Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry

Abstract

Targeted protein degradation (TPD) is a promising approach in drug discovery for degrading proteins implicated in diseases. A key step in this process is the formation of a ternary complex where a heterobifunctional molecule induces proximity of an E3 ligase to a protein of interest (POI), thus facilitating ubiquitin transfer to the POI. In this work, we characterize 3 steps in the TPD process. (1) We simulate the ternary complex formation of SMARCA2 bromodomain and VHL E3 ligase by combining hydrogen-deuterium exchange mass spectrometry with weighted ensemble molecular dynamics (MD). (2) We characterize the conformational heterogeneity of the ternary complex using Hamiltonian replica exchange simulations and small-angle X-ray scattering. (3) We assess the ubiquitination of the POI in the context of the full Cullin-RING Ligase, confirming experimental ubiquitinomics results. Differences in degradation efficiency can be explained by the proximity of lysine residues on the POI relative to ubiquitin.

Protein–protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction

“…This has been thoroughly discussed in the review on enzymology of degraders 152 . A few recent studies have used physics modeling 153,154 and ML techniques 155 to predict or rationalize degradability of PROTAC molecules. These studies all point to lysines, especially those that are E2-accesible ubiquitination sites, are indicative of degradation potential.…”

Modeling the Effect of Cooperativity in Ternary Complex Formation and Targeted Protein Degradation Mediated by Heterobifunctional Degraders

“…Our model suggests that the optimal range of cooperativity depends on the ubiquitination rate (Figure a). The target in the ternary complexes of different HBF molecules may have different ubiquitination rates because of the difference in their structural ensembles, , which affects the exposure of lysines on the target surface to ubiquitination . If ubiquitination is fast, a transient ternary complex is sufficient for ubiquitination to take place, and fast dissociation of the ternary complexcorresponding to a low cooperativityleads to both high turnover of the HBF molecules and rapid production of free, polyubiquitinated target ready for degradation; in contrast, high cooperativityand thus a very stable ternary complexmay hinder the catalytic turnover and slow down the degradation.…”

Investigation into the Use of Encorafenib to Develop Potential PROTACs Directed against BRAFV600E Protein

“…Indeed, a recent paper by Eron et al reports that PPIs stabilized by PROTACs can still be very dynamic, and X-ray structures of ternary complexes can also not correspond to a biologically relevant conformation, as they only represent a ‘crystallization snapshot’ of a highly dynamic interaction [ 42 ]. Demonstrating the efficacy of combining in silico methods with experimental data for studying the dynamics of PPIs in PROTACs design, a freshly published work by Dixon et al was able to eventually predict the structural basis of targeted protein degradation [ 43 ]. In this work, the authors showed that productive ternary complexes, modelled in the context of the full Cullin-RING ligase, are characterized by the proximity of lysine residues of the target protein to the E2 ligase.…”