Cyclic ss-peptoids

Article abstract of DOI:10.1021/ol7030763

The first synthesis of functionalized ss-peptoid macrocycles is reported. X-ray crystallographic structure of tetramer 9 reveals a C ₂-symmetrical derivative with unexpected a//-cis-amide bonds and spatial disposition of the appendages toward the two opposite faces of the ring. Quantum calculations suggest that 9 is locked in this layout. These macrocycles constitute novel promising templates for multimeric ligation of biologically active ligands. The concept was exemplified by chemical decoration of tetramer 9 via click reactions.

Full text of DOI:10.1021/ol7030763

ORGANIC
LETTERS
2008
Vol. 10, No. 5
921-924
Cyclic
â-Peptoids
Olivier Roy,† Sophie Faure,† Vincent Thery,† Claude Didierjean,‡ and
Claude Taillefumier*,†
Laboratoire de Synthe`se et Etude de Syste`mes d’Inte´reˆt Biologique, SEESIB (UMR
6504 - CNRS), UniVersite´ Blaise Pascal - Clermont-Ferrand II, 24 aVenue des
Landais, 63177 Aubie`re Cedex, France, and LCM3B, Equipe Biocristallographie,
UMR 7036 CNRS-UHP, Faculte´ des Sciences et Techniques, Nancy UniVersite´,
BP 239, 54506 VandoeuVre-le`s-Nancy, France
claude.taillefumier@uniV-bpclermont.fr
Received December 21, 2007
ABSTRACT
The first synthesis of functionalized â-peptoid macrocycles is reported. X-ray crystallographic structure of tetramer 9 reveals a C2-symmetrical
derivative with unexpected all-cis-amide bonds and spatial disposition of the appendages toward the two opposite faces of the ring. Quantum
calculations suggest that 9 is locked in this layout. These macrocycles constitute novel promising templates for multimeric ligation of biologically
active ligands. The concept was exemplified by chemical decoration of tetramer 9 via “click” reactions.
The development of oligomers with artificial backbones
carrying diverse side chains, capable of mimicking bioactive
peptides, is an area of intense research activity.1 These so-
called peptidomimetics can be designed for conformational
rigidity of the backbone, their resistance to hydrolytic
peptidases and proteases,2 and their folding properties.3
Oligoureas,4 azapeptides,5 peptoids,6 γ-peptides,7 and â-pep-
tides8 are representative oligomers that belong to this class
of peptidomimetic. Among them, â-peptides have been
particularly studied in this regard as â-peptides can adopt a
large variety of secondary structures from very short
sequences.9 This unique feature makes them not only
interesting oligomers as peptidomimetics but also as fol-
damers for multimeric attachment of biologically active
pharmacophoric groups.10 â-Peptoids represent a new class
(5) (a) Han, H.; Janda, K. D. J. Am. Chem. Soc. 1996, 118, 2539-2544.
(b) Yoon, J.; Han, H.; Janda, K. D. Solution and soluble polymer syntheses
of azatides and aza peptides. AdV. Amino Acid Mimetics Peptidomimetics
1999, 2, 247-262.
(6) (a) Zuckermann, R. N.; Kerr, J. M.; Kent, S. B. H.; Moos, W. H. J.
Am. Chem. Soc. 1992, 114, 10646-10647. (b) Wu, C. W.; Seurynck, S.
L.; Lee, K. Y.; Barron, A. E. Chem. Biol. 2003, 10, 1057-1063. (c) Sanborn,
T. J.; Wu, C. W.; Zuckermann, R. N.; Barron, A. E. Biopolymers 2002, 63,
12-20. (d) Burkoth, T. S.; Fafarman, A. T.; Charych, D. H.; Connolly, M.
D.; Zuckermann, R. N. J. Am. Chem. Soc. 2003, 125, 8841-8845. (e)
Fafarman, A. T.; Borbat, P. P.; Freed, J. H.; Kirshenbaum, K. Chem.
Commun. 2007, 377-379. (f) Gorske, B. C.; Jewell, S. A.; Guerard, E. J.;
Blackwell, H. E. Org. Lett. 2005, 7, 1521-1524. (g) Kruijtzer, J. A. W.;
Hofmeyer, L. J. F.; Heerma, W.; Versluis, C.; Liskamp, R. M. J. Chem.
Eur. J. 1998, 4, 1570-1580.
†
Universite´ Blaise Pascal - Clermont-Ferrand II.
Nancy Universite´.
‡
(1) (a) Barron, A. E.; Zuckermann, R. N. Curr. Opin. Chem. Biol. 1999,
3, 681-687. (b) Kirshenbaum, K.; Zuckermann, R. N.; Dill, K. A. Curr.
Opin. Struct. Biol. 1999, 9, 530-535. (c) Solid-Phase Synthesis; Kates, S.
A., Albericio, F., Eds.; CRC Press: Boca Raton, 2000; pp 649-703.
(2) (a) Frackenpohl, J.; Arvidsson, P. I.; Schreiber, J. V.; Seebach, D.
ChemBioChem 2001, 2, 445-455. (b) Schreiber, J.; Frackenpohl, J.; Moser,
F.; Fleischmann, T.; Kohler, H. P.; Seebach, D. ChemBioChem 2002, 3,
424-432.
(3) (a) Gellman, S. H. Acc. Chem. Res. 1998, 31, 173-180. (b) Price, J.
L.; Horne, W. S.; Gellman, S. H. J. Am. Chem. Soc. 2007, 129, 6376-
6377.
(4) (a) Hemmerlin, C.; Marraud, M.; Rognan, D.; Graff, R.; Semetey,
V.; Briand, J. P.; Guichard, G. HelV. Chim. Acta 2002, 85, 3692-3711.
(b) Violette, A.; Averlant-Petit, M. C.; Semetey, V.; Hemmerlin, C.; Casimir,
R.; Graff, R.; Marraud, M.; Briand, J. P.; Rognan, D.; Guichard, G. J. Am.
Chem. Soc. 2005, 127, 2156-2164.
(7) Pseudo-Peptides in Drug DiscoVery; Nielsen, P. E., Ed.; Wiley-
VCH: Weinheim, 2004; pp 33-120.
(8) (a) Seebach, D.; Matthews, J. L. Chem. Commun. 1997, 2015-2022.
(b) Seebach, D.; Beck, A. K.; Bierbaum, D. J. Chem. BiodiVersity 2004, 1,
1111-1239.
(9) (a) Martinek, T. A.; Fu¨lo¨p, F. Eur. J. Biochem. 2003, 270, 3657-
3666. (b) Seebach, D.; Hook, D. F.; Glattli, A. Biopolymers 2006, 84, 23-
37.
10.1021/ol7030763 CCC: $40.75
© 2008 American Chemical Society
Published on Web 02/06/2008

of synthetic polyamides structurally related to â-peptides in
which the amino acid side chain is switched from the CR or
Câ carbon to the amide nitrogen. Since the concept was
introduced by Hamper11 in 1998, very few reports have
concerned this class of compounds,12 and to date, their cyclic
counterparts have not been investigated at all. Interesting
biological properties are associated to cyclo â-peptides;13
however, the poor solubility encountered with â-peptides13a
may hamper their cyclization. It is expected that the lack of
hydrogen on the amide can greatly modify the physical as
well the folding properties of â-peptoids related to â-pep-
tides.14 Cyclization of molecules containing tertiary amide
is often facilitated due to the easy trans-cis isomerization
of the amide bond.15 With all these considerations in mind,
we therefore decided to investigate the synthesis and further
cyclization of short functionalized â-peptoids. To the best
of our knowledge, cyclic â-peptoids have never been
reported, and therefore, conformational aspects including the
general shape of such macrocycles, cisoid/transoid geometry
of the amide bonds, the relative orientation of the CO as
well as orientation of the appendages on the backbone merit
investigation.
oligomers, was prepared quantitatively on a gram-scale
(Supporting Information). From this monomer, elongation
according to a two-step iterative procedure (acylation with
acryloyl chloride followed by 1,4-addition with the appropri-
ate amine) allowed the facile preparation of varying chain
length oligomers 2-6 depending on the number of cycles
(Scheme 1). Each two-step elongation required one purifica-
Scheme 1. Iterative Solution-Phase Synthesis of
Oligo-â-peptoids
Since the final objective of our work was to ligate the
template to key elements like carbohydrate for multimeric
recognition events, we decided first to anchor cyclo-â-
peptoids with terminal alkyne groups ready for click
chemistry approach.
tion stage and furnished the n + 1 oligomer with yields
ranging from 86 to 48%. After each cycle, a portion was
deprotected (TFA) for cyclization reaction.
As indicated by recent studies, the most convenient route
to â-peptoids is a two-step iterative methodology involving
acryloyl chloride as acylating agent for amide bond formation
and aza-Michael addition of primary amines to the resulting
R,â-unsaturated amide. Repeating this chemistry for several
cycles allows the synthesis of â-peptoid oligomers. This
methodology is also convenient in solid-phase organic
synthesis (SPOS); this is of great interest in case of
combinatorial approaches, but it is limited to small quantities,
yields seem to be affected after five to six repetitive cycles,12b
and byproducts corresponding to shorter and/or longer
oligomers have also been isolated.14a Therefore, we found it
more convenient to conduct solution-phase synthesis, al-
though some purification steps were expected.
Macrocyclization study started with the medium size linear
tetramer 4 using O-(7-azabenzotriazol-1-yl)-N,N,N′,N′-
tetramethyluronium hexafluorophosphate (HATU) and diphe-
nylphosphoryl azide (DPPA) acylating agents at moderate
dilution (5-10 mM). All experimental conditions (entries
8-12, Table 1) successfully furnished the expected cyclotet-
ramer 9 in good isolated yields (flash chromatography, SiO2)
ranging from 48 to 65%. Cyclization of 4 to 16-membered
macrocycle 9 appears to be not very sensitive to the
conditions, indicating a favorable process. Liquid chroma-
tography/mass spectrometry (LC/MS) of the crude showed
that formation of cyclotetramer 9 was only contaminated by
trace amount of a cyclic homodimer compound (<1%,
estimated by RP-HPLC at 214 nm). Pentamer 5 and hexamer
6 were also converted to the corresponding macrocycles 10
and 11 in good isolated yields, 67 and 68%, respectively,
with DPPA in acetonitrile (entries 14 and 16). LC/MS
profiles of the crude products allowed the detection of
cyclodimeric compounds; further estimated by RP-HPLC in
a range of 1-2%. Difficulties are often encountered with
the cyclization of short oligomers due to ring strain.
Cyclization of trimer 3 supposed to form the 12-membered
ring 8 was assessed under a set of conditions (entries 3-7,
Table 1). Whatever the coupling reagent and conditions, an
inseparable mixture of 8 and cyclodimeric product 11, having
a 24-membered ring was formed. HATU proved to be the
more efficient reagent, while benzotriazolyloxytris(pyrroli-
dino)phosphonium hexafluorophosphate (PyBOP) used by
others15 for cyclization of peptoids (poly-N-substituted
glycine) was in our hand deleterious. As anticipated, cy-
clization of dimer 2 proved challenging. The expected cyclic
N-Propargyl-functionalized â-alanine 1, the key building
block for the synthesis of the expected short â-peptoids
(10) (a) Norgren, A. S.; Arvidsson, P. I. Org. Biomol. Chem. 2005, 3,
1359-1361. (b) Simpson, G. L.; Gordon, A. H.; Lindsay, D. M.;
Promsawan, N.; Crump, M. P.; Mulholland, K.; Hayter, B. R.; Gallagher,
T. J. Am. Chem. Soc. 2006, 128, 10638-10639.
(11) Hamper, B. C.; Kolodziej, S. A.; Scates, A. M.; Smith, R. G.; Cortez,
E. J. Org. Chem. 1998, 63, 708-718.
(12) (a) Mejias, X.; Feliu, L.; Planas, M.; Bardaji, E. Tetrahedron Lett.
2006, 47, 8069-8071. (b) Shuey, S. W.; Delaney, W. J.; Shah, M. C.;
Scialdone, M. A. Biorg. Med. Chem. Lett. 2006, 16, 1245-1248. (c) Olsen,
C. A.; Bonke, G.; Vedel, L.; Adsersen, A.; Witt, M.; Franzyk, H.;
Jaroszewski, J. W. Org. Lett. 2007, 9, 1549-1552.
(13) (a) Gademann, K.; Seebach, D. HelV. Chim. Acta 2001, 84, 2924-
2937. (b) Gademann, K.; Ernst, M.; Hoyer, D.; Seebach, D. Angew. Chem.,
Int. Ed. 1999, 38, 1223-1226. (c) Gademann, K.; Seebach, D. HelV. Chim.
Acta 1999, 82, 957-962.
(14) (a) Norgren, A. S.; Zhang, S.; Arvidsson, P. I. Org. Lett. 2006, 8,
4533-4536. (b) Baldauf, C.; Gu¨nther, R.; Hofmann, H.-J. Phys. Biol. 2006,
3, S1-S9.
(15) Shin, S. B.; Yoo, B.; Todaro, L. J.; Kirshenbaum, K. J. Am. Chem.
Soc. 2007, 129, 3218-3225.
922
Org. Lett., Vol. 10, No. 5, 2008

our knowledge, structure 9 is the first macrocyclic oligoamide
containing only cis-amide bonds. All four carbonyl groups
are directed outside of the ring and make two subsequent
angles of 54° and 126° with the vertical 2-fold symmetry
axis. This is also a major difference with previous work on
cyclo-â-peptides describing a unidirectional arrangement of
the amides with NH and CdO groups oriented to opposite
faces of the peptide ring, perpendicularly to the ring. As a
consequence, cyclic â-peptides are known to form unique
nanotube assemblies17 due to supramolecular staking medi-
ated by intermolecular hydrogen-bonding both in the solid
state and in solution.
Table 1. Macrocyclization of Linear â-Peptoids 2-6
compd
yielda
entry
1
conditions
linear cyclic (%)
HATU (1.2 equiv), DIEA (2 equiv),
CH2Cl2/DMF 4:1 (5 mM)
DPPA (2 equiv), DIEA (3 equiv),
CH3CN (5 mM)
HATU (1.2 equiv), DIEA (2 equiv),
CH2Cl2 + ꢀ DMF (10 mM)
DPPA (1.5 equiv), NaHCO3 (9 equiv),
DMF (10 mM)
DPPA (2 equiv), DIEA (3 equiv),
DMF (10 mM)
DPPA (2 equiv), DIEA (3 equiv),
CH3CN (5 mM)
PyBOP (2 equiv), DIEA (3 equiv),
CH2Cl2 (5 mM)
HATU (1.2 equiv), DIEA (2 equiv),
CH2Cl2/DMF 4:1 (10 mM)
DPPA (2 equiv), NaHCO3 (9 equiv),
CH3CN/DMF 8:2 (10 mM)
2
2
3
3
3
3
3
4
4
4
4
4
5
5
6
6
7/9 16/12b
The crystal packing can be described as layers of
molecules perpendicular to the 2-fold symmetry axis (Figure
1a) and as column of molecules along the C2 axis (Figure
2
3
4
5
6
7
8
9
7/9
8/11
8/11
8/11
8/11
8/11
9
26
69c
30c
27c
66c
d
57
48
65
63
55
52
67
59
68
9
10 DPPA (2 equiv), NaHCO3 (9 equiv),
CH3CN/DMF 9:1 (5 mM)
11 DPPA (2 equiv), DIEA (3 equiv),
CH3CN (10 mM)
12 DPPA (2 equiv), DIEA (3 equiv),
CH3CN (5 mM)
13 HATU (1.2 equiv), DIEA (2 equiv),
CH2Cl2/DMF 4:1 (5 mM)
14 DPPA (2 equiv), DIEA (3 equiv),
CH3CN (5 mM)
15 HATU(1.2 equiv), DIEA (2 equiv),
CH2Cl2/DMF 4:1 (5 mM)
16 DPPA (2 equiv), DIEA (3 equiv),
CH3CN (5 mM)
9
9
9
10
10
11
11
Figure 1. Crystal structure of 9: (a) four cyclic subunits in one
layer showing the formation of the 18-membered pseudorings, (b)
column-like crystal packing and interlayer stabilization via CH‚‚‚
O interactions. The intermolecular interactions are shown as dashed
lines.
a Yield of pure isolated products. b Not separated. c Inseparable mixture
by silica gel chromatography. d No reaction.
dipeptoid 7 was isolated as a pure compound in low yield
(16%) beside cyclotetramer 9 (12%) (entry 1).
1b). The molecules in a layer are held together via inter-
molecular CH‚‚‚O hydrogen bonds18 involving carbonyl
groups and acetylenic H atoms (D ) 3.223 Å, d ) 2.34 Å,
Colorless prismatic crystals suitable for X-ray structure
analysis of tetramer 9 were grown by slow evaporation from
deuterated methanol solution at room temperature. The
crystal structure of 9, the first to be solved for a cyclic
â-peptoid compound, adopts a C2-symmetrical nonplanar
square-shaped conformation with dimensions 4.89 × 4.89
Å. All amide bonds are in the cis configuration, in sharp
contrast with the solid-state structure of known cyclo-â-
tetrapeptides which have all the peptide bonds in trans
geometry.16 In the field of peptoids, a leading publication
from Kirshenbaum et al.15 reports on cyclic R-peptoids
containing cis- and trans-amides; however, to the best of
(16) (a) Seebach, D.; Matthews, J. L.; Meden, A.; Wessels, T.; Baer-
locher, C.; McCusker, L. B. HelV. Chim. Acta 1997, 80, 173-182. (b)
Sutton, Peter, W.; Bradley, A.; Elsegood, M. R. J.; Farra`s, J.; Jackson, R.
F. W.; Romea, P.; Urpf, F.; Vilarrasa, J. Tetrahedron Lett. 1999, 40, 2629-
2632. (c) Buttner, F.; Norgren, A. S.; Zhang, S.; Prabpai, S.; Kongsaeree,
P.; Arvidsson, P. I. Chem. Eur. J. 2005, 11, 6145-6158.
(17) (a) Tereshko, V.; Monserrat, J. M.; Pe´rez-Folch, J.; Aymam´ı, J.;
Fita, I.; Subirana, J. A. Acta Crystallogr. 1994, B50, 243-251. (b) Clark,
T. D.; Buehler, L. K.; Ghadiri, R. J. Am. Chem. Soc. 1998, 120, 651-656.
(18) Desiraju, G. R.; Steiner, T. The Weak Hydrogen bond in Structural
Chemistry and Biology; Oxford University Press: Oxford, U.K., 1999.
Org. Lett., Vol. 10, No. 5, 2008
923

θ ) 159°), leading to the formation of 18-membered
pseudorings. Interlayer CH‚‚‚O interactions were also ob-
served between the carbonyl and the methylene groups of
the cyclic â-peptoid (D ) 3.485 Å, d ) 2.57 Å, θ ) 157°).
It should also be noted that two propargyl groups are pointing
toward one face and the other two toward the opposite face
in an alternative manner. That is a very interesting feature
considering the design of well-defined template for multi-
valent ligands anchoring.19
spectra complexity (1H and 13C), comparable to those of
linear peptoids is likely due to cis-trans isomerizations, a
characteristic that, in addition to a large size of the ring
increases its conformational flexibility.
Cylic â-peptoids have been prepared as new promising
template for multimeric bioactive ligands anchoring. We
chose to synthesize compounds 12 and 13 to demonstrate
proof of principle for the efficient functionalization of these
macrocycles using click chemistry.22 Conjugation was achieved
by reacting 9 with benzyl azide or 6-deoxy-6-azido-1,2-
3,4-diisopropylidene R-D-galactopyranose in the presence of
CuSO4, ascorbic acid, and tris(benzyltriazolylmethyl)amine
(TBTA) as a ligand or a hydrosoluble analogue (Scheme 2).23
Due to a small energy difference between cis and trans
tertiary amide bonds, linear peptoids 2-6 were observed as
mixtures of cis/trans configurational isomers.20 However,
1
both H and 13C NMR spectrum of 9 were very simple,
showing only one resonance for each kind of proton and
carbon, in agreement with a symmetrical structure. Thus, only
one configurational isomer exists in solution, tentatively
assigned to the all-cis isomer found in the solid. For that
purpose the all-cis cyclic tetramer 9 was sampled by
simulating annealing method and the energetically most
favorable structure was optimized at the DFT (B3LYP/6-
31G**) level. Geometry optimization was also performed
with an all-trans and an alternate cis-trans arrangement, both
in agreement with NMR data, and the thermodynamic
properties were evaluated. According to DFT calculations,
the all-trans cyclic tetramer is 7.3 kcal more stable than the
isolated all-cis compound and 4.7 kcal more stable than the
alternate cis-trans structure. From these results, one can
roughly estimate that for each amide bond in the ring, the
cis configuration, compared to the trans, is unfavored by
about 2 kcal‚mol-1, in the order of what is known for
secondary amide bonds.21
Scheme 2. Functionalized Cyclic â-Peptoids
a 4 mol % for 12, 8 mol % for 13. b12 mol % for 12, 24 mol %
for 13. c4 mol % of TBTA for 12, 8 mol % of hydrosoluble TBTA
for 13 (see the Supporting Information).
Since large ∆(∆G) are measured between the three
putative symmetrical arrangements, one can reasonably
assume that the all-cis configurational isomer is the primary
product from macrocyclization; i.e., it does not arise from
the equilibration of a more stable isomer during crystalliza-
tion. These results would suggest that the all-cis compound
exists both in the solid and in solution. The kinetic all-cis
compound is likely obtained, from an all-cis open-chain
isomer, displaying the most favorable conformation for
cyclization. At the moment, no suitable crystals have been
obtained to perform X-ray diffraction studies of cyclic
pentamer 10 and hexamer 11. However, their NMR spectra
are very instructive. The magnetic equivalence of the
different protons and carbons of all five residues in 10
(DMSO-d6) clearly indicates that 10 possesses a 5-fold
molecular symmetry. This symmetry implies that the 20-
membered ring should possess only one type of amide bonds,
cis or trans and that all the side chains should point toward
the same face of the ring. In the case of hexamer 11, the
In summary, we have described the first macrocyclization
study of â-peptoids. Functionalization of tetramer 9 was
addressed via “click” reactions. X-ray analysis of tetramer
9 has revealed an unprecedent all-cis cyclic structure. For
cyclic â-peptoids larger than a 20-membered ring, it is likely
that the conformational behavior of â-peptoids macrocycles
depends on cis-trans isomerizations.
Acknowledgment. We thank Bertrand Legeret (Univer-
site´ Blaise Pascal - Clermont-Ferrand II) for LC-MS
analysis and HRMS measurements
Supporting Information Available: Experimental de-
tails, characterization of new compounds, X-ray crystal-
lography data for 9, RP-HPLC data, NMR spectra, and total
energies. This material is available free of charge via the
Internet at http://pubs.acs.org.
(19) Boturyn, D.; Coll, J. C.; Garanger, E.; Favrot, M. C.; Dumy, P. J.
Am. Chem. Soc. 2004, 126, 5730-5739.
OL7030763
(20) Linear peptoids with cis amide bonds have been repeatedly
described, see for example the following reference describing a pentamer
with all-cis-amide bonds: Armand, P.; Kirshenbaum, K.; Goldsmith, R.
A.; Farr-Jones, S.; Barron, A. E.; Truong, K. T. V.; Dill, K. A.; Mierke, D.
F.; Cohen, F. E.; Zuckermann, R. N.; Bradley, E. K. Proc. Natl. Acad. Sci.
U.S.A. 1998, 95, 4309-4314.
(22) Jang, H.; Fafarman, A.; Holub, J. M.; Kirshenbaum, K. Org. Lett.
2005, 7, 1951-1954. Holub, J. M.; Jang, H.; Kirshenbaum, K. Org. Biomol.
Chem. 2006, 4, 1497-1502.
(23) Chan, T. R.; Hilgraf, R.; Sharpless, K. B.; Fokin, V. V Org. Lett.
2004, 6, 2853-2855.
(21) Poteau, R.; Trinquier, G. J. Am. Chem. Soc. 2005, 127, 13875-
13889 and references cited therein.
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