Expedient route to functionalized and water soluble 5-6-5 imidazole-phenyl-thiazole based α-helix mimetics

Article abstract of DOI:10.1016/j.tet.2012.11.070

A range of small molecule scaffolds have been shown to act as structural and functional mimics of α-helices by mimicking the i, i+4, and i+7 positions, often found at the interface of PPIs. These molecules, though potent, possess complicating features - either low water solubility, or maintenance of conformation by hydrogen-bonding networks. We have addressed these limitations by developing a scaffold with increased water solubility. Herein we present a rapid synthetic pathway to a library of 56 compounds based on a 5-6-5 scaffold, containing an imidazole-phenyl-thiazole core; the route is flexible and allows rapid installation of different substituents via high-yielding Ullman and Suzuki couplings and Hantsch thiazole syntheses.

Full text of DOI:10.1016/j.tet.2012.11.070

Tetrahedron 69 (2013) 1663e1668
Contents lists available at SciVerse ScienceDirect
Tetrahedron
journal homepage: www.elsevier.com/locate/tet
Expedient route to functionalized and water soluble 5-6-5
imidazole-phenyl-thiazole based a-helix mimetics
,b,
Christopher G. Cummings a, Andrew D. Hamilton a
*
a Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06520-8107, USA
b Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX13TA, UK
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 24 August 2012
Received in revised form 30 October 2012
Accepted 20 November 2012
Available online 10 December 2012
A range of small molecule scaffolds have been shown to act as structural and functional mimics of a-
helices by mimicking the i, iþ4, and iþ7 positions, often found at the interface of PPIs. These molecules,
though potent, possess complicating featuresdeither low water solubility, or maintenance of confor-
mation by hydrogen-bonding networks. We have addressed these limitations by developing a scaffold
with increased water solubility. Herein we present a rapid synthetic pathway to a library of 56 com-
pounds based on a 5-6-5 scaffold, containing an imidazole-phenyl-thiazole core; the route is flexible and
allows rapid installation of different substituents via high-yielding Ullman and Suzuki couplings and
Hantsch thiazole syntheses.
Keywords:
a
-Helix mimetic
Heterocyclic compounds
Hantsch thiazole synthesis
Suzuki coupling
Ó 2012 Published by Elsevier Ltd.
Fluorescent
1. Introduction
an a-helix mimetic based on a 5-6-5 imidazole-phenyl-thiazole
scaffold that replaces the terminal six-membered aromatic end
units with more water soluble five-membered heterocyclic
groups.22 This core scaffold possesses increased water solubility
relative to the terphenyl, the more water soluble terpyridine and
even the terephthalamide. In addition, we focused on designing
a synthetic approach that would allow rapid construction of a di-
verse array of compounds. To that end, we relied on high-yielding
coupling reactions, nucleophilic aromatic substitution (SNAr) and
the Hantsch thiazole synthesis to install the i, iþ4, and iþ7 side-
chain mimics and contribute to an efficient and flexible five-step
Proteineprotein interactions (PPIs) play critical roles in many
biological processes and have been implicated in numerous dis-
eases, including HIV, diabetes, and neurodegeneration, making
them important targets for disruption.1,2 Recognition between
proteins is often facilitated by secondary structure elements, such
as a-helices, which interact via one helical face, where interacting
residues predominantly occupy the i, iþ3 or iþ4, and iþ7 posi-
tions.3e12 Accordingly, these surfaces are critical targets for small
molecule mimicry. In an ongoing effort to disrupt
PPIs, we have reported several small molecules that act as struc-
tural and functional mimetics of
-helices.3e8 However, our pre-
vious focus has yielded -helix mimetics with inherently
a-helix mediated
route to
a-helix mimetics. The water soluble core and modular
a
synthetic route suggest that the 5-6-5 imidazole-phenyl-thiazole
scaffold will be applicable to various protein targets by simply
changing the appended substituents.
a
complicating features, either low solubility (terphenyl13 and ter-
pyridine14 scaffolds) or hydrogen-bonding networks to maintain
their correct orientation (terephthalamide,15 enaminone,16 ben-
zoylurea,17 and trispyridylamide18 scaffolds). The demand for water
Herein, we investigate substitution patterns designed to mimic
the PPI between Cdc42 and Dbs, a guanine nucleotide triphos-
phatase (GTPase) and its corresponding GEF (Guanine nucleotide
exchange factor) that have been linked to diabetes and cardiovas-
cular and neurodegenerative diseases.23 The crystal structure of the
complex of these two proteins has been solved and shows that
contact is mediated by the Q770, K774, and L777 residues of Dbs,
soluble
a
-helix mimetics has been addressed in recent work by
€
Rebek and Konig by making one side of the scaffold hydrophilic or
via a 1,4-dipiperazinobenzene scaffold.19e21 As a mechanism to
overcome the limitations of previous designs, we have developed
which correspond to the i, iþ4, and iþ7 of a key Dbs
Because this PPI is mediated by an -helix with two polar resi-
dues, our strategy incorporates mimics of polar sidechains, high-
a
-helix.24
a
* Corresponding author. Tel.: þ44 1865 275494; fax: þ44 1865 285002; e-mail
addresses: andrew.hamilton@chem.ox.ac.uk, andrew.hamilton@admin.ox.ac.uk
(A.D. Hamilton).
lighting an area of
a-helix mimicry that has not been generally
explored.1,22
0040-4020/$ e see front matter Ó 2012 Published by Elsevier Ltd.
http://dx.doi.org/10.1016/j.tet.2012.11.070

1664
C.G. Cummings, A.D. Hamilton / Tetrahedron 69 (2013) 1663e1668
2. Discussion
The 3-position of the central phenyl ring (iþ4 position, Fig. 2b
and c, R2), could be readily functionalized with various amines
through Suzuki coupling, between an aryl bromide and the nec-
essary boronic acid, or through SNAr displacement of an aryl fluo-
ride with a suitably substituted alkyl alcohol.
2.1. Design
Our initial goal for this investigation was to explore scaffolds for
a
-helix mimicry with increased water solubility in the expectation
that this would lead to improved biological properties. Our aim was
to develop a novel class of -helix mimetics that overcame the low
The final thiazole ring could be installed through Hantsch con-
ditions involving conversion of a nitrile at the 4-position of the
a
phenyl ring to a thioamide followed by treatment with an
oketone or -haloketoester, to give the substituent at the 4-position
of the thiazole (Fig. 2b and c, R3).
a-hal-
water solubility (cf. oligophenylenes) but did not rely on hydrogen-
bonding networks to maintain proper orientation (cf. tereph-
thalamides or pyridylcarboxamides). The 5-6-5 imidazole-phenyl-
thiazole scaffold offered a possible solution to this goal as it
maintains the three substituents (R1, R2, R3) in a similar orientation
to those on a terphenyl and has a calculated log P (o/w) value of 2.3,
substantially lower than the terphenyl, terpyridine, and tereph-
thalamide scaffolds (log P (o/w) values of 7.3, 3.4, and 4.4,
respectively-calculated for trimethyl or tetramethyl (tereph-
thalamide) substituted core scaffold, Fig. 1).22
a
Merging high-yielding coupling reactions, SNAr and the Hantsch
thiazole synthesis with highly functionalized, commercially avail-
able starting materials allows installation of different substituents
and rapid accessibility to water soluble
steps.
a-helix mimetics in five
2.2. Synthesis
Two distinct synthetic routes were followed; the benzonitrile
starting material chosen and the synthetic route undertaken de-
pend on the iþ4 position mimic installed. For mimetics with flex-
ible amines at the iþ4 position, 4-bromo-2-fluorobenzonitrile was
subjected to nucleophilic aromatic substitution with tert-butyl 3-
hydroxypropylcarbamate or tert-butyl 2-hydroxyethylcarbamate
(KHMDS in THF) to produce 1a,b, in quantitative yield (Scheme 1).
Attempts were made to couple 1a with methyl 3-(1H-imidazol-2-
yl)propanoate or dimethyl 1H-benzo[d]imidazole-5,6-dicarboxylate
via BuchwaldeHartwig amination, but no product was observed.
Ullmann conditions successfully coupled 1a,b with methyl 3-(1H-
imidazol-2-yl) propanoate or dimethyl 1H-benzo[d]imidazole-5,6-
dicarboxylate to furnish 2a,b and 6a,b in high yield. Subsequent
treatment with phosphorous pentasulfide failed to convert the ni-
trile in 2a,b and 6a,b to the expected product but aqueous (20%)
ammonium sulfide did furnish thioamides 3a,b and 7a,b in excellent
yield.25 Hantsch thiazole conditions16 with various chloroacetates
and bromoacetophenones, and heating for 2 h, converted the thio-
amides to thiazoles. Subsequent treatment with TFA in DCM re-
moved the Boc protection. Interestingly, increasing the reaction time,
for Hantsch thiazole formation, from 2 to 12 h resulted in both thi-
azole formation and Boc deprotection, presumably by the HCl or HBr
by-product, furnishing compounds 4aen and 8aen. Acknowledging
this success, future efforts bypassed the two-step route, in favor of
the one-step alternative, which showed a negligible loss in totalyield
over the two steps; subsequent hydrolysis produced 5aen and 9aen.
For mimetics with a rigid amine (aniline) at the iþ4 position,
SNAr between 2-bromo-4-fluorobenzonitrile and either methyl 3-
(1H-imidazol-2-yl) propanoate or dimethyl 1H-benzo[d]imidazole-
5,6-dicarboxylate yielded 10 or 15, respectively (Scheme 2). Treat-
ment with aqueous (20%) ammonium sulfide and then Hantsch
thiazole conditions with various chloroacetates and bromoaceto-
phenones converted thioamides 11 and 16 to thiazoles 12aeg and
17aeg.26 Suzuki coupling with 3-aminophenylboronic acid or 4-
(4,4,5,5)-tetramethyl-1,3,2 dioxaborolan-2-yl aniline in the pres-
ence of PdCl2(dppf), followed by hydrolysis furnished 14aen and
19aen.27 Incorporating the Hantsch thiazole synthesis and Suzuki
couplings facilitated late stage installation of diversity and rapid
accessibility to this 56 compound library.
Fig. 1. Energy minimized (a) poly-alanine
(b) trimethyl substituted terphenyl, (c) trimethyl substituted terpyridine, (d) tetra-
methyl substituted terephthalamide, and (d) trimethyl substituted 5-6-5 imidazole-
a
-helix displaying i, iþ4, and iþ7 positions,
phenyl-thiazole based
(o/w) values.
a-helix mimetics along with their respective calculated log P
A modular synthetic approach was developed capable of func-
tionalizing the 5-6-5 imidazole-phenyl-thiazole scaffolds with
a series of amino acid-like sidechains to mimic the i, iþ4, and iþ7
positions. Our design involved incorporating, onto the N-aryl im-
idazole ring, either flexible or rigid acid groups (R1 position, Fig. 2b
and c), in place of the Q770 residue in the protein.22 The diacid
(Fig. 2c, R1) serves as a rigidified version of the monoacid (Fig. 2b,
R1) with the second carboxylic acid potentially allowing for in-
creased hydrogen-bonding. Installation of the monoacid and diacid
proceeded via Ullman coupling of the corresponding imidazole or
benzimidazole with an aryl bromide or SNAr with an aryl fluoride,
depending on the substitution pattern at the iþ4 position.
A crystal structure of a fully functionalized 5-6-5 a-helix mi-
metic, compound 19i (Fig. 3), confirmed the extended shape of the
molecule and the staggered projections of the substituents in
a nonplanar orientation (5-6-5 dihedral angles 42.3ꢀ and 39.0ꢀ). In
addition to projecting functionality in a similar orientation to that
of an a-helix, a subset of these compounds, upon conversion from
Fig. 2. Schematic representations of (a) an energy minimized poly-alanine
a-helix
thioamides 7a,b to thiazoles 8aec and hej, were found to
be fluorescent under long wave (365 nm) UV light exposure
(Fig. S4).28,29
displaying i, iþ4, and iþ7 positions (b) the flexible acid based 5-6-5 imidazole-phenyl-
thiazole core scaffold and (c) the rigid diacid based 5-6-5 imidazole-phenyl-thiazole
based core scaffold a-helix mimetics.

C.G. Cummings, A.D. Hamilton / Tetrahedron 69 (2013) 1663e1668
1665
Scheme 1. Conditions: (a) tert-butyl 3-hydroxypropylcarbamate or tert-butyl 2-hydroxyethylcarbamate, KHMDS, THF (99%); (b) methyl 3-(1H-imidazol-2-yl)propanoate, L-proline,
CuI, K2CO3, DMSO, 130 ꢀC (80e84%); (b0) dimethyl 1H-benzo[d]imidazole-5,6-dicarboxylate, L-proline, CuI, K2CO3, DMSO, 130 ꢀC (76e81%); (c) (NH4)2S (aq) (20%), EtOH, 90 ꢀC
(83e92%); (d) R3COCH2X (X¼Cl or Br), R3OH or EtOH, 80 ꢀC, 2 h (75e88%); (d0) R3COCH2X (X¼Cl or Br), R3OH or EtOH, 80 ꢀC, 12 h (69e84%); (e) TFA, CH2Cl2 (99%); (f) LiOH$H2O, THF,
H2O, MeOH (99%).
Scheme 2. Conditions: (a) methyl 3-(1H-imidazol-2-yl)propanoate, DIPEA, DMSO, 90 ꢀC (81%); (a0) dimethyl 1H-benzo[d]imidazole-5,6-dicarboxylate, DIPEA, DMSO, 90 ꢀC (93%);
(b) (NH4)2S (aq) (20%), EtOH, 90 ꢀC (86e91%); (c) R3COCH2X (X¼Cl or Br), R3OH or EtOH, 80 ꢀC, 12 h (81e87%); (d) 3-aminophenylboronic acid or 4-(4,4,5,5)-tetramethyl-1,3,2
dioxaborolan-2-yl aniline, CsF, PdCl2(dppf), DMF, 90 ꢀC (84e93%); (e) LiOH$H2O, THF, H2O, MeOH (99%).

1666
C.G. Cummings, A.D. Hamilton / Tetrahedron 69 (2013) 1663e1668
performed using electrospray ionization on either a Varian MAT-
CH-5 (HRMS) or a Waters Micromass ZQ (LRMS) instrument.
Analysis and purification by rpHPLC were performed using either
Phenomenex Luna 5
at 15 mL/min (preparative) or
m
m C18 (2) 250 mmꢁ21 mm column run
ꢀ
a
Microsorb-MV 300 A C18
250 mmꢁ4.6 mm column run at 1 mL/min (analytical), using gra-
dient mixtures of (A) water with 0.1% TFA and (B) 10:1 acetonitrile/
water with 0.1% TFA. Appropriate product fractions were pooled
and lyophilized to dryness, affording the inhibitors as fluffy white
powders as their TFA salts. Inhibitor purity was confirmed by an-
alytical rpHPLC using linear gradients from 100% A to 100% B, with
changing solvent composition of either (I) 4.5% or (II) 1.5% per min
after an initial 2 min of 100% A.
4.2. General procedure for preparation of 5a
4.2.1. Methyl 3-(1H-imidazol-2-yl) propanoate. To a round bottom
flask charged with 143 mL of methanol was added 1 g (g) (1 equiv,
7.15 mmol) of 3-(1H-imidazol-2-yl)propanoic acid (Astatech Inc.).
This solution was cooled to 0 ꢀC, then 5.2 mL (10 equiv, 71.5 mmol)
of thionyl chloride was added and the reaction stirred for 5 h.
Upon completion, the reaction was reduced, diluted with
dichloromethane, and washed three times with 0.1 M K2CO3. The
organic portions were dried with sodium sulfate, filtered, and
reduced to afford the HCl salt of methyl 3-(1H-imidazol-2-yl)
propanoate as a white powder in quantitative yield (1.35 g, 99%).
dH (500 MHz, DMSO-d6) 2.98 (s, 2H, CH2CH2Im), 3.16 (s, 2H,
CH2CH2Im), 3.59 (s, 3H, CH3), 7.52 (s, 2H, Im), 14.58 (s, 1H, NH); dC
(125 MHz, DMSO-d6) 20.44, 29.98, 51.45, 118.20, 145.76, 171.31;
HRMS (ESþ) calcd for [C7H10N2O2þH] 155.08205, found
155.08202.
Fig. 3. Stereoview of the X-ray crystal structure of
a fully functionalized 5-6-5
imidazole-phenyl-thiazole a
-helix mimetic30 (compound 19i).
3. Conclusions
In summary, the 5-6-5 imidazole-phenyl-thiazole scaffold
avoids the inherent disadvantages of previous mimetics, such as
poor water solubility or relying on hydrogen-bonding networks
to maintain their proper orientation. Crystal structures of
model12 and fully functionalized 5-6-5 imidazole-phenyl-
thiazole
a
-helix mimetics30 confirm that substituents are stag-
gered in a nonplanar orientation. Analysis of the 5-6-5 dihedral
angles suggests that the i, iþ4, and iþ7 sidechain mimics are
projected in a similar orientation to the corresponding residues
4.2.2. tert-Butyl3-(5-bromo-2-cyanophenoxy)propylcarbamate(1a). To
a 0 ꢀC stirring solution of 100 mL tetrahydrofuran, 3 g (1 equiv,
15 mol) 4-bromo-2-fluorobenzonitrile, 2.63 g (1 equiv, 15 mol) tert-
butyl 3-hydroxypropylcarbamate was added 30 mL (1 equiv, 15 mol)
of 0.5 M potassium hexamethyldisilane solution in toluene. The re-
action mixture was allowed to warm to room temperature over the
course of 6 h. Upon completion the reaction was reduced, then di-
luted with dichloromethane and washed repeatedly with 0.1 M HCl.
The organic portions were collected, dried with sodium sulfate, fil-
tered, and reduced to produce tert-butyl 3-(5-bromo-2-
cyanophenoxy) propylcarbamate as an off white powder in quanti-
tative yield (5.31 g, 99%).dH (500 MHz, DMSO-d6) 1.37 (s, 9H, C(CH3)3),
1.84e1.86 (m, 2H, CH2CH2CH2), 3.09e3.11 (m, 2H, NCH2), 4.17 (t,
J¼6.75 Hz, 2H, CH2O), 6.90 (br s, 1H, NH), 7.30 (d, J¼8.25 Hz, 1H, Ar),
7.49 (s, 1H, Ar), 7.68 (d, J¼8.25 Hz, 1H, Ar); dC (125 MHz, DMSO-d6)
27.77, 28.35, 36.03, 54.43, 66.67, 77.07, 99.58, 116.04, 123.65, 128.05,
134.39, 155.14, 160.26; HRMS (ESþ) calcd for [C15H19BrN2O3þH]
355.06573, found 355.06533.
on a natural a-helix.
Incorporation of high-yielding Ullman and Suzuki coupling
reactions, along with SNAr and the Hantsch thiazole synthesis
form the foundation of five step synthetic routes to fully func-
tionalized, water soluble 5-6-5 imidazole-phenyl-thiazole a-helix
mimetics, with total overall yields of 42e67%, from commercially
available starting materials. The innate heterocyclic core, in-
stalled with Ullman coupling or SNAr and Hantsch thiazole
synthesis, increases water solubility, which may translate to
improved bioavailability, protein binding, and pharmacokinetic
properties. The ability of these compounds to disrupt PPIs, in-
cluding studies against GTPase-GEF target proteins, are currently
under investigation.
4. Experimental section
4.1. General
All chemicals were obtained from Sigma/Aldrich, Fluka, Lan-
caster, Atlantic SciTech, TCI America, and Astatech Inc. unless oth-
erwise noted. Solvents CH2Cl2, THF, CH3CN, and DMF were dried
using an Innovative Technology SPS-400 dry solvent system. An-
hydrous MeOH, EtOH, iPrOH, and DMSO were purchased from
SigmaeAldrich and used directly from their Sure-Seal bottles. All
reactions were performed under an atmosphere of dry nitrogen in
oven-dried glassware and were monitored for completeness by
thin-layer chromatography (TLC) using silica gel (visualized by UV
light or developed by treatment with KMnO4 stain or Hanessian’s
stain). 1H and 13C NMR spectra were recorded on Bruker AM
400 MHz and Bruker AM 500 MHz spectrometers in either CDCl3,
4.2.3. Methyl 3-(1-(3-(3-(tert-butoxycarbonyl amino)propoxy)-4-
cyanophenyl)-1H-imidazol-2-yl) propanoate (2a). To a pressure
flask charged with 24 mL anhydrous dimethyl sulfoxide was added
3.04 g (8.56 mmol, 1.1 equiv) tert-butyl 3-(5-bromo-2-cyanoph-
enoxy) propylcarbamate, 1.48 g (7.80 mmol, 1.0 equiv) HCl salt of
methyl 3-(1H-imidazol-2-yl)propanoate, 2.02 g (15.6 mmol, 2 equiv)
potassium carbonate, 900 mg (7.8 mmol, 1 equiv) L-proline, and
296 mg (1.56 mmol, 0.2 equiv) copper iodide. The pressure flask was
stirred at 130 ꢀC for 48 h, upon completion the reaction mixture was
diluted with ethyl acetate and washed three times with 0.1 M HCl
solution. The organic portions were collected, dried with sodium
sulfate, and the reduced to afford the crude reaction mixture as a
brown oil. The crude reaction mixture was dry loaded and purified by
silica gel flash column chromatography (eluent: CH2Cl2:MeOH:N-
H4OH, 92:7:1) to afford methyl 3-(1-(3-(3-(tert-butoxycarbony-
MeOH-d4 or DMSO-d6. Chemical shifts (d) are reported in parts per
million after calibration to residual isotopic solvent. Coupling
constants (J) are reported in Hertz. Mass spectrometry (MS) was

C.G. Cummings, A.D. Hamilton / Tetrahedron 69 (2013) 1663e1668
1667
lamino)propoxy)-4-cyanophenyl)-1H-imidazol-2-yl)propanoate as
a brown oil (2.5 g, 80%). dH (400 MHz, DMSO-d6) 1.36 (s, 9H, C(CH3)3),
1.88 (q, J¼6.38 Hz, 2H, CH2CH2CH2), 2.77 (t, J¼7.0 Hz, 2H, CH2CH2Im),
2.92 (t, J¼7.0 Hz, 2H, CH2CH2Im), 3.12 (q, J¼6.35 Hz, 2H, NCH2), 3.55 (s,
3H, CH3), 4.21 (t, J¼6.5 Hz, 2H, CH2O), 6.91 (br t, J¼5.5, 1H, NH), 6.98
(d, J¼1.0 Hz, 1H, Im), 7.21e7.19 (m, 1H, Ar), 7.12 (d, J¼1.0 Hz, 1H, Ar),
7.34 (br s, 1H, Ar), 7.92 (d, J¼8 Hz, 1H, Im), dC (125 MHz, DMSO-d6)
21.91, 28.07, 28.66, 30.80, 36.47, 51.19, 66.99, 77.39, 99.90, 110.26,
115.58, 117.61, 120.83, 127.55, 134.55, 142.41, 145.90, 155.48, 160.85,
172.38; HRMS (ESþ) calcd for [C22H28N4O5þH] 429.21380, found
429.21377.
salt of 5a, this salt was used to determine the NMR spectrum. dH
(500 MHz, DMSO-d6) 1.87 (t, J¼6.0 Hz, 2H, CH2), 2.56 (s, 3H, CH3),
2.71 (t, J¼5.0 Hz, 2H, CH2), 3.02 (q, J¼5.0 Hz, 2H, CH2), 3.12 (m, 2H,
CH2), 4.19 (t, J¼5.0 Hz, 2H, CH2), 6.93 (m, 2H, Ar), 7.31 (d, J¼5.0 Hz,
1H, Ar), 7.50 (s, 1H, Ar), 7.72 (m, 1H, Ar), 8.02 (d, J¼8.0 Hz, 1H, Ar); dC
(125 MHz, DMSO-d6) 21.26, 27.05, 31.31, 50.18, 99.24, 110.64, 114.65,
125.38, 129.31, 130.99, 140.05, 141.57, 143.90, 146.62, 148.30, 153.76,
158.00, 160.89, 172.10; HRMS (ESþ) calcd for [C19H22N4O4SþH]
403.14400, found 403.14409.
4.3. General procedure for preparation of 19b
4.2.4. Methyl 3-(1-(3-(3-(tert-butoxycarbonyl amino)propoxy)-4-
carbamothioylphenyl)-1H-imidazol-2-yl) propanoate (3a). To a round
bottom flask was added 1.00 g (2.34 mmol, 1 equiv) methyl 3-(1-(3-
(3-(tert-butoxycarbonyl amino)propoxy)-4-cyanophenyl)-1H-imida-
zol-2-yl) propanoate, 30 mL ethanol and 2.0 mL 20% ammonium
sulfide (aq). The reaction stirred at 90 ꢀC for 2 h. The crude mixture
was dry loaded and purified by silica gel flash column chromatog-
raphy (eluent: CH2Cl2:MeOH:NH4OH, 92:7:1) to produce methyl 3-
(1-(3-(3-(tert-butoxycarbonylamino)propoxy)-4-carbamothioyl phe-
4.3.1. Dimethyl 1H-benzo[d]imidazole-5,6-dicarboxylate. To a pres-
sure flask was added 2.0 g (9.71 mmol, 1 equiv) of benzimidazole
dicarboxylic acid and 97.1 mL methanol. After stirring for 10 min,
7.0 mL (97.1 mmol, 10 equiv) of thionyl chloride was added drop-
wise. Continuous stirring for 10 min allowed the components to
mix thoroughly and then the pressure flask was placed at 80 ꢀC for
12 h. The reaction was reduced and then diluted with dichloro-
methane and washed three times with 0.1 M K2CO3. The organic
layer was dried and reduced to furnish dimethyl 1H-benzo[d]im-
idazole-5,6-dicarboxylate in 95% yield (2.16 g) with no further
purification necessary. dH (500 MHz, DMSO-d6) 3.82 (s, 6H, CH3),
7.89 (s, 1H, Ar), 8.00 (s, 1H, Ar), 8.50 (s, 1H, Ar), 12.99 (br, 1H, NH);
dC (125 MHz, DMSO-d6) 52.32, 112.94, 119.97, 134.31, 145.92, 167.78;
HRMS (ESþ) calcd for [C11H10N2O4þH] 235.07188, found
235.07137.
nyl)-1H-imidazol-2-yl)propanoate as
a bright yellow powder
(860 mg, 92%).dH (400 MHz, DMSO-d6) 1.34 (s, 9H, C(CH3)3),
1.81e1.84 (m, 2H, CH2CH2CH2), 2.78 (t, J¼6.9 Hz, 2H, CH2CH2Im), 2.89
(t, J¼6.9 Hz, 2H, CH2CH2Im), 3.10e3.13 (m, 2H, NCH2), 3.56 (s, 3H,
CH3), 4.06 (t, J¼6.2 Hz, 2H, CH2O), 6.91 (br t, J¼5.8, 1H, NH), 6.95 (d,
J¼1.6,1H, Im), 7.02e7.03 (m, 1H, Ar), 7.12 (d, J¼2.0 Hz, 1H, Ar), 7.30 (d,
J¼1.6,1H, Im), 7.76 (d, J¼8.0 Hz,1H, Ar), 9.39 (s,1H, NH2), 10.09 (s,1H,
NH2); dC (125 MHz, DMSO-d6) 21.85, 28.04, 30.82, 35.64, 36.28, 51.20,
65.74, 77.51, 109.70, 116.64, 120.91, 127.17, 130.27, 131.44, 139.03,
145.78, 153.82, 155.64, 172.41, 197.91; HRMS (ESþ) calcd for
[C22H30N4O5SþH] 463.20152, found 463.20150.
4.3.2. Dimethyl 1-(3-bromo-4-cyanophenyl)-1H-benzo[d]imidazole-
5,6-dicarboxylate (15). A pressure flask was charged with 20 mL
DMSO, 3.8 g (16.2 mmol, 1 equiv) dimethyl 1H-benzo[d]imidazole-
5,6-dicarboxylate, and 3.24 g (16.2 mmol, 1 equiv) 2-bromo-4-
fluorobenzonitrile. After stirring for 10 min, 14 mL (81.0 mmol,
5 equiv) of DIPEA was added and the reaction was placed at 90 ꢀC
for 30 h. The reaction was diluted with minimal ethyl acetate and
washed three times with 0.1 M K2CO3, then dried and reduced. The
crude reaction mixture was dry loaded and purified by silica gel
flash column chromatography (eluent: CH2Cl2:MeOH:NH4OH,
92:7:1) to afford dimethyl 1-(3-bromo-4-cyanophenyl)-1H-benzo
[d] imidazole-5,6-dicarboxylate in 93% yield (1.46 g). dH (500 MHz,
CDCl3 and MeOD) 3.92 (s, 3H, CH3), 3.94 (s, 3H, CH3), 7.65e7.63 (m,
1H, Ar), 7.87 (s, 1H, Ar), 7.90 (s, 1H, Ar), 7.92 (s, 1H, Ar), 8.25 (s, 1H,
Ar), 8.28 (s, 1H, Ar); dC (125 MHz, CDCl3) 52.49, 52.59, 111.57, 115.46,
115.83, 121.79, 121.80, 122.76, 127.64, 127.94, 128.61, 133.45, 135.87,
139.25, 144.47, 144.92, 167.68(2); HRMS (ESþ) calcd for
[C18H12BrN3O4þH] 414.00894, found 414.00843.
4.2.5. Methyl 3-(1-(3-(3-aminopropoxy)-4-(4-methoxythiazol-2-yl)
phenyl)-1H-imidazol-2-yl) propanoate (4a). To a pressure flask
charged with 1 mL methanol was added 70 mg (0.156 mmol,
1 equiv) methyl 3-(1-(3-(3-(tert-butoxycarbonylamino)propoxy)-
4-carbamo thioylphenyl)-1H-imidazol-2-yl) propanoate and 19 mg
(0.172 mmol, 1.1 equiv) methyl 2-chloroacetate. The pressure flask
stirred at 90 ꢀC for 14 h. The crude reaction mixture was dry loaded
and purified by silica gel flash column chromatography (eluent:
CH2Cl2:MeOH:NH4OH, 92:7:1) to yield methyl 3-(1-(3-(3-amino-
propoxy)-4-(4-methoxythiazol-2-yl)phenyl)-1H-imidazol-2-yl)
propanoate as a reddish powder (49 mg, 78%). dH (500 MHz,
DMSO-d6) 2.07 (t, J¼5.0 Hz, 2H, CH2), 2.56 (s, 3H, CH3), 2.83 (t,
J¼5.0 Hz, 2H, CH2), 3.00 (q, J¼5.0 Hz, 2H, CH2), 3.28 (m, 2H,
CH2), 3.62 (s, 3H, CH3), 4.34 (t, J¼5.0 Hz, 2H, CH2), 6.38 (s, 1H,
Ar), 7.07 (s, 1H, Ar), 7.22 (d, J¼8.0 Hz, 1H, Ar), 7.34 (s, 1H, Ar),
7.44 (s, 1H, Ar), 8.36 (d, J¼8.0 Hz, 1H, Ar); dC (125 MHz, DMSO-
d6) 21.94, 28.21, 31.01, 36.86, 50.99, 91.53, 109.84, 112.17, 117.64,
121.00, 124.85, 127.99, 130.96, 132.24, 135.62, 145.90, 155.62,
156.26, 162.20, 172.33; HRMS (ESþ) calcd for [C19H22N4O4SþH]
403.1440, found 403.1451.
4.3.3. Dimethyl 1-(3-bromo-4-carbamothioyl phenyl)-1H-benzo[d]
imidazole-5,6-dicarboxylate (16). To a pressure flask was added
6.70 g (16.2 mmol, 1 equiv) dimethyl 1-(3-bromo-4-cyanophenyl)-
1H-benzo[d]imidazole-5,6-dicarboxylate, 40 mL ethanol and
10.0 mL 20% ammonium sulfide (aq). The reaction stirred at 90 ꢀC
for 1.5 h. The crude mixture was dry loaded and purified by silica
gel flash column chromatography (eluent: CH2Cl2:MeOH:NH4OH,
92:7:1) to produce dimethyl 1-(3-bromo-4-carbamothioylphenyl)-
1H-benzo [d] imidazole-5,6-dicarboxylate as a yellow powder
(5.43 g, 91%). dH (500 MHz, DMSO-d6) 3.82 (s, 3H, CH3), 3.85 (s, 3H,
CH3), 7.65 (d, J¼9.2, 1H, Ar), 7.80 (d, J¼8.0, 1H, Ar), 7.92 (s, 1H, Ar),
8.01 (s,1H, Ar), 8.16 (s,1H, Ar), 8.22 (s,1H, Ar), 9.81 (s,1H, NH),10.33
(s, 1H, NH); dC (125 MHz, DMSO-d6) 53.05, 53.13, 111.98, 119.01,
122.57, 123.38, 123.90, 128.67, 129.37, 131.35, 134.53, 136.71, 143.75,
145.05, 145.16, 168.20(2), 201.23; HRMS (ESþ) calcd for
[C18H14BrN3O4SþH] 447.99666, found 447.99633.
4.2.6. 3-(1-(3-(3-Aminopropoxy)-4-(4-methoxy thiazol-2-yl) phe-
nyl)-1H-imidazol-2-yl) propanoic acid (5a). A round bottom flask
was charged with
1 mL of 3:1:1 (MeOH:THF:H2O), 20 mg
(0.049 mmol, 1 equiv) methyl 3-(1-(3-(3-aminopropoxy)-4-(4-
methoxy thiazol-2-yl) phenyl)-1H-imidazol-2-yl) propanoate and
7.0 mg (0.150 mmol, 3 equiv) lithium hydroxide monohydrate. The
reaction mixture stirred at room temperature for 20 h. The crude
reaction mixture was dry loaded and purified by silica gel flash
column chromatography (eluent: CH2Cl2:MeOH:NH4OH, 92:7:1)
to afford 3-(1-(3-(2-aminoethoxy)-4-(4-methoxythiazol-2-yl)phe-
nyl)-1H -imidazol-2-yl) propanoic acid (19 mg, 99%). The final
compound, 5a, was additionally purified by HPLC to obtain the TFA
4.3.4. Dimethyl 1-(3-bromo-4-(4-ethoxythiazol-2-yl)phenyl)-1H-benzo
[d]imidazole-5,6-dicarboxylate (17b). A pressure flask was charged

1668
C.G. Cummings, A.D. Hamilton / Tetrahedron 69 (2013) 1663e1668
1.5 mL ethanol and (0.150 mmol, 1.1 equiv) ethyl 2-chloroacetate and
50 mg (0.136 mmol, 1 equiv) dimethyl 1-(3-bromo-4-carbamoth-
ioylphenyl)-1H-benzo[d] imidazole-5,6-dicarboxylate. The reaction
stirred at 80 ꢀC for 4 h, the crude mixture was dry loaded and purified
by silica gel flash column chromatography (eluent: CH2Cl2:MeOH:N-
H4OH, 92:7:1)to produce dimethyl 1-(3-bromo-4-(4-ethoxythiazol-2-
yl) phenyl)-1H-benzo[d]imidazole-5,6-dicarboxylate as a reddish
powder (50 mg, 82%). dH (500 MHz, CDCl3) 1.39 (t, J¼7.5 Hz, 3H, CH3),
3.83 (s, 3H, CH3), 3.86 (s, 3H, CH3), 4.15 (q, J¼6.3 Hz, 2H, CH2), 6.25 (s,
1H, Ar), 7.48e7.50 (m,1H, Ar), 7.79 (d, J¼4.0 Hz,1H, Ar), 7.81 (s,1H, Ar),
8.16 (s, 1H, Ar), 8.24 (s, 1H, Ar), 8.36 (d, J¼4.0 Hz, 1H, Ar); dC
(125 MHz, CDCl3) 14.71, 31.56, 34.85, 67.21, 111.23, 115.89, 117.84,
121.43, 122.98, 123.90, 125.67, 128.58, 129.21, 131.99, 132.84, 135.67,
137.92, 143.66, 144.12, 152.87, 167.69, 168.11; HRMS (ESþ) calcd for
[C22H18BrN3O5SþH] 516.02288, found 516.02281.
131.54, 133.23, 135.13, 139.00, 161.24, 162.96, 168.01(2); HRMS
(ESþ) calcd for [C26H20N4O5SþH] 501.12327, found 501.12320.
Acknowledgements
The authors would like to thank the National Institutes of Health
for financial support of this work (CA67771) and our collaborators
Channing Der, Adrienne Cox, John Sondek (UNC) and Said Sebti (H.
Lee Moffitt Cancer Center and Research Institute) for invaluable
discussions. We would also like to thank Dr. Steven Fletcher and Dr.
Patrick Gunning for initial discussions and Dr. Christopher Incarvito
for X-ray crystallographic analysis.
Supplementary data
Supplementary data related to this article can be found at http://
dx.doi.org/10.1016/j.tet.2012.11.070.
4.3.5. Dimethyl 1-(40-amino-6-(4-ethoxythiazol-2-yl)biphenyl-3-yl)-
1H-benzo[d]imidazole-5,6-dicarboxylate (18i). A pressure flask was
charged with 22 mg (0.052 mmol, 1 equiv) dimethyl 1-(3-bromo-4-
(4-ethoxythiazol-2-yl)phenyl)-1H-benzo[d]imidazole-5,6-dicarbo-
xylate, 34.2 mg (0.156 mmol, 3 equiv) 4-(4,4,5,5)-tetramethyl-1,3,2
dioxaborolan-2-yl aniline, 43 mg (0.220 mmol, 5.2 equiv) cesium
fluoride, 10 mg (0.0104 mmol, 20 mol %) PdCl2(dppf)2, and 1.0 mL
DMF. The reaction mixture stirred for 12 h at 90 ꢀC and was then
diluted with ethyl acetate and washed three times with 0.1 M HCl.
The organic layers were combined and then dried and reduced, the
crude reaction mixture was dry loaded and purified by silica gel
flash column chromatography (eluent: CH2Cl2:MeOH:NH4OH,
92:7:1) to produce dimethyl 1-(40-amino-6-(4-ethoxythiazol-2-yl)
biphenyl-3-yl)-1H-benzo[d]imidazole-5,6-dicarboxylate in 89%
yield (20.3 mg). dH (500 MHz, DMSO-d6) 1.34 (t, J¼7.5 Hz, 3H, CH3),
3.82 (s, 3H, CH3), 3.85 (s, 3H, CH3), 4.10 (q, J¼6.3 Hz, 2H, CH2), 5.35
(br, 2H, NH2), 6.53 (s, 1H, Ar), 6.62 (d, J¼8.0 Hz, 2H, Ar), 7.02 (d,
J¼8.0 Hz, 1H, Ar), 7.62 (s, 1H, Ar), 7.76 (d, J¼8.0 Hz, 1H, Ar), 7.95 (s,
1H, Ar), 8.00 (s, 1H, Ar), 8.15 (d, J¼4 Hz, 2H, Ar), 8.95 (s, 1H, Ar); dC
(125 MHz, DMSO-d6) 30.75, 35.89, 52.63, 64.97, 92.84, 112.10,
113.70, 121.07, 122.39, 125.23, 126.38, 127.24, 130.44, 130.59, 131.66,
134.18, 135.43, 143.03, 144.78, 149.21, 161.93, 162.27, 162.33, 163.01,
167.54(2); HRMS (ESþ) calcd for [C28H24N4O5SþH] 529.15457,
found 529.15468.
References and notes
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biphenyl-3-yl)-1H-
benzo [d]imidazole-5,6-dicarboxylic acid (19i). To a round bottom
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amino-6-(4-ethoxythiazol-2-yl)biphenyl-3-yl)-1H-benzo [d] imid-
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