Structure of Rhinovirus A9 and Infection Inhibition with Benzene Sulfonamide Derivatives

Rhinovirus infections cause the common cold, for which there is no cure. The consequences of the disease are mainly seen as absence from school or work, as the disease is usually mild, self-limiting and symptoms disappear in a few days, but infections can also lead to severe asthma exacerbations and hospitalization. This research is based on earlier findings of benzene sulfonamide derivative compounds that inhibited a broad range of enteroviruses by binding to a newly identified capsid pocket. Here, four promising compounds were tested against four different rhinoviruses belonging to Rhinovirus A and B species in a cell-based inhibition assay. After identification of a potential inhibitory compound against rhinovirus A9 and rhinovirus B14, a rhinovirus A9 homology model was generated, and then the binding was predicted with computational analysis using the rhinovirus A9 homology model and the published structure for rhinovirus B14. As the same compound has previously been shown to bind and inhibit coxsackievirus B4, this virus was used a control. Thermal stability testing of rhinovirus A9 revealed that the virus survives heat treatment up to at least 58°C, in contrast to previously published results. An efficient rhinovirus A9 purification protocol was established and high- quality cryo electron microscopy data were collected for structure determination of rhinovirus A9, which resulted in a 3.1 Å resolution map. The map was used for building the first atomic model of rhinovirus A9. The atomic model revealed that rhinovirus A9 has the expected T=1, pseudo T=3 capsid structure composed primarily of the three β-barrel proteins VP1, VP2 and VP3, with VP4 between the inside of the capsid and the RNA genome. The model confirmed the presence of the interprotomer pocket and VP1 pocket, although density for lipid factor was not detected. The final atomic model was compared to the homology model and used for comparative docking of the inhibitory compound to the pocket. The results revealed that empirical structure determination is still more accurate for large macromolecule complexes than modelling and that empirical data of the binding is required for reliable computational work