Using protein structures obtained in part at the Advanced Light Source (ALS), researchers from the University of California San Francisco (UCSF) produced simplified antibodies (“nanobodies”) engineered to be highly effective at blocking SARS-CoV-2, the virus that causes COVID-19. Because they are extremely stable, these nanobodies can be aerosolized, stored at room temperature, and self-administered as needed, directly to affected nasal or lung tissues using nasal sprays or inhalers.
The researchers sifted through over two billion synthetic nanobody sequences available in databases and identified a few most likely to bind to and neutralize the SARS-CoV-2 spike protein—the distinctive protrusions on the coronavirus surface that facilitate entry to a host cell.
To better understand how the nanobodies interact with the spike protein in different conformations, they obtained structural maps of nanobody–spike complexes using cryo-electron microscopy (cryo-EM) at UCSF. In addition, protein crystallography at ALS Beamline 8.3.1 yielded atomic-level close-ups of nanobody regions that directly interact with the spike. In cases where cryo-EM provided inconclusive data, the researchers relied on a relatively new technique called x-ray footprinting at ALS Beamline 3.2.1. This technique provides structural information similar to crystallography, but is done with molecules in solution and doesn’t require protein crystals.
The structural work gave the researchers enough information to optimize the potency of the nanobodies through strategies such as the linking of two or three nanobodies together to attach to the spike at multiple points and the targeted replacement of amino acids to increase nanobody affinity for the spike. They are currently moving forward to the animal testing phase for these synthetic nanobodies, as their combined stability, potency, and multiple modes of action provide a distinctive potential prophylactic and therapeutic approach to limiting the continued toll of the COVID-19 pandemic.
Read more in this ALS Science Highlight.