Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge

Abstract

In the context of the SAMPL5 blinded challenge standard free energies of binding were predicted for a dataset of 22 small guest molecules and three different host molecules octa-acids (OAH and OAMe) and a cucurbituril (CBC). Three sets of predictions were submitted, each based on different variations of classical molecular dynamics alchemical free energy calculation protocols based on the double annihilation method. The first model (model A) yields a free energy of binding based on computed free energy changes in solvated and host-guest complex phases; the second (model B) adds long range dispersion corrections to the previous result; the third (model C) uses an additional standard state correction term to account for the use of distance restraints during the molecular dynamics simulations. Model C performs the best in terms of mean unsigned error for all guests (MUE \(3.2\,<\,3.4\,<\,3.6\,\text{kcal}\,\text{mol}^{-1}\)—95 % confidence interval) for the whole data set and in particular for the octa-acid systems (MUE \(1.7\,<\,1.9\,<\,2.1\,\text{kcal}\,\text{mol}^{-1}\)). The overall correlation with experimental data for all models is encouraging (\(R^2\, 0.65\,<\,0.70<0.75\)). The correlation between experimental and computational free energy of binding ranks as one of the highest with respect to other entries in the challenge. Nonetheless the large MUE for the best performing model highlights systematic errors, and submissions from other groups fared better with respect to this metric.

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Notes

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    A fourth model that corrects for finite-effects on electrostatic interactions was also submitted by our group, but the results are not discussed here as it was subsequently established that a coding error led to incorrect evaluation of the correction terms.

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Acknowledgments

J. M. is supported by a Royal Society University Research Fellowship. The research leading to these results has received funding from the European Research Council under the European Unions Seventh Framework Programme (FP7/ 2007-2013)/ERC Grant Agreement No. 336289.

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Correspondence to Julien Michel.

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Bosisio, S., Mey, A.S.J.S. & Michel, J. Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge. J Comput Aided Mol Des 31, 61–70 (2017). https://doi.org/10.1007/s10822-016-9933-0

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Keywords

  • SAMPL5
  • Binding free energies
  • Host-guest systems