Article
Author: Freedman, Benjamin S. ; Thomson, Christy A. ; Green, Lydia B. ; Yeh, Hsien-Wei ; Boyken, Scott E. ; Krüger, Antje ; Stewart, Lance ; Bloom, Jesse D. ; Ueda, George ; Chow, Cameron M. ; Chen, Rita E. ; Cao, Longxing ; Edman, Natasha ; Bowen, John E. ; Hunt, Andrew C. ; Zhao, Yan Ting ; Liu, Zhuoming ; VanBlargan, Laura A. ; Gale, Michael ; Ruohola-Baker, Hannele ; Johnson, Max ; Matochko, Wadim L. ; Saini, Shally ; Diamond, Michael S. ; Whelan, Sean P. J. ; Kozodoy, Lisa ; Baker, David ; Carter, Lauren ; Vögeli, Bastian ; Navarro, Mary-Jane ; Ravichandran, Rashmi ; Park, Young-Jun ; Hsiang, Tien-Ying ; Wu, Kejia ; Addetia, Amin ; Case, James Brett ; Bailey, Adam L. ; Veesler, David ; Walls, Alexandra C. ; Helms, Louisa ; Ljubetič, Ajasja ; Goreshnik, Inna ; Panpradist, Nuttada ; Kafai, Natasha M. ; Starr, Tyler N. ; Jewett, Michael C. ; Ying, Baoling
New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the coronavirus disease 2019 (COVID-19) pandemic. Here, we used a cell-free expression workflow to rapidly screen and optimize constructs containing multiple computationally designed miniprotein inhibitors of SARS-CoV-2. We found the broadest efficacy was achieved with a homotrimeric version of the 75-residue angiotensin-converting enzyme 2 (ACE2) mimic AHB2 (TRI2-2) designed to geometrically match the trimeric spike architecture. Consistent with the design model, in the cryo-electron microscopy structure TRI2-2 forms a tripod at the apex of the spike protein that engaged all three receptor binding domains simultaneously. TRI2-2 neutralized Omicron (B.1.1.529), Delta (B.1.617.2), and all other variants tested with greater potency than the monoclonal antibodies used clinically for the treatment of COVID-19. TRI2-2 also conferred prophylactic and therapeutic protection against SARS-CoV-2 challenge when administered intranasally in mice. Designed miniprotein receptor mimics geometrically arrayed to match pathogen receptor binding sites could be a widely applicable antiviral therapeutic strategy with advantages over antibodies in greater resistance to viral escape and antigenic drift, and advantages over native receptor traps in lower chances of autoimmune responses.