Biosynthetic proteins targeting the SARS-CoV-2 spike as anti-virals

PLoS Pathog. 2022 Sep 6;18(9):e1010799. doi: 10.1371/journal.ppat.1010799. eCollection 2022 Sep.

Abstract

The binding of the SARS-CoV-2 spike to angiotensin-converting enzyme 2 (ACE2) promotes virus entry into the cell. Targeting this interaction represents a promising strategy to generate antivirals. By screening a phage-display library of biosynthetic protein sequences build on a rigid alpha-helicoidal HEAT-like scaffold (named αReps), we selected candidates recognizing the spike receptor binding domain (RBD). Two of them (F9 and C2) bind the RBD with affinities in the nM range, displaying neutralisation activity in vitro and recognizing distinct sites, F9 overlapping the ACE2 binding motif. The F9-C2 fusion protein and a trivalent αRep form (C2-foldon) display 0.1 nM affinities and EC50 of 8-18 nM for neutralization of SARS-CoV-2. In hamsters, F9-C2 instillation in the nasal cavity before or during infections effectively reduced the replication of a SARS-CoV-2 strain harbouring the D614G mutation in the nasal epithelium. Furthermore, F9-C2 and/or C2-foldon effectively neutralized SARS-CoV-2 variants (including delta and omicron variants) with EC50 values ranging from 13 to 32 nM. With their high stability and their high potency against SARS-CoV-2 variants, αReps provide a promising tool for SARS-CoV-2 therapeutics to target the nasal cavity and mitigate virus dissemination in the proximal environment.

MeSH terms

  • Angiotensin-Converting Enzyme 2* / chemistry
  • Angiotensin-Converting Enzyme 2* / metabolism
  • Antiviral Agents / chemistry
  • Antiviral Agents / pharmacology
  • COVID-19 Drug Treatment*
  • Humans
  • Peptidyl-Dipeptidase A / metabolism
  • Protein Binding
  • Recombinant Fusion Proteins* / pharmacology
  • Recombinant Fusion Proteins* / therapeutic use
  • Recombinant Proteins / pharmacology
  • Recombinant Proteins / therapeutic use
  • SARS-CoV-2 / genetics
  • Spike Glycoprotein, Coronavirus* / metabolism

Substances

  • Antiviral Agents
  • Recombinant Fusion Proteins
  • Recombinant Proteins
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2
  • Peptidyl-Dipeptidase A
  • Angiotensin-Converting Enzyme 2

Supplementary concepts

  • SARS-CoV-2 variants

Grants and funding

B.D. was supported by the Agence Nationale de la Recherche (ANR) and by the Fédération pour la recherche médicale (ANR 20 Flash Covid 19 – FRM program). S.T. received salary from the Fédération pour la recherche médicale. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.