOF + SMV). No factors associated with SVR were identified according to the statistical analysis. The most common adverse reactions were anemia, nausea, headache and fatigue. No evidence of association was found between the presence of mutations associated with treatment resistance and treatment failure. Conclusion: The use of treatment regimens composed of SOF and DCV or SOF and SMV showed a high rate of SVR and a good tolerability profile in patients with HCV genotype 1.

Sofosbuvir is a uridine based nucleotide inhibitor of the hepatitis C viral (HCV) polymerase that is the backbone of many treatment regimens. In combination with drugs targeting other viral enzymes (including the poorly potent guanosine analogue ribavirin or highly potent inhibitors of viral NS5A or protease) most patients clear virus and resistance to sofosbuvir is rare, allowing effective retreatment with sofosbuvir. Patients with Genotype 3 HCV respond less well than other genotypes and response is reduced in those previously exposed to interferon. Here we show that patientderived virus from patients with Genotype 3 HCV who relapse to sofosbuvir-based therapies have a reduced sensitivity to SOF in an in-vitro phenotyping assay. Analysis of viral sequencing data revealed two distinct polymorphisms (A150V and K206E) in the HCV polymerase that are associated with treatment failure and in-vitro; they reduce sofosbuvir sensitivity against genotype 3 hepatitis C virions. However both polymorphisms modify the cellular response to type I interferon and in cells lacking response to interferon the impact on sofosbuvir sensitivity is minimal. The A150V polymorphism reduces the response to interferon 70 fold whereas the K206E substitution has minimal effects on interferon in isolation but in combination with A150V reduces the response 100 fold. Preliminary data indicates that the A150V polymorphism interferes with the late response to type I interferons enabling the virus to overcome the induction of interferon-stimulated genes. These data indicate a complex interaction between direct acting antiviral drugs and the innate antiviral response.

Around 130-150 million people are chronically infected with hepatitis C-virus today. Personal suffering and great societal costs aside, this also causes around 400 000 deaths every year due to complications. Earlier treatments with pegylated interferon and ribavirin were both ineffective and had a lot of side effects, but in recent years new treatments using direct-acting antivirals that are both more effective and has less side effects have been introduced. The downside with these are that their effectiveness depends on which HCV genotype the patient has, which requires costly and time consuming pre-treatment examinations before treatment can begin. This paper investigates clinical studies in which the effectiveness and side effects of a new combination of drugs containing sofosbuvir and velpatasvir is tested. The studies where found through PubMed, and they are what the usage of these drugs in health care is based on. The studies show that the combination of sofosbuvir and velpatasvir is effective, measured by sustained virological response, against all HCV genotypes irrespective of if the patient has a compensated or decompensated cirrhosis, or if the patient has had a previously failed treatment. The patients with decompensated cirrhosis also had an early improvement in liver function, but it is too early to say if the improvement is long lasting. The treatment also gave less side effects compared to pegylated interferon and ribavirin. The combination of sofosbuvir and velpatasvir was also shown to have a good effect amongst patients where resistance associated variants of NS5A and NS5B where found. The conclusion is that the combination of sofosbuvir and velpatasvir is an effective, but also at the moment expensive, treatment for HCV independent of genotype.

This dissertation is divided into two main sections describing major portions of my Ph.D. research: (1) development of two enzymatic assays for identifying inhibitors of SARS-CoV-2 RNA dependent RNA polymerase (RdRp) and the associated proofreading exonuclease complexes, two key enzymatic activities of SARS-CoV-2, the virus responsible for the COVID-19 pandemic and (2) the design and implementation of four novel single-color fluorescent DNA sequencing by synthesis (SBS) methods, including the synthesis of many of the key nucleotide analogues required for these studies. In response to the COVID-19 pandemic, the first part of my research is focused on the discovery of potential therapeutics for combating coronavirus infections. Chapter 1 describes the identification of several polymerase and exonuclease inhibitors for SARS-CoV-2 using novel mass spectrometry-based molecular assays. SARS-CoV-2 has an exonuclease complex, which removes nucleotide inhibitors such as Remdesivir that are incorporated into the viral RNA during replication, reducing the efficacy of these drugs for treating COVID-19. Combinations of inhibitors of both the viral RdRp and the exonuclease could overcome this deficiency. Chapter 1 reports the identification of hepatitis C virus NS5A inhibitors Pibrentasvir and Ombitasvir as SARS-CoV-2 exonuclease inhibitors. In the presence of identified exonuclease inhibitors, RNAs terminated with the active forms of the prodrugs like Sofosbuvir, Remdesivir and Favipiravir were largely protected from excision by the exonuclease, while in the absence of exonuclease inhibitors, there was rapid excision. Viral cell culture studies also demonstrate significant synergy using this combination strategy. This study supports the use of combination drugs that inhibit both the SARS-CoV-2 polymerase and exonuclease for effective COVID-19 treatment. Chapters 2-6 describe the single-color DNA SBS studies. Chapter 2 provides essential background on the structure of DNA, the DNA polymerase reaction, and several key DNA sequencing technologies, with an emphasis on the design of nucleotide analogues for the DNA SBS approach. Chapter 3 delineates a one-color fluorescent DNA SBS method based on a set of nucleotide reversible terminators (NRTs) comprising two orthogonal cleavable linkers, one fluorescent dye and one anchor. Chapter 4 describes a one-color hybrid DNA sequencing approach using a set of dideoxynucleotide analogues bearing two orthogonal cleavable linkers, one fluorophore and one anchor as well as a set of unlabeled NRTs. By introducing a pH responsive fluorophore into the design of nucleotide analogues, Chapter 5 demonstrates a novel type of single-color DNA SBS method using a set of NRTs comprising one pH-responsive fluorescent dye or one non-responsive fluorescent dye tethered with one cleavable linker. Chapter 6 presents another option for the single-color DNA sequencing technique using a set of deoxynucleotide analogues comprising the above pH responsive or non-responsive dyes tethered with a cleavable linker, along with a set of unlabeled NRTs. The one-color SBS approaches have the potential for higher sensitivity, miniaturization and cost effectiveness compared with four-color SBS methods. Finally, Chapter 7 summarizes the SARS-CoV-2 antiviral drug discovery and one-color sequencing techniques and discusses potential follow-up research on these projects.

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Charles University Faculty of Pharmacy in Hradec Králové Department of Pharmacology & Toxicology Student: Zdeněk Záboj Supervisor: PharmDr. Lukáš Červený, Ph.D. Title of diploma thesis: Study of drugs interactions of antiviral drugs with intestinal transporters Sofosbuvir is an antiviral agent widely used in the treatment of chronic hepatitis C. This orally administered prodrug is a designed substrate of ATP-binding (ABC) efflux transporters, P- glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2). ABCB1 and ABCG2 are important determinants of intestinal absorption and are the site of significant pharmacokinetic drug interactions, leading to changes in drug exposure. Pharmacokinetic drug interactions may be undesirable (increasing the toxicity of the treatment) or desirable (allowing dose reduction). Because sofosbuvir is often administered in combination regimens with other anti(retro)virotics, the aim of this thesis was to study the ability to enhance intestinal absorption of sofosbuvir. To study the pharmacokinetic drug interactions on ABCB1 and ABCG2, a widely established in vitro bi-directional transport method through a polarized monolayer formed by the Caco-2 cell line derived from colorectal cancer has been used. We analyzed the drug interactions of sofosbuvir on these efflux...