A Peptoid Square Helix via Synergistic Control of Backbone Dihedral Angles

Article abstract of DOI:10.1021/jacs.7b02319

The continued expansion of the fields of macromolecular chemistry and nanoscience has motivated the development of new secondary structures that can serve as architectural elements of innovative materials, molecular machines, biological probes, and even commercial medicines. Synthetic foldamers are particularly attractive systems for developing such elements because they are specifically designed to facilitate synthetic manipulation and functional diversity. However, relatively few predictive design principles exist that permit both rational and modular control of foldamer secondary structure, while maintaining the capacity for facile diversification of displayed functionality. We demonstrate here that the synergistic application of two such principles in the design of peptoid foldamers yields a new and unique secondary structure that we term an η-helix due to its repeating turns, which are highly reminiscent of peptide β-turns. Solution-phase structures of η-helices were obtained by simulated annealing using NOE-derived distance restraints, and the NMR spectra of a series of designed helices were altogether consistent with the primary adoption of this structure. The structure is resilient to solvent and temperature changes, and accommodates diversification without requiring postsynthetic manipulation. The unique shape, broad structural stability, and synthetic accessibility of helices could facilitate their utilization in a wide range of applications.

Full text of DOI:10.1021/jacs.7b02319

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A Peptoid Square Helix via Synergistic Control of Backbone Dihedral Angles.
Benjamin Craig Gorske, Emily M Mumford, Charles G Gerrity, and Imelda Ko
J. Am. Chem. Soc., Just Accepted Manuscript • Publication Date (Web): 24 May 2017
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A Peptoid Square Helix via Synergistic Control of Backbone Dihe-
dral Angles.
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Benjamin C. Gorske,* Emily M. Mumford, Charles G. Gerrity, and Imelda Ko.
*Department of Chemistry, Bowdoin College, 6600 College Station, Brunswick, Maine 04011-8466.
Email: bgorske@bowdoin.edu
Supporting Information Placeholder
4
weak intramolecular interactions, which have been
ABSTRACT: The continued expansion of the fields of
macromolecular chemistry and nanoscience has moti-
engineered to stabilize new secondary structures such
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as peptoid ribbons, helices, and Σ-strands. The ca-
pacity to rationally program the ω-dihedral angle simp-
ly by sidechain choice and without additional synthetic
manipulation distinguishes peptoids from most other
foldamers and endows them with unique structural and
functional capabilities. The peptoid ribbon secondary
structure that arises from alternating incorporation of
cis- and trans-amide-promoting 1-naphthylethyl and
phenyl sidechains, respectively, aptly demonstrates the
vated the development of new secondary structures
that can serve as architectural elements of innovative
materials, molecular machines, biological probes, and
even commercial medicines. Synthetic foldamers are
particularly attractive systems for developing such el-
ements because they are specifically designed to facili-
tate synthetic manipulation and functional diversity.
However, relatively few predictive design principles
exist that permit both rational and modular control of
foldamer secondary structure, while maintaining the
capacity for facile diversification of displayed func-
tionality. We demonstrate here that the synergistic ap-
plication of two such principles in the design of pep-
toid foldamers yields a new and unique secondary
structure that we term an “η-helix” due to its repeating
turns, which are highly reminiscent of peptide β-turns.
Solution-phase structures of η-helices were obtained
by simulated annealing using nOe-derived distance
restraints, and the NMR spectra of a series of designed
η-helices were altogether consistent with the primary
adoption of this structure. The structure is resilient to
solvent and temperature changes, and accommodates
diversification without requiring post-synthetic manip-
ulation. The unique shape, broad structural stability,
and synthetic accessibility of η-helices could facilitate
their utilization in a wide range of applications.
5
application of this design principle. However, design
strategies of comparable scope for per-residue control
of the other peptoid backbone dihedral angles (ψ and
φ) are much less developed. We recently reported one
such strategy entailing the tandem incorporation of
enantiomeric 1-naphthylethyl sidechains that can be
8
used to rationally “switch” the backbone φ angle.
However, the “ω-strand" structures resulting from al-
ternation of (S)- and (R)-1-naphthylethyl sidechains did
not dominate the conformational manifold at oligomer
lengths exceeding four residues.
R
N
O
R
N
O
χ1
ω
H
N
R
N
ψ
φ
O
n
R =
Interest in developing foldameric, and particularly
peptidomimetic, oligomers is on the rise as evidence of
their remarkable utility and versatility in the develop-
ment of new bioactive compounds, catalysts, materials,
s1npe
r1npe
ph
,
1 2
and even medicines continues to accrue. Peptoids (N-
alkylglycine oligomers) have proven to be especially
adaptable platforms for such applications, as their con-
ception was strongly motivated by considerations of
F
3
synthetic facility and structural diversity. The nearly
equal energies of peptoid amide bond rotamers enable
control of the ω-dihedral angle (Figure 1) via relatively
4fph
2,6mph
3,5mph
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(Figure 2). Notably, the incorporation of enantiomeric
FIGURE 1. Structures of the peptoid oligomers and side
chains examined in this study.
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2
3
4
5
6
7
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1npe residues provided sufficient dispersion to unam-
biguously assign each peak of interest without isotopic
labeling. Consistent with previously reported solution-
and solid-phase structures of peptoid helices and rib-
bons, the 1-naphthylethyl sidechains clearly enforced
the adoption of the cis-rotamer (ω dihedral angle ≈ 0°)
by the preceding residue, as evidenced by strong nOes
We now report that the synergistic application of the
two strategies above — incorporation of both enantio-
meric side chains and side chains that alternately pro-
mote cis- and trans-amides in the backbone — yields a
new and unique peptoid secondary structure. We refer
to this structure as an “η-helix” since it resembles a
peptide π helix with longer facets. NMR spectroscopy
revealed that these structures exhibit high conforma-
tional homogeneity, are highly insensitive to solvent
perturbation, and tolerate phenyl sidechain diversity.
We thus envision that η-helices will complement emi-
nent peptoid secondary structures such as helices, rib-
bons, and Σ-strands in the construction of new materi-
als, catalysts, and biologically active compounds.
4d,5
between the i and i-1 methylene protons. In contrast,
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the achiral but trans-amide-promoting (ω dihedral an-
gle ≈ 180°) N-aryl residues produced nOes between the
methylene and sidechain protons within the residue, as
observed in previous studies of N-aryl PPII-like helices
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5,6c
and peptoid ribbons. Restraining the simulated an-
nealing using these nOe-based ω-angle restraints,
along with key nOes observed between the 1npe me-
thyl groups and sidechain protons of the i+1 and i+2
residues, yielded several compact structures that were
inconsistent with the paucity of additional inter-residue
nOes observed. Thus, absent distance restraints
(ADRs) were used (in a manner consistent with that
employed to determine the extended peptoid helix
We first examined trimer 1 representing the shortest
possible unit that permits both alternation of the cis-
and trans-promoting sidechains (1-naphthylethyl and
various phenyl residues, respectively) and alternation
of the 1-naphthylethyl sidechain stereoconfiguration
(Figure 1, Table 1). Although other peptoid secondary
structures can require up to 12 residues to achieve con-
formational homogeneity due to reliance on coopera-
6a
structure ) to penalize structures that would give rise
to strong but unobserved nOes to the 3,5mph methyl
groups.
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tive folding, we observed a dominant conformation by
NMR spectroscopy in CD3OD for trimer 1, suggesting
that the sidechains exert a high degree of local struc-
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tural control, as observed in peptoid ribbons. In con-
O
O
N
N
NH
trast to the peptoid ω-strands that we recently report-
N
N
8
O
O
O
ed, elongation of the trimer up to octamer length (2–5)
in accordance with the design principal above did not
significantly impact conformational homogeneity.
Table 1. Peptoid oligomer structures.
com-
monomer sequence
pound
1
2
3
4
5
r1npe-ph-s1npe
3,5mph-r1npe-ph-s1npe
s1npe-3,5mph-r1npe-ph-s1npe
4fph-s1npe-3,5mph-r1npe-ph-s1npe
2,6mph-r1npe-4fph-
-s1npe-3,5mph-r1npe-ph-s1npe
6
7
4fph-r1npe-3,5mph-s1npe
s1npe-4fph-r1npe-3,5mph-s1npe
2,6mph-r1npe-3,5mph-s1npe
r1npe-2,6mph-s1npe
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9
10
11
2,6mph-r1npe-ph-s1npe
r1npe-3,5mph-s1npe
The solution-phase structure of pentamer 3 in
CD3OD was obtained by simulated annealing using
distance restraints derived from key inter-residue nOes
FIGURE 2. Top: Chemical structure of 3. Middle: Views
of the lowest energy structure obtained from nOe-
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restrained simulated annealing of 3. (Hydrogen atoms and
dihedral angle, with the S- and R-enantiomers enforc-
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2
3
4
sidechains removed for clarity.) Bottom: Lowest energy
structure from simulated annealing with key nOes and
ADRs in green and red, respectively.
ing φ angles of approximately −60° and +60°, respec-
tively; this particular relationship between primary and
secondary peptoid structure is precedented within the
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context of peptoid ω-strands. As is typical for pep-
5
toids, the ψ angles uniformly cluster near 180°. The
minimal repeating unit containing both S- and R-
sidechains is tetrameric and contains both central and
terminal turns for which the η-helix is named. The
NMR spectra of both longer peptoids (4 and 5) and
peptoids containing differently substituted phenyl
groups in various positions (6–11) are also universally
consistent with the elucidated structures, regardless of
solvent (see Supporting Information). The similar nOe
patterns observed in CD3OD, CD3CN, and CDCl3 for
the principal conformations of compounds 1–11 sug-
gest that steric interactions play the dominant role in
their folding. Variable-temperature NMR spectroscopy
of trimer 1 in CD3CN revealed no spectral perturbation
of consequence between -40 and 80 ºC, further sup-
porting this hypothesis.
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O
O
O
O
N
N
N
NH
N
N
F
N
N
O
O
O
O
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In order to further explore the structural space acces-
sible using the titular design strategy, we also obtained
a solution-phase structure for octamer 5 in CD3CN
(Figure 3) using nOe-restrained simulated annealing
and assignments of the backbone methylene protons
based on the NMR-derived structure of 3. (Although 5
was also soluble in CD3OD, insufficient dispersion
was obtained for unambiguous assignment of the reso-
nances.) In addition to the inter-residue nOes of the
types observed for 3, 5 also exhibited several nOes
between the C- and N-termini, and between the termini
and central residues, that collectively focused the simu-
lated annealing outcomes to yield the compact solu-
tion-phase structure shown. The ensemble of lowest
energy structures reveals consecutive pairs of 90° turns
that completely reverse the direction of the backbone.
As a result, the residues appended to the termini of
internal turns (e.g. 4fph and ph, 2,6mph and 3,5mph)
are arrayed approximately parallel to each other, anal-
ogously to a peptide β-hairpin. (The C-terminal residue
containing the secondary amide once again adopted an
outlying conformation as observed in pentamer 3.)
This parallel orientation is enabled in part by the coun-
terbalancing of the gentle backbone curvatures pro-
duced by the s1ne and r1ne residues, leading to a more
flattened structure compared to peptoid ribbons com-
FIGURE 3. Chemical structure of 5, and the lowest ener-
gy structure obtained from nOe-restrained simulated an-
nealing of octamer 5 with (top) and without (bottom)
sidechains. (Hydrogen atoms removed for clarity.)
The ensemble of the ten lowest energy structures ex-
hibited a RMSD of 1.05 Å, and each of these structures
was wholly consistent with the complete set of ob-
served nOes (see Supporting Information). Aside from
the C-terminal residue containing a unique secondary
amide, the dihedral angles closely correspond to those
of a peptoid ribbon, except that the signs of the φ an-
gles alternate between positive and negative for s1ne
and r1ne, respectively. Thus, the stereoconfiguration of
the 1-naphthylethyl sidechain apparently dictates the φ
5
prised of only one of these enantiomeric residues. The
antiparallel alignment of the residues protruding from
the turns distinguishes them from the more obtuse,
corkscrew-like turns observed in peptoid ribbons. We
attribute the unique, ≈90° angles in the η-helix back-
bone to steric interactions between these antiparallel
residues that force slight deviations of the backbone
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dihedral angles from their predicted optimal values. ACKNOWLEDGMENT
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1
Thus, the backbone flexibility afforded by relying sole-
ly upon noncovalent interactions for folding appears to
play a critical role in the formation of these helices.
This flexibility is presumably also responsible for the
planar displacement of the C- and N-termini, resulting
in one terminus “tucking under” the other to provide a
slight pitch to the nascent square helix. In conclusion,
we have elucidated a new peptoid secondary structure
realized by rational, synergistic control of both the ω
and φ backbone dihedral angles using only noncovalent
interactions. To our knowledge, this particular folda-
mer construction approach, which maximizes synthetic
and structural flexibility by obviating covalent cycliza-
tion of backbone atoms, has not been reported previ-
ously. The insensitivity of the structure to variation of
solvent and temperature indicates that steric interac-
tions provide the primary impetus for folding. Such
broad structural competence suggests that η-helices
that are appropriately functionalized and solubilized
We wish to thank Dr. Ronald Zuckermann for helpful and
contributive discussions, and Prof. Amelia Fuller for CD
spectroscopy. Acknowledgment is made to the Donors of
the American Chemical Society Petroleum Research Fund
for support of this research. Support for the LCMS in-
strumentation at Bowdoin College by the NSF (CHE-
1126657) is gratefully acknowledged.
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using existing, well-developed strategies for peptoids
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talysis, we are currently developing η-helix-derived
β-hairpins as catalysts. Indeed, the internal turns of
octamer 5 place the side chains of the antiparallel resi-
dues in close proximity, which could facilitate both
mimicry of multifunctional enzyme active sites and
cyclization. Furthermore, such hairpins could serve to
11
nucleate strand-like structures as they do in peptides.
We thus envision grafting more linear peptoid struc-
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tures such as ω- or Σ-strands, and perhaps even PPI-
6
and PPII-type helices, to isolated η-helix turns to gen-
erate peptoid β-sheet mimics. The structure of octamer
5 suggests that such sheets could be stabilized by π-
stacking of interdigitated aromatic groups rather than
by interstrand hydrogen bonding, and we are thus ac-
tively investigating these possibilities in our laborato-
ry. We also submit that η-helical peptidic structures
can be accessed using suitably modified D- and L-
amino acids; such residues might be used within the
context of η-helix/peptide hybrid oligomers to control
the ψ dihedral angles, potentially yielding complete
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modular control of the entire backbone. Overall, this
work demonstrates the generality of structural control
achievable using enantiomeric sidechains in pep-
tidomimetics, and further illustrates the versatility of
peptoids as a foldameric system.
Supporting Information. The Supporting Information is
available free of charge on the ACS Publications website.
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