The Science

Pandemics caused by emerging human viruses are a persistent global threat. Current antiviral therapies often fail because they directly target the virus, which rapidly mutates to evade immune responses and treatments. Under the Predictive Phenomics Initiative, researchers at Pacific Northwest National Laboratory (PNNL) pursued an alternative strategy aimed at fortifying host cells against viral takeover. They applied a newer molecular phenotyping workflow, limited proteolysis combined with mass spectrometry (LiP-MS), designed to capture subtle structural changes in cellular proteins following infection. This powerful tool revealed previously undetectable vulnerabilities in lung cell protein complexes exploited by human coronaviruses during replication. By targeting these cellular vulnerabilities, researchers successfully protected host cells against viral takeover.

The Impact

This research marks a paradigm shift in antiviral strategy from directly targeting viruses to fortifying host cells against viral exploitation. Using LiP-MS, researchers revealed critical vulnerabilities in lung cell protein complexes that human coronaviruses hijack for replication. This tool enables researchers to pinpoint key molecular control points within cells, allowing for prediction and control of cellular responses. LiP-MS is broadly applicable and is already being leveraged to explore cellular responses to toxic chemical exposures and microbial adaptation to changing environments. By revealing how structural changes in proteins occur under varied conditions, this approach will accelerate therapeutic discovery and deepen our understanding of a variety of molecular phenotypes.

Summary

Proteins orchestrate the cellular processes that enable them to respond to environmental challenges, such as viral infections. Traditionally, PNNL researchers have studied these phenotypic changes by measuring changes in protein abundance using PNNL’s fleet of advanced mass spectrometers. However, proteins are highly dynamic, shifting their shapes to interact with complementary partners and regulate functional pathways within the cell. To capture these structural dynamics, researchers under the Predictive Phenomics Initiative developed a suite of “structural proteomics” tools, such as LiP-MS. Unlike conventional methods, LiP-MS identifies which proteins are undergoing structural changes in response to infection and maps the locations of these alterations.

Using LiP-MS, researchers analyzed protein assemblies in different human lung cells with differing levels of resistance to coronavirus infection. Despite the varied cellular responses, the tool revealed shared vulnerabilities within the cellular protein production complexes that are exploited by the virus. Specifically, the virus shuts down host cell protein production, suppressing immune responses, while hijacking this machinery to synthesize components for new viral progeny. These subtle changes, missed with traditional methods, highlight critical weak points in the host machinery, which researchers targeted to strengthen cellular response. Modulating these assemblies successfully aided the cells in warding off viral infection.

The structural insights from LiP-MS not only provided information on functional responses but also laid a foundation for developing targeted therapies that block viral replication while minimizing side effects. This approach advances our understanding of host-virus interactions and offers a universal framework for combating diverse virus strains through advancements in precision medicine.

Contact

• Snigdha Sarkar, snigdha.sarkar@pnnl.gov, PNNL
• Amy C. Sims, amy.sims@pnnl.gov, PNNL
• John T. Melchior, john.melchior@pnnl.gov, PNNL

Funding

The research described in this paper is part of the Predictive Phenomics Initiative at Pacific Northwest National Laboratory (PNNL) and was conducted under the Laboratory Directed Research and Development Program. PNNL is a multiprogram national laboratory operated by Battelle for the Department of Energy under contract no. DE-AC05-76RL01830.