Journal of Computer-Aided Molecular Design

, Volume 26, Issue 12, pp 1293–1309 | Cite as

Free enthalpies of replacing water molecules in protein binding pockets

  • Sereina Riniker
  • Luzi J. Barandun
  • François Diederich
  • Oliver Krämer
  • Andreas Steffen
  • Wilfred F. van Gunsteren


Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH3 group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH3 at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design.


Water sites Binding pocket Molecular dynamics Free energy Enveloping distribution sampling 



This work was financially supported by the National Center of Competence in Research (NCCR) in Structural Biology and by grant number 200020-137827 of the Swiss National Science Foundation, and by grant number 228076 of the European Research Council, which is gratefully acknowledged.

Supplementary material

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Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • Sereina Riniker
    • 1
  • Luzi J. Barandun
    • 2
  • François Diederich
    • 2
  • Oliver Krämer
    • 3
  • Andreas Steffen
    • 3
  • Wilfred F. van Gunsteren
    • 1
  1. 1.Laboratory of Physical ChemistryETH ZurichZurichSwitzerland
  2. 2.Laboratory of Organic ChemistryETH ZurichZurichSwitzerland
  3. 3.Boehringer Ingelheim RCV GmbH & Co KGViennaAustria

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