In vitro neutralisation of Zika virus by an engineered protein targeting the viral envelope fusion loop

The development of therapeutics against Zika virus (ZIKV) requires the design of molecules capable of neutralising the virus and preventing cell infection. Among the known ZIKV epitopes for neutralising antibodies, the fusion loop (FL), located in the envelope (E) protein, is of particular interest since it mediates the first step of cell infection, and it is highly conserved among flaviviruses. Here, small synthetic proteins were computationally engineered to bind to the ZIKV FL with high affinity. The candidate with the highest predicted affinity was experimentally synthesised. It binds to its target epitope with high affinity, either in the context of the E protein or within the whole virus. The protein also showed cross-reactive neutralising capacity against ZIKV and dengue virus 1 and 2 in vitro. X-ray crystallography was used to validate the computational design, as well as to offer additional insights into the structural basis of flavivirus neutralisation targeting the FL envelope protein.