Synthesis and crystal structure of a chiral lactam and three amino alcohols as potential protein tyrosine phosphates 1B inhibitors

Article abstract of DOI:10.1016/j.tetasy.2017.09.014

Chiral lactam 2 and three chiral β-amino alcohols 3–5 have been synthesized and characterized by spectroscopic techniques. Regioselective ring opening reaction of chiral styrene oxide by an amine nucleophile was confirmed by X-ray diffraction data. Ligand 2–4 crystallizes in the tetragonal, orthorhombic and tetragonal crystal lattice system respectively. Ligands 2–6 have been used as potential inhibitors for protein tyrosine phosphatase 1B enzyme (PTP1B). The potential inhibitor effect of these molecules to the target protein was investigated by Dock and molecular dynamics calculations. Dock score analysis and Lipinski parameters suggested that ligands 1, 2, 4–6 are potential inhibitors towards PTP1B, thus indicating that the residues Arg24, Arg254 and Met258, Asp29 in the second active site of PTP1B are essential for the high selectivity of inhibitors. The results indicate that the polar hydrogen bonding interacts with Asp29, Gln102, and the amino acid residues of PTP1B are responsible for governing inhibitory potency of ligands 1–6.

Full text of DOI:10.1016/j.tetasy.2017.09.014

Tetrahedron: Asymmetry xxx (2017) xxx–xxx
Contents lists available at ScienceDirect
Tetrahedron: Asymmetry
journal homepage: www.elsevier.com/locate/tetasy
Synthesis and crystal structure of a chiral lactam and three amino
alcohols as potential protein tyrosine phosphates 1B inhibitors
b
Sßafak Özhan Kocakaya a, Mehmet Karakaplan a, , Rosario Scopelliti
⇑
a Department of Chemistry, Faculty of Science, Dicle University, 21280 Diyarbakır, Turkey
b Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
a r t i c l e i n f o
a b s t r a c t
Article history:
Chiral lactam 2 and three chiral b-amino alcohols 3–5 have been synthesized and characterized by spec-
troscopic techniques. Regioselective ring opening reaction of chiral styrene oxide by an amine nucle-
ophile was confirmed by X-ray diffraction data. Ligand 2–4 crystallizes in the tetragonal, orthorhombic
and tetragonal crystal lattice system respectively. Ligands 2–6 have been used as potential inhibitors
for protein tyrosine phosphatase 1B enzyme (PTP1B). The potential inhibitor effect of these molecules
to the target protein was investigated by Dock and molecular dynamics calculations. Dock score analysis
and Lipinski parameters suggested that ligands 1, 2, 4–6 are potential inhibitors towards PTP1B, thus
indicating that the residues Arg24, Arg254 and Met258, Asp29 in the second active site of PTP1B are
essential for the high selectivity of inhibitors. The results indicate that the polar hydrogen bonding inter-
acts with Asp29, Gln102, and the amino acid residues of PTP1B are responsible for governing inhibitory
potency of ligands 1–6.
Received 30 June 2017
Revised 5 September 2017
Accepted 15 September 2017
Available online xxxx
Dedicated to the memory of Dr. Howard
Flack
Ó 2017 Elsevier Ltd. All rights reserved.
1. Introduction
Ser118). The other important parts of PTP1B are S loops (Ser201-
Gly209), R3-helix (Glu186-Glu200), R6-helix (Ala264-Ile281), and
Protein tyrosine phosphatase 1B (PTP1B) is an intracellular pro-
tein expressed in insulin responsive tissues including the classical
insulin targeted tissues such as liver, muscle and fat.1 PTP1B plays
an important role in insulin receptor signaling.2 PTP1B dephospho-
rylates the insulin receptor during its biosynthesis in endoplasmic
reticulum as well as after it has been stimulated by the insulin, and
thus plays a central role in the negative regulation of the insulin
signalling pathway.3 Studies on mice have shown that insulin sen-
sitivity and obesity correspond with an increase in PTP1B enzyme
deficiency. Several experiments have also demonstrated that the
knockout of PTP1B in mice can result in insulin hypersensitivity,
even in a high-fat diet.4–9
Therefore, small molecular inhibitors of PTP1B are promising
drugs for potentially curing type II diabetes. The full length of
PTP1B comprises of 435 amino acids, constituting the major cellu-
lar form; however, only a shorter length of 298 or 321 residues is
typically considered in biochemical studies. The model used herein
is the one coded 1wax.pdb in the protein Data Bank which contains
298 amino acids. The active site of PTP1B consists of residues
R7-helix, (Val287-Ser295) which take part in the catalysis sub-
strate binding.10–15 The second binding active site, close to the con-
served primary active site, also referred to as site B, which was
determined by Zhang et al., is not so conserved, and therefore it
is believed that it should be exploited in the design PTP1B enzyme
inhibitors with good selectivity.6
The design of small molecules that can inhibit the PTP1B
enzyme is an area of research that has raised considerably interest
in the medicinal chemistry field and is being actively pursued by
many academic and industrial organizations. In clinical trials, the
association between insulin resistance and PTP1B levels in fat
and muscle tissues has been determined. A variety of PTP1B inhi-
bitors have been reported over the last decade.16–22 The discovery
of potent, selective, cell permeable and orally bioavailable PTP1B
inhibitors is a challenging medicinal chemistry objective. Out of
several small molecule PTP1B inhibitors, only three small molecule
PTP1B inhibitors have entered clinical trials and finally discontin-
ued due to insufficient efficacy and unwanted side effects.23
The synthesis of new chiral ligands is the subject of ongoing sci-
entific research.24–26 The common route to b-amino alcohol ligands
is the ring-opening reaction of epoxides by amines.27–31 The out-
come of the ring-openings strongly depends on the electronic
and steric effects on reactants. Concerning the regioselectivity,
the favoured product is the result of nucleophilic attack at the less
His214-Arg221 and loops WPD (Thr177-Pro185),
R (Val113-
⇑
Corresponding authors. Tel.: +90 4122488550.
E-mail addresses: safakozhan@dicle.edu.tr (Sß. Özhan Kocakaya), mkkaplan@
dicle.edu.tr (M. Karakaplan).
https://doi.org/10.1016/j.tetasy.2017.09.014
0957-4166/Ó 2017 Elsevier Ltd. All rights reserved.
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2
Sß. Özhan Kocakaya et al. / Tetrahedron: Asymmetry xxx (2017) xxx–xxx
hindered epoxide carbon (b-attack), except in the case of styrene
oxide, where an
-attack was the major one.32 Concerning the
2.2. Molecular docking
a
stereochemistry, under neutral or basic conditions, an SN2 mecha-
nism was operating to trans-b-amino alcohols.
Dock 6.0 module allows all stages of a docking process to be
performed with the generation of ligand conformations, ligand
docking, and the scoring of the binding modes. As in this case,
where a rigid receptor approximation was used, it is expected that
the different receptors considered will lead to different ligand-
binding modes depending on the initial size of the PTP1B-binding
cavity. Thus, the six new PTP1B inhibitors were docked on the
available receptor following a multistep procedure. In order to
describe receptor-binding properties, a grid of potential energy
was calculated for atoms taking part in the binding pocket. These
atoms were obtained from the analysis of each protein–ligand
complex. In this step, default parameters were used. The ligand
was then docked using the calculated grid to place it into the cavity
and score the proposed binding modes.
The identification of selective, safe and readily available inhibi-
tors of these PTP1B has proven difficult and it still represents a
challenge for medicinal chemists. Herein we report the synthesis
of a lactam and five b-amino alcohols derived from (R,R)-1,2-
diaminocyclohexane as potential PTP1B inhibitors (Scheme 1).
Molecular modelling was used to understand the possible binding
mode of proposed compounds.
2. Computational section
2.1. Molecular dynamics simulations
The ligands were then applied with partial atomic charges
derived by fitting Antechamber obtained by electronic structure
calculation module in AMBER and assigned the AM1-BCC
charges.33–36 Atoms on PTP1B were assigned the PARM99 charges,
and all ionisable residues were set at their default protonation
states at neutral pH. Parameters for the ligands were generated
using XLEAP the general amber force field (GAFF).37 Molecular
Dynamics runs were in general for 1 ns at 300 K.
The coordinates of the protein mentioned above were taken
from the Protein Data Bank (1wax PDB). Crystallographic water
molecules were removed from all the structures. In 1wax.pdb,
the missing coordinates were modelled using XLEAP and a ff99SB
force field. Atoms on PTP1B were assigned the PARM99 charges,
and all ionizable residues were set at their default protonation
states at neutral pH. All structures were further processed by the
xLeAP module of AMBER. The molecular systems were neutralized
by the addition of counterions. The systems and then the energy
were minimized in two steps; in the first step, the protein and
ligand were kept fixed, only the water molecules were allowed
to move, and in the second step, all atoms were allowed to move.
For the first step, the energy minimization was performed in 500
and 2500 steps with the steepest descent and conjugate gradient
methods, respectively. For the second step, the energy minimiza-
tions were performed in 500 and 2500 steps using the steepest
descent and conjugant gradient methods, respectively.
3. Results and discussions
The chiral unit of 1,2-diaminocyclohexane has the most suit-
able geometry parameters and commercial availability; therefore
it is the one of the most important parts of the ligand
structure.38,39 Chiral ligands 2–5 were synthesized by starting
from cis/trans mixtures of 1,2-diaminocyclohexane. The struc-
tures of all compounds were ambiguously assigned by means of
analytical and spectroscopic data. The absolute configurations of
compound 2–4 were assigned by X- ray crystallographic data
(Figs. 1–3).
The known ligand 1 was prepared by the condensation of ben-
zaldehyde and (R,R)-1,2-diaminocyclohexane obtained from classi-
cal resolution of cis/trans mixtures of 1,2-diaminocyclohexane to
form an imine intermediate.40 These intermediates were reduced
by NaBH4 to afford the desired ligand. Lactam 2 was easily pre-
pared from ligand 1 and oxalyl chloride in 71% yield. The atom
numbering scheme of 2 drawn at the 50% probability level is given
in Figure 1. Lactam 2 crystallized into a tetragonal crystal lattice
system with space group P41212 (Table 1). The crystal packing of
C2 symmetric lactam 2 contains one ethanol molecule having
hydrogen bonds with the carbonyl oxygen of lactam 2. Bond
distances N(1)AC(1) and N(2)AC(2) are 1.356 and 1.350 Å respec-
tively. These bond lengths are shorter than those in amino alcohols
H2N
NH2
a
O
O
Ph
Ph
N
N
Ph
Ph
Ph
N
N
Ph
Ph
c
c
Ph
N
H
N
H
Ph
OH
HO
OH
HO
1
3
5
b
d
d
Ph
Ph
N
H
N
H
N
H
N
H
Ph
N
O
N
O
Ph
OH
OH
OH
OH
6
2
4
Scheme 1. Reagents: (a) PhCHO/MeOH than NaBH4, (b) Oxalyl chloride, (c) Pd(OH2)/C, [H2].
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Sß. Özhan Kocakaya et al. / Tetrahedron: Asymmetry xxx (2017) xxx–xxx
3
Figure 1. ORTEP diagram of the lactam 2. Ellipsoids are shown at the 50% probability threshold.
Figure 2. ORTEP plot of amino alcohol 3. Ellipsoids are shown at the 50% probability threshold.
3 and 4, which depend on the symmetrical electron withdrawing of
carbonyl groups with bond lengths 1.2206 and 1.2246 Å. It has
been shown that the lactam ring is planar; the C(1)AN(1)AC(8)
and C(2)AN(2)AC(3) bond angels are 121.05 and 119.62°, respec-
tively. The bond angels indicate that the cyclohexyl ring is in the
chair confirmation and both stereogenic centers are (R)-
configurations.
Epoxides are small molecules with a wide range of synthetic
applications as intermediates in the pharmaceutical and agro-
chemical industries. It is susceptible to attack by a range of
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4
Sß. Özhan Kocakaya et al. / Tetrahedron: Asymmetry xxx (2017) xxx–xxx
Figure 3. IR spectrum and ball-and-stick view of chiral amino alcohol 3.
Table 1
Crystal data and structure refinement details for ligands 2–4
2
3
4
Formula, formula weight
Temperature
C
23H27N2O2.5, 371.47
C36H42N2O2, 534.72
140(2) K
C22H30N2O2, 354.48
140(2) K
100(2) K
Radiation
0.71073 Å
0.71073 Å
0.71073 Å
Crystal system, space group
Unit cell dimensions
Tetragonal, P41212
a = 10.1214(9) Å
b = 10.1214(9) Å
c = 37.475(7) Å
3839.0(8) Å3
8, 1.285 Mg/m3
0.084 mmꢀ1
Orthorhombic, P212121
a = 10.6029(4) Å
b = 16.0647(6) Å
c = 17.4065(8) Å
2964.9(2) Å3
Tetragonal, P43
a = 11.364(3) Å
b = 11.364(3) Å
c = 16.250(10) Å
2098.5(8) Å3
4, 1.122 Mg/m3
0.072 mmꢀ1
a
= 90°
b = 90°
= 90°
a
= 90°
b = 90°
= 90°
a
= 90°
b = 90°
= 90°
c
c
c
Volume (Å3)
Z, density (g/cm3)
Absorption coefficient m (mꢀ1
F (000)
4, 1.198 Mg/m3
0.073 mmꢀ1
)
1592
1152
768
Crystal size (mm)
Theta range
0.44 ꢁ 0.40 ꢁ 0.29 mm3
0.34 ꢁ 0.32 ꢁ 0.21 mm3
0.32 ꢁ 0.25 ꢁ 0.22 mm3
3.28–27.49°
3.03–28.79°
2.53–24.48°
Index ranges
Index ranges
Reflection collected/unique
Independent reflections
Completeness to theta = 24.48°
Absorption correction
ꢀ12 ꢂ h ꢂ 13, ꢀ13 ꢂ k ꢂ 13,
ꢀ48 ꢂ l ꢂ 48
ꢀ14 ꢂ h ꢂ 14, ꢀ20 ꢂ k ꢂ 21,
ꢀ22 ꢂ l ꢂ 23
ꢀ13 ꢂ h ꢂ 13, ꢀ13 ꢂ k ꢂ 13,
ꢀ18 ꢂ l ꢂ 17
3376
65,734
29,766
4401 [R(int) = 0.0270]
99.7%
Semi-empirical from equivalents
Full-matrix least-squares on F2
4401/0/264
7226 [R(int) = 0.0435]
99.8%
Semi-empirical from equivalents
Full-matrix least-squares on F2
7226/0/369
3376 [R(int) = 0.0000]
99.2%
None
Refinement method
Full-matrix least-squares on F2
3376/1/252
Data/restraints/parameters
Goodness-of-fit on F2
1.127
1.026
1.131
Final R indices [I > 2
r
(I)]
R1 = 0.0344, wR2 = 0.0845
R1 = 0.0371, wR2 = 0.0868
ꢀ0.1(10)
R1 = 0.0428, wR2 = 0.0817
R1 = 0.0628, wR2 = 0.0898
ꢀ0.6(11)
R1 = 0.0486, wR2 = 0.0914
R1 = 0.0600, wR2 = 0.0954
2.2(14)
R indices (all data) data]
Absolute structure parameter
Largest diff. peak and hole
0.232 and ꢀ0.202 e Åꢀ3
0.154 and ꢀ0.189 e Åꢀ3
0.147 and ꢀ0.146 e Åꢀ3
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Sß. Özhan Kocakaya et al. / Tetrahedron: Asymmetry xxx (2017) xxx–xxx
5
nucleophiles, including nitrogen, oxygen, and sulfur containing
compounds, leading to bifunctional molecules of great industrial
value. Chiral amino alcohol 3 was synthesized by ring opening of
(R)-styrene oxide with amine nucleophile 1 in a catalyst free
medium using methanol. Although the synthesis of compound 3
was reported, its solid state form has not been reported so far.41
A single crystal of compound 3 was obtained as a bright colour-
less crystal by dissolving the crude product in n-hexane and a few
drops of ethanol at room temperature. Its crystallographic image
provides evidence to the regioselectivity about the attack of amine
nucleophile to the styrene oxide. It showed that compound 3 is
formed by a b-attack of nucleophile to the less hindered terminal
carbon of styrene oxide without any racemisation (Fig. 2).
The IR spectrum of amino alcohols 3 also showed a free hydro-
xyl absorption band at approximately 3429 cmꢀ1 (Fig. 3). This
point was clarified by the crystallographic image of this compound.
As can be seen from Figure 3, one of the phenyl ring of benzyl
groups bearing to the nitrogen atom inhibits the formation of
intramolecular hydrogen bonds between hydroxyl groups.
Through X-ray crystal structure analysis, amino alcohol 3 crystal-
lized into an orthorhombic crystal lattice system with space group
P21212 (Table 1).
Amino alcohol 4 with a secondary amine functionality was
obtained by debenzylation of compound 3 with Pd(OH)2/C in high
yields (70%). As can be seen from Figure 4, diastereomer of amino
alcohol 4 crystallized into a tetragonal crystal lattice system with
space group P43 (Table 1). The cyclohexyl ring is in a chair confirma-
tion and has a (1S,1S)-configuration (Fig. 4). This was attributed to
the enantiomeric impurity of compound 1. Consequently, the struc-
tures of compound 2–4 derived from chiral 1,2-diaminocyclohexane
were evaluated by their single crystal forms. In order to investigate
the effect of a substituent on the second stereogenic center bearing a
hydroxyl functional group, we designed chiral ligands 5 and 6.
The 1,2-diamino moiety of ligands was selected in order to
improve the stability of the inhibitor/enzyme complex through
contacts with residues bearing a hydroxyl active site, which sug-
gested a marked influence on the potential potency and selectivity.
Molecular docking experiments into the PTP1B active site indicate
that the 1,2-diamino moiety of compounds 2–6 fitted the binding
site very well by establishing favourable polar and hydrogen bond-
ing. All compounds showed similar interaction modes of binding in
the second active site of PTP1B (Fig. 5).
With regards to the potential inhibitory effectiveness, PTP1B
was shown to be enhanced by the apolar interactions of ligands
investigated. The potential of the inhibitors is mainly governed
by hydrophobic interactions, van der Waals contacts of the inhibi-
tors with the Arg24, Arg257, Met258, Arg254, and Phe182 and
hydrogen bonding. The calculated thermodynamic parameters for
the complexation of (1R,2R)-1,2-diaminocyclohexane derivatives
1–6 by Docking method analysis are shown in Table 2. The energy
of complexation was observed in the range from ꢀ16.98 to
42.22 kcal/mol, respectively. The orientations of these potential
inhibitors in the enzyme B site indicate that the interaction of
the hydrogen bond is of great importance during binding. In gener-
ally, the hydrogen bonds place the amine and hydroxyl functional
groups of ligands between the Gln102 and Asp29 residues of the
protein as shown in Figure 6.
The lactam functionality of ligand 2 has better calculated
enzyme inhibitor properties than the more flexible ligand 1. It is
thought that the fixed geometry of ligand 2 would infer a powerful
ability to bind with the target enzyme via apolar and polar
interactions (Fig. 6). The hindrance of benzyl group on nitrogen
atom of ligand 3 would make it less effective than ligand 4, having
a high total enclosed volume, occupying effectively van der
Waals contacts of by Lys58, His60, Gln102 together with hydrogen
bonds.
The similar chemical structures and stereochemistry of ligands
5 and 6 make them better potential inhibitors when compared
with ligand 3 (Table 2). This was attributed to their lower lipophilic
or more hydrophilic character. It was also found that the residues
adjacent to the second active site of PTP1B, including Asp29, Arg24,
Arg254, and Met258, might be partially responsible for the poten-
tial high inhibition activity and selectivity of ligand 6 by analyzing
their interactions.
The potential inhibitor effect of ligands 1–6 has also been inves-
tigated by using calculated Lipinski parameters (Table 3). The
results indicate that five of the ligands have a powerful enzyme
inhibitor potent. These results are agreement with the litera-
ture.42,43 Ligand 3 showed the lowest potential inhibitor efficiency
for PTP1B due to the higher molecular weight, rotation bonds and
logP value, as shown in Table 3.
Lipinski values have been supported Dock Score results showed
that ligands 1, 2 and 4–6 have a good potential inhibitor efficiency
toward PTP1B enzyme.
Figure 4. ORTEP diagram of diastereomer of chiral amino alcohol 4. Ellipsoids are shown at the 50% probability threshold.
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Sß. Özhan Kocakaya et al. / Tetrahedron: Asymmetry xxx (2017) xxx–xxx
A
B
Figure 5. (A) Docking results of potential ligands 2–6 in the PTP1B catalytic pocket. Ligand 1–6 are coloured in pink, cyan, yellow, red, blue and green respectively. (B)
Docking results of ligand 1–6 in the PTP1B second active site.
Table 2
Calculated thermodynamic parameters for complexation of ligands 1–6 as potential inhibitors for PTP1B by docking method
Ligand
Electrostatic energy
van der Waals energy
Dock score energy
Internal energy
1
2
3
4
5
6
ꢀ2.145
ꢀ4.852
ꢀ0.435
ꢀ3.909
ꢀ2.695
ꢀ4.500
ꢀ14.850
ꢀ31.47
ꢀ16.985
ꢀ36.32
1.150
18.585
1.876
7.734
30.708
18.547
ꢀ24.911
ꢀ37.297
ꢀ39.349
ꢀ37.716
ꢀ25.346
ꢀ41.206
ꢀ42.044
ꢀ42.216
(d, 2H, J = 13.2 Hz), 2.36 (m, 2H, J = 3.6), 2.24 (d, 2H, J = 13.2 Hz),
2.15 (br s, 2H), 1.81–1.85 (m, 2H), 1.30–1.36 (m, 2H), 1.10–1.15
(m, 2H). 13C NMR (CDCI3): d (ppm) 141.01, 128.38, 128.19,
126.79, 60.90, 50.89, 31.56, 25.08.
4. Conclusion
Herein, a lactam and five chiral amino alcohols derived from
chiral 1,2-diaminocyclohexane have been designed for potential
PTP1B inhibition. We have demonstrated that the regioselective
ring opening reaction of (R)-styrene oxide by amine nucleophile
and absolute configuration of desired product 2–4 could be
assigned by their X-ray diffraction data. In the design of more
effective medicines, the development of such molecules and tar-
geting the surface residues, for example, the region containing
Met258, Arg254, Gln102 and Asp29 of the second phosphate bind-
ing site, might be advantageous. Dock score analysis demonstrated
that ligands 4–6 are potential inhibitors towards PTP1B by hydro-
gen bonds especially with Gln102 and Asp29 of the second phos-
phate binding site.
5.3. N,N0-Dibenzyl-(1R,2R)-1,2-Diaminocyclohexaneoxalylamide 2
N,N0-Dibenzyl-(1R,2R)-1,2-diaminocyclohexane
1
(500 mg,
1.7 mmol) and oxalyl chloride (200 mg, 1.7 mmol) was refluxed
in toluene (3 mL) under argon for 24 h. After evaporation of the sol-
vent, the crude product was purified by flash column chromatogra-
phy eluted with hexane/EtOH (9:1) to give 0.42 g (71%), mp 166–
167 °C, [a]
20 = +70.3 (c 0.5, CHCl3). IR (cmꢀ1): 3254, 3219, 3102,
D
3033, 2994, 2939, 2878, 1676, 1402, 1355, 1256, 1041, 810, 794,
771, 708, 665. 1H NMR d: 7.36–7.24 (m, 5H), 5.295 (d, 15.96 Hz,
1H); 4.55 (d, 15.96 Hz, 1H); 3.48–3.46 (m, 1H); 2.26–2.18 (m,
1H); 1.74–1.72 (m, 1H); 1.31–1.11 (m, 2H). 13C NMR (d, ppm):
158.66, 136.62, 128.83, 127.45, 127.11, 58.12, 45.59, 28.75, 23.80.
Anal. Calcd. for C23H27N2O2.5 C: 74.29, H: 7.27, N: 7.53. Found; C:
74.73, H: 7.08, N: 7.32.
5. Experimental
5.1. Apparatus and chemicals
Melting points were determined with GALLENKAMP Model
apparatus with open capillaries. Infrared spectra were recorded
on a MIDAC-FTIR Model 1700 spectrophotometer. The Elemental
5.4.
N,N0-Dibenzyl-N,N0-bis[(S)-2-hydroxy(2-phenyl)ethyl]-
(1R,2R)-1,2-diaminocyclo-hexane 3
_
analyses were obtained with CARLO-ERBA Model 1108 apparatus.
Optical rotations were recorded using PERKIN ELMER Model 341
polarimeter. 1H NMR (400 MHz) and 13C NMR (100 MHz) spectra
were recorded on BRUKER DPX-400 high performance digital FT-
NMR spectrometer, with tetramethysilane as the internal standard
solutions in deuteriochloroform.
(S)-Styrene oxide (1.63 g, 13.6 mmol) was added to a solution of
N,N0-Dibenzyl-(1R,2R)-1,2-diaminocyclohexane 1 (2 g, 6.8 mmol) in
methanol (3 mL) and stirred at 40, 50 and 60 °C, for 24 h for each
temperature. The solvent was evaporated and the remaining epoxide
and amine were removed by Kugelrohr distillation apparatus. The
crude product was purified by crystallization from n-hexane and
ethanol to give 3 (2.72 g, 75%) as a white powder. Mp 202–203 °C;
5.2. N,N0-Dibenzyl-(1R,2R)-1,2-diaminocyclohexane 1
[
a D
]
20 = ꢀ147.6 (c 1 CHCl3). IR (
m
: cmꢀ1): 3429, 3242, 3063, 3030,
This compound was synthesized by a previous method40,41 by
2928, 2851, 1490, 1458, 1336, 1240, 1195, 1105, 1066, 1022, 758,
714 cmꢀ1 1H (400 MHz, CDCl3) 7.71–7.07 (20H, m), 5.78 (2H, br s,
;
using (1R,2R)-1,2-diaminocyclohexane (1.0 g, 8.77 mmol) to give
20 = ꢀ79.7 (c 2.5, CHCl3) 1H NMR
OH), 5.02 (1H, br s), 4.73 (1H, br s), 4.0–3.50 (4H, m), 3.19–2.55
2.60 g, 99% of compound 1. [
(CDCI3): (d, ppm) 7.20–7.50(m, 10H), 3.98(d, 2H, J = 13.2 Hz), 3.75
a
]
D
(6H, m), 2.23–1.69 (4H, m), 1.28–1.23 (4H, m). 13C (100 MHz, CDCl3):
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Sß. Özhan Kocakaya et al. / Tetrahedron: Asymmetry xxx (2017) xxx–xxx
7
1
2
3
4
5
6
Figure 6. The orientation of the residues shown as sticks around inhibitor compounds in the final snophot of Dock result.
Table 3
Calculated Lipinski parameters for complexation of ligands 1–6 by Molinspiration method
Ligand
LogP
Mw
nON
nOHNH
nRotb
1
2
3
4
5
6
4.07
3.06
6.16
2.90
4.02
0.73
294
348
534
354
430
230
2
4
4
4
4
4
2
0
2
4
2
4
6
4
12
8
10
6
LogP: octanol/water partition coefficient, Mw: molecular weight, nON: number of hydrogen bond acceptors, nOHNH: number of hydrogen bond donors, nRotb: number of
rotatable bonds.
143.23, 138.39, 130.55, 130.08, 128.43, 127.27, 126.01, 76.80, 72.27,
69.02, 58.43, 25.69, 24.27. Anal. Calcd. for C36H42N2O2: C, 80.89; H,
7.86; N, 5.24, Found: C, 80.25; H, 7.46; N, 5.30.
[(S)-2-hydroxy-(2-phenyl)ethyl]-1,2-diaminocyclohexane
(400 mg, 0.75 mmol) in methanol (2 mL) as described.44 The mix-
ture was stirred under hydrogen and the reaction was monitored
by TLC. After completion of the reaction, sodium carbonate
(80 mg, 0.75 mmol) was added and stirred for 1 h. The solution
was filtered and washed with methanol, then concentrated in
vacuo. The crude product was purified by flash chromatography
on silica gel H/EA/EtOH/TEA (4:1:1:0.5 as eluent) to give 186 mg
% 70.05 of compound 2 as a viscous oil. Diastereomer single
5.5. N,N0-Bis[(S)-2-hydroxy(2-phenyl)ethyl]-(1R,2R)-1,2-diamino-
cyclohexane 4
At first, Pd(OH)2/C (20%, 75 mg) was added in one portion to a
solution of the appropriate compound (1R,2R)-N,N0-dibenzyl-bis
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8
Sß. Özhan Kocakaya et al. / Tetrahedron: Asymmetry xxx (2017) xxx–xxx
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crystals could be obtained from this oil by dissolving n-hexane and
ethanol. IR (cmꢀ1): 3346, 3250, 3057, 3030, 2926, 2860, 1493,
1453, 1348, 1310, 1195, 1139, 1056, 924, 893, 854, 791, 756,
701. 1H NMR (CDCl3) d: 7.41–7.27 (m, 10H), 4.55 (dd, 4, 8.12 Hz,
2H), 2.90–2.71 (m, 8H), 2.32–2.27 (m, 2H), 2.12–1.99 (m, 2H),
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of N,N0-Dibenzyl-(1R,2R)-1,2-diaminocyclohexane
1
(250 mg,
0.82 mmol) in methanol (3 mL) and stirred at 40 °C for 24 h, and
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a pure product (340 mg, 99%). IR:
1953, 1600, 1452, 1296, 1388, 1336, 1253, 1132, 1060, 964,
746 cmꢀ1 1H NMR (CDCl3): d (ppm) 7.36–7.15(m, 10H), 5.92 (br
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.
s, 2H), 3.74 (d, 2H, J = 12.8 Hz), 3.49–3.40 (m, 4H), 2.70–2.60 (m,
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