It is widely understood that antibodies neutralize viruses by latching onto
their surfaces and blocking them from infecting host cells. But new research
reveals that this barrier method isn’t the only way that antibodies disable
viruses. An international team of researchers led by Penn State has
discovered that antibodies also distort viruses, thereby preventing them
from properly attaching to and entering cells.
“Everybody thinks of antibodies as binding to viruses and blocking them from
entering cells — essentially locking them down,” said Ganesh Anand,
associate professor of chemistry at Penn State. “But our research reveals
for the first time that antibodies may also physically distort viruses, so
they are unable to properly attach to and infect host cells.”
In their study, which published online today (Nov. 30) in the journal Cell,
Anand and his colleagues investigated the interactions between human
monoclonal antibody (HMAb) C10 and two disease-causing viruses: Zika and
dengue. The HMAb C10 antibodies they used had previously been isolated from
patients infected with dengue virus and also had been shown to neutralize
Zika virus.
The researchers used a combination of techniques, including cryogenic
electron microscopy (cryo-EM) to visualize the viruses and
hydrogen/deuterium exchange mass spectrometry (HDXMS) to understand their
movement.
“Cryo-EM involves flash-freezing a solution containing molecules of interest
and then targeting them with electrons to generate numerous images of
individual molecules in different orientations,” explained Anand. “These
images are then integrated into one snapshot of what the molecule looks
like. The technique provides much more accurate pictures of molecules than
other forms of microscopy.”
To document the effects of antibodies on Zika and dengue viruses, the team
collected cryo-EM snapshots of the viruses under conditions of increasing
concentrations of antibodies.
In parallel, the team applied HDXMS, a technique in which molecules of
interest — in this case Zika and dengue virus, along with HMAb C10
antibodies — are submerged in heavy water. Heavy water, Anand explained, has
had its hydrogen atoms replaced with deuterium, hydrogen’s heavier isotopic
cousin.
“When you submerge a virus in heavy water, the hydrogen atoms on the surface
of the virus exchange with deuterium,” he said. “You can then use mass
spectrometry to measure the heaviness of the virus as a function of this
deuterium exchange. By doing this, we observed that dengue virus, but not
Zika virus, became heavier with deuterium as more antibodies were added to
the solution. This suggests that for dengue virus, the antibodies are
distorting the virus and allowing more deuterium to get in. It’s as if the
virus is getting squished and more surface area becomes exposed where
hydrogen can be exchanged for deuterium.”
In contrast, Zika virus did not become heavier when placed in heavy water,
suggesting that its surface, while fully occupied by antibodies, is not
distorted by the antibodies.
Anand explained that by combining cryo-EM and HDXMS, the team was able to
get a comprehensive picture of what happens when antibodies attach to Zika
and dengue viruses.
“It’s like those cartoon flipbooks, where each page has a slightly different
image, and when you flip through the book, you see a short movie,” he said.
“Imagine a flipbook with drawings of a racehorse. Cryo-EM shows you what the
racehorse looks like and HDXMS shows you how fast the racehorse is moving.
You need both techniques to be able to describe a racehorse in motion. This
complementary set of tools enabled us to understand how one type of antibody
differentially affects two types of viruses.”
He noted that the fact that the more antibodies they added, the more
distorted the dengue virus particles became, suggests that stoichiometry —
the relationship between the quantities of the reactants and the products
before, during and after a chemical reaction — matters.
“It’s not enough to just have antibodies present,” he said. “How much
antibody you add determines the extent of neutralization.”
In fact, the team found that at saturating conditions, in which antibodies
were added at high enough concentrations to fill all the available binding
locations on the dengue viruses, 60% of the virus’ surfaces became
distorted. This distortion was enough to protect the cells from infection.
“If you have enough antibodies, they will distort the virus particle enough
so that it’s preemptively destabilized before it even reaches its target
cells,” Anand said.
Indeed, when the scientists incubated the antibody-bound dengue viruses with
BHK-21 cells, a cell line from the kidneys of baby hamsters that is often
used in viral infection research, they found that 50%-70% fewer cells were
infected.
Anand explained that with some viruses, including Zika, antibodies work by
jamming the exits so the passenger cannot get out of the car.
“We have found a new mechanism in dengue virus whereby antibodies basically
total the car so it cannot even travel to a cell,” he said.
How are the antibodies distorting the dengue virus particles?
Anand explained that contrary to the now-familiar SARS-CoV-2, which has
spike proteins protruding in all directions, the surfaces of both Zika and
dengue are smoother with peaks and valleys.
Anand noted that for dengue virus, antibodies especially prefer binding the
‘peaks’ known as five-fold vertices. Once all the proteins on the five-fold
vertices have been bound, antibodies will turn to their second-favorite
peaks — the three-fold vertices. Finally, they are left with only the
two-fold vertices.
“Antibodies do not like two-fold vertices because they are very mobile and
difficult to bind to,” said Anand. “We found that once the five- and
three-fold vertices have been fully bound with antibodies, if we add more
antibodies to the solution, the virus starts to shudder. There’s this
competition taking place between antibodies trying to get in and the virus
trying to shake them off. As a result, these antibodies end up burrowing
into the virus rather than binding onto the two-fold vertices, and we think
it’s this digging into the virus particle that causes the virus to shake and
distort and ultimately become nonfunctional.”
What is the difference between Zika and dengue?
Anand explained that Zika is a much more stable, less dynamic virus than
dengue, which has a lot of moving parts.
“Dengue and Zika look similar but each one has a different give. Dengue may
have evolved as a more mobile virus as a way of avoiding being caught by
antibodies. Its moving parts confuse and throw off the immune system.
Unfortunately for dengue, antibodies have evolved a way around this by
burrowing into the virus and distorting it.”
It appears, he said, that the same type of antibody can neutralize Zika and
dengue in two different ways — one where it binds to the virus and
deactivates it, which is the traditional way we think about antibody
activity, and the other where it burrows in and distorts the virus.
What about other viruses?
Anand said the distortion strategy his team discovered may be used by
antibodies when they are confronted with other types of viruses as well.
“Dengue is just a model virus that we used in our experiments, but we think
this preemptive destabilization strategy may be broadly applicable to any
virus,” he said. “It may be that the antibodies first attempt to neutralize
viruses through the barrier method and if they are unsuccessful, they resort
to the distortion method.”
Are there any potential applications of the findings?
The findings could be useful in designing therapeutic antibodies, Anand
said.
“HMAb C10 antibodies are specific to dengue and Zika viruses, and happen to
be capable of neutralizing Zika and dengue viruses in two different ways,”
he said. “But you could potentially design therapeutics with the same
capabilities for treating other diseases, such as COVID-19. By creating a
therapeutic with antibodies that can both block and distort viruses, we can
possibly achieve greater neutralization.”
He added, “You don’t want to wait for a virus to reach its target tissue, so
if you can introduce such a therapeutic cocktail as a nasal spray where the
virus first enters the body, you can prevent it from even entering the
system. By doing this, you may even be able to use less antibody since our
research shows that it takes less antibody to neutralize a virus through the
distortion method. You can get better bang for the buck.”
Overall, Anand stressed that the importance of the study is that it reveals
an entirely new strategy that some antibodies use to disable some viruses.
“Previously, all we knew about antibodies was that they bind and neutralize
viruses,” he said. “Now we know that antibodies can neutralize viruses in at
least two different ways, and perhaps even more. This research opens the
door to a whole new avenue of exploration.”
Reference:
Xin-Xiang Lim, Bo Shu, Shuijun Zhang, Aaron W.K. Tan, Thiam-Seng Ng, Xin-Ni
Lim, Valerie S.-Y. Chew, Jian Shi, Gavin R. Screaton, Shee-Mei Lok, Ganesh
S. Anand. Human antibody C10 neutralizes by diminishing Zika but enhancing
dengue virus dynamics. Cell, 2021;
DOI: 10.1016/j.cell.2021.11.009
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