Pharmacophore-based peptide biologics neutralize SARS-CoV-2 S1 and deter S1-ACE2 interactionin vitro

Abstract

Effective therapeutics and stable vaccine are the urgent need of the day to combat COVID-19 pandemic. SARS-CoV-2 spike protein has a pivotal role in cell-entry and host immune response, thus regarded as potential drug- and vaccine-target. As the virus utilizes the S1 domain of spike to initiate cell-attachment and S2 domain for membrane fusion, several attempts have been made to design viral-receptor and viral-fusion blockers. Here, by deploying interactive structure-based design and pharmacophore-based approaches, we designed short and stable peptide-biologics i.e. CoV-spike-neutralizing peptides (CSNPs) including CSNP1, CSNP2, CSNP3, CSNP4. We could demonstrate in cell culture experiments that CSNP2 binds to S1 at submicromolar concentration and abrogates the S1-hACE2 interaction. CSNP3, a modified and downsized form of CSNP2, could neither interfere with the S1-hACE2 interaction nor bind to S1. CSNP4 exhibited dose-dependent binding to both S1 and hACE2 and abolished the S1-hACE2 interaction in vitro. CSNP4 possibly enhance the mAb-based S1 neutralization by limiting the spontaneous movement of spike receptor-binding domain (RBD), whereas CSNP2 allowed RBD-mAb binding without any steric hindrance. Taken together, we suggest that CSNP2 and CSNP4 are potent and stable candidate peptides that can neutralize the SARS-CoV-2 spike and possibly pose the virus to host immune surveillance.

Shedding Light on the Inhibitory Mechanisms of SARS-CoV-1/CoV-2 Spike Proteins by ACE2-Designed Peptides

“…The full ACE2 enzyme dissociation constant of the SARS-CoV-2 spike protein is reported to be on the higher end, the nanomolar binding affinity, though that of SARS-CoV-1 were reported by different BLI experiments to be similar , or to have an up to 20-fold higher K D , meaning lowered affinity to CoV1. The de novo designed ACE2-based peptide and miniprotein affinities to CoV2 were also reported to have comparable or lower affinity to CoV1. ,,,− This is an indication that ACE2-derived peptides might be, in some cases, more sensitive to CoV2 than to CoV1, that is, qualitatively in line with the theoretical binding affinities estimated in Table . The natural peptides 1 and 2 and the designed 3 are based on the original sequence of the human ACE2 that is shown to be suboptimal for binding CoV2 in the nanomolar range.…”