Immunity: Designing and validating promising HIV vaccine strategies

Scientists at Scripps Research, IAVI, the Ragon Institute and Moderna, Inc.
have worked together to make important progress
in developing an effective human immunodeficiency virus (HIV) vaccine.

The results of the study were published in
two separate papers by Immunity on September 29, 2022.
The study describes the first step in a vaccine approach designed to promote the production of broadly neutralizing antibodies (bnAbs) — antibodies broad enough to fight and protect against many different variants
of a virus.
By identifying the most promising bnAbs and the human genes needed to make them, as well as designing protein and mRNA vaccine candidates to begin the creation of bnAbs and validate the vaccine candidates, the team is paving the way
for the creation of effective HIV vaccines.

"Our two studies describe a collaborative effort to understand bnAbs genetically and structurally, and ultimately 'reverse engineer' vaccines to induce these bnAbs," said senior author William Schief, PhD, executive director for
vaccine design at the Scripps Research Center's IAVI Neutralizing Antibodies Center.
"HIV has always been one of the hardest viruses to prevent because of its innate ability
to mutate quickly and evade capture by the immune system.
Our team's findings mark a critical step
in overcoming these historic barriers and creating an effective HIV vaccine.
”

Researchers have long studied how a small percentage of people living with HIV make
bnAbs.
Even in these cases, bnAbs do arise during infection, they appear too late to help stop the virus
.
However, researchers have shown that if bnAbs are present before a person is infected with HIV, then it can protect against the virus
.
This observation prompted scientists to try to develop a vaccine that induces bnAbs in healthy individuals, but designing such a vaccine proved difficult
.

The new work by the Scripps Institute, IAVI and Lagan aims to break the ice by carefully selecting the bnAbs to induce and then designing a custom vaccine that induces the immune system to progressively produce the targeted bnAbs
.
The team focused on bnAbs
that bind to the tip of the HIV spike protein, a spike protein similar to SARS-CoV-2.
These apical bnAbs use extremely long rings, called HCDR3 rings, to pierce puncture the spike protein
like a spear.
By binding to the apex of HIV synapes, bnAbs prevent HIV from infecting human cells
.

immunity

The scientists first needed to determine if there were precursor cells
in the general population that eventually led to the production of these potent BNBs.

"Finding the bnab we need is like finding a needle in a haystack," said
Dr.
Zachary Berndsen, co-first author of both papers and an assistant professor of biochemistry at the University of Missouri.
"To make an effective vaccine, we must first find precursor antibodies that can eventually become bnAbs, while also observing whether these precursor antibodies are common enough in the general population to be stimulated," added Berndsen, who was previously a research assistant
in the lab of Scripps Research Institute professor Andrew Ward.

All bnbs develop from a type of white blood cell that produces antibodies, called naïve B cells
.
These B cells are often referred to as "germline" precursors
.
Through bioinformatics analysis of a large database containing 1.
2 billion human antibody sequences, the researchers learned that the two top bnAbs host the most common precursor B cells
.
This discovery prompted the team to focus on developing a vaccine to induce both types of bnAbs
.

Dr.
Jordan Veilles, senior lead scientist and co-first author of the Neutralizing Antibodies Center at the IAVI at Scripps Research Center, said: "Long HCDR3 rings in vertex bnAbs are rare in human antibodies, so one might think that precursors of these vertex bnAbs are also rare
.
" "However, we found that the two top classes of bnAbs had relatively common precursors, so we decided to focus our vaccine design strategy on these two bnAbs
.
"

The researchers then found that the native HIV spike protein did not bind to the germline precursors of the two target bnAbs, meaning that using the native HIV spike protein as a vaccine would not induce the expected bnAb response
.
To solve this problem, the researchers designed a modified HIV spike protein that binds to the germline precursors of two target bnAbs
.
This engineered spike protein acts as a "priming immunogen," where the first shot of the vaccine binds and activates the correct precursor B cells, beginning the process of
producing the desired apical bnAbs.

Co-first author Krystal Ma, a PhD student at the Scripps Research Institute, said: "The first step in designing a vaccine that induces these apical bnAbs is to design a primer immunogen
with a high binding affinity for the right germline precursors.
" "The next step will be to design a range of immunoenhancing gens to mature precursors into bnAbs
.
"

After multiple rounds of design and extensive in vitro testing, combined with a "snapshot" of Ward's cryo-electron microscope, the team provided insight into how the virus would eventually fight back against BABS—and the team succeeded in creating the priming immunogen
.

One last step

Scientists at the Scripps Institute and IAVI, in collaboration with the lab of Dr.
Facundo Batista, associate director of the Lagan Institute, showed that the new immunogen was able to successfully bind germline precursor B cells and elicit the desired response in mice expressing bnAb germline genes at the same
frequency as they would appear in humans.

"This is a very important step because it shows that vaccination with our immunogens can actually elicit a response from
the precursors we target.
" "We also showed that vaccination with unmodified HIV protein could not elicit these responses, proving that our affinity engineering was necessary
.
"

This antibody response has the potential to develop into a bnb that can fight HIV, and scientists will try to achieve this goal
in future studies using different boosting immunogens that are still in the design phase.

"We and our collaborators are building on this approach to develop and test immunogens to drive the later stages of
bnAb maturation," Batista said.

Since a successful vaccine also needs to be feasible from a production standpoint, the team worked with scientists at Moderna to successfully target their germ cells to immunogens to make an mRNA vaccine (similar to a COVID-19 vaccine).

This approach produced a better antibody response in mice than typical vaccine formulations, while also being easier and faster to produce
.

With this validation, the researchers are continuing to refine their vaccine approach and testing it in other models, with the goal of eventually moving into the clinic for human trials
.