Efficient assembly of threaded molecular machines for sequence-specific synthesis

Article abstract of DOI:10.1021/ja5022415

We report on an improved strategy for the preparation of artificial molecular machines that can pick up and assemble reactive groups in sequence by traveling along a track. In the new approach a preformed rotaxane synthon is attached to the end of an otherwise fully formed strand of building blocks. This rotaxane-capping protocol is significantly more efficient than the final-step-threading method employed previously and enables the synthesis of threaded molecular machines that operate on extended oligomer, and potentially polymer, tracks. The methodology is exemplified through the preparation of a machine that adds four amino acid building blocks from a strand in sequence, featuring up to 20-membered ring native chemical ligation transition states.

Full text of DOI:10.1021/ja5022415

Article
pubs.acs.org/JACS
Efficient Assembly of Threaded Molecular Machines for
Sequence-Specific Synthesis
Guillaume De Bo, Sonja Kuschel, David A. Leigh,* Bartosz Lewandowski, Marcus Papmeyer,
and John W. Ward
School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL United Kingdom
S
* Supporting Information
ABSTRACT: We report on an improved strategy for the preparation of artificial molecular machines that can pick up and
assemble reactive groups in sequence by traveling along a track. In the new approach a preformed rotaxane synthon is attached to
the end of an otherwise fully formed strand of building blocks. This “rotaxane-capping” protocol is significantly more efficient
than the “final-step-threading” method employed previously and enables the synthesis of threaded molecular machines that
operate on extended oligomer, and potentially polymer, tracks. The methodology is exemplified through the preparation of a
machine that adds four amino acid building blocks from a strand in sequence, featuring up to 20-membered ring native chemical
ligation transition states.
Scheme 1. Assembling Threaded Molecular Machines for
Sequence-Specific Synthesis
INTRODUCTION
■
Many biological molecular machines responsible for sequence-
specific synthesis, including the ribosome1 and various DNA
polymerases,2 travel along tracks in order to assemble reactive
building blocks in a precise order.3 An artificial rotaxane-based
molecular machine4 was recently described that successively
adds three amino acids to a growing peptide chain in such a
fashion.5,6 The macrocycle moves along a thread derivatized
with amino acid phenolate esters, picking up the groups that
block its path and linking them together through successive
native chemical ligation7 (NCL) reactions to form a new peptide
oligomer. The sequence of the product corresponds to the order
of the building blocks on the original track.
building blocks it is clearly necessary to find a more efficient
strategy to assemble such machine-track conjugates. Here
we report on a molecular peptide synthesizer containing four
amino acids loaded onto the building block strand, pre-
pared using a “rotaxane-capping” strategy (Schemes 1b). The
operation of the molecular device yields an oligopeptide with
four amino acids added from the track in the desired sequence
(Scheme 3).
The key reaction to form the interlocked machine
architecture involves threading of the ring onto the full strand
of building blocks (Scheme 1a).5 Unfortunately, the active
template8,9 reaction employed to do this is low yielding and
comes as the last step of a long synthetic route, limiting the
utility of this approach for longer tracks. The low efficiency of
the threading is probably due to the number of amide groups
on the completed track that can sequester the Cu(I) catalyst
from the pyridine group of the macrocycle used to promote
the active template threading reaction.9a In order to produce
machines that can operate on extended strands with more
Received: March 4, 2014
Published: March 28, 2014
© 2014 American Chemical Society
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a
Scheme 2. Synthesis of Rotaxane Synthon 1
RESULTS AND DISCUSSION
■
A simple [2]rotaxane synthon, 1, bearing no persistent recogni-
tion elements between the macrocycle and sites on the thread,
which would retard free movement of the macrocycle toward
the reactive building blocks, and a N-Boc-Phe group, which
is sufficiently large to prevent dethreading, was prepared
from macrocycle 2, azide 3, and alkyne 4 by an active template9
Cu(I)-catalyzed alkyne−azide cycloaddition (CuAAC) reaction10
(Scheme 2). Rotaxane 1 was isolated in 50% yield in a procedure
that could be conveniently run on a scale that provided hundreds
of milligrams of the threaded building block. Rotaxane 1 was
subsequently attached to a molecular strand containing a further
three amino acids in its structure, 5, using a conventional
CuAAC ligation to afford 6 (Scheme 3). The CysGlyGly “arm”,
responsible for removing and joining together the track amino
acid groups, was then added (in protected form) to the extended
machine assembly through hydrazone exchange of 6 with 7,
under aniline catalysis.11
The fully assembled molecular machine, 8, had the acid-
labile protecting groups removed (20% CF3CO2H in CH2Cl2;
Scheme 2 (iii)) and was allowed to operate at 60 °C in
3:1 CH3CN:(CH3)2NCHO, in the presence of iPr2NEt
a
Reagents and conditions: (i) 2 (2 equiv), 3 (10 equiv), 4 (1 equiv),
Cu(CH3CN)4.PF6 (0.5 equiv), 6:1 CH2Cl2/t-BuOH, RT, 24 h, 50%.
a
Scheme 3. Synthesis and Operation of Four-Barrier Molecular Machine 8
a
Reagents and conditions: (i) TentaGel-TBTA/Cu(CH3CN)4·PF6 (0.5 equiv), 4:1 CH2Cl2/t-BuOH, RT, 48 h, 70%. (ii) PhNH2,
BocGlyGlyCys(S-Trt)NHNCHC6H4OCH3 (7) in 3:1 dimethyl sulfoxide: 2-(N-morpholino)ethanesulfonic acid aqueous buffer (pH 6.0),
60 °C, 2 days, 90%. (iii) CF3CO2H (20% in CH2Cl2), RT, 2 h. (iv) ((CH3)2CH)2NEt, (HO2CCH2CH2)3P in 3:1 CH3CN:(CH3)2NCOH, 60 °C,
microwave, 48 h, 9 (80%) and 10 (53%).
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The sequence of the newly formed heptapeptide was con-
firmed as AlaLeuPhePheGlyGlyCys by tandem mass spectrom-
etry on an S,N-acetal derivative of the operation product
(Figure 1a).5a Comparison of the fragmentation pattern of the
isolated product with an authentic sample of the heptapeptide,
prepared by conventional peptide synthesis, confirmed that the
operation product had the amino acid groups in the anticipated
order (Figure 1b). No other products featuring the macrocycle
bearing other peptide sequences or missing amino acid residues
were detected, indicating the high sequence specificity of the
peptide synthesis by the molecular machine. The efficiency
of even the fourth successive NCL reaction, featuring a
20-membered ring S,N-acyl transfer transition state, without the
need for a significant increase in reaction time nor to optimize
conditions, suggests that we are not yet approaching the limit
of the number of amino acids that can be added through this
mechanism.
CONCLUSIONS
■
The potential utility of artificial polymers made from precise
sequences of building blocks is apparent from the diverse
properties of the four controlled-sequence macromolecules
exploited throughout biology (DNA, RNA, proteins, and
oligosaccharides).3 Currently, however, sequence-specific syn-
thesis using unnatural building blocks or chemistries remains an
unsolved problem in polymer science.14 The facile connection of
a prethreaded ring to the end of a strand, without leaving residual
recognition elements between the macrocycle and track to
hinder the rings movement, should greatly assist the develop-
ment of artificial molecular machines for this purpose.5b−d
ASSOCIATED CONTENT
* Supporting Information
■
S
Detailed descriptions of synthetic procedures, characterization
of new compounds, and spectroscopic data. This material is
available free of charge via the Internet at http://pubs.acs.org.
AUTHOR INFORMATION
Corresponding Author
david.leigh@manchester.ac.uk
Notes
■
Figure 1. Tandem mass spectra of 2+ ions of S,N-acetal-
derivatized macrocycles bearing the peptide sequence (Piv)-
AlaLeuPhePheGlyGlyCys: (a) Product of the operation of molecular
machine 8 in Scheme 2 (2+ ion isotope-selected m/z = 951.42). (b)
The identical compound prepared unambiguously by conventional
peptide synthesis (2+ ion isotope-selected m/z = 951.58). The m/z
values observed correspond to the loss of peptide fragments at various
points along the chain (a7, a6, a5, ... etc.), and therefore the peptide
sequence can be read directly simply by considering the fragmentation
from high m/z value to low. Fragment a1 is observed as a singly
charged adduct of the aldehyde macrocycle (m/z = 561) and the
corresponding methanol or hydrazone adduct (m/z = 576).
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
This research was funded by the Engineering and Physical
Sciences Research Council (UK). We are grateful to the
following organizations for postdoctoral fellowships: Fundacja
na Rzecz Nauki Polskiej (to B.L.), Fonds Spec
́
ial de
Recherche−Fed
́ ́
eration Wallonie-Bruxelles and Wallonie-Brux-
elles International (to G.D.B.)
(to promote NCL reactions12) and (HO2CCH2CH2)3P (to
reduce any cysteine disulfides formed in situ back to thiols13)
(Scheme 3 (iv)). After 48 h mass spectrometry showed two
major products present in the postoperation mixture which
were isolated by preparative thin layer chromatography. One
of the products was identified as the noninterlocked thread
with four phenol groups, 9 (80% isolated yield); the other was
the macrocycle bearing a peptide chain that mass spectrometry
showed had a molecular mass (m/z = 1355 [M + H]+)
corresponding to the tripeptide of the original arm with four
further amino acids added, one from each site of the thread, 10
(53% isolated yield).
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