Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA

@article{Genheden2011BindingAO,
  title={Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA},
  author={Samuel Genheden and Ingemar Nilsson and Ulf Ryde},
  journal={Journal of chemical information and modeling},
  year={2011},
  volume={51 4},
  pages={947-58}
}
We present free energy estimates of nine 3-amidinobenzyl-1H-indole-2-carboxamide inhibitors of factor Xa. Using alchemical thermodynamic integration (TI) calculations, we estimate the difference in binding free energies with high accuracy and precision, except for mutations involving one of the amidinobenzyl rings. Crystal studies show that the inhibitors may bind in two distinct conformations, and using TI, we show that the two conformations give a similar binding affinity. Furthermore, we… CONTINUE READING

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