Reovirus is internalized after interaction of the outer proteins μ1, σ1 and σ3 with the host cell. Proteolysis of σ3 and cleavage of μ1 (into δ and φ) eventually leads to the formation of a more infectious subviral particle named “ISVP”. The infectious entry of viruses, but not of ISVPs, can be blocked using various entry inhibitors and therefore, suggests that there is a threshold of σ3 digestion required to allow particle to bypass entry blockers. By combining protease and detergent to the digestion of virions, data from this work showed distinct particles generated along the transition pathway. In addition, studies involving flow cytometry and specific antibodies (anti-μ1) showed that between virus and ISVP there is a gradual yet heterogeneous particle proteolysis that is directly related to the virus infectivity. The findings and approaches taken for this thesis work can possibly be extended for studying other non-enveloped viruses. Moreover, it may help to shed some light on the development of safe and effective oncolytic agents.

Reovirus is internalized after interaction of the outer proteins μ1, σ1 and σ3 with the host cell. Proteolysis of σ3 and cleavage of μ1 (into δ and φ) eventually leads to the formation of a more infectious subviral particle named “ISVP”. The infectious entry of viruses, but not of ISVPs, can be blocked using various entry inhibitors and therefore, suggests that there is a threshold of σ3 digestion required to allow particle to bypass entry blockers. By combining protease and detergent to the digestion of virions, data from this work showed distinct particles generated along the transition pathway. In addition, studies involving flow cytometry and specific antibodies (anti-μ1) showed that between virus and ISVP there is a gradual yet heterogeneous particle proteolysis that is directly related to the virus infectivity. The findings and approaches taken for this thesis work can possibly be extended for studying other non-enveloped viruses. Moreover, it may help to shed some light on the development of safe and effective oncolytic agents.

In the infection process, native poliovirus (160S) first converts to a cell-entry intermediate (135S) particle, which causes the externalization of capsid proteins VP4 and the N-terminus of VP1 (residues 1-53). The externalization of these entities is followed by release of the RNA genome, leaving an empty (80S) particle. Three antibodies were utilized to track the location of VP1 residues in different states of poliovirus by cryogenic electron microscopy (cryo-EM). "P1" antibody binds to N-terminal residues 24-40 of VP1. Three-dimensional reconstruction of 135S-P1 showed that P1 binds to a prominent capsid peak known as the "propeller tip". In contrast, our initial 80S-P1 reconstruction showed P1 Fabs also binding to a second site, ~60 Å distant, at the icosahedral twofold axes. Analysis of 80S-P1 reconstructions showed that the overall population of 80S-P1 particles consisted of three kinds of capsids: those with P1 Fabs bound only at the propeller tips; only at the twofold axes; or simultaneously at both positions. Our results indicate that, in 80S particles, a significant fraction of VP1 can deviate from icosahedral symmetry. Similar deviations from icosahedral symmetry may be biologically significant during other viral transitions. "C3" antibody binds to 93-103 residues (BC loop) of VP1. The C3 epitope shifts outwards in radius by 4.5% and twists through 15° in the 160S-to-135S transition, but appears unchanged in the 135S-to-80S transition. In addition, binding of C3 to either 160S or 135S particles causes residues of the BC loop to move an estimated 5 (±2) Å, indicating flexibility. The flexibility of BC loop may play a role in cell-entry interactions. At 37°C, the structure of poliovirus is dynamic, and internal polypeptides VP4 and the N-terminus of VP1 externalize reversibly. An antibody, binding to the residues 39-55 of VP1, was utilized to track the location of the N-terminus of VP1 in 160S particle in the "breathing" state. The resulting reconstruction showed the capsid expands similarly to the irreversibly altered 135S particle, but the N-terminus of VP1 is located near the twofold axes, instead of the propeller tip as in 135S particles.

L'infection par le virus de l'hépatite C (VHC) est un problème de santé publique majeur car en absence de vaccin et de thérapie suffisamment efficace, l’infection peut dégénérer en carcinome hépatocellulaire. Il est alors important d’identifier de nouvelles cibles thérapeutiques et de développer de nouveaux antiviraux. Ainsi, nous avons étudié l'activité anti-VHC de différents composés : l'arbidol (Arb), la silymarine (SM) et les molécules la composant, notamment la silibinine (SbN). Ces composés ont l'avantage d'être déjà utilisés en médecine humaine depuis de nombreuses années et ont ainsi prouvé leur innocuité. Ils présentent un large spectre antiviral et inhibent plusieurs étapes du cycle viral, dont la fusion membranaire. Cette étape du cycle est intéressante à cibler car le virus serait bloqué précocement, avant de provoquer des dommages cellulaires.Nous avons approfondi notre connaissance du mécanisme d'inhibition de la fusion par Arb en montrant par différentes stratégies qu'il s'associe avec les phospholipides à l'interface membranaire et interagit avec des résidus aromatiques. Cela suggère que Arb pourrait former durant le processus de fusion un complexe entre glycoprotéine virale et membrane, permettant d'inhiber les changements conformationnels de la glycoprotéine, nécessaires à la fusion. De même SM et ses composés inhibent la fusion de pseudoparticules de HCV, probablement en stabilisant les membranes impliquées dans le processus. Enfin, nous avons observé une activité antivirale et anti-inflammatoire très différente entre deux formulations de SbN. Tous ces résultats sont discutés dans le contexte actuel d'un arsenal thérapeutique anti-HCV qui reste limité. / Infection by the hepatitis C virus (HCV) is a major public health problem since the infection can lead to hepatocellular carcinoma in the current absence of vaccine and effective treatment. It is therefore important to identify new therapeutic targets and to develop novel antiviral drugs. Here we studied the anti-HCV activity of two compounds : arbidol (Arb), the herbal extract silymarin (SM) and molecules therein, including silibinin (SbN). These compounds are already in use in human medicine for several years and have proven safety. They display a broad antiviral spectrum and inhibit several steps of the virus life cycle, including membrane fusion. This step is very interesting to target, since the virus could be blocked upstream the cellular damages it could induce. Using different biophysical strategies, we showed that Arb associates with phospholipids at the membrane interface and interacts with aromatic residues. This suggests that Arb could form during the fusion process a complex between viral glycoprotein(s) and membrane, leading to the inhibition of the conformational changes within the glycoprotein that are required during the fusion process. SM and its components inhibit fusion of HCV pseudoparticles, probably by stabilizing the membranes involved in this process. Finally, we observed different antiviral and anti-inflammatory activities between two different formulations of SbN. Knowledge of these antiviral mechanisms should lead to innovative therapeutic strategies against HCV.

Le virus de l'hépatite C (HCV) infecte environ 180 millions de personnes à travers le monde. De nouveaux antiviraux ont récemment été mis sur le marché mais ils présentent des effets indésirables. La recherche de nouvelles cibles thérapeutiques reste donc d'actualité. Mes principaux travaux ont consisté à développer des approches de biochimie et d'imagerie sur cellules vivantes pour étudier les mécanismes moléculaires d'action des antiviraux silibinine (SbN) et arbidol (ARB) sur HCV. Nous avons montré que SbN et ARB inhibent des vésicules entourées de clathrine et ne sont pas délivrés aux endosomes précoces. SbN et ARB inhibent également l'infection d'autres virus entrant par endocytose clathrine-dépendante, ce qui expliquerait leur activité à large spectre. J'ai également contribué à un projet initié depuis quelques mois au sein de l'équipe. L'hypothèse était qu'un élément présent dans le microenvironnement hépatique (MEH) jouerait un rôle essentiel dans l'infection par HCV. Nous nous sommes intéressés au syndécan-1 (SDC1) car il est fortement exprimé à la surface des hépatocytes. Nos travaux montrent que la déplétion de SDC1 diminue fortement l'infection. SDC1 colocalise à la surface des hépatocytes non infectés avec CD81, un récepteur connu de HCV. Dans les jours suivant l'infection, cette colocalisation est perturbée. Ces données suggèrent que SDC1 serait un co-facteur d'entrée de HCV, agissant en combinaison avec CD81, et que l'infection réorganiserait les molécules du MEH, ce qui pourrait à long terme contribuer à la persistance de l'infection / Hepatitis C virus (HCV) is a global health concern infecting 170 million people worldwide. New antivirals recently received the approval for the treatment against HCV infection but they display many side effects. Research for new therapeutic targets therefore remains an important topic. My main work was to develop approaches in biochemistry and live cell imaging to study the molecular mechanisms of action of antivirals silibinin (SbN) and arbidol (ARB) on HCV infection. We show that SbN and ARB alter clathrin-mediated endocytosis. Viral particles are trapped in clathrin-positive structures and cannot be delivered to the early endosomal compartment, thereby preventing infection. SbN and ARB also prevent cell infection by viruses that enter through clathrin-mediated endocytosis, which could explain their broad spectrum activity. I also contribute to a project initiated for a few months in the lab. We hypothsized that a molecule present in the immediate surrouding of the hepatocyte microenvironment could play a role in HCV infection. We focused on the syndecan-1 (SDC1) because it is essentially anchored on the surface of hepatocytes. We show that SDC1 depletion leads to a drastic decrease of the viral infectivity. SDC1 colocalizes on the unfected hepatocyte surface with the already identified HCV recptor CD81. This colocalization vanished within days in infected cells. These data suggest that SDC1 could act as a cellular co-factor for HCV entry, in combination with CD81; thus infection could reorganized molecules of the hepatocyte microenvironment and contribute to HCV hepatotropism and the peristence of infection

Die Fusionsreaktion des Coronavirus MHV wird vom S-Protein vermittelt. In der vorliegenden Arbeit wurde der Eintrittsweg von MHV-A59 in Mauszellen untersucht. Die Infektivität kann durch lysosomotrope Substanzen und Inhibitoren der Clathrin-abhängigen Endozytose gehemmt werden. Der Eintritt von MHV-A59 in Mauszellen erfolgt über die Clathrin-abhängige Endozytose und setzt die anschließende Fusion der viralen und zellulären Membran bei niedrigem pH-Wert voraus. Fluoreszenzmikroskopische Studien zur Interaktion fluoreszenzmarkierter MHV-A59 Partikel mit Mauszellen bestätigen, dass MHV-A59 über Endozytose aufgenommen wird. Nach Bindung der Viren an die Zellen und anschließende Erniedrigung des pH-Wertes kommt es zur Färbung der Plasmamembran. Die Erniedrigung des pH-Wertes in Abwesenheit des Rezeptors führt zu einer irreversiblen Konformationsumwandlung im viralen Fusionsprotein, die die Inaktivierung der Fusionsaktivität und den Verlust der Infektivität zur Folge hat. Die Ergebnisse deuten auf die Beteiligung des endozytotischen Weges für den viralen Eintritt von MHV-A59 hin. Ein niedriger pH-Wert eines zellulären endosomalen Kompartiments induziert vermutlich die Konformationsänderung im S-Protein und löst die Fusionsreaktion aus. Ein vorläufiges 3D-Modell des S-Proteins von MHV-A59 konnte erstellt werden. Darüber hinaus wurde die Struktur und Fusionsfähigkeit des S-Proteins von SARS-CoV analysiert. Ein Zell-Zell-Fusionsassay konnte nachweisen, dass die Fusion zwischen S-Protein und ACE2-exprimierenden Zellen sowohl abhängig vom pH-Wert als auch von der proteolytischen Spaltung in S1- und S2-Untereinheit ist und durch Erniedrigung des pH-Wertes zusätzlich verstärkt werden kann. Im abschließenden Teil der Arbeit wurde auf Basis theoretischer Untersuchungen eine Vorhersage des mutmaßlichen Fusionspeptids des S-Proteins von MHV-A59, welches alle wesentlichen Merkmale eines internen Fusionspeptids aufweist, vorgenommen. Es liegt nahe der "Heptad-Repeat" (HR) Domäne HR1. / Fusion of the Coronavirus MHV-A59 is mediated by the viral S-protein. The entry pathway of MHV-A59 into murine cells was studied in this work. Infection was strongly inhibited by lysosomotropic compounds and substances interfering with clathrin-dependent endocytosis, suggesting that MHV-A59 is taken up via endocytosis and delivered to acidic compartments. Fluorescence microscopy of labeled MHV-A59 confirmed that the virus is taken up via endocytosis. When the virus was bound to cells and the pH was lowered to 5.0, we observed a strong labeling of the plasma membrane. Electron microscopy revealed low pH triggered conformational alterations of the S-ectodomain. These alterations are likely to be irreversible because low pH-treatment of viruses caused an irreversible loss of fusion activity. The results imply that endocytosis plays a major role in MHV-A59 infection and that the acidic pH of the endosomal compartment triggers a conformational change of the S-protein mediating fusion. Furthermore the conformation of the trimeric spike protein of the murine hepatitis virus A59 was characterized by cryoelectron microscopy. A preliminary 3D-reconsruction of the native structure could be accomplished. Besides we studied the structure and fusion capability of the spike protein expressed by SARS-CoV. The cell-based fusion assay revealed that fusion of spike protein and ACE2-receptor expressing cells was strongly dependent on low pH and on proteolytic cleavage of the S-protein into S1 and S2 subunit. Additionally fusion could be significantly increased by lowering of the pH. The theoretical part of the thesis allowed the identification of the putative fusion peptide, which showed main characteristics of internal fusion peptides. It allows the heptad regions of the spike protein to assemble in the six-helix bundle structure (6HB). This structure is of great importance to initiate the approximation of viral and cellular membrane and thus to induce fusion.