More than a simple lipophilic contact: a detailed thermodynamic analysis of nonbasic residues in the s1 pocket of thrombin

J Mol Biol. 2009 Jul 3;390(1):56-69. doi: 10.1016/j.jmb.2009.04.051. Epub 2009 May 3.


The field of medicinal chemistry aims to design and optimize small molecule leads into drug candidates that may positively interfere with pathological disease situations in humans or combat the growth of infective pathogens. From the plethora of crystal structures of protein-inhibitor complexes we have learned how molecules recognize each other geometrically, but we still have rather superficial understanding of why they bind to each other. This contribution surveys a series of 26 thrombin inhibitors with small systematic structural differences to elucidate the rationale for their widely deviating binding affinity from 185 microM to 4 nM as recorded by enzyme kinetic measurements. Five well-resolved (resolution 2.30 - 1.47 A) crystal structures of thrombin-inhibitor complexes and an apo-structure of the uncomplexed enzyme (1.50 A) are correlated with thermodynamic data recorded by isothermal titration calorimetry with 12 selected inhibitors from the series. Taking solubility data into account, the variation in physicochemical properties allows conclusions to be reached about the relative importance of the enthalpic binding features as well as to estimate the importance of the parameters more difficult to capture, such as residual ligand entropy and desolvation properties. The collected data reveal a comprehensive picture of the thermodynamic signature that explains the so far poorly understood attractive force experienced by m-chloro-benzylamides to thrombin.

MeSH terms

  • Entropy
  • Humans
  • Kinetics
  • Models, Molecular
  • Protease Inhibitors / chemistry*
  • Protease Inhibitors / metabolism*
  • Protein Binding
  • Protein Structure, Quaternary
  • Thermodynamics
  • Thrombin / antagonists & inhibitors
  • Thrombin / chemistry*
  • Thrombin / metabolism*


  • Protease Inhibitors
  • Thrombin

Associated data

  • PDB/2ZC9
  • PDB/2ZDA
  • PDB/2ZDV
  • PDB/2ZF0
  • PDB/2ZFF
  • PDB/3D49