Cytokine storms are potentially life-threatening overreactions of the immune system provoked by viral infection and other “threats.” Two key players are cytokines interleukin-6 (IL-6) and interleukin-1 (IL-1). Currently available inhibitors of IL-6 and IL-1 relieve the cytokine storm associated with rheumatoid arthritis, but not with COVID-19.
Now, scientists from the University of Washington have computationally designed protein inhibitors that may prevent the COVID-19-related cytokine storm. X-ray crystallography revealed a near-perfect match between the computational designs and their real-life counterparts, which blocked the cytokine storm in a human heart organoid. This suggests that computational design has the power to create entirely new proteins that function as viable therapeutics against the cytokine storm associated with COVID-19.
Researchers used the resources of the Advanced Photon Source (APS), a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory.
Cytokine storm became a household term during the COVID-19 pandemic. Also known as cytokine release syndrome (CRS), this process happens when the immune system grossly overreacts to a threat and produces too many inflammatory immune cells. A cytokine storm can also be triggered by certain autoimmune diseases and CAR-T cell therapy.
The major players in a cytokine storm are cytokines IL-6 and IL-1. They bind to receptors on the surface of inflammatory immune cells, among others, sending signals to the cell’s DNA. These signals may activate the cell, amplify production of more inflammatory cells, or recruit cells to various locations. During a cytokine storm associated with COVID-19, too many inflammatory cells are activated and directed to the lungs and heart, where they can destroy tissue and cause fatal organ failure.
Binding is essential to the signal being sent; if there is no binding, there is no signal, and no cytokine storm. A few drugs on the market currently inhibit IL-6 and IL-1 binding, but they are better suited for long-term conditions like rheumatoid arthritis rather than short-term, acute events like COVID-19. To fill the void, a team of scientists led by 2024 Nobel Prize winner David Baker set out to design proteins from scratch that could effectively inhibit IL-6 and IL-1 binding.
Both IL-6 and IL-1 rely on a third protein—GP130 in the case of IL-6, and an accessory protein in the case of IL-1—to send a signal when they bind with their receptors. The scientists used Rosetta, a proprietary protein design program, to create inhibitors that would occupy (a) binding sites on the IL-6 receptor, (b) the site on GP130 where IL-6 and its receptor would bind, and (c) the site on IL-1 where it would bind to both its receptor and the accessory protein.
After generating their initial designs, the scientists tweaked them to improve the structure and amino acid sequence, then chose the top 100,000 candidates to test experimentally. First, they expressed the designs as real-life proteins in yeast cells. Then they optimized binding affinity by mutating each of the amino acids in the proteins. Finally, they used E. coli to express the optimized proteins.
Read more on APS website
Image: Advances in computational design tools now enable functional proteins to be created from scratch.