Overcoming Resistance in the Androgen Receptor: Rational and Strategic Design of Advanced Antagonists

ConspectusProstate cancer (PCa) is the most prevalent malignancy among men worldwide, with its pathogenesis and progression heavily reliant on the sustained activation of the androgen receptor (AR) signaling pathway. The AR, a transcription factor of nuclear receptor superfamily, serves as the most privileged therapeutic target in PCa, as evidenced by the clinical efficacy of first- and second-generation AR antagonists. Current clinically available AR antagonists exclusively target the ligand binding pocket (LBP), suppressing tumor proliferation through competitive inhibition of androgen binding and subsequent blockade of AR signaling transduction. However, their therapeutic utility is invariably limited by acquired resistance mechanisms, including point mutations that alter LBP specificity, AR gene amplification leading to receptor overexpression, and the emergence of constitutively active splice variants that bypass ligand-dependent activation. Thus, the development of novel AR antagonists featuring innovative mechanisms and structural scaffolds is imperative to overcome resistance to antiandrogen therapy. However, the AR exhibits significant structural flexibility, and the lack of antagonist-bound crystal structures has hindered structure-based rational drug design. In this Article, we summarize our advances in elucidating the molecular mechanisms underlying AR conformational regulation and highlight our progress in the structure-based design and development of novel AR antagonists. First, our molecular dynamic (MD) studies collectively elucidate the molecular mechanisms by which the AR ligand binding domain (LBD) regulates its functional states through dynamic conformational changes mediated by distinct allosteric pathways when bound to agonists or antagonists, providing atomic-level insights and structural basis for drug development. Then, we successfully identified structurally diverse lead compounds targeting the LBP through various integrated approaches combining MD simulations, structure-based virtual screening (SBVS), and systematic biological evaluation. These compounds exhibited potent activity against clinically relevant AR mutations F877L, W742C, T878A, and H875Y, demonstrating their potential to overcome mutations-driven resistance. Further, we explored non-LBP mediated strategies for AR antagonism, including: (1) targeting the allosteric binding sites on LBD; (2) identification of novel druggable binding sites; and (3) targeting alternative domains beyond the LBD. As a paradigm-shifting example, we proposed inhibition of AR LBD dimerization as a novel mechanism of action for LBP-targeting AR antagonists. Building upon this insight, we characterized a promising pocket at the dimer interface, designated the Dimerization Interface Pocket (DIP), and developed first-in-class antagonists specifically targeting this site, which exhibit exceptional therapeutic potential. Collectively, these multipronged strategies not only highlight the power of computation-driven approaches in drug discovery but also yield a diverse pipeline of resistance-targeting candidates, directly addressing the unmet clinical need in advanced PCa.