The SARS-CoV-2 viral spike protein S receptor-binding domain (S-RBD) binds ACE2 on host
cells to initiate molecular events, resulting in intracellular release of the viral
genome. Therefore, antagonists of this interaction could allow a modality for
therapeutic intervention. Peptides can inhibit the S-RBD:ACE2 interaction by interacting
with the protein–protein interface. In this study, protein contact atlas data and
molecular dynamics simulations were used to locate interaction hotspots on the secondary
structure elements α1, α2, α3, β3, and β4 of ACE2. We
designed a library of discontinuous peptides based upon a combination of the hotspot
interactions, which were synthesized and screened in a bioluminescence-based assay. The
peptides demonstrated high efficacy in antagonizing the SARS-CoV-2 S-RBD:ACE2
interaction and were validated by microscale thermophoresis which demonstrated strong
binding affinity (∼10 nM) of these peptides to S-RBD. We anticipate that such
discontinuous peptides may hold the potential for an efficient therapeutic treatment for
COVID-19.