A fragment-based approach to probing adenosine recognition sites by using dynamic combinatorial chemistry

Chembiochem. 2009 Nov 23;10(17):2772-9. doi: 10.1002/cbic.200900537.


A new strategy that combines the concepts of fragment-based drug design and dynamic combinatorial chemistry (DCC) for targeting adenosine recognition sites on enzymes is reported. We demonstrate the use of 5'-deoxy-5'-thioadenosine as a noncovalent anchor fragment in dynamic combinatorial libraries templated by Mycobacterium tuberculosis pantothenate synthetase. A benzyl disulfide derivative was identified upon library analysis by HPLC. Structural and binding studies of protein-ligand complexes by X-ray crystallography and isothermal titration calorimetry informed the subsequent optimisation of the DCC hit into a disulfide containing the novel meta-nitrobenzyl fragment that targets the pantoate binding site of pantothenate synthetase. Given the prevalence of adenosine-recognition motifs in enzymes, our results provide a proof-of-concept for using this strategy to probe adjacent pockets for a range of adenosine binding enzymes, including other related adenylate-forming ligases, kinases, and ATPases, as well as NAD(P)(H), CoA and FAD(H2) binding proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine / analogs & derivatives*
  • Adenosine / chemical synthesis
  • Adenosine / chemistry
  • Combinatorial Chemistry Techniques / methods*
  • Crystallography, X-Ray
  • Disulfides / chemistry
  • Drug Design*
  • Molecular Sequence Data
  • Molecular Structure
  • Mycobacterium tuberculosis / enzymology
  • Peptide Synthases / metabolism
  • Protein Conformation
  • Thionucleosides / chemical synthesis
  • Thionucleosides / chemistry*


  • Disulfides
  • Thionucleosides
  • 5'-thioadenosine
  • Peptide Synthases
  • pantothenate synthetase
  • Adenosine

Associated data

  • PDB/3IOB
  • PDB/3IOC
  • PDB/3IOD
  • PDB/3IOE