Quaternary centres as a tool for modulating foldamer conformation

Article abstract of DOI:10.1002/chem.201102103

Centre refold: (3R,4S,1′S)-4-Amino-1-(1′-(4-methoxyphenyl) ethyl)-3-methyl-5-oxopyrrolidine-3-carboxylic acid (AMMOPC) gives a foldamer with an 8-helix conformation. When it was inserted in the 12-helix foldamer of (3R,4S,1′S)-4-amino-1-(1′-(4-methoxyphenyl)ethyl) -5-oxo-pyrrolidine-3-carboxylic acid (AMOPC), it locally induced formation of an 8-helix conformation (see figure).

Full text of DOI:10.1002/chem.201102103

DOI: 10.1002/chem.201102103
Quaternary Centres as a Tool for Modulating Foldamer Conformation
Roberta Galeazzi,[a] Gianluca Martelli,*[a] Andrea Mazzanti,[b] Mario Orena,*[a] and
Samuele Rinaldi[a]
Dedicated to Professor Giuliana Cardillo
In recent years, oligomers of unnatural peptidic resi-
dues,[1–3] mainly built up with b-amino acids[4–5] or their hy-
brids with natural a-amino acids,[6] have emerged as versa-
tile structural templates (foldamers) that exhibit predictable
and well-defined secondary structures, such as helices, turns
and strands, and offer a variety of possibilities for orienting
functional side-chains. When a linear a-polypeptide folds
into well-ordered and compact secondary structures,[7–11] the
preferred backbone conformation arises in part from mini-
mization of Newman and Pitzer strain, as well as pseudo-
Scheme 1. b-Amino acids leading to foldamers displaying an 8-helix con-
formation.
impose angular constraints that translate the robust 314-helix
sustained by trans-ACHC-b2,3 amino acid units into a new
folding pattern.[1,20,21] Eventually, homo-oligomers derived
from nucleoside b-amino acids 4, in which strain probably
arises from 1,3-cis-disubstitution at the oxygen bridge, dis-
play a similar conformational pattern.[22] However, all these
results do not question the proposal formulated by Gellman
allylic AACHTUNGTRENNUNG(1,3) strain, which restricts the f and c torsion angle
values accessible to proteinogenic amino acid residues.[12] In
addition, proteinogenic a-amino acids display intrinsic and
distinct propensities for helices and sheets and can be select-
ed accordingly to stabilise a given fold,[13–15] but a higher sta-
bilisation can be achieved by further restricting the available
conformational space of amino acids in the sequence.[5]
Thus, in a-peptides, Thorpe–Ingold effects (C(a)-tetrasub-
stitution) have been used extensively to impose such a re-
striction on f and c angles[16] and Aib (a-aminoisobutyric
acid) is a very strong promoter of helical (310 and a-helices)
and b-turn structures.[5,11] On the other hand, b-peptides
mostly occur in the 12- or 14-helical conformation, but olig-
omers consisting of b2,3-amino acids of unlike configuration
or of geminally disubstituted amino acids cannot fit in any
of the two folds. In fact, (2R,3S)-a-hydroxy b2,3-amino acid 1
gives a foldamer, which in polar solvent, displays a helical
conformation based on repetitive 8-membered H bonded
!
that 1 3 H bonding between nearest-neighbour amide
groups in b-peptides is not favoured, but rather suggest that
extra interactions or specific angular constraints can over-
come this general feature.[23]
Since the change from 12- or 14-helix into a 8-helix con-
formation for a b-foldamer seems to arise from conforma-
tional restrictions, we investigated whether introducing a
quaternary centre in (3R,4S,1’S)-4-amino-1-(1’-(4-methoxy-
phenyl)ethyl)-5-oxopyrrolidine-3-carboxylic
acid
((3S,4R,1’S)
AHCTUNGTRENNUNG
MOPC; 5a)[24] could also give rise to a confor-
mational change. In fact, in connection with our interest to-
wards applications, such as peptidomimetics,[25] antimicrobial
agents[26] and components in nanostructured materials,[27] we
had already prepared a foldamer starting from 5b, the di-
protected form of 5a, the secondary structure of which was
!
ꢀ
rings resulting from 1 3 H bond interactions (C=Oi···H
N
i+2).[17] A remarkably similar C8-based conformation has
1
also been reported for oligomers consisting of 1-aminometh-
yl cyclopropane carboxylic acid residues (2, Scheme 1).[18]
Moreover, the b-peptide consisting of trans-oxabornene-
b-amino acid 3 adopts a C8-based helix conformation;[19] this
causes the cyclohexyl ring bridging and unsaturation to
determined to be a 12-helix by means of H NMR spectros-
copy data and supported by molecular dynamics (MD) sim-
ulations.[28]
Directed towards the preparation of an amphiphilic folda-
mer, we envisaged the more rigid 8-helix conformation can
allow a better separation between the substituents at the
lactam nitrogen on the two sides of the helix. In fact, owing
to the easy removal of the 4-methoxyphenylethyl group, the
N-1 of the pyrrolidin-2-one ring could be appropriately func-
tionalised with polar chains. Thus, stereoselective alkylation
of 5b led to the corresponding derivative 6b, the fully pro-
tected (3R,4S,1’S)-4-amino-1-(1’-(4-methoxyphenyl)ethyl)-3-
[a] Dr. R. Galeazzi, Dr. G. Martelli, Prof. M. Orena, Dr. S. Rinaldi
Di.S.V.A. Chemistry, Polytechnic University of Marche
Via Brecce Bianche, I-60131 Ancona (Italy)
Fax : (+39)071-2204714
E-mail: gmartell@univpm.it
m.orena@univpm.it
[b] Prof. A. Mazzanti
Department of Organic Chemistry “A. Mangini”
University of Bologna, Via Risorgimento, I-40126 Bologna (Italy)
methyl-5-oxopyrrolidine-3-carboxylic
acid
((3R,4S,1’S)-
AMMOPC; 6a, Scheme 2),[29] and this unit was employed in
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/chem.201102103.
an attempt to modify the foldamer conformation to intro-
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Chem. Eur. J. 2011, 17, 12564 – 12568

COMMUNICATION
mained identical (see the Supporting Information). The out-
come of these titrations was in perfect agreement with re-
sults arising from ROESY spectral data, as the NH protons
of 7 are nearly insensitive to DMSO; this confirms that this
hexamer is able to form a H bond-driven secondary struc-
ture. Then, ROESY spectral data were used in order to
assign non-adjacent NOE interactions, and the correlation
types observed were consistent with a population of secon-
dary structures identified as an 8-helix (see the Supporting
Information).
Scheme 2. Structures
AMMOPC (6a) and of their derivatives, 5b and 6b.
of
(3S,4R,1’S)-AMOPC
(5a), (3R,4S,1’S)-
duce a quaternary centre in the monomer. Thus, by using
standard homogeneous peptide synthesis, starting from 6b
the corresponding hexamer 7 was obtained and its confor-
mation was first assigned by means of NMR analysis and
then confirmed by MD simulations.
In order to definitely confirm the real strong preference
for this conformational structure, totally unconstrained MD
simulations were carried out by using the protocol described
in the Supporting Information. The cluster analysis (RMS=
0.39) pointed out the existence of 72 conformers grouped
into three clusters, all showing the same 8-helix backbone
arrangement, whereas the main differences concern the ori-
entation of the side-chains. The lowest energy conformer
with its 8-helix structure and the most populated cluster in-
cluding the lowest energy conformer (number of members
70) are reported in Figures 2 and 3, respectively.
ꢀ
First, the occurrence of intramolecular C=O···H N hydro-
gen bonds in the foldamer leading to an 8-helix was con-
firmed by investigation of the [D6]DMSO dependence of
NH proton chemical shifts.[30] This solvent is a strong hydro-
gen-bond acceptor and if it is bound to a free NH proton, it
is expected to dramatically move its chemical shift down-
field. The results for the [D6]DMSO/CDCl3 titrations of the
NH protons of hexamer 7 are reported in Figure 1. The olig-
omers are not aggregated under the experimental conditions
since even on changing the concentration the spectra re-
Figure 2. Minimum energy structure for hexamer 7 showing the hydrogen
bonds implicated in the 8-helix conformation.
These findings were confirmed by high temperature
quenched molecular dynamics (QMD) simulations by using
ROESY distance restrained QMD simulations. In fact, a
total agreement was observed between these two independ-
ently obtained results and the NOE interatomic distances.
Figure 1. Variation of NH proton chemical shifts (ppm) of hexamer 7 as a
function of increasing percentage of [D6]DMSO added to the CDCl3 so-
lution (v/v; concentration 5 mm). From top to bottom: NH-Res2, NH-
Res3, NH-Res4, NH-Res5, NH-Res6, NH-Res1.
1
Thus, as observed from the H NMR spectroscopy data and
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M. Orena, G. Martelli et al.
conformational changes being unit 3. On the other hand,
when monomers 5a and 6a were alternated, the conforma-
tion changed dramatically from 12- to 8-helix, which was
Figure 3. Most populated cluster for compound 7.
Figure 4. Minimum energy structure for hexamer 8 showing the hydrogen
bonds implicated in the 8-helix!12-helix conformation.
MD simulations, foldamer 7 displays an 8-helical secondary
structure in CDCl3 solution.
Having assigned the conformation of 7, using MD simula-
tions we started a preliminary computational analysis direct-
ed to ascertain whether introduction of (3S,4R,1’S)-
AMMOPC (6a) within a structure built up with (3S,4R,1’S)-
AMOPC (5a) could give rise to significant conformational
changes. From the MD simulations carried out without any
experimental restraints, the introduction of a sole 6a unit at
any position of the hexamer built up with 5a led only to
minor effects. Random conformational changes perturbed
the population distribution of the 12-helix structure, which
was locally distorted, with the position most prone to give
Scheme 3. Structures of the hexamers 8 and 9 showing the insertion of
(3R,4S,1’S)-AMMOPC (6a).
Figure 5. Minimum energy structure for hexamer 9 showing the hydrogen
bonds implicated in the mixed 8-helix!12-helix conformation.
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Modulating Foldamer Conformation
COMMUNICATION
most stable when the double substitution occurred at posi-
tions 2 and 4.
6a could be a useful tool to generate local changes of the
conformationally preferred 12-helix in a b-foldamer, and
this behaviour was ascribed to the presence of the quaterna-
ry carbon centre.
With the aim to confirm these results, following a stan-
dard homogeneous phase synthesis (see the Supporting In-
formation) the mixed hexamers 8 and 9 were prepared, in
which 6a was introduced at positions 3 and (2,4), respective-
ly, and the remaining building blocks were 5a (Scheme 3).
From both NMR spectroscopy data and MD simulations, it
was found that 6a is able to modify the 12-helix of the hexa-
mer built up from 5a, and the new conformation was as-
signed as a mixed 8-helix–12-helix. In fact, for compound 8
we observed a large conformational variability and only a
locally induced 8-helix folding within 12-helix structural ele-
ments (see the Supporting Information for further details;
Figure 4). On the contrary, cluster analysis of compound 9
carried out with NOE restricted MD simulations pointed
out the existence of 22 conformers, arranged into 13 clusters,
and the minimum energy structures alternate 8-helix and 12-
helix conformations (Figure 5).
In summary, we have found that the hexamer of
(3S,4R,1’S)-AMMOPC (6a) in CDCl3 folds around short-
range hydrogen bonds leading to eight-membered rings (8-
helix conformation). In addition, insertion of 6a into the b-
peptide built up from (3S,4R,1’S)-AMOPC (5a), which
shows a clear preference for longer-range hydrogen bonding
interactions that lead to a stabilised 12-helix, changed its
conformation from 12- to 8-helix. This behaviour might en-
hance the understanding of the principles behind the design
of functionally folded architectures in large synthetic struc-
tures. To this end, synthesis of a series of b-amino acids teth-
ered on a g-lactam containing a quaternary centre is under-
way, and results arising from their insertion into b-foldamers
will be reported in due course.
For a better insight, a comparison between the backbones
of hexamers 7–9 is reported in Figure 6. From these results,
Figure 6. Comparison of lateral and perpendicular views of backbones of foldamers 7, 8 and 9 (from left to right).
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Keywords: conformation analysis
structures · lactams · quaternary carbon
· foldamers · helical
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Received: July 8, 2011
Published online: October 4, 2011
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