Virtual screen to NMR (VS2NMR): Discovery of fragment hits for the CBP bromodomain

Area of Science:

• Biochemistry
• Structural Biology
• Medicinal Chemistry

Background:

• CREB-binding protein (CBP) is a transcriptional coactivator implicated in various cellular functions.
• Overexpression of CBP is linked to increased aggressiveness in several cancer types.
• Targeting the CBP bromodomain presents a potential therapeutic strategy for cancer.

Purpose of the Study:

• To identify small molecules that can bind to the CBP bromodomain using virtual screening.
• To validate the identified compounds through experimental biophysical and structural methods.
• To establish the efficacy of high-throughput docking for CBP bromodomain inhibitor discovery.

Main Methods:

• High-throughput virtual screening of a 1500-fragment library against the CBP bromodomain.
• Binding energy evaluation using a force field with electrostatic solvation.
• Ligand-observed nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography for validation.
• In vitro binding assays to assess ligand efficiency.

Main Results:

• Virtual screening identified 39 potential fragments, with 20 showing positive results in NMR experiments.
• Four crystal structures confirmed the docking poses of selected fragments.
• The high-throughput docking approach demonstrated a 50% success rate with NMR validation and 10% with X-ray crystallography.
• Compounds 1 and 3 exhibited favorable ligand efficiency in binding assays.

Conclusions:

• High-throughput docking is an effective strategy for identifying CBP bromodomain binders.
• The validated compounds serve as starting points for developing novel cancer therapeutics.
• Fragment-based drug design, including fragment growing via Suzuki coupling, is feasible for CBP inhibitors.