Hit clustering can improve virtual fragment screening: CDK2 and PARP1 case studies

J Mol Model. 2012 Jun;18(6):2553-66. doi: 10.1007/s00894-011-1280-4. Epub 2011 Nov 9.


Virtual fragment screening could be a promising alternative to existing experimental screening techniques. However, reliable methods of in silico fragment screening are yet to be established and validated. In order to develop such an approach we first checked how successful the existing molecular docking methods can be in predicting fragment binding affinities and poses. Using our Lead Finder docking software the RMSD of the binding energy prediction was observed to be 1.35 kcal/mol(-1) on a set of 26 experimentally characterized fragment inhibitors, and the RMSD of the predicted binding pose from the experimental one was <1.5 Å. Then, we explored docking of 68 fragments obtained from 39 drug molecules for which co-crystal structures were available from the PDB. It appeared that fragments that participate in oriented non-covalent interactions, such as hydrogen bonds and metal coordination, could be correctly docked in 70-80% of cases suggesting the potential success of rediscovering of corresponding drugs by in silico fragment approach. Based on these findings we've developed a virtual fragment screening technique which involved structural filtration of protein-ligand complexes for specific interactions and subsequent clustering in order to minimize the number of preferable starting fragment candidates. Application of this method led to 2 millimolar-scale fragment PARP1 inhibitors with a new scaffold.

MeSH terms

  • Binding Sites
  • Computer Simulation
  • Cyclin-Dependent Kinase 2 / chemistry*
  • Drug Design*
  • Enzyme Inhibitors / chemistry*
  • Humans
  • Hydrogen Bonding
  • Models, Chemical
  • Models, Molecular
  • Poly (ADP-Ribose) Polymerase-1
  • Poly(ADP-ribose) Polymerases / chemistry*
  • Protein Binding
  • Protein Structure, Secondary
  • Small Molecule Libraries
  • Thermodynamics


  • Enzyme Inhibitors
  • Small Molecule Libraries
  • PARP1 protein, human
  • Poly (ADP-Ribose) Polymerase-1
  • Poly(ADP-ribose) Polymerases
  • CDK2 protein, human
  • Cyclin-Dependent Kinase 2