# A 5-Br-1-Propylisatin Derivative as a Promising BRD9 Ligand: Insights from Computational and STD NMR Investigation

## TL;DR

This study identifies a new compound that binds to BRD9, a protein linked to diseases with faulty epigenetic control, using advanced techniques like NMR and virtual screening.

## Contribution

The study introduces a novel isatin derivative as a potential BRD9 ligand and validates the use of STD NMR in fragment-based drug discovery.

## Key findings

- A new isatin derivative (compound 2) was identified as a BRD9 ligand through virtual screening and confirmed via AlphaScreen assays.
- STD NMR experiments confirmed the binding of compound 2 and mapped its interaction epitope on BRD9.
- Compound 2 was shown to bind in the canonical BRD9 pocket, as confirmed by competitive displacement with a reference ligand.

## Abstract

Bromodomain-containing protein 9 (BRD9) belongs to the non-canonical BAF chromatin remodeling complex and represents a relevant therapeutic target in pathologies featuring dysregulated epigenetic control. The absence of clinically validated inhibitors and the need for diversified chemical entities highlight the interest in identifying new scaffolds targeting this protein. In this study, Saturation Transfer Difference Nuclear Magnetic Resonance (STD NMR) was employed to assess its suitability for characterizing BRD9–ligand interactions within a fragment-based discovery framework. STD NMR conditions were first optimized using the known BRD9 ligand 1, verifying the presence of interaction signals. A pharmacophore-based virtual screening campaign was then performed using libraries of commercially available fragments, leading to the selection of a novel isatin derivative, i.e., compound 2, whose binding was demonstrated in AlphaScreen assays. STD NMR experiments provided epitope mapping consistent with the predicted binding mode, thus supporting the stability of the interaction in solution. Moreover, a competitive STD experiment demonstrated displacement of 2 by a reference ligand, confirming the binding within the canonical BRD9 pocket. Overall, this study establishes STD NMR as a reliable approach for probing BRD9–ligand interactions and for the identification and validation of BRD9-targeting scaffolds suitable for future structure-guided optimization.