A ligand-observed mass spectrometry approach integrated into the fragment based lead discovery pipeline

Sci Rep. 2015 Feb 10:5:8361. doi: 10.1038/srep08361.


In fragment-based lead discovery (FBLD), a cascade combining multiple orthogonal technologies is required for reliable detection and characterization of fragment binding to the target. Given the limitations of the mainstream screening techniques, we presented a ligand-observed mass spectrometry approach to expand the toolkits and increase the flexibility of building a FBLD pipeline especially for tough targets. In this study, this approach was integrated into a FBLD program targeting the HCV RNA polymerase NS5B. Our ligand-observed mass spectrometry analysis resulted in the discovery of 10 hits from a 384-member fragment library through two independent screens of complex cocktails and a follow-up validation assay. Moreover, this MS-based approach enabled quantitative measurement of weak binding affinities of fragments which was in general consistent with SPR analysis. Five out of the ten hits were then successfully translated to X-ray structures of fragment-bound complexes to lay a foundation for structure-based inhibitor design. With distinctive strengths in terms of high capacity and speed, minimal method development, easy sample preparation, low material consumption and quantitative capability, this MS-based assay is anticipated to be a valuable addition to the repertoire of current fragment screening techniques.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Drug Discovery / methods*
  • Hepacivirus* / chemistry
  • Hepacivirus* / metabolism
  • Hepatitis C* / drug therapy
  • Hepatitis C* / metabolism
  • Mass Spectrometry / methods*
  • Viral Nonstructural Proteins* / antagonists & inhibitors
  • Viral Nonstructural Proteins* / chemistry
  • Viral Nonstructural Proteins* / metabolism


  • Viral Nonstructural Proteins
  • NS-5 protein, hepatitis C virus