Melatonin, a widely applied cosmetic active ingredient,
has a variety
of uses as a skin protector through antioxidant and anti-inflammatory
functions as well as giving the body UV-induced defenses and immune
system support. In the body, melatonin is synthesized from a tryptophan
amino acid in a cascade of reactions, but as melatonin is toxic at
high concentrations, it is metabolized in the human skin by the cytochrome
P450 enzymes. The P450s are diverse heme-based mono-oxygenases that
catalyze oxygen atom-transfer processes that trigger metabolism and
detoxification reactions in the body. In the catalytic cycle of the
P450s, a short-lived high-valent iron(IV)–oxo heme cation radical
is formed that has been proposed to be the active oxidant. How and
why it activates melatonin in the human body and what the origin of
the product distributions is, are unknown. This encouraged us to do
a detailed computational study on a typical human P450 isozyme, namely
CYP1A1. We initially did a series of molecular dynamics simulations
with substrate docked into several orientations. These simulations
reveal a number of stable substrate-bound positions in the active
site, which may lead to differences in substrate activation channels.
Using tunneling analysis on the full protein structures, we show that
two of the four binding conformations lead to open substrate-binding
pockets. As a result, in these open pockets, the substrate is not
tightly bound and can escape back into the solution. In the closed
conformations, in contrast, the substrate is mainly oriented with
the methoxy group pointing toward the heme, although under a different
angle. We then created large quantum cluster models of the enzyme
and focused on the chemical reaction mechanisms for melatonin activation,
leading to competitive O-demethylation and C6-aromatic
hydroxylation pathways. The calculations show that active site positioning
determines the product distributions, but the bond that is activated
is not necessarily closest to the heme in the enzyme–substrate
complex. As such, the docking and molecular dynamics positioning of
the substrate versus oxidant can give misleading predictions on product
distributions. In particular, in quantum mechanics cluster model I,
we observe that through a tight hydrogen bonding network, a preferential
6-hydroxylation of melatonin is obtained. However, O-demethylation
becomes possible in alternative substrate-binding orientations that
have the C6-aromatic ring position shielded. Finally, we
investigated enzymatic and non-enzymatic O-demethylation processes
and show that the hydrogen bonding network in the substrate-binding
pocket can assist and perform this step prior to product release from
the enzyme.