Structural Diversity of Ligand-Binding Androgen Receptors Revealed by Microsecond Long Molecular Dynamics Simulations and Enhanced Sampling

Abstract

Androgen receptor (AR) plays important roles in the development of prostate cancer (PCa). The antagonistic drugs, which suppress the activity of AR, are widely used in the treatment of PCa. However, the molecular mechanism of antagonism about how ligands affect the structures of AR remains elusive. To better understand the conformational variability of ARs bound with agonists or antagonists, we performed long time unbiased molecular dynamics (MD) simulations and enhanced sampling simulations for the ligand binding domain of AR (AR-LBD) in complex with various ligands. Based on the simulation results, we proposed an allosteric pathway linking ligands and helix 12 (H12) of AR-LBD, which involves the interactions among the ligands and the residues W741, H874, and I899. The interaction pathway provides an atomistic explanation of how ligands affect the structure of AR-LBD. A repositioning of H12 was observed, but it is facilitated by the C-terminal of H12, instead of by the loop between helix 11 (H11) and H12. The bias-exchange metadynamics simulations further demonstrated the above observations. More importantly, the free energy profiles constructed by the enhanced sampling simulations revealed the transition process between the antagonistic form and agonistic form of AR-LBD. Our results would be helpful for the design of more efficient antagonists of AR to combat PCa.

Computational chemistry in drug lead discovery and design

“…Antagonists HF and R‐bicalutamide introduce a certain degree of dynamic instability in helix 12, though due to insufficient simulation length, it could not be assessed at that time whether this translates into passive antagonism or helix 12 relocation. Recently, significantly longer simulations on these systems confirmed many of our findings …”

“…Recently, significantly longer simulations on these systems confirmed many of our findings. [51,52] 3 | METHODOLOGICAL DEVELOPMENTS IN DOCKING-BASED DRUG LEAD DISCOVERY In molecular docking, the pose of a small-molecule is optimized within the receptor binding site, and then the best (or the few lowest-energy poses) are assigned a score which is a measure of the likelihood of binding. In docking-based SBVS, this docking process is performed in a highthroughput fashion (high-throughput docking, HTD) using chemical libraries of small-molecules, with the aim of prioritizing a hit-list enriched with potential ligands.…”

A magic drug target: Androgen receptor

“…It is believed that the antagonist binding would destabilize the AF2 site and then damage the interaction between the LBD and NTD of AR. Recently, the microsecond long molecular dynamics simulations for the AR LBDs in complex with various ligands reveal that the binding of an antagonist would not only change the orientation of H12 but also impair the helical structure of H12 . Moreover, the enhanced sampling simulations illustrate that the relatively small free energy barrier for the antagonist binding allows the easy transition among different intermediate states with distinct structures, so that the crystal structures of the antagonistic AR LBDs are hard to be determined …”

“…| 1489 microsecond long molecular dynamics simulations for the AR LBDs in complex with various ligands reveal that the binding of an antagonist would not only change the orientation of H12 but also impair the helical structure of H12. 38 Moreover, the enhanced sampling simulations illustrate that the relatively small free energy barrier for the antagonist binding allows the easy transition among different intermediate states with distinct structures, so that the crystal structures of the antagonistic AR LBDs are hard to be determined. 38 The binding of agonistic ligands would induce the formation of the AF2 site ( Figure 2D, PDB ID: 2PIU), a hydrophobic groove encircled by a number of residues in H3, H4, and H12, which is important for the recruitment of coactivators and amplifying the activity of AR.…”

“…38 Moreover, the enhanced sampling simulations illustrate that the relatively small free energy barrier for the antagonist binding allows the easy transition among different intermediate states with distinct structures, so that the crystal structures of the antagonistic AR LBDs are hard to be determined. 38 The binding of agonistic ligands would induce the formation of the AF2 site ( Figure 2D, PDB ID: 2PIU), a hydrophobic groove encircled by a number of residues in H3, H4, and H12, which is important for the recruitment of coactivators and amplifying the activity of AR. At the bottom of the AF2 groove, there are some nonpolar residues including Leu713, Val717, Met735, Ile738, Met895, and Ile899, and above these hydrophobic residues, several acidic residues (Glu894 and Glu898) and basic residues (Lys718, Lys721, and Arg727) located at two nearly opposed sides assemble into a "charge clamp."…”