Synthesis and structural study of cyclic 5-aminovaleric acid-linked β-Ala-β-Ala dipeptides

Article abstract of DOI:10.1016/j.bmcl.2008.07.082

5-Aminovaleric acid and ornithine were evaluated as linkers for the cyclization of β-dipeptides. Two linked examples of β-Ala-β-Ala were prepared by standard coupling methods and their conformations probed by NMR, CD, and computational means. The data sug

Full text of DOI:10.1016/j.bmcl.2008.07.082

Bioorganic & Medicinal Chemistry Letters 18 (2008) 5975–5977
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis and structural study of cyclic 5-aminovaleric acid-linked
b-Ala–b-Ala dipeptides q
Anne Mengel a,b, Oliver Reiser a, Jeffrey Aubé b,
*
a Institut für Organische Chemie, Universität Regensburg, Universitätsstrasse. 31, 93053 Regensburg, Germany
b Department of Medicinal Chemistry, 1251 Wescoe Hall Drive, Malott Hall, Room 4070, University of Kansas, Lawrence, KS 66045-5782, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
5-Aminovaleric acid and ornithine were evaluated as linkers for the cyclization of b-dipeptides. Two
linked examples of b-Ala-b-Ala were prepared by standard coupling methods and their conformations
probed by NMR, CD, and computational means. The data suggest that these non- or monosubstituted ver-
sions of the target compounds are flexible in solution.
Received 28 June 2008
Revised 18 July 2008
Accepted 21 July 2008
Available online 24 July 2008
Ó 2008 Elsevier Ltd. All rights reserved.
Keywords:
b-Peptide
Cyclic peptide
Peptidomimetics
b-Peptides have captured the imagination of a wide range of
researchers, from those interested in basic principles of macromo-
lecular design to nanotechnologists.1 For medicinal chemists,
b-amino acids hold promise as components of potential therapeu-
tic agents because they provide a diversity of shape and function-
ality similar to that found in standard peptides.2 In addition, b-
peptides may be less likely to undergo deleterious metabolism.
Cyclization is a useful strategy for the discovery of b-peptide-based
Me
Me
O
H
N
HN
N
H
O
O
O
NH
O
HN
Aca
NH
O
O--H
1.94-2.65 Å
1, cyclo(Aca-Ala-Ala)
X
2a, X = H
2b, X = NHCbz
therapeutics for the same reason as in
a-peptides: to bias com-
pound conformation in
a
given (hopefully bioactive)
conformation.3
Figure 1. Structures of an Aca-cyclized Ala–Ala dipeptide (1) and the two cyclized
b-Ala–b-Ala-containing structures targeted in this study (2 and 3). Note the C–N
distance in 1, which complies with one standard definition of a b-turn.6
The use of unsubstituted4 and substituted5 versions of
e-amino-
caproic acid (Aca) as a linker in cyclic peptide derivates has become
well established as a means of constraining a dipeptide into a b-
turn-like conformation. In some cases, control over the conforma-
tion of the mimetic (e.g., type I vs type II b-turns) may be exerted
by either the dipeptide or the Aca linker portion of the molecule.
Given the success of the Aca cyclization strategy in conferring
b-turn conformations onto standard dipeptides, we decided to
pursue the synthesis and evaluation of two cyclic versions of
b-Ala–b-Ala using a related strategy (Fig. 1).
(Fig. 2). These studies also suggested that a turn structure includ-
ing the depicted intramolecular NH–OC hydrogen bond would also
be favored for these structures. Thus, for 2a, an energy minimum
O
O---H
Molecular modeling7 carried out in a series of
a,x-amino acids
1.8 Å
N
(n = 1–3, Fig. 1) combined with b-Ala–b-Ala suggested that the
optimal spacer length in structures of type 2 would be n = 2
H
O
NH
HN
O
2
2a
q
In honor of the bestowal of the 2008 Tetrahedron Young Investigator Award in
Bioorganic and Medicinal Chemistry to Professor Benjamin F. Cravatt.
* Corresponding author. Tel.: +1 785 864 4496; fax: +1 785 864 5326.
E-mail address: jaube@ku.edu (J. Aubé).
Figure 2. Energy minimum found for 2a by molecular modeling.
0960-894X/$ - see front matter Ó 2008 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2008.07.082

5976
A. Mengel et al. / Bioorg. Med. Chem. Lett. 18 (2008) 5975–5977
Boc-β-Ala-OH
O
O
b
a
3
BocHN
N
OH
+
O
H
H-β-Ala-OBn
H2N
OR
4
5
X
6a: X = H, R = Bn
6b: X = NHCbz, R = t-Bu
O
O
O
O
d
HN
N
H
YHN
N
N
H
OR
H
O
N
O
X
H
X
7a: X = H, Y = Boc, R = Bn
7b: X = NHCbz, Y = Boc, R = t-Bu
2a: X = H
2b: X = NHCbz
c
8a: X = H, Y = Boc, R = H
8b: X = NHCbz, Y = H, R = H
Scheme 1. Synthesis of cyclic peptides 2. Reagents and conditions: (a) i—EDC, HOBt, NEt3, 81%; ii—Pd/C, H2, 91%; (b) 7a: 6a HCl, EDC, HOBt, NEt3, 81%; 7b: 6b, EDC, HOBt,
NEt3, 57%; (c) 8a: Pd/C, H2, trifluoroethanol, 96%; 8b: TFA, CH2Cl2, quant. (crude); (d) 2a: i—EDC, C6F5OH 53%; ii—TFA, CH2Cl2; iii—DIPEA, 43% (2 steps); 2b: (EtO)2P(O)CN, NEt3,
27%.
was found in which NH–OC of the C- and N-terminal part of the b-
Ala–b-Ala fragment was aligned with a distance of 1.8 Å. Shorter
(n = 1) or longer (n = 3; i.e., Aca) spacers resulted in minimized con-
formations that did not reside in b-turn-like structures, and fur-
thermore lacked hydrogen bonding between the NH and CO
fragments.
values of less than 3400 cmÀ1 are generally considered consistent
with internal hydrogen bond formation under standard conditions
(typically 1 mmol in DCM),9 we hesitate to read too much into
these results due to the differences in solvent and concentration.
However, it is not unreasonable to suggest that the hydrogen
bonding pattern indicated in Figure 2 is at least possible. In addi-
tion, ROESY NMR studies were done on 2a and 2b. These results
were ambiguous, suggesting that these macrocycles have a highly
dynamic structure. Only a few significant crosspeaks were ob-
served between distant protons (defined as 1,6 relationship or lar-
ger). There were a greater number of these peaks in the ROESY of
2b, suggesting a greater population in this compound, possibly
due to the conformational bias of NHZ substituent. One approach
that will be taken in future work will be to add further substituents
and other constraints to try to add more of a bias to the
macrocycles.
Compound 2b was also subjected to circular dichroism spec-
troscopy in methanol solution (Fig. 3a). The resulting spectrum,
as well as that of the b-peptide-derived macrocycle 9 reported by
Seebach (Fig. 3b, spectrum not shown),10 was similar to that ex-
pected for a random coil. The structural differences between these
different systems preclude any meaningful interpretation of this
result at the present time.
Consequently, 5-aminovaleric acid (Ava) and ornithine were
chosen as spacers to bridge the b-Ala–b-Ala dipeptide. N-Boc-b-
Ala–b-Ala-OH 5, readily prepared from N-Boc-b-Ala-OH (3) and
H-b-Ala-OBn (4) by standard peptide coupling followed by hydro-
genation of the benzylic ester, served as a convenient starting
material for the envisaged peptides 2 (Scheme 1). Elongation of 5
by coupling with 6a or 6b again followed by deprotection gave rise
to 8. Solubility problems of 7a called for its hydrogenation in an
alcoholic solvent: while methanol resulted in some transesterifica-
tion of 7a to the corresponding methyl ester, the use of trifluoro-
ethanol cleanly allowed deprotection of the benzyl ester to give
8a in almost quantitative yield. For the final cyclization, activation
of 8a as its pentafluorophenyl ester turned out to be necessary be-
cause the acid was not soluble in standard peptide coupling sol-
vents. N-deprotection of this ester then led to the cyclized
peptide 2a. The amine-containing analog 8b could be directly cyc-
lized by activation with diethylcyanophosphonate, yielding 2b. The
moderate yields in which 2 was obtained in the final cyclization
were a result of the very low solubility of the products, making
purification a laborious task. In both cases, sufficient quantities
of peptides were made available for standard characterization.8
The structural analysis of 2a and 2b was hampered by solubility
concerns. For example, it proved necessary to obtain IR spectra in
pyridine at relatively high concentrations (ca. 5 mmol). Under
these conditions, N–H stretching bands were observed at
3272 cmÀ1 for 2a and 3276 cmÀ1 and 3296 cmÀ1 for 2b. Although
In conclusion, the present work demonstrates the synthetic fea-
sibility of cyclizing b-dipeptides with Ava linkers in a manner sim-
ilar to our previously published use of Aca linkers with
a-
dipeptides. The resulting compounds are likely to take up turn con-
formations due to the simple fact that they are cyclic, but prelimin-
ary data are most consistent with a fairly extensive range of
possible interconverting conformations for the simple substitution
types shown. Future work will add substituents and further con-
straints11 in attempts to obtain more highly ordered and possible
biologically interesting structures.
Acknowledgments
4
2
0
-2
-4
-6
-8
O
O
NH HN
The present work was supported by the National Science Foun-
dation and the DFG-Graduiertenkolleg 760 Medizinische Chemie.
NH HN
CD
O
-10
-12
190
O
References and notes
210
230
250
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9
Wavelength (nm)
Figure 3. (a) CD spectrum of 2b taken in methanol. (b) Cyclic b-peptide reported by
Seebach.10

A. Mengel et al. / Bioorg. Med. Chem. Lett. 18 (2008) 5975–5977
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;
NMR (400 MHz, MeOH-d4) d 1.49–1.55 (m, 2H, 4-H), 1.64 (quin, J = 7.0 Hz, 2H, 3-
H), 2.20 (t, J = 6.9 Hz, 2H, 2-H), 2.37 (t, J = 5.7 Hz, 2H, 7/10-H), 2.46 (t, J = 5.9 Hz,
2H, 7/10-H), 3.25 (t, J = 5.6 Hz, 2H, 5-H), 3.46 (t, J = 5.7 Hz, 2H, 8/11-H), 3.50 (t,
J = 5.9 Hz, 2H, 8/11-H); 13C NMR (100.6 MHz, MeOH-d4) 24.0 (4-C), 28.8 (3-C),
35.0 (CH2), 35.2 (CH2), 35.4 (CH2), 35.7 (CH2), 36.1 (CH2), 37.7 (CH2), 172.6 (CO),
172.9 (CO), 175.6 (CO). MS (DCI–NH3): m/z (%) = 242 (60) [MH+], 207 (45), 143
(70), 60 (100). C11H20N3O3 (POS FAB VSCAN): 242.1505 (cal), 242.1501 (found).
Compound 2b: [
a
] À38 (MeOH, c 0.06). IR (TeflonÒ film) 3301, 3083, 2925, 1684,
1649, 1571, 1431 cmÀ1 1H NMR (400 MHz, DMSO-d6) 1.37–1.50 (m, 4H, 3-H
;
and 4-H), 2.03–2.09 (m, 1H, 7/10-H), 2.13–2.19 (m, 1H, 7/10-H), 2.20–2.26 (m,
1H, 7/10-H), 2.42–2.48 (m, 1H, 7/10-H), 2.97–3.18 (m, 4H, 5/8/11-H), 3.45–3.60
(m, 2H, 5/8/11-H), 3.99–4.04 (m, 1H, 2-H), 5.00 (s, 2H, CH2Ph), 7.23 (d, J = 7.9 Hz,
1H, NHCbz), 7.31–7.39 (m, 6H, Ph, NH), 7.78 (t, J = 5.7 Hz, 1H, NH), 7.85 (t,
J = 5.3 Hz, 1H, NH). MS (DCI–NH3): m/z (%) = 391 (60) [MH+], 283 (100), 225 (20).
C19H27N4O5 (POS FAB VSCAN): 391.1981 (cal), 391.1967 (found).
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