Expedient synthesis of a novel asymmetric selectively deprotectable derivative of the ATAC scaffold

Article abstract of DOI:10.1016/j.tet.2014.04.084

An efficient multigram scale synthesis of a new asymmetric triazacyclophane scaffold, the ATAC (Asymmetric-TAC) scaffold, bearing three selectively removable groups is described. This scaffold is slightly more rigid than our frequently used TAC (TriAzaCyc

Full text of DOI:10.1016/j.tet.2014.04.084

Tetrahedron 70 (2014) 4002e4007
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Expedient synthesis of a novel asymmetric selectively deprotectable
derivative of the ATAC scaffold
,
,
,b,
Arwin J. Brouwer a y, Helmus van de Langemheen a y, Rob M.J. Liskamp a
*
a Department of Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University,
PO Box 80082, 3508 TB Utrecht, The Netherlands
b School of Chemistry, Joseph Black Building, University of Glasgow, University Avenue, Glasgow G12 8QQ, UK
a r t i c l e i n f o
a b s t r a c t
Article history:
An efficient multigram scale synthesis of a new asymmetric triazacyclophane scaffold, the ATAC
(Asymmetric-TAC) scaffold, bearing three selectively removable groups is described. This scaffold is
slightly more rigid than our frequently used TAC (TriAzaCyclophane) scaffold. The synthesis of the re-
quired triamine is very high yielding without difficult steps or purifications and was also applied to
a much improved synthesis of our original TAC scaffold. Especially the tedious first reaction step, that is,
mono-oNBS-protection of a triamine could be omitted. The rigidity of the triazacyclophane ring in both
TAC- and ATAC scaffolds has also been investigated using variable temperature 1H NMR experiments.
Ó 2014 Elsevier Ltd. All rights reserved.
Received 15 January 2014
Received in revised form 8 April 2014
Accepted 25 April 2014
Available online 2 May 2014
Keywords:
TAC scaffold
ATAC scaffold
Tripodal scaffold
Orthogonal protecting groups
Asymmetric scaffold
1. Introduction
Several scaffolds have been described in the literature to which
three or more identical ligands, such as peptides can be attached,
but only relatively few scaffolds capable of selective attachment of
three different ligands are available.1 One of the first representa-
tives of this class of selectively deprotectable scaffolds, originating
from our group, is the TAC (TriAzaCyclophane) scaffold (1), which
was originally developed for the preparation of synthetic re-
ceptors.2 It consists of a disubstituted benzoic acid hinge connected
to a symmetric cyclophane bridge containing three amine func-
tions, which carry three different selectively removable protecting
groups (Fig. 1).1g,3
In addition to the use of the TAC scaffold in the preparation of
synthetic receptors we have extended its applications greatly to the
preparation of synthetic vaccines,4 involving mimicry of discon-
tinuous epitopes,5 as well as combinatorial libraries,2,6 for example,
toward artificial enzymes.6 So far our work has been mainly focused
on selective introduction of different ligands with relatively defined
distances between points of attachment, especially for peptide
ligands.
Fig. 1. Structures of the TAC (1) and ATAC (asymmetric-TAC) (2) scaffolds.
Since we have described several successful applications of site
selective introduction of ligands onto the TAC scaffold, we are now
increasingly directing our attention to the much more difficult issue
of attempting to orient the ligands with respect to each other in
space. Recently, we strongly varied the rigidity of the scaffold to
influence the relative position in space of peptide loops.5c
While the relatively rigid scaffolds, such as CTV,5c,7 calixarene8
and the steroid skeleton9 are strongly organizing, we were won-
dering whether we could effect directionality in space in a more
subtle way by influencing the conformation of the cyclophane ring.
One of the first things we wanted to investigate was reduction of
cyclophane flexibility by removal of a rotatable single bond in the
TAC scaffold (1), that is, removal of one carbon atom leading to
ATAC (Asymmetric-TAC) scaffold 2 (Fig. 1). Relatively undemanding
molecular modeling experiments (molecular mechanics energy
minimization) showed that in the TAC scaffold the ligands are lo-
calized on average more above and below the plane of the
* Corresponding author. Tel.: þ31 (0) 30 253 7307; fax: þ31 (0) 30 253 6655;
e-mail addresses: R.M.J.Liskamp@uu.nl, robert.liskamp@glasgow.ac.uk, r.m.j.lis-
kamp@pharm.uu.nl (R.M.J. Liskamp).
y
These authors contributed equally to this research.
0040-4020/$ e see front matter Ó 2014 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.tet.2014.04.084

A.J. Brouwer et al. / Tetrahedron 70 (2014) 4002e4007
4003
Fig. 2. Molecular modeling images for comparison of the spatial orientation of three
attached peptides between the TAC (18, left) and ATAC (19, right) scaffolds. Both
scaffolds contain three di-alanine peptides (see Supplementary data for both
structures).
cyclophane ring as compared to being present within the plane. In
the ATAC scaffold this is the other way around, that is, the ligands
are predominantly located in the plane of the cyclophane ring
(Fig. 2). This increased inclination towards a more defined position
on the cyclophane ring might be favorable for a better orientation
of ligands in a similar direction.
This asymmetric triazacyclophane (ATAC) scaffold (2) has been
prepared and applied earlier by us, containing three identical
peptide sequences.2a However, for our applications it is essential
that any future scaffold including the ATAC scaffold should be se-
lectively deprotectable for introduction of at least three different
ligands.
For synthesis of the ATAC scaffold with three selectively re-
movable protecting groups on the amino functionalities, it was
decided to adapt the original TAC synthetic route. The first step in
this
synthesis
was
a
mono-oNBS-protection
(o-nitro-
benzenesulfonyl) of bis(3-aminopropyl) amine (3, Scheme 1, left),
which was a low yielding step due to the tedious workup.1g This
adaptation was also required for the synthesis of the ATAC scaffold,
since the required triamine is not symmetrical and mono-oNBS-
protection according to the previous route (Scheme 1, left) will
result in a complex mixture and an even further lower yield.
Therefore, a stepwise and much more selective approach was
chosen, starting with a reaction between oNBS-protected 3-
bromopropylamine (4) and propyl or ethyl di-amine. This novel
approach was first evaluated for an alternative synthesis of the TAC
scaffold. An improvement of its synthesis was also desirable in view
of our continuing demands for large amounts of the TAC scaffold.
Scheme 1. Synthesis routes of the TAC scaffold (left: original route; right: new route).
2. Results and discussion
synthetic route with an overall yield of 44%. Subsequently, reaction
of 8 with dibromide 911 using cesium carbonate as a base gave the
TAC scaffold. Treatment with Tesser’s base12 for saponification of
the methyl ester and cleavage of the trifluoroacetyl group was
followed by Fmoc-protection, which afforded the desired protected
TAC scaffold 1 in 41% yield, containing the oNBS, Aloc and Fmoc
protecting groups in addition to the carboxylic acid moiety, which,
for example, can be used for attachment to the solid phase or other
purposes.
This approach was now applied to the synthesis of the ATAC
scaffold (Scheme 2). Thus, oNBS-protected 3-bromopropylamine
(4) was reacted with 10 equiv of 1,2-diaminoethane (10) in DMA,
to give mono-oNBS-protected triamine 11. Removal of excess of the
more volatile diamine by co-evaporation with DMA was clearly
easier than removal of 1,3-diaminopropane. The purity of crude 11
was very good (TLC) and comparable to 6 in the TAC synthesis.
Trifluoroacetylation to afford bis-protected triamine 12, was fol-
lowed by introduction of the Aloc-group, yielding tri-protected
amine 13 in high yield (74%, 90% per step), after column
oNBS-protected 3-bromopropylamine (4)10 was reacted with
10 equiv of 1,3-diaminopropane (5) in DMA as a solvent (Scheme 1).
After stirring overnight, 1 equiv of NaOH (4.0 M) was added to
liberate all protonated amines, which was necessary for removal of
excess diamine by evaporation. After co-evaporation with DMA
until the receiving flask was pH neutral, the crudedalmost pure-
dmono-protected triamine 6 was obtained. This was directly used
for selective introduction of a trifluoroacetyl group on the free
primary amine by treatment with ethyl trifluoroacetate. The
workup was again only evaporation of the solvents and excess ethyl
trifluoroacetate, leading to bis-protected triamine 7 in relatively
high purity (based on TLC). Introduction of the last protecting
group, the Aloc-group, took place by reaction with Aloc-chloride
under Schotten Baumann conditions using NaHCO3 as a base in
a water/dioxane mixture. Purification by column chromatography
afforded tri-protected amine 8 in a high yield of 75% (91% average
per step), which was a huge improvement over the previous

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A.J. Brouwer et al. / Tetrahedron 70 (2014) 4002e4007
Scheme 2. Synthesis of the ATAC scaffold (2).
chromatography. Cyclization with dibromide 9 in the presence of
cesium carbonate afforded ATAC scaffold 14 in 54% yield. Treatment
with Tesser’s base,12 followed by Fmoc-protection afforded the
desired protected ATAC scaffold 2 in 82% yield.
After characterization of both ATAC scaffolds (2 and 14), we were
wondering whether ring flipping would occur as easily as with the
TAC scaffold (Scheme 3).
than that of TAC, it was expected that ring flipping would be more
difficult. Ring flipping was monitored using variable temperature
1H NMR experiments (Fig. 3).13 At room temperature, the benzylic
CH2 groups in the scaffold were visible as a singlet for the TAC
scaffold, and two slightly broader singlets for the ATAC scaffold, due
to the asymmetry of this scaffold.
When measured at ꢀ40 ꢁC, the TAC scaffold still showed a sin-
glet (broader), but in the 1H NMR spectrum of ATAC three very
broad peaks were visible now instead of the earlier two singlets.
This indicated that ATAC scaffold ring flipping at about ꢀ40 ꢁC is
very slow on the NMR timescale, in contrast to the TAC scaffold. The
singlet of the TAC scaffold started to broaden significantly after
further cooling to ꢀ80 ꢁC, indicating a slower ring flipping, whereas
the ATAC scaffold stopped ring flipping at about ꢀ80 ꢁC, shown by
the double AB system for the benzylic CH2 protons. Determination
of the coalescence temperatures gave ꢀ80 ꢁC for the TAC scaffold,
and ꢀ35 ꢁC for the ATAC scaffold. These results showed that the
ATAC scaffold represents a more constrained system, which might
be beneficial for alignment of ligands attached to it.
3. Conclusions
Scheme 3. Superimposed conformers resulting from-cyclophane ring flipping of TAC
(15, left) and the ATAC (16, right) scaffolds (P1e3¼oNBS).2a
In search of approaches for influencing the conformation of the
cyclophane ring of the TAC scaffold, we have reduced the size of the
cyclophane ring. To realize this, we have described an efficient
method for the multigram scale synthesis of a novel asymmetric
selectively deprotectable ATAC scaffold. Although this scaffold is
very similar to our TAC scaffold, its cyclophane ring is only one CH2-
unit smaller, it is considerably less flexible. The same new synthetic
approach was also very useful for a convenient large scale high
Ring flipping is a phenomenon, which can occur with macro-
cycles, leading to different conformers, which can be observed in 1H
NMR spectra.13 The ease of ring flipping is proportional/correlated
to the rigidity of the triazacyclophane ring.13d
Thus, ring flipping properties of both oNBS-protected TAC and
ATAC scaffolds (15 and 16, Scheme 3)2a were studied by 1H NMR.
Since the ATAC triazacyclophane ring is one carbon atom smaller
Fig. 3. Variable temperature 1H NMR (acetone-d6) signals for the diastereotopic benzylic CH2 protons from TAC scaffold 15 (a) and ATAC scaffold 16 (b). *¼A solvent peak, which
shifts with temperature change.

A.J. Brouwer et al. / Tetrahedron 70 (2014) 4002e4007
4005
yielding synthesis of the TAC scaffold. The crucial step in the syn-
slowly. Directly
a
precipitate formed, which was probably
thesis of both scaffolds is the stepwise synthetic approach of
a mono oNBS-protected triamine.
Et3N$HBr. The mixture was stirred overnight at rt, affording a yel-
low suspension. After evaporation in vacuo, EtOAc (1.2 L) was added
and the mixture was washed with a KHSO4 solution (1.0 M, 600 mL,
twice), a NaHCO3 solution (5% w/w, 600 mL, twice) and brine.
Drying (Na2SO4) followed by concentration in vacuo and by co-
evaporation with CHCl3 yielded 4 as an off-white solid (117.7 g,
92%). All spectroscopic data were in agreement with the
literature.10
Investigation of the conformational behavior by 1H NMR of both
the TAC and ATAC scaffolds showed that ring flipping of the latter
was more difficult. This increasing rigidity, due to the smaller size of
the triazacyclophane ring, may affect the orientation of ligands to
the ATAC scaffold and is therefore interesting for mimicry of dis-
continuous epitopes in protein mimics.
Under present investigation are additional structural modifica-
tions including those of the aromatic ring, which could provide
additional pre-organization and therefore an increased capacity of
the TAC-ring system to direct the positioning of substituents.14
4.2.2. Allyl (3-(2-nitrophenylsulfonamido)propyl)(3-(2,2,2-
trifluoroacetamido)propyl)carbamate (8). To a cooled (ice bath)
solution of 1,3-diaminopropane (5) (50.5 mL, 600 mmol) in DMA
(250 mL), was added dropwise a solution of N-(3-bromopropyl)-
2-nitrobenzenesulfonamide (4) (19.5 g, 60 mmol) in DMA
(180 mL). During addition the solution slowly turned green. After
stirring overnight at rt, the reaction mixture turned yellow with
a white precipitate. A solution of NaOH (4.0 M, 15 mL, 1.0 equiv)
was added, after which the precipitate fully dissolved. The mix-
ture was concentrated in vacuo until a third of the volume. DMA
(200 mL) was added and again the mixture was concentrated until
a third of the volume. This co-evaporation was repeated (usually
three times) until the collected DMA was not basic anymore (pH
indicator paper). After evaporation in vacuo of all the DMA, crude
6 was obtained as a yellow oil. To crude 6 was added acetonitrile
(200 mL), water (1.08 mL, 60 mmol) and ethyl trifluoroacetate
(28.6 mL, 240 mmol). After stirring overnight under reflux, the
mixture was concentrated in vacuo to afford crude 7. To a cooled
(ice bath) solution of crude 7, NaHCO3 (20.2 g, 240 mmol), water
(200 mL) and dioxane (200 mL), was added dropwise a solution of
allyl chloroformate (7.68 mL, 72 mmol) in 100 mL dioxane. After
stirring overnight, the dioxane was evaporated in vacuo and
EtOAc (400 mL) was added. The organic layer was washed with
a solution of NaHCO3 (5%, w/w, 200 mL), KHSO4 (1.0 M, 200 mL,
twice) and brine. Drying (Na2SO4) and concentration afforded
crude 8 as a yellow oil (30 g). Column chromatography (eluent:
EtOAc/hexanes, 4/6 until first a yellow band was eluted, then 1/1
until the product started to elute, then 6/4 until all product had
eluted) afforded 8 as a thick yellowish oil, which slowly solidified
(22.3 g, 75%). Rf¼0.28 (acetone/CH2Cl2; 5/95). 1H NMR (500 MHz,
4. Experimental section
4.1. Materials and methods
Chemicals were purchased from Aldrich. Peptide grade and
HPLC grade solvents for synthesis and HPLC were purchased from
Biosolve (The Netherlands). All solvent mixtures (eluents) are given
in v/v. Reactions were carried out at ambient temperature unless
stated otherwise. TLC analysis was performed on Merck pre-coated
silica gel 60 F-254 (0.25 mm) plates. Spots were visualized with UV
light, ninhydrin or Cl2-TDM.15 Solvents were evaporated under re-
duced pressure at 40 ꢁC. Column chromatography was performed
on Siliaflash P60 (40e63 mm) from Silicycle (Canada). Analytical
HPLC was performed on a Shimadzu HPLC using a C18 Gemini
column at a flow rate of 1.0 mL/min. Buffers used: buffer A (0.1% TFA
in CH3CN/H2O, 5/95) and buffer B (0.1% TFA in CH3CN/H2O, 95/5).
Runs started with an isocratic flow of buffer A (100%, 2 min), fol-
lowed by a linear gradient of buffer B (100% in 48 min). Sub-
sequently an isocratic flow of buffer B (100%, 2 min) was performed
followed by a linear gradient to buffer A (100%, 5 min). The run
ended with an isocratic flow of buffer A (100%, 5 min). Elemental
analyses were carried out at Kolbe Mikroanalytisches Laboratorium
€
(Mulheim an der Ruhr, Germany). High resolution mass spec-
trometry (HRMS) spectra were measured on an ESI-MS instrument.
13C NMR (75 MHz), COSY and 19F NMR (282 MHz) were recorded on
a Varian M-300 spectrometer, 1H NMR (500 MHz), TOCSYand HSQC
spectra were recorded on a Varian Inova 500 spectrometer. Variable
temperature 1H NMR spectra (400 MHz) were recorded on a Varian
DMSO-d6)
d
: 1.65 (m, 4H, 2ꢂ NCH2CH2CH2N), 2.88 (t, J¼7.0 Hz, 2H,
oNBSNHCH2CH2CH2NAloc), 3.16 (m, 6H, TFANHCH2CH2CH2N,
CH2NHoNBS), 4.46 (d, J¼5.0 Hz, 2H, OCH2 (Aloc)), 5.14, 5.22 (2d,
JAx¼10.4 Hz, JBx¼16.25 Hz, 2H, ]CH2 (Aloc)), 5.86 (m, 1H, ]CH
(Aloc)), 7.86, 7.98 (2m, 4H, AreCH (oNBS)). 13C NMR (75 MHz,
S400 spectrometer. Chemical shifts (
million relative to DMSO (2.50 ppm) for 1H NMR, to DMSO-d6
(39.52 ppm) for 13C NMR and to
-trifluorotoluene
d) are reported in parts per
a,a,a
(ꢀ63.72 ppm) for 19F NMR as internal standards. Some of the 13C
NMR spectra were recorded using the attached proton test (apt)
pulse sequence. The 1H NMR spectra of 13 and scaffolds containing
a TFA-group (14, 17 (see Supplementary data)) contained many
additional peaks, due the cis/trans isomers of the TFA-amide. The 1H
NMR spectra of scaffolds 1 and 2 also contained additional peaks
due to the presence of Fmoc-rotamers. Some 13C spectra contain an
additional peak at 79.2 ppm, which was caused by an interference
with the spectrometer. This peak was not visible in the 13C spectra
obtained using the attached proton sequence.
DMSO-d6) d: 27.1, 27.6, 27.9, 28.5 (CH2CH2CH2N), 37.0 (NCH2), 40.5
(oNBSNHCH2CH2CH2NAloc), 44.1, 44.3 (2ꢂ NCH2), 65.1 (OCH2
(Aloc)), 110.2, 114.0, 117.9, 121.7 (q, J¼288 Hz, CF3), 117.0 (]CH2
(Aloc)), 124.4, 132.6, 133.4, 134.0, 147.8 (AreC (oNBS)), 129.5 (]CH
(Aloc)), 155.0 (C]O (Aloc)), 155.5, 156.0, 156.5, 156.9 (q, J¼36 Hz,
C(O)CF3). 19F NMR (282 MHz, DMSO-d6)
d
: ꢀ77.0 (s). HRMS: calcd
for C18H24F3N4O7S [MþH]þ 497.1318, found 497.1317. Anal. Calcd
for C18H23F3N4O7S: C, 43.55; H, 4.67; F, 11.48; N, 11.29. Found: C,
43.43; H, 4.41; F, 11.12; N, 11.00.
4.2.3. TAC scaffold 1. A suspension of triamine
8 (4.68 g,
4.2. Synthesis
10.0 mmol), dibromide 911 (3.22 g, 10.0 mmol), and Cs2CO3 (13.0 g,
40.0 mmol) in DMF (1.0 L) was stirred at rt overnight (16 h). The
color of the reaction mixture changed from yellow to light orange.
After evaporation of the DMF in vacuo, EtOAc (500 mL) and water
(300 mL) were added. The organic layer was washed with an
aqueous solution of KHSO4 (1 M, 250 mL) and with brine. Drying
(Na2SO4) and concentration in vacuo afforded the crude product as
an orange oil or foam, which was purified using column chroma-
tography (eluent: acetone/CH2Cl2; 2/98). The cyclic product (17, see
Supplementary data) was obtained as a yellowish foam (3.37 g,
4.2.1. N-(3-Bromopropyl)-2-nitrobenzenesulfonamide (4). N-(3-Bro
mopropyl)-2-nitrobenzenesulfonamide (4) was prepared accord-
ing to the literature.10 This procedure was slightly modified for use
on a large scale.
To a cooled (ice bath) mixture of 3-bromopropylamine (113.3 g,
517.5 mmol), 2-nitrobenzenesulfonyl chloride (88.6 g, 388 mmol)
and dichloromethane (800 mL) was added dropwise triethylamine
(140 mL, 1.0 mol). During addition, 3-bromopropylamine dissolves

4006
A.J. Brouwer et al. / Tetrahedron 70 (2014) 4002e4007
51%). Rf¼0.30 (acetone/CH2Cl2; 5/95). 1H NMR (500 MHz, DMSO-d6)
NMR (75 MHz, DMSO-d6) d: 27.7, 28.3 (CH2CH2CH2N), 36.2, 36.9, 37.5,
d
: 1.25 (m, 3H, 1½ꢂ NCH2CH2CH2N), 1.46 (m, 1H, ½ꢂ NCH2CH2),
37.8 (NCH2CH2N), 40.4 (CH2CH2CH2NAloc), 44.0, 44.4, 44.6, 45.0,
45.2, 45.6 (oNBSNHCH2, NCH2CH2N), 65.2 (OCH2 (Aloc)), 110.2, 114.0,
117.8, 121.6 (q, J¼288 Hz, CF3), 116.8 (]CH2 (Aloc)), 124.4, 129.5,
132.6, 133.2, 134.0, 147.8 (AreC (oNBS)), 129.5 (]CH (Aloc)), 155.1,
155.3 (C]O (Aloc)), 155.7, 156.2, 156.7, 157.2 (q, J¼35.9 Hz, C(O)CF3).
2.81 (t, J¼7.6 Hz, 1H, ½ꢂ NCH2CH2), 2.94 (m, 3H, 1½ꢂ NCH2CH2),
3.30 (m, 3H, 1½ꢂ NCH2CH2), 3.51 (t, J¼6.4 Hz, 1H, ½ꢂ NCH2CH2),
3.86, 3.88 (2s, 3H, OCH3), 4.41 (d, J¼3.9 Hz, 2H, OCH2 (Aloc)), 4.56,
4.59, 4.76, 4.82 (4s, 4H, PhCH2), 5.12 (dd, JAx¼10.5 Hz, JAB¼1.3 Hz,
1H, ]CHA (Aloc)), 5.17 (dd, JBx¼17.3 Hz, JAB¼1.3 Hz, 1H, ]CHB
19F NMR (282 MHz, DMSO-d6)
d
: ꢀ70.0 (s), ꢀ70.9 (s), ꢀ77.1 (s), ꢀ77.2
(Aloc)), 5.83 (m, 1H, ]CH (Aloc)), 7.90e8.12 (2m, 7H, AreCH). 13
C
(s). The 19F NMR spectrum showed four peaks, while only one or two
peaks were expected (cis/trans isomers of the TFA-amide bond).
Therefore, its purity was confirmed by analytical HPLC (retention
time: 33.3 min, see Supplementary data), showing that the extra
peaks were not from an impurity, but possibly from a conformer. This
conformer was also visible in the 1H NMR spectrum, which con-
tained some small additional peaks with a similar pattern in the
TOCSY spectrum as 13. VT NMR up to 70 ꢁC supported the presence
of conformers. HRMS: calcd for C17H22F3N4O7S [MþH] 483.1161,
found 483.1117. Anal. Calcd for C17H21F3N4O7S$½ H2O: C, 41.55; H,
4.51; F, 11.60; N, 11.40. Found: C, 41.74; H, 4.15; F, 11.23; N, 11.40.
NMR (75 MHz, DMSO-d6) d: 27.9, 28.3 (NCH2CH2CH2N), 44.6, 45.1,
46.3, 46.7, 47.4, 47.6 (NCH2), 51.0, 51.8, 52.4 (PhCH2), 52.3 (OCH3),
65.0 (OCH2 (Aloc)), 110.7, 114.6, 118.4,122.2 (q, J¼288 Hz, CF3), 116.6,
116.7 (]CH2 (Aloc)), 124.5, 128.9, 129.1, 129.3, 129.5, 129.7, 130.8,
131.0, 132.7, 133.3, 133.9, 134.8, 136.9, 138.3, 138.9, 147.9 (AreC, ]
CH (Aloc)), 154.7, 154.8 (C]O (Aloc)), 155.5, 156.0, 156.4, 156.9 (q,
J¼35 Hz, C(O)CF3), 156.3, 156.8, 157.3, 157.7 (q, J¼35 Hz, C(O)CF3),
165.5, 165.6 (CO2Me). 19F NMR (282 MHz, DMSO-d6)
d
: ꢀ69.2 (s),
ꢀ70.2 (s). HRMS: calcd for C28H32F3N4O9S [MþH]þ 657.1842, found
657.1824.
A solution of cyclic product 17 (2.51 g, 4.0 mmol) in Tesser’s base
(140 mL, 28 mmol, dioxane/methanol/4 M NaOH; 15/4/1) was
stirred overnight (16 h) at rt. The reaction mixture changed from
clear yellow to turbid yellow. The pH of the mixture was adjusted to
neutral (indicator paper) by addition of an aqueous solution of HCl
(1.0 M, 24 mL), leading to a slight warming-up of the reaction
mixture and a yellow solution. After addition of CH3CN (65 mL) and
water (65 mL), the pH was adjusted to approximately eight using
DiPEA (using pH electrode). Then, a solution of Fmoc-OSu (1.48 g,
4.4 mmol) in CH3CN (15 mL) was added, followed by dropwise
addition of DiPEA to maintain the pH around 8. The reaction was
considered complete when no more DiPEA was needed to maintain
the pH above 7.5 during 10 min, under nitrogen atmosphere. Ad-
dition of an aqueous solution of HCl (1.0 M, 30 mL) and water
(400 mL) was followed by extraction with EtOAc (twice; first with
250 mL, then with 150 mL). The combined organic layers were
washed with brine, dried (Na2SO4), and concentrated in vacuo
affording a yellow oil or foam. Column chromatography (eluent:
gradient from EtOAc/hexanes 2/1 to 3/1, and finally to EtOAc)
afforded TAC scaffold 1 as a yellowish foam (2.48 g, 81%). Rf¼0.30
4.2.5. ATAC scaffold 14. Cyclization was performed as described for
the synthesis of 1, using triamine 13 (4.82 g, 10.0 mmol), dibromide
911 (3.22 g, 10.0 mmol), and Cs2CO3 (13.0 g, 40.0 mmol) in DMF
(1.0 L). The color of the reaction mixture changed overnight from
yellow to light orange. After extraction, the crude product was
obtained as an orange oil or foam, which was purified using column
chromatography (eluent: acetone/CH2Cl2; 2/98). ATAC scaffold 14
was obtained as a yellowish foam (3.48 g, 54%). Rf¼0.31 (acetone/
CH2Cl2; 5/95). 1H NMR (500 MHz, DMSO-d6)
d: 1.08 (m, 2H,
NCH2CH2CH2N), 1.36, 2.50 (2m, 2H, NCH2CH2N), 3.13, 3.23, 3.49
(3m, 4H, NCH2CH2CH2N), 3.60 (m, 2H, NCH2CH2N), 3.87, 3.97 (2s,
3H, OCH3), 4.46 (m, 2H, OCH2 (Aloc)), 4.66, 4.81, 4.94 (3s, 4H,
PhCH2), 5.14, 5.16 (2d, J¼8.3 Hz (2ꢂ), ]CHA (Aloc)), 5.20, 5.29 (2d,
J¼17.4 Hz (2ꢂ), 1H, ]CHB (Aloc)), 5.86 (m, 1H, ]CH (Aloc)),
7.86e8.08 (m, 7H, AreCH). 13C NMR (75 MHz, DMSO-d6)
d: 24.7,
25.2, 25.8 (NCH2CH2CH2N), 40.8, 41.0, 42.5, 42.7, 43.2, 43.4, 45.7,
48.8, 48.9 (NCH2), 51.4, 52.0, 53.1, 53.3 (PhCH2), 52.5 (2ꢂ) (OCH3),
65.2, 65.4, 65.6 (OCH2 (Aloc)), 110.7, 114.5, 118.3, 122.2 (q, J¼288 Hz,
CF3), 110.8, 114.6, 118.5, 122.3 (q, J¼288 Hz, CF3), 116.3, 117.0, 117.2
(]CH2 (Aloc)), 124.6, 128.4, 128.9, 129.3, 129.4, 131.2, 131.3, 131.5,
132.9, 133.0, 134.8, 136.6, 138.0, 139.9, 140.0, 148.1 (AreC), 133.4 (]
CH (Aloc)), 154.6, 154.7, 154.9 (C]O (Aloc)), 154.9, 155.3, 155.8,
156.3 (q, J¼35 Hz, C(O)CF3), 155.8, 156.3, 156.8, 157.2 (q, J¼35 Hz,
C(O)CF3), 155.9,156.4,156.8,157.3 (q, J¼36 Hz, C(O)CF3), 165.5,165.6
(EtOAc). 1H NMR (500 MHz, DMSO-d6)
d: 0.82 (m, 1.3H,
NCH2CH2CH2N), 1.17, 1.30 (2m, 2.7H, NCH2CH2CH2N), 2.32, 2.84,
3.27 (3m, 8H, 2ꢂ NCH2CH2CH2N), 4.31 (m, 1H, CH (Fmoc)),
4.42e4.66 (m, 8H, OCH2 (Aloc), 2ꢂ PhCH2, CH2 (Fmoc)), 5.15 (m, 2H,
]CH2 (Aloc)), 5.84 (m, 1H, ]CH (Aloc)), 7.27e8.31 (m, 15H,
AreCH). 13C NMR (75 MHz, DMSO-d6)
d
: 27.7, 28.1 (NCH2CH2CH2N),
(CO2Me). 19F NMR (282 MHz, DMSO-d6)
d
: ꢀ69.2 (s), ꢀ70.2 (s).
44.5, 44.9, 45.7, 47.7 (NCH2CH2CH2N), 46.8 (CH (Fmoc)), 51.5, 52.8
(PhCH2), 64.9, 66.2, 66.9 (OCH2 (Aloc), CH2 (Fmoc)), 116.7 (]CH2
(Aloc)), 120.0, 124.5, 124.9, 127.0, 127.4, 128.8, 129.1, 129.6, 130.9,
131.7, 132.1, 132.6, 134.7, 138.1, 140.3, 140.9, 144.0, 147.9 (AreC),
133.5 (]CH (Aloc)), 154.7, 155.4, 156.0 (C]O (Aloc, Fmoc)), 166.8
(CO2H). HRMS: calcd for C40H41N4O10S [MþH]þ 769.2543, found
769.2564. Anal. Calcd for C40H40N4O10S.H2O: C, 61.06; H, 5.38; N,
7.12. Found: C, 61.20; H, 4.95; N, 7.00.
HRMS: calcd for C27H30F3N4O9S [MþH]þ 643.1686, found 643.1665.
Anal. Calcd for C27H29F3N4O9S$½ H2O: C, 49.77; H, 4.64; F, 8.75; N,
8.60. Found: C, 49.77; H, 4.43; F, 8.58; N, 8.38.
4.2.6. ATAC scaffold 2. TFA-removal and hydrolysis of the methyl
ester was performed as was described for the synthesis of 1, using
the cyclic product (2.57 g, 4.0 mmol), and Tesser’s base (140 mL,
28 mmol, dioxane/methanol/4 M NaOH; 15/4/1). The reaction
mixture changed overnight from clear yellow to turbid yellow.
Fmoc-protection was performed as described for the synthesis of 1,
using CH3CN (65 mL) and water (65 mL), DiPEA as a base, and
a solution of Fmoc-OSu (1.48 g, 4.4 mmol) in CH3CN (15 mL). After
workup, a yellow oil or foam was obtained. Column chromatogra-
phy (eluent: gradient from EtOAc/hexanes 2/1 to 3/1, and finally to
EtOAc) afforded ATAC scaffold 2 as an off-white foam (2.46 g, 82%).
4.2.4. Allyl (3-(2-nitrophenylsulfonamido)propyl)(2-(2,2,2-
trifluoroacetamido)ethyl)carbamate (13). Triamine 13 was prepared
using the same procedure as for the synthesis of 8. The synthesis was
performed on 56.7 mmol scale, solvent volumes were the same as
used for 8. 1,2-Diaminoethane (10) was used as the diamine. Purifi-
cation was performed using the same eluent for column chroma-
tography as used for 8, affording 13 as a yellowish solid (20.4 g, 74%).
Rf¼0.33 (EtOAc). 1H NMR (500 MHz, DMSO-d6)
d: 1.07 (m, 2H,
Rf¼0.22 (acetone/CH2Cl2; 5/95). 1H NMR (500 MHz, DMSO-d6)
d
: 1.71
NCH2CH2), 2.36, 2.50 (m, 2H, NCH2CH2N), 3.18, 3.27, 3.51 (3m, 4H,
NCH2CH2CH2N), 3.35, 3.58 (2m, 2H, NCH2CH2N), 4.22e4.67 (m, 9H,
OCH2 (Aloc), 2ꢂ PhCH2, CHCH2 (Fmoc)), 4.88e5.12 (m, 2H, ]CH2
(Aloc)), 5.68, 5.83 (2m, 1H, ]CH (Aloc)), 7.33e8.31 (m, 15H,
(m, 2H, NCH2CH2CH2), 2.90 (m, 2H, oNBSNHCH2CH2CH2NAloc), 3.19
(m, 2H, CH2NHoNBS), 3.41 (m, 4H, HNCH2CH2NH), 4.46 (d, J¼5.0 Hz,
2H, OCH2 (Aloc)), 5.16 (2d, J¼8.7 Hz (2ꢂ), 1H, ]CHA (Aloc)), 5.24 (2d,
J¼15.8 Hz (2ꢂ),1H, ]CHB (Aloc)), 5.87 (m,1H, ]CH (Aloc)), 7.86, 7.98
AreCH). 13C NMR (75 MHz, DMSO-d6)
d: 24.7, 25.3 (NCH2CH2CH2N),
(2m, 4H, AreCH (oNBS)), 8.10 (br s, 1H, NH), 9.45 (br s, 1H, NH). 13
C
42.8, 45.3, 48.8 (NCH2), 46.7 (CH (Fmoc), 51.3, 51.6, 53.3 (PhCH2),

A.J. Brouwer et al. / Tetrahedron 70 (2014) 4002e4007
4007
65.1, 67.2, 67.8 (OCH2 (Aloc), CH2 (Fmoc)), 116.2, 116.5, 116.9 (]CH2
References and notes
(Aloc)), 120.8, 124.6, 125.0, 125.1, 125.4, 127.2, 127.7, 128.0, 129.2,
129.3,131.1,131.2, 132.3, 132.8,134.7, 139.1, 139.4, 139.8,140.6,140.8,
143.7, 143.9, 148.0 (AreC), 133.2 (]CH (Aloc)), 154.7, 155.7 (C]O
(Aloc, Fmoc)), 166.8 (CO2H). HRMS: calcd for C39H39N4O10S [MþH]þ
755.2387, found 755.2344. Anal. Calcd for C39H38N4O10S$1½ H2O:
C, 59.91; H, 5.29; N, 7.17. Found: C, 60.16; H, 5.06; N, 6.72.
1. (a) Van der Plas, S. E.; Gea, A.; Figaroli, S.; De Clercq, P. J.; Madder, A. Eur. J. Org.
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Molecular modeling was performed using the program Yasara
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tached to each scaffold. The following settings were used: Yamber3
ꢀ
force field; Force cutoff at 7.86 A; temperature control: simulated
ꢀ
annealing; the simulation cell was 50ꢂ50ꢂ50 A; no extra water
molecules were added. The minimization was carried out starting
at 300 K until it reached 0 K.
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Acknowledgements
We would like to thank dr Johann Jastrzebski and dr Ties Kor-
stanje for the help with the variable temperature NMR measure-
ments, dr Johan Kemmink for measuring some of the NMR spectra,
and dr Jack Slootweg for helping with the conversion of these
measurements into Fig. 3. We also would like to thank Javier Sastre
8. Park, H. S.; Lin, Q.; Hamilton, A. D. J. Am. Chem. Soc. 1999, 121, 8e13.
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Torano for measuring the HRMS data.
Supplementary data
€
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M. J. submitted for publication.
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Structures of compounds 17, 18, and 19, NMR spectra, and
a HPLC trace of 13. Supplementary data related to this article can be
found at http://dx.doi.org/10.1016/j.tet.2014.04.084.