De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2

Science. 2020 Dec 4;370(6521):1208-1214. doi: 10.1126/science.abe0075. Epub 2020 Nov 5.

Abstract

We developed a de novo protein design strategy to swiftly engineer decoys for neutralizing pathogens that exploit extracellular host proteins to infect the cell. Our pipeline allowed the design, validation, and optimization of de novo human angiotensin-converting enzyme 2 (hACE2) decoys to neutralize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The best monovalent decoy, CTC-445.2, bound with low nanomolar affinity and high specificity to the receptor-binding domain (RBD) of the spike protein. Cryo-electron microscopy (cryo-EM) showed that the design is accurate and can simultaneously bind to all three RBDs of a single spike protein. Because the decoy replicates the spike protein target interface in hACE2, it is intrinsically resilient to viral mutational escape. A bivalent decoy, CTC-445.2d, showed ~10-fold improvement in binding. CTC-445.2d potently neutralized SARS-CoV-2 infection of cells in vitro, and a single intranasal prophylactic dose of decoy protected Syrian hamsters from a subsequent lethal SARS-CoV-2 challenge.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Angiotensin-Converting Enzyme 2 / antagonists & inhibitors*
  • Animals
  • Antiviral Agents / chemistry
  • Antiviral Agents / pharmacology*
  • Antiviral Agents / therapeutic use
  • COVID-19 / drug therapy*
  • Cricetinae
  • Cryoelectron Microscopy
  • Directed Molecular Evolution / methods
  • Protein Binding
  • Protein Domains
  • Protein Engineering / methods
  • Receptors, Virus / antagonists & inhibitors*
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / pharmacology*
  • Recombinant Proteins / therapeutic use
  • SARS-CoV-2 / drug effects*
  • Spike Glycoprotein, Coronavirus / antagonists & inhibitors*
  • Spike Glycoprotein, Coronavirus / chemistry

Substances

  • Antiviral Agents
  • Receptors, Virus
  • Recombinant Proteins
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2
  • Angiotensin-Converting Enzyme 2