Lipidated macrocyclic peptide S-880008 as a broad-spectrum SARS-CoV-2 fusion inhibitor

Coronavirus disease 2019, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a threat to public health and the economy. Although several SARS-CoV-2 vaccines exist, they have failed to elicit effective neutralizing antibody responses against emerging SARS-CoV-2 variants harboring spike protein mutations. Moreover, while certain neutralizing-antibody-based therapies were effective in the early stages of the SARS-CoV-2 pandemic, their performance declined with the emergence of spike protein mutations. Thus, it is essential to develop antiviral agents that inhibit the early stages of viral infection by effectively targeting spike protein mutants. Broad-spectrum anti-SARS-CoV-2 activity relies on the targeting of conserved sites within the spike protein. Herein, we used mRNA display screening and chemical modification to generate S-880008, a lipid-modified macrocyclic peptide. S-880008 exhibited efficacy against a broad range of SARS-CoV-2 (including Omicron) variants and inhibited SARS-CoV-2 fusion rather than attachment via a novel mechanism. Cryo-electron microscopy analysis revealed that, unexpectedly, S-880008 simultaneously recognized the vulnerable sites of both the interface between the receptor-binding domain (RBD) and subdomain 1 (via the macrocyclic peptide portion) and the N-terminal domain of the adjacent protomer (via the acyl chain) to enforce a RBD 3-up conformation. The results of the structure-activity relationship experiments with S-880008 derivatives supported the notion that S-880008 binding inhibited fusion by suppressing protomer dissociation. Crucially, the intranasal administration of S-880008 to mouse-adapted SARS-CoV-2-infected mice significantly reduced the viral titer in lung homogenates and improved survival rates in a dose-dependent manner. Our findings show that S-880008 has the potential to overcome the increasing threat posed by emerging SARS-CoV-2 variants, providing a rationale for the design of a broad range of antiviral fusion inhibitors.