Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice

AC Hunt, JB Case, YJ Park, L Cao, K Wu… - Science translational …, 2022 - science.org
AC Hunt, JB Case, YJ Park, L Cao, K Wu, AC Walls, Z Liu, JE Bowen, HW Yeh, S Saini
Science translational medicine, 2022science.org
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 …
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.
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