Targeting Human Bromodomain Proteins for the Treatment of Medulloblastoma

Author

Zalak Sheth, University of Nebraska Medical CenterFollow

Graduation Date

Summer 8-15-2025

Document Type

Thesis

Degree Name

Master of Science (MS)

Programs

Pharmaceutical Sciences

First Advisor

Dr. Donald Ronning

Second Advisor

Dr. Jered Garrison

Third Advisor

Dr. Gloria Borgstahl

Fourth Advisor

Dr. Ram Mahato

Abstract

Medulloblastoma (MB) is a malignant pediatric brain tumor, where MYC overexpression is associated with poor prognosis and reduced survival. Directly targeting MYC remains difficult due to the lack of a druggable site. Targeting epigenetic readers such as BET bromodomain proteins, particularly BRD4, has emerged as a promising strategy. In MYC-driven MB, the BD1 and BD2 domains of BRD4 recognize acetylatedlysine residues, and the C-terminal motif recruits transcriptional machinery to promote MYC transcription. Most pan-BET inhibitors (iBET) bind equipotently to all bromodomains (BRD2/3/4/T), exhibiting no domain selectivity and dose-limiting toxicity. While these compounds highlight the therapeutic potential of iBETs, domain selectivity remains a challenge. We structurally characterized two ligands SRX3305, a BRD4 inhibitor exhibiting nanomolar-range affinity but lacked structural characterization, and MDP20, a structural analog of MDP5, a known iBET. We solved the crystal structure of a BRD4-BD2/SRX3305 complex, which reveals a ligand-induced conformational change within the acetyl-lysine binding pocket that could be leveraged to improve BD2 selectivity. Several Fluorescence Polarization-based probes have been developed to aid iBET drug discovery, but few have been characterized. To address this, we developed and characterized a fluorescent chemical probe based on structural insights from BRD4-BD2/SRX3305 complex. The probe demonstrated an affinity in the 2-25 µM range across BD1/BD2 of BRD2 and BRD4, with preference for BD1. To further assess the possible selectivity of these iBETs, we determined the crystal structure of the BRD2-BD2/SRX3305 complex along with MDP20 in complex with BRD2-BD2 and BRD4-BD2. These structural insights will guide the design of domain-selective iBET.

Comments

2025 Copyright, the authors

Recommended Citation

Sheth, Zalak, "Targeting Human Bromodomain Proteins for the Treatment of Medulloblastoma" (2025). Theses & Dissertations. 992.
https://digitalcommons.unmc.edu/etd/992