A hybrid structure determination approach to investigate the druggability of the nucleocapsid protein of SARS-CoV-2

Nucleic Acids Res. 2023 May 22;51(9):4555-4571. doi: 10.1093/nar/gkad195.


The pandemic caused by SARS-CoV-2 has called for concerted efforts to generate new insights into the biology of betacoronaviruses to inform drug screening and development. Here, we establish a workflow to determine the RNA recognition and druggability of the nucleocapsid N-protein of SARS-CoV-2, a highly abundant protein crucial for the viral life cycle. We use a synergistic method that combines NMR spectroscopy and protein-RNA cross-linking coupled to mass spectrometry to quickly determine the RNA binding of two RNA recognition domains of the N-protein. Finally, we explore the druggability of these domains by performing an NMR fragment screening. This workflow identified small molecule chemotypes that bind to RNA binding interfaces and that have promising properties for further fragment expansion and drug development.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 Drug Treatment*
  • COVID-19* / virology
  • Coronavirus Nucleocapsid Proteins* / antagonists & inhibitors
  • Coronavirus Nucleocapsid Proteins* / chemistry
  • Coronavirus Nucleocapsid Proteins* / metabolism
  • Drug Development*
  • Humans
  • Mass Spectrometry
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Binding
  • RNA, Viral / metabolism
  • SARS-CoV-2* / drug effects
  • SARS-CoV-2* / metabolism
  • Workflow


  • RNA, Viral
  • nucleocapsid phosphoprotein, SARS-CoV-2
  • Coronavirus Nucleocapsid Proteins