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Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

Abstract

Proteins fluctuate between alternative conformations, which presents a challenge for ligand discovery because such flexibility is difficult to treat computationally owing to problems with conformational sampling and energy weighting. Here we describe a flexible docking method that samples and weights protein conformations using experimentally derived conformations as a guide. The crystallographically refined occupancies of these conformations, which are observable in an apo receptor structure, define energy penalties for docking. In a large prospective library screen, we identified new ligands that target specific receptor conformations of a cavity in cytochrome c peroxidase, and we confirm both ligand pose and associated receptor conformation predictions by crystallography. The inclusion of receptor flexibility led to ligands with new chemotypes and physical properties. By exploiting experimental measures of loop and side-chain flexibility, this method can be extended to the discovery of new ligands for hundreds of targets in the Protein Data Bank for which similar experimental information is available.

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Figure 1: Experimental occupancies of apo loop conformations set the penalties for docking.
Figure 2: Predicting loop occupancies in holo complexes.
Figure 3: Experimental binding poses versus prospective docking predictions.
Figure 4: Predicting loop occupancies in bound complexes.
Figure 5: Enrichment alone cannot distinguish first-in-class from best-in-class.

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Acknowledgements

We thank G. Rocklin for enlightening discussions, P. Afonine for advice and bug fixing of the occupancy refinement in PHENIX, A. Doak for protein preparation and H. Lin, J. Karpiak and T. Balius for reading this manuscript. This work was supported by US National Institutes of Health grants GM59957 (B.K.S.), DP5OD009180 (J.S.F.) and NRSA F32GM096544 (R.G.C.).

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M.F., R.G.C., J.S.F. and B.K.S. designed the study and wrote the paper, M.F. performed all experiments and refined structures with the assistance of J.S.F. R.G.C. wrote the computer code and performed all computational work.

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Correspondence to James S. Fraser or Brian K. Shoichet.

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The authors declare no competing financial interests.

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Fischer, M., Coleman, R., Fraser, J. et al. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nature Chem 6, 575–583 (2014). https://doi.org/10.1038/nchem.1954

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