Another Angle of Attack

HMS researchers explore protein-based vaccines against COVID-19

Stylized photograph of unlabeled bottles of vaccine
Image: Toshe_O/iStock/Getty Images Plus

This article is part of Harvard Medical School’s continuing coverage of medicine, biomedical research, medical education, and policy related to the SARS-CoV-2 pandemic and the disease COVID-19.

Vaccines play a critical role in helping the world quell the COVID-19 pandemic.

Those already on the market—such as the messenger RNA-based vaccines by Pfizer–BioNTech and Moderna and the adeno-associated virus or AAV-based vaccines by Johnson & Johnson and AstraZeneca—are protecting billions of people from becoming seriously ill or dying from COVID-19.

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But the vaccine story isn’t over. There aren’t yet enough doses to protect everyone willing and able to be vaccinated. Special storage requirements for mRNA vaccines make it difficult or impossible to deliver doses to under-resourced areas of the world. Manufacturing can be complicated and expensive. Emerging viral variants threaten to circumvent hard-won immunity.

And so scientists continue to investigate new strategies for developing vaccines against COVID-19. Among the most anticipated candidates are protein-based vaccines, which have been used for years to protect against diseases such as hepatitis B, whooping cough, and shingles. Experts suspect that these will be cheaper to make and easier to transport than existing COVID-19 vaccines.

Whereas mRNA and AAV-based vaccines use pieces of a virus’s genetic code to teach cells to make proteins that attack the virus, protein-based vaccines provide cells with pieces of viral proteins along with immune-boosting substances.

Protein-based vaccines against SARS-CoV-2, including one by the U.S. company Novavax, are beginning to receive emergency authorization in various countries.

Two more candidates are being developed by Harvard Medical School researchers at Boston Children’s Hospital. Both show promise in mice and in human cell samples, although they are many steps away from being proven safe and effective against COVID-19 in humans.

Both vaccine candidates use a portion of the spike protein called the receptor-binding domain, or RBD—the part that latches onto cells’ angiotensin-converting enzyme 2 (ACE2) receptors.

Each one, however, uses a different method to stimulate an immune response.

Illustration of SARS-CoV-2 receptor-binding domain in blobby pink, attached to an ACE2 receptor in blobby purple
Illustration of the receptor-binding domain (pink) on a SARS-CoV-2 spike protein bound to the ACE2 receptor (blue) on a human cell. Image: vdvornyk/iStock/Getty Images Plus

Alpacas and antigens

A team led by Novalia Pishesha, HMS instructor in pediatrics at Boston Children’s, Thibault Harmand, HMS research fellow in pediatrics at Boston Children’s, and Hidde Ploegh, senior investigator in the Boston Children’s Program in Cellular and Molecular Medicine, attached the RBD to a special kind of antibody derived from alpacas.

This nanobody, smaller than human antibodies, steers the RBD protein segment directly to antigen-presenting cells—key immune cells that then show RBD to other immune cells, stimulating a broader immune response.

Current COVID-19 vaccines are presumed to stimulate antigen-presenting cells, but only indirectly, said Ploegh. “Taking out the middleman and talking directly to antigen-presenting cells is much more efficient,” he said. “The secret sauce is the targeting.”

To target the antigen-presenting cells, the team engineered the nanobodies to recognize and zero in on class II major histocompatibility complex antigens on the cells’ surfaces.

As reported in PNAS, the team’s vaccine elicited strong immune responses against SARS-CoV-2 and its variants in mice, stimulating high amounts of neutralizing antibodies against the RBD protein. It also elicited strong cellular immunity, stimulating the T helper cells that rally other immune defenses.

In tests, the team successfully freeze-dried the vaccine and then reconstituted it without loss of efficacy. It also remained stable and potent for at least seven days at room temperature.

The team has filed a patent on this technology and hopes to engage biotech or pharmaceutical companies to take the vaccine into further testing and eventually a clinical trial.

Adjuvants for older adults

In the Precision Vaccines Program at Boston Children’s, David Dowling, HMS instructor in pediatrics at Boston Children’s, Ofer Levy, HMS professor of pediatrics at Boston Children’s, and colleagues have created a COVID-19 vaccine formulation that may work especially well in older people. It combines the RBD with two vaccine adjuvants: molecules that boost the immune response.

“The RBD protein by itself is poorly immunogenic,” said Dowling. “That’s why people have used the full spike protein, which is harder to produce at scale. With the adjuvants we selected, we were able to make an RBD-based protein vaccine as effective as a full spike-based mRNA vaccine.”

The adjuvants emerged through an exhaustive screening process that compared multiple molecules head-to-head in different combinations. As reported in Science Translational Medicine, two adjuvants—aluminum hydroxide and CpG—proved to be the most successful combination when added to the RBD protein.

Aluminum hydroxide, a commonly used adjuvant, helps vaccine antigens persist longer in the body so the immune system can better detect them. CpG expands the immune response by stimulating Toll-like receptors in the innate immune system.

In tests, the RBD–adjuvant combination elicited strong innate immune responses in white blood cells from older adults, equivalent to those in cells from younger adults.

In mice, it elicited large numbers of neutralizing antibodies across all age groups, similar to current spike-based mRNA vaccines.

In a live challenge, it fully protected elderly mice against SARS-CoV-2 infection.

“Our immunized aged mice still had high levels of functional antibodies nearly a year later,” noted Dowling.

Omicron and on

The omicron variant of SARS-CoV-2 includes 15 genetic mutations in the RBD protein. Whether RBD-based COVID-19 vaccines would protect against it remains to be seen.

“We do not know enough about omicron, so it is difficult to assess its effects on protein-based vaccines,” said Pishesha.

She noted that because her team’s nanobody vaccine induced CD8 T cell responses against a portion of the RBD that remains intact in the omicron strain, the researchers are “cautiously optimistic.”

Dowling noted that his team’s formulation similarly drove a robust T cell and B cell response against the RBD. The researchers are actively investigating the vaccine’s effectiveness against omicron and other variants and expect to have results soon.

Adapted from a Boston Children’s blog post.