Computational mapping of productive POI–E3 ligase conformations to guide de novo degrader design: application to WEE1 and PKMYT1 PROTACs

Targeted protein degradation has emerged as a promising therapeutic strategy, yet rational degrader design remains challenged by the dynamic nature of protein of interest (POI)-E3 ligase interactions. While X-ray crystallography and cryo-EM provide valuable structural snapshots, they are insufficient for capturing the conformational heterogeneity underpinning efficient ubiquitination and degradation. Here, we present a unified computational workflow to systematically generate and evaluate POI-E3 ligase conformational states for CRBN- and VHL-mediated proteolysis-targeting chimeras (PROTACs). The workflow integrates warhead connectivity analysis, conformational clustering, ubiquitination accessibility assessment and molecular dynamics simulations to identify productive POI-E3 ligase geometries. Analysis of experimental structures revealed that PROTAC linkers do not exceed 15 Å, providing a practical attachment-atom distance based filter for docking-derived models. Furthermore, POI-E3 ligase conformations differing by more than 7.5 Å Cα RMSD exhibited distinct ubiquitination profiles, offering quantitative guidance for defining structurally and functionally divergent states. Experimental ternary complexes consistently positioned one or more solvent-exposed POI lysine residues within 50 Å of the E2 catalytic Cys111, establishing a mechanistically grounded criterion for ubiquitination competence. Validation against 34 experimentally determined PROTAC ternary complexes achieved a 97% recovery rate and identified multiple ubiquitination competent conformations beyond experimental snapshots. The workflow was subsequently applied to model productive WEE1-CRBN and PKMYT1-CRBN conformations, for which no experimental structures are available. PROTAC induced-fit docking demonstrated that active PROTACs selectively engage productive POI-E3 ligase geometries with linker-compatible attachment atom distances. Overall, this study provides a quantitative, structure-based framework for guiding the rational design of ubiquitination-based degraders. The code and example data supporting this workflow are openly available at https://github.com/Husam-PSE/PROTACMap .Scientific contributionThis study offers a generalizable computational framework for identifying productive POI-E3 ligase conformations. It demonstrates that effective degradation depends on the interplay between conformational diversity, feasible warhead connectivity and preserved ubiquitination competence, rather than solely on ternary complex stability or binding affinity. Our computational approach was applied on WEE1 and PKMYT1 PROTACs for which no experimental ternary structure is available.