A R T I C L E S
Vial et al.
Scheme 1. Synthesis of Building Block 2
bath. Dimethylthiocarbamoyl chloride (19 g, 157 mmol) dissolved in
dry DMA (50 mL) was added dropwise under nitrogen. The mixture
was stirred for 16 h at room temperature. The off-white precipitate
was filtered, washed extensively with water (300 mL), and dried under
vacuum, yielding compound 8 (16 g, 97%). 1H NMR (400 MHz,
CDCl3): δ 7.73 (s, 2H, CHAr), 4.30 (q, J ) 7.1 Hz, 4H, CH2), 3.46
(s, 6H, CH3), 3.40 (s, 6H, CH3), 1.33 (t, J ) 7.1 Hz, 6H, CH3).
2,5-Bis(dimethylthiocarbamoylsulfanyl)terephthalic Acid Diethyl
Ester (9).25 Compound 8 (650 mg, 1.51 mmol) was heated under
nitrogen at 215 °C for 1 h. The brownish mixture was cooled to 70 °C,
and EtOH (20 mL) was added. Pale brown crystals appeared as the
sample was slowly cooled to room temperature. The crystals were
filtered off, yielding compound 9 (626 mg, 97%). 1H NMR (400 MHz,
CDCl3): δ 8.11 (s, 2H, CHAr), 4.34 (q, J ) 7.1 Hz, 4H, CH2), 3.12
(s, 6H, CH3), 3.02 (s, 6H, CH3), 1.37 (t, J ) 7.1 Hz, 6H, CH3).
2,5-Dimercaptoterephthalic Acid (2). A solution of compound 9
(1.3 g, 3.03 mmol) in degassed 1.3 M KOH in EtOH/H2O (1:1, 40
mL) was refluxed under an inert atmosphere for 3 h. The reaction
mixture was cooled in ice, and concentrated HCl (15 mL) was added.
A bright yellow precipitate was formed, filtered, and washed extensively
with water, yielding compound 2 as a yellow solid (663 mg, 95%). 1H
NMR (400 MHz, CD3OD): δ 8.02 (s, 2H, CHAr).
Subsequent addition of one-half an equivalent of 6 to the
resulting Z-DNA solution reversed the transition, regenerating
the original B-DNA, indicating that the receptor is indeed able
to unbind spermine from DNA and thereby control the helicity
of DNA.31
Dynamic Combinatorial Libraries. In a typical experiment, the
thiols (10 mM overall) were suspended in water, and the pH was
adjusted to 8.25 by addition of a 1 M solution of NaOH. Where
appropriate, spermine (2.5 mM) was added. The mixtures were allowed
to oxidize and equilibrate by stirring in an open vial at room
temperature. Evaporated water was replenished every day.
Library Analysis. Analyses were performed using an Agilent 1100
series HPLC and Agilent XCT ion-trap mass spectrometer. Solvents
and formic acid were acquired from Romil. Analyses were performed
using a reversed phase HPLC column (Agilent C8 Zorbax Eclipse XBD,
4.6 × 150 mm, 5 µm), using an injection volume of 10 µL, a flow rate
of 1 mL/min, and a gradient (5-95% in 40 min) of acetonitrile in water
(both containing 0.1% formic acid) at 303 K. Negative ion mass spectra
were acquired in ultrascan mode using electrospray ionization (drying
temperature, 350 °C; nebulizer pressure, 55 psi; drying gas flow, 12
L/min; HV capillary, 4000 V; ICC target, 200 000).
Conclusions
Our results demonstrate that, after the design of only
rudimentary molecular recognition elements, dynamic combi-
natorial chemistry can be used to guide their assembly into a
high-affinity receptor. Thus, starting from a dynamic combi-
natorial library made from two building blocks that contain
carboxylate groups as recognition units, a new macrocyclic
receptor for the oligoamine spermine was obtained that binds
this guest with a dissociation constant of 22 ((1) nM. Water-
soluble synthetic receptors for biologically relevant guests with
such high affinities are extremely rare. Analysis of the host-
guest complex by NMR and computer simulations indicates a
pseudo-rotaxane structure in which spermine is threaded through
the macrocyclic host and bound through a series of hydrogen
bonds and anion-cation interactions. The host was shown to
interfere efficiently with spermine-DNA interactions, being able
to prevent and reverse the binding of spermine to DNA and
thereby indirectly control the conformation of DNA; while
spermine can induce a change in the conformation of DNA from
a right-handed (B-form) to a left-handed (Z-form) helix, the
addition of the synthetic spermine receptor reverts the DNA
back to its original B-form. These results suggest that our
spermine receptor may be a promising lead for the development
of novel therapeutics or molecular probes that may help unravel
the still poorly understood role of oligoamines in cell biology.
Purification of Receptor 6. Receptor 6 was isolated from a dynamic
“library” made from thiol 2 (10 mM) and spermine (2.5 mM) in water
at pH 8.25. Aliquots of 700 µL of this solution were injected onto a
reversed phase preparative HPLC column (Agilent C8 Zorbax Eclipse
XBD, 21.2 × 150 mm, 5 µm) at 303 K. Using a flow rate of 5 mL/
min and a gradient (5-95% over 30 min) of acetonitrile in water (both
containing 0.1% formic acid), the receptor was collected from 14 runs.
The solvents were removed under reduced pressure keeping the
temperature below 40 °C. The last traces of solvent were removed under
high vacuum for 2-3 h. The crude host was dissolved in 12 mL of
borate buffer (10 mM pH 9.0) and sonicated for 2 min. The resulting
solution was centrifuged and decanted. Hydrochloric acid (3 mL of a
2.0 M solution) was added to the supernatant. The resulting suspension
was centrifuged and the pellet resuspended in dilute hydrochloric acid
(30 mL of a 40 mM solution) and centrifuged. The solid (6 mg) was
dried under vacuum overnight. The LC-MS analysis of 6 is shown in
Experimental Section
Materials and Methods. Chemicals were purchased from Aldrich
or Fluka. Building block 2 was synthesized on the basis of a method
described by Field and Engelhardt (Scheme 1).25 NMR analyses were
performed using an Advance 500 Bruker instrument equipped with a
standard TCI Cryoprobe. Spectra were recorded at 300 K with water
presaturation during relaxation delay and mixing time.
2,5-Bis(dimethylthiocarbamoyloxy)terephthalic Acid Diethyl Es-
ter (8).25 2,5-Dihydroxyterephthalic acid diethyl ester 7 (10 g, 39.00
mmol) and DABCO (18 g, 157 mmol) were dissolved in dry DMA
(100 mL) under a nitrogen atmosphere and cooled to 0 °C in an ice
1
the Supporting Information. H NMR (500 MHz, DMSO-d6): δ 8.34
(s, 8H). Anal. Calcd for 6‚5H2O: C, 38.32; H, 2.61. Found: C, 38.06;
H, 2.76.
Isothermal Titration Calorimetry (ITC). The binding studies
between 1 and 6 were conducted at three different concentrations using
isothermal titration microcalorimetry (MCS-ITC, Microcal LLC,
Northampton, MA). Solutions of guest 1 (in 3 mM TRIS buffer pH
7.4) were titrated into solutions of host 6 (in 3 mM TRIS buffer pH
7.4). Binding constants and enthalpies of binding were obtained by
curve fitting of the titration data using the one-site binding model
available in the Origin 2.9 software as shown in the Supporting
Information. The thermodynamic parameters were averaged over three
(31) The amplitude of the CD signals after addition of spermine and after addition
of 6 is somewhat lower than the original value as a result of partial
precipitation of the DNA-spermine complex. This does not affect the
conclusions.
9
10256 J. AM. CHEM. SOC. VOL. 128, NO. 31, 2006