Atomic-Resolution Prediction of Degrader-mediated Ternary Complex Structures by Combining Molecular Simulations with Hydrogen Deuterium Exchange

Abstract

Targeted protein degradation (TPD) has recently emerged as a powerful approach for removing (rather than inhibiting) proteins implicated in diseases. A key step in TPD is the formation of an induced proximity complex where a degrader molecule recruits an E3 ligase to the protein of interest (POI), facilitating the transfer of ubiquitin to the POI and initiating the proteasomal degradation process. Here, we address three critical aspects of the TPD process using atomistic simulations: 1) formation of the ternary complex induced by a degrader molecule, 2) conformational heterogeneity of the ternary complex, and 3) degradation efficiency via the full Cullin Ring Ligase (CRL) macromolecular assembly. The novel approach described here combines experimental biophysical data with molecular dynamics (MD) simulations to accurately predict ternary complex structures at atomic resolution. We integrate hydrogen-deuterium exchange mass spectrometry (HDX-MS, which measures the solvent exposure of protein residues) directly into the MD simulation algorithm to improve the efficiency and accuracy of the ternary structure predictions of the bromodomain of the cancer target SMARCA2 with the E3 ligase VHL, as mediated by three different degrader molecules. The simulations accurately reproduce X-ray crystal structures–including a new structure that we determined in this work (PDB ID: 7S4E)–with root mean square deviations (RMSD) of 1.1 to 1.6 Å. The simulations also reveal a structural ensemble of low-energy conformations of the ternary complex. Snapshots from these simulations are used as seeds for additional simulations, where we perform 5.7 milliseconds of aggregate simulation time using Folding@home, the world’s largest distributed supercomputer. The detailed free energy surface captures the crystal structure conformation within the low-energy basin and is consistent with solution-phase experimental data (HDX-MS and SAXS). Finally, we graft a structural ensemble of the ternary complexes onto the full CRL and perform enhanced sampling simulations. Our results suggest that differences in degradation efficiency may be related to the proximity distribution of lysine residues on the POI relative to the E2-loaded ubiquitin. We make source code and the simulation and experimental datasets from this work publicly available for researchers to further advance the field of induced proximity modulation.