The global pandemic may be over, but SARS-CoV-2 continues to infect people around the world. Indeed, the United States has recorded roughly 750 deaths from COVID-19 over the past month.

Now, an siRNA screen performed by scientists at Scripps Research has pinpointed dozens of human proteins that SARS-CoV-2 uses to complete its replication cycle. These findings could open the door to new drugs that target host proteins rather than the virus. This strategy may lead to new treatments effective against SARS-CoV-2 and other coronaviruses, even as the pathogens continue to evolve.

This work is published in PLOS Biology in the paper, “Global siRNA screen identifies human host factors critical for SARS-CoV-2 replication and late stages of infection.”

The team used genome-wide siRNA screening to uncover the human proteins that SARS-CoV-2 relies on. Unlike the pooled genome-scale CRISPR libraries that have been done in the past, the screening method used here can individually inhibit human genes in cells that are susceptible to SARS-CoV-2, revealing which proteins the virus requires to replicate. The team uncovered 32 proteins essential for the earliest stages of infection, 27 proteins that the virus uses later, as well as cellular pathways it exploits—some previously known and others newly discovered.

The authors write that the work revealed: “common pathways that were identified in all OMICs datasets—including regulation of Wnt signaling and gap junctions, pathways uniquely identified in this screen—including NADH oxidation, and pathways supported by this screen and proteomics data but not published functional screens—including arachidonate production and MAPK signaling.”

“By identifying the human proteins that coronaviruses rely on, we can now think about developing the next generation of pan-coronavirus therapies—treatments that could be effective not just against today’s SARS-CoV-2, but even a future SARS-CoV-3. Because these strategies target the host, they’re also less likely to be undermined by viral mutations and drug resistance,” notes Sumit Chanda, PhD, a professor of immunology and microbiology at Scripps Research.

Two proteins emerged as promising drug targets. The first is the large extracellular matrix protein perlecan. The research team discovered that SARS-CoV-2’s spike protein can latch directly onto perlecan’s sugar chains. “Perlecan could be acting almost like a co-receptor for the virus,” says Laura Martin-Sancho, PhD, who was formerly a staff research scientist at Scripps Research and is now an assistant professor of molecular virology at Imperial College London. “If we can target that interaction, we may be able to stop infection right at the door.”

The second protein, Baculoviral IAP Repeat Containing 2 (BIRC2), is part of a cellular inflammation pathway. In cultures of human cells and in mice infected with SARS-CoV-2, drug compounds known as second mitochondria-derived activators of caspases (Smac) mimetics—originally developed to trigger cell death in cancer and to activate dormant HIV so it can be targeted by the therapy—successfully inhibited BIRC2, slashing viral levels in an animal model.

The team tested the same human proteins against three other coronaviruses: SARS-CoV-1, MERS-CoV and a seasonal coronavirus. Of the 47 proteins tested, 17 were consistently used by all three viruses, including proteins that help viruses fuse with cells, copy themselves, and exit to infect new cells. This suggests that blocking human proteins the viruses depend on could form the basis of drugs effective against past, current, and potentially future pandemic coronaviruses.

“If we have such antivirals ready ahead of time, we could deploy them early in a future coronavirus outbreak,” points out Chanda. “That gives us a higher barrier to resistance and the potential to block multiple viruses with a single therapy.”

Next, the researchers plan to explore whether the same host proteins are also used by other respiratory pathogens such as influenza and RSV. They’ll also continue testing the safety and efficacy of promising compounds in future studies.