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Computational peptide design for targeting homodimerization of BACH2 BTB domain and in vitro validations

By
Assoc. Prof. Ahmet Can Timuçin, PhD
Title Computational peptide design for targeting homodimerization of BACH2 BTB domain and in vitro validations
Speaker Assoc. Prof. Ahmet Can Timuçin, PhD
Department of Molecular Biology and Genetics
Faculty of Engineering and Natural Sciences
Acıbadem University
Date February 12th, 2026
Thursday
Time 15:00 (GMT+3)
Location ITU Informatics Institute
Room 413
Abstract
This talk will present the computational framework employed to identify a peptide capable of interfering with homodimerization of nuclear repressor BACH2 BTB domain, alongside wet lab validations. Activating master regulator of antioxidant response, the transcription factor NRF2 (Nuclear Factor Erythroid 2–Related Factor 2) through targeting its nuclear suppressor BACH2 represents an unexplored therapeutic strategy. Furthermore, the established role of BACH2 in tumor immunosuppression underscores the necessity of developing modulators against this repressor. To date, no peptide-based inhibitor targeting the BACH2 BTB domain has been reported. Therefore, this study aimed to identify a BACH2 inhibitory peptide using integrated computational and experimental approaches by characterizing its binding affinity and demonstrating its disruptive effect on homodimerization. As a preliminary step, a peptide library targeting the BACH2 BTB homodimerization interface was generated and screened via molecular docking to assess binding capacity at the dimerization surface. Subsequently, selected BACH2 BTB domain-peptide complexes were evaluated for binding stability through 500 ns molecular dynamics simulations, and trajectories were analyzed using MM-PBSA to estimate relative binding free energies. For experimental validation, selected peptides were ranked based on their dissociation constants to full-length BACH2 using supernatant depletion assays, with peptide 13 demonstrating higher affinity. Co-immunoprecipitation studies further revealed functionality of peptide 13 through disruption of BACH2 BTB domain homodimerization. Collectively, these findings established peptide 13 as a putative BACH2 negative regulator. Limitations of these findings and future directions on enhanced sampling-based peptide design towards intrinsically disordered regions will also be discussed.

 

Date 03 Feb 2026

İTÜ Informatics Institute

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ITU Informatics Institute provides graduate-level education and research in applied informatics, computer sciences, computational science and engineering, communication systems under the following programs.

Faculty members and students conduct research supported by national and international organızatıons in the fields of electromagnetic fields, communication systems/regulations, computational materials design, computational chemistry/biology, cryptography, signal/data processing/visualization, big data management, climate and ocean sciences, 

  • The paper titled “Non-Invasive Complete Hemodynamic Model to Investigate the Effect of Multi-Stenosis in Patient-Specific Coronary Arteries”, jointly prepared by research assistants Hacer Duzman and E. Cenk Ersan, andProf. Dr. M. Serdar Çelebi from the Computational Science and Engineering Program, has been awarded the Best Paper Award at the ESM’25. (22-24 Oct. 2025 Belgium)
  • Hacer Duzman and Muhammed Enis Şen, PhD students of Computational Science and Engineering Program, received awards in the "5 Minute Thesis Competition" organized at the "Başarım 2024 8th National High Performance Computing Conference".

There is also a High Performance Computing Laboratory established with the support of the State Planning Organization within the Institute.

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