Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 is a novel and highly pathogenic coronavirus and is the causative agent of the coronavirus disease 2019 (COVID-19). The high morbidity and mortality associated with COVID-19 and the lack of an approved drug or vaccine for SARS-CoV-2 underscores the urgent need for developing effective antiviral therapies. Therapeutics that target essential viral proteins are effective at controlling virus replication and spread. Coronavirus Spike glycoproteins mediate viral entry and fusion with the host cell, and thus, are essential for viral replication. To enter host cells, the Spike proteins of SARS-CoV-2 and related coronavirus, SARS-CoV, bind the host angiotensin-converting enzyme 2 (ACE2) receptor through their receptor binding domains (RBDs).
We performed comparative analyses of the SARS-CoV and SARS-CoV-2 RBD-ACE2 interaction interfaces to rationally design a panel of Spike-targeting ACE2-derived peptides (SAPs). Antiviral potencies of SAPs were evaluated against lentiviral vectors pseudotyped with SARS-CoV-2 or SARS-CoV Spike glycoproteins. Affinity precipitation assays were employed to determine the binding affinities of SAPs to recombinant SARS-CoV-2 RBD. Antiviral potential of selected SAPs was also validated against two pathogenic human coronaviruses, SARS-CoV-2 and HCoV-NL63, both of which use ACE2 as entry receptors.
We designed six SAPs – four derived from ?1, one derived from ?3, and one derived from ?11 helix of ACE2. Three of the six SAPs inhibited SARS-CoV-2 and SARS-CoV Spike-mediated virus infection with IC50 values in the low millimolar range. The in vitro SAP-RBD binding affinities tracked closely with their antiviral IC50 values. Importantly, two SAPs inhibited SARS-CoV-2 and HCoV-NL63 infections. Results from the infection experiments and modeling of the peptides with RBD identified a six amino acid (Glu37-Gln42) ACE2 motif that is important for SARS-CoV-2 inhibition.
We rationally designed a panel of ACE2-derived peptides based on the RBD-ACE2 binding interfaces of SARS-CoV-2 and SARS-CoV. We identified two peptides that inhibited infection with genuine SARS-CoV-2. Our work demonstrates the feasibility of inhibiting SARS-CoV-2 with peptide-based inhibitors. These findings will allow for the successful development of engineered peptides and peptidomimetic-based compounds for the treatment of COVID-19.