A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge

J Comput Aided Mol Des. 2017 Jan;31(1):29-44. doi: 10.1007/s10822-016-9956-6. Epub 2016 Sep 30.


As part of the SAMPL5 blinded experiment, we computed the absolute binding free energies of 22 host-guest complexes employing a novel approach based on the BEDAM single-decoupling alchemical free energy protocol with parallel replica exchange conformational sampling and the AGBNP2 implicit solvation model specifically customized to treat the effect of water displacement as modeled by the Hydration Site Analysis method with explicit solvation. Initial predictions were affected by the lack of treatment of ionic charge screening, which is very significant for these highly charged hosts, and resulted in poor relative ranking of negatively versus positively charged guests. Binding free energies obtained with Debye-Hückel treatment of salt effects were in good agreement with experimental measurements. Water displacement effects contributed favorably and very significantly to the observed binding affinities; without it, the modeling predictions would have grossly underestimated binding. The work validates the implicit/explicit solvation approach employed here and it shows that comprehensive physical models can be effective at predicting binding affinities of molecular complexes requiring accurate treatment of conformational dynamics and hydration.

Keywords: AGBNP2; BEDAM; Debye–Hückel; Hydration Site Analysis (HSA); SAMPL5; Salt effects.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Drug Design
  • Humans
  • Ligands
  • Molecular Conformation
  • Molecular Dynamics Simulation*
  • Protein Binding
  • Proteins / chemistry*
  • Solvents / chemistry*
  • Thermodynamics
  • Water / chemistry*


  • Ligands
  • Proteins
  • Solvents
  • Water