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

Samuel Genheden, Ingemar Nilsson, Ulf Ryde

Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskriftPeer review

211 Nedladdningar (Pure)


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 show that we can reduce the computational demand, while still retaining a high accuracy and precision, by using fewer integration points and shorter protein-ligand simulations. Finally, we have compared the TI results to those obtained with the simpler MM/GBSA method (molecular-mechanics with generalized Born surface-area solvation). MM/GBSA gives better results for the mutations that involve a change of net charge, but if a precision similar to that of the TI method is required, the MM/GBSA method is actually slightly more expensive. Thus, we have shown that TI could be a valuable tool in drug design.
Sidor (från-till)947-958
TidskriftJournal of Chemical Information and Modeling
NummerOnline March 18, 2011
StatusPublished - 2011

Bibliografisk information

The information about affiliations in this record was updated in December 2015.
The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039)

Ämnesklassifikation (UKÄ)

  • Teoretisk kemi


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