A single-molecule atomic force microscopy study reveals the antiviral mechanism of tannin and its derivatives

Antiviral agents work by stopping or intervening the virus replication. Virus replication is a fast and multi-step process while effective antiviral intervention requires agents to interact with the protein coat, genetic RNA/DNA or both during virus replication. Thus, quantifying these interactions at the molecular level, although it is quite challenging, is very important for an understanding of the underlying molecular mechanism of antiviral intervention. Here, at the single molecule level, we employ single molecule force spectroscopy (SMFS) in combination with AFM imaging and choose tobacco mosaic virus (TMV)/tannin as a model system of tubular virus to directly study how the inhibitor influences the interactions of RNA and coat protein. We illustrated the antiviral mechanism of tannin during the three main stages of TMV infection, i.e., before the entry of cells, the disassembly of genetic RNA and reassembly of genetic RNA, respectively. Our SMFS results show that tannin and its derivatives can stabilize the TMV complex by enhancing the interactions between RNA and coat protein via weak interactions, such as hydrogen bonding and hydrophobic interactions. In addition, the stabilization effect showed molecular weight dependence, i.e., for higher molecular weight tannin the stabilization occurs after genetic RNA gets partially disassembled from the protein coat, while the lower molecular weight tannin hydrolyte starts experiencing the stabilization effect before the RNA disassembly. Furthermore, the cycling stretching-relaxation experiments in the presence/absence of tannin proved that tannin can prevent the assembling of RNA and coat protein. In addition, the AFM imaging results demonstrate that tannin can cause the aggregation of TMV particles in a concentration-dependent manner; a higher concentration of tannin will cause more severe aggregations. These results deepen our understanding of the antiviral mechanism of tannin and its derivatives, which facilitate the rational design of efficient agents for antiviral therapy.