Characterizing the Cooperative Effect of PROTAC Systems with End-Point Binding Free Energy Calculation

Proteolytic targeting chimeras (PROTACs), as an emerging type of drug, function by proximity-based modalities that narrow the distance between a target protein and the E3 ubiquitin ligase to facilitate the ubiquitination labeling of the target protein for degradation. Although it is evidenced that the cooperativity of the PROTAC ternary interaction is one of the key factors affecting the degradation rate of a target protein, PROTAC design utilizing this indicator is still challenging because of the complicated/flexible interactions in a target-PROTAC-E3 ternary system. Therefore, developing reliable and practicable computational methods is of great interest for PROTAC design. Hence, in this study, we investigate the feasibility of using the end-point binding free energy calculation method, represented by molecular mechanics/Poisson-Boltzmann (generalized-Born) surface area (MM/PB(GB)SA), for characterizing cooperativity (including the stabilization and hook effects) of the PROTAC systems. The result shows that MM/GBSA is a good predictor in characterizing these effects under a relatively long molecular dynamics adjustment (50-100 ns) and low dielectric constant (ε_in = 1), with the Pearson correlation coefficient (<i>r</i>_p) > 0.5 and 0.6 for the stabilization and hook effect, respectively. This study provides a feasible strategy for characterizing the cooperativity of the PROTAC systems, facilitating the rational design of PROTAC molecules.