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 hACE2 decoys to neutralize SARS-CoV-2. The best decoy, CTC-445.2, binds with low nanomolar affinity and high specificity to the RBD of the spike protein. Cryo-EM shows 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, shows ~10-fold improvement in binding. CTC-445.2d potently neutralizes 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.
The synthesis, structure, and magnetic behavior of the complexes Cu(qnx)Br(2) (1), Cu(2,3-dmpz)Br(2) (2), Cu(qnx)Cl(2) (3), and Cu(2,3-dmpz)Cl(2) (4) (qnx = quinoxaline, dmpz = dimethylpyrazine) are described. Both X-ray structural data and fitting of the magnetic data suggest that the compounds are well-described as strong-rung, two-leg magnetic ladders with J(rung) ranging from -30 K to -37 K, and J(rail) ranging from -14 K to -24 K. An unexpected decrease in the exchange constant for J(rail) (through the diazine ligand) is observed when the halide ion is changed from bromide to chloride, along with a small decrease in the magnetic exchange through the halide ion. Theoretical calculations on 2 and 4 via a first-principles bottom-up approach confirmed the description of the complexes as two-leg magnetic ladders. Furthermore, the calculations provide an explanation for the experimentally observed change in the value of the magnetic exchange through the dmpz ligand when the halide ion is changed from bromide to chloride, and for the very small change observed in the exchange through the different halide ions themselves via a combination of changes in geometry, bond lengths, and anion volume.
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