Atropisomerism in azadipeptides: evaluation of N1-methylation and thioamide introduction

Article abstract of DOI:10.1016/j.tetlet.2015.06.074

Abstract Cbz-protected azadipeptides, designed as structurally reduced model compounds, were synthesized and investigated with respect to the occurrence of atropisomerism. Methylation at the carbamate nitrogen caused mixtures of E and Z isomers in Cbz-sar

Full text of DOI:10.1016/j.tetlet.2015.06.074

Tetrahedron Letters 56 (2015) 4889–4891
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Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Atropisomerism in azadipeptides: evaluation of N1-methylation and
thioamide introduction
Philipp A. Ottersbach a, Gregor Schnakenburg b, Michael Gütschow a,
⇑
a Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
b Institute of Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
a r t i c l e i n f o
a b s t r a c t
Article history:
Cbz-protected azadipeptides, designed as structurally reduced model compounds, were synthesized and
investigated with respect to the occurrence of atropisomerism. Methylation at the carbamate nitrogen
caused mixtures of E and Z isomers in Cbz-sarcosyl-azaglycine-amide (9) and Cbz-sarcosyl-methylazaala-
nine-amide (10). A formal O/S exchange led to Cbz-glycyl-azaglycine-thioamide (11) and Cbz-glycyl-
methylazaalanine-thioamide (12), respectively. The (MeN)2 fragment, present in 10 and 12 (but not 9
and 11), serves as a chirality-inducing element owing to a restricted rotation around the N–N axis.
Ó 2015 Elsevier Ltd. All rights reserved.
Received 22 May 2015
Revised 22 June 2015
Accepted 24 June 2015
Available online 30 June 2015
Keywords:
Atropisomers
Azapeptides
Diastereotopicity
Peptide thioamides
Azapeptides are peptides in which the C H unit of at least one
pharmacological effects, particular attention in drug discovery pro-
jects has been paid to atropisomerism only in the last decade.11
In a previous investigation it was demonstrated that the methy-
lation of N2 and N3 of the structurally reduced model azadipeptide
amide Cbz-Gly-azaGly-NH2 (1) led to an E configuration of respec-
a
amino acid in the peptide has been replaced by nitrogen. This
replacement is an important element in the design of pep-
tidomimetics.1 Azapeptides can improve potency and selectivity
and possess superior pharmacokinetics such as proteolytic
resistance and higher bioavailability compared to their natural
‘carbapeptide’ counterparts. Recent examples for the manifold
biological activities of azapeptides include enzyme inhibitory
properties, such as inhibition of cysteine cathepsins,2 caspases,3
human neutrophil proteinase 3 (PR3),4 and modulation of the insu-
lin receptor tyrosine kinase (IRTK).5 Other receptors have also been
addressed by azapeptides, such as the cluster of differentiation 36
(CD36) receptor by analogues of the growth hormone releasing
peptide-6 (GHRP-6),6 and cyclic azapeptides were identified as
potent antagonists of integrin receptors.7 Moreover, successful
attempts to convert azapeptides into activity-based probes
(ABPs) and positron emission tomography (PET) tracers have been
reported.8
tive CO–N bonds in the resulting Cbz-Gly[WCONMe]-azaAla-NH2
(2) and hence to atropisomerism due to a restricted rotation
around the N–N axis (Fig. 1).12 Vice versa, removal of the methyl
groups of 2 gave rise to a regular Z configuration of the CO–N bonds
and to a loss of chirality in 1. N-methylation is a simple but mean-
ingful manipulation of naturally occurring and synthetic peptides.
It has a significant impact on the secondary structure of (aza)pep-
tides and influences the E/Z equilibrium of peptide bonds.13
The O/S-exchange, has also been established as an important
strategy in the design of peptidomimetics, which can lead to
improved potency and stability.14 Although the thioamide group
is one of the closest mimics of an amide linkage, remarkably
different properties result from the O/S-exchange, due to the better
polarizability and lower electrophilicity of sulfur, the larger C–S
bond (1.65 Å vs 1.20 Å), the higher acidity of the thioamide NH,
and the stronger double bond character between carbon and nitro-
gen in case of the thio analogs with a somewhat higher rotational
barrier.14,15
Getting insights into the secondary structure of (aza)peptides is
an important field of research to understand the respective pro-
tein–ligand interactions. The structural properties of azapeptides
have been examined by theoretical techniques and experimental
approaches, respectively.9,10 Although it has been known for a long
time that chirality enables distinct enantiomers to have different
In the current letter, we report on the impact of N1-methylation
as well as the amide O/S-exchange in model azadipeptide amides
on atropisomerism.16,17 Axial chirality was diagnosed on the basis
of 1H NMR signals of diastereotopic Gly-methylene protons.12
⇑
Corresponding author. Tel.: +49 228 732317; fax: +49 228 732567.
E-mail address: guetschow@uni-bonn.de (M. Gütschow).
http://dx.doi.org/10.1016/j.tetlet.2015.06.074
0040-4039/Ó 2015 Elsevier Ltd. All rights reserved.

4890
P. A. Ottersbach et al. / Tetrahedron Letters 56 (2015) 4889–4891
O
O
O
S
Thus, a mixture of E/Z isomers has been produced as a result of
introducing a methyl group to the carbamate nitrogen N1 of the
achiral azadipeptide 1. The Z configuration of the CO–NH bonds
can be anticipated from previous investigations of related com-
pounds.12 However, raising the temperature to 343 K caused a coa-
lescence of the respective signals, indicating that the E/Z isomers
are not separable due to the known low rotational barrier of CN
bonds of alkylated carbamates.19
H
H
Z
N2
N2
Z
Z
BnO
N1
Me
N3
H
NH2
BnO
N1
N3
H
NH2
Z
Z
H
O
O
9
,
11
,
(
)-
(
)-
Z Z,Z
Cbz-Gly-azaGly[ΨCSNH]-NH2
Z Z
Cbz-Sar-azaGly-NH2
1-methylation
N
/
-exchange
O S
This finding was confirmed by analyzing the NMR data of Cbz-
Sar[WCONMe]-azaAla-NH2 (10). Again, the doubling of all signals
1
Cbz-Gly-azaGly-NH2 ( , non atropisomeric)
in 1H and 13C NMR spectra disappeared when recording the spectra
at 343 K and single signals were obtained. However, a geminal cou-
pling of the Gly-methylene protons was still apparent, indicating a
restricted rotation around the N–N axis, which can be explained by
an E configuration of the central peptide bond. The E configuration
is adopted owing to methylation of the N2 nitrogen in 10.12 This
structural change results in steric and electronic repulsions
between the N3 substituents and the Gly-methylene protons as
well as between the N3 substituents and the N2 methyl group.
Cbz-Gly[ΨCONMe]-azaAla-NH2 (2, atropisomeric)
1-methylation
N
/
-exchange
NH2
O S
O
S
NOE
E
E
N3
Me
H
Me
H
N3
NH2
O
O
H
N1
Me
H
N2
N2
Z
BnO
N1
Me
Me
BnO
E
E
H
Gà298 value for the barrier of rotation in 10 is expected to
O
O
The
be in
D
K
10
12
a
similar range than that of 2, that is, approximately
110 kJ molÀ1, because of the structural similarity of the E-configured
azadipeptide amides 2 and 10.
(a
,
, )-
S E E
Cbz-Sar[ΨCONMe]-azaAla-NH2
(a
,
,
,
)-
S Z E E
Cbz-Gly[ΨCONMe]-azaAla[ΨCSNH]-NH2
Turning our interest to azadipeptide thioamides, we observed a
Figure 1. N1-methylation and O/S-exchange of non-atropisomeric (1)12 or atropi-
someric (2)12 azadipeptides.
regular doublet for the Gly-methylene protons in the 1H NMR spec-
trum of Cbz-Gly-azaGly[
neighboring carbamate proton, which refers to achirality. In case
of the N2/N3-bis-methylated analog Cbz-Gly[
CONMe]-
azaAla[ CSNH]-NH2 (12) an ABX spin system was observed.
WCSNH]-NH2 (11) due to coupling to the
To obtain the N1-methylated compounds Cbz-Sar-azaGly-NH2
W
(9) and Cbz-Sar[W
CONMe]-azaAla-NH2 (10), Cbz-Sar-OH (3)18
W
After assignment of the N2 and the N3 methyl groups by HMBC
and HMQC techniques, an NOE experiment was performed. NOE
correlations between the N3 methyl group and one proton of the
diastereotopic Gly-methylene fragment were detected (Fig. 1, for
spectra, see Supplementary material). This indicated the adoption
of an E configuration of the methylated CO–N bond in 12, as it
has also been reported for the oxo analog 2.12 X-ray crystallo-
graphic analysis gave further evidence for this finding (Fig. 2).
To get more insights into the stereochemical stability of 12 and
to address a possible atropisomerism in 12, the minimum energy
conformations were computed at the non-local density functional
level of theory and the rotational barrier around the N–N bond was
calculated (see Supplementary material). Atropisomerism arises
from a sterically hindered rotation about a single bond leading to
two separable individual conformers.16 Two rotational barriers
were obtained for 12 and the energies of the corresponding transi-
was reacted with semicarbazide (5) and 1,2-dimethylsemicar-
bazide (6),12 respectively, via the mixed anhydride method
(Table 1). Azadipeptide thioamide Cbz-Gly-azaGly[WCSNH]-NH2
(11) was prepared from Cbz-Gly-OH (4) and thiosemicarbazide
(7) by applying the same coupling procedure. However, synthesis
of Cbz-Gly[
W
CONMe]-azaAla[
W
CSNH]-NH2 (12) required
a
different approach, in which 1,2-dimethylthiosemicarbazide (8),
prepared from 1,2-dimethylhydrazine and potassium thiocyanate
(see Supplementary material), was reacted with the acid chloride
of 4.
When inspecting the NMR spectra (500 MHz, DMSO-d6) of the
sarcosine-derived compound 9, we observed a doubling of all sig-
nals in the 1H and 13C NMR spectra (see Supplementary material).
Table 1
tion states
D
Gà298K are 122 and 135 kJ molÀ1. This demonstrates that
Coupling of amino acids 3, 4 with (thio)semicarbazides 5–8 to azadipeptide amides
9–12
R2
N2
X
Cbz
OH 1. ClCO2i-Bu, NMM, THF, -30 °C
Cbz
N1
R1
N3 NH2
R3
N
R1
O
R2
HN
X
O
9-12
2.
-30 °C to rt
3, 4
N
NH2
5-8
R3
C11
S
R1
R2/R3
X
Yield (%)
92
N2
N3
Compound
3
4
Me
H
C13
5
6
7
H
Me
H
O
O
S
N1
8
9
10
11
12a
Me
H
Me
H
S
77
42
72
44
31
C8
O1
Me
Me
H
O
O
S
C1
C7
H
Me
S
a
Coupling procedure applied: 3, (COCl)2, cat. DMF, CH2Cl2, rt, then DMAP, DIPEA,
6, CH2Cl2, rt.
Figure 2. Molecular plot of (Z,E,E)-Cbz-Gly[
WCONMe]-azaAla[WCSNH]-NH2 (12).
Displacement ellipsoids are drawn at 30% probability level.20

P. A. Ottersbach et al. / Tetrahedron Letters 56 (2015) 4889–4891
4891
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atropisomers.
In conclusion, four model azadipeptide (thio)amides 9–12 have
been designed on the basis of N1-methylation and O/S exchange of
structurally reduced azadipeptide amides 1 and 2. To experimen-
tally elucidate structural features of 9–12, diastereotopicity of
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Acknowledgments
G.S. thanks Prof. A. C. Filippou for support. This work has been
supported by the Deutsche Forschungsgemeinschaft – Germany
(GRK 804).
Supplementary data
Supplementary data (detailed synthetic procedures, analytical
data, NMR spectra, an X-ray crystallographic file in CIF format,
electronic structure calculations) associated with this article can
be found, in the online version, at http://dx.doi.org/10.1016/j.tet-
let.2015.06.074.
15. For a computational study on thioamide containing azapeptides, see: Lee, H.-J.;
Kim, J. H.; Jung, H. J.; Kim, K.-Y.; Kim, E.-J.; Choi, Y.-S.; Yoon, C.-J. J. Comput.
Chem. 2004, 25, 169.
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temperature: (a) Oki, M. Top. Stereochem. 1983, 14, 1; (a) Bringmann, G.; Price
Mortimer, A. J.; Keller, P. A.; Gresser, M. J.; Garner, J.; Breuning, M. Angew.
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