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[摘要]：challenge in the field of structure-based inhibitor design and is a requirement for accurate binding free energy predictions with structure-based methods. A series of HIV-1 reverse transcriptase inhibitors was cross-docked using a non-native crystal structure that resulted in two distinct clusters of possible conformations. One of these clusters was compatible with an existing crystal structure, whereas the other displayed a flipped heterocyclic group. Binding free energies, using the non-native crystal structure, calcd. from several scoring functions, were similar for the two clusters, and no conclusion about the binding mode could be drawn from these results. The two clusters could be sepd. through rescoring with the linear interaction method (LIE) in combination with mol. dynamics simulations, which leads to a binding mode prediction in line with exptl. crystallog. data. Further, the LIE model produces the best correlation between exptl. and calcd. binding free energies among the tested scoring methods. |
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