Uncovering the Kinetic Characteristics and Degradation Preference of PROTAC Systems with Advanced Theoretical Analyses

Proteolysis-targeting chimeras (PROTACs), which can selectivelyinduce the degradation of target proteins, represent an attractivetechnology in drug discovery. A large number of PROTACs have beenreported, but due to the complicated structural and kinetic characteristicsof the target-PROTAC-E3 ligase ternary interaction process, the rationaldesign of PROTACs is still quite challenging. Here, we characterizedand analyzed the kinetic mechanism of MZ1, a PROTAC that targets thebromodomain (BD) of the bromodomain and extra terminal (BET) protein(Brd2, Brd3, or Brd4) and von Hippel-Lindau E3 ligase (VHL), fromthe kinetic and thermodynamic perspectives of view by using enhancedsampling simulations and free energy calculations. The simulationsyielded satisfactory predictions on the relative residence time andstandard binding free energy (r (p) >0.9)for MZ1 in different Brd(BD)-MZ1-VHL ternary complexes. Interestingly,the simulation of the PROTAC ternary complex disintegration illustratesthat MZ1 tends to remain on the surface of VHL with the BD proteinsdissociating alone without a specific dissociation direction, indicatingthat the PROTAC prefers more to bind with E3 ligase at the first stepin the formation of the target-PROTAC-E3 ligase ternary complex. Furtherexploration of the degradation difference of MZ1 in different Brdsystems shows that the PROTAC with higher degradation efficiency tendsto leave more lysine exposed on the target protein, which is guaranteedby the stability (binding affinity) and durability (residence time)of the target-PROTAC-E3 ligase ternary complex. It is quite possiblethat the underlying binding characteristics of the Brd(BD)-MZ1-VHL systems revealed by this study may be shared by differentPROTAC systems as a general rule, which may accelerate rational PROTACdesign with higher degradation efficiency.