Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2

Area of Science:

• Epigenetics
• Cancer Biology
• Structural Biology

Background:

• Bromodomains, particularly ATAD2 (ATPase family AAA domain-containing 2 isoform A), are implicated in cancer progression.
• Targeting ATAD2 offers a promising strategy for epigenetic cancer therapy due to its overexpression in cancer cells.

Purpose of the Study:

• To develop an in vitro assay for identifying small molecule ligands targeting the ATAD2 bromodomain.
• To conduct structure-guided studies to understand the ATAD2 bromodomain's conformational flexibility and ligand-binding mechanisms.

Main Methods:

• Structure-guided studies including co-crystallization to determine the structures of apo-, peptide-, and small molecule-ATAD2 complexes.
• Development of an in vitro assay for screening and identifying small molecule binders.
• Analysis of conformational changes in the ATAD2 bromodomain and its interaction with ligands.

Main Results:

• The ATAD2 bromodomain exhibits conformational flexibility, adopting distinct 'closed' (histone-compatible) and 'open' (ligand-compatible) states.
• An unexpected conformational change in a conserved asparagine residue was identified as crucial for peptide-binding conformation remodeling.
• Dimethylisoxazole-containing small molecules were identified as ATAD2 binders, validating the in vitro assay and aiding conformational analysis.

Conclusions:

• The ATAD2 bromodomain's conformational flexibility is key to its function and interaction with both histones and small molecules.
• The identified small molecule ligands provide a basis for developing novel epigenetic therapeutics targeting ATAD2 in cancer.
• Understanding these conformational dynamics is essential for the rational design of ATAD2-specific inhibitors.