A rigid helical peptide axle for a [2]rotaxane molecular machine

Article abstract of DOI:10.1002/anie.200904749

Spinning around? A series of peptido[2]rotaxanes have been designed which contain a rigid helix as a significant part of their axle. One such rotaxane has been used to construct a reversible molecular device, in which, by virtue of the size of the inner c

Full text of DOI:10.1002/anie.200904749

Communications
DOI: 10.1002/anie.200904749
Rotaxanes
A Rigid Helical Peptide Axle for a [2]Rotaxane Molecular Machine**
Alessandro Moretto,* Ileana Menegazzo, Marco Crisma, Elizabeth J. Shotton, Harriott Nowell,
Stefano Mammi, and Claudio Toniolo
Rotaxanes are mechanically interlocked molecular architec-
tures in which a central linear molecule (axle) passes through
the cavity of a macrocycle (wheel).[1] The axle is held in place
by the presence of sterically bulky stoppers at both ends.
Oligomeric systems, which typically consist of repeating
oxyethylene or methylene units, are often exploited as axles
in the construction of rotaxanes.
containing such a motif is expected to template the formation
of the tetramide macrocycle to afford a rotaxane through a
five-component clipping reaction. Following the protocol
developed by Leigh and co-workers,[2,7] we synthesized a
macrocycle (from xylylenediamine and isophthaloyl dichlor-
ide) on the fumardiamide station in yields of 78 and 72% for
n = 1 and n = 4, respectively.
Peptido[2]rotaxanes, based on various -Gly-Xxx- dipep-
tide stations in the axle, were first reported by Leigh and co-
workers[2] and subsequently by Onagi and Rebek.[3] More
recently, the Leigh research group described a rotaxane in
which the wheel is able to protect a bioactive pentapeptide
axle from peptidase-catalyzed hydrolysis.[4] We are currently
investigating the synthesis and properties of a new set of
symmetrical and nonsymmetrical peptido[2]rotaxanes with
amino acid repeating units (oligopeptide systems) in their
axles. Herein we describe our results on a [2]rotaxane shuttle
in which the longest part of the axle is a rigid helical peptide,
which was planned to act as a track for the reversible motion
of a tetramide macrocyclic wheel.
The X-ray diffraction structures of the two resulting
highly crystalline, peptido[2]rotaxanes (Figure 1 and see the
As a first step in this study, we chose two symmetrical
axles, each characterized by either two a-aminoisobutyric
acid (Aib) residues or by two -(Aib)4- homopeptide ester
sequences; the latter sequence is known to generate incipient
310-helices,[5a,b] that is, secondary structures stabilized by two
Figure 1. Two representations each of the two X-ray diffraction struc-
tures of the symmetrical [Fmoc-(Aib)n-O-(CH2)2-NH]2-FUM (A: n=1;
B: n=4) [2]rotaxanes. Left: the carbon, oxygen, and nitrogen atoms
are depicted in gray, red, and blue, respectively. The intramolecular
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intramolecular, consecutive i i + 3 C O···H N hydrogen
bonds.[5c–e] A fumardiamide-derived central station,[2] two
ethoxy linkers, and two 9-fluorenylmethoxycarbonyl (Fmoc)
Na-protecting group[6] stoppers completed the chemical
structures of the [Fmoc-(Aib)n-O-(CH2)2-NH]2-FUM (n =
1,4; FUM = fumaric unit) axles. Each step of the synthesis
of the axle was performed by using solution methods. The
tetramide macrocycle[2,7] developed by Leigh and co-workers
was used as the wheel. The fumardiamide unit has multiple
hydrogen-bonding sites. In solvents of low polarity an axle
=
ꢀ
C O···H N hydrogen bonds are shown as black dotted lines. Right:
space-filling representations (macrocycle in blue and axle in green).
Supporting Information) show that the fumardiamide-dieth-
oxy moiety is an excellent station for the chair conformation
of the aromatic tetramide ring,[7] despite the proximity of the
bulky Aib residues or -(Aib)4- homopeptide helices.[8] The
ring is held in place by two sets of hydrogen bonds from the
two NH groups of each of its two isophthaldiamide moieties
to each of the two double-acceptor fumardiamide carbonyl
groups. The overall architecture is further stabilized by two
fluorenyl···isophthaloyl (stopper···macrocycle) face-to-edge
[*] Dr. A. Moretto, Dr. I. Menegazzo, Dr. M. Crisma, Prof. S. Mammi,
Prof. C. Toniolo
Istituto di Chimica Biomolecolare, CNR, Unitꢀ di Padova
Dipartimento di Scienze Chimiche, Universitꢀ di Padova
via Marzolo 1, 35131 Padova (Italy)
Fax: (+39)049-827-5239
E-mail: alessandro.moretto.1@unipd.it
interactions and
a xylylene···olefin···xylylene (macrocy-
cle···axle···macrocycle) p-stacking interaction. The inner
cavity of the macrocycle is roughy rectangular, with van der
Waals dimensions of 5.4 ꢀ 4.0 ꢁ and 7.4 ꢀ 3.4 ꢁ in the mono-
and tetrapeptide-based peptido[2]rotaxanes, respectively. The
lumen of the wheel is, therefore, significantly smaller than the
outer diameter of the -(Aib)4- 310-helix (about 10 ꢁ).
Whereas the NH group of each of the two amidoethoxy
linkers forms an intramolecular hydrogen bond with the
urethane Fmoc-Aib carbonyl group (C10 pseudocyclic struc-
Dr. E. J. Shotton, Dr. H. Nowell
Diamond Light Source
Didcot, Oxfordshire OX11 0DE (UK)
[**] A.M. thanks the University of Padova for financial support
(“Progetto Strategico” HELIOS). The technical assistance of S.
Spatola (Padova) is gratefully acknowledged.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.200904749.
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ture) in the Aib rotaxane, this same NH group in the -(Aib)4-
rotaxane is hydrogen bonded to the Aib(2) carbonyl group to
afford a C13 pseudocyclic structure. Moreover, in the -(Aib)4-
rotaxane the regularity of the two incipient 310-helices (one
right handed, the other left handed), including the presence of
the diphenylacetyl and diphenylmethyl amino moieties (at
the N and C terminus, respectively) and the aromatic
tetramide ring developed by Leigh and co-workers for the
stoppers and macrocycle.[2,7]
The results of the TOCSY and ROESY NMR analyses on
the (E)-FUM axle in CD3CN solution confirmed the pre-
dicted -(Aib)6- helical secondary structure (see Figure S7 and
Table S1 in the Supporting Information). By using the
protocol developed by Leigh and co-workers,[2,7] the macro-
cycle self-assembled on the fumardiamide station of the (E)-
FUM axle (I) in 95% yield, thus producing the (E)-FUM
peptido[2]rotaxane (III) (Figure 2). Evidence for the regio-
selective positioning of the macrocycle is provided by the
differences in the CH olefin proton resonances between I and
III (Figure 3 and Figure S9 in the Supporting Information).
The axle contains as many as 12 amide (or peptide) bonds
which could act as templates for the assembly of the
macrocycle. However, in solvents of low polarity such as
CHCl3 (the solvent used in the synthesis), most of the
carbonyl groups of Aib-rich peptides are so strongly intra-
molecularly hydrogen bonded that they are not available for
templation of the macrocycle. A comparison of the FTIR
absorption spectra of I and III corroborates the structural
!
[5]
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two intramolecular i i + 3 C O···H N hydrogen bonds, is
not disturbed by the formation of the macrocycle. Also, in
these structures the two helices are almost antiparallel and
orthogonal to the fumardiamide-diethoxy station, thereby
affording an overall S-shaped conformation of the axle. The
breaking points of the axle linearity are given by the gauche
disposition of two consecutive torsion angles of the -O-CH2-
CH2-NH- linker moiety.
We then moved to the second step of our study, namely to
attempt to create a peptido[2]rotaxane molecular machine.
To this end, we envisaged the nonsymmetrical (E)-FUM
configured axle shown in Figure 2A. The N terminus is based
on a 9-mer peptide with the sequence -d-Leu-(Gly)2-(Aib)6-,
followed by an ethoxyamide-FUM unit and a l-Leu residue.
The two stations of opposite chirality (-d-Leu-Gly-Gly- and
-(E)-FUM-l-Leu-) were expected to offer the possibility to
also check the system by using CD spectroscopy. The -(Aib)6-
sequence is known to fold in a robust 310-helix.[5,9] We selected
Figure 2. A) Chemical structure of the nonsymmetrical (E)-FUM axle I. B) Computer generated structures of I, the (Z)-MAL axle II, the (E)-FUM
peptido[2]rotaxane III, and the (Z)-MAL peptido[2]rotaxane IVa. The wheel is highlighted in yellow.
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To activate the molecular machine we heated IVa to 508C
for 60 minutes in CH3CN solution. This results in the macro-
cycle wheel moving to the -d-Leu-Gly-Gly- N-terminal
station, thus affording the (Z)-MAL peptido[2]rotaxane
(IVb) (Figure 4) in 90% yield. The 1H NMR data supporting
Figure 4. Reversible interconversion of the peptido[2]rotaxane IVa
(top) and IVb (bottom). The wheel is highlighted in yellow. The
proposed mechanism for the concomitant rotation and translation of
the wheel along the helical axle is depicted schematically in the center.
Figure 3. 1H NMR spectra (400 MHz, CD3CN, 318 K) of the (E)-FUM
axle I, (E)-FUM peptido[2]rotaxane III, (Z)-MAL peptido[2]rotaxane IVa,
(Z)-MAL peptido[2]rotaxane IVb, and (Z)-MAL axle II.
this conclusion (Figure 3 as well as Table S1 and Figure S10 in
the Supporting Information) are as follows: 1) The resonan-
ces of the olefin CH protons of IVb and those of the protons
of the two methylene groups of the amidoethoxy linker move
back to the same positions as those of the corresponding axle
II; 2) the Gly2 NH and aCH protons, as well as the d-Leu NH
proton are downfield shifted with respect to the correspond-
ing protons of II and IVa. Our interpretation of the NMR
results is corroborated by the switchable CD response of the
two translational isomers IVa and IVb of (Z)-MAL pepti-
do[2]rotaxane (see Figure S4 in the Supporting Information).
In particular, the induced ellipticities at about 230 nm, where
the benzamido chromophore of the achiral wheel absorbs
strongly,[10] are quite different, being close to zero for IVb
(with the wheel on the d-Leu-containing station) and very
strongly negative for isomer IVa (with the wheel on the l-Leu
maleidiamide station).[2d] It is noteworthy that this motion of
the wheel can be reversed (Figure 4) by heating IVb in either
CHCl3 or 1,1,2,2-tetrachloroethane solution at 558C for three
days, which results in a 95% conversion into IVa, as
demonstrated by the HPLC profiles (see Figure S3 in the
Supporting Information). Our long-standing experience on
medium-sized 310-helical peptides based entirely on the
strongly helicogenic Ca-tetrasubstituted a-amino acid
Aib,[5d,e] along with literature data on a variety of peptides
from this series from other research groups,[11] make us quite
confident that the overwhelmingly preferred conformation
(310-helix) of the -CO-(Aib)6-O- sequence used in this study is
extremely resistant to melting, particularly under the rela-
assignment of the latter, as it highlights the contribution of the
four macrocyclic hydrogen-bonded NH groups to the absorp-
tion band at about 3320 cmꢀ1 (see Figure S5 in the Supporting
Information). In agreement with all of the NMR and FTIR
absorption data collected, we propose that I and III adopt the
3D structures shown in Figure 2B. Moreover, from our NMR
findings it is evident that the macrocycle assembled onto the
axle does not affect the helical domain of the axle.
We then applied photon stimuli (254 nm) and switched the
fumardiamide unit of I and III to a maleidiamide. We
obtained the (Z)-MAL (MAL = maleic) axle (II; 100% yield
in 15 min) and the (Z)-MAL peptido[2]rotaxane (IVa; 49%
yield in 45 min); in the latter case the wheel is on the
1
maleidiamide station. Comparisons of the H NMR spectra
of: 1) axles I and II, and 2) peptido[2]rotaxanes III and IVa
(Figure 3 and Table S1 in the Supporting Information) show
clearly the differences between the E and Z olefin CH proton
dyads. Moreover, the resonances corresponding to the pro-
tons of the two methylene groups of the amidoethoxy linker
are remarkably downfield shifted in the case of the (Z)-MAL
peptido[2]rotaxane IVa compared to its (E)-FUM counter-
part III. Therefore, in the former the macrocycle is located
over the Z olefin unit through multiple intercomponent
hydrogen bonding. Again, the presence of the macrocycle
on the axle does not alter the helical stretch of the axle.
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tively mild experimental conditions (heating to 50–558C in
solvents of low polarity, such as CHCl3 or CH3CN) required
for activating our peptido[2]rotaxane molecular machine.
Our results also suggest that changing the solvent from CHCl3
to CH3CN results in modification of the relative stabilities of
the two stations (Z)-MAL diamide and -d-Leu-Gly-Gly- in
IVa and IVb, respectively. Acetonitrile, which is known to
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the N-terminal -Gly-Gly- dipeptide unit, which we believe
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on one such rotaxane. In this case: 1) the wheel switches
almost quantitatively between two, unambiguously identified,
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in this molecular machine in detail.
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Received: August 25, 2009
Published online: October 22, 2009
Keywords: molecular devices · NMR spectroscopy · peptides ·
.
rotaxanes · structure elucidation
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