Viral Protein Analysis Used To Design New Vaccines Against Respiratory Viruses

In most people, the lung-infecting pathogens known as respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) trigger mild cold-like symptoms. But in infants and seniors, these viruses can cause severe pneumonia and even death.

Vaccines against both viruses, however, have been difficult to design. Now, Scripps Research scientists have analyzed the structure and stability of a critical RSV and hMPV protein to better design vaccines that target it. Their research, published in Nature Communications on November 16, 2024, points toward RSV vaccines that may be more effective than existing ones, as well as a vaccine against hMPV, for which there are no commercially available options. 

“Creating a combination vaccine for these viruses could significantly reduce viral hospitalizations for both babies and the elderly,” says study senior author Jiang Zhu, PhD, an associate professor in the Department of Integrative Structural and Computational Biology at Scripps Research. “This could alleviate the overall health burden during flu season, which is also when most RSV and hMPV cases occur.”

Scientists have long attempted to create vaccines that coax the immune system into recognizing the fusion (F) proteins present on the surfaces of RSV, hMPV and related viruses. These proteins play a key role in letting the viruses infect human cells. However, the F protein has a delicate structure that changes rapidly from a “pre-fusion” form to a “post-fusion” form when the viruses fuse with cells. Ideally, a vaccine would teach the immune system to recognize the closed pre-fusion F protein so it could stop infection.

“The problem is that this pre-fusion structure is so fragile and volatile,” says Zhu. “If you change the environment even a tiny bit, the protein is like a transformer that suddenly flips from a car into a robot.”

This means that scientists cannot simply use an isolated pre-fusion F protein as a vaccine—its structure would change too quickly for the immune system to react. And a vaccine targeting the post-fusion version of the protein wouldn’t teach the immune system to attack the virus before it has a chance to infect the body.

Zhu, who has a background in biophysics and has recently designed new vaccines for viruses including HIV, SARS-CoV-2 and hepatitis C, thought that if he could understand the precise mechanism of why the pre-fusion F protein was so unstable, especially why it is so easy to open, he could make a more stable form—and, in turn, a better vaccine.

Zhu and his research team first analyzed the F proteins used in development of four existing RSV vaccines—the commercially available Arexvy, mResvia and Abrysvo, and an experimental vaccine that has reached phase 3 trials. They discovered that some of the pre-fusion F proteins appeared to be unstable and sometimes converted to an open form, or even less desirable, a post-fusion form. A detailed structural analysis revealed an “acidic patch” sitting at the center of the pre-fusion structure with three positively charged molecules repelling each other, ready to push open the RSV F protein at the slightest perturbation, like a spring-loaded transformer.

“This is an incredible trait for a virus to acquire during evolution to control the movement of its key protein,” says Zhu. “Luckily, it’s also something we can overcome, either with brute force or, better, with a smart mutation directly tackling the source of the problem, the acidic patch.”

Zhu reengineered the RSV F protein by changing a pair of molecules at its center, turning the outward repelling force into an attracting one. Then, his team showed that this new F protein was both more stable in the lab and successfully worked to vaccinate mice against RSV.

“This suggests that we might be able to take a similar approach for other viral F proteins,” says Zhu. “At the very least, we can look for similar repulsive patches in their structure as we design vaccines.”

In the hMPV F protein, Zhu didn’t find the same patch of repellant molecules—instead, he used a strong chemical bond as a “brute force” solution to hold the protein together. Once again, the modified protein was stable enough to remain intact as a vaccine.

In future studies, Zhu plans to develop an experimental vaccine using a self-assembling protein nanoparticle (SApNP) platform reported in his recent work to deliver the RSV and hMPV F proteins to the human body. “That would be our next-generation RSV/hMPV combo vaccine,” says Zhu.

Reference: Lee YZ, Han J, Zhang YN, et al. Rational design of uncleaved prefusion-closed trimer vaccines for human respiratory syncytial virus and metapneumovirus. Nat Commun. 2024;15(1):9939. doi: 10.1038/s41467-024-54287-x

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