Synthesis and structure of oxetane containing tripeptide motifs

Article abstract of DOI:10.1039/c4cc03507k

A new class of peptidomimetic is reported in which one of the amide CO bonds of the peptide backbone is replaced by an oxetane ring. They are synthesised by conjugate addition of various α-amino esters to a 3-(nitromethylene)oxetane, reduction of the nitro group and further coupling with N-Z protected amino acids to grow the peptide chain. Structural insights are provided by X-ray diffraction and molecular dynamics simulations.

Full text of DOI:10.1039/c4cc03507k

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Synthesis and structure of oxetane containing
tripeptide motifs†‡
Cite this: Chem. Commun., 2014,
50, 8797
Nicola H. Powell,a Guy J. Clarkson,a Rebecca Notman,a Piotr Raubo,b
Nathaniel G. Martinb and Michael Shipman*a
Received 9th May 2014,
Accepted 16th June 2014
DOI: 10.1039/c4cc03507k
www.rsc.org/chemcomm
A new class of peptidomimetic is reported in which one of the
Q
amide C O bonds of the peptide backbone is replaced by an
oxetane ring. They are synthesised by conjugate addition of various
a-amino esters to a 3-(nitromethylene)oxetane, reduction of the
nitro group and further coupling with N–Z protected amino acids
to grow the peptide chain. Structural insights are provided by X-ray
diffraction and molecular dynamics simulations.
Fig. 1 Replacement of amide CQO by oxetane ring in peptide chain.
Peptidomimetics are extremely important in medicinal chemistry
offering a number of advantages over physiologically active pep-
tides.1 Consequently, there is an ongoing search for new motifs
that effectively mimic the structure and conformation of natural
peptides.2 A highly productive approach is to replace one or more
of the amide bonds of the backbone with a peptide bond isostere
such as an E-alkene, thioamide or sulfonamide.1a,c Since the four-
membered oxetane ring has emerged as an excellent replacement
for the carbonyl group in medicinal chemistry,3 we reasoned that
substituting one or more of the CQO bonds within the backbone
of a peptide with oxetane units could yield an interesting new class
of peptidomimetic with greatly reduced vulnerability to proteases
(Fig. 1).4 Through the preparation and study of representative
peptide-like motifs containing this bioisosteric replacement, we
sought to understand how the introduction of a 3-aminooxetane
subunit into the peptide backbone modulates its physicochemical
properties, conformational preferences and receptor binding.
Scheme 1 Synthetic strategy to new oxetane based peptidomimetics.
is replaced by the oxetane nucleus, e.g. 1. The generalised
In this communication, we report on the preparation of synthetic strategy is given in Scheme 1. It was envisaged that
derivatives in which the central CQO amide bond of a tripeptide introduction of the 3-aminooxetane subunit might be realised by
conjugate addition of chiral a-amino ester 3 to readily accessible
oxetane containing nitroalkene 2. Highly nucleophilic primary
amines (e.g. BnNH2) are known to undergo rapid conjugate
a Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry,
CV4 7AL, UK. E-mail: m.shipman@warwick.ac.uk; Fax: +44 2476 524112;
addition to 2 (R = Bn) at room temperature suggesting that this
Tel: +44 2476 523186
b AstraZeneca, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
transformation would be facile.3a For general applicability, this
† This communication is dedicated to Prof. Richard Taylor on the occasion of his interconversion would need to be effective for amino esters
65th birthday.
derived from a broad spectrum of a-amino acids, and tolerate
variation in R within nitroalkene 2. Further chemoselective
reduction of the nitro group in 4, and coupling of the resulting
‡ Electronic supplementary information (ESI) available: Synthetic procedures and
spectroscopic data for 1a–f, 4a–k, 7, chiral HPLC analysis of 4a, X-ray depictions
of 1c and 1e, MD simulations for 1e and 8, and the computational methodologies.
amine 5 with an N-protected amino acid would allow the oxetane
residue to be positioned centrally within the peptide backbone.
CCDC 996043 and 996044. For ESI and crystallographic data in CIF or other
electronic format see DOI: 10.1039/c4cc03507k
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Finally, removal of the C- and N-terminal protecting groups work well. However, the use of benzyl esters was favoured as it
would yield the oxetane based peptidomimetic 1. Importantly, allows concomitant deprotection of the N- and C-termini later in
knowledge obtained from making these simple tripeptide motifs the sequence (vide infra). Although our study of amino ester
would be applicable to the production of larger peptidomimetics nucleophiles is not exhaustive, success has been achieved with a
through the use of longer peptide fragments as the nucleophile wide selection of polar and hydrophobic amino acids including
in the conjugate addition step (vide infra); or through further Gly (4c,d), Val (4a,b), Thr (4e), Leu (4f), Ile (4g), Phe (4h), and
extension of the N-terminus by conventional peptide couplings. Ser (4i). Moreover, dipeptide based nucleophiles have also been
Two nitroalkenes 2a (R = H) and 2b (R = Bn) were used in this successfully used, enabling the synthesis of 4j and 4k containing
investigation, to produce peptidomimetics of glycine and phenyl- longer peptide backbones.¶
alanine respectively (Scheme 2). These were made from commer-
The completion of the synthesis of the tripeptide analogues
cially available oxetan-3-one (6) and the appropriate nitroalkane required reduction of the nitro group to enable homologation
by Henry reaction and elimination of the resulting alcohol by way of the peptide backbone via the corresponding amine. Initially,
of the mesylate according to published methods.3a,c Conjugate we tried to isolate these amines but observed the formation of
addition of (S)-valine methyl ester (2.0 equiv.) to 2a (1.0 equiv.) diketopiperazine-like compounds by way of unwanted ring
provided 4a in 68% yield. In fact, it proved more convenient closure. For example, reduction of 4h with Zn–AcOH yielded
to generate 2a in situ from 6 (1.0 equiv.) and nitromethane 7 in 68% after chromatography (Scheme 3). Better results were
(1.4 equiv.), and react it directly with the (S)-valine methyl ester achieved by immediately coupling the free amine with the
(2.0 equiv.) without work-up. In this way, 4a was obtained in 65% appropriate N–Z protected amino acid using EDC–HOBt in
over the three steps (see ESI‡). Reducing the amount of (S)-valine EtOH after reduction.5 Excess SmI2 (14 equiv.) in THF–MeOH6
methyl ester (1.2 equiv.) led to lower yields (40%) and so the was an effective reducing agent but in some instances
amine nucleophile was typically used in 2-fold excess. Using (R)- unwanted transesterification of the benzyl ester was observed.
and (S)-4a, made from D- and L-valine methyl ester respectively, it Indium (4 equiv.) in aq. HCl–THF7 proved more reliable for a
was confirmed by chiral HPLC analysis that no detectable race- range of amines. These amines were immediately coupled
mization occurs during these conjugate additions (see ESI‡). using 1-ethyl-3-(3-dimethylamino-propyl)carbodiimide (EDC)
Similar efficiency was achieved using tetrasubstituted nitroalkene with representative Cbz-protected amino acids, then the Cbz
2b as the acceptor. For example, 4c and 4k were both produced in and benzyl ester groups removed by hydrogenolysis. A selection
good yields.§ With respect to the nucleophile, various ester groups of representative tripeptide analogues 1a–f were made in high
purity and good overall yields using this 3-step sequence
(Scheme 3).
X-ray diffraction studies performed on single crystals of 1c
and 1e grown from methanol unambiguously confirmed their
gross structures and provided insights into their conformational
a
Scheme 2 Conjugate addition of a variety of amino esters and dipeptides
to oxetane substituted nitroalkene (2).
Scheme 3 Homologation to tripeptide derivatives 1a–f. Produced in
68% yield upon reaction of 4h with Zn–AcOH.
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Fig. 2 Solid state structure of 1e showing the 4 crystallographically
independent molecules in the unit cell, and part of the infinite
H-bonded sheet formed by the antiparallel arrangement of the tripeptide
chains.
Fig. 3 Snapshots of the two most populated clusters of 8 and 1e derived
from MD simulations, along with the percentages of total structures
accounted for by each cluster. Hydrogen atoms omitted for clarity.
preferences and crystal packing.8 Both these tripeptide mimetics
are zwitterionic with the terminal amine, not the central sec-
ondary amine, ionised as the ammonium ion. They display
antiparallel sheet-like arrangements in the solid state as illu-
strated for 1e in Fig. 2 (also see ESI‡).
to demonstrating the use of oxetane containing peptidomimetics
as ligands for biological receptors.
We thank EPSRC, the Royal Society and AstraZeneca for
financial support. We acknowledge the Centre for Scientific
Computing at the University of Warwick for the provision of
computing facilities. The Oxford Diffraction Gemini XRD
system was obtained, through the Science City Advanced Mate-
rials project: Creating and Characterizing Next Generation
Advanced Materials.
Molecular dynamics (MD) simulations were conducted on a
representative analogue (1e) and the results compared to those
for the parent tripeptide sequence: Leu-Gly-Ile (8). To enable
simulations of these molecules, CHARMM-compatible force-
field parameters for the 3-aminooxetane residue were first
derived from quantum mechanical calculations (see ESI‡). Each
peptide was then simulated for 100 ns in water at 500 K and
from this trajectory 10 distinct conformations of each peptide
were selected for an additional 100 ns of simulation at 300 K, to
yield a total simulation time of 1 ms per peptide. Cluster
analysis was performed using 100 000 structures extracted from
the trajectories at 10 ps intervals. Eleven distinct structures
were found for 1e, compared to seven for 8, indicating that the
oxetane based peptidomimetic has greater conformational
flexibility. Snapshots of the two most populated clusters for
1e and 8 are presented in Fig. 3 with further analysis provided
in the ESI.‡ The conformations explored by the natural peptide
are dominated by extended structures where the C and N
termini are separated by 47 Å. In contrast, the most populated
cluster of 1e is a folded conformation (C to N separation
distance of the order of 3–4ÀÅ) that benefits from close contact
Notes and references
§ Phenylalanine analogues 4c and 4k were produced as racemates.
Addition of chiral amino esters to 2b such as (S)-valine methyl ester
proceeded in high yield but low diastereoselectivity (d.r. = 45 : 55).
¶ Amino ester nucleophile = (S)-H2NCH(iPr)C(QO)NHCH2CO2Bn for 4j;
amino ester = H2NCH2C(QO)NHCH2CO2Bn for 4k.
8 CCDC 996044 crystal data: 1c, C19H29N3O4, 0.1 (CH4O) (M = 366.65):
triclinic, space group P1 (no. 1), a = 8.4127(4) Å, b = 9.5002(5) Å,
c
=
13.3202(8) Å,
a = 96.096(5)1, b = 104.312(5)1, g = 90.121(4)1,
V = 1025.27(10) Å3, Z = 2, T = 150(2) K, m(CuKa) = 0.683 mmÀ1, Dcalc
=
1.188 g mmÀ3, 19 052 reflections measured (6.89 r 2Y r 158.46), 8088
unique (Rint = 0.0470, Rsigma = 0.0526) which were used in all calculations.
The final R1 was 0.0506 (I 4 2s(I)) and wR2 was 0.1426 (all data). CCDC
996043 crystal data: 1e, C16H31N3O4 (M = 329.44): triclinic, space group P1
(no. 1), a = 8.5557(2) Å, b = 14.0932(5) Å, c = 16.3070(4) Å, a = 77.134(3)1,
b = 81.935(2)1, g = 80.958(2)1, V = 1881.70(9) Å3, Z = 4, T = 150(2) K, m(CuKa) =
0.679 mmÀ1, Dcalc = 1.163 g mmÀ3, 34 050 reflections measured (6.488 r
2Y r 156.87), 14 895 unique (Rint = 0.0468, Rsigma = 0.0504) which were used
in all calculations. The final R1 was 0.0646 (I 4 2s(I)) and wR2 was 0.1839
(all data).
+
between the terminal –CO2 and –NH3 ions. The ability of 1e
to more readily accommodate a turn-like feature likely arises
from the change in hybridisation and dihedral angle at the
central amino oxetane unit.**
** From the X-ray crystal structure of 1e, the nitrogen atom adjacent to
the oxetane is pyramidal and the averaged C–N–Cox–C torsional angle,
o = 60.21 (cf. o E 1801 in a conventional sp2-hybridised peptide bond).
In summary, we have developed practical methodology for the
synthesis of oxetane containing tripeptide motifs, and begun to
explore the conformational changes that result from the intro-
duction of the 3-aminooxetane subunit into the peptide back-
bone. Current work is focused on extending this chemistry to the
synthesis and study of larger and more complex derivatives, and
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8800 | Chem. Commun., 2014, 50, 8797--8800
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