Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available
COVID-19 vaccines and
monoclonal antibody therapies through
epitope change on the receptor binding domain of the viral spike
glycoprotein. Hence, there is a specific urgent need for alternative
antivirals that target processes less likely to be affected by mutation, such as the membrane fusion step of viral entry into the host cell. One such
antiviral class includes
peptide inhibitors which block formation of the so-called HR1HR2 six-helix bundle of the SARS-CoV-2 spike (S)
protein and thus interfere with viral membrane fusion. Here we performed structural studies of the HR1HR2 bundle, revealing an extended, well-folded N-terminal region of HR2 that interacts with the HR1 triple helix. Based on this structure, we designed an extended HR2
peptide that achieves single-digit nanomolar inhibition of SARS-CoV-2 in cell-based fusion, VSV-SARS-CoV-2 chimera, and authentic
SARS-CoV-2 infection assays without the need for modifications such as lipidation or chemical stapling. The
peptide also strongly inhibits all major SARS-CoV-2 variants to date. This extended
peptide is ~100-fold more potent than all previously published short, unmodified HR2
peptides, and it has a very long inhibition lifetime after washout in
virus infection assays, suggesting that it targets a pre-hairpin intermediate of the
SARS-CoV-2 S protein. Together, these results suggest that regions outside the HR2 helical region may offer new opportunities for potent
peptide-derived
therapeutics for SARS-CoV-2 and its variants, and even more distantly related viruses, and provide further support for the pre-hairpin intermediate of the S
protein.
Significance Statement:
SARS-CoV-2 infection requires fusion of viral and host membranes, mediated by the viral spike
glycoprotein (S). Due to the importance of viral membrane fusion, S has been a popular target for developing
vaccines and
therapeutics. We discovered a simple
peptide that inhibits
infection by all major variants of SARS-CoV-2 with nanomolar efficacies. In marked contrast, widely used shorter
peptides that lack a key N-terminal extension are about 100 x less potent than this
peptide. Our results suggest that a simple
peptide with a suitable sequence can be a potent and cost-effective therapeutic against
COVID-19 and they provide new insights at the virus entry mechanism.