Discovery of N-(4-(Benzyloxy)-phenyl)-sulfonamide Derivatives as Novel Antagonists of the Human Androgen Receptor Targeting the Activation Function 2

Estrogenic disruption effects and formation mechanisms of transformation products during photolysis of preservative parabens

The ubiquitous presence of emerging contaminants (ECs) in the environment and their associated adverse effects has raised concerns about their potential risks. The increased toxicity observed during the environmental transformation of ECs is often linked to the formation of their transformation products (TPs). However, comprehension of their formation mechanisms and contribution to the increased toxicity remains an unresolved challenge. To address this gap, by combining quantum chemical and molecular simulations with photochemical experiments in water, this study investigated the formation of TPs and their molecular interactions related to estrogenic effect using the photochemical degradation of benzylparaben (BZP) preservative as a representative example. A non-targeted analysis was carried out and three previously unknown TPs were identified during the transformation of BZP. Noteworthy, two of these novel TPs, namely oligomers BZP-o-phenol and BZP-m-phenol, exhibited higher estrogenic activities compared to the parent BZP. Their IC50 values of 0.26 and 0.50 μM, respectively, were found to be lower than that of the parent BZP (6.42 μM). The binding free energies (ΔGbind) of BZP-o-phenol and BZP-m-phenol (-29.71 to -23.28 kcal·mol-1) were lower than that of the parent BZP (-20.86 kcal·mol-1), confirming their stronger binding affinities toward the estrogen receptor (ER) α-ligand binding domain. Subsequent analysis unveiled that these hydrophobic residues contributed most favorably to ER binding, with van der Waals interactions playing a significant role. In-depth examination of the formation mechanisms indicated that these toxic TPs primarily originated from the successive cleavage of ester bonds (OCH2C6H5 and COO group), followed by their combination with BZP*. This study provides valuable insight into the mechanisms underlying the formation of toxic TPs and their binding interactions causing the endocrine-disrupting effects. It offers a crucial framework for elucidating the toxicological patterns of ECs with similar structures.

Discovery of Novel Anti-Resistance AR Antagonists Guided by Funnel Metadynamics Simulation

Androgen receptor (AR) antagonists are widely used for the treatment of prostate cancer (PCa), but their therapeutic efficacy is usually compromised by the rapid emergence of drug resistance. However, the lack of the detailed interaction between AR and its antagonists poses a major obstacle to the design of novel AR antagonists. Here, funnel metadynamics is employed to elucidate the inherent regulation mechanisms of three AR antagonists (hydroxyflutamide, enzalutamide, and darolutamide) on AR. For the first time it is observed that the binding of antagonists significantly disturbed the C-terminus of AR helix-11, thereby disrupting the specific internal hydrophobic contacts of AR-LBD and correspondingly the communication between AR ligand binding pocket (AR-LBP), activation function 2 (AF2), and binding function 3 (BF3). The subsequent bioassays verified the necessity of the hydrophobic contacts for AR function. Furthermore, it is found that darolutamide, a newly approved AR antagonist capable of fighting almost all reported drug resistant AR mutants, can induce antagonistic binding structure. Subsequently, docking-based virtual screening toward the dominant binding conformation of AR for darolutamide is conducted, and three novel AR antagonists with favorable binding affinity and strong capability to combat drug resistance are identified by in vitro bioassays. This work provides a novel rational strategy for the development of anti-resistant AR antagonists.

Current and emerging approaches to noncompetitive AR inhibition

The androgen receptor (AR) has been shown to be a key determinant in the pathogenesis of castration-resistant prostate cancer (CRPC). The current standard of care therapies targets the ligand-binding domain of the receptor and can afford improvements to life expectancy often only in the order of months before resistance occurs. Emerging preclinical and clinical compounds that inhibit receptor activity via differentiated mechanisms of action which are orthogonal to current antiandrogens show promise for overcoming treatment resistance. In this review, we present an authoritative summary of molecules that noncompetitively target the AR. Emerging small molecule strategies for targeting alternative domains of the AR represent a promising area of research that shows significant potential for future therapies. The overall quality of lead candidates in the area of noncompetitive AR inhibition is discussed, and it identifies the key chemotypes and associated properties which are likely to be, or are currently, positioned to be first in human applications.

Computationally guided discovery of novel non-steroidal AR-GR dual antagonists demonstrating potency against antiandrogen resistance

As a major class of medicine for treating the lethal type of castration-resistant prostate cancer (PCa), long-term use of androgen receptor (AR) antagonists commonly leads to antiandrogen resistance. When AR signaling pathway is blocked by AR-targeted therapy, glucocorticoid receptor (GR) could compensate for AR function especially at the late stage of PCa. AR-GR dual antagonist is expected to be a good solution for this situation. Nevertheless, no effective non-steroidal AR-GR dual antagonist has been reported so far. In this study, an AR-GR dual binder H18 was first discovered by combining structure-based virtual screening and biological evaluation. Then with the aid of computationally guided design, the AR-GR dual antagonist HD57 was finally identified with antagonistic activity towards both AR (IC₅₀ = 0.394 μM) and GR (IC₅₀ = 17.81 μM). Moreover, HD57 could effectively antagonize various clinically relevant AR mutants. Further molecular dynamics simulation provided more atomic insights into the mode of action of HD57. Our research presents an efficient and rational strategy for discovering novel AR-GR dual antagonists, and the new scaffold provides important clues for the development of novel therapeutics for castration-resistant PCa.

Discovery of 2-(1-(3-Chloro-4-cyanophenyl)-1H-pyrazol-3-yl)acetamides as Potent, Selective, and Orally Available Antagonists Targeting the Androgen Receptor

The androgen receptor (AR) antagonists are efficient therapeutics for the treatment of prostate cancer (PCa). All the approved AR antagonists to date are targeted to the ligand-binding pocket (LBP) of AR and have suffered from various drug resistances, whereas AR antagonist targeting non-LBP site of AR is conceived as a promising strategy. Through the scaffold hopping of AR LBP antagonists, the 2-chloro-4-(1H-pyrazol-1-yl)benzonitrile was designed as a new core structure for AR antagonists. A total of 46 compounds were synthesized and biologically evaluated to disclose compounds 2f, 2k, and 4c, exhibiting potent AR antagonistic activities (IC₅₀ up to 69 nM), force against antiandrogen resistance, and untraditional targeting site of probably AR binding function 3. Therein, 4c exhibited effective tumor growth inhibition in LNCaP xenograft study upon oral administration. This work provides a novel chemical scaffold for AR antagonists and offers new perspective for the development of PCa therapy.

Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning

The mechanism of transcriptional activation/repression of the nuclear receptors (NRs) involves two main conformations of the NR protein, namely, the active (agonistic) and inactive (antagonistic) conformations. Binding of agonists or antagonists to the ligand-binding pocket (LBP) of NRs can regulate the downstream signaling pathways with different physiological effects. However, it is still hard to determine the molecular type of a LBP-bound ligand because both the agonists and antagonists bind to the same position of the protein. Therefore, it is necessary to develop precise and efficient methods to facilitate the discrimination of agonists and antagonists targeting the LBP of NRs. Here, combining structural and energetic analyses with machine-learning (ML) algorithms, we constructed a series of structure-based ML models to determine the molecular category of the LBP-bound ligands. We show that the proposed models work robustly and with high accuracy (ACC > 0.9) for determining the category of molecules derived from docking-based and crystallized poses. Furthermore, the models are also capable of determining the molecular category of ligands with dual opposite functions on different NRs (i.e., working as an agonist in one NR target, whereas functioning as an antagonist in another) with reasonable accuracy. The proposed method is expected to facilitate the determination of the molecular properties of ligands targeting the LBP of NRs with structural interpretation.