Novel hydrazine molecules as tools to understand the flexibility of vascular adhesion protein-1 ligand-binding site: Toward more selective inhibitors

Article abstract of DOI:10.1021/jm200059p

Vascular adhesion protein-1 (VAP-1) belongs to a family of amine oxidases. It plays a role in leukocyte trafficking and in amine compound metabolism. VAP-1 is linked to various diseases, such as Alzheimer's disease, psoriasis, depression, diabetes, and obesity. Accordingly, selective inhibitors of VAP-1 could potentially be used to treat those diseases. In this study, eight novel VAP-1 hydrazine derivatives were synthesized and their VAP-1 and monoamine oxidase (MAO) inhibition ability was determined in vitro. MD simulations of VAP-1 with these new molecules reveal that the VAP-1 ligand-binding pocket is flexible and capable of fitting substantially larger ligands than was previously believed. The increase in the size of the VAP-1 ligands, together with the methylation of the secondary nitrogen atom of the hydrazine moiety, improves the VAP-1 selectivity over MAO.

Full text of DOI:10.1021/jm200059p

ARTICLE
pubs.acs.org/jmc
Novel Hydrazine Molecules as Tools To Understand the Flexibility of
Vascular Adhesion Protein-1 Ligand-Binding Site: Toward More
Selective Inhibitors
Elisa M. Nurminen,† Marjo Pihlavisto,‡ Lꢀaszlꢀo Lꢀazꢀar,§ Ulla Pentik€ainen,† Ferenc F€ul€op,§ and
Olli T. Pentik€ainen*,†
†Department of Biological and Environmental Science and Nanoscience Center, University of Jyv€askyl€a, P.O. Box 35, FI-40014
Jyv€askyl€a, Finland
‡BioTie Therapies Corporation, Tykist€okatu 6, FI-20520 Turku, Finland
§Institute of Pharmaceutical Chemistry, University of Szeged, H-6720 Eotvos 6, Szeged, Hungary
ABSTRACT: Vascular adhesion protein-1 (VAP-1) belongs to
a family of amine oxidases. It plays a role in leukocyte trafficking
and in amine compound metabolism. VAP-1 is linked to various
diseases, such as Alzheimer’s disease, psoriasis, depression,
diabetes, and obesity. Accordingly, selective inhibitors of
VAP-1 could potentially be used to treat those diseases. In this
study, eight novel VAP-1 hydrazine derivatives were synthesized
and their VAP-1 and monoamine oxidase (MAO) inhibition ability was determined in vitro. MD simulations of VAP-1 with these
new molecules reveal that the VAP-1 ligand-binding pocket is flexible and capable of fitting substantially larger ligands than was
previously believed. The increase in the size of the VAP-1 ligands, together with the methylation of the secondary nitrogen atom of
the hydrazine moiety, improves the VAP-1 selectivity over MAO.
mine oxidases (AOs) are enzymes that metabolize diverse
amine compounds by converting them into corresponding
Alterations in reaction product levels and corresponding diseases
can arise from either overexpression5-11 or underexpression of VAP-
112-16 or from increased enzymatic activities of VAP-1.17-22
VAP-1 is a potential target for drug development because it is
involved in many diseases. Various VAP-1 inhibitors have already
been developed, such as phenylallylhydrazines23 thiocarbamoyl
derivatives,24 carboxamides and sulfonamides,25 and hydrazines1,26
(Figure 1). VAP-1 function can also be modulated by using (1)
peptides with NH3þ functionality (lysine side chain),27-29 (2) func-
tion blocking antibodies (to inhibit the leukocyte trafficking),30
and (3) small interfering RNAs (to inhibit both adhesion and
enzymatic functions).31 Because amine oxidases have partly
overlapping substrate specificities, it is challenging to design
selective inhibitors for one member of an AO family. The
compounds mentioned above establish a promising starting
point for VAP-1 blocking pharmaceuticals, but they are not
selective or safe enough yet.
A
aldehydes with concomitant hydrogen peroxide and ammonia
production. AOs can be divided into two families based on their
cofactors. The first family of AOs includes monoamine oxidases
A and B (MAOs A and B, EC 1.4.3.4.) and polyamine oxidase
(EC 1.5.3.11.), which have flavin adenosine dinucleotide as a
cofactor. The second family of AOs include diamine oxidase
(DAO, EC 1.4.3.22.), lysyl oxidase (EC 1.4.3.13.), and vascular
adhesion protein-1 (VAP-1, EC 1.4.3.21.), which all have mod-
ified tyrosine (topaquinone, TPQ) or lysine residue as a cofactor.
VAP-1 is an interesting member of the AO family. In addition
to being an enzyme, it also has an adhesive task in leukocyte
extravasation.1 VAP-1 is a type II transmembrane glycoprotein
with a large glycosylated extracellular domain and a short
N-terminal intracellular domain, which is involved in the adhe-
sion of lymphocytes to endothelial cells and lymphocyte recircu-
lation.1 VAP-1 is primarily expressed on endothelial cells, but
some expression is also detected in nonendothelial cells, e.g.,
blood vessel smooth muscle cells.2 VAP-1 activity can exert
insulin-like effects on glucose metabolism via hydrogen
peroxide.3 Hydrogen peroxide acts as a local signaling molecule,
but excess amounts can cause oxidative stress. Other reaction
products are potential toxins as well; for example, methylglyoxal
can form advanced glycation end products.4 Maintenance of
constant levels of the reaction products is crucial because in
normal concentrations, they are beneficial and necessary, but
increased or decreased amounts can cause severe diseases.
The crystal structures determined for human VAP-132-34
show that the structure of VAP-1 is homodimeric. The active
site is located near the dimerization interface, buried deep within
the protein, and includes the TPQ cofactor and the catalytic base
(Asp386).32-34 The accessibility of the active site is restricted by
Leu469, which blocks the entrance to the ligand-binding site.34
We have recently reported that hydrazine derivatives are
potential selective VAP-1 inhibitors.26 The reaction mechanism
Received: October 17, 2010
Published: March 15, 2011
r
2011 American Chemical Society
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Figure 1. Structures of some known small molecule VAP-1 inhibitors: phenylallylhydrazines,23 thiocarbamoyl derivatives,24 carboxamides and
sulfonamides,25 hydrazines,1,26 and pyrroline derivatives.63
Figure 2. Binding of 2-hydrazinopyridine (2-HP) to TPQ: (A) reaction mechanism of VAP-1;36 (B) resonance structures of 2-HP-TPQ complex, the
prevalent hydrazone form in physiological pH and the distinctive azo form, detected at pH > 9; (C) 3D crystal structure of bound 2-HP in human VAP-1
(PDB code 2C1133); (D) 3D crystal structure of 2-HP in E. coli amine oxidase (PDB code 1SPU35).
of the TPQ catalyzed reaction has been studied extensively
(Figure 2A), and it appears that the efficacy of hydrazine
molecules to inhibit copper amine oxidases is based on their
ability to form a mimic of the substrate Schiff base intermediate
with the enzyme.35 In the case of a natural substrate, the catalytic
aspartic acid participates in the deamination reaction where its
role is to abstract a proton from the natural substrate. When a
hydrazine compound is bound, instead of a substrate molecule,
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Table 1. Novel VAP-1 Inhibitor Compounds
compd
R1
R2
relative configuration
IC50 VAP-1 (μM)a
IC50 MAO (μM)b
selectivityc
2a
H
H
H
1R
0.04 ( 0.01
0.15 ( 0.01
50 ( 3
9.90 ( 2.20
9.80 ( 1.00
34 ( 3
250
65
2b
H
1S
5
H
C6H5
1R*,2S*
d
0.7
9
8
H
(CH2)2CH3
C6H5
1.20 ( 0.16
0.28 ( 0.03
1.18 ( 0.08
1.06 ( 0.04
0.33 ( 0.02
0.26 ( 0.04
11 ( 2
11a
11b
11c
11d
12e
CH3
CH3
CH3
CH3
CH3
1R,2S
1S,2S
1R,2R
1S,2R
1R*,2S*
70 ( 12
85 ( 9
250
72
C6H5
C6H5
99 ( 10
105 ( 13
28 ( 1
90
C6H5
320
(CH2)2CH3
110
a IC50 data for VAP-1 in μM, mean ( SEM of two to four similar experiments. b IC50 data for MAO in μM, mean ( SEM of two to four similar
experiments. c Calculated IC50(MAO)/IC50(VAP-1). d Mixture of diastereomers. e Reference 26.
the enzymatic reaction is halted because the catalytic aspartic acid
cannot abstract a proton from the secondary amine group.35 The
reactivity of the hydrazines also makes these molecules excellent
inhibitors for AOs.
of VAP-1 flexibility and its inhibitor binding capability. These
molecules show high VAP-1 selectivity over MAO. Additionally,
molecular dynamics (MD) simulations were used to study the
effect of bulky inhibitor binding onto the VAP-1 structure. These
simulations visualize the high reorganization capability of the
amino acids that line the ligand-binding cavity, providing a new,
extra space to accommodate the ligands. This space could be
utilized in the development of new, better, and more selective
VAP-1 inhibitors. We also show that, compared to the 2-hydra-
zinopyridine and other nonsubstituted hydrazine molecules,
substitution on the secondary amine group results in a distinct
binding mode.
The available 3D crystal structure of VAP-1 with bound
inhibitor 2-hydrazinopyridine (PDB code 2C1133) shows the
general mechanism by which an unsubstituted hydrazine binds to
VAP-1 (Figure 2B and Figure 2C). The primary amine group of
the hydrazine binds covalently to the TPQ cofactor. The secon-
dary amine group of the hydrazine participates in a hydrogen
bond, with the C4 oxygen of the TPQ (Figure 2B and
Figure 2C), with the Asp386 carboxyl group, or with both
(Figure 2D). This strongly determines the conformation of the
rest of a molecule.36 On the basis of the crystal structure of VAP-1
with 2-hydrazinopyridine (PDB code 2C1133), the distances and
angles from the secondary nitrogen atom to the C4 oxygen atom
of the TPQ cofactor and the Asp386 carboxylate group are
appropriate for hydrogen bonding, suggesting a positively
charged amine group (Figure 2C). The crystal structure of
Escherichia coli amine oxidase, in complex with 2-hydrazinopyr-
idine (1SPU35), demonstrates another type of binding. In this
complex structure, the C4 oxygen atom of the TPQ is situated
close to the conserved Tyr369, which suggests a shared proton35
(Figure 2D). The secondary amine of the 2-hydrazinopyridine
turns toward the C6 of the TPQ rather than toward C4, as it does
in the 2C11 structure,33 showing that hydrogen bonding of the
secondary amine group occurs to catalytic Asp383 and in the
main chain of Val463. Furthermore, this also suggests a positively
charged secondary amine group.
’ RESULTS AND DISCUSSION
Design of Novel Hydrazines. Previously, we reported the
construction of 3D-QSAR models, based on 47 hydrazine
molecules and their IC50 values for VAP-1 and MAO.26 The
VAP-1 model suggested that introduction of steric groups to
position C2 (Table 1) would be beneficial for VAP-1 potency.
Therefore, we designed a small series of novel hydrazine mole-
cules with varied C2 substituents. The molecules used for model
building were smaller than the newly designed molecules
(Table 1). Thus, the prediction of novel molecules, using the
QSAR model, was omitted prior to the synthesis and the in vitro
testing of molecules.
Synthesis. In the syntheses of 2a,b, 5, 8, and 11a-d,
conventional methods for the preparation of hydrazino
alcohols37 were applied. Enantiomers of 2-hydrazino-1-pheny-
lethanol (2a,b) were prepared by hydrazinolysis of the corre-
sponding (S)- or (R)-styrene oxide (1a,b), resulting in a mixture
of the regioisomeric products, 2 and 3, in a ratio of about 2:1,
from which the main components (2a,b) were isolated by
fractional crystallization of the hydrogen maleate salt. Similarly,
(1R*,2S*)-2-hydrazino-1,2-diphenylethanol (5) was obtained
The previously published three-dimensional quantitative
structure-activity relationship model of VAP-1 hydrazine-de-
rived inhibitors26 predicted that the larger ligands could show
even higher VAP-1 selectivity over MAO than was earlier
reported. Here, we have designed, synthesized, and tested the
in vitro VAP-1 and MAO inhibition potency of eight novel
hydrazine molecules that substantially enlarge the understanding
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Scheme 1a
Scheme 3a
a Reagents: (a) NaNO2, AcOH, H2O (yield, 95-97%); (b) LiAlH4,
THF (yield, 58-65%).
model, where Leu469 is rotated, as described above, resulting in a
similar binding conformation, as seen in the VAP-1-bound 2-hydra-
zinopyridine (Figure 2C). To understand the binding of 2a and 2b in
more detail, MD simulations were used to study the complexes
obtained from the docking. These simulations of VAP-1, with bound
2a,b, show that the surrounding amino acids Tyr384, Phe389,
Tyr394, Leu468, and Leu469 form a hydrophobic pocket that nicely
accommodates the phenyl rings of 2a and 2b (Figure3). Both2a and
2b can form a tight hydrogen bond network (Figure 3), which
explains their excellent potency for VAP-1. The orientation of the
hydroxyl group (1R = 2a and 1S = 2b) represents the greatest
difference in the ability of 2a and 2b to bind to VAP-1. The hydroxyl
group of 2a points away from Tyr384, where it has more space
(Figure 3A), while the hydroxyl group of 2b has difficulties
accommodating itself between the aromatic rings of Tyr384 and
Phe389 (Figure 3B). This may explain why 2a binds 4 times better to
VAP-1 than does 2b. The binding of 2a and 2b induce conforma-
tional changes in two amino acid side chains: Met211 and Leu469
(shown with 2a in Figure 3A). This reveals new free space near C2 of
2a,b (Figure 3).
Effect of Propyl Substitution at C2. Docking simulations
indicated that the addition of a propyl group to C2, compound 8
(Table 1), can utilize the additional space (Figure 4A), revealed
by the rotation of Met211 and Leu469, during the MD simula-
tion of VAP-1 with bound 2a and 2b (parts A and B of Figure 3,
respectively). On the basis of the binding of 2a and 2b (parts A
and B of Figure 3), the 1R,2S enantiomer of 8 is optimal for
binding to VAP-1 because (a) the hydroxyl group can freely
interact with the Asp386 and (b) the 2S-propyl can accommo-
date itself into the space formed by the rotation of Met211 and
Leu469, during the MD simulation of VAP-1 with bound 2a,b
(Figure 4A). Although compound 8 seems to fit into the VAP-1
ligand-binding site, its inhibitory activity is clearly worse than the
inhibitory activity of 2a and 2b (Table 1).
As previously reported, the methylation of the secondary
amine at the hydrazine moiety (N-methylation) can lower the
potency of ligands.26 However, the N-methylation of 8 increases
the potency because the IC50 value of N-methylated 12 is 0.26
μM while the IC50 value of nonmethylated 8 is 1.20 μM
(Table 1). In order to study the binding of the N-methylated
compound 12 (1R,2S), it was docked into the VAP-1 conforma-
tion obtained from the MD simulations with 2a. As expected, the
N-methylated compound 12 yielded a distinct conformation
than did the nonmethylated compound 8 (Figure 4). The N-
methyl group of 12 points toward the main chain of Leu469,
whereas in compound 8, the hydrogen of the same nitrogen atom
is hydrogen-bonded with Asp386 and the hydroxyl group of
TPQ (Figure 4). The conformation of 8 is further stabilized by
a Reagents: (a) H2NNH2, H2O, and EtOH (yield, 52-62%).
Scheme 2a
a Reagents: (a) NaBH4, MeOH (yield, ∼100%); (b) H2NNH2, H2O,
and EtOH (yield, 53%).
from the ring-opening reaction of (()-trans-stilbene oxide (4)
with hydrazine hydrate (Scheme 1).38
A nucleophilic substitution reaction of the corresponding bromo-
substituted alcohol (7) with hydrazine was applied for the synthesis
of 2-hydrazino-1-phenylpentanol (8) (Scheme2).37,39 Compound 7
was formed as a diastereomeric mixture in the reduction of (()-2-
bromo-1-phenylpentanone40 (6) with NaBH4.41 All our efforts to
separate the diastereomers of 8 have failed.
Isomeric 2-(1-methylhydrazino)-1,2-diphenylethanols 11a-
d were prepared from enantiomerically pure amino alcohols 9a-
d,42-44 using a two-step procedure that included N-nitrosation
and subsequent LiAlH4 reductions of the N-nitroso intermedi-
ates 10a-d (Scheme 3).
In Vitro Potency. In vitro potencies were determined for the
synthesized inhibitors 2a,b, 5, 8, and 11a-d (Table 1). The in
vitro potency of 12 was reported earlier.26 The results indicate
that the compounds 2a, 11a, and 11d are highly specific
inhibitors of human VAP-1 activity. The IC50 for VAP-1 inhibi-
tion varies from 50 to 0.04 μM (Table 1). Major differences were
found in the selectivity of the inhibitors against the total MAO
potency, with selectivity ranging from nonselective to 320-fold
selective (Table 1).
Binding of 1R- and 1S-2-Hydrazinyl-1-phenylethanol to
VAP-1. In the crystal structure of VAP-1 with a bound inhibitor,
2-hydrazinopyridine, Leu469 blocks the ligand-binding cavity.33
However, as we recently reported, during the MD simulations of
VAP-1 with inhibitors larger than 2-hydrazinopyridine, Leu469
rotates and unblocks the ligand-binding cavity, providing to the
ligands free access from the solvent to the ligand-binding
pocket.26 This rotated Leu469 conformation was used here as
the starting structure.
Two stereoisomers of 2-hydrazinyl-1-phenylethanol (1R = 2a
and 1S = 2b; Table 1) are the simplest molecules studied in this
research. Both stereoisomers were docked to the VAP-1 structural
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Figure 3. Binding of 2a,b to VAP-1 (parallel stereoview). (A) In the course of MD simulation the side chains of Met211 and Leu469 change their
conformation (black sticks) but the rest of the side chains remain close to the starting conformations (gray sticks). TPQ-2a is shown in ball-and-stick.
The phenyl ring of 2a is surrounded by hydrophobic Leu468 and Leu469 and aromatic Tyr384, Phe389, and Tyr394 (surface rendering). Multiple
hydrogen bonds are present: Asp386 forms hydrogen bonds (black dashed lines) (1) to TPQ hydroxyl group, (2) to second nitrogen of the hydrazine
functionality, and (3) to the hydroxyl group of the 2a. The second nitrogen of 2a forms a hydrogen bond with TPQ hydroxyl group. (B) The surface
rendering of the amino acids closest to 2b reveals space near C2 of 2b. The hydrogen bond network (black dashed lines) between TPQ, 2b, and Asp386
is as tight as in the case of 2a. The movement of Met211 is not as prominent as in the case of 2a.
the hydrogen bond between the hydroxyl group of 8 and Asp386
(Figure 4A). Compound 12 forms only two hydrogen bonds: (1)
Asp386, the hydroxyl group of TPQ, and (2) Asp386, the
hydroxyl group of 12 (Figure 4B). Accordingly, the conforma-
tion of 8 is more strongly determined by hydrogen bonding, and
these interactions force 8 into a bended conformation. This
bended conformation restricts the C2 propyl substituent of 8
from taking advantage of all the extra space created by the
rotation of the Met211 side chain. In compound 12, whose
conformation is not strictly determined by hydrogen bonding,
the propyl substituent can extend deeper into the extra space
(Figure 4). This can be seen as the difference in IC50 values
between 8 and 12, which are 1.20 and 0.26 μM, respectively
(Table 1).
Effect of Phenyl Substitution at C2. The MD simulations of
VAP-1 with bound 2a and 2b (Figure 3) and the dockings of 8
and 12 (Figure 4) into VAP-1 clearly show that in compounds 8
and 12, it is possible to add an even larger substituent than propyl
to the C2-position. In the compound series 11, the C2 sub-
stituent is phenyl (R2 in Table 1) while the C1 substituent is
methyl (R1 in Table 1), which is the same as in compound 12.
The docking of the 11a (1R, 2S) into VAP-1 conformation,
obtained in the MD simulation of VAP-1 with bound 2a,b, shows
that the phenyl might fit into the VAP-1 ligand-binding site.
However, it is difficult to use static protein conformation to
predict the binding of other enantiomers of 11, i.e., 11b, 11c, and
11d. Therefore, to understand the exact binding modes of the
enantiomers, we docked all four enantiomers (11a-d) into a
VAP-1 crystal structure33 where the Leu469 side chain was rotated,
as described above, and then the complexes were simulated
with MD.
The IC50 data of VAP-1 inhibition of 11a-d are intriguing.
Although these molecules differ significantly in their stereo
configuration, and thus also in their three-dimensional structure,
their VAP-1 inhibition potencies show some similarities (11a is
only 4 times more potent than 11b) (Table 1). The MD
simulations performed for 11a-d bound to VAP-1 indicate
two different hydrogen bonding partners for the C1 hydroxyl
group, which (1) in 11a and 11b form a hydrogen bond to the
TPQ (parts A and B of Figure 5, respectively) while (2) in 11c
(Figure 5C) and 11d (Figure 5D) form a hydrogen bond to the
Asp386. Regardless of whether the hydroxyl group of the ligand is
hydrogen-bonded with the TPQ or the Asp386, one of the
phenyl rings is turned into the hydrophobic pocket formed by
Tyr384, Phe389, Tyr394, Leu468, and Leu469 (Figure 5) and
the N-methyl is pointed toward Ala370. In the conformation in
which an intramolecular hydrogen bond with TPQ exists, the
phenyl ring at carbon 2 points toward the hydrophobic pocket
(11a and 11b, parts A and B of Figure 5). However, with the 11c
and 11d enantiomers, whose conformation is driven by the
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Figure 4. Binding modes of (A) 8 and (B) 12 based on docking simulations to VAP-1 conformation obtained from MD simulations (parallel
stereoview). (A) The bound 8 and TPQ are shown in ball-and-stick. A groove formed between Ser496, Met211, and Leu469 can accommodate the C2
substituent. A similar hydrogen bond network is formed as in 2a. (B) The binding of 12 is distinct to 8 because of the methylation of the second nitrogen
atom. Asp386 can form hydrogen bonds to (1) hydroxyl group of 12 and (2) hydroxyl group of TPQ. The phenyl ring of 12 is buried inside the
hydrophobic pocket, similar to that in 8. The propyl substituent extends toward Met211. The N-methyl substituent points toward Leu469 main chain.
The hydroxyl group of 12 is closer to the hydroxyl group of TPQ than the hydroxyl group of 8.
hydrogen bonding with the Asp386 (parts C and D of Figure 5),
the phenyl ring attached to carbon 1 points toward the hydro-
phobic pocket. The phenyl ring that is not buried inside the
hydrophobic pocket forms a π-π interaction either with Tyr372
or with Tyr384 (Figure 5).
It was expected that the removal of the N-methyl from 11
would reduce inhibitory activity, just as it did in the molecule pair
8 and 12. Indeed, the IC50 for 5 is 50 μM, whereas those of 11a-
d vary between 0.28 and 1.18 μM (Table 1). Accordingly,
N-methylation increases the VAP-1 potency if, simultaneously,
C2 has a large substituent. This is interesting because without the
C2-substitution the N-methylation has an opposite effect.26
VAP-1 over MAO Selectivity. All the compounds evaluated in
this study are weak MAO inhibitors showing only a 10-fold
variation in MAO inhibition: 2a (9.90 μM), 2b (9.80 μM), 8 (11
μM), 11a (70 μM), 11b (85 μM), 11c (99 μM), 11d (105 μM),
12 (28 μM), and 5 (34 μM). Thus, in general, N-methylated
compounds with a phenyl substituent at the R2-position (11a-
d) are slightly worse inhibitors of MAO than those that do not
have this type of substituent (2, 5, 8, and 12) (Table 1). In
contrast, the N-methylation for VAP-1 inhibition has an opposite
effect; in this set of compounds, the N-methylation significantly
increases the selectivity toward VAP-1 over MAOs (Table 1).
The size of the molecule has a negative effect on the MAO
binding(Figure 6) becausethe ligand-binding pocket in the MAO
is smaller than it is in the VAP-1. On the basis of the crystal
structure of human MAO B in complex with phenylethylhydra-
zine, i.e., phenelzine,45 it can be postulated that both nitrogens of
hydrazine moiety are cleaved off during the course of the reaction
and the remaining part of the ligand forms a covalent bond with
The conformational changes observed in the MD simulations of
VAP-1 with bound inhibitors are predominantly rotational changes
in the side chains of the amino acids. The most substantial changes in
the conformations of the amino acids in the ligand-binding pocket
are related to Met211, Leu469, and TPQ conformations. Interest-
ingly, the conformation of Leu469 seems to be dependent upon the
C2 configuration of the ligand. Here, with 11c and 11d, the Leu469
returns to the conformation seen in the crystal structure (i.e., to block
the ligand-binding cavity33). However, with the 11a and 11b
diastereomers, Leu469 remains in the conformation, where access
to the ligand-binding cavity is free. The conformation of Met211 is
not dependent upon configurations of C1 and C2. In compounds
11a-d, Met211 turns away from the bound ligand revealing extra
space (Figure 5). This is similar to the conformation of Met211 in
compounds 2a and 2b (Figure 3). The conformation of TPQ also
alters on the course of MD simulation, depending upon the C2
configuration of the ligand. With 11c and 11d, the TPQ moves to
resemble the inactive conformation34 more than the active
conformation.33 This change in TPQ conformation does not affect
the hydrogen-bonding network.
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Figure 5. Continued
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Figure 5. Binding conformations of 11a-d to VAP-1 based on MD simulations (parallel stereoview). Starting structure of VAP-1 MD simulation is
visualized in gray and final structure in green. TPQ-ligand complexes and surrounding amino acids are represented in ball-and-sticks and sticks,
respectively. Hydrogen bonds in MD starting structure are drawn with dotted black line, and those in MD final structure are drawn with dotted orange
line. All main chain atoms are omitted. (A) The binding of 11a to VAP-1. In the MD simulation starting structure the ligand forms hydrogen bond with
Asp386. In the final structure the ligand OH group has moved markedly. This change recruits Tyr372 and Tyr384 to form hydrogen bonds that were
initially absent, resembling the final structure of the 11b. (B) Binding of 11b to VAP-1. The ligand has formed a hydrogen bond with the TPQ OH group.
The surrounding tyrosines Tyr372 and Tyr384 also form hydrogen bonds to the ligand and TPQ. Tyr372 changes its conformation during the
simulation, and in the final structure it is close enough to be hydrogen-bonded to Tyr384. The overall conformation of the ligand does not change
markedly. (C) Binding of 11c to VAP-1. Ligand OH group forms a hydrogen bond with Asp386. Surrounding aromatic amino acids (Tyr372, Tyr384,
and Phe389) undergo conformational changes during simulation as the ligand moves. TPQ moves toward the protein core. (D) Binding of 11d to VAP-
1. The ligand is hydrogen-bonded to the Asp386 throughout the simulation. The TPQ-ligand complex moves slightly toward the protein core. A
hydrogen bond between Tyr372 and TPQ OH group can be detected.
Figure 6. Binding of 5 and 8 into MAO B ligand binding site. The ligand binding pocket of MAO is small and narrow (represented as green surface).
The ligands, 5 and 8, are covalently docked to the nitrogen of cofactor FAD and are represented as ball-and-sticks. The reaction product of 8 (A) fits
slightly better into the ligand binding pocket of MAO than that of 5 (B), thus explaining their difference in inhibitor potency to MAO. The surrounding
tyrosines, Tyr60, Tyr398, and Tyr435, of the ligand binding pocket are shown as transparent ball-and-sticks.
the nitrogen atom at the central ring of the FAD. The docking
simulations of the probable covalent reaction product of 8
(1-phenyl-2-propanylethanol, Figure 6A) and 5 (1,2-dipheny-
lethanol, Figure 6B) to MAO B indicate that the MAO ligand-
binding site is too small to properly accommodate these
compounds. Furthermore, the MAO ligand-binding site is too
small to accommodate compounds 11a-d (data not shown).
However, it is notable that the propyl group of 8, at R2-position,
fits slightly better into the MAO ligand-binding site (Figure 6A),
possibly explaining the small difference in their potency
(Table 1). Additionally, the docking of 8 into the MAO ligand-
binding site is easier because of the flexibility of the propyl group
in contrast to the phenyl group in 5.
molecules compared to the reactivity of the nonsubst-
ituted molecules. Even though molecules 8 and 12 yield
the same reaction product in MAO, N-methylated compound
12 has only half of the inhibition activity for MAO than does
compound 8, which is not N-methylated (Table 1). Similarly,
non-N-methylated compound 5 has twice the potency to
MAO than do the N-methylated compounds 11a-d
(Table 1).
’ CONCLUSIONS
This study has explored the flexibility of the VAP-1 ligand-
binding site and developed several novel VAP-1 selective in-
hibitors over MAO. The MD simulations show that the static
crystal structures of VAP-1 provide only a limited view into
The negative effect of N-methylation on MAO binding
may be explained by the lowered reactivity of the N-methylated
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Journal of Medicinal Chemistry
ARTICLE
ligand-binding capability. The VAP-1 ligand-binding site can
accommodate bulkier inhibitors than can MAO. Additionally, the
N-methylation of large hydrazines increases the potency of VAP-
1 while the inhibition of MAO is simultaneously reduced, thus
leading to VAP-1 selectivity. Altogether, these findings open up
new avenues into the discovery of novel and selective inhibitors
to treat diseases related to VAP-1.
extracted with Et2O (2 ꢀ 25 mL). The combined organic phases were
dried (Na2SO4) and evaporated to give compound 7 as an oily product
which was used in the next step without further purification. Yield: 2.42 g
(∼100%).
To a solution of compound 7 (2.42 g, 10 mmol) in ethanol (30 mL)
hydrazine hydrate (2.50 g, 50 mmol) was added, and the mixture was
heated under reflux for 6 h. The solvent and the unreacted hydrazine
hydrate were evaporated off, and evaporation was repeated twice after
addition of toluene (10 mL). The oily residue was treated with an
equivalent amount of fumaric acid in a mixture of EtOH and Et2O to give
crystalline fumarate salt which was filtered off and recrystallized. Beige
crystalline substance; yield 1.64 g (53%); mp 170 °C (decomposition)
(EtOH-Et2O). 1H NMR (DMSO-d6) δ (ppm): 0.68 (t, 3H, J = 7.0 Hz,
CH3), 0.94-1.36 (m, 4H, 2 ꢀ CH2), 2.80-2.91 (m, 1H, NCH), 4.53
(d, 1H, J = 8.2 Hz, OCH), 6.51 (s, 2H, CHCOOH), 7.16-7.42 (m, 5H,
C6H5). Anal. Calcd for C15H22N2O5: C, 58.05; H, 7.15; N, 9.03. Found:
C, 57.75; H, 6.94; N, 8.89.
’ MATERIALS AND METHODS
Materials. Cell culture reagents were supplied by Gibco. Other
chemicals were of analytical or reagent grade and were purchased from
commercial suppliers.
Synthesis of the Novel Hydrazine-like Molecules. General
Methods. Melting points were measured on a Kofler hot-plate micro-
scope apparatus and are uncorrected. For routine thin-layer chromatog-
raphy (TLC), silica gel 60 F254 plates (Merck, Germany) were used.
Elemental analyses were performed with a Perkin-Elmer 2400 CHNS
elemental analyzer. 1H NMR spectra were recorded in CDCl3, in
DMSO-d6, or in D2O solutions on a Bruker DRX 400 spectrometer.
These spectra indicated the >95% purities of the prepared compounds.
Chemical shifts are given in δ (ppm) relative to TMS (DMSO-d6) or to
TSP (D2O) as internal standards.
General Procedure for the Preparation of Hydrazino Alcohols 2a,b.
To a stirred solution of hydrazine hydrate (5.01 g, 0.10 mol) in EtOH
(10 mL) a solution of (R)- or (S)-styrene oxide (1a or 1b, 1.20 g, 10
mmol) in EtOH (5 mL) was added dropwise. After addition was
complete, the mixture was kept at 60 °C for 10 min. The solvent was
evaporated off, and the oily residue was dissolved in EtOH and treated
with an equivalent amount of maleic acid. The separated crystals of the
corresponding maleates (2a,b) were filtered off and recrystallized.
(R)-2-Hydrazino-1-phenylethanol Hydrogen Maleate (2a Hydro-
gen Maleate). Beige crystalline solid; yield 1.45 g (54%); mp 98-
103 °C (EtOH-Et2O); [R]D -44 (MeOH, c 0.50). 1H NMR (D2O) δ
3.38 (m, 2H, J = 7.9 Hz, NCH2), 5.07 (dd, 1H, J = 7.1, 5.7 Hz, OCH),
6.30 (s, 2H, CHdCH), 7.38-7.50 (m, 5H, C6H5). Anal. Calcd for
C12H16N2O5: C, 53.73; H, 6.01; N, 10.44. Found: C, 53.51; H, 5.93;
N, 10.28.
General Procedure for the Preparation of N-Nitrosoamino Alcohols
10a-d. A solution of NaNO2 (1.38 g, 20 mmol) in H2O (10 mL) was
added dropwise to a suspension of the corresponding isomer of
2-methylamino-1,2-diphenyl-1-ethanol (7a-d, 2.27 g, 10 mmol) (10
mmol) in H2O (25 mL) with vigorous stirring on an ice-cold bath, and
then AcOH (0.90 g, 15 mmol) was added dropwise. The mixture was
stirred at room temperature for 8 h, then was extracted with EtOAc (4 ꢀ
30 mL). The combined organic phases were dried (Na2SO4) and
evaporated under reduced pressure to give the N-nitroso derivative as
a crystalline product, which was filtered and washed with n-hexane.
Yield: 2.44-2.49 g (95-97%). The crude product was used in the next
step without further purification.
General Procedure for the Preparation of Hydrazino Alcohols 11a-
d. A solution of the corresponding isomer of 2-methylamino-N-nitroso-
1,2-diphenyl-1-ethanol (10a-d, 1.54 g, 6 mmol) in THF (12 mL) was
added dropwise to a strirred and ice-cooled suspension of LiAlH4 (0.46
g, 12 mmol) in THF (25 mL), and the mixture was stirred at ambient
temperature for 3 h. The excess of LiAlH4 was decomposed with a
mixture of H2O (1.0 mL) and THF (20 mL). The resulting precipitate
was filtered off and washed with EtOAc (3 ꢀ 25 mL). The combined
filtrate and washings were dried (Na2SO4) and evaporated under
reduced pressure. The oily residue was treated with an equivalent
amount of fumaric acid (11b,c) or (S,S)-tartaric acid (11a,d) in a
mixture of EtOH and Et2O to give crystalline salts which was filtered off
and recrystallized. The salt formations of 11b and 11c with fumaric acid
occurred in 1:1 ratio, while tartrates of 11a and 11d could be character-
ized by the 2:1 ratios of the base and acid components.
(S)-2-Hydrazino-1-phenylethanol Hydrogen Maleate (2b Hydro-
gen Maleate). Beige crystalline solid; yield 1.40 g (52%); mp 99-
1
104 °C (EtOH-Et2O); [R]D þ43 (MeOH, c 0.50). The H NMR
(D2O) spectrum was identical to that of the (R)-enantiomer (2a
hydrogen maleate). Anal. Calcd for C12H16N2O5: C, 53.73; H, 6.01;
N, 10.44. Found: C, 53.64; H, 5.85; N, 10.38.
(1R*,2R*)-2-Hydrazino-1,2-diphenylethanol Hydrogen Maleate (5
Hydrogen Maleate). To a solution of (()-trans-stilbene oxide (4, 1.57 g,
8 mmol) in EtOH (10 mL) hydrazine hydrate (5.01 g, 100 mmol) was
added. The mixture was heated under reflux for 12 h. The solvent and
the unreacted hydrazine hydrate were evaporated off, and evaporation
was repeated twice after addition of toluene (10 mL). The oily residue
was treated with an equivalent amount of maleic acid in a mixture of
EtOH and Et2O to give crystalline maleate salt which was filtered off and
recrystallized. White crystalline substance; yield 1.71 g (62%); mp 159-
160 °C (EtOH-Et2O). 1H NMR (D2O) δ (ppm): 4.41 (d, 1H, J = 6.5
Hz, NCH), 5.10 (d, 1H, J = 6.5 Hz, OCH), 6.30 (s, 2H, CHCOOH)
7.28-7.49 (m, 10H, 2 ꢀ C6H5). Anal. Calcd for C18H20N2O5: C, 62.78;
H, 5.85; N, 8.13. Found: C, 62.50; H, 5.67; N, 7.96.
2-Hydrazino-1-phenylpentanol Hydrogen Fumarate (8 Hydrogen
Fumarate). To a stirred and ice-cooled solution of (()-2-bromo-1-
phenyl-1-pentanone (6, 2.41 g, 10 mmol) in methanol (30 mL) NaBH4
(0.38 g, 10 mmol) was added in small portions, and the resulting mixture
was stirred for 2 h with ice-water bath. The mixture was then acidified
with 10% HCl and evaporated in vacuo. The residue was partitionated
between water (30 mL) and Et2O (25 mL), and the aqueous phase was
(1R,2S)-2-(1-Methylhydrazino)-1,2-diphenylethanol (S,S)-Tartrate
[11a (S,S)-Tartrate]. White crystalline substance; yield 1.10 g (58%);
mp 141-143 °C (EtOH-Et2O); [R]D -85 (MeOH, c 0.57). 1H NMR
(D2O) δ (ppm): 2.95 (s, 3H, NCH3), 4.35 (s, 1H, CHOHCOOH), 4.45
(d, 1H, J = 4.8 Hz, NCH), 5.67 (d, 1H, J = 4.8 Hz, OCH), 7.18-7.46 (m,
10H, 2 ꢀ C6H5). Anal. Calcd for C17H21N2O4: C, 64.34; H, 6.67; N,
8.83. Found: C, 64.28; H, 6.31; N, 8.99.
(1S,2S)-2-(1-Methylhydrazino)-1,2-diphenylethanol Hydrogen Fu-
marate (11b Hydrogen Fumarate). White crystalline substance; yield
1.33 g (62%); mp 153-154 °C (EtOH-Et2O); [R]D -44 (MeOH, c
1
0.40). H NMR (D2O) δ (ppm): 2.83 (s, 3H, NCH3), 4.62 (d, 1H,
J = 10.3 Hz, NCH), 5.43 (d, 1H, J = 10.3 Hz, OCH), 6.60 (s, 2H,
CHCOOH), 7.10-7.46 (m, 10H, 2 ꢀ C6H5). Anal. Calcd for
C19H22N2O5: C, 63.67; H, 6.19; N, 7.82. Found: C, 63.68; H, 5.93;
N, 7.66.
(1R,2R)-2-(1-Methylhydrazino)-1,2-diphenylethanol Hydrogen Fu-
marate (11c Hydrogen Fumarate). White crystalline substance; yield
1.40 g (65%); mp 150-152 °C (EtOH-Et2O); [R]D þ41 (MeOH, c
0.40). The 1H NMR (D2O) spectrum was identical to that of the (1S,2S)
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Journal of Medicinal Chemistry
ARTICLE
enantiomer (11b hydrogen fumarate). Anal. Calcd for C19H22N2O5: C,
63.67; H, 6.19; N, 7.82. Found: C, 63.45; H, 6.08; N, 7.71.
using MMFF94s force field with MMFF94 charges and conjugate
gradient method until the energy gradient was less than 0.05 kcal/
mol. Bioactive conformations for studied ligands were predicted with
GOLD 3.1.1. The ligand binding pocket was defined using the CβH
from Leu468 as a central atom with radius of 20 Å. The ligands were
docked covalently to TPQ. Each ligand was docked 10 times; however,
the docking simulation was allowed to terminate in cases where the root-
mean-squared deviations of the three best conformations were within
1.5 Å. Compounds 5, 8, and 12 were docked on the final conformation of
the MD simulation of VAP-1 with 2a instead of the modified crystal
structure of VAP-1 described above. Docking of ligands into crystal
structures of MAO A52 and MAO B45 was performed with GOLD 3.1.1
similarly as docking to VAP-1. Molecules were docked covalently to the
nitrogen atom of cofactor FAD.
Starting Structures for Molecular Dynamics Simulations.
The starting structure of VAP-1 with an active conformation of cofactor
TPQ32 was retrieved from the Protein Data Bank.48 Leu469 side chain
was turned as described earlier.26 As all studied inhibitor molecules bind
covalently to TPQ, the TPQ-ligand systems were parametrized as
follows. TPQ-ligand complexes were built with SYBYL 7.351 and
optimized with Gaussian 0353 at the HF/6-31þG* level. The electro-
static potentials of the ligands were calculated with Gaussian 03 (HF/6-
31þG*) for the optimized TPQ-ligand complexes, and the RESP
methodology54 was used to create atom-centered point charges from the
electrostatic potentials. Finally, hydrogens, neutralizing counterions
(Naþ ions), and TIP3P water molecules extending 13 Å around the
protein complex (rectangular box) were added with LEAP.55
Molecular Dynamics Simulations. All energy minimizations and
molecular dynamics simulations were performed with NAMD 2.656 using
ff03 force field parameters57 for the protein and gaff99 parameters58 for the
ligands (TPQ þ compounds 2a,b and 11a-d). The whole MD simulation
procedure comprised two minimization runs (the minimization of water
molecules, counterions, and amino acid side chains, followed by the
minimization for the whole complex) and two MD simulations. The first
MD simulation (360 ps) where the CR atoms were restrained was
performed at constant pressure. The 2.4 ns production simulation was
performed without constraints. The simulated complexes were held at
constant temperature (300 K) with Langevin dynamics for all non-hydrogen
atoms, using a Langevin damping coefficient of 5 ps -1. A constant pressure
of 1 atm was upheld by a Nosꢀe-Hoover-Langevin piston59 with an
oscillation time scale of 200 fs and a damping time scale of 100 fs. An
integration time step of 2 fs was used under a multiple time stepping
scheme.60 The bonded and short-range interactions were calculated every
third step. A cutoff value of 12 Å was used for the van der Waals and short-
range van der Waals forces to smoothen the cutoff. The simulations were
conducted under the periodic boundary conditions with the full system, and
the long-range electrostatics were counted with the particle-mesh Ewald
method.61 The bonds involving hydrogen atoms were restrained by the
SHAKE algorithm.62 Snapshot structures from the MD trajectories were
visually inspected to understand the potencies and effects of inhibitors to the
structure of the catalytic site.
(1S,2R)-2-(1-Methylhydrazino)-1,2-diphenylethanol (S,S)-Tartrate
[11d (S,S)-Tartrate]. White crystalline substance; yield 1.24 g (65%);
mp 167-170 °C (EtOH-Et2O); [R]D þ78 (MeOH, c 0.55). 1H NMR
(D2O) δ (ppm): 2.94 (s, 3H, NCH3), 4.35 (s, 1H, CHOHCOOH), 4.44
(d, 1H, J = 4.9 Hz, NCH), 5.66 (d, 1H, J = 4.9 Hz, OCH), 7.18-7.46 (m,
10H, 2 ꢀ C6H5). Anal. Calcd for C17H21N2O4: C, 64.34; H, 6.67; N,
8.83. Found: C, 64.07; H, 6.48; N, 8.51.
Expression of Recombinant VAP-1. Recombinant VAP-1 pro-
tein was obtained from Chinese hamster ovary (CHO) cells stably
transfected with a full-length human VAP-1 cDNA. Recombinant
human VAP-1 SSAO expressed in CHO cells was used as a source of
VAP-1 for activity measurements. Native CHO cells have negligible
VAP-1 activity. These cells and their culture have previously been
described.46 A cell lysate was prepared by suspending approximately
3.6 ꢀ 108 cells in 25 mL of lysis buffer (150 mM NaCl, 10 mM Tris base,
pH 7.2, 1.5 mM MgCl2, 1% NP40) and incubating at 4 °C overnight on a
rotating table. The lysate was clarified by centrifugation at 18000g for 5
min at room temperature and the supernatant used directly in the assay.
Mitochondrial MAO Extract. Rat total monoamine oxidase
enzyme (MAO, mixture of MAO A and MAO B) was prepared from
rat liver tissues by rinsing the liver sample several times in KCl-EDTA
solution to remove all blood. Then the liver sample was homogenized in
ice-cold potassium phosphate buffer (0.1 M, pH 7.4) with an Ultra-
Turax homogenizer (setting 11 000 rpm, 4 ꢀ 10 s). After centrifugation
at 500g for 10 min at 4 °C the supernatant was carefully withdrawn and
was centrifuged at 12300g for 15 min at 4 °C. The supernatant was
discharged, and sedimented mitochondria were resuspended in fresh
phosphate buffer and centrifuged as previously. The mitochondria were
suspended in phosphate buffer and homogenized with an Ultra-Turax
homogenizer (setting 11 000 rpm, 2 ꢀ 10 s). Mitochondrial preparate
was aliquoted and stored at -70 °C.
In Vitro Inhibition Activity. VAP-1 activity was measured as
described previously26 using the coupled colorimetric method essen-
tially as described for monoamine oxidase and related enzymes.47 In
short, the assay was performed in 96-well microtiter plates as follows.
The inhibitor concentrations used varied between 1 nM and 50 μM. The
assay was performed in a final volume of 200 μL consisting of 0.2 M
potassium phosphate buffer (pH 7.6) and freshly made chromogenic
solution containing 1 mM 2,4-dichlorophenol, 500 μM 4-aminoanti-
pyrine, and 4 U/mL horseradish peroxidase and an amount of CHO cell
lysate containing VAP-1 SSAO that caused a change of 0.6A490 per h.
The plates were incubated for 30 min at 37 °C. To initiate the enzymatic
reaction, 1 mM benzylamine was added and the plate incubated for 1 h at
37 °C. The increase in absorbance, reflecting VAP-1 SSAO activity, was
measured at 490 nm by using Wallac Victor II multilabel counter. The
IC50 values for the inhibitors were calculated using GraphPad Prism
software. Since MAO A and MAO B have similar amino acids at the
proposed inhibitor binding site (Figure 6), the IC50 values for MAOs
were measured only for the mixture of MAO A and MAO B. Total MAO
activity was measured in a similar way as for VAP-1 SSAO except that
2,4-dichlorophenol was replaced by 1 mM vanillic acid, and benzylamine
was replaced by tyramine in 0.5 mM final concentration.
’ AUTHOR INFORMATION
Corresponding Author
*Phone: þ358-40-521-6913. Fax: þ358-14-260-2221. E-mail:
Docking of Ligands to VAP-1 and MAO B Ligand Binding
Pockets. The crystal structure of VAP-1 in complex with
2-hydrazinopyridine33 was retrieved from the Protein Data Bank.48
The conformation of the side chain of Leu469 was changed to resemble
that obtained from MD simulations26 using amino acid side chain
rotamer library49 incorporated into BODIL modeling environment.50
In addition, the water molecules and the atoms of bound inhibitor
molecule 2-hydrazinopyridine (C1, C2, C3, C4, C5, and N3 in the
crystal structure) were removed. Hydrogen atoms were added using
SYBYL.51 Ligands were sketched in SYBYL and energy-minimized by
olli.t.pentikainen@jyu.fi.
’ ACKNOWLEDGMENT
This study was financially supported by Academy of Finland
(Grant 121393 for U.P. and Grant 129175 for O.T.P.). CSC-
Finnish IT Center for Science is thanked for generous computa-
tional grant (Grant jyy2516 for O.T.P.).
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ARTICLE
’ ABBREVIATIONS USED
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