Rational Prediction of PROTAC-Compatible Protein–Protein Interfaces by Molecular Docking

Abstract

Proteolysis targeting chimeras (PROTACs) are heterobifunctional ligands that mediate the interaction between a protein target and an E3 ligase, resulting in a ternary complex, whose interaction with the ubiquitination machinery leads to target degradation. This technology is emerging as an exciting new avenue for therapeutic development, with several PROTACs currently undergoing clinical trials targeting cancer. Here, we describe a general and computationally efficient methodology combining restraint-based docking, energy-based rescoring, and a filter based on the minimal solvent-accessible surface distance to produce PROTAC-compatible PPIs suitable for when there is no a priori known PROTAC ligand. In a benchmark employing a manually curated data set of 13 ternary complex crystals, we achieved an accuracy of 92% when starting from bound structures and 77% when starting from unbound structures, respectively. Our method only requires that the ligand-bound structures of the monomeric forms of the E3 ligase and target proteins be given to run, making it general, accurate, and highly efficient, with the ability to impact early-stage PROTAC-based drug design campaigns where no structural information about the ternary complex structure is available.

AlphaFold-Multimer struggles in predicting PROTAC-mediated protein-protein interfaces

“…While some groups have developed tools for this purpose [32][33][34][35][36] , they are typically not general because they require that the PROTAC molecule be known a priori. Within our group we developed PROTACability 25 , which by-passes this constraint and achieves satisfactory accuracy but fails to produce high quality solutions. Thus, there is significant room for improvement and a general tool that uses minimal information and achieves high prediction quality would significantly impact the field of PROTAC-based drug discovery.…”

“…DockQ: To evaluate the similarity between the experimental structures and the predicted structures from AF-Multimer, the DockQ criteria were employed 28 . In short, DockQ provides a continuous score from 0 to 1 (with 1 being perfect similarity) which takes into account the fraction of conserved native contacts, RMSD of the target protein and the interface RMSD between a reference structure and a predicted structure 25 . This metric can be employed either quantitatively or qualitatively, with possible classifications being inaccurate (0-0.229), acceptable (0.23-0.49), medium (0.50-0.799) or high quality(0.80-1) predictions.…”

“…We have reported in another work 25 that PROTAC-mediated interfaces are typically shallow and small and thus, represent a significant challenge to machine learning-based approaches such as AF2. In this letter, we evaluate the accuracy of AlphaFold-Multimer in predicting the structure of heterodimeric protein-protein complexes.…”

Revolutionizing Drug Targeting Strategies: Integrating Artificial Intelligence and Structure-Based Methods in PROTAC Development

“…It can be used to design PROTACs that have optimal binding affinity for both the target protein and the E3 ligase, which is necessary for the targeted degradation of the protein. The advancement in AlphaFold, which predicts protein structure and interactions, is considered one of the most promising tools for designing PROTAC constructs [73]. It can predict protein-protein complexes in the multimer variant, which can be helpful in correctly predicting the PROTAC-mediated PPI interfaces.…”

PROTAC-induced Protein Structural Dynamics in Targeted Protein Degradation

“…For example, several studies have employed protein-protein docking, linker conformational searching [14][15][16][17] , and machine learning approaches 18,19 to generate ensembles of E3-PROTAC-POI complexes in silico. Recent advancement in docking algorithms aim to provide higher accuracy and energetically favorable ternary complexes 20,21 . Notably, recent studies suggest that, in addition to forming a ternary complex, the orientations of E3-PROTAC-POI allowing accessibility of the surface Lys residues of the POI are important for ubiquitination.…”