Complementarity between in silico and biophysical screening approaches in fragment-based lead discovery against the A(2A) adenosine receptor

J Chem Inf Model. 2013 Oct 28;53(10):2701-14. doi: 10.1021/ci4003156. Epub 2013 Sep 18.


Fragment-based lead discovery (FBLD) is becoming an increasingly important method in drug development. We have explored the potential to complement NMR-based biophysical screening of chemical libraries with molecular docking in FBLD against the A(2A) adenosine receptor (A(2A)AR), a drug target for inflammation and Parkinson's disease. Prior to an NMR-based screen of a fragment library against the A(2A)AR, molecular docking against a crystal structure was used to rank the same set of molecules by their predicted affinities. Molecular docking was able to predict four out of the five orthosteric ligands discovered by NMR among the top 5% of the ranked library, suggesting that structure-based methods could be used to prioritize among primary hits from biophysical screens. In addition, three fragments that were top-ranked by molecular docking, but had not been picked up by the NMR-based method, were demonstrated to be A(2A)AR ligands. While biophysical approaches for fragment screening are typically limited to a few thousand compounds, the docking screen was extended to include 328,000 commercially available fragments. Twenty-two top-ranked compounds were tested in radioligand binding assays, and 14 of these were A(2A)AR ligands with K(i) values ranging from 2 to 240 μM. Optimization of fragments was guided by molecular dynamics simulations and free energy calculations. The results illuminate strengths and weaknesses of molecular docking and demonstrate that this method can serve as a valuable complementary tool to biophysical screening in FBLD.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine A2 Receptor Agonists / chemistry*
  • Adenosine A2 Receptor Antagonists / chemistry*
  • Anti-Inflammatory Agents / chemistry*
  • Antiparkinson Agents / chemistry*
  • Binding Sites
  • Drug Discovery
  • High-Throughput Screening Assays
  • Humans
  • Kinetics
  • Ligands
  • Magnetic Resonance Spectroscopy
  • Molecular Docking Simulation*
  • Protein Binding
  • Radioligand Assay
  • Receptor, Adenosine A2A / chemistry*
  • Small Molecule Libraries / chemistry*
  • Structure-Activity Relationship
  • Thermodynamics
  • User-Computer Interface


  • Adenosine A2 Receptor Agonists
  • Adenosine A2 Receptor Antagonists
  • Anti-Inflammatory Agents
  • Antiparkinson Agents
  • Ligands
  • Receptor, Adenosine A2A
  • Small Molecule Libraries