Synthesis of a novel 14-membered highly constrained cyclic peptidic scaffold

Article abstract of DOI:10.1016/j.tetlet.2004.03.131

The synthesis and NMR analysis of a novel highly constrained scaffold is described. The 14-membered macrocyclic ring structure was inspired by many medicinally relevant natural products that also contain the bi-aryl ether moiety. The synthesis required on

Full text of DOI:10.1016/j.tetlet.2004.03.131

Tetrahedron
Letters
Tetrahedron Letters 45 (2004) 4153–4156
Synthesis of a novel 14-membered highly constrained
cyclic peptidic scaffold
Christopher J. Arnusch and Roland J. Pieters*
Department of Medicinal Chemistry, Utrecht Institute of Pharmaceutical Sciences, Utrecht University,
PO Box 80082, 3508 TB Utrecht, The Netherlands
Received 26 February 2004; revised 15 March 2004; accepted 22 March 2004
Abstract—The synthesis and NMR analysis of a novel highly constrained scaffold is described. The 14-membered macrocyclic ring
structure was inspired by many medicinally relevant natural products that also contain the bi-aryl ether moiety. The synthesis
required only commercially available starting materials and involved a base mediated SNAr cyclization. A conformational search
was performed, which indicated a strong preference for a single conformation, which was consistent with observed ROE signals by
NMR.
Ó 2004 Elsevier Ltd. All rights reserved.
Cyclic peptides1 are important compounds for medicinal
purposes and represent an important class of natural
products. Compared to their acyclic counterparts, cyclic
peptides have more constrained conformations and are
more resistant to degradation in vivo. The constriction
of a peptide into a certain conformation can greatly
enhance its binding to receptors due to reduced entropy
loss upon binding. Many efforts have been made to
develop methods of cyclization and a variety of reagents
and catalysts have been developed for this purpose.
Macrolactamization,2 disulfide formation,3 ring closing
olefin metathesis,4 and various cycloetherification tech-
niques such as SNAr cyclizations5 are important meth-
ods for a synthetic chemist in the design of a desired
cyclic peptide. By the same token, these tools are
essential for the synthesis of mimics or derivatives
of biologically active compounds aiming at improved
activity or function. We here present a short synthesis of
a highly constrained cyclic peptide scaffold that includes
several sites that allow the introduction of structural
variations.
piperazinomycin,8 deoxybouvardin,9 K-13,10 and
OF494911 (Fig. 1). The medicinal functions of these
products range from antitumor agents, enzyme inhibi-
tors (including HIV integrase, and angiotensin I con-
verting enzyme), and antibiotics.
A feature that differentiates the structure of these
medicinally relevant molecules is the size of the
OH
OH
O
O
H
N
N
N
H
H
N
O
H
O
O
NH
(+)-piperazinomycin
HN
N
O
O
O
NO2
O
HN
The bi-aryl ether moiety is a common element in many
natural products and also in synthetically constrained
peptides. Numerous examples include the vancomycin
class of antibiotics,6 cycloisodityrosine derivatives,7
O2N
O
O
HN
N
H
O
O
1
deoxybouvardin
Figure 1. Structures of (þ)-piperazinomycin and deoxybouvardin
compared with 1. These 14-membered macrocyclic examples contain a
biphenyl ether moiety.
Keywords: SNAR reaction; Cyclic peptide; Bi-aryl ether.
* Corresponding author. Tel.: +31-30-253-6944; fax: +31-30-253-6655;
e-mail: r.j.pieters@pharm.uu.nl
0040-4039/$ - see front matter Ó 2004 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2004.03.131

4154
C. J. Arnusch, R. J. Pieters / Tetrahedron Letters 45 (2004) 4153–4156
macrocyclic ring, which ranges from 14 to 17. Without
considering the differences in functionality elsewhere in
the molecule, a general scaffold that harbors such a
highly constrained macrocyclic ring, and that allows
functionalization could be a useful starting point to find
novel biologically active entities. Previously in our lab-
oratory small mimics for vancomycin were studied.12;13
An SNAr cyclization was employed to form biphenyl
ether macrocyclic compounds (16-membered rings) and
was successful for solution and solid-phase applications.
Described herein is the solution phase synthesis of 1, a
mimic for piperazinomycin and deoxybouvardin. Simi-
lar to these natural products, the novel highly con-
strained scaffold 1 also contains a 14-membered ring,
and includes a biphenyl ether bridge. Compound 1 was
synthesized using commercially available starting
materials in five steps, which included 1,5-difluoro-2,4-
dinitrobenzene, an inexpensive reagent used for protein
crosslinking14 but also used in organic synthesis.15
isolated yield of 38%. Mass spectrometry confirmed the
cyclization to 1, which proved to be very stable in air at
room temperature.
Scaffold 1 is highly functionalizable due to its five
potential points of derivatization (Fig. 2). The C-ter-
minus can be easily functionalized, the secondary aro-
matic amine is a possible second point of variation,
and upon reduction of the nitro functionalities, a third
and fourth handle for functionalization are possible
although no differentiation is easily envisioned. A fifth
potential point of derivatization represents the amino
acid side chain by using other amino acids instead of
glycine.
The structural identity of 1 was confirmed by NMR. To
this end TOCSY, ROESY, and HSQC experiments
measured at 500 MHz were performed. The cyclization
reaction was clearly observed by the disappearance
of the fluorine–hydrogen coupling observed in 3. The
aromatic proton flanked by both nitro groups was seen
at 8.87 ppm (JH–F ¼ 8 Hz), and the other aromatic
hydrogen on the nitro-aromatic was seen at 6.68 ppm
(JH–F ¼ 14:6 Hz). Upon cyclization, these signals became
singlets and were observed at 8.82 and 4.02 ppm! The
large pronounced shift in the latter can be explained by
The solution phase synthesis began with tyrosine, which
was protected with a methyl ester on the C-terminus and
a benzyl group on the phenolic OH (Scheme 1). This
compound was coupled to Boc-protected glycine with
BOP and i-Pr2NEt in CH2Cl2. Removal of the protect-
ing groups was achieved by sequential hydrogenation on
Pd/C and TFA/CH2Cl2 1:1 treatment. The N-terminus
of the dipeptide was first linked to 1,5-difluoro-2,4-
dinitrobenzene using NEt3 as a base to give 3,16 which
was isolated in 58% overall yield after column chroma-
tography. 1,5-Difluoro-2,4-dinitrobenzene is highly
reactive in nucleophilic aromatic substitutions because
of the nitro functionalities ortho and para to the carbons
bearing a fluorine. Upon substitution with the first
nucleophile, the second point of substitution was
observed to be slightly less electrophilic since compound
3 was a stable yellow solid, and could be stored at room
temperature for months without degradation. Cycliza-
tion was achieved by treatment with 4 equiv of K2CO3 in
DMF, which gave the highly constrained 117 in an
4
NO2
O
1
O2N
O
O
HN
N
H
3
O
2
5
Figure 2. Potential points of variation in 1.
BnO
HO
a,b,c
d
O
-
CF3CO2 +H3N
O
O
Cl- +H3N
N
H
O
O
2
NO2
HO
O
e
O
H
N
O2N
O
F
O
N
O
HN
H
N
O
H
O2N
NO2
O
3
1
Scheme 1. Reagents and conditions: (a) Boc–Gly–OH, BOP, i-Pr2NEt, CH2Cl2, 3 h. (b) H2 Pd/C, EtOAc/MeOH, 3 h. (c) TFA/CH2Cl2 1:1, 1 h. (d)
1,5-Difluoro-2,4-dinitrobenzene 1 equiv, NEt3, EtOAc, 30 min., steps a–d 58%. (e) K2CO3, DMF, 3 d. rt 38%.

C. J. Arnusch, R. J. Pieters / Tetrahedron Letters 45 (2004) 4153–4156
4155
NO2
yield of 22%. Its identity and conformation were eluci-
dated by NMR and molecular modeling.
NO2
O
O
O
H
O
O2N
H
O
H
N
H
N
+
O
HN
N
H
NH3
H2N
N
H
O
O
O
Acknowledgements
~ 6 ppm
4.02 ppm
We would like to thank Hans Hilbers for help with
modeling and Dr. Johan Kemmink for help with NMR.
We also would like to thank the Royal Netherlands
Academy of Arts and Sciences (KNAW) for a fellowship
to R.J.P. and acknowledge support from Prof. Dr. R.
M. J. Liskamp.
1
1
Figure 3. Chemical shifts of 1 in DMSO-d6 and vancomycin mimic 4.
its close proximity to the flanking aromatic ring. This
effect was also previously seen in our 16-membered
vancomycin mimics,12;13 although less pronounced as
the relevant resonance was observed at ꢀ6 ppm (Fig. 3).
The assignment of the high-field aromatic proton was
confirmed by the observation of a signal at 4.02 (1H) and
References and notes
106 (13C) ppm in the H–13C HSQC spectrum of 1. The
1
1. For a review on the synthesis of cyclic peptides, see:
Lambert, J. N.; Mitchell, J. P.; Roberts, K. D. J. Chem.
Soc., Perkin Trans. 1 2001, 471–474.
2. Pant, N.; Hamilton, A. D. J. Am. Chem. Soc. 1988, 110,
2002–2003.
3. Rosek, A.; Powers, J. P. S.; Friedrich, C. L.; Hancock, R.
E. W. Biochemistry 2003, 42, 14130–14138.
4. Reichwein, J. F.; Wels, B.; Kruijtzer, J. A. W.; Versluis,
C.; Liskamp, R. M. J. Angew. Chem., Int. Ed. 1999, 38,
3684–3687.
5. (a) Feng, Y.; Burgess, K. Chem. Eur. J. 1999, 5, 3261–
3272; (b) Goldberg, M.; Smith, L., II; Tamayo, N.;
Kiselyov, A. S. Tetrahedron 1999, 55, 13887–13898; (c)
Kohn, W. D.; Zhang, L.; Weigel, J. A. Org. Lett. 2001, 3,
971–974; (d) For a review on SNAr cyclizations see: Zhu, J.
Synlett 1997, 133–144.
6. Singh, G. H.; Jayasuriya, H.; Hazudda, D. L.; Felock, P.;
Homnick, C. F.; Sardana, M.; Patane, A. Tetrahedron
Lett. 1998, 39, 8769–8770.
7. (a) Bigot, A.; Zhu, J. Tetrahedron Lett. 1998, 38, 551–554;
(b) Krenitsky, P. J.; Boger, D. L. Tetrahedron Lett. 2002,
43, 407–410; (c) Poupaardin, O.; Ferreira, F.; Genet, J. P.;
Greck, C. Tetrahedron Lett. 2001, 42, 1523–1526; (d)
Bigot, A.; Dau, M. E. T. H.; Zhu, J. J. Org. Chem. 1999,
64, 6283–6296.
13C chemical shift confirmed the aromatic nature of the
carbon. Another interesting observation was the differ-
entiation of all the tyrosine aromatic protons due to
their distinct chemical environments, resulting in four
unique chemical shifts: 7.52, 7.36, 7.28, 6.94 ppm (in
CD3OD).
In order to obtain an idea about the preferred confor-
mation of the rigid structure of 1, a conformational
search18 was undertaken using MacroModel v. 7.0.19
A
group of highly similar conformations was found to
have the lowest energy (Fig. 4). This conformation was
consistent with ROE signals observed by NMR. The
ROESY experiment indicated a short interproton dis-
tance between the amide NH and one of the glycine CH
signals (3.28 ppm) and a significant longer one to the
other glycine CH signal (4.07 ppm). Furthermore only a
weak ROE signal was observed between the amide NH
and the aromatic-H at 4.02 ppm. This profile is consis-
tent with the structure shown and not with higher energy
alternative structures with either the glycine CH2 group
or the amide bond rotated away.
8. Tamai, S.; Kaneda, M.; Nakamura, S. J. Antibiot. 1982,
35, 1130–1136.
In summary, the synthesis of a novel bio-inspired scaf-
fold was achieved in five synthetic steps in an overall
9. Jolad, S. D.; Hoffmann, J. J.; Torrance, S. J.; Wiedhopf,
R. M.; Cole, J. R.; Arora, S. K.; Bates, R. B.; Gargiulo, R.
L.; Kriek, G. R. J. Am. Chem. Soc. 1977, 99, 8040.
10. Kase, H.; Kaneko, M.; Yamado, K. J. Antibiot. 1987, 40,
450–454.
11. (a) Sano, S.; Ikai, K.; Kuroda, H.; Nakamura, T.;
Obayashi, A.; Ezure, Y.; Enomoto, H. J. Antibiot. 1986,
39, 1674–1684; (b) Sano, S.; Ikai, K.; Katayama, K.;
Takesako, K.; Nakamura, T.; Obayashi, A.; Ezure, Y.;
Enomoto, H. J. Antibiot. 1986, 39, 1685–1696; (c) Sano,
S.; Ueno, M.; Katayama, K.; Nakamura, T.; Obayashi, A.
J. Antibiot. 1986, 39, 1697–1703; (d) Sano, S.; Ikai, K.;
Yoshikawa, Y.; Nakamura, T.; Obayashi, A. J. Antibiot.
1987, 40, 512–518; (e) Sano, S.; Kuroda, H.; Ueno, M.;
Yoshikawa, Y.; Nakamura, T.; Obayashi, A. J. Antibiot.
1987, 40, 519–525.
12. Pieters, R. J. Tetrahedron Lett. 2000, 41, 7541–7545.
13. Arnusch, C. J.; Pieters, R. J. Eur. J. Org. Chem. 2003,
3131–3138.
Figure 4. Lowest energy structure of 1 found by molecular modeling.
Chemical shift assignment in DMSO-d6 are indicated and also the
observed ROE signals labeled as strong.
14. (a) Kornblatt, J. A.; Lake, D. F. Can. J. Biochem. 1980,
58, 219–224; (b) Fitzgerald, T. J.; Carlson, G. M. J. Biol.
Chem. 1984, 259, 3266–3274.

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C. J. Arnusch, R. J. Pieters / Tetrahedron Letters 45 (2004) 4153–4156
1
15. (a) Mazurov, A. Tetrahedron Lett. 2000, 41, 7–10;
(b) Shivanyuk, A.; Far, A. R.; Rebek, J., Jr. Org. Lett.
2002, 4, 1555–1558; (c) Liu, G.; Fan, Y.; Carlson, J. R.;
Zhao, Z. G.; Lam, K. S. J. Comb. Chem. 2000, 467–
474.
17. Compound 1: Rf ¼ 0:47 (EtOAc). H NMR (DMSO-d6):
d ¼ 2:72 (t, J ¼ 12:6 Hz, 1H), 3.28 (d, J ¼ 17:0 Hz, 1H),
3.48 (dd, J ¼ 4:6 Hz, J ¼ 12:6 Hz, 1H), 3.71 (s, 3 H), 4.02
(s, 1H), 4.07 (d, J ¼ 16:5 Hz, 1H), 4.79 (m, 1H), 7.02 (dd,
J ¼ 2:2 Hz, J ¼ 8:5 Hz, 1H), 7.33 (m, 2 H), 7.51 (dd,
J ¼ 1:7 Hz, J ¼ 7:2 Hz, 1H), 8.35 (d, J ¼ 10:1 Hz, 1H),
8.55 (br s, 1H), 8.82 (s, 1H). MS: m=z ¼ 417:2 [M þ H]þ.
18. A 1000 step Monte Carlo search using the MMFF force
field, in vacuum.
1
16. Compound 3: Rf ¼ 0:63 (EtOAc). H NMR (DMSO-d6):
d ¼ 2:78 (dd, J ¼ 9:3 Hz, J ¼ 13:7 Hz, 1H), 2.93 (dd,
J ¼ 5:2 Hz, J ¼ 14 Hz, 1H), 3.60 (s, 3H), 4.13 (d,
J ¼ 5:5 Hz, 2H), 4.40–4.49 (m, 1H), 6.60 (d, J ¼ 8:2 Hz,
2H), 6.68 (d, J ¼ 14:6 Hz, 1H), 6.95 (d, J ¼ 8:2 Hz, 2H),
8.63 (d, J ¼ 7:7 Hz, 1H), 8.87 (d, J ¼ 8 Hz, 1H), 9.05 (br s,
1H), 9.22 (s, 1H).
19. Mohamadi, F.; Richards, N. G. J.; Guida, W. C.;
Liskamp, R.; Caufield, C.; Chang, G.; Hendrickson, T.;
Still, W. C. J. Comput. Chem. 1990, 11, 440–467.