# Discovering Uncharted Binding Pockets on E3 Ligases Leads to the Identification of FBW7 Allosteric Modulators

## TL;DR

Researchers discovered new binding sites on E3 ligases and identified small molecules that modulate FBW7 activity, enhancing the degradation of specific proteins.

## Contribution

The study introduces a novel computational method to identify ligandable pockets on E3 ligases and reports the first allosteric modulators of FBW7.

## Key findings

- A computational approach identified ligandable pockets on 22 diverse E3 ligases.
- Small molecules were discovered that bind to FBW7 and enhance the degradation of c-MYC and c-JUN.
- The binding site and functional impact of these molecules were confirmed through biophysical and structural studies.

## Abstract

E3 ligases are key regulators of the ubiquitin‐proteasome system (UPS) and have emerged as attractive drug target candidates for precise therapeutic intervention. Additionally, their ligands are extremely valuable as handles for Targeted Protein Degradation (TPD). However, only a limited number of E3 ligases have been targeted with small molecules. An efficient approach to identify ligandable surfaces on 22 structurally diverse E3 ligases has been developed, revealing that they offer significant binding opportunities through allosteric pockets. As a proof of concept, an allosteric pocket identified in FBW7 has been targeted, leading to the discovery of the first potent and reversible small‐molecule binders of this E3 ligase. Biophysical and structural studies have confirmed the binding site, while functional cell assays have showed that some of these molecules act as allosteric enhancers of c‐MYC and c‐JUN degradation in an FBW7‐dependent manner. These allosteric modulators of E3 ligases represent a novel mechanism of action in the TPD landscape and could be used as PROTAC handles.

A computational approach to identify and characterize ligandable binding pockets on E3 ligases is presented. As a validation case, the first low‐micromolar small moleculesthat bind to the FBW7 E3 ligase are identified and confirmed to bind at the intended site. Some of the molecules identified are capable of allosterically enhance the natural degradation of c‐MYC and c‐JUN by FBW7 in an E3 ligase‐dependent manner.