Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties

J Mol Biol. 2011 Feb 4;405(5):1170-87. doi: 10.1016/j.jmb.2010.11.038. Epub 2010 Nov 25.


A congeneric series of benzamidine-type ligands with a central proline moiety and a terminal cycloalkyl group--linked by a secondary amine, ether, or methylene bridge--was synthesized as trypsin inhibitors. This series of inhibitors was investigated by isothermal titration calorimetry, crystal structure analysis in two crystal forms, and molecular dynamics simulations. Even though all of these congeneric ligands exhibited essentially the same affinity for trypsin, their binding profiles at the structural, dynamic, and thermodynamic levels are very distinct. The ligands display a pronounced enthalpy/entropy compensation that results in a nearly unchanged free energy of binding, even though individual enthalpy and entropy terms change significantly across the series. Crystal structures revealed that the secondary amine-linked analogs scatter over two distinct conformational families of binding modes that occupy either the inside or of the outside the protein's S3/S4 specificity pocket. In contrast, the ether-linked and methylene-linked ligands preferentially occupy the hydrophobic specificity pocket. This also explains why the latter ligands could only be crystallized in the conformationally restricting closed crystal form whereas the derivative with the highest residual mobility in the series escaped our attempts to crystallize it in the closed form; instead, a well-resolved structure could only be achieved in the open form with the ligand in disordered orientation. These distinct binding modes are supported by molecular dynamics simulations and correlate with the shifting enthalpic/entropic signatures of ligand binding. The examples demonstrate that, at the molecular level, binding modes and thermodynamic binding signatures can be very different even for closely related ligands. However, deviating binding profiles provide the opportunity to optimally address a given target.

MeSH terms

  • Animals
  • Benzamidines / chemistry*
  • Binding Sites
  • Calorimetry
  • Crystallography, X-Ray
  • Humans
  • Hydrogen Bonding
  • Ligands
  • Molecular Conformation
  • Molecular Dynamics Simulation
  • Substrate Specificity
  • Thermodynamics*
  • Trypsin / chemistry*
  • Trypsin Inhibitors / chemical synthesis
  • Trypsin Inhibitors / chemistry*


  • Benzamidines
  • Ligands
  • Trypsin Inhibitors
  • Trypsin
  • benzamidine

Associated data

  • PDB/2ZDK
  • PDB/2ZDL
  • PDB/2ZDM
  • PDB/2ZDN
  • PDB/2ZFS
  • PDB/2ZFT
  • PDB/2ZHD
  • PDB/2ZQ1
  • PDB/2ZQ2
  • PDB/3LJJ
  • PDB/3LJO