Unveiling Ligand-Induced Conformational Changes in Mutant AR-LBD: Molecular Dynamics Insights into the Androgen Receptor-Coactivator Mechanism

The androgen receptor (AR) is a nuclear receptor involved in regulating gene expression, maintaining the sexual phenotype, and contributing to the development of prostate cancer (PCa). The binding of agonists, such as dihydrotestosterone (DHT), triggers conformational changes in the AR, affecting coactivator interactions, and regulates downstream signaling pathways. Although AR activation depends on interactions between its ligand-binding domain (LBD) and coactivators, the precise impact of ligand binding on these interactions remains unclear. Antagonists such as apalutamide, bicalutamide, and enzalutamide inhibit AR activation and are used to treat PCa. However, their long-term effectiveness is often reduced due to mutations in AR-LBD, which can shift the AR from an antagonistic to an agonistic state, diminishing treatment efficacy. The mechanisms driving this conversion have not been fully elucidated. This study employed atomic-level investigations through molecular dynamics simulation with multiple replicas covering a total time frame of 10.5 μs, to investigate ligand induced perturbations in mutants AR_LBD, particularly focusing on conformational changes and the effect on AR-coactivator interaction. The results demonstrated that DHT, an agonist, stabilizes the activation function-2 region (AF-2), thereby promoting AR-coactivator interactions, while antagonists induce distinct changes in helix 12 that disrupt these interactions. In addition, F876L and T877A mutations in AR-LBD alter the ligand-to-coactivator allosteric pathway involving the coactivator, helix 3 (H3), helix 4 (H4), the loop between H3–H4, and helix 12 (H12), potentially converting the AR-apalutamide complex from an antagonistic to an agonistic state. The free energy decomposition calculations exhibited that AR mutant systems possess higher binding affinities than antagonistic ARs, with electrostatic interactions and conformational entropies associated with the determination of the binding free energies. The study suggests that point mutations in AR-LBD induce a shift from an antagonistic to an agonistic state by altering the AR and AF-2 structure, resulting in continuous coactivator recruitment and sustained AR activity. Through the application of a dynamic cross-correlation matrix, principal component analysis, free energy landscape computation, and structural community analysis, this research offers valuable insights into AR-coactivator interactions, paving the way for more effective treatments against castration-resistant prostate cancer.