Communication between the Ligand-Binding Pocket and the Activation Function-2 Domain of Androgen Receptor Revealed by Molecular Dynamics Simulations

Abstract

Androgen receptor (AR), as a member of the nuclear receptor (NR) superfamily, regulates the gene transcription in response to the sequential binding of diverse agonists and coactivators. Great progress has been made in studies on the pharmacology and structure of AR, but the atomic level mechanism of the bidirectional communications between the ligand-binding pocket (LBP) and the activation function-2 (AF2) region of AR remains poorly understood. Therefore, in this study, molecular dynamics (MD) simulations and free energy calculations were carried out to explore the interactions among water, agonist (DHT) or antagonist (HFT), AR, and coactivator (SRC3). Upon the binding of an agonist (DHT) or antagonist (HFT), the LBP structure would transform to the agonistic or antagonistic state, and the conformational changes of the LBP would regulate the structure of the AF2 surface. As a result, the binding of the androgen DHT could promote the recruitment of the coactivator SRC3 to the AF2, and on the contrary, the binding of the antagonist HFT would induce a perturbation to the shape of the AF2 and then weaken its accommodating capability of the coactivators with the LXXLL motif. The simulation results illustrated that the DHT-AR binding affinity was enhanced by the association of the coactivator SRC3, which would reduce the conformational fluctuation of the AR-LBD and expand the size of the AR LBP. On the other hand, the coactivator-to-HFT allosteric pathway, which involves the SRC3, helix 3 (H3), helix 4 (H4), the loop (L1−3) between helix 1 (H1) and H3, and HFT, was characterized. The HFT's skewness and different interactions between HFT and the LBP were observed in the SRC3-present AR. The mutual communications between the AF2 surface and LBP, together with the processes involving the interplay of the ligand binding and coactivator recruitment events, would help in understanding the association of coactivators and rationally develop potent drugs to inhibit the activity of AR.

Ligand Binding Mechanism and Its Relationship with Conformational Changes in Adenine Riboswitch

“…This is also in agreement with the experimental data (Table 1) [16,26]. The total binding free energy was decomposed into individual energies in the MM-PBSA method, which is helpful when evaluating the binding mechanism of a complex in detail [49][50][51]. The sum of van der Waals interactions and nonpolar solvation energies (∆G vdw+nonpol ) was favorable for all complexes, which was responsible for the burial of the inhibitor's hydrophobic groups upon binding.…”

Structural Dynamics of Agonist and Antagonist Binding to the Androgen Receptor

“…34 Recently, Li et al, investigated the interaction between the AR agonist and antagonist and their influence on the co-activator binding using MD simulations. 34 Smieško et al utilized molecular docking and MD simulation to discriminate the agonistic and antagonist conformation of AR, showing that distinguishing AR antagonists from agonists is not possible with their current approach alone. 35 Hong et al, studied the structural changes in AR upon binding to agonist and antagonist using bicalutamide as their example antagonist, but bicalutamide is known to act as agonist in the absence of androgen and thus is not a good model.…”

Identifying New Liver X Receptor Alpha Modulators and Distinguishing Between Agonists and Antagonists By Crystal Ligand Pocket Screening

“…According to the recognized concepts of nuclear receptor transactivation mechanisms, a ligand is necessary to bind to the AF2 function site for the activation of a specific nuclear receptor [14][15][16]. In LXRα (as well as other nuclear receptors), we can also see that a full agonist always exhibits a feature whereby the head of the ligand structure body has a direct hydrogen bond link with the AF2 Helix12 His421 in x-ray crystallography images.…”

“…The volumes of different binding sites, as well as the largest-size ligand-binding pocket (PDB ID: 3FC6), are listed in Table 1 (binding site columns) and illustrated in Figure 4A and B. Our aim was to see if hits could dock into the LBD and whether the hit furthered show a hydrogen bond link with 3FC6 LXRα AF2 His421 [14][15][16] or not. As a result of all simulation observations, the best antagonist (compound 5) and the best agonist (compound 11) in our study were taken as examples.…”

“…To differentiate types of modulators, we needed to choose another suitable binding site model to distinguish the agonism of the hits by structure-based molecular docking screening. According to the standard theory of nuclear receptor transactivation mechanisms, an agonist binding in the core of the LBD with contact to the AF2 function site induces a conformational change which can introduce a binding site for coactivators in a groove formed majorly by Helix12, leading to effective transactivation [14][15][16]. Molecular docking to see whether a hit can dock into the LBD and whether the hit can also show contact with LXRα Helix12 His421, which may denote its agonism.…”