Facile synthesis of benzamides to mimic an α-helix

Article abstract of DOI:10.1016/j.tetlet.2007.03.108

A new α-helix mimetic was designed by using a benzamide as a rigid scaffold. It presents three functional groups corresponding to side chains of amino acids found at the i, i + 4, and i + 7 positions of an ideal α-helix, which are displayed on the same he

Full text of DOI:10.1016/j.tetlet.2007.03.108

Tetrahedron Letters 48 (2007) 3543–3547
Facile synthesis of benzamides to mimic an a-helix
Jung-Mo Ahn* and Sun-Young Han
Department of Chemistry, University of Texas at Dallas, 2601 North Floyd Road, Richardson, TX 75080, USA
Received 21 November 2006; revised 19 March 2007; accepted 19 March 2007
Available online 23 March 2007
Abstract—A new a-helix mimetic was designed by using a benzamide as a rigid scaffold. It presents three functional groups corre-
sponding to side chains of amino acids found at the i, i + 4, and i + 7 positions of an ideal a-helix, which are displayed on the same
helical face. Its efficient synthesis was achieved by employing simple alkylation and amidation reactions which can be easily adapted
for solid-phase synthesis. As a result, two tris-benzamides were produced to mimic two helical regions found in a peptide hormone,
glucagon.
Ó 2007 Elsevier Ltd. All rights reserved.
An a-helix is one of the most common structural motifs
a
c
d
e
in proteins and widely used for diverse functions includ-
ing recognition of other proteins.1 The formation of
protein–protein complex is essential for numerous regu-
latory processes in cells and paramount for survival.
Thus, modulation of the protein–protein interaction is
extremely valuable to comprehending biochemical path-
ways and eventually may lead to develop new therapeu-
tic candidates.2–5 However, short peptide segments
corresponding to helical regions of proteins have diffi-
culty binding to their target proteins because they tend
to adopt significantly less organized conformations in
solution.6 Several approaches have been pursued to
stabilize a-helices, including making a non-covalent
interaction or a covalent bond between side chains of
amino acid residues as well as incorporating unnatural
amino acids.7–12
Ri
NH2
Ri
RO
H
ORi
M
Ri+1
O
H
H
H
H
H
H
Ri
O
O
O
N
N
H
Ri+3
O
ORi+4
ORi+8
O
H
O
H
N
Ri+7
Ri+4
H
N
N
O
b
H
i+4
Cβ
O
Cα
O
Cβ
i+3
Cα
Ri+7
Cα
i+1
Cβ
Cβ
i
Cα
O
OCH3
Figure 1. Structures of a-helix mimetics reported previously. (a)
Indane; (b) biphenyl; (c) terphenyl; (d) tris-pyridylamide; (e) polycyclic
ether.
Another approach is to develop nonpeptidic a-helix
mimetics. While a number of amino acids are required
to construct a highly ordered, helical structure, it is often
found that side chains on one face of a helix are mainly
responsible for the interaction with its target proteins.
For the development of a-helix mimetics, it is thereby
important to retain characteristic structural features of
a helix, and only a handful of a-helix mimetics
have been created using rigid and pre-organized scaf-
folds13–18 (Fig. 1).
1,1,6-Trisubstituted indanes (Fig. 1a) reported by Wil-
lems and co-workers are to represent amino acids at
the i and i + 1 positions of an a-helix, and the designed
mimetics of dipeptides (Phe–Phe and Trp–Phe) showed
micromolar affinity similar to the original dipeptides in
an attempt to mimic tachykinins and other neuropeptide
targets.13 However, the indanes can mimic only two
amino acids, thereby are not suitable to cover more resi-
dues in a helix. On the other hand, Jacoby suggested
2,6,30,50-tetrasubstituted biphenyl analogues (Fig. 1b)
to mimic one helical turn.14 Recently, Hamilton and
co-workers have reported scaffolds which can represent
two helical turns. Trifunctionalized 3,20,200-terphenyl
Keywords: a-Helix mimetics; Benzamide scaffold; Glucagon antago-
nists; Inhibitors for protein–protein interaction.
*
Corresponding author. Tel.: +1 972 883 2917; fax: +1 972 883
2925; e-mail: jungmo@utdallas.edu
0040-4039/$ - see front matter Ó 2007 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2007.03.108

3544
J.-M. Ahn, S.-Y. Han / Tetrahedron Letters 48 (2007) 3543–3547
derivatives (Fig. 1c) hold side chains located at the i,
i + 3, and i + 7 positions in two helical turns and are
found to be potent antagonists against calmodulin15
and inhibitors to disrupt p53/MDM2 complex,16 dem-
onstrating the potential use of a-helix mimetics as ther-
apeutics. A tris-pyridylamide scaffold (Fig. 1d) was also
designed to display side chains found at the i, i + 4, and
i + 7 positions to inhibit the formation of Bak BH3/Bcl-
xL complex.17 In addition, ladder-like polycyclic ethers
(Fig. 1e) were developed by Hirama and co-workers to
mimic the i, i + 4, and i + 8 positions in a helix.18
may result in a weak binding affinity for a protein,
Bcl-xL.17 Although high degree of structural rigidity is
prerequisite for a scaffold of a mimetic, small degree of
flexibility is also necessary to optimally interact with tar-
get proteins that change their structures dynamically.
To demonstrate its a-helix mimicry, computer modeling
of a tris-benzamide with the attachment of three func-
tional groups (R1ꢀ3) was carried out using MacroModel
(version 9, Schro¨dinger, New York, NY).19 A Monte
Carlo conformational search (5000 steps) was conducted
using a MM3 force field20 implemented into the soft-
ware. The energy-minimized structure of the lowest
energy conformation showed that all three functional
groups in the tris-benzamide mimetic are found to be
well overlaid over the corresponding side chains of an
ideal a-helix. (Fig. 2).
In this study, we have focused on developing a new
a-helix mimetic using a benzamide as a scaffold. Substi-
tution on a tris-benzamide structure allows placement of
three functional groups corresponding to the side chains
of amino acids found at the i, i + 4, and i + 7 positions
of an ideal a-helix, representing one helical face. Despite
its structural similarity to the tris-pyridylamide, the syn-
thesis of the tris-benzamides can be easily carried out
(vide infra), and the high synthetic efficiency will be
quite valuable for facile production of a large number
of derivatives. Achieving high molecular diversity is
often necessary in drug discovery since there is always
a possibility of trial and error; thus the synthetic effi-
ciency, such as high yields, easy derivatization, ready
availability of starting materials, and synthetic chemis-
tries suitable for automation, should be considered as
an important factor when developing mimetics.
The synthesis of tris-benzamides starts from an alkyl-
ation reaction, placing a functional group corresponding
to an amino acid at the i position of a helix. The hydro-
xyl group in methyl 4-(t-butoxycarbonylamino)-3-
hydroxybenzoate (1), which was readily prepared from
a commercially available 4-amino-3-hydroxybenzoic
acid, was reacted with a series of alkyl halides in the
presence of a base as described in Table 1. Several bases
and solvents were examined to optimize the reaction
condition, and the use of NaH in DMF at room temper-
ature resulted in the highest yield. Sodium methoxide
also provided comparable yield as NaH, whereas
K2CO3 and a hindered organic base, 1,8-diazabicyclo-
[5.4.0]undec-7-ene (DBU) were found to be inefficient.
As a solvent, DMF appears to be more effective than
THF since the benzylation in THF required refluxing
even with the most efficient base found for the reac-
tion (NaH), whereas DMF provided higher yield at
much lower ambient temperature. The alkylation reac-
tion was also carried out with various alkyl halides
under the optimized reaction condition, resulting in
the desired products in high yield (70–80%). Methyl
and benzyl halides mimicking Ala and Phe, respectively,
In addition, the tris-benzamide possesses slightly higher
conformational flexibility compared to the tris-pyridyl-
amide due to the lack of a hydrogen bond between an
amide proton and a nitrogen on a pyridine ring of the
tris-pyridylamide. This hydrogen bond as well as a
hydrogen bond between the amide proton and an oxy-
gen in an adjacent ether linkage, significantly rigidifies
the tris-pyridylamide as a flat structure, and places its
three functional groups on a straight line. This spatial
arrangement by the tris-pyridylamide does not properly
represent the i, i + 4, and i + 7 positions in a helix and
Figure 2. Structures of an a-helix mimetic using a tris-benzamide scaffold. (a) a-Helix; (b) tris-benzamide; (c) energy-minimized structure of a tris-
benzamide; (d) superimposition of a tris-benzamide (orange) to an ideal a-helix (green).

J.-M. Ahn, S.-Y. Han / Tetrahedron Letters 48 (2007) 3543–3547
3545
Table 1. Alkylation of the 3-hydroxyl group of benzoate (1)
NHBoc
OR
NHBoc
O
NHBoc
O
NHBoc
OH
R-X
a or b
base
O
O
OH
3
X
+
O
NH
O
O
O
O
2
1
O
NH2
Product R–X
Reaction condition
Yielda (%)
33
O
2a
K2CO3 (1.2 equiv),
acetone, reflux, 24 h
Br
Br
6
O
O
4
O
c
2a
2a
2a
2a
2a
NaH (1.1 equiv),
DMF, rt, 1.5 h
83
53
73
72
19
a or b
(5-10%)
NHBoc
O
(86%)
Br
Br
Br
Br
NaH (1.1 equiv),
THF, reflux, 2.5 h
NHBoc
O
3
O
O
OH
+
NaOMe (1.2 equiv),
DMF, rt, 1.5 h
a or b
NH2
O
NH
OH
(70-80%)
OH
NaOMe (1.2 equiv),
THF, reflux, 2.5 h
5
7
O
DBU (5 equiv),
DMF, rt, 12 h
O
O
Scheme 1. Formation of an amide bond for the synthesis of dialkoxy-
bis-benzamide (6). Reagents and conditions: (a) (i) 3, SOCl2, THF,
DMF (cat), 60 °C, 2 h; (ii) 4 or 5, DIPEA, DCM, 0 °C!rt, 2 h; (b) 4 or
5, BOP, DIPEA, DCM, rt, 2 h; (c) 2-bromomethylnaphthalene, NaH,
DMF, rt, 2 h.
2b
2c
CH3l
Br
NaH (1.1 equiv),
DMF, rt, 1.5 h
86
78
NaH (1.1 equiv),
DMF, rt, 24 h
Br
2d
2e
NaH (1.1 equiv),
DMF, rt, 24 h
73
83
using unalkylated aminobenzoate (5) instead of alkyl-
ated (4). Using SOCl2 or BOP as a coupling reagent,
monoalkoxy-bis-benzamide (7) was synthesized in high
yield (70–80%), and a subsequent alkylation produced
the desired bis-benzamide (6) possessing two functional
groups corresponding to the i and i + 4 positions in a
helix.
Br
NaH (1.1 equiv),
DMF, rt, 1.5 h
a Yield was determined after purification by column chromatography.
gave slightly better yields compared to aliphatic alkyl
halides, such as 2-bromopropane and 2-bromobutane
representing Val and Ile, respectively. 2-Naphthylmethyl
group was introduced to represent the indole side chain
of Trp.
For the evaluation of the tris-benzamides as a-helix
mimetics, we have synthesized two analogues to mimic
a-helical regions found in glucagon. Glucagon is a 29
amino acid-containing peptide hormone and plays a
critical role in glucose homeostasis by stimulating glu-
cose release upon binding to its membrane receptor in
liver.21 Therefore, potent glucagon antagonists22–24 have
been pursued as a potential therapeutic candidate for
diabetes mellitus, and nonpeptidic glucagon receptor
antagonists25–28 have also been reported while most of
them turned out to be noncompetitive. Recently, gluca-
gon is found to adopt helical conformations in two sep-
arate regions when it binds to the receptor,29 thus two
tris-benzamides were designed to mimic hydrophobic
faces of the two helical regions in glucagon. Two tris-
benzamides (17 and 18) contain benzyl, 4-fluorobenzyl,
and 4-fluorobenzyl; and methyl, benzyl, and 2-naph-
thylmethyl groups as three functional groups which
represent Phe,6 Tyrp,10 and Tyr;13 and Ala,19 Phe,22
and Trp,25 respectively. The 4-fluorobenzyl group was
employed to substitute the side chain of Tyr because
the 4-hydroxybenzyl group was unstable during the
synthesis.
After the alkylation, formation of an amide bond to
produce dialkoxy-bis-benzamide (6) was attempted
(Scheme 1). Free carboxylic acid and amine groups were
released by hydrolysis of a methyl ester and removal of
an N-Boc group from two methyl alkoxybenzoates,
respectively. Several coupling reagents were examined
including SOCl2, (COCl)2, DCC, EDC, HBTU, BOP,
PyBrOP, and TFFH, however all of them failed to pro-
duce the desired bis-benzamide (6), presumably due to
substantially reduced nucleophilicity of the amine and
electrophilicity of the benzoic acid as well as steric hin-
drance caused by the alkoxy group of aniline (4). While
the starting materials were mostly recovered after the
reaction, it is quite interesting that the reaction yielded
monoalkylated bis-benzamide (7) as a byproduct (5–
10% conversion). Hinted by the formation of byproduct
(7), the coupling reaction was successfully carried out

3546
J.-M. Ahn, S.-Y. Han / Tetrahedron Letters 48 (2007) 3543–3547
NHR1
OR2
concept, two tris-benzamides were prepared to represent
two helical regions in glucagon and will be evaluated for
receptor binding and biological activity.
NHR1
OR2
NHR1
OR2
a
d,e
f
O
NH
OH
Acknowledgments
O
O
O
OH
2a: R1=Boc, R2=Bn
2b: R1=Boc, R2=Me
8: R1=Ac, R2=Bn
9: R1=Ac, R2=Bn
10: R1=Boc, R2=Me
We gratefully acknowledge the University of Texas at
Dallas for start-up funds. This material is based in part
upon work supported by the Welch Foundation (Grant
No. AT-1595) and the Texas Advanced Research Pro-
gram (Grant No. 009741-0031-2006).
b,c
O
O
11: R1=Ac, R2=Bn
12: R1=Boc, R2=Me
NHR1
OR2
NHR1
OR2
NHR1
OR2
Supplementary data
O
NH
O
NH
Available for experimental procedures and spectral
characterization. Supplementary data associated with
this article can be found, in the online version, at
doi:10.1016/j.tetlet.2007.03.108.
OR3
OR3
a,g
h
O
NH
OR3
O
NH
O
NH
OR4
OH
O
O
References and notes
13: R1=Ac, R2=Bn
R3=4-F-Bn
14: R1=Boc, R2=Me
R3=Bn
O
O
O
O
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was achieved by using simple alkylation and amide
bond-formation reactions which can be easily adapted
for solid-phase synthesis to construct a combinatorial li-
brary of a-helix mimetics. To demonstrate the proof of

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3547
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