In a scene not unlike a sci-fi blockbuster, flaviviruses such as dengue and Zika glide through the bloodstream, their spherical outer surfaces cloaked in a layer of flat-lying envelope proteins. Once these viruses invade a host cell and find themselves within an intracellular compartment called an endosome, an acidic trigger causes these viral proteins to morph dramatically, sprouting spikes that pierce the endosome’s membrane.
“These spikes facilitate the fusion of the viral membrane with the endosomal membrane, enabling the virus to release its genetic material into the cytoplasm,” said Peter J. Bond, a Senior Principal Scientist at the Multiscale Simulation, Modelling and Design (MSMD) group within A*STAR’s Bioinformatics Institute (BII).
As this shapeshifting ability poses significant challenges for vaccine development, Bond's team aimed to identify a weak spot—a hidden 'cryptic pocket' on flavivirus envelope proteins that only reveals itself under specific conditions.
To explore the pocket further, Bond and first author, Lorena Zuzic, together with researchers from the National University of Singapore; Pennsylvania State University, US; and University of Manchester, UK; turned to large-scale molecular dynamics (MD) simulations for a high-resolution view of viral protein dynamics in atomic detail.
The team first created digital models, or 'rafts', that represented a significant portion of the flaviviral envelope. By simulating the different pH conditions that the virus encounters from the bloodstream to the cell's interior, the team observed how these proteins form the spikes that facilitate the virus’s entry. To locate potential drug-binding hotspots, the team then introduced benzene probes: tiny molecules that latch onto protein surfaces. This dynamic pocket is otherwise difficult to study with conventional methods due to its transient nature.
“We were able to calculate how these potential drug-binding sites change over time, and could also compare their behaviour across multiple flaviviruses, which could be useful in the context of pan-flavivirus inhibitor development,” said Bond.
A key discovery was a cluster of charge-sensitive particles within the cryptic pocket, which includes amino acids, like histidine, known for their pH-responsive behaviour. This cluster acts as a pH sensor, altering its charge in response to the acidic environment inside the host cell, prompting the virus to rearrange itself for entry.
"Targeting these pockets could allow us to stop the virus at an early stage, potentially preventing the progression to severe disease," said Bond, citing the successful antiviral targeting of viral proteins in the treatment of HIV and hepatitis C.
Bond added that this strategy holds a vast potential not just for flaviviruses, but also for other enveloped viruses that rely on similar mechanisms to invade host cells.
The A*STAR-affiliated researchers contributing to this research are from the Bioinformatics Institute (BII).
