Amphiphilic α-helix mimetics based on a benzoylurea scaffold

Article abstract of DOI:10.1039/c2ob25273b

The design and synthesis of amphiphilic benzoylurea α-helix mimetics is described. These conformationally constrained molecules allow for the correct angular and spatial projection of hydrophobic and hydrophilic groups and thus the reproduction of side-chains on both faces of an α-helix.

Full text of DOI:10.1039/c2ob25273b

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COMMUNICATION
Amphiphilic α-helix mimetics based on a benzoylurea scaffold†‡
Sam Thompson and Andrew D. Hamilton*
Received 6th February 2012, Accepted 19th March 2012
DOI: 10.1039/c2ob25273b
give 4. The allyl 6 and 3-butenyl 7 amides were prepared in
The design and synthesis of amphiphilic benzoylurea α-helix
mimetics is described. These conformationally constrained
molecules allow for the correct angular and spatial projec-
tion of hydrophobic and hydrophilic groups and thus the
reproduction of side-chains on both faces of an α-helix.
excellent yields via hydrogenolysis of the benzyl ester and car-
boxyl activation through acid chloride formation (Scheme 1).
To simplify the synthesis we initially designed a route to an
i + 6, i + 7 component (rather than i + 6, i + 8). Dialkylation of
2-nitroresorcinol, followed by reduction of the nitro group and
isocyanate formation, afforded a precursor of the i + 6, i + 7
component 11 in an overall yield of 52% (Scheme 2).
The inhibition of aberrant protein–protein interactions using
small molecules is an attractive approach for the treatment of a
range of pathological conditions.1 One strategy for the design of
such agents involves the mimicry of common intrafacial
domains such as α-helices where key side-chain residues (often
the i, i + 4, i + 7 positions) play an important role.2 Exploitation
of this approach led to the discovery of a compound based on
the benzoylurea scaffold I that has shown 2.4 μM inhibition of
the Bcl-xL–Bak interaction in a fluorescence polarization assay.3
However, there are few examples of non-peptidic molecules
able to reproduce the position and angular projection of side-
chains on two faces of an α-helix.4 The side-chains projecting
from the exterior face of an α-helix have been widely implicated
in the binding of multiple proteins, bacterial cell wall sensing
and membrane penetration.5
Under our standard conditions of benzoylurea formation with
lithium bis(trimethylsilyl)amide (LiHMDS) in tetrahydrofuran at
The benzoylurea scaffold offered a logical extension to an
amphiphilic mimic II of the i, i + 1, i + 4, i + 6 and i + 8 pos-
itions of a peptide (Fig. 1). To the best of our knowledge there
are currently no mimics of this selection of amino acid side-
chains. We rationalised that commercially available dihydroxy-
lated aromatics would serve as good starting materials for our
syntheses. These molecules allow for a range of straight-forward
alkylation reactions and thus the creation of bespoke mimics in
which both lipophilic and hydrophilic amino acid side-chains are
reproduced. As targets for mimicry we selected aspartic acid,
leucine and methionine as representative examples of amino
acids with polar and non-polar side-chains.
Fig. 1 A synthetic scaffold for mimicry of an α-helix. (a) I benzoyl-
urea scaffold with R1, R2, R3 mimicking the i, i + 4, i + 7 side-chains on
one face of an α-helix; (b) II amphiphilic mimic of the i, i + 1, i + 4, i +
6 and i + 8 side-chains on both faces of an α-helix. (c) Superimposition
of the calculated lowest energy conformer of II (orange, R1 = R5
=
CH2CO2H, R2 = R4 = i-Pr, R3 = CH2CHCH2) with an α-helix (grey
bonds) showing good spatial and angular agreement of substituents with
side-chains.6
Synthesis of the i, i + 1, i + 4 component commenced with
protection of 3,5-dihydroxybenzoic acid as the benzyl ester7 and
alkylation with iso-propyl iodide and tert-butyl bromoacetate to
Department of Chemistry, Chemistry Research Laboratory, University of
Oxford, Mansfield Road, Oxford OX1 3TA, UK.
E-mail: andrew.hamilton@chem.ox.ac.uk; Tel: +44 (0)1865 270242
†This article is part of the Organic & Biomolecular Chemistry 10th
Anniversary issue.
‡Electronic supplementary information (ESI) available: Experimental
procedures, compound characterization data (1H & 13C NMR—includ-
ing spectra, HRMS, IR). CCDC 861447. For ESI and crystallographic
data in CIF or other electronic format see DOI: 10.1039/c2ob25273b
Scheme 1 Synthesis of the i, i + 1, i + 4 component.
5780 | Org. Biomol. Chem., 2012, 10, 5780–5782
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Scheme 2 Synthesis of the i + 6, i + 7 component.
Scheme 4 Synthesis of the i + 6, i + 8 component.
Scheme 3 Fragment union giving a benzoylurea mimic of the i, i + 1,
i + 4, i + 7 and i + 8 side-chain residues.
Scheme 5 Fragment union giving a benzoylurea mimic of the i, i + 1,
i + 4, i + 6 and i + 8 side-chain residues.
−78 °C,8 there was little reaction between amide 6 and isocya-
nate 11. Since we were able to recover significant amounts of the
starting amide and inseparable mixtures of compounds appar-
ently derived from the isocyanate, we reasoned that the extra
steric bulk of the 6-substituent was hindering nucleophilic
approach of the lithiated amide. Raising the temperature of the
reaction mixture during addition of the isocyanate failed to give
desired product, however generating a more reactive amide with
potassium bis(trimethylsilyl)amide (KHMDS) allowed isolation
of 13 in low yield. It was important to maintain the reaction at
−78 °C and to quench the mixture with acetic acid. Removal of
the t-butyl protecting groups with trifluoroacetic acid proceeded
in excellent yield (Scheme 3).
In order to form an i + 6, i + 8 component we synthesised a
2,5-disubstituted isocyanate 20 from 4-fluoro-3-nitrobenzoic acid
in 6 steps and 66% overall yield. Whilst more direct approaches
from 4-chloro-3-nitrobenzaldehyde and 4-hydroxy-3-chloro-
benzaldehyde were unsuccessful, we were able to synthesise 18
on a gram scale with a single chromatographic step in 67% yield
(Scheme 4).
When treated with KHMDS in tetrahydrofuran at −78 °C,
N-allyl 6 and N-butenyl 7 amides reacted with 2,5-disubstituted
isocyanate 20 to give benzoylureas 21 and 22 in 61% and 64%
yields respectively. Acidic deprotection of the t-butyl esters gave
di-carboxylic acid 23 (Scheme 5).
Fig. 2 (a) X-ray crystal structure of benzoylurea 22 with two intra-mol-
ecular hydrogen bonds providing a constrained conformation (values in
Å, t-butyl groups shown in grey). (b) Superimposition of X-ray structure
22 (orange) with an α-helix (grey bonds). There is good agreement
between the side-chain angles and positions of the i, i + 1, i + 4, i + 6
and i + 8 residues (t-butyl groups omitted for clarity).
A single crystal X-ray structure of 22‡ confirmed the connec-
tivity and the presence of N–H⋯OvC (1.9 Å) and N–H⋯Oi-Pr
(2.2 Å) hydrogen bonds (Fig. 2a).9 Superimposition of this struc-
ture with a model peptide shows good overlap of substituents
with the i, i + 1, i + 4, i + 6 and i + 8 side-chain residues
(Fig. 2b), and is in accordance with our computational modelling
work (Fig. 1c). The root mean square deviation (RMSD) for the
five peptide α-carbon atoms and the corresponding scaffold pos-
itions was calculated as 1.25 Å.10 While this value is larger than
those often reported for peptidomimetics it is important to
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consider that the RMSD value will not scale linearly with the
number of positions considered. Previous reports have generally
measured the ‘goodness-of-fit’ of only three groups and not the
five substituents of molecule 22. In this scaffold the RMSD
value for the groups on one face of the molecule (i, i + 4 and
i + 8) is 0.84 Å, which compares comparably to the previously
reported benzoylurea mimic of the i, i + 4 and i + 7 side-chains
(0.67 Å).3
Notes and references
1 (a) M. J. Adler et al., in Small-Molecule Inhibitors of Protein–Protein
Interactions, L. Vassilev and D. Fry, Springer, Berlin, Heidelberg, 2011;
(b) J. A. Wells and C. L. McClendon, Nature, 2007, 450, 1001;
(c) S. Fletcher and A. D. Hamilton, Curr. Top. Med. Chem., 2007, 7, 922;
(d) S. Fletcher and A. D. Hamilton, J. R. Soc. Interface, 2006, 3, 215.
2 (a) E. Ko, J. Liu and K. Burgess, Chem. Soc. Rev., 2011, 40, 4411;
(b) J. M. Davis, L. K. Tsou and A. D. Hamilton, Chem. Soc. Rev., 2007,
36, 326.
3 (a) I. C. Kim and A. D. Hamilton, Org. Lett., 2006, 8, 1751;
(b) J. Becerril and A. D. Hamilton, Angew. Chem., Int. Ed., 2007, 46,
4471; (c) S. Marimganti, M. N. Cheemala and J.-M. Ahn, Org. Lett.,
2009, 11, 4418; (d) S. Thompson, R. Vallinayagam, M. J. Adler,
R. T. W. Scott and A. D. Hamilton, Tetrahedron, 2011, DOI: 10.1016/j.
tet.2011.11.010.
4 J. M. Rodriguez, N. T. Ross, W. P. Katt, D. Dhar, G. I. Lee and
A. D. Hamilton, ChemMedChem, 2009, 4, 649.
5 Molecular Operating Environment, MMFF94(s); Chemical Computing
Group Inc.
6 (a) S. Hirano, M. Kawasaki, H. Ura, R. Kato, C. Raiborg, H. Stenmark
and S. Wakatsuki, Nat. Struct. Mol. Biol., 2006, 13, 272; (b) I. Huber,
M. Rotman, E. Pick, V. Makler, L. Rothem, E. Cukierman and D. Cassel,
Methods Enzymol., 2001, 329, 307; (c) S. Runge, H. Thøgersen,
K. Madsen, J. Lau and R. Rudolph, J. Biol. Chem., 2008, 283, 11340;
(d) R. E. W. Hancock and A. Rozek, FEMS Microbiol. Lett., 2002, 206,
143.
1H NMR of the deprotected molecule 23 shows the benzoyl-
urea N–H resonance as a sharp singlet at 11.38 (CDCl3) and
11.46 (DMSO-d6) consistent with previous studies,8 and sup-
ports the existence of an intra-molecular hydrogen bond and thus
a linear scaffold conformation in both of these solvent systems.
In summary, we have designed a route to amphiphilic α-helix
mimetics based on the well-established benzoylurea scaffold,
and have implemented this in a modular and scalable synthesis
of molecules accurately reproducing the spatial and angular pro-
jection of five amino acid side-chains on both sides of an
α-helical strand. This represents a significant improvement in the
scope of non-peptidic peptidomimetics, allowing for mimicry of
hydrophobic and hydrophilic side-chains on two faces of an
α-helix.
7 W. Guo, J. F. Li, N. J. Fan, W. W. Wu, P. W. Zhou and C. Z. Xia, Synth.
Commun., 2005, 35, 145.
8 J. M. Rodriguez and A. D. Hamilton, Angew. Chem., Int. Ed., 2007, 46,
8614.
Acknowledgements
9 Crystal structure data for compound 22 has been deposited with the
Cambridge Crystallographic Data Centre (CCDC number 861447‡).
10 Chimera. University of California, San Francisco (supported by NIH P41
RR001081): C. C. Huang, G. S. Couch, E. F. Pettersen and T. E. Ferrin,
Pacific Symposium on Biocomputing, 1996, 1, 724.
We thank Richard T. W. Scott (X-ray crystallography), James
W. Luccarelli (modelling), The University of Oxford for funding
(ST) and Dr Martin D. Smith (Oxford) for helpful discussions.
5782 | Org. Biomol. Chem., 2012, 10, 5780–5782
This journal is © The Royal Society of Chemistry 2012