Synthesis and structural characterisation as 12-helix of the hexamer of a β-amino acid tethered to a pyrrolidin-2-one ring

Article abstract of DOI:10.1039/b612071g

Starting from (3S,4R,1′S)-3-amino-2-oxo-1-[1′-(4- methoxyphenylethyl)]pyrrolidine carboxylic acid (2), the first synthesis of a β-foldamer containing pyrrolidin-2-one rings is described, whose 12-helix conformation is assigned by NMR analysis and confirme

Full text of DOI:10.1039/b612071g

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Synthesis and structural characterisation as 12-helix of the hexamer of
a b-amino acid tethered to a pyrrolidin-2-one ring{
Ileana Menegazzo,a Alexander Fries,a Stefano Mammi,*a Roberta Galeazzi,b Gianluca Martelli,b
Mario Orena*b and Samuele Rinaldib
Received (in Cambridge, UK) 22nd August 2006, Accepted 20th September 2006
First published as an Advance Article on the web 10th October 2006
DOI: 10.1039/b612071g
Starting from (3S,4R,19S)-3-amino-2-oxo-1-[19-(4-methoxyphe-
nylethyl)]pyrrolidine carboxylic acid (2), the first synthesis of a
b-foldamer containing pyrrolidin-2-one rings is described,
whose 12-helix conformation is assigned by NMR analysis
and confirmed by molecular dynamics (MD) simulations.
Non-natural polymers able to form organized secondary structures
in solution (‘‘foldamers’’), can be a useful alternative to peptides.1
Among them, oligomers of b-amino acids (‘‘b-peptides’’) are of
particular interest, since they display a high tendency to give
defined secondary structures2 and are unaffected by proteases, thus
being very attractive for molecular biology and drug discovery.3
Although many pyrrolidine ring-based foldamers have been
studied,4 to the best of our knowledge, amino acids tethered to a
pyrrolidin-2-one (c-lactam) ring were not used to build b-folda-
mers. We therefore planned to investigate the effect of the lactam
moiety on the conformational behaviour of such molecules.5 In
addition, if the group attached to the nitrogen of the lactam ring
can be easily removed, subsequent alkylation carried out with
appropriate functionalised alkyl halides could afford a new class of
foldamers where the conformational constriction due to the lactam
ring affects the orientation of the side chain. Here, we report both
Scheme 1 Preparation of hexamer 1. Reagents and conditions: (t-Boc =
the synthesis and the structural characterization of hexamer 1,
tert-butyloxycarbonyl; PMP = 4-methoxyphenyl): (i) (Boc)2O, TEA,
built from the b-amino acid (3S,4R,19S)-3-amino-2-oxo-1-[19-(4-
methoxyphenylethyl)]pyrrolidine carboxylic acid [(3S,4R,19S)-
AOMPC], 2, recently synthesized in our laboratory.5 First, the
(3S,4R,19S)-AOMPC 2 hydrochloride was converted into the key
intermediate, 3, precursor of both building blocks 4 and 5
(Scheme 1).
MeOH, rt, then CH2N2; (ii) 0.5 M NaOH, MeOH, then 2 M HCl; (iii)
TFA, DCM, rt. (iv) EDAC, TEA, DCM, 0 uC.
carboxy and amino groups, respectively. Finally, coupling of 9 and
10 led to the hexamer t-Boc-(AOMPC)6-OMe, 1 (Scheme 1 and
Fig. 1).
The synthesis of the homo-oligomers of (3S,4R,19S)-AOMPC 2
was carried out according to standard peptide synthesis in the
homogeneous phase. Starting from the monoprotected derivatives
4 and 5, the dimer t-Boc-(AOMPC)2-OMe, 6, was first isolated.
The trimer t-Boc-(AOMPC)3-OMe, 8, was subsequently synthe-
sized by coupling the dimer 7, which has a free amino group, and
4. Starting from 8, the trimers 9 and 10 were prepared, with free
The 12-helical conformation of 1 was elucidated by NMR
analysis. Assignment of the backbone proton resonances of each
1
monomer was achieved with standard H-homonuclear spectra6
and assignment of the carbon backbone resonances was achieved
using 1H/13C HMQC and HMBC experiments.7 Long-range
couplings between CONH(i) and H4(i) and between CO(i) and
NH(i + 1) detected in the HMBC spectrum provided the sequence-
specific assignment (Fig. 2). The complete backbone assignment is
reported in the electronic supplementary information (ESI).{
aDipartimento di Scienze Chimiche, Universita` di Padova, ICB-CNR,
Via Marzolo 1, I-35131 Padova, Italy. E-mail: stefano.mammi@unipd.it;
Fax: +39 049 8275239; Tel: +39 049 8275293
bDipartimento di Scienze dei Materiali e della Terra, Universita`
Politecnica delle Marche, Via Brecce Bianche, I-60131 Ancona, Italy.
E-mail: m.orena@univpm.it; Fax: +39 071 2204714;
Tel: +39 071 2204720
{ Electronic supplementary information (ESI) available: Detailed synthetic
procedures, characterization data for all compounds, spectra for
compounds 1, 2, 4, and 5 and molecular dynamics (MD) simulations.
See DOI: 10.1039/b612071g
Fig. 1 The structure of hexamer 1.
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Fig. 2 Example of spectral assignment of t-Boc-(AOMPC)6-OMe, 1, in
CDCl3 at 298 K.
Fig. 3 The 12-helix structure for hexamer
1 arising from MD
Medium-range correlations detected in the ROESY spectrum
(see ESI{) strongly suggested a 12-helical conformation: H3(i)–
NH(i + 2), H3(i)–H4(i + 2), H3(i)–NH(i + 3), and H5(i)–
NH(i + 3). The conformation of 1 was also studied by molecular
dynamics (MD) simulations8–10 and at first ROESY distance
restraints were used.11–13
simulations showing intramolecular H-bonding.
A detailed cluster analysis was carried out and the results, given
in the form of torsion angles w, h, and y population distributions
(clustering level 42, RMS 0.53), showed 48 structures grouped into
7 families (clusters). The lowest energy structures for 1 all provided
a 12-helical conformation and the differences in energy between
the conformations mainly arose from the side chain arrangements
which strongly differ from each other. In Fig. 3, the lowest energy
conformer is represented and its 12-helix like geometry is clearly
visible, whereas the superposition of the lowest energy structures of
1 from cluster 1 is reported in Fig. 4.
In addition, an unconstrained molecular dynamics simulation
was carried out, and the cluster analysis (clustering level 38,
RMS 0.52) showed 44 structures grouped into 7 families (see
ESI{). For the set clusters, we could identify a backbone structure
highly compatible with a 12-helical conformation, and the results
were in total agreement with the observed ROE interproton
distances.
In summary, we have reported the synthesis and the structural
elucidation of hexamer 1 which displays a 12-helix secondary
structure. The possibility of linking further substituents at the ring
nitrogen, exploiting the rigid sp2 moiety make this compound
synthetically useful since a lot of cationic or anionic functionalities
can be placed at specific sites along the helix. Thus, with the aim to
synthesize foldamers useful for their antibiotic activity14 and/or for
generation of nanostructures,15 work is currently in progress in our
laboratory and will be reported in due course.
Fig. 4 The cluster for 12-helix structure of hexamer 1 arising from MD
simulations (intramolecular H-bonding shown in green).
4916 | Chem. Commun., 2006, 4915–4917
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5 R. Galeazzi, G. Martelli, M. Orena, S. Rinaldi and P. Sabatino,
Tetrahedron, 2005, 61, 5465–5473.
Financial support is acknowledged from M.U.R. (Roma, Italy)
within the PRIN 2004 framework.
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J. Am. Chem. Soc., 1987, 109, 607–609; B. Ancian, I. Bourgeois,
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