Structure-Based Stabilization of Non-native Protein-Protein Interactions of Coronavirus Nucleocapsid Proteins in Antiviral Drug Design

J Med Chem. 2020 Mar 26;63(6):3131-3141. doi: 10.1021/acs.jmedchem.9b01913. Epub 2020 Mar 11.


Structure-based stabilization of protein-protein interactions (PPIs) is a promising strategy for drug discovery. However, this approach has mainly focused on the stabilization of native PPIs, and non-native PPIs have received little consideration. Here, we identified a non-native interaction interface on the three-dimensional dimeric structure of the N-terminal domain of the MERS-CoV nucleocapsid protein (MERS-CoV N-NTD). The interface formed a conserved hydrophobic cavity suitable for targeted drug screening. By considering the hydrophobic complementarity during the virtual screening step, we identified 5-benzyloxygramine as a new N protein PPI orthosteric stabilizer that exhibits both antiviral and N-NTD protein-stabilizing activities. X-ray crystallography and small-angle X-ray scattering showed that 5-benzyloxygramine stabilizes the N-NTD dimers through simultaneous hydrophobic interactions with both partners, resulting in abnormal N protein oligomerization that was further confirmed in the cell. This unique approach based on the identification and stabilization of non-native PPIs of N protein could be applied toward drug discovery against CoV diseases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alkaloids / chemistry
  • Alkaloids / metabolism
  • Alkaloids / pharmacology*
  • Amino Acid Sequence
  • Animals
  • Antiviral Agents / chemistry
  • Antiviral Agents / metabolism
  • Antiviral Agents / pharmacology*
  • Chlorocebus aethiops
  • Crystallography, X-Ray
  • Drug Design
  • Hydrophobic and Hydrophilic Interactions
  • Indoles / chemistry
  • Indoles / metabolism
  • Indoles / pharmacology*
  • Middle East Respiratory Syndrome Coronavirus / chemistry
  • Middle East Respiratory Syndrome Coronavirus / drug effects
  • Molecular Docking Simulation
  • Nucleocapsid Proteins / chemistry
  • Nucleocapsid Proteins / metabolism*
  • Protein Binding
  • Protein Domains
  • Protein Multimerization / drug effects*
  • Sequence Alignment
  • Vero Cells


  • Alkaloids
  • Antiviral Agents
  • Indoles
  • Nucleocapsid Proteins
  • nucleocapsid protein, Coronavirus
  • 5-benzyloxygramine