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Protein Sequences Yield Clues About How Coronavirus Hijacks Cells

SARS-CoV2 engulfing a cell
SARS-CoV-2 (yellow) may use some amino acid sequences called SliMs to enter and hijack cells. | NIAID

SARS-CoV-2 — the virus that causes COVID-19 — may enter and replicate in human cells by exploiting newly-identified strings of amino acids within cellular proteins, according to work from two teams of scientists published in the January 12 issue of Science Signaling.

Although researchers know broadly how the virus enters human cells, the molecular mechanisms have remained murky. The two new research papers paint a more complete portrait of the exact cellular processes that SARS-CoV-2 targets to not only enter cells, but to then multiply and spread.

The scientists also compiled a collection of drugs that could potentially be repurposed to disrupt the interactions between the virus and its protein targets within cells. The collection could aid the development of new treatment strategies for patients with COVID-19, although studies in cells and animal models are needed.

As the COVID-19 pandemic approaches its second year, scientists have made large strides in understanding the biology of the disease and of SARS-CoV-2. For example, researchers now know that SARS-CoV-2 binds with the ACE2 protein receptor on the surface of human cells, after which it enters the cell through a process known as endocytosis.

These discoveries have informed the development of new vaccines based on the spike protein, a section of the virus that binds with ACE2. However, researchers are still uncertain about whether the virus might target other proteins besides ACE2 to gain entry, as well as exactly how SARS-CoV-2 replicates once it has entered cells.

Understanding the Virus Targets

Previous experiments have suggested that coronaviruses may hijack or interfere with a form of cellular housekeeping called autophagy by interacting with other proteins called integrins on the surface of cells.

But as with endocytosis, not much is known about exactly how the virus takes advantage of integrins on the biochemical level to disrupt autophagy, according to Bálint Mészáros, a postdoctoral fellow at the European Molecular Biology Laboratory in Heidelberg, Germany and lead author of the first study.

"In broad outline, it is known how the virus enters and exits cells, how its genetic material is replicated and where new viruses are assembled," he said. "However, the molecular details are largely unknown … [and] little is known about the function of certain parts of ACE2."

Adding to the mystery, it's also unclear how SARS-CoV-2 infects cells that don't have ACE2, such as many of the cells inside of the lungs that the virus invades, according to Mészáros.

"If we knew enough about the proteins that are responsible for these processes, it might be possible to slow them down using appropriate drugs," he said. "Stopping viral entry is thus the first line of defense against the infection."

SARS-CoV-2 micrograph
SARS-CoV-2 virus particles | NIAID

As Mészáros and his team entered lockdown in Heidelberg, they decided to find out as much as they could about the life cycle of SARS-CoV-2. The researchers focused most of their attention on what they call short linear motifs, or SLiMs, which are small sequences of amino acids within proteins that control many processes within cells.

The team had previously developed a database called the Eukaryotic Linear Motif resource, which has become the largest known collection of SLiMs to date. In the new study, they searched through the database for SLiMs that matched sequences of amino acids within the ACE2 protein.

The search revealed that both ACE2 and several integrins contain various SLiMs that play a role in both autophagy and endocytosis in human cells.

The scientists then compiled a list of current experimental treatments and approved drugs that can target the interactions between SARS-CoV-2 and SLiMs. Some examples they identified include chlorpromazine, an approved antipsychotic drug that interferes with endocytosis, and metformin, a well-known diabetes drug that triggers autophagy.

This discovery "creates an opportunity for drugging these interactions, or the processes they control, through treatments directed at the host to prevent viral entry," the researchers concluded.

Lab Results May Empower Viral Research

Excited by their results, Mészáros and colleagues invited another group of researchers led by Johanna Kliche, a researcher at Uppsala University in Sweden, to test their findings in the lab.

Kliche's team performed molecular experiments with isolated protein fragments and showed that two SLiMs in ACE2 identified by Mészáros' team could bind with proteins related to endocytosis. They also discovered that one SLiM in the integrin β 3 bound with two proteins involved in autophagy.

"We are hopeful that this new autophagy motif in integrins could kickstart a new wave of research seeking to understand how integrins function under normal conditions and how they behave in disease," said Mészáros.

In addition to providing a resource for repurposing drugs to treat SARS-CoV-2, Mészáros and colleagues say their prediction methods could help identify similar under-the-radar SLiMs that assist with the replication of other bacteria and viruses, including Salmonella, HIV and the Ebola virus.

They predict that as new SLiMs are identified, they could be passed on to other laboratory groups that work with the related pathogen. This extra information could then inform ongoing efforts to repurpose drugs that can interrupt viral entry or replication within cells — an approach Mészáros referred to as "drugging the cell to cure the pathogen".