Weaknesses in the Spike Protein of SARS-CoV-2 Revealed

The visual features of coronaviruses, namely, nodular protrusions protruding outwards in all directions: spike proteins, are also key to their entry into cells. These spike proteins bind to cells—in the case of SARS-CoV-2, they bind to human cells—thereby triggering infection. To prevent this from happening, scientists around the world are focusing on spike proteins to reveal how they work and find potential weaknesses from them to exploit.

This spike structure itself is actually a spike protein trimer. The presence of a site on top of the spike structure allows SARS-CoV-2 viral particles to bind an enzyme called the ACE2 receptor on the surface of human cells.

Rommie Amaro, a biophysical chemist at the University of California, San Diego, USA, says this site must be located in an "open" or "up" position, bent and ready to bind itself to host cell receptors. An animation published online by Greg Bowman, a biophysicist at Washington University School of Medicine, shows that this looks like a creature opening its chin. But Amaro says an important feature is essentially missing in the pictures of many SARS-CoV-2 spike structures that have been made to date.

This spike structure is covered by sugars called glycan. They are thought to allow this coronavirus to camouflage the human immune system, making it look like a harmless cell because cells are also often covered with sugars. In pictures and three-dimensional models of coronavirus spike structure, these sugars are usually represented as small and thick protrusions, but in fact they are more blurred and hindered than this, Amaro says.

"They protect it like a physical shield," she explains. Indeed, these glycans are so protective that spike proteins may have to bend and protrude just to cross these glycans and bind to ACE2 on the surface of human cells. Any antibody targeting spike structures must insert between these glycans and bind to the spike protein itself.

To simulate which defensive glycans cover the SARS-CoV-2 spike protein, Amaro used mass spectrometry data of spike protein, which were published on March 28 on the preprinted server bioRxiv. This reveals the location of these glycans in greater detail than before.

A recent online animation by Amaro shows how these glycans wrap around spike proteins and shake, which may further affect their ability to block antibodies outside spike structures. In the animation, spike proteins protrude from the lipid membrane of this coronavirus.

Chris Oostenbrink, an expert in molecular modeling at the Austrian University of Natural Resources and Life Sciences, is also conducting similar research work. He explained that his approach involves using a glycan shape database and matching it to the shape of known coronavirus spike structures, which is the molecular puzzle.

"Basically, we put them all up, and we choose the most appropriate model as a representative," he said. A picture constructed by his graduate student, Jan Walther Perthold, shows these glycans as blurred globules covering the spike structure. Like Amaro's model, this reveals how common these glycans are, and they pose a serious obstacle to any antibody that may bind to spike structures.

By mapping the glycan shield, scientists should more easily find the right antibody to cross from the pores of this glycan barrier, Amaro says. For example, a vaccine could be designed that elicits the human immune system to produce antibodies that successfully bind spike structures, disrupt its open mechanism, or otherwise prevent it from binding to ACE2. Amaro suggests that it can be imagined as tapping a wrench into the machine and stopping it.

A special antibody called CR3022 can bind to SARS-CoV-2 spike protein, according to a study published in the April 3 issue of Science. This antibody was isolated as early as 2006 from a patient who recovered from SARS and was able to better target the SARS-CoV virus that led to the 2003 SARS outbreak.

In laboratory tests, the researchers mixed this antibody with SARS-CoV or SARS-CoV-2 in vitro. The antibody failed to neutralize SARS-CoV-2, suggesting that it is not strongly bound to this novel coronavirus. After all, it is an older weapon and is not specific to SARS-CoV-2 targets.

The authors of the Science paper write that they believe that this antibody may still be effective against this novel coronavirus in vivo, but more experiments are needed to prove it.

Jeremy Rossman, a virologist at the University of Kent in the UK (who was not involved in the study), has an interesting research work. He pointed out that these data show how the CR3022 antibody binds this protein slightly below the binding site of the SARS-CoV spike protein to the host cell. This means that it apparently does not act by physically blocking binding. He added, “It is not clear how the antibody neutralizes and prevents the virus.”

Perhaps more hopefully, the researchers found that antibodies isolated from llamas fused with human antibodies could better neutralize SARS-CoV-2, a two-pronged attack. In a paper published on March 28 in the preprint server bioRxiv, they write that this specially designed double antibody effectively prevents its infection by binding to binding sites located at the tips of spike structures in host cells.

These authors also proposed that treatment can be performed by means of a spray that allows the patient to inhale. In this way, these antibodies can be inhaled directly to the site of infection.

There are other ways. Several pharmaceutical companies have initiated projects to develop laboratory cloned antibodies. For example, GlaxoSmithKline is using antibodies isolated from a SARS patient to determine whether they are effective in fighting COVID-19.

Antibodies or other molecules may also hinder SARS-CoV-2 viruses in other ways that target spike structures. For example, they can prevent the human body's furin from interacting with this novel coronavirus. This would be useful because researchers believe that Flynn helps the two subunits of this spike structure separate from each other, a process that allows this virus to break open and enter host cells. Flynn protease happens to be abundant in the human body, which means that we provide an ideal infection environment for SARS-CoV-2. It is possible that there are molecules that can isolate Flynn protease from this virus, and they may prevent this pathogen from entering the human body. Several teams are currently evaluating whether Flynn protease inhibitors can do this.

Akiko Iwasaki, an immunobiologist at Yale University School of Medicine in the United States, said that no matter what method we use to target spike proteins, we need to be careful. Scientists must determine which antibodies can bind to spike structures, but also to ensure that they do not simultaneously trigger a bad immune response. She pointed out that a paper published last year in the journal JCI Insight showed that antibodies in macaques infected with SARS-CoV sometimes exacerbate the disease rather than quell it.

In macaques, an anti-spike protein antibody stimulates blood cells called macrophages, which causes inflammation in the lungs of this primate. These authors noted that patients who died of SARS had similar lung inflammation.

Iwasaki said, “I am concerned that this may be the case in SARS-CoV-2. A truly serious disease does not occur within two weeks. And then the antibody appears.”

If scientists can find antibodies that do not trigger dangerous immune responses, Rossman says, it is possible to provide them to infected patients to help them overcome COVID-19. However, it would be better if we could find a peptide that could prompt the production of such antibodies so that patients could be immunized before they contracted the disease.