Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19

Sci Rep. 2021 Jun 10;11(1):12310. doi: 10.1038/s41598-021-91625-1.

Abstract

The novel SARS-CoV-2 virus emerged in December 2019 and has few effective treatments. We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. We utilized three independent published studies to acquire or generate lists of differentially expressed genes between control and SARS-CoV-2-infected samples. Using a rank-based pattern matching strategy based on the Kolmogorov-Smirnov Statistic, the signatures were queried against drug profiles from Connectivity Map (CMap). We validated 16 of our top predicted hits in live SARS-CoV-2 antiviral assays in either Calu-3 or 293T-ACE2 cells. Validation experiments in human cell lines showed that 11 of the 16 compounds tested to date (including clofazimine, haloperidol and others) had measurable antiviral activity against SARS-CoV-2. These initial results are encouraging as we continue to work towards a further analysis of these predicted drugs as potential therapeutics for the treatment of COVID-19.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Antiviral Agents / pharmacology*
  • COVID-19 / genetics
  • COVID-19 Drug Treatment*
  • Computational Biology / methods
  • Drug Repositioning / methods*
  • Humans
  • SARS-CoV-2 / drug effects*
  • SARS-CoV-2 / physiology
  • Transcriptome / drug effects*

Substances

  • Antiviral Agents