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© 2023. The Author(s). SynOpen 2023, 7, 401–407
Georg Thieme Verlag KG, Rüdigerstraße 14, 70469 Stuttgart, Germany
N. Long et al. Letter
SynOpen
Synthesis of Squaric Acid Monoamides as Building Blocks for Drug
Discovery
Nathan Longa
Adam Le Gresleya
Arran Solomonszb
Antony Wozniakb
Steve Broughc
Stephen P. Wren*a
0000-0001-7184-9528
aSchool of Life Sciences , Pharmacy and Chemistry, Faculty of
Health, Science, Social Care and Education, Kingston University,
Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
s.wren@kingston.ac.uk
bAsynt Ltd., Hall Barn Road Industrial Estate, Hall Barn Rd, Isle-
ham, Ely, CB7 5RJ, UK
cKey Organics Ltd., Highfield Road Insutrial Estate Camelford,
Cornwall, PL32 9RA, UK
The Wren Group would like to dedicate this article to Tory May Wren who sadly passed away on the 28th October 2022.
She is a constant source of inspiration for her dad (Stephen P. Wren).
Corresponding Author
Aniline
Derivative O O
OEtEtO
Benzylamine
Derivative
8 Examples
19 Examples
OO
N
HOEt
Ar
OO
EtO N
H
Bn
Received: 03.07.2023
Accepted after revision: 03.08.2023
Published online: 04.08.2023 (Accepted Manuscript), 29.08.2023 (Version of Record)
DOI: 10.1055/a-2148-9518; Art ID: SO-2023-07-0043-L
License terms:
© 2023. The Author(s). This is an open access article published by Thieme under the
terms of the Creative Commons Attribution License, permitting unrestricted use, dis-
tribution and reproduction, so long as the original work is properly cited.
(https://creativecommons.org/licenses/by/4.0/)
Abstract Herein, we present a synthetic compound library compris-
ing of 28 anilino and benzylamino monosquarate-amide derivatives.
Members of this library were designed as bioisosteric replacements for
groups such as the ubiquitous carboxylic acid moiety. Further to their
synthesis, we have shown the potential of these chemical building
blocks for the generation of additional novel compounds. This work
forms part of our efforts aimed at the assembly of 96-well plates loaded
with bioisosteric analogues that may be used to enrich drug discovery
programs. The research presented in this work focuses on the chemis-
try of 3,4-dihydroxycyclobut-3-ene-1,2-dione, a known carboxylic acid
bioisostere.
Key words squaric acid, squaramide, bioisostere, carboxylic acid,
compound library
The carboxylic acid moiety is a ubiquitously recognised
functional group in the sphere of organic chemistry. The
importance of this group is easily justified both by its prev-
alence and the number of endogenous biological processes
which rely on its intrinsic chemical nature.1 Over 450 mar-
keted drug compounds worldwide are known to possess a
carboxylic acid group within their chemical structure. Such
drug classes include nonsteroidal anti-inflamatory drugs
(NSAIDs) (such as naproxen (1) and indomethacin (2)), anti-
coagulants, statins, betafucin (which contains fusidic acid
(3)), -lactam antibiotics, and GPR40 agonists to name but
a few (Figure 1).2–4
Figure 1 Examples of marketed drug compounds featuring a carboxyl-
ic acid
Despite its prevalence, and often acting directly as a
pharmacophore to invoke a biological response, the pres-
ence of this polar moiety can also confer significant draw-
backs. One such pitfall involves extensive metabolism of the
carboxylic acid functional group through glucoconjuga-
tion.5 Another potential complication is a diminished abili-
ty to diffuse across biological membranes and this can be a
particular issue in the context of developing agents which
act on the central nervous system (CNS). In order for drugs
to be CNS active they must successfully permeate the blood
brain barrier, a highly lipophilic membrane which does not
tolerate the charged carboxylate ion present at physiologi-
cal pH.6 Further, the presence of the carboxylic acid func-
tionality can lead to idiosyncratic toxicity and result in a
drug candidate being withdrawn from the market (for ex-
ample, benoxaprofen).7
Frequently, replacement of the carboxylic acid motif or
other structural units with a suitable surrogate or bio-
isostere (such as a squaramide) is undertaken in order to
avoid suboptimal properties that may give rise to unsuit-
ability for lead compound generation, or undesirable phar-
macokinetic effects.1,8 In this paper, we describe our con-
O
HO
OMe
Naproxen
1
N
OCl
O
OH
MeO
O
O
OH
O
HO
H
H
HO
Indomethacin
2
Fucidic Acid
3
SYNOPEN
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2023, 7, 401–407
letter
en
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N. Long et al. Letter
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tinuing efforts to develop a toolbox of bioisosteric building
blocks for use by the medicinal chemistry community. This
work builds on our recent review of the synthesis of novel
thiazolidinedione-containing derivatives used to replace
carboxylic acid moieties in druglike structures.9 Consulta-
tion of the literature, specifically works published by
Lassalas and co-workers, highlighted 3,4-dihydroxycy-
clobut-3-ene-1,2-dione (squaric acid) as a recognised bio-
isostere for the carboxylic acid functionality.10
Since its first synthesis, in 1959, by Cohen and col-
leagues, there has been continuous interest into the chem-
istry of squaric acid and its functionalised nitrogenous de-
rivatives (Figure 2).11 Squaric acid is a highly versatile or-
ganic framework which can be derivatised extensively and
has seen use in the fields of optoelectronic materials, inor-
ganic dyes, organocatalysis, and in the development of new
pharmaceuticals.12–14
Figure 2 Squaric acid and functionalised squaric acid derivatives
Squaric acid functionalised derivatives have been used
in the field of medicinal chemistry. The majority of such
structures usually fall into the class of bis-squaramides 7,
though some squarate esters 6 also are used clinically. One
common clinically used example of a squarate ester is the
dibutyl ester of squaric acid (SADBE).15 SADBE is a known
potent allergen and strong irritant and has been used in the
treatment of alopecia areata. As a topical immunotherapy
treatment it is a good alternative treatment method to pa-
tients with refractory alopecia who do not tolerate stan-
dard treatments, such as corticosteroids, phototherapy,
topical Minoxidil, topical irritating agents, or immunosup-
pressives.16,17
Amino/nitrogen-functionalised squaric acid derivatives
are far more common in the literature. Generally, the
squaric acid core is chemically stable in an aqueous envi-
ronment and therefore often stable in vivo (a largely aque-
ous environment). Other studies have revealed that where
squaramides are used as isosteres for amino acids, they are
often more resistant to decarboxylase action as they do not
possess the nucleophilic nitrogen atom essential for the de-
carboxylation mechanism.13 Squaric acid derivatives have
been researched to combat a large multitude of different
disease areas including, but not limited to, antibacterial, cy-
totoxic, antiprotozoal, and antiviral agents (Figure 3).15 We
commenced our investigations by targeting compounds
that resemble 8 (where the squaric acid ring is function-
alised once with a primary amine, and specifically, with the
use of substituted anilines or benzylamines as library in-
puts).
Due to the poor solubility exhibited by squaric acid (5)
in organic solvents, diethyl squarate (DES) (14, an example
of 6) was used as the precursor for all the following trans-
formations.18 We turned our attention to couple benzyl-
amine (15) with diethyl squarate (14) by combining the
two substrates in MeOH at room temperature. After 1 h the
desired monosquarate-amide product 16 was isolated fol-
lowing purification, as a white solid, in 33% yield (Scheme
1). The structure of 16 was determined and confirmed by IR
spectroscopy, NMR spectroscopy, and HRMS.
O O
OHHO
Squaric Acid
5
Bis-squaramides
7
O O
ORRO
Squarate Ester
6
O O
NRO H/R
R/H
Monosquarate-amide
8
O O
NN
H/R
H/R
H/R
R/H
Figure 3 Functionalised squaric acid medicinal agents
HN N PO
O
OH
O O
9
Perzinfotel
(NMDA Antagonist)
OO
N
H
O
NH
N
O
OH
10
Navarixin
(CXCR1/2 Antagonist)
OO
N
H
H2N
11
BMY-25368
(H2 Antagonist)
ON
O O
N
HN
N
O
12
TB Drug
Lead Optimisation
O
O
N
H
O
N
N
NH2
13
Pibutidine
(H2 Antagonist)
403
SynOpen 2023, 7, 401–407
N. Long et al. Letter
SynOpen
Scheme 1 Coupling of diethyl squarate with benzylamine
With compound 16 in hand, attention then turned to
accessing the aniline derivative 18. Analysis of the reaction
mechanism (which proceeds via nucleophilic addition then
elimination) involves EtOH leaving as a byproduct of the re-
action. Consequently, we exchanged the reaction solvent
from MeOH to EtOH when trying to access the aniline scaf-
fold. However, the attempted reaction failed to initiate, and
no product formation was observed after 24 h (Scheme 2).
Scheme 2 Coupling of aniline to DES with and without Zn(OTf)2
This reaction failure was attributed to the poor nucleop-
hilicity of aniline as compared to benzylamine. Consulta-
tion of the literature revealed that, in many cases, a Lewis
acid catalyst is introduced into the reaction which serves to
coordinate to the carbonyl oxygens.19 The presence of such
a Lewis acid draws electron density away from the planar
carbonyl carbons making them more electrophilic and the
compounds more susceptible to substitution. Furthermore,
the cationic zinc species can act as a steric block and (as a
result of its coordination) prevents nucleophilic attack of
the amine directly onto the carbonyl oxygens. With the in-
clusion of the Zn(OTf)2 catalyst, loaded at 13 mol%, the de-
sired aniline scaffold was yielded as an off-white solid in a
37% yield (Scheme 2). Ethyl alcohol is the only reaction sol-
vent that we have evaluated to date. This decision was
based on literature precedent.20–23 While this is not an ex-
cellent yield, Zn(OTf)2 was chosen as a suitable catalyst fol-
lowing literature precedent published by Taylor et al.19 We
are in the process of screening a series of potential Lewis
acid catalysts in an effort to increase the yield of product.
Inspired by our own success in yielding the unsubstitut-
ed analogues 16 and 18 we sought to generate a monosub-
stituted compound library by adding functionality to access
further derivatives. Simple, yet functionalised, anilines and
benzylamines were chosen on the basis of low cost and
ability for varied substrate scope. This chemistry proved to
have extensive substrate scope (Table 1). The isolated com-
pounds listed in Table 1 were all initially attempted without
the presence of the Zn(OTf)2 catalyst. If the reaction failed
to initiate after a period of 24 h, then the reaction was re-
started, and the catalyst was included. Table 1 shows the re-
action conditions used and associated yields for the com-
pound library generation plus an assessment of each reac-
tion product’s novelty. In cases where the reaction failed to
show significant consumption of the reacting amine the re-
action was brought to reflux to try and drive the reaction
forward. In many cases, and with TLC monitoring, heating
the reaction at reflux for prolonged periods did not cause
any further consumption of the starting amine and hence
did not increase product yield. Overall, we have not only
generated novel composition of matter for some of the
monosquarate-amides, but we have also shown an im-
proved yield for the synthesis of compound 25 (compared
to a previous route).24
Table 1 Overview of Synthetic Reactions Used to Yield Monosquarate-amide Derivatives
OO
EtO OEt
NH2
OO
EtO N
H
MeOH
r.t., 1 h
+
14 15 16
33%
OO
EtO OEt
NH2
OO
EtO N
H
EtOH
r.t., 24 h
+
14 17 18
No Reaction
OO
EtO OEt
NH2
OO
EtO N
H
EtOH, r.t., 24 h
+
14 17 18
37%
Zn(OTf)2 (13 mol%)
Compound ID Structure Solvent Temp Time (h) Catalyst presence Yield (%) Is product novel?
16 MeOH r.t. 1 no 33 no24
18 EtOH r.t. 4 13 mol% 37 no20
Alcohol, 0 °C to reflux, Time,
Optional Zn(OTf2) Catalyst
Alcohol, 0 °C to reflux, Time,
Optional Zn(OTf2) Catalyst
Aniline
Derivative O O
OEtEtO
Benzylamine
Derivative
8 Examples
19 Examples
OO
N
HOEt
Ar
OO
EtO N
H
Bn
O O
EtO N
H
O O
EtO N
H
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SynOpen 2023, 7, 401–407
N. Long et al. Letter
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19 EtOH r.t. 12 20 mol% 75 no
(patent)21
20 EtOH r.t. 14 10 mol% 26 yes
21 EtOH r.t. 4 10 mol% 60 no
(patent)22
22 EtOH r.t. 8 10 mol% 64 no25
23 EtOH r.t. 1 10 mol% 66 no19
24 EtOH r.t. 24 no 44 no26
25 EtOH 0 °C to r.t. 24 no 54 no24
26 EtOH 0 °C to r.t. 12 no 45 yes
27 EtOH r.t. 24 13 mol% 18 yes
28 EtOH r.t. 24 13 mol% 94 yes
29 EtOH r.t 36 13 mol% 49 no20
30 EtOH r.t 50 no 29 no27
31 EtOH r.t 48 no 89 no27
32 EtOH r.t 12 no 75 no27
33 EtOH r.t 10 no 54 no
(patent)28
O O
EtO N
H
F
O O
EtO N
HCl
O O
EtO N
H
Cl
O O
EtO N
HBr
O O
EtO N
H
Br
O O
EtO N
H
HO
O O
EtO N
HOH
O O
EtO N
H
OH
O O
EtO N
H
MeO
O O
EtO N
HOMe
O O
EtO N
H
OMe
O O
EtO N
H
O O
EtO N
H
O O
EtO N
H
O O
EtO N
HCF3
405
SynOpen 2023, 7, 401–407
N. Long et al. Letter
SynOpen
It can be witnessed that the coupling of DES (14) with
one equivalent of amine leads to the generation of the cor-
responding monosquarate-amides in moderate to excellent
yield (Table 1). Compound 37 was obtained in 99% yield, but
these refluxing conditions have not yet proved to be trans-
ferable to the reactions run at room temperature. This se-
ries of compounds exhibit significant halide functionalisa-
tion as well as the presence of some electron-donating and
electron-withdrawing groups (e.g., hydroxy, tolyl and tri-
fluoromethyl derivatives 24–26, 30–32, and 33, 34 respec-
tively). Also, current research being conducted within our
group is centered on extending this compound library to in-
corporate anilines adorned with fused ring systems and
carbonyl-containing functional groups that are suitably
protected.
34 EtOH r.t 40 20 mol% 48 no23
35 EtOH r.t 48 10 mol% 38 yes
36 EtOH r.t 48 no 25 yes
37 EtOH reflux 24 no 99 yes
38 EtOH r.t 4 no 34 yes
39 EtOH 0 °C to r.t 5 no 57 yes
40 EtOH r.t 24 no 41 yes
41 EtOH r.t 24 no 91 yes
42 EtOH reflux 6 20 mol% 31 yes
43 EtOH reflux 5 no 48 yes
O O
EtO N
H
CF3
O O
EtO N
H
Cl
O O
EtO N
H
Cl
O O
EtO N
H
Cl
O O
EtO N
H
Br
O O
EtO N
H
Br
O O
EtO N
H
Br
O O
EtO N
Br
O O
EtO N
H
O
OH
O O
EtO N
H
O
O
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N. Long et al. Letter
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It should be noted, however, that coupling reactions be-
tween 14 and ortho-halogenated aniline derivatives failed
to proceed even when re-attempted with the inclusion of
Zn(OTf)2 and heating at reflux for a period of 48 h (see 44,
Scheme 3). The failure in these instances has been attribut-
ed both to the poor nucleophilicity of the anilines and the
physical parameter of steric crowding. In the case of ortho-
halogenated benzylamine derivatives (35 and 38), the reac-
tions did yield the desired monosquarate-amides, presum-
ably due to the fact that the requisite amines are sufficient-
ly nucleophilic.
Scheme 3 Reactions of diethyl squarate with ortho halogenated ani-
lines
In all cases, where reactions yielded the desired prod-
ucts, they existed as amorphous solids when free of reac-
tion solvent. The crude products were purified via column
chromatography over silica gel without any aqueous work-
up being conducted. After accessing the purified compound,
derivatives which were prepared using Zn(OTf)2 were sub-
jected to an aqueous workup to remove any transition-met-
al impurities.
With a significant series of analogues in hand, we began
to explore the use of some of them in further chemical re-
actions in order to provide proof-of-concept applications
for these versatile building blocks.
Brominated analogues are often targeted in synthetic
studies due to their ability to act as substrates in cross-cou-
pling reactions.29,30 Thus, we attempted to use substrate 23
in a novel Suzuki cross-coupling reaction. For simplicity,
PhB(OH)2 was selected as a model coupling partner,
Pd(dba)2 as the palladium catalyst, and K2CO3 as the accom-
panying base. A three-component solvent mixture compris-
ing of DME, H2O, and EtOH, was used in the reaction. Unfor-
tunately, after heating at 120 °C for 30 min, with microwave
irradiation, no discernable product was detected by TLC and
1H NMR spectroscopy (Scheme 4). We are currently study-
ing alternative reaction conditions aimed at the discovery of
a suitable methodology that allows the Pd-catalysed cou-
pling of squaric acid derivatives (45, see Scheme 4).
Our intention to develop methods that demonstrate fur-
ther functionality can be attached to our library com-
pounds was exemplified by the addition of a Me group to
the ‘amidic’ NH. Whilst being a relatively straightforward
procedure, this reaction provided proof of concept that the
synthesised substrates can afford more complex structural
features.
The methyl adduct 47 was successfully obtained as a
white solid in a 29% yield. It was isolated following the dis-
solution of 23 (which was prepared from 14 and 46) and K2-
CO3 in DMF. Following dissolution and allowing 30 min for
deprotonation, 2 equiv of MeI were added dropwise to the
reaction mixture. After allowing the reaction to proceed for
24 h, the desired product was isolated the following aqueous
workup, trituration with Et2O and column chromatography
(eluting with 50% EtOAc in hexane; see Scheme 5).
Scheme 5 Conducted methylation of a synthesised analogue with MeI
In summary, we have managed to assemble an initial li-
brary of monosquarate-amide building blocks derived from
DES and a series of functionalised aniline and benzylamine
precursors. We have demonstrated a proof-of-concept
progress that compounds of this class can act as substrates
in further chemical transformations. These innovations are
continuing within our laboratory. We are looking to further
extend this platform technology with the main goal of as-
sembling 96-well plates of proprietary building blocks
bearing biosisosteric replacements for the carboxylic acid
moiety and other groups. Our continuing studies on the
formation of novel analogues of marketed drugs will be re-
ported on in due course.
Conflict of Interest
The authors declare no conflict of interest.
OO
EtO N
HX
O O
EtO OEt
Ortho Halogenated Aniline
Zn(OTf)2 (10 mol%)
EtOH, Reflux, 48 h
14 44
No Reaction
Scheme 4 Attempted Suzuki cross-coupling reaction utilising a syn-
thesised derivative
O O
EtO N
H
Br
O O
EtO N
H
PhB(OH)2 (1 Equiv)
Pd(dba)2 (10 mol%)
K2CO2 (1.3 Equiv)
DME:H2O:EtOH (7:3:1)
MW 120 °C, 30 min
23 45
No Reaction
O O
EtO N
H
Br
O O
EtO N
H
23 45
Pd
OO
EtO OEt
O
O
EtO N
H
EtOH, r.t., 1 h
+
Zn(OTf)2 (10 mol%)
H2N
14 46 23
66%
Br
Br
O
O
EtO N
H
23
Br O
O
EtO N
47
29%
Br
K2CO3 (1.5 Equiv)
CH3I (2,0 Equiv)
DMF, r.t., 24 h
407
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N. Long et al. Letter
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Acknowledgment
We thank Mr Reece Bristow and Mr James Scanlon (two previous un-
dergraduate students working within the Wren Group) very much for
their hard work establishing some preliminary results for this work.
Our extensive gratitude is offered to both Mr Arran Solomonsz and
Mr Antony Wozniak from Asynt Ltd. for the supply of glassware and
heating utilities. We are also very grateful to Steve Brough, and the
rest of the team at Key Organics Ltd. for their support and their supply
of tert-butyl 3-aminobenzoate (which was used in this research to
synthesise derivative 37 and 38).
Supporting Information
Supporting information for this article is available online at
https://doi.org/10.1055/a-2148-9518.
Supporting InformationSupporting Information
References and Notes
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mation. Two example syntheses are given here.
Compound 26
To 3,4-diethoxycyclobut-3-ene-1,2-dione (500 mg, 0.43 mL,
2.94 mmol, 1 equiv) dissolved in EtOH (15 mL) at 0 °C was
added 4-hydroxyaniline (321 mg, 2.94 mmol, 1 equiv) in EtOH
(10 mL). The reaction was allowed to warm to r.t. and stirred for
12 h before being concentrated under reduced pressure and
purified via column chromatography (5% MeOH in DCM). The
desired compound was obtained as a tan solid (311 mg, 45%);
mp 208–213 °C. FTIR: max = 3695 (NH), 3212 (OH stretch), 2982
(CH aromatic), 1807 (CH alkyl), 1728 (C=O) cm–1. 1H NMR (400
MHz, DMSO-d6): = 10.56 (s, 1 H), 9.42 (s, 1 H), 7.14 (s, 2 H),
6.75–6.69 (m, 2 H), 4.72 (q, J = 7.1 Hz, 2 H), 1.44–1.32 (m, 3 H).
13C NMR (101 MHz, acetone-d6): = 155.6, 131.2, 122.5, 116.5,
70.3, 16.1. HRMS (ESI): m/z [M + Na]+ calcd for C12H11NO4Na:
256.0580; found: 256.0603.
Compound 41
To 3,4-diethoxycyclobut-3-ene-1,2-dione (500 mg, 0.43 mL,
2.94 mmol, 1 equiv) dissolved in EtOH (7 mL) was added 1-(4-
bromophenyl)-N-methylmethanamine (588 mg, 0.59 mL, 2.94
mmol, 1 equiv) dropwise. The reaction was then stirred at r.t.
for 24 h before being concentrated under reduced pressure and
purified via column chromatography (55% EtOAc–hexane). The
product was obtained as a white solid (870 mg, 91%); mp 110–
114 °C. FTIR: max = 2988 (NH), 2928 (CH aromatic), 1802 (CH
alkyl), 1703 (C=O), 1591 (CO) cm–1. 1H NMR (400 MHz, DMSO-
d6): = 7.59 (d, J = 8.4 Hz, 2 H), 7.28 (d, J = 8.4 Hz, 2 H), 4.75 (s, 1
H), 4.67 (p, J = 6.8 Hz, 2 H), 4.52 (s, 1 H), 3.05 (d, J = 63.5 Hz, 3 H),
1.35 (q, J = 7.3 Hz, 3 H). 13C NMR (151 MHz, DMSO-d6): =
188.8, 181.6, 176.5, 171.4, 134.9, 131.7, 130.3, 130.2, 121.2,
69.2, 53.0, 36.0, 15.5. HRMS (ESI): m/z [M + H]+ calcd for
C14H1581BrNO3: 326.02298; found: 326.0203.
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