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

## TL;DR

Researchers used computational methods to design covalent inhibitors that target the TRIM28–EZH2 protein interaction, a key driver in cancer progression.

## Contribution

A novel computational blueprint for targeting the TRIM28–EZH2 interface using cysteine-reactive covalent inhibitors is proposed.

## Key findings

- Compound C87 showed the most favorable binding free energy (-57.2 kcal/mol) and stable interactions.
- Four lead covalent inhibitors were identified with potential to disrupt oncogenic TRIM28–EZH2 complexes.
- Molecular dynamics simulations confirmed the stability of the inhibitors at the protein interface.

## Abstract

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.

Graphical overview of the computational strategy employed to disrupt the oncogenic TRIM28EZH2 proteinprotein interaction. The workflow illustrates proteinprotein docking to define the interaction interface, cysteine‐focused covalent virtual screening targeting EZH2 Cys144, covalent docking, molecular dynamics simulations, and MM‐GBSA binding free‐energy calculations, leading to the identification of C87, C470, C128, and C508 as thermodynamically stable covalent inhibitors with potential anticancer relevance.