Targeting the TRIM28–EZH2 Protein–Protein Interface With Cysteine‐Reactive Covalent Inhibitors: A Computational Blueprint for Cancer Therapy

Aberrant protein-protein interactions (PPIs) play crucial roles in cancer progression by driving transcriptional repression and epigenetic silencing. Among these, the TRIM28-EZH2 interaction is central to maintaining repressive chromatin states that promote tumorigenesis. In this study, we modeled the TRIM28-EZH2 complex using protein-protein docking, revealing a stable interface dominated by the RBCC domain of TRIM28 and the PRC2 catalytic domain of EZH2. A cysteine-focused covalent inhibitor library was screened to identify small molecules capable of targeting reactive cysteines at the interface. Four lead compounds were identified, with compound C87 exhibiting the most favorable binding free energy (ΔG_bind = -57.2 kcal/mol) and stable interactions throughout molecular dynamics simulations. These findings highlight the potential of covalent inhibition as a novel strategy to disrupt oncogenic TRIM28-EZH2 complexes and restore tumor suppressor gene expression.