De novo design of picomolar SARS-CoV-2 miniprotein inhibitors
View ORCID ProfileLongxing Cao1,2, Inna Goreshnik1,2, View ORCID ProfileBrian Coventry1,2,3, View ORCID ProfileJames Brett Case4, View ORCID ProfileLauren Miller1,2, Lisa Kozodoy1,2, Rita E. Chen4,5, View ORCID ProfileLauren Carter1,2, View ORCID ProfileAlexandra C. Walls1, Young-Jun Park1, View ORCID ProfileEva-Maria Strauch6, View ORCID ProfileLance Stewart1,2, View ORCID ProfileMichael S. Diamond4,7, View ORCID ProfileDavid Veesler1, View ORCID ProfileDavid Baker1,2,8,*
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Science 09 Sep 2020:
eabd9909
DOI: 10.1126/science.abd9909
Abstract
Targeting the interaction between the SARS-CoV-2 Spike protein and the human ACE2 receptor is a promising therapeutic strategy. We designed inhibitors using two de novo design approaches. Computer generated scaffolds were either built around an ACE2 helix that interacts with the Spike receptor binding domain (RBD), or docked against the RBD to identify new binding modes, and their amino acid sequences designed to optimize target binding, folding and stability. Ten designs bound the RBD with affinities ranging from 100pM to 10nM, and blocked ARS-CoV-2 infection of Vero E6 cells with IC 50 values between 24 pM and 35 nM; The most potent, with new binding modes, are 56 and 64 residue proteins (IC 50 ~ 0.16 ng/ml). Cryo-electron microscopy structures of these minibinders in complex with the SARS-CoV-2 spike ectodomain trimer with all three RBDs bound are nearly identical to the computational models. These hyperstable minibinders provide starting points for SARS-CoV-2 therapeutics.
