Molecular Simulations of Aromatase Reveal New Insights Into the Mechanism of Ligand Binding

Abstract

CYP19A1, also known as aromatase or estrogen synthetase, is the rate-limiting enzyme in the biosynthesis of estrogens from their corresponding androgens. Several clinically used breast cancer therapies target aromatase. In this work, explicitly solvated all-atom molecular dynamics simulations of aromatase with a model of the lipid bilayer and the transmembrane helix are performed. The dynamics of aromatase and the role of titration of an important amino acid residue involved in aromatization of androgens are investigated via two 250-ns long simulations. One simulation treats the protonated form of the catalytic aspartate 309, which appears more consistent with crystallographic data for the active site, while the simulation of the deprotonated form shows some notable conformational shifts. Ensemble-based computational solvent mapping experiments indicate possible novel druggable binding sites that could be utilized by next-generation inhibitors. In addition, the effects of protonation on the ligand positioning and channel dynamics are investigated using geometrical models that estimate the opening width of critical channels. Significant differences in channel dynamics between the protonated and deprotonated trajectories are exhibited, suggesting that the mechanism for substrate and product entry and the aromatization process may be coupled to a “locking” mechanism and channel opening. Our results may be particularly relevant in the design of novel drugs, which may be useful therapeutic treatments of cancers such as those of the breast and prostate.

Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4

“…6 It is worth noting that despite some differences in membrane immersion depths and orientations of individual CYPs, all recent studies have consistently reported insertion of the N-terminal, F' and G' helices into the membrane interior, 9,11,16,21 , while the B/C loop and F and G helices in CYP3A4 11 have been reported to interact with the membrane. Figure 5 shows that with increasing content of cholesterol, the F and (Table 1).…”

“…16 A recent study on membrane anchored aromatase considered the more complex composition of the ER membrane. 21 However, to date, no systematic study into the effect of membrane composition on the positioning of CYP has been published.…”

Computational Approaches Elucidate the Allosteric Mechanism of Human Aromatase Inhibition: A Novel Possible Route to Small-Molecule Regulation of CYP450s Activities?

“…32 According to previous computational and experimental studies [33][34][35] Asp309 was simulated in its neutral form. 33,34 However, considering the large number of drug/DNA adducts under investigation and that the membrane environment should similarly influence all systems, all the simulations were run considering only the cytosolic portion of HA immersed in a box of pure water simulated using the TIP3P model. 33,34 However, considering the large number of drug/DNA adducts under investigation and that the membrane environment should similarly influence all systems, all the simulations were run considering only the cytosolic portion of HA immersed in a box of pure water simulated using the TIP3P model.…”

Recent Progress in the Discovery of Next Generation Inhibitors of Aromatase from the Structure–Function Perspective

“…Results from other dynamical simulations also have demonstrated similar flexibility of the AROM structure, especially in the access channel region, even on membrane insertion. 153,154 Despite the observed rigidity of the active site core, the likelihood of some ligand-induced flexibility cannot be ruled out. In addition, inhibition kinetics data 47 as well as computational analysis 117 suggest possible secondary binding sites for nonsteroidal ligands.…”