Structure-based phylogeny identifies avoralstat as a TMPRSS2 inhibitor that prevents SARS-CoV-2 infection in mice

J Clin Invest. 2021 May 17;131(10):e147973. doi: 10.1172/JCI147973.


Drugs targeting host proteins can act prophylactically to reduce viral burden early in disease and limit morbidity, even with antivirals and vaccination. Transmembrane serine protease 2 (TMPRSS2) is a human protease required for SARS coronavirus 2 (SARS-CoV-2) viral entry and may represent such a target. We hypothesized that drugs selected from proteins related by their tertiary structure, rather than their primary structure, were likely to interact with TMPRSS2. We created a structure-based phylogenetic computational tool named 3DPhyloFold to systematically identify structurally similar serine proteases with known therapeutic inhibitors and demonstrated effective inhibition of SARS-CoV-2 infection in vitro and in vivo. Several candidate compounds, avoralstat, PCI-27483, antipain, and soybean trypsin inhibitor, inhibited TMPRSS2 in biochemical and cell infection assays. Avoralstat, a clinically tested kallikrein-related B1 inhibitor, inhibited SARS-CoV-2 entry and replication in human airway epithelial cells. In an in vivo proof of principle, avoralstat significantly reduced lung tissue titers and mitigated weight loss when administered prophylactically to mice susceptible to SARS-CoV-2, indicating its potential to be repositioned for coronavirus disease 2019 (COVID-19) prophylaxis in humans.

Keywords: COVID-19; Drug screens; Infectious disease; Molecular biology; Proteases.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • COVID-19* / enzymology
  • COVID-19* / genetics
  • COVID-19* / prevention & control
  • Chlorocebus aethiops
  • Female
  • HEK293 Cells
  • Humans
  • Male
  • Mice
  • Phylogeny*
  • SARS-CoV-2 / physiology*
  • Serine Endopeptidases* / chemistry
  • Serine Endopeptidases* / genetics
  • Serine Endopeptidases* / metabolism
  • Serine Proteinase Inhibitors* / chemistry
  • Serine Proteinase Inhibitors* / pharmacology
  • Structure-Activity Relationship
  • Vero Cells
  • Virus Internalization / drug effects*
  • Virus Replication / drug effects*


  • Serine Proteinase Inhibitors
  • Serine Endopeptidases
  • TMPRSS2 protein, human
  • TMPRSS2 protein, mouse