ACS Medicinal Chemistry Letters
Letter
blood−brain barrier permeability (see Table S1). Then,
docking calculations into representative conformations of the
MAO-B were studied by X-ray crystallography. The three-
dimensional structures of human MAO-B in complex with 13
24,26
In
particular, two different binding modes between 13 and MAO-
B were predicted (termed binding modes a and b), while a
single binding mode was observed for MAO-A. Figure 2a
shows the binding mode of 13 in MAO-A, and Figure 2b
depicts the more stable binding mode of 13 in MAO-B (herein
in MAO-B (binding mode a) is shown in Figure S1. The two
binding modes in MAO-B are likely due to the peculiar
morphology of this isoform, which is composed of two similar
27,28
subcavities separated by the Ile199 and Tyr326 side chains.
The binding modes are similar to those previously reported for
21,29
other chalcone inhibitors.
The docking scores in MAO-B were −10 kcal·mol for
−
1
−
1
binding mode a and −11 kcal·mol for binding mode b. The
docking score in MAO-A was −7.5 kcal/mol. To better
discriminate between the two binding modes in MAO-B, a
rescoring of the predicted docking poses was performed with a
more rigorous free-energy-based screening methodology (i.e.,
Figure 3. Overall structure of the MAO-B dimer represented as a pink
ribbon diagram (chain A is on the left) with the membrane-spanning
C-terminal helix pointing to the bottom of the figure. The FAD
cofactor is shown in stick representation with carbon, nitrogen,
oxygen, and phosphorus atoms colored in yellow, blue, red, and
magenta, respectively. The structure in complex with 13 (in green,
with fluorine atoms in light blue and oxygen in red) is shown. The
overall fold is identical to that of the enzyme in complex with 14.
30
BEAR) to evaluate the binding free energy of the ligand.
According to the binding free energy scores (ΔGbind)
−
1
kcal·mol more stable than binding mode a (Table S2). In
binding mode b, the B phenyl ring of 13 establishes
hydrophobic interactions with the aromatic rings of the
Tyr398, Tyr435, and Tyr60 side chains and the flavine ring
of FAD. The α,β-unsaturated ketone binds close to the Ile198
and Leu171 side chains, with the carbonyl moiety forming a
hydrogen bond with the Cys172 side chain, as previously
.1 Å resolution, respectively (statistics are reported in Table
S3). For both structures, the overall fold and, in particular, the
active site and the bound inhibitor display the same
conformation between the two monomers of the dimer
contained in the asymmetric unit (the root-mean-square
deviations for Cα atoms are 0.30 and 0.27 Å between chains
A and B for the structures in complex with compounds 13 and
14, respectively). Hereafter, we will refer to subunit A of each
structure for the following discussion.
29
observed for other chalcone compounds. The A ring forms
hydrophobic contacts with the Leu164, Leu167, Phe168 and
Trp119 side chains, as previously observed in ref 29. In
particular, the trifluoromethyl moiety was predicted to be
accommodated near the Trp119 and Leu164 side chains,
establishing close contacts. The hydrogen bond of the carbonyl
with the Cys172 residue is of special interest because this
residue, which is mutated to Asn181 in MAO-A, has a
Inspection of the electron density in the enzyme active site
revealed that 13 and 14 bind in the hydrophobic cavity of
MAO-B (Figure 4a,b, respectively). In both cases the chalcone
moiety is accommodated with the carbonyl oxygen pointing
toward the bottom of the active site and establishing a
hydrogen bond with Cys172 in one of the two conformations
that this residue adopts. This feature was also found in the
21,29
recognized role in MAO-B/MAO-A selectivity.
Impor-
tantly, docking of 13 into MAO-A did not provide an
orientation similar to that of MAO-B. In MAO-A, the
trifluoromethylbenzene moiety (ring A) was predicted to be
accommodated toward the entrance of the MAO-A binding
site near residues Leu97, Ile335, and Leu337 because of steric
clashes with the Phe208 side chain. Moreover, the carbonyl
group of 13 did not establish hydrogen bonds with MAO-A
residues. Interestingly, the lack of a hydrogen bond with
residues in this region of the MAO-A binding pocket, like
those previously observed with Cys172 or Tyr326 into MAO-
B, has been reported to play an important role in isoform
32
MAO-B structures in complex with chromone inhibitors.
The distances between the cysteine side chain and the
chalcone alkene unit are 4.0 and 4.6 Å for 13 and 14,
respectively, both of which are too long for the formation of a
33
covalent bond as previously observed for other targets.
Compound 13 binds with the CF substituent in the entrance
3
cavity space (Figure 4a), which is in agreement with the most
stable orientation predicted by modeling as described above
and is consistent with previous studies highlighting this part of
the active site as a favorable niche for halogen atoms (such as
in the case of safinamide; see Figure 5). Most likely, in the
crystallized MAO-B−13 complex the predicted binding mode
b of 13 is selected. Interestingly, 14 is bound in the opposite
way with respect to the flavin compared with 13, with the CF3
group positioned within the aromatic cage formed by residues
Tyr398 and Tyr435 in front of the flavin (Figure 4b). This is
unique in MAO-B structures and is probably due to the para
position of the substituent on the aromatic ring, which would
clash with the residues belonging to the gating loop formed by
residues 99−110 (on the left in Figure 4). Similar to the
27,28,31
selectivity for the MAO proteins.
The B phenyl ring is
accommodated close to the Tyr60 and Tyr407 side chains and
FAD, similar to what was observed in MAO-B. Altogether,
these differences help explain the experimentally observed
selectivity of compound 13 for MAO-B over MAO-A.
Considering that docking calculations on 13 suggested two
alternative orientations, one of which was clearly favored over
the other, we sought to investigate whether para (compound
1
4) instead of meta (compound 13) trifluorocarbon
substitution could play a role in discriminating the ligand
orientation. To this aim, the binding modes of 13 and 14 in
1
155
ACS Med. Chem. Lett. 2021, 12, 1151−1158