Shotgun Approach for PROTAC Ternary Complex Modeling and Evaluation

Proteolysis targeting chimeras (PROTACs) are bifunctional
molecules
that induce protein degradation by forming ternary complexes with
the target protein (protein of interest, POI) and the E3 ubiquitin
ligase. Most commonly used degrader design strategies start with known
POI and E3 binders, followed by the replacement of different linkers.
Structure-based linker design is promising, yet successful cases using
ternary complex structures to guide linker design remain scarce, primarily
due to the inherent flexibility and conformational diversity of the
complexes. This challenge is compounded by two key limitations: first,
obtaining high-quality POI–egrader–E3 ternary complex
crystal structures faces major technical hurdles; second, existing
crystal structures in the PDB only capture static snapshots of these
dynamically changing systems, with some even biased by crystal packing.
Although many computational tools for ternary complex modeling have
been developed so far, their accuracy still needs improvement. Currently,
the commonly used methods for evaluating ternary complex modeling
all rely on comparison with crystal structures while ignoring potential
issues that may exist. Therefore, it is necessary to develop new modeling
and evaluation methods to guide degrader design. In this study, the
conformation distribution extracted from multiple parallel MD trajectories
for a ternary complex is used as a reference, and we propose a framework
consisting of a new modeling protocol and a scoring to generate and
evaluate a ternary complex ensemble. The results of 5 tested cases
demonstrate that our protocol generates complexes that can cover or
are at least close to the high-density regions of the MD trajectory.
This framework is particularly suitable for the POI–degrader–E3
system, which has multiple possible stable conformations and PPIs.