Download MendeleyIntegrating Hydrogen Exchange with Molecular Dynamics for Improved Ligand Binding Predictions.
Walters, B.T., Patapoff, A.W., Kiefer, J.R., Wu, P., Wang, W.(2025) J Chem Inf Model 65: 6144-6154
- PubMed: 40495786 Search on PubMed
- DOI: https://doi.org/10.1021/acs.jcim.5c00397
- Primary Citation Related Structures:
9N48, 9N4U, 9N7R, 9N9X, 9NAC, 9NBS, 9NBX, 9NC2 - PubMed Abstract:
We introduce hydrogen-exchange experimental structure prediction (HX-ESP), a method that integrates hydrogen exchange (HX) data with molecular dynamics (MD) simulations to accurately predict ligand binding modes, even for targets requiring significant conformational changes. Benchmarking HX-ESP by fitting two ligands to PAK1 and four ligands to MAP4K1 (HPK1) and comparing the results to X-ray crystallography structures, demonstrates that HX-ESP can identify binding modes across a range of affinities significantly outperforming flexible docking for ligands necessitating large conformational adjustments. By objectively guiding simulations with experimental HX data, HX-ESP overcomes the long time scales required for binding predictions using traditional MD. This advancement enhances the accuracy of computational modeling in drug discovery and thus will accelerate the development of effective therapeutics.
- Department of Biochemistry and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States.
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