Engineered ACE2 receptor traps potently neutralize SARS-CoV-2

Abstract

An essential mechanism for severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection begins with the viral spike protein binding to the human receptor protein angiotensin-converting enzyme II (ACE2). Here, we describe a stepwise engineering approach to generate a set of affinity optimized, enzymatically inactivated ACE2 variants that potently block SARS-CoV-2 infection of cells. These optimized receptor traps tightly bind the receptor binding domain (RBD) of the viral spike protein and prevent entry into host cells. We first computationally designed the ACE2–RBD interface using a two-stage flexible protein backbone design process that improved affinity for the RBD by up to 12-fold. These designed receptor variants were affinity matured an additional 14-fold by random mutagenesis and selection using yeast surface display. The highest-affinity variant contained seven amino acid changes and bound to the RBD 170-fold more tightly than wild-type ACE2. With the addition of the natural ACE2 collectrin domain and fusion to a human immunoglobulin crystallizable fragment (Fc) domain for increased stabilization and avidity, the most optimal ACE2 receptor traps neutralized SARS-CoV-2–pseudotyped lentivirus and authentic SARS-CoV-2 virus with half-maximal inhibitory concentrations (IC50s) in the 10- to 100-ng/mL range. Engineered ACE2 receptor traps offer a promising route to fighting infections by SARS-CoV-2 and other ACE2-using coronaviruses, with the key advantage that viral resistance would also likely impair viral entry. Moreover, such traps can be predesigned for viruses with known entry receptors for faster therapeutic response without the need for neutralizing antibodies isolated from convalescent patients.

Pilot Production of SARS-CoV-2 Related Proteins in Plants: A Proof of Concept for Rapid Repurposing of Indoor Farms Into Biomanufacturing Facilities

“…Passive immunization with recombinant antibody cocktails resembles a natural response more than a monoclonal therapy, requires shorter developmental times and is probably more robust against the development of resistances. Additionally, other antibody-based therapeutics, such as receptor decoys fused to Fc of IgG1 (such as ACE-Fc described recently; Glasgow et al, 2020 ), could be designed and produced rapidly in plants followed a similar scheme as described here.…”

BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2

“…Recombinant biotinylated SARS-CoV2 spike Spike-receptor-binding domain with a C-terminal human IgG Fc domain fusion (referred to as Spike-RBD) was prepared as previously described 43 . Calu-3 cells were grown in 96-well flat bottom plates until >50% confluent.…”

An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants

“…In principle, the virus has limited potential to escape sACE2-mediated neutralization without simultaneously decreasing affinity for the native ACE2 receptor, rendering the virus less virulent. Wild-type (WT) sACE2 is currently in a phase 2 clinical trial ( 28 ), and multiple groups have now engineered sACE2 to create high-affinity decoys for SARS-CoV-2 that rival matured monoclonal antibodies for potent neutralization of infection ( 27 , 29 , 30 ). In our group, deep mutagenesis was used to identify a large number of mutations in ACE2 that increase affinity for S ( 27 ).…”