Sequence-specific binding of m-phenylene ethynylene foldamers to a piperazinium dihydrochloride salt

Article abstract of DOI:10.1021/ol0500721

(Chemical Equation Presented) Binding properties of a series of isomeric m-phenylene ethynylene oligomers containing short amide sequences to a piperazinium dihydrochloride salt were investigated by using circular dichroism (CD) measurements. Although the

Full text of DOI:10.1021/ol0500721

ORGANIC
LETTERS
2005
Vol. 7, No. 9
1683-1686
Sequence-Specific Binding of
m-Phenylene Ethynylene Foldamers to a
Piperazinium Dihydrochloride Salt
Kazuki Goto and Jeffrey S. Moore*
Roger Adams Laboratory, Department of Chemistry and Materials Science &
Engineering, UniVersity of Illinois at Urbana-Champaign, Urbana, Illinois 61801
moore@scs.uiuc.edu
Received January 13, 2005
ABSTRACT
Binding properties of a series of isomeric m-phenylene ethynylene oligomers containing short amide sequences to a piperazinium dihydrochloride
salt were investigated by using circular dichroism (CD) measurements. Although these isomeric oligomers exhibited similar helical conformations,
high affinity was observed only for one oligomer. This behavior is presumably controlled by the orientation of amino groups of the amide
sequence and the folded conformation of the oligomer.
While the “binding pocket” concept is well understood for
globular proteins, it has yet to be widely implemented with
synthetic macromolecules. In principle, compact polymer
chains of all types can generate three-dimensional cavities
and crevices. Lining these surfaces with specific functional
groups whose spatial position is determined by chain
sequence and conformation offers a potentially powerful and
general platform for high-affinity and high-specificity mo-
lecular recognition.1 A major challenge, however, is the need
to control the conformation of chain molecules in solution,
such that only a small ensemble of cavity shapes and sizes
is generated in the collapsed state. Recent advances in the
field of foldamers2 have provided oligomers with a high
degree of conformational order. For example, we have
previously shown that m-phenylene ethynylene oligomers in
polar solvents exhibit a unique helical conformation stabilized
by solvophobic interactions.3 This helical conformation
produces an internal cavity with nonpolar surfaces capable
of binding hydrophobic molecules of appropriate size in polar
solvents.4 Here we report a series of hybrid backbones
derived from m-phenylene ethynylene oligomers and short,
isomeric amide sequences. Their association with a piper-
azinium dihydrochloride salt demonstrates that functional
groups in the helical cavity control binding selectivity.
(2) (a) Hill, D. J.; Mio, M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S.
Chem. ReV. 2001, 101, 3893-4012. (b) Zhu, J.; Parra, R. D.; Zeng, H.;
Skrypczak-Jankun, E.; Zeng, X. C.; Gong, B. J. Am. Chem. Soc. 2000,
122, 4219-4220. (c) Berl, V.; Huc, I.; Khoury, R. G.; Krische, M. J.; Lehn,
J.-M. Nature 2000, 407, 720-723. (d) Hirschberg, J. H. K. K.; Brunsveld,
L.; Ramzi, A.; Vekemans, J. A. J. M.; Sijbesma, R. P.; Meijer, E. W. Nature
2000, 407, 167-170.
(3) (a) Nelson, J. C.; Saven, J. G.; Moore, J. S.; Wolynes, P. G. Science
1997, 277, 1793-1796. (b) Prince, R. B.; Saven, J. G.; Wolynes, P. G.;
Moore, J. S. J. Am. Chem. Soc. 1999, 121, 3114-3121. (c) Prince, R. B.;
Moore, J. S.; Brunsverd, L.; Meijer, E. W. Chem. Eur. J. 2001, 7, 4150-
4154.
(4) (a) Prince, R. B.; Barnes, S. A.; Moore, J. S. J. Am. Chem. Soc.
2000, 122, 2758-2762. (b) Tanatani, A.; Mio, M. J.; Moore, J. S. J. Am.
Chem. Soc. 2001, 123, 1792-1793. (c) Inouye, M.; Waki, M.; Abe, H. J.
Am. Chem. Soc. 2004, 126, 2022-2027.
(1) Szwajkajzer, D.; Carey, J. Biopolymers 1997, 44, 181-198.
10.1021/ol0500721 CCC: $30.25
© 2005 American Chemical Society
Published on Web 04/02/2005

A short amide sequence inserted into the middle of a
m-phenylene ethynylene oligomer introduces hydrogen bond-
ing and ion recognition capabilities into the backbone.
Assuming that the solvophobically driven helical conforma-
tion is preserved in these hybrid backbones, the cavity will
display anion and/or cation interaction receptors that are
buried in the otherwise nonpolar cavity environment. The
specific arrangement of these receptors in the cavity interior
will depend on the amide sequence (Figure 1). For example,
Figure 3. UV titration curves of oligomer 1 ([), 2 (9), and 3
(2).
Isomeric oligomers 1-3 were synthesized by coupling
short amide sequences capped with terminal acetylene end
groups to a m-phenylene ethynylene heptamer.6,7 UV-vis
spectra of these three oligomers in a series of chloroform/
acetonitrile binary solvent compositions are similar to those
of the m-phenylene ethynylene oligomers previously re-
ported, suggesting a random conformation in chloroform and
a helical conformation in acetonitrile (Figure 2).3
In addition, solvent denaturation studies indicate that these
hybrid oligomers undergo a folding transition at a composi-
tion similar to the parent phenylene ethynylene backbone
(Figure 3 and Table 1).8,9
Figure 1. Structures of isomeric oligomers 1-3, rodlike ligand 4,
and piperazinium dihydrochloride salt 5.
the conformations of sequence 1 are commensurate with the
phenylene ethynylene helix orienting amino groups as
H-bond donors into the cavity.5 In contrast, the helical
conformations of sequence 2 position carbonyl groups as
H-bond acceptors into the cavity. Sequence 3, derived from
aminobenzoic acid, is expected to create a helical cavity that
has one H-bond donor and one H-bond acceptor.
Table 1. Comparison of the Free Energy of Folding of
Denaturation for Oligomers
oligomer
-∆G(CH3CN) (kcal/mol)
[CHCl3]1/2
1
2
3
3.9 ( 0.1
3.5 ( 0.1
3.5 ( 0.1
52
56
54
On the basis of earlier studies,4b ligand 4 was expected to
have a shape and size complementary to the helical cavity
generated from oligomers 1-3. However, in acetonitrile, no
induced CD signal was observed when ligand 4 was added
to solutions of 1, 2, or 3 (Figure 4 A curves labeled i). When
HCl was added to the solution, there was an induced signal
observed for oligomer 1 (Figure 4A curves labeled ii).10 In
contrast, without ligand 4, oligomers 1-3 do not exhibit any
(5) Coles, S. J.; Frey, J. G.; Gale P. A.; Hursthouse, M. B.; Light, M.
E.; Navakhun K.; Thomas, G. L. Chem. Commun. 2003, 568-569.
(6) See Supporting Information.
(7) On the basis of a previous study,3b chiral side chains were introduced
to both ends to gain information about the conformation of these oligomers.
The CD signals induced by these side chains are much weaker than
complexation-induced CD seen in Figure 5A.
(8) For detailed description of experimental procedure and data analysis,
see Supporting Information.
Figure 2. UV absorption spectra of oligomer 1 in mixed solvents.
[1] ) 4.3 µM. Volume % of chloroform/acetonitrile was from 100
to 0.
(9) Apparent reduction in folding at 90-100% chloroform is likely to
be caused by amide H-bonding in these nonpolar solvent conditions.
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Org. Lett., Vol. 7, No. 9, 2005

Figure 4. CD spectra of oligomers 1 (black), 2 (red), and 3 (blue)
in acetonitrile with ligand 4 (A) and without ligand 4 as a control
(B): (i) no HCl, (ii) [HCl] ) 840 µM, [oligomer] ) 4.2 µM; [ligand
4] ) 840 µM in A.
significant CD signals (Figure 4B) regardless of whether HCl
is added or not. These results suggested that oligomer 1
specifically interacts with the protonated form of ligand 4.
Given these observations, we decided to investigate the
binding of oligomers 1-3 to the dication ligand 5. The
binding isotherm for each oligomer to ligand 5 was measured
in acetonitrile by circular dichroism (CD) spectroscopy.4b,11
Figure 5 shows a series of CD spectra obtained from the
addition of different concentrations of enantiomerically pure
ligand 5 to oligomers 1-3 in acetonitrile. For sequence 1,
ligand 5 induces a significant Cotton effect at ca. 314 nm
corresponding to the backbone’s diphenylacetylene chro-
mophore. An isodichroic point is observed at ca. 292 nm.
The spectra have band shapes similar to those observed for
the 1:1 complex formed between m-phenylene ethynylene
oligomers and ligand 4 in 40% aqueous acetonitrile.4b
As seen in Figure 5A (inset), the CD signal at 314 nm
recorded over a range of ligand concentrations showed
saturation behavior expected for complex-induced CD signal.
The intensity of the CD signal at 314 nm plotted against the
concentration of 5 can be fitted to a 1:1 binding isotherm
by nonlinear least-squares analysis,12 yielding an association
constant, K11, of 1.0 × 103 M-1. In contrast to sequence 1,
when oligomer 2 or 3 was exposed to ligand 5, the induced
CD signal was much smaller over the entire range of ligand
concentrations. No induced Cotton effect or saturation
behavior was evident (Figures 5B and 5C).
Figure 5. CD spectra of oligomer 1 (A), 2 (B), and 3 (C) as a
function of concentration of 5 (range, 4.0-400 µM) in acetonitrile.
[Oligomer] ) 4.2 µM. The insets show plots of the ∆∆ꢀ values at
314 nm against the concentration of ligand 5. The solid curve is
the best fit to the data using a 1:1 binding model.
Although we have not been able to rule out the possibility
that this behavior stems from an insignificant helical twist
sense bias in the diastereomeric complex between 5 and 2
or 3, the most plausible explanation is a significantly lower
affinity for 5 by these two sequences.
sequences capped with terminal trimethylsilylacetylene end
groups (6-8) were also investigated. When ligand 5 was
added to acetonitrile solutions of these short amide se-
quences, only 6, which has the same amide arrangement as
oligomer 1, showed chemical shift changes of NH protons
and aromatic proton.13 For further investigation, a Job’s plot
analysis was performed. Keeping the total concentration of
6 and ligand 5 at 1 mM, the concentrations of 6 were varied.
When products of chemical shift change by the mole fraction
of 6 were plotted against the mole fraction of 6, there was
To further support the mechanism of the specific interac-
tion between oligomer 1 and the ligand 5, clear, short amide
(10) CD spectra of each oligomer in the absence of 5 do not have any
significant signals. Induced CD spectra were obtained by subtracting the
CD spectrum of ligand 5 from that of the complex.
(11) m-Phenylene ethynylene oligomers without an amide sequence do
not bind 5 in pure acetonitrile.
(12) Program “Dynafit” was used for nonlinear least-squares fitting:
Kuzmic, P. Anal. Biochem. 1996, 237, 260-273.
(13) For the binding study between oligomers 1-3 and ligand 5, 1H NMR
was unsuccessful because of line broadening due to aggregation.
Org. Lett., Vol. 7, No. 9, 2005
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a peak observed at 0.67 of the mole fraction of the short
amide sequence. This result suggested that the stoichiometry
of the complex between 6 and ligand 5 is 2:1, rather than
1:1.14 In addition, 1H NMR titration data were also obtained
by progressive addition of ligand 5 to 6 in acetonitrile. The
chemical shift changes of NH protons against the concentra-
tion of ligand 5 can be fitted to a 2:1 binding, yielding
association constants Ka1 of 1.0 × 103 M-1 and Ka2 of 1.0 ×
105 M-1.14
groups of the amide sequence are oriented toward the interior
of the cavity. The presence of H-bond donors in the helical
cavity and chloride anion of piperazinium salt 5 provides
favorable ion interactions between 1 and 5. We investigated
the role of counterion through the study of dications of 4
with H-F, H-Br, and H-I. No clear evidence of induced
CD was observed in these cases. We thus conclude that the
chloride anion plays an important role in the sequence-
selective binding between 1 and 5.
In conclusion, we have demonstrated that hybrid back-
bones derived from m-phenylene ethynylene oligomers and
short, isomeric amide sequences can be used to introduce
ion-selective interactions into the helical cavity. The specific
binding properties observed between these oligomers and
piperazinium salt 5 are consistent with H-bond donor groups
being oriented according to the amide sequence and con-
trolled by the folded conformation of the m-phenylene
ethynylene oligomer. Further studies to gain more details
about the specific interactions involved in binding and the
role of chlorine ion are currently underway.
Acknowledgment. This work was supported by the
National Science Foundation under Grant CHE 01-03447 and
the U.S. Department of Energy, Division of Materials
Sciences, under Award DEFG02-91ER45439, through the
Frederick Seitz Materials Research Laboratory at the Uni-
versity of Illinois at Urbana-Champaign. This work was also
financially supported by TORAY Industries, Inc. K.G. thanks
Prof. Thomas S. Hughes at University of Vermont for
discussions on the molecular modeling of the helical
structures and binding properties of the oligomers.
Figure 6. Structures of short amide sequences 6-8.
These experiments support the notion that oligomer 1
specifically interacts with the protonated form of ligand 4.
These results are consistent with our assumption that
oligomer 1 adopts a helical conformation in which the amino
Supporting Information Available: Binding study of
short amide sequences and the ligand 5, experimental
procedures, and synthesis of 1-3, 5, and 6-8. This material
is available free of charge via the Internet at http://pubs.acs.org.
(14) See Supporting Information.
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