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Turkish Journal of Biology

Abstract

Background/aim: 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.Materials and methods: 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.Results: 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.Conclusion: 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.

Author ORCID Identifier

MERVE YILMAZ: 0000-0003-3346-2781

BELGİN SEVER: 0000-0003-4847-9711

YİĞİT KUTLU: 0000-0001-5917-2550

MEHMET GÜL: 0000-0001-5513-1866

CEREN OKUDUCU: 0009-0008-8976-0204

SERRA TAVLI: 0000-0001-9362-8013

MASAMI OTSUKA: 0000-0002-2968-3939

MIKAKO FUJITA: 0000-0001-6705-4052

TURKAN HALİLOĞLU: 0000-0002-1279-5803

HALİLİBRAHİM ÇİFTÇİ: 0000-0002-9796-7669

HASAN DEMİRCİ: 0000-0002-9135-5397

DOI

10.55730/1300-0152.2742

Keywords

Keap1, Nrf2, Kelch domain, dimethyl fumarate, CNN, structural dynamics

First Page

247

Last Page

260

Publisher

The Scientific and Technological Research Council of Türkiye (TÜBİTAK)

Creative Commons License

Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.

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