Homogeneous and Robust Polyproline Type i Helices from Peptoids with Nonaromatic α-Chiral Side Chains

Article abstract of DOI:10.1021/jacs.7b07475

Peptoids that are oligomers of N-substituted glycines represent a class of peptide mimics with great potential in areas ranging from medicinal chemistry to biomaterial science. Controlling the equilibria between the cis and trans conformations of their backbone amides is the major hurdle to overcome for the construction of discrete folded structures, particularly for the development of all-cis polyproline type I (PPI) helices, as tools for modulating biological functions. The prominent role of backbone to side chain electronic interactions (n → π) and side chains bulkiness in promoting cis-amides was essentially investigated with peptoid aromatic side chains, among which the chiral 1-naphthylethyl (1npe) group yielded the best results. We have explored for the first time the possibility to achieve similar performances with a sterically hindered α-chiral aliphatic side chain. Herein, we report on the synthesis and detailed conformational analysis of a series of (S)-N-(1-tert-butylethyl)glycine (Ns1tbe) peptoid homo-oligomers. The X-ray crystal structure of an Ns1tbe pentamer revealed an all-cis PPI helix, and the CD curves of the Ns1tbe oligomers also resemble those of PPI peptide helices. Interestingly, the CD data reported here are the first for any conformationally homogeneous helical peptoids containing only α-chiral aliphatic side chains. Finally we also synthesized and analyzed two mixed oligomers composed of NtBu and Ns1tbe monomers. Strikingly, the solid state structure of the mixed oligomer Ac-(tBu)₂-(s1tbe)₄-(tBu)₂-COOtBu, the longest to be solved for any linear peptoid, revealed a PPI helix of great regularity despite the presence of only 50% of chiral side chain in the sequence.

Full text of DOI:10.1021/jacs.7b07475

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Article
Highly homogeneous and robust PolyProline type I helices
from peptoids with non-aromatic #-chiral side chains
Olivier Roy, Geoffrey Dumonteil, Sophie Faure, Laurent Jouffret, Alexandre Kriznik, and Claude Taillefumier
J. Am. Chem. Soc., Just Accepted Manuscript • DOI: 10.1021/jacs.7b07475 • Publication Date (Web): 24 Aug 2017
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Journal of the American Chemical Society
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Homogeneous and robust PolyProline type I helices from peptoids
with non-aromatic α-chiral side chains
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Olivier Roy,*,† Geoffrey Dumonteil,† Sophie Faure,† Laurent Jouffret,† Alexandre Kriznik,‡ and
Claude Taillefumier*,†
†Université Clermont Auvergne, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP 10448, F-
63000 Clermont-Ferrand, France and CNRS, UMR 6296, ICCF, F-63178 Aubière Cedex, France
‡Université de Lorraine, Fédération de Recherche CNRS 3209, Service Commun de Biophysique Interactions Molé-
culaires, and Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire, CNRS, UMR 7365, BP 20199, F-
54505 Vandoeuvre les Nancy, France
ABSTRACT: Peptoids which are oligomers of Nꢀsubstituted glycines represent a class of peptide mimics
with great potential in areas ranging from medicinal chemistry to biomaterial science. Controlling the
equilibria between the cis and trans conformations of their backbone amides is the major hurdle to overꢀ
come for the construction of discrete folded structures, particularly for the development of allꢀcis Polyꢀ
Prolineꢀtype I (PPI) helices, as tools for modulating biological functions. The prominent role of backꢀ
bone to side chain electronic interactions (n→π*) and side chains bulkiness in promoting cisꢀamides
was essentially investigated with peptoid aromatic side chains among which the chiral 1ꢀnaphthylethyl
(1npe) group yielded the best results. We have explored for the first time the possibility to achieve simiꢀ
lar performances with a sterically hindered αꢀchiral aliphatic side chain. Herein, we report on the synꢀ
thesis and detailed conformational analysis of a series of (S)ꢀNꢀ(1ꢀtertꢀbutylethyl)glycine (Ns1tbe) pepꢀ
toid homooligomers. The Xꢀray crystal structure of an Ns1tbe pentamer revealed an allꢀcis PPI helix and
the CD curves of the Ns1tbe oligomers also resemble those of PPI peptide helices. Interestingly, the CD
data reported here are the first for any conformationally homogeneous helical peptoids containing only
αꢀchiral aliphatic side chains. Finally we also synthesized and analysed two mixed oligomers composed
of NtBu and Ns1tbe monomers. Strikingly, the solid state structure of the mixed oligomer Acꢀ(tBu)2ꢀ
(s1tbe)4ꢀ(tBu)2ꢀCOOtBu, the longest to be solved for any linear peptoid revealed a PPI helix of great
regularity despite the presence of only 50% of chiral side chain in the sequence.
cases the cis and trans conformations of the amide bonds
1. INTRODUCTION
are very close in energy giving rise to cis/trans equilibria.5
Despite their inherent flexibility, peptoids have been
shown to adopt preferential folded conformations, includ-
ing the PolyProline-type II (PPII) 6 and PolyProline-type I
(PPI) helical structures.7 The potential of foldamer helices
from a drug discovery standpoint has been recognized but
for some of them a limitation exists in term of diversity of
accessible monomers.8 In the case of peptoids a huge
diversity of side chains can be incorporated but only few
of them are capable of promoting a stable secondary
structure. The canonical PPI helix with all-cis amide
bonds was the first to be predicted by molecular mechan-
ics calculations from prototypical oligopeptoids com-
posed of chiral (S)-N-(1-phenylethyl)glycine residues
(spe).7 Soon after, the PPI-type conformation was con-
Peptoids are artificial oligomers/polymers composed of
N-Substituted Glycine (NSG) monomers that are becom-
ing a valuable class of compounds in biosciences1 as well
as in important chemical areas including catalysis,2 self-
assembly3 and metal binding.4 Compared to natural pep-
tides, the side chains are shifted from the Cα carbons to
the amide bond nitrogen atoms. This change has im-
portant implications on the conformational behaviour of
this class of compounds whose main chain is more flexi-
ble than that of their parent peptides. This difference is
essentially due to the presence of N,N-disubstituted am-
ide bonds, often referred as tertiary amides, with no hy-
drogen bond donor atoms for establishing intramolecular
H-bonding interactions, and also to the fact that in most
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firmed by NMR of the (Nspe)5 homopentamer, the all-cis
structure being the major solution conformation among a
mixture of cis/trans isomers.9 In a recent past, intensive
efforts have been made for a clear understanding of the
local stereoelectronic factors that govern the cis/trans
peptoid amides equilibria. This research led to the devel-
opment of side chains capable of exercising a strong steric
and/or electronic control over the amide geometry and
consequently on the conformation in the vicinity of the
studied amide. Thus, a number of side chains were exam-
ined with respect to their ability to promote the cis con-
formation. Those that yielded the best performances to
date are presented in Figure 1B.10 11 12 13 It must be pointed
out here that most of them have an aromatic group in
their structure which is a limitation in term of physico-
chemical properties in a drug discovery context as for
example the disruption of protein-protein interactions. In
this work we have sought to identify a non-aromatic cis-
peptoid amide inducer allowing the formation of discrete
PPI helices of defined handedness. This challenge was
never achieved from peptoid oligomers with α-chiral
aliphatic side chains. Thus our goal was also to describe
more precisely the CD signature of non-aromatic PPI
peptoid. In view of our understanding of the noncovalent
interactions that govern local peptoid folding, the first
objective was to identify a chiral aliphatic side chain
bringing the maximum of steric hindrance. As a precursor
of this ideal side chain, it was also important for this work
to identify a commercially primary amine available in the
R and S configurations. We report here the synthesis of a
series of (S)-N-(1-tert-butylethyl)glycine (Ns1tbe) homo-
oligomers and two mixed oligomers composed of Ns1tbe
and NtBu monomers, and their detailed structural analy-
sis by NMR spectroscopy, X-ray crystallography and CD
analysis.
all attempts of solid-phase synthesis yielded mixtures of
truncated (NtBu) oligomers.15 The solution-phase sub-
monomer synthesis was therefore preferred for this study.
In order to compare the efficacy of the new s1tbe side
chain to the past work with the s1npe side chain,11a which
can be considered today as the reference for constructing
robust peptoid helical structures, we chose to synthesize a
series of acetamide-capped (N1tbe) homooligomers with
tBu esters at their C-termini. This series comprises all the
oligomers from the monomer till the hexamer (1-6), the
octamer (8) and the nonamer (9) (Table 1). The synthesis
started by substitution of the bromine atom of tertbutyl
bromoacetate by the s1tbe amine, yielding a N1tbe mono-
mer which was then elongated by the iterative submono-
1
2
3
4
5
6
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,
,
,
mer method consisting in
a
two-step acylation-
substitution cycle. Bromoacetic anhydride, freshly pre-
pared from bromoacetic acid and DCC, was systematically
used for the acylation steps and the substitutions were
carried out with 3 equivalents of the s1tbe amine.13 After
each iteration, with the exception of the heptamer stage, a
portion of the formed amine was acetylated to yield pep-
toids 1-6, 8 and 9. The same procedure was applied for
synthesizing the mixed oligomers 6’and 8’ (Table 1) by
using when required tBuNH2 instead of the s1tbe amine
(see Scheme S1 for details). The Nsch hexamer 7 com-
posed of (S)-N-(1-cyclohexylethyl)glycine units with an
acetylated N-terminus and a tert-butyl ester at the C-
terminus, was also synthesised as a key control to allow
for spectroscopic comparison. 16
Table 1. Structures for peptoids 1-9, 6’ and 8’
peptoid
Monomer sequence
Ac-s1tbe-COOtBu
1
2
Ac-(s1tbe)2-COOtBu
Ac-(s1tbe)3-COOtBu
Ac-(s1tbe)4-COOtBu
Ac-(s1tbe)5-COOtBu
Ac-(s1tbe)6-COOtBu
Ac-(sch)6-COOtBu
3
2. RESULTS AND DISCUSSIONS
2.1 Synthesis of peptoid oligomers
4
5
The commercially available (2S)-3,3-dimethylbutan-2-
amine was used as the precursor of the s1tbe side chain.
Its enantiomeric R form is also commercially available.
Peptoids are most often synthesized by the so-called sol-
id-phase submonomer synthesis14 but this method can
results in low yields in case of very bulky amines like the
1-naphthylethyl amine or the tert-butyl amine for which
6
7
6’
8
8’
9
Ac-tBu(s1tbe)4tBu-COOtBu
Ac-(s1tbe)8-COOtBu
Ac-(tBu)2(s1tbe)4(tBu)2-COOtBu
Ac-(s1tbe)9-COOtBu
2.2. NMR analysis of peptoid oligomers
1H NMR of monomer 1 was recorded at a concentration of
10 mM in various solvents (CDCl3, CD3CN and CD3OD) for
determining the Kcis/trans ratios (Table 2). They were calcu-
lated by averaging the integration of three sets of related
rotamer signals, including when possible the NCα
methyne protons. The chemical shift of the methyne
proton in monomer 1 is remarkably deshielded in the cis
conformation relative to the trans (~ 1 ppm in CDCl3),
Figure 1. (A) Cis-trans peptoid amide equilibrium. (B)
Chemical structure of side chains promoting the cis confor-
mation: a) (S)-1-phenylethyl (spe); b) 4-methylpyridinium
(4mpy);10 c) (S)-1-naphthylethyl (s1npe);10,11 d) with R1 = Bn, 1-
(benzyltriazolium)ethyl (bte+);12 e) tert-butyl (tBu).13
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Table 2. Overall Kcis/trans values as determined by H
NMR integration and/or H-COSY in CDCl3, CD3CN
aliphatic cyclohexyl (ch) side chain, which served as a
baseline indicator of chiral aliphatic side chain.16 The
bulky s1tbe side chain in monomer 1, however, cannot
compete with the tBu side chain which suppressed com-
pletely the trans rotamers, based on steric hindrance
(Kcis/trans ≥ 19 for E and F) and with the s1npe in the mon-
omer compound G (n=1) for which the high Kcis/trans value
1
1
2
and CD3OD
3
4
5
6
7
8
9
CDCl3
Kcis/trans
0.64a
0.98a
1.95a
>19b
18.92a
>19 a
2.71c
>19b
>19a
>19b
>19a
CD3CN
Kcis/trans
0.67a
1.60a
CD3OD
Kcis/trans
0.77a
1.68a
3.00a
>19b
peptoid
1
2
results from complementary steric and n → π*Ar effects. A
greater sensitivity to solvent polarity was observed from
2.61a
the dimer stage. Notably, the Ns1tbe dimer exhibits a
3
larger overall Kcis/trans value in acetonitrile (CD3CNKcis/trans
=
10
11
12
13
14
15
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4
5
10.89a
7.96a
10.39a
1.39c
>19b
8.08a
>19b
1.60) relative to the value observed in chloroform
>19b
>19b
CDCl3
(
K
= 0.98). One possible explanation is that
cis/trans
6
7
acetonitrile, by minimizing inter amide n → π*C=O interac-
tions, would destabilize trans-amide rotamers. What is
striking and deserves to be mentioned on how the overall
backbone Kcis/trans evolve with the oligomer length, is the
great leap between the trimer and tetramer stage, particu-
larly in chloroform and methanol. Taking the example of
chloroform, the Kcis/trans increased from 1.95 to ≥ 19, which
mean that overall, the population of trans rotamers de-
creased from 66% to < 4%. The same tendency, through
less marked was observed in CD3CN between trimer 3 and
tetramer 4. Extension of the trimer by one residue thus
induced a dramatic increase of conformational ordering.
This phenomenon is much more pronounced with the
Ns1tbe system as compared with the Ns1npe for which
progression of the Kcis/trans is more regular going from the
monomer to the tetramer (G, Figure 2). A direct compari-
son of these two systems is particularly relevant since
they possess identical N- and C-capping groups and have
been studied both in acetonitrile. A Kcis/trans of 3.3 for Ac-
(Nspe)5-CO2tBu in CD3CN (B, Figure 2), has also been
described as part of the study of the N1snpe system.11a
6’
8
8’
9
>19b
>19b
12.13a
aDetermined by integration of 1D-1H NMR spectrum. bDetermined by
integration of 2D-1H-COSY spectrum. Determined by integration of
c
2D-HSQC spectrum.
1
in accordance with previously H NMR reported data on
aliphatic and aromatic side chains.10,11a,12,17 The methyne
protons resonances are thus a good way for discriminat-
ing the cis and trans rotamers of the Ns1tbe family. Mon-
omer 1 which exhibits Kcis/trans ranging between 0.64 and
0.77 displays only slight sensitivity with solvent polarity,
in line with previous observations of ester-capped mono-
mer models, relative to related amide-capped systems.10
These values are similar to those observed for the pe side
chain in the methyl ester model A (Figure 2) for which an
n →
π*
interaction stabilizing the cis rotamer has been
Ar
suggested.10 Interestingly, the Kcis/trans for compound 1 are
2-fold higher than those for the model C containing the
Figure 2. Kcis/trans values (the number in brackets) of various model peptoids and oligomers as determined by NMR measure-
ments in different solvents. In the lower right corner, the structure of the homo-oligomers synthesized in this work.
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