This thesis describes the design and synthesis of compounds that are intended to inhibit serine and aspartic proteases. The first part of the text deals with preparation of inhibitors of the hepatitis C virus (HCV) NS3 serine protease. Hepatitis C is predominantly a chronic disease that afflicts about 170 million people worldwide. The NS3 protease, encoded by HCV, is essential for replication of the virus and has become one of the main targets when developing drugs to fight HCV. The inhibitors discussed here constitute surrogates for the widely used N-acyl-hydroxyproline isostere designated 4-hydroxy-cyclopentene. The stereochemistry of the 4-hydroxy-cyclopentene scaffold was determined by nuclear overhauser effect spectroscopy (NOESY) and the regiochemistry by heteronuclear multiple bond correlation (HMBC). The scaffold was decorated with different substituents to obtain both linear and macrocyclic HCV NS3 protease inhibitors that display low nanomolar activity. The second part of the thesis describes the design and synthesis of potential aspartic protease inhibitors. The hydroxyethylene motif was used as a noncleavable transition state isostere. The synthetic route yielded a pivotal intermediate with excellent stereochemical control, which was corroborated by NOESY experiments. This intermediate can be diversified with different substituents to furnish novel aspartic protease inhibitors. / <p>Report code: LIU-TEK-LIC-2006:45</p>

Les cellules dendritiques plasmacytoïdes (pDC) sont responsables de la production d'IFN de type I au cours des infections virales. L'élimination du virus de l’hépatite C (VHC) par une thérapie basée sur l'IFN-α chez plus de 50% des patients chroniquement infectés suggère une diminution possible de la production d'IFN-α endogène par les pDC. Cependant, les pDC exposées à des hépatocytes infectés par le VHC produisent de l'IFN de type I via la signalisation du TLR7. Dans cette étude, nous avons étudié l'impact du virion du VHC sur les différentes fonctions des pDC que sont la production d’IFN-α et de TNF-α, l’expression de marqueurs de maturation et de la protéine cytotoxique TRAIL. De plus, nous sommes posés la question de l’effet de l'exposition des pDC à des hépatocytes infectés par le VHC sur l’induction des autres voies de signalisation que celle de l'IRF-7 et de l'IFN- et impliquant NF-κB nécessaire à d’autres fonctions des pDC. Nous montrons que l'exposition des pDC au virion du VHC extrait du sérum de patients ou produit en culture cellulaire induit une très faible production d'IFN-α et de TNF-α par les pDC par rapport à celle induite par le virus de l’Influenza et le virus de l'herpès de type 1 (HHV-1). Les virions complets du VHC ainsi que les particules dépourvues d’ARN viral (HCV-like particles) inhibent la production d'IFN-α des pDC stimulées avec les agonistes du récepteur « Toll-like Recptor 9 » (TLR9) (CpG-A ou HHV-1). Cependant, ils ne bloquent pas la production d'IFN-α induite par les agonistes du TLR7 (R848, virus de l’Influenza). Le niveau d’ARN messager de l'IFN-α traduit aussi de l’inhibition par le virion du VHC de la voie du TLR9 dès deux heures après stimulation par le CpG-A et corrèle avec régulation à la baisse de l'expression des ARN messagers du facteur de transcription IRF-7 et du récepteur TLR9. De plus, contrairement aux virus de l'influenza, R848 et CpG-B, les hépatocytes infectés par le VHC ne stimulent de façon significative ni la phosphorylation de la sous-unité p65 de NF-B ni la sécrétion de « tumor necrosis factor » (TNF)- par les pDC. Les cellules infectées par le VHC n'induisent pas non plus de façon significative l'expression de marqueurs de différenciation importants CD40, CCR7, et de la molécule de co-stimulation CD86 ni l’expression de TRAIL à la surface des pDC en comparaison avec les virus de l'influenza, R848 et CpG-B. Le profil de signalisation induit par les cellules infectées par le VHC chez les pDC ressemble à celui induit par le CpG-A et diffère de ceux induits par le CpG-B, R848 ou le virus de l’influenza. En conclusion, les premières interactions des particules virales aves des protéines cellulaires des pDC suivies de l'internalisation des particules et du blocage de la voie du TLR9 pourraient être à l’origine d’une détection moins efficace du virion du VHC par les pDC, et d’une production réduite d'IFN-α. De plus, nos résultats suggèrent que les hépatocytes infectées par le VHC signalisent uniquement dans les pDC via les endosomes recrutant IRF7, et que, tout comme le virion du VHC, ils n'induisent pas une réponse fonctionnelle complète des pDC. Nos résultats montrent donc un lien entre les voies de signalisation des pDC et leurs fonctions, et sont importants pour notre compréhension les mécanismes amenant à l’établissement d’une infection chronique par le VHC. / Plasmacytoid dendritic cells (pDCs) are responsible for the production of type I IFN during viral infections. The elimination of hepatitis C virus (HCV) is based on IFN-alpha therapy and is effective in more than 50% of chronically infected patients. This suggests a possible decrease in production of IFN-alpha by endogenous pDCs. However, pDCs exposed to HCV-infected hepatocytes produce type I IFN via TLR7 signaling. In this study, we investigated the impact of HCV virions and of HCV-infected hepatoma cells on pDC functions such as production of IFN-alpha and TNF-alpha, expression of maturation markers and cytotoxic TRAIL protein. In addition, we evaluated the effect of exposure of pDCs to cell-asociated and cell-freed HCV on induction of IRF-7 and NF-kB signaling pathways. We show that exposure of pDCs to HCV virions from serum of patients or produced in cell culture induces a very low production of IFN-alpha and TNF-alpha by pDCs compared to that induced by Influenza virus and herpes virus type 1 (HHV-1). The complete HCV virions and particles lacking viral RNA (HCV-like particles) inhibit the production of IFN-α in pDCs stimulated with agonists of Toll-like Recptor 9 (TLR9) (CpG-A or HHV-1). However, they do not block the production of IFN-alpha induced by agonists of TLR7 (R848, influenza virus). The level of IFN-alpha mRNA also show the inhibition of TLR9 pathway by HCV virions from two hours after stimulation with CpG-A and correlates with downregulation of expression of mRNA of the transcription factor IRF-7 and TLR9. Moreover, unlike influenza virus, R848 and CpG-B, hepatocytes infected with HCV do not significantly stimulate the phosphorylation of p65 subunit of NF- B or the secretion of tumor necrosis factor (TNF) -  by pDCs. Cells infected with HCV do not induce significant expression of differentiation markers CD40, CCR7, and of costimulatory molecule CD86, nor the expression of TRAIL on the surface of pDC compared with the influenza virus, and with synthetic agonists of TLR7 (R848) and TLR9 (CpG-B). The signaling profile induced by cells infected with HCV is similar to that induced by CpG-A on pDCs and differs from those induced by CpG-B, R848 or influenza virus. In conclusion, the initial interations of viral particles with cellular proteins of pDC, followed by the internalization of particles and blockade of TLR9 pathway could cause a less efficient detection of HCV virions by pDCs, and reduced production of IFN-α. Moreover, our results suggest that hepatocytes infected with HCV signalize via endosomes recruiting IRF7, and that, like the HCV virion, they do not induce a complete functional response of pDCs. Our results show a link between the signaling pathways of pDCs and their functions, and are important for understanding the mechanisms leading to the establishment of chronic infection with HCV.

The clearance of viruses is largely dependent upon the activation of T cells to generate a robust immune response. However, host responses are suppressed during chronic viral infections. In this thesis, we explored the role of Top2α in DNA topology in individuals with chronic HBV, HCV, and HIV infections. We found that Top2α protein expression and activity were low in T cells derived from chronically virus-infected individuals compared to healthy subjects. Using CD4+ T cells treated with Top2α inhibitor or poisoner as a model, we demonstrated that Top2α inhibition disrupts the DNA topology, suppresses DNA repair kinase (ATM), and telomere protein (TRF2) expression, and induces T cell dysfunction. These findings reveal that Top2α inhibition is a mechanism by which viruses evade the host responses and establish persistent infection, and thus, restoring Top2α levels could be a way of boosting immune responses during chronic viral infections.

Background: Rural people who inject drugs (PWID) have been disproportionately affected by the ongoing hepatitis C virus (HCV) epidemic. Methods: Using data from a cross-sectional study of PWID from rural New Hampshire, Vermont, and Massachusetts, we evaluated the potential for syringe services programs (SSPs) to lower the risk of HCV infection among rural PWID via their influence on the physical and social environment. The specific aims were to evaluate: 1) the association of spatial proximity to the nearest SSP with HCV seroprevalence and injection risk behaviors; 2) the association of indirect SSP use (secondary syringe exchange) with HCV seroprevalence and injection risk behaviors; and to 3) explore PWIDs’ perceptions and experiences with obtaining injection supplies, injection risk behaviors, and HCV. Results: Living farther from an SSP was associated with a higher prevalence of HCV seropositivity and injection risk behaviors. Indirect SSP use was weakly and imprecisely associated with lower prevalence of injection risk behaviors, while direct SSP and pharmacy use were both associated with a higher prevalence of HCV seropositivity and injection risk behaviors. Participants described sharing syringes in response to limited access to syringe sources. Syringe sharing behavior was influenced by perceptions of HCV risk, HCV status, and emotions of trust and intimacy. Conclusion: Spatial proximity to an SSP and direct use of an SSP may lower the risk of HCV infection among rural PWID. HCV prevention efforts in rural New England need to address syringe access and cultivate the perception that HCV is a serious but preventable risk.

Drug injection is an increasingly important risk factor in the transmission of blood-borne pathogens, including the hepatitis C virus (HCV) and human immunodeficiency virus (HIV). The purpose of the study was to examine the influence of social network factors on HCV and HIV. The study was grounded in social network theory and sought to determine whether social network characteristics affect high-risk sexual and drug injection behavior as well as self-reported HIV and HCV status. The study design was a quantitative cross-sectional survey. A total of 181 participants in a needle exchange program completed a survey in Spanish assessing individual drug and sex risk practices as well as gathering information to describe the characteristics of participants' personal networks from an egocentric perspective. General estimating equation techniques were used to analyze the data. Results showed that only social network size was related to risky sexual behavior. Injecting risk behaviors were only impacted by personal network exposures, measured by the average number of years network members had injected. HIV self-reported serum status was correlated with trust, closeness, and number of family members named among the closest 5 network members. Last, HCV self-reported serum status was only related to the years that network members had been injecting drugs. This study has implications for positive social change in that public health practitioners may gain a better understanding of the social network characteristics associated with high-risk behaviors of those infected with HCV and HIV in order to develop health promotion programs to lower infections and mortality.

Contents of the present thesis were published in the following articles. 1. Suzuki S, Mori K, Higashino A, Iwasaki Y, Yasutomi Y, Maki N, Akari H. 2016. Persistent replication of a hepatitis C virus genotype 1b-based chimeric clone carrying E1, E2 and p6 regions from GB virus B in a New World monkey. Microbiol Immunol 60:26-34. Copyright © 1999-2016 John Wiley & Sons, Inc.2. Yoshida T, Suzuki S, Iwasaki Y, Kaneko A, Saito A, Enomoto Y, Higashino A, Watanabe A, Suzuki J, Inoue K, Kuroda T, Takada M, Ito R, Ito M, Akari H. 2013. Efficient in vivo depletion of CD8+ T lymphocytes in common marmosets by novel CD8 monoclonal antibody administration. Immunol Lett 154:12-17.Copyright © 2013 Elsevier B. V. / 京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第19546号 / 理博第4206号 / 新制||理||1604(附属図書館) / 32582 / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 明里 宏文, 教授 岡本 宗裕, 教授 中村 克樹 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

Hepatitis-C Virus (HCV) remains the leading cause of liver transplant in the US and the UK, and the World Health Organization (WHO) estimates that 71 million people are infected worldwide. A vaccine would drastically impact the healthcare-associated burdens that HCV causes globally. The objective of this master’s thesis project is to produce human antibody (IgG) against HCV. This project will focus on the monoclonal antibodies (mAbs) HEPC3, AR3C, HEPC74, and HCV1. These four antibodies have been isolated from patients who have successfully cleared the infection, and their sequences and structures are available in the public domain. These four antibodies have also shown to bind to E2, a glycoprotein on the surface HCV that is crucial for viral binding and entry. This interaction of the mABs with E2 has been implicated in viral neutralization, making them promising choices for this study. Overall, 3 out of 4 mAbs were successfully cloned and produced. The unsuccessful antibody, HEPC74, was discovered to have failed due to an error in the plasmid sequence. Just as the western blot to confirm secretion was ready to be run, the laboratory closed due the Covid-19 outbreak. Therefore, the data can officially declare a ¾ mAb production success, however it is safe to assume that the alternative clone for HEPC74 was also a success due to a perfect sequence match. Since the primary objective of this project was to successfully clone and produce these four antibodies, then this study is considered an overall success. Lastly, this study examined how the same protocol  could be applied the SARS-CoV-2 outbreak, by the cloning and production of anti-RBD IgG and testing them for viral neutralization. / Hepatit-C (HCV) är fortsatt den enskilt största orsaken till levertransplantationer med uppskattningsvis 71 miljoner infekterade globalt sett, enligt världshälsoorganisationen (WHO).Ett vaccin mot HCV skulle drastiskt minska trycket på global hälso- och sjukvård. Syftet med detta projekt är att producera antikroppar (igG) mot HCV. Projektet fokuserar på HEPC3, AR3C, HEPC74 och HCV1 som är monoklonala antikroppar (mAbs). Dessa antikroppsvarianter har isolerats från patienter som tillfrisknat från infektion. Både DNA-sekvenser och strukturer av antikropparna finns offentligt tillgängliga. Dessa fyra antikroppar har också visats kunna binda till E2 som är ett membranbundet glykoprotein hos HCV som är centralt för viral adhesion och fusion. Interaktionen mellan dessa mAbs och E2 har visat sig neutralisera virulens, vilket gör dem till lovande kandidater för denna studie. Tre av fyra mAbs kunde klonas och produceras framgångsrikt. Försöket med HEPC74 misslyckades på grund av ett fel i plasmidsekvensen och just som western blot skulle genomföras för att bekräfta sekretion av en alternativ klon avslutades the praktiska arbetet med anledning av Covid-19 utbrottet. Resultaten visar entydigt att tre av fyra mAb producerades framgångsrikt. Det går dock att anta att det andra försöket med HEPC74 sannolikt också lyckades pga perfekt sekventiell matchning. Då det huvudsakliga syftet med projektet var att framgångsrikt klona och producera dessa fyra antikroppar så kan studien anses vara framgångsrik. Slutligen så undersöktes huruvida samma förfarande kunde appliceras mot SARS-CoV-2 genom kloning och produktion av anti-RBD IgG och tester av viral neutralisering.

Two polymorphisms in the promoter region of macrophage migration inhibitory factor (MIF)—rs755622 and rs5844572—exhibit prognostic relevance in inflammatory diseases. The aim of this study was to investigate a correlation between these MIF promoter polymorphisms and the severity of hepatitis C virus (HCV)-induced liver fibrosis. Our analysis included two independent patient cohorts with HCV-induced liver fibrosis (504 and 443 patients, respectively). The genotype of the single nucleotide polymorphism (SNP) -173 G/C and the repeat number of the microsatellite polymorphism -794 CATT5–8 were determined in DNA samples and correlated with fibrosis severity. In the first cohort, homozygous carriers of the C allele in the rs755622 had lower fibrosis stages compared to heterozygous carriers or wild types (1.25 vs. 2.0 vs. 2.0; p = 0.03). Additionally, 7 microsatellite repeats were associated with lower fibrosis stages (<F2) (p = 0.04). Comparable tendencies were observed in the second independent cohort, where fibrosis was assessed using transient elastography. However, once cirrhosis had been established, the C/C genotype and higher microsatellite repeats correlated with impaired liver function and a higher prevalence of hepatocellular carcinoma. Our study demonstrates that specific MIF polymorphisms are associated with disease severity and complications of HCV-induced fibrosis in a stage- and context-dependent manner.

No description available.

Chronic hepatitis C virus (HCV) infection exhibits persistent high viral load, inducing T cells differentiation and dysfunction in chronically infected individuals. Recent longitude studies in both HCV specific- and bulk T cells reveal that chronic immune stimulation is the driving force for the impaired T cell functions, however, the underlying mechanisms remain elusive. Here, we show that peripheral CD4+ T cells from chronically HCV-infected patients exhibit lymphopenia with the reduction of naïve population and expansion of effector memory T cells. CD4+ T cells from HCV patient also display elevated activation markers. including HLA-DR, GLUT1, Granzyme B, and short-lived effector marker CD127- KLRG1+, whereas stem cell-liked transcription factor TCF1 and telomere sheterin subunit TRF2 are significant reduced, comparing to age- and gender-matched healthy controls. Mechanistically, ex vivo T cell differentiation revealed that CD4+ T cells from HCV patients exhibit PI3K/Akt/mTOR signaling hyperactivation upon TCR stimulation, favoring pro-inflammatory effector differentiation with TRF2 downregulation, rendering telomere dysfunction induced foci (TIFs) accumulation, resulting in telomeric DNA damage and cellular apoptosis. Importantly, exacerbation of telomere deprotection by knockdown of TRF2 expression in healthy T cells resulted in an increase in telomeric DNA damage and T cell apoptosis; whereas overexpression of TRF2 in HCV-T cells led to an alleviation of telomeric DNA damage and T cell death. Additionally, inhibition of Akt signaling during T cell activation can preserve precursor memory population, while limiting inflammatory effector expansion, DNA damage, and cell death. Taken together, these results suggest that modulation of immune activation by inhibiting Akt signaling and protection of telomeres by enforcing TRF2 expression could open new therapeutic strategies to balance adaptive immune responses in the setting of chronic immune activation and inflammatory in vulnerable populations such as chronically viral infected individuals.