# Insights into therapeutic discovery through the Kelch domain structure of Keap1 at ambient temperature

## TL;DR

This study explores the structure of the Keap1 protein at room temperature to identify potential drug candidates that can inhibit its interaction with Nrf2.

## Contribution

The study provides new insights into the conformational dynamics of the Keap1 Kelch domain at ambient temperature and identifies promising inhibitor compounds.

## Key findings

- The Keap1 Kelch domain structure at ambient temperature reveals potential conformational changes at key binding sites.
- Molecular docking identified CNN, ZINC 12433145, and ZINC 10550867 as potential inhibitors of the Keap1/Nrf2 complex.
- GNM analysis showed that DMF binding residues exhibit allosteric behavior in the ambient temperature structure.

## Abstract

The Kelch-like-ECH associated protein 1 (Keap1) is an integral component of the E3-ubiquitin ligase complex, which binds to Nuclear factor erythroid 2-related factor 2 (Nrf2) and facilitates its degradation by the 26S proteasome. The Kelch domain of Keap1, composed of six repeated structural motifs, plays a key role in this interaction. This study aims to investigate the dimeric structure of the Keap1 Kelch domain at ambient temperature and to examine its implications for conformational dynamics, particularly in relation to the DMF and Nrf2 binding sites.

The dimeric crystal structure of the Keap1 Kelch domain was determined at 3.0 Å resolution using data collected at the Turkish Light Source ‘Turkish DeLight.’ To analyze structural dynamics, Gaussian Network Model (GNM) analysis was applied, and molecular docking studies were performed using the ambient temperature structure to evaluate the binding of compounds acting as inhibitors of the Keap1/Nrf2 complex.

The study reveals significant potential conformational changes in Keap1 residues, especially at the DMF and Nrf2 binding sites, driven by temperature-induced shifts. GNM analysis suggests that the allosteric behavior of DMF binding residues is fully realized in the ambient temperature structure. Molecular docking of various compounds, including CNN (a hybrid of L-carnosine and L-histidyl hydrazide), ZINC 12433145, and ZINC 105508677, demonstrated favorable binding interactions with key Keap1 residues, highlighting their potential as inhibitors.

Our in silico and crystallo results suggest that CNN is a promising lead compound for Keap1 inhibition. Understanding the dimeric form of the Keap1 Kelch domain and its conformational changes at ambient temperature is crucial for elucidating the dynamics of the Keap1-Nrf2 interaction.