M. Petaccia et al.
Bioorganic & Medicinal Chemistry 29 (2021) 115881
pyrene moiety and a 5-FU derivative, where the fluorescence signal
occurred upon the interaction of 5-FU derivative with TP, due to the
variation of excimer/monomer ratio of pyrene residues.14 In that case
the sensor elements were not covalently linked. Here we report the
synthesis and the characterization of new extrinsic fluorescent molecu-
lar probes (1, 2 and 3, Chart 2) designed to detect the target enzymes of
as a function of the aminoacidic composition of the enzymatic pocket
and of its conformation. The ability of the three MRs to trigger an optical
signal upon the interaction with the target enzyme was investigated by
fluorescent measurements.
2. Experimental section
5
-FU. The evaluation of binding and sensor capabilities was carried out
on TP because it is the only commercially available among the three
target enzymes.
2.1. Instrumentation
The three newly synthesized fluorescent molecules differ for the
length of the alkyl spacer joining the receptor unit, a thymine moiety,
and the fluorophore residue responsible of signaling the recognition
event, a [4-(1-dimethylamino)phenyl]-pyridinium bromide, a molecular
rotor (MR). Among MRs, the fluorescence properties of p-(dimethyla-
1H and 13C NMR spectra were carried out on a Varian NMR 500 MHz;
δ in ppm relative to the residual solvent peak of CDCl
ppm for 1H and 13C, respectively; J in Hz.
3
at 7.26 and 77.0
Steady-state fluorescence experiments were carried out on
Fluoromax-4 Horiba-Jobin Yvon spectrofluorimeter.
a
1
5–18
mino)-benzene derivatives have been extensively studied.
probes 1, 2 and 3, belonging to this class of MRs, exhibit the so-called
turn-on” emission as a function of their chemical microenvironment.
The
High-resolution electrospray ionisation mass spectrometry (HRE-
SIMS) spectra were recorded using a Micromass Q-TOF Micromass
spectrometer (Waters) in the electrospray-ionization mode.
“
The presence of the electron donating dimethyl amino group coupled
opposite to the electron withdrawing N-methylpyridinium ring yields a
molecule with strong charge transfer character in the planar locally
excited (LE) state. Another feature that contributes to the high sensi-
tivity of these compounds is the ability of the molecule to twist from
coplanarity, that is, to form a dihedral angle φ between the aniline and
pyridinium rings (Figure 1) significantly different from zero.
2.2. Materials
Phosphate–buffered saline (PBS, 0.01 M phosphate buffer; 0.0027 M
KCl; 0.137 M NaCl; pH 7.4), TP recombinant from Escherichia coli and all
reagents employed for the synthesis of 1–3 were purchased from Sigma-
Aldrich and were used without further purification.
The minimum excited-state energy is reached when the aniline
◦
(
donor) and pyridinium ring (acceptor) planes are rotated 90 relative to
2.2.1. Synthesis of pyrimidines 1b, 2b and 3b
each other (Figure 1). In this geometrical condition the energy gap be-
tween the twisted intramolecular charge transfer (TICT) state and the
α
, -Alkyldibromide 1a (2a, 3a) (1 eq) was added to a solution of
ω
thymine (4 eq) dissolved in DMF (“purum” grade bottle) (26 eq) fol-
lowed by anhydrous potassium carbonate (2 eq). The mixture was stir-
red for 48 h at room temperature. The resulting slurry was filtered
through a Celite pad and the cake washed two times with DMF (5 mL).
The solvent was removed under reduced pressure to give 1b (2b, 3b) as
a white solid that was purified by column chromatography on silica gel
using CH C1 /ETOAc 9:1 as eluent (yield 37% for 1b, 45% for 2b and
ground state (GS) becomes dramatically small and the relaxation from
this twisted state is practically radiationless.1
7,19
Polar solvents
conceivably help to stabilize the TICT state resulting in a shift to lower
emission energies as well as lead to emission quenching. On the other
hand, apolar solvents do not particularly favor the formation of TICT
state with consequent increase of emission intensity.18 The twisting is
also supposed to be limited in viscous solvents or in geometrically
confined environments hence resulting in a sharp increase of emission.20
The binding of the new fluorescent molecules with the binding site of the
target enzymes, promoted by the presence of thymine, should place the
MR in a less polar and restrictive environment compared to the free
molecule in aqueous solvent. In this configuration turn-on emission of
the MR should occur. This approach offers the advantage of minimizing
background emission from unbound MR, because the emission in
aqueous solvent is turned-off.
2
2
1
55% for 3b). Compound 1b: H NMR (CDCl ) δ ppm 1.86 (d, 3H, J = 1.5
3
Hz), 2.51 (t, 3H, J = 2 Hz), 4.16 (t, J = 8 Hz, 2H), 4.67 (t, J = 8 Hz, 2H),
1
3
7.57 (d, J = 1 Hz, 1H) C NMR (500 MHz, CDCI3) 8 12.44, 42.45,
1
66.17, 116.93, 151.01, 158.43, 161.55. Compound 2b: H NMR (CDCl )
3
δ ppm 1.31 (m, J = 1.2, 4H), 2.05 (s, 3H), 3.44 (t, J = 8.5 Hz, 2H), 3.88
1
3
(t, J = 8.5 Hz, 2H), 7.53 (s, 1H), 11.2 (s, 1H). C NMR (500 MHz,
CDCI3) δ ppm 12.4, 30.1, 35.9, 48.9, 110.9, 139.2, 150.8, 163.7.
Compound 3b: 1H NMR (CDCl ) δ ppm 1.67–1.71 (m, 3H, J = 6 Hz),
3
1.74–1.79 (m, 3H, J = 6 Hz), 2.50 (s, 3H) 3.55 (t, J = 6.5 Hz, 2H), 3.65
1
3
The different length of the alkylic spacer of the three new fluorescent
MRs 1–3 might affect the ability to show the turn-on emission upon the
binding with TP because the fluorophore should be located in environ-
ments characterized by different local polarity and/or steric hindrance
(t, J = 6.5 Hz, 2H), 7.54 (s, 1H), 11.23 (s, 1H). C NMR (CDCl ) δ ppm
3
12.43, 27.67, 29.64, 34.98, 46.73, 109, 141.81, 151.37, 164.74.
2.2.2. Synthesis of 4-[4-(1-Dimethylamino)phenyl]-pyridine (DMAPP)
Palladium (II) acetate (5% mol) and triphenylphosphine (10% mol)
were added to a mixture of 4-bromopyridine HCl (1.2 eq), then a solu-
tion of 4-(dimethylamino)phenylboronic (1 eq), and potassium car-
bonate (3 eq) in dimethylformamide (DMF, 1.5 mL) was added. The
reaction mixture was kept at reflux overnight, then filtered through a
celite plug and concentrated. The crude product was purified by flash
chromatography (silica, CH
2
Cl
2
/ETOAc = 99:1 → 95:5) to give the
1
product, DMAPP, as a tan solid (30%). H NMR (CDCl
3
): δ ppm 8.56 (d,
J = 4.9 Hz, 2H), 7.61 – 7.55 (m, 2H), 7.46 (dd, J = 4.7, 1.5 Hz, 2H), 6.82
–
1
6.76 (m, 2H), 3.02 (s, 6H) 13C NMR (CDCl
28.3, 131.2, 147.2, 149.7, 155.8.
3
): δ ppm 41.3, 112.7, 120.6,
2
.2.3. Synthesis of MRs 1, 2 and 3
4
-[4-(1-Dimethylamino)phenyl]-pyridine (1 eq) was combined with
1
eq of 1b (2b, 3b) and 0.5–4.0 mL of DMF. The reaction mixture was
◦
heated at 80 C for 48 h to observe the formation of a yellow precipitate.
After cooling the reaction mixture, the crude product was isolated by
suction filtration and rinsed with EtOAc. The crude product was crys-
tallized from MeOH/EtOAc to yield 32% for 1, 62% for 2 and 75% for 3
Fig. 1. Intramolecular twisting of MR of 1, 2 and 3.
2