Integrating Hydrogen Exchange with Molecular Dynamics for Improved Ligand Binding Predictions

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, demonstrated that HX-ESP successfully identified 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 timescales required for binding predictions using traditional MD. This advancement promises to enhance the accuracy of computational modeling in drug discovery, potentially accelerating the development of effective therapeutics.