Possible Pathway(s) of Metyrapone Egress from the Active Site of Cytochrome P450 3A4: A Molecular Dynamics Simulation

Abstract

ABSTRACT:To identify a possible pathway(s) for metyrapone egress from the active site of P450 3A4, a 5-ns conventional molecular dynamics simulation followed by steered molecular dynamics simulations was performed on the complex with metyrapone. The steered molecular dynamics simulations showed that metyrapone egress via channel 1, threading through the B-C loop, only required a relatively small rupture force and small displacement of residues, whereas egress via the third channel, between helix I and helices F and G, required a relatively large force and perturbation of helices I, B, and C. The conventional dynamics simulation indicated that channel 2, located between the ␤1 sheet, B-B loop, and F-G region, is closed because of the movement of residues in the mouth of this channel. The findings suggest that channel 1 can be used for metyrapone egress, whereas both channel 2 and channel 3 have a low probability of serving as an exit channel for metyrapone. In addition, residues F108 and I120 appear to act as two gatekeepers to prevent the inhibitor from leaving the active site. These results are in agreement with previous site-directed mutagenesis experiments.

The Cytochrome P450 3A4 has three Major Conformations: New Clues to Drug Recognition by this Promiscuous Enzyme

“…Our calculations focussed on the entrance channels while the egress ways were considered in the literature through molecular dynamics simulations. [32][33][34][35] The crystallographic structures are snapshots of the 3A4 isoform. Despite that the number of available snapshots is much smaller than the ones usually got from costly molecular dynamics simulations, the detailed analysis of these snapshots gives an insight on the dynamic nature of this isoform and its malleability.…”

Molecular modeling of human cytochrome P450 2W1 and its interactions with substrates

“…The pw2e is penetrating through the B 0 helix/B-C loop. This channel was also suggested to be the possible substrate channel in CYP3A4 [32] and CYP51 [35]. The solvent channel is located between helix I, helix F and the loop preceding C-terminus.…”

“…Previous evidence from both crystal structures and theoretic simulations suggests that different CYPs have different ligand access channels [31][32][33]. For a given CYP, there might exist multiple channels for ligand passage.…”

Anticushing Drug Metyrapone Exhibits Specific Interactions with Serine Containing Systems. A Possible Molecular Target?

“…Some works have focused on the mechanisms by which metyrapone interacts with P450. Its fixation on P450 is independent from the redox state of the enzyme and the availability of oxygen [33,34] and does not modify the conformation of the protein P450A3 [35,36]. Another mechanisms suggested was the possible implication of membrane components, phospholipids or cholesterol [37,38].…”