A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike

Xia, Shuai; Yan, Lei; Xu, Wei; Agrawal, Anurodh Shankar; Algaissi, Abdullah; Tseng, Chien-Te K.; Wang, Qian; Du, Lanying; Tan, Wenjie; Wilson, Ian A.; Jiang, Shibo; Yang, Bei; Lu, Lu

We and others have reported that peptides derived from the HR2 regions of SARS-CoV and MERS-CoV S proteins can competitively inhibit viral 6-HB formation, thereby preventing viral fusion and entry into host cells (18, 27) . For example, the peptide CP-1, derived from the SARS-CoV spike protein HR2 region, was able to inhibit SARS-CoV entry in a manner similar to that of MERS-HR2P against MERS-CoV infection (18, 27) . However, we note that those peptides lack broad-spectrum antiviral activity against heterologous HCoVs. For example, CP-1 and MERS-HR2P peptides failed to cross-inhibit MERS-CoV and SARS-CoV infection, respectively. Furthermore, the CoV fusion core HR regions can be divided into two groups (28, 29) : short HRs, such as MERS-CoV, SARS-CoV, and OC43 HRs; and long HRs, such as 229E and NL63 HRs. The difference between short and long HRs arises from an insertion of 14 amino acids in the long HRs, further increasing the difficulty in designing broad-spectrum peptide fusion inhibitors. To address this challenge, we herein report the successful screening of a peptide OC43-HR2P with broad-spectrum fusion inhibitory activity. Furthermore, a modified OC43-HR2P peptide, EK1, shows promising potency and breadth in inhibiting infection by multiple HCoVs. In vivo studies demonstrate that administration of EK1 via the nasal route exhibits highly protective effects and safety profiles, highlighting its clinical potential. Moreover, structural studies of EK1 in complex with HR1s from different HCoVs explain the conserved basis for the HR1-EK1 interaction, further indicating that HR1 region could serve as a promising target site for the development of broad-spectrum pan-CoV fusion inhibitors.