Fragment-Based Protein-Protein Interaction Antagonists of a Viral Dimeric Protease

ChemMedChem. 2016 Apr 19;11(8):862-9. doi: 10.1002/cmdc.201500526. Epub 2016 Jan 28.


Fragment-based drug discovery has shown promise as an approach for challenging targets such as protein-protein interfaces. We developed and applied an activity-based fragment screen against dimeric Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) using an optimized fluorogenic substrate. Dose-response determination was performed as a confirmation screen, and NMR spectroscopy was used to map fragment inhibitor binding to KSHV Pr. Kinetic assays demonstrated that several initial hits also inhibit human cytomegalovirus protease (HCMV Pr). Binding of these hits to HCMV Pr was also confirmed by NMR spectroscopy. Despite the use of a target-agnostic fragment library, more than 80 % of confirmed hits disrupted dimerization and bound to a previously reported pocket at the dimer interface of KSHV Pr, not to the active site. One class of fragments, an aminothiazole scaffold, was further explored using commercially available analogues. These compounds demonstrated greater than 100-fold improvement of inhibition. This study illustrates the power of fragment-based screening for these challenging enzymatic targets and provides an example of the potential druggability of pockets at protein-protein interfaces.

Keywords: NMR spectroscopy; dimer disruption; fragment-based screening; human herpesviruses; proteases.

Publication types

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

MeSH terms

  • Dose-Response Relationship, Drug
  • Herpesvirus 8, Human / enzymology*
  • High-Throughput Screening Assays
  • Humans
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Structure
  • Peptide Hydrolases / metabolism*
  • Protease Inhibitors / chemical synthesis
  • Protease Inhibitors / chemistry
  • Protease Inhibitors / pharmacology*
  • Protein Binding / drug effects
  • Serine Endopeptidases / metabolism*
  • Structure-Activity Relationship


  • Protease Inhibitors
  • Peptide Hydrolases
  • Serine Endopeptidases
  • assemblin