Covalent Adducts Formed by the Androgen Receptor Transactivation Domain and Small Molecule Drugs Remain Disordered

Area of Science:

• Biochemistry
• Structural Biology
• Computational Chemistry

Background:

• Intrinsically disordered proteins (IDPs) are crucial in human diseases.
• Small molecules targeting the androgen receptor transactivation domain (AR-TAD) are in clinical trials for castration-resistant prostate cancer.
• These molecules form covalent adducts with AR-TAD cysteine residues, but their structural impact is unknown.

Purpose of the Study:

• To investigate the conformational changes induced by covalent binding of small molecules (EPI-002, EPI-7170) to the intrinsically disordered androgen receptor transactivation domain (AR-TAD).
• To provide atomically detailed insights into the protein-ligand interactions within covalent adducts.
• To inform the design of more effective covalent inhibitors for IDPs.

Main Methods:

• All-atom molecular dynamics (MD) computer simulations.
• Simulation of covalent adducts of AR-TAD with EPI-002 and EPI-7170.
• Comparison of conformational ensembles between covalent and non-covalent ligand-bound states.

Main Results:

• Covalent adducts of AR-TAD exhibit heterogeneous and disordered conformational ensembles.
• Covalent attachment of EPI-002 and EPI-7170 increases the population of collapsed helical AR-TAD conformations compared to non-covalent binding.
• Distinct protein-ligand interaction networks stabilize these collapsed conformations in covalent adducts.

Conclusions:

• Covalent modification significantly alters the conformational landscape of the disordered AR-TAD.
• Understanding these altered ensembles and stabilizing interactions is key for designing potent covalent inhibitors.
• This study offers a detailed molecular perspective on covalent inhibition of IDPs.