A new protein-based antiviral nasal spray developed by Baker lab researchers in collaboration with scientists Northwestern University, UW Medicine, and Washington University at St. Louis is being advanced toward Phase I human clinical trials to treat COVID-19.
Designed computationally and refined in the laboratory, the new protein therapies thwarted infection by interfering with the virus’ ability to enter cells. The top protein neutralized the virus with similar or greater potency than antibody treatments with Emergency Use Authorization status from the U.S. Food and Drug Administration (FDA). Notably, the top protein also neutralized all tested SARS-CoV-2 variants, something that many clinical antibodies have failed to do.
When administered to mice as a nasal spray, the best of the new antiviral proteins reduced symptoms of infection — or even prevented infection outright.
The findings were published this week in the journal Science Translational Medicine.
To begin, the team first used supercomputers to design proteins that could stick to vulnerable sites on the surface of the novel coronavirus, targeting the spike protein. This work was originally reported in 2020 in the journal Science.
In the new work, the team reengineered the proteins — called minibinders — to make them even more potent. Rather than targeting just one site of the virus’ infectious machinery, the minibinders simultaneously bind to three sites, making the drug less likely to detach.
“SARS-CoV-2’s spike protein has three binding domains, and common antibody therapies may only block one,” said co-senior author Michael Jewett. “Our minibinders sit on top of the spike protein like a tripod and block all three. The interaction between the spike protein and our antiviral is among the tightest interactions known in biology. When we put the spike protein and our antiviral therapeutic in a test tube together for a week, they stayed connected and never fell apart.”
Jewett is a professor of chemical and biological engineering at Northwestern’s McCormick School of Engineering and director of Northwestern’s Center for Synthetic Biology.
As the SARS-CoV-2 virus has mutated to create new variants, some treatments have become less effective in fighting the ever-evolving virus. Just last month, the FDA paused several monoclonal antibody treatments, for example, due to their failure against the BA.2 omicron subvariant.
Unlike these antibody treatments, which failed to neutralize omicron, the new minibinders maintained potency against the omicron variant of concern. By blocking the virus’ spike protein, the new antiviral prevents it from binding to the human angiotensin-converting enzyme 2 (ACE2) receptor, which is the entry point for infecting the body. Because the novel coronavirus and its mutant variants cannot infect the body without binding to the ACE2 receptor, the antiviral also should work against future variants.
Korea’s SK bioscience has announced that it will initiate preclinical development of an antiviral nasal spray for preventing COVID-19 based on similar designed minibinder technology first developed in the Baker lab.
The new study, “Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice,” was supported by The Audacious Project at the Institute for Protein Design; Bill & Melinda Gates Foundation (OPP1156262, INV-004949); Burroughs Wellcome Fund; Camille Dreyfus Teacher-Scholar Program; David and Lucile Packard Foundation; Helen Hay Whitney Foundation; Open Philanthropy Project; Pew Biomedical Scholars Award; Schmidt Futures; Wu Tsai Translational Investigator Fund; Howard Hughes Medical Institute, including a fellowship from the Damon Runyon Cancer Research Foundation; Department of Defense (NDSEG-36373, W81XWH-21-1-0006, W81XWH-21-1-0007, W81XWH-20-1-0270-2019, AI145296, and AI143265); Defense Advanced Research Project Agency (HR0011835403 contract FA8750-17-C-0219); Defense Threat Reduction Agency (HDTRA1-15-10052, HDTRA1-20-10004); European Commission (MSCA CC-LEGO 792305); National Institutes of Health (1P01GM081619, R01GM097372, R01GM083867, T32GM007270, S10OD032290); National Institute of Allergy and Infectious Diseases (DP1AI158186, HHSN272201700059C, R37 AI1059371, R01 AI145486); National Institute of Diabetes and Digestive and Kidney Diseases (R01DK117914, R01DK130386, U01DK127553, F31DK130550); National Institute of General Medical Sciences (R01GM120553); NHLBI Progenitor Cell Biology Consortium (U01HL099997, UO1HL099993); National Center for Advancing Translational Sciences (UG3TR002158); United World Antiviral Research Network; Fast Grants; T90 Training Grant; and with federal funds from the Department of Health and Human Services (HHSN272201700059C).