Hydration site analysis and molecular simulations highlight drug repurposing opportunities for TRIM24 bromodomain inhibition

TRIM24, a transcriptional co-activator of multiple nuclear receptors, recruits these receptors to acetylated chromatin via its bromodomain (BRD) module, promoting the upregulation of oncogenic pathways. Overexpression of TRIM24 has been linked to enhanced cancer cell proliferation, while BRD inhibition suppresses tumor growth. Although several small-molecule inhibitors and PROTACs targeting the TRIM24 BRD have been developed, none have advanced to clinical trials, underscoring the need for novel scaffolds with optimized ADMET properties. In this study, we employed computational approaches to characterize hydration sites within the TRIM24 BRD binding pocket and identify putative inhibitors from FDA-approved drugs and InterBioScreen (IBS) natural compounds. WaterMap was used to analyze hydration thermodynamics, followed by molecular docking, molecular dynamics (MD) simulations, and free energy calculations to evaluate binding interactions. Furthermore, density probability map and survival analyses of water were performed to assess ligand-induced displacement of conserved water molecules. Our results reveal that the ZA channel of TRIM24 BRD contains thermodynamically unfavorable hydration sites, which may be exploitable for inhibitor design. MD simulation and binding free energy calculations suggested rosiglitazone and esculin (FDA-approved drugs) as promising computationally identified candidates, along with IBS-90266, a natural compound exhibiting strong binding affinity. These hits demonstrated stable binding poses, favorable interactions with the BRD pocket, and efficient displacement of key hydration sites. Notably, these compounds feature unique scaffolds and moderate ADMET profiles, suggesting their potential as candidate TRIM24 BRD inhibitors. Further in vitro validation is warranted to confirm their biological activity.