S. A. Ohnmacht et al. / Bioorg. Med. Chem. Lett. 23 (2013) 5351–5355
5355
(4H, m, 4 ꢀ Ar–H), 8.19 (2H, t, J = 1.8 Hz, 2 ꢀ Ar–H), 8.46–8.48 (4H, m, 4 ꢀ Ar–
H). 13C NMR (100 MHz, CDCl3) d 148.2 (2 ꢀ CH), 143.2 (2 ꢀ CH), 138.0 (2 ꢀ CH),
133.6 (quat), 133.3 (quat), 131.0 (2 ꢀ CH), 128.8 (2 ꢀ quat), 128.1 (2 ꢀ quat),
125.0 (2 ꢀ CH), 124.3 (2 ꢀ quat), 118.6 (2 ꢀ quat), 118.2 (2 ꢀ CH), 118.1
(2 ꢀ CH), 110.7 (2 ꢀ CH), 54.4 (2 ꢀ CH2), 53.3 (4 ꢀ CH2), 50.7 (4 ꢀ CH2), 43.8
(2 ꢀ CH2), 41.7 (2 ꢀ CH2), 23.3 (2 ꢀ CH3). HRMS (ES+) calculated for C42H52N12
[M+1]+ 725.4516, found 725.4482.
19. Sulforhodamine B assay (SRB). Cells were counted and diluted to the required
concentration in 20 mL medium. For cell lines MCF7, A549, RCC4 and 786-0,
1000–4000 cells with 160
well of 96 well plate (Nunc, Denmark). After incubation for 24 h, the
compound to be tested was dissolved in 40 L of medium and was added in a
range of concentrations, and the cells incubated for 96 h. The medium was
then removed and the cells fixed by incubation with TCA (10%, Sigma–Aldrich,
UK) for 30 min at 4 °C. After removal of the TCA, the cells were washed with
deionised water five times and dried at 60 °C for 1 h. The cells were then
lL media (WI38: 6000/well) were seeded into each
a
l
incubated with sulforhodamine B (80
UK) for 15 min at rt. The SRB was removed, the wells washed with 1% acetic
acid (200 L), and dried at 60 °C for 1 h. Tris-base (100 L, 10 mM, Acros
Organics, UK) solution was added to each well, and the plates were gently
shaken for 5 min. The absorbance at 540 nm was measured with a plate reader
(Spectrostar Omega, BMG Labtech, Germany). The data were normalized to the
value of 100 for the control experiment (untreated cells), and the IC50 values
were obtained by interpolation from a plot with Origin (Version 7.0, OriginLab
Corp.), as the concentration leading to an absorbance intensity of 50%.
lL, 0.4% in 1% acetic acid, Acros Organics,
17. Direct arylation: 3,30-(5,50-(1,3-phenylene)bis(oxazole-5,2-diyl))bis(N-(3-(4-
methylpiperazine-1-yl)propyl)aniline) (3, 4). An oven dried microwave vial
was charged with Pd(OAc)2 (0.1 equiv), K2CO3 (3 equiv), ligand (2-
l
l
dicyclohexylphosphino-20,60-diisopropoxybiphenyl,
0.2 equiv),
oxazole
precursor (1 equiv) and arylbromide (2.2 equiv). The microwave vial was
capped, evacuated and backfilled with argon and then pivalic acid (0.4 equiv)
and toluene were added. The vial was heated at 110 °C for 72 h. After cooling to
room temperature, the reaction mixture was concentrated and purified using
silica gel. (400 MHz, CDCl3) d 1.26 (4H, s, 2 ꢀ CH2), 1.65 (4H, br s, 2 ꢀ CH2), 1.85
(4H, quintet, J = 6.3 Hz, 2 ꢀ CH2), 2.31 (6H, s, 2 ꢀ CH3), 2.51–2.55 (12H, m,
6 ꢀ CH2), 3.30 (4H, t, J = 6.3 Hz, 2 ꢀ CH2), 6.72 (2H, dd, J = 1.6, 8.1 Hz, 2 ꢀ Ar–
H), 7.29 (2H, t, J = 7.8 Hz, 2 ꢀ Ar–H), 7.35 (2H, t, J = 1.6 Hz, 2 ꢀ Ar–H), 7.46 (2H,
d, J = 7.8 Hz, 2 ꢀ Ar–H), 7.49–7.53 (2H, m, 2 ꢀ Ar–H), 7.69 (2H, dd, J = 1.5,
7.8 Hz, 2 ꢀ Ar–H), 8.01 (1H, br s, Ar–H). 13C NMR (100 MHz, CDCl3) d 162.1
(2 ꢀ quat), 150.4 (CH), 149.1 (2 ꢀ CH), 129.7 (2 ꢀ CH), 129.6 (2 ꢀ CH), 129.0
(2 ꢀ CH), 128.1 (2 ꢀ CH), 124.1 (2 ꢀ quat), 124.0 (2 ꢀ quat), 119.7 (2 ꢀ quat),
115.3 (CH), 115.2 (2 ꢀ CH), 109.8 (2 ꢀ CH), 57.2 (2 ꢀ CH2), 55.3 (4 ꢀ CH2), 53.2
(4 ꢀ CH2), 46.0 (2 ꢀ CH2), 43.5 (2 ꢀ CH2), 25.6 (2 ꢀ CH3). HRMS (ES+)
calculated for C40H50N8O2 [M+1]+ 675.4135, found 675.4125.
20. FRET DNA melting assays on compounds 1–8 were performed as previously
described (Guyen, B. Schultes, C. M. Hazel, P. Mann, J. Neidle, S. Org. Biomol.
Chem. 2004, 2, 981) using a fluorescence resonance energy transfer (FRET)
assay modified as a high-throughput screen in a 96-well format. The labelled
oligonucleotides had attached the donor fluorophore FAM: 6-
carboxyfluorescein
carboxytetramethyl-rhodamine. The FRET probe sequences were diluted
from stock to the correct concentration (400 nM) in 60 mM potassium
and
the
acceptor
fluorophore
TAMRA:
6-
a
cacodylate buffer (pH 7.4) and then annealed by heating to 95 °C for 10 min,
followed by cooling to room temperature in the heating block (3–3.5 h). The
compounds were stored as a 1 mM stock solution in 10% DMSO/90% 1 mmol
HCl; final solutions (at 2 ꢀ concentration) were prepared using 60 mM
potassium cacodylate buffer (pH 7.4). Relevant controls using BRACO-19 (in
addition to blank runs) were also performed to check for quality of DNA
samples (e.g., F21T). 96-Well plates (MJ Research, Waltham, MA) were
18. Click
reaction:
3,30-(4,40-(naphthalene-2,7-diyl)bis(1H-1,2,3-triazole-4,1-
diyl))bis(N-(3-(4-methylpiperazin-1-yl)-propyl) aniline) (1, 2). Dialkyne
(1 equiv) was dissolved in the appropriate volume of solvent (H2O:tBuOH
1:1), followed by the addition of required azide (3 equiv) and the catalytic
mixture of CuSO4 ꢀ 5H2O (0.05 equiv), sodium ascorbate (0.5 equiv) and
bathophenanthroline disulfonic acid disodium salt hydrate (0.1 equiv). The
reaction was performed with excess of the required amine (6 equiv). The
mixture was heated under microwave irradiation for 15 min at 120 °C. Crude
product was obtained following evaporation of solvents and subsequent C18
reversed phase semi-prep purification. 1H NMR (400 MHz, CDCl3) d 1.81 (4H,
quintet, J = 6.6 Hz, 2 ꢀ CH2), 2.45 (4H, t, J = 6.6 Hz, 2 ꢀ CH2), 2.58 (6H, s,
2 ꢀ CH3), 2.67 (8H, br s, 4 ꢀ CH2), 2.94 (8H, br s, 4 ꢀ CH2), 4.16 (4H, t, J = 7.3 Hz,
2 ꢀ CH2), 7.64–7.68 (2H, m, 2 ꢀ Ar–H), 7.75–7.77 (4H, m, 4 ꢀ Ar–H), 7.93–8.03
prepared by aliquoting 50
lL of the annealed DNA into each well, followed
by 50 L of the compound solutions. Measurements were made on a DNA
l
Engine Opticon (MJ Research) with excitation at 450–495 nm and detection at
515–545 nm. Fluorescence readings were taken at intervals of 0.5 °C in the
range 30–100 °C, with a constant temperature being maintained for 30 s prior
to each reading to ensure a stable value. Final analysis of the data was carried
out using
Northampton, MA). The advanced curve-fitting function in Origin 7.0 was
used for calculation of Tm values. Esds in Tm are 0.1 °C.
a script written in the program Origin 7.0 (OriginLab Corp.,
D
D