Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via New In Silico Methodologies

Abstract

methods are presented to model PROTAC-mediated ternary complex structures, which are then used to predict the efficacy of any accompanying protein degradation. Method 4B, an extension to one of our previous approaches, incorporates a clustering procedure uniquely suited for considering ternary complexes. Method 4B yields the highest proportion to date of crystal-like poses in modeled ternary complex ensembles, nearing 100% in two cases and always giving a hit rate of at least 10%. Techniques to further improve this performance for particularly troublesome cases are suggested and validated. This demonstrated ability to reliably reproduce known crystallographic ternary complex structures is further established through modeling of a newly released crystal structure. Moreover, for the far more common scenario where the structure of the ternary complex intermediate is unknown, the methods detailed in this work nonetheless consistently yield results that reliably follow experimental protein degradation trends, as established through seven retrospective case studies. These various case studies cover challenging yet common modeling situations, such as when the precise orientation of the PROTAC binding moiety in one (or both) of the protein pockets has not been experimentally established. Successful results are presented for one PROTAC targeting many proteins, for different PROTACs targeting the same protein, and even for degradation effected by an E3 ligase that has not been structurally characterized in a ternary complex. Overall, the computational modeling approaches detailed in this work should greatly facilitate PROTAC screening and design efforts, so that the many advantages of a PROTAC-based degradation approach can be effectively utilized both rapidly and at reduced cost.

Proteolysis targeting chimeras (PROTACs) come of age: entering the third decade of targeted protein degradation

“…The two available models can be run using the Molecular Operating Environment (MOE) or Rosetta. [123][124][125] Development of the MOE based software was a pioneering achievement of in silico docking of PROTAC ternary complexes. The program uses four different methods to predict ternary complex formation:…”

“…Clustering of ternary complex ensembles has been found to increase the accuracy of identifying viable ternary complex structures. 124 Additionally, two crystal structures of binary protein–ligand complexes can be used to predict optimal linker lengths to bridge the gap between the E3 and POI.…”

Major advances in targeted protein degradation: PROTACs, LYTACs, and MADTACs

“…The Williams group has further refined their computational model using more constrained PROTAC conformations ( 110 ). As more atomic-resolution structures are solved, we anticipate that the accuracies of these models will be even further refined.…”

Exploiting Folding and Degradation Machineries To Target Undruggable Proteins: What Can a Computational Approach Tell Us?

“…Such method is shown to reproduce crystal-like poses in a significant fraction of modeled ternary complex ensembles. [19] Lately, machine-and deep-learning approaches have started to be applied to molecular design problems. The DeLinker method [20] is a novel graph-based deep generative model that combines machine learning and structural knowledge: starting with two PROTAC fragments or partial structures, a molecule is designed to incorporate both through a linker fragment.…”

“…In a subsequent extension of the latter method, a clustering approach specific for ternary complexes is introduced to detect and isolate possible solutions. Such method is shown to reproduce crystal‐like poses in a significant fraction of modeled ternary complex ensembles [19] …”