In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses

Abstract

Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that can induce the ubiquitination of targeted proteins via the formation of ternary complexes between an E3 ubiquitin ligase and a target protein. The poly-ubiquitinated target protein will be escorted to the proteasome for degradation. Rational design of PROTACs require knowledge of an accurate configuration of the PROTAC induced ternary complex. This study demonstrates that native ternary poses can be distinguished by scoring candidate poses based on the pose residence time. The scoring is essentially heat-and-dissociate trials of candidate poses sampled by MD and pre-ranked by the classic MM/GBSA method. It is practical, simple to use and self-intuitive, relying on the observation that the assumed more stable native crystal ternary poses maintained a longer residence time than non-native ones at both room and higher temperatures. A time score and temperature score were generated from multiple replicate trajectories. These scores were able to correctly identify the native pose from non-native ones in all the systems examined. The absolute numbers were comparable across different systems in all currently available VHL and CRBN-containing ternary crystal structures. Therefore, it is also possible to provide an empirical criteria for unresolved ternary structures that under the conditions of this study. If a ternary pose is stable up to over a certain threshold score, it is likely a native pose. The success of the method is in part attributed to the dynamic nature of the pose change analysis which naturally involves entropic effects, one that is intrinsically unavailable with faster static scoring methods that consider molecular mechanical energy only. Protein-protein binding entropy is much more significant than in protein-ligands binding. The success is also attributed to the fact that the protein structures themselves were all stable in the short heating trials.

Development of Substituted Phenyl Dihydrouracil as the Novel Achiral Cereblon Ligands for Targeted Protein Degradation

“…The MD refinement procedure is similar to our previous method used for PROTAC modeling. 32 From these results, we observed that the carbamate carbonyl oxygen of 6F forms a H-bond with neighboring Histidine 353. The phenyl, 2-methyl, 3-alkyne group, and Boc t-butyl all form hydrophobic contacts with the protein.…”

Exploring PROTAC Cooperativity with Coarse-Grained Alchemical Methods

“…Sophisticated enhanced sampling techniques and distributed computing are needed to sample an ensemble of low-energy conformations that are consistent with experimental data. 40 Due to the difficulties in modeling the ternary complex, direct calculation of the binding cooperativities was not attempted until two recent studies 41,42 that explored the molecular mechanics with the generalized Born and surface area continuum solvation (MM/GBSA).…”

A New In-Silico Approach for PROTAC Design and Quantitative Rationalization of PROTAC mediated Ternary Complex Formation

“…This deficiency has been addressed in the next generation of methods which begin to appear in the 2022 literature. Liao, Junzhuo, et al (2022) [3] and Li, Wenqing, et al (2022) [4] have reported methods that use molecular mechanics combined with the generalized Born and surface area continuum solvation (MMGBSA) and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculated ΔGs to relatively rank PROTAC candidates and achieved a good correlation (R 2 > 0.9) with ranking based on experimentally measured quantities from PROTAC assays. This we call as the third generation of methods.…”