Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion

Cell Res. 2020 Apr;30(4):343-355. doi: 10.1038/s41422-020-0305-x. Epub 2020 Mar 30.

Abstract

The recent outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 infection in Wuhan, China has posed a serious threat to global public health. To develop specific anti-coronavirus therapeutics and prophylactics, the molecular mechanism that underlies viral infection must first be defined. Therefore, we herein established a SARS-CoV-2 spike (S) protein-mediated cell-cell fusion assay and found that SARS-CoV-2 showed a superior plasma membrane fusion capacity compared to that of SARS-CoV. We solved the X-ray crystal structure of six-helical bundle (6-HB) core of the HR1 and HR2 domains in the SARS-CoV-2 S protein S2 subunit, revealing that several mutated amino acid residues in the HR1 domain may be associated with enhanced interactions with the HR2 domain. We previously developed a pan-coronavirus fusion inhibitor, EK1, which targeted the HR1 domain and could inhibit infection by divergent human coronaviruses tested, including SARS-CoV and MERS-CoV. Here we generated a series of lipopeptides derived from EK1 and found that EK1C4 was the most potent fusion inhibitor against SARS-CoV-2 S protein-mediated membrane fusion and pseudovirus infection with IC50s of 1.3 and 15.8 nM, about 241- and 149-fold more potent than the original EK1 peptide, respectively. EK1C4 was also highly effective against membrane fusion and infection of other human coronavirus pseudoviruses tested, including SARS-CoV and MERS-CoV, as well as SARSr-CoVs, and potently inhibited the replication of 5 live human coronaviruses examined, including SARS-CoV-2. Intranasal application of EK1C4 before or after challenge with HCoV-OC43 protected mice from infection, suggesting that EK1C4 could be used for prevention and treatment of infection by the currently circulating SARS-CoV-2 and other emerging SARSr-CoVs.

MeSH terms

  • Administration, Intranasal
  • Amino Acid Sequence
  • Animals
  • Betacoronavirus / drug effects
  • Betacoronavirus / physiology*
  • Cell Fusion
  • Chlorocebus aethiops
  • Coronavirus Infections / prevention & control*
  • HEK293 Cells
  • Humans
  • Lipopeptides / pharmacology*
  • Membrane Fusion*
  • Mice
  • Pandemics / prevention & control*
  • Pneumonia, Viral / prevention & control*
  • Protein Interaction Domains and Motifs
  • Protein Structure, Secondary
  • SARS Virus
  • Sequence Alignment
  • Spike Glycoprotein, Coronavirus / antagonists & inhibitors*
  • Structure-Activity Relationship
  • Vero Cells

Substances

  • Lipopeptides
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2

Supplementary concepts

  • COVID-19
  • severe acute respiratory syndrome coronavirus 2