Ternary Complex Geometry and Lysine Positioning Guide the Generation of PROTAC-Induced Degradable Complexes

Targeted protein degradation via PROTACs (PROteolysis TArgeting Chimaeras) has transformed drug discovery by enabling the elimination of disease-driving proteins, including those previously considered undruggable. However, rational PROTAC design remains hindered by the lack of systematic approaches to evaluate the geometry of ternary complexes, ubiquitination feasibility, and the influence of linker architecture on degradation potential. Here, we present an integrative computational framework that addresses these challenges by combining ternary complex generation, pairwise RMSD-based clustering, full CRL2 VHL RING-like complex modeling, lysine proximity analysis, and structure-guided dynamics. As a representative system, we applied this workflow to PTP1B, a phosphatase implicated in oncogenic signaling yet long considered therapeutically challenging. Over 6900 ternary complex poses were generated across diverse linker designs and systematically filtered using custom Python scripts that automate pose clustering and lysine-to-E2 distance evaluation. Critical ternary complexes were subjected to molecular dynamics simulations, PCA, TICA, and Markov state modeling to reveal degradation-competent conformations and dynamic transitions. We additionally assessed AlphaFold-Multimer and Arg69-guided docking approaches. AlphaFold-Multimer produced few lysine-accessible poses, whereas Arg69-guided docking enriched degradation-competent geometries via biologically relevant interactions. This framework offers a mechanistically grounded and generalizable strategy for rational PROTAC development across protein targets.